diff options
Diffstat (limited to 'sci-libs')
1333 files changed, 64495 insertions, 0 deletions
diff --git a/sci-libs/Fiona/Fiona-1.5.1.ebuild b/sci-libs/Fiona/Fiona-1.5.1.ebuild new file mode 100644 index 000000000000..85394dcc60ec --- /dev/null +++ b/sci-libs/Fiona/Fiona-1.5.1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python2_7 python3_4 ) + +inherit distutils-r1 + +DESCRIPTION="OGR's neat, nimble, no-nonsense API" +HOMEPAGE="https://pypi.python.org/pypi/Fiona" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + >=sci-libs/gdal-1.8 + dev-python/click[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + test? ( + dev-python/nose[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + )" + +PATCHES=( "${FILESDIR}"/scriptname.patch ) + +python_test() { + esetup.py test +} diff --git a/sci-libs/Fiona/Fiona-1.7.6.ebuild b/sci-libs/Fiona/Fiona-1.7.6.ebuild new file mode 100644 index 000000000000..2b00c823c1bb --- /dev/null +++ b/sci-libs/Fiona/Fiona-1.7.6.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python{2_7,3_{3,4,5,6}} ) + +inherit distutils-r1 + +DESCRIPTION="OGR's neat, nimble, no-nonsense API" +HOMEPAGE="https://pypi.python.org/pypi/Fiona" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + >=sci-libs/gdal-1.8 + dev-python/click[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + test? ( + dev-python/nose[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/cligj[${PYTHON_USEDEP}] + dev-python/munch[${PYTHON_USEDEP}] + dev-python/click-plugins[${PYTHON_USEDEP}] + )" + +PATCHES=( "${FILESDIR}"/scriptname-${PV}.patch ) + +python_test() { + esetup.py test +} diff --git a/sci-libs/Fiona/Fiona-9999.ebuild b/sci-libs/Fiona/Fiona-9999.ebuild new file mode 100644 index 000000000000..a4322b36330a --- /dev/null +++ b/sci-libs/Fiona/Fiona-9999.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="OGR's neat, nimble, no-nonsense API" +HOMEPAGE="https://pypi.python.org/pypi/Fiona" +SRC_URI="" +EGIT_REPO_URI="https://github.com/Toblerity/${PN}.git" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="" +IUSE="test" + +RDEPEND=" + >=sci-libs/gdal-1.8 + dev-python/click[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + test? ( + dev-python/nose[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + )" + +PATCHES=( "${FILESDIR}"/scriptname.patch ) + +python_test() { + esetup.py test +} diff --git a/sci-libs/Fiona/Manifest b/sci-libs/Fiona/Manifest new file mode 100644 index 000000000000..3cde0bf9788d --- /dev/null +++ b/sci-libs/Fiona/Manifest @@ -0,0 +1,10 @@ +AUX scriptname-1.7.6.patch 362 SHA256 ce48d1e3410257e5c2d805d49732595bc86b4ee7a4cacbfaa94d3c63fb3dd1ba SHA512 2c5e5c6c08274f75fe5306c8318a375a81ec08a3c3978cd8412c2cbe16bd5790b821bb0fce85d37f9af6238cc0f8e96740e9e72c66c213a74ad43d0e9ef916b8 WHIRLPOOL 2b25c60e1015e5095257ff4840c15c4341f5d125882747cc655ca23d5e6a4cded9a8eb9738a95f41ed1e9238aa3a8924b23f54fa7e914b58f3de29d1515de0a4 +AUX scriptname.patch 353 SHA256 d68af1bca4a036c54016028e25c507857815ef557d5a099d0fef6515ecde640e SHA512 f9a0c51fbdc5bf99eb9a2b94c0f27f7f6fef7ebab94d9e575f34594e31dcb624e4c327e147e5b4955b5434b54cd2179b985bc64a9410bdb792b93f45375838c9 WHIRLPOOL 0432177f8585292af401811a09fda058f49fef4a0cae2d0c14c74ffd691e60d99ee5be0054d0999c3fe4df3ece45455b47bc956f473b8f26539c9b7c277a29aa +DIST Fiona-1.5.1.tar.gz 1117361 SHA256 2e2469190107dc671b4aa05d5b8bed5c01ffeb9de79525c91129bad76915e095 SHA512 06a2f091138b455355aa24bdd3cace48a3ccbbcb8b680f8009862a9ef3bdc217b68ba4596c51caaa9d09d2fad606a581d50f2fc9f2d0636bfec459e2022546a7 WHIRLPOOL 47d274f1755aa875273f1c8b4ce8949fe9a22b237fff90bdf71aa3ff7a6a4a18ff9016ebe3cdf8b323a2d67fa45b6cb8c8e8bfc20c2c57e01df0aa7cf8733330 +DIST Fiona-1.7.6.tar.gz 641013 SHA256 d0ab7d04556005a6354c4edfd820a4001a4ad7b57332e28f7dd6c4cdab9a0e3c SHA512 a988772cd8d9cf7ee6862b87c91d18d5caf78f81c35c018e815dfb0000502a0768d9ce6c580a8ef9a9a652c64c4b6027685d597766f851563a70db07db0de4f3 WHIRLPOOL 451cad50035918b29576fd865d475249719d426ceae59bffb387422dfc2ffb8e09aa2b634b610e97e266979f5313d7ae6b2ded328012381dfd45dca008e811ed +EBUILD Fiona-1.5.1.ebuild 715 SHA256 84e1cbc7842bb2b1a13ccf303b0731cb1fe70edeff8ecb90f4634f305790720a SHA512 c90b22be37d75e1e75e98f3882b981064d8794b8b5122645b68fa14a3d41ff238eb899fff9866610a80f0c666c9068dedd68ea3a3379531932d6ef07ecab6c95 WHIRLPOOL ee193aa0ab5ad022e604f685dfa637970799d104a9d3093111116806412b69acf3ac6365c8f2f38bfcab9e33b54db3c0e0f8d6f61cf33864bf87150bffd7ab9f +EBUILD Fiona-1.7.6.ebuild 844 SHA256 a390d2d9c1cffa909f4393733afbafc9b5b2323414202641788173eb15760e2c SHA512 a15eaf2c62a4c454ee0cf7c925aeea4f416d7769d3b24d91fde24e68a3bfe6ba1f4f000291f23acccb77ded1fbfbdf39b4eba77ae787752dfb4d2fce7e8fe5cf WHIRLPOOL b6c61093d4e4eda46f75b4ea82614f7758088b3d0e414c7bdf045abb9dde6f8aeb786f0f5abeb0c679e36e04b19d3dbf21ce97661e3910b58d3e8c39b3ff5775 +EBUILD Fiona-9999.ebuild 731 SHA256 818aee6c45a516d44473d38d04f15c092406a568e9e80970891a5cbd138e7fb6 SHA512 3a72cff9872a1730f781220fe5295dea890e08d5a24b1d22f4bad1c737087208bddfb2f2bd9c3c5c8812d8cf0c2009a3313dbed7c2871bd30b81cf0ff0920550 WHIRLPOOL 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de0472e2bb3e03ab9d0c4639274c82fd0019054b5bae99294b82d24f5af057737c61b58065db930088d7021aeaf3e18b520733bb7a2ca5e8eb567d7ee82e5ac1 WHIRLPOOL 0f99b183ce31c8fcac468c1df55f9e81d6c9230215c56f44443736d14dc7e8aeda235fb4f6a19db3241a2b2518ac95c545bfca8d9e61cdd124b7184d9019d93d diff --git a/sci-libs/Fiona/files/scriptname-1.7.6.patch b/sci-libs/Fiona/files/scriptname-1.7.6.patch new file mode 100644 index 000000000000..410caf39da55 --- /dev/null +++ b/sci-libs/Fiona/files/scriptname-1.7.6.patch @@ -0,0 +1,11 @@ +--- setup.py.orig 2017-05-30 10:51:33.369935784 +0200 ++++ setup.py 2017-05-30 10:51:45.793269042 +0200 +@@ -251,7 +251,7 @@ + packages=['fiona', 'fiona.fio'], + entry_points=''' + [console_scripts] +- fio=fiona.fio.main:main_group ++ Fiona=fiona.fio.main:main_group + + [fiona.fio_commands] + bounds=fiona.fio.bounds:bounds diff --git a/sci-libs/Fiona/files/scriptname.patch b/sci-libs/Fiona/files/scriptname.patch new file mode 100644 index 000000000000..227e644f0759 --- /dev/null +++ b/sci-libs/Fiona/files/scriptname.patch @@ -0,0 +1,11 @@ +--- setup.py.orig 2015-03-27 21:34:22.790592037 +0100 ++++ setup.py 2015-03-27 21:34:54.247259049 +0100 +@@ -150,7 +150,7 @@ + packages=['fiona', 'fiona.fio'], + entry_points=''' + [console_scripts] +- fio=fiona.fio.fio:cli ++ Fiona=fiona.fio.fio:cli + ''', + install_requires=requirements, + tests_require=['nose'], diff --git a/sci-libs/Fiona/metadata.xml b/sci-libs/Fiona/metadata.xml new file mode 100644 index 000000000000..8260bf3a55b3 --- /dev/null +++ b/sci-libs/Fiona/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>slis@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="pypi">Fiona</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/Rtree/Manifest b/sci-libs/Rtree/Manifest new file mode 100644 index 000000000000..b3b4812ea313 --- /dev/null +++ b/sci-libs/Rtree/Manifest @@ -0,0 +1,5 @@ +DIST Rtree-0.8.2.tar.gz 55813 SHA256 064ecd9791fe170a8492f4ae75b0cbe8e62b5392f136a159a24d1b70c86d3c3f SHA512 c0c1091c21e92022540a0aed09c00f3b2b6abb2869757e0cb7a68a120e3a289f275cea824a72172ea5b327696a67024894f5f01354f0cd5ec5b05d9b3ec130e0 WHIRLPOOL 3167258f8a1480b2af65ebe6b6070870f6ad8dd2c5045285cb4babdff64a0bd85a4c434bf9b2a7908e211ec16be268482eacf2de8390afb27f06e8084c7b8db4 +EBUILD Rtree-0.8.2.ebuild 457 SHA256 91a530909d990c0d512fc370938d6e0d6cdf894bfc5a9cce8d162c6f90d4b834 SHA512 bc28ffe5084192a5a3a38c8734b19baa5c9b74fdb55edaab0f198c3219abf59f2202b0d35e6dd6c2d41c4deb541e570905351f64f287c1567bdfcd7bab6ee8f0 WHIRLPOOL 7480bf80462e4bf000c133b178be3d332392110675b776f5382a4860520cde44dde2d55960904ef4ce84b4b7fb12f2dacd864b2d437068369b1b087a71383fb7 +MISC ChangeLog 2170 SHA256 1974284adca84b6d99f278b34490dc2995406df0b93cc941fb3b5ce99baa0d56 SHA512 27de83c4722801ef8ce2d4198df15371913e2f1d13b1eed5692bfc95eb7168a28303310abf3c2200f2cf5b1eedc0a9ba369f5bf483cb83690af1776b92095249 WHIRLPOOL 04b8f08680b11892b26b618f133c0af40eee94b83284955abc741a2a77fbe582202b39d0ee87b7306262148b3ba240bcf5d1fc500bfc2f568b1890903d2d8a52 +MISC ChangeLog-2015 432 SHA256 7ddc20500b16efdd875cb49e8cd67ef5376967e82fb4009942b52992edd3256d SHA512 a7a39419fd349cd4ce900b6ec76ad4fda3949eaa9fdc2aea0640ce1a53f3cb31d9512ac9f65e584cbcfadc59856cfa53a8a9221e47a786a9f2f69a3379320f1d WHIRLPOOL 10b543505f02d69338657663b755b91969ee8aa0c40f464676d8d2da1b58d2c0219494db85b7dc86a519ca8b395f6e370810aa084b68308a0ac1973b5e1f8caf +MISC metadata.xml 291 SHA256 0cd38fd68b4391c716c4ff7d9ac763199d48b52d5e5dce2cf0b1a1d82611e892 SHA512 1dc1aaee480103b3d6f3cbdc7612960d422407ceed6e9014a28438bb19d61657291fe7df764928e1cbabb53e7b611afe70ea00c2eb2fb5e5c65a973cadedf367 WHIRLPOOL d5771d118e712995ac027c1db37372bb3a10a317b3f3659ed74e1a62754c558abd635bfdc694505170987a68d0be20bddd745da1464762b401db2f7cc64321d6 diff --git a/sci-libs/Rtree/Rtree-0.8.2.ebuild b/sci-libs/Rtree/Rtree-0.8.2.ebuild new file mode 100644 index 000000000000..de9e5b077474 --- /dev/null +++ b/sci-libs/Rtree/Rtree-0.8.2.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="R-Tree spatial index for Python GIS" +HOMEPAGE="https://pypi.python.org/pypi/Rtree" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="sci-libs/libspatialindex + sci-libs/scipy" +DEPEND="dev-python/setuptools" diff --git a/sci-libs/Rtree/metadata.xml b/sci-libs/Rtree/metadata.xml new file mode 100644 index 000000000000..150a150f5ebe --- /dev/null +++ b/sci-libs/Rtree/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>slis@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="pypi">Rtree</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/Shapely/Manifest b/sci-libs/Shapely/Manifest new file mode 100644 index 000000000000..1d0ee3046c76 --- /dev/null +++ b/sci-libs/Shapely/Manifest @@ -0,0 +1,12 @@ +AUX setup_unicode.patch 698 SHA256 507d6fb5a65ceeceb788c1a17efc96cd34fbd5912c2ddb37f606ffab2dc3d927 SHA512 f3e2766a1da5586a5c534d4e2eae1a00545d5af90e0f7ce92d2a1e38644f07b6db90c7ab20742d390e79198b6d5957900a7cd6777515a773fab2f1f98e09c8dd WHIRLPOOL fdf1f6badda690465169a9f7a660f78fec54b94ea60f36ab33bc7d529223df9f3d894607754c6659fefb1702c1bc73412c33961ccb7367782c3bd0105f4e2924 +DIST Shapely-1.3.0.tar.gz 118863 SHA256 297df004aec27e38ed93987e93ff5f8187cd0299394fe8b0b9028566015a9bb5 SHA512 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850b4e0ef0b365030c29a55c20eba931ea283a3f1603d0c0f887e80fad352ffcee0c546cd68ada65d4ba9f33fc0bfb2a817b11e630e704a22928380c7180deb4 WHIRLPOOL 0813d1f462e8f281191ef755748ff1af35113644666c2da2b50f5a24273c70589ca0d09e66f63e9bd11103a4c2ff7f241eb3b84f033e8c929bfb6bf38a303bbf diff --git a/sci-libs/Shapely/Shapely-1.3.0.ebuild b/sci-libs/Shapely/Shapely-1.3.0.ebuild new file mode 100644 index 000000000000..290fdf25740f --- /dev/null +++ b/sci-libs/Shapely/Shapely-1.3.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python2_7 python3_4 ) + +inherit distutils-r1 + +DESCRIPTION="Geometric objects, predicates, and operations" +HOMEPAGE="https://pypi.python.org/pypi/Shapely" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=">=sci-libs/geos-3.1" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +PATCHES=( "${FILESDIR}"/setup_unicode.patch ) + +python_test() { + esetup.py test +} diff --git a/sci-libs/Shapely/Shapely-1.3.2.ebuild b/sci-libs/Shapely/Shapely-1.3.2.ebuild new file mode 100644 index 000000000000..290fdf25740f --- /dev/null +++ b/sci-libs/Shapely/Shapely-1.3.2.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python2_7 python3_4 ) + +inherit distutils-r1 + +DESCRIPTION="Geometric objects, predicates, and operations" +HOMEPAGE="https://pypi.python.org/pypi/Shapely" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=">=sci-libs/geos-3.1" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +PATCHES=( "${FILESDIR}"/setup_unicode.patch ) + +python_test() { + esetup.py test +} diff --git a/sci-libs/Shapely/Shapely-1.5.17-r1.ebuild b/sci-libs/Shapely/Shapely-1.5.17-r1.ebuild new file mode 100644 index 000000000000..9dc9f27b2a21 --- /dev/null +++ b/sci-libs/Shapely/Shapely-1.5.17-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 + +DESCRIPTION="Geometric objects, predicates, and operations" +HOMEPAGE="https://pypi.python.org/pypi/Shapely" + +if [[ ${PV} == "9999" ]] ; then + inherit git-r3 + SRC_URI="" + EGIT_REPO_URI="https://github.com/Toblerity/${PN}.git" +else + SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="BSD" +SLOT="0" +IUSE="test" + +RDEPEND=">=sci-libs/geos-3.3 + dev-python/numpy[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/cython[${PYTHON_USEDEP}] + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +python_prepare_all() { + # fix install path for Cython definition file + sed -i \ + -e "s|\(data_files.*\)'shapely'|\1'share/shapely'|" \ + setup.py || die + + distutils-r1_python_prepare_all +} + +python_test() { + distutils_install_for_testing + cd "${TEST_DIR}/lib" || die + cp -r "${S}/tests" . || die + py.test tests || die +} diff --git a/sci-libs/Shapely/Shapely-1.5.17.ebuild b/sci-libs/Shapely/Shapely-1.5.17.ebuild new file mode 100644 index 000000000000..a90108d26d17 --- /dev/null +++ b/sci-libs/Shapely/Shapely-1.5.17.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" +PYTHON_COMPAT=( python{2_7,3_{4,5}} ) + +inherit distutils-r1 + +DESCRIPTION="Geometric objects, predicates, and operations" +HOMEPAGE="https://pypi.python.org/pypi/Shapely" + +if [[ ${PV} == "9999" ]] ; then + inherit git-r3 + SRC_URI="" + EGIT_REPO_URI="https://github.com/Toblerity/${PN}.git" +else + SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="BSD" +SLOT="0" +IUSE="test" + +RDEPEND=">=sci-libs/geos-3.1" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +python_test() { + esetup.py test +} diff --git a/sci-libs/Shapely/Shapely-9999.ebuild b/sci-libs/Shapely/Shapely-9999.ebuild new file mode 100644 index 000000000000..efa8587ea42e --- /dev/null +++ b/sci-libs/Shapely/Shapely-9999.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="Geometric objects, predicates, and operations" +HOMEPAGE="https://pypi.python.org/pypi/Shapely" +SRC_URI="" +EGIT_REPO_URI="https://github.com/Toblerity/${PN}.git" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="" +IUSE="test" + +RDEPEND=">=sci-libs/geos-3.1" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +python_test() { + esetup.py test +} diff --git a/sci-libs/Shapely/files/setup_unicode.patch b/sci-libs/Shapely/files/setup_unicode.patch new file mode 100644 index 000000000000..89e1b058f0f8 --- /dev/null +++ b/sci-libs/Shapely/files/setup_unicode.patch @@ -0,0 +1,23 @@ +--- setup.py.orig 2014-06-20 10:27:26.638779565 +0200 ++++ setup.py 2014-06-20 10:27:29.885446151 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++# -*- coding: utf-8 -*- + + from __future__ import print_function + +@@ -74,8 +75,12 @@ + readme_text = fp.read() + readme_text = readme_text.replace(".. include:: CREDITS.txt", "") + +-with open('CREDITS.txt', 'r') as fp: +- credits = fp.read() ++if sys.version_info[0] == 3: ++ with open('CREDITS.txt', 'r', encoding='utf-8') as fp: ++ credits = fp.read() ++elif sys.version_info[0] == 2: ++ with open('CREDITS.txt', 'r') as fp: ++ credits = fp.read().decode('utf-8') + + with open('CHANGES.txt', 'r') as fp: + changes_text = fp.read() diff --git a/sci-libs/Shapely/metadata.xml b/sci-libs/Shapely/metadata.xml new file mode 100644 index 000000000000..a97d495a34c5 --- /dev/null +++ b/sci-libs/Shapely/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>slis@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="pypi">Shapely</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/ViSP/Manifest b/sci-libs/ViSP/Manifest new file mode 100644 index 000000000000..df59675033bb --- /dev/null +++ b/sci-libs/ViSP/Manifest @@ -0,0 +1,7 @@ +AUX ViSP-3.0.0-ffmpeg3.patch 4291 SHA256 9afb4a33dd65a3cd07638ed0a7284f14c4bb9478cf72a4c29592ea5f629bc3dd SHA512 fed1699ccaba5baa67e0fde19abc5ae828c51c88bf761a9d6784b8ad858230cca7e11bfbc1fb7661bca0a666c49ff9915e0a771909bf42493229165d1131b3a9 WHIRLPOOL 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a47e3d09ebcf9d27349fd9f568168efe56b503479e887a4e4f4b308293e4d65db2a10a2a1727245c3d7bd84124473f1dc5cd248dc5bf9fc091dbf1e8675dedb6 WHIRLPOOL d371d4dd084e34488ba5fdeaff812f16772be534919e4d7cdebde1d120fb0ce964e681a7c02e61afb383b181e8cf5792fd2c5c02752b70eb87fc1eac3f2b9d78 +MISC ChangeLog 3870 SHA256 fc10538840344796527d38e8f3996f4f67e9111df6ddde26e2dbafbdb2d4350d SHA512 16ec980eb40a76dd576654babe408733a3e82521f5487d3b97cbdbd011c1307036d10eb6f411bfb94165c8bf35ed3a67dbdcfb164d32892bf9b0439680ff210d WHIRLPOOL 0b644b43ebb2f5d9711a6c70948755467fa7d05e26769087ae390acaaccec955606a850155d7ccb5153937cd32488a520895507565f112e145ed4bd82c306974 +MISC ChangeLog-2015 712 SHA256 06f16b06376a8809501b369a8a46fc7753743d59a346b7da7750a25be668f54f SHA512 6e655228d267f3dc90a34bf5f53edf5d1e17f98dc3bf425963f249317c219c0dcb2252ad624ff4cd1fd33fcf89f96ec0d878253cdd4523d5910e2304783ab8bc WHIRLPOOL 8fe255d3f578eaa72bd9a3abe5996e763ff24554c42270b17a0b6e4ed31bd3107a384072799d98616823355ef0a4f994dc534bde7b621fab48b7b754241e1cd2 +MISC metadata.xml 1377 SHA256 6fc75621bf9f3f4802008433b73046ce83505c431528d87256aaff49cc435c06 SHA512 a830ac98ca671d7ffedc8d891b3ab5aadfc6da9251fa1b45fa5df6076add1c8d4cf03eca3581c7dca83c97fb3b8d871559d409cdf2d1267adf1e4a5132ae83a7 WHIRLPOOL a091127ecfa1fee0865b1457b8f75fec176c662fdbd594c5849c4c4d5f9b5fbc1347964b0ea4454a78eaf8319bc747918e0bd4a10d8793779e5dca6b84314a4e diff --git a/sci-libs/ViSP/ViSP-3.0.1.ebuild b/sci-libs/ViSP/ViSP-3.0.1.ebuild new file mode 100644 index 000000000000..390e20cb18a2 --- /dev/null +++ b/sci-libs/ViSP/ViSP-3.0.1.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Visual Servoing Platform: visual tracking and visual servoing library" +HOMEPAGE="http://www.irisa.fr/lagadic/visp/visp.html" +SRC_URI="http://gforge.inria.fr/frs/download.php/latestfile/475/visp-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0/3" +KEYWORDS="~amd64 ~arm" +IUSE=" + +coin demos +dmtx doc examples ffmpeg gsl ieee1394 jpeg lapack motif ogre + ois opencv png qt4 test tutorials usb v4l X xml +zbar zlib + cpu_flags_x86_sse2 cpu_flags_x86_sse3 cpu_flags_x86_ssse3 +" + +RDEPEND=" + coin? ( media-libs/coin virtual/opengl ) + dmtx? ( media-libs/libdmtx ) + ffmpeg? ( virtual/ffmpeg ) + gsl? ( sci-libs/gsl ) + ieee1394? ( media-libs/libdc1394 ) + jpeg? ( virtual/jpeg:0 ) + lapack? ( virtual/lapack ) + !qt4? ( motif? ( media-libs/SoXt ) ) + ogre? ( dev-games/ogre[ois?] dev-libs/boost:=[threads] ) + opencv? ( media-libs/opencv:= qt4? ( media-libs/opencv[-qt5(-)] ) ) + png? ( media-libs/libpng:0= ) + qt4? ( media-libs/SoQt dev-qt/qtgui:4 ) + usb? ( virtual/libusb:1 ) + v4l? ( media-libs/libv4l ) + X? ( x11-libs/libX11 ) + xml? ( dev-libs/libxml2 ) + zbar? ( media-gfx/zbar ) + zlib? ( sys-libs/zlib ) +" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen virtual/latex-base media-gfx/graphviz ) + virtual/pkgconfig + test? ( sci-misc/ViSP-images ) + v4l? ( virtual/os-headers )" +RDEPEND="${RDEPEND} + demos? ( sci-misc/ViSP-images )" +REQUIRED_USE=" + ffmpeg? ( opencv ) + ois? ( ogre ) + qt4? ( coin ) + motif? ( coin ) +" + +S="${WORKDIR}/visp-${PV}" +PATCHES=( "${FILESDIR}/${PN}-3.0.1-opencv.patch" "${FILESDIR}/${PN}-3.0.0-ffmpeg3.patch" ) + +src_configure() { + local mycmakeargs=( + "-DBUILD_EXAMPLES=$(usex examples ON OFF)" + "-DBUILD_TESTS=$(usex test ON OFF)" + "-DBUILD_DEMOS=$(usex demos ON OFF)" + "-DBUILD_TUTORIALS=$(usex tutorials ON OFF)" + "-DUSE_COIN3D=$(usex coin ON OFF)" + "-DUSE_DC1394=$(usex ieee1394 ON OFF)" + "-DUSE_DMTX=$(usex dmtx ON OFF)" + "-DUSE_FFMPEG=$(usex ffmpeg ON OFF)" + "-DUSE_GSL=$(usex gsl ON OFF)" + "-DUSE_LAPACK=$(usex lapack ON OFF)" + "-DUSE_JPEG=$(usex jpeg ON OFF)" + "-DUSE_PNG=$(usex png ON OFF)" + "-DUSE_LIBUSB_1=$(usex usb ON OFF)" + "-DUSE_OGRE=$(usex ogre ON OFF)" + "-DUSE_OIS=$(usex ois ON OFF)" + "-DUSE_OPENCV=$(usex opencv ON OFF)" + "-DUSE_SOQT=$(usex qt4 ON OFF)" + "-DUSE_SOXT=$(usex motif "$(usex qt4 OFF ON)" OFF)" + "-DUSE_V4L2=$(usex v4l ON OFF)" + "-DUSE_X11=$(usex X ON OFF)" + "-DUSE_XML2=$(usex xml ON OFF)" + "-DUSE_ZBAR=$(usex zbar ON OFF)" + "-DUSE_ZLIB=$(usex zlib ON OFF)" + "-DCOIN3D_INCLUDE_DIR=${EPREFIX:-${SYSROOT}}/usr/include/coin" + "-DSOQT_INCLUDE_DIR=${EPREFIX:-${SYSROOT}}/usr/include/coin" + "-DENABLE_SSE2=$(usex cpu_flags_x86_sse2 ON OFF)" + "-DENABLE_SSE3=$(usex cpu_flags_x86_sse3 ON OFF)" + "-DENABLE_SSSE3=$(usex cpu_flags_x86_ssse3 ON OFF)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + cd "${BUILD_DIR}" + use doc && emake visp_doc +} + +src_install() { + cmake-utils_src_install + if use tutorials ; then + dodoc -r tutorial + docompress -x /usr/share/doc/${PF}/tutorial + fi + cd "${BUILD_DIR}" + use doc && dohtml -r doc/html/* +} diff --git a/sci-libs/ViSP/files/ViSP-3.0.0-ffmpeg3.patch b/sci-libs/ViSP/files/ViSP-3.0.0-ffmpeg3.patch new file mode 100644 index 000000000000..8fd3c8b1edb3 --- /dev/null +++ b/sci-libs/ViSP/files/ViSP-3.0.0-ffmpeg3.patch @@ -0,0 +1,78 @@ +Index: visp-3.0.0/modules/io/src/video/vpFFMPEG.cpp +=================================================================== +--- visp-3.0.0.orig/modules/io/src/video/vpFFMPEG.cpp ++++ visp-3.0.0/modules/io/src/video/vpFFMPEG.cpp +@@ -180,7 +180,7 @@ bool vpFFMPEG::openStream(const char *fi + if (pFrameRGB == NULL) + return false; + +- numBytes = avpicture_get_size (PIX_FMT_RGB24,pCodecCtx->width,pCodecCtx->height); ++ numBytes = avpicture_get_size (AV_PIX_FMT_RGB24,pCodecCtx->width,pCodecCtx->height); + } + + else if (color_type == vpFFMPEG::GRAY_SCALED) +@@ -194,7 +194,7 @@ bool vpFFMPEG::openStream(const char *fi + if (pFrameGRAY == NULL) + return false; + +- numBytes = avpicture_get_size (PIX_FMT_GRAY8,pCodecCtx->width,pCodecCtx->height); ++ numBytes = avpicture_get_size (AV_PIX_FMT_GRAY8,pCodecCtx->width,pCodecCtx->height); + } + + /* +@@ -211,10 +211,10 @@ bool vpFFMPEG::openStream(const char *fi + } + + if (color_type == vpFFMPEG::COLORED) +- avpicture_fill((AVPicture *)pFrameRGB, buffer, PIX_FMT_RGB24, pCodecCtx->width, pCodecCtx->height); ++ avpicture_fill((AVPicture *)pFrameRGB, buffer, AV_PIX_FMT_RGB24, pCodecCtx->width, pCodecCtx->height); + + else if (color_type == vpFFMPEG::GRAY_SCALED) +- avpicture_fill((AVPicture *)pFrameGRAY, buffer, PIX_FMT_GRAY8, pCodecCtx->width, pCodecCtx->height); ++ avpicture_fill((AVPicture *)pFrameGRAY, buffer, AV_PIX_FMT_GRAY8, pCodecCtx->width, pCodecCtx->height); + + streamWasOpen = true; + +@@ -231,10 +231,10 @@ bool vpFFMPEG::openStream(const char *fi + bool vpFFMPEG::initStream() + { + if (color_type == vpFFMPEG::COLORED) +- img_convert_ctx= sws_getContext(pCodecCtx->width, pCodecCtx->height, pCodecCtx->pix_fmt, pCodecCtx->width,pCodecCtx->height,PIX_FMT_RGB24, SWS_BICUBIC, NULL, NULL, NULL); ++ img_convert_ctx= sws_getContext(pCodecCtx->width, pCodecCtx->height, pCodecCtx->pix_fmt, pCodecCtx->width,pCodecCtx->height,AV_PIX_FMT_RGB24, SWS_BICUBIC, NULL, NULL, NULL); + + else if (color_type == vpFFMPEG::GRAY_SCALED) +- img_convert_ctx= sws_getContext(pCodecCtx->width, pCodecCtx->height, pCodecCtx->pix_fmt, pCodecCtx->width,pCodecCtx->height,PIX_FMT_GRAY8, SWS_BICUBIC, NULL, NULL, NULL); ++ img_convert_ctx= sws_getContext(pCodecCtx->width, pCodecCtx->height, pCodecCtx->pix_fmt, pCodecCtx->width,pCodecCtx->height,AV_PIX_FMT_GRAY8, SWS_BICUBIC, NULL, NULL, NULL); + + int ret = av_seek_frame(pFormatCtx, (int)videoStream, 0, AVSEEK_FLAG_ANY) ; + if (ret < 0 ) +@@ -703,7 +703,7 @@ bool vpFFMPEG::openEncoder(const char *f + pCodecCtx->time_base.den = framerate_encoder; + pCodecCtx->gop_size = 10; /* emit one intra frame every ten frames */ + pCodecCtx->max_b_frames=1; +- pCodecCtx->pix_fmt = PIX_FMT_YUV420P; ++ pCodecCtx->pix_fmt = AV_PIX_FMT_YUV420P; + + /* open it */ + #if LIBAVCODEC_VERSION_INT < AV_VERSION_INT(53,35,0) // libavcodec 53.35.0 +@@ -726,15 +726,15 @@ bool vpFFMPEG::openEncoder(const char *f + outbuf_size = 100000; + outbuf = new uint8_t[outbuf_size]; + +- numBytes = avpicture_get_size (PIX_FMT_YUV420P,pCodecCtx->width,pCodecCtx->height); ++ numBytes = avpicture_get_size (AV_PIX_FMT_YUV420P,pCodecCtx->width,pCodecCtx->height); + picture_buf = new uint8_t[numBytes]; +- avpicture_fill((AVPicture *)pFrame, picture_buf, PIX_FMT_YUV420P, pCodecCtx->width, pCodecCtx->height); ++ avpicture_fill((AVPicture *)pFrame, picture_buf, AV_PIX_FMT_YUV420P, pCodecCtx->width, pCodecCtx->height); + +- numBytes = avpicture_get_size (PIX_FMT_RGB24,pCodecCtx->width,pCodecCtx->height); ++ numBytes = avpicture_get_size (AV_PIX_FMT_RGB24,pCodecCtx->width,pCodecCtx->height); + buffer = new uint8_t[numBytes]; +- avpicture_fill((AVPicture *)pFrameRGB, buffer, PIX_FMT_RGB24, pCodecCtx->width, pCodecCtx->height); ++ avpicture_fill((AVPicture *)pFrameRGB, buffer, AV_PIX_FMT_RGB24, pCodecCtx->width, pCodecCtx->height); + +- img_convert_ctx= sws_getContext(pCodecCtx->width, pCodecCtx->height, PIX_FMT_RGB24, pCodecCtx->width,pCodecCtx->height,PIX_FMT_YUV420P, SWS_BICUBIC, NULL, NULL, NULL); ++ img_convert_ctx= sws_getContext(pCodecCtx->width, pCodecCtx->height, AV_PIX_FMT_RGB24, pCodecCtx->width,pCodecCtx->height,AV_PIX_FMT_YUV420P, SWS_BICUBIC, NULL, NULL, NULL); + + encoderWasOpened = true; + diff --git a/sci-libs/ViSP/files/ViSP-3.0.1-opencv.patch b/sci-libs/ViSP/files/ViSP-3.0.1-opencv.patch new file mode 100644 index 000000000000..c50dcb6d182e --- /dev/null +++ b/sci-libs/ViSP/files/ViSP-3.0.1-opencv.patch @@ -0,0 +1,12 @@ +Index: visp-3.0.1/modules/core/CMakeLists.txt +=================================================================== +--- visp-3.0.1.orig/modules/core/CMakeLists.txt ++++ visp-3.0.1/modules/core/CMakeLists.txt +@@ -182,6 +182,7 @@ if(USE_OPENCV) + if(OpenCV_INCLUDE_DIRS) + list(APPEND opt_incs ${OpenCV_INCLUDE_DIRS}) + endif() ++ list(APPEND opt_libs ${OpenCV_LIBS}) + endif(USE_OPENCV) + + if(USE_YARP) diff --git a/sci-libs/ViSP/metadata.xml b/sci-libs/ViSP/metadata.xml new file mode 100644 index 000000000000..abab5bed6646 --- /dev/null +++ b/sci-libs/ViSP/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="person"> +<email>aballier@gentoo.org</email> +<name>Alexis Ballier</name> +</maintainer> +<use> + <flag name="coin">Enables Coin3D support.</flag> + <flag name="dmtx">Enables barcode data matrix support.</flag> + <flag name="demos">Installs demo programs.</flag> + <flag name="ogre">Enables <pkg>dev-games/ogre</pkg> support.</flag> + <flag name="ois">Enables <pkg>dev-games/ois</pkg> support via ogre.</flag> + <flag name="opencv">Enables <pkg>media-libs/opencv</pkg> support.</flag> + <flag name="tutorials">Installs tutorials.</flag> + <flag name="zbar">Enables barcodes reading.</flag> +</use> +<longdescription lang="en"> + ViSP standing for Visual Servoing Platform is a modular cross platform library that allows prototyping and developing applications using visual tracking and visual servoing technics at the heart of the researches done by Inria Lagadic team. + ViSP is able to compute control laws that can be applied to robotic systems. + It provides a set of visual features that can be tracked using real time image processing or computer vision algorithms. + ViSP provides also simulation capabilities. + + ViSP can be useful in robotics, computer vision, augmented reality and computer animation. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/adolc/Manifest b/sci-libs/adolc/Manifest new file mode 100644 index 000000000000..0f824dda406a --- /dev/null +++ b/sci-libs/adolc/Manifest @@ -0,0 +1,19 @@ +AUX adolc-2.4.0-no-colpack.patch 580 SHA256 75b7b059336059383c8e0e08da8176f7f8084576397341858a93a88b2c6817cd SHA512 974e538343c377ce286c63b5206a5c3c33d9b5995addac07860ca52f6e1d3ca42d1fe8c1384b6d5d0ac39c062d8dc1f984262172b347f273c0e4c7d43fd120a2 WHIRLPOOL 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bab109356a0cfc40b0c21518628774bdbb35874247fa71baf12a6755a41fc6d6cd5a8551ae568f3d24e84d7a5ef4026ea2cbda182724ed78d0d962b0c5a80c89 WHIRLPOOL 80e2efe5ae5573db0d64de59a192648e720858ae771422ae6d91650c4da393eca51fdd3a16fe5d712481c80f1865aab2d5165ffad499b01d2af636d66a44106a diff --git a/sci-libs/adolc/adolc-2.4.1.ebuild b/sci-libs/adolc/adolc-2.4.1.ebuild new file mode 100644 index 000000000000..d8eda2e65133 --- /dev/null +++ b/sci-libs/adolc/adolc-2.4.1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes +AUTOTOOLS_IN_SOURCE_BUILD=yes +inherit autotools-utils toolchain-funcs + +MYPN=ADOL-C + +DESCRIPTION="Automatic differentiation system for C/C++" +HOMEPAGE="https://projects.coin-or.org/ADOL-C/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="|| ( EPL-1.0 GPL-2 )" +SLOT="0/1" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="sparse static-libs" + +RDEPEND="sparse? ( sci-libs/colpack )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}-${PV}" + +PATCHES=( "${FILESDIR}"/${PN}-2.4.0-no-colpack.patch ) + +src_configure() { + local myeconfargs=( + $(use_enable sparse) + $(use_with sparse colpack "${EPREFIX}"/usr) + ) + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test test +} diff --git a/sci-libs/adolc/adolc-2.5.0.ebuild b/sci-libs/adolc/adolc-2.5.0.ebuild new file mode 100644 index 000000000000..8b54bd951b7b --- /dev/null +++ b/sci-libs/adolc/adolc-2.5.0.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes +#AUTOTOOLS_IN_SOURCE_BUILD=yes + +inherit autotools-utils toolchain-funcs + +MYPN=ADOL-C + +DESCRIPTION="Automatic differentiation system for C/C++" +HOMEPAGE="https://projects.coin-or.org/ADOL-C/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="|| ( EPL-1.0 GPL-2 )" +SLOT="0/1" +KEYWORDS="~amd64 ~hppa ~x86 ~amd64-linux ~x86-linux" +IUSE="mpi sparse static-libs" + +RDEPEND="mpi? ( sys-cluster/ampi:0= ) + sparse? ( sci-libs/colpack:0= )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}-${PV}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.5.0-no-colpack.patch + "${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch +) + +src_configure() { + local myeconfargs=( + $(use_enable mpi ampi) + $(use_enable sparse) + $(use_with sparse colpack "${EPREFIX}"/usr) + ) + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test test +} diff --git a/sci-libs/adolc/adolc-2.5.2.ebuild b/sci-libs/adolc/adolc-2.5.2.ebuild new file mode 100644 index 000000000000..b625ae76398f --- /dev/null +++ b/sci-libs/adolc/adolc-2.5.2.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes +#AUTOTOOLS_IN_SOURCE_BUILD=yes + +inherit autotools-utils toolchain-funcs + +MYPN=ADOL-C + +DESCRIPTION="Automatic differentiation system for C/C++" +HOMEPAGE="https://projects.coin-or.org/ADOL-C/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="|| ( EPL-1.0 GPL-2 )" +SLOT="0/1" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="mpi sparse static-libs" + +RDEPEND=" + mpi? ( sys-cluster/ampi:0= ) + sparse? ( sci-libs/colpack:0= )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}-${PV}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.5.0-no-colpack.patch + "${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch + "${FILESDIR}"/${P}-dash.patch +) + +src_configure() { + local myeconfargs=( + $(use_enable mpi ampi) + $(use_enable sparse) + $(use_with sparse colpack "${EPREFIX}"/usr) + ) + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test test +} diff --git a/sci-libs/adolc/adolc-2.6.2.ebuild b/sci-libs/adolc/adolc-2.6.2.ebuild new file mode 100644 index 000000000000..52b9d2868659 --- /dev/null +++ b/sci-libs/adolc/adolc-2.6.2.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs eutils + +MYPN=ADOL-C + +DESCRIPTION="Automatic differentiation system for C/C++" +HOMEPAGE="https://projects.coin-or.org/ADOL-C/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="|| ( EPL-1.0 GPL-2 )" +SLOT="0/2" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="mpi sparse static-libs" + +RDEPEND=" + mpi? ( sys-cluster/ampi:0= ) + sparse? ( sci-libs/colpack:0= ) +" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}-${PV}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.5.0-no-colpack.patch + "${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch + "${FILESDIR}"/${PN}-2.6.2-dash.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_enable mpi ampi) \ + $(use_enable sparse) \ + $(use_with sparse colpack "${EPREFIX}"/usr) +} + +src_test() { + emake test +} + +src_install() { + default + use static-libs || prune_libtool_files --all +} diff --git a/sci-libs/adolc/adolc-2.6.3.ebuild b/sci-libs/adolc/adolc-2.6.3.ebuild new file mode 100644 index 000000000000..eb2ddb931e3d --- /dev/null +++ b/sci-libs/adolc/adolc-2.6.3.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs eutils + +MYPN=ADOL-C + +DESCRIPTION="Automatic differentiation system for C/C++" +HOMEPAGE="https://projects.coin-or.org/ADOL-C/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="|| ( EPL-1.0 GPL-2 )" +SLOT="0/2" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="mpi sparse static-libs" + +RDEPEND=" + mpi? ( sys-cluster/ampi:0= ) + sparse? ( sci-libs/colpack:0= ) +" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}-${PV}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.5.0-no-colpack.patch + "${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch + "${FILESDIR}"/${PN}-2.6.2-dash.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_enable mpi ampi) \ + $(use_enable sparse) \ + $(use_with sparse colpack "${EPREFIX}"/usr) +} + +src_test() { + emake test +} + +src_install() { + default + use static-libs || prune_libtool_files --all +} diff --git a/sci-libs/adolc/adolc-9999.ebuild b/sci-libs/adolc/adolc-9999.ebuild new file mode 100644 index 000000000000..c029efc2ea29 --- /dev/null +++ b/sci-libs/adolc/adolc-9999.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs eutils git-r3 + +MYPN=ADOL-C + +DESCRIPTION="Automatic differentiation system for C/C++" +HOMEPAGE="https://projects.coin-or.org/ADOL-C/" + +if [[ ${PV} = *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="https://gitlab.com/adol-c/adol-c.git" + SRC_URI="" + KEYWORDS="" +else + SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc64 ~x86 ~amd64-linux ~x86-linux" + S="${WORKDIR}/${MYPN}-${PV}" +fi + +LICENSE="|| ( EPL-1.0 GPL-2 )" +SLOT="0/2" +IUSE="mpi sparse static-libs" + +RDEPEND=" + mpi? ( sys-cluster/ampi:0= ) + sparse? ( sci-libs/colpack:0= ) +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.5.0-no-colpack.patch + "${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch + "${FILESDIR}"/${PN}-2.6.2-dash.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_enable mpi ampi) \ + $(use_enable sparse) \ + $(use_with sparse colpack "${EPREFIX}"/usr) +} + +src_test() { + emake test +} + +src_install() { + default + use static-libs || prune_libtool_files --all +} diff --git a/sci-libs/adolc/files/adolc-2.4.0-no-colpack.patch b/sci-libs/adolc/files/adolc-2.4.0-no-colpack.patch new file mode 100644 index 000000000000..e3b5a4a2ca5f --- /dev/null +++ b/sci-libs/adolc/files/adolc-2.4.0-no-colpack.patch @@ -0,0 +1,24 @@ +do not test colpack when user says no even when it is installed + +--- configure.ac.orig 2012-07-19 13:04:37.426461811 -0700 ++++ configure.ac 2012-07-19 13:06:06.477916144 -0700 +@@ -281,7 +281,7 @@ + COLPACK_LIBDIR="" + COLPACK_LIBS="-lColPack" + ]) +- ++if test x$colpack != xno; then + AC_LANG_PUSH([C++]) + save_CPPFLAGS="$CPPFLAGS" + save_LIBS="$LIBS" +@@ -301,7 +301,9 @@ + CPPFLAGS="$save_CPPFLAGS" + LIBS="$save_LIBS" + AC_LANG_POP([C++]) +- ++else ++ have_colpack=no ++fi + AM_CONDITIONAL(HAVE_LIBCOLPACK,[test x$have_colpack = xyes]) + if test x$have_colpack = xyes; then + sparse=yes diff --git a/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch b/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch new file mode 100644 index 000000000000..779890c8cf2b --- /dev/null +++ b/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch @@ -0,0 +1,57 @@ + autoconf/colpack.m4 | 23 +++++++++++++---------- + 1 file changed, 13 insertions(+), 10 deletions(-) + +diff --git a/autoconf/colpack.m4 b/autoconf/colpack.m4 +index 9792786..bd4ba5e 100644 +--- a/autoconf/colpack.m4 ++++ b/autoconf/colpack.m4 +@@ -8,20 +8,20 @@ AC_ARG_WITH(colpack, + AS_HELP_STRING([--with-colpack=DIR],[path to the colpack library and headers [default=system libraries]])], + [ + colpack=$withval +-COLPACK_CFLAGS="-I$colpack/include" +-if test x${_lib} != xlib ; then +- D[[0]]="$colpack/${_lib}" +- D[[1]]="$colpack/lib" +-else +- D[[0]]="$colpack/${_lib}" +-fi + ], + [ + COLPACK_CFLAGS="" + COLPACK_LIBS="-lColPack" + D[[0]]="" + ]) +- ++if test x$colpack != xno; then ++COLPACK_CFLAGS="-I$colpack/include" ++if test x${_lib} != xlib ; then ++ D[[0]]="$colpack/${_lib}" ++ D[[1]]="$colpack/lib" ++else ++ D[[0]]="$colpack/${_lib}" ++fi + AC_LANG_PUSH([C++]) + save_CXXFLAGS="$CXXFLAGS" + save_CPPFLAGS="$CPPFLAGS" +@@ -33,8 +33,8 @@ have_colpackheaders=no + CPPFLAGS="$save_CPPFLAGS" + CXXFLAGS="$save_CXXFLAGS" + ]) +-for ((i=0; i < ${#D[@]} ; i++)); do +-COLPACK_LIBDIR="${D[[$i]]}" ++for i in ${D[@]}; do ++COLPACK_LIBDIR="${i}" + if test -n "$COLPACK_LIBDIR" ; then + COLPACK_LIBS="-L$COLPACK_LIBDIR -lColPack -Wl,-rpath,$COLPACK_LIBDIR" + fi +@@ -56,6 +56,9 @@ else + fi + done + AC_LANG_POP([C++]) ++else ++ have_colpack=no ++fi + + AM_CONDITIONAL(HAVE_LIBCOLPACK,[test x$have_colpack = xyes]) + if test x$have_colpack = xyes; then diff --git a/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch b/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch new file mode 100644 index 000000000000..258f835ca9e8 --- /dev/null +++ b/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch @@ -0,0 +1,9 @@ +--- a/adolclib.pc.in 2014-05-21 09:09:10.060824555 -0700 ++++ b/adolclib.pc.in 2014-05-21 09:09:10.060824555 -0700 +@@ -7,5 +7,5 @@ + Version: @PACKAGE_VERSION@ + Description: Algorithmic Differentiation Library for C/C++ + Requires: +-Libs: -L${libdir} -l@adolclib@ -Wl,-rpath,${libdir} @LDFLAGS@ @LIBS@ ++Libs: -L${libdir} -l@adolclib@ @LIBS@ + Cflags: -I${includedir} diff --git a/sci-libs/adolc/files/adolc-2.5.2-dash.patch b/sci-libs/adolc/files/adolc-2.5.2-dash.patch new file mode 100644 index 000000000000..3aa5a3035a14 --- /dev/null +++ b/sci-libs/adolc/files/adolc-2.5.2-dash.patch @@ -0,0 +1,148 @@ + configure.ac | 45 +++++++++++++++++---------------------------- + 1 file changed, 17 insertions(+), 28 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 926832c..1310025 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -29,12 +29,12 @@ AM_SILENT_RULES([yes]) + + adolclib=adolc + +-if test "x$CFLAGS" == x ; then ++if test "x$CFLAGS" = x ; then + ac_shell_cflags="not_set" + else + ac_shell_cflags="$CFLAGS" + fi +-if test "x$CXXFLAGS" == x ; then ++if test "x$CXXFLAGS" = x ; then + ac_shell_cxxflags="not_set" + else + ac_shell_cxxflags="$CXXFLAGS" +@@ -225,12 +225,12 @@ AS_HELP_STRING([--enable-harddebug],[enable ADOL-C hard debug mode + AC_MSG_RESULT(no) + ]) + +-if test x$adolc_harddebug == xyes ; then ++if test x$adolc_harddebug = xyes ; then + adolc_debug=yes + AC_DEFINE(ADOLC_HARDDEBUG,1,[ADOL-C hard debug mode]) + fi + +-if test x$adolc_debug == xyes ; then ++if test x$adolc_debug = xyes ; then + AC_DEFINE(ADOLC_DEBUG,1,[ADOL-C debug mode]) + fi + +@@ -248,7 +248,7 @@ AS_HELP_STRING([--disable-stdczero],[adouble default constructor does not initia + AC_MSG_RESULT(yes) + ]) + +-if test x$adolc_stdczero == xyes; then ++if test x$adolc_stdczero = xyes; then + AC_DEFINE(ADOLC_ADOUBLE_STDCZERO,1,[ADOL-C adouble zeroing mode]) + fi + +@@ -265,7 +265,7 @@ AS_HELP_STRING([--enable-lateinit],[adouble constructors need to be called. With + AC_MSG_RESULT(no) + ]) + +-if test x$adolc_late_init == xyes; then ++if test x$adolc_late_init = xyes; then + AC_DEFINE(ADOLC_ADOUBLE_LATEINIT,1,[ADOL-C adouble late initialization mode]) + fi + +@@ -282,7 +282,7 @@ AS_HELP_STRING([--enable-tserrno],[use errno as thread number cache [default=no] + AC_MSG_RESULT(no) + ]) + +-if test x$adolc_tserrno == xyes ; then ++if test x$adolc_tserrno = xyes ; then + AC_DEFINE(ADOLC_THREADSAVE_ERRNO,1,[ADOL-C thread save errno mode]) + fi + +@@ -351,8 +351,8 @@ AC_ARG_WITH(cflags, + [AS_HELP_STRING([--with-cflags=FLAGS], + [use CFLAGS=FLAGS (default: -O2)])], + [ac_adolc_cflags="$withval" +- if test x${adolc_debug} == xyes || +- test x${adolc_harddebug} == xyes ; then ++ if test "x${adolc_debug}" = xyes || ++ test "x${adolc_harddebug}" = xyes ; then + ac_adolc_cflags="$ac_adolc_cflags -g -O0" + fi + ac_adolc_cflags="$ac_adolc_cflags $ac_adolc_openmpflag" +@@ -360,8 +360,8 @@ AC_ARG_WITH(cflags, + AC_MSG_RESULT($ac_adolc_cflags)], + [if test "$ac_shell_cflags" = "not_set"; then + ac_adolc_cflags="-O2" +- if test x${adolc_debug} == xyes || +- test x${adolc_harddebug} == xyes ; then ++ if test "x${adolc_debug}" = xyes || ++ test "x${adolc_harddebug}" = xyes ; then + ac_adolc_cflags="-g -O0 -Wall -ansi" + fi + else +@@ -377,8 +377,8 @@ AC_ARG_WITH(cxxflags, + [AS_HELP_STRING([--with-cxxflags=FLAGS], + [use CXXFLAGS=FLAGS (default: -O2)])], + [ac_adolc_cxxflags="$withval" +- if test x${adolc_debug} == xyes || +- test x${adolc_harddebug} == xyes ; then ++ if test x${adolc_debug} = xyes || ++ test x${adolc_harddebug} = xyes ; then + ac_adolc_cxxflags="$ac_adolc_cxxflags -g -O0" + fi + ac_adolc_cxxflags="$ac_adolc_cxxflags $ac_adolc_openmpflag" +@@ -386,8 +386,8 @@ AC_ARG_WITH(cxxflags, + AC_MSG_RESULT($ac_adolc_cxxflags)], + [if test "$ac_shell_cxxflags" = "not_set"; then + ac_adolc_cxxflags="-O2" +- if test x${adolc_debug} == xyes || +- test x${adolc_harddebug} == xyes ; then ++ if test x${adolc_debug} = xyes || ++ test x${adolc_harddebug} = xyes ; then + ac_adolc_cxxflags="-g -O0 -Wall" + fi + else +@@ -420,7 +420,7 @@ AC_ARG_ENABLE(tapedoc_values, + ]) + AC_MSG_RESULT($tapedoc_values) + +-if test x$tapedoc_values == xyes; then ++if test x$tapedoc_values = xyes; then + AC_DEFINE(ADOLC_TAPE_DOC_VALUES,1,[ADOL-C tape_doc routine computes values]) + fi + +@@ -583,7 +583,7 @@ while test "x${pdir}" != "x/" ; do + break + fi + done +-if test "x${pdir}" == "x/" ; then ++if test "x${pdir}" = "x/" ; then + writable=false + fi + if ! ${writable} ; then +@@ -595,15 +595,6 @@ if ! ${writable} ; then + warn=true + fi + +-case ${prefix} in +- ${HOME}|${HOME}/*) +-if $warn ; then +- for (( i=5; i>0; i-- )); do +- echo -ne "\rPlease read the above messages carefully, continuing in ${i} seconds" +- sleep 1 +- done +- echo -e "\rPlease read the above messages carefully " +-fi + echo \ + " + ***************************************************************************** +@@ -629,5 +620,3 @@ echo \ + + ***************************************************************************** + " +-;; +-esac diff --git a/sci-libs/adolc/files/adolc-2.6.2-dash.patch b/sci-libs/adolc/files/adolc-2.6.2-dash.patch new file mode 100644 index 000000000000..b8d4fe5ad64d --- /dev/null +++ b/sci-libs/adolc/files/adolc-2.6.2-dash.patch @@ -0,0 +1,146 @@ +--- a/configure.ac 2016-08-31 12:49:35.000000000 +0000 ++++ b/configure.ac 2017-03-04 00:58:02.354372332 +0000 +@@ -29,12 +29,12 @@ + + adolclib=adolc + +-if test "x$CFLAGS" == x ; then ++if test "x$CFLAGS" = x ; then + ac_shell_cflags="not_set" + else + ac_shell_cflags="$CFLAGS" + fi +-if test "x$CXXFLAGS" == x ; then ++if test "x$CXXFLAGS" = x ; then + ac_shell_cxxflags="not_set" + else + ac_shell_cxxflags="$CXXFLAGS" +@@ -231,12 +231,12 @@ + AC_MSG_RESULT(no) + ]) + +-if test x$adolc_harddebug == xyes ; then ++if test x$adolc_harddebug = xyes ; then + adolc_debug=yes + AC_DEFINE(ADOLC_HARDDEBUG,1,[ADOL-C hard debug mode]) + fi + +-if test x$adolc_debug == xyes ; then ++if test x$adolc_debug = xyes ; then + AC_DEFINE(ADOLC_DEBUG,1,[ADOL-C debug mode]) + fi + +@@ -254,7 +254,7 @@ + AC_MSG_RESULT(yes) + ]) + +-if test x$adolc_stdczero == xyes; then ++if test x$adolc_stdczero = xyes; then + AC_DEFINE(ADOLC_ADOUBLE_STDCZERO,1,[ADOL-C adouble zeroing mode]) + fi + +@@ -271,7 +271,7 @@ + AC_MSG_RESULT(no) + ]) + +-if test x$adolc_late_init == xyes; then ++if test x$adolc_late_init = xyes; then + AC_DEFINE(ADOLC_ADOUBLE_LATEINIT,1,[ADOL-C adouble late initialization mode]) + fi + +@@ -288,7 +288,7 @@ + AC_MSG_RESULT(no) + ]) + +-if test x$adolc_tserrno == xyes ; then ++if test x$adolc_tserrno = xyes ; then + AC_DEFINE(ADOLC_THREADSAVE_ERRNO,1,[ADOL-C thread save errno mode]) + fi + +@@ -376,8 +376,8 @@ + [AS_HELP_STRING([--with-cflags=FLAGS], + [use CFLAGS=FLAGS (default: -O2)])], + [ac_adolc_cflags="$withval" +- if test x${adolc_debug} == xyes || +- test x${adolc_harddebug} == xyes ; then ++ if test "x${adolc_debug}" = xyes || ++ test "x${adolc_harddebug}" = xyes ; then + ac_adolc_cflags="$ac_adolc_cflags -g -O0" + fi + ac_adolc_cflags="$ac_adolc_cflags $ac_adolc_openmpflag" +@@ -385,8 +385,8 @@ + AC_MSG_RESULT($ac_adolc_cflags)], + [if test "$ac_shell_cflags" = "not_set"; then + ac_adolc_cflags="-O2" +- if test x${adolc_debug} == xyes || +- test x${adolc_harddebug} == xyes ; then ++ if test "x${adolc_debug}" = xyes || ++ test "x${adolc_harddebug}" = xyes ; then + ac_adolc_cflags="-g -O0 -Wall -ansi" + fi + else +@@ -402,8 +402,8 @@ + [AS_HELP_STRING([--with-cxxflags=FLAGS], + [use CXXFLAGS=FLAGS (default: -O2)])], + [ac_adolc_cxxflags="$withval" +- if test x${adolc_debug} == xyes || +- test x${adolc_harddebug} == xyes ; then ++ if test x${adolc_debug} = xyes || ++ test x${adolc_harddebug} = xyes ; then + ac_adolc_cxxflags="$ac_adolc_cxxflags -g -O0" + fi + ac_adolc_cxxflags="$ac_adolc_cxxflags $ac_adolc_openmpflag" +@@ -411,8 +411,8 @@ + AC_MSG_RESULT($ac_adolc_cxxflags)], + [if test "$ac_shell_cxxflags" = "not_set"; then + ac_adolc_cxxflags="-O2" +- if test x${adolc_debug} == xyes || +- test x${adolc_harddebug} == xyes ; then ++ if test x${adolc_debug} = xyes || ++ test x${adolc_harddebug} = xyes ; then + ac_adolc_cxxflags="-g -O0 -Wall" + fi + else +@@ -445,7 +445,7 @@ + ]) + AC_MSG_RESULT($tapedoc_values) + +-if test x$tapedoc_values == xyes; then ++if test x$tapedoc_values = xyes; then + AC_DEFINE(ADOLC_TAPE_DOC_VALUES,1,[ADOL-C tape_doc routine computes values]) + fi + +@@ -614,7 +614,7 @@ + break + fi + done +-if test "x${pdir}" == "x/" ; then ++if test "x${pdir}" = "x/" ; then + writable=false + fi + if ! ${writable} ; then +@@ -626,15 +626,6 @@ + warn=true + fi + +-case ${prefix} in +- ${HOME}|${HOME}/*) +-if $warn ; then +- for (( i=5; i>0; i-- )); do +- echo -ne "\rPlease read the above messages carefully, continuing in ${i} seconds" +- sleep 1 +- done +- echo -e "\rPlease read the above messages carefully " +-fi + echo \ + " + ***************************************************************************** +@@ -660,8 +651,6 @@ + + ***************************************************************************** + " +-;; +-esac + if test "x$enable_static" != "xno" ; then + echo \ + " Linking a user program with a static ADOL-C library will always result diff --git a/sci-libs/adolc/metadata.xml b/sci-libs/adolc/metadata.xml new file mode 100644 index 000000000000..150156feaded --- /dev/null +++ b/sci-libs/adolc/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The ADOLC system automatically calculates exact derivatives of a + C/C++ function. It uses C++ overloading to record arithmetic + operations, which it plays back later in various ways to calculate + the requested values. +</longdescription> + <use> + <flag name="sparse">Add support for sparse matrix algebra with <pkg>sci-libs/colpack</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-libs/alglib/Manifest b/sci-libs/alglib/Manifest new file mode 100644 index 000000000000..09a3b856f589 --- /dev/null +++ b/sci-libs/alglib/Manifest @@ -0,0 +1,9 @@ +AUX CMakeLists.txt 1076 SHA256 362393e6e363e739d9aeac7bebe84fce6848efc954f8dbcebed3d954163c947f SHA512 e5a10fe01c313863e23e9b61eef64e0b08232bf324d50ab6583bbb085cba5722c190bbdfca7bee485c65c8cd7e713300ced4a8feb2cdba0bee07244d5154de25 WHIRLPOOL 5e189008438a4791f278e27b180c557077b5951d617a2c690a0b19c9f900378be454c5aa07d2517ca8bbb7d8d57e01f5adda65f9785b39bd4af4d935823924d3 +AUX CMakeLists.txt-3.8.2 1159 SHA256 53ed7a133b27e83bf1a0255153a6d7b36924d59a7f0e40b8f688898640f53f15 SHA512 193661b9f949972048132bc07b4619c2f0d38135d6f0030621cd8aabf87e9e78a6bec18cdb4fb9cb9e547fee9f4387e21ba3a02d45c41033a9c0be9221cf7d3c WHIRLPOOL a02fa5b7833d6ff19f6987904c737bc24578d992c173a50a4a51d250fe25c363fa3268cb002863f94aa318fbb74d3b090bc489340aebb37816fc70ca662b3c54 +DIST alglib-3.10.0.cpp.gpl.tgz 1991101 SHA256 26a6aa966da5bba01da1bebddc0acb0a8fc579f07d53a2cbcfa5dfcaf612aaeb SHA512 f02b3db5ab8dee841f27186b6693997c4e6876e75310b0a31a04593dbcb41d300920404e32e7aecb39c8dd15e54cfee05b725caa27397a67b453f6e64cd1ef5e WHIRLPOOL c0092a82404b060de0bc01d3cba731eac0a5a8f17cea736b784091cadf672883438fdd9c3ab37efa764b8e57fb9a1d7ca3eb7a842b863c22d9961307041e5d66 +DIST alglib-3.8.2.cpp.tgz 1674260 SHA256 c02944558849c8b22f32f8dea03ebf3b77a0aab9aa2518927d25f6bfe7cb06a2 SHA512 3d7b6e3b5a29f25aee476bdd69e583d7504a2e06d390822b4aa2792eeb500e08c13477176be348a9dd560bad358e423465c9086f0c7c12f73dc88024364aed50 WHIRLPOOL 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31cfe5e7f1c79dfda9cacc53e35a60146218d7a244ad04c260d3c8869786a5d30309624520014f8343a8215e0935807db95d7fcb91c065c0e48fab9dfaf9dc79 diff --git a/sci-libs/alglib/alglib-3.10.0-r1.ebuild b/sci-libs/alglib/alglib-3.10.0-r1.ebuild new file mode 100644 index 000000000000..4144904b8fb4 --- /dev/null +++ b/sci-libs/alglib/alglib-3.10.0-r1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Numerical analysis and data processing library" +HOMEPAGE="http://www.alglib.net/" +SRC_URI="http://www.alglib.net/translator/re/${P}.cpp.gpl.tgz" + +SLOT="0/3.8" +LICENSE="GPL-2+" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +S="${WORKDIR}"/cpp/ + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt-3.8.2 CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( $(cmake-utils_use_build test) ) + cmake-utils_src_configure +} diff --git a/sci-libs/alglib/alglib-3.8.2-r1.ebuild b/sci-libs/alglib/alglib-3.8.2-r1.ebuild new file mode 100644 index 000000000000..6e725a2cd3d1 --- /dev/null +++ b/sci-libs/alglib/alglib-3.8.2-r1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Numerical analysis and data processing library" +HOMEPAGE="http://www.alglib.net/" +SRC_URI="http://www.alglib.net/translator/re/${P}.cpp.tgz" + +SLOT="0/3.7" +LICENSE="GPL-2+" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="test" + +S="${WORKDIR}"/cpp/ + +src_prepare() { + cp "${FILESDIR}"/CMakeLists.txt-${PV} CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( $(cmake-utils_use_build test) ) + cmake-utils_src_configure +} diff --git a/sci-libs/alglib/files/CMakeLists.txt b/sci-libs/alglib/files/CMakeLists.txt new file mode 100644 index 000000000000..6455423b0fe9 --- /dev/null +++ b/sci-libs/alglib/files/CMakeLists.txt @@ -0,0 +1,32 @@ +project(alglib CXX) +cmake_minimum_required(VERSION 2.8) + +INCLUDE(GNUInstallDirs) +INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/src) +SET(VERSION 3.7.0) +SET(SOVERSION 3.7) + +FILE(GLOB ALGLIB_SRC_LIB "src/*.cpp") +FILE(GLOB ALGLIB_HDR_LIB "src/*.h") + +ADD_LIBRARY(alglib SHARED ${ALGLIB_SRC_LIB}) +SET_TARGET_PROPERTIES(alglib PROPERTIES + VERSION ${VERSION} + SOVERSION ${SOVERSION}) + +INSTALL(TARGETS alglib DESTINATION ${CMAKE_INSTALL_LIBDIR}/) +INSTALL(FILES ${ALGLIB_HDR_LIB} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) + +#=========================================================== +ADD_EXECUTABLE(test_c tests/test_c.cpp) +TARGET_LINK_LIBRARIES(test_c alglib) +#INSTALL(TARGETS test_c DESTINATION ${CMAKE_INSTALL_BINDIR}/) +#=========================================================== +ADD_EXECUTABLE(test_i tests/test_i.cpp) +TARGET_LINK_LIBRARIES(test_i alglib) +#INSTALL(TARGETS test_i DESTINATION ${CMAKE_INSTALL_BINDIR}/) +#=========================================================== + +enable_testing() +add_test( test_c ${CMAKE_BUILD_DIR}/test_c) +add_test( test_i ${CMAKE_BUILD_DIR}/test_i) diff --git a/sci-libs/alglib/files/CMakeLists.txt-3.8.2 b/sci-libs/alglib/files/CMakeLists.txt-3.8.2 new file mode 100644 index 000000000000..483c63dc7f59 --- /dev/null +++ b/sci-libs/alglib/files/CMakeLists.txt-3.8.2 @@ -0,0 +1,36 @@ +project(alglib CXX) +cmake_minimum_required(VERSION 2.8) + +INCLUDE(GNUInstallDirs) +INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/src) +SET(VERSION 3.8.2) +SET(SOVERSION 3.8) + +option(BUILD_TEST "Build tests" OFF) + +FILE(GLOB ALGLIB_SRC_LIB "src/*.cpp") +FILE(GLOB ALGLIB_HDR_LIB "src/*.h") + +ADD_LIBRARY(alglib SHARED ${ALGLIB_SRC_LIB}) +SET_TARGET_PROPERTIES(alglib PROPERTIES + VERSION ${VERSION} + SOVERSION ${SOVERSION}) + +INSTALL(TARGETS alglib DESTINATION ${CMAKE_INSTALL_LIBDIR}/) +INSTALL(FILES ${ALGLIB_HDR_LIB} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) + +if (BUILD_TEST) + #=========================================================== + ADD_EXECUTABLE(test_c tests/test_c.cpp) + TARGET_LINK_LIBRARIES(test_c alglib) + #INSTALL(TARGETS test_c DESTINATION ${CMAKE_INSTALL_BINDIR}/) + #=========================================================== + ADD_EXECUTABLE(test_i tests/test_i.cpp) + TARGET_LINK_LIBRARIES(test_i alglib) + #INSTALL(TARGETS test_i DESTINATION ${CMAKE_INSTALL_BINDIR}/) + #=========================================================== + + enable_testing() +endif (BUILD_TEST) +add_test( test_c ${CMAKE_BUILD_DIR}/test_c) +add_test( test_i ${CMAKE_BUILD_DIR}/test_i) diff --git a/sci-libs/alglib/metadata.xml b/sci-libs/alglib/metadata.xml new file mode 100644 index 000000000000..dc39a23a79e8 --- /dev/null +++ b/sci-libs/alglib/metadata.xml @@ -0,0 +1,38 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> +ALGLIB is a cross-platform numerical analysis and data processing library. It +supports several programming languages (C++, C#, Pascal, VBA) and several +operating systems (Windows, Linux, Solaris). ALGLIB features include: + +* Linear algebra (direct algorithms, EVD/SVD) +* Solvers (linear and nonlinear) +* Interpolation +* Optimization +* Fast Fourier transforms +* Numerical integration +* Linear and nonlinear least-squares fitting +* Ordinary differential equations +* Special functions +* Statistics (descriptive statistics, hypothesis testing) +* Data analysis (classification/regression, including neural networks) +* Multiple precision versions of linear algebra, interpolation optimization and +* others algorithms (using MPFR for floating point computations) + +Why to choose ALGLIB? Because it is: + +* portable. It can be compiled almost anywhere using almost any compiler +(see compatibility matrix for more info). +* easy to use. It supports many programming languages. If you use one language, +you don't need to study another (FORTRAN, for example) to compile and link an +external library. +* open source. It can be used for free under GPL 2+. +* suited for commercial users too. Those who want to use ALGLIB in commercial +applications can buy commercial license without copyleft requirement. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/amd/Manifest b/sci-libs/amd/Manifest new file mode 100644 index 000000000000..5ab4e7ff484f --- /dev/null +++ b/sci-libs/amd/Manifest @@ -0,0 +1,5 @@ +DIST amd-2.3.1.tar.bz2 339970 SHA256 35f60a47000ec39c8328d621b6d8f249ccf6c12f0ebc809272e16f7d4a8a430c SHA512 19b8c010e0f7a5a96e60fe52904b2b548fb89dfaf9d6f99184df955a732ec3edef04acff01a82a909e030c3bf78c9eccfe0c329731edb29f4b936507e39d885e WHIRLPOOL 737fe5eb785f09bea7a693421b547a0ec18c8428b19efb2890c8573895333862522ece1af00c24156d83ed0888b11c59d9c0ee3ea125ed8cb216d718343f6874 +EBUILD amd-2.3.1.ebuild 754 SHA256 6914801ba302e2ac9ee7132356f0307fefbbf4a127f680a6940993f56e90c66c SHA512 79c19cb2b6260d19d7f9378472e645f43d62b1ea3d5a085d8a502c262ee3b29027c3768ae57821633d25921e90a8585f0e5f25ad1f2f9d51f28d15ea07cfc531 WHIRLPOOL e51a1452eeda1434f880414018ff1abf2f6292d419ce3dbf72308b0fff406f83d7da634fa6db2435015dda4b1f9f7abdd58fc7b18c3f2822b9840058fe1c1b2a +MISC ChangeLog 2597 SHA256 eb9f07ff9ec07ff81a373699f2bdc6437a28fa1ec6b40b87222bb40abf7e13c2 SHA512 f91acdfdab1f78b0590a5571d8969d949d4ddf16730d8add8977672dafba791bc824fbb96da0ca13f4f79eda3355e33aa8b20b69040ec8754940b818ed539a64 WHIRLPOOL d58bb771d74a03e619447a2c819345511d5b694e2927f752682eafcf46aa4d6eb2af7400050529438ffef781de08ac80d313e42db162d450267e186aa8b38f05 +MISC ChangeLog-2015 5520 SHA256 ac170b0ab8a65131701f3a894efb9722f69240c967029c92cbd9f7e10245a01b SHA512 3920ed96d1bbf67b3eaacf459000f4884d6e447f998cc166741554ef43764900c64d368219b287f0521d43888e70b8b4b64b8d09bdac6e076af28570ff5f7b65 WHIRLPOOL 7607eddc6c35b4b6b1d68eccbe6374fe280fea882a7e87cfff417d203d2fcedbd78a78622e3033d3a2a724ae61478a19993e08a8d6c529a202791ce936e34af7 +MISC metadata.xml 492 SHA256 711568b1dc32e94f9a8da88d200b14a87a3906e79dc3f96194f25b68cb5fdfc3 SHA512 1c53658e87337e1e43149c363c901dabfdde52b647891d8026a7ce9ddcd5e36b0121948d169d446e5a78d05c26301bd4f8c7c06665506ebc0999c259b709a6b6 WHIRLPOOL f79288749a64dad7105050ca29171fa389338b0b66d9a953edf2c3c5dc90455d7904d9c9d9cd608f1188d73b468e8dbd9d0dff7a9c496b2c3e57259f343dba16 diff --git a/sci-libs/amd/amd-2.3.1.ebuild b/sci-libs/amd/amd-2.3.1.ebuild new file mode 100644 index 000000000000..e799ab899a0a --- /dev/null +++ b/sci-libs/amd/amd-2.3.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils fortran-2 + +DESCRIPTION="Library to order a sparse matrix prior to Cholesky factorization" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/amd" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~alpha amd64 ~arm ~arm64 hppa ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc fortran static-libs" + +RDEPEND="sci-libs/suitesparseconfig" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base )" + +src_configure() { + local myeconfargs=( + $(use_enable fortran) + $(use_with doc) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/amd/metadata.xml b/sci-libs/amd/metadata.xml new file mode 100644 index 000000000000..353c2f00738d --- /dev/null +++ b/sci-libs/amd/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + AMD is a set of routines for ordering a sparse matrix prior to Cholesky + factorization (or for LU factorization with diagonal pivoting). There + are versions in both C and Fortran. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest new file mode 100644 index 000000000000..25bf8e0a1334 --- /dev/null +++ b/sci-libs/armadillo/Manifest @@ -0,0 +1,11 @@ +DIST armadillo-6.200.3.tar.gz 5442342 SHA256 4e436704a3b0824be6286ffa7c71c91ef783699889fa0992897d446b7ed82b28 SHA512 598ba8be19971fc0e44703b17be922568e697c592ed85d0148c31f8476ecd7b5a0e6185918763bc063ba68244330b17594333c1453e9c1cfd39b9fefe85be222 WHIRLPOOL b774fd736a55c6bad44f26ed839ef7539784be494e9379b2c9fd7ff47363cfe304c23baedd24fa0c990fb94f73ce10db77a32dab77b2d6cc549e61ec83a6e33e +DIST armadillo-7.800.2.tar.xz 4001664 SHA256 efd70600ab6f30449d90a3e58ff7499937985209bb0a03ce4e322474dbf11fe3 SHA512 bd6a718d9aff5d87ae3bb792405e634e58249e74c8b49e31e6c3a1d77f7537b3e2f04f9fb10fc34279673126a1069cd43e991fb03fdf82ce77a00541ab6bd2fc WHIRLPOOL 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+CMAKE_IN_SOURCE_BUILD=1 + +inherit cmake-utils toolchain-funcs multilib eutils + +DESCRIPTION="Streamlined C++ linear algebra library" +HOMEPAGE="http://arma.sourceforge.net/" +SRC_URI="mirror://sourceforge/arma/${P}.tar.gz" + +LICENSE="MPL-2.0" +SLOT="0/6" +KEYWORDS="amd64 ~arm ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="arpack blas debug doc examples hdf5 lapack mkl superlu tbb test" +REQUIRED_USE="test? ( lapack )" + +RDEPEND=" + dev-libs/boost + arpack? ( sci-libs/arpack ) + blas? ( virtual/blas ) + lapack? ( virtual/lapack ) + superlu? ( sci-libs/superlu ) +" +DEPEND="${RDEPEND} + arpack? ( virtual/pkgconfig ) + blas? ( virtual/pkgconfig ) + hdf5? ( sci-libs/hdf5 ) + lapack? ( virtual/pkgconfig ) + mkl? ( sci-libs/mkl ) + tbb? ( dev-cpp/tbb )" +PDEPEND="${RDEPEND} + hdf5? ( sci-libs/hdf5 ) + mkl? ( sci-libs/mkl ) + tbb? ( dev-cpp/tbb )" + +src_prepare() { + # avoid the automagic cmake macros + sed -i -e '/ARMA_Find/d' CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)" + $(cmake-utils_use debug ARMA_EXTRA_DEBUG) + $(cmake-utils_use mkl ARMA_USE_MKL_ALLOC) + $(cmake-utils_use tbb ARMA_USE_TBB_ALLOC) + ) + if use arpack; then + mycmakeargs+=( + -DARPACK_FOUND=ON + -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)" + ) + fi +# if use atlas; then +# local c=atlas-cblas l=atlas-clapack +# $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads +# $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads +# mycmakeargs+=( +# -DCBLAS_FOUND=ON +# -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')" +# -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})" +# -DCLAPACK_FOUND=ON +# -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')" +# -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})" +# ) +# fi + if use blas; then + mycmakeargs+=( + -DBLAS_FOUND=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + ) + fi + if use hdf5; then + mycmakeargs+=( + -DHDF5_FOUND=ON + -DHDF5_LIBRARIES="-lhdf5" + ) + fi + if use lapack; then + mycmakeargs+=( + -DLAPACK_FOUND=ON + -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + fi + if use superlu; then + mycmakeargs+=( + -DSuperLU_FOUND=ON + -DSuperLU_LIBRARIES="$($(tc-getPKG_CONFIG) --libs superlu)" + ) + fi + + cmake-utils_src_configure +} + +src_test() { + pushd examples > /dev/null + emake \ + CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \ + EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)" + LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die + LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die + emake clean + popd > /dev/null +} + +src_install() { + cmake-utils_src_install + dodoc README.txt + use doc && dodoc *pdf && dohtml *html + if use examples; then + insinto /usr/share/examples/${PF} + doins -r examples/* + fi +} diff --git a/sci-libs/armadillo/armadillo-7.800.2-r1.ebuild b/sci-libs/armadillo/armadillo-7.800.2-r1.ebuild new file mode 100644 index 000000000000..d582395e08ec --- /dev/null +++ b/sci-libs/armadillo/armadillo-7.800.2-r1.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_IN_SOURCE_BUILD=1 + +inherit cmake-utils toolchain-funcs multilib eutils + +DESCRIPTION="Streamlined C++ linear algebra library" +HOMEPAGE="http://arma.sourceforge.net/" +SRC_URI="mirror://sourceforge/arma/${P}.tar.xz" + +LICENSE="Apache-2.0" +SLOT="0/7" +KEYWORDS="~amd64 ~arm ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="arpack blas debug doc examples hdf5 lapack mkl superlu tbb test" +REQUIRED_USE="test? ( lapack )" + +RDEPEND=" + dev-libs/boost + arpack? ( sci-libs/arpack ) + blas? ( virtual/blas ) + lapack? ( virtual/lapack ) + superlu? ( >=sci-libs/superlu-5 ) +" + +DEPEND="${RDEPEND} + arpack? ( virtual/pkgconfig ) + blas? ( virtual/pkgconfig ) + hdf5? ( sci-libs/hdf5 ) + lapack? ( virtual/pkgconfig ) + mkl? ( sci-libs/mkl ) + tbb? ( dev-cpp/tbb )" +PDEPEND="${RDEPEND} + hdf5? ( sci-libs/hdf5 ) + mkl? ( sci-libs/mkl ) + tbb? ( dev-cpp/tbb )" + +src_prepare() { + # avoid the automagic cmake macros + sed -i -e '/ARMA_Find/d' CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)" + -DARMA_EXTRA_DEBUG="$(usex debug)" + -DARMA_USE_MKL_ALLOC="$(usex mkl)" + -DARMA_USE_TBB_ALLOC="$(usex tbb)" + ) + if use arpack; then + mycmakeargs+=( + -DARPACK_FOUND=ON + -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)" + ) + else + mycmakeargs+=( + -DARPACK_FOUND=OFF + ) + fi +# if use atlas; then +# local c=atlas-cblas l=atlas-clapack +# $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads +# $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads +# mycmakeargs+=( +# -DCBLAS_FOUND=ON +# -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')" +# -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})" +# -DCLAPACK_FOUND=ON +# -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')" +# -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})" +# ) +# fi + if use blas; then + mycmakeargs+=( + -DBLAS_FOUND=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + ) + else + mycmakeargs+=( + -DBLAS_FOUND=OFF + ) + fi + if use hdf5; then + mycmakeargs+=( + -DHDF5_FOUND=ON + -DHDF5_LIBRARIES="-lhdf5" + ) + else + mycmakeargs+=( + -DHDF5_FOUND=OFF + ) + fi + if use lapack; then + mycmakeargs+=( + -DLAPACK_FOUND=ON + -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + else + mycmakeargs+=( + -DLAPACK_FOUND=OFF + ) + fi + if use superlu; then + mycmakeargs+=( + -DSuperLU_FOUND=ON + -DSuperLU_LIBRARIES="$($(tc-getPKG_CONFIG) --libs superlu)" + ) + else + mycmakeargs+=( + -DSuperLU_FOUND=OFF + ) + fi + + cmake-utils_src_configure +} + +src_test() { + pushd examples > /dev/null + emake \ + CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \ + EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)" + LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die + LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die + emake clean + popd > /dev/null +} + +src_install() { + cmake-utils_src_install + dodoc README.txt + + if use doc ; then + dodoc *pdf + dodoc *html + fi + + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r examples/* + fi +} diff --git a/sci-libs/armadillo/armadillo-7.950.0.ebuild b/sci-libs/armadillo/armadillo-7.950.0.ebuild new file mode 100644 index 000000000000..d582395e08ec --- /dev/null +++ b/sci-libs/armadillo/armadillo-7.950.0.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_IN_SOURCE_BUILD=1 + +inherit cmake-utils toolchain-funcs multilib eutils + +DESCRIPTION="Streamlined C++ linear algebra library" +HOMEPAGE="http://arma.sourceforge.net/" +SRC_URI="mirror://sourceforge/arma/${P}.tar.xz" + +LICENSE="Apache-2.0" +SLOT="0/7" +KEYWORDS="~amd64 ~arm ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="arpack blas debug doc examples hdf5 lapack mkl superlu tbb test" +REQUIRED_USE="test? ( lapack )" + +RDEPEND=" + dev-libs/boost + arpack? ( sci-libs/arpack ) + blas? ( virtual/blas ) + lapack? ( virtual/lapack ) + superlu? ( >=sci-libs/superlu-5 ) +" + +DEPEND="${RDEPEND} + arpack? ( virtual/pkgconfig ) + blas? ( virtual/pkgconfig ) + hdf5? ( sci-libs/hdf5 ) + lapack? ( virtual/pkgconfig ) + mkl? ( sci-libs/mkl ) + tbb? ( dev-cpp/tbb )" +PDEPEND="${RDEPEND} + hdf5? ( sci-libs/hdf5 ) + mkl? ( sci-libs/mkl ) + tbb? ( dev-cpp/tbb )" + +src_prepare() { + # avoid the automagic cmake macros + sed -i -e '/ARMA_Find/d' CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)" + -DARMA_EXTRA_DEBUG="$(usex debug)" + -DARMA_USE_MKL_ALLOC="$(usex mkl)" + -DARMA_USE_TBB_ALLOC="$(usex tbb)" + ) + if use arpack; then + mycmakeargs+=( + -DARPACK_FOUND=ON + -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)" + ) + else + mycmakeargs+=( + -DARPACK_FOUND=OFF + ) + fi +# if use atlas; then +# local c=atlas-cblas l=atlas-clapack +# $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads +# $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads +# mycmakeargs+=( +# -DCBLAS_FOUND=ON +# -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')" +# -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})" +# -DCLAPACK_FOUND=ON +# -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')" +# -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})" +# ) +# fi + if use blas; then + mycmakeargs+=( + -DBLAS_FOUND=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + ) + else + mycmakeargs+=( + -DBLAS_FOUND=OFF + ) + fi + if use hdf5; then + mycmakeargs+=( + -DHDF5_FOUND=ON + -DHDF5_LIBRARIES="-lhdf5" + ) + else + mycmakeargs+=( + -DHDF5_FOUND=OFF + ) + fi + if use lapack; then + mycmakeargs+=( + -DLAPACK_FOUND=ON + -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + else + mycmakeargs+=( + -DLAPACK_FOUND=OFF + ) + fi + if use superlu; then + mycmakeargs+=( + -DSuperLU_FOUND=ON + -DSuperLU_LIBRARIES="$($(tc-getPKG_CONFIG) --libs superlu)" + ) + else + mycmakeargs+=( + -DSuperLU_FOUND=OFF + ) + fi + + cmake-utils_src_configure +} + +src_test() { + pushd examples > /dev/null + emake \ + CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \ + EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)" + LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die + LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die + emake clean + popd > /dev/null +} + +src_install() { + cmake-utils_src_install + dodoc README.txt + + if use doc ; then + dodoc *pdf + dodoc *html + fi + + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r examples/* + fi +} diff --git a/sci-libs/armadillo/armadillo-7.950.1.ebuild b/sci-libs/armadillo/armadillo-7.950.1.ebuild new file mode 100644 index 000000000000..f51cc63bdf42 --- /dev/null +++ b/sci-libs/armadillo/armadillo-7.950.1.ebuild @@ -0,0 +1,143 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_IN_SOURCE_BUILD=1 + +inherit cmake-utils toolchain-funcs multilib eutils + +DESCRIPTION="Streamlined C++ linear algebra library" +HOMEPAGE="http://arma.sourceforge.net/" +SRC_URI="mirror://sourceforge/arma/${P}.tar.xz" + +LICENSE="Apache-2.0" +SLOT="0/7" +KEYWORDS="~amd64 ~arm ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="arpack blas debug doc examples hdf5 lapack mkl superlu tbb test" +REQUIRED_USE="test? ( lapack )" + +# atlas? ( sci-libs/atlas[lapack] ) + +RDEPEND=" + dev-libs/boost + arpack? ( sci-libs/arpack ) + blas? ( virtual/blas ) + lapack? ( virtual/lapack ) + superlu? ( >=sci-libs/superlu-5 ) +" + +DEPEND="${RDEPEND} + arpack? ( virtual/pkgconfig ) + blas? ( virtual/pkgconfig ) + hdf5? ( sci-libs/hdf5 ) + lapack? ( virtual/pkgconfig ) + mkl? ( sci-libs/mkl ) + tbb? ( dev-cpp/tbb )" +PDEPEND="${RDEPEND} + hdf5? ( sci-libs/hdf5 ) + mkl? ( sci-libs/mkl ) + tbb? ( dev-cpp/tbb )" + +src_prepare() { + # avoid the automagic cmake macros + sed -i -e '/ARMA_Find/d' CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)" + -DARMA_EXTRA_DEBUG="$(usex debug)" + -DARMA_USE_MKL_ALLOC="$(usex mkl)" + -DARMA_USE_TBB_ALLOC="$(usex tbb)" + ) + if use arpack; then + mycmakeargs+=( + -DARPACK_FOUND=ON + -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)" + ) + else + mycmakeargs+=( + -DARPACK_FOUND=OFF + ) + fi +# if use atlas; then +# local c=atlas-cblas l=atlas-clapack +# $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads +# $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads +# mycmakeargs+=( +# -DCBLAS_FOUND=ON +# -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')" +# -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})" +# -DCLAPACK_FOUND=ON +# -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')" +# -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})" +# ) +# fi + if use blas; then + mycmakeargs+=( + -DBLAS_FOUND=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + ) + else + mycmakeargs+=( + -DBLAS_FOUND=OFF + ) + fi + if use hdf5; then + mycmakeargs+=( + -DHDF5_FOUND=ON + -DHDF5_LIBRARIES="-lhdf5" + ) + else + mycmakeargs+=( + -DHDF5_FOUND=OFF + ) + fi + if use lapack; then + mycmakeargs+=( + -DLAPACK_FOUND=ON + -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + else + mycmakeargs+=( + -DLAPACK_FOUND=OFF + ) + fi + if use superlu; then + mycmakeargs+=( + -DSuperLU_FOUND=ON + -DSuperLU_LIBRARY="$($(tc-getPKG_CONFIG) --libs superlu)" + -DSuperLU_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I superlu | awk '{print $1}' | sed 's/-I//')" + ) + else + mycmakeargs+=( + -DSuperLU_FOUND=OFF + ) + fi + + cmake-utils_src_configure +} + +src_test() { + pushd examples > /dev/null + emake \ + CXX="$(tc-getCXX)" \ + CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \ + LIB_FLAGS="-L.. -larmadillo $($(tc-getPKG_CONFIG) --libs blas lapack)" + LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die + emake clean + popd > /dev/null +} + +src_install() { + cmake-utils_src_install + dodoc README.txt + use doc && dodoc *pdf *html + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r examples/* + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-libs/armadillo/metadata.xml b/sci-libs/armadillo/metadata.xml new file mode 100644 index 000000000000..b2dad09a9172 --- /dev/null +++ b/sci-libs/armadillo/metadata.xml @@ -0,0 +1,42 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>dilfridge@gentoo.org</email> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Armadillo is a C++ linear algebra library (matrix maths) aiming + towards a good balance between speed and ease of use. Integer, + floating point and complex numbers are supported, as well as a + subset of trigonometric and statistics functions. Various matrix + decompositions are provided through optional integration with LAPACK + and ATLAS libraries. + A delayed evaluation approach is employed (during compile time) to + combine several operations into one and reduce (or eliminate) the + need for temporaries. This is accomplished through recursive + templates and template meta-programming. +</longdescription> + <use> + <flag name="arpack"> + Link with <pkg>sci-libs/arpack</pkg> libraries for eigen decomposition + </flag> + <flag name="mkl"> + Use matrix allocation from the Intel MKL <pkg>sci-libs/mkl</pkg> + </flag> + <flag name="tbb"> + Use matrix allocation from the Threads Building Blocks + <pkg>dev-cpp/tbb</pkg> + </flag> + <flag name="superlu"> + Use SuperLU for sparse linear equation solving + <pkg>sci-libs/superlu</pkg> + </flag> + </use> + <upstream> + <remote-id type="sourceforge">arma</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/arpack/Manifest b/sci-libs/arpack/Manifest new file mode 100644 index 000000000000..66c9695bb5ee --- /dev/null +++ b/sci-libs/arpack/Manifest @@ -0,0 +1,11 @@ +DIST arpack-3.4.0.tar.gz 942149 SHA256 69e9fa08bacb2475e636da05a6c222b17c67f1ebeab3793762062248dd9d842f SHA512 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c3e094cab53fb61c9acf3eff6ca0c0fc53a71ec135315ba833fbfe6a5ae9481f2b4de5270ccd19ec84cf85dfb18df179e1e234d268eef1af98be218575dcd4bf WHIRLPOOL b016ca376fb949c2f9e854356826c89692d86803c6cbb7f5d7642554da326f9d9376a59a46b8c4044a93d002e31c8e374d060dc6c28e63408d8ac17ff084a171 diff --git a/sci-libs/arpack/arpack-3.1.5.ebuild b/sci-libs/arpack/arpack-3.1.5.ebuild new file mode 100644 index 000000000000..ff9435a97943 --- /dev/null +++ b/sci-libs/arpack/arpack-3.1.5.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +#AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils eutils flag-o-matic fortran-2 toolchain-funcs + +MY_P="${PN}-ng_${PV}" + +DESCRIPTION="Arnoldi package library to solve large scale eigenvalue problems" +HOMEPAGE="http://www.caam.rice.edu/software/ARPACK/ http://forge.scilab.org/index.php/p/arpack-ng/" +SRC_URI=" + http://forge.scilab.org/upload/arpack-ng/files/${MY_P}.tar.gz + doc? ( + http://www.caam.rice.edu/software/ARPACK/SRC/ug.ps.gz + http://www.caam.rice.edu/software/ARPACK/DOCS/tutorial.ps.gz )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 ~arm hppa ppc ppc64 x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc examples mpi static-libs" + +RDEPEND=" + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[fortran] )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MY_P/_/-}" + +src_configure() { + tc-export PKG_CONFIG + local myeconfargs=( + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + $(use_enable mpi) + ) + autotools-utils_src_configure +} + +src_test() { + cp "${S}"/TESTS/testA.mtx "${BUILD_DIR}"/TESTS || die + autotools-utils_src_test +} + +src_install() { + autotools-utils_src_install + + dodoc DOCUMENTS/*.doc + newdoc DOCUMENTS/README README.doc + use doc && dodoc "${WORKDIR}"/*.ps + if use examples; then + insinto /usr/share/doc/${PF} + doins -r EXAMPLES + if use mpi; then + insinto /usr/share/doc/${PF}/EXAMPLES/PARPACK + doins -r PARPACK/EXAMPLES/MPI + fi + fi +} diff --git a/sci-libs/arpack/arpack-3.4.0.ebuild b/sci-libs/arpack/arpack-3.4.0.ebuild new file mode 100644 index 000000000000..8f4688842a61 --- /dev/null +++ b/sci-libs/arpack/arpack-3.4.0.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils fortran-2 toolchain-funcs + +MY_P="${PN}-ng_${PV}" + +DESCRIPTION="Arnoldi package library to solve large scale eigenvalue problems" +HOMEPAGE="http://www.caam.rice.edu/software/ARPACK/ http://forge.scilab.org/index.php/p/arpack-ng/" +SRC_URI=" + https://github.com/opencollab/${PN}-ng/archive/${PV}.tar.gz -> ${P}.tar.gz + doc? ( + http://www.caam.rice.edu/software/ARPACK/SRC/ug.ps.gz + http://www.caam.rice.edu/software/ARPACK/DOCS/tutorial.ps.gz )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc examples mpi static-libs" + +RDEPEND=" + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[fortran] )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}-ng-${PV}" + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \ + $(use_enable mpi) +} + +src_install() { + default + + dodoc DOCUMENTS/*.doc + newdoc DOCUMENTS/README README.doc + use doc && dodoc "${WORKDIR}"/*.ps + if use examples; then + insinto /usr/share/doc/${PF} + doins -r EXAMPLES + if use mpi; then + insinto /usr/share/doc/${PF}/EXAMPLES/PARPACK + doins -r PARPACK/EXAMPLES/MPI + fi + fi +} diff --git a/sci-libs/arpack/arpack-3.5.0.ebuild b/sci-libs/arpack/arpack-3.5.0.ebuild new file mode 100644 index 000000000000..8f4688842a61 --- /dev/null +++ b/sci-libs/arpack/arpack-3.5.0.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils fortran-2 toolchain-funcs + +MY_P="${PN}-ng_${PV}" + +DESCRIPTION="Arnoldi package library to solve large scale eigenvalue problems" +HOMEPAGE="http://www.caam.rice.edu/software/ARPACK/ http://forge.scilab.org/index.php/p/arpack-ng/" +SRC_URI=" + https://github.com/opencollab/${PN}-ng/archive/${PV}.tar.gz -> ${P}.tar.gz + doc? ( + http://www.caam.rice.edu/software/ARPACK/SRC/ug.ps.gz + http://www.caam.rice.edu/software/ARPACK/DOCS/tutorial.ps.gz )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc examples mpi static-libs" + +RDEPEND=" + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[fortran] )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}-ng-${PV}" + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \ + $(use_enable mpi) +} + +src_install() { + default + + dodoc DOCUMENTS/*.doc + newdoc DOCUMENTS/README README.doc + use doc && dodoc "${WORKDIR}"/*.ps + if use examples; then + insinto /usr/share/doc/${PF} + doins -r EXAMPLES + if use mpi; then + insinto /usr/share/doc/${PF}/EXAMPLES/PARPACK + doins -r PARPACK/EXAMPLES/MPI + fi + fi +} diff --git a/sci-libs/arpack/metadata.xml b/sci-libs/arpack/metadata.xml new file mode 100644 index 000000000000..c38e598bbdac --- /dev/null +++ b/sci-libs/arpack/metadata.xml @@ -0,0 +1,21 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The ARnoldi PACKage is a library of routines capable of solving large scale symmetric, + nonsymmetric, and generalized eigenproblems. The software is designed to compute a few + eigenvalues with user specified features such as those of largest real + part or largest magnitude. Storage requirements are on the order of + n*k locations. No auxiliary storage is required. A set of Schur basis + vectors for the desired k-dimensional eigen-space is computed which is + numerically orthogonal to working precision. Numerically accurate + eigenvectors are available on request. + </longdescription> + <upstream> + <remote-id type="github">opencollab/arpack-ng</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/arprec/Manifest b/sci-libs/arprec/Manifest new file mode 100644 index 000000000000..3bc900ab3aad --- /dev/null +++ b/sci-libs/arprec/Manifest @@ -0,0 +1,7 @@ +AUX arprec-2.2.18-fix-c++14.patch 368 SHA256 351181564f61c4f8ac363b753007f829918cfde4b85ec44abe5073865223015c SHA512 9763bd97dd8b678195c3967296deaf4b2d9c3853c5f35b4b9c31a02bbd1ba810809585c46a9bdf42f5b56dc6abf4e326f5d3ab0665cd3aff0f363a77598ec029 WHIRLPOOL bf58d43883c7b597aa5629ffc6111ef4d1ed09bcfe2e2fd13cfcdf225b2acb183f3d69eef9965fbb1d0e848a71070d6d90707fe3615268923514d4743c9caf1a +AUX arprec-2.2.18-gold.patch 545 SHA256 0cfbca8d88c20821878c8ca143e8ebc3c8e1a76655668b34be8396086b56bd77 SHA512 09368abacb24ea28e7ff32f1638526e17a0928e3f37f3d216b6918666ac86df8cd447400e2aa3bae6e81c6037ac43ce4b2af9c3dae79b322fa934b36f727a032 WHIRLPOOL a572f8bf8530d8fb8b52cdf2ba4c7b253dd545fca9197adc1df9c4a9f77551433361ba185d45f78dc9539c869ae61e5e340e3a54732d2cac3da8bbd3a2419c54 +DIST arprec-2.2.18.tar.gz 1751743 SHA256 12bcbaabbbd475bdcd0f4983bc280bd3888972ed32bcc8fe5f09fb94b7a85ed5 SHA512 372eb0a0c3aceac0d222679058f47c4d1037b5a51524b752b87f1b61c1b25101c34d4e56d9da45b4075ea7040dd59a597e0add4f34be902955dcf209423a6579 WHIRLPOOL 41322123ca1e444dfea5d678fb435dede56ba9704fdec04a0ae3d98766cad431b350652babaa431d579fe7e9e611b8d2e4c60d70c82d38e8699d33c103ef2ac1 +EBUILD arprec-2.2.18.ebuild 1533 SHA256 f2cfce2aca572c7b8cfbf3c3df55c1f6d240d6c26ee45212f029a63af471e1c7 SHA512 0b4d377fda48265a8671123a752044ec70ea58f28bb471744c0e5f9138711269d1284c7feb678388e62a2e771d876a0f0e28a4307700bab9184959e60af0c118 WHIRLPOOL 90e8292e47aa7094c572ed076da271708ef6c63f2b3da25ae0590328e8b10eca5b6348b577ee181c47cc10641e98c5690c0246b10336ec17ba448536a2e364da +MISC ChangeLog 2888 SHA256 28faee6183234ef3e1b432820a9116ce2a4f93334fef8f4d2972c8621f7efd9b SHA512 c480fe528c326c486425effb709e98e6b40b856b06844260428fd28d39ca843f032369c321ef4f449b17208abb0f075e7b7a64c4b5f56ab323d858e0ba695a1d WHIRLPOOL 1dad6904f443747f172ba0e6214c1410b51c62d6ad076b14a1851883c401c6f6883469d5a3a255ef7e965a70e65a3cbfc80d1f488057299e18a7bd65e28ff56c +MISC ChangeLog-2015 3418 SHA256 cb228ef1a825030eff57ee656d4564ace5624d799957856b379d6bbe090c39c9 SHA512 822de0e218949f78df7254eee639842bd91ba3431f8dacc585459871e14ef8f39f79d1858f7f13ae20236b1ba23ed1900fb2010e9107beb7cc6980aa59264923 WHIRLPOOL 55d2045f2a085bdec0d8e4436f549bcc292ea457c04f781c8c2e013d0d6a30f0b818c0805599c42ed1391c5e4adf97439be5b869bc0be6382770878e2847fc39 +MISC metadata.xml 587 SHA256 c26beaee09b12e3316e4ea0b2e609437462b71ceeb360eb2e943f0dcafd039fa SHA512 710dad7df63809653fef4e68e109304fcc1e6ac97d164efdfb5e294634b996ead15fa4a02f0f7ed8031b9df2fc8b0630be591c4ec14b3845cde9cf61efa53432 WHIRLPOOL 042475284bd3b8b5149758dd4b8e8a8964dd3150b0138ea065df427b6b698a52aca014df949f325f78a48556532b01e13f266bd0224a095a12435fb9f9edb4a4 diff --git a/sci-libs/arprec/arprec-2.2.18.ebuild b/sci-libs/arprec/arprec-2.2.18.ebuild new file mode 100644 index 000000000000..b7ba9c00b8df --- /dev/null +++ b/sci-libs/arprec/arprec-2.2.18.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran +FORTRAN_STANDARD=90 + +inherit autotools fortran-2 + +DESCRIPTION="Arbitrary precision float arithmetics and functions" +HOMEPAGE="http://crd-legacy.lbl.gov/~dhbailey/mpdist/" +SRC_URI="http://crd.lbl.gov/~dhbailey/mpdist/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_fma3 cpu_flags_x86_fma4 doc fortran qd static-libs" + +DEPEND="qd? ( sci-libs/qd[fortran=] )" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.2.18-fix-c++14.patch + "${FILESDIR}"/${P}-gold.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable static-libs static) \ + $(use_enable cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4) fma) \ + $(use_enable fortran) \ + $(use_enable qd) +} + +src_compile() { + default + + if use fortran; then + emake toolkit + cd toolkit || die + ./mathinit || die "mathinit failed" + fi +} + +src_install() { + default + + if use fortran; then + cd toolkit || die + + exeinto /usr/libexec/${PN} + doexe mathtool + + insinto /usr/libexec/${PN} + doins *.dat + + cat > mathtool.exe <<- _EOF_ || die + #!/usr/bin/env sh + cd "${EPREFIX}/usr/libexec/${PN}" && exec ./mathtool + _EOF_ + + newbin mathtool.exe mathtool + newdoc README README.mathtool + fi + + if ! use doc; then + rm "${ED%/}"/usr/share/doc/${PF}/*.pdf || die + fi + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} diff --git a/sci-libs/arprec/files/arprec-2.2.18-fix-c++14.patch b/sci-libs/arprec/files/arprec-2.2.18-fix-c++14.patch new file mode 100644 index 000000000000..680e921d6807 --- /dev/null +++ b/sci-libs/arprec/files/arprec-2.2.18-fix-c++14.patch @@ -0,0 +1,13 @@ +Fix compiling with C++14, due to changed operator T* -> operator bool semantics. +See also: https://bugs.gentoo.org/show_bug.cgi?id=593872 + +--- a/src/write.cpp ++++ b/src/write.cpp +@@ -196,6 +196,6 @@ + + string str = to_string(precision, width, expn_width, + fmt, showpos, uppercase, fill); +- return (s << str) != 0; ++ return static_cast<bool>(s << str); + } + diff --git a/sci-libs/arprec/files/arprec-2.2.18-gold.patch b/sci-libs/arprec/files/arprec-2.2.18-gold.patch new file mode 100644 index 000000000000..293b495f10a7 --- /dev/null +++ b/sci-libs/arprec/files/arprec-2.2.18-gold.patch @@ -0,0 +1,15 @@ + fortran/Makefile.am | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/fortran/Makefile.am b/fortran/Makefile.am +index 8eb4d19..91a125c 100644 +--- a/fortran/Makefile.am ++++ b/fortran/Makefile.am +@@ -4,6 +4,7 @@ LDADD = libarprec_f_main.la libarprecmod.la $(top_builddir)/src/libarprec.la $(F + + lib_LTLIBRARIES = libarprecmod.la libarprec_f_main.la + libarprecmod_la_SOURCES = f_mp.cpp mp_mod.f mp_modm.f mp_modx.f ++libarprecmod_la_LIBADD = $(top_builddir)/src/libarprec.la $(FCLIBS) + libarprec_f_main_la_SOURCES = main.cpp + + if UPCASE_MODULE diff --git a/sci-libs/arprec/metadata.xml b/sci-libs/arprec/metadata.xml new file mode 100644 index 000000000000..55cd058d02de --- /dev/null +++ b/sci-libs/arprec/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>grozin@gentoo.org</email> + <name>Andrey Grozin</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + Arbitrary precision library for float arithmetics and mathematical functions. +</longdescription> + <use> + <flag name="qd">Use <pkg>sci-libs/qd</pkg> for quad-double datatype</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/atlas/Manifest b/sci-libs/atlas/Manifest new file mode 100644 index 000000000000..d1066c7a3fbb --- /dev/null +++ b/sci-libs/atlas/Manifest @@ -0,0 +1,7 @@ +AUX atlas-3.10.2-format-security.patch 8872 SHA256 7615ad2d61edf6990d6a4afc6596571bf669437cc1a0c52762522f8a510de8c6 SHA512 151add96a1e34f99eb37d83e31018797a5737cf9e1ffb9d2fa459f9811dabae1e8fada3a8790618fd24abc7a43255b3694d4f3b9775d3478f1ffe4bc9c314252 WHIRLPOOL 10ad107c3bc1243e2d2b6d7f8d1897cf9385c7f8b986413bd5a1db81bca975cf09763971e86a6b07bfaee6291b7dd2b20a79a3414bd4b81336a23973b4384dfd +AUX atlas-3.10.2-x32-support.patch 3410 SHA256 2f360ef3231c68a7d125373bb5631553f8ef2771b2edce6e4db9718f63013597 SHA512 ba30f795031457a4416978fadd76870aa09fa7af93f10bc5f0258a44d98151fa37c72813a999048927fc9a521e52d2eb9f01b4f7423baa4d0bad099eb0ee06cb WHIRLPOOL e35952a24d78f8f6547350098537143f6ab3de436d6da1f99e5ea9945544adcce5a2b2bb43eaee286f554a0e02f96744e9e31b52f3f6a3094d28f8a71afa4169 +DIST atlas3.10.2.tar.bz2 4904923 SHA256 3aab139b118bf3fcdb4956fbd71676158d713ab0d3bccb2ae1dc3769db22102f SHA512 9fe04cfa1f89449db047d1a4659a656964d13117c783cbbe43344eb32555736f037d9cd30c5ae1514c08ad5b8949a3982d7fe102d707ddb62288e76b2607fbb1 WHIRLPOOL e56936da713b0a1eb560d993bd29da0ac65923bdd2298c0a240a933fbf8961cd151020756ab550e716eae153d97c96d713512cda208a9c1a7c34467bd591fcd5 +DIST lapack-3.6.0.tgz 6792324 SHA256 a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3 SHA512 bc50441d415ef8896dd7626d77c6104184b996e758704366288089f03d4c99d068e33153b0d13305310886017e5d2e716130f812a95cfcad36ef37fe20417ab8 WHIRLPOOL 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4ddc44385911499badf07f1695614bfec44a935442c4361e8e30d4fe65f882fd2b15881b70d7f6be00c27d80a770b7a8683b6a7b6191de66184fea6ba742ea77 WHIRLPOOL 65ef35bbb0863bc3c4446848651f61716de18d9d17fd791e78bf953a7716f63eaa8ad1b985b70b576f49ce39c856974bed31ea37a607fc8bf4deafe22f398049 diff --git a/sci-libs/atlas/atlas-3.10.2.ebuild b/sci-libs/atlas/atlas-3.10.2.ebuild new file mode 100644 index 000000000000..fcc3e5e0b331 --- /dev/null +++ b/sci-libs/atlas/atlas-3.10.2.ebuild @@ -0,0 +1,220 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit fortran-2 toolchain-funcs versionator + +LAPACKP=lapack-3.6.0.tgz + +DESCRIPTION="Automatically Tuned Linear Algebra Software" +HOMEPAGE="http://math-atlas.sourceforge.net/" +SRC_URI="mirror://sourceforge/math-atlas/${PN}${PV}.tar.bz2 + fortran? ( lapack? ( http://www.netlib.org/lapack/${LAPACKP} ) )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc fortran generic lapack static-libs threads" + +RDEPEND="" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/ATLAS" + +PATCHES=( + "${FILESDIR}/${P}-x32-support.patch" + "${FILESDIR}/${P}-format-security.patch" +) + +pkg_setup() { + local _cpufreq + for _cpufreq in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor; do + if [ -f ${_cpufreq} ]; then + if ! grep -q performance ${_cpufreq}; then + echo 2> /dev/null performance > ${_cpufreq} || \ + die "${PN} needs all cpu set to performance" + fi + fi + done + use fortran && fortran-2_pkg_setup +} + +src_configure() { + # hack needed to trick the flaky gcc detection + local mycc="$(type -P $(tc-getCC))" + [[ ${mycc} == *gcc* ]] && mycc=gcc + atlas_configure() { + local myconf=( + --prefix="${ED}/usr" + --libdir="${ED}/usr/$(get_libdir)" + --incdir="${ED}/usr/include" + --cc="$(tc-getCC)" + "-D c -DWALL" + "-C acg '${mycc}'" + "-F acg '${CFLAGS}'" + "-Ss pmake '\$(MAKE) ${MAKEOPTS}'" + ) + + # OpenMP shown to decreased performance over POSIX threads + # (at least in 3.9.x, see atlas-dev mailing list) + if use threads; then + if use generic; then # 2 threads is most generic + myconf+=( "-t 2" "-Si omp 0" ) + else + myconf+=( "-t -1" "-Si omp 0" ) + fi + else + myconf+=( "-t 0" "-Si omp 0" ) + fi + + if use amd64 || use ppc64 || use sparc; then + if [ ${ABI} = amd64 ] || [ ${ABI} = ppc64 ] || [ ${ABI} = sparc64 ] ; then + myconf+=( "-b 64" ) + elif [ ${ABI} = x86 ] || [ ${ABI} = ppc ] || [ ${ABI} = sparc32 ] ; then + myconf+=( "-b 32" ) + elif [ ${ABI} = x32 ] ; then + myconf+=( "-b 48" ) + else + myconf+=( "-b 64" ) + fi + elif use ppc || use x86; then + myconf+=( "-b 32" ) + elif use ia64; then + myconf+=( "-b 64" ) + fi + if use fortran; then + myconf+=( + "-C if '$(type -P $(tc-getFC))'" + "-F if '${FFLAGS}'" + ) + if use lapack; then + myconf+=( + "-Si latune 1" + "--with-netlib-lapack-tarfile=${DISTDIR}/${LAPACKP}" + ) + else + myconf+=( "-Si latune 0" ) + fi + else + myconf+=( "-Si latune 0" "--nof77" ) + fi + # generic stuff found by make make xprint_enums in atlas build dir + # basically assuming sse2+sse1 and 2 threads max + use generic && use x86 && myconf+=( "-V 384 -A 13") + use generic && use amd64 && myconf+=( "-V 384 -A 24") + + local confdir="${S}_${1}"; shift + myconf+=( $@ ) + mkdir "${confdir}" && cd "${confdir}" + # for debugging + echo ${myconf[@]} > myconf.out + "${S}"/configure ${myconf[@]} || die "configure in ${confdir} failed" + } + + atlas_configure shared "-Fa alg -fPIC" ${EXTRA_ECONF} + use static-libs && atlas_configure static ${EXTRA_ECONF} +} + +src_compile() { + atlas_compile() { + pushd "${S}_${1}" > /dev/null + # atlas does its own parallel builds + emake -j1 build + cd lib + emake libclapack.a + [[ -e libptcblas.a ]] && emake libptclapack.a + popd > /dev/null + } + + atlas_compile shared + use static-libs && atlas_compile static +} + +src_test() { + cd "${S}_shared" + emake -j1 check time +} + +# transform a static archive into a shared library and install them +# atlas_install_libs <mylib.a> [extra link flags] +atlas_install_libs() { + local libname=$(basename ${1%.*}) + einfo "Installing ${libname}" + local soname=${libname}.so.$(get_major_version) + shift + pushd "${S}_shared"/lib > /dev/null + ${LINK:-$(tc-getCC)} ${LDFLAGS} -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libname}.a -Wl,--no-whole-archive \ + "$@" -o ${soname} || die "Creating ${soname} failed" + dolib.so ${soname} + ln -s ${soname} ${soname%.*} + dosym ${soname} /usr/$(get_libdir)/${soname%.*} + popd > /dev/null + use static-libs && dolib.a "${S}_static"/lib/${libname}.a +} + +src_install() { + cd "${S}_shared/lib" + # rename to avoid collision with other packages + local l + for l in {,c}{blas,lapack}; do + if [[ -e lib${l}.a ]]; then + mv lib{,atl}${l}.a + use static-libs && mv "${S}"_static/lib/lib{,atl}${l}.a + fi + done + + [[ -e libptcblas.a ]] && PTLIBS="-lpthread" + + # atlas + atlas_install_libs libatlas.a -lm ${PTLIBS} + + # cblas + atlas_install_libs libatlcblas.a -lm -L. -latlas + + # cblas threaded + [[ -e libptcblas.a ]] && \ + atlas_install_libs libptcblas.a -lm -L. -latlas ${PTLIBS} + + if use lapack; then + # clapack + atlas_install_libs libatlclapack.a -lm -L. -latlas -latlcblas + + # clapack threaded + [[ -e libptclapack.a ]] && \ + atlas_install_libs libptclapack.a -lm -L. -latlas -lptcblas ${PTLIBS} + fi + + if use fortran; then + LINK=$(tc-getF77) + + # blas + atlas_install_libs libf77blas.a -lm -L. -latlas + + # blas threaded + [[ -e libptf77blas.a ]] && \ + atlas_install_libs libptf77blas.a -lm -L. -latlas ${PTLIBS} + + if use lapack; then + # lapack + atlas_install_libs libatllapack.a \ + -lm -L. -latlas -latlcblas -lf77blas + # lapack threaded + [[ -e libptlapack.a ]] && \ + atlas_install_libs libptlapack.a -lm -L. -latlas -lptcblas -lptf77blas ${PTLIBS} + fi + fi + + cd "${S}" + insinto /usr/include/${PN} + doins include/*.h + + cd "${S}/doc" + dodoc INDEX.txt AtlasCredits.txt ChangeLog + use doc && dodoc atlas*pdf cblas.pdf cblasqref.pdf + use doc && use fortran && dodoc f77blas*pdf + use doc && use fortran && use lapack && dodoc *lapack*pdf +} diff --git a/sci-libs/atlas/files/atlas-3.10.2-format-security.patch b/sci-libs/atlas/files/atlas-3.10.2-format-security.patch new file mode 100644 index 000000000000..f3f45d774510 --- /dev/null +++ b/sci-libs/atlas/files/atlas-3.10.2-format-security.patch @@ -0,0 +1,198 @@ + bin/atlas_install.c | 46 +++++++++++++++++++++++----------------------- + 1 file changed, 23 insertions(+), 23 deletions(-) + +diff --git a/bin/atlas_install.c b/bin/atlas_install.c +index 2753cbf..21b716d 100644 +--- a/bin/atlas_install.c ++++ b/bin/atlas_install.c +@@ -483,9 +483,9 @@ void PrintStartStop(FILE *fp0, FILE *fp1, int nspc, int START, int sec, + fprintf(fp1, "\n\n"); + } + if (fp0) +- fprintf(fp0, ln); ++ fprintf(fp0, "%s", ln); + if (fp1) +- fprintf(fp1, ln); ++ fprintf(fp1, "%s", ln); + } + + int LnIsCont(char *ln) +@@ -776,11 +776,11 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + if (DefInstall) + { + sprintf(ln, "%s IRunMMDef pre=%c %s %s\n", fmake, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2); + } + sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2); + PrintBanner(ln2, 0, 2, ip+1, 1); + } +@@ -836,7 +836,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + if (!FileExists(fnam)) + { + sprintf(ln, "%s %s pre=%c %s %s", fmake, fnam, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2); + } + fp = fopen(fnam, "r"); +@@ -854,7 +854,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + { + sprintf(ln, "%s %s pre=%c nb=%d %s %s", + fmake, fnam, pre, ncnb, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2); + } + GetInstLogFile(fnam, pre, &muladd, &pf, &lat, &nb, &mu, &nu, &ku, +@@ -881,7 +881,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + } + + sprintf(ln, "%s MMinstall pre=%c %s %s\n", fmake, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "BUILDING BLOCK MATMUL TUNE", ln2); + + fprintf(fpsum, "\n"); +@@ -896,7 +896,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + PrintBanner(ln2, 1, 2, ip+1, 2); + sprintf(ln, "%s INSTALL_LOG/atlas_cacheedge.h pre=%c %s %s\n", + fmake, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "CACHEEDGE DETECTION", ln2); + PrintBanner(ln2, 0, 2, ip+1, 2); + } +@@ -922,7 +922,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + { + sprintf(ln, "%s %s pre=%c %s %s\n", + fmake, ln3, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "CACHEEDGE DETECTION", ln2); + } + fp = fopen(ln3, "r"); +@@ -955,7 +955,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + "\n\n STAGE 2-%d-3: COPY/NO-COPY CROSSOVER DETECTION\n", ip+1); + + sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "COPY/NO-COPY CROSSOVER DETECTION", ln2); + PrintBanner(ln2, 0, 2, ip+1, 3); + fprintf(stdout, " done.\n"); +@@ -970,17 +970,17 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + { + sprintf(ln, "%s INSTALL_LOG/atlas_%ctrsmXover.h pre=%c %s %s\n", + fmake, pre, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "L3BLAS TUNING", ln2); + } + else + { + sprintf(ln, "%s Il3lib pre=%c %s %s\n", fmake, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "L3BLAS TUNING", ln2); + } + sprintf(ln, "%s %ccblaslib %s %s\n", fmake, pre, redir, ln2); /* cblas */ +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "L3BLAS TUNING", ln2); + PrintBanner(ln2, 0, 2, ip+1, 5); + PrintStartStop(stdout, fpsum, 3, 0, 2, ip+1, 4, "L3BLAS TUNE"); +@@ -993,7 +993,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + sprintf(ln2, "INSTALL_LOG/%cMVNTUNE.LOG", pre); + PrintBanner(ln2, 1, 2, ip+1, 7); + sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "MVNTUNE", ln2); + ATL_Cassert(FileIsThere(fnam), "MVNTUNE", ln2); + PrintBanner(ln2, 0, 2, ip+1, 7); +@@ -1026,7 +1026,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + sprintf(ln2, "INSTALL_LOG/%cMVTTUNE.LOG", pre); + PrintBanner(ln2, 1, 2, ip+1, 7); + sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "MVTTUNE", ln2); + ATL_Cassert(FileIsThere(fnam), "MVTTUNE", ln2); + PrintBanner(ln2, 0, 2, ip+1, 7); +@@ -1061,7 +1061,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + sprintf(ln2, "INSTALL_LOG/%cR1TUNE.LOG", pre); + PrintBanner(ln2, 1, 2, ip+1, 7); + sprintf(ln, "%s %s pre=%c %s %s\n", fmake, fnam, pre, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "R1TUNE", ln2); + ATL_Cassert(FileIsThere(fnam), "R1TUNE", ln2); + PrintBanner(ln2, 0, 2, ip+1, 7); +@@ -1099,7 +1099,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + sprintf(ln2, "INSTALL_LOG/LIBBUILD.LOG"); + PrintBanner(ln2, 1, 3, 1, 1); + sprintf(ln, "%s IBuildLibs %s %s\n", fmake, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "LIBRARY BUILD", ln2); + ATL_Cassert(FileIsThere(fnam), "LIBRARY BUILD", ln2); + PrintBanner(ln2, 0, 3, 1, 1); +@@ -1110,7 +1110,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + PrintBanner(ln2, 1, 4, 1, 1); + PrintStartStop(stdout, fpsum, 3, 1, 4, 1, 1, "TRSM TUNE"); + sprintf(ln, "%s IPostTune %s %s\n", fmake, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "POST-BUILD TUNE", ln2); + PrintStartStop(stdout, fpsum, 3, 0, 4, 1, 0, NULL); + ATL_Cassert(FileIsThere(fnam), "POST-BUILD TUNE", ln2); +@@ -1121,7 +1121,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + sprintf(ln2, "INSTALL_LOG/PTTUNE.LOG"); + PrintBanner(ln2, 1, 4, 2, 0); + sprintf(ln, "%s IPTtune %s %s\n", fmake, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "THREADING TUNE", ln2); + PrintStartStop(stdout, fpsum, 3, 0, 4, 2, 0, "THREADING TUNE"); + +@@ -1129,7 +1129,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + sprintf(ln2, "INSTALL_LOG/LIBPTBUILD.LOG"); + PrintBanner(ln2, 1, 4, 2, 1); + sprintf(ln, "%s IBuildPtlibs %s %s\n", fmake, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "PTLIBRARY BUILD", ln2); + PrintBanner(ln2, 0, 4, 2, 1); + PrintStartStop(stdout, fpsum, 3, 0, 4, 2, 1, "THREADING BUILD"); +@@ -1144,7 +1144,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + PrintStartStop(stdout, fpsum, 6, 1, 4, 3, ip+1, ln2); + sprintf(ln2, "INSTALL_LOG/%cLATUNE.LOG", pre); + PrintBanner(ln2, 1, 4, 3, ip+1); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + sprintf(ln, "%s ILATune pre=%c %s %s\n", fmake, pre, redir, ln2); + ATL_Cassert(system(ln)==0, "LAPACK TUNE", ln2); + PrintStartStop(stdout, fpsum, 6, 0, 4, 3, ip+1, NULL); +@@ -1162,7 +1162,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + #else + sprintf(ln, "%s IBuildLibs %s %s\n", fmake, redir, ln2); + #endif +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "STATIC LIBRARY UPDATE", ln2); + PrintBanner(ln2, 0, 5, 1, 1); + PrintStartStop(stdout, fpsum, 3, 0, 5, 1, 0, "FINAL STATIC LIBRARY UPDATE"); +@@ -1172,7 +1172,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA) + sprintf(ln2, "INSTALL_LOG/LIBDYBUILD.LOG"); + PrintBanner(ln2, 1, 5, 2, 1); + sprintf(ln, "%s IBuildDyLibs %s %s\n", fmake, redir, ln2); +- fprintf(stdout, ln); ++ fprintf(stdout, "%s", ln); + ATL_Cassert(system(ln)==0, "DYLIBRARY BUILD", ln2); + PrintBanner(ln2, 0, 5, 2, 1); + PrintStartStop(stdout, fpsum, 3, 0, 5, 2, 0, NULL); diff --git a/sci-libs/atlas/files/atlas-3.10.2-x32-support.patch b/sci-libs/atlas/files/atlas-3.10.2-x32-support.patch new file mode 100644 index 000000000000..82e6980690cb --- /dev/null +++ b/sci-libs/atlas/files/atlas-3.10.2-x32-support.patch @@ -0,0 +1,93 @@ +--- ATLAS/CONFIG/src/SpewMakeInc.c.orig 2012-05-24 00:56:27.000000000 +0200 ++++ ATLAS/CONFIG/src/SpewMakeInc.c 2012-06-06 15:17:40.000000000 +0200 +@@ -370,7 +370,7 @@ + } + *f2cdefs = fdefs; + *ecdefs = cdefs; +- if (*ptrbits != 32 && *ptrbits != 64) ++ if (*ptrbits != 32 && *ptrbits != 64 && *ptrbits != 48) + *ptrbits = 0; + } + char *GetPtrbitsFlag(enum OSTYPE OS, enum MACHTYPE arch, int ptrbits, +@@ -418,6 +418,8 @@ + sp = "-m64"; + else if (ptrbits == 32) + sp = "-m32"; ++ else if (ptrbits == 48 && MachIsX86(arch)) ++ sp = "-mx32"; + } + return(sp); + } +--- ATLAS/CONFIG/src/gnuccw.c.orig 2012-06-06 15:30:05.000000000 +0200 ++++ ATLAS/CONFIG/src/gnuccw.c 2012-06-06 15:33:29.000000000 +0200 +@@ -363,7 +363,7 @@ + * -m64/32 args get passed to comp, asm & linker + */ + else if (at->len == 4 && +- (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32"))) ++ (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32") || !strcmp(at->arg, "-mx32"))) + { + if (at->arg[2] == '6') + *BITS = 64; +--- ATLAS/CONFIG/src/gcc3p.c.orig 2012-06-06 15:29:38.000000000 +0200 ++++ ATLAS/CONFIG/src/gcc3p.c 2012-06-06 15:31:17.000000000 +0200 +@@ -352,7 +352,7 @@ + * -m64/32 args get passed to comp, asm & linker + */ + else if (at->len == 4 && +- (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32"))) ++ (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32") || !strcmp(at->arg, "-mx32"))) + { + if (at->arg[2] == '6') + { +--- ATLAS/CONFIG/src/gnuf90w.c.orig 2012-06-06 15:29:28.000000000 +0200 ++++ ATLAS/CONFIG/src/gnuf90w.c 2012-06-06 15:30:36.000000000 +0200 +@@ -363,7 +363,7 @@ + * -m64/32 args get passed to comp, asm & linker + */ + else if (at->len == 4 && +- (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32"))) ++ (!strcmp(at->arg, "-m64") || !strcmp(at->arg, "-m32") || !strcmp(at->arg, "-mx32"))) + { + if (at->arg[2] == '6') + *BITS = 64; +--- ATLAS/CONFIG/src/probe_comp.c.orig 2012-06-06 15:29:51.000000000 +0200 ++++ ATLAS/CONFIG/src/probe_comp.c 2012-06-06 15:32:50.000000000 +0200 +@@ -614,6 +614,8 @@ + sp = "-m64"; + else if (ptrbits == 32) + sp = "-m32"; ++ else if (ptrbits == 48) ++ sp = "-mx32"; + } + return(sp); + } +@@ -1691,7 +1693,7 @@ + } + } + } +- if (*ptrbits != 32 && *ptrbits != 64) ++ if (*ptrbits != 32 && *ptrbits != 64 && *ptrbits != 48) + *ptrbits = 0; + } + +--- ATLAS/CONFIG/src/config.c.orig 2012-06-06 15:59:53.000000000 +0200 ++++ ATLAS/CONFIG/src/config.c 2012-06-06 16:00:07.000000000 +0200 +@@ -183,7 +183,7 @@ + i = sprintf(ln, "make IRun_comp args=\"-v %d -o atlconf.txt -O %d -A %d -Si nof77 %d -V %d %s %s", + verb, OS, arch, nof77, vecext, targarg, flags); + free(flags); +- if (ptrbits == 64 || ptrbits == 32) ++ if (ptrbits == 64 || ptrbits == 32 || ptrbits == 48) + { + sprintf(stmp, "-b %d", ptrbits); + ln = NewAppendedString(ln, stmp); +@@ -1272,7 +1272,7 @@ + } + *f2cdefs = fdefs; + *ecdefs = cdefs; +- if (*ptrbits != 32 && *ptrbits != 64) ++ if (*ptrbits != 32 && *ptrbits != 64 && *ptrbits != 48) + *ptrbits = 0; + } + diff --git a/sci-libs/atlas/metadata.xml b/sci-libs/atlas/metadata.xml new file mode 100644 index 000000000000..ac115a049487 --- /dev/null +++ b/sci-libs/atlas/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + ATLAS is an approach for the automatic generation and optimization of + numerical software. Currently ATLAS supplies optimized versions for the + complete set of linear algebra kernels known as the Basic Linear Algebra + Subroutines (BLAS) for both c and F77 interfaces. It can also build + a subset of the linear algebra routine LAPACK library or the full + LAPACK using the reference LAPACK from Netlib. +</longdescription> + <use> + <flag name="generic">Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)</flag> + </use> + <upstream> + <remote-id type="sourceforge">math-atlas</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/avogadrolibs/Manifest b/sci-libs/avogadrolibs/Manifest new file mode 100644 index 000000000000..f2afc22581d7 --- /dev/null +++ b/sci-libs/avogadrolibs/Manifest @@ -0,0 +1,11 @@ +AUX avogadrolibs-0.7.2-6464.patch 902 SHA256 e4d0e73683ffd6da1a039bf6ea6544065c1d45533633c7793fb2329c924625d7 SHA512 3851a3c5f7c599e439b4faa491ea080264e60bf2a7c4d35e01a10726f901a5797026bf32535107b46ca44335c5723d9ec7f0b6a46e9eebf7ffd9f90c7f2103d3 WHIRLPOOL 2622bc8408f69f4deb0084d78265fe5c70f05f6095f94b1cb0a4b25793ec1d1c4e9f7ef8a13043ea1b6f185d1a7ea11579675ae8a5360e2582fd2e87dcd91074 +AUX avogadrolibs-0.8.0-underlinking.patch 1170 SHA256 51c69e4b440c6d8056c3a8facc45a8771301da6d73abe83afc983b26e57f5104 SHA512 2520af361e250dc2459beec78d073686f44b41166cf81fd7c2a98e2ed30c5f20b5c910fb3808a56202420068043044900e7a504657506a12d16bd0acac87a466 WHIRLPOOL 25bdb409dcd93369b13ade06615f869f20ef758394f0a5a3fdc29d28401a8d48baf2557fa8def9d5906c40b54e6e5c9e945498bcf64c60825bcf6c31807fe549 +DIST avogadrolibs-0.7.2.tar.gz 637001 SHA256 217eb5d62082bbaacefe8ad3c8c8ddbbd41931d306038774f761c0155aeccc76 SHA512 a796af1ab3eb77eb2e5484e9e9cb9d7cf68759c9afbd48ddeb237513583e2c207c7c70b2e87b37843886fc737410456ee451e8fe5a21707bdc01fdf600d4cbb8 WHIRLPOOL 81f0d1949c0a93b9efd1f47f276929b01ca761a5875015be3feafb493be3629b0b8e00c0ba930e1ca73b79fc621a67f7e2ab41ae5e4fc10dddd18449238d933f +DIST avogadrolibs-0.8.0.tar.bz2 619784 SHA256 0f9a39e3469c4b4622a55ceeace3565c5f7f4df13fdadb73aa1f7d9bba43856c SHA512 edcd220e7c05962543b3cdd61faacb838060a69acb61677150256e2e8f36cad513f58a5071b6ef20510aa4aa6699e517c57d70017d8f1b57936c7f87c9da21c7 WHIRLPOOL 87ea3436af93ec860e90bdbe1b7c24408dae69e17755300f526a03b4e5d0f76217d0d3b695e917c5bf315758b4e2d3ee0c1511734d13e58251ade1d63709949b +DIST avogadrolibs-0.9.0.tar.gz 742370 SHA256 be627991148ebcc50153ff5838ac147b6de2d90d25f1eeba700619810d353f69 SHA512 7cb000cd6399f33483c38b4f8a9c4a4688f5054cba35e101bed0f2371cea614ace6b3fc65c3ed1418976afef4462a09be868500435a5ae9c98a7ac496c10c36f WHIRLPOOL 9f7d10b2748b370a77ea22aa14abc50afefc49f23554e84600061d52b8c06c36953d1540d142068e4afa9a626b57a201720d9fae567d9a01bce9fca8e191e635 +EBUILD avogadrolibs-0.7.2-r1.ebuild 1134 SHA256 4d2d24e2268196656d6f03299b356c0bd1d40f116844fcf213d47df82b4e9f55 SHA512 647996bc7599e95c89f65e0527d682bab720a0b3c34f96ba979a41d8c4b5efde12de572d98146310a67cff8a8709cf0cc67f4ea49f93aab4cabbf80eb45f6572 WHIRLPOOL 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0b9d6c1de7321db3cae6a2e307a1a0569c3a42a8f9464835865696da83e69174182f0325bb4e1629d91f6c1ec5f9356ba2ec8319e3593f2a2f8c23dd3f30ce2c WHIRLPOOL 58a4ff0e716850a43edde9705fbf06b6c652f854491b8f1f62720f25a5389e7112e4b8e33006711956d3fecbc1930870f4c73600b1108682c73f8cdc23f14ca8 +MISC ChangeLog-2015 1728 SHA256 854ce6d73ee64d3675d9aeb9450af44f9f2936835f17f728a1fc88dfa4a859a3 SHA512 cd403669a5ea336bc3a6ac16afa4939aa515ec3d4c81f9c6e7fb9b01b1fdde75fc6c6089944b9052e3c1dd1ea562c45e8cb8d4788e4da2fdb301ab38e9e6840f WHIRLPOOL 147a0bdaf79c36d347067ce4e448b81ee7b9cad59ee329d3579e42ebe5e48f1d384106d45bbc85b97131f95c39b69a802d06ba93e39130236fd6c23188cde4a3 +MISC metadata.xml 561 SHA256 f7a56fafd1cd4aa6c8a2c9b49a185fbb0320897a991817f35581ecde95b72785 SHA512 20bee27014f13bcb3d1ca6addad61f4553fb77197c6113d65e71f97cbd6bda4a69e5db7f3ca12db41dc5d4afb09882bb89312a8e4babf5110957d6e86c1cbc81 WHIRLPOOL 8a3961c0d7ed2ab533f389b2147573efb44d0807d7796adbdcac27f4661530f381f4f5a8b476fe4f53138c7a59903792a69bf37210de126de16392b0c54708cd diff --git a/sci-libs/avogadrolibs/avogadrolibs-0.7.2-r1.ebuild b/sci-libs/avogadrolibs/avogadrolibs-0.7.2-r1.ebuild new file mode 100644 index 000000000000..ea3c49c5231f --- /dev/null +++ b/sci-libs/avogadrolibs/avogadrolibs-0.7.2-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries" +HOMEPAGE="http://www.openchemistry.org/" +SRC_URI="mirror://sourceforge/project/avogadro/avogadro2/${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD GPL-2+" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc opengl qt4 static-plugins test vtk" + +REQUIRED_USE="qt4? ( opengl )" + +RDEPEND=" + >=sci-chemistry/molequeue-0.7 + sci-libs/chemkit + sci-libs/hdf5:= + opengl? ( + dev-qt/qtopengl:4 + media-libs/glew + ) + qt4? ( + dev-qt/qtcore:4 + dev-qt/qtgui:4 + ) + vtk? ( sci-libs/vtk ) +" +DEPEND="${DEPEND} + test? ( dev-cpp/gtest )" + +PATCHES=( "${FILESDIR}"/${P}-6464.patch ) + +src_configure() { + local mycmakeargs=( + -DUSE_PROTOCALL=OFF + -DBUILD_GPL_PLUGINS=ON + $(cmake-utils_use_build doc DOCUMENTATION) + $(cmake-utils_use_use opengl OPENGL) + $(cmake-utils_use_use qt4 QT) + $(cmake-utils_use_build static-plugins STATIC_PLUGINS) + $(cmake-utils_use_enable test TESTING) + $(cmake-utils_use_use vtk VTK) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/avogadrolibs/avogadrolibs-0.8.0.ebuild b/sci-libs/avogadrolibs/avogadrolibs-0.8.0.ebuild new file mode 100644 index 000000000000..489784bb1736 --- /dev/null +++ b/sci-libs/avogadrolibs/avogadrolibs-0.8.0.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries" +HOMEPAGE="http://www.openchemistry.org/" +SRC_URI="mirror://sourceforge/project/avogadro/avogadro2/${PV}/${P}.tar.bz2" + +SLOT="0" +LICENSE="BSD GPL-2+" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc opengl qt5 static-plugins test vtk" + +REQUIRED_USE="qt5? ( opengl )" + +RDEPEND=" + >=sci-chemistry/molequeue-0.7 + sci-libs/chemkit + sci-libs/hdf5:= + opengl? ( + dev-qt/qtopengl:5 + media-libs/glew + ) + qt5? ( + dev-qt/qtconcurrent:5 + dev-qt/qtcore:5 + dev-qt/qtnetwork:5 + dev-qt/qtwebkit:5 + dev-qt/qtwidgets:5 + ) + vtk? ( sci-libs/vtk ) +" +DEPEND="${DEPEND} + dev-cpp/eigen:3 + test? ( dev-cpp/gtest )" + +PATCHES=( "${FILESDIR}"/${PN}-0.7.2-6464.patch "${FILESDIR}/"${P}-underlinking.patch ) + +src_configure() { + local mycmakeargs=( + -DUSE_PROTOCALL=OFF + -DBUILD_GPL_PLUGINS=ON + -DUSE_MOLEQUEUE=ON + $(cmake-utils_use_build doc DOCUMENTATION) + $(cmake-utils_use_use opengl OPENGL) + $(cmake-utils_use_use qt5 QT) + $(cmake-utils_use_build static-plugins STATIC_PLUGINS) + $(cmake-utils_use_enable test TESTING) + $(cmake-utils_use_use vtk VTK) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/avogadrolibs/avogadrolibs-0.9.0.ebuild b/sci-libs/avogadrolibs/avogadrolibs-0.9.0.ebuild new file mode 100644 index 000000000000..ea71fa95ce6e --- /dev/null +++ b/sci-libs/avogadrolibs/avogadrolibs-0.9.0.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +DESCRIPTION="Advanced molecule editor and visualizer 2 - libraries" +HOMEPAGE="http://www.openchemistry.org/" +SRC_URI="https://github.com/OpenChemistry/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="BSD GPL-2+" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc hdf5 opengl qt5 static-plugins test vtk" + +REQUIRED_USE="qt5? ( opengl )" + +RDEPEND=" + >=sci-chemistry/molequeue-0.7 + sci-libs/chemkit + hdf5? ( sci-libs/hdf5:= ) + opengl? ( + dev-qt/qtopengl:5 + media-libs/glew + ) + qt5? ( + dev-qt/qtconcurrent:5 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtnetwork:5 + dev-qt/qtwidgets:5 + ) + vtk? ( sci-libs/vtk ) +" +DEPEND="${DEPEND} + dev-cpp/eigen:3 + test? ( dev-cpp/gtest )" + +PATCHES=( + "${FILESDIR}"/${PN}-0.7.2-6464.patch + "${FILESDIR}/"${PN}-0.8.0-underlinking.patch +) + +src_configure() { + local mycmakeargs=( + -DUSE_PROTOCALL=OFF + -DBUILD_GPL_PLUGINS=ON + -DUSE_MOLEQUEUE=ON + -DUSE_HDF5=$(usex hdf5) + -DBUILD_DOCUMENTATION=$(usex doc) + -DUSE_OPENGL=$(usex opengl) + -DUSE_QT=$(usex qt5) + -DBUILD_STATIC_PLUGINS=$(usex static-plugins) + -DENABLE_TESTING=$(usex test) + -DUSE_VTK=$(usex vtk) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + + # TODO: bundles jsoncpp + rm "${ED%/}"/usr/lib64/libjsoncpp.a || die +} diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-0.7.2-6464.patch b/sci-libs/avogadrolibs/files/avogadrolibs-0.7.2-6464.patch new file mode 100644 index 000000000000..f763c242cc48 --- /dev/null +++ b/sci-libs/avogadrolibs/files/avogadrolibs-0.7.2-6464.patch @@ -0,0 +1,16 @@ + cmake/AvogadroLibsConfig.cmake.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/cmake/AvogadroLibsConfig.cmake.in b/cmake/AvogadroLibsConfig.cmake.in +index ad57195..8a63400 100644 +--- a/cmake/AvogadroLibsConfig.cmake.in ++++ b/cmake/AvogadroLibsConfig.cmake.in +@@ -10,7 +10,7 @@ set(AvogadroLibs_VERSION "${AvogadroLibs_VERSION_MAJOR}.${AvogadroLibs_V + + set(AvogadroLibs_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@") + set(AvogadroLibs_INCLUDE_DIRS "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_INCLUDE_DIR@") +-set(AvogadroLibs_LIBRARY_DIR "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_LIBRARY_DIR@@LIB_SUFFIX@") ++set(AvogadroLibs_LIBRARY_DIR "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_LIBRARY_DIR@") + set(AvogadroLibs_RUNTIME_DIR "${AvogadroLibs_INSTALL_PREFIX}/@INSTALL_RUNTIME_DIR@") + set(AvogadroLibs_CMAKE_DIR "${AvogadroLibs_LIBRARY_DIR}/cmake/avogadrolibs") + diff --git a/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch b/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch new file mode 100644 index 000000000000..b29f3afe7613 --- /dev/null +++ b/sci-libs/avogadrolibs/files/avogadrolibs-0.8.0-underlinking.patch @@ -0,0 +1,34 @@ +Fix underlinking problems in shared libraries. + +--- avogadrolibs-0.8.0/avogadro/qtplugins/apbs/CMakeLists.txt ++++ avogadrolibs-0.8.0/avogadro/qtplugins/apbs/CMakeLists.txt +@@ -23,4 +23,4 @@ + "${apbs_uis}" + ) + +-target_link_libraries(apbs LINK_PRIVATE AvogadroIO MoleQueueClient) ++target_link_libraries(apbs LINK_PRIVATE AvogadroIO MoleQueueClient AvogadroMoleQueue) +--- avogadrolibs-0.8.0/avogadro/qtplugins/playertool/CMakeLists.txt ++++ avogadrolibs-0.8.0/avogadro/qtplugins/playertool/CMakeLists.txt +@@ -7,3 +7,5 @@ + "" + playertool.qrc + ) ++ ++target_link_libraries(PlayerTool LINK_PRIVATE Qt5OpenGL) +--- avogadrolibs-0.8.0/avogadro/qtplugins/povray/CMakeLists.txt ++++ avogadrolibs-0.8.0/avogadro/qtplugins/povray/CMakeLists.txt +@@ -8,3 +8,5 @@ + "povray.cpp" + "" + ) ++ ++target_link_libraries(POVRay LINK_PRIVATE AvogadroRendering) +--- avogadrolibs-0.8.0/avogadro/qtplugins/qtaim/CMakeLists.txt ++++ avogadrolibs-0.8.0/avogadro/qtplugins/qtaim/CMakeLists.txt +@@ -34,3 +34,5 @@ + + target_link_libraries(QTAIMScenePlugin + LINK_PRIVATE AvogadroRendering ${Qt5Concurrent_LIBRARIES}) ++target_link_libraries(QTAIMExtension ++ LINK_PRIVATE ${Qt5Concurrent_LIBRARIES}) diff --git a/sci-libs/avogadrolibs/metadata.xml b/sci-libs/avogadrolibs/metadata.xml new file mode 100644 index 000000000000..ea8e4fdee064 --- /dev/null +++ b/sci-libs/avogadrolibs/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="static-plugins">Build all plugins statically into main plugin modules</flag> + <flag name="vtk">include vtk support</flag> + </use> + <upstream> + <remote-id type="github">OpenChemistry/avogadrolibs</remote-id> + <remote-id type="sourceforge">avogadro</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/beagle/Manifest b/sci-libs/beagle/Manifest new file mode 100644 index 000000000000..d86363a8b2f3 --- /dev/null +++ b/sci-libs/beagle/Manifest @@ -0,0 +1,8 @@ +AUX beagle-3.0.3-fix-c++14.patch 1087 SHA256 307180f16a137175b3700fbd309070222ba048a37c3b196b88bda177c7b3ba96 SHA512 fdbcd7bbde24943ad3327ee98078e25eea9c1a450c52594f50e59b3344a6c7a9a8d9be81665ccdef1dd95d2bc5945c8001309d4df013491238add0036835caca WHIRLPOOL 515adfa015fd7ce85ae21832c7ea00623ac7caa5f2211816f5adb15f678a100a635f041ee89092bf8efe2b0e30291764c81aaf06654a3ed76232d3df18df38b9 +AUX beagle-3.0.3-gcc43.patch 3096 SHA256 2c54696275ac9653fa30eddc1bc1640fffd5f68a7153fab896634b0b553f9487 SHA512 3611b41ea82030b192cf36cfa9636a72e874e69b60f69dcbe0745b21c98e8d89e09f52f902b6d4e174a5a64e05b14352227610b4780f917d29122ef03270e702 WHIRLPOOL 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SHA512 f95698da02a85c615c966a723dc464cf0b55ebeac3ba5e4ed41be6d9b7bb7db605f2e34dd949089ee6a5bd768eb7114c8d2600be97c61700c102f74f438a11b2 WHIRLPOOL efb6d1fefe16dd3f2b611fa81a39cc189f2a226943e00908578e01a5869232491d3f99369507eff6226c9c3279de718228e217831e1d7e8c7b96930daa90e8c3 +MISC ChangeLog 2928 SHA256 804c7b4f024aacff468d612689197c832364aa40a169aaf04ce97d7b52300117 SHA512 7097d251e33cd417598c858b21edf7064c7080df237ffa2caacf6a567bc15c440a8d8d908caf81a3925e2271359ffbb8b41cad9f1a1a2df7c1c825ebdda18c62 WHIRLPOOL 97a31956603023ef6b77fee60597cf3b719046aaffdd9efd436257475a46bf46200bb11cf768fdb0082648effdf3e9d7a21621d6e81e89e2d092866a6455f3df +MISC ChangeLog-2015 2360 SHA256 b8a6c4098d8fe9c969c06b169ca9d06745dc53cec854433e2b447129ff5a2e72 SHA512 68d153c45046d06e165ad5e0f45d2b8f433137e959657ffe174fabf0ad849810f2549477fed1db8537a025a3f7c34c0e9f9feec3d2f18b304530374be4fb875a WHIRLPOOL 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+SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples static-libs" + +RDEPEND=" + sys-libs/zlib + !app-misc/beagle + !dev-libs/libbeagle" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +PATCHES=( + "${FILESDIR}/${PN}-3.0.3-gcc43.patch" + "${FILESDIR}/${PN}-3.0.3-gcc47.patch" + "${FILESDIR}/${PN}-3.0.3-fix-c++14.patch" +) + +src_prepare() { + default + sed -e "s:@LIBS@:@LIBS@ -lpthread:" \ + -i PACC/Threading/Makefile.in || die +} + +src_configure() { + econf \ + --enable-optimization \ + $(use_enable static-libs static) +} + +src_compile() { + default + use doc && emake doc +} + +src_install () { + use doc && local HTML_DOCS=( refman/. ) + if use examples; then + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi + + default + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} diff --git a/sci-libs/beagle/files/beagle-3.0.3-fix-c++14.patch b/sci-libs/beagle/files/beagle-3.0.3-fix-c++14.patch new file mode 100644 index 000000000000..896b58225890 --- /dev/null +++ b/sci-libs/beagle/files/beagle-3.0.3-fix-c++14.patch @@ -0,0 +1,30 @@ +Fix building with C++14, where destructors are noexcept(true) by default. +See also: https://bugs.gentoo.org/show_bug.cgi?id=597342 + +--- a/PACC/Threading/Thread.cpp ++++ b/PACC/Threading/Thread.cpp +@@ -79,6 +79,9 @@ + \attention If the destructor in the derived thread class (e.g. MyThread above) does not wait for thread termination, the potential hazardous situation is that the runtime system will have deleted all of its members before calling this destructor (in C++, class destructors are called in reversed sequence). Thus, the still running thread could access deleted data members with unpredictable and unexpected results. So beware! + */ + Threading::Thread::~Thread(void) ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + lock(); + if(mThread) { +--- a/PACC/Threading/Thread.hpp ++++ b/PACC/Threading/Thread.hpp +@@ -53,7 +53,11 @@ + class Thread : public Condition { + public: + Thread(void); +- virtual ~Thread(void); ++ virtual ~Thread(void) ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ ; + + void cancel(void); + bool isRunning(void) const; diff --git a/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch b/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch new file mode 100644 index 000000000000..608ce388e793 --- /dev/null +++ b/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch @@ -0,0 +1,89 @@ +diff -rupN beagle-3.0.3b/PACC/Math/Matrix.cpp beagle-3.0.3/PACC/Math/Matrix.cpp +--- beagle-3.0.3b/PACC/Math/Matrix.cpp 2009-01-20 23:38:39.000000000 -0400 ++++ beagle-3.0.3/PACC/Math/Matrix.cpp 2009-01-21 00:26:46.000000000 -0400 +@@ -40,6 +40,7 @@ + #include <stdexcept> + #include <iomanip> + #include <cmath> ++#include <climits> + + using namespace std; + using namespace PACC; +diff -rupN beagle-3.0.3b/PACC/Math/Vector.hpp beagle-3.0.3/PACC/Math/Vector.hpp +--- beagle-3.0.3b/PACC/Math/Vector.hpp 2009-01-20 23:38:39.000000000 -0400 ++++ beagle-3.0.3/PACC/Math/Vector.hpp 2009-01-21 00:26:29.000000000 -0400 +@@ -42,6 +42,7 @@ + #include "XML/Document.hpp" + #include "XML/Streamer.hpp" + #include <cmath> ++#include <algorithm> + + namespace PACC { + +diff -rupN beagle-3.0.3b/PACC/Socket/Cafe.cpp beagle-3.0.3/PACC/Socket/Cafe.cpp +--- beagle-3.0.3b/PACC/Socket/Cafe.cpp 2009-01-20 23:38:39.000000000 -0400 ++++ beagle-3.0.3/PACC/Socket/Cafe.cpp 2009-01-21 00:31:09.000000000 -0400 +@@ -35,6 +35,7 @@ + + #include "Socket/Cafe.hpp" + #include <iostream> ++#include <cstring> + + #ifdef WIN32 + ///////////// specifics for windows ///////////// +diff -rupN beagle-3.0.3b/PACC/Socket/Port.cpp beagle-3.0.3/PACC/Socket/Port.cpp +--- beagle-3.0.3b/PACC/Socket/Port.cpp 2009-01-20 23:38:39.000000000 -0400 ++++ beagle-3.0.3/PACC/Socket/Port.cpp 2009-01-21 00:30:54.000000000 -0400 +@@ -34,6 +34,7 @@ + */ + + #include "Socket/Port.hpp" ++#include <cstring> + + #ifdef WIN32 + ///////////// specifics for windows ///////////// +diff -rupN beagle-3.0.3b/PACC/Threading/Thread.cpp beagle-3.0.3/PACC/Threading/Thread.cpp +--- beagle-3.0.3b/PACC/Threading/Thread.cpp 2009-01-20 23:38:39.000000000 -0400 ++++ beagle-3.0.3/PACC/Threading/Thread.cpp 2009-01-21 00:28:02.000000000 -0400 +@@ -35,6 +35,7 @@ + + #include "Threading/Thread.hpp" + #include "Util/Assert.hpp" ++#include <cstdlib> + + #ifdef WIN32 + #include <windows.h> +diff -rupN beagle-3.0.3b/PACC/Util/SignalHandler.cpp beagle-3.0.3/PACC/Util/SignalHandler.cpp +--- beagle-3.0.3b/PACC/Util/SignalHandler.cpp 2009-01-20 23:38:39.000000000 -0400 ++++ beagle-3.0.3/PACC/Util/SignalHandler.cpp 2009-01-20 23:44:20.000000000 -0400 +@@ -37,6 +37,7 @@ + #include "Util/Assert.hpp" + #include <signal.h> + #include <stdexcept> ++#include <cstdlib> + + using namespace std; + using namespace PACC; +diff -rupN beagle-3.0.3b/PACC/Util/Tokenizer.cpp beagle-3.0.3/PACC/Util/Tokenizer.cpp +--- beagle-3.0.3b/PACC/Util/Tokenizer.cpp 2009-01-20 23:38:39.000000000 -0400 ++++ beagle-3.0.3/PACC/Util/Tokenizer.cpp 2009-01-20 23:44:10.000000000 -0400 +@@ -36,6 +36,8 @@ + #include "Util/Tokenizer.hpp" + #include "Util/Assert.hpp" + #include <stdexcept> ++#include <cstring> ++#include <cstdlib> + + using namespace std; + using namespace PACC; +diff -rupN beagle-3.0.3b/PACC/XML/Node.cpp beagle-3.0.3/PACC/XML/Node.cpp +--- beagle-3.0.3b/PACC/XML/Node.cpp 2009-01-20 23:38:39.000000000 -0400 ++++ beagle-3.0.3/PACC/XML/Node.cpp 2009-01-20 23:45:09.000000000 -0400 +@@ -39,6 +39,7 @@ + #include "Util/Assert.hpp" + #include <sstream> + #include <stdexcept> ++#include <cstring> + + using namespace std; + using namespace PACC; diff --git a/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch b/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch new file mode 100644 index 000000000000..b74fb32b9989 --- /dev/null +++ b/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch @@ -0,0 +1,10 @@ +--- a/beagle/include/beagle/RouletteT.hpp ++++ b/beagle/include/beagle/RouletteT.hpp +@@ -87,7 +87,7 @@ + Beagle_StackTraceBeginM(); + Beagle_AssertM(inWeight>=0.0); + if(VectorType::empty()==false) inWeight += VectorType::back().first; +- push_back(std::make_pair(inWeight,inValue)); ++ this->push_back(std::make_pair(inWeight,inValue)); + Beagle_StackTraceEndM("void RouletteT<T>::insert(const T& inValue, double inWeight)"); + } diff --git a/sci-libs/beagle/metadata.xml b/sci-libs/beagle/metadata.xml new file mode 100644 index 000000000000..c7ddf2e763fe --- /dev/null +++ b/sci-libs/beagle/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + Open BEAGLE is a C++ Evolutionary Computation (EC) framework. It provides an high-level software environment to do any kind of EC, with support for tree-based genetic programming, bit string and real-valued genetic algorithms, and evolution strategy. + </longdescription> + <upstream> + <remote-id type="sourceforge">beagle</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/blas-reference/Manifest b/sci-libs/blas-reference/Manifest new file mode 100644 index 000000000000..3155242ef956 --- /dev/null +++ b/sci-libs/blas-reference/Manifest @@ -0,0 +1,15 @@ +AUX blas-reference-20070226-autotool.patch 4245 SHA256 637c9a5af75ff4eb4cf8c7ae2ddbefda087d9b861d2fc2214cb865648d7ae093 SHA512 01abdad5d93466bcfbc832548a57248050d0e362090ba33b497e3e4d5b39cb078cbec44f07f709a90e6e89b9e9eb49f040e9f6b600058044534d4473d2cc3830 WHIRLPOOL bdd17169ad553f1c54f4cd1bd8ecb91edbe0502a838232667415d739c7cc91c7e58650d103a7ec21b7f75e69c7b125836244a8d2a1c939fb9c6d25cb810d6074 +AUX blas-reference-20070226-pkg-config.patch 354 SHA256 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+LAPACKPN="lapack-lite" + +DESCRIPTION="Basic Linear Algebra Subprograms F77 reference implementations" +HOMEPAGE="http://www.netlib.org/blas/" +SRC_URI="http://www.netlib.org/lapack/${LAPACKPN}-${LAPACKPV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="alpha amd64 arm hppa ia64 ~mips ppc ppc64 ~s390 sparc x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos" +IUSE="doc" + +DEPEND="app-eselect/eselect-blas" +RDEPEND="${DEPEND} + doc? ( app-doc/blas-docs )" + +S="${WORKDIR}/${LAPACKPN}-${LAPACKPV}" + +src_prepare() { + ESELECT_PROF=reference + epatch \ + "${FILESDIR}"/${P}-autotool.patch \ + "${FILESDIR}"/${P}-pkg-config.patch + eautoreconf + + cp "${FILESDIR}"/eselect.blas.reference "${T}"/eselect.blas.reference || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.blas.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.blas.reference || die + fi +} + +src_configure() { + econf \ + --libdir="${EPREFIX}"/usr/$(get_libdir)/blas/reference +} + +src_compile() { + emake LDFLAGS="${LDFLAGS}" +} + +src_install() { + default + eselect blas add $(get_libdir) "${T}"/eselect.blas.reference ${ESELECT_PROF} +} + +pkg_postinst() { + local p=blas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/blas-reference/blas-reference-20151113-r1.ebuild b/sci-libs/blas-reference/blas-reference-20151113-r1.ebuild new file mode 100644 index 000000000000..6a37c36168fc --- /dev/null +++ b/sci-libs/blas-reference/blas-reference-20151113-r1.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils fortran-2 cmake-utils multilib flag-o-matic toolchain-funcs + +LPN=lapack +LPV=3.6.0 + +DESCRIPTION="Basic Linear Algebra Subprograms F77 reference implementations" +HOMEPAGE="http://www.netlib.org/blas/" +SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos" +IUSE="doc" + +DEPEND="app-eselect/eselect-blas" +RDEPEND="${DEPEND} + doc? ( app-doc/blas-docs ) + virtual/pkgconfig" + +S="${WORKDIR}/${LPN}-${LPV}" +PATCHES=( "${FILESDIR}/lapack-reference-${LPV}-fix-build-system.patch" ) + +src_prepare() { + epatch "${PATCHES[@]}" + + eapply_user + + ESELECT_PROF=reference + + cp "${FILESDIR}"/eselect.blas.reference-r1 "${T}"/eselect.blas.reference || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.blas.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.blas.reference || die + fi +} + +src_configure() { + local mycmakeargs=( + -Wno-dev + -DUSE_OPTIMIZED_BLAS=OFF + -DCMAKE_Fortran_FLAGS="$(get_abi_CFLAGS) ${FCFLAGS}" + -DBUILD_SHARED_LIBS=ON + -DBUILD_STATIC_LIBS=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile -C BLAS +} + +src_install() { + cmake-utils_src_install -C BLAS + + mkdir -p "${ED}/usr/$(get_libdir)/blas/reference" || die + mv "${ED}/usr/$(get_libdir)"/lib* "${ED}/usr/$(get_libdir)/pkgconfig"/* \ + "${ED}/usr/$(get_libdir)/blas/reference" || die + rmdir "${ED}/usr/$(get_libdir)/pkgconfig" || die + + eselect blas add $(get_libdir) "${T}"/eselect.blas.reference ${ESELECT_PROF} +} + +pkg_postinst() { + local p=blas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/blas-reference/blas-reference-20161223.ebuild b/sci-libs/blas-reference/blas-reference-20161223.ebuild new file mode 100644 index 000000000000..f24a30a53724 --- /dev/null +++ b/sci-libs/blas-reference/blas-reference-20161223.ebuild @@ -0,0 +1,91 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils fortran-2 cmake-utils multilib flag-o-matic toolchain-funcs + +LPN=lapack +LPV=3.7.0 + +DESCRIPTION="Basic Linear Algebra Subprograms F77 reference implementations" +HOMEPAGE="http://www.netlib.org/blas/" +SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos" +IUSE="doc" + +DEPEND="app-eselect/eselect-blas" +RDEPEND="${DEPEND} + doc? ( app-doc/blas-docs ) + virtual/pkgconfig" + +S="${WORKDIR}/${LPN}-${LPV}" +PATCHES=( "${FILESDIR}/lapack-reference-${LPV}-fix-build-system.patch" ) + +src_prepare() { + epatch "${PATCHES[@]}" + + eapply_user + + ESELECT_PROF=reference + + cp "${FILESDIR}"/eselect.blas.reference-r1 "${T}"/eselect.blas.reference || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.blas.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.blas.reference || die + fi +} + +src_configure() { + local mycmakeargs=( + -Wno-dev + -DUSE_OPTIMIZED_BLAS=OFF + -DCMAKE_Fortran_FLAGS="$(get_abi_CFLAGS) ${FCFLAGS}" + -DBUILD_SHARED_LIBS=ON + -DBUILD_STATIC_LIBS=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile -C BLAS +} + +src_install() { + cmake-utils_src_install -C BLAS + + mkdir -p "${ED}/usr/$(get_libdir)/blas/reference" || die + mv "${ED}/usr/$(get_libdir)"/lib* "${ED}/usr/$(get_libdir)/pkgconfig"/* \ + "${ED}/usr/$(get_libdir)/blas/reference" || die + if [[ ${CHOST} == *-darwin* ]] ; then + # modify install_names accordingly, bug #605214 + local lib + for lib in "${ED}"/usr/$(get_libdir)/blas/reference/*.dylib ; do + install_name_tool -id "${lib#${D%/}}" "${lib}" + done + fi + rmdir "${ED}/usr/$(get_libdir)/pkgconfig" || die + + eselect blas add $(get_libdir) "${T}"/eselect.blas.reference ${ESELECT_PROF} +} + +pkg_postinst() { + local p=blas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/blas-reference/files/blas-reference-20070226-autotool.patch b/sci-libs/blas-reference/files/blas-reference-20070226-autotool.patch new file mode 100644 index 000000000000..8d8192fc0254 --- /dev/null +++ b/sci-libs/blas-reference/files/blas-reference-20070226-autotool.patch @@ -0,0 +1,243 @@ +--- configure.ac 1970-01-01 01:00:00.000000000 +0100 ++++ configure.ac 2007-07-16 10:14:29.000000000 +0100 +@@ -0,0 +1,14 @@ ++AC_PREREQ(2.59) ++AC_INIT(blas, 20070226, lapack@cs.utk.edu) ++AM_INIT_AUTOMAKE([foreign]) ++ ++AC_LANG(Fortran 77) ++AC_PROG_F77 ++AC_PROG_LIBTOOL ++ ++AC_CONFIG_FILES([Makefile ++ BLAS/Makefile ++ BLAS/SRC/Makefile ++ BLAS/TESTING/Makefile ++ BLAS/blas.pc]) ++AC_OUTPUT +--- Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Makefile.am 2007-07-16 01:51:11.000000000 +0100 +@@ -0,0 +1 @@ ++SUBDIRS = BLAS +--- BLAS/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ BLAS/Makefile.am 2007-08-14 11:38:42.000000000 +0100 +@@ -0,0 +1,7 @@ ++SUBDIRS = SRC TESTING ++ ++pkgconfigdir = $(libdir) ++pkgconfig_DATA = blas.pc ++ ++EXTRA = blas.pc ++ +--- BLAS/blas.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ BLAS/blas.pc.in 2007-08-17 11:38:23.000000000 +0100 +@@ -0,0 +1,11 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: @PACKAGE_NAME@ ++Description: Basic Linear Algebra Subprograms F77 reference implementations ++Version: @PACKAGE_VERSION@ ++URL: http://www.netlib.org/blas ++Libs: -lblas ++Libs.private: -lm +--- BLAS/SRC/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ BLAS/SRC/Makefile.am 2007-07-16 01:50:12.000000000 +0100 +@@ -0,0 +1,153 @@ ++lib_LTLIBRARIES = libblas.la ++ ++libblas_la_SOURCES = \ ++ caxpy.f \ ++ ccopy.f \ ++ cdotc.f \ ++ cdotu.f \ ++ cgbmv.f \ ++ cgemm.f \ ++ cgemv.f \ ++ cgerc.f \ ++ cgeru.f \ ++ chbmv.f \ ++ chemm.f \ ++ chemv.f \ ++ cher2.f \ ++ cher2k.f \ ++ cher.f \ ++ cherk.f \ ++ chpmv.f \ ++ chpr2.f \ ++ chpr.f \ ++ crotg.f \ ++ cscal.f \ ++ csrot.f \ ++ csscal.f \ ++ cswap.f \ ++ csymm.f \ ++ csyr2k.f \ ++ csyrk.f \ ++ ctbmv.f \ ++ ctbsv.f \ ++ ctpmv.f \ ++ ctpsv.f \ ++ ctrmm.f \ ++ ctrmv.f \ ++ ctrsm.f \ ++ ctrsv.f \ ++ dasum.f \ ++ daxpy.f \ ++ dcabs1.f \ ++ dcopy.f \ ++ ddot.f \ ++ dgbmv.f \ ++ dgemm.f \ ++ dgemv.f \ ++ dger.f \ ++ dnrm2.f \ ++ drot.f \ ++ drotg.f \ ++ drotm.f \ ++ drotmg.f \ ++ dsbmv.f \ ++ dscal.f \ ++ dsdot.f \ ++ dspmv.f \ ++ dspr2.f \ ++ dspr.f \ ++ dswap.f \ ++ dsymm.f \ ++ dsymv.f \ ++ dsyr2.f \ ++ dsyr2k.f \ ++ dsyr.f \ ++ dsyrk.f \ ++ dtbmv.f \ ++ dtbsv.f \ ++ dtpmv.f \ ++ dtpsv.f \ ++ dtrmm.f \ ++ dtrmv.f \ ++ dtrsm.f \ ++ dtrsv.f \ ++ dzasum.f \ ++ dznrm2.f \ ++ icamax.f \ ++ idamax.f \ ++ isamax.f \ ++ izamax.f \ ++ lsame.f \ ++ scabs1.f \ ++ sasum.f \ ++ saxpy.f \ ++ scasum.f \ ++ scnrm2.f \ ++ scopy.f \ ++ sdot.f \ ++ sdsdot.f \ ++ sgbmv.f \ ++ sgemm.f \ ++ sgemv.f \ ++ sger.f \ ++ snrm2.f \ ++ srot.f \ ++ srotg.f \ ++ srotm.f \ ++ srotmg.f \ ++ ssbmv.f \ ++ sscal.f \ ++ sspmv.f \ ++ sspr2.f \ ++ sspr.f \ ++ sswap.f \ ++ ssymm.f \ ++ ssymv.f \ ++ ssyr2.f \ ++ ssyr2k.f \ ++ ssyr.f \ ++ ssyrk.f \ ++ stbmv.f \ ++ stbsv.f \ ++ stpmv.f \ ++ stpsv.f \ ++ strmm.f \ ++ strmv.f \ ++ strsm.f \ ++ strsv.f \ ++ xerbla.f \ ++ zaxpy.f \ ++ zcopy.f \ ++ zdotc.f \ ++ zdotu.f \ ++ zdrot.f \ ++ zdscal.f \ ++ zgbmv.f \ ++ zgemm.f \ ++ zgemv.f \ ++ zgerc.f \ ++ zgeru.f \ ++ zhbmv.f \ ++ zhemm.f \ ++ zhemv.f \ ++ zher2.f \ ++ zher2k.f \ ++ zher.f \ ++ zherk.f \ ++ zhpmv.f \ ++ zhpr2.f \ ++ zhpr.f \ ++ zrotg.f \ ++ zscal.f \ ++ zswap.f \ ++ zsymm.f \ ++ zsyr2k.f \ ++ zsyrk.f \ ++ ztbmv.f \ ++ ztbsv.f \ ++ ztpmv.f \ ++ ztpsv.f \ ++ ztrmm.f \ ++ ztrmv.f \ ++ ztrsm.f \ ++ ztrsv.f +--- BLAS/TESTING/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ BLAS/TESTING/Makefile.am 2007-07-16 01:50:12.000000000 +0100 +@@ -0,0 +1,27 @@ ++TESTS = blas_tests ++ ++blas_tests: ++ @install -m0755 blas_tests.sh blas_tests ++ ++check_PROGRAMS = \ ++ xsblat1 xdblat1 xcblat1 xzblat1 \ ++ xsblat2 xdblat2 xcblat2 xzblat2 \ ++ xsblat3 xdblat3 xcblat3 xzblat3 ++ ++LDADD = $(top_builddir)/BLAS/SRC/libblas.la ++ ++xsblat1_SOURCES = sblat1.f ++xdblat1_SOURCES = dblat1.f ++xcblat1_SOURCES = cblat1.f ++xzblat1_SOURCES = zblat1.f ++ ++xsblat2_SOURCES = sblat2.f ++xdblat2_SOURCES = dblat2.f ++xcblat2_SOURCES = cblat2.f ++xzblat2_SOURCES = zblat2.f ++ ++xsblat3_SOURCES = sblat3.f ++xdblat3_SOURCES = dblat3.f ++xcblat3_SOURCES = cblat3.f ++xzblat3_SOURCES = zblat3.f ++ +--- BLAS/TESTING/blas_tests.sh 1970-01-01 01:00:00.000000000 +0100 ++++ BLAS/TESTING/blas_tests.sh 2007-07-16 01:50:12.000000000 +0100 +@@ -0,0 +1,9 @@ ++#!/bin/sh ++ ++for t in cblat1 sblat1 dblat1 zblat1; do ++ ./x${t} ++done ++ ++for t in cblat2 sblat2 dblat2 zblat2 cblat3 sblat3 dblat3 zblat3; do ++ ./x${t} < ../${t}.in ++done diff --git a/sci-libs/blas-reference/files/blas-reference-20070226-pkg-config.patch b/sci-libs/blas-reference/files/blas-reference-20070226-pkg-config.patch new file mode 100644 index 000000000000..14190f41e7d5 --- /dev/null +++ b/sci-libs/blas-reference/files/blas-reference-20070226-pkg-config.patch @@ -0,0 +1,11 @@ +diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in +index 367c87b..44b86db 100644 +--- a/BLAS/blas.pc.in ++++ b/BLAS/blas.pc.in +@@ -7,5 +7,5 @@ Name: @PACKAGE_NAME@ + Description: Basic Linear Algebra Subprograms F77 reference implementations + Version: @PACKAGE_VERSION@ + URL: http://www.netlib.org/blas +-Libs: -lblas ++Libs: -L@libdir@ -lblas + Libs.private: -lm diff --git a/sci-libs/blas-reference/files/eselect.blas.reference b/sci-libs/blas-reference/files/eselect.blas.reference new file mode 100644 index 000000000000..edb10ddd10d9 --- /dev/null +++ b/sci-libs/blas-reference/files/eselect.blas.reference @@ -0,0 +1,4 @@ +blas/reference/libblas.so /usr/@LIBDIR@/libblas.so +blas/reference/libblas.so.0 /usr/@LIBDIR@/libblas.so.0 +blas/reference/libblas.a /usr/@LIBDIR@/libblas.a +../blas/reference/blas.pc /usr/@LIBDIR@/pkgconfig/blas.pc diff --git a/sci-libs/blas-reference/files/eselect.blas.reference-r1 b/sci-libs/blas-reference/files/eselect.blas.reference-r1 new file mode 100644 index 000000000000..f032181beb67 --- /dev/null +++ b/sci-libs/blas-reference/files/eselect.blas.reference-r1 @@ -0,0 +1,4 @@ +blas/reference/libblas.so /usr/@LIBDIR@/libblas.so +blas/reference/libblas.so.3 /usr/@LIBDIR@/libblas.so.3 +blas/reference/libblas.a /usr/@LIBDIR@/libblas.a +../blas/reference/blas.pc /usr/@LIBDIR@/pkgconfig/blas.pc diff --git a/sci-libs/blas-reference/files/lapack-reference-3.6.0-fix-build-system.patch b/sci-libs/blas-reference/files/lapack-reference-3.6.0-fix-build-system.patch new file mode 100644 index 000000000000..8661709d369b --- /dev/null +++ b/sci-libs/blas-reference/files/lapack-reference-3.6.0-fix-build-system.patch @@ -0,0 +1,92 @@ +--- lapack-3.6.0/BLAS/blas.pc.in ++++ lapack-3.6.0/BLAS/blas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: blas + Description: Basic Linear Algebra Subprograms F77 reference implementations +--- lapack-3.6.0/BLAS/CMakeLists.txt ++++ lapack-3.6.0/BLAS/CMakeLists.txt +@@ -2,7 +2,7 @@ + if(BUILD_TESTING) + add_subdirectory(TESTING) + endif(BUILD_TESTING) +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/blas.pc + DESTINATION ${PKG_CONFIG_DIR} +--- lapack-3.6.0/CBLAS/cblas.pc.in ++++ lapack-3.6.0/CBLAS/cblas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: lapacke + Description: C Standard Interface to BLAS Linear Algebra PACKage +--- lapack-3.6.0/CBLAS/CMakeLists.txt ++++ lapack-3.6.0/CBLAS/CMakeLists.txt +@@ -71,7 +71,7 @@ + ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc + DESTINATION ${PKG_CONFIG_DIR} +--- lapack-3.6.0/CMakeLists.txt ++++ lapack-3.6.0/CMakeLists.txt +@@ -333,7 +333,7 @@ + ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc + DESTINATION ${PKG_CONFIG_DIR} +--- lapack-3.6.0/LAPACKE/CMakeLists.txt ++++ lapack-3.6.0/LAPACKE/CMakeLists.txt +@@ -65,7 +65,7 @@ + endif(BUILD_TESTING) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc + DESTINATION ${PKG_CONFIG_DIR} +--- lapack-3.6.0/LAPACKE/lapacke.pc.in ++++ lapack-3.6.0/LAPACKE/lapacke.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: lapacke + Description: C Standard Interface to LAPACK Linear Algebra PACKage +--- lapack-3.6.0/lapack.pc.in ++++ lapack-3.6.0/lapack.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: lapack + Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage diff --git a/sci-libs/blas-reference/files/lapack-reference-3.7.0-fix-build-system.patch b/sci-libs/blas-reference/files/lapack-reference-3.7.0-fix-build-system.patch new file mode 100644 index 000000000000..70f7cb0ee926 --- /dev/null +++ b/sci-libs/blas-reference/files/lapack-reference-3.7.0-fix-build-system.patch @@ -0,0 +1,56 @@ +diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in +index 7fd6f1e..e52f3ad 100644 +--- a/BLAS/blas.pc.in ++++ b/BLAS/blas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: BLAS + Description: FORTRAN reference implementation of BLAS Basic Linear Algebra Subprograms +diff --git a/CBLAS/cblas.pc.in b/CBLAS/cblas.pc.in +index 4a938fe..311aed9 100644 +--- a/CBLAS/cblas.pc.in ++++ b/CBLAS/cblas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: CBLAS + Description: C Standard Interface to BLAS Basic Linear Algebra Subprograms +diff --git a/LAPACKE/lapacke.pc.in b/LAPACKE/lapacke.pc.in +index 028f8da..dc092b1 100644 +--- a/LAPACKE/lapacke.pc.in ++++ b/LAPACKE/lapacke.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: LAPACKE + Description: C Standard Interface to LAPACK Linear Algebra PACKage +diff --git a/lapack.pc.in b/lapack.pc.in +index 878efc2..2cca4c2 100644 +--- a/lapack.pc.in ++++ b/lapack.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: LAPACK + Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage diff --git a/sci-libs/blas-reference/metadata.xml b/sci-libs/blas-reference/metadata.xml new file mode 100644 index 000000000000..1bde80743687 --- /dev/null +++ b/sci-libs/blas-reference/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +The BLAS (Basic Linear Algebra Subprograms) are high quality "building +block" routines for performing basic vector and matrix operations. Level 1 +BLAS do vector-vector operations, Level 2 BLAS do matrix-vector operations, +and Level 3 BLAS do matrix-matrix operations. Because the BLAS are +efficient, portable, and widely available, they're commonly used in the +development of high quality linear algebra software, LAPACK for +example. This packages implements the reference FORTRAN 77 library. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/bliss/Manifest b/sci-libs/bliss/Manifest new file mode 100644 index 000000000000..56f3f18ebf0b --- /dev/null +++ b/sci-libs/bliss/Manifest @@ -0,0 +1,9 @@ +AUX bliss-0.73-autotools.patch 3117 SHA256 bdfb47b25d02b4cd7300381ce4fe416507644f91ecccb6830cce957594e0feea SHA512 98333e4d97eca83776148b06e8ec41b283fa2a85a77a2c1281084a5af5efefb22ca34b9b6a11e2b9fdb71af944c6c56247291ea6721bd6d6dcf855e73116351e WHIRLPOOL 3904d788687f9da80934579d437b2736f5b326f4cf1c21df5143a4f77713c3518c42fe32c1c3013840d6f3debf62c2dd0e937e9d92fd45686f6abb8150727c80 +AUX bliss-0.73-error.patch 14317 SHA256 75a3833f7b61a0059f1076ad4bdf9f2857447c214013b524867dc7505380b79a SHA512 d4adcd652016d4b62e4b366cdbd5bd60f1dbaf89619e1d8d4dad6092a3dbb4e27e12aa13c1fc1f12481f144696b2e1392ecbc67dab0485959450d39013613a14 WHIRLPOOL 385a41cef1ceeb8fc13ed15b359861377e85bb0d862edebf9666f27f324294f5073ebe9d5ca03ae558e42d4a087f9bdba1ffabc1869af2cc652a866403a1891a +AUX bliss-0.73-rehn.patch 1669 SHA256 b03799a0cc7f8377b2f640ff57cd7dd67a50361c37f58ba81b0afad6cf94d767 SHA512 ae70ebcd3d9ef2f744e951dfb9cc2b48bee741ee7ead557a0fdfdacbd1895b015bb9a8da986fa36b084d4c92f7a28adad1df14c0814847d84c46f73cb69123b7 WHIRLPOOL f06a7ca86b030c6bda0c03332f4daec6af6f261cb52d54a02ec1e0fd2cc7855c48419de64dd8076d76674a27a30531969123d6dd8f092082b754c3d1b6194775 +AUX bliss-0.73.1.in 1482 SHA256 3fdbf91955a075ff40c647ed2076442594531aff65bc0f2b082798503a066d9d SHA512 7eb1d08f9c40358ef986d8fe31d42eb90dc57879cb399f45dcf5df85eecdc6fd86208f1bf06c21a6875e5a3fb5a634d818edd75ce2ccd855910feeb22b714f4b WHIRLPOOL 711be890a84f02993de7c04c0deb6b555b737897126544caaba4839a08b27477f4c726518f8963d593d77619ac9c36b5abeef6a3fb88be81cef530fa96e3da9c +DIST bliss-0.73.zip 94108 SHA256 f57bf32804140cad58b1240b804e0dbd68f7e6bf67eba8e0c0fa3a62fd7f0f84 SHA512 30f505945c577d8bcb265a349f5bc9d4dcd96555fa3add285199cdd95ea2710f04409008ff06432daffab62c132e884845eae7f823191407906202862509e05d WHIRLPOOL 08402453515e092604105f17f5889d252c0207fa31a1125e87e04c4792cbeb77b7a585a134fd2b3108e8620bbd643cd8b7826dee8a56cf47908a922298b70ad1 +EBUILD bliss-0.73-r1.ebuild 1043 SHA256 9d0ab0c652d946a8995409edd9556c48cda0091719315bafe4acefe274067bfa SHA512 81c15201073a7151be82baeb4438f9677332c30b89f9154c55e62e4438caa8992558f307f60f068d53f216bddbf9b9fa7006d44bb1afbba29db4d7ca562b0b46 WHIRLPOOL ed4d81d688617a25c87eaa2c2b8f8b44a70a3c3cff623ffe3b588bcd04565c9640d08ed1be6c5d0d613d935789fc3b10e1766ba27b05763100a1b11632e0278c +MISC ChangeLog 2753 SHA256 d761ffe8bef6dc4eedb6112e42f6dbb4ff51fc2f1eded49242ee15b708138ac8 SHA512 ce3a2d7f5ada218b8305308caf4987be550efeba9b5da1f915e359f8976fe3126f2f6ae43bfff1ae5b0cf1c20b647a2543410299cf9945a77bc1ffa0e15e4ff4 WHIRLPOOL c14c187969b26dab8b04d531f5368e0041716951f5a052e1787eb39661a0a29302f72275e2354d7dbccd49fe0db4f5b79496c0aa117ad04e6980654a80b956ad +MISC ChangeLog-2015 602 SHA256 faa76a783fffa957ce5d4c4fd90ecfd0039c2d06bfdfa28880cec3a0dec2f53f SHA512 16273c662bb222dc3552ab46b60d183a7eb9dcbd3f64394fb1c87d9f5f2893aa1f3b9cb7706d963bcf65db7f0f2bdf3fdc0fc97f021b4913b7d1c6265dbf3f33 WHIRLPOOL 1c141e7285d68a73b1be8754326bd61eff955f05b1226dcb6a8f9da5eb8e0c422a33d5c9356f9d66ece316bf11c96446c40f90ee0618203600cede69b2e92462 +MISC metadata.xml 377 SHA256 0792512ebf944eec93eb89c9cb406e981cff319977e4518f949d3bce971d9752 SHA512 c1a74f1feabe9c0b1179889514cffb7bf130a483990de7d235e177e345c0d1813c09b9751a1c94ced6f9d5c19b1428a0d62ab4d2e8876502dfeb5b7f5806afbf WHIRLPOOL 25d2f8442e8f5fc281448744d8b5c380d39ca0b28c02f3cda844aedc21074359f9fa99b7f3c1eb97369ea4152a6a5f047533d10a0812daae13aa0a7e35cc3fbf diff --git a/sci-libs/bliss/bliss-0.73-r1.ebuild b/sci-libs/bliss/bliss-0.73-r1.ebuild new file mode 100644 index 000000000000..de9e1f385274 --- /dev/null +++ b/sci-libs/bliss/bliss-0.73-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +SRC_URI="http://www.tcs.hut.fi/Software/${PN}/${P}.zip" +DESCRIPTION="Compute Automorphism Groups and Canonical Labelings of Graphs" +HOMEPAGE="http://www.tcs.hut.fi/Software/bliss/" + +LICENSE="LGPL-3" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc gmp static-libs" + +RDEPEND="gmp? ( dev-libs/gmp:0= )" +DEPEND="${RDEPEND} + app-arch/unzip + doc? ( app-doc/doxygen )" + +#patches from http://pkgs.fedoraproject.org/cgit/rpms/bliss.git/tree/ +PATCHES=( + "${FILESDIR}"/${P}-error.patch + "${FILESDIR}"/${P}-rehn.patch + "${FILESDIR}"/${P}-autotools.patch +) + +src_prepare() { + default + cp "${FILESDIR}/${P}.1.in" "${PN}.1.in" || die + rm Makefile || die + eautoreconf +} + +src_configure() { + econf $(use_with gmp) $(use_enable static-libs static) +} + +src_compile() { + emake all $(usex doc html "") +} + +src_install() { + default + use static-libs || find "${ED}" -name '*.la' -delete + use doc && dodoc -r html +} diff --git a/sci-libs/bliss/files/bliss-0.73-autotools.patch b/sci-libs/bliss/files/bliss-0.73-autotools.patch new file mode 100644 index 000000000000..efdbcb81b42a --- /dev/null +++ b/sci-libs/bliss/files/bliss-0.73-autotools.patch @@ -0,0 +1,99 @@ +Replace simple Makefile by autotools +- allow shared library +- parallel build +- added pkg-config support + +Author: Christoph Junghans <junghans@gentoo.org> + +diff -Naur bliss-0.72-fedora/config/.dummy bliss-0.72/config/.dummy +--- bliss-0.72-fedora/config/.dummy 1969-12-31 17:00:00.000000000 -0700 ++++ bliss-0.72/config/.dummy 2013-04-28 14:43:06.143760368 -0600 +@@ -0,0 +1 @@ ++Dummy file to make patch create config dir, which is needed for autotools +diff -Naur bliss-0.72-fedora/configure.ac bliss-0.72/configure.ac +--- bliss-0.72-fedora/configure.ac 1969-12-31 17:00:00.000000000 -0700 ++++ bliss-0.72/configure.ac 2013-04-28 14:40:42.283242722 -0600 +@@ -0,0 +1,32 @@ ++AC_PREREQ([2.65]) ++AC_INIT([bliss], [0.73], [Tommi.Junttil@kk.fi]) ++ ++AC_CONFIG_AUX_DIR(config) ++AC_CONFIG_MACRO_DIR(config) ++ ++AM_INIT_AUTOMAKE([1.8 foreign]) ++ ++SHARED_VERSION_INFO="1:0:0" ++AC_SUBST(SHARED_VERSION_INFO) ++ ++# Checks for programs. ++AC_PROG_CXX ++ ++LT_INIT ++# Checks for libraries. ++AC_ARG_WITH([gmp], ++ [AS_HELP_STRING([--with-gmp], [enable support for GNU Multiple Precision Arithmetic Library @<:@default=check@:>@])], ++ [], [with_gmp=no]) ++AS_IF([test "x$with_gmp" != xno], ++ [AC_CHECK_HEADERS([gmp.h],,AC_MSG_ERROR([Cannot find gmp.h header])) ++ AC_CHECK_LIB([gmp],_init,,AC_MSG_ERROR([Cannot find gmp library])) ++ AC_SUBST([GMP],[-lgmp]) ++ [CPPFLAGS="$CPPFLAGS -DBLISS_USE_GMP"]]) ++ ++AC_CHECK_PROG(DOXYGEN,doxygen,doxygen,no) ++AM_CONDITIONAL(HAVE_DOXYGEN,[test .$DOXYGEN != .no]) ++ ++AC_CONFIG_FILES([Makefile]) ++AC_CONFIG_FILES([bliss.pc]) ++AC_CONFIG_FILES([bliss.1]) ++AC_OUTPUT +diff -Naur bliss-0.72-fedora/bliss.pc.in bliss-0.72/bliss.pc.in +--- bliss-0.72-fedora/bliss.pc.in 1969-12-31 17:00:00.000000000 -0700 ++++ bliss-0.72/bliss.pc.in 2013-04-28 14:40:54.223285686 -0600 +@@ -0,0 +1,13 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: bliss ++Description: Library for Computing Automorphism Groups and Canonical Labelings of Graphs ++URL: http://www.tcs.hut.fi/Software/bliss/index.shtml ++Version: @VERSION@ ++Requires: ++Libs: -L${libdir} -lbliss @GMP@ ++Libs.private: -lm ++Cflags: -I${includedir} +diff -Naur bliss-0.72-fedora/Makefile.am bliss-0.72/Makefile.am +--- bliss-0.72-fedora/Makefile.am 1969-12-31 17:00:00.000000000 -0700 ++++ bliss-0.72/Makefile.am 2013-04-28 14:47:26.944698789 -0600 +@@ -0,0 +1,30 @@ ++ACLOCAL_AMFLAGS = -I config ++ ++lib_LTLIBRARIES = libbliss.la ++ ++libbliss_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@ ++libbliss_la_SOURCES = \ ++ defs.cc graph.cc partition.cc orbit.cc uintseqhash.cc heap.cc \ ++ timer.cc utils.cc bliss_C.cc ++ ++pkginclude_HEADERS = \ ++ bignum.hh bliss_C.h defs.hh graph.hh heap.hh kqueue.hh kstack.hh \ ++ orbit.hh partition.hh timer.hh uintseqhash.hh utils.hh ++ ++bin_PROGRAMS = bliss ++bliss_SOURCES = bliss.cc ++bliss_LDADD = libbliss.la ++dist_man1_MANS = bliss.1 ++ ++pkgconfigdir = $(libdir)/pkgconfig ++pkgconfig_DATA = bliss.pc ++ ++html-local: Doxyfile ++if HAVE_DOXYGEN ++ $(DOXYGEN) $(srcdir)/Doxyfile ++else ++ @echo "doxygen was not found, please re-run configure" ++endif ++ ++clean-local: ++ -rm -rf html diff --git a/sci-libs/bliss/files/bliss-0.73-error.patch b/sci-libs/bliss/files/bliss-0.73-error.patch new file mode 100644 index 000000000000..cd0f5457219f --- /dev/null +++ b/sci-libs/bliss/files/bliss-0.73-error.patch @@ -0,0 +1,471 @@ +--- ./bliss.cc.orig 2015-09-01 10:23:10.000000000 -0600 ++++ ./bliss.cc 2015-09-04 15:04:09.946602735 -0600 +@@ -276,13 +276,16 @@ main(const int argc, const char** argv) + if(opt_canonize == false) + { + /* No canonical labeling, only automorphism group */ +- g->find_automorphisms(stats, &report_aut, stdout); ++ if (!g->find_automorphisms(stats, &report_aut, stdout)) ++ exit(1); + } + else + { + /* Canonical labeling and automorphism group */ + const unsigned int* cl = g->canonical_form(stats, &report_aut, stdout); + ++ if (!cl) ++ exit(1); + fprintf(stdout, "Canonical labeling: "); + bliss::print_permutation(stdout, g->get_nof_vertices(), cl, 1); + fprintf(stdout, "\n"); +@@ -290,6 +293,8 @@ main(const int argc, const char** argv) + if(opt_output_can_file) + { + bliss::AbstractGraph* cf = g->permute(cl); ++ if (!cf) ++ exit(1); + FILE* const fp = fopen(opt_output_can_file, "w"); + if(!fp) + _fatal("Cannot open '%s' for outputting the canonical form, aborting", opt_output_can_file); +--- ./bliss_C.cc.orig 2015-09-01 10:23:10.000000000 -0600 ++++ ./bliss_C.cc 2015-09-04 15:04:09.945602814 -0600 +@@ -131,7 +131,7 @@ BlissGraph *bliss_permute(BlissGraph *gr + } + + extern "C" +-void ++int + bliss_find_automorphisms(BlissGraph *graph, + void (*hook)(void *user_param, + unsigned int n, +@@ -142,7 +142,8 @@ bliss_find_automorphisms(BlissGraph *gra + bliss::Stats s; + assert(graph); + assert(graph->g); +- graph->g->find_automorphisms(s, hook, hook_user_param); ++ if (!graph->g->find_automorphisms(s, hook, hook_user_param)) ++ return 0; + + if(stats) + { +@@ -154,6 +155,7 @@ bliss_find_automorphisms(BlissGraph *gra + stats->nof_generators = s.get_nof_generators(); + stats->max_level = s.get_max_level(); + } ++ return 1; + } + + +@@ -173,7 +175,7 @@ bliss_find_canonical_labeling(BlissGraph + + canonical_labeling = graph->g->canonical_form(s, hook, hook_user_param); + +- if(stats) ++ if(canonical_labeling && stats) + { + stats->group_size_approx = s.get_group_size_approx(); + stats->nof_nodes = s.get_nof_nodes(); +--- ./bliss_C.h.orig 2015-09-01 10:23:10.000000000 -0600 ++++ ./bliss_C.h 2015-09-04 15:04:09.947602656 -0600 +@@ -156,6 +156,7 @@ unsigned int bliss_hash(BlissGraph *grap + * The argument \a perm should be an array of + * N=bliss::bliss_get_nof_vertices(\a graph) elements describing + * a bijection on {0,...,N-1}. ++ * Returns NULL if insufficient memory or internal error. + */ + BlissGraph *bliss_permute(BlissGraph *graph, const unsigned int *perm); + +@@ -174,8 +175,9 @@ BlissGraph *bliss_permute(BlissGraph *gr + * if you want to use the automorphism later, you have to take a copy of it. + * Do not call bliss_* functions in the hook. + * If \a stats is non-null, then some search statistics are copied there. ++ * \return nonzero if successful, zero if insufficient memory or internal error + */ +-void ++int + bliss_find_automorphisms(BlissGraph *graph, + void (*hook)(void *user_param, + unsigned int N, +@@ -194,6 +196,7 @@ bliss_find_automorphisms(BlissGraph *gra + * then bliss_permute() with the returned canonical labeling. + * Note that the computed canonical version may depend on the applied version + * of bliss. ++ * Returns NULL if insufficient memory or internal error. + */ + const unsigned int * + bliss_find_canonical_labeling(BlissGraph *graph, +--- ./defs.cc.orig 2015-09-01 10:23:12.000000000 -0600 ++++ ./defs.cc 2015-09-04 15:04:09.947602656 -0600 +@@ -32,7 +32,6 @@ fatal_error(const char* fmt, ...) + vfprintf(stderr, fmt, ap); + fprintf(stderr, "\nAborting!\n"); + va_end(ap); +- exit(1); + } + + } +--- ./graph.cc.orig 2015-09-01 10:23:10.000000000 -0600 ++++ ./graph.cc 2015-09-04 15:04:09.927604245 -0600 +@@ -34,7 +34,10 @@ + namespace bliss { + + #define _INTERNAL_ERROR() fatal_error("%s:%d: internal error",__FILE__,__LINE__) +-#define _OUT_OF_MEMORY() fatal_error("%s:%d: out of memory",__FILE__,__LINE__) ++#define _OUT_OF_MEMORY(label) do { \ ++ fatal_error("%s:%d: out of memory",__FILE__,__LINE__); \ ++ goto label; \ ++ } while (0) + + /*------------------------------------------------------------------------- + * +@@ -279,20 +282,6 @@ AbstractGraph::reset_permutation(unsigne + *perm = i; + } + +-bool +-AbstractGraph::is_automorphism(unsigned int* const perm) +-{ +- _INTERNAL_ERROR(); +- return false; +-} +- +-bool +-AbstractGraph::is_automorphism(const std::vector<unsigned int>& perm) const +-{ +- _INTERNAL_ERROR(); +- return false; +-} +- + + + +@@ -618,7 +607,7 @@ typedef struct { + } PathInfo; + + +-void ++bool + AbstractGraph::search(const bool canonical, Stats& stats) + { + const unsigned int N = get_nof_vertices(); +@@ -658,7 +647,7 @@ AbstractGraph::search(const bool canonic + if(N == 0) + { + /* Nothing to do, return... */ +- return; ++ return true; + } + + /* Initialize the partition ... */ +@@ -696,10 +685,10 @@ AbstractGraph::search(const bool canonic + */ + if(first_path_labeling) free(first_path_labeling); + first_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int)); +- if(!first_path_labeling) _OUT_OF_MEMORY(); ++ if(!first_path_labeling) _OUT_OF_MEMORY(oom1); + if(best_path_labeling) free(best_path_labeling); + best_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int)); +- if(!best_path_labeling) _OUT_OF_MEMORY(); ++ if(!best_path_labeling) _OUT_OF_MEMORY(oom2); + + /* + * Is the initial partition discrete? +@@ -710,7 +699,7 @@ AbstractGraph::search(const bool canonic + update_labeling(best_path_labeling); + /* Update statistics */ + stats.nof_leaf_nodes = 1; +- return; ++ return true; + } + + /* +@@ -718,20 +707,39 @@ AbstractGraph::search(const bool canonic + */ + if(first_path_labeling_inv) free(first_path_labeling_inv); + first_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int)); +- if(!first_path_labeling_inv) _OUT_OF_MEMORY(); ++ if(!first_path_labeling_inv) _OUT_OF_MEMORY(oom3); + if(best_path_labeling_inv) free(best_path_labeling_inv); + best_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int)); +- if(!best_path_labeling_inv) _OUT_OF_MEMORY(); ++ if(!best_path_labeling_inv) _OUT_OF_MEMORY(oom4); + + /* + * Allocate space for the automorphisms + */ + if(first_path_automorphism) free(first_path_automorphism); + first_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int)); +- if(!first_path_automorphism) _OUT_OF_MEMORY(); ++ if(!first_path_automorphism) _OUT_OF_MEMORY(oom5); + if(best_path_automorphism) free(best_path_automorphism); + best_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int)); +- if(!best_path_automorphism) _OUT_OF_MEMORY(); ++ if(!best_path_automorphism) { ++ _OUT_OF_MEMORY(oom6); ++ oom6: ++ free(first_path_automorphism); ++ first_path_automorphism = NULL; ++ oom5: ++ free(best_path_labeling_inv); ++ best_path_labeling_inv = NULL; ++ oom4: ++ free(first_path_labeling_inv); ++ first_path_labeling_inv = NULL; ++ oom3: ++ free(best_path_labeling); ++ best_path_labeling = NULL; ++ oom2: ++ free(first_path_labeling); ++ first_path_labeling = NULL; ++ oom1: ++ return false; ++ } + + /* + * Initialize orbit information so that all vertices are in their own orbits +@@ -1203,8 +1211,10 @@ AbstractGraph::search(const bool canonic + + #if defined(BLISS_VERIFY_EQUITABLEDNESS) + /* The new partition should be equitable */ +- if(!is_equitable()) ++ if(!is_equitable()) { + fatal_error("consistency check failed - partition after refinement is not equitable"); ++ return false; ++ } + #endif + + /* +@@ -1596,8 +1606,10 @@ AbstractGraph::search(const bool canonic + + #if defined(BLISS_VERIFY_AUTOMORPHISMS) + /* Verify that it really is an automorphism */ +- if(!is_automorphism(best_path_automorphism)) ++ if(!is_automorphism(best_path_automorphism)) { + fatal_error("Best path automorhism validation check failed"); ++ return false; ++ } + #endif + + unsigned int gca_level_with_first = 0; +@@ -1664,6 +1676,7 @@ AbstractGraph::search(const bool canonic + + + _INTERNAL_ERROR(); ++ return false; + + + handle_first_path_automorphism: +@@ -1699,8 +1712,10 @@ AbstractGraph::search(const bool canonic + + #if defined(BLISS_VERIFY_AUTOMORPHISMS) + /* Verify that it really is an automorphism */ +- if(!is_automorphism(first_path_automorphism)) ++ if(!is_automorphism(first_path_automorphism)) { + fatal_error("First path automorphism validation check failed"); ++ return false; ++ } + #endif + + if(opt_use_long_prune) +@@ -1747,12 +1762,13 @@ AbstractGraph::search(const bool canonic + /* Release component recursion data in partition */ + if(opt_use_comprec) + p.cr_free(); ++ return true; + } + + + + +-void ++bool + AbstractGraph::find_automorphisms(Stats& stats, + void (*hook)(void *user_param, + unsigned int n, +@@ -1762,7 +1778,8 @@ AbstractGraph::find_automorphisms(Stats& + report_hook = hook; + report_user_param = user_param; + +- search(false, stats); ++ if (!search(false, stats)) ++ return false; + + if(first_path_labeling) + { +@@ -1774,6 +1791,7 @@ AbstractGraph::find_automorphisms(Stats& + free(best_path_labeling); + best_path_labeling = 0; + } ++ return true; + } + + +@@ -1788,7 +1806,8 @@ AbstractGraph::canonical_form(Stats& sta + report_hook = hook; + report_user_param = user_param; + +- search(true, stats); ++ if (!search(true, stats)) ++ return NULL; + + return best_path_labeling; + } +@@ -3479,15 +3498,17 @@ Digraph::initialize_certificate() + * Check whether perm is an automorphism. + * Slow, mainly for debugging and validation purposes. + */ +-bool ++int + Digraph::is_automorphism(unsigned int* const perm) + { + std::set<unsigned int, std::less<unsigned int> > edges1; + std::set<unsigned int, std::less<unsigned int> > edges2; + + #if defined(BLISS_CONSISTENCY_CHECKS) +- if(!is_permutation(get_nof_vertices(), perm)) ++ if(!is_permutation(get_nof_vertices(), perm)) { + _INTERNAL_ERROR(); ++ return -1; ++ } + #endif + + for(unsigned int i = 0; i < get_nof_vertices(); i++) +@@ -3506,7 +3527,7 @@ Digraph::is_automorphism(unsigned int* c + ei++) + edges2.insert(*ei); + if(!(edges1 == edges2)) +- return false; ++ return 0; + + edges1.clear(); + for(std::vector<unsigned int>::iterator ei = v1.edges_out.begin(); +@@ -3519,10 +3540,10 @@ Digraph::is_automorphism(unsigned int* c + ei++) + edges2.insert(*ei); + if(!(edges1 == edges2)) +- return false; ++ return 0; + } + +- return true; ++ return 1; + } + + bool +@@ -4337,8 +4358,10 @@ Graph* + Graph::permute(const unsigned int* perm) const + { + #if defined(BLISS_CONSISTENCY_CHECKS) +- if(!is_permutation(get_nof_vertices(), perm)) ++ if(!is_permutation(get_nof_vertices(), perm)) { + _INTERNAL_ERROR(); ++ return NULL; ++ } + #endif + + Graph* const g = new Graph(get_nof_vertices()); +@@ -5278,15 +5301,17 @@ Graph::initialize_certificate() + * + *-------------------------------------------------------------------------*/ + +-bool ++int + Graph::is_automorphism(unsigned int* const perm) + { + std::set<unsigned int, std::less<unsigned int> > edges1; + std::set<unsigned int, std::less<unsigned int> > edges2; + + #if defined(BLISS_CONSISTENCY_CHECKS) +- if(!is_permutation(get_nof_vertices(), perm)) ++ if(!is_permutation(get_nof_vertices(), perm)) { + _INTERNAL_ERROR(); ++ return -1; ++ } + #endif + + for(unsigned int i = 0; i < get_nof_vertices(); i++) +@@ -5306,10 +5331,10 @@ Graph::is_automorphism(unsigned int* con + edges2.insert(*ei); + + if(!(edges1 == edges2)) +- return false; ++ return 0; + } + +- return true; ++ return 1; + } + + +--- ./graph.hh.orig 2015-09-01 10:23:10.000000000 -0600 ++++ ./graph.hh 2015-09-04 15:09:17.261182632 -0600 +@@ -159,7 +159,7 @@ public: + * Check whether \a perm is an automorphism of this graph. + * Unoptimized, mainly for debugging purposes. + */ +- virtual bool is_automorphism(const std::vector<unsigned int>& perm) const; ++ virtual bool is_automorphism(const std::vector<unsigned int>& perm) const = 0; + + + /** Activate/deactivate failure recording. +@@ -211,8 +211,10 @@ public: + * if you want to use the automorphism later, you have to take a copy of it. + * Do not call any member functions in the hook. + * The search statistics are copied in \a stats. ++ * \return true if successful, false if insufficient memory to search or ++ * other internal error. + */ +- void find_automorphisms(Stats& stats, ++ bool find_automorphisms(Stats& stats, + void (*hook)(void* user_param, + unsigned int n, + const unsigned int* aut), +@@ -232,6 +234,8 @@ public: + * Note that the computed canonical version may depend on the applied version + * of bliss as well as on some other options (for instance, the splitting + * heuristic selected with bliss::Graph::set_splitting_heuristic()). ++ * This function returns NULL if there is insufficient memory, or another ++ * internal error occurs. + */ + const unsigned int* canonical_form(Stats& stats, + void (*hook)(void* user_param, +@@ -436,7 +440,7 @@ protected: + void reset_permutation(unsigned int *perm); + + /* Mainly for debugging purposes */ +- virtual bool is_automorphism(unsigned int* const perm); ++ virtual int is_automorphism(unsigned int* const perm) = 0; + + std::vector<unsigned int> certificate_current_path; + std::vector<unsigned int> certificate_first_path; +@@ -450,7 +454,11 @@ protected: + virtual Partition::Cell* find_next_cell_to_be_splitted(Partition::Cell *cell) = 0; + + +- void search(const bool canonical, Stats &stats); ++ /** ++ * \return true if successful, false if insufficient memory to complete or ++ * other internal error ++ */ ++ bool search(const bool canonical, Stats &stats); + + + void (*report_hook)(void *user_param, +@@ -634,7 +642,7 @@ protected: + + void initialize_certificate(); + +- bool is_automorphism(unsigned int* const perm); ++ int is_automorphism(unsigned int* const perm); + + + bool nucr_find_first_component(const unsigned int level); +@@ -875,7 +883,7 @@ protected: + + void initialize_certificate(); + +- bool is_automorphism(unsigned int* const perm); ++ int is_automorphism(unsigned int* const perm); + + void sort_edges(); + diff --git a/sci-libs/bliss/files/bliss-0.73-rehn.patch b/sci-libs/bliss/files/bliss-0.73-rehn.patch new file mode 100644 index 000000000000..f37eedb4a6bd --- /dev/null +++ b/sci-libs/bliss/files/bliss-0.73-rehn.patch @@ -0,0 +1,74 @@ +--- ./graph.cc.orig 2015-09-04 15:04:09.927604245 -0600 ++++ ./graph.cc 2015-09-04 15:09:46.999819514 -0600 +@@ -597,16 +597,6 @@ public: + }; + + +- +- +-typedef struct { +- unsigned int splitting_element; +- unsigned int certificate_index; +- unsigned int subcertificate_length; +- UintSeqHash eqref_hash; +-} PathInfo; +- +- + bool + AbstractGraph::search(const bool canonical, Stats& stats) + { +@@ -753,7 +743,6 @@ AbstractGraph::search(const bool canonic + initialize_certificate(); + + std::vector<TreeNode> search_stack; +- std::vector<PathInfo> first_path_info; + std::vector<PathInfo> best_path_info; + + search_stack.clear(); +@@ -5477,7 +5466,7 @@ Graph::nucr_find_first_component(const u + component.clear(); + component_elements = 0; + sh_return = 0; +- unsigned int sh_first = 0; ++ unsigned int sh_first = 1 << 31; + unsigned int sh_size = 0; + unsigned int sh_nuconn = 0; + +--- ./graph.hh.orig 2015-09-04 15:09:17.261182632 -0600 ++++ ./graph.hh 2015-09-04 15:09:47.001819355 -0600 +@@ -109,9 +109,12 @@ public: + unsigned long int get_max_level() const {return max_level;} + }; + +- +- +- ++typedef struct { ++ unsigned int splitting_element; ++ unsigned int certificate_index; ++ unsigned int subcertificate_length; ++ UintSeqHash eqref_hash; ++} PathInfo; + + + /** +@@ -524,7 +527,7 @@ protected: + */ + unsigned int cr_component_elements; + +- ++ std::vector<PathInfo> first_path_info; + + + }; +@@ -756,6 +759,10 @@ public: + void set_splitting_heuristic(const SplittingHeuristic shs) {sh = shs; } + + ++ /** ++ * Get an information vector about the first path. ++ */ ++ std::vector<PathInfo> get_first_path_info() { return first_path_info; } + }; + + diff --git a/sci-libs/bliss/files/bliss-0.73.1.in b/sci-libs/bliss/files/bliss-0.73.1.in new file mode 100644 index 000000000000..f652c3d1307a --- /dev/null +++ b/sci-libs/bliss/files/bliss-0.73.1.in @@ -0,0 +1,55 @@ +.TH "BLISS" "1" "@VERSION@" "Tommi Junttila & Petteri Kaski" "User Commands" +.SH "NAME" +bliss \- Compute automorphism groups and canonical labelings of graphs +.SH "SYNOPSIS" +.B bliss +[\fIOPTIONS\fR] [<\fIGRAPH FILE\fR>] +.SH "DESCRIPTION" +.PP +Bliss is an open source tool for computing automorphism groups and +canonical forms of graphs. The graphs are specified in DIMACS format. +.TP +\fB\-directed\fR +the input graph is directed +.TP +\fB\-can\fR +compute canonical form +.TP +\fB\-ocan\fR=\fIf\fR +compute canonical form and output it in file \fIf\fR +.TP +\fB\-v\fR=\fIN\fR +set verbosity level to N [N >= 0, default: 1] +.TP +\fB\-sh\fR=\fIX\fR +select splitting heuristics, where X is: +.TS +tab(;); +R L. +f;first non-singleton cell +fl;first largest non-singleton cell +fs;first smallest non-singleton cell +fm;first maximally non-trivially connected non-singleton cell +flm;first largest maximally non-trivially connected +;non-singleton cell +fsm;first smallest maximally non-trivially connected +;non-singleton cell (default) +.TE +.TP +\fB\-fr\fR=\fIX\fR +use failure recording? [X=y/n, default: y] +.TP +\fB\-cr\fR=\fIX\fR +use component recursion? [X=y/n, default: y] +.TP +\fB\-version\fR +print the version number and exit +.TP +\fB\-help\fR +print this help and exit +.SH "AUTHORS" +Bliss was written by Tommi Junttila <Tommi.Junttila@tkk.fi> and +Petteri Kaski <petteri.kaski@aalto.fi>. +.PP +This man page was written by Jerry James <loganjerry@gmail.com>. +It is distributed under the same terms as bliss. diff --git a/sci-libs/bliss/metadata.xml b/sci-libs/bliss/metadata.xml new file mode 100644 index 000000000000..0668c1ada0d5 --- /dev/null +++ b/sci-libs/bliss/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/bmrblib/Manifest b/sci-libs/bmrblib/Manifest new file mode 100644 index 000000000000..836b38a3d87d --- /dev/null +++ b/sci-libs/bmrblib/Manifest @@ -0,0 +1,5 @@ +DIST bmrblib-1.0.3.tar.bz2 51246 SHA256 583e8d8f4ea2aaffec5eb30edfb4a840f1222512ad4f17c2d0d2c885a5afe3f6 SHA512 b03ad9e4ca035439165ebd1b7ba93ede427b2a233a4179be4e8089db988f1dcdce68b1e97348fe22fe7f2c3827ed003b654e0674a4d16a9e32a8a7c255c4b248 WHIRLPOOL 65b3a62142092af882be8d45fa84dd5b80e983c6bfb36d98b5ab444d6b0e4b0523ca64977a6643f27be9d64448a0c7e0ee2021bcbc306cbaa2101dcc3a1f6e1a +EBUILD bmrblib-1.0.3.ebuild 465 SHA256 f91f7144bde62e810d2a8d2c22a97c60b5eec9b536fc037d551fa60ebdea1934 SHA512 151733614dc3c6b770f97fba0350bef1f711e68292f72978da780f0b6c31cc2b176a09174ba080b84eb1f0e7de8abd728d33040d65d17b0ff5b0e5da23f017b1 WHIRLPOOL 686f36b72619621829a02c0b15cb073209b4bcde609810f7d7aeeda0b40af8ab55d8609315fbb7c3a8f7d2551ab3d77648039b859ca95aa0aa57457ef3248a65 +MISC ChangeLog 2695 SHA256 5772519bc351b51fc851062dfc5a4925fd1d51c3553b86b241dff46fff9afa86 SHA512 a03077f6b5ff9c72ecd395ee9e8fd1c1d02f7c66822cbb198a6e0de156266e4f22f1d5149109fada747284cfafd5f4e1cec10db471ba01e2f0ce09a4bcdf8c51 WHIRLPOOL f442cf4b5faed2c319d1c9477277e18c2e5a9ed55640d0a145035132d2f80d184ac6d4ce5dcfc0cfd201bd71f2a6561161be4023461142c441fe4eac2448df82 +MISC ChangeLog-2015 1624 SHA256 52ea1659eeee30a7893b369d1c1a2357f3e893c4aeffba5d7313ebf4d1f4a175 SHA512 173f835f1c55fe50729f4c80e197ca408c69ae88972201c5e3e7887b38ad898157998e9db26206b653540f5cd2322e285e59b7287989f5c9e36d466b592321d6 WHIRLPOOL 37e32e60563525531816d7d7b8cefa4c181e3bd7cacdf4cf1b758354ea3b5fea16466606e5716b585d21fc5e0ddde298334e9dc1de941c6cb5817a34084df008 +MISC metadata.xml 702 SHA256 813c9e63af37114d23976e63722824f29f5307b38d31c95b0447bcc95df27967 SHA512 57112dfdf8c732ea4ab256646e86016735d19a0a91df7c69179dafa72d8dbc498a2813df52883c11f3294a2b42563ce48117dc541c943e3f0f421af673d592bf WHIRLPOOL 335be13f975eaa8b52c4149bfe330275b9fd16422c0c799e531cd20e058ee091e93ad5e6957fef026301acc2d42469db365aab42497cebf3722509128eb233e2 diff --git a/sci-libs/bmrblib/bmrblib-1.0.3.ebuild b/sci-libs/bmrblib/bmrblib-1.0.3.ebuild new file mode 100644 index 000000000000..0b1e918d5776 --- /dev/null +++ b/sci-libs/bmrblib/bmrblib-1.0.3.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} pypy ) + +inherit distutils-r1 + +DESCRIPTION="API abstracting the BioMagResBank (BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/)" +HOMEPAGE="http://gna.org/projects/bmrblib/" +SRC_URI="http://download.gna.org/${PN}/${P}.tar.bz2" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-libs/bmrblib/metadata.xml b/sci-libs/bmrblib/metadata.xml new file mode 100644 index 000000000000..df11d311c7dd --- /dev/null +++ b/sci-libs/bmrblib/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + Bmrblib is an API abstracting the BioMagResBank (BMRB) NMR-STAR format + (http://www.bmrb.wisc.edu/). It allows the writing of NMR-STAR files + for BMRB data deposition and the reading and easy extraction of data + from files residing in the BMRB data bank, all without knowledge of + the Self-Defining Text Archive and Retrieval (STAR) format. 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+HOMEPAGE="http://www.cise.ufl.edu/research/sparse/btf/" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND="sci-libs/ufconfig" +RDEPEND="" + +DOCS=( README.txt Doc/ChangeLog ) +PATCHES=( "${FILESDIR}"/${PN}-1.0.1-autotools.patch ) + +S="${WORKDIR}/${MY_PN}" diff --git a/sci-libs/btf/btf-1.2.0.ebuild b/sci-libs/btf/btf-1.2.0.ebuild new file mode 100644 index 000000000000..d89070b87566 --- /dev/null +++ b/sci-libs/btf/btf-1.2.0.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Algorithm for matrix permutation into block triangular form" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/btf/" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" + +KEYWORDS=" ~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" + +RDEPEND="sci-libs/suitesparseconfig" +DEPEND="${RDEPEND} + virtual/pkgconfig" diff --git a/sci-libs/btf/files/btf-1.0.1-autotools.patch b/sci-libs/btf/files/btf-1.0.1-autotools.patch new file mode 100644 index 000000000000..4156c2dfeb70 --- /dev/null +++ b/sci-libs/btf/files/btf-1.0.1-autotools.patch @@ -0,0 +1,34 @@ +--- configure.ac 1970-01-01 01:00:00.000000000 +0100 ++++ configure.ac 2008-01-30 12:29:44.232979678 +0000 +@@ -0,0 +1,10 @@ ++# -*- Autoconf -*- ++AC_PREREQ(2.59) ++AC_INIT(btf, 1.0.1, davis@cise.ufl.edu) ++AM_INIT_AUTOMAKE([foreign]) ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++AC_CHECK_LIB(m, sqrt) ++AC_CHECK_HEADERS(UFconfig.h) ++AC_CONFIG_FILES([Makefile Source/Makefile]) ++AC_OUTPUT +--- Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Makefile.am 2008-01-30 12:30:12.862611188 +0000 +@@ -0,0 +1,3 @@ ++SUBDIRS = Source ++EXTRA_DIST = README.txt ++include_HEADERS = Include/btf.h Include/btf_internal.h +--- Source/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Source/Makefile.am 2008-01-30 12:37:00.857861512 +0000 +@@ -0,0 +1,12 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include ++ ++BTFSRC = btf_order.c btf_maxtrans.c btf_strongcomp.c ++ ++lib_LTLIBRARIES = libbtf.la ++noinst_LTLIBRARIES = libbtfi.la libbtfl.la ++libbtfi_la_SOURCES = $(BTFSRC) ++libbtfi_la_CPPFLAGS = $(AM_CPPFLAGS) ++libbtfl_la_SOURCES = $(BTFSRC) ++libbtfl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG ++libbtf_la_SOURCES = ++libbtf_la_LIBADD = libbtfl.la libbtfi.la diff --git a/sci-libs/btf/metadata.xml b/sci-libs/btf/metadata.xml new file mode 100644 index 000000000000..3979193d3287 --- /dev/null +++ b/sci-libs/btf/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The Block Triangular Form is a library of routines offering + permutation of an unsymmetric matrix (square or rectangular) into + its block upper triangular form (more precisely, it computes a + Dulmage-Mendelsohn decomposition). +</longdescription> +</pkgmetadata> diff --git a/sci-libs/buddy/Manifest b/sci-libs/buddy/Manifest new file mode 100644 index 000000000000..ff206164825a --- /dev/null +++ b/sci-libs/buddy/Manifest @@ -0,0 +1,7 @@ +AUX buddy-2.4-gcc43.patch 807 SHA256 ea1aace88336f4f10cb214beb3657672eb64f7996af3b4f84fbdbad4d1ccaf26 SHA512 da8069bb467ad1a159036a6d39c8ab5ad75ecf1d69b00b2db8b2de5f279a8cf807fc0f93ae9e0b0b9512d4b33c0889318463e1f34ec10f34415be76ebb1c9a20 WHIRLPOOL 6f92229dca96dc0f1f646d218520c257401d6023b802ffb2d120aebf078cb4c961d9a5fc3813a289ef1ea88f64c5e8b6aef03c3baba2a245e3e9d6f2afb21cfb +AUX buddy-2.4-gold.patch 596 SHA256 03c0e11c889de894267148f0d10bab150d07e8054a8b11e0f027184b3ad09c83 SHA512 46f8077fc2c10479b083d3b9cda2905baa8c06739e3de47ebf1535b77229a21811f47f33d5de1431ea634e97baa9950496ab46bc69974830f1f13a1c2e2444ee WHIRLPOOL ba63ef0d0c2480d8107f40ee66e43715caf32a7c1e26c2a33788d036171bc8e2090c530d21b0f4cccb321839ad7afa356a2352572c337a1a7a8aa5354429158d +DIST buddy-2.4.tar.gz 766523 SHA256 d3df80a6a669d9ae408cb46012ff17bd33d855529d20f3a7e563d0d913358836 SHA512 43984969359ac363141ee8a67538ceeae1412efa172432a8355f6ce68ab5ffab12470ad7a2e0d7a6a557b8bf55e98b2f2dc5cc6710466403d45fab2195ba2e23 WHIRLPOOL 448c1eacc61a238083723693abca6f1600198e9ebd420a9b21179d82fd717c697bfe39758bffda1d96e3ace1a160da5cde91094bd67d9d288a632f1d03f2170a +EBUILD buddy-2.4-r1.ebuild 707 SHA256 9dc1a40a957709aeb2eabf6a3d0c1c9a2dea857773bdabd62be6c496e614728b SHA512 3b1f8f9db8f7946de4b518c7dc62abe0b111cdafca153ac7426ac6dfb5c1f856357bcaf6d7d962d6160960373ab27fd27ceb30a6fa7f131de97d5f8e6590eee7 WHIRLPOOL 504ad17a81723143df50170d824c7857643765913b3fcd91d70a3755a7dd0258bc9d8b06c73c17504aae1d16f2135262b6f3899243ea2947e286d73ae53e5506 +MISC ChangeLog 3137 SHA256 38351a9a6068bc2ff071fdb3947aba8a869adf1081555e4b3894c49de8e74c11 SHA512 a7ad3c61b51a6891ef225480422ee0ff4039c407d1ba1a5cac5e073d84c6da1eff461bf7d0103a8ead22d9e6bbcc7a43cc6f77733975d51029e611f9cf6ea7f5 WHIRLPOOL d7a590032ceb8a5fb84ffcb888746395b20cad6d662ec5c933bbce7ed7a736b3acde522ec5dcaa74e09485974ea4ca3ea087ee38640efd9922e30872a208b81f +MISC ChangeLog-2015 2433 SHA256 cd9ac6258c525280094fd4aa5b3e3f3a70bd9f5ffdb4f0669674d75717511b0b SHA512 91ef17b013d9bf6976c8c005d92303145d8f38381d195b529a2c5b63386adf1c0d5482fbcc5961a79ea35ed9f11135846f3094fdbb6e64a068fb824c8571fd04 WHIRLPOOL f80552657514b89506611db63d6e43c2fd0e14c07f0a5efb43593d72b85f456a65921431eabf1b0b88c8225c69c7905969b9d3f8fe086782219a8e9a2973e117 +MISC metadata.xml 606 SHA256 dbec072ccda0f4a01013ee83aea0ec7697653f40a4e3e4a47876f2087f7de585 SHA512 b89f749637d1b732bb8bb6ce33d8ca9445e388ee6bf0870e01781a3eec0a8a4bb3fe88c0ed618b0e3a4f2c793655fa3ba3184d84857754782b5c2a777f3f847a WHIRLPOOL 4929655b455a4c1bab5c5af935dc46eda794760e7ee1104379cea341c01daf736e0b7faac9ff11f5aee4c91c75442fa2328069462a74f16b3db4809f95392511 diff --git a/sci-libs/buddy/buddy-2.4-r1.ebuild b/sci-libs/buddy/buddy-2.4-r1.ebuild new file mode 100644 index 000000000000..c5dfddbbe1e1 --- /dev/null +++ b/sci-libs/buddy/buddy-2.4-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit fortran-2 + +DESCRIPTION="Binary Decision Diagram Package" +HOMEPAGE="https://sourceforge.net/projects/buddy/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="buddy" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="doc examples static-libs" + +DOCS=( doc/tech.txt ) +PATCHES=( + "${FILESDIR}"/${P}-gcc43.patch + "${FILESDIR}"/${P}-gold.patch +) + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + + use doc && docinto ps && dodoc doc/*.ps + + if use examples; then + insinto /usr/share/${PN}/ + doins -r examples + fi +} diff --git a/sci-libs/buddy/files/buddy-2.4-gcc43.patch b/sci-libs/buddy/files/buddy-2.4-gcc43.patch new file mode 100644 index 000000000000..c7b9f85688eb --- /dev/null +++ b/sci-libs/buddy/files/buddy-2.4-gcc43.patch @@ -0,0 +1,22 @@ +diff -Naurp buddy-2.4-orig/src/bddtest.cxx buddy-2.4/src/bddtest.cxx +--- buddy-2.4-orig/src/bddtest.cxx 2004-06-25 07:22:26.000000000 -0600 ++++ buddy-2.4/src/bddtest.cxx 2009-02-09 22:14:19.000000000 -0600 +@@ -28,6 +28,7 @@ + ========================================================================*/ + + #include <string> ++#include <cstdlib> + #include "bdd.h" + #include "bvec.h" + +diff -Naurp buddy-2.4-orig/examples/bddcalc/parser_.h buddy-2.4/examples/bddcalc/parser_.h +--- buddy-2.4-orig/examples/bddcalc/parser_.h 2004-06-25 07:21:43.000000000 -0600 ++++ buddy-2.4/examples/bddcalc/parser_.h 2009-02-09 22:21:09.000000000 -0600 +@@ -9,6 +9,7 @@ + #define _PARSER_H + + #include <stdio.h> ++#include <stdlib.h> + #include "bdd.h" + + #define MAXIDLEN 32 /* Max. number of allowed characters in an identifier */ diff --git a/sci-libs/buddy/files/buddy-2.4-gold.patch b/sci-libs/buddy/files/buddy-2.4-gold.patch new file mode 100644 index 000000000000..dc30a642141d --- /dev/null +++ b/sci-libs/buddy/files/buddy-2.4-gold.patch @@ -0,0 +1,16 @@ + examples/cmilner/Makefile.in | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/examples/cmilner/Makefile.in b/examples/cmilner/Makefile.in +index 9b49e9d..f7a9b8a 100644 +--- a/examples/cmilner/Makefile.in ++++ b/examples/cmilner/Makefile.in +@@ -217,7 +217,7 @@ clean-checkPROGRAMS: + done + cmilner$(EXEEXT): $(cmilner_OBJECTS) $(cmilner_DEPENDENCIES) + @rm -f cmilner$(EXEEXT) +- $(LINK) $(cmilner_LDFLAGS) $(cmilner_OBJECTS) $(cmilner_LDADD) $(LIBS) ++ $(LINK) $(cmilner_LDFLAGS) $(cmilner_OBJECTS) $(cmilner_LDADD) $(LIBS) -lm + + mostlyclean-compile: + -rm -f *.$(OBJEXT) diff --git a/sci-libs/buddy/metadata.xml b/sci-libs/buddy/metadata.xml new file mode 100644 index 000000000000..2cbfbe4b7bfa --- /dev/null +++ b/sci-libs/buddy/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + A Binary Decision Diagram library, with :many highly efficient + vectorized BDD operations,dynamic variable reordering,automated + garbage collection,a C++ interface with automatic reference + counting,and much more. +</longdescription> + <upstream> + <remote-id type="sourceforge">buddy</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/camd/Manifest b/sci-libs/camd/Manifest new file mode 100644 index 000000000000..b066dbba8925 --- /dev/null +++ b/sci-libs/camd/Manifest @@ -0,0 +1,5 @@ +DIST camd-2.3.1.tar.bz2 319766 SHA256 bb3fcb577307fa4a70281bea8db896b2300a484f27cb61b392be2c4cf7cd5a2e SHA512 13c5d687b9314f43a6c7237c7541e0c21cc544ffe52f8a984f64c5177a9f1f6b5ab07e9190388587f273424db8e6076ef050f836dbc9f33ca44e94d0034c8070 WHIRLPOOL a53b09c002b930a78055742f507b3ea7b14906378edb6808e65e4aac16dcad8178cc16de6373d633356b501fb8a5939737f8c4966d94c1162076be5b1b15c2ad +EBUILD camd-2.3.1.ebuild 716 SHA256 d0f499c0401b2edebd558c20bc6fb0a0b8d3200b8a3cf9ce1d24a86dda62c3eb SHA512 ac6c70deaf50bd24fe2f69a7c37434ec2679aebdcfc9ca5d9a873bf1fb60ddefb5f9a73c47ba8713ec2c4cf2483f031e27aa0dd8d47373a27fda7cb1870ceffb WHIRLPOOL 6779880adcbcb723e9a1c03cf0c4ea6b1f496f48885876b177f7537428c6dfb5ca97999435a4f60064cc6e2de3ed6bca4783331af339a9baf78163cb7a03fcb8 +MISC ChangeLog 2639 SHA256 753bde19c7c631942f20e971a67d83b780e1c3d49600c4194e247e4dd4016a80 SHA512 17977213115383136a924bb22c334a905972bb9eb78a5a307df94542220c8f7d860735a3f4f2322b6c1453d99730f939db98888cf3fe36979368611c99f7318d WHIRLPOOL a6291af89b1aa4da6d0b356effe12b9365f6688db380e941ff1549214f7588e98793f6bb5830e1c84134f04317aef8a14eb9ea2b0d36bd23b566d750e5cd5d96 +MISC ChangeLog-2015 4152 SHA256 3d926c73986209900d3651da4b5e77d356e2fd4b2a224066dfe3671142cd5f25 SHA512 678234dc70e765d26312ffccf917a239eaaa7382fe9ad27a0e4f0701e2a1e24f8aade689f66eb67840bad10182d5194214e23a579dfda7533d5505e5163b2bde WHIRLPOOL ea6c71a062f0cd403f223c52e745d5da16914df00bdbc6ad26d8fed7f2d7a920b7d9b78c400b888093de28a496a1dbab414ae87889d14b2d2e0be5e7169e2726 +MISC metadata.xml 494 SHA256 3a1b85db61ebd4fa60e9d0a2dd5ceed4c5e2ee895a0a179cb31d41f56c3c5551 SHA512 6402783aec0922669bbf45477074644a9b10f44b0b06bf86ad9b4ecbab124076ee7f19c2c68c6eb3bf21a1569a3410f1ed0ac12f653dd5808559da133613d09f WHIRLPOOL 5606e05bf229e8fdbc361581ae59f0f953b148ae9ee76a5d2ab218c65f07573186a8839a6c336e67e37f73d3c5abf24ce6a2c394b4100e572d241a830570190c diff --git a/sci-libs/camd/camd-2.3.1.ebuild b/sci-libs/camd/camd-2.3.1.ebuild new file mode 100644 index 000000000000..acd75e0feb53 --- /dev/null +++ b/sci-libs/camd/camd-2.3.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Library to order a sparse matrix prior to Cholesky factorization" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/camd/" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" + +KEYWORDS="~alpha amd64 ~arm ~arm64 hppa ~ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc static-libs" + +RDEPEND="sci-libs/suitesparseconfig" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base )" + +src_configure() { + local myeconfargs=( + $(use_with doc) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/camd/metadata.xml b/sci-libs/camd/metadata.xml new file mode 100644 index 000000000000..f543de2655de --- /dev/null +++ b/sci-libs/camd/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Constrained Approximate Minimum Degree ordering is a set of routines + for ordering a sparse matrix prior to Cholesky factorization (or for + LU factorization with diagonal pivoting). +</longdescription> +</pkgmetadata> diff --git a/sci-libs/cbflib/Manifest b/sci-libs/cbflib/Manifest new file mode 100644 index 000000000000..9b096ee2591d --- /dev/null +++ b/sci-libs/cbflib/Manifest @@ -0,0 +1,6 @@ +AUX cbflib-0.9.3.3-unbundle.patch 8308 SHA256 edb391b86b8157ce2cc84c23e167ae2ac1bea945543eed1ae03746c931e895be SHA512 21f39214e188cc8fb76326765aba7da4d15c1b70d41c193016733d5b3d14e499178e25c45c807e7c9cabaf3a7f4e3e97c5ed2a8b383472ec9f4e4cbea9b3522d WHIRLPOOL 8dc05512d5797a4e9e3c90363fe0c13d1a30c86e2b37b7f9134c4881b514d1b1505583592a71ef16002ef0b2751b77950dd68dd2ac00c1228220429fce5ec9dd +DIST CBFlib-0.9.3.3.tar.gz 5787633 SHA256 d6c3cc2c6c0aed2a3aa7c74dc645ad223470dc76bb2181242534d4c322bb00dc SHA512 e041c26770e12e09110d7c4f39737406c6ade6cae6fa941cd31dd3b90432a034426272b8daa851a8a23baceb7189479d2d8bde882b7cfdb8ae666fadc5be57ff WHIRLPOOL 8e9e0004cdd2411c9d37b588afa274e1c2b955fe361fc3df597acc30526958d5722993f36f33672769ef55eca51b87917f57ec56528a7711a934d9f8de2b8019 +EBUILD cbflib-0.9.3.3.ebuild 1259 SHA256 215301b82cffeea07285e3e09dc01e8079801f28a9516474747dbb72f723045d SHA512 e7ce226580ddf3184aa3f511fe8a2cd1d3a41313dacba256c9eddd657691ef60996f2e1504f369972bc945270eaaf30b05c916c0972d69099debc9bf617f23d5 WHIRLPOOL 7f1adcfdf624cabfbc766cd80ab02397883dc02f171e239930667c5c03a5ce7bc0a483448ece51cec501167c8a538fb3cc66e22317bb8793149e4a00a179532e +MISC ChangeLog 4045 SHA256 a87b35490f90b7d30152d13126669bf5e18231b44991593b0cad03f6cde2e30f SHA512 da21a767820e2a800b2c7f4258cede6cb7d16c3f185a18d7af904738d0360b3ad34d251cb2ab31218a150c818a1b19689dbe4c391422abbe851ebc7ec4ff75af WHIRLPOOL fc5e6d66330d27b83a8de2f7f8506ff7efabcf45f9e108dedc1a434a774200aca6a310c7f70df785163d00cf74386907e57dca8e908acb32fc03ba03dca9fa28 +MISC ChangeLog-2015 5903 SHA256 b9a4402bab656bbab69af9cedfd71353e62a74b7cf6434bfc9339ff67b06cfb5 SHA512 4f34ff58268e419bf92e68da5927c33b8860d5b0c24099e65c116ac2d35e13ca581308a7290dc48a68e562c401cab5c8cc545c7a39d136bc80f10271f7fae51e WHIRLPOOL ab4278a96557e1a2374c91231428736c115d51339a8a00b2c5e7b4fc8407e3443bb628c7d06b78aca4e98fcf61124c2dc3b86c5474b11014441b63e4c9014a54 +MISC metadata.xml 987 SHA256 14b84adad09029a8dedf88f306171d6f9353340875549dc39a8bc126a1730ee1 SHA512 1917afb5bc1a5dbcd9e5ec175ac355e79929fd5ece8be7ea8606bf1ef7329affffa56efa5281df7d2c2eea4e1e3ef224c8310ee8cbeb1c44a0b32b232dadf007 WHIRLPOOL 777d5adc3a47b0fbf3a6274041768a4550cb82d155428e7095b992379ccbd9e1a48fb7bad79d327ac7d8cdc98912b2be7f65a117ae17741f1a6984417d626fcc diff --git a/sci-libs/cbflib/cbflib-0.9.3.3.ebuild b/sci-libs/cbflib/cbflib-0.9.3.3.ebuild new file mode 100644 index 000000000000..066ea3ca26ea --- /dev/null +++ b/sci-libs/cbflib/cbflib-0.9.3.3.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +CMAKE_MAKEFILE_GENERATOR=emake + +inherit cmake-utils eutils flag-o-matic fortran-2 toolchain-funcs + +MY_P1="CBFlib-${PV}" +#MY_P2="CBFlib_${PV}" +MY_P2="CBFlib_0.9.3" + +DESCRIPTION="Library providing a simple mechanism for accessing CBF files and imgCIF files" +HOMEPAGE="http://www.bernstein-plus-sons.com/software/CBF/" +BASE_TEST_URI="http://arcib.dowling.edu/software/CBFlib/downloads/version_${PV}/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P1}.tar.gz" +# test? ( +# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Input.tar.gz +# mirror://sourceforge/${PN}/${MY_P2}_Data_Files_Output.tar.gz +# )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="doc test" + +S=${WORKDIR}/${MY_P1} + +RDEPEND="sci-libs/hdf5:=" +DEPEND="${RDEPEND}" + +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/${P}-unbundle.patch +) + +src_prepare(){ + rm -rf Py* drel* dRel* ply* || die + + append-fflags -fno-range-check + + tc-export CC CXX AR RANLIB FC F77 + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DUNPACKED_DIRECTORY="${S}" + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + dosym ${PN} /usr/include/cbf +} diff --git a/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch b/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch new file mode 100644 index 000000000000..ef24c4b94b22 --- /dev/null +++ b/sci-libs/cbflib/files/cbflib-0.9.3.3-unbundle.patch @@ -0,0 +1,181 @@ + CMakeLists.txt | 118 +++------------------------------------------------------ + 1 file changed, 6 insertions(+), 112 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 75054d6..15bab99 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -279,7 +279,7 @@ project (CBFlib C CXX Fortran) + enable_testing() + set (CBF_CMAKE_DEBUG "ON") + +-set(CMAKE_C_FLAGS "-Wall -fno-strict-aliasing") ++set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -fno-strict-aliasing") + + # + # User setable parameters +@@ -530,42 +530,6 @@ find_package(ZLIB) + + + +-#Load external packages in build directory at cmake time +-add_subdirectory(${CBF__EXTERNAL_PACKAGES} "${CBF__EXT_PKG}") +- +-find_file(CBF_EXT_PKG_BLD_RUNNING cbf_ext_pkg_build_running "${CBF__EXT_PKG}") +-if (${CBF_EXT_PKG_BLD_RUNNING} STREQUAL "CBF_EXT_PKG_BLD_RUNNING-NOTFOUND") +- file(WRITE "${CBF__EXT_PKG}/cbf_ext_pkg_build_running" "cbf_ext_pkg_build_running") +- CBF_DEBUG_MESSAGE("CMAKE_COMMAND: ${CMAKE_COMMAND}") +- CBF_DEBUG_MESSAGE("CBFlib_SOURCE_DIR: ${CBFlib_SOURCE_DIR} ") +- execute_process( +- COMMAND ${CMAKE_COMMAND} ${CBFlib_SOURCE_DIR} +- RESULT_VARIABLE CBF_BUILD_RESULT) +- CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}") +- execute_process( +- COMMAND ${CMAKE_COMMAND} --build ${CBFlib_BINARY_DIR} --target HDF5 +- RESULT_VARIABLE CBF_BUILD_RESULT) +- CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}") +- execute_process( +- COMMAND ${CMAKE_COMMAND} --build ${CBFlib_BINARY_DIR} --target TIFF +- RESULT_VARIABLE CBF_BUILD_RESULT) +- CBF_DEBUG_MESSAGE("CBF_BUILD_RESULT: ${CBF_BUILD_RESULT}") +- file(REMOVE "${CBF__EXT_PKG}/cbf_ext_pkg_build_running") +-endif (${CBF_EXT_PKG_BLD_RUNNING} STREQUAL "CBF_EXT_PKG_BLD_RUNNING-NOTFOUND") +- +- +-file(GLOB CBF_HDF5_LIBRARY_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib/*hdf5*") +-CBF_DEBUG_MESSAGE( "CBF_HDF5_LIBRARY_PATH: ${CBF_HDF5_LIBRARY_PATH}") +-file(GLOB CBF_TIFF_LIBRARY_PATH "${CMAKE_CURRENT_BINARY_DIR}/lib/*tif*") +-CBF_DEBUG_MESSAGE( "CBF_TIFF_LIBRARY_PATH: ${CBF_TIFF_LIBRARY_PATH}") +- +-if ("|${CBF_HDF5_LIBRARY_PATH}|" STREQUAL "||" OR "|${CBF_TIFF_LIBRARY_PATH}|" STREQUAL "||") +- MESSAGE(STATUS "Must build external packages in ${CBF__EXT_PKG}") +- MESSAGE(STATUS "Then rerun cmake") +- MESSAGE(WARNING "Finishing run to make Makefiles") +-endif ("|${CBF_HDF5_LIBRARY_PATH}|" STREQUAL "||" OR "|${CBF_TIFF_LIBRARY_PATH}|" STREQUAL "||") +- +- + # + # Data Directories + # +@@ -579,35 +543,6 @@ set(CBF_DATAURLBASE "http://downloads.sf.net/cbflib") + set(CBF_DATAURLI "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Input.tar.gz") + set(CBF_DATAURLO "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Output.tar.gz") + set(CBF_DATAURLS "${CBF_DATAURLBASE}/CBFlib_${CBF_VERSION}_Data_Files_Output_Sigs_Only.tar.gz") +-# +-# Load and unpack the Data Files +-# +-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRI} ${CBF_DATAURLI}) +-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRO} ${CBF_DATAURLO}) +-CBF_LOAD_TARBALL(${CBF__DATA} ${CBF_DATADIRS} ${CBF_DATAURLS}) +-# +-# Verify the checksums +-# +-file(GLOB CBF_DATADIRI_FILES "${CBF_DATADIRI}/*") +-file(GLOB CBF_DATADIRO_FILES "${CBF_DATADIRO}/*") +-foreach(loop_file ${CBF_DATADIRI_FILES} ) +- if (NOT "${loop_file}" MATCHES "[*.]md5") +- file(MD5 "${loop_file}" loop_file_md5) +- file(STRINGS "${loop_file}.md5" loop_file_md5_orig LIMIT_COUNT 1) +- if (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}")) +- message(WARNINH "loop_file: ${loop_file}:|${loop_file_md5}|${loop_file_md5_orig}|") +- endif (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}")) +- endif (NOT "${loop_file}" MATCHES "[*.]md5") +-endforeach(loop_file) +-foreach(loop_file ${CBF_DATADIRO_FILES} ) +- if (NOT "${loop_file}" MATCHES "[*.]md5") +- file(MD5 "${loop_file}" loop_file_md5) +- file(STRINGS "${loop_file}.md5" loop_file_md5_orig LIMIT_COUNT 1) +- if (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}")) +- message(WARNING "loop_file: ${loop_file}:|${loop_file_md5}|${loop_file_md5_orig}|") +- endif (NOT ("${loop_file_md5}" STREQUAL "${loop_file_md5_orig}")) +- endif (NOT "${loop_file}" MATCHES "[*.]md5") +-endforeach(loop_file) + + + # +@@ -775,7 +710,7 @@ add_library(cbf_shared SHARED ${CBF_C_SOURCES}) + set_target_properties(cbf_shared PROPERTIES OUTPUT_NAME "cbf") + set_target_properties(cbf_shared PROPERTIES LINKER_LANGUAGE C) + set_target_properties(cbf_shared PROPERTIES SOVERSION "${CBF_APIVERSION}") +-target_link_libraries(cbf_shared ${CBF_HDF5_LIBRARY_PATH}) ++target_link_libraries(cbf_shared hdf5) + + # + # Build the static and shared IMG libraries +@@ -791,7 +726,7 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CBFlib_BINARY_DIR}/solib") + add_library(img_shared SHARED ${CBF__EXAMPLES}/img.c) + set_target_properties(img_shared PROPERTIES OUTPUT_NAME "img") + set_target_properties(img_shared PROPERTIES LINKER_LANGUAGE C) +-target_link_libraries(img_shared ${CBF_HDF5_LIBRARY_PATH}) ++target_link_libraries(img_shared hdf5 m ) + + + # +@@ -829,26 +764,6 @@ target_link_libraries(fcb_shared ${CBF_HDF5_LIBRARY_PATH}) + # + # C and C++ examples + # +-CBF_ADD_C_EXAMPLE(convert_image "${CBF__EXAMPLES}" "" "img_static") +-CBF_ADD_C_EXAMPLE(convert_minicbf "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(makecbf "${CBF__EXAMPLES}" "" "img_static") +-CBF_ADD_C_EXAMPLE(adscimg2cbf "${CBF__EXAMPLES}" "${CBF__EXAMPLES}/adscimg2cbf_sub.c" "") +-CBF_ADD_C_EXAMPLE(cbf2adscimg "${CBF__EXAMPLES}" "${CBF__EXAMPLES}/cbf2adscimg_sub.c" "") +-CBF_ADD_C_EXAMPLE(cbf_tail "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(changtestcompression "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(img2cif "${CBF__EXAMPLES}" "" "img_static") +-CBF_ADD_C_EXAMPLE(cif2cbf "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(cbf2nexus "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(minicbf2nexus "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(cbf_template_t "${CBF__DECTRIS_EXAMPLES}" "" "") +-CBF_ADD_CXX_EXAMPLE(testcell "${CBF__EXAMPLES}" "" "") +-CBF_ADD_CXX_EXAMPLE(sauter_test "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(sequence_match "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(tiff2cbf "${CBF__EXAMPLES}" "${CBF__EXT_PKG}/${CBF_TIFF}/libtiff/tif_sprint.c" "${CBF_TIFF_LIBRARY_PATH}") +-CBF_ADD_C_EXAMPLE(testulp "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(testhdf5 "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(testtree "${CBF__EXAMPLES}" "" "") +-CBF_ADD_C_EXAMPLE(testalloc "${CBF__EXAMPLES}" "" "") + + + +@@ -876,26 +791,9 @@ target_link_libraries(test_xds_binary fcb_static) + # + # install + # +-install (TARGETS makecbf DESTINATION bin) +-install (TARGETS img2cif DESTINATION bin) +-install (TARGETS cif2cbf DESTINATION bin) +-install (TARGETS adscimg2cbf DESTINATION bin) +-install (TARGETS cbf2adscimg DESTINATION bin) +-install (TARGETS changtestcompression DESTINATION bin) +-install (TARGETS convert_image DESTINATION bin) +-install (TARGETS convert_minicbf DESTINATION bin) +-install (TARGETS minicbf2nexus DESTINATION bin) +-install (TARGETS cbf_template_t DESTINATION bin) +-install (TARGETS testcell DESTINATION bin) +-install (TARGETS sauter_test DESTINATION bin) +-install (TARGETS sequence_match DESTINATION bin) +-install (TARGETS tiff2cbf DESTINATION bin) +-install (TARGETS cbf_static DESTINATION lib) +-install (TARGETS cbf_shared DESTINATION lib) +-install (TARGETS fcb_static DESTINATION lib) +-install (TARGETS fcb_shared DESTINATION lib) +-install (TARGETS img_static DESTINATION lib) +-install (TARGETS img_shared DESTINATION lib) ++install (TARGETS cbf_shared DESTINATION lib${LIB_SUFFIX}) ++install (TARGETS fcb_shared DESTINATION lib${LIB_SUFFIX}) ++install (TARGETS img_shared DESTINATION lib${LIB_SUFFIX}) + install (DIRECTORY ${CBF__INCLUDE}/ DESTINATION include/cbflib FILES_MATCHING PATTERN "*.h") + install (DIRECTORY ${CBF__BIN_INCLUDE}/* DESTINATION include/cbflib FILES_MATCHING PATTERN "*.h") + +@@ -914,10 +812,6 @@ endif () + # + # tests -- to be extended + # +-add_test(NAME cbftest_makecbf +- COMMAND ${CMAKE_COMMAND} +- -DCMD1=$<TARGET_FILE:makecbf> -DARG11=${CBF_DATADIRI}/example.mar2300 -DARG12=makecbf.cbf +- -P ${CMAKE_CURRENT_SOURCE_DIR}/runcommands.cmake) + add_test(cbftest_testalloc ${VALGRIND_COMMAND} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testalloc) + add_test(cbftest_testhdf5 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testhdf5) + add_test(cbftest_testtree ${VALGRIND_COMMAND} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/testtree) diff --git a/sci-libs/cbflib/metadata.xml b/sci-libs/cbflib/metadata.xml new file mode 100644 index 000000000000..e0080f59068f --- /dev/null +++ b/sci-libs/cbflib/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> +CBFLIB is a library of ANSI-C functions providing a simple mechanism +for accessing Crystallographic Binary Files (CBF files) and Image-supporting +CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for +mmCIF files. Starting with this release, CBFLIB performs validation checks +on reading of a CBF. If a dictionary is provided, values will be validated +against dictionary ranges and enumerations. Tags missing under parent-child +relationships or category key requirements will be reported. CBFlib provides +functions to create, read, modify and write CBF binary data files and imgCIF +ASCII data files. +</longdescription> + <upstream> + <remote-id type="sourceforge">cbflib</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/cblas-reference/Manifest b/sci-libs/cblas-reference/Manifest new file mode 100644 index 000000000000..d23317673115 --- /dev/null +++ b/sci-libs/cblas-reference/Manifest @@ -0,0 +1,14 @@ +AUX cblas-reference-20030223-autotool.patch 13378 SHA256 a264b4cc35da214982a8ee0e49e5ee8a94ae23299df2cb0ca1a6286cf5fb694c SHA512 45d07414acd5251d162ccc2b3f8f126665e110348797f97df472ba38ecce46c3c91359d3f37a83f9763f756246e04b5756710ea0e2d2a74b4485968707262393 WHIRLPOOL 03a4d3c4f1c5d8f1802fa8899c0a59879f0edfa367e87d7b4ac30c76f8e10ab40d4e16c4f72992feb32b8e2be00abbdd52611ce77f2af9dfaa28f79ccac8058a +AUX eselect.cblas.reference 256 SHA256 8562e2dd7abd83ca4d5ce2f20e5f2669a1ce26931e27836d4348897d4535d237 SHA512 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20c5144410588e803afde01ca85aca278814e644dd16dcfeb4dd7e4f2b712438a24639898eb531c2787af7b446d18a6469d70271052f1810fdeabd7c13c36b21 diff --git a/sci-libs/cblas-reference/cblas-reference-20030223-r6.ebuild b/sci-libs/cblas-reference/cblas-reference-20030223-r6.ebuild new file mode 100644 index 000000000000..cf8b726cddc3 --- /dev/null +++ b/sci-libs/cblas-reference/cblas-reference-20030223-r6.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils fortran-2 multilib toolchain-funcs + +MyPN="${PN/-reference/}" + +DESCRIPTION="C wrapper interface to the F77 reference BLAS implementation" +HOMEPAGE="http://www.netlib.org/blas/" +SRC_URI="http://www.netlib.org/blas/blast-forum/${MyPN}.tgz" + +SLOT="0" +LICENSE="public-domain" +IUSE="" +KEYWORDS="alpha amd64 hppa ppc ppc64 ~s390 sparc x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos" + +RDEPEND=" + virtual/blas + app-eselect/eselect-cblas" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +ESELECT_PROF=reference +S="${WORKDIR}/CBLAS" + +src_prepare() { + epatch "${FILESDIR}"/${P}-autotool.patch + eautoreconf + + cp "${FILESDIR}"/eselect.cblas.reference "${T}"/ || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.cblas.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.cblas.reference || die + fi +} + +src_configure() { + econf \ + --libdir="${EPREFIX}"/usr/$(get_libdir)/blas/reference \ + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" +} + +src_install() { + default + dodoc cblas_example*c + eselect cblas add $(get_libdir) "${T}"/eselect.cblas.reference ${ESELECT_PROF} +} + +pkg_postinst() { + local p=cblas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/cblas-reference/cblas-reference-20151113-r2.ebuild b/sci-libs/cblas-reference/cblas-reference-20151113-r2.ebuild new file mode 100644 index 000000000000..723c8287af30 --- /dev/null +++ b/sci-libs/cblas-reference/cblas-reference-20151113-r2.ebuild @@ -0,0 +1,94 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils fortran-2 cmake-utils multilib flag-o-matic toolchain-funcs + +LPN=lapack +LPV=3.6.0 + +DESCRIPTION="C wrapper interface to the F77 reference BLAS implementation" +HOMEPAGE="http://www.netlib.org/cblas/" +SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~hppa ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos" +IUSE="" + +DEPEND="app-eselect/eselect-cblas + >=virtual/blas-3.6 + virtual/pkgconfig" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${LPN}-${LPV}" +PATCHES=( "${FILESDIR}/lapack-reference-${LPV}-fix-build-system.patch" ) + +src_prepare() { + epatch "${PATCHES[@]}" + + eapply_user + + ESELECT_PROF=reference + + cp "${FILESDIR}"/eselect.cblas.reference-r2 "${T}"/eselect.cblas.reference || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.cblas.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.cblas.reference || die + fi + + sed -i \ + -e 's:/CMAKE/:/cmake/:g' \ + CBLAS/CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -Wno-dev + -DCBLAS=ON + -DUSE_OPTIMIZED_BLAS=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + -DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags blas) ${CFLAGS}" + -DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags blas) $(get_abi_CFLAGS) ${FCFLAGS}" + -DBUILD_SHARED_LIBS=ON + -DBUILD_STATIC_LIBS=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile -C CBLAS +} + +src_install() { + cmake-utils_src_install -C CBLAS + + mkdir -p "${ED}/usr/$(get_libdir)/blas/reference" || die + mv "${ED}/usr/$(get_libdir)"/lib* "${ED}/usr/include"/cblas* \ + "${ED}/usr/$(get_libdir)/pkgconfig"/* \ + "${ED}/usr/$(get_libdir)/blas/reference" || die + + rmdir "${ED}/usr/$(get_libdir)/pkgconfig" || die + rmdir "${ED}/usr/include" || die + + eselect cblas add $(get_libdir) "${T}"/eselect.cblas.reference ${ESELECT_PROF} +} + +pkg_postinst() { + local p=cblas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/cblas-reference/cblas-reference-20161223.ebuild b/sci-libs/cblas-reference/cblas-reference-20161223.ebuild new file mode 100644 index 000000000000..e03c6408cb89 --- /dev/null +++ b/sci-libs/cblas-reference/cblas-reference-20161223.ebuild @@ -0,0 +1,94 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils fortran-2 cmake-utils multilib flag-o-matic toolchain-funcs + +LPN=lapack +LPV=3.7.0 + +DESCRIPTION="C wrapper interface to the F77 reference BLAS implementation" +HOMEPAGE="http://www.netlib.org/cblas/" +SRC_URI="http://www.netlib.org/${LPN}/${LPN}-${LPV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm64 ~hppa ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos" +IUSE="" + +DEPEND="app-eselect/eselect-cblas + >=virtual/blas-3.6 + virtual/pkgconfig" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${LPN}-${LPV}" +PATCHES=( "${FILESDIR}/lapack-reference-${LPV}-fix-build-system.patch" ) + +src_prepare() { + epatch "${PATCHES[@]}" + + eapply_user + + ESELECT_PROF=reference + + cp "${FILESDIR}"/eselect.cblas.reference-r2 "${T}"/eselect.cblas.reference || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.cblas.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.cblas.reference || die + fi + + sed -i \ + -e 's:/CMAKE/:/cmake/:g' \ + CBLAS/CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -Wno-dev + -DCBLAS=ON + -DUSE_OPTIMIZED_BLAS=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + -DCMAKE_C_FLAGS="$($(tc-getPKG_CONFIG) --cflags blas) ${CFLAGS}" + -DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags blas) $(get_abi_CFLAGS) ${FCFLAGS}" + -DBUILD_SHARED_LIBS=ON + -DBUILD_STATIC_LIBS=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile -C CBLAS +} + +src_install() { + cmake-utils_src_install -C CBLAS + + mkdir -p "${ED}/usr/$(get_libdir)/blas/reference" || die + mv "${ED}/usr/$(get_libdir)"/lib* "${ED}/usr/include"/cblas* \ + "${ED}/usr/$(get_libdir)/pkgconfig"/* \ + "${ED}/usr/$(get_libdir)/blas/reference" || die + + rmdir "${ED}/usr/$(get_libdir)/pkgconfig" || die + rmdir "${ED}/usr/include" || die + + eselect cblas add $(get_libdir) "${T}"/eselect.cblas.reference ${ESELECT_PROF} +} + +pkg_postinst() { + local p=cblas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/cblas-reference/files/cblas-reference-20030223-autotool.patch b/sci-libs/cblas-reference/files/cblas-reference-20030223-autotool.patch new file mode 100644 index 000000000000..0dd595bf4a21 --- /dev/null +++ b/sci-libs/cblas-reference/files/cblas-reference-20030223-autotool.patch @@ -0,0 +1,567 @@ +--- configure.ac 1970-01-01 01:00:00.000000000 +0100 ++++ configure.ac 2007-11-09 17:59:16.000000000 +0000 +@@ -0,0 +1,24 @@ ++AC_PREREQ(2.59) ++AC_INIT(cblas, 20030223, lapack@cs.utk.edu) ++AC_CONFIG_SRCDIR([cblas_example2.c]) ++AC_CONFIG_HEADER([config.h]) ++AM_INIT_AUTOMAKE([foreign]) ++ ++AC_LANG(C) ++AC_PROG_CC ++AC_PROG_F77 ++AC_F77_LIBRARY_LDFLAGS ++AC_PROG_LIBTOOL ++ ++sinclude(acx_blas.m4) ++ACX_BLAS ++if test x"$BLAS_LIBS" = x; then ++ AC_MSG_ERROR([Cannot find blas libraries]) ++fi ++ ++ ++AC_CONFIG_FILES([Makefile ++ src/Makefile ++ testing/Makefile ++ cblas.pc]) ++AC_OUTPUT +--- Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Makefile.am 2007-11-09 16:20:41.000000000 +0000 +@@ -0,0 +1,8 @@ ++SUBDIRS = src testing ++ ++pkgconfigdir = $(libdir) ++pkgconfig_DATA = cblas.pc ++ ++EXTRA = cblas.pc ++ ++ +--- cblas.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ cblas.pc.in 2007-11-09 16:20:41.000000000 +0000 +@@ -0,0 +1,13 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: @PACKAGE_NAME@ ++Description: Basic Linear Algebra Subprograms C reference wrapper ++Version: @PACKAGE_VERSION@ ++Requires: blas ++URL: http://www.netlib.org/blas/ ++Libs: -lcblas ++Libs.private: @FLIBS@ ++Cflags: -I${includedir} +--- acx_blas.m4 1970-01-01 01:00:00.000000000 +0100 ++++ acx_blas.m4 2007-08-04 22:50:48.000000000 +0100 +@@ -0,0 +1,191 @@ ++##### http://autoconf-archive.cryp.to/acx_blas.html ++# ++# SYNOPSIS ++# ++# ACX_BLAS([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]) ++# ++# DESCRIPTION ++# ++# This macro looks for a library that implements the BLAS ++# linear-algebra interface (see http://www.netlib.org/blas/). On ++# success, it sets the BLAS_LIBS output variable to hold the ++# requisite library linkages. ++# ++# To link with BLAS, you should link with: ++# ++# $BLAS_LIBS $LIBS $FLIBS ++# ++# in that order. FLIBS is the output variable of the ++# AC_F77_LIBRARY_LDFLAGS macro (called if necessary by ACX_BLAS), and ++# is sometimes necessary in order to link with F77 libraries. Users ++# will also need to use AC_F77_DUMMY_MAIN (see the autoconf manual), ++# for the same reason. ++# ++# Many libraries are searched for, from ATLAS to CXML to ESSL. The ++# user may also use --with-blas=<lib> in order to use some specific ++# BLAS library <lib>. In order to link successfully, however, be ++# aware that you will probably need to use the same Fortran compiler ++# (which can be set via the F77 env. var.) as was used to compile the ++# BLAS library. ++# ++# ACTION-IF-FOUND is a list of shell commands to run if a BLAS ++# library is found, and ACTION-IF-NOT-FOUND is a list of commands to ++# run it if it is not found. If ACTION-IF-FOUND is not specified, the ++# default action will define HAVE_BLAS. ++# ++# This macro requires autoconf 2.50 or later. ++# ++# LAST MODIFICATION ++# ++# 2007-07-29 ++# ++# COPYLEFT ++# ++# Copyright (c) 2007 Steven G. Johnson <stevenj@alum.mit.edu> ++# ++# This program is free software: you can redistribute it and/or ++# modify it under the terms of the GNU General Public License as ++# published by the Free Software Foundation, either version 3 of the ++# License, or (at your option) any later version. ++# ++# This program is distributed in the hope that it will be useful, but ++# WITHOUT ANY WARRANTY; without even the implied warranty of ++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ++# General Public License for more details. ++# ++# You should have received a copy of the GNU General Public License ++# along with this program. If not, see ++# <http://www.gnu.org/licenses/>. ++# ++# As a special exception, the respective Autoconf Macro's copyright ++# owner gives unlimited permission to copy, distribute and modify the ++# configure scripts that are the output of Autoconf when processing ++# the Macro. You need not follow the terms of the GNU General Public ++# License when using or distributing such scripts, even though ++# portions of the text of the Macro appear in them. The GNU General ++# Public License (GPL) does govern all other use of the material that ++# constitutes the Autoconf Macro. ++# ++# This special exception to the GPL applies to versions of the ++# Autoconf Macro released by the Autoconf Macro Archive. When you ++# make and distribute a modified version of the Autoconf Macro, you ++# may extend this special exception to the GPL to apply to your ++# modified version as well. ++ ++AC_DEFUN([ACX_BLAS], [ ++AC_PREREQ(2.50) ++AC_REQUIRE([AC_F77_LIBRARY_LDFLAGS]) ++acx_blas_ok=no ++ ++AC_ARG_WITH(blas, ++ [AC_HELP_STRING([--with-blas=<lib>], [use BLAS library <lib>])]) ++case $with_blas in ++ yes | "") ;; ++ no) acx_blas_ok=disable ;; ++ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;; ++ *) BLAS_LIBS="-l$with_blas" ;; ++esac ++ ++# Get fortran linker names of BLAS functions to check for. ++AC_F77_FUNC(sgemm) ++AC_F77_FUNC(dgemm) ++ ++acx_blas_save_LIBS="$LIBS" ++LIBS="$LIBS $FLIBS" ++ ++# First, check BLAS_LIBS environment variable ++if test $acx_blas_ok = no; then ++if test "x$BLAS_LIBS" != x; then ++ save_LIBS="$LIBS"; LIBS="$BLAS_LIBS $LIBS" ++ AC_MSG_CHECKING([for $sgemm in $BLAS_LIBS]) ++ AC_TRY_LINK_FUNC($sgemm, [acx_blas_ok=yes], [BLAS_LIBS=""]) ++ AC_MSG_RESULT($acx_blas_ok) ++ LIBS="$save_LIBS" ++fi ++fi ++ ++# BLAS linked to by default? (happens on some supercomputers) ++if test $acx_blas_ok = no; then ++ save_LIBS="$LIBS"; LIBS="$LIBS" ++ AC_CHECK_FUNC($sgemm, [acx_blas_ok=yes]) ++ LIBS="$save_LIBS" ++fi ++ ++# BLAS in ATLAS library? (http://math-atlas.sourceforge.net/) ++if test $acx_blas_ok = no; then ++ AC_CHECK_LIB(atlas, ATL_xerbla, ++ [AC_CHECK_LIB(f77blas, $sgemm, ++ [AC_CHECK_LIB(cblas, cblas_dgemm, ++ [acx_blas_ok=yes ++ BLAS_LIBS="-lcblas -lf77blas -latlas"], ++ [], [-lf77blas -latlas])], ++ [], [-latlas])]) ++fi ++ ++# BLAS in PhiPACK libraries? (requires generic BLAS lib, too) ++if test $acx_blas_ok = no; then ++ AC_CHECK_LIB(blas, $sgemm, ++ [AC_CHECK_LIB(dgemm, $dgemm, ++ [AC_CHECK_LIB(sgemm, $sgemm, ++ [acx_blas_ok=yes; BLAS_LIBS="-lsgemm -ldgemm -lblas"], ++ [], [-lblas])], ++ [], [-lblas])]) ++fi ++ ++# BLAS in Alpha CXML library? ++if test $acx_blas_ok = no; then ++ AC_CHECK_LIB(cxml, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-lcxml"]) ++fi ++ ++# BLAS in Alpha DXML library? (now called CXML, see above) ++if test $acx_blas_ok = no; then ++ AC_CHECK_LIB(dxml, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-ldxml"]) ++fi ++ ++# BLAS in Sun Performance library? ++if test $acx_blas_ok = no; then ++ if test "x$GCC" != xyes; then # only works with Sun CC ++ AC_CHECK_LIB(sunmath, acosp, ++ [AC_CHECK_LIB(sunperf, $sgemm, ++ [BLAS_LIBS="-xlic_lib=sunperf -lsunmath" ++ acx_blas_ok=yes],[],[-lsunmath])]) ++ fi ++fi ++ ++# BLAS in SCSL library? (SGI/Cray Scientific Library) ++if test $acx_blas_ok = no; then ++ AC_CHECK_LIB(scs, $sgemm, [acx_blas_ok=yes; BLAS_LIBS="-lscs"]) ++fi ++ ++# BLAS in SGIMATH library? ++if test $acx_blas_ok = no; then ++ AC_CHECK_LIB(complib.sgimath, $sgemm, ++ [acx_blas_ok=yes; BLAS_LIBS="-lcomplib.sgimath"]) ++fi ++ ++# BLAS in IBM ESSL library? (requires generic BLAS lib, too) ++if test $acx_blas_ok = no; then ++ AC_CHECK_LIB(blas, $sgemm, ++ [AC_CHECK_LIB(essl, $sgemm, ++ [acx_blas_ok=yes; BLAS_LIBS="-lessl -lblas"], ++ [], [-lblas $FLIBS])]) ++fi ++ ++# Generic BLAS library? ++if test $acx_blas_ok = no; then ++ AC_CHECK_LIB(blas, $sgemm, [acx_blas_ok=yes; BLAS_LIBS="-lblas"]) ++fi ++ ++AC_SUBST(BLAS_LIBS) ++ ++LIBS="$acx_blas_save_LIBS" ++ ++# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND: ++if test x"$acx_blas_ok" = xyes; then ++ ifelse([$1],,AC_DEFINE(HAVE_BLAS,1,[Define if you have a BLAS library.]),[$1]) ++ : ++else ++ acx_blas_ok=no ++ $2 ++fi ++])dnl ACX_BLAS +--- src/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ src/Makefile.am 2007-11-09 16:20:41.000000000 +0000 +@@ -0,0 +1,232 @@ ++lib_LTLIBRARIES = libcblas.la ++ ++pkgincludedir = $(includedir)/cblas ++pkginclude_HEADERS = cblas.h ++ ++AM_CPPFLAGS = -DADD_ ++ ++ERRHAND_SOURCES = \ ++ cblas_globals.c \ ++ cblas_xerbla.c \ ++ xerbla.c ++ ++SINGLE_SOURCES = \ ++ cblas_scasum.c \ ++ cblas_scnrm2.c \ ++ scasumsub.f \ ++ scnrm2sub.f ++ ++SLEV_SOURCES = \ ++ isamaxsub.f \ ++ sdotsub.f \ ++ sdsdotsub.f \ ++ snrm2sub.f \ ++ sasumsub.f ++ ++SLEV1_SOURCES = \ ++ cblas_srotg.c \ ++ cblas_srotmg.c \ ++ cblas_srot.c \ ++ cblas_srotm.c \ ++ cblas_sswap.c \ ++ cblas_sscal.c \ ++ cblas_scopy.c \ ++ cblas_saxpy.c \ ++ cblas_sdot.c \ ++ cblas_sdsdot.c \ ++ cblas_snrm2.c \ ++ cblas_sasum.c \ ++ cblas_isamax.c ++ ++SLEV2_SOURCES = \ ++ cblas_sgemv.c \ ++ cblas_sgbmv.c \ ++ cblas_sger.c \ ++ cblas_ssbmv.c \ ++ cblas_sspmv.c \ ++ cblas_sspr.c \ ++ cblas_sspr2.c \ ++ cblas_ssymv.c \ ++ cblas_ssyr.c \ ++ cblas_ssyr2.c \ ++ cblas_stbmv.c \ ++ cblas_stbsv.c \ ++ cblas_stpmv.c \ ++ cblas_stpsv.c \ ++ cblas_strmv.c \ ++ cblas_strsv.c ++ ++SLEV3_SOURCES = \ ++ cblas_sgemm.c \ ++ cblas_ssymm.c \ ++ cblas_ssyrk.c \ ++ cblas_ssyr2k.c \ ++ cblas_strmm.c \ ++ cblas_strsm.c ++ ++DLEV_SOURCES = \ ++ ddotsub.f \ ++ dsdotsub.f \ ++ dnrm2sub.f \ ++ dasumsub.f \ ++ idamaxsub.f ++ ++DLEV1_SOURCES = \ ++ cblas_drotg.c \ ++ cblas_drotmg.c \ ++ cblas_drot.c \ ++ cblas_drotm.c \ ++ cblas_dswap.c \ ++ cblas_dscal.c \ ++ cblas_dcopy.c \ ++ cblas_daxpy.c \ ++ cblas_ddot.c \ ++ cblas_dsdot.c \ ++ cblas_dnrm2.c \ ++ cblas_dasum.c \ ++ cblas_idamax.c ++ ++DLEV2_SOURCES = \ ++ cblas_dgemv.c \ ++ cblas_dgbmv.c \ ++ cblas_dger.c \ ++ cblas_dsbmv.c \ ++ cblas_dspmv.c \ ++ cblas_dspr.c \ ++ cblas_dspr2.c \ ++ cblas_dsymv.c \ ++ cblas_dsyr.c \ ++ cblas_dsyr2.c \ ++ cblas_dtbmv.c \ ++ cblas_dtbsv.c \ ++ cblas_dtpmv.c \ ++ cblas_dtpsv.c \ ++ cblas_dtrmv.c \ ++ cblas_dtrsv.c ++ ++DLEV3_SOURCES = \ ++ cblas_dgemm.c \ ++ cblas_dsymm.c \ ++ cblas_dsyrk.c \ ++ cblas_dsyr2k.c \ ++ cblas_dtrmm.c \ ++ cblas_dtrsm.c ++ ++CLEV_SOURCES = \ ++ cdotcsub.f \ ++ cdotusub.f \ ++ icamaxsub.f ++ ++CLEV1_SOURCES = \ ++ cblas_cswap.c \ ++ cblas_cscal.c \ ++ cblas_csscal.c \ ++ cblas_ccopy.c \ ++ cblas_caxpy.c \ ++ cblas_cdotu_sub.c \ ++ cblas_cdotc_sub.c \ ++ cblas_icamax.c ++ ++CLEV2_SOURCES = \ ++ cblas_cgemv.c \ ++ cblas_cgbmv.c \ ++ cblas_chemv.c \ ++ cblas_chbmv.c \ ++ cblas_chpmv.c \ ++ cblas_ctrmv.c \ ++ cblas_ctbmv.c \ ++ cblas_ctpmv.c \ ++ cblas_ctrsv.c \ ++ cblas_ctbsv.c \ ++ cblas_ctpsv.c \ ++ cblas_cgeru.c \ ++ cblas_cgerc.c \ ++ cblas_cher.c \ ++ cblas_cher2.c \ ++ cblas_chpr.c \ ++ cblas_chpr2.c ++ ++CLEV3_SOURCES = \ ++ cblas_cgemm.c \ ++ cblas_csymm.c \ ++ cblas_chemm.c \ ++ cblas_cherk.c \ ++ cblas_cher2k.c \ ++ cblas_ctrmm.c \ ++ cblas_ctrsm.c \ ++ cblas_csyrk.c \ ++ cblas_csyr2k.c ++ ++ZLEV_SOURCES = \ ++ zdotcsub.f \ ++ zdotusub.f \ ++ dzasumsub.f \ ++ dznrm2sub.f \ ++ izamaxsub.f ++ ++ZLEV1_SOURCES = \ ++ cblas_zswap.c \ ++ cblas_zscal.c \ ++ cblas_zdscal.c \ ++ cblas_zcopy.c \ ++ cblas_zaxpy.c \ ++ cblas_zdotu_sub.c \ ++ cblas_zdotc_sub.c \ ++ cblas_dznrm2.c \ ++ cblas_dzasum.c \ ++ cblas_izamax.c ++ ++ZLEV2_SOURCES = \ ++ cblas_zgemv.c \ ++ cblas_zgbmv.c \ ++ cblas_zhemv.c \ ++ cblas_zhbmv.c \ ++ cblas_zhpmv.c \ ++ cblas_ztrmv.c \ ++ cblas_ztbmv.c \ ++ cblas_ztpmv.c \ ++ cblas_ztrsv.c \ ++ cblas_ztbsv.c \ ++ cblas_ztpsv.c \ ++ cblas_zgeru.c \ ++ cblas_zgerc.c \ ++ cblas_zher.c \ ++ cblas_zher2.c \ ++ cblas_zhpr.c \ ++ cblas_zhpr2.c ++ ++ZLEV3_SOURCES = \ ++ cblas_zgemm.c \ ++ cblas_zsymm.c \ ++ cblas_zhemm.c \ ++ cblas_zherk.c \ ++ cblas_zher2k.c \ ++ cblas_ztrmm.c \ ++ cblas_ztrsm.c \ ++ cblas_zsyrk.c \ ++ cblas_zsyr2k.c ++ ++libcblas_la_SOURCES = \ ++ cblas_f77.h \ ++ cblas.h \ ++ $(ERRHAND_SOURCES) \ ++ $(SINGLE_SOURCES) \ ++ $(SLEV_SOURCES) \ ++ $(DLEV_SOURCES) \ ++ $(CLEV_SOURCES) \ ++ $(ZLEV_SOURCES) \ ++ $(SLEV1_SOURCES) \ ++ $(DLEV1_SOURCES) \ ++ $(CLEV1_SOURCES) \ ++ $(ZLEV1_SOURCES) \ ++ $(SLEV2_SOURCES) \ ++ $(DLEV2_SOURCES) \ ++ $(CLEV2_SOURCES) \ ++ $(ZLEV2_SOURCES) \ ++ $(SLEV3_SOURCES) \ ++ $(DLEV3_SOURCES) \ ++ $(CLEV3_SOURCES) \ ++ $(ZLEV3_SOURCES) ++ ++libcblas_la_LIBADD = @BLAS_LIBS@ ++ +--- testing/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ testing/Makefile.am 2007-11-09 17:20:37.000000000 +0000 +@@ -0,0 +1,70 @@ ++TESTS = cblas_tests ++ ++cblas_tests: ++ @install -m0755 cblas_tests.sh cblas_tests ++ ++check_PROGRAMS = \ ++ xscblat1 xdcblat1 xccblat1 xzcblat1 \ ++ xscblat2 xdcblat2 xccblat2 xzcblat2 \ ++ xscblat3 xdcblat3 xccblat3 xzcblat3 ++ ++LDADD = $(top_builddir)/src/libcblas.la @BLAS_LIBS@ ++ ++AM_CPPFLAGS = -I$(top_srcdir)/src -DADD_ ++ ++AUX_SOURCES = \ ++ auxiliary.c \ ++ c_xerbla.c ++ ++xscblat1_SOURCES = \ ++ c_sblas1.c \ ++ c_sblat1.f ++xscblat2_SOURCES = \ ++ c_sblas2.c \ ++ c_s2chke.c \ ++ c_sblat2.f \ ++ $(AUX_SOURCES) ++xscblat3_SOURCES = \ ++ c_sblas3.c \ ++ c_s3chke.c \ ++ c_sblat3.f \ ++ $(AUX_SOURCES) ++xdcblat1_SOURCES = \ ++ c_dblas1.c \ ++ c_dblat1.f ++xdcblat2_SOURCES = \ ++ c_dblas2.c \ ++ c_d2chke.c \ ++ c_dblat2.f \ ++ $(AUX_SOURCES) ++xdcblat3_SOURCES = \ ++ c_dblas3.c \ ++ c_d3chke.c \ ++ c_dblat3.f \ ++ $(AUX_SOURCES) ++xccblat1_SOURCES = \ ++ c_cblas1.c \ ++ c_cblat1.f ++xccblat2_SOURCES = \ ++ c_cblas2.c \ ++ c_c2chke.c \ ++ c_cblat2.f \ ++ $(AUX_SOURCES) ++xccblat3_SOURCES = \ ++ c_cblas3.c \ ++ c_c3chke.c \ ++ c_cblat3.f \ ++ $(AUX_SOURCES) ++xzcblat1_SOURCES = \ ++ c_zblas1.c \ ++ c_zblat1.f ++xzcblat2_SOURCES = \ ++ c_zblas2.c \ ++ c_z2chke.c \ ++ c_zblat2.f \ ++ $(AUX_SOURCES) ++xzcblat3_SOURCES = \ ++ c_zblas3.c \ ++ c_z3chke.c \ ++ c_zblat3.f \ ++ $(AUX_SOURCES) +--- testing/cblas_tests.sh 1970-01-01 01:00:00.000000000 +0100 ++++ testing/cblas_tests.sh 2007-11-09 16:20:41.000000000 +0000 +@@ -0,0 +1,8 @@ ++#!/bin/sh ++ ++for t in x*blat1; do ++ ./${t} ++done ++for t in x*blat{2,3}; do ++ ./${t} < ${t:1:1}in${t:7:1} ++done diff --git a/sci-libs/cblas-reference/files/eselect.cblas.reference b/sci-libs/cblas-reference/files/eselect.cblas.reference new file mode 100644 index 000000000000..62b581860fc7 --- /dev/null +++ b/sci-libs/cblas-reference/files/eselect.cblas.reference @@ -0,0 +1,5 @@ +blas/reference/libcblas.so /usr/@LIBDIR@/libcblas.so +blas/reference/libcblas.so.0 /usr/@LIBDIR@/libcblas.so.0 +blas/reference/libcblas.a /usr/@LIBDIR@/libcblas.a +../blas/reference/cblas.pc /usr/@LIBDIR@/pkgconfig/cblas.pc +cblas/cblas.h /usr/include/cblas.h diff --git a/sci-libs/cblas-reference/files/eselect.cblas.reference-r2 b/sci-libs/cblas-reference/files/eselect.cblas.reference-r2 new file mode 100644 index 000000000000..b02188c8a9da --- /dev/null +++ b/sci-libs/cblas-reference/files/eselect.cblas.reference-r2 @@ -0,0 +1,8 @@ +blas/reference/libcblas.so /usr/@LIBDIR@/libcblas.so +blas/reference/libcblas.so.3 /usr/@LIBDIR@/libcblas.so.3 +blas/reference/libcblas.a /usr/@LIBDIR@/libcblas.a +../blas/reference/cblas.pc /usr/@LIBDIR@/pkgconfig/cblas.pc +../@LIBDIR@/blas/reference/cblas_test.h /usr/include/cblas_test.h +../@LIBDIR@/blas/reference/cblas_mangling.h /usr/include/cblas_mangling.h +../@LIBDIR@/blas/reference/cblas_f77.h /usr/include/cblas_f77.h +../@LIBDIR@/blas/reference/cblas.h /usr/include/cblas.h diff --git a/sci-libs/cblas-reference/files/lapack-reference-3.6.0-fix-build-system.patch b/sci-libs/cblas-reference/files/lapack-reference-3.6.0-fix-build-system.patch new file mode 100644 index 000000000000..a187dac21a12 --- /dev/null +++ b/sci-libs/cblas-reference/files/lapack-reference-3.6.0-fix-build-system.patch @@ -0,0 +1,124 @@ + BLAS/CMakeLists.txt | 2 +- + BLAS/blas.pc.in | 6 ++++-- + CBLAS/CMakeLists.txt | 2 +- + CBLAS/cblas.pc.in | 9 ++++++--- + CMakeLists.txt | 2 +- + LAPACKE/CMakeLists.txt | 2 +- + LAPACKE/lapacke.pc.in | 6 ++++-- + lapack.pc.in | 6 ++++-- + 8 files changed, 22 insertions(+), 13 deletions(-) + +diff --git a/BLAS/CMakeLists.txt b/BLAS/CMakeLists.txt +index 45e68e9..56c8354 100644 +--- a/BLAS/CMakeLists.txt ++++ b/BLAS/CMakeLists.txt +@@ -2,7 +2,7 @@ add_subdirectory(SRC) + if(BUILD_TESTING) + add_subdirectory(TESTING) + endif(BUILD_TESTING) +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/blas.pc + DESTINATION ${PKG_CONFIG_DIR} +diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in +index 845a25c..7a53ea5 100644 +--- a/BLAS/blas.pc.in ++++ b/BLAS/blas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: blas + Description: Basic Linear Algebra Subprograms F77 reference implementations +diff --git a/CBLAS/CMakeLists.txt b/CBLAS/CMakeLists.txt +index 98b481f..8f98b04 100644 +--- a/CBLAS/CMakeLists.txt ++++ b/CBLAS/CMakeLists.txt +@@ -71,7 +71,7 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/cblas-config-build.cmake.in + ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc + DESTINATION ${PKG_CONFIG_DIR} +diff --git a/CBLAS/cblas.pc.in b/CBLAS/cblas.pc.in +index ee20206..14a141e 100644 +--- a/CBLAS/cblas.pc.in ++++ b/CBLAS/cblas.pc.in +@@ -1,9 +1,12 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include/@PROFNAME@ + +-Name: lapacke ++Name: cblas-reference + Description: C Standard Interface to BLAS Linear Algebra PACKage + Version: @LAPACK_VERSION@ + URL: http://www.netlib.org/lapack/ + Libs: -L${libdir} -lcblas ++Cflags: -I${includedir} + Requires: blas +diff --git a/CMakeLists.txt b/CMakeLists.txt +index ab29bd2..31b878a 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -333,7 +333,7 @@ configure_file(${LAPACK_SOURCE_DIR}/CMAKE/lapack-config-build.cmake.in + ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc + DESTINATION ${PKG_CONFIG_DIR} +diff --git a/LAPACKE/CMakeLists.txt b/LAPACKE/CMakeLists.txt +index 008f24c..d8c4cb0 100644 +--- a/LAPACKE/CMakeLists.txt ++++ b/LAPACKE/CMakeLists.txt +@@ -65,7 +65,7 @@ if(BUILD_TESTING) + endif(BUILD_TESTING) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc + DESTINATION ${PKG_CONFIG_DIR} +diff --git a/LAPACKE/lapacke.pc.in b/LAPACKE/lapacke.pc.in +index 75e6871..ce5201b 100644 +--- a/LAPACKE/lapacke.pc.in ++++ b/LAPACKE/lapacke.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: lapacke + Description: C Standard Interface to LAPACK Linear Algebra PACKage +diff --git a/lapack.pc.in b/lapack.pc.in +index d34c870..0d0750f 100644 +--- a/lapack.pc.in ++++ b/lapack.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: lapack + Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage diff --git a/sci-libs/cblas-reference/files/lapack-reference-3.7.0-fix-build-system.patch b/sci-libs/cblas-reference/files/lapack-reference-3.7.0-fix-build-system.patch new file mode 100644 index 000000000000..70f7cb0ee926 --- /dev/null +++ b/sci-libs/cblas-reference/files/lapack-reference-3.7.0-fix-build-system.patch @@ -0,0 +1,56 @@ +diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in +index 7fd6f1e..e52f3ad 100644 +--- a/BLAS/blas.pc.in ++++ b/BLAS/blas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: BLAS + Description: FORTRAN reference implementation of BLAS Basic Linear Algebra Subprograms +diff --git a/CBLAS/cblas.pc.in b/CBLAS/cblas.pc.in +index 4a938fe..311aed9 100644 +--- a/CBLAS/cblas.pc.in ++++ b/CBLAS/cblas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: CBLAS + Description: C Standard Interface to BLAS Basic Linear Algebra Subprograms +diff --git a/LAPACKE/lapacke.pc.in b/LAPACKE/lapacke.pc.in +index 028f8da..dc092b1 100644 +--- a/LAPACKE/lapacke.pc.in ++++ b/LAPACKE/lapacke.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: LAPACKE + Description: C Standard Interface to LAPACK Linear Algebra PACKage +diff --git a/lapack.pc.in b/lapack.pc.in +index 878efc2..2cca4c2 100644 +--- a/lapack.pc.in ++++ b/lapack.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: LAPACK + Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage diff --git a/sci-libs/cblas-reference/metadata.xml b/sci-libs/cblas-reference/metadata.xml new file mode 100644 index 000000000000..f77724cb6a54 --- /dev/null +++ b/sci-libs/cblas-reference/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +The BLAS (Basic Linear Algebra Subprograms) are high quality "building +block" routines for performing basic vector and matrix operations. Level 1 +BLAS do vector-vector operations, Level 2 BLAS do matrix-vector operations, +and Level 3 BLAS do matrix-matrix operations. Because the BLAS are +efficient, portable, and widely available, they're commonly used in the +development of high quality linear algebra software, LAPACK for +example. This packages implements the reference C library as a wrapper +to the FORTRAN 77 BLAS library. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/ccfits/Manifest b/sci-libs/ccfits/Manifest new file mode 100644 index 000000000000..88f0d9304114 --- /dev/null +++ b/sci-libs/ccfits/Manifest @@ -0,0 +1,8 @@ +AUX ccfits-2.2-makefile.patch 710 SHA256 fc6af44d3aee9652570f5e82633f2449bf00f654cac93d5d3d10c9961b6f8294 SHA512 ea4553b9a794131fe1b90172d49623bb97c6d78c52a3cdbdd43c8bb3ec23ae535081a981f83c61d425fc9fe1b6258e7ef78cea580f7df302893840ab3a35e7e5 WHIRLPOOL 5cf32898d320d8d27a74bf269c7b3575857d7f8cdfbb5b2825362d13db427fd270190423bb91bca84e4fc31622794906ee606a07658f7b34ea4e4f358cd99c5f +DIST CCfits-2.4.tar.gz 1792643 SHA256 ba6c5012b260adf7633f92581279ea582e331343d8c973981aa7de07242bd7f8 SHA512 b12d455bb6dd631056e02a12e996d3bf0b6169f8922011e4b64f979b08d2ab8f405e14947c6f5d26ad18bf2f5764854a84987ae105944515f533fe6b0b4ef7be WHIRLPOOL 7f0ca6f0e684f7d66d7272a89dbeb8fa95e3907f358ec624f5f817311288fdfb6467ec915d0ab9f2eee753fcaee3f4b68f497c2dffcf7a38bdce9a7f97681e2a +DIST CCfits-2.5.tar.gz 1416358 SHA256 938ecd25239e65f519b8d2b50702416edc723de5f0a5387cceea8c4004a44740 SHA512 63ab4d153063960510cf60651d5c832824cf85f937f84adc5390c7c2fb46eb8e9f5d8cda2554d79d24c7a4f1b6cf0b7a6e20958fb69920b65d7c362c0a5f26b5 WHIRLPOOL 2bd2834d9c113b0dd3cceba381ad186bd13ccfa7184a8b4a314f4b5a8034121481e8ed68fe50dd25484ddce0f0391f884cde6783db72bf9cc61044e540c9d4be +EBUILD ccfits-2.4-r1.ebuild 889 SHA256 a51f675ab4b385d9a9c5ecd8d06ca6473a8cbc2a9059143b0e813b77c345191b SHA512 da0b9d7138dc9b5438c46cbdba15a8a49bc744e45f4ba872d8597521e272368b1ad2454f027faa937f30ca2f5b1b4b8415ee7923cecb4649d026d18608779113 WHIRLPOOL 1278be4a0d88af95a9abab2b5e326f21609be94de1d08da6308fe2f54d24fb542808495962eaf66f7d6e353f41ac2c3e055cc79d2dbe5a0d11f70b662f013885 +EBUILD ccfits-2.5.ebuild 901 SHA256 2c6186299819813ef2ceaa1e3cd9899fe79c563cd28b31eba5da99084d86ea6f SHA512 382efb11b57f290d250d599f641b7edb37c2f87cf61580a37ef94ecd2ed80eb8b4b4f2938fce9d9aea6b462bd79b534ff67f06a54646c2a43b88989994256128 WHIRLPOOL 2033ce42de6455bee6b53467296d50de17e850a9bd2984f8f637360689f399b0f2cb8041a85d19f0de2fafcd3e9b536091ca06f66dae742a0be11d1b99a14112 +MISC ChangeLog 3208 SHA256 599f7b0e83106d975c04a68f6c2beeb2a77db6eed66c8a0370a4861c79bbf1d0 SHA512 2f1d17b6ce604b1535f7eb687949a974f288541c5534e6f88dfc0d68c22b73e67d4a258a3e8215567f4605c0f29993c5aaddf40479841f90e696514465628964 WHIRLPOOL 43bef34b8be5a65cc32e6260aea5ebacd37012f7455b182df84306636638640f58463e999c6a5544050b85d609f209f92bd784eb61bcaaf1275f13b1dd55e04c +MISC ChangeLog-2015 752 SHA256 c3bed0e690061bdaa0170ba8bc21e2474033eafc3ffa1c929b9d0692a24131d4 SHA512 4f9cdeffb8ab2c968f4409e52f93c520070471bd43d0b47cb3007a14b6ada868d17ca2441b07c1de4bc72abdc8289d1aa9f5fa9a9da28a5a2d6de12cf62b7676 WHIRLPOOL 6f2801b1afdc504d2958ba85141f3cf84b5143087054745ec0d64dc26e37c1e1bcaaabfaf08219534cf8df0ab64e03d36068627bfb82652d0aacda32bb040b12 +MISC metadata.xml 639 SHA256 8740fd8eefba94194724e26d0d426919a1d09254f124ab91457df89f9521716f SHA512 163801f94ad9076cf5306b4f06682fc7186e724704b4ad1e5dfca871fc770ed0b06827caa2aa83eeebc7bb65b5bbc27f254431d6472735abb30f0872eeccf721 WHIRLPOOL 57eccb2d4a76a1b61926b69ef785dfdbaa2f0b3d0657375574b5c2d389102d48ee02d65c01965792d2b2b84992dd4dbdfca850e7b46659d5cb6a2c52263f21f6 diff --git a/sci-libs/ccfits/ccfits-2.4-r1.ebuild b/sci-libs/ccfits/ccfits-2.4-r1.ebuild new file mode 100644 index 000000000000..a053f0dd3a6e --- /dev/null +++ b/sci-libs/ccfits/ccfits-2.4-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +MYPN=CCfits +MYP=${MYPN}-${PV} + +DESCRIPTION="C++ interface for cfitsio" +HOMEPAGE="http://heasarc.gsfc.nasa.gov/fitsio/CCfits/" +SRC_URI="${HOMEPAGE}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +RDEPEND=">=sci-libs/cfitsio-3.080" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}" + +DOCS=( CHANGES README.INSTALL ) +PATCHES=( + "${FILESDIR}"/${PN}-2.2-makefile.patch # avoid building cookbook by default and no rpath +) + +src_prepare() { + default + mv configure.{in,ac} || die + AT_M4DIR=config/m4 eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install () { + if use doc; then + DOCS+=( *.pdf ) + HTML_DOCS=( html/. ) + fi + default + + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-libs/ccfits/ccfits-2.5.ebuild b/sci-libs/ccfits/ccfits-2.5.ebuild new file mode 100644 index 000000000000..9530618f2c8c --- /dev/null +++ b/sci-libs/ccfits/ccfits-2.5.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils + +MYPN=CCfits +MYP=${MYPN}-${PV} + +DESCRIPTION="C++ interface for cfitsio" +HOMEPAGE="http://heasarc.gsfc.nasa.gov/fitsio/CCfits/" +SRC_URI="${HOMEPAGE}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +RDEPEND=">=sci-libs/cfitsio-3.080" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}" + +DOCS=( CHANGES README.INSTALL ) +PATCHES=( + "${FILESDIR}"/${PN}-2.2-makefile.patch # avoid building cookbook by default and no rpath +) + +src_prepare() { + default + mv configure.{in,ac} || die + AT_M4DIR=config/m4 eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install () { + if use doc; then + DOCS+=( *.pdf ) + HTML_DOCS=( html/. ) + fi + default + use static-libs || prune_libtool_files --all +} diff --git a/sci-libs/ccfits/files/ccfits-2.2-makefile.patch b/sci-libs/ccfits/files/ccfits-2.2-makefile.patch new file mode 100644 index 000000000000..f8fa5d518591 --- /dev/null +++ b/sci-libs/ccfits/files/ccfits-2.2-makefile.patch @@ -0,0 +1,26 @@ +--- a/Makefile.am ++++ b/Makefile.am +@@ -26,12 +26,11 @@ + EXTRA_DIST = config CHANGES README.INSTALL License.txt file1.pha $(MSVC_FILES) + + +-bin_PROGRAMS = cookbook ++check_PROGRAMS = cookbook + + cookbook_SOURCES = cookbook.cxx + + cookbook_LDADD = libCCfits.la +-cookbook_LDFLAGS = -R $(R_LIB_PATH) -R $(CXX_LIB_PATH) + + pkgconfigdir = $(libdir)/pkgconfig + pkgconfig_DATA = CCfits.pc +@@ -64,8 +63,7 @@ + + # This will tell shared library which STD C++ library to use without + # needing the user to use LD_LIBRARY_PATH environment variable +-libCCfits_la_LIBADD = $(LIBSTDCPP) +-libCCfits_la_LDFLAGS = -R $(R_LIB_PATH) -R $(CXX_LIB_PATH) ++#libCCfits_la_LIBADD = $(LIBSTDCPP) + + libCCfits_ladir = $(pkgincludedir) + diff --git a/sci-libs/ccfits/metadata.xml b/sci-libs/ccfits/metadata.xml new file mode 100644 index 000000000000..e4f684da7916 --- /dev/null +++ b/sci-libs/ccfits/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-astronomy@gentoo.org</email> + <name>Gentoo Astronomy Project</name> + </maintainer> + <longdescription lang="en"> + CCfits is an object oriented interface to the cfitsio library. It is + designed to make the capabilities of cfitsio available to + programmers working in C++. It is written in ANSI C++ and + implemented using the C++ Standard Library with namespaces, + exception handling, and member template functions. + </longdescription> +</pkgmetadata> diff --git a/sci-libs/ccolamd/Manifest b/sci-libs/ccolamd/Manifest new file mode 100644 index 000000000000..53235d3e13ca --- /dev/null +++ b/sci-libs/ccolamd/Manifest @@ -0,0 +1,5 @@ +DIST ccolamd-2.8.0.tar.bz2 309907 SHA256 0e3d0d147f22ef6d3e6eedc7540be6135303a064dae9f10ff443ade1196d12eb SHA512 6a515a8250ed98d52aa932a6f93170174ff32f76c1ecedcedeb1540a471416d0cd40b5613a839b96fbc79c66b3cb5106c6a340a33fafdd695c83b7d949756e77 WHIRLPOOL f999836681321d0f1ee0ccaae8cbc86b934220eb4151792b5163a7a1f115319442a9a3db8cb707b7e42cd50fa092765a0fc49c8e60daf756aaff56fa8eb93169 +EBUILD ccolamd-2.8.0.ebuild 592 SHA256 77087ef68018989eddb8fcb09808780bb2cfb9d38fa82c47e49db78f117231d7 SHA512 03774bcd9d15a7bf4238fcbd2a1cceeced9131a53c8ab4a3d45b9929c716361c288675ec7486363ba68876f9cb5c77ffcd02d1af0260415ca7c082358816bfbb WHIRLPOOL a616417d720703d6803b7953bfa22a9b72a162842fd3b7dfc67eb5e1f666b8742b994d8c4a91deecb0fee0422f877c3c37f73ffaf111b55a048fa4a96fdc7ab6 +MISC ChangeLog 2657 SHA256 d09f5fb22ec8aaa348fc17d074965e508af8e3e08c9c4edb1e27c97fb7cbf37c SHA512 990e2ebb9484a88312d126c5ce469b78d3d9ef4b2dba5f387b28b9418e43f33e8498cb3d2d1d6e830a22442ecca53856d65f007adfdfdfe80b74a398028be0b8 WHIRLPOOL ce20f8d3d6dd47c4de11ecde5c1800346177a44c394356ea2020141ba3cc350a8163dbe07eefd76799f966ee83a26035e0abb762420c54648c715a99041bf4d9 +MISC ChangeLog-2015 5020 SHA256 6cb0e08666cfa696ac7791a4565bee2ee9773a18a57c2b4dc7efab05cbfa34c0 SHA512 97ee2eb1bab54b4771b9f40faa1362d8b72a93f97048145d7805e65eee14796d95be3d61c738d6e4d9da7c2d2dd09704f9f9351e91ba8cf7c56bc24cbc95c4f3 WHIRLPOOL 0e66825ad975c0e6ad7f02f2192a07664550943a1a66751b4b39074937c143cbc609a40d926991f0f7a8649996d3c4395c4820f53317ae08462f81dde880b9ba +MISC metadata.xml 470 SHA256 7bc846e6b6654c1bf4c0fdfd115167617b1c11136400b46dbd279a13741f49b9 SHA512 99c2d290fea618dfd8997209d8e6db971a2ab74d1be5fb270f2177c9843b0f324710491977c7cf2427806295d05e341ece4399afd8a0d43bca8b42b0fdea7beb WHIRLPOOL fb9447fabe59268f9d977fd4b9ddd37c4289920afb0f2a34aac1a99e0a267d1ab940121820e2b00894dd21369143c0e862d7b6338f3cc2067138c6790723c9dc diff --git a/sci-libs/ccolamd/ccolamd-2.8.0.ebuild b/sci-libs/ccolamd/ccolamd-2.8.0.ebuild new file mode 100644 index 000000000000..a631cbdf4641 --- /dev/null +++ b/sci-libs/ccolamd/ccolamd-2.8.0.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Constrained Column approximate minimum degree ordering algorithm" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/ccolamd/" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" + +KEYWORDS="~alpha amd64 ~arm ~arm64 hppa ~ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" + +RDEPEND="sci-libs/suitesparseconfig" +DEPEND="${RDEPEND} + virtual/pkgconfig" diff --git a/sci-libs/ccolamd/metadata.xml b/sci-libs/ccolamd/metadata.xml new file mode 100644 index 000000000000..23373de57a20 --- /dev/null +++ b/sci-libs/ccolamd/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Constrained COLAMD computes an column approximate minimum degree ordering + algorithm, (like COLAMD), but it can also be given a set of ordering + constraints. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/ccpn-data/Manifest b/sci-libs/ccpn-data/Manifest new file mode 100644 index 000000000000..567b420a239c --- /dev/null +++ b/sci-libs/ccpn-data/Manifest @@ -0,0 +1,14 @@ +AUX 312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml 6672 SHA256 31230ff89f2a44d3f29784da721dbca0493467c28b0b725f31de8b37e4532183 SHA512 ce23efeaed52a460979c99b6e60ffaee427a8e5df191132755c7c4bdd36e1246e709cae49643eb5de950668ebc0616e90d872c4092f6a52989d0e0ec224c3845 WHIRLPOOL 03d01f3995d65a22a3c1e812e82b336d2a50eb1828a79e9ab6be9efeba8f6831779d41bd3fe96acc97b227a006c53dbeb261155391c8c1c8666a993d72af2492 +DIST analysis2.3.1r2.tar.gz 21683215 SHA256 a9e47a24d84f7b8261c6c23a8607af5a6ba2f2db9e161a7f873794c1ba8663ef SHA512 96bf75d1e958340d83836348f5a3045e5b2632913c66d9d74272140085800ea096f1ae53eadfb5bc0eba76804f1864553e82a517d637bdc3bace71b0c1c785ee WHIRLPOOL 2d1e55a4d8e62decc649a885d767dc5a2bdec701447a97ef8bc5e15ddde8c6add5fb0606c0cdd5871bbb9af74c163a13a28207b3e254fb41ba56293c88d6bc85 +DIST analysis2.4.0.tar.gz 36047222 SHA256 efde9f398bb62cb79e32cfe3118fe2af4ff6c56e5a9068bee654b3aa00f20ae1 SHA512 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v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils portability python-r1 versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN/-data}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})r2" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR - Data" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www2.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + !<sci-chemistry/ccpn-${PVR}" +DEPEND="" + +RESTRICT="binchecks strip" + +S="${WORKDIR}"/ccpnmr/ccpnmr2.3 + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + cp "${FILESDIR}"/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml data/ccp/nmr/NmrExpPrototype/ || die +} + +src_install() { + local i pydocs in_path ein_path + + dodir /usr/share/doc/${PF}/html + sed \ + -e "s:../ccpnmr2.1:${EPREFIX}/usr/share/doc/${PF}/html:g" \ + ../doc/index.html > "${ED}"/usr/share/doc/${PF}/html/index.html || die + treecopy $(find python/ -name doc -type d) "${ED}"/usr/share/doc/${PF}/html/ + + pydocs="$(find python -name doc -type d)" + + symlinking() { + in_path=$(python_get_sitedir)/ccpn + ein_path="${in_path#${EPREFIX}}" + dosym ../../../../share/doc/${PF}/html ${ein_path}/doc + for i in ${pydocs}; do + dosym /usr/share/doc/${PF}/html/${i} ${ein_path}/${i} + done + dosym /usr/share/ccpn/data ${ein_path}/data + dosym /usr/share/ccpn/model ${ein_path}/model + } + python_foreach_impl symlinking + + dohtml -r doc/* + insinto /usr/share/ccpn + doins -r data model +} diff --git a/sci-libs/ccpn-data/ccpn-data-2.4.0_p140425.ebuild b/sci-libs/ccpn-data/ccpn-data-2.4.0_p140425.ebuild new file mode 100644 index 000000000000..359f1f2acb84 --- /dev/null +++ b/sci-libs/ccpn-data/ccpn-data-2.4.0_p140425.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils portability python-r1 versionator + +PATCHSET="${PV##*_p}" +MY_PN="${PN/-data}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR - Data" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www2.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + !<sci-chemistry/ccpn-${PVR}" +DEPEND="" + +RESTRICT="binchecks strip" + +S="${WORKDIR}"/ccpnmr/ccpnmr2.4 + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + cp "${FILESDIR}"/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml data/ccp/nmr/NmrExpPrototype/ || die +} + +src_install() { + local i pydocs in_path ein_path + + dodir /usr/share/doc/${PF}/html + sed \ + -e "s:../ccpnmr2.1:${EPREFIX}/usr/share/doc/${PF}/html:g" \ + ../doc/index.html > "${ED}"/usr/share/doc/${PF}/html/index.html || die + treecopy $(find python/ -name doc -type d) "${ED}"/usr/share/doc/${PF}/html/ + + pydocs="$(find python -name doc -type d)" + + symlinking() { + in_path=$(python_get_sitedir)/ccpn + ein_path="${in_path#${EPREFIX}}" + dosym ../../../../share/doc/${PF}/html ${ein_path}/doc + for i in ${pydocs}; do + dosym /usr/share/doc/${PF}/html/${i} ${ein_path}/${i} + done + dosym /usr/share/ccpn/data ${ein_path}/data + dosym /usr/share/ccpn/model ${ein_path}/model + } + python_foreach_impl symlinking + + dohtml -r doc/* + insinto /usr/share/ccpn + doins -r data model +} diff --git a/sci-libs/ccpn-data/ccpn-data-2.4.1.ebuild b/sci-libs/ccpn-data/ccpn-data-2.4.1.ebuild new file mode 100644 index 000000000000..ef092feed4b2 --- /dev/null +++ b/sci-libs/ccpn-data/ccpn-data-2.4.1.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils portability python-r1 versionator + +#PATCHSET="${PV##*_p}" +MY_PN="${PN/-data}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR - Data" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www2.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + !<sci-chemistry/ccpn-${PVR}" +DEPEND="" + +RESTRICT="binchecks strip" + +S="${WORKDIR}"/ccpnmr/ccpnmr2.4 + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + cp "${FILESDIR}"/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml data/ccp/nmr/NmrExpPrototype/ || die +} + +src_install() { + local i pydocs in_path ein_path + + dodir /usr/share/doc/${PF}/html + sed \ + -e "s:../ccpnmr2.1:${EPREFIX}/usr/share/doc/${PF}/html:g" \ + ../doc/index.html > "${ED}"/usr/share/doc/${PF}/html/index.html || die + treecopy $(find python/ -name doc -type d) "${ED}"/usr/share/doc/${PF}/html/ + + pydocs="$(find python -name doc -type d)" + + symlinking() { + in_path=$(python_get_sitedir)/ccpn + ein_path="${in_path#${EPREFIX}}" + dosym ../../../../share/doc/${PF}/html ${ein_path}/doc + for i in ${pydocs}; do + dosym /usr/share/doc/${PF}/html/${i} ${ein_path}/${i} + done + dosym /usr/share/ccpn/data ${ein_path}/data + dosym /usr/share/ccpn/model ${ein_path}/model + } + python_foreach_impl symlinking + + dohtml -r doc/* + insinto /usr/share/ccpn + doins -r data model +} diff --git a/sci-libs/ccpn-data/ccpn-data-2.4.2.ebuild b/sci-libs/ccpn-data/ccpn-data-2.4.2.ebuild new file mode 100644 index 000000000000..624c6fee4867 --- /dev/null +++ b/sci-libs/ccpn-data/ccpn-data-2.4.2.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils portability python-r1 versionator + +#PATCHSET="${PV##*_p}" +MY_PN="${PN/-data}mr" +MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})" +MY_MAJOR="$(get_version_component_range 1-3)" + +DESCRIPTION="The Collaborative Computing Project for NMR - Data" +HOMEPAGE="http://www.ccpn.ac.uk/v2-software/software" +SRC_URI="http://www2.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz" +[[ -n ${PATCHSET} ]] && SRC_URI+=" https://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz" + +SLOT="0" +LICENSE="|| ( CCPN LGPL-2.1 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + !<sci-chemistry/ccpn-${PVR}" +DEPEND="" + +RESTRICT="binchecks strip" + +S="${WORKDIR}"/ccpnmr/ccpnmr2.4 + +src_prepare() { + [[ -n ${PATCHSET} ]] && \ + epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch + cp "${FILESDIR}"/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml data/ccp/nmr/NmrExpPrototype/ || die +} + +src_install() { + local i pydocs in_path ein_path + + dodir /usr/share/doc/${PF}/html + sed \ + -e "s:../ccpnmr2.1:${EPREFIX}/usr/share/doc/${PF}/html:g" \ + ../doc/index.html > "${ED}"/usr/share/doc/${PF}/html/index.html || die + treecopy $(find python/ -name doc -type d) "${ED}"/usr/share/doc/${PF}/html/ + + pydocs="$(find python -name doc -type d)" + + symlinking() { + in_path=$(python_get_sitedir)/ccpn + ein_path="${in_path#${EPREFIX}}" + dosym ../../../../share/doc/${PF}/html ${ein_path}/doc + for i in ${pydocs}; do + dosym /usr/share/doc/${PF}/html/${i} ${ein_path}/${i} + done + dosym /usr/share/ccpn/data ${ein_path}/data + dosym /usr/share/ccpn/model ${ein_path}/model + } + python_foreach_impl symlinking + + dohtml -r doc/* + insinto /usr/share/ccpn + doins -r data model +} diff --git a/sci-libs/ccpn-data/files/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml b/sci-libs/ccpn-data/files/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml new file mode 100644 index 000000000000..60e8041c99da --- /dev/null +++ b/sci-libs/ccpn-data/files/312+ccpn_rhf22_2013-10-02-16-17-30-923_00001.xml @@ -0,0 +1,140 @@ +<?xml version="1.0" encoding="UTF-8"?> +<_StorageUnit release="2.1.2" originator="CCPN Python XmlIO" packageGuid="www.ccpn.ac.uk_Fogh_2006-08-16-14:22:45_00019" time="Wed Oct 2 16:22:49 2013"> + +<NMRX.NmrExpPrototype _ID="_1" createdBy="ccpnRef" guid="ccpn_rhf22_2013-10-02-16-17-30-923_00001" lastUnlockedBy="editor" serial="312"> + <NMRX.NmrExpPrototype.category> + <NMRX.ExpCategory>through-bond</NMRX.ExpCategory> + </NMRX.NmrExpPrototype.category> + <NMRX.NmrExpPrototype.details> + <IMPL.Text>e.g. POST-C7, INADEQUATE</IMPL.Text> + </NMRX.NmrExpPrototype.details> + <NMRX.NmrExpPrototype.name> + <IMPL.Line>C[DQ(CC)]_C.through-space</IMPL.Line> + </NMRX.NmrExpPrototype.name> + <NMRX.NmrExpPrototype.synonym> + <IMPL.Line>13C DQ</IMPL.Line> + </NMRX.NmrExpPrototype.synonym> + <NMRX.NmrExpPrototype.atomSites> + <NMRX.AtomSite _ID="_2" isotopeCode="13C" name="C" serial="1"> + <NMRX.AtomSite.expMeasurements> _3 _4</NMRX.AtomSite.expMeasurements> + <NMRX.AtomSite.expTransfers> _5 _6</NMRX.AtomSite.expTransfers> + </NMRX.AtomSite> + <NMRX.AtomSite _ID="_7" isotopeCode="13C" name="C" serial="2"> + <NMRX.AtomSite.expMeasurements> _4</NMRX.AtomSite.expMeasurements> + <NMRX.AtomSite.expTransfers> _5</NMRX.AtomSite.expTransfers> + </NMRX.AtomSite> + <NMRX.AtomSite _ID="_8" isotopeCode="13C" name="C" serial="3"> + <NMRX.AtomSite.expMeasurements> _9</NMRX.AtomSite.expMeasurements> + <NMRX.AtomSite.expTransfers> _6</NMRX.AtomSite.expTransfers> + </NMRX.AtomSite> + </NMRX.NmrExpPrototype.atomSites> + <NMRX.NmrExpPrototype.expGraphs> + <NMRX.ExpGraph _ID="_10" serial="1"> + <NMRX.ExpGraph.expSteps> + <NMRX.ExpStep _ID="_11" serial="1" stepNumber="1"> + </NMRX.ExpStep> + <NMRX.ExpStep _ID="_12" serial="2" stepNumber="2"> + </NMRX.ExpStep> + <NMRX.ExpStep _ID="_13" serial="3" stepNumber="3"> + </NMRX.ExpStep> + <NMRX.ExpStep _ID="_14" serial="4" stepNumber="4"> + </NMRX.ExpStep> + </NMRX.ExpGraph.expSteps> + <NMRX.ExpGraph.expTransfers> + <NMRX.ExpTransfer _ID="_5" serial="1" transferType="onebond"> + <NMRX.ExpTransfer.atomSites> _7 _2</NMRX.ExpTransfer.atomSites> + </NMRX.ExpTransfer> + <NMRX.ExpTransfer _ID="_6" serial="2" transferToSelf="true" transferType="through-space"> + <NMRX.ExpTransfer.atomSites> _8 _2</NMRX.ExpTransfer.atomSites> + </NMRX.ExpTransfer> + </NMRX.ExpGraph.expTransfers> + </NMRX.ExpGraph> + </NMRX.NmrExpPrototype.expGraphs> + <NMRX.NmrExpPrototype.expMeasurements> + <NMRX.ExpMeasurement _ID="_3" serial="1"> + <NMRX.ExpMeasurement.measurementType> + <NMRX.ExpMeasurementType>Shift</NMRX.ExpMeasurementType> + </NMRX.ExpMeasurement.measurementType> + <NMRX.ExpMeasurement.atomSites> _2</NMRX.ExpMeasurement.atomSites> + <NMRX.ExpMeasurement.expSteps> _11 _13</NMRX.ExpMeasurement.expSteps> + <NMRX.ExpMeasurement.refExpDimRefs> _15</NMRX.ExpMeasurement.refExpDimRefs> + </NMRX.ExpMeasurement> + <NMRX.ExpMeasurement _ID="_4" serial="2"> + <NMRX.ExpMeasurement.atomSiteWeights> 1.0 1.0</NMRX.ExpMeasurement.atomSiteWeights> + <NMRX.ExpMeasurement.measurementType> + <NMRX.ExpMeasurementType>MQShift</NMRX.ExpMeasurementType> + </NMRX.ExpMeasurement.measurementType> + <NMRX.ExpMeasurement.atomSites> _2 _7</NMRX.ExpMeasurement.atomSites> + <NMRX.ExpMeasurement.expSteps> _12</NMRX.ExpMeasurement.expSteps> + <NMRX.ExpMeasurement.refExpDimRefs> _16 _17</NMRX.ExpMeasurement.refExpDimRefs> + </NMRX.ExpMeasurement> + <NMRX.ExpMeasurement _ID="_9" serial="3"> + <NMRX.ExpMeasurement.measurementType> + <NMRX.ExpMeasurementType>Shift</NMRX.ExpMeasurementType> + </NMRX.ExpMeasurement.measurementType> + <NMRX.ExpMeasurement.atomSites> _8</NMRX.ExpMeasurement.atomSites> + <NMRX.ExpMeasurement.expSteps> _14</NMRX.ExpMeasurement.expSteps> + <NMRX.ExpMeasurement.refExpDimRefs> _18 _19</NMRX.ExpMeasurement.refExpDimRefs> + </NMRX.ExpMeasurement> + </NMRX.NmrExpPrototype.expMeasurements> + <NMRX.NmrExpPrototype.refExperiments> + <NMRX.RefExperiment _ID="_20" serial="3"> + <NMRX.RefExperiment.name> + <IMPL.Line>C[DQ(CC)]_C.through-space</IMPL.Line> + </NMRX.RefExperiment.name> + <NMRX.RefExperiment.synonym> + <IMPL.Line>13C DQ-SQ-SQ</IMPL.Line> + </NMRX.RefExperiment.synonym> + <NMRX.RefExperiment.refExpDims> + <NMRX.RefExpDim _ID="_21" dim="1"> + <NMRX.RefExpDim.refExpDimRefs> + <NMRX.RefExpDimRef _ID="_19" serial="1"> + <NMRX.RefExpDimRef.validScalingFactors> 1.0</NMRX.RefExpDimRef.validScalingFactors> + </NMRX.RefExpDimRef> + </NMRX.RefExpDim.refExpDimRefs> + </NMRX.RefExpDim> + <NMRX.RefExpDim _ID="_22" dim="2"> + <NMRX.RefExpDim.refExpDimRefs> + <NMRX.RefExpDimRef _ID="_15" serial="1"> + <NMRX.RefExpDimRef.validScalingFactors> 1.0</NMRX.RefExpDimRef.validScalingFactors> + </NMRX.RefExpDimRef> + </NMRX.RefExpDim.refExpDimRefs> + </NMRX.RefExpDim> + <NMRX.RefExpDim _ID="_23" dim="3"> + <NMRX.RefExpDim.refExpDimRefs> + <NMRX.RefExpDimRef _ID="_17" serial="1"> + <NMRX.RefExpDimRef.validScalingFactors> 1.0</NMRX.RefExpDimRef.validScalingFactors> + </NMRX.RefExpDimRef> + </NMRX.RefExpDim.refExpDimRefs> + </NMRX.RefExpDim> + </NMRX.RefExperiment.refExpDims> + </NMRX.RefExperiment> + <NMRX.RefExperiment _ID="_24" serial="4"> + <NMRX.RefExperiment.name> + <IMPL.Line>c[DQ(CC)]_C.through-space</IMPL.Line> + </NMRX.RefExperiment.name> + <NMRX.RefExperiment.synonym> + <IMPL.Line>13C DQ-SQ-SQ</IMPL.Line> + </NMRX.RefExperiment.synonym> + <NMRX.RefExperiment.refExpDims> + <NMRX.RefExpDim _ID="_25" dim="1"> + <NMRX.RefExpDim.refExpDimRefs> + <NMRX.RefExpDimRef _ID="_18" serial="1"> + <NMRX.RefExpDimRef.validScalingFactors> 1.0</NMRX.RefExpDimRef.validScalingFactors> + </NMRX.RefExpDimRef> + </NMRX.RefExpDim.refExpDimRefs> + </NMRX.RefExpDim> + <NMRX.RefExpDim _ID="_26" dim="2"> + <NMRX.RefExpDim.refExpDimRefs> + <NMRX.RefExpDimRef _ID="_16" serial="1"> + <NMRX.RefExpDimRef.validScalingFactors> 1.0</NMRX.RefExpDimRef.validScalingFactors> + </NMRX.RefExpDimRef> + </NMRX.RefExpDim.refExpDimRefs> + </NMRX.RefExpDim> + </NMRX.RefExperiment.refExpDims> + </NMRX.RefExperiment> + </NMRX.NmrExpPrototype.refExperiments> +</NMRX.NmrExpPrototype> + +</_StorageUnit> +<!--End of Memops Data--> diff --git a/sci-libs/ccpn-data/metadata.xml b/sci-libs/ccpn-data/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/ccpn-data/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest new file mode 100644 index 000000000000..a7323ca2432a --- /dev/null +++ b/sci-libs/cctbx/Manifest @@ -0,0 +1,13 @@ +AUX 2010.03.29.2334-boost.patch 18175 SHA256 f6a8a246dfd42e7981687802a0e00d933759d3c749c0344bfbfbfde12814f4d7 SHA512 e722312a878be229a24269471902bd1febe98c5510bfc50e1ba3a841c1a0228cdb7964e69703083850052e49e91899b229bc3543d90485ba50e79e7eceb11e2e WHIRLPOOL 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100644 index 000000000000..5ac1e461f684 --- /dev/null +++ b/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild @@ -0,0 +1,189 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils fortran-2 multilib prefix python-single-r1 toolchain-funcs + +MY_PV="${PV//./_}" + +DESCRIPTION="Computational Crystallography Toolbox" +HOMEPAGE="http://cctbx.sourceforge.net/" +SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz" + +LICENSE="cctbx-2.0" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="+minimal openmp threads" + +REQUIRED_USE=" + ${PYTHON_REQUIRED_USE} + ?? ( openmp threads )" + +RDEPEND=" + ${PYTHON_DEPS} + >=dev-libs/boost-1.48[python,${PYTHON_USEDEP}] + sci-libs/clipper + sci-libs/fftw:3.0= + !minimal? ( + sci-chemistry/cns + sci-chemistry/shelx )" +DEPEND="${RDEPEND} + !prefix? ( >=dev-util/scons-1.2[${PYTHON_USEDEP}] )" + +S="${WORKDIR}" +MY_S="${WORKDIR}"/cctbx_sources +MY_B="${WORKDIR}"/cctbx_build + +pkg_setup() { + use openmp && FORTRAN_NEED_OPENMP="1" + if use openmp && ! tc-has-openmp; then + ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 and icc" + ewarn "If you want to build ${PN} with OpenMP, abort now," + ewarn "and switch CC to an OpenMP capable compiler" + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + python-single-r1_pkg_setup +} + +src_prepare() { + local opts + local optsld + + epatch \ + "${FILESDIR}"/${PV}-tst_server.py.patch \ + "${FILESDIR}"/${PV}-boost.patch \ + "${FILESDIR}"/${PV}-clipper.patch \ + "${FILESDIR}"/${PV}-flags.patch \ + "${FILESDIR}"/${PV}-soname.patch \ + "${FILESDIR}"/${PV}-gcc-4.6.patch \ + "${FILESDIR}"/${PV}-gcc-4.7.patch \ + "${FILESDIR}"/${PV}-format-security.patch + + eprefixify "${MY_S}"/scitbx/libtbx_refresh.py + + rm -rvf "${MY_S}/boost" "${MY_S}/PyCifRW" >> "${T}"/clean.log || die + if ! use prefix; then + rm -rvf "${MY_S}/scons" >> "${T}"/clean.log || die + echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py || die + fi + + find "${MY_S}/clipper" -name "*.h" -print -delete >> "${T}"/clean.log || die + + sed \ + -e "/LIBS/s:boost_python:boost_python-$(echo ${EPYTHON} | sed 's/python//'):g" \ + -i "${MY_S}"/boost_adaptbx/SConscript "${MY_S}"/scitbx/boost_python/SConscript || die +} + +src_configure() { + local compiler + local myconf + + myconf="${MY_S}/libtbx/configure.py" + + compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') + myconf="${myconf} --compiler=${compiler}" + + # Additional USE flag usage + myconf="${myconf} --enable-openmp-if-possible=$(usex openmp true false)" + + use threads && USEthreads="--enable-boost-threads" + + myconf="${myconf} ${USE_threads} --scan-boost --use_environment_flags" + + mkdir "${MY_B}" && myconf="${myconf} --current_working_directory=${MY_B}" + cd "${MY_B}" + + myconf="${myconf} --build=release fftw3tbx rstbx smtbx mmtbx clipper_adaptbx fable" + einfo "configuring with ${python} ${myconf}" + + ${EPYTHON} ${myconf} || die "configure failed" +} + +src_compile() { + local makeopts_exp + + cd "${MY_B}" + + makeopts_exp=${MAKEOPTS/j/j } + makeopts_exp=${makeopts_exp%-l[0-9]*} + + source setpaths_all.sh + + einfo "compiling with libtbx.scons ${makeopts_exp}" + libtbx.scons ${makeopts_exp} .|| die "make failed" +} + +src_test(){ + source "${MY_B}"/setpaths_all.sh + libtbx.python $(libtbx.show_dist_paths boost_adaptbx)/tests/tst_rational.py && \ + libtbx.python ${SCITBX_DIST}/run_tests.py ${MAKEOPTS_EXP} && \ + libtbx.python ${CCTBX_DIST}/run_tests.py ${MAKEOPTS_EXP} \ + || die "test failed" +} + +src_install(){ + local lib baselib +# find cctbx_build/ -type f \( -name "*.py" -o -name "*sh" \) -exec \ +# sed -e "s:${MY_S}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_sources:g" \ +# -e "s:${MY_B}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build:g" \ +# -i '{}' \; || die "Fail to correct path" + + sed \ + -e "s:${MY_B}:${EPREFIX}/usr:g" \ + -e "s:${MY_S}:${EPREFIX}/$(python_get_sitedir):g" \ + -i "${MY_B}/libtbx_env" || die + + insinto /usr/share/cctbx + doins "${MY_B}/libtbx_env" || die + + ebegin "removing unnessary files" + rm -r "${S}"/cctbx_sources/{clipper,ccp4io,ucs-fonts,TAG} || die "failed to remove uneeded scons" + find -O3 "${S}" -type f \ + \( -name "*conftest*" -o -name "*.o" -o -name "*.c" -o -name "*.f" -o -name "*.cpp" -o \ + -name "*.pyc" -o -name "SCons*" -o -name "Makefile" -o -name "config.log" \) -delete \ + -print >> "${T}"/clean.log || die + find "${S}" -type d -empty -delete -print >> "${T}"/clean.log || die + find "${MY_B}" -maxdepth 1 -type f -delete -print >> "${T}"/clean.log || die + eend + + dobin "${MY_B}"/bin/* + rm -vrf "${MY_B}/bin" >> "${T}"/clean.log || die + dolib.so "${MY_B}"/lib/lib* + mv "${ED}"/usr/$(get_libdir)/libscitbx_min{,i}pack.so || die + rm -vf "${MY_B}"/lib/lib* >> "${T}"/clean.log || die + + for lib in "${ED}"/usr/$(get_libdir)/*.so; do + baselib=$(basename ${lib}) + mv ${lib}{,.0.0} || die + dosym ${baselib}.0.0 /usr/$(get_libdir)/${baselib} + done + + insinto /usr/include + doins -r "${MY_B}"/include/* || die + rm -rvf "${MY_B}/include" >> "${T}"/clean.log || die + + insinto /usr/libexec/${PN} + doins -r "${MY_B}"/* || die + find "${ED}"/usr/libexec/${PN} -type f -exec chmod 755 '{}' \; + + cd "${MY_S}" + python_domodule * "${MY_B}"/lib/* + rm -rvf "${MY_B}/lib" >> "${T}"/clean.log || die + + sed \ + -e "/PYTHONPATH/s:${MY_S}:$(python_get_sitedir):g" \ + -e "/PYTHONPATH/s:${MY_B}:$(python_get_sitedir):g" \ + -e "/LD_LIBRARY_PATH/s:${MY_B}/lib:${EPREFIX}/usr/$(get_libdir):g" \ + -e "/PATH/s:${MY_B}/bin:${EPREFIX}/usr/bin:g" \ + -e "/PATH/s:${MY_B}/exe:${EPREFIX}/usr/bin:g" \ + -e "/exec/s:${MY_S}:$(python_get_sitedir):g" \ + -e "/LIBTBX_BUILD/s:${MY_B}:${EPREFIX}/usr/share/cctbx:g" \ + -e "s:${MY_B}/exe_dev/:${EPREFIX}/usr/libexec/${PN}/exe_dev/:g" \ + -i "${ED}"/usr/bin/* || die + + python_optimize +} diff --git a/sci-libs/cctbx/files/2010.03.29.2334-boost.patch b/sci-libs/cctbx/files/2010.03.29.2334-boost.patch new file mode 100644 index 000000000000..5b4439ee6780 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-boost.patch @@ -0,0 +1,516 @@ +From 7e77ff8694b87e95efe56ed961fbc8dd30d8c238 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <gentoo@mgorny.alt.pl> +Date: Sun, 4 Jul 2010 12:21:10 +0200 +Subject: [PATCH] Unbundle boost. + +--- + work/cctbx_sources/boost_adaptbx/SConscript | 260 ------------------------- + work/cctbx_sources/cbflib_adaptbx/SConscript | 1 - + work/cctbx_sources/cctbx/SConscript | 1 - + work/cctbx_sources/clipper_adaptbx/SConscript | 1 - + work/cctbx_sources/fable/SConscript | 1 - + work/cctbx_sources/fable/libtbx_config | 2 +- + work/cctbx_sources/fftw3tbx/SConscript | 1 - + work/cctbx_sources/gltbx/SConscript | 1 - + work/cctbx_sources/iotbx/SConscript | 2 - + work/cctbx_sources/mmtbx/SConscript | 1 - + work/cctbx_sources/omptbx/libtbx_config | 2 +- + work/cctbx_sources/rstbx/SConscript | 1 - + work/cctbx_sources/scitbx/SConscript | 1 - + work/cctbx_sources/scitbx/libtbx_config | 2 +- + work/cctbx_sources/scitbx/libtbx_refresh.py | 3 +- + work/cctbx_sources/smtbx/SConscript | 1 - + work/cctbx_sources/spotfinder/SConscript | 1 - + work/cctbx_sources/tntbx/SConscript | 1 - + 18 files changed, 4 insertions(+), 279 deletions(-) + +diff --git a/work/cctbx_sources/boost_adaptbx/SConscript b/work/cctbx_sources/boost_adaptbx/SConscript +index 0701816..9f8cbf9 100644 +--- a/work/cctbx_sources/boost_adaptbx/SConscript ++++ b/work/cctbx_sources/boost_adaptbx/SConscript +@@ -8,39 +8,9 @@ import string + import sys, os + op = os.path + Import("env_base", "env_etc") +-env_etc.boost_dist = libtbx.env.dist_path("boost") +-env_etc.boost_include = env_etc.boost_dist + env_etc.boost_adaptbx_dist = libtbx.env.dist_path("boost_adaptbx") + env_etc.boost_adaptbx_include = os.path.dirname(env_etc.boost_adaptbx_dist) + +-def build_boost_thread(): +- if (not libtbx.env.build_options.enable_boost_threads): +- return +- if (sys.platform == "win32"): s = "win32" +- else: s = "pthread" +- join = os.path.join +- src = join("libs", "thread", "src", s) +- prefix = "#" + join(os.path.basename(env_etc.boost_dist), src) +- source = [] +- for node in sorted(os.listdir(join(env_etc.boost_dist, src))): +- if (not node.lower().endswith(".cpp")): continue +- source.append(join(prefix, node)) +- env = env_base.Clone( +- SHLINKFLAGS=env_etc.shlinkflags) +- env.Append(SHCXXFLAGS=["-DBOOST_THREAD_BUILD_DLL"]) +- env_etc.include_registry.append( +- env=env, +- paths=[env_etc.boost_include]) +- darwin_shlinkcom(env_etc, env, +- lo="boost/libs/thread/src/libboost_thread.lo", +- dylib="lib/libboost_thread.dylib") +- env.Repository(os.path.dirname(env_etc.boost_dist)) +- env.SharedLibrary( +- target='#lib/boost_thread', +- source=source) +- +-build_boost_thread() +- + if (not env_etc.no_boost_python): + env_etc.cxxflags_bpl_defines_base = [ + "-DBOOST_PYTHON_MAX_BASES=2"] +@@ -64,12 +34,10 @@ if (not env_etc.no_boost_python): + ' /manifest ${TARGET}.manifest']) + Export("env_no_includes_boost_python_ext") + env_pure_boost_python_ext = env_no_includes_boost_python_ext.Clone() +- env_etc.include_registry.set_boost_dir_name(env_etc.boost_dist) + env_etc.include_registry.append( + env=env_pure_boost_python_ext, + paths=[ + "#include", +- env_etc.boost_include, + env_etc.python_include]) + env_boost_python_ext = env_pure_boost_python_ext.Clone() + env_etc.include_registry.prepend( +@@ -113,234 +81,6 @@ if (not env_etc.no_boost_python): + target="tests/tst_optional_copy", + source="tests/tst_optional_copy.cpp") + +- import os, os.path +- env = env_base.Clone(LIBS=env_etc.libs_python) +- env.Append(LIBPATH=env_etc.libpath_python) +- env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base) +- env.Append(SHCXXFLAGS=["-DBOOST_PYTHON_SOURCE"]) +- if (libtbx.env.build_options.boost_python_bool_int_strict): +- env.Append(SHCXXFLAGS=["-DBOOST_PYTHON_BOOL_INT_STRICT"]) +- env.Replace(SHLINKFLAGS=env_etc.shlinkflags) +- env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base) +- env.Append(CXXFLAGS="-DBOOST_PYTHON_SOURCE") +- env.Replace(LINKFLAGS=env_etc.shlinkflags) +- env_etc.include_registry.append( +- env=env, +- paths=[env_etc.boost_include, env_etc.python_include]) +- +- darwin_shlinkcom(env_etc, env, +- lo="boost/libs/python/src/libboost_python.lo", +- dylib="lib/libboost_python.dylib") +- +- # fixed list of file names introduced 2009-09-29, due to major changes in +- # boost/libs/python/build/Jamfile.v2 svn rev. 56305 (new Python 3 support) +- bpl_dll_sources = """\ +-numeric.cpp +-list.cpp +-long.cpp +-dict.cpp +-tuple.cpp +-str.cpp +-slice.cpp +-converter/from_python.cpp +-converter/registry.cpp +-converter/type_id.cpp +-object/enum.cpp +-object/class.cpp +-object/function.cpp +-object/inheritance.cpp +-object/life_support.cpp +-object/pickle_support.cpp +-errors.cpp +-module.cpp +-converter/builtin_converters.cpp +-converter/arg_to_python_base.cpp +-object/iterator.cpp +-object/stl_iterator.cpp +-object_protocol.cpp +-object_operators.cpp +-wrapper.cpp +-import.cpp +-exec.cpp +-object/function_doc_signature.cpp +-""".splitlines() +- prefix = "#"+os.path.join( +- os.path.basename(env_etc.boost_dist), "libs", "python", "src") +- bpl_dll_sources = [os.path.join(prefix, path) for path in bpl_dll_sources] +- # +- env.Repository(os.path.dirname(env_etc.boost_dist)) +- if (env_etc.static_bpl): +- env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources) +- else: +- env.SharedLibrary(target="#lib/boost_python", source=bpl_dll_sources) +- if (int(ARGUMENTS.get("boost_python_tests", 0))): +- warn_if_unexpected_md5_hexdigest( +- path=libtbx.env.under_dist("boost", "libs/python/test/Jamfile.v2"), +- expected_md5_hexdigests=[ +- "c7a3dd81bf730635146f5c908ac982eb", # svn revision 39065M +- "d40aac0029bcd28f6e205ae3b30a1284", # svn revision 40216 +- "b79f016d3ec10cf1625a9e006e605428", # svn revision 40714 +- "f948983d970fd47e83a3a785bb54520a", # svn revision 41550 +- "c3d84006331d534840c42ab956fdfa05", # svn revision 50367M +- "cedfd061d767a27413ef4a75ee0e446f", # svn revision 56310 +- "e5507482a1937825e4c9f3ffe555fc59", # svn revision 59331 +- ]) +- bpl_tests = Split(""" +-staticmethod +-shared_ptr +-enable_shared_from_this +-andreas_beyer +-polymorphism +-polymorphism2 +-auto_ptr +-minimal +-args +-numpy +-enum +-exception_translator +-test_pointer_adoption +-operators +-callbacks +-defaults +-object +-list +-long +-dict +-tuple +-str +-virtual_functions +-back_reference +-implicit +-data_members +-ben_scott1 +-bienstman1 +-bienstman2 +-bienstman3 +-multi_arg_constructor +-extract +-opaque +-pickle1 +-pickle2 +-pickle3 +-pickle4 +-nested +-docstring +-pytype_function +-bienstman4 +-bienstman5 +-test_builtin_converters,builtin_converters_ext,test_builtin_converters +-cltree,cltree,test_cltree +-m1,m1,newtest +-m2,m2,newtest +-iterator,iterator_ext,iterator +-input_iterator,input_iterator,iterator +-crossmod_exception_a,crossmod_exception_a,crossmod_exception +-crossmod_exception_b,crossmod_exception_b,crossmod_exception +-vector_indexing_suite +-return_arg +-keywords,keywords,keywords_test +-properties +-map_indexing_suite;int_map_indexing_suite;a_map_indexing_suite,map_indexing_suite_ext,map_indexing_suite +-injected +-slice +-const_argument +-raw_ctor +-pointer_vector +-wrapper_held_type +-polymorphism2_auto_ptr +-stl_iterator +-voidptr +-crossmod_opaque_a,crossmod_opaque_a,crossmod_opaque +-crossmod_opaque_b,crossmod_opaque_b,crossmod_opaque +-""") +-# non-portable tests are not included above: +-# calling_conventions +-# calling_conventions_mf +-# +- Import("env_boost_python_ext") +- test_dir = libtbx.env.under_dist("boost", "libs/python/test") +- prefix = "#"+os.path.join( +- os.path.basename(env_etc.boost_dist), "libs", "python", "test") +- all_tst = [] +- for bpl_test in bpl_tests: +- flds = bpl_test.split(",") +- assert len(flds) in (1,3) +- if (len(flds) == 1): +- src = bpl_test +- pyd = bpl_test + "_ext" +- tst = bpl_test +- else: +- src = flds[0] +- pyd = flds[1] +- tst = flds[2] +- env = env_pure_boost_python_ext.Clone() +- env.Repository(os.path.dirname(env_etc.boost_dist)) +- ok = True +- source = [] +- for s in src.split(";"): +- cpp = "%s.cpp" % s +- file_name = os.path.join(test_dir, cpp) +- if (not os.path.isfile(file_name)): +- print "Warning: source file not available:", show_string(file_name) +- ok = False +- else: +- source.append(os.path.join(prefix, cpp)) +- if (ok): +- if (not tst in all_tst): +- all_tst.append(tst) +- env.SharedLibrary(target="#lib/%s" % pyd, source=source) +- all_tst = [os.path.join(test_dir, tst+".py") for tst in all_tst] +- # +- if (sys.platform == "linux2"): +- base_lib = libtbx.env.under_build(path="base/lib") +- if (os.path.isdir(base_lib)): +- env_prog = env.Clone() +- env_prog.Append(LIBPATH=[base_lib]) +- env_prog.Append(LIBS=[ +- "-lpython%d.%d" % sys.version_info[:2], +- "-lpthread", +- "-lutil", +- "-ldl"]) +- exe = env_prog.Program( +- target="boost/libs/python/test/exec_dynamic", +- source=[os.path.join(prefix, "exec.cpp")]) +- libtbx.env.write_dispatcher_in_bin( +- source_file=exe[0].get_abspath(), +- target_file="boost_libs_python_test_exec_dynamic") +- all_tst.append("$ boost_libs_python_test_exec_dynamic %s" +- % show_string(os.path.join(test_dir, "exec.py"))) +- # +- if (os.name != "nt"): +- env.SharedLibrary( +- target="#lib/boost_adaptbx_char_array_ext", +- source=["char_array_ext.cpp"]) +- all_tst.append( +- libtbx.env.under_dist("boost_adaptbx", "tests/tst_char_array.py")) +- # +- if (os.name == "nt"): +- boost_python_run_tests = \ +- "%s\\boost_python_run_tests.bat" % libtbx.env.build_path +- f = open(boost_python_run_tests, "w") +- for tst in all_tst: +- if (tst.startswith("$ ")): +- print >> f, 'call %s' % tst[2:] +- else: +- print >> f, 'call libtbx.python %s' % show_string(tst) +- f.close() +- else: +- boost_python_run_tests = \ +- "%s/boost_python_run_tests.csh" % libtbx.env.build_path +- f = open(boost_python_run_tests, "w") +- print >> f, "#! /bin/csh -f" +- print >> f, "set verbose" +- for tst in all_tst: +- if (tst.startswith("$ ")): +- print >> f, tst[2:] +- else: +- print >> f, 'libtbx.python "%s"' % show_string(tst) +- f.close() +- os.chmod(boost_python_run_tests, 0755) +- + def write_type_id_eq_h(): + unsigned_types = [ + "unsigned short", +diff --git a/work/cctbx_sources/cbflib_adaptbx/SConscript b/work/cctbx_sources/cbflib_adaptbx/SConscript +index 78c1297..dffc247 100644 +--- a/work/cctbx_sources/cbflib_adaptbx/SConscript ++++ b/work/cctbx_sources/cbflib_adaptbx/SConscript +@@ -14,7 +14,6 @@ env_etc.cbflib_common_includes = [ + env_etc.libtbx_include, + env_etc.scitbx_include, + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + env_etc.cbflib_dist, # for the adaptor cpp files + env_etc.cbflib_include[0], # for the cbflib c-files + env_etc.cbflib_include[1], # for the cbflib c-files +diff --git a/work/cctbx_sources/cctbx/SConscript b/work/cctbx_sources/cctbx/SConscript +index 6ec7c93..2dfb442 100644 +--- a/work/cctbx_sources/cctbx/SConscript ++++ b/work/cctbx_sources/cctbx/SConscript +@@ -10,7 +10,6 @@ env_etc.cctbx_common_includes = [ + env_etc.scitbx_include, + env_etc.chiltbx_include, + env_etc.omptbx_include, +- env_etc.boost_include, + ] + + env = env_base.Clone( +diff --git a/work/cctbx_sources/fable/SConscript b/work/cctbx_sources/fable/SConscript +index bf8e198..b6acccf 100644 +--- a/work/cctbx_sources/fable/SConscript ++++ b/work/cctbx_sources/fable/SConscript +@@ -13,7 +13,6 @@ if (not env_etc.no_boost_python): + env_etc.libtbx_include, + env_etc.fable_include, + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + env_etc.python_include]) + env.SharedLibrary( + target="#lib/fable_ext", +diff --git a/work/cctbx_sources/fable/libtbx_config b/work/cctbx_sources/fable/libtbx_config +index d456588..f00ae86 100644 +--- a/work/cctbx_sources/fable/libtbx_config ++++ b/work/cctbx_sources/fable/libtbx_config +@@ -1,4 +1,4 @@ + { +- "modules_required_for_build": ["boost"], ++ "modules_required_for_build": [], + "modules_required_for_use": ["boost_adaptbx"], + } +diff --git a/work/cctbx_sources/fftw3tbx/SConscript b/work/cctbx_sources/fftw3tbx/SConscript +index ecc3a03..4fc1ec1 100755 +--- a/work/cctbx_sources/fftw3tbx/SConscript ++++ b/work/cctbx_sources/fftw3tbx/SConscript +@@ -8,7 +8,6 @@ env_etc.fftw3tbx_dist = libtbx.env.dist_path("fftw3tbx") + env_etc.fftw3tbx_common_includes = [ + env_etc.libtbx_include, + env_etc.scitbx_include, +- env_etc.boost_include, + ] + + base_include = libtbx.env.under_build("base/include") +diff --git a/work/cctbx_sources/gltbx/SConscript b/work/cctbx_sources/gltbx/SConscript +index 56a7115..f6214a4 100644 +--- a/work/cctbx_sources/gltbx/SConscript ++++ b/work/cctbx_sources/gltbx/SConscript +@@ -7,7 +7,6 @@ env_etc.gltbx_common_includes = [ + env_etc.libtbx_include, + env_etc.gltbx_include, + env_etc.scitbx_include, +- env_etc.boost_include, + ] + + if (not env_etc.no_boost_python): +diff --git a/work/cctbx_sources/iotbx/SConscript b/work/cctbx_sources/iotbx/SConscript +index df17856..c5cf7da 100644 +--- a/work/cctbx_sources/iotbx/SConscript ++++ b/work/cctbx_sources/iotbx/SConscript +@@ -10,7 +10,6 @@ env_etc.iotbx_common_includes = [ + env_etc.iotbx_include, + env_etc.cctbx_include, + env_etc.scitbx_include, +- env_etc.boost_include, + env_etc.boost_adaptbx_include, + ] + +@@ -37,7 +36,6 @@ if (not env_etc.no_boost_python): + env_etc.include_registry.append( + env=env, + paths=[env_etc.libtbx_include, +- env_etc.boost_include, + env_etc.python_include]) + env.SharedLibrary( + target="#lib/iotbx_wildcard_ext", +diff --git a/work/cctbx_sources/mmtbx/SConscript b/work/cctbx_sources/mmtbx/SConscript +index 0532878..9bcaeb2 100755 +--- a/work/cctbx_sources/mmtbx/SConscript ++++ b/work/cctbx_sources/mmtbx/SConscript +@@ -10,7 +10,6 @@ env_etc.mmtbx_common_includes = [ + env_etc.mmtbx_include, + env_etc.cctbx_include, + env_etc.scitbx_include, +- env_etc.boost_include, + ] + + if (not env_etc.no_boost_python): +diff --git a/work/cctbx_sources/omptbx/libtbx_config b/work/cctbx_sources/omptbx/libtbx_config +index d456588..f00ae86 100644 +--- a/work/cctbx_sources/omptbx/libtbx_config ++++ b/work/cctbx_sources/omptbx/libtbx_config +@@ -1,4 +1,4 @@ + { +- "modules_required_for_build": ["boost"], ++ "modules_required_for_build": [], + "modules_required_for_use": ["boost_adaptbx"], + } +diff --git a/work/cctbx_sources/rstbx/SConscript b/work/cctbx_sources/rstbx/SConscript +index 2213c2f..232b5d7 100644 +--- a/work/cctbx_sources/rstbx/SConscript ++++ b/work/cctbx_sources/rstbx/SConscript +@@ -11,7 +11,6 @@ env_etc.rstbx_common_includes = [ + env_etc.scitbx_include, + env_etc.chiltbx_include, + env_etc.omptbx_include, +- env_etc.boost_include, + ] + + env = env_base.Clone(SHLINKFLAGS=env_etc.shlinkflags) +diff --git a/work/cctbx_sources/scitbx/SConscript b/work/cctbx_sources/scitbx/SConscript +index f30b9db..10e0967 100644 +--- a/work/cctbx_sources/scitbx/SConscript ++++ b/work/cctbx_sources/scitbx/SConscript +@@ -9,7 +9,6 @@ env_etc.scitbx_common_includes = [ + env_etc.scitbx_include, + env_etc.omptbx_include, + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + ] + + SConscript("error/SConscript") +diff --git a/work/cctbx_sources/scitbx/libtbx_config b/work/cctbx_sources/scitbx/libtbx_config +index 87cc3c7..d147819 100644 +--- a/work/cctbx_sources/scitbx/libtbx_config ++++ b/work/cctbx_sources/scitbx/libtbx_config +@@ -1,4 +1,4 @@ + { +- "modules_required_for_build": ["boost"], ++ "modules_required_for_build": [], + "modules_required_for_use": ["boost_adaptbx", "omptbx"], + } +diff --git a/work/cctbx_sources/scitbx/libtbx_refresh.py b/work/cctbx_sources/scitbx/libtbx_refresh.py +index 10d4ee0..c8374b2 100644 +--- a/work/cctbx_sources/scitbx/libtbx_refresh.py ++++ b/work/cctbx_sources/scitbx/libtbx_refresh.py +@@ -13,8 +13,7 @@ if (self.env.is_ready_for_build()): + generate_all.refresh(array_family=os.path.dirname(target_dir)) + # + warn_if_unexpected_md5_hexdigest( +- path=self.env.under_dist( +- module_name="boost", path="boost/random/mersenne_twister.hpp"), ++ path="@GENTOO_PORTAGE_EPREFIX@/usr/include/boost/random/mersenne_twister.hpp", + expected_md5_hexdigests=[ + "a2533c79a21f0f773f2e0d29a37371b0", # CVS revision 1.21 + "378432b5b280c9c0c894f7c80f0dad92", # CVS revision 1.20 +diff --git a/work/cctbx_sources/smtbx/SConscript b/work/cctbx_sources/smtbx/SConscript +index f5031ee..02f81a4 100644 +--- a/work/cctbx_sources/smtbx/SConscript ++++ b/work/cctbx_sources/smtbx/SConscript +@@ -7,7 +7,6 @@ env_etc.smtbx_common_includes = [ + env_etc.cctbx_include, + env_etc.scitbx_include, + env_etc.chiltbx_include, +- env_etc.boost_include, + ] + + env = env_base.Clone( +diff --git a/work/cctbx_sources/spotfinder/SConscript b/work/cctbx_sources/spotfinder/SConscript +index 1d280d4..9dc9195 100644 +--- a/work/cctbx_sources/spotfinder/SConscript ++++ b/work/cctbx_sources/spotfinder/SConscript +@@ -13,7 +13,6 @@ env_etc.spotfinder_common_includes = [ + env_etc.iotbx_include, + os.path.dirname(env_etc.spotfinder_dist), + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + env_etc.annlib_dist, + env_etc.annlib_include[0], + env_etc.annlib_include[1], +diff --git a/work/cctbx_sources/tntbx/SConscript b/work/cctbx_sources/tntbx/SConscript +index e773186..ee29f10 100755 +--- a/work/cctbx_sources/tntbx/SConscript ++++ b/work/cctbx_sources/tntbx/SConscript +@@ -10,7 +10,6 @@ env_etc.tntbx_common_includes = [ + env_etc.tntbx_include, + env_etc.tntbx_tnt_include, + env_etc.scitbx_include, +- env_etc.boost_include, + ] + + Import("env_base", "env_etc") +-- +1.7.1.1 diff --git a/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch b/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch new file mode 100644 index 000000000000..8830dd8a054e --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch @@ -0,0 +1,77 @@ +diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript +index 9cce49e..1046ed0 100644 +--- a/cctbx_sources/clipper_adaptbx/SConscript ++++ b/cctbx_sources/clipper_adaptbx/SConscript +@@ -1,56 +1,13 @@ + import libtbx.load_env + Import("env_base", "env_etc") + +-env_etc.clipper_dist = libtbx.env.dist_path("clipper") +-env_etc.clipper_include = env_etc.clipper_dist +- + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags, + LIBS=env_etc.libm) +-env.Prepend(CPPPATH=[env_etc.clipper_include]) +- +-if (env_etc.static_libraries): builder = env.StaticLibrary +-else: builder = env.SharedLibrary +-builder(target='#lib/clipper', +- source = ["../clipper/clipper/core/"+file_name for file_name in """ +- atomsf.cpp +- cell.cpp +- clipper_memory.cpp +- clipper_message.cpp +- clipper_stats.cpp +- clipper_types.cpp +- clipper_util.cpp +- container.cpp +- container_hkl.cpp +- container_map.cpp +- container_types.cpp +- coords.cpp +- derivs.cpp +- hkl_compute.cpp +- hkl_data.cpp +- hkl_datatypes.cpp +- hkl_info.cpp +- hkl_lookup.cpp +- hkl_operators.cpp +- map_interp.cpp +- map_utils.cpp +- nxmap.cpp +- nxmap_operator.cpp +- ramachandran.cpp +- resol_basisfn.cpp +- resol_fn.cpp +- resol_targetfn.cpp +- rotation.cpp +- spacegroup.cpp +- spacegroup_data.cpp +- symop.cpp +- xmap.cpp +-""".split()]) +-# fftmap_sparse.cpp +-# fftmap.cpp + + env_exe = env.Clone() +-env_exe.Prepend(LIBS=["clipper"]) ++env_exe.Prepend(LIBS=["clipper-minimol","clipper-mmdb","clipper-cns","clipper-cif","clipper-contrib","clipper-ccp4","clipper-phs","clipper-core"]) ++env_exe.Prepend(SHLINKFLAGS=["-Wl,--as-needed"]) + + exe = env_exe.Program( + target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest' +@@ -76,12 +33,10 @@ if (hasattr(env_etc, "cctbx_include")): + env_etc.include_registry.append( + env=env_clipper_boost_python_ext, + paths=[ +- env_etc.clipper_include, + env_etc.libtbx_include, + env_etc.cctbx_include, + env_etc.scitbx_include, + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + env_etc.python_include]) + Export("env_clipper_boost_python_ext") +- SConscript("clipper/SConscript") ++ diff --git a/sci-libs/cctbx/files/2010.03.29.2334-flags.patch b/sci-libs/cctbx/files/2010.03.29.2334-flags.patch new file mode 100644 index 000000000000..8a8033234713 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-flags.patch @@ -0,0 +1,94 @@ +diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript +index 16d22b6..f85b664 100644 +--- a/cctbx_sources/libtbx/SConscript ++++ b/cctbx_sources/libtbx/SConscript +@@ -5,6 +5,7 @@ from libtbx.str_utils import show_string + from libtbx.path import norm_join, full_command_path + import platform + import sys, os ++import SCons.Util + + if (hasattr(Environment, "Clone")): + Environment.Copy = Environment.Clone # XXX backward compatibility 2008_03_30 +@@ -132,9 +133,7 @@ if (env_etc.compiler == "unix_icpc"): + static_exe = libtbx.env.build_options.static_exe + + def gcc_common_warn_options(): +- result = ["-Wall", "-Wno-sign-compare", "-Wno-unknown-pragmas"] +- if (env_etc.gcc_version >= 40000): +- result.append("-Winit-self") ++ result = [""] + return result + + def enable_more_warnings(env): +@@ -355,16 +354,22 @@ else: + cc = env_etc.compiler.replace("unix_", "") + cxx = cc.replace("gcc", "g++") + env_etc.gcc_version = libtbx.env_config.get_gcc_version(command_name=cc) ++# linkerflags = os.environ.get("LDFLAGS") ++# link_flags=env_etc.ldflags ++ link_flags=os.environ.get("LDFLAGS") ++ linker_options=SCons.Util.CLVar(os.environ['LDFLAGS']) + env_base.Replace( + CC=cc, + SHCC=cc, + CXX=cxx, + LINK=cxx, ++ LINKFLAGS=linker_options, + SHCXX=cxx, + SHLINK=cxx, + SHLIBSUFFIX=env_etc.shlibsuffix, + ) +- env_etc.c_link = cc ++# linkerflags = env_etc.ldflags ++# env_etc.c_link = cc + " " + linkerflags + env_etc.ccflags_base = [ + "-fPIC", + "-fno-strict-aliasing"] +@@ -380,7 +385,7 @@ else: + warn_options = gcc_common_warn_options() + ["-Werror"] + env_etc.ccflags_base.extend(warn_options) + if (libtbx.env.build_options.optimization): +- opts = ["-DNDEBUG", "-O3", "-ffast-math"] ++ opts = ["-DNDEBUG"] + if (env_etc.gcc_version >= 40300): + opts.append("-fno-associative-math") + opts.append("-ftrapping-math") +@@ -401,6 +406,7 @@ else: + env_base.Prepend(LINKFLAGS=["-static"]) + static_exe = None + env_etc.shlinkflags = ["-shared"] ++ env_etc.shlinkflags.append(linker_options) + env_etc.shlinkflags_bpl = env_etc.shlinkflags + if (libtbx.env.build_options.mode == "profile"): + env_base.Prepend(LINKFLAGS=["-pg"]) +diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py +index ca510b9..68c58ea 100644 +--- a/cctbx_sources/libtbx/env_config.py ++++ b/cctbx_sources/libtbx/env_config.py +@@ -1608,6 +1608,7 @@ class build_options: + self.env_cxxflags = "" + self.env_cflags = "" + self.env_cppflags = "" ++ self.env_ldflags = "" + flg = os.environ.get("CXXFLAGS") + if flg is not None: + self.env_cxxflags = flg +@@ -1617,6 +1618,9 @@ class build_options: + flg = os.environ.get("CPPFLAGS") + if flg is not None: + self.env_cppflags = flg ++ flg = os.environ.get("LDFLAGS") ++ if flg is not None: ++ self.env_ldflags = flg + + def report(self, f=None): + if (f is None): f = sys.stdout +@@ -1640,6 +1644,7 @@ class build_options: + print >>f, " CXXFLAGS = ", self.env_cxxflags + print >>f, " CFLAGS = ", self.env_cflags + print >>f, " CPPFLAGS = ", self.env_cppflags ++ print >>f, " LDFLAGS = ", self.env_ldflags + + class include_registry: + diff --git a/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch b/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch new file mode 100644 index 000000000000..057c135f9953 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch @@ -0,0 +1,117 @@ + cctbx_sources/scitbx/lbfgsb/raw.h | 54 +++++++++++++++++++-------------------- + 1 file changed, 27 insertions(+), 27 deletions(-) + +diff --git a/cctbx_sources/scitbx/lbfgsb/raw.h b/cctbx_sources/scitbx/lbfgsb/raw.h +index 21afed7..5b15055 100644 +--- a/cctbx_sources/scitbx/lbfgsb/raw.h ++++ b/cctbx_sources/scitbx/lbfgsb/raw.h +@@ -853,7 +853,7 @@ namespace raw { + if (iprint >= 99) { + printf(" LINE SEARCH%12d times; norm of step = %.15G\n", + iback, xstep); +- printf(fmt_2001, iter,f,sbgnrm); ++ printf("%s %i %f %f", fmt_2001, iter,f,sbgnrm); + if (iprint > 100) { + write_ref1(" X =", x); + write_ref1(" G =", g); +@@ -862,7 +862,7 @@ namespace raw { + else if (iprint > 0) { + int imod = iter % iprint; + if (imod == 0) { +- printf(fmt_2001, iter,f,sbgnrm); ++ printf("%s %i %f %f", fmt_2001, iter,f,sbgnrm); + } + } + if (iprint >= 1) { +@@ -967,9 +967,9 @@ namespace raw { + " 2 rounding error dominate computation.\n"; + if (task.substr(0,5) == "ERROR") goto lbl_999; + if (iprint >= 0) { +- printf(fmt_3003); +- printf(fmt_3004); +- printf(fmt_3005, n,iter,nfgv,nintol,nskip,nact,sbgnrm,f); ++ printf("%s", fmt_3003); ++ printf("%s", fmt_3004); ++ printf("%s %i %i %i %i %i %i %f %f", fmt_3005, n,iter,nfgv,nintol,nskip,nact,sbgnrm,f); + if (iprint >= 100) { + write_ref1(" X =", x); + } +@@ -977,40 +977,40 @@ namespace raw { + } + lbl_999: + if (iprint >= 0) { +- printf(fmt_3009, task.c_str()); ++ printf("%s %s", fmt_3009, task.c_str()); + if (info != 0) { +- if (info == -1) printf(fmt_9011); +- if (info == -2) printf(fmt_9012); +- if (info == -3) printf(fmt_9013); +- if (info == -4) printf(fmt_9014); +- if (info == -5) printf(fmt_9015); ++ if (info == -1) printf("%s", fmt_9011); ++ if (info == -2) printf("%s", fmt_9012); ++ if (info == -3) printf("%s", fmt_9013); ++ if (info == -4) printf("%s", fmt_9014); ++ if (info == -5) printf("%s", fmt_9015); + if (info == -6) { + printf(" Input nbd(%12d) is invalid.\n", k); + } + if (info == -7) { + printf(" l(%12d) > u(%12d). No feasible solution.\n", k, k); + } +- if (info == -8) printf(fmt_9018); +- if (info == -9) printf(fmt_9019); ++ if (info == -8) printf("%s", fmt_9018); ++ if (info == -9) printf("%s", fmt_9019); + } +- if (iprint >= 1) printf(fmt_3007, cachyt,sbtime,lnscht); +- printf(fmt_3008, time); ++ if (iprint >= 1) printf("%s %f %f %f", fmt_3007, cachyt,sbtime,lnscht); ++ printf("%s %f", fmt_3008, time); + if (iprint >= 1) { + if (info == -4 || info == -9) { +- printf(fmt_3002, ++ printf("%s %i %i %i %i %s %i %f %f", fmt_3002, + iter,nfgv,nint,nact,word.c_str(),iback,stp,xstep); // itfile + } +- printf(fmt_3009, task.c_str()); // itfile ++ printf("%s %s", fmt_3009, task.c_str()); // itfile + if (info != 0) { +- if (info == -1) printf(fmt_9011); // itfile +- if (info == -2) printf(fmt_9012); // itfile +- if (info == -3) printf(fmt_9013); // itfile +- if (info == -4) printf(fmt_9014); // itfile +- if (info == -5) printf(fmt_9015); // itfile +- if (info == -8) printf(fmt_9018); // itfile +- if (info == -9) printf(fmt_9019); // itfile ++ if (info == -1) printf("%s", fmt_9011); // itfile ++ if (info == -2) printf("%s", fmt_9012); // itfile ++ if (info == -3) printf("%s", fmt_9013); // itfile ++ if (info == -4) printf("%s", fmt_9014); // itfile ++ if (info == -5) printf("%s", fmt_9015); // itfile ++ if (info == -8) printf("%s", fmt_9018); // itfile ++ if (info == -9) printf("%s", fmt_9019); // itfile + } +- printf(fmt_3008, time); // itfile ++ printf("%s %f", fmt_3008, time); // itfile + } + } + } +@@ -3902,7 +3902,7 @@ namespace raw { + " refresh the lbfgs memory and restart the iteration.\n"; + if (info != 0) { + // singular triangular system detected; refresh the lbfgs memory. +- if(iprint >= 1) printf(fmt_1005); ++ if(iprint >= 1) printf("%s", fmt_1005); + info = 0; + col = 0; + head = 1; +@@ -3968,7 +3968,7 @@ namespace raw { + if (info != 0) { + // singular triangular system detected; + // refresh the lbfgs memory and restart the iteration. +- if(iprint >= 1) printf(fmt_1005); ++ if(iprint >= 1) printf("%s", fmt_1005); + info = 0; + col = 0; + head = 1; diff --git a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch new file mode 100644 index 000000000000..e54cfa16838b --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch @@ -0,0 +1,29 @@ + cctbx_sources/scitbx/array_family/detail/misc.h | 1 + + .../scitbx/fortran_io/details/istream_scanner.h | 2 +- + 2 files changed, 2 insertions(+), 1 deletions(-) + +diff --git a/cctbx_sources/scitbx/array_family/detail/misc.h b/cctbx_sources/scitbx/array_family/detail/misc.h +index 6ed881e..d7f7f52 100644 +--- a/cctbx_sources/scitbx/array_family/detail/misc.h ++++ b/cctbx_sources/scitbx/array_family/detail/misc.h +@@ -2,6 +2,7 @@ + #define SCITBX_ARRAY_FAMILY_MISC_H + + #include <scitbx/array_family/type_traits.h> ++#include <memory> + + namespace scitbx { namespace af { + +diff --git a/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h b/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h +index 8a0ac25..03a0e20 100644 +--- a/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h ++++ b/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h +@@ -32,7 +32,7 @@ class istream_scanner + } + + private: +- mutable std::basic_istream<CharType> &input; ++ std::basic_istream<CharType> &input; + mutable value_t current; + }; + diff --git a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch new file mode 100644 index 000000000000..96cb21531bbf --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch @@ -0,0 +1,154 @@ + .../scitbx/math/boost_python/distributions.cpp | 60 +++++++++++++------ + cctbx_sources/scitbx/rigid_body/spatial_lib.h | 1 + + cctbx_sources/scitbx/rigid_body/tardy.h | 4 +- + .../refinement/boost_python/weighting_schemes.cpp | 4 +- + .../smtbx/structure_factors/direct/standard_xray.h | 4 +- + 5 files changed, 48 insertions(+), 25 deletions(-) + +diff --git a/cctbx_sources/scitbx/math/boost_python/distributions.cpp b/cctbx_sources/scitbx/math/boost_python/distributions.cpp +index a676798..68818e7 100644 +--- a/cctbx_sources/scitbx/math/boost_python/distributions.cpp ++++ b/cctbx_sources/scitbx/math/boost_python/distributions.cpp +@@ -59,29 +59,51 @@ namespace { + { + typedef Distribution wt; + ++ #define NEW_MEMBER(name) \ ++ static FloatType name(wt const &self) { \ ++ return boost::math::name(self); \ ++ } ++ ++ NEW_MEMBER(mean); ++ NEW_MEMBER(median); ++ NEW_MEMBER(mode); ++ NEW_MEMBER(variance); ++ NEW_MEMBER(standard_deviation); ++ NEW_MEMBER(skewness); ++ NEW_MEMBER(kurtosis); ++ ++ #undef NEW_MEMBER ++ ++ #define NEW_MEMBER(name) \ ++ static FloatType name(wt const &self, FloatType arg) { \ ++ return boost::math::name(self, arg); \ ++ } ++ ++ NEW_MEMBER(pdf); ++ NEW_MEMBER(cdf); ++ NEW_MEMBER(quantile); ++ ++ #undef NEW_MEMBER ++ ++ static scitbx::af::shared<FloatType> quantiles(wt const &self, std::size_t n) { ++ return scitbx::math::quantiles<FloatType>(self, n); ++ } ++ + static void + wrap() + { + using namespace boost::python; +- def("mean", (FloatType(*)(wt const&)) boost::math::mean); +- def("median", (FloatType(*)(wt const&)) boost::math::median); +- def("mode", (FloatType(*)(wt const&)) boost::math::mode); +- def("variance", (FloatType(*)(wt const&)) boost::math::variance); +- def("standard_deviation", +- (FloatType(*)(wt const&)) boost::math::standard_deviation); +- def("skewness", (FloatType(*)(wt const&)) boost::math::skewness); +- def("kurtosis", (FloatType(*)(wt const&)) boost::math::kurtosis); +- def("pdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::pdf); +- def("cdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::cdf); +- def("quantile", (FloatType(*)(wt const&, FloatType const&)) +- boost::math::quantile); +- def("quantiles", +-#if BOOST_WORKAROUND(__EDG_VERSION__, BOOST_TESTED_AT(306)) +- (scitbx::af::shared<FloatType>(*)(wt const&, std::size_t)) quantiles +-#else +- quantiles<FloatType, wt> +-#endif +- ); ++ def("mean" , mean); ++ def("median" , median); ++ def("mode" , mode); ++ def("variance" , variance); ++ def("standard_deviation", standard_deviation); ++ def("skewness" , skewness); ++ def("kurtosis" , kurtosis); ++ def("pdf" , pdf); ++ def("cdf" , cdf); ++ def("quantile" , quantile); ++ def("quantiles" , quantiles); + } + }; + +diff --git a/cctbx_sources/scitbx/rigid_body/spatial_lib.h b/cctbx_sources/scitbx/rigid_body/spatial_lib.h +index a084f0f..e377292 100755 +--- a/cctbx_sources/scitbx/rigid_body/spatial_lib.h ++++ b/cctbx_sources/scitbx/rigid_body/spatial_lib.h +@@ -2,6 +2,7 @@ + #define SCITBX_RIGID_BODY_SPATIAL_LIB_H + + #include <scitbx/rotr3.h> ++#include <scitbx/rigid_body/matrix_helpers.h> + #include <scitbx/array_family/versa_matrix.h> + + namespace scitbx { namespace rigid_body { +diff --git a/cctbx_sources/scitbx/rigid_body/tardy.h b/cctbx_sources/scitbx/rigid_body/tardy.h +index 104f16b..a8f76cc 100755 +--- a/cctbx_sources/scitbx/rigid_body/tardy.h ++++ b/cctbx_sources/scitbx/rigid_body/tardy.h +@@ -346,7 +346,7 @@ namespace tardy { + unsigned nb = this->bodies_size(); + af::shared<af::small<ft, 7> > result((af::reserve(nb))); + af::shared<af::small<ft, 6> > +- tau_array = f_ext_as_tau(f_ext_array().const_ref()); ++ tau_array = this->f_ext_as_tau(f_ext_array().const_ref()); + for(unsigned ib=0;ib<nb;ib++) { + result.push_back( + this->bodies[ib]->joint->tau_as_d_e_pot_d_q(tau_array[ib])); +@@ -379,7 +379,7 @@ namespace tardy { + qdd_array() + { + if (!qdd_array_) { +- qdd_array_ = forward_dynamics_ab( ++ qdd_array_ = this->forward_dynamics_ab( + /*tau_array*/ af::const_ref<af::small<ft, 6> >(0, 0), + f_ext_array().const_ref(), + /*grav_accn*/ af::const_ref<ft>(0, 0)); +diff --git a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp +index ce0c27b..904e8d7 100644 +--- a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp ++++ b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp +@@ -25,9 +25,9 @@ namespace smtbx { namespace refinement { namespace least_squares { + : base_t(name, boost::python::no_init) + { + using namespace boost::python; +- def("__call__", &wt::operator(), ++ this->def("__call__", &wt::operator(), + (arg("fo_sq"), arg("sigma"), arg("fc_sq"))); +- def("__call__", weights, ++ this->def("__call__", weights, + (arg("fo_sq"), arg("sigmas"), arg("fc_sq"))); + } + }; +diff --git a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h +index 5e2df76..911bfde 100644 +--- a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h ++++ b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h +@@ -161,7 +161,7 @@ namespace smtbx { namespace structure_factors { namespace direct { + for (int k=0; k < hr_ht.groups.size(); ++k) { + hr_ht_group<float_type> const &g = hr_ht.groups[k]; + float_type hrx = g.hr * scatterer.site; +- complex_type f = exp_i_2pi(hrx + g.ht); ++ complex_type f = this->exp_i_2pi(hrx + g.ht); + if (scatterer.flags.use_u_aniso()) { + float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star); + f *= dw; +@@ -336,7 +336,7 @@ namespace smtbx { namespace structure_factors { namespace direct { + for (int k=0; k < hr_ht.groups.size(); ++k) { + hr_ht_group<float_type> const &g = hr_ht.groups[k]; + float_type hrx = g.hr * scatterer.site; +- complex_type f = exp_i_2pi(hrx + g.ht); ++ complex_type f = this->exp_i_2pi(hrx + g.ht); + float_type fa = f.real(), fb = f.imag(); + if (scatterer.flags.use_u_aniso()) { + float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star); diff --git a/sci-libs/cctbx/files/2010.03.29.2334-soname.patch b/sci-libs/cctbx/files/2010.03.29.2334-soname.patch new file mode 100644 index 000000000000..2c0efcabeb13 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-soname.patch @@ -0,0 +1,123 @@ +diff --git a/cctbx_sources/ccp4io_adaptbx/SConscript b/cctbx_sources/ccp4io_adaptbx/SConscript +index 4ff2232..2ee3991 100644 +--- a/cctbx_sources/ccp4io_adaptbx/SConscript ++++ b/cctbx_sources/ccp4io_adaptbx/SConscript +@@ -40,6 +40,7 @@ def replace_printf(file_name): + + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libccp4io.so.0.0"]) + env.Append(CCFLAGS=env_etc.ccp4io_defines) + env.Append(SHCCFLAGS=env_etc.ccp4io_defines) + env_etc.include_registry.append( +diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript +index 6ec7c93..7f2e788 100644 +--- a/cctbx_sources/cctbx/SConscript ++++ b/cctbx_sources/cctbx/SConscript +@@ -15,6 +15,7 @@ env_etc.cctbx_common_includes = [ + + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libcctbx.so.0.0"]) + env_etc.include_registry.append( + env=env, + paths=env_etc.cctbx_common_includes) +diff --git a/cctbx_sources/iotbx/mtz/SConscript b/cctbx_sources/iotbx/mtz/SConscript +index c0a4bb0..d3c1e45 100644 +--- a/cctbx_sources/iotbx/mtz/SConscript ++++ b/cctbx_sources/iotbx/mtz/SConscript +@@ -6,6 +6,7 @@ ccp4io_lib = getattr(env_etc, "ccp4io_lib", "cmtz") + env.Prepend(LIBS=["cctbx", ccp4io_lib]+env_etc.libm) + env.Append(CXXFLAGS=env_etc.ccp4io_defines) + env.Append(SHCXXFLAGS=env_etc.ccp4io_defines) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libiotbx_mtz.so.0.0"]) + env_etc.enable_more_warnings(env=env) + if (env_etc.static_libraries): builder = env.StaticLibrary + else: builder = env.SharedLibrary +diff --git a/cctbx_sources/iotbx/pdb/SConscript b/cctbx_sources/iotbx/pdb/SConscript +index c1415c8..9e1af8d 100644 +--- a/cctbx_sources/iotbx/pdb/SConscript ++++ b/cctbx_sources/iotbx/pdb/SConscript +@@ -2,6 +2,7 @@ Import("env_base", "env_etc") + + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libiotbx_pdb.so.0.0"]) + env_etc.enable_more_warnings(env=env) + env_etc.include_registry.append( + env=env, +diff --git a/cctbx_sources/mmtbx/masks/SConscript b/cctbx_sources/mmtbx/masks/SConscript +index e70ab3c..cf2f530 100755 +--- a/cctbx_sources/mmtbx/masks/SConscript ++++ b/cctbx_sources/mmtbx/masks/SConscript +@@ -17,7 +17,9 @@ builder( + target="#lib/mmtbx_masks", + source=lib_sources) + +-env = env.Clone() ++env = env.Clone( ++ SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libmmtbx_masks.so.0.0"]) + env.Prepend(LIBS=["mmtbx_masks", "iotbx_pdb", "cctbx_sgtbx_asu"]) + env.Program( target = "tst_mask", source="tst_mask.cpp") + +diff --git a/cctbx_sources/omptbx/SConscript b/cctbx_sources/omptbx/SConscript +index 43aac91..ce4b4f3 100644 +--- a/cctbx_sources/omptbx/SConscript ++++ b/cctbx_sources/omptbx/SConscript +@@ -7,6 +7,7 @@ env_etc.omptbx_include = os.path.dirname(env_etc.omptbx_dist) + + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libomptbx.so.0.0"]) + env_etc.include_registry.append( + env=env, + paths=[env_etc.omptbx_include]) +diff --git a/cctbx_sources/rstbx/SConscript b/cctbx_sources/rstbx/SConscript +index 2213c2f..cae7542 100644 +--- a/cctbx_sources/rstbx/SConscript ++++ b/cctbx_sources/rstbx/SConscript +@@ -15,6 +15,7 @@ env_etc.rstbx_common_includes = [ + ] + + env = env_base.Clone(SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,librstbx.so.0.0"]) + env.Append(LIBS=["cctbx"] + env_etc.libm) + env_etc.include_registry.append( + env=env, +diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript +index 6f221d0..c4698d8 100644 +--- a/cctbx_sources/scitbx/boost_python/SConscript ++++ b/cctbx_sources/scitbx/boost_python/SConscript +@@ -4,6 +4,7 @@ Import("env_scitbx_boost_python_ext") + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) + env_etc.enable_more_warnings(env=env) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_boost_python.so.0.0"]) + env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base) + env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base) + env.Append(LIBS=["boost_python"]) +diff --git a/cctbx_sources/scitbx/minpack/SConscript b/cctbx_sources/scitbx/minpack/SConscript +index 7c325cb..cc23a04 100644 +--- a/cctbx_sources/scitbx/minpack/SConscript ++++ b/cctbx_sources/scitbx/minpack/SConscript +@@ -3,6 +3,7 @@ Import("env_base", "env_etc") + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) + env_etc.enable_more_warnings(env=env) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_minipack.so.0.0"]) + env_etc.include_registry.append( + env=env, + paths=env_etc.scitbx_common_includes) +diff --git a/cctbx_sources/scitbx/slatec/SConscript b/cctbx_sources/scitbx/slatec/SConscript +index ca9b6da..9c79d47 100644 +--- a/cctbx_sources/scitbx/slatec/SConscript ++++ b/cctbx_sources/scitbx/slatec/SConscript +@@ -3,6 +3,7 @@ Import("env_base", "env_etc") + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) + env_etc.enable_more_warnings(env=env) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_slatec.so.0.0"]) + env.Append(LIBS=env_etc.libm) + if (env_etc.static_libraries): builder = env.StaticLibrary + else: builder = env.SharedLibrary diff --git a/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch b/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch new file mode 100644 index 000000000000..f6509260d313 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch @@ -0,0 +1,15 @@ +diff --git a/mmtbx/monomer_library/tst_server.py b/mmtbx/monomer_library/tst_server.py +index 519d203..91ba783 100644 +--- cctbx_sources/mmtbx/monomer_library/tst_server.py ++++ cctbx_sources/mmtbx/monomer_library/tst_server.py +@@ -86,8 +86,8 @@ def exercise(): + for base_code in ["A", "C", "G"]: + rna_atoms = srv.get_comp_comp_id_direct(base_code+"r").atom_dict() + dna_atoms = srv.get_comp_comp_id_direct(base_code+"d").atom_dict() +- for as,bs,c in [(rna_atoms,dna_atoms,"d"), (dna_atoms,rna_atoms,"r")]: +- for a in as.keys(): ++ for as_,bs,c in [(rna_atoms,dna_atoms,"d"), (dna_atoms,rna_atoms,"r")]: ++ for a in as_.keys(): + b = bs.get(a, None) + if (b is None): + print "Not in %s: %s" % (base_code+c, a) diff --git a/sci-libs/cctbx/metadata.xml b/sci-libs/cctbx/metadata.xml new file mode 100644 index 000000000000..3288d4956c5a --- /dev/null +++ b/sci-libs/cctbx/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + The Computational Crystallography Toolbox (cctbx) is being developed + as the open source component of the PHENIX system. The goal of + the PHENIX project is to advance automation of macromolecular structure + determination. PHENIX depends on the cctbx, but not vice versa. This + hierarchical approach enforces a clean design as a reusable library. + The cctbx is therefore also useful for small-molecule crystallography + and even general scientific applications. + </longdescription> + <upstream> + <remote-id type="sourceforge">cctbx</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/cdd+/Manifest b/sci-libs/cdd+/Manifest new file mode 100644 index 000000000000..435de08878d2 --- /dev/null +++ b/sci-libs/cdd+/Manifest @@ -0,0 +1,9 @@ +AUX cdd+-077a-gcc-5.patch 369 SHA256 6ae57cabdc68ce2de089144b9d2a07673e60e4a582b769401e3d6f826078ba84 SHA512 36804d2cf1f8ac137b2ef5b1991e5e73a2ab40f8391a813f07b3d1ba6d5556bf852f07f25567a3696f9c1fa5927ef23f3364125af50136d0954723fee8d80059 WHIRLPOOL 94092f9746ced2c1852d3cd7b63c14392fc10d318ba749d8e09fbd59fa50bd4950376559f95444a904945a4222cceb54b321caa0b44678455fdffbd48ef4b60a +AUX cdd+-077a-gentoo.patch 1141 SHA256 8a97bc1fc44397dfab71064807f2add136a30477018087a7ad648c54c1d839ab SHA512 7b05ac66c6b4205c5434dc63ca46f2fbd88c115fa3bdae92ad8014fe5c70daf256b24ec1d7a0f7697e78868f78afd3ea6d5e23ed294433c2507fd8b1be510e61 WHIRLPOOL 78506d5cb56d8d1aabbcaa704d15c120144913f5bde65736bb629771c3b47e2cfa245e1b32c82be7cce08c48405f8a68b96e5306352070e616559a3b0afde431 +AUX cdd+-077a-headers.patch 1993 SHA256 05dd3e77c3e27f07ee02ab35e9eb7206d214a9438c0bf630eaf52c476ae2b450 SHA512 8b141789efea76eba1256c0f9c882dc7920169c39b80040f8c7a0238cede399b69094cf3352b26c3996d0d9ced650c654cb12d07996d0c6466a7efa1069e609f WHIRLPOOL 4702f26ef696bcfb0ddac5de1d8223cb992f9b3280e6cf8c8b4eeb68941e547fb698aeb4db8044e541fdf87116acf0db2d769ad876046e91f0e6f9f61ee2d153 +AUX cdd+-077a-qa-const-char.patch 1469 SHA256 d9750fa6ac9dd90bd69d0dbfc9a7d7073f357b88b1ad67d37f65c491bfe20297 SHA512 fb9165442197cdbe5c1994d1759eed4c7948ce2fd89dc15b10012684be5749e9cdff548d0809f7dbf6f07141d608b71f990c10d4fbe089c73abeda8519158ab5 WHIRLPOOL 4f121cf09faac488f09d90e0e8b90eda3c18511f0126120ee8103caaf237acfd046420b7c0d3ff9ea78d3d7a67ef5a55013656b14d21c592a9cda6d08fe74078 +DIST cdd+-077a.tar.gz 186771 SHA256 bace5c6c62fc48938b04a7b80fc55935e1bfe56cfb0b80f803842173a40ad616 SHA512 cb151274adec502420e5e931d2f248d62b26d5797f7d55f6db9c947f8e9d715a864c88ad08ad2cd74ada237789de5ca3c49dc04dc55e63d4101f07cc1685ab12 WHIRLPOOL a36abf5d5654a786844543f78126d60ec9c0326966570674e63f02251aa2fce72a640eda5ad1893cd5b3e7592f53f0fbd96887107d4e53fcf15100e8a6bea73d +EBUILD cdd+-077a.ebuild 855 SHA256 c26aca05ca23f0360e0bf148559f43812cb02b72bbc38788901db23dd50fa60d SHA512 03c514c3bd410826e8a5c1ff69c35e397014fc40c9bd94ade0f5e06a876860ab942bd30b82dcfa675ce5455f6e35fcbaff229f7f2658ebdea046c5bde3f2f7b7 WHIRLPOOL 34618058f9a5aee3afd3316653f2ae860db2da200257a771384023ba092522e22441f0b5bb47dbaa852d76521ea9202ae45e4cff95864c15b04923761ef60f92 +MISC ChangeLog 2863 SHA256 736bf44f4a07558463f3e5840ab8485551072c6e08b855074abb1a8cf125dbb8 SHA512 fe5730a33da31b2b54a021df645decb78d781af09f99e29fcf775db2b85c009e147bbfcc5a475e1f11d67ca0cac4c41a0b0deb6801c91ca3f12d76ef1c3b8989 WHIRLPOOL 25d24a7dbcbd956f58d65ac5032b31b79ae64815276ea56aa69037e3b2afdaa613be3e8233a4702cc61fc8e1fe880f7eb3a248fa4a1ba3cbbb31d0810d864a31 +MISC ChangeLog-2015 756 SHA256 237122d9b6098f37f458a09d70c80dc1ecea62f42f5d4263882777e36155820e SHA512 0eff630bf31aa3ab597d48f6e1ac921088470673e529310dfe2237a7b68ca6e47c8d0188c3ca1e1d4efb2f0303417218b41468ca4a484ce2a7ee15e3011936c6 WHIRLPOOL e1b232d269d47debd825398dd35cf2c17b384b7b0bb84c2555ef92d73832e00f762a5a58ddb892f4a91d7fcc364d869a3fd2e2c63ea01d5a1a992a6cdb43156a +MISC metadata.xml 661 SHA256 653432af3decb7d7be85069bd82e9df761e4608d42d9a3477c6c60a7d63f8703 SHA512 cefc0b38a9d11cd66ef0646a3bad907d3fc4d78aa6cf24e594efd40b8114293c94255c3fea1bb54f66f5e1beeb6a732fe1809ffb62d4528ef3f63b6f7e4a73e8 WHIRLPOOL cf87f7af62267c805757fd5f8f1f697ab9381e01a6facdb7768f110757fef49488e46f96f815d380544cc07d8cb6a9ed573eff948f25b04eb6db0ebdec14f3f8 diff --git a/sci-libs/cdd+/cdd+-077a.ebuild b/sci-libs/cdd+/cdd+-077a.ebuild new file mode 100644 index 000000000000..ac7812bf9f08 --- /dev/null +++ b/sci-libs/cdd+/cdd+-077a.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +DESCRIPTION="Another implementation of the double description method" +HOMEPAGE="http://www.ifor.math.ethz.ch/~fukuda/cdd_home/" +SRC_URI="ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~arm x86" +IUSE="" + +DEPEND="dev-libs/gmp:0=" +RDEPEND="${DEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-headers.patch \ + "${FILESDIR}"/${P}-gentoo.patch \ + "${FILESDIR}"/${P}-gcc-5.patch \ + "${FILESDIR}"/${P}-qa-const-char.patch +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + LIBDIR="${EPREFIX}/usr/$(get_libdir)" \ + GMPLIBDIR="${EPREFIX}/usr/$(get_libdir)" \ + GMPINCLUDE="${EPREFIX}/usr/include" \ + all + +} + +src_install() { + dobin cddr+ cddf+ +} diff --git a/sci-libs/cdd+/files/cdd+-077a-gcc-5.patch b/sci-libs/cdd+/files/cdd+-077a-gcc-5.patch new file mode 100644 index 000000000000..cd2d32a8a31b --- /dev/null +++ b/sci-libs/cdd+/files/cdd+-077a-gcc-5.patch @@ -0,0 +1,14 @@ +Fix check for GCC version beyond major version 4. +Gentoo bug #569222 + +--- cdd+-077a/gmp_init.cc ++++ cdd+-077a/gmp_init.cc +@@ -31,7 +31,7 @@ + # define pm_gmp_reallocate std::__alloc::reallocate + #endif // gcc 3.3 + +-#if __GNUC__==3 && __GNUC_MINOR__==4 || __GNUC__==4 ++#if __GNUC__==3 && __GNUC_MINOR__==4 || __GNUC__>=4 + # include <ext/pool_allocator.h> + + namespace { diff --git a/sci-libs/cdd+/files/cdd+-077a-gentoo.patch b/sci-libs/cdd+/files/cdd+-077a-gentoo.patch new file mode 100644 index 000000000000..efe6d7035e99 --- /dev/null +++ b/sci-libs/cdd+/files/cdd+-077a-gentoo.patch @@ -0,0 +1,43 @@ +--- makefile.orig 2010-01-19 20:22:59.000000000 +0100 ++++ makefile 2010-01-19 20:52:01.000000000 +0100 +@@ -6,21 +6,21 @@ + #CC = /bin/cc + + # Location of gnu c++ library. +-#LIBDIR = /usr/lib +-LIBDIR = /usr/local/lib ++LIBDIR = /usr/lib ++#LIBDIR = /usr/local/lib + + # Location of gnu gmp library libgmp.a +-#GMPLIBDIR = /usr/lib +-GMPLIBDIR = /usr/local/lib ++GMPLIBDIR = /usr/lib ++#GMPLIBDIR = /usr/local/lib + + # Location of gnu gmp-library include file gmp.h +-#GMPINCLUDEDIR = /usr/include +-GMPINCLUDEDIR = /usr/local/include ++GMPINCLUDEDIR = /usr/include ++#GMPINCLUDEDIR = /usr/local/include + + # Compiler optimization/debug options + #OPTFLAGS = -g -static -O + #OPTFLAGS = -g -static -pg -O +-OPTFLAGS = -O3 ++#OPTFLAGS = -O3 + + ########## You shouldn't have to change anything after this point ########## + +@@ -29,9 +29,8 @@ + RATOBJ = gmp_init.o Integer.o Rational.o + RATEXE = cddr+ + +-CFLAGS = $(OPTFLAGS) -I$(INCLUDEDIR) -I$(GMPINCLUDEDIR) -I. $(GMPFLAG) +- +-LDFLAGS = -L$(LIBDIR) -L$(GMPLIBDIR) ++CFLAGS += -I$(INCLUDEDIR) -I$(GMPINCLUDEDIR) -I. $(GMPFLAG) ++LDFLAGS += -L$(LIBDIR) -L$(GMPLIBDIR) + + LIBS = -lstdc++ -l$(RATLIB) + diff --git a/sci-libs/cdd+/files/cdd+-077a-headers.patch b/sci-libs/cdd+/files/cdd+-077a-headers.patch new file mode 100644 index 000000000000..c6ceb93bfaad --- /dev/null +++ b/sci-libs/cdd+/files/cdd+-077a-headers.patch @@ -0,0 +1,69 @@ +Index: Integer.h +=================================================================== +RCS file: /home/imocvs/cdd+/Integer.h,v +retrieving revision 1.1.1.1 +diff -u -p -r1.1.1.1 Integer.h +--- Integer.h 2008/12/15 01:19:52 1.1.1.1 ++++ Integer.h 2008/12/15 01:24:04 +@@ -23,6 +23,7 @@ + #include <gmp_init.h> + #include <cctype> + #include <limits> ++#include <climits> + + class Integer; class Rational; + +Index: Rational.cc +=================================================================== +RCS file: /home/imocvs/cdd+/Rational.cc,v +retrieving revision 1.1.1.1 +diff -u -p -r1.1.1.1 Rational.cc +--- Rational.cc 2008/12/15 01:19:52 1.1.1.1 ++++ Rational.cc 2008/12/15 01:25:14 +@@ -17,6 +17,7 @@ + + #include <cctype> + #include "Rational.h" ++#include <cstring> + + Rational& Rational::set(const char* s) throw (gmp_error) + { +Index: Rational.h +=================================================================== +RCS file: /home/imocvs/cdd+/Rational.h,v +retrieving revision 1.1.1.1 +diff -u -p -r1.1.1.1 Rational.h +--- Rational.h 2008/12/15 01:19:52 1.1.1.1 ++++ Rational.h 2008/12/15 01:27:08 +@@ -17,6 +17,7 @@ + #define _POLYMAKE_GMP_RATIONAL_H "$Project: polymake $$Id$ + + #include <Integer.h> ++#include <cstring> + + #if __GNU_MP_VERSION < 4 + #define _tmp_little_Integer(x) \ +@@ -1178,7 +1179,7 @@ std::basic_ostream<char, Traits>& operat + Integer::little_buffer buf(s); + numerator(a).putstr(os.flags(), buf); + if (show_den) { +- char *den_buf=buf+strlen(buf); ++ char *den_buf=buf+std::strlen(buf); + *den_buf++ = '/'; + denominator(a).putstr(os.flags(), den_buf); + } +Index: gmp_init.cc +=================================================================== +RCS file: /home/imocvs/cdd+/gmp_init.cc,v +retrieving revision 1.1.1.1 +diff -u -p -r1.1.1.1 gmp_init.cc +--- gmp_init.cc 2008/12/15 01:19:52 1.1.1.1 ++++ gmp_init.cc 2008/12/15 01:23:45 +@@ -16,6 +16,7 @@ + #ident "$Project: polymake $$Id$ + + #include <memory> ++#include <cstring> + #include "gmp_init.h" + + #if defined(__GNUC__) diff --git a/sci-libs/cdd+/files/cdd+-077a-qa-const-char.patch b/sci-libs/cdd+/files/cdd+-077a-qa-const-char.patch new file mode 100644 index 000000000000..a2304725990f --- /dev/null +++ b/sci-libs/cdd+/files/cdd+-077a-qa-const-char.patch @@ -0,0 +1,47 @@ +Silence warnings produced by passing a string literal to a 'char*': + +cddio.C: In function ‘void SetWriteFileName(char*, char, char*)’: +cddio.C:103:20: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] + extension=".ine"; break; /* output file for ine data */ + +--- cdd+-077a/cdd.h ++++ cdd+-077a/cdd.h +@@ -185,8 +185,8 @@ + extern int output_digits; /* Float digits for output. Does not affect the computation. */ + + void SetInputFile(boolean *); +-void SetWriteFileName(DataFileType, char, char *); +-void SetReadFileName(DataFileType, char, char *); ++void SetWriteFileName(DataFileType, char, const char *); ++void SetReadFileName(DataFileType, char, const char *); + + myTYPE FABS(myTYPE); + void SetNumberType(string); +--- cdd+-077a/cddio.C ++++ cdd+-077a/cddio.C +@@ -90,10 +90,10 @@ + } + } + +-void SetWriteFileName(DataFileType fname, char cflag, char *fscript) ++void SetWriteFileName(DataFileType fname, char cflag, const char *fscript) + { + boolean quit=False; +- char *extension; ++ const char *extension; + DataFileType newname; + + switch (cflag) { +@@ -192,10 +192,10 @@ + if (DynamicWriteOn) printf("Open %s file %s.\n",fscript,fname); + } + +-void SetReadFileName(DataFileType fname, char cflag, char *fscript) ++void SetReadFileName(DataFileType fname, char cflag, const char *fscript) + { + boolean quit=False; +- char *extension; ++ const char *extension; + DataFileType newname; + + switch (cflag) { diff --git a/sci-libs/cdd+/metadata.xml b/sci-libs/cdd+/metadata.xml new file mode 100644 index 000000000000..1745610437d5 --- /dev/null +++ b/sci-libs/cdd+/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-mathematics@gentoo.org</email> + <name>Gentoo Mathematics Project</name> + </maintainer> + <longdescription> + The program cdd+ is a C++ implementation of the Double Description Method of Motzkin et al. for generating all + vertices (i.e. extreme points) and extreme rays of a general convex polyhedron in R^d given by a system of linear + inequalities: P = { x : A x <= b } where A is an m x d real matrix and b is a real m dimensional vector. + </longdescription> +</pkgmetadata> diff --git a/sci-libs/cddlib/Manifest b/sci-libs/cddlib/Manifest new file mode 100644 index 000000000000..b952037a9d1c --- /dev/null +++ b/sci-libs/cddlib/Manifest @@ -0,0 +1,11 @@ +AUX cdd_both_reps.c 6439 SHA256 a0a799dfffd38447cf4e513e92780ca89429abf0c2ea6d983811fdf856613e65 SHA512 5aaf99344a823f908ffb54dc5fa153a865f11c7a4fdcde8773627de794a55f376f78f8cc19e40f6e62aceeec2d855aedcf43b0d332dc3c7231356a43b6a6715e WHIRLPOOL 0afc3949188620cdad182528dd4c99e2c1361b31ba0ba8e7070439f470bfc2f9285f53880590ee45354c06f01feeda09ce65e8ed8efa6dfa8c80b1f66a3372c3 +AUX cddlib-094g-add-cdd_both_reps-binary.patch 1210 SHA256 f0a317406ef224f392813e94d2d92615e91c9e2303b812b3c4bdc3e73f22075a SHA512 c69c6d2ebbfbf132a287032ac1470fcce0c0d1e000dd96501f271ff200034567056d3948626023722c83082289f40122b0eacf35d10d2497f36ab226a9316348 WHIRLPOOL 3d7723421b10af94284291ebbd45202522a14cf57316f981081a4fdca5b677f21bef38ae431b2604b20b834f41be11d5de75cd7f581141dc1468948d91706346 +AUX cddlib-094h-add-cdd_both_reps-binary.patch 1601 SHA256 ec750d791829f3124787e2d4a376ff8316e179600505fee5513ca0e3320535d2 SHA512 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9bad11da28535e89323be8a456ba1c925c2bdc1e49f13b21bf6fe7eac00f752e93bce7e753794930eefce3886120b385e4f516320909c0482aafbf469dd2cb1c +MISC metadata.xml 1238 SHA256 9be90eff3a68c0fabe14e2eafdf53f0164533eb076662416665751fd8a438d05 SHA512 f9422c30988d6e2ef87f650906dc500fd3dc8203745c5a8e261dbce3dd2daa307c9e8245deb64dad70a594a92f78ec2add3d77aacc94d2490ac2e9c1bfe1e4b1 WHIRLPOOL 6abcdd244f366ce01e9fbf4b9c29051201052c2c09b7005f6da3aad1063af712f2e23125f8ecfed1597befa2bfce9869c954432d088cc780bdfc59db12049ce9 diff --git a/sci-libs/cddlib/cddlib-094g.ebuild b/sci-libs/cddlib/cddlib-094g.ebuild new file mode 100644 index 000000000000..6a37b6d4ec1e --- /dev/null +++ b/sci-libs/cddlib/cddlib-094g.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="C implementation of the Double Description Method of Motzkin et al" +HOMEPAGE="http://www.ifor.math.ethz.ch/~fukuda/cdd_home/" +SRC_URI="ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="amd64 ~arm ppc x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +DEPEND=">=dev-libs/gmp-4.2.2:0=" +RDEPEND="${DEPEND}" + +AUTOTOOLS_IN_SOURCE_BUILD="1" + +DOCS=( ChangeLog README ) + +PATCHES=( + "${FILESDIR}"/${P}-add-cdd_both_reps-binary.patch +) + +src_prepare() { + autotools-utils_src_prepare + + cp "${FILESDIR}"/cdd_both_reps.c "${S}"/src/ \ + || die "failed to copy source file" + ln -s "${S}"/src/cdd_both_reps.c "${S}"/src-gmp/cdd_both_reps.c \ + || die "failed to make symbolic link to source file" +} + +src_install() { + use doc && DOCS+=( doc/cddlibman.pdf doc/cddlibman.ps ) + + autotools-utils_src_install +} diff --git a/sci-libs/cddlib/cddlib-094h.ebuild b/sci-libs/cddlib/cddlib-094h.ebuild new file mode 100644 index 000000000000..d9dd28bdddb4 --- /dev/null +++ b/sci-libs/cddlib/cddlib-094h.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils + +DESCRIPTION="C implementation of the Double Description Method of Motzkin et al" +HOMEPAGE="https://www.inf.ethz.ch/personal/fukudak/cdd_home/" +SRC_URI="ftp://ftp.math.ethz.ch/users/fukudak/cdd/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~arm ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs tools" + +DEPEND="dev-libs/gmp:0=" +RDEPEND="${DEPEND}" + +DOCS=( ChangeLog README ) + +PATCHES=( + "${FILESDIR}"/${P}-add-cdd_both_reps-binary.patch + "${FILESDIR}"/${P}-enforce-no-gmp.patch +) + +src_prepare() { + default + sed -e 's|localdebug=dd_TRUE|localdebug=dd_FALSE|g' \ + -i lib-src/cddlp.c -i lib-src-gmp/cddlp.c -i lib-src-gmp/cddlp_f.c || die + cp "${FILESDIR}"/cdd_both_reps.c src || die + ln -s "${S}"/src/cdd_both_reps.c "${S}"/src-gmp/cdd_both_reps.c || die + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + use tools || rm "${ED}"/usr/bin/* + use static-libs || prune_libtool_files --all + use doc && dodoc doc/cddlibman.pdf +} diff --git a/sci-libs/cddlib/files/cdd_both_reps.c b/sci-libs/cddlib/files/cdd_both_reps.c new file mode 100644 index 000000000000..3de4247e3016 --- /dev/null +++ b/sci-libs/cddlib/files/cdd_both_reps.c @@ -0,0 +1,255 @@ +/* cdd_both_reps.c: compute reduced H and V representation of polytope + by Volker Braun <vbraun@stp.dias.ie> + + The input is taken from stdin and can be either a + H or V representation, not necessarily reduced. + + based on testcdd1.c, redcheck.c, and of course the cdd library + written by Komei Fukuda, fukuda@ifor.math.ethz.ch + Standard ftp site: ftp.ifor.math.ethz.ch, Directory: pub/fukuda/cdd +*/ + +/* This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. +*/ + +#include "setoper.h" +#include "cdd.h" +#include <stdio.h> +#include <stdlib.h> +#include <time.h> +#include <math.h> +#include <string.h> + + + + + +void compute_adjacency(dd_MatrixPtr Rep, dd_ErrorType* err_ptr) +{ + dd_SetFamilyPtr AdjacencyGraph; + if (*err_ptr != dd_NoError) return; + + switch (Rep->representation) { + case dd_Inequality: + printf("Facet graph\n"); + break; + case dd_Generator: + printf("Vertex graph\n"); + break; + case dd_Unspecified: + printf("unknown representation type!\n"); + default: + printf("This should be unreachable!\n"); + exit(2); + } + + /* Output adjacency of vertices/rays/lines */ + if (Rep->rowsize > 0) { /* workaround for bug with empty polyhedron */ + /* compute adjacent vertices/rays/lines */ + AdjacencyGraph = dd_Matrix2Adjacency(Rep, err_ptr); + if (*err_ptr == dd_NoError) { + dd_WriteSetFamily(stdout,AdjacencyGraph); + dd_FreeSetFamily(AdjacencyGraph); + } + } else { + printf("begin\n"); + printf(" 0 0\n"); + printf("end\n"); + } + + printf("\n"); +} + + +void minimal_Vrep_Hrep(dd_MatrixPtr M, + dd_MatrixPtr* Vrep_ptr, dd_MatrixPtr* Hrep_ptr, + dd_ErrorType* err_ptr) +{ + dd_PolyhedraPtr poly; + dd_rowindex newpos; + dd_rowset impl_linset,redset; + dd_MatrixPtr Vrep, Hrep; + + if (*err_ptr != dd_NoError) return; + + /* compute the second representation */ + poly = dd_DDMatrix2Poly(M, err_ptr); + if (*err_ptr != dd_NoError) return; + + if (*err_ptr == dd_NoError) { + /* compute canonical H-representation */ + Hrep = dd_CopyInequalities(poly); + if (Hrep->rowsize > 0) { /* workaround for bug with empty matrix */ + dd_MatrixCanonicalize(&Hrep, &impl_linset, &redset, &newpos, err_ptr); + if (*err_ptr == dd_NoError) { + set_free(redset); + set_free(impl_linset); + free(newpos); + } + } + if (*err_ptr == dd_NoError) (*Hrep_ptr) = Hrep; + } + + if (*err_ptr == dd_NoError) { + /* compute canonical V-representation */ + Vrep = dd_CopyGenerators(poly); + if (Vrep->rowsize > 0) { /* workaround for bug with empty matrix */ + dd_MatrixCanonicalize(&Vrep, &impl_linset, &redset, &newpos, err_ptr); + if (*err_ptr == dd_NoError) { + set_free(redset); + set_free(impl_linset); + free(newpos); + } + } + if (*err_ptr == dd_NoError) (*Vrep_ptr) = Vrep; + } + + dd_FreePolyhedra(poly); +} + + +void print_both_reps(dd_MatrixPtr Vrep, dd_MatrixPtr Hrep) +{ + /* Output V-representation */ + dd_WriteMatrix(stdout,Vrep); + printf("\n"); + + /* Output H-representation */ + dd_WriteMatrix(stdout,Hrep); + printf("\n"); +} + + +void compute_both_reps(dd_MatrixPtr M, dd_ErrorType* err_ptr) +{ + dd_MatrixPtr Vrep, Hrep; + minimal_Vrep_Hrep(M, &Vrep, &Hrep, err_ptr); + if (*err_ptr != dd_NoError) return; + + print_both_reps(Vrep, Hrep); + dd_FreeMatrix(Hrep); + dd_FreeMatrix(Vrep); +} + + +void compute_all(dd_MatrixPtr M, dd_ErrorType* err_ptr) +{ + dd_MatrixPtr Vrep, Hrep; + minimal_Vrep_Hrep(M, &Vrep, &Hrep, err_ptr); + if (*err_ptr != dd_NoError) return; + + print_both_reps(Vrep, Hrep); + compute_adjacency(Vrep, err_ptr); + compute_adjacency(Hrep, err_ptr); + dd_FreeMatrix(Hrep); + dd_FreeMatrix(Vrep); +} + + + +void usage(char *name) +{ + printf("No known option specified, I don't know what to do!\n" + "Usage:\n" + "%s --option\n" + "where --option is precisely one of the following:\n\n" + " --all: Compute everything.\n" + " This will compute minimal H-,V-representation and vertex and facet graph.\n" + "\n" + " --reps: Compute both a minimal H- and minimal V-representation.\n" + "\n" + " --adjacency: Compute adjacency information only.\n" + " The input is assumed to be a minimal representation, as, for example, computed\n" + " by --reps. Warning, you will not get the correct answer if the input\n" + " representation is not minimal! The output is the vertex or facet graph,\n" + " depending on the input.\n" + "\n" + "The input data is a H- or V-representation in cdd's ine/ext format and\n" + "is in each case read from stdin.\n", + name); +} + + +enum command_line_arguments { ALL, REPS, ADJACENCY }; + + +int parse_arguments(char* arg, enum command_line_arguments* option) +{ + if (strcmp(arg,"--all")==0) { + *option = ALL; + return 0; + } + if (strcmp(arg,"--reps")==0) { + *option = REPS; + return 0; + } + if (strcmp(arg,"--adjacency")==0) { + *option = ADJACENCY; + return 0; + } + printf("Unknown option: %s\n", arg); + return 1; +} + + +int main(int argc, char *argv[]) +{ + dd_ErrorType err=dd_NoError; + dd_MatrixPtr M; + enum command_line_arguments option; + + if (argc!=2 || parse_arguments(argv[1],&option)) { + usage(argv[0]); + return 0; + } + + dd_set_global_constants(); + + /* Read data from stdin */ + M = dd_PolyFile2Matrix(stdin, &err); + if (err != dd_NoError) { + printf("I was unable to parse the input data!\n"); + dd_WriteErrorMessages(stdout,err); + dd_free_global_constants(); + return 1; + } + + switch (option) { + case ALL: + compute_all(M,&err); + break; + case REPS: + compute_both_reps(M,&err); + break; + case ADJACENCY: + compute_adjacency(M,&err); + break; + default: + printf("unreachable option %d\n", option); + exit(3); /* unreachable */ + } + + /* cleanup */ + dd_FreeMatrix(M); + if (err != dd_NoError) { + dd_WriteErrorMessages(stdout,err); + } + + dd_free_global_constants(); + return 0; +} + + + diff --git a/sci-libs/cddlib/files/cddlib-094g-add-cdd_both_reps-binary.patch b/sci-libs/cddlib/files/cddlib-094g-add-cdd_both_reps-binary.patch new file mode 100644 index 000000000000..3aa5912b7460 --- /dev/null +++ b/sci-libs/cddlib/files/cddlib-094g-add-cdd_both_reps-binary.patch @@ -0,0 +1,41 @@ +--- src-gmp/Makefile.am 2009-01-26 09:30:16.000000000 +0000 ++++ src-gmp/Makefile.am 2009-10-04 10:36:17.000000000 +0100 +@@ -11,7 +11,8 @@ + testcdd2_gmp \ + testlp1_gmp \ + testlp2_gmp \ +-testlp3_gmp ++testlp3_gmp \ ++cdd_both_reps_gmp + #cddmathlink + + scdd_gmp_SOURCES = simplecdd.c +@@ -27,6 +28,7 @@ + testlp1_gmp_SOURCES = testlp1.c + testlp2_gmp_SOURCES = testlp2.c + testlp3_gmp_SOURCES = testlp3.c ++cdd_both_reps_gmp_SOURCES = cdd_both_reps.c + # cddmathlink_SOURCES = cddmathlink.c cddmlio.h cddmlio.c + + LDADD = ../lib-src-gmp/libcddgmp.la +--- src/Makefile.am 2009-01-26 09:30:03.000000000 +0000 ++++ src/Makefile.am 2009-10-04 10:36:17.000000000 +0100 +@@ -11,7 +11,8 @@ + testcdd2 \ + testlp1 \ + testlp2 \ +-testlp3 ++testlp3 \ ++cdd_both_reps + #cddmathlink + + scdd_SOURCES = simplecdd.c +@@ -27,6 +28,7 @@ + testlp1_SOURCES = testlp1.c + testlp2_SOURCES = testlp2.c + testlp3_SOURCES = testlp3.c ++cdd_both_reps_SOURCES = cdd_both_reps.c + # cddmathlink_SOURCES = cddmathlink.c cddmlio.h cddmlio.c + + LDADD = ../lib-src/libcdd.la + diff --git a/sci-libs/cddlib/files/cddlib-094h-add-cdd_both_reps-binary.patch b/sci-libs/cddlib/files/cddlib-094h-add-cdd_both_reps-binary.patch new file mode 100644 index 000000000000..ba9a909abb19 --- /dev/null +++ b/sci-libs/cddlib/files/cddlib-094h-add-cdd_both_reps-binary.patch @@ -0,0 +1,43 @@ +diff -up cddlib-094g/src-gmp/Makefile.am.orig cddlib-094g/src-gmp/Makefile.am +--- cddlib-094g/src-gmp/Makefile.am.orig 2012-07-05 13:30:30.982562213 -0400 ++++ cddlib-094g/src-gmp/Makefile.am 2012-07-05 13:31:14.576563881 -0400 +@@ -11,7 +11,8 @@ testcdd1_gmp \ + testcdd2_gmp \ + testlp1_gmp \ + testlp2_gmp \ +-testlp3_gmp ++testlp3_gmp \ ++cdd_both_reps_gmp + #cddmathlink + + scdd_gmp_SOURCES = simplecdd.c +@@ -27,6 +28,7 @@ testcdd2_gmp_SOURCES = tes + testlp1_gmp_SOURCES = testlp1.c + testlp2_gmp_SOURCES = testlp2.c + testlp3_gmp_SOURCES = testlp3.c ++cdd_both_reps_gmp_SOURCES = cdd_both_reps.c + # cddmathlink_SOURCES = cddmathlink.c cddmlio.h cddmlio.c + + LDADD = ../lib-src-gmp/libcddgmp.la +diff -up cddlib-094g/src-gmp/Makefile.in.orig cddlib-094g/src-gmp/Makefile.in +diff -up cddlib-094g/src/Makefile.am.orig cddlib-094g/src/Makefile.am +--- cddlib-094g/src/Makefile.am.orig 2012-07-05 13:34:07.449570501 -0400 ++++ cddlib-094g/src/Makefile.am 2012-07-05 13:34:32.128571446 -0400 +@@ -11,7 +11,8 @@ testshoot \ + testcdd2 \ + testlp1 \ + testlp2 \ +-testlp3 ++testlp3 \ ++cdd_both_reps + #cddmathlink + + scdd_SOURCES = simplecdd.c +@@ -27,6 +28,7 @@ testcdd2_SOURCES = testcdd + testlp1_SOURCES = testlp1.c + testlp2_SOURCES = testlp2.c + testlp3_SOURCES = testlp3.c ++cdd_both_reps_SOURCES = cdd_both_reps.c + # cddmathlink_SOURCES = cddmathlink.c cddmlio.h cddmlio.c + + LDADD = ../lib-src/libcdd.la diff --git a/sci-libs/cddlib/files/cddlib-094h-enforce-no-gmp.patch b/sci-libs/cddlib/files/cddlib-094h-enforce-no-gmp.patch new file mode 100644 index 000000000000..bab20025a793 --- /dev/null +++ b/sci-libs/cddlib/files/cddlib-094h-enforce-no-gmp.patch @@ -0,0 +1,37 @@ +Description: Don't link against gmp in the non-gmp version + Using AC_CHECK_LIB will add -lgmp to all children, but we don't want this + for the non-gmp variants. Instead, add -lgmp explicitly in gmp variants. +Author: Ximin Luo <infinity0@debian.org> +Forwarded: TBD +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/configure.in ++++ b/configure.in +@@ -14,8 +14,6 @@ + dnl AC_CHECK_LIB(g, main) + dnl Replace `main' with a function in -lstdc: + dnl AC_CHECK_LIB(stdc, main) +-dnl look for gmp: +-AC_CHECK_LIB(gmp, main) + + dnl Checks for header files. + AC_HEADER_STDC +--- a/lib-src-gmp/Makefile.am ++++ b/lib-src-gmp/Makefile.am +@@ -25,4 +25,4 @@ + setoper.h + + AM_CPPFLAGS = -I$(gmpincludedir) -DGMPRATIONAL +-AM_LDFLAGS = -version-info 0:0:0 ++AM_LDFLAGS = -lgmp -version-info 0:0:0 +--- a/src-gmp/Makefile.am ++++ b/src-gmp/Makefile.am +@@ -32,7 +32,7 @@ + # cddmathlink_SOURCES = cddmathlink.c cddmlio.h cddmlio.c + + LDADD = ../lib-src-gmp/libcddgmp.la +-AM_LDFLAGS = -L$(gmplibdir) ++AM_LDFLAGS = -lgmp -L$(gmplibdir) + INCLUDES = -I../lib-src-gmp + INCLUDES += -I$(gmpincludedir) + AM_CPPFLAGS = -DGMPRATIONAL diff --git a/sci-libs/cddlib/metadata.xml b/sci-libs/cddlib/metadata.xml new file mode 100644 index 000000000000..a93a12f9174f --- /dev/null +++ b/sci-libs/cddlib/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-mathematics@gentoo.org</email> + <name>Gentoo Mathematics Project</name> + </maintainer> + <longdescription lang="en"> + The C-library cddlib is a C implementation of the Double Description + Method of Motzkin et al. for generating all vertices (i.e. extreme points) + and extreme rays of a general convex polyhedron in R^d given by a system + of linear inequalities: + + P = { x=(x1, ..., xd)^T : b - A x >= 0 } + + where A is a given m x d real matrix, b is a given m-vector + and 0 is the m-vector of all zeros. + + The program can be used for the reverse operation (i.e. convex hull + computation). This means that one can move back and forth between + an inequality representation and a generator (i.e. vertex and ray) + representation of a polyhedron with cdd. Also, cdd can solve a linear + programming problem, i.e. a problem of maximizing and minimizing + a linear function over P. + </longdescription> + <use> + <flag name="tools">Add a few executables and tests for cddlib</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/cdf/Manifest b/sci-libs/cdf/Manifest new file mode 100644 index 000000000000..ab7076e392ec --- /dev/null +++ b/sci-libs/cdf/Manifest @@ -0,0 +1,25 @@ +AUX 50cdf 124 SHA256 030452ff70f6c05eca8776976b7f2ab15c74a189065a6dda1a7b8eb32de953a2 SHA512 4fe515d03379f2b6e1723c771f73e65be9f67365a46e75dbeb3358bbdc6f3446b91efd989363bf229b7ae93a446ddedeefd883a0d59d28c1480a10a8994eeadc WHIRLPOOL f017286eee25e2bfc081fe8d9eb85e30207adedfac4a3687f73a71d2c880e13db84bbf7d83b3d45d929f32b175a4feed449805f09d856a43c506a22f1cfad9f6 +AUX cdf-3.2-soname.patch 738 SHA256 df148aad093d5ac4a51e2d2805f36e3fb3156979a4b1cff34d8e9ba2619741ff SHA512 f3bb09e43b3b36ed346dc7690cc0c75a28e8dcfb2c1ebbf8a0577abdc2d15bbcbce7b0da9c5de23ef65e669bd118692db498aef230e9395dd4b67dba48258a8d WHIRLPOOL 5771aebab646b35bca54ded793a5428dfa22c528e062f60041e0d9cdd60b2ddf0f796081d025675020b6558313362d063e2a6a06180101dbcca7cdd2591942b7 +AUX cdf-3.4-Makefile.patch 3838 SHA256 271962757be1d5f9f87aea8f4f0c4cd1fea44f0297231e2ad79dc945eca3c1ff SHA512 f8eb1b78b5a8e466dff38fa8108ac7316bd171e50e7e9125a99b10482994f02b86656d2d3e34a29c1a384beab6c0fd97ddf6e4697c18657d189620a9efcd1e47 WHIRLPOOL 3fcfa15abe8f69934c461c2d3f172b441eefe0cb37b54d66bd1c9b98a8d20bcae96d15766b22a6f3e210ce4a8ce0871f91a4bed1ed4a4b9d9e944f386d420158 +AUX cdf-3.5.0.2-Makefile.patch 3973 SHA256 e9c8df363f40aa0004d30b8d6bded4b453589cf8a114949506c7bada89a4cd08 SHA512 9842d43d8e2910f8d7cc00c27711f84cde622ab69084ce1c798625475034b73db857410d6fc1311933512bb3a235cfe2fb0808d2eebfc6165e3962e04aaed4e1 WHIRLPOOL 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SHA512 cbc8a4b6237632147de24c0eecaaff0f7fa6551eec08f68ebc72c79aff71a99608c309874bd07e9dca6203868171159556a29a7669ecb7e45e60a5cef8d81cb4 WHIRLPOOL 35a01d1cae36d683c232fc3de779c3541b209d303edebdec254eebbba88b10063cd632d0a36bf18b82f47e002695ad858801359b75af7fbf7b1282a1f97ea575 +DIST cdf34frm.pdf 1968381 SHA256 a725ee218c00fd544fdce4c7868d49b1c6128077ba60c2eebf19d7357bfbb8a4 SHA512 c5402db80c05192430e1ca7142d356a8224c52f128fe8c1be937767623c12a7ed55d7afaa0955a00e9ebcace87ba5fed977fc8020a71cdac40fb44326c5f8f65 WHIRLPOOL 7ce91654405d8e80c81b775d931fdf676b00987406fc608df19f69278a5f362f83c30c6e8c4986bd064f1f32f3ce48fb03e2cd8e39a785fa53335a95c4a83d7d +DIST cdf34ifd.pdf 415359 SHA256 3bf7b3ec80c8be85425bb632a9da34142eabc7a26f5c1cdb6208eb47095922ec SHA512 1ab42f8677fbbb7cb477c6cbbfe632a8569c6a78fee07dd32c42f549b7d451faaf0ca61ba03f2ea5ba4de2a3a71cc40e4de6ca3dcf86b7caef7594cefc9f2246 WHIRLPOOL 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+MY_P="${MY_DP}_$(get_version_component_range 3)" + +DESCRIPTION="Common Data Format I/O library for multi-dimensional data sets" +HOMEPAGE="http://cdf.gsfc.nasa.gov/" +SRC_BASE="ftp://cdaweb.gsfc.nasa.gov/pub/${PN}/dist/${MY_P}/unix" + +SRC_URI="${SRC_BASE}/${MY_P}-dist-${PN}.tar.gz + java? ( ${SRC_BASE}/${MY_P}-dist-java.tar.gz ) + doc? ( + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}crm.pdf + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}frm.pdf + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}ifd.pdf + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}prm.pdf + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}ug.pdf + java? ( ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}jrm.pdf ) + )" + +LICENSE="CDF" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="doc examples java ncurses static-libs" + +RDEPEND=" + java? ( >=virtual/jre-1.5:= ) + ncurses? ( sys-libs/ncurses:0= ) + " +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}-dist" + +src_prepare() { + # respect cflags, remove useless scripts + epatch \ + "${FILESDIR}"/${PN}-3.4-Makefile.patch \ + "${FILESDIR}"/${PN}-3.2-soname.patch + # use proper lib dir + sed -i \ + -e "s:\$(INSTALLDIR)/lib:\$(INSTALLDIR)/$(get_libdir):g" \ + Makefile || die "sed failed" +} + +src_compile() { + PV_SO=${PV:0:1} + emake \ + OS=linux \ + CC=$(tc-getCC) \ + ENV=gnu \ + SHARED=yes \ + SHAREDEXT_linux=so.${PV_SO} \ + CURSESLIB_linux_gnu="$(usex ncurses "$($(tc-getPKG_CONFIG) --libs ncurses)" "")" \ + CURSES=$(usex ncurses) \ + ${myconf} \ + all + + if use java; then + export CDF_BASE="${S}" + export CDF_LIB="${S}/src/lib" + cd cdfjava/jni + $(tc-getCC) \ + ${CFLAGS} -fPIC \ + -I${CDF_BASE}/src/include \ + -I$(java-config -O)/include \ + -I$(java-config -O)/include/linux \ + -c cdfNativeLibrary.c \ + -o cdfNativeLibrary.o \ + || die "compiling java lib failed" + $(tc-getCC) \ + ${LDFLAGS} \ + -shared cdfNativeLibrary.o \ + -Wl,-soname=libcdfNativeLibrary.so.${PV_SO} \ + -L${CDF_LIB} -lcdf -lm \ + -o libcdfNativeLibrary.so.${PV_SO} \ + || die "linking java lib failed" + fi +} + +src_test() { + emake -j1 test +} + +src_install() { + dodir /usr/bin /usr/$(get_libdir) + # -j1 (fragile non-autotooled make) + emake -j1 \ + INSTALLDIR="${ED}/usr" \ + SHAREDEXT=so.${PV_SO} \ + install + dosym libcdf.so.${PV_SO} /usr/$(get_libdir)/libcdf.so + use static-libs || rm "${ED}"/usr/$(get_libdir)/libcdf.a + dodoc Release.notes CHANGES.txt Welcome.txt + doenvd "${FILESDIR}"/50cdf + + if use doc; then + dodoc "${DISTDIR}"/${MY_DP}{crm,frm,ifd,prm,ug}.pdf + use java && dodoc "${DISTDIR}"/${MY_DP}jrm.pdf + fi + + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins samples/* + fi + + if use java; then + cd cdfjava || die + dolib.so jni/libcdfNativeLibrary.so.${PV_SO} + dosym libcdfNativeLibrary.so.${PV_SO} \ + /usr/$(get_libdir)/libcdfNativeLibrary.so + java-pkg_dojar */*.jar + if use examples; then + insinto /usr/share/doc/${PF}/examples/java + doins examples/* + fi + fi +} diff --git a/sci-libs/cdf/cdf-3.5.0.2.ebuild b/sci-libs/cdf/cdf-3.5.0.2.ebuild new file mode 100644 index 000000000000..9956ff0e3fa8 --- /dev/null +++ b/sci-libs/cdf/cdf-3.5.0.2.ebuild @@ -0,0 +1,122 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils java-pkg-opt-2 multilib toolchain-funcs versionator + +MY_DP="${PN}$(get_version_component_range 1)$(get_version_component_range 2)" +MY_P="${MY_DP}_$(get_version_component_range 3)" + +DESCRIPTION="Common Data Format I/O library for multi-dimensional data sets" +HOMEPAGE="http://cdf.gsfc.nasa.gov/" +SRC_BASE="http://cdaweb.gsfc.nasa.gov/pub/software/${PN}/dist/${MY_P}/unix/" + +SRC_URI="${SRC_BASE}/${MY_P}-dist-${PN}.tar.gz + java? ( ${SRC_BASE}/${MY_P}-dist-java.tar.gz ) + doc? ( + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}0crm.pdf + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}0frm.pdf + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}ifd.pdf + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}0prm.pdf + ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}0ug.pdf + java? ( ${SRC_BASE}/${MY_DP}_documentation/${MY_DP}0jrm.pdf ) + )" + +LICENSE="CDF" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples java ncurses static-libs" + +RDEPEND=" + java? ( >=virtual/jre-1.5:= ) + ncurses? ( sys-libs/ncurses:0= ) + " +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}-dist" + +src_prepare() { + # respect cflags, remove useless scripts + epatch \ + "${FILESDIR}"/${P}-Makefile.patch \ + "${FILESDIR}"/${PN}-3.2-soname.patch + # use proper lib dir + sed -i \ + -e "s:\$(INSTALLDIR)/lib:\$(INSTALLDIR)/$(get_libdir):g" \ + Makefile || die "sed failed" +} + +src_compile() { + PV_SO=${PV:0:1} + emake \ + OS=linux \ + CC=$(tc-getCC) \ + ENV=gnu \ + SHARED=yes \ + SHAREDEXT_linux=so.${PV_SO} \ + CURSESLIB_linux_gnu="$(usex ncurses "$($(tc-getPKG_CONFIG) --libs ncurses)" "")" \ + CURSES=$(usex ncurses) \ + ${myconf} \ + all + + if use java; then + export CDF_BASE="${S}" + export CDF_LIB="${S}/src/lib" + cd cdfjava/jni + $(tc-getCC) \ + ${CFLAGS} -fPIC \ + -I${CDF_BASE}/src/include \ + -I$(java-config -O)/include \ + -I$(java-config -O)/include/linux \ + -c cdfNativeLibrary.c \ + -o cdfNativeLibrary.o \ + || die "compiling java lib failed" + $(tc-getCC) \ + ${LDFLAGS} \ + -shared cdfNativeLibrary.o \ + -Wl,-soname=libcdfNativeLibrary.so.${PV_SO} \ + -L${CDF_LIB} -lcdf -lm \ + -o libcdfNativeLibrary.so.${PV_SO} \ + || die "linking java lib failed" + fi +} + +src_test() { + emake -j1 test +} + +src_install() { + dodir /usr/bin /usr/$(get_libdir) + # -j1 (fragile non-autotooled make) + emake -j1 \ + INSTALLDIR="${ED}/usr" \ + SHAREDEXT=so.${PV_SO} \ + install + dosym libcdf.so.${PV_SO} /usr/$(get_libdir)/libcdf.so + use static-libs || rm "${ED}"/usr/$(get_libdir)/libcdf.a + dodoc Release.notes CHANGES.txt Welcome.txt + doenvd "${FILESDIR}"/50cdf + + if use doc; then + dodoc "${DISTDIR}"/${MY_DP}{0{crm,frm,prm,ug},ifd}.pdf + use java && dodoc "${DISTDIR}"/${MY_DP}jrm.pdf + fi + + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins samples/* + fi + + if use java; then + cd cdfjava || die + dolib.so jni/libcdfNativeLibrary.so.${PV_SO} + dosym libcdfNativeLibrary.so.${PV_SO} \ + /usr/$(get_libdir)/libcdfNativeLibrary.so + java-pkg_dojar */*.jar + if use examples; then + insinto /usr/share/doc/${PF}/examples/java + doins examples/* + fi + fi +} diff --git a/sci-libs/cdf/files/50cdf b/sci-libs/cdf/files/50cdf new file mode 100644 index 000000000000..d967cbee6f22 --- /dev/null +++ b/sci-libs/cdf/files/50cdf @@ -0,0 +1,5 @@ +CDF_BASE=/usr +CDF_INC=${CDF_BASE}/include +CDF_LIB=${CDF_BASE}/lib +CDF_BIN=${CDF_BASE}/bin +CDF_HELP=${CDF_BASE}/lib/cdf/help diff --git a/sci-libs/cdf/files/cdf-3.2-soname.patch b/sci-libs/cdf/files/cdf-3.2-soname.patch new file mode 100644 index 000000000000..e4f28617faca --- /dev/null +++ b/sci-libs/cdf/files/cdf-3.2-soname.patch @@ -0,0 +1,22 @@ +--- src/lib/Makefile.orig 2007-12-03 17:47:58.476149933 +0000 ++++ src/lib/Makefile 2007-12-03 17:50:34.353032850 +0000 +@@ -94,7 +94,7 @@ + + shared.yes: libcdf.$(SHAREDEXT) + +-libcdf.so \ ++libcdf.$(SHAREDEXT) \ + libcdf.dylib \ + libcdf.sl: $(OBJs) + @if [ -f $@ ] ; then rm $@ ; else $(NULL) ; fi +@@ -102,8 +102,8 @@ + echo $(LD) $(LDFLAGS) -o $@ $(OBJs) $(SYSLIBS); \ + $(LD) $(LDFLAGS) -o $@ $(OBJs) $(SYSLIBS); \ + else \ +- echo $(LD) $(LDFLAGS) -o $@ $(OBJs) $(SYSLIBS); \ +- $(LD) $(LDFLAGS) -o $@ $(OBJs) $(SYSLIBS); \ ++ echo $(LD) $(LDFLAGS) -Wl,-soname,libcdf.$(SHAREDEXT) -o $@ $(OBJs) $(SYSLIBS); \ ++ $(LD) $(LDFLAGS) -Wl,-soname,libcdf.$(SHAREDEXT) -o $@ $(OBJs) $(SYSLIBS); \ + fi + + libcdf.o: $(OBJs) diff --git a/sci-libs/cdf/files/cdf-3.4-Makefile.patch b/sci-libs/cdf/files/cdf-3.4-Makefile.patch new file mode 100644 index 000000000000..4a6c0a0ef266 --- /dev/null +++ b/sci-libs/cdf/files/cdf-3.4-Makefile.patch @@ -0,0 +1,102 @@ +diff -Nur cdf34_1-dist.orig/Makefile cdf34_1-dist/Makefile +--- cdf34_1-dist.orig/Makefile 2012-06-19 06:05:21.000000000 -0700 ++++ cdf34_1-dist/Makefile 2012-08-03 10:11:38.672992055 -0700 +@@ -715,17 +715,17 @@ + "PIC=$(PIC_$(OS)_$(ENV))" \ + "CCx=$(CC_$(OS)_$(ENV))" \ + "LDx=$(LD_$(OS)_$(ENV))" \ +-"COPTIONS=$(UCOPTIONS) $(COPTIONS_$(OS)_$(ENV))" \ ++"COPTIONS=$(CFLAGS) $(COPTIONS_$(OS)_$(ENV))" \ + "SYSLIBS=$(SYSLIBSshr_$(OS)_$(ENV))" \ + "SHAREDEXT=$(SHAREDEXT_$(OS))" \ +-"LDOPTIONS=$(LDOPTIONS_$(OS)_$(ENV))" \ ++"LDOPTIONS=$(LDFLAGS) $(LDOPTIONS_$(OS)_$(ENV))" \ + "AROPTIONS=$(AROPTIONS_$(OS))" \ + "RANLIB=$(RANLIB_$(OS))" \ + all + @cd $(TOOLSsrcDIR); $(MAKE) \ + "CURSES=$(AND.$(CURSES).$(CURSES_$(OS)_$(ENV)))" \ + "CCx=$(CC_$(OS)_$(ENV))" \ +-"COPTIONS=$(COPTIONS_$(OS)_$(ENV))" \ ++"COPTIONS=$(CFLAGS) $(COPTIONS_$(OS)_$(ENV))" \ + "COPTIONSld=$(COPTIONSld_$(OS)_$(ENV))" \ + "SYSLIBS=$(SYSLIBSexe_$(OS)_$(ENV))" \ + "CURSESLIB=$(CURSESLIB_$(OS)_$(ENV))" \ +@@ -735,9 +735,9 @@ + "FCx=$(FC_$(OS))" \ + "CCx=$(CC_$(OS)_$(ENV))" \ + "SHARED=$(AND.$(SHARED).$(SHARED_$(OS)))" \ +-"FOPTIONS=$(FOPTIONS_$(OS)) $(FOPTIONS_$(OS)_$(ENV))" \ ++"FOPTIONS=$(FFLAGS) $(FOPTIONS_$(OS)) $(FOPTIONS_$(OS)_$(ENV))" \ + "FOPTIONSld=$(FOPTIONSld_$(OS)) $(FOPTIONSld_$(OS)_$(ENV))" \ +-"COPTIONS=$(COPTIONS_$(OS)_$(ENV))" \ ++"COPTIONS=$(CFLAGS) $(COPTIONS_$(OS)_$(ENV))" \ + "COPTIONSld=$(COPTIONSld_$(OS)_$(ENV))" \ + "SYSLIBS=$(SYSLIBSexe_$(OS)_$(ENV))" \ + "SHAREDEXT=$(SHAREDEXT_$(OS))" \ +@@ -773,12 +773,17 @@ + install.all: install.definitions install.include install.lib \ + install.tools install.help_ notify.user copy.leapseconds + +-install.definitions: create.bin copy.definitions change.definitions ++install.definitions: create.bin + install.include: create.include copy.include + install.tools: create.bin copy.tools + install.help_: create.help copy.help + + install.lib: create.lib copy.lib.a ++ @if [ -f $(LIBsrcDIR)/libcdf.$(SHAREDEXT) ] ; then \ ++ $(MAKE) "INSTALLDIR=$(INSTALLDIR)" install.lib.so ; \ ++ else \ ++ $(NULL) ; \ ++ fi + @if [ -f $(LIBsrcDIR)/libcdf.so ] ; then \ + $(MAKE) "INSTALLDIR=$(INSTALLDIR)" install.lib.so ; \ + else \ +@@ -884,8 +889,8 @@ + cp $(INCsrcDIR)/cdfconfig.h $(INSTALLDIR)/include + + copy.lib.so: +- @echo cp $(LIBsrcDIR)/libcdf.so $(INSTALLDIR)/lib +- cp $(LIBsrcDIR)/libcdf.so $(INSTALLDIR)/lib ++ @echo cp $(LIBsrcDIR)/libcdf.$(SHAREDEXT) $(INSTALLDIR)/lib ++ cp $(LIBsrcDIR)/libcdf.$(SHAREDEXT) $(INSTALLDIR)/lib + + copy.lib.sl: + @echo cp $(LIBsrcDIR)/libcdf.sl $(INSTALLDIR)/lib +@@ -1964,15 +1969,15 @@ + show.supported: + @echo SHARED is $(SUPPORTED.$(SHARED_$(OS))) + @echo CURSES is $(SUPPORTED.$(CURSES_$(OS)_$(ENV))) +- @echo FOPTIONS=$(FOPTIONS_$(OS)) ++ @echo FOPTIONS=$(FFLAGS) $(FOPTIONS_$(OS)) + @echo FOPTIONSld=$(FOPTIONSld_$(OS)) + @echo SHAREDEXT=$(SHAREDEXT_$(OS)) +- @echo LDOPTIONSlibcdf=$(LDOPTIONS_$(OS)_$(ENV)) ++ @echo LDOPTIONSlibcdf=$(LDFLAGS) $(LDOPTIONS_$(OS)_$(ENV)) + @echo RANLIB=$(RANLIB_$(OS)) + @echo FCx=$(FC_$(OS)) + @echo CCx=$(CC_$(OS)_$(ENV)) + @echo PIC=$(PIC_$(OS)_$(ENV)) +- @echo COPTIONS=$(COPTIONS_$(OS)_$(ENV)) ++ @echo COPTIONS=$(CFLAGS) $(COPTIONS_$(OS)_$(ENV)) + @echo COPTIONSld=$(COPTIONSld_$(OS)_$(ENV)) + @echo CURSESLIB=$(CURSESLIB_$(OS)_$(ENV)) + @echo SYSLIBSexe=$(SYSLIBSexe_$(OS)_$(ENV)) +diff -Nur cdf34_1-dist.orig/src/tools/Makefile cdf34_1-dist/src/tools/Makefile +--- cdf34_1-dist.orig/src/tools/Makefile 2012-06-15 09:22:16.000000000 -0700 ++++ cdf34_1-dist/src/tools/Makefile 2012-08-03 10:11:38.685992724 -0700 +@@ -35,10 +35,10 @@ + INCLUDEcdf= ../include + + CC=$(CCx) +-CFLAGS=$(COPTIONS) -I$(INCLUDEcdf) +-CFLAGSld=$(COPTIONSld) ++CFLAGS:=$(CFLAGS) $(COPTIONS) -I$(INCLUDEcdf) ++CFLAGSld=$(LDFLAGS) $(COPTIONSld) + +-LIBCDFa=../lib/libcdf.a ++LIBCDFa=../lib/libcdf.so.3 + LIBs1=$(LIBCDFa) $(SYSLIBS) + LIBs2=$(LIBCDFa) $(CURSESLIB) $(SYSLIBS) + diff --git a/sci-libs/cdf/files/cdf-3.5.0.2-Makefile.patch b/sci-libs/cdf/files/cdf-3.5.0.2-Makefile.patch new file mode 100644 index 000000000000..3bab69dfc6ac --- /dev/null +++ b/sci-libs/cdf/files/cdf-3.5.0.2-Makefile.patch @@ -0,0 +1,110 @@ + Makefile | 27 ++++++++++++++++----------- + src/tools/Makefile | 6 +++--- + 2 files changed, 19 insertions(+), 14 deletions(-) + +diff --git a/Makefile b/Makefile +index 7f240db..222c4f1 100644 +--- a/Makefile ++++ b/Makefile +@@ -771,17 +771,17 @@ all + "PIC=$(PIC_$(OS)_$(ENV))" \ + "CCx=$(CC_$(OS)_$(ENV))" \ + "LDx=$(LD_$(OS)_$(ENV))" \ +-"COPTIONS=$(UCOPTIONS) $(COPTIONS_$(OS)_$(ENV))" \ ++"COPTIONS=$(CFLAGS) $(COPTIONS_$(OS)_$(ENV))" \ + "SYSLIBS=$(SYSLIBSshr_$(OS)_$(ENV))" \ + "SHAREDEXT=$(SHAREDEXT_$(OS))" \ +-"LDOPTIONS=$(LDOPTIONS_$(OS)_$(ENV))" \ ++"LDOPTIONS=$(LDFLAGS) $(LDOPTIONS_$(OS)_$(ENV))" \ + "AROPTIONS=$(AROPTIONS_$(OS))" \ + "RANLIB=$(RANLIB_$(OS))" \ + all + @cd $(TOOLSsrcDIR); $(MAKE) \ + "CURSES=$(AND.$(CURSES).$(CURSES_$(OS)_$(ENV)))" \ + "CCx=$(CC_$(OS)_$(ENV))" \ +-"COPTIONS=$(COPTIONS_$(OS)_$(ENV))" \ ++"COPTIONS=$(CFLAGS) $(COPTIONS_$(OS)_$(ENV))" \ + "COPTIONSld=$(COPTIONSld_$(OS)_$(ENV))" \ + "SYSLIBS=$(SYSLIBSexe_$(OS)_$(ENV))" \ + "CURSESLIB=$(CURSESLIB_$(OS)_$(ENV))" \ +@@ -791,9 +791,9 @@ all + "FCx=$(FC_$(OS))" \ + "CCx=$(CC_$(OS)_$(ENV))" \ + "SHARED=$(AND.$(SHARED).$(SHARED_$(OS)))" \ +-"FOPTIONS=$(FOPTIONS_$(OS)) $(FOPTIONS_$(OS)_$(ENV))" \ ++"FOPTIONS=$(FFLAGS) $(FOPTIONS_$(OS)) $(FOPTIONS_$(OS)_$(ENV))" \ + "FOPTIONSld=$(FOPTIONSld_$(OS)) $(FOPTIONSld_$(OS)_$(ENV))" \ +-"COPTIONS=$(COPTIONS_$(OS)_$(ENV))" \ ++"COPTIONS=$(CFLAGS) $(COPTIONS_$(OS)_$(ENV))" \ + "COPTIONSld=$(COPTIONSld_$(OS)_$(ENV))" \ + "SYSLIBS=$(SYSLIBSexe_$(OS)_$(ENV))" \ + "SHAREDEXT=$(SHAREDEXT_$(OS))" \ +@@ -829,12 +829,17 @@ install: install.$(PART) + install.all: install.definitions install.include install.lib \ + install.tools install.help_ notify.user copy.leapseconds + +-install.definitions: create.bin copy.definitions change.definitions ++install.definitions: create.bin + install.include: create.include copy.include + install.tools: create.bin copy.tools + install.help_: create.help copy.help + + install.lib: create.lib copy.lib.a ++ @if [ -f $(LIBsrcDIR)/libcdf.$(SHAREDEXT) ] ; then \ ++ $(MAKE) "INSTALLDIR=$(INSTALLDIR)" install.lib.so ; \ ++ else \ ++ $(NULL) ; \ ++ fi + @if [ -f $(LIBsrcDIR)/libcdf.so ] ; then \ + $(MAKE) "INSTALLDIR=$(INSTALLDIR)" install.lib.so ; \ + else \ +@@ -940,8 +945,8 @@ copy.include: + cp $(INCsrcDIR)/cdfconfig.h $(INSTALLDIR)/include + + copy.lib.so: +- @echo cp $(LIBsrcDIR)/libcdf.so $(INSTALLDIR)/lib +- cp $(LIBsrcDIR)/libcdf.so $(INSTALLDIR)/lib ++ @echo cp $(LIBsrcDIR)/libcdf.$(SHAREDEXT) $(INSTALLDIR)/lib ++ cp $(LIBsrcDIR)/libcdf.$(SHAREDEXT) $(INSTALLDIR)/lib + + copy.lib.sl: + @echo cp $(LIBsrcDIR)/libcdf.sl $(INSTALLDIR)/lib +@@ -2128,15 +2133,15 @@ show.posix.alphaI: show.supported + show.supported: + @echo SHARED is $(SUPPORTED.$(SHARED_$(OS))) + @echo CURSES is $(SUPPORTED.$(CURSES_$(OS)_$(ENV))) +- @echo FOPTIONS=$(FOPTIONS_$(OS)) ++ @echo FOPTIONS=$(FFLAGS) $(FOPTIONS_$(OS)) + @echo FOPTIONSld=$(FOPTIONSld_$(OS)) + @echo SHAREDEXT=$(SHAREDEXT_$(OS)) +- @echo LDOPTIONSlibcdf=$(LDOPTIONS_$(OS)_$(ENV)) ++ @echo LDOPTIONSlibcdf=$(LDFLAGS) $(LDOPTIONS_$(OS)_$(ENV)) + @echo RANLIB=$(RANLIB_$(OS)) + @echo FCx=$(FC_$(OS)) + @echo CCx=$(CC_$(OS)_$(ENV)) + @echo PIC=$(PIC_$(OS)_$(ENV)) +- @echo COPTIONS=$(COPTIONS_$(OS)_$(ENV)) ++ @echo COPTIONS=$(CFLAGS) $(COPTIONS_$(OS)_$(ENV)) + @echo COPTIONSld=$(COPTIONSld_$(OS)_$(ENV)) + @echo CURSESLIB=$(CURSESLIB_$(OS)_$(ENV)) + @echo SYSLIBSexe=$(SYSLIBSexe_$(OS)_$(ENV)) +diff --git a/src/tools/Makefile b/src/tools/Makefile +index 3773c0c..1cabf61 100644 +--- a/src/tools/Makefile ++++ b/src/tools/Makefile +@@ -40,12 +40,12 @@ CURSESLIB=-lncurses + INCLUDEcdf= ../include + + CC=$(CCx) +-CFLAGS=$(COPTIONS) -I$(INCLUDEcdf) +-CFLAGSld=$(COPTIONSld) ++CFLAGS:=$(CFLAGS) $(COPTIONS) -I$(INCLUDEcdf) ++CFLAGSld=$(LDFLAGS) $(COPTIONSld) + + WHICHOS=$(shell uname -a | cut -f1 -d" ") + ifeq ("$(WHICHOS)","Darwin") +- LIBCDFa=../lib/libcdf.a ++ LIBCDFa=../lib/libcdf.so.3 + else + WHICHOS=$(shell uname -a | cut -f7 -d" ") + ifeq ("$(WHICHOS)","Cygwin") diff --git a/sci-libs/cdf/metadata.xml b/sci-libs/cdf/metadata.xml new file mode 100644 index 000000000000..1021bdd389ce --- /dev/null +++ b/sci-libs/cdf/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +Common Data Format (CDF) is a conceptual data abstraction for storing +multi-dimensional data sets. The basic component of CDF is a software +programming interface that is a device independent view of the CDF data +model. The application developer is insulated from the actual physical +file format for reasons of conceptual simplicity, device independence, +and future expandability. CDF files created on any given platform can +be transported to any other platform on to which CDF is ported and used +with any CDF tools or layered applications. A more detailed introduction +to CDF can be found in the CDF User's Guide. +A comparison between CDF, netCDF, HDF and HDF5 is available at +http://cdf.gsfc.nasa.gov/html/FAQ.html. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/ceres-solver/Manifest b/sci-libs/ceres-solver/Manifest new file mode 100644 index 000000000000..b8404e2c9b45 --- /dev/null +++ b/sci-libs/ceres-solver/Manifest @@ -0,0 +1,7 @@ +DIST ceres-solver-1.11.0.tar.gz 3944965 SHA256 4d666cc33296b4c5cd77bad18ffc487b3223d4bbb7d1dfb342ed9a87dc9af844 SHA512 4941538e6ec31e2ee56a24446748dc5d6dd02ba9c151e4320a2db943fd1a377455b0ee23d56780e1f05322b30e25057145c540fde901d7fd2244ec630a73527c WHIRLPOOL 82e8c9f8fcf66f20dea28c5ddcfc4ac030a20d86c498eda487899b090fb67e7e44e3e1a76d3b689a409860c83713005e4f889814707d25cf298892ae9ea78890 +DIST ceres-solver-1.12.0.tar.gz 5008861 SHA256 745bfed55111e086954126b748eb9efe20e30be5b825c6dec3c525cf20afc895 SHA512 485eece0471cf05d31b5dd7e133e23115a334a4ed557a3c1bd0b715a063f840738af8f507e935522a0dae90ce6851984c0002a25e9b445b90889792f68a05571 WHIRLPOOL 80d884cd62b80b80927c451a2bea0d02dfe120acd98cfa8b6d1b2b9adf74a50242c7dd25e0d445d6454a919c03fc2e64479c7abea100231bcaad5c4b1ff541bc +EBUILD ceres-solver-1.11.0.ebuild 2390 SHA256 ca8fb5a8f45136317a867bd989dc3379d484b2ce29501e02c2fd937bd52492c3 SHA512 4f85570276c40e2c6800a429b26c7b3769c715181bc1242ef3e0d77fbe9292086061d1f804c642a56737d69d5d951a5852cf546a2e0a15df02eec9f0067e6ebe WHIRLPOOL 450ff257dd0e5d6ea7614767197f0e90a148eca71bdbbd65e88cdc9ba80e89a8fd32bccb318f7cd9e2ef1bf5d57f6d1443696d9f8bf75731481d4d66d4b54a73 +EBUILD ceres-solver-1.12.0.ebuild 2399 SHA256 6942ca6c66d515dab345e7fe2ac06abbf0b51b1a92358f6beab5df823b2811af SHA512 258eb56d4aa6d4ad9587cc825b18abc8cc90a921ba1733d6d18094704386ddda19aee9260c7dbc21d9f9bd9d8f9b55a4cacd2437b798be73e9b80b7c21dae239 WHIRLPOOL bed9968397096abc27e7cd114128e921ad1829bc8070c2628ef6b4f0cc5ffe273f4790f73e196caafd5ffa66c31366abd3c6eb52ce6db36216e23b19943780bf +MISC ChangeLog 2896 SHA256 f16ad4cf0dc9688c12377e4af9752c445a695d76ecd2e90c2d8518e1684c9585 SHA512 8f50844626d6b1065f1ce31daa18e0d168f5df6aa6f24cb1a1ae102e4d66bd0d1615174201f617c0fa48ee5e663c9dcea759e5fc91140ea22dbe2b411cb4b9da WHIRLPOOL d0152859480b9fea5ca6a3bef8129ff221e59e1d5725e2b96a4f239a67612974725aef80ddec274a8b069050ea57d8f0415623757cb5ad9c1959bcdc8ead0066 +MISC ChangeLog-2015 2001 SHA256 89f5dee254f7e114465bda52db77ed7810c427e62f9a18283d93f70e2f6d6d99 SHA512 ac35af703912b19697390c6f48ef3dbc08c9e787c913469df056a25dc6dc691a0395ee95845b56eb213d0c327dbd60f52888e69570b9f990086d4841609ff9e2 WHIRLPOOL 6675fa854fa217b84fc8e9a1b9c83e342b8b34d94d5ac210fe5581dac64a749f09ee2580b42d8cb588fce0cb94d202ae15bd0f91cfee09566ca4d162b10c08c3 +MISC metadata.xml 1525 SHA256 67dc2f63f3b707d750481c23d8ac5a9213238735401e43472d432cea9c04941f SHA512 4c95aef23ce327f9cd11b53638e1b6485eb789cd296ad8a571278b65c9001465f56c97b97db6e2c4a4ed76336f0e33684958adef593d74193cb73930e7ea5ad2 WHIRLPOOL a66358aa3c44a29d855be15d9c636599786445e7a663a8da4be035953397594ee56f2998382312dcda0ae73701ce11d4f53df007b633b50d10d1c07d84a027f1 diff --git a/sci-libs/ceres-solver/ceres-solver-1.11.0.ebuild b/sci-libs/ceres-solver/ceres-solver-1.11.0.ebuild new file mode 100644 index 000000000000..f9643b670583 --- /dev/null +++ b/sci-libs/ceres-solver/ceres-solver-1.11.0.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5} ) + +inherit cmake-multilib eutils python-any-r1 toolchain-funcs + +DESCRIPTION="Nonlinear least-squares minimizer" +HOMEPAGE="http://ceres-solver.org/" +SRC_URI="${HOMEPAGE}/${P}.tar.gz" + +LICENSE="sparse? ( BSD ) !sparse? ( LGPL-2.1 ) cxsparse? ( BSD )" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cxsparse c++11 doc examples gflags lapack openmp +schur sparse test" + +REQUIRED_USE="test? ( gflags ) sparse? ( lapack ) abi_x86_32? ( !sparse !lapack )" + +RDEPEND=" + dev-cpp/glog[gflags?,${MULTILIB_USEDEP}] + cxsparse? ( sci-libs/cxsparse:0= ) + lapack? ( virtual/lapack ) + sparse? ( + sci-libs/amd:0= + sci-libs/camd:0= + sci-libs/ccolamd:0= + sci-libs/cholmod:0= + sci-libs/colamd:0= + sci-libs/spqr:0= + )" + +DEPEND="${RDEPEND} + dev-cpp/eigen:3 + doc? ( dev-python/sphinx dev-python/sphinx_rtd_theme ) + lapack? ( virtual/pkgconfig ) + ${PYTHON_DEPS}" + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if [[ $(tc-getCXX) == *g++* ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + fi +} + +pkg_setup() { + use doc && python-any-r1_pkg_setup +} + +src_prepare() { + # search paths work for prefix + sed -e "s:/usr:${EPREFIX}/usr:g" \ + -i cmake/*.cmake || die + + # remove Werror + sed -e 's/-Werror=(all|extra)//g' \ + -i CMakeLists.txt || die + + # respect gentoo doc install directory + sed -e "s:share/doc/ceres:share/doc/${PF}:" \ + -i docs/source/CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + # CUSTOM_BLAS=OFF EIGENSPARSE=OFF MINIGLOG=OFF CXX11=OFF + local mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DBUILD_EXAMPLES=OFF + -DENABLE_TESTING="$(usex test)" + -DCXX11="$(usex c++11)" + -DBUILD_DOCUMENTATION="$(usex doc)" + -DGFLAGS="$(usex gflags)" + -DLAPACK="$(usex lapack)" + -DOPENMP="$(usex openmp)" + -DSCHUR_SPECIALIZATIONS="$(usex schur)" + -DCXSPARSE="$(usex cxsparse)" + -DSUITESPARSE="$(usex sparse)" + ) + use sparse || use cxsparse || mycmakeargs+=( -DEIGENSPARSE=ON ) + cmake-multilib_src_configure +} + +src_install() { + cmake-multilib_src_install + dodoc README.md VERSION + + if use examples; then + insinto /usr/share/doc/${PF} + docompress -x /usr/share/doc/${PF}/examples + doins -r examples data + fi +} diff --git a/sci-libs/ceres-solver/ceres-solver-1.12.0.ebuild b/sci-libs/ceres-solver/ceres-solver-1.12.0.ebuild new file mode 100644 index 000000000000..d9c8044cdb33 --- /dev/null +++ b/sci-libs/ceres-solver/ceres-solver-1.12.0.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit cmake-multilib eutils python-any-r1 toolchain-funcs + +DESCRIPTION="Nonlinear least-squares minimizer" +HOMEPAGE="http://ceres-solver.org/" +SRC_URI="${HOMEPAGE}/${P}.tar.gz" + +LICENSE="sparse? ( BSD ) !sparse? ( LGPL-2.1 ) cxsparse? ( BSD )" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cxsparse c++11 doc examples gflags lapack openmp +schur sparse test" + +REQUIRED_USE="test? ( gflags ) sparse? ( lapack ) abi_x86_32? ( !sparse !lapack )" + +RDEPEND=" + dev-cpp/glog[gflags?,${MULTILIB_USEDEP}] + cxsparse? ( sci-libs/cxsparse:0= ) + lapack? ( virtual/lapack ) + sparse? ( + sci-libs/amd:0= + sci-libs/camd:0= + sci-libs/ccolamd:0= + sci-libs/cholmod:0=[metis] + sci-libs/colamd:0= + sci-libs/spqr:0= + )" + +DEPEND="${RDEPEND} + dev-cpp/eigen:3 + doc? ( dev-python/sphinx dev-python/sphinx_rtd_theme ) + lapack? ( virtual/pkgconfig ) + ${PYTHON_DEPS}" + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if [[ $(tc-getCXX) == *g++* ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + fi +} + +pkg_setup() { + use doc && python-any-r1_pkg_setup +} + +src_prepare() { + # search paths work for prefix + sed -e "s:/usr:${EPREFIX}/usr:g" \ + -i cmake/*.cmake || die + + # remove Werror + sed -e 's/-Werror=(all|extra)//g' \ + -i CMakeLists.txt || die + + # respect gentoo doc install directory + sed -e "s:share/doc/ceres:share/doc/${PF}:" \ + -i docs/source/CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + # CUSTOM_BLAS=OFF EIGENSPARSE=OFF MINIGLOG=OFF CXX11=OFF + local mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DBUILD_EXAMPLES=OFF + -DENABLE_TESTING="$(usex test)" + -DCXX11="$(usex c++11)" + -DBUILD_DOCUMENTATION="$(usex doc)" + -DGFLAGS="$(usex gflags)" + -DLAPACK="$(usex lapack)" + -DOPENMP="$(usex openmp)" + -DSCHUR_SPECIALIZATIONS="$(usex schur)" + -DCXSPARSE="$(usex cxsparse)" + -DSUITESPARSE="$(usex sparse)" + ) + use sparse || use cxsparse || mycmakeargs+=( -DEIGENSPARSE=ON ) + cmake-multilib_src_configure +} + +src_install() { + cmake-multilib_src_install + dodoc README.md VERSION + + if use examples; then + insinto /usr/share/doc/${PF} + docompress -x /usr/share/doc/${PF}/examples + doins -r examples data + fi +} diff --git a/sci-libs/ceres-solver/metadata.xml b/sci-libs/ceres-solver/metadata.xml new file mode 100644 index 000000000000..42d1cafcb8bf --- /dev/null +++ b/sci-libs/ceres-solver/metadata.xml @@ -0,0 +1,34 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Ceres Solver is a portable C++ library that allows for + modeling and solving large complicated nonlinear least squares + problems. It features: + * automatic differentiation + * robust loss functions + * local parameterizations + * threaded Jacobian evaluators and linear solvers + * Levenberg-Marquardt and Dogleg (Powell, Subspace) solvers + * Dense QR and Cholesky factorization (using Eigen) for small problems + * Sparse Cholesky factorization (using SuiteSparse) for large sparse + problems + * Specialized solvers for bundle adjustment problems in computer vision + * Iterative linear solvers for general sparse and bundle + adjustment problems +</longdescription> + <use> + <flag name="cxsparse">Enable simple support for sparse matrix algebra from + <pkg>sci-libs/cxsparse</pkg> with no LAPACK dependencies</flag> + <flag name="schur">Enable fixed-size schur specializations (disable if + binary size is an issue)</flag> + <flag name="sparse">Enable support for sparse matrix algebra with various + packages from SuiteSparse</flag> + <flag name="gflags">Use <pkg>dev-cpp/gflags</pkg> for flag parsing</flag> + <flag name="c++11">Build ceres-solver using the C++11 standard</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/cfitsio/Manifest b/sci-libs/cfitsio/Manifest new file mode 100644 index 000000000000..c4ae952ebd72 --- /dev/null +++ b/sci-libs/cfitsio/Manifest @@ -0,0 +1,11 @@ +DIST cfitsio-3.360.tar.gz 4104894 SHA256 b5fb209583c76a0bcc39808e55ebf2417b9c26114c59db1a3f49ea1ede5fa95d SHA512 158819b4a3a29c29a5f017283e2b20067420994e881d202dbf3ba199c9e564dc1e74f8be5ce84f78107126d2a8688cc55cc7ed284540ca647e44cdc3b0b02072 WHIRLPOOL 05589a27c6fa83a0240b26924954c1c6d25d985ad609dfbd37fccfe5758fd28efbd97a5ec289803053e2f53e053e51c017292845de1b4368bcd1725fa2eccdb7 +DIST cfitsio-3.38.tar.gz 4142236 SHA256 d4aef44401b1d2142a13ffc3a28cce7c77264ca0ddce164d87fdcb275503dd5d SHA512 7428c1c87736ca384153f7f810e0bdbccdcc2f41892b0b9ceda9e5efb20655585c2789b16510a5362f8b67ef53a0ac443094786966e5748cbe7ad828599723fc WHIRLPOOL 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+FORTRAN_NEEDED=fortran + +inherit autotools-utils fortran-2 + +DESCRIPTION="C and Fortran library for manipulating FITS files" +HOMEPAGE="http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0/1" +KEYWORDS="alpha amd64 hppa ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris" +IUSE="doc examples fortran static-libs +tools threads" + +RDEPEND="sys-libs/zlib" +DEPEND="${RDEPEND} + fortran? ( dev-lang/cfortran )" + +pkg_setup() { + use fortran && fortran-2_pkg_setup +} + +src_prepare() { + # avoid internal cfortran + if use fortran; then + mv cfortran.h cfortran.h.disabled + ln -s "${EPREFIX}"/usr/include/cfortran.h . || die + fi + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable fortran) + $(use_enable threads) + $(use_enable tools) + ) + autotools-utils_src_configure +} + +src_install () { + autotools-utils_src_install + dodoc README* Changes* docs/changes.txt docs/cfitsio.doc + use fortran && dodoc docs/fitsio.doc + use doc && dodoc docs/{quick,cfitsio,fpackguide}.pdf + use doc && use fortran && dodoc docs/fitsio.pdf + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins cookbook.c testprog.c speed.c smem.c + use fortran && doins cookbook.f testf77.f + fi +} diff --git a/sci-libs/cfitsio/cfitsio-3.38-r1.ebuild b/sci-libs/cfitsio/cfitsio-3.38-r1.ebuild new file mode 100644 index 000000000000..7d3f7ad294b0 --- /dev/null +++ b/sci-libs/cfitsio/cfitsio-3.38-r1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit autotools-multilib fortran-2 + +DESCRIPTION="C and Fortran library for manipulating FITS files" +HOMEPAGE="http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0/2" +KEYWORDS="~alpha ~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris" +IUSE="bzip2 doc examples fortran static-libs +tools threads" + +RDEPEND=" + sys-libs/zlib[${MULTILIB_USEDEP}] + bzip2? ( app-arch/bzip2[${MULTILIB_USEDEP}] )" +DEPEND="${RDEPEND} + fortran? ( dev-lang/cfortran )" + +pkg_setup() { + use fortran && fortran-2_pkg_setup +} + +src_prepare() { + # avoid internal cfortran + if use fortran; then + mv cfortran.h cfortran.h.disabled + ln -s "${EPREFIX}"/usr/include/cfortran.h . || die + fi + autotools-multilib_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable fortran) + $(use_enable threads) + $(use_enable tools) + $(use_with bzip2) + ) + autotools-multilib_src_configure +} + +src_install () { + autotools-multilib_src_install + dodoc README README.md CHANGES.md docs/changes.txt docs/cfitsio.doc + use fortran && dodoc docs/fitsio.doc + use doc && dodoc docs/{quick,cfitsio,fpackguide}.pdf + use doc && use fortran && dodoc docs/fitsio.pdf + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins cookbook.c testprog.c speed.c smem.c + use fortran && doins cookbook.f testf77.f + fi +} diff --git a/sci-libs/cfitsio/cfitsio-3.39.ebuild b/sci-libs/cfitsio/cfitsio-3.39.ebuild new file mode 100644 index 000000000000..9a75291ffa74 --- /dev/null +++ b/sci-libs/cfitsio/cfitsio-3.39.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit fortran-2 multilib-minimal + +DESCRIPTION="C and Fortran library for manipulating FITS files" +HOMEPAGE="http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0/5" +KEYWORDS="~alpha ~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris" +IUSE="bzip2 doc examples fortran static-libs +tools threads" + +RDEPEND=" + sys-libs/zlib[${MULTILIB_USEDEP}] + bzip2? ( app-arch/bzip2[${MULTILIB_USEDEP}] )" +DEPEND="${RDEPEND} + fortran? ( dev-lang/cfortran )" + +pkg_setup() { + use fortran && fortran-2_pkg_setup +} + +src_prepare() { + # avoid internal cfortran + if use fortran; then + mv cfortran.h cfortran.h.disabled + ln -s "${EPREFIX}"/usr/include/cfortran.h . || die + fi + default +} + +multilib_src_configure() { + ECONF_SOURCE="${S}" econf \ + $(use_enable fortran) \ + $(use_enable static-libs static) \ + $(use_enable threads) \ + $(use_enable tools) \ + $(use_with bzip2) +} + +multilib_src_install_all() { + dodoc README README.md CHANGES.md docs/changes.txt docs/cfitsio.doc + use fortran && dodoc docs/fitsio.doc + use doc && dodoc docs/{quick,cfitsio,fpackguide}.pdf + use doc && use fortran && dodoc docs/fitsio.pdf + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins cookbook.c testprog.c speed.c smem.c + use fortran && doins cookbook.f testf77.f + fi + prune_libtool_files --all +} diff --git a/sci-libs/cfitsio/cfitsio-3.410.ebuild b/sci-libs/cfitsio/cfitsio-3.410.ebuild new file mode 100644 index 000000000000..9a75291ffa74 --- /dev/null +++ b/sci-libs/cfitsio/cfitsio-3.410.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit fortran-2 multilib-minimal + +DESCRIPTION="C and Fortran library for manipulating FITS files" +HOMEPAGE="http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0/5" +KEYWORDS="~alpha ~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris" +IUSE="bzip2 doc examples fortran static-libs +tools threads" + +RDEPEND=" + sys-libs/zlib[${MULTILIB_USEDEP}] + bzip2? ( app-arch/bzip2[${MULTILIB_USEDEP}] )" +DEPEND="${RDEPEND} + fortran? ( dev-lang/cfortran )" + +pkg_setup() { + use fortran && fortran-2_pkg_setup +} + +src_prepare() { + # avoid internal cfortran + if use fortran; then + mv cfortran.h cfortran.h.disabled + ln -s "${EPREFIX}"/usr/include/cfortran.h . || die + fi + default +} + +multilib_src_configure() { + ECONF_SOURCE="${S}" econf \ + $(use_enable fortran) \ + $(use_enable static-libs static) \ + $(use_enable threads) \ + $(use_enable tools) \ + $(use_with bzip2) +} + +multilib_src_install_all() { + dodoc README README.md CHANGES.md docs/changes.txt docs/cfitsio.doc + use fortran && dodoc docs/fitsio.doc + use doc && dodoc docs/{quick,cfitsio,fpackguide}.pdf + use doc && use fortran && dodoc docs/fitsio.pdf + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins cookbook.c testprog.c speed.c smem.c + use fortran && doins cookbook.f testf77.f + fi + prune_libtool_files --all +} diff --git a/sci-libs/cfitsio/metadata.xml b/sci-libs/cfitsio/metadata.xml new file mode 100644 index 000000000000..70b6e88c674a --- /dev/null +++ b/sci-libs/cfitsio/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-astronomy@gentoo.org</email> + <name>Gentoo Astronomy Project</name> + </maintainer> + <longdescription lang="en"> + CFITSIO is a library of C and Fortran subroutines for reading and + writing data files in FITS (Flexible Image Transport System) data + format. CFITSIO provides simple high-level routines for reading and + writing FITS files that insulate the programmer from the internal + complexities of the FITS format. CFITSIO also provides advanced + features for manipulating and filtering the information in FITS + files. +</longdescription> + <use> + <flag name="tools">Build execs fpack, funpack, imcopy, fitscopy, listhead + </flag> + </use> +</pkgmetadata> diff --git a/sci-libs/cgcode/Manifest b/sci-libs/cgcode/Manifest new file mode 100644 index 000000000000..054dfb1804fe --- /dev/null +++ b/sci-libs/cgcode/Manifest @@ -0,0 +1,6 @@ +AUX 1.0-gentoo.patch 2363 SHA256 0ebe39ee8df88f40c25fd0cbc36e10d25c7e6d3427071c6545e81fd4df439c58 SHA512 2daaf89d275a325404ec6804389a45fe02361e4e517a146dd329b9155a2200b4151bb559f4aad87055ed5d6da4227e0a30683ba82cfa1bb5f54c6cc40a76aea7 WHIRLPOOL 53ddf08427dc010665ecbdca794491ea295bdc1c762c6b1d651fb857fb746147a2bbf2a406fc61883370a944d3b8dd7089faf5302101757e3c77c20d89673815 +DIST cgcode-1.0.tar.gz 77941 SHA256 41dd5a8d388b234c26dbc514f61883530be3d0bd56abdbbde94b8724d266f594 SHA512 df76a2f8a0c00924af3d6933487a363fe23ded8281b392d40f240074c8643219f99dda9b6b6d515a281827d657a27ab06416ce152e65c5fead7549bb96be9621 WHIRLPOOL bcd4f00b4698c6b023a6458c5466f979ae726625b54014ee47a84864c5dc7ac783a8ffcb452e0990f1cfce3093f5c33c131b948a6436b04b0e314e0507d0b538 +EBUILD cgcode-1.0-r2.ebuild 773 SHA256 d916a8c8cdd583568b49c47bc5c2591b1a7fd4cd7ffbd5c7f76044f4ff65923a SHA512 a2bae62a4a82aca54d10e4ccbe941deb78f59eaa743458ff620729f298debeaf9af093e39e1260a8a7f594328980ec8081dc44c24a8d258b322362c4fa3fce23 WHIRLPOOL c46a3fa124bdde37d534640e2b711b821b6c22751b090cbfbf83e56d4cea6693661ab696725f691e423892e0db7caaf8966c0128582a5efc2fec0eb295fda97f +MISC ChangeLog 2591 SHA256 dce7d42357a1e61d6fad22796ea63b426e016b3d7a23aba96b04c889bd153264 SHA512 b9be2cfe9e7fe817928d1581f6ae686b9822f3593a3bdc9273bcc68788e445d0d8af53ed19e46b47f1f4bce04767d6a5ef60d567231ed5a11c51e28eca9e6de5 WHIRLPOOL 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000000000000..90160c444ea9 --- /dev/null +++ b/sci-libs/cgcode/cgcode-1.0-r2.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="Conjugate gradient Codes for large sparse linear systems" +HOMEPAGE="http://fetk.org/codes/cgcode/index.html" +SRC_URI="http://www.fetk.org/codes/download/${P}.tar.gz" + +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="" + +RDEPEND="virtual/blas" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}"/${PN} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + + cat >> make.inc <<- EOF + F77 = $(tc-getFC) + FFLAGS = ${FFLAGS} + BLASLIBS = $($(tc-getPKG_CONFIG) --libs blas) + EOF +} + +src_install() { + dobin goos good + dolib.so src/lib${PN}.so* + dodoc INTRODUCTION NOTE README +} diff --git a/sci-libs/cgcode/files/1.0-gentoo.patch b/sci-libs/cgcode/files/1.0-gentoo.patch new file mode 100644 index 000000000000..612ca9e06497 --- /dev/null +++ b/sci-libs/cgcode/files/1.0-gentoo.patch @@ -0,0 +1,83 @@ +diff --git a/makefile b/makefile +index 4813b55..f20af02 100644 +--- a/makefile ++++ b/makefile +@@ -1,21 +1,23 @@ + + include make.inc + +-THELIBS = libcgcode.a libblas_mini.a ++THELIBS = -lcgcode + + default : goos good + +-libs : +- cd src ; make ; cd ../util ; make ++libs : src/libcgcode.so ++ ++src/libcgcode.so: ++ $(MAKE) -C src + + goos : mains.o libs +- $(F77) $(DEBUG) $(OFLAGS) $(LFLAGS) mains.o $(THELIBS) -o goos ++ $(F77) $(LDFLAGS) mains.o -L./src $(THELIBS) $(BLASLIBS) -o goos + + good : maind.o libs +- $(F77) $(DEBUG) $(OFLAGS) $(LFLAGS) maind.o $(THELIBS) -o good ++ $(F77) $(LDFLAGS) maind.o -L./src $(THELIBS) $(BLASLIBS) -o good + +-.f.o : +- $(F77) $(CFLAGS) $(DEBUG) $(OFLAGS) $*$ .f ++%.o : %.f ++ $(F77) $(FFLAGS) -c $< + + clean : + rm -f *.o goos good +diff --git a/src/makefile b/src/makefile +index 10cf6c3..1dfd02d 100644 +--- a/src/makefile ++++ b/src/makefile +@@ -1,16 +1,17 @@ + + include ../make.inc + +-THISLIB = libcgcode.a ++THISLIB = libcgcode.so + SOBJLIB = scgdrv.o scg.o scr.o scrind.o spcg.o scgnr.o scgne.o spcgnr.o spcgne.o sppcg.o spcgca.o sdpchb.o scbfix.o sckchb.o scgchk.o sonest.o msstop.o r1mach.o sratqr.o + DOBJLIB = dcgdrv.o dcg.o dcr.o dcrind.o dpcg.o dcgnr.o dcgne.o dpcgnr.o dpcgne.o dppcg.o dpcgca.o ddpchb.o dcbfix.o dckchb.o dcgchk.o donest.o mdstop.o d1mach.o dratqr.o depsln.o + + $(THISLIB) : $(SOBJLIB) $(DOBJLIB) +- $(AR) $(THISLIB) $(SOBJLIB) $(DOBJLIB) +- cp $(THISLIB) ../. ++ $(F77) $(FFLAGS) $(LDFLAGS) -shared -fPIC -Wl,--soname,$(THISLIB).1 -o $(THISLIB).1.0 $(SOBJLIB) $(DOBJLIB) $(BLASLIBS) ++ ln -sf $(THISLIB).1.0 $(THISLIB).1 ++ ln -sf $(THISLIB).1.0 $(THISLIB) + +-.f.o : +- $(F77) $(CFLAGS) $(DEBUG) $(OFLAGS) $*$ .f ++%.o : %.f ++ $(F77) $(FFLAGS) -fPIC -c $< + + clean : + rm -f *.o $(THISLIB) +diff --git a/util/makefile b/util/makefile +index 6dad0d1..5c9d24f 100644 +--- a/util/makefile ++++ b/util/makefile +@@ -6,11 +6,12 @@ SOBJLIB = saxpy.o scopy.o sdot.o snrm2.o sscal.o + DOBJLIB = daxpy.o dcopy.o ddot.o dnrm2.o dscal.o + + $(THISLIB) : $(SOBJLIB) $(DOBJLIB) +- $(AR) $(THISLIB) $(SOBJLIB) $(DOBJLIB) +- cp $(THISLIB) ../. ++ $(F77) $(FFLAGS) $(LDFLAGS) -shared -Wl,--soname,$(THISLIB).1 -o $(THISLIB).1.0 $(SOBJLIB) $(DOBJLIB) $(BLASLIBS) ++ ln -sf $(THISLIB).1.0 $(THISLIB) ++ cp $(THISLIB)* ../. + +-.f.o : +- $(F77) $(CFLAGS) $(DEBUG) $(OFLAGS) $*$ .f ++%.o : %.f ++ $(F77) $(FFLAGS) -c $< + + clean : + rm -f *.o $(THISLIB) diff --git a/sci-libs/cgcode/metadata.xml b/sci-libs/cgcode/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-libs/cgcode/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/cgnslib/Manifest b/sci-libs/cgnslib/Manifest new file mode 100644 index 000000000000..81fc7353cd41 --- /dev/null +++ b/sci-libs/cgnslib/Manifest @@ -0,0 +1,8 @@ +AUX cgnslib-3.2.1-cmake.patch 4758 SHA256 d7de564429cef417c98c146283e0e3370b148a93b78b0be5ebcac58821cc838f SHA512 c55279d0c5d26bb8c0ed41e637d7cd417e84f6896fa76c81d5c47d2fd7491e2889e739606e52763bca184f1775da6ee4d0be55d8fab7f6d2e2a73b87fa593f0f WHIRLPOOL c859798c4fd024be14b7c85867347d3ca8a6432a01048d4042200786c925a82337a5492f37f8564d5b89c13e0bd3263b371c9ed481e2c3072c364f14b1b3a897 +DIST cgnslib-3.3.0.tar.gz 3314889 SHA256 8422c67994f8dc6a2f201523a14f6c7d7e16313bdd404c460c16079dbeafc662 SHA512 eb5c79d3830f8ee1fa30a67fbf32133c13a276c4b18a553826e4670bd4aa7262d7751bccb74c5e208cd47703f9076bde2e2e0db70408c88fde3ac11b638e6ff3 WHIRLPOOL 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+MY_S="${PN}_$(get_version_component_range 1-2)" + +DESCRIPTION="The CFD General Notation System (CGNS) is a standard for CFD data" +HOMEPAGE="http://www.cgns.org/" +SRC_URI="mirror://sourceforge/project/cgns/${MY_S}/${MY_P}.tar.gz" + +LICENSE="ZLIB" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="fortran hdf5 legacy mpi szip zlib" + +DEPEND=" + hdf5? ( >=sci-libs/hdf5-1.8[mpi=] ) + szip? ( virtual/szip ) + zlib? ( sys-libs/zlib )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${PN}_${PV} + +PATCHES=( + "${FILESDIR}"/${P}-cmake.patch +) + +pkg_setup() { + use fortran && fortran-2_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DCGNS_ENABLE_64BIT=ON + $(usex x86 -DCGNS_ENABLE_LFS=ON) + $(cmake-utils_use fortran CGNS_ENABLE_FORTRAN) + $(cmake-utils_use hdf5 CGNS_ENABLE_HDF5) + $(cmake-utils_use legacy CGNS_ENABLE_LEGACY) + $(cmake-utils_use mpi HDF5_NEED_MPI) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/cgnslib/cgnslib-3.3.0.ebuild b/sci-libs/cgnslib/cgnslib-3.3.0.ebuild new file mode 100644 index 000000000000..e3e6d2d56d92 --- /dev/null +++ b/sci-libs/cgnslib/cgnslib-3.3.0.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED="fortran" +FORTRAN_STANDARD="90 2003" + +inherit cmake-utils fortran-2 + +DESCRIPTION="CFD General Notation System standard library" +HOMEPAGE="http://www.cgns.org/" +SRC_URI="https://github.com/CGNS/CGNS/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="ZLIB" +SLOT="0/3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples fortran hdf5 legacy mpi static-libs szip test tools" + +RDEPEND="hdf5? ( sci-libs/hdf5:=[mpi=,szip=] ) + tools? ( + dev-lang/tcl:= + dev-lang/tk:= + x11-libs/libXmu:= + virtual/glu + virtual/opengl + )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/CGNS-${PV}" + +pkg_setup() { + use fortran && fortran-2_pkg_setup +} + +src_prepare() { + # gentoo libdir + sed -e '/DESTINATION/s|lib)|lib${LIB_SUFFIX})|g' \ + -e 's|lib LIBDIR|lib${LIB_SUFFIX} LIBDIR|' \ + -e 's|/lib"|/lib${LIB_SUFFIX}"|'\ + -i CMakeLists.txt src/CMakeLists.txt || die + # dont hard code link + sed -e '/link_directories/d' \ + -i src/tools/CMakeLists.txt src/cgnstools/*/CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCGNS_BUILD_SHARED=ON + -DCGNS_USED_SHARED=ON + -DCGNS_BUILD_CGNSTOOLS="$(usex tools)" + -DCGNS_ENABLE_FORTRAN="$(usex fortran)" + -DCGNS_ENABLE_HDF5="$(usex hdf5)" + -DCGNS_ENABLE_LEGACY="$(usex legacy)" + -DCGNS_ENABLE_TESTS="$(usex test)" + -DHDF5_NEED_MPI="$(usex mpi)" + -DHDF5_NEED_SZIP="$(usex szip)" + -DHDF5_NEED_ZLIB="$(usex szip)" + ) + cmake-utils_src_configure +} + +src_compile() { + # hack to allow parallel building by first producing fortran module + use fortran && cd "${BUILD_DIR}"/src && emake cgns_f.o + cmake-utils_src_compile +} + +src_install() { + cmake-utils_src_install + dodoc README.md changelog release_docs/Release.txt + use static-libs || rm "${ED}"/usr/$(get_libdir)/libcgns.a + use doc && dodoc *pdf release_docs/*.pdf + insinto /usr/share/doc/${PF} + use examples && doins -r src/examples +} diff --git a/sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch b/sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch new file mode 100644 index 000000000000..bf8ea5f2bfeb --- /dev/null +++ b/sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch @@ -0,0 +1,149 @@ + CMakeLists.txt | 20 +-------------- + src/CMakeLists.txt | 72 +++++++++++++++++++++++++++--------------------------- + 2 files changed, 37 insertions(+), 55 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index d9c1b3c..d4c2bf7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -81,7 +81,7 @@ if (CGNS_ENABLE_LFS) + if (HAVE_OPEN64) + add_definitions(-DHAVE_LSEEK64) + endif (HAVE_OPEN64) +- if (HAVE_OPEN64) ++ if (HAVE_LSEEK64) + add_definitions(-DHAVE_LSEEK64) + endif (HAVE_LSEEK64) + endif (WIN32) +@@ -254,24 +254,6 @@ else (CGNS_ENABLE_HDF5 AND HDF5_NEED_MPI) + mark_as_advanced(FORCE CGNS_ENABLE_PARALLEL) + endif (CGNS_ENABLE_HDF5 AND HDF5_NEED_MPI) + +-#################### +-# RPATH Management # +-#################### +- +-# use, i.e. don't skip the full RPATH for the build tree +-set(CMAKE_SKIP_BUILD_RPATH FALSE) +- +-# when building, don't use the install RPATH already +-# (but later on when installing) +-set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) +- +-# the RPATH to be used when installing +-set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") +- +-# add the automatically determined parts of the RPATH +-# which point to directories outside the build tree to the install RPATH +-set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) +- + ######## + # CGNS # + ######## +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 3c12c6d..694da42 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -69,7 +69,7 @@ set(SYSCFLAGS "") + set(CFGFLAGS "") + set(LIBS "") + +-file(TO_NATIVE_PATH ${CMAKE_INSTALL_PREFIX}/lib LIBDIR) ++file(TO_NATIVE_PATH ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX} LIBDIR) + file(TO_NATIVE_PATH ${CMAKE_INSTALL_PREFIX}/include INCLUDEDIR) + file(TO_NATIVE_PATH ${CMAKE_C_COMPILER} CC) + if (WIN32) +@@ -102,42 +102,42 @@ set(ZLIBLIB "") + set(MPIINC "") + set(MPILIBS "") + +-macro(native_paths INPUT_PATH_VARIABLE RESULT_VARIABLE)
+- set(${RESULT_VARIABLE} "")
+- foreach(PATH ${${INPUT_PATH_VARIABLE}})
+- file(TO_NATIVE_PATH ${PATH} NATIVE_PATH)
+- list(APPEND ${RESULT_VARIABLE} ${NATIVE_PATH})
+- endforeach(PATH ${${INPUT_PATH_VARIABLE}})
+-endmacro(native_paths)
++macro(native_paths INPUT_PATH_VARIABLE RESULT_VARIABLE) ++ set(${RESULT_VARIABLE} "") ++ foreach(PATH ${${INPUT_PATH_VARIABLE}}) ++ file(TO_NATIVE_PATH ${PATH} NATIVE_PATH) ++ list(APPEND ${RESULT_VARIABLE} ${NATIVE_PATH}) ++ endforeach(PATH ${${INPUT_PATH_VARIABLE}}) ++endmacro(native_paths) + + if (CGNS_ENABLE_HDF5) + set(BUILDHDF5 1) +- if (HDF5_INCLUDE_PATH)
+- native_paths(HDF5_INCLUDE_PATH HDF5INC)
+- endif (HDF5_INCLUDE_PATH)
+- if (HDF5_LIBRARY)
+- native_paths(HDF5_LIBRARY HDF5LIB)
+- endif (HDF5_LIBRARY)
+- if (HDF5_NEED_SZIP)
+- set(H5NEEDSZIP 1)
+- if (SZIP_LIBRARY)
+- native_paths(SZIP_LIBRARY SZIPLIB)
+- endif (SZIP_LIBRARY)
+- endif (HDF5_NEED_SZIP)
+- if (HDF5_NEED_ZLIB)
+- set(H5NEEDZLIB 1)
+- if (ZLIB_LIBRARY)
+- native_paths(${ZLIB_LIBRARY} ZLIBLIB)
+- endif (ZLIB_LIBRARY)
+- endif (HDF5_NEED_ZLIB)
+- if (HDF5_NEED_MPI)
+- set(H5NEEDMPI 1)
+- if (MPI_INC)
+- native_paths(MPI_INC MPIINC)
+- endif (MPI_INC)
+- if (MPI_LIBS)
+- native_paths(MPI_LIBS MPILIBS)
+- endif (MPI_LIBS)
++ if (HDF5_INCLUDE_PATH) ++ native_paths(HDF5_INCLUDE_PATH HDF5INC) ++ endif (HDF5_INCLUDE_PATH) ++ if (HDF5_LIBRARY) ++ native_paths(HDF5_LIBRARY HDF5LIB) ++ endif (HDF5_LIBRARY) ++ if (HDF5_NEED_SZIP) ++ set(H5NEEDSZIP 1) ++ if (SZIP_LIBRARY) ++ native_paths(SZIP_LIBRARY SZIPLIB) ++ endif (SZIP_LIBRARY) ++ endif (HDF5_NEED_SZIP) ++ if (HDF5_NEED_ZLIB) ++ set(H5NEEDZLIB 1) ++ if (ZLIB_LIBRARY) ++ native_paths(${ZLIB_LIBRARY} ZLIBLIB) ++ endif (ZLIB_LIBRARY) ++ endif (HDF5_NEED_ZLIB) ++ if (HDF5_NEED_MPI) ++ set(H5NEEDMPI 1) ++ if (MPI_INC) ++ native_paths(MPI_INC MPIINC) ++ endif (MPI_INC) ++ if (MPI_LIBS) ++ native_paths(MPI_LIBS MPILIBS) ++ endif (MPI_LIBS) + if (CGNS_ENABLE_PARALLEL) + set(BUILDPARALLEL 1) + endif (CGNS_ENABLE_PARALLEL) +@@ -251,7 +251,7 @@ if(CGNS_BUILD_SHARED) + endif(CGNS_BUILD_SHARED) + + # Set the install path of the static library +-install(TARGETS cgns_static ARCHIVE DESTINATION lib) ++install(TARGETS cgns_static ARCHIVE DESTINATION lib${LIB_SUFFIX}) + # Set the install path of the shared library + if(CGNS_BUILD_SHARED) + # for windows, need to install both cgnsdll.dll and cgnsdll.lib +@@ -259,7 +259,7 @@ if(CGNS_BUILD_SHARED) + install(TARGETS cgns_shared ARCHIVE DESTINATION lib) + install(TARGETS cgns_shared RUNTIME DESTINATION lib) + else (WIN32 OR CYGWIN) +- install(TARGETS cgns_shared LIBRARY DESTINATION lib) ++ install(TARGETS cgns_shared LIBRARY DESTINATION lib${LIB_SUFFIX}) + endif (WIN32 OR CYGWIN) + endif(CGNS_BUILD_SHARED) + diff --git a/sci-libs/cgnslib/metadata.xml b/sci-libs/cgnslib/metadata.xml new file mode 100644 index 000000000000..0edf2c837c09 --- /dev/null +++ b/sci-libs/cgnslib/metadata.xml @@ -0,0 +1,30 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription lang="en"> + The Computational Fluid Dynamics General Notation System (CGNS) provides a + general, portable, and extensible standard for the storage and retrieval of + computational fluid dynamics (CFD) analysisdata. It consists of a collection + of conventions, and free and open software implementing those conventions. It + is self-descriptive, machine-independent, well-documented, and administered by + an international steering committee. + </longdescription> + <use> + <flag name="legacy">Enable or disable building legacy code (3.0 compatible)</flag> + <flag name="tools"> + A number of utility programs: + cgnscheck, cgnscompress, cgnsdiff, cgnslist, cgnsnames, cgnsupdate, cgnsconvert, adf2hdf, hdf2adf. + </flag> + </use> + <maintainer type="person"> + <email>slis@gentoo.org</email> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">CGNS/CGNS</remote-id> + <remote-id type="sourceforge">cgns</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/chemkit/Manifest b/sci-libs/chemkit/Manifest new file mode 100644 index 000000000000..cab15ca5db29 --- /dev/null +++ b/sci-libs/chemkit/Manifest @@ -0,0 +1,7 @@ +AUX chemkit-0.1-multilib.patch 4694 SHA256 9c9402535a1afc727d96d6415dcf16780c0f29998ea7bac3e1e4c3b89ecf3af2 SHA512 dedde9e5db14f088e5a70ebfcd9f46b6fbb2d60b1800a61ece1f7afef24caac502f129573823807caec050ba1515ad402a3615953b903a239c5287a5b96aa8b8 WHIRLPOOL 4e86024cc5dd39af48133c43f477ca4c69fa21d88498fb7af95f1565c6785e2fac39cd1724129db1c390cbdb723a8deee9fab82e6aceae8ed6dfcae0e0a3a646 +AUX chemkit-0.1-unbundle.patch 6103 SHA256 0fb331b49205fc55e00404dec5dbbfc70f5d80b5a64ae06c6aeb7a6971f42552 SHA512 9edd39008763b56eb7697562536c4c4d476880a414ae1a305d1af64cee04e4ccb82585cfd15d2f7608b5200e39863a9a97c2a152110b28e501fbd055737ce015 WHIRLPOOL 1bfe931e706d7259dbf2a5527b1e75cbfa1ca09148fffd25c4e4cc986112fd1cb18730b462c29fcae553b6bbdefcb5c895934b96fb5e141a307fa67eb0becc23 +DIST chemkit-0.1.tar.gz 5842235 SHA256 bec718ce4ae2fcb4cda63004d05a6e6bf65c1887179f665fcee118cbe7bec11b SHA512 0273f8735333000b04007ccd7adc58f0c4809a570fa5a72e4161652d72e8953bf89cad0893c20ecbb3484d6c13a8828c92f12366dddeedaf591815c35f6ef011 WHIRLPOOL 30c73d5d2bb7e946204d3dcdd87b82fa3e5278e799b06df523557f46ca4c71ae7d5b9c37d82af8dcdee48bb83f8840c5f2900b4331c3cf643c323ef20abc1883 +EBUILD chemkit-0.1-r1.ebuild 1838 SHA256 b93c38a6167a09526421e7d44da225178725ecbc9a7274f74545fb954430bd7b SHA512 d1726b0239454b00623c807337341ff4bf5ad5da889e492da0613e09e34422c566322d2ceb68ebffcea52fd499d42c7678c7640b044d7b7a7312c84b4e322cb0 WHIRLPOOL 5c2b2c11d64d63e75d4ad21d03efd9231332dc04b694624fddc68b2e83ea6ef43605d80914a6b051039c40ed9502f7d58578aa11a563ac4d4f0859c22b1e55af +MISC ChangeLog 2689 SHA256 905f93d2a880dff2c014dcf2196ea45ee33e72e176347b8087c0b329668bff7c SHA512 5dbc79de565751e085de846a95cf4c85bdbfa256dd9b0016eb43f8d7ffdd409e2d7342bb9966c1fe8a6789cbd05fcdb8326fe95f572dbde403729b2723cc3428 WHIRLPOOL 41e5a82dab3b398fbf8e5f1c81e9c13d44114fc72c24fe02d3e8f554cea511a0294a621d2704ef99917e52df577925a9a06ed692ede6ca0490207e7d6fcf3cfd +MISC ChangeLog-2015 1121 SHA256 827207ab1d87618d48c2bca3e172225d76a1ae86d6aa6bc94f86b23f80bf77a8 SHA512 fdb871617cdafc76b4f8c094d61847286d83289b1fe89220afd64f289c6b53de3012db9042ae827609544c3c951a93292ffcea375229068415b5eec598e92657 WHIRLPOOL 486be8176ec3d1028c965a111e3ddf056a5fb5ee34d65d70e98909d6188385eaab5504ba970ada14152301960351d1fef83d6e53ab54f232c74c7d9b1bcab27a +MISC metadata.xml 453 SHA256 e2e8ab9cb866c65794124f2a6c54fbb921de29173a083bf55cd637f4848699d5 SHA512 4a492fc1856ccc3eda100f356ef4699bbbc9e51719015ffab0d14d6bf1077cd07f7be3a7113e93f9a1fb2acdc347dffe2fb68e6076c00e80f265cd35ec80019a WHIRLPOOL d9cc84fd96a0718df26cafa8aa1caceac17bb230538b8d4a2817564bf68d506fbe3f2fa1486dc5d0a0fd4fdc5eb83c5b34969bf2d6de4925cc74ba3c80f500d1 diff --git a/sci-libs/chemkit/chemkit-0.1-r1.ebuild b/sci-libs/chemkit/chemkit-0.1-r1.ebuild new file mode 100644 index 000000000000..b620a1e9f7fd --- /dev/null +++ b/sci-libs/chemkit/chemkit-0.1-r1.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils multilib python-single-r1 virtualx + +DESCRIPTION="Library for chemistry applications" +HOMEPAGE="http://www.chemkit.org/" +SRC_URI="mirror://sourceforge/project/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD PSF-2.2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="applications examples python test" + +REQUIRED_USE="${PYTHON_REQUIRED_USE} + test? ( applications python )" + +RDEPEND=" + dev-libs/boost + dev-libs/rapidxml + dev-cpp/eigen:3 + dev-qt/qtcore:4 + dev-qt/qtgui:4 + dev-qt/qtopengl:4 + media-libs/glu + sci-libs/inchi + sci-libs/lemon + virtual/opengl + examples? ( + x11-libs/libX11 + x11-libs/libXext + ) + python? ( ${PYTHON_DEPS} ) +" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${PN} + +PATCHES=( + "${FILESDIR}"/${P}-multilib.patch + "${FILESDIR}"/${P}-unbundle.patch + ) + +src_prepare() { + # jsoncpp API change + # xdrf != xdrfile + rm -rvf src/3rdparty/{inchi,khronos,lemon,rapidxml} || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCHEMKIT_BUILD_PLUGIN_BABEL=on + -DUSE_SYSTEM_INCHI=ON + -DUSE_SYSTEM_JSONCPP=OFF + -DUSE_SYSTEM_RAPIDXML=ON + -DUSE_SYSTEM_XDRF=OFF + $(cmake-utils_use applications CHEMKIT_BUILD_APPS) + $(cmake-utils_use applications CHEMKIT_BUILD_QT_DESIGNER_PLUGINS) + $(cmake-utils_use examples CHEMKIT_BUILD_EXAMPLES) + $(cmake-utils_use examples CHEMKIT_BUILD_DEMOS) + $(cmake-utils_use python CHEMKIT_BUILD_BINDINGS_PYTHON) + $(cmake-utils_use test CHEMKIT_BUILD_TESTS) + ) + cmake-utils_src_configure +} + +src_test() { + VIRTUALX_COMMAND="cmake-utils_src_test" + virtualmake +} + +src_install() { + use examples && \ + dobin \ + "${BUILD_DIR}"/demos/*-viewer/*-viewer \ + "${BUILD_DIR}"/examples/uff-energy/uff-energy + + cmake-utils_src_install +} diff --git a/sci-libs/chemkit/files/chemkit-0.1-multilib.patch b/sci-libs/chemkit/files/chemkit-0.1-multilib.patch new file mode 100644 index 000000000000..b6a61d58ed8c --- /dev/null +++ b/sci-libs/chemkit/files/chemkit-0.1-multilib.patch @@ -0,0 +1,90 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index e531be4..e0d6b2d 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -44,7 +44,7 @@ configure_file( + "${CMAKE_MODULE_PATH}/ChemkitConfig.cmake.in" + "${CMAKE_BINARY_DIR}/ChemkitConfig.cmake" + IMMEDIATE @ONLY) +-install(FILES ${CMAKE_BINARY_DIR}/ChemkitConfig.cmake DESTINATION lib/chemkit) ++install(FILES ${CMAKE_BINARY_DIR}/ChemkitConfig.cmake DESTINATION lib${LIB_SUFFIX}/chemkit) + + # Create a ChemkitBuildTreeSettings.cmake file for the use from the build tree + configure_file( +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 88c6b5f..1100c3b 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -8,12 +8,12 @@ macro(add_chemkit_library library_name) + add_library(${library_name} SHARED ${ARGN}) + + # add install target +- install(TARGETS ${library_name} DESTINATION lib) ++ install(TARGETS ${library_name} DESTINATION lib${LIB_SUFFIX}) + + # copy library into build directory + get_target_property(library_location ${library_name} LOCATION) + get_filename_component(library_filename ${library_location} NAME) +- add_custom_command(TARGET ${library_name} POST_BUILD COMMAND ${CMAKE_COMMAND} ARGS -E copy ${library_location} ${CMAKE_BINARY_DIR}/lib/${library_filename}) ++ add_custom_command(TARGET ${library_name} POST_BUILD COMMAND ${CMAKE_COMMAND} ARGS -E copy ${library_location} ${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/${library_filename}) + + endmacro(add_chemkit_library) + +diff --git a/src/plugins/CMakeLists.txt b/src/plugins/CMakeLists.txt +index dc8970f..77029b7 100644 +--- a/src/plugins/CMakeLists.txt ++++ b/src/plugins/CMakeLists.txt +@@ -3,7 +3,7 @@ macro(add_chemkit_plugin plugin_name) + add_library(${plugin_name} SHARED ${ARGN}) + + # add install target +- install(TARGETS ${plugin_name} DESTINATION lib/chemkit/plugins/) ++ install(TARGETS ${plugin_name} DESTINATION lib${LIB_SUFFIX}/chemkit/plugins/) + + # remove 'lib' prefix + set_target_properties(${plugin_name} PROPERTIES PREFIX "") +@@ -11,15 +11,15 @@ macro(add_chemkit_plugin plugin_name) + # copy plugin into build directory + get_target_property(plugin_location ${plugin_name} LOCATION) + get_filename_component(plugin_filename ${plugin_location} NAME) +- add_custom_command(TARGET ${plugin_name} POST_BUILD COMMAND ${CMAKE_COMMAND} ARGS -E copy ${plugin_location} ${CMAKE_BINARY_DIR}/lib/chemkit/plugins/${plugin_filename}) ++ add_custom_command(TARGET ${plugin_name} POST_BUILD COMMAND ${CMAKE_COMMAND} ARGS -E copy ${plugin_location} ${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/chemkit/plugins/${plugin_filename}) + + # plugin data + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/data) + # copy plugin data into build directory +- file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION ${CMAKE_BINARY_DIR}/lib/chemkit/plugins/data/${plugin_name}/) ++ file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION ${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/chemkit/plugins/data/${plugin_name}/) + + # install plugin data directory +- install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION lib/chemkit/plugins/data/${plugin_name}) ++ install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION lib${LIB_SUFFIX}/chemkit/plugins/data/${plugin_name}) + endif() + endmacro(add_chemkit_plugin) + +diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt +index b191b82..a4ea0b0 100644 +--- a/tests/CMakeLists.txt ++++ b/tests/CMakeLists.txt +@@ -4,7 +4,7 @@ endif() + + macro(add_chemkit_test test_name test_executable) + add_test(NAME ${test_name} COMMAND ${test_executable}) +- set_tests_properties(${test_name} PROPERTIES ENVIRONMENT "CHEMKIT_PLUGIN_PATH=${CMAKE_BINARY_DIR}/lib/chemkit/plugins/") ++ set_tests_properties(${test_name} PROPERTIES ENVIRONMENT "CHEMKIT_PLUGIN_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/chemkit/plugins/") + endmacro(add_chemkit_test) + + add_subdirectory(auto) +diff --git a/tests/auto/bindings/python/CMakeLists.txt b/tests/auto/bindings/python/CMakeLists.txt +index 9859867..70da693 100644 +--- a/tests/auto/bindings/python/CMakeLists.txt ++++ b/tests/auto/bindings/python/CMakeLists.txt +@@ -5,7 +5,7 @@ endif() + macro(add_chemkit_python_test test_name test_script) + add_test(${test_name} ${PYTHON_EXECUTABLE} ${test_script}) + set_tests_properties(${test_name} PROPERTIES +- ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/bindings/python/;CHEMKIT_PLUGIN_PATH=${CMAKE_BINARY_DIR}/lib/chemkit/plugins") ++ ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/bindings/python/;CHEMKIT_PLUGIN_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/chemkit/plugins") + endmacro(add_chemkit_python_test) + + add_chemkit_python_test(python.Atom ${CMAKE_CURRENT_SOURCE_DIR}/atomtest.py) diff --git a/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch b/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch new file mode 100644 index 000000000000..e8c9d18dca6e --- /dev/null +++ b/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch @@ -0,0 +1,191 @@ + CMakeLists.txt | 21 +++++++++++++++++++++ + src/plugins/chemjson/CMakeLists.txt | 6 +++++- + src/plugins/chemjson/chemjsonfileformat.cpp | 4 ++++ + src/plugins/cml/cmlfileformat.h | 4 ++++ + src/plugins/inchi/CMakeLists.txt | 4 +++- + src/plugins/inchi/inchikeylineformat.cpp | 4 ++++ + src/plugins/inchi/inchilineformat.cpp | 4 ++++ + src/plugins/pdb/pdbmlfileformat.cpp | 4 ++++ + src/plugins/xtc/CMakeLists.txt | 9 +++++++-- + src/plugins/xtc/xtcfileformat.cpp | 4 ++++ + 10 files changed, 60 insertions(+), 4 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index e531be4..622ea9d 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -55,6 +55,27 @@ configure_file( + # export the Chemkit package + export(PACKAGE Chemkit) + ++option(USE_SYSTEM_INCHI "Use inchi installed in system" OFF) ++option(USE_SYSTEM_JSONCPP "Use json cpp installed in system" OFF) ++option(USE_SYSTEM_RAPIXML "Use rapidxml installed in system" OFF) ++option(USE_SYSTEM_XDRF "Use xdrflib installed in system" OFF) ++ ++if(USE_SYSTEM_INCHI) ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_INCHI") ++endif() ++ ++if(USE_SYSTEM_JSONCPP) ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_JSONCPP") ++endif() ++ ++if(USE_SYSTEM_RAPIDXML) ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_RAPIDXML") ++endif() ++ ++if(USE_SYSTEM_XDRF) ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_XDRF") ++endif() ++ + # build options + option(CHEMKIT_WITH_GRAPHICS "Build the chemkit-graphics library." ON) + option(CHEMKIT_WITH_IO "Build the chemkit-io library." ON) +diff --git a/src/plugins/chemjson/CMakeLists.txt b/src/plugins/chemjson/CMakeLists.txt +index 0e115b5..a5e6f48 100644 +--- a/src/plugins/chemjson/CMakeLists.txt ++++ b/src/plugins/chemjson/CMakeLists.txt +@@ -10,7 +10,11 @@ set(SOURCES + chemjsonplugin.cpp + ) + +-aux_source_directory(../../3rdparty/jsoncpp/ JSONCPP_SOURCES) ++if(NOT USE_SYSTEM_JSONCPP) ++ aux_source_directory(../../3rdparty/jsoncpp/ JSONCPP_SOURCES) ++else() ++ target_link_libraries(chemjson jsoncpp) ++endif() + + add_chemkit_plugin(chemjson ${SOURCES} ${JSONCPP_SOURCES}) + target_link_libraries(chemjson ${CHEMKIT_LIBRARIES}) +diff --git a/src/plugins/chemjson/chemjsonfileformat.cpp b/src/plugins/chemjson/chemjsonfileformat.cpp +index a0d271e..3cd5827 100644 +--- a/src/plugins/chemjson/chemjsonfileformat.cpp ++++ b/src/plugins/chemjson/chemjsonfileformat.cpp +@@ -43,7 +43,11 @@ + #include <chemkit/molecule.h> + #include <chemkit/moleculefile.h> + ++#ifdef SYSTEM_JSONCPP ++#include <jsoncpp/json/json.h> ++#else + #include "../../3rdparty/jsoncpp/json/json.h" ++#endif + + namespace { + +diff --git a/src/plugins/cml/cmlfileformat.h b/src/plugins/cml/cmlfileformat.h +index e813223..61a547d 100644 +--- a/src/plugins/cml/cmlfileformat.h ++++ b/src/plugins/cml/cmlfileformat.h +@@ -38,7 +38,11 @@ + + #include <chemkit/moleculefileformat.h> + ++#ifdef SYSTEM_RAPIDXML ++#include <rapidxml/rapidxml.hpp> ++#else + #include "../../3rdparty/rapidxml/rapidxml.hpp" ++#endif + + class CmlFileFormat : public chemkit::MoleculeFileFormat + { +diff --git a/src/plugins/inchi/CMakeLists.txt b/src/plugins/inchi/CMakeLists.txt +index 2b25d9b..5f45f8a 100644 +--- a/src/plugins/inchi/CMakeLists.txt ++++ b/src/plugins/inchi/CMakeLists.txt +@@ -7,7 +7,9 @@ set(SOURCES + inchiplugin.cpp + ) + +-aux_source_directory(../../3rdparty/inchi/ IUPAC_INCHI_SOURCES) ++if(NOT USE_SYSTEM_INCHI) ++ aux_source_directory(../../3rdparty/inchi/ IUPAC_INCHI_SOURCES) ++endif() + + add_chemkit_plugin(inchi ${SOURCES} ${IUPAC_INCHI_SOURCES}) + target_link_libraries(inchi ${CHEMKIT_LIBRARIES}) +diff --git a/src/plugins/inchi/inchikeylineformat.cpp b/src/plugins/inchi/inchikeylineformat.cpp +index 2682f95..cec0a17 100644 +--- a/src/plugins/inchi/inchikeylineformat.cpp ++++ b/src/plugins/inchi/inchikeylineformat.cpp +@@ -38,7 +38,11 @@ + #include <boost/format.hpp> + + #include "inchilineformat.h" ++#ifdef SYSTEM_INCHI ++#include <inchi_api.h> ++#else + #include "../../3rdparty/inchi/inchi_api.h" ++#endif + + InchiKeyLineFormat::InchiKeyLineFormat() + : chemkit::LineFormat("inchikey") +diff --git a/src/plugins/inchi/inchilineformat.cpp b/src/plugins/inchi/inchilineformat.cpp +index 5b9bc42..ea5977c 100644 +--- a/src/plugins/inchi/inchilineformat.cpp ++++ b/src/plugins/inchi/inchilineformat.cpp +@@ -42,7 +42,11 @@ + + #include <boost/algorithm/string.hpp> + ++#ifdef SYSTEM_INCHI ++#include <inchi_api.h> ++#else + #include "../../3rdparty/inchi/inchi_api.h" ++#endif + + #include <chemkit/atom.h> + #include <chemkit/bond.h> +diff --git a/src/plugins/pdb/pdbmlfileformat.cpp b/src/plugins/pdb/pdbmlfileformat.cpp +index 081a4ec..2ca4269 100644 +--- a/src/plugins/pdb/pdbmlfileformat.cpp ++++ b/src/plugins/pdb/pdbmlfileformat.cpp +@@ -35,7 +35,11 @@ + + #include "pdbmlfileformat.h" + ++#ifdef SYSTEM_RAPIDXML ++#include <rapidxml/rapidxml.hpp> ++#else + #include "../../3rdparty/rapidxml/rapidxml.hpp" ++#endif + + #include <chemkit/atom.h> + #include <chemkit/polymer.h> +diff --git a/src/plugins/xtc/CMakeLists.txt b/src/plugins/xtc/CMakeLists.txt +index 98d8ba7..8c09e64 100644 +--- a/src/plugins/xtc/CMakeLists.txt ++++ b/src/plugins/xtc/CMakeLists.txt +@@ -13,7 +13,12 @@ set(SOURCES + xtcplugin.cpp + ) + +-aux_source_directory(../../3rdparty/xdrf/ XDRF_SOURCES) ++ ++if(USE_SYSTEM_XDRF) ++ find_library(XDRF_LIBRARY NAMES xdrfile libxdrfile) ++else() ++ aux_source_directory(../../3rdparty/xdrf/ XDRF_SOURCES) ++endif() + + add_chemkit_plugin(xtc ${SOURCES} ${XDRF_SOURCES}) +-target_link_libraries(xtc ${CHEMKIT_LIBRARIES} ${Boost_LIBRARIES}) ++target_link_libraries(xtc ${CHEMKIT_LIBRARIES} ${Boost_LIBRARIES} ${XDRF_LIBRARY} ) +diff --git a/src/plugins/xtc/xtcfileformat.cpp b/src/plugins/xtc/xtcfileformat.cpp +index 0f00cb6..f8659ca 100644 +--- a/src/plugins/xtc/xtcfileformat.cpp ++++ b/src/plugins/xtc/xtcfileformat.cpp +@@ -47,7 +47,11 @@ + #include <chemkit/trajectoryframe.h> + #include <chemkit/cartesiancoordinates.h> + ++#ifdef SYSTEM_XDRF ++#include <xdrfile/xdrfile.h> ++#else + #include "../../3rdparty/xdrf/xdrf.h" ++#endif + + XtcFileFormat::XtcFileFormat() + : chemkit::TrajectoryFileFormat("xtc") diff --git a/sci-libs/chemkit/metadata.xml b/sci-libs/chemkit/metadata.xml new file mode 100644 index 000000000000..d2802f9728df --- /dev/null +++ b/sci-libs/chemkit/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="applications">Build also applications not only the libraries</flag> + </use> + <upstream> + <remote-id type="sourceforge">chemkit</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/cholmod/Manifest b/sci-libs/cholmod/Manifest new file mode 100644 index 000000000000..dd9c7e598d76 --- /dev/null +++ b/sci-libs/cholmod/Manifest @@ -0,0 +1,6 @@ +AUX cholmod-1.7.4-parmetis32.patch 702 SHA256 fb8f2950c908d21ee649c16f8e26bbe5e37284c1417cf9b7f22e6f82532944f8 SHA512 a1694a7f42f10c7619e23817e93f76df35bc208200918b74a6dd68bb4662d57ce2f3665be424ad4b5c8a4ea9c3957676c48716aa0e47d9fb19337dc43e759ecc WHIRLPOOL ce45b6ad88acebba64df6209d12cfca54a22d7cee9b529b8f20d9f8d855dcdcda6d9485e110bac15b99a86af8b996fccedc0fd43f87bdff83a824d1c2cba1aa6 +DIST cholmod-2.1.2.tar.bz2 656458 SHA256 eea80ad7b797866df1505feafa8c33279f6bc7e7e5aec4f00a167a0a0e73675f SHA512 7aca97de4c60ff2d7a76a776be4c2d61243a159a51b9e147fa2480f2aaf61a5d966eb0f1cb57c0145510437f6c478fa30384b741709d0a02432b74ada3e78089 WHIRLPOOL 8f8f2c4f504f30905c442422042d0b3a203cb24ab289b51bdb4ee6606ca006eef3afb2611bcc6074c1532893caa5ec5a63e4c4d46d115e2528700d98b65dcb27 +EBUILD cholmod-2.1.2.ebuild 1776 SHA256 854badc928abd84bbeea9cd6a1a5f6f0c61e49498f7510ab6b427f52341956b2 SHA512 f83dc657b727a3b160fa8491d013e3c78a401ab9e1e79d620c2db23e003c84ac5375d6651ccacf8bafc0bd00e983effa382710fb092e1e99ff48cf8992c7200d WHIRLPOOL 560d9127b01ba49e2606a3e6ed7c728339fe6011434ace34879c67c3b62e405fdecc8bd2e9235d18a89967bbb6d703de1f5a54ac7a55c7fe3d2c4d29d51b812b +MISC ChangeLog 2658 SHA256 ef0bb84fbc202ea953bff7019e80bb49f50e961b6dda7c87146ad75071c0c400 SHA512 2b01eb2340b2169a336c4215b148c8b4288a8d64434ce2ebc4689d651243f90c8a9f8359f1fe0769b7396892a92986db8d2c9dc8ea4d4bebc1eb1ddde898f748 WHIRLPOOL 65c2196421e027e52a213d03a7855d1edef22ab72f90ad6125cd0d7cad4f5bb4f3b52b09855352ce4da0b6b5d1a97d2984b876f6455bb050c37c95caec76af27 +MISC ChangeLog-2015 6846 SHA256 0bce94bab45022b8bca8d584227b24c799e58ce573d7309fb6323934e21c6515 SHA512 6c804d678836283443a25cb7af76bee629c0fc6d08d62c108598ad641b8c3d12c661a7d0b69da93b34b0bd7dbf39602deac6cd23eab6b073b6ed183449357617 WHIRLPOOL 5334066f64b241ac47a8774d02afb8f3b3c2412f289096ed3cc866efdba40816b8d790f9575af4fa82baf191a4c133a22ddf5576f0daac16c4c3e462576ffe90 +MISC metadata.xml 603 SHA256 fb114028f8b69f3352fcc875d0a4da48f3fffd42e59f980414d47f8f78a23406 SHA512 da9db58edeab0b40813e47567cbaa4e54ae8aa9f4cdc89cd87f1e35bb65991c305bc955e6aba744d322c6375de0e8ba1253415814175cf1f4bc2a01de2e11d22 WHIRLPOOL befdf5d17aae08a5d9eb0f59597f2c74bd9ad3f463df759c9eb5b4b03dcc602dfed11262e852dfb55d8ce13943d6b174d22b3b3d87bf7fbd9c95c545c8d87ac1 diff --git a/sci-libs/cholmod/cholmod-2.1.2.ebuild b/sci-libs/cholmod/cholmod-2.1.2.ebuild new file mode 100644 index 000000000000..32bd49515a4b --- /dev/null +++ b/sci-libs/cholmod/cholmod-2.1.2.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib toolchain-funcs + +DESCRIPTION="Sparse Cholesky factorization and update/downdate library" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/cholmod/" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="minimal? ( LGPL-2.1 ) !minimal? ( GPL-2 )" +SLOT="0" +KEYWORDS="~alpha amd64 ~arm ~arm64 hppa ~ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="cuda doc lapack metis minimal static-libs" + +RDEPEND=" + >=sci-libs/amd-2.3 + >=sci-libs/colamd-2.8 + cuda? ( x11-drivers/nvidia-drivers dev-util/nvidia-cuda-toolkit ) + lapack? ( virtual/lapack ) + metis? ( + >=sci-libs/camd-2.3 + >=sci-libs/ccolamd-2.8 + || ( sci-libs/metis sci-libs/parmetis ) )" + +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base )" + +src_prepare() { + # bug #399483 does not build with parmetis-3.2 + has_version "=sci-libs/parmetis-3.2*" && \ + epatch "${FILESDIR}"/${PN}-1.7.4-parmetis32.patch +} + +src_configure() { + local lapack_libs=no + local blas_libs=no + if use lapack; then + blas_libs=$($(tc-getPKG_CONFIG) --libs blas) + lapack_libs=$($(tc-getPKG_CONFIG) --libs lapack) + fi + local myeconfargs=( + --with-blas="${blas_libs}" + --with-lapack="${lapack_libs}" + $(use_with doc) + $(use_with !minimal modify) + $(use_with !minimal matrixops) + $(use_with !minimal partition) + $(use_with metis camd) + $(use_with metis partition) + $(use_with lapack supernodal) + ) + if use cuda; then + myeconfargs+=( + --with-cuda + --with-cublas-libs="-L${EPREFIX}/opt/cuda/$(get_libdir) -lcublas" + --with-cublas-cflags="-I${EPREFIX}/opt/cuda/include" + ) + fi + autotools-utils_src_configure +} diff --git a/sci-libs/cholmod/files/cholmod-1.7.4-parmetis32.patch b/sci-libs/cholmod/files/cholmod-1.7.4-parmetis32.patch new file mode 100644 index 000000000000..6b50ae8bcea7 --- /dev/null +++ b/sci-libs/cholmod/files/cholmod-1.7.4-parmetis32.patch @@ -0,0 +1,20 @@ +diff -Nur CHOLMOD.orig/Partition/cholmod_metis.c CHOLMOD/Partition/cholmod_metis.c +--- CHOLMOD.orig/Partition/cholmod_metis.c 2012-03-13 03:57:37.000000000 +0000 ++++ CHOLMOD/Partition/cholmod_metis.c 2012-03-13 04:02:22.000000000 +0000 +@@ -216,6 +216,7 @@ + int Opt [8], nn, csp ; + size_t n1 ; + DEBUG (Int nsep) ; ++ float ubfactor = 1.05; + + /* ---------------------------------------------------------------------- */ + /* check inputs */ +@@ -370,7 +371,7 @@ + #endif + + nn = n ; +- METIS_NodeComputeSeparator (&nn, Mp, Mi, Mnw, Mew, Opt, &csp, Mpart) ; ++ METIS_NodeComputeSeparator (&nn, Mp, Mi, Mnw, Mew, &ubfactor, Opt, &csp, Mpart) ; + n = nn ; + csep = csp ; + diff --git a/sci-libs/cholmod/metadata.xml b/sci-libs/cholmod/metadata.xml new file mode 100644 index 000000000000..79ccb35047bf --- /dev/null +++ b/sci-libs/cholmod/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + CHOLMOD is a set of ANSI C routines for sparse Cholesky + factorization and update/downdate. +</longdescription> + <use> + <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag> + <flag name="metis">Enable the Partition module to cholmod using <pkg>sci-libs/metis</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-libs/cifparse-obj/Manifest b/sci-libs/cifparse-obj/Manifest new file mode 100644 index 000000000000..2f8a991763a5 --- /dev/null +++ b/sci-libs/cifparse-obj/Manifest @@ -0,0 +1,13 @@ +AUX cifparse-obj-7.025-gcc4.3.patch 3926 SHA256 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1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild new file mode 100644 index 000000000000..647673dcd240 --- /dev/null +++ b/sci-libs/cifparse-obj/cifparse-obj-7.025-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +MY_P="${PN}-v${PV}-prod-src" + +DESCRIPTION="Provides an object-oriented application interface to information in mmCIF format" +HOMEPAGE="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/index.html" +SRC_URI="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/source/${MY_P}.tar.gz" + +LICENSE="PDB" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="" + +RDEPEND="" +DEPEND=" + sys-devel/bison + sys-devel/flex" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-makefile.patch \ + "${FILESDIR}"/${P}-gcc4.3.patch \ + "${FILESDIR}"/${P}-gcc4.7.patch \ + "${FILESDIR}"/${P}-gcc5_6.patch \ + "${FILESDIR}"/${PN}-7.025-strncasecmp-declaration.patch + + sed \ + -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ + -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ + -e "s:^\(F77=\).*:\1${FORTRANC}:g" \ + -e "s:^\(F77_LINKER=\).*:\1${FORTRANC}:g" \ + -e "s:-static::g" \ + -i "${S}"/etc/make.* || die "Failed to fix makefile" +} + +src_compile() { + # parallel make fails + emake -j1 +} + +src_install() { + dolib.a lib/* + insinto /usr/include/${PN} + doins include/* +} diff --git a/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild b/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild new file mode 100644 index 000000000000..622af4794346 --- /dev/null +++ b/sci-libs/cifparse-obj/cifparse-obj-7.105.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils toolchain-funcs + +MY_P="${PN}-v${PV}-prod-src" + +DESCRIPTION="Provides an object-oriented application interface to information in mmCIF format" +HOMEPAGE="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/index.html" +SRC_URI="http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/source/${MY_P}.tar.gz" + +LICENSE="PDB" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="" + +RDEPEND="" +DEPEND=" + sys-devel/bison + sys-devel/flex" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${PN}-7.025-gcc5_6.patch +) + +src_prepare() { + default + + sed \ + -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ + -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ + -e "s:^\(F77=\).*:\1${FORTRANC}:g" \ + -e "s:^\(F77_LINKER=\).*:\1${FORTRANC}:g" \ + -e "s:-static::g" \ + -i "${S}"/etc/make.* || die "Failed to fix makefile" +} + +src_compile() { + # parallel make fails + emake -j1 \ + C_OPT="${CFLAGS}" \ + CXX_OPT="${CXXFLAGS}" +} + +src_install() { + dolib.a lib/* + insinto /usr/include/${PN} + doins include/* +} diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch new file mode 100644 index 000000000000..1715f493a6e0 --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.3.patch @@ -0,0 +1,87 @@ +diff -Naur cifparse-obj-v7.025-prod-src/cif-file-v1.0/src/CifFile.C cifparse-obj-v7.025-prod-src.new/cif-file-v1.0/src/CifFile.C +--- cifparse-obj-v7.025-prod-src/cif-file-v1.0/src/CifFile.C 2008-02-06 07:17:50.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/cif-file-v1.0/src/CifFile.C 2008-09-03 09:36:41.000000000 -0400 +@@ -153,6 +153,7 @@ + // VLAD - Carefully examine all methods that accept with, for cases where + // with is 0. This may happen if the value is empty !! + ++#include <algorithm> + #include "GenString.h" + #include "CifString.h" + #include "regex.h" +diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest3.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest3.C +--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest3.C 2008-02-06 07:17:51.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest3.C 2008-09-03 09:40:12.000000000 -0400 +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdlib> + #include "GenString.h" + #include "CifFile.h" + +diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest7.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest7.C +--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest7.C 2008-02-06 07:17:51.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest7.C 2008-09-03 09:40:42.000000000 -0400 +@@ -3,6 +3,7 @@ + */ + #include "CifFile.h" + #include <iostream> ++#include <cstdlib> + + void FillTestTable(ISTable *s); + void TwoCifFileObj(); +diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest8.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest8.C +--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/FOtest8.C 2008-02-06 07:17:51.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/FOtest8.C 2008-09-03 09:41:06.000000000 -0400 +@@ -1,6 +1,7 @@ + /* Test for reading binary files of two different versions*/ + #include "CifFile.h" + #include <iostream> ++#include <cstdlib> + + + #define FALSE 0 +diff -Naur cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/SdbReader.C cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/SdbReader.C +--- cifparse-obj-v7.025-prod-src/cifparse-test-v1.0/src/SdbReader.C 2008-02-06 07:17:51.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/cifparse-test-v1.0/src/SdbReader.C 2008-09-03 09:41:50.000000000 -0400 +@@ -1,4 +1,5 @@ + #include <iostream> ++#include <cstdlib> + #include "CifFile.h" + + +diff -Naur cifparse-obj-v7.025-prod-src/common-v4.5/src/GenString.C cifparse-obj-v7.025-prod-src.new/common-v4.5/src/GenString.C +--- cifparse-obj-v7.025-prod-src/common-v4.5/src/GenString.C 2008-02-06 07:17:49.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/common-v4.5/src/GenString.C 2008-09-03 09:32:17.000000000 -0400 +@@ -138,7 +138,7 @@ + POSSIBILITY THEREOF. + */ + +- ++#include <cstring> + // Needed, since some platforms do not define std:: elsewhere + #include <ctype.h> + +diff -Naur cifparse-obj-v7.025-prod-src/tables-v8.0/src/ISTable.C cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ISTable.C +--- cifparse-obj-v7.025-prod-src/tables-v8.0/src/ISTable.C 2008-02-06 07:17:50.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ISTable.C 2008-09-03 09:35:57.000000000 -0400 +@@ -150,6 +150,8 @@ + #include <sstream> + #include <iostream> + #include <iomanip> ++#include <algorithm> ++#include <climits> + + #include "Exceptions.h" + #include "GenString.h" +diff -Naur cifparse-obj-v7.025-prod-src/tables-v8.0/src/ITTable.C cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ITTable.C +--- cifparse-obj-v7.025-prod-src/tables-v8.0/src/ITTable.C 2008-02-06 07:17:50.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/tables-v8.0/src/ITTable.C 2008-09-03 09:35:29.000000000 -0400 +@@ -150,6 +150,8 @@ + #include <sstream> + #include <iostream> + #include <iomanip> ++#include <algorithm> ++#include <climits> + + #include "Exceptions.h" + #include "GenString.h" diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch new file mode 100644 index 000000000000..b828ae618caa --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc4.7.patch @@ -0,0 +1,64 @@ + common-v4.5/src/mapped_ptr_vector.C | 14 +++++++------- + 1 files changed, 7 insertions(+), 7 deletions(-) + +diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C +index 0ffff35..993d0b9 100644 +--- a/common-v4.5/src/mapped_ptr_vector.C ++++ b/common-v4.5/src/mapped_ptr_vector.C +@@ -256,12 +256,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP, + _vector.push_back(inP); + + typename tIndex::value_type valuePair(inP->GetName(), +- make_pair(_vector.size() - 1, fileIndex)); ++ std::make_pair(_vector.size() - 1, fileIndex)); + + _index.insert(valuePair); + + _currentName = inP->GetName(); +- _currentIndices = make_pair(_vector.size() - 1, fileIndex); ++ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); + + } + +@@ -274,12 +274,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name, + _vector.push_back(NULL); + + typename tIndex::value_type valuePair(name, +- make_pair(_vector.size() - 1, fileIndex)); ++ std::make_pair(_vector.size() - 1, fileIndex)); + + _index.insert(valuePair); + + _currentName = name; +- _currentIndices = make_pair(_vector.size() - 1, fileIndex); ++ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); + } + + +@@ -447,7 +447,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name) + if (is_equal(_currentName, name, keyComp)) + { + _currentName.clear(); +- _currentIndices = make_pair(_vector.size(), (unsigned int)0); ++ _currentIndices = std::make_pair(_vector.size(), (unsigned int)0); + } + + } +@@ -532,7 +532,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic + if (_vector.empty()) + { + // Empty container. Return invalid index. +- return(make_pair(_vector.size(), (unsigned int)0)); ++ return(std::make_pair(_vector.size(), (unsigned int)0)); + } + + typename tIndex::key_compare keyComp = _index.key_comp(); +@@ -556,7 +556,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic + else + { + // Not found. Return invalid index. +- return(make_pair(_vector.size(), (unsigned int)0)); ++ return(std::make_pair(_vector.size(), (unsigned int)0)); + } + } + diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch new file mode 100644 index 000000000000..2ac0ec220d9e --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-gcc5_6.patch @@ -0,0 +1,16 @@ + etc/platform.sh | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/etc/platform.sh b/etc/platform.sh +index ff0ab51..1b56ab1 100755 +--- a/etc/platform.sh ++++ b/etc/platform.sh +@@ -60,7 +60,7 @@ case `uname -s` in + # Check if it is a Linux platform + Linux) + # Check if it is GCC version 4.x +- gcc_ver=`gcc --version | grep -e " 4\."` ++ gcc_ver=`gcc --version | grep -e " [456]\."` + if [[ -z $gcc_ver ]] + then + # It is not GCC version 4.x. Check if it is GCC version 3.x diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch new file mode 100644 index 000000000000..9e9a61788ddf --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-makefile.patch @@ -0,0 +1,115 @@ +diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3 +--- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu3 2008-02-06 07:17:49.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu3 2008-09-03 09:18:55.000000000 -0400 +@@ -107,8 +107,8 @@ + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ ++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ + $(INCLUDES) + + ## C++ compiler +@@ -128,13 +128,13 @@ + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ ++C++FLAGS=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ + $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +-C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ ++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ + $(INCLUDES) + + ## Fortran compiler +@@ -144,7 +144,7 @@ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -157,7 +157,7 @@ + STATIC_LINKING=-static + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT) + LDFLAGS_NO_STATIC=$(ABI) -w + + # Fortran linker +diff -Naur cifparse-obj-v7.025-prod-src/etc/make.platform.gnu4 cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu4 +--- cifparse-obj-v7.025-prod-src/etc/make.platform.gnu4 2008-02-06 07:17:49.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/etc/make.platform.gnu4 2008-09-03 09:20:16.000000000 -0400 +@@ -107,12 +107,12 @@ + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ ++CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ + $(INCLUDES) + + ## C++ compiler +-## This part defines C++ compiler information ++ + + # C++ compiler executable + CCC=g++ +@@ -128,13 +128,13 @@ + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ ++C++FLAGS=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ + $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +-C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ ++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ + $(INCLUDES) + + ## Fortran compiler +@@ -144,7 +144,7 @@ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -157,7 +157,7 @@ + STATIC_LINKING=-static + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT) + LDFLAGS_NO_STATIC=$(ABI) -w + + # Fortran linker +diff -Naur cifparse-obj-v7.025-prod-src/Makefile cifparse-obj-v7.025-prod-src.new/Makefile +--- cifparse-obj-v7.025-prod-src/Makefile 2008-02-06 07:17:48.000000000 -0500 ++++ cifparse-obj-v7.025-prod-src.new/Makefile 2008-09-03 09:19:12.000000000 -0400 +@@ -62,7 +62,7 @@ + echo "------------------------------------------------------------"; \ + echo "**** Making $$libdir ****"; \ + echo "------------------------------------------------------------"; \ +- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ ++ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CXX_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LD_OPT="${LDFLAGS}" install) || exit 1; \ + done + + debug: diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch new file mode 100644 index 000000000000..9222ff27699e --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.025-strncasecmp-declaration.patch @@ -0,0 +1,16 @@ +Remove incorrect prototypes of the 'strcasecmp' and 'strncasecmp' functions. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594054 + +--- a/misclib-v2.2/include/ndb_misclib.h ++++ b/misclib-v2.2/include/ndb_misclib.h +@@ -167,10 +167,6 @@ + #define NDB_MSG_BUFFER_LEN 200000 + + +-#if !defined(HAVE_STRCASECMP) +-int strcasecmp (const char *s1, const char *s2); +-int strncasecmp (const char *s1, const char *s2, unsigned int n); +-#endif + /* + * ndb_misclib.c prototypes + */ diff --git a/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch b/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch new file mode 100644 index 000000000000..1716cd6390a4 --- /dev/null +++ b/sci-libs/cifparse-obj/files/cifparse-obj-7.105-makefile.patch @@ -0,0 +1,110 @@ + etc/make.platform.gnu3 | 14 +++++++------- + etc/make.platform.gnu4 | 16 ++++++++-------- + 2 files changed, 15 insertions(+), 15 deletions(-) + +diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3 +index 54b0297..138fa47 100644 +--- a/etc/make.platform.gnu3 ++++ b/etc/make.platform.gnu3 +@@ -107,8 +107,8 @@ NON_ANSI_C_FLAG= + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(C_WARNINGS) \ ++CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(C_WARNINGS) \ + $(DEFINES) $(INCLUDES) + + ## C++ compiler +@@ -128,14 +128,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ ++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ + $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES) + + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +-C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ ++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + $(DEFINES) $(INCLUDES) + + ## Fortran compiler +@@ -145,7 +145,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -158,7 +158,7 @@ F77LIBS= + STATIC_LINKING=-static + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT) + LDFLAGS_NO_STATIC=$(ABI) -w + + # Fortran linker +diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4 +index 6676f35..51681fa 100644 +--- a/etc/make.platform.gnu4 ++++ b/etc/make.platform.gnu4 +@@ -107,11 +107,11 @@ NON_ANSI_C_FLAG= + C_WARNINGS=$(WARNINGS) + + # C compiler flags +-CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) +-CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) ++CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) ++CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) + + ## C++ compiler +-## This part defines C++ compiler information ++ + + # C++ compiler executable + CCC=g++ +@@ -127,14 +127,14 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) + EXT=C + + # C++ compiler flags +-C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ ++C++FLAGS=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ + $(DEFINES) $(INCLUDES) +-C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ ++C++FLAGS_NONANSI=$(CXX_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ + $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES) + + # C++FLAGS_RELAXED should be set to avoid warnings reported by third party + # source code that is not maintained by PDB +-C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ ++C++FLAGS_RELAXED=$(CXX_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + $(DEFINES) $(INCLUDES) + + ## Fortran compiler +@@ -144,7 +144,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ + F77=f77 + + # Fortran compiler flags +-FFLAGS=-O -u ++FFLAGS=$(F_OPT) + + # Additional Fortran libraries + F77LIBS= +@@ -157,7 +157,7 @@ F77LIBS= + STATIC_LINKING=-static + + # Linker flags +-LDFLAGS=$(ABI) -w $(STATIC_LINKING) ++LDFLAGS=$(ABI) -w $(STATIC_LINKING) $(LD_OPT) + LDFLAGS_NO_STATIC=$(ABI) -w + + # Fortran linker diff --git a/sci-libs/cifparse-obj/metadata.xml b/sci-libs/cifparse-obj/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/cifparse-obj/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/clapack/Manifest b/sci-libs/clapack/Manifest new file mode 100644 index 000000000000..2cc41bfddf3a --- /dev/null +++ b/sci-libs/clapack/Manifest @@ -0,0 +1,9 @@ +AUX clapack-3.2.1-findblas-r7.patch 3163 SHA256 fd01b1709b1beb97fc69332b0ced2a703c30f4ba92fbad7d5666bb1eebb91437 SHA512 84010f10a0d7932597638018ee607414ff5420ba168dc7b3200caeecaf3afdf3e17af9fdee558ce919c67d66c2c795a290fd0d882bfcc53a2e9f7afec0879c57 WHIRLPOOL b07c35288de19653df7e5df20facde32b1093966ec4a3abf2415ed82c303b25e2e796be4d8c9ccbc5818b3ef4b802df82d9a0d915b8a5f264e6dbfbe5bb94e71 +AUX clapack-3.2.1-fix_include_file.patch 689 SHA256 9b6024cecbfb152d910b8fb878db6918704388479876719b43f4378992581603 SHA512 74bddac93db98e2752eb7064578e246e113bc850fe8671ecd129f05490345130ded6c5188eb07cc6a086b8044959a4595ee46912af30ee39b9f80244d7b8335b WHIRLPOOL 99732f878d800cacaa819fe211a6109b4a4426971dae808357fc7425d92ad6144f160c4ff897be66504e891295fb7aebc9fcc7036930f22eda3549eca951ce92 +AUX clapack-3.2.1-hang.patch 641 SHA256 19322ccb00dea5abdd28aaad5c25ad58c4a6bb8b5ad15e9dad329fa6c113f9a8 SHA512 a6e7461bfe7bddd2120c46e3629a899cc12c23669b22b562675922bf11d2fb69793e8093d24773d688e0d7e1f24c08b16ccd2b01631b23f55fbb7a10c29ed036 WHIRLPOOL 066c25f92ef6354c113f3ccc46f50fc884c323d718e5db50a68fa7981e1e7e5366f1ca847901f3fb7c9e73d1a5ebe061c4342d2819ed9d06cefd3c0df2818599 +AUX clapack-3.2.1-noblasf2c.patch 5841 SHA256 37525a9099aba9130346abd2b765d05b7164c880a45b0b231b9bedfd63894fc2 SHA512 68571f682e7015c75104494f8d156cd0c1f758aa03d9c2614f93db418c8d4f9c9c2e7b5d965022060f776a9baa8d48c15bbfa30dbcada03bccffa4ebb3c4deef WHIRLPOOL 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071bc02d47c79e4e359ab77a19fe60f6b10f8b42262f2be048e6f1de61ed57334c9d6f41114a96775bc956dd8460e3bf6d7042916857f74f439bef700fd1542f WHIRLPOOL 9ee1847de2e0aa89f04035335eeb2439d384750ada623324126f06a5fb2a6918a8292da6fd09c8a261375259844810cd3714f2346c6fe252c4c9aa7aa0ccdbb5 +MISC ChangeLog-2015 4333 SHA256 262a6ac6978faff15abd8dc5546488487cb1136acc655bebb5f26e6c92310470 SHA512 4a12a81ba1010730819efa3b8352dc5c28799933ece0a770bd1f3fcf664d0df5708cb8f439c14ccc6e6c63297c570bb0eeb353759b6fbacdca3cf400670ac25d WHIRLPOOL 5d6697fe02e892766aed70df7b0cb4d7010afabd9d4c6cd56021325df6e08211bb0340731ea74bbec503b4ee7761bb383d40d76199e5dac0114afab561f07fcb +MISC metadata.xml 725 SHA256 d4c049aa4012ef5e6bb169f1187dc84f3489975ff1c510d7041e113f6a750f69 SHA512 78f3e4fc5bf308d619a1544d5e5125dce565fe7b9a4c563b25096c137bf2edee3a17b9c91f50442b8d2498bd1bd37c0d44b39f7e0dcdfd3a0e5583f01eb93c19 WHIRLPOOL cd37260192cea1cdecc6acce04942a19b19d1c973235babcf9467e2998329369389959e747957a2bf0f984b138f6e5faffd8c67cb280177d8c6fb3edde084ade diff --git a/sci-libs/clapack/clapack-3.2.1-r8.ebuild b/sci-libs/clapack/clapack-3.2.1-r8.ebuild new file mode 100644 index 000000000000..ac9a2c73f97e --- /dev/null +++ b/sci-libs/clapack/clapack-3.2.1-r8.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic cmake-utils + +DESCRIPTION="f2c'ed version of LAPACK" +HOMEPAGE="http://www.netlib.org/clapack/" +SRC_URI="http://www.netlib.org/${PN}/${P}-CMAKE.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + >=dev-libs/libf2c-20090407-r1 + virtual/blas" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${P}-CMAKE + +PATCHES=( + "${FILESDIR}/${P}-fix_include_file.patch" + "${FILESDIR}/${P}-noblasf2c.patch" + "${FILESDIR}/${P}-hang.patch" + "${FILESDIR}/${P}-findblas-r7.patch" +) + +# bug 433806 +RESTRICT="test" + +src_prepare() { + rm INCLUDE/f2c.h F2CLIBS/libf2c/f2c.h || die + cmake-utils_src_prepare +} + +src_configure() { + filter-flags -ftree-vectorize + # causes an internal compiler error with gcc-4.6.2 + + local mycmakeargs=( -DENABLE_TESTS=$(usex test) ) + cmake-utils_src_configure +} diff --git a/sci-libs/clapack/files/clapack-3.2.1-findblas-r7.patch b/sci-libs/clapack/files/clapack-3.2.1-findblas-r7.patch new file mode 100644 index 000000000000..c82cd50a2c5b --- /dev/null +++ b/sci-libs/clapack/files/clapack-3.2.1-findblas-r7.patch @@ -0,0 +1,84 @@ + CMakeLists.txt | 29 +++++++++++++++++++++++++++-- + SRC/CMakeLists.txt | 7 ++++++- + TESTING/CMakeLists.txt | 5 +++++ + 3 files changed, 38 insertions(+), 3 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 37fb433..fe29d4c 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -28,7 +28,33 @@ set(CPACK_PACKAGE_VERSION_MAJOR 3) + set(CPACK_PACKAGE_VERSION_MINOR 2) + set(CPACK_PACKAGE_VERSION_PATCH 1) + +-set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") ++if(BLAS_LIBRARIES) ++ include(CheckFortranFunctionExists) ++ set(CMAKE_REQUIRED_LIBRARIES ${BLAS_LIBRARIES}) ++ CHECK_FORTRAN_FUNCTION_EXISTS("dgemm" BLAS_FOUND) ++ unset( CMAKE_REQUIRED_LIBRARIES ) ++ if(BLAS_FOUND) ++ message(STATUS "--> BLAS supplied by user is WORKING, will use ${BLAS_LIBRARIES}.") ++ else(BLAS_FOUND) ++ message(ERROR "--> BLAS supplied by user is not WORKING, CANNOT USE ${BLAS_LIBRARIES}.") ++ message(ERROR "--> Will use REFERENCE BLAS (by default)") ++ message(ERROR "--> Or Correct your BLAS_LIBRARIES entry ") ++ message(ERROR "--> Or Consider checking USE_OPTIMIZED_BLAS") ++ endif(BLAS_FOUND) ++else(BLAS_LIBRARIES) ++ # User did not provide a BLAS Library ++ find_package(PkgConfig) ++ pkg_check_modules(BLAS blas) ++endif (BLAS_LIBRARIES) ++ ++if(NOT BLAS_FOUND) ++ message(FATAL_ERROR "--> BLAS libraries needed but not found.") ++endif(NOT BLAS_FOUND) ++ ++if(BLAS_LIBRARY_DIRS) ++# SET_TARGET_PROPERTIES(clapack PROPERTIES LINK_FLAGS ${LINK_FLAGS} -L"${BLAS_LIBRARY_DIRS}") ++ SET (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -L\"${BLAS_LIBRARY_DIRS}\"") ++endif() + + add_subdirectory(SRC) + +@@ -44,4 +70,3 @@ configure_file(${CLAPACK_SOURCE_DIR}/clapack-config-version.cmake.in + ${CLAPACK_BINARY_DIR}/clapack-config-version.cmake @ONLY) + configure_file(${CLAPACK_SOURCE_DIR}/clapack-config.cmake.in + ${CLAPACK_BINARY_DIR}/clapack-config.cmake @ONLY) +- +diff --git a/SRC/CMakeLists.txt b/SRC/CMakeLists.txt +index 7b75ee9..39380ed 100644 +--- a/SRC/CMakeLists.txt ++++ b/SRC/CMakeLists.txt +@@ -376,8 +376,13 @@ if(BUILD_COMPLEX16) + set(ALLOBJ ${ZLASRC} ${ALLAUX} ${DZLAUX}) + endif() + ++set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") ++ + add_library(clapack SHARED ${ALLOBJ} ${ALLXOBJ}) +-target_link_libraries(clapack blas f2c m) ++target_link_libraries(clapack ${BLAS_LIBRARIES} f2c m) ++if(BLAS_LIBRARY_DIRS) ++ SET_TARGET_PROPERTIES(clapack PROPERTIES LINK_FLAGS ${LINK_FLAGS} -L"${BLAS_LIBRARY_DIRS}") ++endif() + set_target_properties(clapack PROPERTIES SOVERSION "${CLAPACK_VERSION}") + + install( +diff --git a/TESTING/CMakeLists.txt b/TESTING/CMakeLists.txt +index d59359d..174672e 100644 +--- a/TESTING/CMakeLists.txt ++++ b/TESTING/CMakeLists.txt +@@ -4,6 +4,11 @@ if(MSVC_VERSION) + string(REGEX REPLACE "(.*)/STACK:(.*) (.*)" "\\1/STACK:900000000000000000 \\3" + CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}") + endif() ++if(BLAS_LIBRARY_DIRS) ++# SET_TARGET_PROPERTIES(clapack PROPERTIES LINK_FLAGS ${LINK_FLAGS} -L"${BLAS_LIBRARY_DIRS}") ++ SET (CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -L\"${BLAS_LIBRARY_DIRS}\"") ++endif() ++ + add_subdirectory(MATGEN) + add_subdirectory(LIN) + add_subdirectory(EIG) diff --git a/sci-libs/clapack/files/clapack-3.2.1-fix_include_file.patch b/sci-libs/clapack/files/clapack-3.2.1-fix_include_file.patch new file mode 100644 index 000000000000..002336f2d124 --- /dev/null +++ b/sci-libs/clapack/files/clapack-3.2.1-fix_include_file.patch @@ -0,0 +1,25 @@ +diff -urN clapack-3.2.1-CMAKE.old/INCLUDE/clapack.h clapack-3.2.1-CMAKE/INCLUDE/clapack.h +--- clapack-3.2.1-CMAKE.old/INCLUDE/clapack.h 2011-04-30 11:39:51.000000000 +0200 ++++ clapack-3.2.1-CMAKE/INCLUDE/clapack.h 2011-04-30 11:40:39.000000000 +0200 +@@ -3,6 +3,12 @@ + #ifndef __CLAPACK_H + #define __CLAPACK_H + ++#include <f2c.h> ++ ++#ifdef __cplusplus ++extern "C" { ++#endif ++ + /* Subroutine */ int caxpy_(integer *n, complex *ca, complex *cx, integer * + incx, complex *cy, integer *incy); + +@@ -7250,5 +7256,8 @@ + integer ilaenv_(integer *ispec, char *name__, char *opts, integer *n1, + integer *n2, integer *n3, integer *n4); + ++#ifdef __cplusplus ++} ++#endif + + #endif /* __CLAPACK_H */ diff --git a/sci-libs/clapack/files/clapack-3.2.1-hang.patch b/sci-libs/clapack/files/clapack-3.2.1-hang.patch new file mode 100644 index 000000000000..f9ec2e0ec18c --- /dev/null +++ b/sci-libs/clapack/files/clapack-3.2.1-hang.patch @@ -0,0 +1,13 @@ +diff -ruN clapack-3.2.1-CMAKE.orig/SRC/CMakeLists.txt clapack-3.2.1-CMAKE/SRC/CMakeLists.txt +--- clapack-3.2.1-CMAKE.orig/SRC/CMakeLists.txt 2011-06-21 00:29:16.275749375 +0200 ++++ clapack-3.2.1-CMAKE/SRC/CMakeLists.txt 2011-06-21 00:31:06.133749448 +0200 +@@ -355,6 +355,9 @@ + zla_heamv.c zla_hercond_c.c zla_hercond_x.c zla_herpvgrw.c + zla_lin_berr.c zlarscl2.c zlascl2.c zla_wwaddw.c) + ++if(CMAKE_COMPILER_IS_GNUCC) ++ set_source_files_properties(../INSTALL/dlamch.c ../INSTALL/slamch.c PROPERTIES COMPILE_FLAGS "-ffloat-store -O0") ++endif() + + if( USEXBLAS) + set(ALLXOBJ ${SXLASRC} ${DXLASRC} ${CXLASRC} ${ZXLASRC} ${ALLXAUX}) diff --git a/sci-libs/clapack/files/clapack-3.2.1-noblasf2c.patch b/sci-libs/clapack/files/clapack-3.2.1-noblasf2c.patch new file mode 100644 index 000000000000..5ae9e63977c6 --- /dev/null +++ b/sci-libs/clapack/files/clapack-3.2.1-noblasf2c.patch @@ -0,0 +1,189 @@ +diff -u -r -N clapack-3.2.1-CMAKE.orig/CMakeLists.txt clapack-3.2.1-CMAKE/CMakeLists.txt +--- clapack-3.2.1-CMAKE.orig/CMakeLists.txt 2009-08-10 20:46:33.000000000 +0200 ++++ clapack-3.2.1-CMAKE/CMakeLists.txt 2010-08-28 14:04:30.000000000 +0200 +@@ -1,7 +1,10 @@ + cmake_minimum_required(VERSION 2.6) + project(CLAPACK C) +-enable_testing() +-include(CTest) ++ ++if(ENABLE_TESTS) ++ enable_testing() ++ include(CTest) ++endif(ENABLE_TESTS) + + if(WIN32 AND NOT CYGWIN) + set(SECOND_SRC ${CLAPACK_SOURCE_DIR}/INSTALL/winsecond.c) +@@ -11,24 +14,34 @@ + set(SECOND_SRC ${CLAPACK_SOURCE_DIR}/INSTALL/second.c) + set(DSECOND_SRC ${CLAPACK_SOURCE_DIR}/INSTALL/dsecnd.c) + endif() +-enable_testing() ++ + option(USE_BLAS_WRAP "pre-pend f2c_ to each function in blas" OFF) + if(NOT USE_BLAS_WRAP) + # _zrotg_ seems to be missing in the wrap header + add_definitions(-DNO_BLAS_WRAP) + endif() ++ + include_directories(${CLAPACK_SOURCE_DIR}/INCLUDE) +-add_subdirectory(F2CLIBS) +-add_subdirectory(BLAS) +-add_subdirectory(SRC) +-add_subdirectory(TESTING) ++ + set(CLAPACK_VERSION 3.2.1) + set(CPACK_PACKAGE_VERSION_MAJOR 3) + set(CPACK_PACKAGE_VERSION_MINOR 2) + set(CPACK_PACKAGE_VERSION_PATCH 1) ++ ++set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") ++ ++add_subdirectory(SRC) ++ ++if(ENABLE_TESTS) ++ add_subdirectory(TESTING) ++endif(ENABLE_TESTS) ++ + include(CPack) +-export(TARGETS f2c blas lapack FILE clapack-targets.cmake) ++ ++export(TARGETS clapack FILE clapack-targets.cmake) ++ + configure_file(${CLAPACK_SOURCE_DIR}/clapack-config-version.cmake.in + ${CLAPACK_BINARY_DIR}/clapack-config-version.cmake @ONLY) + configure_file(${CLAPACK_SOURCE_DIR}/clapack-config.cmake.in + ${CLAPACK_BINARY_DIR}/clapack-config.cmake @ONLY) ++ +diff -u -r -N clapack-3.2.1-CMAKE.orig/SRC/CMakeLists.txt clapack-3.2.1-CMAKE/SRC/CMakeLists.txt +--- clapack-3.2.1-CMAKE.orig/SRC/CMakeLists.txt 2009-08-10 19:47:54.000000000 +0200 ++++ clapack-3.2.1-CMAKE/SRC/CMakeLists.txt 2010-08-28 14:32:17.000000000 +0200 +@@ -375,6 +375,20 @@ + if(BUILD_COMPLEX16) + set(ALLOBJ ${ZLASRC} ${ALLAUX} ${DZLAUX}) + endif() +-add_library(lapack ${ALLOBJ} ${ALLXOBJ}) +-target_link_libraries(lapack blas) + ++add_library(clapack SHARED ${ALLOBJ} ${ALLXOBJ}) ++target_link_libraries(clapack blas f2c m) ++set_target_properties(clapack PROPERTIES SOVERSION "${CLAPACK_VERSION}") ++ ++install( ++ TARGETS clapack EXPORT clapack ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ++) ++ ++install( ++ FILES ../INCLUDE/clapack.h DESTINATION include/clapack ++) ++ ++install( ++ EXPORT clapack DESTINATION "share/cmake/Modules" FILE clapack-config.cmake ++) +diff -u -r -N clapack-3.2.1-CMAKE.orig/TESTING/EIG/CMakeLists.txt clapack-3.2.1-CMAKE/TESTING/EIG/CMakeLists.txt +--- clapack-3.2.1-CMAKE.orig/TESTING/EIG/CMakeLists.txt 2009-08-10 19:47:54.000000000 +0200 ++++ clapack-3.2.1-CMAKE/TESTING/EIG/CMakeLists.txt 2010-08-28 13:46:40.000000000 +0200 +@@ -119,7 +119,7 @@ + + macro(add_eig_executable name ) + add_executable(${name} ${ARGN}) +- target_link_libraries(${name} tmglib lapack ) ++ target_link_libraries(${name} tmglib clapack ) + endmacro(add_eig_executable) + + add_eig_executable(xeigtsts ${SEIGTST} ${SCIGTST} ${AEIGTST} +diff -u -r -N clapack-3.2.1-CMAKE.orig/TESTING/LIN/CMakeLists.txt clapack-3.2.1-CMAKE/TESTING/LIN/CMakeLists.txt +--- clapack-3.2.1-CMAKE.orig/TESTING/LIN/CMakeLists.txt 2009-08-10 20:06:06.000000000 +0200 ++++ clapack-3.2.1-CMAKE/TESTING/LIN/CMakeLists.txt 2010-08-28 13:46:40.000000000 +0200 +@@ -189,7 +189,7 @@ + + macro(add_lin_executable name ) + add_executable(${name} ${ARGN}) +- target_link_libraries(${name} tmglib lapack) ++ target_link_libraries(${name} tmglib clapack) + endmacro(add_lin_executable) + + add_lin_executable(xlintsts ${ALINTST} ${SCLNTST} ${SLINTST} +diff -u -r -N clapack-3.2.1-CMAKE.orig/TESTING/MATGEN/CMakeLists.txt clapack-3.2.1-CMAKE/TESTING/MATGEN/CMakeLists.txt +--- clapack-3.2.1-CMAKE.orig/TESTING/MATGEN/CMakeLists.txt 2009-08-10 19:47:54.000000000 +0200 ++++ clapack-3.2.1-CMAKE/TESTING/MATGEN/CMakeLists.txt 2010-08-28 13:46:40.000000000 +0200 +@@ -65,5 +65,6 @@ + if(BUILD_COMPLEX16) + set(ALLOBJ $(ZMATGEN) $(DZATGEN)) + endif() +-add_library(tmglib ${ALLOBJ} ) ++ ++add_library(tmglib ${ALLOBJ} i_len_trim.c i_ceiling.c ) + +diff -u -r -N clapack-3.2.1-CMAKE.orig/TESTING/MATGEN/i_ceiling.c clapack-3.2.1-CMAKE/TESTING/MATGEN/i_ceiling.c +--- clapack-3.2.1-CMAKE.orig/TESTING/MATGEN/i_ceiling.c 1970-01-01 01:00:00.000000000 +0100 ++++ clapack-3.2.1-CMAKE/TESTING/MATGEN/i_ceiling.c 2010-08-28 13:46:40.000000000 +0200 +@@ -0,0 +1,38 @@ ++/* file has been copied from the included f2c library - dilfridge */ ++ ++#include <f2c.h> ++ ++#ifdef KR_headers ++integer i_sceiling(x) real *x; ++#else ++#ifdef __cplusplus ++extern "C" { ++#endif ++integer i_sceiling(real *x) ++#endif ++{ ++#define CEIL(x) ((int)(x) + ((x) > 0 && (x) != (int)(x))) ++ ++ return (integer) CEIL(*x); ++} ++#ifdef __cplusplus ++} ++#endif ++ ++ ++#ifdef KR_headers ++integer i_dceiling(x) doublereal *x; ++#else ++#ifdef __cplusplus ++extern "C" { ++#endif ++integer i_dceiling(doublereal *x) ++#endif ++{ ++#define CEIL(x) ((int)(x) + ((x) > 0 && (x) != (int)(x))) ++ ++ return (integer) CEIL(*x); ++} ++#ifdef __cplusplus ++} ++#endif +diff -u -r -N clapack-3.2.1-CMAKE.orig/TESTING/MATGEN/i_len_trim.c clapack-3.2.1-CMAKE/TESTING/MATGEN/i_len_trim.c +--- clapack-3.2.1-CMAKE.orig/TESTING/MATGEN/i_len_trim.c 1970-01-01 01:00:00.000000000 +0100 ++++ clapack-3.2.1-CMAKE/TESTING/MATGEN/i_len_trim.c 2010-08-28 13:46:40.000000000 +0200 +@@ -0,0 +1,25 @@ ++/* file has been copied from the included f2c library - dilfridge */ ++ ++#include <f2c.h> ++ ++#ifdef __cplusplus ++extern "C" { ++#endif ++ ++#ifdef KR_headers ++integer i_len_trim(s, n) char *s; ftnlen n; ++#else ++integer i_len_trim(char *s, ftnlen n) ++#endif ++{ ++ int i; ++ ++ for(i=n-1;i>=0;i--) ++ if(s[i] != ' ') ++ return i + 1; ++ ++ return(0); ++} ++#ifdef __cplusplus ++} ++#endif diff --git a/sci-libs/clapack/metadata.xml b/sci-libs/clapack/metadata.xml new file mode 100644 index 000000000000..5f899e3c2212 --- /dev/null +++ b/sci-libs/clapack/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + LAPACK is a comprehensive library that does linear algebra + operations including matrix inversions, least squared solutions to + linear sets of equations, eigenvector analysis, singular value + decomposition, etc. It is a very comprehensive and reputable package + that has found extensive use in the scientific community. + This package installs the reference C implementation from Netlib, + generated from f2c. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/clashscore-db/Manifest b/sci-libs/clashscore-db/Manifest new file mode 100644 index 000000000000..f8108bd10e50 --- /dev/null +++ b/sci-libs/clashscore-db/Manifest @@ -0,0 +1,5 @@ +DIST molprobity-3.17.tgz 26429898 SHA256 2e70814efb4f566a522762a626f69669c09285cbb6fc26444eb947fde9b30f25 SHA512 a6e986f285ff7e8d167e2d1c935a55b080446c9809d352c95e2ffa32265892b59cd1611730e75ca88aa28387495d3ebd84226e1a9cdd33f0b27b1a8a1b6a469f WHIRLPOOL 3981522eeacaa589530e7d268cda786bebeaf676f7fa5c26508798022126bd1a1c8ea193f65e3c5c739fb3b516b26c3cf24ac0e7898e764a9cffab6637dcd5a9 +EBUILD clashscore-db-3.17.ebuild 469 SHA256 ebfd9bad425f5e3f22b2a698b6d1a46fec0cfa390535db20607754f7c4bda230 SHA512 ae1407f0c51e0197bab1971ec8abb23ff5b99c300be8d8e30848748e72ed62051f9d3970bd1ffea3de6dd016aedd3c3d850d93de1ffabd960a436bd680c8ada5 WHIRLPOOL fe22fe6754fbff7e7e8535bc781abce7a3fd27ea3f76d0956ba474e9a35234734f6ba62501fe66bee4f5a692054196222d5be2494659b6fcd7218243da85594c +MISC ChangeLog 2583 SHA256 67494c92503d0e8c67a73cbd293c87050e3641693a26671854f958a08e957e37 SHA512 4a2e5f99cc393d0576245da3347826343e1757f0d84357a12d0d0304b0e17e748d5a81a3cff0a534b82216da42bebcbde4bf15202c932179df488b8abb1c6354 WHIRLPOOL e12f8bf2b3d4e050eb28c39d10251a72c80c3778b2b262e09fbfb73b1e2d6ff2c0868736a4cad5cba4e9518c4b74c87fb7f2ea48a803ecd37c7465d342434aba +MISC ChangeLog-2015 1036 SHA256 7758b710cca4ccf076e45f3350ddafa26e6c14dcf47edb94f9061eca8f99f99d SHA512 20e960542d4e7bbcbc7a1f1b4d3a2152fe4b55c55c7e7a8aad4335bfdf5f58945fc5b8a74dc1a5829034f21efd657f76ef7c30b16df12321519c78d28f33afc1 WHIRLPOOL d3431a42a5f087c17eee833a701dd04783bd2a833fcdbd160ba501e48a94ec6f9b1d4da86a5558afd8e1dc4496ae2a4af1adca8da6fb120aaffb8e4af1970af7 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 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000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/clashscore-db/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/clblas/Manifest b/sci-libs/clblas/Manifest new file mode 100644 index 000000000000..db0565b0be3b --- /dev/null +++ b/sci-libs/clblas/Manifest @@ -0,0 +1,9 @@ +AUX clblas-2.10-disable-multilib-cflags.patch 854 SHA256 3aba58803ca8bdae1abfdd66e8f0fa83f7e09aabee8538990729781224265a99 SHA512 39d144be9667b907bdbf1d0d48684196a959801126fa4a9f3b376a1824eaecfc3a5cb3e7d6b8c233e0f8e807b1b241449f6e9554c46ee49d6eca30779c860bff WHIRLPOOL 118a831c51af0d88c7afb8a330d5cc7c68a40de8b8cb8616b46a32b0b54ebbdd11ee725f3d7d5170877b3b6fb1a0b75f7e213ddd902358204f41b8e67deeda63 +AUX clblas-2.10-fix-blas-dot-calls.patch 2732 SHA256 33625fb6b5a7b42b3623a47041c4e8a2f14c5ac945d35e87954528c0e993c980 SHA512 07c1ac79cf9e9432f0f01cfc01c88c88bf4d733de259236eb1087c7e6b6f0539987cb2caf576ec6db24e6efb15de2d1655bdc5afcbd6512e3d15acedbcfbd995 WHIRLPOOL ac4096aa15fcf3c75e17c2f124c27e27e8cd94f8097fa87166e141f088aaf3c54d8352c4e44445eca0e841ceb9f46183363c48291adbf1fc9a8dd24599d2efea +AUX clblas-2.10-fix-doxygen-output-dir.patch 639 SHA256 dd901a8112f21ee8930181295e583b7df3084a19a2b9d11ce1b0cefb00ea674f SHA512 295dfccb9cd860f354abe775c142e0d68b31d2bc25f427b5b8ec4103865e73ce3a4d43967834eaaf3e40f978f48dddcdac1451138b4d53d5f973321d7f27aa74 WHIRLPOOL 55e07544af479b93eb2316c0631d86d6466f10652f9fdf7afc5ab598b9c6551abdbcc7cadee16b31908429d0d3acec70f9fac7b4fcda8b717e25201b83428f07 +AUX clblas-2.10-fix-pthread-linkage.patch 684 SHA256 be1870fe257cbb8ab08fe9a174032cf4d80da23d2a62cc6d2944044e458a95df SHA512 ae42cb7a59caa407df20ec3cfd8e593003bd2653dd43471c39591907159bc6b557c1b7fc4062f662b5986de8fd89cf9b2a287f4b6116701b55baf3ad6acab273 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72a46cb92f6057d10b503ce23d62db73d7332eb0645bb8bca3337f4c0558b429 SHA512 5ed43104aae565292e0df4cc9e014cf483ccc0ff89257ebb5817f6508bfc9593585ed658da639f2167fbfb5d92ef116be4d5de3694f56e1a1e228bd42b1c05c6 WHIRLPOOL 1a96142dc0e7aad076d1e61508b943da8ac176bd889cac89a3cab1aab64a1d8a6bc207bda4483be7dc726af600b660370548ee06db4d28d4b6643b7bff9419e8 +EBUILD clblas-2.10.ebuild 2360 SHA256 aae478b056d18b93a6c32958e8efa5bdc5cdd86982bc20c447a47c5b77bf2407 SHA512 18dd363b3d05ec498c1edcfb86e6c01f0ee1379a21e42ffe6d0a07654c4c3d581cacc94c6a9d6332745fb99f2e04098c96b7e1bd6e2311d56fa53d3a121361bc WHIRLPOOL a5b85e26429b90f85a9f47efcbd5cc6a379a409be62ed4f6669a304eb2f5055f3929edf35f61a2213b28c53dfca7ad5e4d30b1fe0907fb8dd3d5536b2bb3d822 +MISC metadata.xml 1029 SHA256 c583aac269e9107ec05f28a78e3d5e6ff5b41e9ab3fa1ed9b36e1721bfe5cd06 SHA512 62e2f6461060977e68d8f175f40d8de1801f5c4f635e33817ffb04dba9b8a19747bcd99206972e21b8780f5f0499290ff8b0d46bf5bdc1463659a8dd5cebb483 WHIRLPOOL d67a1803c079a4dcafedbfdde75081b7eba04f40a6700e15a19252d3216d610ccbe9daffbe64cc922912f973bb4ee68c37653880a148a2e0c8ba7549d59b1618 diff --git a/sci-libs/clblas/clblas-2.10.ebuild b/sci-libs/clblas/clblas-2.10.ebuild new file mode 100644 index 000000000000..de0b41541ea3 --- /dev/null +++ b/sci-libs/clblas/clblas-2.10.ebuild @@ -0,0 +1,101 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_4,3_5} ) +FORTRAN_NEEDED=test + +inherit cmake-utils python-single-r1 toolchain-funcs fortran-2 + +MYPN="clBLAS" + +DESCRIPTION="Library containing BLAS routines for OpenCL" +HOMEPAGE="https://github.com/clMathLibraries/clBLAS" +SRC_URI="https://github.com/clMathLibraries/${MYPN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0/2" # soname version +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+client doc examples ktest performance test" + +REQUIRED_USE="performance? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + virtual/opencl + doc? ( dev-libs/mathjax ) + performance? ( ${PYTHON_DEPS} ) +" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + test? ( + dev-cpp/gtest + dev-libs/boost + virtual/pkgconfig + virtual/blas + ) +" + +S="${WORKDIR}/${MYPN}-${PV}" +CMAKE_USE_DIR="${S}/src" + +PATCHES=( + "${FILESDIR}"/${P}-disable-multilib-cflags.patch + "${FILESDIR}"/${P}-fix-blas-dot-calls.patch + "${FILESDIR}"/${P}-fix-doxygen-output-dir.patch + "${FILESDIR}"/${P}-fix-pthread-linkage.patch + "${FILESDIR}"/${P}-use-boost-dynamic-libs.patch + "${FILESDIR}"/${P}-use-system-mathjax.patch +) + +src_configure() { + local mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DBUILD_RUNTIME=ON + -DBUILD_SAMPLE=OFF + -DBUILD_CLIENT="$(usex client)" + -DBUILD_KTEST="$(usex ktest)" + -DBUILD_PERFORMANCE="$(usex performance)" + ) + if use test; then + mycmakeargs+=( + -DBUILD_TEST=ON + -DUSE_SYSTEM_GTEST=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + ) + else + mycmakeargs+=( -DBUILD_TEST=OFF ) + fi + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + if use doc; then + cd doc + doxygen clBLAS.doxy || die + fi +} + +src_test() { + pushd "${BUILD_DIR}/staging" > /dev/null + LD_LIBRARY_PATH="${BUILD_DIR}/library:${LD_LIBRARY_PATH}" \ + ./test-short + popd > /dev/null + + # horrible hack to avoid installing compiled tests + # this will trigger some overcompilation + mycmakeargs+=( -DBUILD_TEST=OFF ) + cmake-utils_src_configure +} + +src_install() { + use doc && HTML_DOCS=( doc/html/. ) + cmake-utils_src_install + dodoc CHANGELOG CONTRIBUTING.md NOTICE README.md + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r src/samples/* + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-libs/clblas/files/clblas-2.10-disable-multilib-cflags.patch b/sci-libs/clblas/files/clblas-2.10-disable-multilib-cflags.patch new file mode 100644 index 000000000000..a7e59d913f06 --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.10-disable-multilib-cflags.patch @@ -0,0 +1,20 @@ +Description: disable multilib flags +Author: Ghislain Antony Vaillant <ghisvail@gmail.com> +Forwarded: not-needed +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -296,9 +296,9 @@ + # Don't use -rpath. + set(CMAKE_SKIP_RPATH ON CACHE BOOL "Skip RPATH" FORCE) + +- set(CMAKE_C_FLAGS "-m${TARGET_PLATFORM} ${CMAKE_C_FLAGS}") +- set(CMAKE_CXX_FLAGS "-m${TARGET_PLATFORM} ${CMAKE_CXX_FLAGS}") +- set(CMAKE_Fortran_FLAGS "-m${TARGET_PLATFORM} ${CMAKE_Fortran_FLAGS}") ++ #set(CMAKE_C_FLAGS "-m${TARGET_PLATFORM} ${CMAKE_C_FLAGS}") ++ #set(CMAKE_CXX_FLAGS "-m${TARGET_PLATFORM} ${CMAKE_CXX_FLAGS}") ++ #set(CMAKE_Fortran_FLAGS "-m${TARGET_PLATFORM} ${CMAKE_Fortran_FLAGS}") + + if(TARGET_PLATFORM EQUAL 32) + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-builtin") diff --git a/sci-libs/clblas/files/clblas-2.10-fix-blas-dot-calls.patch b/sci-libs/clblas/files/clblas-2.10-fix-blas-dot-calls.patch new file mode 100644 index 000000000000..cc2c6c3c1766 --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.10-fix-blas-dot-calls.patch @@ -0,0 +1,59 @@ +diff --git a/src/tests/correctness/blas-lapack.c b/src/tests/correctness/blas-lapack.c +index 9687bdf..54666b1 100644 +--- a/src/tests/correctness/blas-lapack.c ++++ b/src/tests/correctness/blas-lapack.c +@@ -655,7 +655,7 @@ complex cdotu( int n, complex *x, int incx, complex *y, int incy) + #elif defined( __APPLE__) + cblas_cdotu_sub(n, x, incx, y, incy, &ans); + #else +- cdotusub_(&n, x, &incx, y, &incy, &ans); ++ ans = cdotu_(&n, x, &incx, y, &incy); + #endif + + return ans; +@@ -670,7 +670,7 @@ doublecomplex zdotu( int n, doublecomplex *x, int incx, doublecomplex *y, int i + #elif defined(__APPLE__) + cblas_zdotu_sub(n, x, incx, y, incy, &ans); + #else +- zdotusub_(&n, x, &incx, y, &incy, &ans); ++ ans = zdotu_(&n, x, &incx, y, &incy); + #endif + + return ans; +@@ -685,7 +685,7 @@ complex cdotc( int n, complex *x, int incx, complex *y, int incy) + #elif defined(__APPLE__) + cblas_cdotc_sub(n, x, incx, y, incy, &ans); + #else +- cdotcsub_(&n, x, &incx, y, &incy, &ans); ++ ans = cdotc_(&n, x, &incx, y, &incy); + #endif + + return ans; +@@ -700,7 +700,7 @@ doublecomplex zdotc( int n, doublecomplex *x, int incx, doublecomplex *y, int i + #elif defined(__APPLE__) + cblas_zdotc_sub(n, x, incx, y, incy, &ans); + #else +- zdotcsub_(&n, x, &incx, y, &incy, &ans); ++ ans = zdotc_(&n, x, &incx, y, &incy); + #endif + + return ans; +diff --git a/src/tests/correctness/blas-lapack.h b/src/tests/correctness/blas-lapack.h +index d2db1aa..8619e1e 100644 +--- a/src/tests/correctness/blas-lapack.h ++++ b/src/tests/correctness/blas-lapack.h +@@ -1170,10 +1170,10 @@ double ddot_(int *n, double *x, int *incx, double* y, int *incy); + complex cdotc_(int *n, complex *x, int *incx, complex* y, int *incy); + doublecomplex zdotc_(int *n, doublecomplex *x, int *incx, doublecomplex* y, int *incy); + #else +- void cdotusub_(int *n, complex *x, int *incx, complex* y, int *incy, complex *ans); +- void zdotusub_(int *n, doublecomplex *x, int *incx, doublecomplex* y, int *incy, doublecomplex *ans); +- void cdotcsub_(int *n, complex *x, int *incx, complex* y, int *incy, complex *ans); +- void zdotcsub_(int *n, doublecomplex *x, int *incx, doublecomplex* y, int *incy, doublecomplex *ans); ++ complex cdotu_(int *n, complex *x, int *incx, complex* y, int *incy); ++ doublecomplex zdotu_(int *n, doublecomplex *x, int *incx, doublecomplex* y, int *incy); ++ complex cdotc_(int *n, complex *x, int *incx, complex* y, int *incy); ++ doublecomplex zdotc_(int *n, doublecomplex *x, int *incx, doublecomplex* y, int *incy); + #endif + + void sswap_(int *n, float *x, int *incx, float* y, int *incy); diff --git a/sci-libs/clblas/files/clblas-2.10-fix-doxygen-output-dir.patch b/sci-libs/clblas/files/clblas-2.10-fix-doxygen-output-dir.patch new file mode 100644 index 000000000000..31abb89b1c3a --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.10-fix-doxygen-output-dir.patch @@ -0,0 +1,16 @@ +Description: use system mathjax instead of remote +Author: Ghislain Antony Vaillant <ghisvail@gmail.com> +Forwarded: not-needed +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/doc/clBLAS.doxy ++++ b/doc/clBLAS.doxy +@@ -52,7 +52,7 @@ + # If a relative path is entered, it will be relative to the location + # where doxygen was started. If left blank the current directory will be used. + +-OUTPUT_DIRECTORY = ..\..\bin\clBLAS.doxy ++OUTPUT_DIRECTORY = + + # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create + # 4096 sub-directories (in 2 levels) under the output directory of each output diff --git a/sci-libs/clblas/files/clblas-2.10-fix-pthread-linkage.patch b/sci-libs/clblas/files/clblas-2.10-fix-pthread-linkage.patch new file mode 100644 index 000000000000..aa99529df034 --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.10-fix-pthread-linkage.patch @@ -0,0 +1,18 @@ +Description: fix missing linkage with pthread +Author: Ghislain Antony Vaillant <ghisvail@gmail.com> +Forwarded: no +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/src/library/CMakeLists.txt ++++ b/src/library/CMakeLists.txt +@@ -888,6 +888,10 @@ + set_target_properties( clBLAS PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" ) + target_link_libraries(clBLAS ${OPENCL_LIBRARIES} ${MATH_LIBRARY}) + ++set(THREADS_PREFER_PTHREAD_FLAG ON) ++find_package(Threads REQUIRED) ++target_link_libraries(clBLAS ${CMAKE_THREAD_LIBS_INIT}) ++ + # CPack configuration; include the executable into the package + install( TARGETS clBLAS + EXPORT Library diff --git a/sci-libs/clblas/files/clblas-2.10-use-boost-dynamic-libs.patch b/sci-libs/clblas/files/clblas-2.10-use-boost-dynamic-libs.patch new file mode 100644 index 000000000000..57c585da11fc --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.10-use-boost-dynamic-libs.patch @@ -0,0 +1,16 @@ +Description: use Boost shared libraries instead of static +Author: Ghislain Antony Vaillant <ghisvail@gmail.com> +Forwarded: no +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -270,7 +270,7 @@ + + # Find Boost on the system, and configure the type of boost build we want + set( Boost_USE_MULTITHREADED ON ) +-set( Boost_USE_STATIC_LIBS ON ) ++set( Boost_USE_STATIC_LIBS OFF ) + set( Boost_DETAILED_FAILURE_MSG ON ) + set( Boost_DEBUG ON ) + set( Boost_ADDITIONAL_VERSIONS "1.44.0" "1.44" "1.47.0" "1.47" ) diff --git a/sci-libs/clblas/files/clblas-2.10-use-system-mathjax.patch b/sci-libs/clblas/files/clblas-2.10-use-system-mathjax.patch new file mode 100644 index 000000000000..775a669e96a8 --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.10-use-system-mathjax.patch @@ -0,0 +1,18 @@ +Description: fix output directory for documentation + Use default doxygen directory, i.e. under docs/html, rather than the + inappropriate path set by upstream. +Author: Ghislain Antony Vaillant <ghisvail@gmail.com> +Forwarded: no +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/doc/clBLAS.doxy ++++ b/doc/clBLAS.doxy +@@ -1223,7 +1223,7 @@ + # installing MathJax. However, it is strongly recommended to install a local + # copy of MathJax from http://www.mathjax.org before deployment. + +-MATHJAX_RELPATH = http://www.mathjax.org/mathjax ++MATHJAX_RELPATH = /usr/share/javascript/mathjax + + # The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension + # names that should be enabled during MathJax rendering. diff --git a/sci-libs/clblas/metadata.xml b/sci-libs/clblas/metadata.xml new file mode 100644 index 000000000000..cad01ed8bce0 --- /dev/null +++ b/sci-libs/clblas/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + clBLAS is the code for the OpenCL BLAS portion of clMath. The + complete set of BLAS level 1, 2 and 3 routines is implemented. See + Netlib BLAS for the list of supported routines. In addition to GPU + devices, the library also supports running on CPU devices to + facilitate debugging and multicore programming. + </longdescription> + <use> + <flag name="client"> + Build a command line clBLAS client program. + </flag> + <flag name="ktest"> + A command line tool for testing single clBLAS kernel. + </flag> + <flag name="performance"> + Copy performance scripts that can measure and graph performance. + </flag> + </use> + <upstream> + <remote-id type="github">clMathLibraries/clBLAS</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/clblast/Manifest b/sci-libs/clblast/Manifest new file mode 100644 index 000000000000..16d646c1dedb --- /dev/null +++ b/sci-libs/clblast/Manifest @@ -0,0 +1,3 @@ +DIST clblast-0.10.0.tar.gz 508763 SHA256 29914462155dba3f5e4f858f6b36601eb77880e4c04bb7ade48e30afb9bf729b SHA512 da1fc659dd470c02c25be0a009b7f5e2333bc590715ac6b90e09e57a25d764479d7e4ecf398f17d0ac0e6bb2eaf24c09082c7f047fb7b3044f4a987e294494ee WHIRLPOOL 115687fae11cb7586993d0f336bf60644ec3ed8eb3566c8e28921779ee7cf66617259f85cb612638ed888391c7d49209f409dbb0dc4b51aa210388a7c42f3dce +EBUILD clblast-0.10.0.ebuild 1506 SHA256 410bb22903291a5ff68cfcba7ffa6764824fe3a4a1e5e1756b05b4bf070c8001 SHA512 fc6b562cba51fdc93f80a266857d33d733d4132d4e7c84d1c8ecac5c7daa8881fed4856f498f56f21674b24a7d98bbe295c46038c4c67ff864160168f6562de5 WHIRLPOOL 84dc6903a75889404ccca42a964f2e59a48ceccedd6bc5ee3ccfcd5ed4f8a2d635a8d477ce9fc87ad93283cf4e2a85668b0dfabf938aadc8873f2e71fdfb1aa3 +MISC metadata.xml 954 SHA256 d7425d86ed45f383f7d90cd3909a018fe8dfcb34fc82343507f5b3d2807c8d6a SHA512 32637508226381a330fbc29874d5d6a157860f16846b0927f9530cc8f2a36c64f40c483ea89d27671f13f600fd560b1d0314846d55a73cf8a2263c7c5860564c WHIRLPOOL aced26e89906f526cdf57eda7b1485d825706e1ded54b60e9bacf573ed49bd8f33d7551878bf84f49988add48195b6b2829d95cd096785bec1e6dd4ab1db6c2b diff --git a/sci-libs/clblast/clblast-0.10.0.ebuild b/sci-libs/clblast/clblast-0.10.0.ebuild new file mode 100644 index 000000000000..0327840fce5b --- /dev/null +++ b/sci-libs/clblast/clblast-0.10.0.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils toolchain-funcs + +MYPN="CLBlast" + +DESCRIPTION="Tuned OpenCL BLAS" +HOMEPAGE="https://github.com/CNugteren/CLBlast" +SRC_URI="https://github.com/CNugteren/${MYPN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="client doc examples test" + +RDEPEND="virtual/opencl" +DEPEND="${RDEPEND} + test? ( + virtual/cblas + virtual/pkgconfig + ) +" +S="${WORKDIR}/${MYPN}-${PV}" + +src_prepare() { + # no forced optimisation, libdir + sed -e 's/-O3//g' \ + -e 's/DESTINATION lib/DESTINATION ${CMAKE_INSTALL_LIBDIR}/g' \ + -i CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + mycmakeargs+=( + -DBUILD_SHARED_LIBS=ON + -DSAMPLES=OFF + -DCLIENTS="$(usex client)" + -DTESTS="$(usex test)" + ) + if use test || use client; then + mycmakeargs+=( + -DNETLIB=ON + -DCBLAS_INCLUDE_DIRS="$($(tc-getPKG_CONFIG) --cflags-only-I cblas| awk '{print $1}' | sed 's/-I//')" + -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs cblas)" + -DREF_LIBRARIES="$($(tc-getPKG_CONFIG) --libs cblas)" + ) + fi + cmake-utils_src_configure +} + +src_test() { + cmake-utils_src_test alltests +} + +src_install(){ + cmake-utils_src_install + dodoc README.md CONTRIBUTING.md CHANGELOG + use doc && dodoc -r doc + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r samples/* + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-libs/clblast/metadata.xml b/sci-libs/clblast/metadata.xml new file mode 100644 index 000000000000..d5ff3a6625c9 --- /dev/null +++ b/sci-libs/clblast/metadata.xml @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + CLBlast is a modern, lightweight, performant and tunable OpenCL + BLAS library written in C++11. It is designed to leverage the full + performance potential of a wide variety of OpenCL devices from + different vendors, including desktop and laptop GPUs, embedded + GPUs, and other accelerators. CLBlast implements BLAS routines: + basic linear algebra subprograms operating on vectors and + matrices. + </longdescription> + <use> + <flag name="client"> + Enable compilation of the clients to test and compare performance with reference libraries + </flag> + </use> + <upstream> + <remote-id type="github">CNugteren/CLBlast</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/clipper/Manifest b/sci-libs/clipper/Manifest new file mode 100644 index 000000000000..8a64ba2f3818 --- /dev/null +++ b/sci-libs/clipper/Manifest @@ -0,0 +1,6 @@ +DIST clipper-2.1.20140911.tar.gz 1922753 SHA256 ced2b2f3a9480805bd111f454742a7152b21212d9749fd5e8fb11e40ecbcd9cf SHA512 1306bd68d40ea6a7d828f58ce276d6f5d05637af8712eeec3528cf0e4b637263b8ab068ec132765fc4167723bf1d43cbb9ffe0eca43dea3742ec273f34947912 WHIRLPOOL cc867a96b8e4a7229a51131292f18db2e5a2398569734347f671078853e5b4a6470e426cbd5c8f49d38a65497270c08118ecf409bc0509bbca98c4df15fc0bc7 +DIST clipper-2.1.20140911_p20160914-fix-c++14.patch.bz2 10551 SHA256 88418a09ce28b8db003a2e561737fc7c29c2d800cc38e57bdeb5bad4d4f5fac4 SHA512 b18a059eb1bfaec18d1f6f104639001074d92b73768ab6ef412828fc21d891d93d15cd50cd41fca1187f4b4f90399e20bf3e6290af695c6bffbff2c85ca028eb WHIRLPOOL af027f9f0b5bed72bfa0875d4d6b7cd532ccc012d820fe14ba55b42b032a5a8c8738faf2f6c71266ea1e86669c5c004c65db374b8a0a04e99be7725a54f8420c +EBUILD clipper-2.1.20140911-r1.ebuild 1434 SHA256 411d5945bd2994c43362328d0124cb6ef3923cd1d65b73658f1c342dafc444c7 SHA512 34816cca8354bccf6508b15e24a699cbf980508b03f3d582f1e3e977e5397354927e75ca8ca0f368ef7e96fdc776bb0968dbfeb1a4a6a3d49efc13d5ebae2558 WHIRLPOOL afb982fb8023aa3ef0ec42800f0320646ede7fc185291acd9df893a3d2fcbbec071de3bc60db62b5e97ce2304f5bc22ab31c5d9c03c9dd198ad73fb9ea0f7b9a +MISC ChangeLog 5127 SHA256 fb87eeb0661beb97c7a375fac9868e3e4930ac413d7ec27fa63150303f544931 SHA512 0d1ce36abcef10cdf5474bf3af42ced123f3f8fe67952df416329d3cf1e3c48ecf27636571ae0741918c319815938c4468004ca1189940a2f16fb64a8467c596 WHIRLPOOL 64030f3552cd6887ea1beb673886b30af07d3eab86831b78a8e37cd5ac35d84ce9ccd143700a5f67d97fd131e47818b23660e53a2b5f724aaecfc24eb224123d +MISC ChangeLog-2015 3640 SHA256 5fa1dae443cc0cfcdcfb2285900938df07271c9031a4a0750a4cadd0c001dfa9 SHA512 6efca10a8e9382d8a9e42497b8963a5f1ee80d217ebc90702d1bd56dda62e14e42113637b0ff1695b27c96ff8a0b66b2d1bd5a6a8f928ae4e8ad7a12df883099 WHIRLPOOL 55ff3096df3eed268cd3c2c57f96a402a44297a312d2d980583fd15ebcf5e6836d8646b0ce36b64dfea8ab3728def977c259d15544e3051b8f7f6136b07adc39 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-libs/clipper/clipper-2.1.20140911-r1.ebuild b/sci-libs/clipper/clipper-2.1.20140911-r1.ebuild new file mode 100644 index 000000000000..249ac435d41b --- /dev/null +++ b/sci-libs/clipper/clipper-2.1.20140911-r1.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit flag-o-matic fortran-2 + +DESCRIPTION="Object-oriented libraries for crystallographic data and computation" +HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html" +SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-2.1.20140911_p20160914-fix-c++14.patch.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="fortran static-libs test" + +RDEPEND=" + sci-libs/libccp4 + sci-libs/fftw:2.1 + sci-libs/mmdb:2" +DEPEND="${RDEPEND} + test? ( app-shells/tcsh )" + +PATCHES=( + # fix building with GCC 6, #585540 + "${WORKDIR}/${PN}-2.1.20140911_p20160914-fix-c++14.patch" +) + +src_configure() { + # Recommended on ccp4bb/coot ML to fix crashes when calculating maps + # on 64-bit systems + append-flags -fno-strict-aliasing + + econf \ + --enable-shared \ + $(use_enable static-libs static) \ + $(use_enable fortran) \ + --enable-ccp4 \ + --enable-cif \ + --enable-cns \ + --enable-contrib \ + --enable-minimol \ + --enable-mmdb \ + --enable-phs +# --enable-cctbx +} + +src_test() { + emake -C examples check + cd examples || die + sed -e '/mtzdump/d' -i test.csh || die + PATH="${S}/examples:${PATH}" csh test.csh || die +} + +src_install() { + default + + # package provides .pc files + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/clipper/metadata.xml b/sci-libs/clipper/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/clipper/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/cln/Manifest b/sci-libs/cln/Manifest new file mode 100644 index 000000000000..1d2fbe84a91a --- /dev/null +++ b/sci-libs/cln/Manifest @@ -0,0 +1,8 @@ +AUX cln-1.3.2-arm.patch 340 SHA256 ff5fd9300bb5a83c64b2c9c416fc5daed13d2a8527df4da021e02f46c5311254 SHA512 b16e00091ade3f77f54a88130a5953a8d677cbcc124a89e632266313b42c042cda57da4bececdc4740c1dce366a06593ad5cec21bf047ea43ea4927d2e08e020 WHIRLPOOL 0533b8c75f43aadd694abbdbb45a9fc5a9ac3fa0c10307bbb8975c9d45498ef3f0aa0f66c3efdcdc8e641a338ff0f67bb071afbe35b6579ea770e60540379c43 +DIST cln-1.3.3.tar.bz2 1300229 SHA256 57fc2ee3ecbb30d4037ff32a9a331804ea7dad8b345e70d42d9991ca659b2612 SHA512 ee829cd03a2d36215a4d4e76cc0aa6c5abe6ff967ed366d752da1dc0c47dbec56e0521e92fb35574c038305fb767991c5c7fd12ad03583080da3f923fbfecdaf WHIRLPOOL fac646fcb8622060917cbe08b232d412459e45f16c4bbe38cd6d1b7296bc259466eba28ddccb66ead435832ea45127e13b4fe0e2601a0f763487144c02e51eb0 +DIST cln-1.3.4.tar.bz2 1281348 SHA256 2d99d7c433fb60db1e28299298a98354339bdc120d31bb9a862cafc5210ab748 SHA512 2178a64b4388b3018c3847f6fb192ea51eb9c8618302986d7706accef17184e3333ddeca218d726f93f3b985598952ad58d705c9081201985611e383f788a631 WHIRLPOOL da1686fa88f7a73e20c60e3116b50dfee0ebe6e4519443df26889f82dd7b9281178c89cea7ab7fe82ed6a6b6fbf91546fc2501da7c56c2375e1f57415f103024 +EBUILD cln-1.3.3.ebuild 1320 SHA256 51ce06d3cebeba513ad1e0216972cca221d5cb64f76f91e427ab9afcc635667b SHA512 22024d622a3ed10ad9b2a7e4d868cff01c5870b2dd549c310779e1fad2db07ee02cf051a2e7f71f9d909869d2359258cd4d15acd82ed6046de1572bd4cdf0aaf WHIRLPOOL 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6254ec3819423ec52d49a21675d944d4d633a88acb4878937238e7b27069419a5d0fe1f00c046541c745a33c04d8fc75f39fc4b21abfa0aff801d404e3dca194 WHIRLPOOL 6a9ceb7a1eaac9a7e07cc3ab158f934c5cba0f5c92da6291eb7daaaf0e102f46340fc3015cc74521ff463083cfcffec49b17b7edb6254c82ef2091c358e05cc7 +MISC metadata.xml 702 SHA256 10840f50fa97482f060acc0bb8c83f3f61400737d55b3884e6a28e45c4bd0d1e SHA512 4b6ddc8f558bc777963dcf271584ba59ba3d8cc3c2c95260a5680eab2a436dca894a2318f5bacdd9c9da68e6c22323d4ef2829b9bb1de0db2467f20ac204d95b WHIRLPOOL 98be8c8fbdcdef3fee7c722988f6d911eacdbffc686dd402f6ac721c5836cb2018a7475c84e4c4931cc1021c74fc39ebd13c2961d21afb2ba7bb0426daca3cdc diff --git a/sci-libs/cln/cln-1.3.3.ebuild b/sci-libs/cln/cln-1.3.3.ebuild new file mode 100644 index 000000000000..26803863a036 --- /dev/null +++ b/sci-libs/cln/cln-1.3.3.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils flag-o-matic + +DESCRIPTION="Class library (C++) for numbers" +HOMEPAGE="http://www.ginac.de/CLN/" +SRC_URI="ftp://ftpthep.physik.uni-mainz.de/pub/gnu/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="1" +KEYWORDS="alpha amd64 arm hppa ia64 ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs" + +RDEPEND="dev-libs/gmp:0=" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +PATCHES=( "${FILESDIR}"/${PN}-1.3.2-arm.patch ) + +pkg_setup() { + use sparc && append-cppflags -DNO_ASM + use hppa && append-cppflags -DNO_ASM + use arm && append-cppflags -DNO_ASM +} + +src_prepare() { + # avoid building examples + # do it in Makefile.in to avoid time consuming eautoreconf + sed -i \ + -e '/^SUBDIRS.*=/s/examples doc benchmarks/doc/' \ + Makefile.in || die + autotools-utils_src_prepare +} + +src_compile() { + autotools-utils_src_compile + if use doc; then + cd "${BUILD_DIR}" + export VARTEXFONTS="${T}/fonts" + emake html pdf + DOCS=("${BUILD_DIR}/doc/cln.pdf") + HTML_DOCS=("${BUILD_DIR}/doc/") + fi +} + +src_install () { + autotools-utils_src_install + if use examples; then + docompress -x /usr/share/doc/${PF}/examples + insinto /usr/share/doc/${PF}/examples + doins examples/*.cc + fi +} diff --git a/sci-libs/cln/cln-1.3.4.ebuild b/sci-libs/cln/cln-1.3.4.ebuild new file mode 100644 index 000000000000..b072885a1307 --- /dev/null +++ b/sci-libs/cln/cln-1.3.4.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils flag-o-matic + +DESCRIPTION="Class library (C++) for numbers" +HOMEPAGE="http://www.ginac.de/CLN/" +SRC_URI="http://www.ginac.de/CLN/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="1" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs" + +RDEPEND="dev-libs/gmp:0=" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +PATCHES=( "${FILESDIR}"/${PN}-1.3.2-arm.patch ) + +pkg_setup() { + use sparc && append-cppflags -DNO_ASM + use hppa && append-cppflags -DNO_ASM + use arm && append-cppflags -DNO_ASM +} + +src_prepare() { + # avoid building examples + # do it in Makefile.in to avoid time consuming eautoreconf + sed -i \ + -e '/^SUBDIRS.*=/s/examples doc benchmarks/doc/' \ + Makefile.in || die + autotools-utils_src_prepare +} + +src_compile() { + autotools-utils_src_compile + if use doc; then + cd "${BUILD_DIR}" + export VARTEXFONTS="${T}/fonts" + emake html pdf + DOCS=("${BUILD_DIR}/doc/cln.pdf") + HTML_DOCS=("${BUILD_DIR}/doc/") + fi +} + +src_install () { + autotools-utils_src_install + if use examples; then + docompress -x /usr/share/doc/${PF}/examples + insinto /usr/share/doc/${PF}/examples + doins examples/*.cc + fi +} diff --git a/sci-libs/cln/files/cln-1.3.2-arm.patch b/sci-libs/cln/files/cln-1.3.2-arm.patch new file mode 100644 index 000000000000..571bd24e68f6 --- /dev/null +++ b/sci-libs/cln/files/cln-1.3.2-arm.patch @@ -0,0 +1,13 @@ +--- src/base/digitseq/cl_asm_arm_.cc 2009-05-10 16:32:30.000000000 -0400 ++++ src/base/digitseq/cl_asm_arm_.cc.new 2009-12-29 09:03:02.161401990 -0500 +@@ -77,8 +77,8 @@ + #else + #define DECLARE_FUNCTION(x) + #endif +-#define GLABEL(x) _##x##: +-#define LABEL(x) x##: ++#define GLABEL(x) _##x: ++#define LABEL(x) x: + #define RRX rrx + #define END + diff --git a/sci-libs/cln/metadata.xml b/sci-libs/cln/metadata.xml new file mode 100644 index 000000000000..3e1bd9fcb042 --- /dev/null +++ b/sci-libs/cln/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-mathematics@gentoo.org</email> + <name>Gentoo Mathematics Project</name> + </maintainer> + <longdescription lang="en"> + A Class Library for Numbers is a library for computations with all + kinds of numbers in arbitrary precision. It has a set of number + classes, including integers (with unlimited precision), reals with + various precisions (including unlimited), rationals, complex numbers + and polynomials. The kernel is written in assembly language. It uses + automatic garbage collection. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/cminpack/Manifest b/sci-libs/cminpack/Manifest new file mode 100644 index 000000000000..ad02faa1ccc6 --- /dev/null +++ b/sci-libs/cminpack/Manifest @@ -0,0 +1,9 @@ +AUX cminpack-1.2.2-underlinking.patch 448 SHA256 b5018d162a045c16cfdd505686b471b8040666e8ff3ac1e7506c297f9f0a8b59 SHA512 319ad720e9fb2fe369fa398adaffc54d3d84dd5deeefe95dba5f46bb35dbdef9229e45e321129581dca7643a58afc0f366ba662d7f3a8a5ca9a9e1211565c60a WHIRLPOOL 2d0035189c3cc1103a7da09f9694965991829b92de384ed1a92d3068da7548dfa29c2fc896c0f62730ca904b94669c297d3f01080ee10d0ebb727997caf357a9 +AUX cminpack-1.3.5-underlinking.patch 338 SHA256 45d055ec8913bf6f09903f072dc6bd9e1f7adc73bb53e0467b389d94cbc97e17 SHA512 e75edbe045d6936d09a2454504fba6b5b5535424aa1c7603df4b55416e801d27f74f1e2db1038193d36262a12734760138df1c66b6c3d9e6d318f124e7409307 WHIRLPOOL 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675884da7afc5193db0977409616101842891ccde2516a1681957641b6fbbd1d6a2ec270fe58b5b32a5a2bfcf5a1c1add060dcfae2b249a8cd23952665a2868f +MISC ChangeLog-2015 1705 SHA256 4252533adc957ad62f5676368cf2cc537b1361ad79b2e5e837fbe7288f9a7239 SHA512 65c3f04d8cfe861c1d00e98633eb8a23824e8d824b274b17fb2783fe151e36877ac605dfa44eedc13b16aee9c5dd59fa8f590cde852170bd60287668cd78edb2 WHIRLPOOL 115f22eaca4b479819b1fcea692a7576ca1794c388e809d784372a61f0d8bae58a8f4da7440b59aa8da20a18cea39bb2d5b8de068b94d211c4dc3c8717c2fc69 +MISC metadata.xml 991 SHA256 42002147eab184ebc273754fd3d7c6ece52a6c9fc429fe0827bc69fdf0fef34b SHA512 1cafc14fcabc7ce953d557c501fb26e698656d334d3af80ce3a3a31b99b3c1f6281babf990ce219f697e505fab4c1764e6c90238d55e98ac0e242e521be08193 WHIRLPOOL bf4d1e2f0c0b0ab4b49b6a228500f860e6f95d2eae50f08fe6c1f83c478f00817fe6d2e2fa42d216314d23bea43fa6832b2d86ed57102be55527df466c82ba86 diff --git a/sci-libs/cminpack/cminpack-1.3.4.ebuild b/sci-libs/cminpack/cminpack-1.3.4.ebuild new file mode 100644 index 000000000000..e4845a26287c --- /dev/null +++ b/sci-libs/cminpack/cminpack-1.3.4.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils multilib + +DESCRIPTION="C implementation of the MINPACK nonlinear optimization library" +HOMEPAGE="http://devernay.free.fr/hacks/cminpack/" +SRC_URI="${HOMEPAGE}/${P}.tar.gz" + +LICENSE="minpack" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc test" + +PATCHES=( "${FILESDIR}"/${PN}-1.2.2-underlinking.patch ) + +src_configure() { + sed -i \ + -e "/CMINPACK_LIB_INSTALL_DIR/s:lib\(\|64\):$(get_libdir):g" \ + cmake/cminpack_utils.cmake || die + local mycmakeargs+=( + -DSHARED_LIBS=ON + $(cmake-utils_use_build test examples) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + dodoc readme* + use doc && dohtml -A .txt doc/* +} diff --git a/sci-libs/cminpack/cminpack-1.3.5.ebuild b/sci-libs/cminpack/cminpack-1.3.5.ebuild new file mode 100644 index 000000000000..7e59ab588eee --- /dev/null +++ b/sci-libs/cminpack/cminpack-1.3.5.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +DESCRIPTION="C implementation of the MINPACK nonlinear optimization library" +HOMEPAGE="http://devernay.free.fr/hacks/cminpack/" +SRC_URI="https://github.com/devernay/cminpack/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="minpack" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc test" + +PATCHES=( "${FILESDIR}"/${P}-underlinking.patch ) + +src_configure() { + local mycmakeargs=( + -DCMINPACK_LIB_INSTALL_DIR=$(get_libdir) + -DBUILD_SHARED_LIBS=ON + -DBUILD_EXAMPLES=$(usex test) + ) + cmake-utils_src_configure + use test && export LD_LIBRARY_PATH="${BUILD_DIR}:${LD_LIBRARY_PATH}" +} + +src_install() { + cmake-utils_src_install + dodoc readme* + use doc && dodoc -r doc/* +} diff --git a/sci-libs/cminpack/files/cminpack-1.2.2-underlinking.patch b/sci-libs/cminpack/files/cminpack-1.2.2-underlinking.patch new file mode 100644 index 000000000000..a042d4c2f72b --- /dev/null +++ b/sci-libs/cminpack/files/cminpack-1.2.2-underlinking.patch @@ -0,0 +1,15 @@ + CMakeLists.txt | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 57394af..5a46a75 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -56,6 +56,7 @@ set (cminpack_hdrs + cminpack.h minpack.h) + + add_library (cminpack ${LIB_TYPE} ${cminpack_srcs}) ++target_link_libraries (cminpack m) + + install (TARGETS cminpack + LIBRARY DESTINATION ${CMINPACK_LIB_INSTALL_DIR} COMPONENT library diff --git a/sci-libs/cminpack/files/cminpack-1.3.5-underlinking.patch b/sci-libs/cminpack/files/cminpack-1.3.5-underlinking.patch new file mode 100644 index 000000000000..5133f5fcd4a8 --- /dev/null +++ b/sci-libs/cminpack/files/cminpack-1.3.5-underlinking.patch @@ -0,0 +1,10 @@ +--- a/CMakeLists.txt 2016-12-29 03:57:50.652989816 +0000 ++++ b/CMakeLists.txt 2016-12-29 03:58:33.882632282 +0000 +@@ -59,6 +59,7 @@ + cminpack.h minpack.h) + + add_library (cminpack ${cminpack_srcs}) ++target_link_libraries (cminpack m) + + install (TARGETS cminpack + LIBRARY DESTINATION ${CMINPACK_LIB_INSTALL_DIR} COMPONENT library diff --git a/sci-libs/cminpack/metadata.xml b/sci-libs/cminpack/metadata.xml new file mode 100644 index 000000000000..1e24c78f14c1 --- /dev/null +++ b/sci-libs/cminpack/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + Minpack includes software for solving nonlinear equations and + nonlinear least squares problems. Five algorithmic paths each + include a core subroutine and an easy-to-use driver. The algorithms + proceed either from an analytic specification of the Jacobian matrix + or directly from the problem functions. The paths include facilities + for systems of equations with a banded Jacobian matrix, for least + squares problems with a large amount of data, and for checking the + consistency of the Jacobian matrix with the functions. + This is the C re-write of the original fortran minpack + implementation. +</longdescription> + <upstream> + <remote-id type="github">devernay/cminpack</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/cmpfit/Manifest b/sci-libs/cmpfit/Manifest new file mode 100644 index 000000000000..d043cdaf2ca9 --- /dev/null +++ b/sci-libs/cmpfit/Manifest @@ -0,0 +1,5 @@ +DIST cmpfit-1.2.tar.gz 30431 SHA256 4b90521d8fe7614e6ce1455aa77ee6eea397acfcdc870019e4351055a0ee0697 SHA512 232a39538396f166efd9c7a9fc687e0ac8fd3090f871f54fb0c131a1ed02cc05a60904894d853d8eb76d88e70a1fbab4bce3ad0b5990408c77d5a6028a3b466c WHIRLPOOL 0cf0eed9e1e1f60ce9a37afffba02155fef5a6bc4ca1b4833bdf1e776d2e01a6b9335f4bf260f311a96ae9e350e92e2e6451003c95ec9789f5fa4df2647b095b +EBUILD cmpfit-1.2-r1.ebuild 1113 SHA256 6fee18d4dd7aedbb586606619db24511f263aebeb93232e149146e8b832d50a4 SHA512 7b5f03cdf045396ec88611dcc75e8776cb1313d707273a538cd05a10ff61c8f99c7cf5db425f1928d0950be627d0a2cee30156476c7df4ee111fd64a8dc3d54e WHIRLPOOL 7fefd38a8b112ceb945c75763e50624c45335f3160f7ef02191ad3132d421def4613fcbbf6a0a9f9ca46b428e8696d4160c83b012328f1b72b3410cfc6177e73 +MISC ChangeLog 2931 SHA256 12092f630926dbdca1eb0d87b06edf23f60dbe6db05a2e46d55205956791d602 SHA512 aaee7dfed18ac8e127fb056d61f8e2acebfda8c691c2522def44c2b96b9f807cae77908f8f9f6a59871173b4cd2193e68140a2eb12d7e239ca495f2e963ee3fa WHIRLPOOL 93826e818a3124ce8103b724a5ae87f67379540e764ee6ab6cd66f093a2e1aaffe54b69bcc7f114da0fffb53d0065bd7304617a685c57d6a7411f25a7f796568 +MISC ChangeLog-2015 470 SHA256 033eb1a3e40a9f98bda3cb46bc7cd1476d6ce3a1d2874fef15d03cb06388da3c SHA512 6069407d86dc80cc566a339f260a4f298a5233940ab9d055221c622bc779fb69af4e371882e9c5c4156d6ae1c240575be4c9c7ee7d69b82b552dd1ceeb339df5 WHIRLPOOL 13c1b3045e96f6468fab09ead0fc0b9095479951719cc472ba109d4a35d06be3f39b0890a7ab150d36feb616ddc3a291997ca9bed120a7ad0f905e5183b20792 +MISC metadata.xml 616 SHA256 7eaee90725ae0495a55cfaf436ffcc99167bfeb400806b3b9e81c0e7185df633 SHA512 4e38bce3a6be5e555dd573d5435b807e7bdda78e002aa896299be521b7cf50a2cd148a25a8ae2dc568a7b730cefa7bf8e2f19d76280654963a870d7d8e60c4d5 WHIRLPOOL 5349de0e4a1746a1797e7e65cd2fca2ed5f236b7ead56db2defe02c18bce6687e0aaf7c5ac3bc29cfcc7f10518af5b5d8380c5f661f734db170d5169501d45dc diff --git a/sci-libs/cmpfit/cmpfit-1.2-r1.ebuild b/sci-libs/cmpfit/cmpfit-1.2-r1.ebuild new file mode 100644 index 000000000000..4ddf2df64b53 --- /dev/null +++ b/sci-libs/cmpfit/cmpfit-1.2-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="MINPACK-1 Least Squares Fitting Library in C" +HOMEPAGE="http://www.physics.wisc.edu/~craigm/idl/cmpfit.html" +SRC_URI="http://www.physics.wisc.edu/~craigm/idl/down/${P}.tar.gz" + +LICENSE="public-domain minpack" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +DOCS=( README DISCLAIMER ) + +src_compile() { + if use static-libs; then + $(tc-getCC) ${CFLAGS} -c mpfit.c || die "non-PIC compilation failed" + $(tc-getAR) cr libmpfit.a mpfit.o || die "creation of static archive failed" + fi + $(tc-getCC) ${CFLAGS} -fPIC -c mpfit.c -o mpfit.so || die "PIC compilation failed" + $(tc-getCC) ${LDFLAGS} -shared -Wl,-soname=libmpfit.so mpfit.so -lm -o libmpfit.so || die "linking failed" +} + +src_test() { + $(tc-getCC) ${CFLAGS} testmpfit.c -L. -lmpfit -lm -o testmpfit || die + LD_LIBRARY_PATH=.:${LD_LIBRARY_PATH} ./testmpfit || die +} + +src_install() { + dolib.so libmpfit.so + use static-libs && dolib.a libmpfit.a + doheader mpfit.h + einstalldocs +} diff --git a/sci-libs/cmpfit/metadata.xml b/sci-libs/cmpfit/metadata.xml new file mode 100644 index 000000000000..bfd0c6bb45fa --- /dev/null +++ b/sci-libs/cmpfit/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + MPFIT uses the Levenberg-Marquardt technique to solve the + least-squares problem. In its typical use, MPFIT will be used to fit + a user-supplied function (the "model") to user-supplied data points + (the "data") by adjusting a set of parameters. MPFIT is based upon + MINPACK-1 (LMDIF.F) by More' and collaborators. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinhsl/Manifest b/sci-libs/coinhsl/Manifest new file mode 100644 index 000000000000..1544f0d13558 --- /dev/null +++ b/sci-libs/coinhsl/Manifest @@ -0,0 +1,5 @@ +DIST coinhsl-2014.01.10.tar.gz 906586 SHA256 7c2be60a3913b406904c66ee83acdbd0709f229b652c4e39ee5d0876f6b2e907 SHA512 fe71b07c4fc11a8a7a40a115457588b91aa4481726e523502d92d6604c5fda13cffcc4620ada64b9332cb3502f8bfbc4ee856125cd5fd987cccf49bae5d46711 WHIRLPOOL 7b59a9d2d532cb494d12485529cf13d14d48a354a622c3d8d2252f46f0aaeb5e60d4ee17f8d11e3e4717cf81d056709b4b03a2dcebbfbf60ea264b55303e4834 +EBUILD coinhsl-2014.01.10.ebuild 673 SHA256 10e43a39a25285096b1b4ce3cb0b09c89949603557e27b0a9f44245585699021 SHA512 b3e8822b42aec6ce25a4ee245d58af417326d8fa2d9937eb30916241811aab75de8ca6ba32e4290659659698245114c55bf189f327fd11e641a5c48f75562f2f WHIRLPOOL dad42b651f4385cc7a6fea915dc30324e1b976e8af1e865294e987d700e1e1555d8f0e9ee84b13e7722a3050bf630c3ee6e85af4ff05ff31e0d99304d25990d6 +MISC ChangeLog 2437 SHA256 fe0a2de5d1cfcb09b3aaa57bfa3d6c25e263a37f971a61ce2932b2de1baeea9e SHA512 7daa483d7452f863a6ca1b5a2ae3715e21ee9e120ac83343767184593bfdfe99e875a318b0061280cf5d762eb2ffa80723e0f274f243f1809e3e3be5909687b7 WHIRLPOOL 37eb6f862a9813ef87f3b7289b5075b5a12e7e58555179ececf9e6517c7ef5d972059d4144cf81b62beb293ac0f347df7c39f7dcc990cde6c8978d09230385b3 +MISC ChangeLog-2015 426 SHA256 829d98f93e62aaa23b9bd05cbf84a961dd63cb5032d38f6bca0f9d557882861e SHA512 7adcb2185c20e2c5e55d5051fd0f1616eb5c8e05c35d5b3567d6010e54fdc4f880e7486fc917619f11ee1a35d4edc31bd5f8935c8a688632bf24a2378e1375e5 WHIRLPOOL b09589c5c17203ea8280de542113ace714c08a06875a13bd75be469b06c6bc0225b21f24ba7d85be0ed62709a98515f587cc90845c5aac6c13af07ab656f5329 +MISC metadata.xml 575 SHA256 2c845f1b48a4a597648b0c97ee566db3ad955176dbdab39ad502cf3fb36902b4 SHA512 71ca7fd62a3cad7eed8726e7a126b0e040029f498096ee50fa9e173dc8de22e76b9cb96553e7daef47d208dc4f91cec5ea3e9d64f5e12a81af6eb57a39a01257 WHIRLPOOL 72e65478d7158d12557cee36f58be0df272989625b5b713b11433275565ca612fd7f9a91bfd768fbf96ffba22c42f5a204aa510038007c60c6c7e9ad2ff10ce8 diff --git a/sci-libs/coinhsl/coinhsl-2014.01.10.ebuild b/sci-libs/coinhsl/coinhsl-2014.01.10.ebuild new file mode 100644 index 000000000000..b750ae79f7ad --- /dev/null +++ b/sci-libs/coinhsl/coinhsl-2014.01.10.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_IN_SOURCE_BUILD=yes +FORTRAN_STANDARD="77 90" + +inherit autotools-utils fortran-2 toolchain-funcs + +DESCRIPTION="HSL mathematical software library for IPOPT" +HOMEPAGE="http://www.hsl.rl.ac.uk/ipopt" +SRC_URI="${P}.tar.gz" + +LICENSE="HSL" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +RDEPEND=" + sci-libs/metis + virtual/blas" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +RESTRICT="mirror fetch" + +src_configure() { + export LIBS="$($(tc-getPKG_CONFIG) --libs metis blas lapack)" + autotools-utils_src_configure + MAKEOPTS+=" -j1" +} diff --git a/sci-libs/coinhsl/metadata.xml b/sci-libs/coinhsl/metadata.xml new file mode 100644 index 000000000000..6816c1c70f8e --- /dev/null +++ b/sci-libs/coinhsl/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + HSL (formerly the Harwell Subroutine Library) is a collection of + state-of-the-art packages for large-scale scientific computation + such as the solution of sparse linear systems of equations and + sparse eigenvalue problems. This package is specific as a plugin for + Ipopt. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-alps/Manifest b/sci-libs/coinor-alps/Manifest new file mode 100644 index 000000000000..98cd4f19596f --- /dev/null +++ b/sci-libs/coinor-alps/Manifest @@ -0,0 +1,7 @@ +DIST Alps-1.4.9.tgz 5564207 SHA256 b1d1636ed16b3a3982d7bc547da9713657cd22cbc3ed4d4323ec63af04d139d2 SHA512 b8f557d33f3d02d0bf98541309934eeebebd21829fe1e2a438b07e6e17f0a1de1a970ed97b28cdaddc8b14eb1092a86db4d44838cef70bae3d091cd48fe8e2d8 WHIRLPOOL dddf890622d44f0c42278a15e0ac979cc6faa9cfa9b26b47fcc785de709098a044bd68d2fe81671b0ab5bae268c18f2ad8b00741bdf96ec7779ce76bf71fc352 +DIST Alps-1.5.4.tgz 5691940 SHA256 e9ca0a3b6f7013b04845935b26ebcda9468eae23b31ae2dcee2dbeb30a046f3a SHA512 eace2f0e3dde682ee92b8e185ba6ea226a681dbcecb5fcf5258334e6deed89705b2c61821896b07323459fbd8575a31fa91c3342becbc9f6173efdf094d39555 WHIRLPOOL 4c77b472bbacb7dcee8f00be91198a17f745769aac00e720b46c034d5e0a8805142efd350eb23a8d3602e4faaa464a6334cd6aa726f8b20b7dccabb6bcd0eebf +EBUILD coinor-alps-1.4.9.ebuild 1562 SHA256 a8c6c267d96c48d221522b40c077053f2c1de0bc87719f93839a55ddc780c623 SHA512 3c84654faf50e541d57a022d117a1eae87e150949153f800b94e3918074cb388beacc175f637418a109b53d91d5a1aafd89d8f090e2e7b2f478b244fb6fa96dc WHIRLPOOL a9b8f821427cafa7e7ec7b356b76e92bd915d0c0245ebe7b05d704272b30cc18bedb0d253b1bd87e3773c0839b12dd2dfbd1cf14641c900077907b7f702c081c +EBUILD coinor-alps-1.5.4.ebuild 1416 SHA256 9be76fa5a2bc996fc51b22f6af3f38d10fbe81ea8baaffb033119b6d08d490b4 SHA512 6543c09a8f88037e18b90ea2c0795a50d8bec3202380fc2ed0ff407b7c3d114a9ac692182e92efee8ba94cc5f8b7f2494095afdfe1f7c27424578f90ac3fb48d WHIRLPOOL 04e12143d2099b85a184e0210f10c7e85442073a91f4fa800796ead905efc99cb6740482ba8c17ab586f385ae5f183985cc4c6ff8d4abbecfa59f0370a70e757 +MISC ChangeLog 2648 SHA256 4177f26f08e6d8d1779aec9fe3d50f277d3b0573c7eaf49b94fb691ca5878f1a SHA512 ed85e4ec5c5d6e661940813cd974cc11ce06b0441c59f3e69a193760c0c7e018fe84edefa39f275dc3e0f8670d709fe99e85abeee790ff2f0cf5fa2204aa92da WHIRLPOOL 7be9cfa04a7f7fe6bb0db37a930f19677d30ecc6968ee19ccebf65467aa71fd4792e570f9cb798a75fee8643046997b3c675f0c1473f32dd024d50299c48420f +MISC ChangeLog-2015 1680 SHA256 898c108e3cdbb40aa4f3178cb5ed3315e8c2d713b4758efbb7d78d7833e65d6c SHA512 946b83d293e543b8997638bec89723b7d311d89be4060bb2642bf2ab315f349981ff2b357dd00fadd7b4329b15ed14701611751e69b4fa0f0d3d421636da3030 WHIRLPOOL 39436d56ae00d05f96d5677332d0c1ddd34c95d14cdf402937d2bec97d7d22d7a20bf670878b24a9553e62164ef5f084c8b30254f1deb52967f1e72900363926 +MISC metadata.xml 676 SHA256 00d63f966d510593d79c04f6ec0a762f01d277d8079dadca45ef3ff3b21c5f51 SHA512 2f9d9fc72a8041d540dee8a9ece59b2cef903d04d8a583522a141f44fdf8f277b9c1e827719aae073ab818626eef9ee0bdedaa972e2894146899fbb7e2334c99 WHIRLPOOL 43e04deeefba84125f12923716dd34d839e37e062c3243c6c4e56f27b50d2ea1d7a970d6e8d0e83cf7e35c4b61ac5bd432a614d03fb435c16ff58628d5f8e108 diff --git a/sci-libs/coinor-alps/coinor-alps-1.4.9.ebuild b/sci-libs/coinor-alps/coinor-alps-1.4.9.ebuild new file mode 100644 index 000000000000..0d32e561166a --- /dev/null +++ b/sci-libs/coinor-alps/coinor-alps-1.4.9.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Alps + +DESCRIPTION="COIN-OR Framework for implementing parallel graph search algorithms" +HOMEPAGE="https://projects.coin-or.org/CHiPPS/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="CPL-1.0" +SLOT="0/3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + sci-libs/coinor-utils:= + sci-libs/coinor-clp:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample sci-libs/coinor-cgl )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # as-needed fix + # hack to avoid eautoreconf (coinor has its own weird autotools) + sed -i \ + -e 's:\(libAlps_la_LIBADD.*=\).*:\1 @ALPSLIB_LIBS@:g' \ + src/Makefile.in || die + # bug for later versions of subversions + sed -i \ + -e 's/xexported/xexported -a "x$svn_rev_tmp" != "xUnversioned directory"/' \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + $(use_with doc dot) + ) + PKG_CONFIG_PATH+="${ED}"/usr/$(get_libdir)/pkgconfig \ + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile all $(usex doc doxydoc "") +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${BUILD_DIR}/doxydocs/html/.") + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-alps/coinor-alps-1.5.4.ebuild b/sci-libs/coinor-alps/coinor-alps-1.5.4.ebuild new file mode 100644 index 000000000000..3418b1c2bf77 --- /dev/null +++ b/sci-libs/coinor-alps/coinor-alps-1.5.4.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils + +MYPN=Alps + +DESCRIPTION="COIN-OR Framework for implementing parallel graph search algorithms" +HOMEPAGE="https://projects.coin-or.org/CHiPPS/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="CPL-1.0" +SLOT="0/3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + sci-libs/coinor-utils:= + sci-libs/coinor-clp:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample sci-libs/coinor-cgl )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + default + # as-needed fix + # hack to avoid eautoreconf (coinor has its own weird autotools) + sed -i \ + -e 's:\(libAlps_la_LIBADD.*=\).*:\1 @ALPSLIB_LIBS@:g' \ + src/Makefile.in || die + # bug for later versions of subversions + sed -i \ + -e 's/xexported/xexported -a "x$svn_rev_tmp" != "xUnversioned directory"/' \ + configure || die +} + +src_configure() { + PKG_CONFIG_PATH+="${ED}"/usr/$(get_libdir)/pkgconfig + export PKG_CONFIG_PATH + econf \ + --enable-dependency-linking \ + $(use_with doc dot) \ + $(use_enable static-libs static) +} + +src_compile() { + emake all $(usex doc doxydoc "") +} + +src_install() { + default + use examples && dodoc -r examples/ + use doc && dodoc -r doxydoc/html/ + + prune_libtool_files --all +} diff --git a/sci-libs/coinor-alps/metadata.xml b/sci-libs/coinor-alps/metadata.xml new file mode 100644 index 000000000000..ca300c0aa7a1 --- /dev/null +++ b/sci-libs/coinor-alps/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + CHiPPS is the COIN-OR High-Performance Parallel Search Framework, a + framework for implementing parallel algorithms based on tree + search. The current CHiPPS architecture consists of three + layers. The Abstract Library for Parallel Search (ALPS) is the base + layer of a hierarchy consisting of implementations of various tree + search algorithms for specific problem types. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-bcp/Manifest b/sci-libs/coinor-bcp/Manifest new file mode 100644 index 000000000000..50636f486d8d --- /dev/null +++ b/sci-libs/coinor-bcp/Manifest @@ -0,0 +1,5 @@ +DIST Bcp-1.3.8.tgz 7086225 SHA256 db0079ba8adc16ca0a3065b385bf27352a27a9e031e8db52e96b4f883d4352f4 SHA512 c599cc60df37cab32cfbf24522efaababbdd2de6144c316390f5e0481863ffd6aec016f97188a610ae6aca8d4e5b1b8088a35bc81bd3448fadb1727a9e9663dd WHIRLPOOL 4bdc2a99bff6ed5b71a978feb224a1c2624b0519e0149b37fbd97c142c617502e46b8bbb9cf3516ebe4bf56c1c29e9cedf6bdcf52d08433fe2f20c7dfe5541b6 +EBUILD coinor-bcp-1.3.8.ebuild 1190 SHA256 a1249c863d15df4a4b289e469653d143f1f427f9e2d729d90a625deba9c6e9e5 SHA512 0ca1fdd104182c7854a783670662eca6b1de5a3eeefdbc199c07749ece648c33c8f3e5c171861025d2f28d2f2ac27e0f6572fdc1c7faf8061ad009681baa9b98 WHIRLPOOL bc6ab63984e7d89045ce5c13daa352956162c083cd4e9fff1013f54e05048b8642e2495b4a3254d8bdee997b2d45ef9b8c7c5ce3c15110afe92971bf2311546a +MISC ChangeLog 2436 SHA256 e7b2554731c2188bddac8d025c37af5f2fca5cca7af7070bc74937ffde1aaf0b SHA512 21e1e3497399568e1bb99a2864301b14592dbca4aaf968e4e66bd2a4c14feeb1d76b46c0daf683f9c4b0f3fb7fe4656c412951b4a47bb0169452e7f0262d8e89 WHIRLPOOL 18d992a113ad44ad542f301e5247c3712345e75ae5a8d5f0dbe8ebb61364ba7c02a13d5724def72a21c0bc63d8a594880989d3661a53015d91b807aaa04b7142 +MISC ChangeLog-2015 1291 SHA256 7cd9e1a7ca32bd10052b304a36214375c0ea31c819bde78ebc29d9beea7b35b8 SHA512 d80d035f7795282236ba114abc654ab1f79fb73d6dafed1b6956a414b54f4611cb6154aea344c3ea3ff578c125b251a9e8d2c5b60682df4f14d050d05a5c6fb9 WHIRLPOOL a59021949654a80c2313110c5596da3c0e95e3bf0e26e6527a29112f3ffa797e3ea5dba2a0052b4d6535f59163570ca5839a4165255846e52887906fc4bef6ae +MISC metadata.xml 672 SHA256 aa8bcff23fb25e63e867bcb0fe9e28dcea03d6c25290f5f7f3f6b7a3a8c68361 SHA512 481d978ffb2f9fd8a82103c85d642902131e3776672b77192e114863f2d9bc3903e24c69d8427bac8ae2701c8136585f1bbc3b46687023e815165b36f5a9315e WHIRLPOOL c688c6edd8950738b882a181b6639d2d9b54921970f0f10ae13796735cbcddc1c24e51b2be288f1a7f055b52d4fb2189dd3c267d9b3ee5af7f20a2585769be61 diff --git a/sci-libs/coinor-bcp/coinor-bcp-1.3.8.ebuild b/sci-libs/coinor-bcp/coinor-bcp-1.3.8.ebuild new file mode 100644 index 000000000000..69080269d02b --- /dev/null +++ b/sci-libs/coinor-bcp/coinor-bcp-1.3.8.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Bcp + +DESCRIPTION="COIN-OR Branch-Cut-Price Framework" +HOMEPAGE="https://projects.coin-or.org/Bcp/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="CPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + sci-libs/coinor-cgl:= + sci-libs/coinor-clp:= + sci-libs/coinor-vol:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + autotools-utils_src_install + use doc && newdoc doc/man.pdf manual.pdf + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-bcp/metadata.xml b/sci-libs/coinor-bcp/metadata.xml new file mode 100644 index 000000000000..9ade151fdc02 --- /dev/null +++ b/sci-libs/coinor-bcp/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + BCP is a parallel framework for implementing branch, cut, and price + algorithms for solving mixed integer programs (MIPs). BCP provides + the user with an object-oriented framework that can be used to + develop an efficient problem class specific MIP solver without all + the implementational effort. involved with implementing a branch and + bound framework from scratch. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-bcps/Manifest b/sci-libs/coinor-bcps/Manifest new file mode 100644 index 000000000000..f93bba715982 --- /dev/null +++ b/sci-libs/coinor-bcps/Manifest @@ -0,0 +1,5 @@ +DIST Bcps-0.93.10.tgz 6270009 SHA256 22c6fbd415fc2a4ca1c98a21c0a909e9fb0fbd8ed472e14bf031f474e0a4fa37 SHA512 4e9348dc1bf75fd9afb74078b55ae0f9a84a99236886552256d7548013c8af4695a4fcc2787ffb0228eba2a870b1cb78c068234048c8650f7d504e1e8d17c549 WHIRLPOOL 7dce76e8bde0d4b266ac597563f04a1e2a290e6d0c1ac9a3ff164a559681f72def1c3009f1b8024b97bac365f0c0b4e63deebfdc2d93f60e9c53075387b85283 +EBUILD coinor-bcps-0.93.10.ebuild 1131 SHA256 4e268dff8a3f1b3175d1073fe49ef035c58cf2dbe8ae622446eca3a3f74db58c SHA512 eeee240cfefd456c18cb8990d2bb381181db256c4dc01c57e619a111c31e545c26e8a199cb97f2a1194bb7a2f7a716548e3b8efd768370de2ffbf3566294d708 WHIRLPOOL 1ebf8b9222d007df4de70de401477204dda4a9fa1aa7360b1703fcc79842277b25b206ac1a1fa544cec6a6bf5638036c2422bba46c86867983aa9b63945da0d7 +MISC ChangeLog 2443 SHA256 67517984f578142b05a024ad683f81be765165a438ba438834d2625cdefdeee5 SHA512 dbc3ec2873ceb8dabf56cf11c3b5f42effe5d73db2bbda4afc3a68b829c96f129c1180e782e93f64124f03bc11d428fc43cc61195b6d9b8a601183c1027534bf WHIRLPOOL b99b928778de0a72b932a01b92fa587e8841ba141a644a1c721ee923aea47f6c7c5338cf5d2853e34c86cd414077cccc722e34092d4355ea7d732b988304f943 +MISC ChangeLog-2015 1219 SHA256 ebf4d452fbe42125d7124b523e95927f7f8a0142f0e859098ffee08e56dc073b SHA512 92659756d6c44423cacf3589f520799a18fed5416eb53bd8939ecba04ddb79d53b20327fed8bc39b5f304b4f5578c45e74335fc05dd8965b5ed4345cb2aae593 WHIRLPOOL 52ba1df6989f1441bac76dcb234cae09e82ba6aa807f1330d1d094c64a1dc62c7c4bf948456bef9f2858a4f7dd91702bcb323a6ba273b4dde7b02a6d9227a394 +MISC metadata.xml 665 SHA256 bcddc0bb8ff7eb1e7cecf0be3f848e81cdcb3b87bd84ef8417cf181758b361b1 SHA512 24ec521cb8142888d8caf95e22399938522da245e167c8adde1cc244e12e0a3dde7d8c4365b03a1890eed9d25ef1f52ff7c75c2a4a7003fba50bd8bc2a2ed3d1 WHIRLPOOL fdccb2250fb19d041247b22a8082a5e86a888f90fc7443b7ada079096d53cf94b98b1b85e45ccabf32a53929864ca56d8fe449a2f98c598db95e124ffe092c49 diff --git a/sci-libs/coinor-bcps/coinor-bcps-0.93.10.ebuild b/sci-libs/coinor-bcps/coinor-bcps-0.93.10.ebuild new file mode 100644 index 000000000000..f9333455ef1b --- /dev/null +++ b/sci-libs/coinor-bcps/coinor-bcps-0.93.10.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Bcps + +DESCRIPTION="COIN-OR BiCEPS data handling library" +HOMEPAGE="https://projects.coin-or.org/CHiPPS/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="CPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples static-libs test" + +RDEPEND=" + sci-libs/coinor-utils:= + sci-libs/coinor-clp:= + sci-libs/coinor-alps:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + ) + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-bcps/metadata.xml b/sci-libs/coinor-bcps/metadata.xml new file mode 100644 index 000000000000..7f491993f450 --- /dev/null +++ b/sci-libs/coinor-bcps/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + CHiPPS is the COIN-OR High-Performance Parallel Search Framework, a + framework for implementing parallel algorithms based on tree + search. The current CHiPPS architecture consists of three + layers. The Branch, Constrain, and Price Software (BiCePS) is a data + management layer built on top of ALPS for implementing + relaxation-based branch and bound algorithms. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-blis/Manifest b/sci-libs/coinor-blis/Manifest new file mode 100644 index 000000000000..357d580b11b2 --- /dev/null +++ b/sci-libs/coinor-blis/Manifest @@ -0,0 +1,5 @@ +DIST Blis-0.93.10.tgz 10612207 SHA256 77f88471b8d04605a19c6ec2371367b226fa4791289d348abaeba1b50fed0aa2 SHA512 ef4c1b7704353e9d2628401d9a47e72d0b26d485ac3951b03fe84fdc98cfbee8e3b9f3412411eca693c8e00bdf97798e08c4dabcf5b8646bbe3d8481c237820e WHIRLPOOL 2f3d24285b9a9e23b43c9a1ea97355319e84ab43feeba05eff23ffc07f2a5a41e99c219c77520fd18968ebe528e24c5c77a45caa6873df1f3e0e5161f5727868 +EBUILD coinor-blis-0.93.10.ebuild 1155 SHA256 641d0ed5ea13b67303c3c40e6f390a5ee1ef17ccbce768dfa20aef1b21a072c8 SHA512 40d3acd8f470d2476c1804803313d014f60088f523b5a8f569157394dd27845b37f9762b831e8df0d38bb62c33c24a6f1f0ae3ce53e804eb32a6541243d67a49 WHIRLPOOL 1e4faa83e5d6e348e19c83120598c91dd3368020dc2b1600c333ea4ffac246487b1302d4cbe085e4d9bd3f8079b3280eb5db2e21264213aa5b611a6e895d9d2a +MISC ChangeLog 2443 SHA256 f4b61eeb77d8fa440eb1bfe05ef057ba5e4f6038e75726d19edbb0b3461ac156 SHA512 63bf6bade3f6560391142ce7d0f1d3d49606ad257c9b80c5130ab99b23be915b56e5452e6563e73f088454715c8caa23d41c93338c33d287b5f62493a044196f WHIRLPOOL 25259cd4120a096f4bd09a3d87fc17937c8657a1fd04a56027d70abee321eb012402ac7355d40dd6bddcfd9a474c45d64fe0b5d188913aaaaeaa540aff3a0b48 +MISC ChangeLog-2015 1547 SHA256 3983cdcb1197b300d06a2320b2d55990a783d1209d8c295917a753fe5f4e47aa SHA512 c0b7f0a767ce7ceb6e19b81170849970ba1d859bc2a1606cc9c8567e3da76de67b8bb95b1983cbfafca2f4dabdcfba09a9bd97597585d60092d953ce3984c39d WHIRLPOOL 852fdf59ddb5cbeb2daa36a0bc7302105241c6bcdcd73f7ecd7863e24ef317fabeeae883744bdd9f606a4dbcceb949bbfb0a7def01bd98af1fedd0e8d2a96db2 +MISC metadata.xml 624 SHA256 a6f5e2a1b8ba3c15fbf6bfbb1e4c6cf31fcf9269906d0ab2ffc2d93164047ca3 SHA512 f7b40d8376c5a8c82c1176a0889e7fd71f056a121149f5e010499d9f3221a05d2db6164ee9ca4f336713705de34970b5360e61f165f68f3ba40af6732680228c WHIRLPOOL 97cf1bd8b6309da3640fb422759d07289f7e0532e4f215e86e2143f275071c2a6ac4dae218b66e75a260e3dad3fa68467d50992b97c9e4f33efe23defbe5e5f2 diff --git a/sci-libs/coinor-blis/coinor-blis-0.93.10.ebuild b/sci-libs/coinor-blis/coinor-blis-0.93.10.ebuild new file mode 100644 index 000000000000..4456ac2e0b37 --- /dev/null +++ b/sci-libs/coinor-blis/coinor-blis-0.93.10.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Blis + +DESCRIPTION="COIN-OR BiCePS Linear Integer Solver" +HOMEPAGE="https://projects.coin-or.org/CHiPPS/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="CPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples static-libs test" + +RDEPEND=" + sci-libs/coinor-utils:= + sci-libs/coinor-bcps:= + sci-libs/coinor-clp:= + sci-libs/coinor-alps:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + ) + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-blis/metadata.xml b/sci-libs/coinor-blis/metadata.xml new file mode 100644 index 000000000000..e680a1e2d381 --- /dev/null +++ b/sci-libs/coinor-blis/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + CHiPPS is the COIN-OR High-Performance Parallel Search Framework, a + framework for implementing parallel algorithms based on tree + search. The current CHiPPS architecture consists of three + layers. The BiCePS Linear Integer Solver (BLIS) is a concretization + of the BiCePS layer for solving mixed-integer linear programs. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-bonmin/Manifest b/sci-libs/coinor-bonmin/Manifest new file mode 100644 index 000000000000..18e7ab79e0f0 --- /dev/null +++ b/sci-libs/coinor-bonmin/Manifest @@ -0,0 +1,5 @@ +DIST Bonmin-1.7.4.tgz 12320747 SHA256 2087ae609ebd237a8f87fd8bdd3ea1cc4700d3f512ccc9e34ec034d52596f809 SHA512 290b1b49e467ab8ce7fc6908d8aa76a3b1ba61f63f44427d3bdd8ff2bed4aa6ef28396f0be59e108038173ea670405b50d3c32636aacdee2c5787765bce763a4 WHIRLPOOL 6be620b5e59f949044dcd78f85e245d4dbdcc03dd25277f822ad1fb3bca796a7fff99e071cb74d19010be682cc58585ac8180e22ebf3d4cafac2757cb5d49178 +EBUILD coinor-bonmin-1.7.4.ebuild 1433 SHA256 680bec1be5d17c32373f7c70421b6e2766de5f93fa0b187b6ade80bb1618587a SHA512 2846881a3f4f14236f5396fb69cd9353cc9a2e1cd5ef0bf02a8a87c92491492dc0d0c65a4f5b9456836968da2087eccffa15d1ab1707676146021337514ab351 WHIRLPOOL fb270ce092d18f296da7d7bc049248388f8ef5ed583ac21b9a466ccddc70032f0473f515e9c47481ec10258146d7c2b927a01f10a0b4e418207edfdd28df0799 +MISC ChangeLog 2445 SHA256 590b9fc39731e5f2aa9506488030bf84e49ac9f3793e48eea3bc23f1b49e27fd SHA512 437a1ff7fa1c894c1338995462a2a74f3e3f21842527e1ad484f71f8e7e81409bfc246df0d24bdfa31e3c28d2f4aeaece008b45549a5043879749c520694b955 WHIRLPOOL 11313e75144f8ea8d061b08432414e886dd9421c2027c7bf04afb5e71a76190766fd06a1c02b86ee330a8d251dd028fe938580af096fb25a41f25caa56d12e85 +MISC ChangeLog-2015 986 SHA256 ca49a8d336cfc6498b3293cd04b3a4e584728c93e6f3813a1424374fcbd7f690 SHA512 fef4bd8b85290d44dbf3220bfb3d0ee74c200cf4d11c4737643623826a11c3aaa555b5c3cd03f8214d37587300b000624c96cace6d139afeb172594f8a0ba991 WHIRLPOOL 26d92cff29a01aa85fc9805b11a640ee1566ba26ce68957a450c272a4899c084b03047ca69ff6febd3e214136bf38796a2efe0dd9aa705191b6e1450f93c451b +MISC metadata.xml 537 SHA256 b0b8f0803976b7424c71fe316c44d605a6fbed8322f100e32c8eec11f217211b SHA512 813db781e346f940d3110f0340208d1400cef20b2dc55b4faafc75c4d71ec0ad3d6cab7638d5afd4e8db7cca1e146bd72f15d45d6e25305961b75e86152377d3 WHIRLPOOL f48e91d26e35d81b5123029af00792f5a9259fc3e55d6eb6c37f284723a57fc4632b3efdc52ed95d52a07ff137d86612efb3db71d6a634f59a62e721b82f2060 diff --git a/sci-libs/coinor-bonmin/coinor-bonmin-1.7.4.ebuild b/sci-libs/coinor-bonmin/coinor-bonmin-1.7.4.ebuild new file mode 100644 index 000000000000..0523a6cf6082 --- /dev/null +++ b/sci-libs/coinor-bonmin/coinor-bonmin-1.7.4.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Bonmin + +DESCRIPTION="COIN-OR Basic Open-source Nonlinear Mixed INteger programming" +HOMEPAGE="https://projects.coin-or.org/Bonmin/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="CPL-1.0" +SLOT="0/4" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples glpk static-libs test" + +RDEPEND=" + sci-libs/coinor-cbc:= + sci-libs/coinor-clp:= + sci-libs/ipopt:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile all $(usex doc doc "") +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + autotools-utils_src_install + # add missing include files needed from coinor-couenne and others + insinto /usr/include/coin + doins \ + src/Interfaces/BonCurvatureEstimator.hpp \ + src/Interfaces/BonExitCodes.hpp \ + src/Algorithms/QuadCuts/BonLinearCutsGenerator.hpp + + use doc && dodoc doc/BONMIN_UsersManual.pdf + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r examples/* + fi +} diff --git a/sci-libs/coinor-bonmin/metadata.xml b/sci-libs/coinor-bonmin/metadata.xml new file mode 100644 index 000000000000..fde4b95c383c --- /dev/null +++ b/sci-libs/coinor-bonmin/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + BONMIN (Basic Open-source Nonlinear Mixed INteger programming) is an + open-source code for solving general MINLP (Mixed Integer NonLinear + Programming) problems. +</longdescription> + <use> + <flag name="glpk">Undocumented USE</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/coinor-cbc/Manifest b/sci-libs/coinor-cbc/Manifest new file mode 100644 index 000000000000..5d439788b6bb --- /dev/null +++ b/sci-libs/coinor-cbc/Manifest @@ -0,0 +1,5 @@ +DIST Cbc-2.8.9.tgz 8231882 SHA256 33b121e43d35fd18b2084cd52a3bfabd5e8e8819bac3c906e33e0b7c017da288 SHA512 ff537a46a8a266767817bc28d61f4541cfda6e8617c857fa0abef4c0b4ef8fbc728dd195645898d94130dfaedb258789bf55e189a0b9665590958355135f020e WHIRLPOOL bb1512065a447f0ec7582076553e06966810d155768cc1277942251c0ad16ba22ad808ed3be7546873ae40ed68f54ae2b342f7906a366991e3ccea56acb45706 +EBUILD coinor-cbc-2.8.9.ebuild 1794 SHA256 9a2cd4d37c9aad93ddca9ccee75175eff1f0898f3723fa77620974d51255119b SHA512 59b82c1d3ac77b01602f49498490ea9ae615dd09343f8649fc01e6924e54bbf4eb2fe8c17abfeb5b3046fd2452cdc3f8a954fa6f4267af0fa94e8022a5dc1175 WHIRLPOOL 809631cbb51131993975e73a4e03da7029b8151b94c9286ebc32d6f161a07ba6486d2dfb2b2cc3b2ae0b38f5d6998162c0a89730047da63db36b97c3e83e2932 +MISC ChangeLog 2436 SHA256 d442e1cc8d8df05a3d9f925ae450a03c56c352cabdaec3eec93473f8b39601a7 SHA512 26c6e358231fb0b9d1b496da29910e6e66e72d3e610c6314fdc3266b195760be20774d9878895c165f7e2646b41da9a01d00e965f61489879264e228ac7dcf96 WHIRLPOOL 7f4c2e4c2653270d3033b9acebbd2301c388cdceafd33ba50a890f75226cccd3746085a7d2a5515fd854c90a28eccfe683b441be8df7882b31b4c471503b76b4 +MISC ChangeLog-2015 1936 SHA256 4614adca6dd4c761023c732db5adbc5fb3733935dbfc175a58a9cfe595488c8e SHA512 49d17ff133626b7f4bb6306a6732d43650a39628577238584ff2486b676d8961045ae1ebef96eed9ed1e83fdb43213ce7fa04804ab220ac23f52efaf83d32a71 WHIRLPOOL 4afdcd1314dbecf0d50aab6be78d07dbeea4253374f0e84e5ce167e78acebe9dbec12d05d6e7a7edcf3860167b66a2991bcd4da0b7167b2c5acf688b84012915 +MISC metadata.xml 542 SHA256 644539a296891be949e00f4ad1b759d20313c0b382bfa4b9ed2a4a8d1e97e490 SHA512 194a75891d6f076bf9771fdb55638db5dc0e94fbed8ea0bfaa8ca7b08634fe406635e58bf8773df9c6a54bbf85c0fe829ef8db675044dd899a1eed8020776bc1 WHIRLPOOL 1d5643f148ae31d4c0dfc0d3916efe3648c997d72ac540b7025d0659da20587b89fd673926dfd72e064f9ebc6b1fae1fdf36df50d723cad239747f594607c731 diff --git a/sci-libs/coinor-cbc/coinor-cbc-2.8.9.ebuild b/sci-libs/coinor-cbc/coinor-cbc-2.8.9.ebuild new file mode 100644 index 000000000000..c820c9d2def4 --- /dev/null +++ b/sci-libs/coinor-cbc/coinor-cbc-2.8.9.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib flag-o-matic + +MYPN=Cbc + +DESCRIPTION="COIN-OR Branch-and-Cut Mixed Integer Programming Solver" +HOMEPAGE="https://projects.coin-or.org/Cbc/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + sci-libs/coinor-clp:= + sci-libs/coinor-cgl:= + sci-libs/coinor-dylp:= + sci-libs/coinor-osi:= + sci-libs/coinor-utils:= + sci-libs/coinor-vol:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + autotools-utils_src_configure +} + +src_compile() { + # hack for parallel build, to overcome not patching Makefile.am above + autotools-utils_src_compile -C src libCbc.la + autotools-utils_src_compile -C src libCbcSolver.la + autotools-utils_src_compile all $(usex doc doxydoc "") +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${BUILD_DIR}/doxydocs/html/") + # hack for parallel install, to overcome not patching Makefile.am above + autotools-utils_src_install -C src install-am + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-cbc/metadata.xml b/sci-libs/coinor-cbc/metadata.xml new file mode 100644 index 000000000000..4826a4e31bb4 --- /dev/null +++ b/sci-libs/coinor-cbc/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + COIN-OR Branch-and-Cut is a Mixed integer linear programming + solver. It uses many of the COIN-OR components and is designed to be + used with COIN-OR CLP or COIN-OR Dylp. It is available as a library and as a + standalone solver. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-cgl/Manifest b/sci-libs/coinor-cgl/Manifest new file mode 100644 index 000000000000..1c47cdcdef20 --- /dev/null +++ b/sci-libs/coinor-cgl/Manifest @@ -0,0 +1,5 @@ +DIST Cgl-0.58.6.tgz 5331274 SHA256 1a690475f3dcd5830949d67dae3669ade4b1b5f8415b30d0759b161c26b9a476 SHA512 28fe2e570cb2ebfa3109ca53e5ebb7dd3a38e2ddcfda4d7a9a1d78d4784abe1b6ab79734e6cbcee48e21791fe8353658df47d11253b04366ccb66c3e566db585 WHIRLPOOL 60627feebe64cedfe26c56aae7c432d409e2136d5a5090569577914343a1248b1e8b695d99808676931bb5b27e7cd4270de2aef0db198fb03b3494e23ff382f8 +EBUILD coinor-cgl-0.58.6.ebuild 1452 SHA256 0ae5b97476353e1e6df88d27b879eb023aab4912d500bae5b03b7248f8fea7f3 SHA512 58b84a1d2b0170a8594f4d7b7da5c9b0673c4664d51c2e75c0b85d48a3e90f9521034203c6afae020dac030913d7d1b2843a24b75fa55afce5d29c677c7cf097 WHIRLPOOL eb094a2b035fa9aaea14178fbb5d8ce46f04141812b3e5a12eb78255a1c23a38acd9361feb57f6c5009088082a66019dbc647ab9345c8aecc34b787b2e40f80c +MISC ChangeLog 2438 SHA256 d24e362ee1a156315a8aaa43821ace115d262b46edb008280bf46889b60dd5ad SHA512 39cdb67566b9fa5970e9bdffa0abfa59d067594e684e81f097d254c43a2b602cb2a5a1f8efcd7196c98ff4139487b71bc45e4686e867a43469cbda483234d622 WHIRLPOOL 51bfdc3ace0b971565af68c6dcac96e0720699e0e7c876e53fdfd7010b5d56d31c273cd60a1ecce3fcfcd332dab2fca5fe63999adcbb08e2d0e5bcd6a9fc2541 +MISC ChangeLog-2015 1908 SHA256 775add9143c9d70441ffe6a097ae9d3057f98fe8a11d14cc0a8ac2dc7c63ca22 SHA512 1992be0133ee57d5776cdf502c9d6d2d984bb7fb8bed941caa1562c07280d01e44d187cd340273b3c9c22f12cd71c7061450933405e3312fad82370d4faaf3f2 WHIRLPOOL 616e916c1de972a0eeb122f45fa9a61b9e78f284fab125e00a8ade16e869c8f829039a9ea534ad9baec8209c7cfd0c4c0aac7db5d09d5aa612c43e25f3eec3ad +MISC metadata.xml 583 SHA256 96b13676d6117c3cfcd12ffb6098ed715846a501b3e06dcccfb7556056185410 SHA512 80bc5b8688aef02cf6c095765b226b13212b18023aa8911dcf20f9f194882434a5c5d6e3d2d243800c5149305b275b494450ae1206efe0ebf44b10180a3deec6 WHIRLPOOL 97e83c89d5611b6beb28afaf98b28e439b9bb3662cc8450b78656a4beb9e96fc669786eeebf7f94c1eeeca9ecaae19310b932cbff41548a487dacd58e8445db0 diff --git a/sci-libs/coinor-cgl/coinor-cgl-0.58.6.ebuild b/sci-libs/coinor-cgl/coinor-cgl-0.58.6.ebuild new file mode 100644 index 000000000000..d165c14a2d71 --- /dev/null +++ b/sci-libs/coinor-cgl/coinor-cgl-0.58.6.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Cgl + +DESCRIPTION="COIN-OR cutting-plane generators library" +HOMEPAGE="https://projects.coin-or.org/Cgl/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + sci-libs/coinor-clp:= + sci-libs/coinor-dylp:= + sci-libs/coinor-osi:= + sci-libs/coinor-utils:= + sci-libs/coinor-vol:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile all $(usex doc doxydoc "") +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${BUILD_DIR}/doxydocs/html/") + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-cgl/metadata.xml b/sci-libs/coinor-cgl/metadata.xml new file mode 100644 index 000000000000..02a1c876c860 --- /dev/null +++ b/sci-libs/coinor-cgl/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The COIN-OR Cut Generation Library (Cgl) is an open collection of + cutting plane implementations ("cut generators") for use in teaching, + research, and applications. Cgl can be used with other COIN-OR + packages that make use of cuts, such as the mixed-integer linear + programming. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-clp/Manifest b/sci-libs/coinor-clp/Manifest new file mode 100644 index 000000000000..a449b67acb1d --- /dev/null +++ b/sci-libs/coinor-clp/Manifest @@ -0,0 +1,7 @@ +AUX coinor-clp-1.15.6-mpi-header.patch 323 SHA256 ba8e50a75385f54ba9cf3bba3f6c8a7171a94161369388dddd33824da6a0a55d SHA512 1f18e00c1a303cffa0ec6244bf1f5dbac83f0a73d1c82f4bf7a4f4df3ce581012a47b044f1d61c140a282e2d262403e76be49892cccec41b191f02edc6fa63a3 WHIRLPOOL 18b7e7916797f5923956d1daa8f69ae28d0987642683e59da26bc1f79ddca2479057334217cb728c17050bc101de43fdfb4c1f85635deb8a944e6beae0c43d76 +AUX coinor-clp-1.15.6-overflow.patch 349 SHA256 e2fbea8a9e6d81e31f5c1b29016b15d64d648979096e2c6fdeb7c335b7fe95bc SHA512 bc467ff47e0c963aa95c84c3321038327ce4bd99119ea7d66337a60aa329ad7ee8c774aa0405c6e089b081aba0c1e3be577661a7425519e8d56a9e7b05cbb01f WHIRLPOOL 67216f2d8a891cd194ce887a9d35c3554156353bbbbbc16203fc9a52a0ae154bccbb8812c984ed98ae2bf4053b4cf1c96805d8361e1891e9117e13cb3cc54244 +DIST Clp-1.15.6.tgz 5644504 SHA256 4f1ff52f7b471d795d395f561bb10cc2d5a11ecd151bc5329f6f60d448b8385f SHA512 a0da0cc5dcdd409c67cb67dd0f126a3d96bf59851543e7e08adbdbf01012a25905b58ded66aac50b06462ee3a147bed912740c00681417f8c228992a917748db WHIRLPOOL 0712972a59790daac6ddbae1b53458361e4f324f84bb5706b4d59e46eb538a69b22b1e236b550fdaa20201fd5adcc33a8f69f296a9ce022a15ea93b73897833c +EBUILD coinor-clp-1.15.6-r1.ebuild 3005 SHA256 07c100abd1fc952686ce42faaede6e896d142c647390f2bdf4ba8b106c159ce6 SHA512 e97784d306e6071e154a2201426e660db12859e86b70c3c0a6d2325734b0a1495cd6742f68c56ed0e8d4aceb9d09da7be03a56350f1ad45fc411cb11cf92db0a WHIRLPOOL 3fb36470af363643a3f6ff8f03c35e44acc95fe474cad04a91aaeb40c9c99218dbafabdb49aa635401c8c45827f2695ba5a674541528080763e93e718952cc59 +MISC ChangeLog 2923 SHA256 3b5808fe947545a5722323bc8c13e2fd17ebbdd94bcc79d1e21c02725e1d9454 SHA512 d758a38e229a33905fb50cf99b23fbbd8e5ba23eb438ba953b8ae239365f2aa8b945ac8105c54b421ec48eb4255ff0cd475d1f566f1d41efc5236fbdc7ec73ca WHIRLPOOL 67c0668653b7e213266860c04e106611c4154187f33ca5f862c74df69f6ad89f70ecb7712637e51b65a88d1708646fa94e4693d6e2cc4589a7b16ec9146378b5 +MISC ChangeLog-2015 2696 SHA256 4784c348a8e86b764135f6c2f5f5fd463d25ecfb85ada6ec4feee38bc1189eaa SHA512 a9ff01252b0c7f037544be7ed25799906396186f462bbb1fdaa1572e4082c9cef17b3d34c2cc74934c48524334d9a629b85ca472e8c1c262de40ea2489580cbe WHIRLPOOL b42f76fbf4fdf9906ace2456439113472c506b4e924ce3b3da679cf25604f91c5fc3a561d4a52ef9cf89acd53652bf2f941b3a4916a90bd22d44e022ce09e218 +MISC metadata.xml 972 SHA256 06a9412b450ba2e0c97aa4ed3c1a48ab06c5c3062697e362d2897c0ec887ebd8 SHA512 45e693abd4af3cf838fb519b5fe9be04c1ebeca4b5494ba0f15b93768273b186d759e73670fef9adbeb3febe2773b33260b2d9e78cecd84a81c03ffe6d2028f3 WHIRLPOOL c3dced5df28d0e1f52a7a6d5eb2f6fe501255f57f88aaecfe0f607ef31caa66c49ab1a6dd09a8c97115ca357ebb917e23ef455093f23328a4c5c7d8de29b04fb diff --git a/sci-libs/coinor-clp/coinor-clp-1.15.6-r1.ebuild b/sci-libs/coinor-clp/coinor-clp-1.15.6-r1.ebuild new file mode 100644 index 000000000000..7bcb4e61b3a4 --- /dev/null +++ b/sci-libs/coinor-clp/coinor-clp-1.15.6-r1.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils eutils multilib toolchain-funcs + +MYPN=Clp + +DESCRIPTION="COIN-OR Linear Programming solver" +HOMEPAGE="https://projects.coin-or.org/Clp/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples glpk metis mumps sparse static-libs test" + +RDEPEND=" + sci-libs/coinor-osi:= + sci-libs/coinor-utils:= + glpk? ( sci-mathematics/glpk:= sci-libs/amd ) + metis? ( || ( sci-libs/metis sci-libs/parmetis ) ) + mumps? ( sci-libs/mumps ) + sparse? ( sci-libs/cholmod )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.15.6-mpi-header.patch + "${FILESDIR}"/${PN}-1.15.6-overflow.patch +) + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + if has_version sci-libs/mumps[-mpi]; then + ln -s "${EPREFIX}"/usr/include/mpiseq/mpi.h src/mpi.h + elif has_version sci-libs/mumps[mpi]; then + export CXX=mpicxx + fi + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-aboca + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + if use glpk; then + myeconfargs+=( + --with-amd-incdir="${EPREFIX}"/usr/include + --with-amd-lib=-lamd + --with-glpk-incdir="${EPREFIX}"/usr/include + --with-glpk-lib=-lglpk ) + else + myeconfargs+=( --without-glpk ) + fi + if use sparse; then + myeconfargs+=( + --with-amd-incdir="${EPREFIX}"/usr/include + --with-amd-lib=-lamd + --with-cholmod-incdir="${EPREFIX}"/usr/include + --with-cholmod-lib=-lcholmod ) + else + myeconfargs+=( --without-amd --without-cholmod ) + fi + if use metis; then + myeconfargs+=( + --with-metis-incdir="$($(tc-getPKG_CONFIG) --cflags metis | sed s/-I//)" + --with-metis-lib="$($(tc-getPKG_CONFIG) --libs metis)" ) + else + myeconfargs+=( --without-metis ) + fi + if use mumps; then + myeconfargs+=( + --with-mumps-incdir="${EPREFIX}"/usr/include + --with-mumps-lib="-lmumps_common -ldmumps -lzmumps -lsmumps -lcmumps" ) + else + myeconfargs+=( --without-mumps ) + fi + autotools-utils_src_configure +} + +src_compile() { + # hack for parallel build, to overcome not patching Makefile.am above + #autotools-utils_src_compile -C src libClp.la + autotools-utils_src_compile all $(usex doc doxydoc "") +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${BUILD_DIR}/doxydocs/html/") + # hack for parallel install, to overcome not patching Makefile.am above + #autotools-utils_src_install -C src install-am + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-clp/files/coinor-clp-1.15.6-mpi-header.patch b/sci-libs/coinor-clp/files/coinor-clp-1.15.6-mpi-header.patch new file mode 100644 index 000000000000..7ad03e8c76c4 --- /dev/null +++ b/sci-libs/coinor-clp/files/coinor-clp-1.15.6-mpi-header.patch @@ -0,0 +1,12 @@ +--- src/ClpCholeskyMumps.cpp.orig 2013-06-19 09:58:02.834485943 -0700 ++++ src/ClpCholeskyMumps.cpp 2013-06-19 09:57:39.013355095 -0700 +@@ -14,8 +14,8 @@ + #define USE_COMM_WORLD -987654 + extern "C" { + #include "dmumps_c.h" +-#include "mpi.h" + } ++#include "mpi.h" + + #include "ClpCholeskyMumps.hpp" + #include "ClpMessage.hpp" diff --git a/sci-libs/coinor-clp/files/coinor-clp-1.15.6-overflow.patch b/sci-libs/coinor-clp/files/coinor-clp-1.15.6-overflow.patch new file mode 100644 index 000000000000..cded22bf384c --- /dev/null +++ b/sci-libs/coinor-clp/files/coinor-clp-1.15.6-overflow.patch @@ -0,0 +1,11 @@ +--- src/ClpPdco.cpp.orig 2014-01-14 11:44:22.717643715 -0800 ++++ src/ClpPdco.cpp 2014-01-14 11:43:12.543202133 -0800 +@@ -316,7 +316,7 @@ + //bool useChol = (LSmethod == 1); + //bool useQR = (LSmethod == 2); + bool direct = (LSmethod <= 2 && ifexplicit); +- char solver[6]; ++ char solver[7]; + strcpy(solver, " LSQR"); + + diff --git a/sci-libs/coinor-clp/metadata.xml b/sci-libs/coinor-clp/metadata.xml new file mode 100644 index 000000000000..49d8540dde00 --- /dev/null +++ b/sci-libs/coinor-clp/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + Clp (Coin-or linear programming) is an open-source linear + programming solver written in C++. It is primarily meant to be used + as a callable library, but a basic, stand-alone executable version + is also available. It is designed to find solutions of constrained + linear mathematical optimization problems. +</longdescription> +<use> + <flag name="glpk">Enable GNU Linear Programming Kit + <pkg>sci-mathematics/glpk</pkg> support</flag> + <flag name="metis">Enable partitioning with + <pkg>sci-libs/metis</pkg></flag> + <flag name="mumps">Enable <pkg>sci-libs/mumps</pkg> support</flag> + <flag name="sparse">Enable support for sparse matrix with <pkg>sci-libs/cholmod</pkg></flag> +</use> +</pkgmetadata> diff --git a/sci-libs/coinor-couenne/Manifest b/sci-libs/coinor-couenne/Manifest new file mode 100644 index 000000000000..7c29de634cca --- /dev/null +++ b/sci-libs/coinor-couenne/Manifest @@ -0,0 +1,5 @@ +DIST Couenne-0.4.7.tgz 12487353 SHA256 23d058aba7564878ec65cdf8aaba6bec83e3809b31520be1ca014444f25badf6 SHA512 ae87ebee778d6782fffe9e6f6c7c8f604140f6134e29824f89e4f87bb86ac00ac1b2d8de274b23de16078a48a1444fbe7960b15ffefdc1798dca8972a8946deb WHIRLPOOL 21d0d1ff4f9d1ea7daf6976546faf6eeaece5205a171763c71813872bd828696bce6b99d7b222e4dd61a637ee053bf5c1271794815eb4e027e5eecac3ace70de +EBUILD coinor-couenne-0.4.7.ebuild 1397 SHA256 002301857a8aebfa71090c6fd99c7b2ce9f73e57d26a20c7c4425255afe88d7a SHA512 e3c41e059cd6f55b79623b3beea791374af75f0d84960cfb608f759727edb367fa23e1c20d25b5e4dd74c9778cdb20fef46c6e2d47c858cda41d8c7099b129b1 WHIRLPOOL 3527456c8a0d4c3d296db046c398789d8a876463003cf9e1b68a5882c56cee8c122d5c7de5dde44cfd86879716bc6b77a5f7c6150ee4df3a120a5590897acc59 +MISC ChangeLog 2448 SHA256 5c6339c93dcceabda2bd274ef28dc4374f4f667995913720a18e2d4d11e11fc1 SHA512 0c695814f29b5367143c39c8cbe0a30b3177b195aefdf1fcd32c8159e1e949297507e52eb657d16baf4a3f9044fd1b169c428e907332abd1a9028967db3a24e7 WHIRLPOOL 131459bf31656659a8a4734abbf51517f695c18ecef9eb78b67cd59b12834d3187b0f172bc39579ebb171f964d857d4cb8205a0c2c507db6d017d599c99a58a9 +MISC ChangeLog-2015 697 SHA256 fcc3b64be4017457b2e402e81e268d526816401198b730c1414835dafcbb91a6 SHA512 68e7ddf71c6b49b30ea50adc30df6659565c14a3c9fd302043769848f62378c434a849d7db4460be425187f8eeae20e625bf50d5cbed3e067eae45e10921d11a WHIRLPOOL e2f656c877a526a51093a450c47061c11862154ec8889199539a1c9c6aef13eedbc51f608dc88572e0a3b1b46eb0396d07a9351b2f5f7a5cb5a12dc95cc7498a +MISC metadata.xml 614 SHA256 1e46ca0c01924b5c32c728fbe278c5468164be23440fc56f60662f48675bd331 SHA512 cdd31b248c01e3ab6c94f4542dd1b5b9cf069d2694e65896031d3457730ae3b5c605661730de615cf46881f776680ee5e3faee16df9fa10b13f288501650b372 WHIRLPOOL c001972594fe73c2d34d281d379b22aa1a376be2ffecb27761059f8407f09a8f5bcd73504ada17f8e3e82003537b425874ef39e04e106a17d43bb813adf8f370 diff --git a/sci-libs/coinor-couenne/coinor-couenne-0.4.7.ebuild b/sci-libs/coinor-couenne/coinor-couenne-0.4.7.ebuild new file mode 100644 index 000000000000..bff100009493 --- /dev/null +++ b/sci-libs/coinor-couenne/coinor-couenne-0.4.7.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Couenne + +DESCRIPTION="COIN-OR Convex Over and Under ENvelopes for Nonlinear Estimation" +HOMEPAGE="https://projects.coin-or.org/Couenne/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs test" + +RDEPEND="sci-libs/coinor-bonmin:=" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + # resolve as-needed + # circular dependencies between libCouenne and libBonCouenne :( + pushd "${BUILD_DIR}"/src > /dev/null + rm libCouenne.la main/libBonCouenne.la || die + emake LIBS+=" -Lmain/.libs -lBonCouenne" libCouenne.la + emake -C main + popd > /dev/null +} + +src_install() { + autotools-utils_src_install + use doc && dodoc doc/couenne-user-manual.pdf + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die +} diff --git a/sci-libs/coinor-couenne/metadata.xml b/sci-libs/coinor-couenne/metadata.xml new file mode 100644 index 000000000000..923d15cb415a --- /dev/null +++ b/sci-libs/coinor-couenne/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + Couenne (Convex Over and Under ENvelopes for Nonlinear Estimation) + is a spatial branch and bound algorithm that implements linearization, bound + reduction, and branching techniques for Mixed-integer, Nonlinear + Programming (MINLP) problems. The purpose of Couenne is to find global + optima of nonconvex MINLPs. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-cppad/Manifest b/sci-libs/coinor-cppad/Manifest new file mode 100644 index 000000000000..ba7083049840 --- /dev/null +++ b/sci-libs/coinor-cppad/Manifest @@ -0,0 +1,10 @@ +AUX coinor-cppad-20140519-boost.patch 2799 SHA256 20a6b1687ef395f9ccbf16dcf1f9758f03dcd8e393e66927818171eb6153c0ed SHA512 fe3af84b635aeefc30dedee488914f1de00d139756b2fa5c1f39c95b3886860c88ce02d8aaea6d0ec467f135bf17e8f2ce6df427fdd4d11188dbfe1a080cc014 WHIRLPOOL cb01bf199bb81f8f1a205c08030df45992af3ca6a167d6dac575f1874be8a1a4ff64c9f94224a84bb39f8cbb758828c8d81965397478a45d9eacac02d5838bfb +AUX coinor-cppad-20140519-dash.patch 7659 SHA256 afedeeb0843f9c4c237d92c576250ca8143987f5370e52af092c4516d80ea53c SHA512 a1aa44e9949d67823492f0296ba51ebdbb2f201855903a9571dfb686b6a42ac3756c577167ee7e8cf664872db0d570ec7576085d0f9d6642b78096708f83cf04 WHIRLPOOL 92120414d6774e1c9f2f0cc5b4b534e476a0e469cd5adb46ebe910a44c648a8c9d07b6e903075505ecd094c0f91a46469d5983f985f8cb05573c0b934bdefacc +DIST cppad-20140204.gpl.tgz 2189463 SHA256 165b416194a41567ff9fccffbf456784f214cb16bb6f77efc6b082d1f8cbf96a SHA512 0cead73e8d2e2da43ea22c003c0feccadefd2f66efbb58df45b79bff51181ad8646063fd053af8d377ce1732609c55175fd53c00142eb6635018878541f6d2ed WHIRLPOOL 258f8a580d5df0056f895c64e898c4b4fbd112b9159f810f45bb01aa3b5610fb9ceff2d4737e585e3e9b41e2f04accd7d6ca7c4a34191319bdf05bae1c4753c1 +DIST cppad-20140519.gpl.tgz 2208236 SHA256 85e36710c0ede5cba2f8c24b9358ec42e36088a469234df006518e5c856e91f2 SHA512 8f47e545bc76f66edccb9ea083ddebcb5852fa1807d727b6e1f445ca74731e74f7614a1d33b48c6eafbc5129b319e513594b415ee838bdc634f9c00a6d9a22af WHIRLPOOL f2a1d6335971f62f7b37558f4bd873710253a62921c311da1c76d3483df927ddc3a0679d8efcf9b2eb3a83bc70925e0c8cfe00f8770cd88cbb8d99af3db7f0e2 +EBUILD coinor-cppad-20140204.ebuild 1039 SHA256 f1fde43cec39dd1ae05ca912f1aea89d0baebd19e75bcacd7c7241edf01f27db SHA512 88d0afbfee4de370dab34ee49d0efce0ef146db2e135e85e1b82c263af0d719957a415f9118fb225c907d7be86ef2ac903976d56e73e8529a84cd2cc9813d06d WHIRLPOOL 0eaa6b4e0b1a258ef8b949a9f6eb6ff18c7ec3e55bf559e346243b05c17fe8bb36276b96e7190891a2e52aed7f5f2b1591be87ac9f55f56b1d8638a1ed5347b6 +EBUILD coinor-cppad-20140519-r1.ebuild 1169 SHA256 d237a85377d033ae5ef3d97908f470d9dc0b87de9709d9ad707652b469406ac3 SHA512 1c9681cb5e7ab7d3d0b7136994acc37f4bf3acd733b80033263b47f8b887e0d727ca062372a55722b83e641f3fdcff134cb85b29b91d6d2a771073cbb5ad3095 WHIRLPOOL 1c68739b72286c40b13ddbd430cfbeeead7cd25fbca7ca10b826d69298b3beeca40ebde6f3cdd6397aec66cacad61dddf01a28c224537fcfe2850b8217b6ce64 +EBUILD coinor-cppad-20140519.ebuild 1041 SHA256 59cc910a6cac5d7cdc9247c6c458b9e96d0f3492babce7cc5218f3dcfb8d0310 SHA512 7b20f8c8e9cbc52397cba87610ba83e79f2006b9b47bfc48b1666505e581736caeafa4e8a4916acbbb112ba69d2d6e01edfdd1dc555c352c42b64c2b6669f857 WHIRLPOOL affadb42d613c7a50797c5a4b6b9a243578c31fbfbd39bd4d76f68fabddd48e59951e26fd93e71caf8bcb2d5f0fffbae00b34da720fe13690cf54e707aa34a6c +MISC ChangeLog 2677 SHA256 4eae51993b194505fa6c195dd0f5c371912f274f56e00fc05dbc1e781afa9801 SHA512 ccf494d57a978cd1c1e75d5f5c5895d17210937f9b3bb1159106d9d112f6e4ad6b6fdf28d62d3b20151d3210187e20975bc6fc1bbafa6e9a2ea84542f8513bd5 WHIRLPOOL 0ecf259f17451be05c8f497a73e545fc1492e8daa574463d2b16d4cd96c1a6914d6aebbec96a4990804b1285210f4f0ac33056627d4b36f2f889a60527ddb0bc +MISC ChangeLog-2015 2323 SHA256 41173aa323d365a7f37a9c7c38d0b227897d1728857c7e2797262c5c0388100b SHA512 5915d446df3f004bd6277d880d92cd7bebc083471590ee2c1fe79c1b836b1ec10567caa652844473fbff26a42ec8e91ee5e5be35c9c77dc52c244df6d80c75dd WHIRLPOOL 7c89998ae922327e0c38137fac83f849fc14a23f2fea85e63aa37847d813c366064bfaf0cb3cc2de532463afa48a7e1739d26649f4468757a44c6fff46ac4f45 +MISC metadata.xml 730 SHA256 343b7f8448266c28fd59a4e04d3e8cefebed58d12a1a530d817de61e86760cdd SHA512 4803e579d3c8d6f83a7ad08658025fe7e366eab3996ba36d6352ef2bf1a36a5b2dce608731604f25a73f23e9ab45a6b100a542ce001408184e799f1def985634 WHIRLPOOL 21488b96b42b0659bee723210ceb16d686308943f0740189ea14409b1bc405545d1224210bf1f46e438e80d2ef1d9e48b1d1acb844e0d42f4558b8fd57059ff7 diff --git a/sci-libs/coinor-cppad/coinor-cppad-20140204.ebuild b/sci-libs/coinor-cppad/coinor-cppad-20140204.ebuild new file mode 100644 index 000000000000..77d4f5ebc898 --- /dev/null +++ b/sci-libs/coinor-cppad/coinor-cppad-20140204.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYP=cppad-${PV} + +DESCRIPTION="COIN-OR C++ Algorithmic Differentiation" +HOMEPAGE="https://projects.coin-or.org/CppAD/" +SRC_URI="http://www.coin-or.org/download/source/CppAD/${MYP}.gpl.tgz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples" + +RDEPEND=" + sci-libs/adolc:= + sci-libs/ipopt:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] )" + +S="${WORKDIR}/${MYP}" + +src_configure() { + local myeconfargs=( $(use doc Documentation) ) + autotools-utils_src_configure CXX_FLAGS="${CXXFLAGS}" +} + +src_compile() { + autotools-utils_src_compile + if use doc; then + ./build.sh doxygen || die + fi +} + +src_test() { + autotools-utils_src_test check test +} + +src_install() { + use doc && HTML_DOC=( "${BUILD_DIR}"/doxydocs/html/. ) + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r example/* + fi +} diff --git a/sci-libs/coinor-cppad/coinor-cppad-20140519-r1.ebuild b/sci-libs/coinor-cppad/coinor-cppad-20140519-r1.ebuild new file mode 100644 index 000000000000..537f051053f1 --- /dev/null +++ b/sci-libs/coinor-cppad/coinor-cppad-20140519-r1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils multilib + +MYP=cppad-${PV} + +DESCRIPTION="COIN-OR C++ Algorithmic Differentiation" +HOMEPAGE="https://projects.coin-or.org/CppAD/" +SRC_URI="http://www.coin-or.org/download/source/CppAD/${MYP}.gpl.tgz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples" + +RDEPEND=" + dev-libs/boost[threads] + sci-libs/adolc:0= + sci-libs/ipopt:0=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] )" + +S="${WORKDIR}/${MYP}" + +PATCHES=( + "${FILESDIR}"/${P}-dash.patch + "${FILESDIR}"/${P}-boost.patch + ) + +src_configure() { + local myeconfargs=( $(use doc Documentation) ) + autotools-utils_src_configure CXX_FLAGS="${CXXFLAGS}" +} + +src_compile() { + autotools-utils_src_compile + if use doc; then + ./build.sh doxygen || die + fi +} + +src_test() { + autotools-utils_src_test check test +} + +src_install() { + use doc && HTML_DOC=( "${BUILD_DIR}"/doxydocs/html/. ) + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r example/* + fi +} diff --git a/sci-libs/coinor-cppad/coinor-cppad-20140519.ebuild b/sci-libs/coinor-cppad/coinor-cppad-20140519.ebuild new file mode 100644 index 000000000000..8294efcbd21d --- /dev/null +++ b/sci-libs/coinor-cppad/coinor-cppad-20140519.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYP=cppad-${PV} + +DESCRIPTION="COIN-OR C++ Algorithmic Differentiation" +HOMEPAGE="https://projects.coin-or.org/CppAD/" +SRC_URI="http://www.coin-or.org/download/source/CppAD/${MYP}.gpl.tgz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples" + +RDEPEND=" + sci-libs/adolc:0= + sci-libs/ipopt:0=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] )" + +S="${WORKDIR}/${MYP}" + +src_configure() { + local myeconfargs=( $(use doc Documentation) ) + autotools-utils_src_configure CXX_FLAGS="${CXXFLAGS}" +} + +src_compile() { + autotools-utils_src_compile + if use doc; then + ./build.sh doxygen || die + fi +} + +src_test() { + autotools-utils_src_test check test +} + +src_install() { + use doc && HTML_DOC=( "${BUILD_DIR}"/doxydocs/html/. ) + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r example/* + fi +} diff --git a/sci-libs/coinor-cppad/files/coinor-cppad-20140519-boost.patch b/sci-libs/coinor-cppad/files/coinor-cppad-20140519-boost.patch new file mode 100644 index 000000000000..7a4d3ae83aca --- /dev/null +++ b/sci-libs/coinor-cppad/files/coinor-cppad-20140519-boost.patch @@ -0,0 +1,79 @@ + configure.ac | 18 ++++++++++-------- + 1 file changed, 10 insertions(+), 8 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 033621f..87e129a 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -550,13 +550,14 @@ dnl check for boost thread library + AC_LANG_PUSH([C++]) + LDFLAGS_save=$LDFLAGS + CXXFLAGS_save=$CXXFLAGS ++LIBS_save=$LIBS + boost_thread_found='no' + if test "$BOOST_DIR" != '' ; then + CXXFLAGS="-I$BOOST_DIR/include $CXXFLAGS" + fi + if test "$BOOST_DIR" = '' && test "$boost_thread_found" = 'no' ; then +- bthread_lib='-lboost_thread-mt' +- LDFLAGS="$LDFLAGS_save $bthread_lib" ++ bthread_lib='-lboost_thread-mt -lboost_system' ++ LIBS="$LIBS_save $bthread_lib" + AC_LINK_IFELSE( + [AC_LANG_PROGRAM( + [# include <boost/thread.hpp>], +@@ -568,7 +569,7 @@ if test "$BOOST_DIR" = '' && test "$boost_thread_found" = 'no' ; then + fi + if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + bthread_lib="$BOOST_DIR/lib/libboost_thread-mt.so" +- LDFLAGS="$LDFLAGS_save $bthread_lib" ++ LIBS="$LIBS_save $bthread_lib" + AC_LINK_IFELSE( + [AC_LANG_PROGRAM( + [# include <boost/thread.hpp>], +@@ -580,7 +581,7 @@ if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + fi + if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + bthread_lib="$BOOST_DIR/lib/libboost_thread-mt.a" +- LDFLAGS="$LDFLAGS_save $bthread_lib" ++ LIBS="$LIBS_save $bthread_lib" + AC_LINK_IFELSE( + [AC_LANG_PROGRAM( + [# include <boost/thread.hpp>], +@@ -591,8 +592,8 @@ if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + ) + fi + if test "$BOOST_DIR" = '' && test "$boost_thread_found" = 'no' ; then +- bthread_lib='-lboost_thread' +- LDFLAGS="$LDFLAGS_save $bthread_lib" ++ bthread_lib='-lboost_thread -lboost_system' ++ LIBS="$LIBS_save $bthread_lib" + AC_LINK_IFELSE( + [AC_LANG_PROGRAM( + [# include <boost/thread.hpp>], +@@ -604,7 +605,7 @@ if test "$BOOST_DIR" = '' && test "$boost_thread_found" = 'no' ; then + fi + if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + bthread_lib="$BOOST_DIR/lib/libboost_thread.so" +- LDFLAGS="$LDFLAGS_save $bthread_lib" ++ LIBS="$LIBS_save $bthread_lib" + AC_LINK_IFELSE( + [AC_LANG_PROGRAM( + [# include <boost/thread.hpp>], +@@ -616,7 +617,7 @@ if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + fi + if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + bthread_lib="$BOOST_DIR/lib/libboost_thread.a" +- LDFLAGS="$LDFLAGS_save $bthread_lib" ++ LIBS="$LIBS_save $bthread_lib" + AC_LINK_IFELSE( + [AC_LANG_PROGRAM( + [# include <boost/thread.hpp>], +@@ -636,6 +637,7 @@ else + fi + LDFLAGS=$LDFLAGS_save + CXXFLAGS=$CXXFLAGS_save ++LIBS=$LIBS_save + AC_LANG_POP([C++]) + # + dnl -------------------------------------------------------------------------- diff --git a/sci-libs/coinor-cppad/files/coinor-cppad-20140519-dash.patch b/sci-libs/coinor-cppad/files/coinor-cppad-20140519-dash.patch new file mode 100644 index 000000000000..fe0b210f1075 --- /dev/null +++ b/sci-libs/coinor-cppad/files/coinor-cppad-20140519-dash.patch @@ -0,0 +1,215 @@ + configure.ac | 56 ++++++++++++++++++++++++++++---------------------------- + 1 file changed, 28 insertions(+), 28 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 9e917dd..033621f 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -194,7 +194,7 @@ AC_ARG_WITH(sparse_list, + ) + AC_MSG_RESULT([$sparse_list]) + if test "$sparse_set" = "yes" ; then +- if test "$sparse_list" == "yes" ; then ++ if test "$sparse_list" = "yes" ; then + AC_MSG_ERROR([cannot --with both sparse_set and sparse_list]) + fi + AC_SUBST(cppad_internal_sparse_set, sparse_set) +@@ -374,7 +374,7 @@ AC_SUBST(cppad_max_num_threads, [$max_num_threads]) + dnl type used for addresses in AD tapes [ default = unsigned int ] ----------- + AC_MSG_CHECKING([TAPE_ADDR_TYPE]) + AC_ARG_VAR(TAPE_ADDR_TYPE, [type used for addresses in AD tapes]) +-if test "$TAPE_ADDR_TYPE" == "" ; then ++if test "$TAPE_ADDR_TYPE" = "" ; then + addr_t="unsigned int" + else + addr_t="$TAPE_ADDR_TYPE" +@@ -382,22 +382,22 @@ fi + AC_SUBST(cppad_tape_addr_type, [$addr_t]) + AC_MSG_RESULT([$addr_t]) + ok="no" +-if test "$addr_t" == "size_t" ; then ++if test "$addr_t" = "size_t" ; then + ok="yes" + fi +-if test "$addr_t" == "int" ; then ++if test "$addr_t" = "int" ; then + AC_MSG_WARN( + [TAPE_ADDR_TYPE=int is for CppAD developers (not users)] + ) + ok="yes" + fi +-if test "$addr_t" == "unsigned int" ; then ++if test "$addr_t" = "unsigned int" ; then + ok="yes" + fi +-if test "$addr_t" == "unsigned short int" ; then ++if test "$addr_t" = "unsigned short int" ; then + ok="yes" + fi +-if test "$ok" == "no" ; then ++if test "$ok" = "no" ; then + AC_MSG_ERROR( + [$addr_t is not a valid choice for TAPE_ADDR_TYPE] + ) +@@ -406,7 +406,7 @@ fi + dnl type used for tape identifier [ default = unsigned int ] ----------- + AC_MSG_CHECKING([TAPE_ID_TYPE]) + AC_ARG_VAR(TAPE_ID_TYPE, [type used for addresses in AD tapes]) +-if test "$TAPE_ID_TYPE" == "" ; then ++if test "$TAPE_ID_TYPE" = "" ; then + tape_id_t="unsigned int" + else + tape_id_t="$TAPE_ID_TYPE" +@@ -414,22 +414,22 @@ fi + AC_SUBST(cppad_tape_id_type, [$tape_id_t]) + AC_MSG_RESULT([$tape_id_t]) + ok="no" +-if test "$tape_id_t" == "size_t" ; then ++if test "$tape_id_t" = "size_t" ; then + ok="yes" + fi +-if test "$tape_id_t" == "int" ; then ++if test "$tape_id_t" = "int" ; then + AC_MSG_WARN( + [TAPE_ID_TYPE=int is for CppAD developers (not users)] + ) + ok="yes" + fi +-if test "$tape_id_t" == "unsigned int" ; then ++if test "$tape_id_t" = "unsigned int" ; then + ok="yes" + fi +-if test "$tape_id_t" == "unsigned short int" ; then ++if test "$tape_id_t" = "unsigned short int" ; then + ok="yes" + fi +-if test "$ok" == "no" ; then ++if test "$ok" = "no" ; then + AC_MSG_ERROR( + [$tape_id_t is not a valid choice for TAPE_ID_TYPE] + ) +@@ -447,7 +447,7 @@ AC_SUBST(cppad_has_rvalue, 0) + dnl Determine if size_t has same size as unsigned int + AC_CHECK_SIZEOF([size_t]) + AC_CHECK_SIZEOF([unsigned int]) +-if test "$ac_cv_size_t" == "$ac_cv_unsigned_int" ; then ++if test "$ac_cv_size_t" = "$ac_cv_unsigned_int" ; then + AC_SUBST(cppad_size_t_same_unsigned_int, 1) + else + AC_SUBST(cppad_size_t_same_unsigned_int, 0) +@@ -485,8 +485,8 @@ AC_PROG_RANLIB + dnl AC_PROG_CXX([compiler-search-list]) outputs CXX as C++ compiler to use + AC_PROG_CXX + AC_MSG_CHECKING([whether using Microsoft C++ compiler]) +-AM_CONDITIONAL(CppAD_MS_COMPILER, test "$CXX" == "cl" || test "$CXX" == "icl") +-if test "$CXX" == "cl" || test "$CXX" == "icl"; then ++AM_CONDITIONAL(CppAD_MS_COMPILER, test "$CXX" = "cl" || test "$CXX" = "icl") ++if test "$CXX" = "cl" || test "$CXX" = "icl"; then + AC_MSG_RESULT([yes]) + else + AC_MSG_RESULT([no]) +@@ -531,7 +531,7 @@ AC_CHECK_LIB( + [pthread="no"] + ) + AM_CONDITIONAL(CppAD_PTHREAD, test "$pthread" = "yes") +-if test "$pthread" == "yes" ; then ++if test "$pthread" = "yes" ; then + AC_SUBST(PTHREAD_LIB,"-lpthread") + else + AC_SUBST(PTHREAD_LIB,"") +@@ -554,7 +554,7 @@ boost_thread_found='no' + if test "$BOOST_DIR" != '' ; then + CXXFLAGS="-I$BOOST_DIR/include $CXXFLAGS" + fi +-if test "$BOOST_DIR" == '' && test "$boost_thread_found" == 'no' ; then ++if test "$BOOST_DIR" = '' && test "$boost_thread_found" = 'no' ; then + bthread_lib='-lboost_thread-mt' + LDFLAGS="$LDFLAGS_save $bthread_lib" + AC_LINK_IFELSE( +@@ -566,7 +566,7 @@ if test "$BOOST_DIR" == '' && test "$boost_thread_found" == 'no' ; then + [boost_thread_found='no'] + ) + fi +-if test "$BOOST_DIR" != '' && test "$boost_thread_found" == 'no' ; then ++if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + bthread_lib="$BOOST_DIR/lib/libboost_thread-mt.so" + LDFLAGS="$LDFLAGS_save $bthread_lib" + AC_LINK_IFELSE( +@@ -578,7 +578,7 @@ if test "$BOOST_DIR" != '' && test "$boost_thread_found" == 'no' ; then + [boost_thread_found='no'] + ) + fi +-if test "$BOOST_DIR" != '' && test "$boost_thread_found" == 'no' ; then ++if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + bthread_lib="$BOOST_DIR/lib/libboost_thread-mt.a" + LDFLAGS="$LDFLAGS_save $bthread_lib" + AC_LINK_IFELSE( +@@ -590,7 +590,7 @@ if test "$BOOST_DIR" != '' && test "$boost_thread_found" == 'no' ; then + [boost_thread_found='no'] + ) + fi +-if test "$BOOST_DIR" == '' && test "$boost_thread_found" == 'no' ; then ++if test "$BOOST_DIR" = '' && test "$boost_thread_found" = 'no' ; then + bthread_lib='-lboost_thread' + LDFLAGS="$LDFLAGS_save $bthread_lib" + AC_LINK_IFELSE( +@@ -602,7 +602,7 @@ if test "$BOOST_DIR" == '' && test "$boost_thread_found" == 'no' ; then + [boost_thread_found='no'] + ) + fi +-if test "$BOOST_DIR" != '' && test "$boost_thread_found" == 'no' ; then ++if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + bthread_lib="$BOOST_DIR/lib/libboost_thread.so" + LDFLAGS="$LDFLAGS_save $bthread_lib" + AC_LINK_IFELSE( +@@ -614,7 +614,7 @@ if test "$BOOST_DIR" != '' && test "$boost_thread_found" == 'no' ; then + [boost_thread_found='no'] + ) + fi +-if test "$BOOST_DIR" != '' && test "$boost_thread_found" == 'no' ; then ++if test "$BOOST_DIR" != '' && test "$boost_thread_found" = 'no' ; then + bthread_lib="$BOOST_DIR/lib/libboost_thread.a" + LDFLAGS="$LDFLAGS_save $bthread_lib" + AC_LINK_IFELSE( +@@ -627,7 +627,7 @@ if test "$BOOST_DIR" != '' && test "$boost_thread_found" == 'no' ; then + ) + fi + AM_CONDITIONAL(CppAD_BTHREAD, test "$boost_thread_found" = 'yes') +-if test "$boost_thread_found" == 'yes' ; then ++if test "$boost_thread_found" = 'yes' ; then + AC_SUBST(BTHREAD_LIB,"$bthread_lib") + AC_MSG_RESULT([boost::thread library... yes]) + else +@@ -650,12 +650,12 @@ fi + AC_SUBST(CPPAD_IPOPT_LD_PATH, "$IPOPT_LD_PATH") + # + AC_SUBST(CPPAD_IPOPT_LIBS, "$IPOPT_LIBS -lipopt") +-if test "$have_pkg_config" == "yes"; then ++if test "$have_pkg_config" = "yes"; then + dnl set CPPAD_IPOPT_LIBS + PKG_CONFIG_PATH="$IPOPT_DIR/lib/pkgconfig:$IPOPT_DIR/share/pkgconfig" + PKG_CONFIG_PATH="$PKG_CONFIG_PATH:$IPOPT_DIR/lib64/pkgconfig" + export PKG_CONFIG_PATH +- if pkg-config --libs ipopt >& /dev/null ; then ++ if pkg-config --libs ipopt > /dev/null 2>&1 ; then + CPPAD_IPOPT_LIBS=`pkg-config --libs ipopt` + else + dnl check for blas library +@@ -696,7 +696,7 @@ dnl + AC_SUBST(cppad_description, "Differentiation of C++ Algorithms") + AC_SUBST(cppad_version, ${PACKAGE_VERSION} ) + AC_SUBST(cppad_url, "http://www.coin-or.org/CppAD") +-if test "$prefix" == "NONE" ; then ++if test "$prefix" = "NONE" ; then + cppad_cflags_value="-I$HOME/include" + cppad_libs_value="-L$HOME/lib" + else +@@ -707,7 +707,7 @@ if test "$POSTFIX_DIR" != "" ; then + cppad_cflags_value="$cppad_cflags_value/$POSTFIX_DIR" + cppad_libs_value="$cppad_libs_value/$POSTFIX_DIR" + fi +-if test "$IPOPT_DIR" == "" ; then ++if test "$IPOPT_DIR" = "" ; then + cppad_libs_value="" + cppad_requires_value="" + else diff --git a/sci-libs/coinor-cppad/metadata.xml b/sci-libs/coinor-cppad/metadata.xml new file mode 100644 index 000000000000..0edc1f35c6e9 --- /dev/null +++ b/sci-libs/coinor-cppad/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + We refer to the step by step conversion from an algorithm that + computes function values to an algorithm that computes derivative + values as Algorithmic Differentiation (AD); often referred to as + automatic differentiation. Given a C++ algorithm that computes + function values, CppAD generates an algorithm that computes + corresponding derivative values (of arbitrary order using either + forward or reverse mode). +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-csdp/Manifest b/sci-libs/coinor-csdp/Manifest new file mode 100644 index 000000000000..8695292d24f3 --- /dev/null +++ b/sci-libs/coinor-csdp/Manifest @@ -0,0 +1,5 @@ +DIST Csdp-6.1.1.tgz 441574 SHA256 0558a46ac534e846bf866b76a9a44e8a854d84558efa50988ffc092f99a138b9 SHA512 ba5dc0faea223bad6293f131ee63daee0a395a6e84c76fe108dbbefb3ab0696b2a59f435766c78a2d22244801a9abda2719798cbfe30dd9e1c32317e0283fd2e WHIRLPOOL 51f4fa92a07e49071581695d31b504b7fa734659ee61387d3f55e7692866dbe68552466b4004104eadde39485c0201455ff18fc5836e50b3ab5cd7b6ae9a52a8 +EBUILD coinor-csdp-6.1.1-r1.ebuild 2924 SHA256 12f8210a2a88ee0a2908c925e81b1403191f8dace973e5de48388affbff8ca6e SHA512 40f824fc2ec8fcc3d2c0bbfbd8425a7153d19b7fc70979c8ea75c60c1bedae14dfbc92604bc28bf5a3340308b2c6747e2fadac6860928a98459ccb902bf8035b WHIRLPOOL 4fb1315b3097dbd403dbac3264b72200ee845ea2f5794ceb38f620f421822158959a0ef6b662601a89e2b7396ac9e901ebec72c578bb01231bb08016c609b447 +MISC ChangeLog 2445 SHA256 ff5871fb1c0169d1a2d16730733a5a2a5e75ebd3e22668497326b6a063ab028f SHA512 cab3de99878ec28d151045e351ab7f1b48cacc9ad7cf3544174fc55695ccd3d948e6da6fed80d87f7c2dd0fd4fc9131c184e7b5a5a3aa16f248688fbf40b6f3b WHIRLPOOL 3737e4b731b85dc85450c2fac1aff039a449a7ad287f9e4d9413ffffffbbfff55c81487fbb5fe0fb4874e67da33a2a5f7f47a3cb78718d4f8623c3e64e4f2728 +MISC ChangeLog-2015 930 SHA256 60d27043525b604f0d4fa2daf1b1194f9ec9eef446a7fd2e6f7afbe88d343f56 SHA512 a868111f865285a8b65d156e7a089cac47e59dfb16275448c94cad25a70610fb1ad5752b0750f65bbf081d8ecbf4a070b6e1e581fd9832a192e4810393012f40 WHIRLPOOL 1f2e668fb85ebc6ef2de87ba5d1e3db275548ecc144a5504790ca7763bb7a781da12b75069dbcb9343a86b02ea0708f72e659160329d144e0e4288b0410efe8d +MISC metadata.xml 886 SHA256 e10c3cb5f90964acf97131a89374954c6cb3d456e218770bb589668b0fa936c5 SHA512 c7d40732c00742e9571ca12b19892083a9a3f2a28000f0e9acb5b868879bb7e0e1fa8d3ade93f6af41b1a2afcce521e1136f7e39cbe227a0c40973afb7a04ab6 WHIRLPOOL b681801caa4c9c972da2879a0665a2a0afe1c1118413dd3d2ba28cd42e2e4bcc2c9f38030cbbfb6aff4c0c8c3bf76e32dcd27624bacae94572ccc2373b3a0640 diff --git a/sci-libs/coinor-csdp/coinor-csdp-6.1.1-r1.ebuild b/sci-libs/coinor-csdp/coinor-csdp-6.1.1-r1.ebuild new file mode 100644 index 000000000000..bc7b2d55620f --- /dev/null +++ b/sci-libs/coinor-csdp/coinor-csdp-6.1.1-r1.ebuild @@ -0,0 +1,101 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit versionator toolchain-funcs flag-o-matic multilib + +MYPN=Csdp + +DESCRIPTION="COIN-OR C Library for Semi-Definite Programming" +HOMEPAGE="https://projects.coin-or.org/Csdp/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="CPL-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples openmp static-libs" + +RDEPEND=" + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MYPN}-${PV}" + +static_to_shared() { + local libstatic=${1}; shift + local libname=$(basename ${libstatic%.a}) + local soname=${libname}$(get_libname $(get_version_component_range 1-2)) + local libdir=$(dirname ${libstatic}) + + einfo "Making ${soname} from ${libstatic}" + if [[ ${CHOST} == *-darwin* ]] ; then + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ + -Wl,-all_load -Wl,${libstatic} \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + else + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + [[ $(get_version_component_count) -gt 1 ]] && \ + ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) + ln -s ${soname} ${libdir}/${libname}$(get_libname) + fi +} + +pkg_setup() { + if use openmp && [[ $(tc-getCC) == *gcc* ]] && ! tc-has-openmp; then + eerror "Your selected gcc compiler does not support OpenMP" + die "OpenMP non capable gcc" + fi +} + +src_prepare() { + find . -name Makefile -exec sed -i -e 's:make:$(MAKE):g' '{}' + || die + append-cflags -DNOSHORTS -DUSEGETTIME -I../include + if use openmp; then + [[ $(tc-getCC) == *gcc* ]] && append-cflags -fopenmp \ + && append-ldflags -fopenmp + [[ $(tc-getCC) == *icc* ]] && append-cflags -openmp + append-cflags -DUSEOPENMP + fi + use amd64 && append-cflags -DBIT64 + [[ $($(tc-getPKG_CONFIG) --libs blas) =~ atlas ]] && append-cflags -DUSEATLAS + sed -i \ + -e "s:-O3:${CFLAGS} ${LDFLAGS}:" \ + -e "s:ar :$(tc-getAR) :" \ + */Makefile || die + + tc-export CC +} + +src_compile() { + emake CFLAGS="${CFLAGS} -fPIC" -C lib + local libs="$($(tc-getPKG_CONFIG) --libs blas lapack)" + static_to_shared lib/libsdp.a ${libs} + use static-libs && emake -C lib clean && emake -C lib + emake -C solver LIBS="${libs} -L../lib -lsdp -lm" + emake -C theta LIBS="${libs} -L../lib -lsdp -lm" +} + +src_test() { + LD_LIBRARY_PATH="${S}/lib" emake -C test +} + +src_install() { + dobin solver/csdp theta/{theta,graphtoprob,complement,rand_graph} + dolib.so lib/libsdp$(get_libname)* + use static-libs && dolib.a lib/libsdp.a + insinto /usr/include/${PN} + doins include/* + dodoc AUTHORS README + use doc && dodoc doc/csdpuser.pdf + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins example/* + fi +} diff --git a/sci-libs/coinor-csdp/metadata.xml b/sci-libs/coinor-csdp/metadata.xml new file mode 100644 index 000000000000..7ff02fb6699f --- /dev/null +++ b/sci-libs/coinor-csdp/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + CSDP is a library of routines that implements a predictor corrector + variant of the semidefinite programming algorithm of Helmberg, + Rendl, Vanderbei, and Wolkowicz. The main advantages of this code + are that it is written to be used as a callable subroutine, it is + written in C for efficiency, the code runs in parallel on shared + memory multi-processor systems, and it makes effective use of + sparsity in the constraint matrices. CSDP has been compiled on many + different systems. The code should work on any system with an ANSI + C Compiler and BLAS/LAPACK libraries. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-dip/Manifest b/sci-libs/coinor-dip/Manifest new file mode 100644 index 000000000000..4381115b93cf --- /dev/null +++ b/sci-libs/coinor-dip/Manifest @@ -0,0 +1,5 @@ +DIST Dip-0.9.8.tgz 10557241 SHA256 d85b5678acf7b9440ef46b04bb602485b6bebe91525d6cf8defe61ea67bb48f6 SHA512 7dfb51f63aab36fe7e894be5f17f8b614bfdf9be1a14b8f8b2ee555dcb8392f82b13d20481d60423d3d375a2e52eebe0439e696e3b3a7dfdd18223829835d361 WHIRLPOOL 324d69725ac94a81b813b9fe2a9437091ba626f5f343f63cf5fb994d9b2ed9ffbe6643fe7b83521a3bd82699bf11a7c9ae3023a3b88b273bce1fc0e61ed9e8c0 +EBUILD coinor-dip-0.9.8.ebuild 1162 SHA256 c850aca660603496ade8f683c7d4fcc13eeacc82cdc5b4721881968fe071f384 SHA512 8d23a5f5f95db8463c5a4eb13277b926ea1c65a089bbbaa2c53713feef531bd60c83098ce751904c9e04534163621d889322ee99295f127e04124884bef7718d WHIRLPOOL e53f58187f3ee5bd268fa93586f7824fc75d788bb329401e417334f142e0307abab370fb400c5431550bbecf6f8c62b65492260c8321865e3e8bb9e3fc65a84c +MISC ChangeLog 2436 SHA256 7e51566d52a7fa78991c28a414b4e1f50f65fe2f752cf1e2c2c5c414963babfd SHA512 70e7d44cebf17b1e535895d38a9420a5c647ecd16e37726566b06d205f17cafe36893b2339d63d2e629623d386c23875c92022ec0b2a28c8daebc00fdb8dbabb WHIRLPOOL 9540da625f77e8d5cc2b3187e628b3d35839576260e3e66ae3d4319070ed515f6f3ae346a3a32f83c493547899e50034fbdfbb95842a0a999ff720b2cecb041c +MISC ChangeLog-2015 918 SHA256 dcdf0250d0cce8fa11bee9c95fb5fa3e731aabe0ba5edc83f3405a71c3854233 SHA512 6805a04b5a58f13817d38c7821d6d1bd5eab08f3f602b820b68d685ff5f7391beb20eaeb145c55abb03959c0a029c20ac979f8d7a546aaaef1fe5e09cd5dc8a2 WHIRLPOOL 49ad9e13ab0242e5c5d892f10241f9a72cae299b76d995367a265aa8057fdd2fc16db23da2e17640b2ccc6f1032243ce27d38d7497ff81ab90d29ea7ce279cfa +MISC metadata.xml 716 SHA256 47a696d886a0be6bfae2ea59013c61cac57d8d4cac0d3531a56cc82a53604ab1 SHA512 2f8a249110f82367361fa63e0ce789eac52a7cbbcbc53c89a665a6f7416ada3c2f772458d33b0a960586bef13442b2598702a23fee65ecbd621c7d68608f9f2b WHIRLPOOL 52c40e87d3f2aa93912d6e1412f6748f47fd07645bab5664bddffb34ca46fce760c38c82c179b02361f4d32e3d4851205b6251fdb56af78cf6cd9f5c7032e213 diff --git a/sci-libs/coinor-dip/coinor-dip-0.9.8.ebuild b/sci-libs/coinor-dip/coinor-dip-0.9.8.ebuild new file mode 100644 index 000000000000..8a74a45423c9 --- /dev/null +++ b/sci-libs/coinor-dip/coinor-dip-0.9.8.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Dip + +DESCRIPTION="COIN-OR Decomposition in Integer Programming library" +HOMEPAGE="https://projects.coin-or.org/Dip/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples static-libs test" + +RDEPEND=" + sci-libs/coinor-alps:= + sci-libs/coinor-cbc:= + sci-libs/coinor-cgl:= + sci-libs/coinor-clp:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + ) + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-dip/metadata.xml b/sci-libs/coinor-dip/metadata.xml new file mode 100644 index 000000000000..9b46cc7b40c7 --- /dev/null +++ b/sci-libs/coinor-dip/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + DIP (Decomposition for Integer Programming) is an open-source + extensible software framework for implementing decomposition-based + bounding algorithms for use in solving large-scale discrete + optimization problems. The framework provides a simple API for + experimenting with various decomposition-based algorithms, such as + Dantzig-Wolfe decomposition, Lagrangian relaxation, and various + cutting plane methods. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-dylp/Manifest b/sci-libs/coinor-dylp/Manifest new file mode 100644 index 000000000000..0e3acbb2ca32 --- /dev/null +++ b/sci-libs/coinor-dylp/Manifest @@ -0,0 +1,5 @@ +DIST DyLP-1.9.4.tgz 5049865 SHA256 b2e7a795927853e3d38f6afa1b787d22f39b630420f54516516e766d3c2b6b35 SHA512 1dcad555f40b88aafaef0ca712731f3d4787900cefd2125eea9171d5dfdbea1888fd08b6767f50dcb915a0e2ad4e3430ed67d68026015b15af9032ed9231a069 WHIRLPOOL f38440bf602e00adc49f4662d7c793e9dd601459d8eb3700326026d6de1ed38c95bda6f9bfaeeb65be1468caad9bc06a6f14128583476b47b551347cac1477cd +EBUILD coinor-dylp-1.9.4.ebuild 1378 SHA256 f50575b82499aba491858f5e45cffb7143aec2cbfa2c77c6d790d5a3d3ac1fcd SHA512 f153e967665f83b2a29b64d06e46fd64388d794542d76ba9c0364662e6de2588f56089efe2c523bf5e5fc2e087804b296e6a4ce99ef1a9123cb28db2dc0621f7 WHIRLPOOL 8fe742c8e2e09ed3264fdcc7c326bab4f3b18c03a3d2995ff91e0cd1d48d29ba1a524bdaabd594c2ee4e7fbff3b96bf73deacce67790f09e8792fb2709be04d5 +MISC ChangeLog 2439 SHA256 5e9876841635beebc4e1d2247506678c8649ae4d29e0a119d7314af352d0e38f SHA512 de74d22358ce0d6b05bb586077dc54412732008de63b62234668a4ebdd4e045bc627f28bbda955456ff18876196f5f9b38039cbe3e5b7a8ab0a7b62bd25a8f7d WHIRLPOOL 7d84460b82a5a08ea5ceebf7b99e62cac699748f78770fa925e70bb5de4d09187cbf037594079158a60285eebd95a62c3e05d1faa12df321c5169a03723b64b8 +MISC ChangeLog-2015 1362 SHA256 e79a8e9819f0ba7c9ac8da59b7e947e6d4cc689311c5aac8431059c0356b58c8 SHA512 a106359ab4c8f4cc70c11a92af3706084019aba1d59e7aca9ef08b484f01d56c0163c865bb9cdef1b2dcbb4d82761b7ae72b5809cd015a3489f169ae3940c9c8 WHIRLPOOL d307ce5fa3802ea2f32a764061bc379cdd0c70bfc6ea56468871e4e039997009adff20d591005456e49d2cb3bb58cf2870888a477dd4219d2091d6ab16d94199 +MISC metadata.xml 615 SHA256 5f97d94150611017193e23ab09067678b7de76fe0d7ecd9292012eed87214b2f SHA512 0ea0ea937fc3bc00892bc25d13807c3db3e42ba21b276a231b3b9bcd541dfa6e0db96de3a53060e09a4e7b13fc70526525de0218d3e6e167102247ee4b0246c6 WHIRLPOOL 433495b8f174ed014aa612aacb58bbdf3e41eca9e23ff2e2d8307eabbfd339860c52db9bee484266fd21a304590b7a4ac6fb524f0137faac83fcdb283a2f07e0 diff --git a/sci-libs/coinor-dylp/coinor-dylp-1.9.4.ebuild b/sci-libs/coinor-dylp/coinor-dylp-1.9.4.ebuild new file mode 100644 index 000000000000..af3785fbe343 --- /dev/null +++ b/sci-libs/coinor-dylp/coinor-dylp-1.9.4.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=DyLP + +DESCRIPTION="COIN-OR using the dynamic simplex linear programming solver" +HOMEPAGE="https://projects.coin-or.org/DyLP/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND="sci-libs/coinor-osi:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile all $(usex doc doxydoc "") +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${BUILD_DIR}/doxydocs/html/") + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-dylp/metadata.xml b/sci-libs/coinor-dylp/metadata.xml new file mode 100644 index 000000000000..2c189040b7fc --- /dev/null +++ b/sci-libs/coinor-dylp/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + DyLp is designed to find solutions of constrained linear mathematical + optimization problems. To this end, it is using a full implementation + of the so called dynamic simplex algorithm for linear programming. + DyLP is part of the larger COIN-OR initiative (Computational + Infrastructure for Operations Research). +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-flopcpp/Manifest b/sci-libs/coinor-flopcpp/Manifest new file mode 100644 index 000000000000..84ec1df63015 --- /dev/null +++ b/sci-libs/coinor-flopcpp/Manifest @@ -0,0 +1,5 @@ +DIST FlopC++-1.1.7.tgz 6631744 SHA256 c5bf2957f48d80638933a95dd1b2575b3b52a211313f664f9896b4c5050ff925 SHA512 40f59cb34f61f6ff1759a90909a81d724a562ee9dbfe91628ad8df1b8049afff254ceeb56f1e68a48d035e6d3a140744b8ebd8815ee39c9f01e17860c904942d WHIRLPOOL 4f2a5104e896980709f8b078c58771331516ed3753005768ec2faee6d6c6b9cedb2fc95cefd9e93c35dda7407094583543e032d0f0a0ca669062211b17ce9ef7 +EBUILD coinor-flopcpp-1.1.7.ebuild 1382 SHA256 47d1f6ec70cb7f87a2a52a480ea995c17a95997acc4e1eaf58257fe0571f8769 SHA512 8b84a8e6653ae8d3c371c354122ae41e307d93ab88699b5e8d6530951aed4b65b9ece3350aaf892e6eaf14db2674e9ad781b058ec52e1e52498eae758e092c50 WHIRLPOOL e574bec08b8bdd72655c5f448562427c49bfb315ba67cdd7a2b539baddd96a63d89bd1dd12dd7bce6c2dc744b278975a30e1c27a88a6513ee33a91925ce50e0d +MISC ChangeLog 2448 SHA256 182701e43325085207c8fd685dee74fff5e553fb99d3fbe9de131294f2ce8433 SHA512 3672104cbb19aa87008360b6e9e3febb8ba9252cff4325605abad4b001e07bf2b5e5fc1ce6de148a25984ddee9016a9584a0ec68e22a01e30ebe7f91005043cc WHIRLPOOL 0d9251d78c6146165dad6a5c04b285540939280d11ff3037cc89ad7c8e6ec6a604c85b68e8d8930cdc3d90c875b4cc3108d1203b7931941d25e3a6f7bef016fd +MISC ChangeLog-2015 1319 SHA256 3847c5113d31859a374e2264007912d1ec256be6a121851264ac064bf34e8f6c SHA512 57dd74ae0e173e9265d85ef445b746f5967d451cbad5ed104d3dd77de0555a01cdb1cbad7da1fafa8ebe28f24976759248a28c3c877af4da524b7ee08d224ad2 WHIRLPOOL dcbedb605f703b891986971d70c10a65f942d1af37922a3e01111b5b311d780b0f2397c2bafd80e78c3adec4266aa0da543984079846a6be6e2ec7ff9f23d13f +MISC metadata.xml 729 SHA256 f4dfa00c58e0209e054c0fb22718ca4fa564717633172a9abb5b8d14b0f240c3 SHA512 bc9e9cd91c9a5a53269c92ee502504f0e05a90c8657a8be511631d1712695345178c8931826af79e0e89c9431799abd99d2df18a7f5b91fad71ad5a3d995e3af WHIRLPOOL 963977325c1c377a79d3a889e05eadb68cfee9a7a1d562f490f854549f52fba9981499f03a688058c386c6d73b024c000a3ca1bc10ec8d1b248aaa41b25a1061 diff --git a/sci-libs/coinor-flopcpp/coinor-flopcpp-1.1.7.ebuild b/sci-libs/coinor-flopcpp/coinor-flopcpp-1.1.7.ebuild new file mode 100644 index 000000000000..015c0264ae52 --- /dev/null +++ b/sci-libs/coinor-flopcpp/coinor-flopcpp-1.1.7.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=FlopC++ + +DESCRIPTION="COIN-OR algebraic modeling language for linear optimization" +HOMEPAGE="https://projects.coin-or.org/FlopC++/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs" + +RDEPEND=" + sci-libs/coinor-cgl:= + sci-libs/coinor-clp:= + sci-libs/coinor-osi:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] )" + +S="${WORKDIR}/${MYPN}-${PV}/FlopCpp" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + if use doc; then + cd "${WORKDIR}/${MYPN}-${PV}/doxydoc" || die + doxygen doxygen.conf || die + fi +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${WORKDIR}/${MYPN}-${PV}/doxydoc/html/") + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-flopcpp/metadata.xml b/sci-libs/coinor-flopcpp/metadata.xml new file mode 100644 index 000000000000..fd5d53dfd884 --- /dev/null +++ b/sci-libs/coinor-flopcpp/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The COIN-OR Formulation of Linear Optimization Problems in C++ + (FLOPC++) is a linear optimization modelling language that can be + specified in a declarative style, similar to algebraic modelling + languages such as GAMS and AMPL, within a C++ program. As a result + the traditional strengths of algebraic modelling languages are + preserved, while embedding linear optimization models in software + applications is facilitated. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-mp/Manifest b/sci-libs/coinor-mp/Manifest new file mode 100644 index 000000000000..d69312bce52d --- /dev/null +++ b/sci-libs/coinor-mp/Manifest @@ -0,0 +1,5 @@ +DIST CoinMP-1.7.6.tgz 10343849 SHA256 86c798780b9e1f5921fe4efe651a93cb420623b45aa1fdff57af8c37f116113f SHA512 1612d43d52d0ee29b4e6ca328e1535c59722dfd5c7a7e0811a4180ad6033ef27111ced6497f9d5cea816c047a4e11c2aed6d1936feac8ded797eeec55d9539ce WHIRLPOOL 32f392e7bc2a0ca1e4a3a7f4ae30d1302cac3e65630cfb8d1483dc5cdf26fb46ba758049f7bd590bb93e7b73018affe05118ebb15fe1e41ffaade8f5a938ea5a +EBUILD coinor-mp-1.7.6.ebuild 1351 SHA256 4da2e2431e5b130a01621e923f2d554de03424442f02c23d490f1bea32cc3c30 SHA512 ea2ef701b4e46d53f25d0d8585c79ebef718fdc77d65ad71fa8b43131dd9d540b87e7afa913a827a1494c40bbbb299c46b6a59cd9bfad8377453c7a35b433b59 WHIRLPOOL 8fb46273d9e21c4165c736a1d2c4816f2d5056aa1baad3f7c94581682690bf3e80564b7d0cb8eb9f40549521f5e86a636ae33fd0e18feeb24d95f2e5f12b1fca +MISC ChangeLog 2433 SHA256 365b2f2c6f7811db1c5c69dc7f56e0ed3e380932efbabe51ade79fd50b173ef8 SHA512 e6a97704e9738aaff4344bf8ac23a1b2ac689a1c862b0071deae1921b283f848addd57217b7f3a2fd88cef3e1065f9628d4a386c8b3d679a1c9db84f6921b359 WHIRLPOOL e9648eef886f351d56dd328ec078c70af408c8b1f0d9336aa1eb2da53d7c6ddddbfa87e74ab841c59ca2d2ffef8504f57c373aead3b30525a633a56f469f9d12 +MISC ChangeLog-2015 1583 SHA256 17b0882d9dc87adbda6a4d05a7b2e96129a902b3573db17121c00023e55a5b05 SHA512 20a172b4b5a209649c82038f2f5601cf04e7829c2f3db4fd2a14dd9e4cb763e0d6f8ef7cc13ad4d8cca23e6c69031a1c50835ee56556f87ac934effe5b30bfd0 WHIRLPOOL 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+HOMEPAGE="https://projects.coin-or.org/CoinMP/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples static-libs" + +RDEPEND="sci-libs/coinor-cbc:=" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + sed -i \ + -e '/^addlibsdir/s/$(DESTDIR)//' \ + -e 's/$(addlibsdir)/$(DESTDIR)\/$(addlibsdir)/g' \ + -e 's/$(DESTDIR)$(DESTDIR)/$(DESTDIR)/g' \ + Makefile.in || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + --datadir=/usr/share + ) + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-mp/metadata.xml b/sci-libs/coinor-mp/metadata.xml new file mode 100644 index 000000000000..5fbc1079f58b --- /dev/null +++ b/sci-libs/coinor-mp/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The COmputational INfrastructure for Operations Research (COIN-OR) + MP is a C-API interface library that supports most of the + functionality of the CLP (Coin LP), CBC (Coin Branch-and-Cut), and + CGL (Cut Generation Library) projects. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-netlib/Manifest b/sci-libs/coinor-netlib/Manifest new file mode 100644 index 000000000000..e4db0fd78b8e --- /dev/null +++ b/sci-libs/coinor-netlib/Manifest @@ -0,0 +1,5 @@ +DIST Netlib-1.2.6.tgz 3960587 SHA256 02b3ef5cc7cce6ecf3778181f34faf8c1733af0e73cba09367d7fbd905b462b7 SHA512 545de8928377fedec44844e0eca02f8aaa0701bcae99ecb0494a01c7f838c6561d66497dde8302a908252198fe2a0b7656241ef26e75d9682f3f4ad1f706b23a WHIRLPOOL 183ee1f325302a38b485a701e9ef2b478c566b05c6eaf97e27e82e6bf030b091dd26b6f26f44382821ca81e919f54a0e22c40b02deb20f7a76cced9fc587d4ea +EBUILD coinor-netlib-1.2.6.ebuild 431 SHA256 b5e7e190cd1a7abca08fb9f558cad71828cec8c8b3beb655446bfcb80f8cecdc SHA512 81c5c0c9b159f5f11fdf1e93ec73891a6c94c8ed05f858fc95f063bf6dcede5680f6f2b8b5e9574e67aa954a2319207a8e78b5abe29b710665f7baebb9e07165 WHIRLPOOL 18f12043e430000aa1b71cdca52c8b63c5cf32346171cfb220f1b10a48d9250a463ef7d1d94bc2fd6f7fa6d004fc2efa2119a9eadb8f3a308b7628723b262843 +MISC ChangeLog 2445 SHA256 74d83f83b92800f97e9e8c1ee4259792b850c94f7472e07d1f8b5cd49ff449fd SHA512 188b8c754d95398b76087c9640a8f5170e08ec7b6e3b5f1dd61f814f0b3b723f27b3e2e93c0bab5945d932be3eac045cd5f53b7e07ddd93d361a8811eb19cb94 WHIRLPOOL efc99b71379fb24e8aa302fe47d28b695a37a34840eb9ce322d32d415521817eb737069f2974c9a350b2782b943f677e8bf8041fdc1883ae371297fcd24e951d +MISC ChangeLog-2015 1134 SHA256 90fd030c912462c87d90055a422ceb919e79fd02538a43249e3df6b3f0cdafec SHA512 d020412f553c74ad40755c76f82c8757987304a15d3f7bd12608637acb0e6fd4c8677c7ccd8d7d4c4c11fa4af2b643b7f635bf71eb56ff70665525ec57a8d75b WHIRLPOOL 980fc96a95e1b3d97b450ee547acfdb1d10a1fdb620b99438ad69abcd33350e985b7b39a290fcc1d569eab71789321f87ace1b81542fcaccb3ff2e07195a7b43 +MISC metadata.xml 399 SHA256 b11d1a44667b7725dc214212927ddbf766732cd070a2aeba27b0bf20b74e323a SHA512 b954652bf69b43fd90b0f207063f58431653153e8ad13cca22acdd369d0b3b4a5d148983810cc5c4103c402526d953e931335783bac3970dca2ba41c5ec091f2 WHIRLPOOL 5a3ae76d620b62516317351d8970a72e4158c36e9241b3693380e57acf6de7c65321dddb079e4e9566f960c29a15d112f4ec292035aa8e6a264adc182e85b86e diff --git a/sci-libs/coinor-netlib/coinor-netlib-1.2.6.ebuild b/sci-libs/coinor-netlib/coinor-netlib-1.2.6.ebuild new file mode 100644 index 000000000000..4eedeac9aa82 --- /dev/null +++ b/sci-libs/coinor-netlib/coinor-netlib-1.2.6.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +MYPN=Netlib + +DESCRIPTION="COIN-OR netlib models" +HOMEPAGE="https://projects.coin-or.org/svn/Data/Netlib" +SRC_URI="http://www.coin-or.org/download/source/Data/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}/${MYPN}-${PV}" diff --git a/sci-libs/coinor-netlib/metadata.xml b/sci-libs/coinor-netlib/metadata.xml new file mode 100644 index 000000000000..7a04ef261601 --- /dev/null +++ b/sci-libs/coinor-netlib/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The COmputational INfrastructure for Operations Research (COIN-OR) + models from netlib for testing. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-os/Manifest b/sci-libs/coinor-os/Manifest new file mode 100644 index 000000000000..93eec4b6e764 --- /dev/null +++ b/sci-libs/coinor-os/Manifest @@ -0,0 +1,6 @@ +AUX coinor-os-2.10.1-fix-c++14.patch 4301 SHA256 90bfec1bc7961b1a0beafbddf75bb0d690e3d645847decd29331fa7941de0501 SHA512 03f53d5a72ad7eef7305fcbd8ee7c07469c418f0e351b7bd84ccba5be0a0395aa5843d84fc7575f5a489a4632dafb651669ef56e760be4c50e69f6c45e24d96e WHIRLPOOL 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0fe71a33dce9767b2bca63b9e8d6421bbf928fd53347a9b11cd5f339a7a25212cb1a995068d2ff0154c43f781273561049d47f25e2ff81b95bb4512cf9f968ac WHIRLPOOL 1283508c07c5a7c272f37cc11bedd44f7867636912bf58ac9fcde3d6b12c5fbc9eb0dd15f189a1e355c0180bd5fa51ad866c8bd0e4c02fa463d9494420b6b2fa +MISC ChangeLog-2015 960 SHA256 8850a98bd54f8345b9be1faf4f423ab843d1c735bfa68de602037526699245cf SHA512 edb3ffb727f3ab6cc8e49ba03968f1817f5f4e73c6a8d5386250d8d812d94baad7b81f0a67ae6a06f48fe2ce8109741fa94dd1d85fc5564dcbb9a7b69035e4d4 WHIRLPOOL 77c176fa070bd9040fb665750453f2bf198fb80e68ea360a6f2d49b88503ab5732b1c512aaef0b75b85d53d39856c30f66b3377039bff43a0ad8e8b11518bdd6 +MISC metadata.xml 542 SHA256 e1a21084c412a8c2db7cb7c4f13f2f057896db04e9c9baf9ec5a3b18bce6fd53 SHA512 6a192caadd1aa4dd532ed2d8ddd17328564af52ffd6f1f9fec9f7eac7bd3f1cf593885e02b3b314d32e21263119883218842b906b51e312703af7603e291f531 WHIRLPOOL 51efd3d704cdad5e88db738a703ef81ed47abcd3bff165184f7e63263ce5c783c2bebce8b2a6b861eec352b73098d4a7ad0969ed21e7b8e9885faadb1c28fa9a diff --git a/sci-libs/coinor-os/coinor-os-2.10.1.ebuild b/sci-libs/coinor-os/coinor-os-2.10.1.ebuild new file mode 100644 index 000000000000..ae0fb46a7469 --- /dev/null +++ b/sci-libs/coinor-os/coinor-os-2.10.1.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic + +MY_PN=OS + +DESCRIPTION="COIN-OR Optimization Services" +HOMEPAGE="https://projects.coin-or.org/OS/" +SRC_URI="http://www.coin-or.org/download/source/${MY_PN}/${MY_PN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/6" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + sci-libs/coinor-bcp:= + sci-libs/coinor-bonmin:= + sci-libs/coinor-couenne:= + sci-libs/coinor-clp:= + sci-libs/coinor-dylp:= + sci-libs/coinor-symphony:= + sci-libs/coinor-utils:= + sci-libs/coinor-vol:= + sci-libs/ipopt:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MY_PN}-${PV}/${MY_PN}" + +PATCHES=( "${FILESDIR}/${PN}-2.10.1-fix-c++14.patch" ) + +src_prepare() { + default + + # needed for the --with-coin-instdir + dodir /usr +} + +src_configure() { + append-cppflags -DNDEBUG + + econf \ + --enable-shared \ + $(use_enable static-libs static) \ + --enable-dependency-linking \ + --with-coin-instdir="${ED%/}"/usr +} + +src_install() { + default + use doc && dodoc doc/*.pdf + + # package provides .pc files + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/coinor-os/files/coinor-os-2.10.1-fix-c++14.patch b/sci-libs/coinor-os/files/coinor-os-2.10.1-fix-c++14.patch new file mode 100644 index 000000000000..a788646abfe1 --- /dev/null +++ b/sci-libs/coinor-os/files/coinor-os-2.10.1-fix-c++14.patch @@ -0,0 +1,100 @@ +Fix building with C++14, which errors out due to bool -> T* conversions +and changed semantics caught by -Werror=terminate. + +See also: https://bugs.gentoo.org/show_bug.cgi?id=594180 +Patch partially taken from: https://projects.coin-or.org/OS/changeset/5137/ + +--- a/src/OSCommonInterfaces/OSInstance.cpp ++++ b/src/OSCommonInterfaces/OSInstance.cpp +@@ -165,6 +165,9 @@ + }
+
+ OSInstance::~OSInstance()
++#if __cplusplus >= 201103L
++ noexcept(false)
++#endif
+ {
+ std::ostringstream outStr;
+
+--- a/src/OSCommonInterfaces/OSInstance.h ++++ b/src/OSCommonInterfaces/OSInstance.h +@@ -2267,7 +2267,11 @@ + OSInstance();
+
+ /** The OSInstance class destructor */
+- ~OSInstance();
++ ~OSInstance()
++#if __cplusplus >= 201103L
++ noexcept(false)
++#endif
++ ;
+
+ /** the instanceHeader is implemented as a general file header object
+ * to allow sharing of classes between schemas
+--- a/src/OSCommonInterfaces/OSMatrix.cpp ++++ b/src/OSCommonInterfaces/OSMatrix.cpp +@@ -2297,7 +2297,7 @@ + + if (!processBlocks(rowPartition, rowPartitionSize, + colPartition, colPartitionSize, false, symmetry)) +- return false; ++ return NULL; + return ExpandedMatrixByBlocks.back(); + }// end of MatrixType::getBlocks + +--- a/src/OSParsers/OSParseosil.tab.cpp ++++ b/src/OSParsers/OSParseosil.tab.cpp +@@ -180,7 +180,7 @@ + + #define GETATTRIBUTETEXT \ + for(; ISWHITESPACE( *ch) || isnewline( *ch, osillineno); ch++ ) ; \ +- if( *ch != '=') { osilerror_wrapper( ch, osillineno, "found an attribute not defined"); return false;} \ ++ if( *ch != '=') { osilerror_wrapper( ch, osillineno, "found an attribute not defined"); return NULL;} \ + ch++; \ + for(; ISWHITESPACE( *ch) || isnewline( *ch, osillineno); ch++ ) ; \ + if(*ch == '\"'){ \ +@@ -196,7 +196,7 @@ + *p = ch; \ + for( ; *ch != '\''; ch++); \ + } \ +- else { osilerror_wrapper( ch, osillineno,"missing quote on attribute"); return false;} \ ++ else { osilerror_wrapper( ch, osillineno,"missing quote on attribute"); return NULL;} \ + }\ + numChar = ch - *p; \ + attText = new char[numChar + 1]; \ +@@ -11070,7 +11070,7 @@ + // eat the white space + for( ; ISWHITESPACE( *ch) || isnewline( *ch, osillineno); ch++ ) ; + for(i = 0; sizeOf[i] == *ch; i++, ch++); +- if(i != 6) { osilerror_wrapper( ch,osillineno,"incorrect sizeOf attribute in <base64BinaryData> element"); return false;} ++ if(i != 6) { osilerror_wrapper( ch,osillineno,"incorrect sizeOf attribute in <base64BinaryData> element"); return NULL;} + // ch should be pointing to the first character after sizeOf + GETATTRIBUTETEXT; + ch++; +@@ -11080,7 +11080,7 @@ + // eat the white space + for( ; ISWHITESPACE( *ch) || isnewline( *ch, osillineno); ch++ ) ; + // better have an > sign or not valid +- if(*ch != '>' ) { osilerror_wrapper( ch,osillineno,"<base64BinaryData> element does not have a proper closing >"); return false;} ++ if(*ch != '>' ) { osilerror_wrapper( ch,osillineno,"<base64BinaryData> element does not have a proper closing >"); return NULL;} + ch++; + // we are now pointing start of the data + const char *b64textstart = ch; +@@ -11089,7 +11089,7 @@ + const char *b64textend = ch; + // we should be pointing to </base64BinaryData> + for(i = 0; endBase64BinaryData[i] == *ch; i++, ch++); +- if(i != 18) { osilerror_wrapper( ch,osillineno," problem with <base64BinaryData> element"); return false;} ++ if(i != 18) { osilerror_wrapper( ch,osillineno," problem with <base64BinaryData> element"); return NULL;} + int b64len = b64textend - b64textstart; + b64string = new char[ b64len + 1]; + for(ki = 0; ki < b64len; ki++) b64string[ki] = b64textstart[ ki]; +@@ -11097,7 +11097,7 @@ + // burn the white space + for( ; ISWHITESPACE( *ch) || isnewline( *ch, osillineno); ch++ ) ; + // better have an > sign or not valid +- if(*ch != '>' ) { osilerror_wrapper( ch,osillineno,"</base64BinaryData> element does not have a proper closing >"); return false;} ++ if(*ch != '>' ) { osilerror_wrapper( ch,osillineno,"</base64BinaryData> element does not have a proper closing >"); return NULL;} + ch++; + for( ; ISWHITESPACE( *ch) || isnewline( *ch, osillineno); ch++ ) ; + *p = ch; diff --git a/sci-libs/coinor-os/metadata.xml b/sci-libs/coinor-os/metadata.xml new file mode 100644 index 000000000000..3d6e1c008811 --- /dev/null +++ b/sci-libs/coinor-os/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The objective of Optimization Services (OS) is to provide a set of + standards for representing optimization instances, results, solver + options, and communication between clients and solvers in a + distributed environment using Web Services. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-osi/Manifest b/sci-libs/coinor-osi/Manifest new file mode 100644 index 000000000000..58b13744fbea --- /dev/null +++ b/sci-libs/coinor-osi/Manifest @@ -0,0 +1,5 @@ +DIST Osi-0.106.6.tgz 7490371 SHA256 aefa3cab599048ed32002d4e5d3bf1a78fd9a48b36a754ca6896d13a65816ec4 SHA512 25d2dd1791b73329fa9bc32f7b4a4f3d0600ce600868bd14d902dd0ea1c6f5a2eca4bff01ac65ea2843e725fd5c218fca6def9d6974e6af9692c47973b6202ef WHIRLPOOL 3a2aa197f11ef48e347e1d730a02b0d9bfa5dce5f804af531a1c612fd786f9c8d3e7cfec37e1bbb395a30f087fd2eb1128572f2460047666f6fcdd4adcb8bfc2 +EBUILD coinor-osi-0.106.6.ebuild 1546 SHA256 973f4a4c78ccb87ff072db4e995d53aa2403e10002ba47752ee41b8ea8eabb9e SHA512 14710fe45e4344eb41bd198fcd4619a31fa1d1c9a74b5fb4e0ae8d5c59cbf10d1efe39b50d070f8bf3e9e4553619dc880f2a2694116da7611b89830be09a2a3d WHIRLPOOL 2ac402c4b6279f96d0c376fcc7692aa4595871db108daf12ec6d5b3335fba0cb0261ff44ff83612056a6cd23066e9601a4463b21ff111e73a6704f2255095e1f +MISC ChangeLog 2833 SHA256 953d811475dd17ca15a7ca3c3e8caf2e287afcd0e126444232960f9a05e3dd25 SHA512 809d49d719bc9f91ef228138d5505ab1a592be59d1c75e2bc442694ed0db81398b6cc667d0b1f078b9c6649e3ae9ad8ee17438df45873d50ad96ebca48452dda WHIRLPOOL 9df0798ede6aeb55d2474995fa40c5c1634f573b4d6fd2191d06dc16d1883089b7de8f544c887a7d4938170facd30a3394e868034aba5a53ec79bdb11c8aab33 +MISC ChangeLog-2015 1719 SHA256 44b4e8899d22e46985342133f6a5c93d712b3cf97ada696f9696b0160744a2a1 SHA512 ee5af1ab7f1e1ae0e10798003a8464f362c33237b47f1bc2f304c5a78115649a038aef580c0cca8b2bee6f30c3e485e901719451a2665da04b539f23f73b9d8f WHIRLPOOL 4941a139035529c6995607107e5c035332276d05772f5624948871d4c505a12e30ce15af83f063a1315798f88c478426b54ea79a3e8b62c54152c04d3722c71e +MISC metadata.xml 664 SHA256 25e0219a14c986804786c7f090f564d9c48ffe076569ee1358920c6676778b12 SHA512 ce3559d0d784f081f901b655c6c9b9005ebc8975838402a2e62c5c3f0874ba5a94b942023fa023850aa41a9c45e82932bd59af74fc6235c4366f16bd9a364626 WHIRLPOOL fa81c4d53a55613d98ccd8ea987c9aa7366352565aabb2adcf77dfbaa451b41a15e8c519fd39d8dad7719ecf3a9f51816ffdec4f601d8761d8250ef75d82fc9e diff --git a/sci-libs/coinor-osi/coinor-osi-0.106.6.ebuild b/sci-libs/coinor-osi/coinor-osi-0.106.6.ebuild new file mode 100644 index 000000000000..59bd9d74227b --- /dev/null +++ b/sci-libs/coinor-osi/coinor-osi-0.106.6.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Osi + +DESCRIPTION="COIN-OR Open Solver Interface" +HOMEPAGE="https://projects.coin-or.org/Osi/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples glpk static-libs test" + +RDEPEND=" + sci-libs/coinor-utils:= + glpk? ( sci-mathematics/glpk:= )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + if use glpk; then + myeconfargs+=( + --with-glpk-incdir="${EPREFIX}"/usr/include + --with-glpk-lib=-lglpk + ) + else + myeconfargs+=( --without-glpk ) + fi + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile all $(usex doc doxydoc "") +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${BUILD_DIR}/doxydocs/html/") + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-osi/metadata.xml b/sci-libs/coinor-osi/metadata.xml new file mode 100644 index 000000000000..17b9b82ecf17 --- /dev/null +++ b/sci-libs/coinor-osi/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The COIN-OR Open Solver Interface is a uniform API for interacting with + callable solver libraries. It supports linear programming solvers as + well as the ability to "finish off" a mixed-integer problem calling the + solver library's MIP solver. +</longdescription> +<use> + <flag name="glpk">Enable GNU Linear Programming Kit + <pkg>sci-mathematics/glpk</pkg> support</flag> +</use> +</pkgmetadata> diff --git a/sci-libs/coinor-sample/Manifest b/sci-libs/coinor-sample/Manifest new file mode 100644 index 000000000000..8e93206ab1c4 --- /dev/null +++ b/sci-libs/coinor-sample/Manifest @@ -0,0 +1,5 @@ +DIST Sample-1.2.9.tgz 367317 SHA256 939f26a915a8180db9bf040fdb2c558da1eabb6055a23120b7105115660d668c SHA512 92af8ad524b8e7efb07a0064591fc8bfeea4235541d7a5f09f05bc33f759668378a49b459e72424ff33e775ab210c5a1ac139f4ff21bb0c9ec63656f4539d8df WHIRLPOOL 79b66575977a805ee8dfa318a64e86adf89018dfca04435bf90d84e6adb99d951ade1eda94f776319a0a5c82626088314397cd1278a61dccb2db2e9805ceab8c +EBUILD coinor-sample-1.2.9.ebuild 431 SHA256 3af14b15e07b5568f86ebd919f0904ade3a9d0dd46491f4be40e84add58a55de SHA512 0db57efdece103d7f7bcf1063c7b4a937c489307e25360e8bf67145f6b24b249a7adccba6aac568de7959da6eb83ae6d47102d5297ac3f45f6897623347adab6 WHIRLPOOL a0706c166c258dced7c8a6c20a6a57bbe28d1e451b97656772259c632a4044f78cfe7b775da62b95d91b42b48db08429d93ccab20b0679fc1ee1f444b7d021c9 +MISC ChangeLog 2445 SHA256 e8c1614cdd360c500d0f38357ef6db4bc8bae1bb038baeafd6c534a88f33b8dc SHA512 d057b28d46b4d68f7d088ca294209f58bb1988a8c0d4dc43063555df4bec229e58389f4b88fd768b89c6e2527f8f8f69db457cd290615e8c68317d14fbf813cc WHIRLPOOL 4e36d15d99e52713d2d15b0deab7a0e7a20e2fb2e5282cbc43ed09cc281eed1d1fd43c875c72af20b8c544aadc184c748e2fcf7072f78389524f4374e96e21a8 +MISC ChangeLog-2015 1707 SHA256 b8cb5a5fb029b880e25cfe7695bbd75f0df46b397240dee24c332bbd30ea5f03 SHA512 9344413487a8b4f21c424767f9eb43a1748d65688fbad23e7eb19a979dca07f91d80bfdc89c280e3bae6f94dad95ef61e70539225c5807ca569afadd645848cc WHIRLPOOL c03768e7d6b627b0edd7f4d17b88eb78cd31be12f8eabef23e4537c60c6e2afa239eb42553b696ec561e274cd9050945b1d8f4488b4bff3cfb20fd3923639773 +MISC metadata.xml 394 SHA256 01f89b8769d586d3f90203825ac761bc53550d94562c8b4bddfdecb7121cff5c SHA512 e54b8d687139e1c3de2b8dffbbbb723f7f5d210a918f1c7e64a301d41cfa29da1d5e89e32ea3392dd87fb9f3ede2ff10deffcb142e262f532ff450b74259bf14 WHIRLPOOL 274d21780d54b40a7e742757e2ba40b18ca92079a5e88a256cf72382afd0f5d5cf0d1f05b5411846a32c27d04bf20292dba2e1850cc3c323e491e5c3855f96dc diff --git a/sci-libs/coinor-sample/coinor-sample-1.2.9.ebuild b/sci-libs/coinor-sample/coinor-sample-1.2.9.ebuild new file mode 100644 index 000000000000..36c4c827e72c --- /dev/null +++ b/sci-libs/coinor-sample/coinor-sample-1.2.9.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +MYPN=Sample + +DESCRIPTION="COIN-OR Sample models" +HOMEPAGE="https://projects.coin-or.org/svn/Data/Sample" +SRC_URI="http://www.coin-or.org/download/source/Data/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +S="${WORKDIR}/${MYPN}-${PV}" diff --git a/sci-libs/coinor-sample/metadata.xml b/sci-libs/coinor-sample/metadata.xml new file mode 100644 index 000000000000..c7a0434f4f28 --- /dev/null +++ b/sci-libs/coinor-sample/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The COmputational INfrastructure for Operations Research (COIN-OR) + sample models for testing. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-smi/Manifest b/sci-libs/coinor-smi/Manifest new file mode 100644 index 000000000000..47516b6d96eb --- /dev/null +++ b/sci-libs/coinor-smi/Manifest @@ -0,0 +1,5 @@ +DIST Smi-0.93.4.tgz 4907130 SHA256 e63ee0f6f6fd20cd7481d7c88fa60980fc1ce8334032a8f4baaad3a88e63004b SHA512 9439b7421475cf5d0c85f529305657e04d1ebb3eca28399b0df0352b52df315e9dceb3f1410ada0b7a6f9447b0e383116fb208d6447994ce1611f019fcace007 WHIRLPOOL a6f6814420111b2e6cf6ae6251aef44f327372bcbe4dff1f9159f95ec4967a77d7912c10d503f480da91143a94a552993a59b9931e893e6c32c21956f93786e9 +EBUILD coinor-smi-0.93.4.ebuild 1494 SHA256 47382db0bfa7995f75cad2825ce4d11ee436caf122fe5628305e79f0bdcc881f SHA512 744f28ce09afd81c17629a750369556337196b1581744e2c093c3a0d98f30305fd3c248c549ad075a6d929e8f69b165e996effc0a9ca29642a3c3f80109e4f34 WHIRLPOOL f8bd298091dfb3a06d843eb727e9116f8e4d596da92cb7b2b7406a7c1688b223a01a4c951126ae7edfe99a24541064e761abc6640852357160558e50ce6542da +MISC ChangeLog 2438 SHA256 93c2635f3467013646ff38dbcf377dbf1c05310a501ee0c0aa866b937f850c23 SHA512 a4d50ecd6486b1a2ee032f508c2d23290ae1bb12c0da2c7393d51ca8be2616ccd20d1ce52d0ec680f44177740c263b300372f72290fb2a80479fa84deac3485e WHIRLPOOL d7b90a1107acaba95d2ab44b8cf51798c9022c1ed25165d51f15efcc78e0d81a002c67f9703d21ce07ed71983c4a0df2a7e2d8011c36a930cda4de06647f1efb +MISC ChangeLog-2015 944 SHA256 8512fa4b88a8bc7182540016e1c45ca985c747b6f7e3396b6f48701ef629975c SHA512 7c86d7e1f706069f88d7410b2f1646ece826fd0ab5a8a1275ac6973ccbd3f686c522e3764d5de3e08a8aaf0aa45a1e1e91577ceb1ece473ded42e9ed338e60b4 WHIRLPOOL 496b380e03ecc8ccb9621f9cd00fc71da89c00ab29eb2a2df33c1dc8695c36a3f9474310446a9a33c33292529865d05622e07deffd03e8b23df86144a38b4a33 +MISC metadata.xml 976 SHA256 bb42b384e8bd84b2de02f2c938fc7f245e600aef3e05b2f70aaa7da8d37399c6 SHA512 b1bec8ccad40e9081d0444de4755b66fca94e515f379a7db2414c45a11f4801eb28bd5aa124eb85b6ab4811b21c6a6453188523a49c391fe5d41a1fb2cd951b8 WHIRLPOOL 1dcaaf41e63c8c09c882472cfe6b591dab24995f9752420189489936194263f8bad469e85966dd456af2461d1308bd866495d7ae119eaff4b536809bc06af4d6 diff --git a/sci-libs/coinor-smi/coinor-smi-0.93.4.ebuild b/sci-libs/coinor-smi/coinor-smi-0.93.4.ebuild new file mode 100644 index 000000000000..1db6ff49b5e2 --- /dev/null +++ b/sci-libs/coinor-smi/coinor-smi-0.93.4.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_IN_SOURCE_BUILD=yes +inherit autotools-utils multilib + +MYPN=Smi + +DESCRIPTION="COIN-OR Stochastic modelling interface" +HOMEPAGE="https://projects.coin-or.org/Smi/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="CPL-1.0" +SLOT="0/2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + sci-libs/coinor-cbc:= + sci-libs/coinor-cgl:= + sci-libs/coinor-clp:= + sci-libs/coinor-flopcpp:= + sci-libs/coinor-osi:= + sci-libs/coinor-utils:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + if use doc; then + cd "${WORKDIR}/${MYPN}-${PV}/doxydoc" || die + doxygen doxygen.conf || die + fi +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${WORKDIR}/${MYPN}-${PV}/doxydoc/html/") + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples flopcpp_examples + fi +} diff --git a/sci-libs/coinor-smi/metadata.xml b/sci-libs/coinor-smi/metadata.xml new file mode 100644 index 000000000000..9918603b2e88 --- /dev/null +++ b/sci-libs/coinor-smi/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The COIN-OR Stochastic Modeling Interface (SMI) is an interface for + problems in which uncertainty and optimization appear + together. There are many modeling and algorithmic approaches that + could belong here, like: recourse programming, chance constrained + programming, stochastic control and dynamic programming, robust + optimization, etc, etc. SMI is intended to be like OSI in the sense + that an SmiXX object is an implementation derived from a base class + that takes care of a number of commonly encountered programming + issues, like handling probability distributions, managing problem + generation, interacting with solvers to obtain solution information, + etc. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/coinor-symphony/Manifest b/sci-libs/coinor-symphony/Manifest new file mode 100644 index 000000000000..4f1219776f06 --- /dev/null +++ b/sci-libs/coinor-symphony/Manifest @@ -0,0 +1,5 @@ +DIST SYMPHONY-5.5.7.tgz 7628863 SHA256 7828620ebe240239f6392a23a54fbacdb39f91c6571f2b98346b5b42436a20f0 SHA512 a3ce66b0b1373c58024ce6840277423a1a3684af8e3179a777fbb33a8d266849ae1cde694a527c3776ff67ce0a5ae3c2bfe0dc29f4e0b3ca51ddc2b299eefb24 WHIRLPOOL aa43df2d558bb328b9d226e7e15f8164cfd18eeac326b6ecd9306887703f2b8619b0343750415b526cfba73eb78319b6509f266ec527fbbb4bb2c84ae134f553 +EBUILD coinor-symphony-5.5.7.ebuild 2052 SHA256 f953449fca6d7ade282606c88f669b2e1be642d0c2bdd8f19c71ae6e5cec2139 SHA512 9e738b42c5555a13a0cec371f4487d70494b1197c95362b9955e5f65358396bb2fee76c5135229af62263bfd48c74dc000e60d4e298e4716155072ae4e92d4b4 WHIRLPOOL ac685b3b709c29d754768824ea3bd4ef1ad003c7a8bafe8df99d65990dd938e958a8c255dd670422bcdbd6eaf806ff00ad413f0d54b20c45b7a542869e7c8ce5 +MISC ChangeLog 2844 SHA256 9cad5d6d592546954ba9f63ff61668575d4652c16af581d0546ac1d34de40c82 SHA512 814963a3316f7c786b9deed5aca6d770458a0cfde754b2cf2c603e41701e3dce13719cd98d3a3de8d537c5b49ba31b6eca5a25ff6bad27edd6368946d6fb9a42 WHIRLPOOL 64973dc2202964d70524f0bad924b4375a8fc91883d0a1ca49165500d31bec95a5c7b0f263f701f2ecc51a76e08be1d93a2789e6bfd578f97a5218ea92fa7a40 +MISC ChangeLog-2015 1735 SHA256 96f675cc8384c739bf67b4598f05ecaa49738708b712df2a253fc5401e3ac9b5 SHA512 1e087efac9a640d505535fc8e9419691462d5eaa3b0eb01ba73dc5f678ba5085501e18d542aaf0eabad8e6ba509c2bfa98a5eabecbb302d0b6e5d44836d5a9f4 WHIRLPOOL a176a6aa3d33fc645bbc18179ea62c58acb753840a16238320a1496947063e87de5a92eb1506c330dbf8ee94fe8eff1a6dbed8692379c179c912100a3fd8b229 +MISC metadata.xml 830 SHA256 8534cafc96a4e99b8f994f4e1b0bf9be1e3e94ce3342c24cf19d10c65da74fd1 SHA512 292f30da8c4b2a847665c848a10b33259c4bb7d89cc9363e75fb167bdbc73e0465697dc9c9979337af438f6f2a9ebba2e51dc32bcd2272ceae741c010e17041d WHIRLPOOL 8f3ad6bb8cbddf64079364f83e73c531e8a0df3a764c5546b26048b837108f2f202fa3c4f6b76ccb2ff9b7fdbbf7d0f8f395e4e371643bedbd441065d326b54e diff --git a/sci-libs/coinor-symphony/coinor-symphony-5.5.7.ebuild b/sci-libs/coinor-symphony/coinor-symphony-5.5.7.ebuild new file mode 100644 index 000000000000..38e4c4e8d5bd --- /dev/null +++ b/sci-libs/coinor-symphony/coinor-symphony-5.5.7.ebuild @@ -0,0 +1,86 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=SYMPHONY + +DESCRIPTION="COIN-OR solver for mixed-integer linear programs" +HOMEPAGE="https://projects.coin-or.org/SYMPHONY/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples glpk static-libs test" + +RDEPEND=" + sci-libs/coinor-cgl:= + sci-libs/coinor-clp:= + sci-libs/coinor-dylp:= + sci-libs/coinor-osi:= + sci-libs/coinor-utils:= + sci-libs/coinor-vol:= + glpk? ( sci-mathematics/glpk:= )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + ) + if use glpk; then + myeconfargs+=( + --with-glpk-incdir="${EPREFIX}"/usr/include + --with-glpk-lib=-lglpk ) + else + myeconfargs+=( --without-glpk ) + fi + autotools-utils_src_configure +} + +src_compile() { + # hack for parallel build, to overcome not patching Makefile.am above + autotools-utils_src_compile -C src libSym.la + autotools-utils_src_compile + if use doc; then + pushd Doc /dev/null + pdflatex Walkthrough && pdflatex Walkthrough + # does not compile and doc is online + #pdflatex man && pdflatex man + popd > /dev/null + fi +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + # hack for parallel install, to overcome not patching Makefile.am above + autotools-utils_src_install -C src install-am + autotools-utils_src_install + use doc && dodoc Doc/Walkthrough.pdf + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r Examples/* + fi +} diff --git a/sci-libs/coinor-symphony/metadata.xml b/sci-libs/coinor-symphony/metadata.xml new file mode 100644 index 000000000000..6933ca7ddab6 --- /dev/null +++ b/sci-libs/coinor-symphony/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + SYMPHONY is a generic mixed-integer linear programs + (MILP) solver, callable library, and extensible framework for implementing + customized solvers. SYMPHONY has a number of advanced capabilities, + including the ability to solve multi-objective MILPs, the ability to + warm start its solution procedure. + SYMPHONY is part of the larger COIN-OR initiative (Computational + Infrastructurefor Operations Research). +</longdescription> +<use> + <flag name="glpk">Enable GNU Linear Programming Kit + <pkg>sci-mathematics/glpk</pkg> support</flag> +</use> +</pkgmetadata> diff --git a/sci-libs/coinor-utils/Manifest b/sci-libs/coinor-utils/Manifest new file mode 100644 index 000000000000..04e24784f50d --- /dev/null +++ b/sci-libs/coinor-utils/Manifest @@ -0,0 +1,5 @@ +DIST CoinUtils-2.9.11.tgz 1740411 SHA256 9c2d9d8f8cb0e249bf3f050afeb02a1a95ad382f55ae98b59d8f7b9ab75cc80b SHA512 3cbbce47cda4d5f63338644853601bf0a3dd9b9388e71a7aea7fedd51dfc007134359e5f12f24d8f6135d86b77a88a95bcb88249b1ba880eb3cd9cf41d039424 WHIRLPOOL 8a2d2b2eea7c11d38f10449ac13bc9c70e1ac6e01469e2d4014d1206cbe48681d949509ec6cc0074e6e603f45152ead6145b6b19e2d2d6c5bf02b572f2174015 +EBUILD coinor-utils-2.9.11.ebuild 1916 SHA256 3eee7a43bba68d64bc9928596102488a10b646f7e1df0ca384b95f1bb62325d6 SHA512 83e8c0509b5c4b26ca9904490d5946a25946413cad38eb5b303e3a07d3b91c8e2c826ee0ccaa25c353aad77c4edf784c38a88354b4a2e04bf455a0e1ac385c98 WHIRLPOOL 6b85fe28332a5cbb5c3f8df90bb66724d4a000ebd78641c37825b9f500c7f29990d9596d39d9fefa496d441e40b301f29adf3786afbda42338dd9e30a5061e8c +MISC ChangeLog 2588 SHA256 ffad22cb5b7faf3dd1724608266cf63e4d42f4c102d294a251827708755fd652 SHA512 2edb3fc5686b819e24a381cc6691eb00b3dc286c160f4074d84e6c6deb8a89322f8072221aa7d84724045696cdac19eb0c265cdcf802c74b7b02ce0197d42cc1 WHIRLPOOL 751d92d7d40b5a705965e01cd68944780bd5b5747bad14b1a6c0895157af9f562e0bee19e610f7826b0f6bedb9e72cf552ea4dd99eec606a6a5e06209012bab7 +MISC ChangeLog-2015 1882 SHA256 fe150051a27bda6952cb566d51e62034a4913d4cb506d13915786dde03601f63 SHA512 f5814db7d0f79fb62b3b445379409de99907298051eb80a79f9baa20e6ac73cef376467ac9522e4ba0b8204d79781ec0f26a9e542839d7426909535c9a54421a WHIRLPOOL 47773e21acfce4b444d025f818dfb0e89f8c7e6eb6662374e3a334cf6ca79186124cc54672a292eab6d9f2f345a3b35defa3c337e0b0958280725d3dae830591 +MISC metadata.xml 653 SHA256 939d9b17271fff5c3586a3f27f3337f3c4139786fded3743cf5c5d6b4644793d SHA512 73fed876146a5d2aea6d7fd5bfb99d938f316cb92022e299c01e04aad218cb75b2745c8e064b9218a96c9b9f9c9e9efb089d38ba930677ce18b71f27667bd0c9 WHIRLPOOL 0db782e9e1911d822c5c063b4e3b46ea2e041dcabdaeca3e9530dc8067696a4ba498b99029d49cfbde1968c3d882a429a2bc93d777813a2f4c3a860e7a3cc339 diff --git a/sci-libs/coinor-utils/coinor-utils-2.9.11.ebuild b/sci-libs/coinor-utils/coinor-utils-2.9.11.ebuild new file mode 100644 index 000000000000..393e7c336efe --- /dev/null +++ b/sci-libs/coinor-utils/coinor-utils-2.9.11.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib toolchain-funcs + +MYPN=CoinUtils + +DESCRIPTION="COIN-OR Matrix, Vector and other utility classes" +HOMEPAGE="https://projects.coin-or.org/CoinUtils/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="bzip2 doc glpk blas lapack static-libs test zlib" + +RDEPEND=" + sys-libs/readline:0= + bzip2? ( app-arch/bzip2 ) + blas? ( virtual/blas ) + glpk? ( sci-mathematics/glpk:= ) + lapack? ( virtual/lapack ) + zlib? ( sys-libs/zlib )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + dodir /usr + sed \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + -i configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_enable zlib) + $(use_enable bzip2 bzlib) + $(use_with doc dot) + ) + if use blas; then + myeconfargs+=( --with-blas-lib="$($(tc-getPKG_CONFIG) --libs blas)" ) + else + myeconfargs+=( --without-blas ) + fi + if use glpk; then + myeconfargs+=( + --with-glpk-incdir="${EPREFIX}"/usr/include + --with-glpk-lib=-lglpk + ) + else + myeconfargs+=( --without-glpk ) + fi + if use lapack; then + myeconfargs+=( --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" ) + else + myeconfargs+=( --without-lapack ) + fi + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile all $(usex doc doxydoc "") +} + +psrc_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${BUILD_DIR}/doxydocs/html/") + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die +} diff --git a/sci-libs/coinor-utils/metadata.xml b/sci-libs/coinor-utils/metadata.xml new file mode 100644 index 000000000000..871e40d0656c --- /dev/null +++ b/sci-libs/coinor-utils/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + CoinUtils (Coin-or Utilities) is a collection of classes that are + generally useful to COmputational INfrastructure for Operations + Research (COIN-OR) projects. These include vector, matrix, mps file + reading classes. +</longdescription> + <use> + <flag name="glpk">Enable GNU Linear Programming Kit + <pkg>sci-mathematics/glpk</pkg> support</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/coinor-vol/Manifest b/sci-libs/coinor-vol/Manifest new file mode 100644 index 000000000000..a59abc4bf7b5 --- /dev/null +++ b/sci-libs/coinor-vol/Manifest @@ -0,0 +1,5 @@ +DIST Vol-1.4.4.tgz 3205621 SHA256 060e2cdd20443507b219192b26bcf8d2559cff2f3061225bb1343a9e569493be SHA512 20e04efac09694ddfa035496ec9b2920ef702e5a2ec4515cd88c52129c783efd3c25e044e6c2cec67ad800b297ebd03f3c3c377f58829790109d8d6dcb40cc39 WHIRLPOOL 01d2a07666bb7fc36eb7539e525ba095ae5efbfaee6c927f9d70d476f05815c1f0737acb6d398357ed0105913b4f4649539a3f5413a833b5e06862897ae5db8d +EBUILD coinor-vol-1.4.4.ebuild 1557 SHA256 343e4430df502e2f67a9a0732d58b88f00c0b5ce07506a14b035ab02070a74e6 SHA512 63ccdab1c71c09820ff2e019e9dd671a476bd8acaa51117f02db916050ac63ed474162deae84bae65707fa2afcffb56b8d15077b2ac9047dbd7733e3df9e73a7 WHIRLPOOL 821de6c4734f16e99c20c5dfe3bde129b3f61b28b0404b477ad7e2f93f56a77b2394488976482046f5e8728c6334cd6398e18128be1d613a23c4033b98483a6b +MISC ChangeLog 2436 SHA256 fba5ddfd6fd244cad0efd8bc31388e692d7696001f0d1adea3c3ff9fe876fd39 SHA512 c1fae571b5922e83fb5ace47a709376d95e0590f2daf6bc56448cf4897aa1eda665e4a95e1eb9339d2bb870c3a5d8ee3edc7ceec073368286a2be8df12806b58 WHIRLPOOL bd0e0bd038ae1cd5e9948ea8601c1f345acfe755f72b85dd15e3aded10b0c63a52e4ad611d2153857107a34bb57ca0675810b826c2bce290eb6e935e36e4b626 +MISC ChangeLog-2015 1424 SHA256 261712b4f5c725820276b80ce08dc505dd67f6173b416f89bade8098e15abbdb SHA512 47515ab5dd3a9ccc9ab8ccc4a1e15be9a6fae75119bf74f421e61ea9df2d3f69e13f0ce5c8e8d59ceef71129e75c374995fde721d13a363e18cb20a829d6c2ca WHIRLPOOL aa598f6d5344f7adc8eb1c434111be5a0c1f6e0efc26d5815892e1817c4ac2314723535676862e5417abc916986420573d03e766910b754166b73988c03f5b83 +MISC metadata.xml 499 SHA256 cd6ca99004fc0673a0c1742daa4a001669fc122fc2bd8455caa505cd246bbe4f SHA512 d629ecca944f6b9d53179044aeff93c5c2fac766766f7c0fa3a7f31a7c2efc44b920460139eb5fb333c8537d3b9d4c59f33461124e0f6fdc53640e4511d121f5 WHIRLPOOL c5aa220a5110ea0610ca6237737cfd3307c30180c910b2fe8b4153277359920a8069650c63273dee4d3d19853ec812e3db0fa2cfc3cd59d5fe47c66c500af04a diff --git a/sci-libs/coinor-vol/coinor-vol-1.4.4.ebuild b/sci-libs/coinor-vol/coinor-vol-1.4.4.ebuild new file mode 100644 index 000000000000..58bba00bd35c --- /dev/null +++ b/sci-libs/coinor-vol/coinor-vol-1.4.4.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +MYPN=Vol + +DESCRIPTION="COIN-OR Volume algorithm linear programming solver" +HOMEPAGE="https://projects.coin-or.org/Vol" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYPN}-${PV}.tgz" + +LICENSE="EPL-1.0" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + sci-libs/coinor-osi:= + sci-libs/coinor-utils:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + # needed for the --with-coin-instdir + dodir /usr + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-dependency-linking + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + autotools-utils_src_configure +} + +src_compile() { + # hack for parallel build, to overcome not patching Makefile.am above + autotools-utils_src_compile -C src libVol.la + autotools-utils_src_compile all $(usex doc doxydoc "") +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${BUILD_DIR}/doxydocs/html/") + autotools-utils_src_install -C src install-am + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/coinor-vol/metadata.xml b/sci-libs/coinor-vol/metadata.xml new file mode 100644 index 000000000000..ac5905e9c285 --- /dev/null +++ b/sci-libs/coinor-vol/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + Volume Algorithm is part of COIN-OR (COmputational INfrastructure + for Operations Research) project. Vol is an implementation of a + subgradient method that produces primal as well as dual solutions. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/colamd/Manifest b/sci-libs/colamd/Manifest new file mode 100644 index 000000000000..f8fbffb08d45 --- /dev/null +++ b/sci-libs/colamd/Manifest @@ -0,0 +1,5 @@ +DIST colamd-2.8.0.tar.bz2 304819 SHA256 a744cbf0f41c76fa1dceae9072204f1d2529cba11851db123c3496a2780839e1 SHA512 36b2e50e01ad44f04f084ebcdcfb7d9d1d1712c6f53c8bce9f46ce39edc418aa64b8e67489fb06cb95d86658fd9f9bad89217a5f9f4777181f0f0e9b58c04aee WHIRLPOOL 0551f47a1af8f46a12b26403b71e14b4caa5e72f03f6f7df285aaf69976264b94ac06803b2c459007c5574fb44282ccfc370c9c28885c4f7ba39bb21af8c880f +EBUILD colamd-2.8.0.ebuild 579 SHA256 3c22d2e714f7bd163491ef411e79aa4b440db1a98e91709d0d3ad85343db9f4d SHA512 c9772321b902395c6a0367a6003c363c95b1073e19b32ed1d4d7263430738c44d5aac4db36b15fae0007f0c956912f6815037e2ce090d37799a820277beb72b6 WHIRLPOOL cdab3569cdf85f9aa42136ffbce5c17298f15c2ae7ad572de69d6b93d73021d9283bb4059510e5f8f778915e8b16698f6406e10bef25ae556dff45f54556f0f9 +MISC ChangeLog 2690 SHA256 f817d32307ea3489cc348952585f1968a2843be64aec182b9f075af7835bdb20 SHA512 c9445b0d42a02e960106a94bb4a1d443fc6a8219e59991f066965baf246d98575394d1225082ab46a45b65180181698b61a933bf4bd56c99762c8f421ae01198 WHIRLPOOL 90c87013d75b162cef8446470ba254812b675772ff1ff2b032879f760da37633baecca7c58d6607ff4b753ec064425a49d5a0b58d1409169ba53b8f144fc9005 +MISC ChangeLog-2015 5227 SHA256 e6759ce0ae8edda105080243b917ac620e62bfdf1808da1d4962ca68906b8917 SHA512 e36fcd0251bd9bbb3ae8df4514baf1f9691a52f4fa139322aa42e423844ead261bb58d14047f5da228ed2aadb15a80a129c019ac00b946c10583443bf3afbfc8 WHIRLPOOL 74bdf27d38f2dfa02d689043f7d5d5c62b3d598f44579f108197a5decb1c1b9de6c877f4e4b6f7e0e01d50421534978aa1ef56ead6d413e801a7072a7b642b33 +MISC metadata.xml 827 SHA256 8e480bd3b0c18936572af8fc5507cd4c8474b93c8dfd95b143ba3e476dcb242f SHA512 367258fb10bcde8e5136c541ef1e134c4e882b296c45300c8d70945222c0730572b1dc116b80057c3a9d6a64c175fb86915847522000740d9a39e6fcd8eb5004 WHIRLPOOL a9e7c79fbe5f3dadf04ddafbad664cfebb3e6aaf9d807f393df0ca7f2400508768ffce3ec428080c6d533ae9dab72162baa2e024134b9b7ab29cd4bb15270b3c diff --git a/sci-libs/colamd/colamd-2.8.0.ebuild b/sci-libs/colamd/colamd-2.8.0.ebuild new file mode 100644 index 000000000000..ffe0436398d7 --- /dev/null +++ b/sci-libs/colamd/colamd-2.8.0.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Column approximate minimum degree ordering algorithm" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/ccolamd/" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" + +KEYWORDS="~alpha amd64 ~arm ~arm64 hppa ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" + +RDEPEND="sci-libs/suitesparseconfig" +DEPEND="${RDEPEND} + virtual/pkgconfig" diff --git a/sci-libs/colamd/metadata.xml b/sci-libs/colamd/metadata.xml new file mode 100644 index 000000000000..73165658cfd6 --- /dev/null +++ b/sci-libs/colamd/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The COLumn Approximate Minimum Degree ordering algorithm + computes a permutation vector P such that the LU factorization of A + (:,P) tends to be sparser than that of A. The Cholesky factorization + of (A (:,P))\'*(A (:,P)) will also tend to be sparser than that of + A\'*A. SYMAMD is a symmetric minimum degree ordering method based on + COLAMD, available as a MATLAB-callable function. It constructs a + matrix M such that M\'*M has the same pattern as A, and then uses + COLAMD to compute a column ordering of M. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/colpack/Manifest b/sci-libs/colpack/Manifest new file mode 100644 index 000000000000..22447c8f1ca1 --- /dev/null +++ b/sci-libs/colpack/Manifest @@ -0,0 +1,13 @@ +AUX colpack-1.0.6-flags.patch 408 SHA256 2a0e0321d7fd3b30a2fee3c8ecbfb3cef7ae1ca75f47d898fe99618216849e4d SHA512 5a614971ea0bb9da829596b352c59455b2a6d892cd96ffd68c5dd6a0f7aea63e35c2fda911a050df55d37109337cb95e52f1bab12174681f964c59c9e0721723 WHIRLPOOL 6ee703a74ff0a9214457b8ffbb0c2ba453eddbb82604a11ba4dcf062d2a36eb4ea47156c138048ca2068d7dab178c7427deeb7c11e15faceba23b3209521f9b8 +AUX colpack-1.0.8-no-bin.patch 442 SHA256 ecb7c0a70bde7fe0550264ab26a1ae4fe25374f2ee6d2196d8d54534f5f3348c SHA512 5424142f844626dca8f71f8deec53c4804c2aba6c618cfab8fb713026a11d6869bab04ed32562f0b77523f27e50db85485ec6346d8ce6f5efb5a1d6aa21b3410 WHIRLPOOL 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+HOMEPAGE="http://cscapes.cs.purdue.edu/coloringpage/" +SRC_URI="https://github.com/CSCsw/${MYPN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +IUSE="openmp static-libs" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}-${PV}" + +pkg_setup() { + if [[ ${MERGE_TYPE} != "binary" ]] && use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then + ewarn "You are using gcc without OpenMP" + die "Need an OpenMP capable compiler" + fi +} + +src_prepare() { + default + sed -e 's/-O3//' -i Makefile.am || die + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable static-libs static) \ + $(use_enable openmp) +} + +src_install() { + default + rm -rf "${ED}"/usr/examples + use static-libs || prune_libtool_files --all +} diff --git a/sci-libs/colpack/colpack-1.0.6.ebuild b/sci-libs/colpack/colpack-1.0.6.ebuild new file mode 100644 index 000000000000..14cc481ca736 --- /dev/null +++ b/sci-libs/colpack/colpack-1.0.6.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs autotools + +MYPN=ColPack + +DESCRIPTION="C++ algorithms for specialized vertex coloring problems" +LICENSE="GPL-3 LGPL-3" +HOMEPAGE="http://www.cscapes.org/coloringpage/software.htm" +SRC_URI="http://www.cscapes.org/download/${MYPN}/${MYPN}-${PV}.tar.gz" + +SLOT="0" +IUSE="openmp static-libs" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYPN}-${PV}" + +pkg_setup() { + if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then + ewarn "You are using gcc without OpenMP" + die "Need an OpenMP capable compiler" + fi +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-flags.patch + eautoreconf +} + +src_configure() { + econf \ + $(use_enable openmp) \ + $(use_enable static-libs static) +} diff --git a/sci-libs/colpack/colpack-1.0.9-r1.ebuild b/sci-libs/colpack/colpack-1.0.9-r1.ebuild new file mode 100644 index 000000000000..bdb0039d0030 --- /dev/null +++ b/sci-libs/colpack/colpack-1.0.9-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs + +MY_PN="ColPack" + +DESCRIPTION="C++ algorithms for specialized vertex coloring problems" +LICENSE="GPL-3 LGPL-3" +HOMEPAGE="http://www.cscapes.org/coloringpage/software.htm" +SRC_URI="http://cscapes.cs.purdue.edu/download/${MY_PN}/${MY_PN}-${PV}.tar.gz" + +SLOT="0" +IUSE="openmp static-libs" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND="" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_PN}-${PV}" + +PATCHES=( + "${FILESDIR}/${PN}-1.0.6-flags.patch" + "${FILESDIR}/${PN}-1.0.8-no-bin.patch" + "${FILESDIR}/${PN}-1.0.9-fix_gcc49_omp.patch" + "${FILESDIR}/${PN}-1.0.9-fix-c++14.patch" +) + +pkg_setup() { + if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then + ewarn "You are using gcc without OpenMP" + die "Need an OpenMP capable compiler" + fi +} + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable static-libs static) \ + $(use_enable openmp) +} + +src_install() { + default + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} diff --git a/sci-libs/colpack/files/colpack-1.0.6-flags.patch b/sci-libs/colpack/files/colpack-1.0.6-flags.patch new file mode 100644 index 000000000000..6d4bb6a0d612 --- /dev/null +++ b/sci-libs/colpack/files/colpack-1.0.6-flags.patch @@ -0,0 +1,10 @@ +diff -Nur ColPack-1.0.6.orig/Makefile.am ColPack-1.0.6/Makefile.am +--- ColPack-1.0.6.orig/Makefile.am 2012-04-13 03:25:37.000000000 +0100 ++++ ColPack-1.0.6/Makefile.am 2012-04-13 03:30:35.000000000 +0100 +@@ -1,5 +1,5 @@ + ACLOCAL_AMFLAGS = ${ACLOCAL_FLAGS} +-COLPACK_COMMON_FLAGS = $(EXTRA_FLAGS) -O5 ++COLPACK_COMMON_FLAGS = $(EXTRA_FLAGS) + + INCLUDES = $(COLPACK_COMMON_FLAGS) \ + -I$(top_srcdir)/Main \ diff --git a/sci-libs/colpack/files/colpack-1.0.8-no-bin.patch b/sci-libs/colpack/files/colpack-1.0.8-no-bin.patch new file mode 100644 index 000000000000..e9230b0ff105 --- /dev/null +++ b/sci-libs/colpack/files/colpack-1.0.8-no-bin.patch @@ -0,0 +1,15 @@ +From: Sebastien Fabbro <bicatali@gentoo.org> +Avoid installing the ColPack binary on an absolute path + +--- a/Makefile.am ++++ b/Makefile.am +@@ -17,8 +17,7 @@ + LDADD = libColPack.la + AM_DEFAULT_SOURCE_EXT = .cpp + +-noinst_bin_PROGRAMS = ColPack +-noinst_bindir = $(abs_top_builddir)/progs ++noinst_PROGRAMS = ColPack + lib_LTLIBRARIES = libColPack.la + pkginclude_HEADERS = \ + Utilities/CoutLock.h Utilities/command_line_parameter_processor.h \ diff --git a/sci-libs/colpack/files/colpack-1.0.9-fix-c++14.patch b/sci-libs/colpack/files/colpack-1.0.9-fix-c++14.patch new file mode 100644 index 000000000000..7076be5426a3 --- /dev/null +++ b/sci-libs/colpack/files/colpack-1.0.9-fix-c++14.patch @@ -0,0 +1,71 @@ +From 44851d9e90d9847fbfeaaea7b0ed1e7c3d093dcb Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Bj=C3=B6rn=20Esser?= <me@besser82.io> +Date: Wed, 24 Feb 2016 23:26:20 +0100 +Subject: [PATCH] fix semantic errors in error-msgs + +--- + Utilities/extra.cpp | 12 +++++------- + 1 file changed, 5 insertions(+), 7 deletions(-) + +diff --git a/Utilities/extra.cpp b/Utilities/extra.cpp +index 21862e6..9f59263 100644 +--- a/Utilities/extra.cpp ++++ b/Utilities/extra.cpp +@@ -49,7 +49,7 @@ int WriteMatrixMarket_ADOLCInput(string s_postfix, int i_mode, ...) { + + ofstream out_Matrix (s_MatrixName.c_str()); + if(!out_Matrix) { +- cout<<"Error creating file: \""<<out_Matrix<<"\""<<endl; ++ cout<<"Error creating file: \""<<s_MatrixName<<"\""<<endl; + exit(1); + } + +@@ -84,7 +84,7 @@ int WriteMatrixMarket_ADOLCInput(string s_postfix, int i_mode, ...) { + string s_MatrixName = "pattern"+s_postfix+s_BaseName; + ofstream out_Matrix (s_MatrixName.c_str()); + if(!out_Matrix) { +- cout<<"Error creating file: \""<<out_Matrix<<"\""<<endl; ++ cout<<"Error creating file: \""<<s_MatrixName<<"\""<<endl; + exit(1); + } + +@@ -111,7 +111,7 @@ int WriteMatrixMarket_ADOLCInput(string s_postfix, int i_mode, ...) { + string s_CompressedMatrixName = "CompressedMatrix"+s_postfix+s_BaseName; + ofstream out_CompressedMatrix (s_CompressedMatrixName.c_str()); + if(!out_CompressedMatrix) { +- cout<<"Error creating file: \""<<out_CompressedMatrix<<"\""<<endl; ++ cout<<"Error creating file: \""<<s_CompressedMatrixName<<"\""<<endl; + exit(1); + } + +@@ -140,7 +140,7 @@ int WriteMatrixMarket_ADOLCInput(string s_postfix, int i_mode, ...) { + string s_MatrixName = "pattern_value"+s_postfix+s_BaseName; + ofstream out_Matrix (s_MatrixName.c_str()); + if(!out_Matrix) { +- cout<<"Error creating file: \""<<out_Matrix<<"\""<<endl; ++ cout<<"Error creating file: \""<<s_MatrixName<<"\""<<endl; + exit(1); + } + +@@ -167,7 +167,7 @@ int WriteMatrixMarket_ADOLCInput(string s_postfix, int i_mode, ...) { + string s_CompressedMatrixName = "CompressedMatrix"+s_postfix+s_BaseName; + ofstream out_CompressedMatrix (s_CompressedMatrixName.c_str()); + if(!out_CompressedMatrix) { +- cout<<"Error creating file: \""<<out_CompressedMatrix<<"\""<<endl; ++ cout<<"Error creating file: \""<<s_CompressedMatrixName<<"\""<<endl; + exit(1); + } + +@@ -671,7 +671,6 @@ int buildDotWithColor(ColPack::GraphColoringInterface &g, vector<string> &ListOf + } + } + } +- + } + } + } +@@ -1483,4 +1482,3 @@ int DisplayADICFormat_Value(std::list<std::vector<double> > &lvd_Value) { + } + + #endif +- diff --git a/sci-libs/colpack/files/colpack-1.0.9-fix_gcc49_omp.patch b/sci-libs/colpack/files/colpack-1.0.9-fix_gcc49_omp.patch new file mode 100644 index 000000000000..0510be9f90ef --- /dev/null +++ b/sci-libs/colpack/files/colpack-1.0.9-fix_gcc49_omp.patch @@ -0,0 +1,26 @@ +Index: ColPack-1.0.9/BipartiteGraphPartialColoring/BipartiteGraphPartialColoring.cpp +=================================================================== +--- ColPack-1.0.9.orig/BipartiteGraphPartialColoring/BipartiteGraphPartialColoring.cpp ++++ ColPack-1.0.9/BipartiteGraphPartialColoring/BipartiteGraphPartialColoring.cpp +@@ -388,8 +388,9 @@ namespace ColPack + if ( m_vi_LeftVertexColors [m_vi_Edges [x]] == m_vi_LeftVertexColors[v] && f(v) > f(m_vi_Edges [x]) ) { + //Algo 4 - Line 18: add [v] to R ; cont <- false; break + #pragma omp critical ++ { + vi_verticesNeedNewColor.push_back(v); +-#pragma omp end critical ++ } + cont = false; + break; + } +@@ -575,8 +576,9 @@ namespace ColPack + if ( m_vi_RightVertexColors [m_vi_Edges [x]] == m_vi_RightVertexColors[v] && f(v) > f(m_vi_Edges [x]) ) { + //Algo 4 - Line 18: add [v] to R ; cont <- false; break + #pragma omp critical ++ { + vi_verticesNeedNewColor.push_back(v); +-#pragma omp end critical ++ } + cont = false; + break; + } diff --git a/sci-libs/colpack/metadata.xml b/sci-libs/colpack/metadata.xml new file mode 100644 index 000000000000..c9aa068b01c3 --- /dev/null +++ b/sci-libs/colpack/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + ColPack is a package comprising of implementations of algorithms for + the specialized vertex coloring problems as well as algorithms for a + variety of related supporting tasks in derivative computation. + </longdescription> + <upstream> + <remote-id type="github">CSCsw/ColPack</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/coot-data/Manifest b/sci-libs/coot-data/Manifest new file mode 100644 index 000000000000..00e0ecdeb9c7 --- /dev/null +++ b/sci-libs/coot-data/Manifest @@ -0,0 +1,5 @@ +DIST coot-data-3.tar.gz 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000000000000..c0ab79993bea --- /dev/null +++ b/sci-libs/coot-data/coot-data-3.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit" +HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/" +SRC_URI="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/dependencies/reference-structures.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="" + +RESTRICT="binchecks strip" + +S="${WORKDIR}" + +src_install() { + insinto /usr/share/coot + doins -r reference-structures + + # Coot looks in the wrong spot for the monomer library + # Listens to ccp4's CCP4_LIB rather than CLIBD_MON + cat >> "${T}"/coot <<- EOF + COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/" + COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/" + EOF + + newenvd "${T}"/coot 20coot +} diff --git a/sci-libs/coot-data/metadata.xml b/sci-libs/coot-data/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/coot-data/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/cqrlib/Manifest b/sci-libs/cqrlib/Manifest new file mode 100644 index 000000000000..1f44b247c20a --- /dev/null +++ b/sci-libs/cqrlib/Manifest @@ -0,0 +1,6 @@ +AUX 1.0.6-gentoo.patch 4265 SHA256 01544406bcdc80222c696365b974fc268efad8081f105f106e493927a62c203b SHA512 9a21d5950e378d041dc5fb318debc1790701fd3a8e2f8c651c9a77b526f641c1a5a2a1615c6c3af114f1a5a6e9246b30bbd774f15fc9eeefaf154a13e561a44e WHIRLPOOL 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6e9280a315096c127251e3acdb891a72b3efb4561b35bf02b35c4282923b2b5a77fe52c4a810ebe5b6a42c6570a44bb884f1b6144c6f4a3b094e19b19228cf83 WHIRLPOOL f6e5808b76c4dba50b111366beb5f5bae8d34c2b3d7958a5d94a0f9519dc6f25aca6fce1124b0ea97c15ea469cda15f599aac9867c6f91e8d4cade7fd87aa16b +MISC ChangeLog-2015 3051 SHA256 0bdc4966f9564d989d5fb874255cb8afbdb0d7a677bd77f4f20a5071fc415b43 SHA512 6de3c22b80c9074d94fea09a7890721d101b4425ba8b59ae6dc43bdbaa9e2cd26a96e2a6777230fca3dbb9f1268b540c63218702f14dd8f60fee152bf4e73f72 WHIRLPOOL 863567553ab55a1fea8f274b6ab8e83dde27ba964467c8a241bfda26e8e3e1c1cb19a1911839df12e91f093af92c88fa8a5296e65eeee8f45cfcfc60f9501ff4 +MISC metadata.xml 339 SHA256 064f882dd5882dddfb4ee718e0599ee083c36b453b393d4301b9f054a62677e0 SHA512 2d9ab4b90ddfdc63db116700f54219dfead1dfee0a80816edce6dd09de412f82e251d0022c9c0cc0770bdf1d726d97ae9bf0ad7207454f2cebbca577d61c573d WHIRLPOOL 8b84a6d60fa06cb0671378ec12d2927127a003de4df54df58866236edb31fe3be9d593445a9b4ad4294218e2c09b21070ffe3e0189640fcf3236860c07469646 diff --git a/sci-libs/cqrlib/cqrlib-1.1.3.ebuild b/sci-libs/cqrlib/cqrlib-1.1.3.ebuild new file mode 100644 index 000000000000..d43706733c17 --- /dev/null +++ b/sci-libs/cqrlib/cqrlib-1.1.3.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +MY_PN=CQRlib +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Utility library for quaternion arithmetic / rotation math (ANSI C implemented)" +HOMEPAGE="http://cqrlib.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="dev-libs/cvector" +DEPEND="${RDEPEND}" + +DOCS=( README_CQRlib.txt ) +HTML_DOCS=( README_CQRlib.html ) +PATCHES=( "${FILESDIR}"/1.0.6-gentoo.patch ) + +S="${WORKDIR}"/${MY_P} + +src_prepare() { + default + sed "s:GENTOOLIBDIR:$(get_libdir):g" -i Makefile || die + append-cflags -std=c90 + append-cxxflags -std=c++98 +} + +src_compile() { + emake \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + CPPFLAGS="${CXXFLAGS} -DCQR_NOCCODE=1" \ + all +} + +src_test() { + emake -j1 \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + CFLAGS="${CFLAGS}" \ + tests +} + +src_install() { + emake -j1 DESTDIR="${ED}" install + einstalldocs + + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/cqrlib/files/1.0.6-gentoo.patch b/sci-libs/cqrlib/files/1.0.6-gentoo.patch new file mode 100644 index 000000000000..64a8eaf3ae26 --- /dev/null +++ b/sci-libs/cqrlib/files/1.0.6-gentoo.patch @@ -0,0 +1,101 @@ + Makefile | 56 +++++++++++++++++--------------------------------------- + 1 files changed, 17 insertions(+), 39 deletions(-) + +diff --git a/Makefile b/Makefile +index 9590e50..1aa14e5 100644 +--- a/Makefile ++++ b/Makefile +@@ -88,7 +88,7 @@ INCLUDES = -I$(INC) + endif + + COMPILE_COMMAND = $(LIBTOOL) --mode=compile $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c +-LIBRARY_LINK_COMMAND = $(LIBTOOL) --mode=link $(CC) -version-info $(VERSION) -rpath $(INSTALLDIR)/lib ++LIBRARY_LINK_COMMAND = $(LIBTOOL) --mode=link $(CC) -shared -version-info $(VERSION) -rpath $(INSTALLDIR)/lib ${LDFLAGS} + BUILD_COMMAND_LOCAL = $(LIBTOOL) --mode=link $(CC) $(CFLAGS) $(INCLUDES) + BUILD_COMMAND_DYNAMIC = $(LIBTOOL) --mode=link $(CC) $(CFLAGS) -dynamic -I $(INSTALLDIR)/include -L$(INSTALLDIR)/lib + BUILD_COMMAND_STATIC = $(LIBTOOL) --mode=link $(CC) $(CFLAGS) -static -I $(INSTALLDIR)/include -L$(INSTALLDIR)/lib +@@ -196,52 +196,30 @@ all: $(LIB) $(BIN) $(SOURCE) $(HEADERS) \ + $(LIB)/libCQRlib.$(LIB_EXT) \ + $(BIN)/CQRlibTest $(BIN)/CPPQRTest + +-install: all $(INSTALLDIR) $(INSTALLDIR)/lib $(INSTALLDIR)/include \ ++install: all $(DESTDIR) $(DESTDIR)/GENTOOLIBDIR $(DESTDIR)/include \ + $(INC) $(LIB)/libCQRlib.$(LIB_EXT) $(INC)/cqrlib.h +- $(INSTALL_COMMAND) $(LIB)/libCQRlib.$(LIB_EXT) $(INSTALLDIR)/lib/libCQRlib.$(LIB_EXT) +- $(INSTALL_FINISH_COMMAND) $(INSTALLDIR)/lib/libCQRlib.$(LIB_EXT) +- -cp $(INSTALLDIR)/include/cqrlib.h $(INSTALLDIR)/include/CQRlib_old.h +- cp $(INC)/cqrlib.h $(INSTALLDIR)/include/cqrlib.h +- chmod 644 $(INSTALLDIR)/include/cqrlib.h +- echo "Testing final install dynamic" +- $(BUILD_COMMAND_DYNAMIC) $(EXAMPLES)/CQRlibTest.c \ +- -lCQRlib -lm -o $(BIN)/CQRlibTest_dynamic +- $(BIN)/CQRlibTest_dynamic > $(TESTDATA)/CQRlibTest_dynamic.lst +- diff -b -c $(TESTDATA)/CQRlibTest_orig.lst \ +- $(TESTDATA)/CQRlibTest_dynamic.lst +- echo "Testing final install static" +- $(BUILD_COMMAND_STATIC) $(EXAMPLES)/CQRlibTest.c \ +- -lCQRlib -lm -o $(BIN)/CQRlibTest_static +- $(BIN)/CQRlibTest_static > $(TESTDATA)/CQRlibTest_static.lst +- diff -b -c $(TESTDATA)/CQRlibTest_orig.lst \ +- $(TESTDATA)/CQRlibTest_static.lst +- $(CPPBUILD_COMMAND_DYNAMIC) $(EXAMPLES)/CPPQRTest.cpp \ +- -lm -o $(BIN)/CPPQRTest_dynamic +- $(BIN)/CPPQRTest_dynamic > $(TESTDATA)/CPPQRTest_dynamic.lst +- diff -b -c $(TESTDATA)/CPPQRTest_orig.lst \ +- $(TESTDATA)/CPPQRTest_dynamic.lst +- $(CPPBUILD_COMMAND_STATIC) $(EXAMPLES)/CPPQRTest.cpp \ +- -lm -o $(BIN)/CPPQRTest_static +- $(BIN)/CPPQRTest_static > $(TESTDATA)/CPPQRTest_static.lst +- diff -b -c $(TESTDATA)/CPPQRTest_orig.lst \ +- $(TESTDATA)/CPPQRTest_static.lst ++ $(INSTALL_COMMAND) $(LIB)/libCQRlib.$(LIB_EXT) $(DESTDIR)/usr/GENTOOLIBDIR/libCQRlib.$(LIB_EXT) ++ $(INSTALL_FINISH_COMMAND) $(DESTDIR)/usr/GENTOOLIBDIR/libCQRlib.$(LIB_EXT) ++ -cp $(INSTALLDIR)/cqrlib.h $(DESTDIR)/usr/include/CQRlib.h ++ cp $(INC)/cqrlib.h $(DESTDIR)/usr/include/cqrlib.h ++ chmod 644 $(DESTDIR)/usr/include/cqrlib.h + + + + # + # Directories + # +-$(INSTALLDIR): +- mkdir -p $(INSTALLDIR) ++$(DESTDIR): ++ mkdir -p $(DESTDIR) + +-$(INSTALLDIR)/lib: $(INSTALLDIR) +- mkdir -p $(INSTALLDIR)/lib ++$(DESTDIR)/GENTOOLIBDIR: $(DESTDIR) ++ mkdir -p $(DESTDIR)/usr/GENTOOLIBDIR + +-$(INSTALLDIR)/bin: $(INSTALLDIR) +- mkdir -p $(INSTALLDIR)/bin ++$(DESTDIR)/bin: $(DESTDIR) ++ mkdir -p $(DESTDIR)/usr/bin + +-$(INSTALLDIR)/include: $(INSTALLDIR) +- mkdir -p $(INSTALLDIR)/include ++$(DESTDIR)/include: $(DESTDIR) ++ mkdir -p $(DESTDIR)/usr/include + + + $(LIB): +@@ -255,7 +233,7 @@ $(BIN): + # + $(LIB)/libCQRlib.$(LIB_EXT): $(SOURCE) $(HEADERS) $(COMMONDEP) + $(COMPILE_COMMAND) -c $(SOURCE) +- $(LIBRARY_LINK_COMMAND) -o $(LIB)/libCQRlib.$(LIB_EXT) *.$(OBJ_EXT) ++ $(LIBRARY_LINK_COMMAND) -o $(LIB)/libCQRlib.$(LIB_EXT) *.$(OBJ_EXT) -lm + + # + # CQRlibTest example program +@@ -274,7 +252,7 @@ $(BIN)/CPPQRTest: $(EXAMPLES)/CPPQRTest.cpp + # + # Tests + # +-tests: $(LIB) $(BIN) $(BIN)/CQRlibTest \ ++tests: $(LIB) $(BIN) $(BIN)/CQRlibTest $(BIN)/CPPQRTest \ + all $(TESTDATA)/CQRlibTest_orig.lst $(TESTDATA)/CPPQRTest_orig.lst + $(BIN)/CQRlibTest > $(TESTDATA)/CQRlibTest.lst + diff -b -c $(TESTDATA)/CQRlibTest_orig.lst \ diff --git a/sci-libs/cqrlib/metadata.xml b/sci-libs/cqrlib/metadata.xml new file mode 100644 index 000000000000..6973deae4ff2 --- /dev/null +++ b/sci-libs/cqrlib/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">cqrlib</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/cxsparse/Manifest b/sci-libs/cxsparse/Manifest new file mode 100644 index 000000000000..4a63ae1ca071 --- /dev/null +++ b/sci-libs/cxsparse/Manifest @@ -0,0 +1,13 @@ +AUX cxsparse-2.2.1-autotools.patch 5606 SHA256 3b801b0a829a78377406fb6531b25c1ba8718faa996b61a88ea87b4a2b0dc295 SHA512 463feef6919f421a27ce43588bfb439a0efd8abc8b51cdc7db36b16f4c858ef396dbbff302b51af73d33ece8f0668acb1aae2de543d25d749cf0125cf8328f7a WHIRLPOOL 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000000000000..8f9796d51e49 --- /dev/null +++ b/sci-libs/cxsparse/cxsparse-2.2.1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit autotools eutils + +MY_PN=CXSparse + +DESCRIPTION="Extended sparse matrix package" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/CXSparse/" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${MY_PN}/versions/${MY_PN}-${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 hppa ppc ppc64 sparc x86" +IUSE="" + +DEPEND="sci-libs/ufconfig" +RDEPEND="" + +S="${WORKDIR}/${MY_PN}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-autotools.patch + eautoreconf +} + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" + dodoc README.txt Doc/ChangeLog || die "dodoc failed" +} diff --git a/sci-libs/cxsparse/cxsparse-2.2.6.ebuild b/sci-libs/cxsparse/cxsparse-2.2.6.ebuild new file mode 100644 index 000000000000..877ce88cdf42 --- /dev/null +++ b/sci-libs/cxsparse/cxsparse-2.2.6.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes +inherit autotools-utils + +MY_PN=CXSparse + +DESCRIPTION="Extended sparse matrix package" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/CXSparse/" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${MY_PN}/versions/${MY_PN}-${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" + +DEPEND="sci-libs/ufconfig" +RDEPEND="" + +DOCS=( README.txt Doc/ChangeLog ) +PATCHES=( "${FILESDIR}"/${PN}-2.2.2-autotools.patch ) + +S="${WORKDIR}/${MY_PN}" diff --git a/sci-libs/cxsparse/cxsparse-3.1.1.ebuild b/sci-libs/cxsparse/cxsparse-3.1.1.ebuild new file mode 100644 index 000000000000..2c43a5c8b88f --- /dev/null +++ b/sci-libs/cxsparse/cxsparse-3.1.1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools-utils + +DESCRIPTION="Extended sparse matrix package" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/CXSparse/" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" + +RDEPEND="sci-libs/suitesparseconfig" +DEPEND="${RDEPEND} + virtual/pkgconfig" diff --git a/sci-libs/cxsparse/cxsparse-3.1.2-r1.ebuild b/sci-libs/cxsparse/cxsparse-3.1.2-r1.ebuild new file mode 100644 index 000000000000..5337d7a95847 --- /dev/null +++ b/sci-libs/cxsparse/cxsparse-3.1.2-r1.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit multilib-minimal + +DESCRIPTION="Extended sparse matrix package" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/CXSparse/" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 ~arm hppa ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" + +RDEPEND="sci-libs/suitesparseconfig[${MULTILIB_USEDEP}]" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +multilib_src_configure() { + ECONF_SOURCE="${S}" econf \ + $(use_enable static-libs static) +} + +multilib_src_install_all() { + einstalldocs + + # package provides .pc files + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/cxsparse/files/cxsparse-2.2.1-autotools.patch b/sci-libs/cxsparse/files/cxsparse-2.2.1-autotools.patch new file mode 100644 index 000000000000..26957d801f13 --- /dev/null +++ b/sci-libs/cxsparse/files/cxsparse-2.2.1-autotools.patch @@ -0,0 +1,152 @@ +--- Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Makefile.am 2008-01-29 19:09:42.000000000 +0000 +@@ -0,0 +1,3 @@ ++SUBDIRS = Demo Source ++EXTRA_DIST = README.txt ++include_HEADERS = Include/cs.h +--- configure.ac 1970-01-01 01:00:00.000000000 +0100 ++++ configure.ac 2008-01-29 19:14:14.000000000 +0000 +@@ -0,0 +1,11 @@ ++# -*- Autoconf -*- ++AC_PREREQ(2.59) ++AC_INIT(cxsparse, 2.2.1, davis@cise.ufl.edu) ++AM_INIT_AUTOMAKE([foreign]) ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++AC_CHECK_LIB(m, sqrt) ++AC_CHECK_HEADERS(UFconfig.h) ++AC_CONFIG_FILES([Makefile Demo/Makefile Source/Makefile]) ++AC_OUTPUT ++ +--- Source/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Source/Makefile.am 2008-01-29 19:09:42.000000000 +0000 +@@ -0,0 +1,24 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include ++CS_SOURCE = cs_add.c cs_amd.c cs_chol.c cs_cholsol.c cs_counts.c cs_cumsum.c \ ++ cs_droptol.c cs_dropzeros.c cs_dupl.c cs_entry.c \ ++ cs_etree.c cs_fkeep.c cs_gaxpy.c cs_happly.c cs_house.c cs_ipvec.c \ ++ cs_lsolve.c cs_ltsolve.c cs_lu.c cs_lusol.c cs_util.c cs_multiply.c \ ++ cs_permute.c cs_pinv.c cs_post.c cs_pvec.c cs_qr.c cs_qrsol.c \ ++ cs_scatter.c cs_schol.c cs_sqr.c cs_symperm.c cs_tdfs.c cs_malloc.c \ ++ cs_transpose.c cs_compress.c cs_usolve.c cs_utsolve.c cs_scc.c \ ++ cs_maxtrans.c cs_dmperm.c cs_updown.c cs_print.c cs_norm.c cs_load.c \ ++ cs_dfs.c cs_reach.c cs_spsolve.c cs_leaf.c cs_ereach.c cs_randperm.c ++ ++lib_LTLIBRARIES = libcxsparse.la ++noinst_LTLIBRARIES = libcxsparse_di.la libcxsparse_dl.la libcxsparse_ci.la libcxsparse_cl.la ++ ++libcxsparse_di_la_SOURCES = $(CS_SOURCE) ++libcxsparse_dl_la_SOURCES = $(CS_SOURCE) ++libcxsparse_dl_la_CPPFLAGS = $(AM_CPPFLAGS) -DCS_LONG ++libcxsparse_ci_la_SOURCES = $(CS_SOURCE) ++libcxsparse_ci_la_CPPFLAGS = $(AM_CPPFLAGS) -DCS_COMPLEX ++libcxsparse_cl_la_SOURCES = $(CS_SOURCE) ++libcxsparse_cl_la_CPPFLAGS = $(AM_CPPFLAGS) -DCS_LONG -DCS_COMPLEX ++ ++libcxsparse_la_SOURCES = cs_convert.c ++libcxsparse_la_LIBADD = libcxsparse_di.la libcxsparse_dl.la libcxsparse_ci.la libcxsparse_cl.la +--- Demo/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Demo/Makefile.am 2008-01-29 19:21:32.000000000 +0000 +@@ -0,0 +1,102 @@ ++check_PROGRAMS = \ ++ cs_ci_demo1 \ ++ cs_ci_demo2 \ ++ cs_ci_demo3 \ ++ cs_cl_demo1 \ ++ cs_cl_demo2 \ ++ cs_cl_demo3 \ ++ cs_demo1 \ ++ cs_demo2 \ ++ cs_demo3 \ ++ cs_di_demo1 \ ++ cs_di_demo2 \ ++ cs_di_demo3 \ ++ cs_dl_demo1 \ ++ cs_dl_demo2 \ ++ cs_dl_demo3 \ ++ cs_idemo \ ++ cs_ldemo ++ ++LDADD = $(top_builddir)/Source/libcxsparse.la -lm ++AM_CPPFLAGS = -I$(top_srcdir)/Include ++ ++cs_ci_demo1_SOURCES = cs_ci_demo1.c ++cs_ci_demo2_SOURCES = cs_ci_demo2.c cs_ci_demo.c ++cs_ci_demo3_SOURCES = cs_ci_demo3.c cs_ci_demo.c ++cs_cl_demo1_SOURCES = cs_cl_demo1.c ++cs_cl_demo2_SOURCES = cs_cl_demo2.c cs_cl_demo.c ++cs_cl_demo3_SOURCES = cs_cl_demo3.c cs_cl_demo.c ++cs_demo1_SOURCES = cs_demo1.c ++cs_demo2_SOURCES = cs_demo2.c cs_demo.c ++cs_demo3_SOURCES = cs_demo3.c cs_demo.c ++cs_di_demo1_SOURCES = cs_di_demo1.c ++cs_di_demo2_SOURCES = cs_di_demo2.c cs_di_demo.c ++cs_di_demo3_SOURCES = cs_di_demo3.c cs_di_demo.c ++cs_dl_demo1_SOURCES = cs_dl_demo1.c ++cs_dl_demo2_SOURCES = cs_dl_demo2.c cs_dl_demo.c ++cs_dl_demo3_SOURCES = cs_dl_demo3.c cs_dl_demo.c ++cs_idemo_SOURCES = cs_idemo.c ++cs_ldemo_SOURCES = cs_ldemo.c ++ ++check-local: $(check_PROGRAMS) ++ - ./cs_demo1 < ../Matrix/t1 ++ - ./cs_demo2 < ../Matrix/t1 ++ - ./cs_demo2 < ../Matrix/fs_183_1 ++ - ./cs_demo2 < ../Matrix/west0067 ++ - ./cs_demo2 < ../Matrix/lp_afiro ++ - ./cs_demo2 < ../Matrix/ash219 ++ - ./cs_demo2 < ../Matrix/mbeacxc ++ - ./cs_demo2 < ../Matrix/bcsstk01 ++ - ./cs_demo3 < ../Matrix/bcsstk01 ++ - ./cs_demo2 < ../Matrix/bcsstk16 ++ - ./cs_demo3 < ../Matrix/bcsstk16 ++ - ./cs_di_demo1 < ../Matrix/t1 ++ - ./cs_di_demo2 < ../Matrix/t1 ++ - ./cs_di_demo2 < ../Matrix/fs_183_1 ++ - ./cs_di_demo2 < ../Matrix/west0067 ++ - ./cs_di_demo2 < ../Matrix/lp_afiro ++ - ./cs_di_demo2 < ../Matrix/ash219 ++ - ./cs_di_demo2 < ../Matrix/mbeacxc ++ - ./cs_di_demo2 < ../Matrix/bcsstk01 ++ - ./cs_di_demo3 < ../Matrix/bcsstk01 ++ - ./cs_di_demo2 < ../Matrix/bcsstk16 ++ - ./cs_di_demo3 < ../Matrix/bcsstk16 ++ - ./cs_dl_demo1 < ../Matrix/t1 ++ - ./cs_dl_demo2 < ../Matrix/t1 ++ - ./cs_dl_demo2 < ../Matrix/fs_183_1 ++ - ./cs_dl_demo2 < ../Matrix/west0067 ++ - ./cs_dl_demo2 < ../Matrix/lp_afiro ++ - ./cs_dl_demo2 < ../Matrix/ash219 ++ - ./cs_dl_demo2 < ../Matrix/mbeacxc ++ - ./cs_dl_demo2 < ../Matrix/bcsstk01 ++ - ./cs_dl_demo3 < ../Matrix/bcsstk01 ++ - ./cs_dl_demo2 < ../Matrix/bcsstk16 ++ - ./cs_dl_demo3 < ../Matrix/bcsstk16 ++ - ./cs_ci_demo1 < ../Matrix/t2 ++ - ./cs_ci_demo2 < ../Matrix/t2 ++ - ./cs_ci_demo2 < ../Matrix/t3 ++ - ./cs_ci_demo2 < ../Matrix/t4 ++ - ./cs_ci_demo2 < ../Matrix/c_west0067 ++ - ./cs_ci_demo2 < ../Matrix/c_mbeacxc ++ - ./cs_ci_demo2 < ../Matrix/young1c ++ - ./cs_ci_demo2 < ../Matrix/qc324 ++ - ./cs_ci_demo2 < ../Matrix/neumann ++ - ./cs_ci_demo2 < ../Matrix/c4 ++ - ./cs_ci_demo3 < ../Matrix/c4 ++ - ./cs_ci_demo2 < ../Matrix/mhd1280b ++ - ./cs_ci_demo3 < ../Matrix/mhd1280b ++ - ./cs_cl_demo1 < ../Matrix/t2 ++ - ./cs_cl_demo2 < ../Matrix/t2 ++ - ./cs_cl_demo2 < ../Matrix/t3 ++ - ./cs_cl_demo2 < ../Matrix/t4 ++ - ./cs_cl_demo2 < ../Matrix/c_west0067 ++ - ./cs_cl_demo2 < ../Matrix/c_mbeacxc ++ - ./cs_cl_demo2 < ../Matrix/young1c ++ - ./cs_cl_demo2 < ../Matrix/qc324 ++ - ./cs_cl_demo2 < ../Matrix/neumann ++ - ./cs_cl_demo2 < ../Matrix/c4 ++ - ./cs_cl_demo3 < ../Matrix/c4 ++ - ./cs_cl_demo2 < ../Matrix/mhd1280b ++ - ./cs_cl_demo3 < ../Matrix/mhd1280b ++ - ./cs_idemo < ../Matrix/t2 ++ - ./cs_ldemo < ../Matrix/t2 diff --git a/sci-libs/cxsparse/files/cxsparse-2.2.2-autotools.patch b/sci-libs/cxsparse/files/cxsparse-2.2.2-autotools.patch new file mode 100644 index 000000000000..f8f26f384c86 --- /dev/null +++ b/sci-libs/cxsparse/files/cxsparse-2.2.2-autotools.patch @@ -0,0 +1,152 @@ +--- Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Makefile.am 2008-01-29 19:09:42.000000000 +0000 +@@ -0,0 +1,3 @@ ++SUBDIRS = Demo Source ++EXTRA_DIST = README.txt ++include_HEADERS = Include/cs.h +--- configure.ac 1970-01-01 01:00:00.000000000 +0100 ++++ configure.ac 2008-01-29 19:14:14.000000000 +0000 +@@ -0,0 +1,11 @@ ++# -*- Autoconf -*- ++AC_PREREQ(2.59) ++AC_INIT(cxsparse, 2.2.2, davis@cise.ufl.edu) ++AM_INIT_AUTOMAKE([foreign]) ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++AC_CHECK_LIB(m, sqrt) ++AC_CHECK_HEADERS(UFconfig.h) ++AC_CONFIG_FILES([Makefile Demo/Makefile Source/Makefile]) ++AC_OUTPUT ++ +--- Source/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Source/Makefile.am 2008-01-29 19:09:42.000000000 +0000 +@@ -0,0 +1,24 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include ++CS_SOURCE = cs_add.c cs_amd.c cs_chol.c cs_cholsol.c cs_counts.c cs_cumsum.c \ ++ cs_droptol.c cs_dropzeros.c cs_dupl.c cs_entry.c \ ++ cs_etree.c cs_fkeep.c cs_gaxpy.c cs_happly.c cs_house.c cs_ipvec.c \ ++ cs_lsolve.c cs_ltsolve.c cs_lu.c cs_lusol.c cs_util.c cs_multiply.c \ ++ cs_permute.c cs_pinv.c cs_post.c cs_pvec.c cs_qr.c cs_qrsol.c \ ++ cs_scatter.c cs_schol.c cs_sqr.c cs_symperm.c cs_tdfs.c cs_malloc.c \ ++ cs_transpose.c cs_compress.c cs_usolve.c cs_utsolve.c cs_scc.c \ ++ cs_maxtrans.c cs_dmperm.c cs_updown.c cs_print.c cs_norm.c cs_load.c \ ++ cs_dfs.c cs_reach.c cs_spsolve.c cs_leaf.c cs_ereach.c cs_randperm.c ++ ++lib_LTLIBRARIES = libcxsparse.la ++noinst_LTLIBRARIES = libcxsparse_di.la libcxsparse_dl.la libcxsparse_ci.la libcxsparse_cl.la ++ ++libcxsparse_di_la_SOURCES = $(CS_SOURCE) ++libcxsparse_dl_la_SOURCES = $(CS_SOURCE) ++libcxsparse_dl_la_CPPFLAGS = $(AM_CPPFLAGS) -DCS_LONG ++libcxsparse_ci_la_SOURCES = $(CS_SOURCE) ++libcxsparse_ci_la_CPPFLAGS = $(AM_CPPFLAGS) -DCS_COMPLEX ++libcxsparse_cl_la_SOURCES = $(CS_SOURCE) ++libcxsparse_cl_la_CPPFLAGS = $(AM_CPPFLAGS) -DCS_LONG -DCS_COMPLEX ++ ++libcxsparse_la_SOURCES = cs_convert.c ++libcxsparse_la_LIBADD = libcxsparse_di.la libcxsparse_dl.la libcxsparse_ci.la libcxsparse_cl.la +--- Demo/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Demo/Makefile.am 2008-01-29 19:21:32.000000000 +0000 +@@ -0,0 +1,102 @@ ++check_PROGRAMS = \ ++ cs_ci_demo1 \ ++ cs_ci_demo2 \ ++ cs_ci_demo3 \ ++ cs_cl_demo1 \ ++ cs_cl_demo2 \ ++ cs_cl_demo3 \ ++ cs_demo1 \ ++ cs_demo2 \ ++ cs_demo3 \ ++ cs_di_demo1 \ ++ cs_di_demo2 \ ++ cs_di_demo3 \ ++ cs_dl_demo1 \ ++ cs_dl_demo2 \ ++ cs_dl_demo3 \ ++ cs_idemo \ ++ cs_ldemo ++ ++LDADD = $(top_builddir)/Source/libcxsparse.la -lm ++AM_CPPFLAGS = -I$(top_srcdir)/Include ++ ++cs_ci_demo1_SOURCES = cs_ci_demo1.c ++cs_ci_demo2_SOURCES = cs_ci_demo2.c cs_ci_demo.c ++cs_ci_demo3_SOURCES = cs_ci_demo3.c cs_ci_demo.c ++cs_cl_demo1_SOURCES = cs_cl_demo1.c ++cs_cl_demo2_SOURCES = cs_cl_demo2.c cs_cl_demo.c ++cs_cl_demo3_SOURCES = cs_cl_demo3.c cs_cl_demo.c ++cs_demo1_SOURCES = cs_demo1.c ++cs_demo2_SOURCES = cs_demo2.c cs_demo.c ++cs_demo3_SOURCES = cs_demo3.c cs_demo.c ++cs_di_demo1_SOURCES = cs_di_demo1.c ++cs_di_demo2_SOURCES = cs_di_demo2.c cs_di_demo.c ++cs_di_demo3_SOURCES = cs_di_demo3.c cs_di_demo.c ++cs_dl_demo1_SOURCES = cs_dl_demo1.c ++cs_dl_demo2_SOURCES = cs_dl_demo2.c cs_dl_demo.c ++cs_dl_demo3_SOURCES = cs_dl_demo3.c cs_dl_demo.c ++cs_idemo_SOURCES = cs_idemo.c ++cs_ldemo_SOURCES = cs_ldemo.c ++ ++check-local: $(check_PROGRAMS) ++ - ./cs_demo1 < ../Matrix/t1 ++ - ./cs_demo2 < ../Matrix/t1 ++ - ./cs_demo2 < ../Matrix/fs_183_1 ++ - ./cs_demo2 < ../Matrix/west0067 ++ - ./cs_demo2 < ../Matrix/lp_afiro ++ - ./cs_demo2 < ../Matrix/ash219 ++ - ./cs_demo2 < ../Matrix/mbeacxc ++ - ./cs_demo2 < ../Matrix/bcsstk01 ++ - ./cs_demo3 < ../Matrix/bcsstk01 ++ - ./cs_demo2 < ../Matrix/bcsstk16 ++ - ./cs_demo3 < ../Matrix/bcsstk16 ++ - ./cs_di_demo1 < ../Matrix/t1 ++ - ./cs_di_demo2 < ../Matrix/t1 ++ - ./cs_di_demo2 < ../Matrix/fs_183_1 ++ - ./cs_di_demo2 < ../Matrix/west0067 ++ - ./cs_di_demo2 < ../Matrix/lp_afiro ++ - ./cs_di_demo2 < ../Matrix/ash219 ++ - ./cs_di_demo2 < ../Matrix/mbeacxc ++ - ./cs_di_demo2 < ../Matrix/bcsstk01 ++ - ./cs_di_demo3 < ../Matrix/bcsstk01 ++ - ./cs_di_demo2 < ../Matrix/bcsstk16 ++ - ./cs_di_demo3 < ../Matrix/bcsstk16 ++ - ./cs_dl_demo1 < ../Matrix/t1 ++ - ./cs_dl_demo2 < ../Matrix/t1 ++ - ./cs_dl_demo2 < ../Matrix/fs_183_1 ++ - ./cs_dl_demo2 < ../Matrix/west0067 ++ - ./cs_dl_demo2 < ../Matrix/lp_afiro ++ - ./cs_dl_demo2 < ../Matrix/ash219 ++ - ./cs_dl_demo2 < ../Matrix/mbeacxc ++ - ./cs_dl_demo2 < ../Matrix/bcsstk01 ++ - ./cs_dl_demo3 < ../Matrix/bcsstk01 ++ - ./cs_dl_demo2 < ../Matrix/bcsstk16 ++ - ./cs_dl_demo3 < ../Matrix/bcsstk16 ++ - ./cs_ci_demo1 < ../Matrix/t2 ++ - ./cs_ci_demo2 < ../Matrix/t2 ++ - ./cs_ci_demo2 < ../Matrix/t3 ++ - ./cs_ci_demo2 < ../Matrix/t4 ++ - ./cs_ci_demo2 < ../Matrix/c_west0067 ++ - ./cs_ci_demo2 < ../Matrix/c_mbeacxc ++ - ./cs_ci_demo2 < ../Matrix/young1c ++ - ./cs_ci_demo2 < ../Matrix/qc324 ++ - ./cs_ci_demo2 < ../Matrix/neumann ++ - ./cs_ci_demo2 < ../Matrix/c4 ++ - ./cs_ci_demo3 < ../Matrix/c4 ++ - ./cs_ci_demo2 < ../Matrix/mhd1280b ++ - ./cs_ci_demo3 < ../Matrix/mhd1280b ++ - ./cs_cl_demo1 < ../Matrix/t2 ++ - ./cs_cl_demo2 < ../Matrix/t2 ++ - ./cs_cl_demo2 < ../Matrix/t3 ++ - ./cs_cl_demo2 < ../Matrix/t4 ++ - ./cs_cl_demo2 < ../Matrix/c_west0067 ++ - ./cs_cl_demo2 < ../Matrix/c_mbeacxc ++ - ./cs_cl_demo2 < ../Matrix/young1c ++ - ./cs_cl_demo2 < ../Matrix/qc324 ++ - ./cs_cl_demo2 < ../Matrix/neumann ++ - ./cs_cl_demo2 < ../Matrix/c4 ++ - ./cs_cl_demo3 < ../Matrix/c4 ++ - ./cs_cl_demo2 < ../Matrix/mhd1280b ++ - ./cs_cl_demo3 < ../Matrix/mhd1280b ++ - ./cs_idemo < ../Matrix/t2 ++ - ./cs_ldemo < ../Matrix/t2 diff --git a/sci-libs/cxsparse/metadata.xml b/sci-libs/cxsparse/metadata.xml new file mode 100644 index 000000000000..fb290bc72702 --- /dev/null +++ b/sci-libs/cxsparse/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + CXSparse is an extended version of CSparse, a sparse matrix package, + with support for double or complex matrices, with int or long + integers. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/dcmtk/Manifest b/sci-libs/dcmtk/Manifest new file mode 100644 index 000000000000..e62a553429b4 --- /dev/null +++ b/sci-libs/dcmtk/Manifest @@ -0,0 +1,12 @@ +AUX 01_fix_perl_script_path.patch 8946 SHA256 94c94e8d557d221310c2b5161cc5085f9e0ca4f86791c12ea4b7fc98d13cf15d SHA512 002b6fe72068a185ecf87ecf04990e8b085593aeee1faa399aacc64de2810f45ecfb181cac9651a37a07719b41cf0029176404ce33264e196350ff701b51f18a WHIRLPOOL 1c4e76cf686393f219bf70bfbecfb054216759acce0224346e771b2115e6b0b6a43f5c16d921d4f52d2d46405dac3d66a9174d11f8ea4de6cd1bca4ea26ac73c +AUX 02_dcmtk_3.6.0-1.patch 3245 SHA256 ef35d208440309579eafe2b6b4cfe7bf323148edc711b9323667f88319876e78 SHA512 369ee28f0d30f7aaa6f204aa45a4314218eb6ed070dc1e3a557802d62956ec3bdf8dcc1490c0b7b879d1a2e9145aa8bf0de691ef32e2bc7dd9270f63cc31f68a WHIRLPOOL 06c759cfa1fbebc4f958cd0ad93448fb2f1fe159f44961bdc2c5c97b4943b35291922b06c027ee33c961f9f7532b74b14a95a5fdcc20bcc4d62d988c8750a154 +AUX 04_nostrip.patch 7339 SHA256 9e0c9249c7915edef4861122c1d51cfcae4483e96fc23e758e785a6b63dd578f SHA512 7f8fb30a4ad4b2b0ab6ace37afb618efc3faed6af3dbed6793ff8c61dfd0a99aa26b880e6c0cc7addfffa008044ba8e81e622f94bebf6152cb0bd273da023e29 WHIRLPOOL 589480f54a8b2230c50681eb957dd6b63377a9cc4b8f0fcf45fda73d04b40cb90e0654b763f243ac82d67a58bf75b00077949db2f4a4208b1dc3861196e1fc35 +AUX dcmtk-asneeded.patch 4403 SHA256 7cb35268b5e6ae3c87a467f07c27fe25985844655a51186c985a4c2c419cecc7 SHA512 629b6cc819c0440b9173ca09343309399abaa1cd23b92f7a2a78b732508140c9b6f9885f38c18328dc9b3dc5e86534940595380fac9223c2fb45c901c9f1222c WHIRLPOOL d477e19f23e623baaa848575a2d41f87abebcb00d6f3da2a50c794846719b0f048667bf0f1981aeeab31fd5f4ec431a135761ebda5f3da19a4adccf04bbc8e03 +AUX dcmtk-gcc472-error.patch 13994 SHA256 1737c0837ae6271eacef4b9d1078826d95ac14fdded119bf846c430b796a80f4 SHA512 d408a83cd7b1de08041ff2c3df7ee3a766ffa31a7085c8a1e853de6fd3d4d871557a5b2a2a417c52953a4bcc4ed2d5f813cd3a5170fb27482caec60ff1361eac WHIRLPOOL 7e4ed9dbc5aa699117d9a1dcde4b0536bd0e09af7fd8fa5bf5e7d675db9d003bc1780dcb27be8181a4c2b5219e5c778326872af882ce0f5556b7e6b729f9ace1 +AUX dcmtk_version_number.patch 5439 SHA256 f2d250b9a2d747b86a0c62ad63e1ff19dda928d09eddf78064800df3782b911c SHA512 22f93c2bd3b1d4ac301653484bf5dca384a65fbc31ee61038c156d285ab587715ed61101761d5edaf4e64c31cd56239fb09c8d81a3aa241772e5c2c0556da872 WHIRLPOOL b43e2eebb2f57cd7a7fbb558db490ec7ee8392eb57e340fc754a582203b4c7d7b68f29a1c3f8bdf789a11521ac59b10e1b3c71b6e15b862a7c31214e7090a29b +AUX png_tiff.patch 620 SHA256 67d413c13185b8d2b17dc6f6743a499e078259bdc615f4c6bf4dea5ec8252cd5 SHA512 b6c30e40ffcabf77f3dd04dbf5ba76ac0e86972e06eec81a1833c472099e7b207c4343208dc756f650f5b5ff77df6b950b0acb24c43029f30e2d67a3f882fab2 WHIRLPOOL 3f87b67965ecaa309a57efb2c2f5ed6fc49fd52fbf5dd03fc624c44825f6ed00af87330eba47ea0c57aeff5e843d93d847b565096b7fbb102764c71d6369b458 +AUX regression_stacksequenceisodd.patch 4989 SHA256 913dc47190c94730021dc3ef466f490b78064529b951b9374c6e030501560bdc SHA512 bb126c947646ca3274863b8517478e738fcbe16f3e1e0bb75b8601ad2b5e6492400f96a89aaf25f683b06f6f3f9dad76391d5adc62177496cbffc0309aa7dc72 WHIRLPOOL 972a12607bb2e98a796af4dfaee679e8ecc4a93fc5f60ba71af568ee1ddf76b479b08469269463329c0810f9105db2a166f19b0e6865f89551dc9284b37b2661 +DIST dcmtk-3.6.0.tar.gz 4673121 SHA256 cfc509701122adfa359f1ee160e943c1548c7696b607dbb646c5a06f015ed33a SHA512 2a9d866bafcaea72d889d24b51ff2341ee39c717aacf9ae5825c8588cd5cb01c3e341b6173abce751f6cb32c45be8888e81ccb08967cae2cca7fdcb2b61be53c WHIRLPOOL 88538048a7534847c5c1450be0ccc94979ab20be8fc1a05a944b4a7f8f627578d585e91a30984f75ae0f1c29bca0c615c3b290cc6c0965b6e7ddd23e31ba3cd9 +EBUILD dcmtk-3.6.0.ebuild 2301 SHA256 2c6fd396452bf03bf4ae5a7f538a7cef8fa442e1804e27a44d5d7999dc291f91 SHA512 5cda12c21fe8acb7ad46a0b5ffb97d5e35fc3d6b77da3465ba08771df7e48b81331217d3a256f821ec5bc14da3f973f9ad012db3af0bb8db9b446bc35fb02ca4 WHIRLPOOL 6a819943545fcc5769bdd337a8cbcfa9966c4d795fbbe7975cdb59182bba8030a1f1f7d4607f82f917042b562c1520fbd5b9df0d35de40d0c702a93646521843 +MISC ChangeLog 1007 SHA256 89c4cf17dd76851de7e684ee5a3f27505a2354a91f486d787dd77fca23b4f76b SHA512 9eb549a4033e8a8bac7c7f3201289ff5b88176afb6f4fc8b294c70fda6ec6b525ca5fe446288fd0767f92aa5b76741b008dd7f26d6ea6fec8723d22296a2d50d WHIRLPOOL f269ab42d9484645ba1def93b51e3c8bc2a61c0b68a6dcbb3fc0a5ef8179691b7010b56bfb5fcdd6b8098720a5967bab2b1931280e53740fea510403af89ea11 +MISC metadata.xml 317 SHA256 bca569e145ba074e5b6882e2a7da0b83e7585fb53f2e1af17aae56b7ec66fd18 SHA512 0c6bb7cc6f8d56a7809354d0630ee49f33b63f7b60ad0a0ccbbfd7f28391a4c6b0c9f56caeb7cefcc74bf169ed6d46adda4fd204ef633311376b3cc3f7193d68 WHIRLPOOL 88873f0aff5d9d811525bff49fff15a985c430f182e53544138515f027406e43a70d670a45deb317e594d5e4afee1fa37b93da570d205a1bece4e4cbafbfe7f1 diff --git a/sci-libs/dcmtk/dcmtk-3.6.0.ebuild b/sci-libs/dcmtk/dcmtk-3.6.0.ebuild new file mode 100644 index 000000000000..afc167d9d7e3 --- /dev/null +++ b/sci-libs/dcmtk/dcmtk-3.6.0.ebuild @@ -0,0 +1,94 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit cmake-utils eutils + +DESCRIPTION="The DICOM Toolkit" +HOMEPAGE="http://dicom.offis.de/dcmtk.php.en" +SRC_URI="ftp://dicom.offis.de/pub/dicom/offis/software/dcmtk/dcmtk360/${P}.tar.gz" + +LICENSE="OFFIS" +KEYWORDS="~amd64 ~arm ~x86" +SLOT="0" +IUSE="doc png ssl tcpd tiff +threads xml zlib" + +RDEPEND=" + virtual/jpeg:0 + png? ( media-libs/libpng:* ) + ssl? ( dev-libs/openssl:0 ) + tcpd? ( sys-apps/tcp-wrappers ) + tiff? ( media-libs/tiff:0 ) + xml? ( dev-libs/libxml2:2 ) + zlib? ( sys-libs/zlib )" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + media-gfx/graphviz" + +src_prepare() { + + epatch \ + "${FILESDIR}"/01_fix_perl_script_path.patch \ + "${FILESDIR}"/02_dcmtk_3.6.0-1.patch \ + "${FILESDIR}"/04_nostrip.patch \ + "${FILESDIR}"/dcmtk_version_number.patch \ + "${FILESDIR}"/png_tiff.patch \ + "${FILESDIR}"/regression_stacksequenceisodd.patch \ + "${FILESDIR}"/${PN}-asneeded.patch \ + "${FILESDIR}"/${PN}-gcc472-error.patch + + sed -e "s:share/doc/dcmtk:&-${PV}:" \ + -e "s:DIR \"/:DIR \"/usr/:" \ + -e "s:usr/etc:etc:" \ + -e "s:/lib\":/$(get_libdir)\":" \ + -e "s:COPYRIGHT::" \ + -i CMakeLists.txt || die + sed -e 's:${CMAKE_INSTALL_PREFIX}/::' \ + -i dcmwlm/data/CMakeLists.txt doxygen/CMakeLists.txt || die + # Temporary workaround: docs are not built with CMake + sed -i -e '/include/d' doxygen/Makefile.in || die + + # fix -D deprecation warnings + sed -i -e "s|_BSD_SOURCE|_DEFAULT_SOURCE|g" \ + "${S}"/config/configure.in \ + "${S}"/CMakeLists.txt +} + +src_configure() { + mycmakeargs="${mycmakeargs} + -DBUILD_SHARED_LIBS=ON + -DCMAKE_INSTALL_PREFIX=/ + $(cmake-utils_use tiff DCMTK_WITH_TIFF) + $(cmake-utils_use png DCMTK_WITH_PNG) + $(cmake-utils_use xml DCMTK_WITH_XML) + $(cmake-utils_use zlib DCMTK_WITH_ZLIB) + $(cmake-utils_use ssl DCMTK_WITH_OPENSSL) + $(cmake-utils_use doc DCMTK_WITH_DOXYGEN) + $(cmake-utils_use threads DCMTK_WITH_THREADS)" + + cmake-utils_src_configure + + if use doc; then + cd "${S}"/doxygen + econf + fi +} + +src_compile() { + cmake-utils_src_compile + + if use doc; then + emake -C "${S}"/doxygen || die + fi +} + +src_install() { + cmake-utils_src_install + + doman doxygen/manpages/man1/* || die + + if use doc; then + dohtml -r "${S}"/doxygen/htmldocs/* || die + fi +} diff --git a/sci-libs/dcmtk/files/01_fix_perl_script_path.patch b/sci-libs/dcmtk/files/01_fix_perl_script_path.patch new file mode 100644 index 000000000000..9f002d85640f --- /dev/null +++ b/sci-libs/dcmtk/files/01_fix_perl_script_path.patch @@ -0,0 +1,222 @@ +Author: Jürgen Salk <jsa@debian.org> +Description: The original maintainer Jürgen Salk applied + a set of patches to the original code. The part which fixes + the path to the perl executable is collected in this patch set. + +--- dcmtk-3.5.5_20101130/dcmwlm/perl/changepw.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/changepw.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/checkvr.ph 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/checkvr.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/isocode.ph 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/isocode.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/layout.ph 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/layout.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/lock.ph 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/lock.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/log.ph 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/log.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/main.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/main.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/password.ph 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/password.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/patidel.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/patidel.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/patiedit.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/patiedit.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/patient.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/patient.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/prefs.ph 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/prefs.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/procdel.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/procdel.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/procedit.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/procedit.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/procedur.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/procedur.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/procstep.pl 2010-10-14 15:02:01.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/procstep.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/prstdel.pl 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/prstdel.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/prstedit.pl 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/prstedit.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/statdel.pl 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/statdel.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/statedit.pl 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/statedit.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/station.pl 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/station.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/urldecod.ph 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/urldecod.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright & Disclaimer. + # This set of routines may be freely distributed, modified and +--- dcmtk-3.5.5_20101130/dcmwlm/perl/workdel.pl 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/workdel.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/workedit.pl 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/workedit.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/worklist.pl 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/worklist.pl 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +--- dcmtk-3.5.5_20101130/dcmwlm/perl/write.ph 2010-10-14 15:02:02.000000000 +0200 ++++ dcmtk-3.5.5_20101130.new/dcmwlm/perl/write.ph 2010-12-09 11:50:35.000000000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # Copyright (C) 1996-2010, OFFIS e.V. + # All rights reserved. See COPYRIGHT file for details. +@@ -59,7 +59,7 @@ + if (open(outfile, ">@_[0]")) + { + print outfile <<EOF; +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # automatically generated by write.pl - do not modify! + # diff --git a/sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch b/sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch new file mode 100644 index 000000000000..11aaaec37646 --- /dev/null +++ b/sci-libs/dcmtk/files/02_dcmtk_3.6.0-1.patch @@ -0,0 +1,89 @@ +Author: Jürgen Salk <jsa@debian.org> +Description: The original maintainer Jürgen Salk applied + a set of patches to the original code. This file contains + changes to C++ code + +Index: dcmtk-3.6.0/dcmqrdb/etc/dcmqrscp.cfg +=================================================================== +--- dcmtk-3.6.0.orig/dcmqrdb/etc/dcmqrscp.cfg 2010-09-09 19:20:25.000000000 +0200 ++++ dcmtk-3.6.0/dcmqrdb/etc/dcmqrscp.cfg 2011-01-28 09:49:02.000000000 +0100 +@@ -10,6 +10,9 @@ + NetworkTCPPort = 104 + MaxPDUSize = 16384 + MaxAssociations = 16 ++UserName = "dcmtk" ++GroupName = "dcmtk" ++ + # + # UserName = <not used> + # GroupName = <not used> +@@ -28,12 +31,13 @@ + # NOTE: in the current implementation you cannot substitute an IP address + # for a hostname. + # +-acme1 = (ACME1, acmehost1, 5678) +-acme2 = (ACME2, acmehost2, 5678) +-acmeCTcompany = acme1, acme2 +-united1 = (UNITED1, unitedhost1, 104) +-united2 = (UNITED2, unitedhost2, 104) +-unitedMRcompany = united1, united2 ++# Example: ++#acme1 = (ACME1, acmehost1, 5678) ++#acme2 = (ACME2, acmehost2, 5678) ++#acmeCTcompany = acme1, acme2 ++#united1 = (UNITED1, unitedhost1, 104) ++#united2 = (UNITED2, unitedhost2, 104) ++#unitedMRcompany = united1, united2 + # + HostTable END + +@@ -51,8 +55,9 @@ + # VendorName = SymbolicName + # The symbolic name should be defined in the HostTable. + # +-"Acme CT Company" = acmeCTcompany +-"United MR Company" = unitedMRcompany ++# Example: ++#"Acme CT Company" = acmeCTcompany ++#"United MR Company" = unitedMRcompany + # + VendorTable END + +@@ -70,8 +75,13 @@ + # Entry in HostTable | + # ANY + # +-COMMON /home/dicom/db/COMMON R (200, 1024mb) ANY +-ACME_STORE /home/dicom/db/ACME_STORE RW (9, 1024mb) acmeCTcompany +-UNITED_STORE /home/dicom/db/UNITED_STORE RW (9, 1024mb) unitedMRcompany ++# Example: ++# ++#ACME_STORE /var/lib/dcmtk/db/ACME_STORE RW (9, 1024mb) acmeCTcompany ++#UNITED_STORE /var/lib/dcmtk/db/UNITED_STORE RW (9, 1024mb) unitedMRcompany ++# ++# Uncomment and adjust the following lines for a common r/rw storage area: ++#READWRITE /var/lib/dcmtk/db/READWRITE RW (10, 1024mb) ANY ++#READ /var/lib/dcmtk/db/READ R (200, 1024mb) ANY + # + AETable END +Index: dcmtk-3.6.0/dcmqrdb/docs/dcmqrcnf.txt +=================================================================== +--- dcmtk-3.6.0.orig/dcmqrdb/docs/dcmqrcnf.txt 2010-09-09 19:20:12.000000000 +0200 ++++ dcmtk-3.6.0/dcmqrdb/docs/dcmqrcnf.txt 2011-01-28 09:46:02.000000000 +0100 +@@ -44,8 +44,8 @@ + NetworkTCPPort = 104 + MaxPDUSize = 8192 + MaxAssociations = 20 +-UserName = (do not change user) +-GroupName = (do not change group) ++UserName = "dcmtk" ++GroupName = "dcmtk" + + NOTE: You must have root privileges to bind port 104 for DICOM association + requests on Unix/Linux/Posix platforms as this is a privileged port number +Index: dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile +=================================================================== +--- /dev/null 1970-01-01 00:00:00.000000000 +0000 ++++ dcmtk-3.6.0/dcmwlm/wlistdb/OFFIS/lockfile 2011-01-28 09:46:02.000000000 +0100 +@@ -0,0 +1 @@ ++ diff --git a/sci-libs/dcmtk/files/04_nostrip.patch b/sci-libs/dcmtk/files/04_nostrip.patch new file mode 100644 index 000000000000..c4a109ca5df8 --- /dev/null +++ b/sci-libs/dcmtk/files/04_nostrip.patch @@ -0,0 +1,171 @@ +Remove all hardcoded calls to `strip` command + +Index: dcmtk-3.6.0/config/templates/Makefile.src +=================================================================== +--- dcmtk-3.6.0.orig/config/templates/Makefile.src 2009-01-30 10:27:58.000000000 +0100 ++++ dcmtk-3.6.0/config/templates/Makefile.src 2011-01-28 09:53:28.000000000 +0100 +@@ -31,7 +31,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmdata/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmdata/apps/Makefile.in 2009-11-04 10:58:05.000000000 +0100 ++++ dcmtk-3.6.0/dcmdata/apps/Makefile.in 2011-01-28 09:53:45.000000000 +0100 +@@ -76,7 +76,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmimage/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmimage/apps/Makefile.in 2009-10-13 16:08:33.000000000 +0200 ++++ dcmtk-3.6.0/dcmimage/apps/Makefile.in 2011-01-28 09:53:59.000000000 +0100 +@@ -42,7 +42,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmimgle/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmimgle/apps/Makefile.in 2009-10-28 10:53:39.000000000 +0100 ++++ dcmtk-3.6.0/dcmimgle/apps/Makefile.in 2011-01-28 09:54:11.000000000 +0100 +@@ -39,7 +39,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmjpeg/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmjpeg/apps/Makefile.in 2009-10-07 14:44:33.000000000 +0200 ++++ dcmtk-3.6.0/dcmjpeg/apps/Makefile.in 2011-01-28 09:54:28.000000000 +0100 +@@ -72,7 +72,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + clean: +Index: dcmtk-3.6.0/dcmnet/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmnet/apps/Makefile.in 2009-11-04 11:24:29.000000000 +0100 ++++ dcmtk-3.6.0/dcmnet/apps/Makefile.in 2011-01-28 09:54:50.000000000 +0100 +@@ -52,7 +52,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmpstat/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmpstat/apps/Makefile.in 2009-10-13 16:57:49.000000000 +0200 ++++ dcmtk-3.6.0/dcmpstat/apps/Makefile.in 2011-01-28 09:55:10.000000000 +0100 +@@ -113,7 +113,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmqrdb/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmqrdb/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ dcmtk-3.6.0/dcmqrdb/apps/Makefile.in 2011-01-28 09:55:24.000000000 +0100 +@@ -57,7 +57,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmsign/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmsign/apps/Makefile.in 2009-09-04 17:42:31.000000000 +0200 ++++ dcmtk-3.6.0/dcmsign/apps/Makefile.in 2011-01-28 09:55:35.000000000 +0100 +@@ -33,7 +33,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmsr/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmsr/apps/Makefile.in 2009-10-13 16:57:49.000000000 +0200 ++++ dcmtk-3.6.0/dcmsr/apps/Makefile.in 2011-01-28 09:55:48.000000000 +0100 +@@ -44,7 +44,7 @@ + install-bin: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmwlm/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmwlm/apps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ dcmtk-3.6.0/dcmwlm/apps/Makefile.in 2011-01-28 09:55:58.000000000 +0100 +@@ -49,7 +49,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmwlm/wwwapps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmwlm/wwwapps/Makefile.in 2009-11-04 11:24:30.000000000 +0100 ++++ dcmtk-3.6.0/dcmwlm/wwwapps/Makefile.in 2011-01-28 09:56:33.000000000 +0100 +@@ -55,7 +55,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + +Index: dcmtk-3.6.0/dcmjpls/apps/Makefile.in +=================================================================== +--- dcmtk-3.6.0.orig/dcmjpls/apps/Makefile.in 2011-01-28 09:56:54.000000000 +0100 ++++ dcmtk-3.6.0/dcmjpls/apps/Makefile.in 2011-01-28 09:57:00.000000000 +0100 +@@ -71,7 +71,7 @@ + install: all + $(configdir)/mkinstalldirs $(DESTDIR)$(bindir) + for prog in $(progs); do \ +- $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir) && strip $(DESTDIR)$(bindir)/$$prog$(BINEXT) ;\ ++ $(INSTALL_PROGRAM) $$prog$(BINEXT) $(DESTDIR)$(bindir);\ + done + + diff --git a/sci-libs/dcmtk/files/dcmtk-asneeded.patch b/sci-libs/dcmtk/files/dcmtk-asneeded.patch new file mode 100644 index 000000000000..a27e46eda2af --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk-asneeded.patch @@ -0,0 +1,63 @@ +--- dcmimgle/libsrc/CMakeLists.txt.orig 2010-10-14 12:19:24.416833916 +0200 ++++ dcmimgle/libsrc/CMakeLists.txt 2010-10-14 12:18:51.682258692 +0200 +@@ -1,5 +1,5 @@ + # create library from source files + ADD_LIBRARY(dcmimgle dcmimage dibaslut diciefn dicielut didislut didispfn didocu digsdfn digsdlut diimage diinpx diluptab dimo1img dimo2img dimoimg dimoimg3 dimoimg4 dimoimg5 dimomod dimoopx dimopx diovdat diovlay diovlimg diovpln diutils) +- ++TARGET_LINK_LIBRARIES(dcmimgle dcmdata) + # declare installation files + INSTALL_TARGETS(${INSTALL_LIBDIR} dcmimgle) +--- dcmpstat/libsrc/CMakeLists.txt.orig 2010-10-14 12:26:05.324680803 +0200 ++++ dcmpstat/libsrc/CMakeLists.txt 2010-10-14 12:26:35.309298272 +0200 +@@ -1,5 +1,5 @@ + # create library from source files + ADD_LIBRARY(dcmpstat dcmpstat dviface dvpsab dvpsabl dvpsal dvpsall dvpscf dvpscu dvpscul dvpsda dvpsdal dvpsfs dvpsga dvpsgal dvpsgl dvpsgll dvpsgr dvpsgrl dvpshlp dvpsib dvpsibl dvpsmsg dvpsov dvpsovl dvpspl dvpspl2 dvpspll dvpspr dvpsprt dvpsri dvpsril dvpsrs dvpsrsl dvpssp dvpsspl dvpssv dvpssvl dvpstat dvpstx dvpstxl dvpsvl dvpsvll dvpsvw dvpsvwl dvsighdl) +- ++TARGET_LINK_LIBRARIES(dcmpstat dcmdsig dcmtls dcmsr) + # declare installation files + INSTALL_TARGETS(${INSTALL_LIBDIR} dcmpstat) +--- dcmsign/libsrc/CMakeLists.txt.orig 2010-10-14 12:37:02.149984538 +0200 ++++ dcmsign/libsrc/CMakeLists.txt 2010-10-14 12:38:53.602332737 +0200 +@@ -1,5 +1,5 @@ + # create library from source files + ADD_LIBRARY(dcmdsig dcsignat siautopr sibrsapr sicert sicertvf sicreapr sidsa simaccon simd5 sinullpr siprivat siripemd sirsa sisha1 sisprof sitypes) +- ++TARGET_LINK_LIBRARIES(dcmdsig ${OPENSSL_LIBS}) + # declare installation files + INSTALL_TARGETS(${INSTALL_LIBDIR} dcmdsig) +--- dcmimage/libsrc/CMakeLists.txt.orig 2010-10-14 12:45:06.926394516 +0200 ++++ dcmimage/libsrc/CMakeLists.txt 2010-10-14 12:46:05.197437359 +0200 +@@ -1,5 +1,5 @@ + # create library from source files + ADD_LIBRARY(dcmimage diargimg dicmyimg dicoimg dicoopx dicopx dihsvimg dilogger dipalimg dipipng dipitiff diqtctab diqtfs diqthash diqthitl diqtpbox diquant diregist dirgbimg diybrimg diyf2img diyp2img) +- ++TARGET_LINK_LIBRARIES(dcmimage ${LIBTIFF_LIBS} ${LIBPNG_LIBS}) + # declare installation files + INSTALL_TARGETS(${INSTALL_LIBDIR} dcmimage) +--- dcmdata/libsrc/CMakeLists.txt.orig 2010-10-14 12:44:00.991741511 +0200 ++++ dcmdata/libsrc/CMakeLists.txt 2010-10-14 12:44:55.918954304 +0200 +@@ -1,5 +1,5 @@ + # create library from source files + ADD_LIBRARY(dcmdata cmdlnarg dcbytstr dcchrstr dccodec dcdatset dcddirif dcdicdir dcdicent dcdict dcdictzz dcdirrec dcelem dcerror dcfilefo dchashdi dcistrma dcistrmb dcistrmf dcistrmz dcitem dclist dcmetinf dcobject dcostrma dcostrmb dcostrmf dcostrmz dcpcache dcpixel dcpixseq dcpxitem dcrleccd dcrlecce dcrlecp dcrledrg dcrleerg dcrlerp dcsequen dcstack dcswap dctag dctagkey dctypes dcuid dcwcache dcvm dcvr dcvrae dcvras dcvrat dcvrcs dcvrda dcvrds dcvrdt dcvrfd dcvrfl dcvris dcvrlo dcvrlt dcvrobow dcvrof dcvrpn dcvrpobw dcvrsh dcvrsl dcvrss dcvrst dcvrtm dcvrui dcvrul dcvrulup dcvrus dcvrut dcxfer dcpath vrscan vrscanl) +- ++TARGET_LINK_LIBRARIES(dcmdata ${ZLIB_LIBS}) + # declare installation files + INSTALL_TARGETS(${INSTALL_LIBDIR} dcmdata) +--- dcmsr/libsrc/CMakeLists.txt.orig 2010-10-14 14:45:48.736866802 +0200 ++++ dcmsr/libsrc/CMakeLists.txt 2010-10-14 14:46:40.910215801 +0200 +@@ -1,5 +1,5 @@ + # create library from source files + ADD_LIBRARY(dcmsr dsrcitem dsrcodtn dsrcodvl dsrcomtn dsrcomvl dsrcontn dsrcsidl dsrdattn dsrdoc dsrdoctn dsrdoctr dsrdtitn dsrimgfr dsrimgtn dsrimgvl dsrnumtn dsrnumvl dsrpnmtn dsrreftn dsrscogr dsrsc3gr dsrscotn dsrsc3tn dsrscovl dsrsc3vl dsrsoprf dsrstrvl dsrtcodt dsrtcosp dsrtcotn dsrtcoto dsrtcovl dsrtextn dsrtimtn dsrtncsr dsrtree dsrtypes dsruidtn dsrwavch dsrwavtn dsrwavvl dsrxmlc dsrxmld dsriodcc dsrbascc dsrenhcc dsrcomcc dsrkeycc dsrmamcc dsrchecc dsrcolcc dsrprocc dsrxrdcc dsrspecc dsrmaccc) +- ++TARGET_LINK_LIBRARIES(dcmsr ${LIBXML_LIBS}) + # declare installation files + INSTALL_TARGETS(${INSTALL_LIBDIR} dcmsr) +--- dcmtls/libsrc/CMakeLists.txt.orig 2012-11-11 19:19:00.832767189 -0800 ++++ dcmtls/libsrc/CMakeLists.txt 2012-11-11 19:29:43.887972426 -0800 +@@ -1,5 +1,6 @@ + # create library from source files + ADD_LIBRARY(dcmtls tlslayer tlstrans tlsscu) + ++TARGET_LINK_LIBRARIES(dcmtls ${OPENSSL_LIBS}) + # declare installation files + INSTALL_TARGETS(${INSTALL_LIBDIR} dcmtls) diff --git a/sci-libs/dcmtk/files/dcmtk-gcc472-error.patch b/sci-libs/dcmtk/files/dcmtk-gcc472-error.patch new file mode 100644 index 000000000000..9d344d7206e8 --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk-gcc472-error.patch @@ -0,0 +1,318 @@ +--- ofstd/include/dcmtk/ofstd/ofoset.h.orig 2013-06-22 09:11:13.000000000 -0700 ++++ ofstd/include/dcmtk/ofstd/ofoset.h 2013-06-22 09:12:07.000000000 -0700 +@@ -146,7 +146,7 @@ + { + // if size equals num, we need more space + if( this->size == this->num ) +- Resize( this->size * 2 ); ++ this->Resize( this->size * 2 ); + + // copy item + T *newItem = new T( item ); +@@ -189,7 +189,7 @@ + { + // if size equals num, we need more space + if( this->size == this->num ) +- Resize( this->size * 2 ); ++ this->Resize( this->size * 2 ); + + // copy item + T *newItem = new T( item ); +--- dcmimage/include/dcmtk/dcmimage/diargpxt.h.orig 2013-06-22 09:32:37.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/diargpxt.h 2013-06-22 09:34:20.000000000 -0700 +@@ -91,7 +91,7 @@ + const unsigned long planeSize, + const int bits) + { // not very much optimized, but no one really uses ARGB !! +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + register T2 value; + const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1)); +--- dcmimage/include/dcmtk/dcmimage/dicmypxt.h.orig 2013-06-22 09:44:02.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/dicmypxt.h 2013-06-22 09:51:29.000000000 -0700 +@@ -87,7 +87,7 @@ + const unsigned long planeSize, + const int bits) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + // use the number of input pixels derived from the length of the 'PixelData' + // attribute), but not more than the size of the intermediate buffer +--- dcmimgle/include/dcmtk/dcmimgle/discalet.h.orig 2013-06-22 09:52:08.000000000 -0700 ++++ dcmimgle/include/dcmtk/dcmimgle/discalet.h 2013-06-22 09:54:35.000000000 -0700 +@@ -206,12 +206,12 @@ + (Left >= OFstatic_cast(signed long, Columns)) || (Top >= OFstatic_cast(signed long, Rows))) + { // no image to be displayed + DCMIMGLE_DEBUG("clipping area is fully outside the image boundaries"); +- fillPixel(dest, value); // ... fill bitmap ++ this->fillPixel(dest, value); // ... fill bitmap + } + else if ((this->Src_X == this->Dest_X) && (this->Src_Y == this->Dest_Y)) // no scaling + { + if ((Left == 0) && (Top == 0) && (Columns == this->Src_X) && (Rows == this->Src_Y)) +- copyPixel(src, dest); // copying ++ this->copyPixel(src, dest); // copying + else if ((Left >= 0) && (OFstatic_cast(Uint16, Left + this->Src_X) <= Columns) && + (Top >= 0) && (OFstatic_cast(Uint16, Top + this->Src_Y) <= Rows)) + clipPixel(src, dest); // clipping +@@ -567,7 +567,7 @@ + if ((xtemp == NULL) || (xvalue == NULL)) + { + DCMIMGLE_ERROR("can't allocate temporary buffers for interpolation scaling"); +- clearPixel(dest); ++ this->clearPixel(dest); + } else { + for (int j = 0; j < this->Planes; ++j) + { +@@ -905,7 +905,7 @@ + if (pTemp == NULL) + { + DCMIMGLE_ERROR("can't allocate temporary buffer for interpolation scaling"); +- clearPixel(dest); ++ this->clearPixel(dest); + } else { + + /* +@@ -1029,7 +1029,7 @@ + if (pTemp == NULL) + { + DCMIMGLE_ERROR("can't allocate temporary buffer for interpolation scaling"); +- clearPixel(dest); ++ this->clearPixel(dest); + } else { + + /* +--- dcmimage/include/dcmtk/dcmimage/dicocpt.h.orig 2013-06-22 10:01:51.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/dicocpt.h 2013-06-22 10:03:10.000000000 -0700 +@@ -86,7 +86,7 @@ + inline void copy(const T *pixel[3], + const unsigned long offset) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + for (int j = 0; j < 3; j++) + OFBitmanipTemplate<T>::copyMem(pixel[j] + offset, this->Data[j], this->getCount()); +--- dcmimage/include/dcmtk/dcmimage/dicosct.h.orig 2013-06-22 10:03:27.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/dicosct.h 2013-06-22 10:04:56.000000000 -0700 +@@ -107,8 +107,8 @@ + inline void scale(const T *pixel[3], + const int interpolate) + { +- if (Init(pixel)) +- scaleData(pixel, this->Data, interpolate); ++ if (this->Init(pixel)) ++ this->scaleData(pixel, this->Data, interpolate); + } + }; + +--- dcmimage/include/dcmtk/dcmimage/dicoflt.h.orig 2013-06-22 10:05:04.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/dicoflt.h 2013-06-22 10:08:17.000000000 -0700 +@@ -98,14 +98,14 @@ + const int horz, + const int vert) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + if (horz && vert) +- flipHorzVert(pixel, this->Data); ++ this->flipHorzVert(pixel, this->Data); + else if (horz) +- flipHorz(pixel, this->Data); ++ this->flipHorz(pixel, this->Data); + else if (vert) +- flipVert(pixel, this->Data); ++ this->flipVert(pixel, this->Data); + } + } + }; +--- dcmimage/include/dcmtk/dcmimage/dicorot.h.orig 2013-06-22 10:08:25.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/dicorot.h 2013-06-22 10:09:57.000000000 -0700 +@@ -98,14 +98,14 @@ + inline void rotate(const T *pixel[3], + const int degree) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + if (degree == 90) +- rotateRight(pixel, this->Data); ++ this->rotateRight(pixel, this->Data); + else if (degree == 180) +- rotateTopDown(pixel, this->Data); ++ this->rotateTopDown(pixel, this->Data); + else if (degree == 270) +- rotateLeft(pixel, this->Data); ++ this->rotateLeft(pixel, this->Data); + } + } + }; +--- dcmimage/include/dcmtk/dcmimage/dihsvpxt.h.orig 2013-06-22 10:10:11.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/dihsvpxt.h 2013-06-22 10:10:54.000000000 -0700 +@@ -87,7 +87,7 @@ + const unsigned long planeSize, + const int bits) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + register T2 *r = this->Data[0]; + register T2 *g = this->Data[1]; +--- dcmimage/include/dcmtk/dcmimage/dipalpxt.h.orig 2013-06-22 10:18:26.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/dipalpxt.h 2013-06-22 10:19:13.000000000 -0700 +@@ -92,7 +92,7 @@ + void convert(const T1 *pixel, + DiLookupTable *palette[3]) + { // can be optimized if necessary ! +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + register const T1 *p = pixel; + register T2 value = 0; +--- dcmimage/include/dcmtk/dcmimage/diybrpxt.h.orig 2013-06-22 10:34:13.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/diybrpxt.h 2013-06-22 10:34:48.000000000 -0700 +@@ -91,7 +91,7 @@ + const int bits, + const OFBool rgb) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1)); + // use the number of input pixels derived from the length of the 'PixelData' +--- dcmimage/include/dcmtk/dcmimage/dirgbpxt.h.orig 2013-06-22 10:35:08.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/dirgbpxt.h 2013-06-22 10:35:39.000000000 -0700 +@@ -87,7 +87,7 @@ + const unsigned long planeSize, + const int bits) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + // use the number of input pixels derived from the length of the 'PixelData' + // attribute), but not more than the size of the intermediate buffer +--- dcmimage/include/dcmtk/dcmimage/diyp2pxt.h.orig 2013-06-22 10:35:45.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/diyp2pxt.h 2013-06-22 10:36:34.000000000 -0700 +@@ -91,7 +91,7 @@ + void convert(const T1 *pixel, + const int bits) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + register T2 *r = this->Data[0]; + register T2 *g = this->Data[1]; +--- dcmimage/include/dcmtk/dcmimage/diyf2pxt.h.orig 2013-06-22 10:36:47.000000000 -0700 ++++ dcmimage/include/dcmtk/dcmimage/diyf2pxt.h 2013-06-22 10:37:19.000000000 -0700 +@@ -95,7 +95,7 @@ + const int bits, + const OFBool rgb) + { +- if (Init(pixel)) ++ if (this->Init(pixel)) + { + const T1 offset = OFstatic_cast(T1, DicomImageClass::maxval(bits - 1)); + register unsigned long i; +--- dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h.orig 2013-06-22 10:44:20.000000000 -0700 ++++ dcmimgle/include/dcmtk/dcmimgle/dimoipxt.h 2013-06-22 10:47:08.000000000 -0700 +@@ -76,10 +76,10 @@ + else if ((this->Modality != NULL) && this->Modality->hasRescaling()) + { + rescale(pixel, this->Modality->getRescaleSlope(), this->Modality->getRescaleIntercept()); +- determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue())); ++ this->determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue())); + } else { + rescale(pixel); // "copy" or reference pixel data +- determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue())); ++ this->determineMinMax(OFstatic_cast(T3, this->Modality->getMinValue()), OFstatic_cast(T3, this->Modality->getMaxValue())); + } + } + } +--- dcmimgle/include/dcmtk/dcmimgle/dimosct.h.orig 2013-06-22 10:47:22.000000000 -0700 ++++ dcmimgle/include/dcmtk/dcmimgle/dimosct.h 2013-06-22 10:48:02.000000000 -0700 +@@ -124,7 +124,7 @@ + { + const T value = OFstatic_cast(T, OFstatic_cast(double, DicomImageClass::maxval(bits)) * + OFstatic_cast(double, pvalue) / OFstatic_cast(double, DicomImageClass::maxval(WIDTH_OF_PVALUES))); +- scaleData(&pixel, &this->Data, interpolate, value); ++ this->scaleData(&pixel, &this->Data, interpolate, value); + } + } + } +--- dcmimgle/include/dcmtk/dcmimgle/dimoflt.h.orig 2013-06-22 10:48:07.000000000 -0700 ++++ dcmimgle/include/dcmtk/dcmimgle/dimoflt.h 2013-06-22 10:48:37.000000000 -0700 +@@ -106,11 +106,11 @@ + if (this->Data != NULL) + { + if (horz && vert) +- flipHorzVert(&pixel, &this->Data); ++ this->flipHorzVert(&pixel, &this->Data); + else if (horz) +- flipHorz(&pixel, &this->Data); ++ this->flipHorz(&pixel, &this->Data); + else if (vert) +- flipVert(&pixel, &this->Data); ++ this->flipVert(&pixel, &this->Data); + } + } + } +--- dcmimgle/include/dcmtk/dcmimgle/dimorot.h,orig 2013-06-22 10:50:38.000000000 -0700 ++++ dcmimgle/include/dcmtk/dcmimgle/dimorot.h 2013-06-22 10:53:57.000000000 -0700 +@@ -105,11 +105,11 @@ + if (this->Data != NULL) + { + if (degree == 90) +- rotateRight(&pixel, &(this->Data)); ++ this->rotateRight(&pixel, &(this->Data)); + else if (degree == 180) +- rotateTopDown(&pixel, &(this->Data)); ++ this->rotateTopDown(&pixel, &(this->Data)); + else if (degree == 270) +- rotateLeft(&pixel, &(this->Data)); ++ this->rotateLeft(&pixel, &(this->Data)); + } + } + } +--- dcmimgle/include/dcmtk/dcmimgle/diflipt.h.orig 2013-06-22 11:03:34.000000000 -0700 ++++ dcmimgle/include/dcmtk/dcmimgle/diflipt.h 2013-06-22 11:04:43.000000000 -0700 +@@ -123,13 +123,13 @@ + if ((src != NULL) && (dest != NULL)) + { + if (horz && vert) +- flipHorzVert(src, dest); ++ this->flipHorzVert(src, dest); + else if (horz) +- flipHorz(src, dest); ++ this->flipHorz(src, dest); + else if (vert) +- flipVert(src, dest); ++ this->flipVert(src, dest); + else +- copyPixel(src, dest); ++ this->copyPixel(src, dest); + } + } + +--- dcmimgle/include/dcmtk/dcmimgle/dirotat.h.orig 2013-06-22 11:06:17.000000000 -0700 ++++ dcmimgle/include/dcmtk/dcmimgle/dirotat.h 2013-06-22 11:07:00.000000000 -0700 +@@ -126,13 +126,13 @@ + const int degree) + { + if (degree == 90) +- rotateRight(src, dest); ++ this->rotateRight(src, dest); + else if (degree == 180) +- rotateTopDown(src, dest); ++ this->rotateTopDown(src, dest); + else if (degree == 270) +- rotateLeft(src, dest); ++ this->rotateLeft(src, dest); + else +- copyPixel(src, dest); ++ this->copyPixel(src, dest); + } + + diff --git a/sci-libs/dcmtk/files/dcmtk_version_number.patch b/sci-libs/dcmtk/files/dcmtk_version_number.patch new file mode 100644 index 000000000000..130a3bfb8efe --- /dev/null +++ b/sci-libs/dcmtk/files/dcmtk_version_number.patch @@ -0,0 +1,131 @@ +From: Joerg Riesmeier <dicom@offis.de> +Date: Tue, 1 Feb 2011 17:01:14 +0000 (+0000) +Subject: Made sure that OFFIS_DCMTK_VERSION_NUMBER is really a number and not a +X-Git-Url: http://git.dcmtk.org/web?p=dcmtk.git;a=commitdiff_plain;h=12c35ca + +Made sure that OFFIS_DCMTK_VERSION_NUMBER is really a number and not a +string. +--- + +Index: dcmtk-3.6.0/CMake/osconfig.h.in +=================================================================== +--- dcmtk-3.6.0.orig/CMake/osconfig.h.in 2010-11-24 14:53:32.000000000 +0100 ++++ dcmtk-3.6.0/CMake/osconfig.h.in 2011-06-17 14:34:56.000000000 +0200 +@@ -677,7 +677,7 @@ + #define PACKAGE_VERSION_SUFFIX "@DCMTK_PACKAGE_VERSION_SUFFIX@" + + /* Define to the version number of this package. */ +-#define PACKAGE_VERSION_NUMBER "@DCMTK_PACKAGE_VERSION_NUMBER@" ++#define PACKAGE_VERSION_NUMBER @DCMTK_PACKAGE_VERSION_NUMBER@ + + /* Define path separator */ + #define PATH_SEPARATOR '@PATH_SEPARATOR@' +Index: dcmtk-3.6.0/CMakeLists.txt +=================================================================== +--- dcmtk-3.6.0.orig/CMakeLists.txt 2011-01-06 11:48:43.000000000 +0100 ++++ dcmtk-3.6.0/CMakeLists.txt 2011-06-17 14:34:56.000000000 +0200 +@@ -21,7 +21,7 @@ + SET(DCMTK_PACKAGE_DATE "2011-01-06") + #SET(DCMTK_PACKAGE_TARNAME "dcmtk-3.6.0") + SET(DCMTK_PACKAGE_VERSION "3.6.0") +-SET(DCMTK_PACKAGE_VERSION_NUMBER "360") ++SET(DCMTK_PACKAGE_VERSION_NUMBER 360) + SET(DCMTK_PACKAGE_VERSION_SUFFIX "") + #SET(DCMTK_PACKAGE_STRING "dcmtk 3.6.0") + #SET(DCMTK_PACKAGE_BUGREPORT "dicom-bugs@offis.de") +Index: dcmtk-3.6.0/config/configure +=================================================================== +--- dcmtk-3.6.0.orig/config/configure 2011-01-06 11:48:47.000000000 +0100 ++++ dcmtk-3.6.0/config/configure 2011-06-17 14:34:56.000000000 +0200 +@@ -1774,13 +1774,13 @@ + + + +-PACKAGE_VERSION_NUMBER="360" ++PACKAGE_VERSION_NUMBER=360 + PACKAGE_VERSION_SUFFIX="" + PACKAGE_DATE="2011-01-06" + + + cat >>confdefs.h <<_ACEOF +-#define PACKAGE_VERSION_NUMBER "${PACKAGE_VERSION_NUMBER}" ++#define PACKAGE_VERSION_NUMBER ${PACKAGE_VERSION_NUMBER} + _ACEOF + + +Index: dcmtk-3.6.0/config/configure.in +=================================================================== +--- dcmtk-3.6.0.orig/config/configure.in 2011-01-06 11:48:47.000000000 +0100 ++++ dcmtk-3.6.0/config/configure.in 2011-06-17 14:34:56.000000000 +0200 +@@ -8,11 +8,11 @@ + dnl Additional Package Information + dnl ------------------------------------------------------- + +-PACKAGE_VERSION_NUMBER="360" ++PACKAGE_VERSION_NUMBER=360 + PACKAGE_VERSION_SUFFIX="" + PACKAGE_DATE="2011-01-06" + +-AC_DEFINE_UNQUOTED(PACKAGE_VERSION_NUMBER,"${PACKAGE_VERSION_NUMBER}",[Define to the version number of this package.]) ++AC_DEFINE_UNQUOTED(PACKAGE_VERSION_NUMBER,${PACKAGE_VERSION_NUMBER},[Define to the version number of this package.]) + AC_DEFINE_UNQUOTED(PACKAGE_VERSION_SUFFIX,"${PACKAGE_VERSION_SUFFIX}",[Define to the version suffix of this package.]) + AC_DEFINE_UNQUOTED(PACKAGE_DATE,"${PACKAGE_DATE}",[Define to the release date of this package.]) + +Index: dcmtk-3.6.0/dcmdata/include/dcmtk/dcmdata/dcuid.h +=================================================================== +--- dcmtk-3.6.0.orig/dcmdata/include/dcmtk/dcmdata/dcuid.h 2010-11-05 11:26:10.000000000 +0100 ++++ dcmtk-3.6.0/dcmdata/include/dcmtk/dcmdata/dcuid.h 2011-06-17 14:34:56.000000000 +0200 +@@ -1,6 +1,6 @@ + /* + * +- * Copyright (C) 1994-2010, OFFIS e.V. ++ * Copyright (C) 1994-2011, OFFIS e.V. + * All rights reserved. See COPYRIGHT file for details. + * + * This software and supporting documentation were developed by +@@ -20,8 +20,8 @@ + * routines for finding and creating UIDs. + * + * Last Update: $Author: joergr $ +- * Update Date: $Date: 2010-11-05 10:26:10 $ +- * CVS/RCS Revision: $Revision: 1.89 $ ++ * Update Date: $Date: 2011-02-01 17:01:33 $ ++ * CVS/RCS Revision: $Revision: 1.90 $ + * Status: $State: Exp $ + * + * CVS/RCS Log at end of file +@@ -165,16 +165,21 @@ + #error Required compiler definition PACKAGE_VERSION_NUMBER undefined + #endif + ++// helper macros for version number conversion ++ ++#define PACKAGE_VERSION_NUMBER_TO_STRING_( x ) #x ++#define PACKAGE_VERSION_NUMBER_TO_STRING( x ) PACKAGE_VERSION_NUMBER_TO_STRING_( x ) ++ + /* NOTE: Implementation version name VR=SH may not be longer than 16 chars + * The second name is used to identify files written without dcmdata + * (i.e. using the --bit-preserving switch in various tools) + */ + + /// implementation version name for this version of the toolkit +-#define OFFIS_DTK_IMPLEMENTATION_VERSION_NAME "OFFIS_DCMTK_" PACKAGE_VERSION_NUMBER ++#define OFFIS_DTK_IMPLEMENTATION_VERSION_NAME "OFFIS_DCMTK_" PACKAGE_VERSION_NUMBER_TO_STRING(PACKAGE_VERSION_NUMBER) + + /// implementation version name for this version of the toolkit, used for files received in "bit preserving" mode +-#define OFFIS_DTK_IMPLEMENTATION_VERSION_NAME2 "OFFIS_DCMBP_" PACKAGE_VERSION_NUMBER ++#define OFFIS_DTK_IMPLEMENTATION_VERSION_NAME2 "OFFIS_DCMBP_" PACKAGE_VERSION_NUMBER_TO_STRING(PACKAGE_VERSION_NUMBER) + + /// release date of current toolkit release + #ifdef DCMTK_BUILD_DATE +@@ -704,6 +709,10 @@ + /* + ** CVS/RCS Log: + ** $Log: dcuid.h,v $ ++** Revision 1.90 2011-02-01 17:01:33 joergr ++** Made sure that OFFIS_DCMTK_VERSION_NUMBER is really a number and not a ++** string. ++** + ** Revision 1.89 2010-11-05 10:26:10 joergr + ** Added new SOP Class UIDs from Supplement 131 and 134 (Implant Templates). + ** diff --git a/sci-libs/dcmtk/files/png_tiff.patch b/sci-libs/dcmtk/files/png_tiff.patch new file mode 100644 index 000000000000..0c498838816a --- /dev/null +++ b/sci-libs/dcmtk/files/png_tiff.patch @@ -0,0 +1,11 @@ +--- dcmtk-3.5.5_20100504/dcmjpls/apps/Makefile.in 2010-12-09 11:27:05.000000000 +0100 ++++ dcmtk-3.5.5_20100504.old/dcmjpls/apps/Makefile.in 2010-12-09 11:27:44.000000000 +0100 +@@ -50,7 +50,7 @@ + LIBDIRS = -L$(top_srcdir)/libsrc $(dcmjplslibdir) $(libcharlslibdir) $(dcmimagelibdir) \ + $(dcmimglelibdir) $(dcmdatalibdir) $(ofloglibdir) $(ofstdlibdir) + LOCALLIBS = $(dcmjplslib) $(dcmimagelib) $(dcmimglelib) $(dcmdatalib) $(ofloglib) $(ofstdlib) \ +- $(libcharlslib) $(ZLIBLIBS) ++ $(libcharlslib) $(ZLIBLIBS) $(TIFFLIBS) $(PNGLIBS) + PNMLIBS = $(TIFFLIBS) $(PNGLIBS) $(ZLIBLIBS) + + objs = dcmdjpls.o dcmcjpls.o dcml2pnm.o diff --git a/sci-libs/dcmtk/files/regression_stacksequenceisodd.patch b/sci-libs/dcmtk/files/regression_stacksequenceisodd.patch new file mode 100644 index 000000000000..f95cb2ef3b38 --- /dev/null +++ b/sci-libs/dcmtk/files/regression_stacksequenceisodd.patch @@ -0,0 +1,98 @@ +From: Joerg Riesmeier <dicom@offis.de> +Date: Tue, 1 Mar 2011 10:04:16 +0000 (+0000) +Subject: Fixed some private tags copied from Philips MR Achieva conformance statement. +X-Git-Url: http://git.dcmtk.org/web?p=dcmtk.git;a=commitdiff_plain;h=0d3d794e71a3b9035c154a266834f93383083819;hp=0025bc0f762e96afec42dfff505386b3d591f6f7 + +Fixed some private tags copied from Philips MR Achieva conformance statement. +Also added a couple of new private tags from the same conformance statement. +--- + +Index: dcmtk-3.6.0/dcmdata/data/private.dic +=================================================================== +--- dcmtk-3.6.0.orig/dcmdata/data/private.dic 2010-11-22 11:39:26.000000000 +0100 ++++ dcmtk-3.6.0/dcmdata/data/private.dic 2011-06-17 14:40:20.000000000 +0200 +@@ -35,6 +35,7 @@ + # - Philips Digital Diagnost 1.3 conformance statement + # - Philips Integris H, catheterization laboratory, RIS-interface + # - Philips Intera Achieva Conformance Statement ++# - Philips MR Achieva Conformance Statement + # - Siemens Somatom syngo VA40B conformance statement + # - Siemens AXIOM Artis VB30 conformance statement + # - SonoWand Invite 2.1.1 conformance statement +@@ -1159,7 +1160,7 @@ + (2001,"Philips Imaging DD 001",35) SS StackSliceNumber 1 + (2001,"Philips Imaging DD 001",36) CS StackType 1 + (2001,"Philips Imaging DD 001",3f) CS ZoomMode 1 +-(2001,"Philips Imaging DD 001",5f) SQ StackSequence 1-n ++(2001,"Philips Imaging DD 001",5f) SQ StackSequence 1 + (2001,"Philips Imaging DD 001",60) SL NumberOfStacks 1 + (2001,"Philips Imaging DD 001",61) CS SeriesTransmitted 1 + (2001,"Philips Imaging DD 001",62) CS SeriesCommitted 1 +@@ -1204,7 +1205,7 @@ + (2001,"PHILIPS IMAGING DD 001",35) SS StackSliceNumber 1 + (2001,"PHILIPS IMAGING DD 001",36) CS StackType 1 + (2001,"PHILIPS IMAGING DD 001",3f) CS ZoomMode 1 +-(2001,"PHILIPS IMAGING DD 001",5f) SQ StackSequence 1-n ++(2001,"PHILIPS IMAGING DD 001",5f) SQ StackSequence 1 + (2001,"PHILIPS IMAGING DD 001",60) SL NumberOfStacks 1 + (2001,"PHILIPS IMAGING DD 001",61) CS SeriesTransmitted 1 + (2001,"PHILIPS IMAGING DD 001",62) CS SeriesCommitted 1 +@@ -1221,12 +1222,6 @@ + (2005,"Philips MR Imaging DD 001",1f) SH MPRProtocol 1 + (2005,"Philips MR Imaging DD 001",20) SL NumberOfChemicalShifts 1 + (2005,"Philips MR Imaging DD 001",2d) SS NumberOfStackSlices 1 +-(2005,"Philips MR Imaging DD 001",32) FL StackRadialAngle 1 +-(2005,"Philips MR Imaging DD 001",33) CS StackRadialAxis 1 +-(2005,"Philips MR Imaging DD 001",35) SS StackSliceNumber 1 +-(2005,"Philips MR Imaging DD 001",36) CS StackType 1 +-(2005,"Philips MR Imaging DD 001",a1) CS SyncraScanType 1 +-(2005,"Philips MR Imaging DD 001",5f) SQ StackSequence 1 + (2005,"Philips MR Imaging DD 001",83) SQ Unknown 1 + + (2005,"Philips MR Imaging DD 005",02) SQ Unknown 1 +@@ -1240,12 +1235,6 @@ + (2005,"PHILIPS MR IMAGING DD 001",1f) SH MPRProtocol 1 + (2005,"PHILIPS MR IMAGING DD 001",20) SL NumberOfChemicalShifts 1 + (2005,"PHILIPS MR IMAGING DD 001",2d) SS NumberOfStackSlices 1 +-(2005,"PHILIPS MR IMAGING DD 001",32) FL StackRadialAngle 1 +-(2005,"PHILIPS MR IMAGING DD 001",33) CS StackRadialAxis 1 +-(2005,"PHILIPS MR IMAGING DD 001",35) SS StackSliceNumber 1 +-(2005,"PHILIPS MR IMAGING DD 001",36) CS StackType 1 +-(2005,"PHILIPS MR IMAGING DD 001",a1) CS SyncraScanType 1 +-(2005,"PHILIPS MR IMAGING DD 001",5f) SQ StackSequence 1 + (2005,"PHILIPS MR IMAGING DD 001",83) SQ Unknown 1 + + (0019,"PHILIPS MR R5.5/PART",1000) DS FieldOfView 1 +Index: dcmtk-3.6.0/dcmdata/libsrc/dcdictzz.cc +=================================================================== +--- dcmtk-3.6.0.orig/dcmdata/libsrc/dcdictzz.cc 2010-11-22 11:48:17.000000000 +0100 ++++ dcmtk-3.6.0/dcmdata/libsrc/dcdictzz.cc 2011-06-17 14:41:07.000000000 +0200 +@@ -20753,11 +20817,11 @@ + DcmDictRange_Unspecified, DcmDictRange_Unspecified, + "PHILIPS IMAGING DD 001" } + , { 0x2001, 0x005f, 0x2001, 0x005f, +- EVR_SQ, "StackSequence", 1, -1, "DICOM", ++ EVR_SQ, "StackSequence", 1, 1, "DICOM", + DcmDictRange_Unspecified, DcmDictRange_Unspecified, + "Philips Imaging DD 001" } + , { 0x2001, 0x005f, 0x2001, 0x005f, +- EVR_SQ, "StackSequence", 1, -1, "DICOM", ++ EVR_SQ, "StackSequence", 1, 1, "DICOM", + DcmDictRange_Unspecified, DcmDictRange_Unspecified, + "PHILIPS IMAGING DD 001" } + , { 0x2001, 0x0060, 0x2001, 0x0060, +@@ -20884,14 +20996,6 @@ + EVR_CS, "StackType", 1, 1, "DICOM", + DcmDictRange_Unspecified, DcmDictRange_Unspecified, + "PHILIPS MR IMAGING DD 001" } +- , { 0x2005, 0x005f, 0x2005, 0x005f, +- EVR_SQ, "StackSequence", 1, 1, "DICOM", +- DcmDictRange_Unspecified, DcmDictRange_Unspecified, +- "Philips MR Imaging DD 001" } +- , { 0x2005, 0x005f, 0x2005, 0x005f, +- EVR_SQ, "StackSequence", 1, 1, "DICOM", +- DcmDictRange_Unspecified, DcmDictRange_Unspecified, +- "PHILIPS MR IMAGING DD 001" } + , { 0x2005, 0x0083, 0x2005, 0x0083, + EVR_SQ, "Unknown", 1, 1, "DICOM", + DcmDictRange_Unspecified, DcmDictRange_Unspecified, diff --git a/sci-libs/dcmtk/metadata.xml b/sci-libs/dcmtk/metadata.xml new file mode 100644 index 000000000000..ed91732eca95 --- /dev/null +++ b/sci-libs/dcmtk/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + </maintainer> + <longdescription>DICOM ToolKit core medical imaging library and tools</longdescription> +</pkgmetadata> diff --git a/sci-libs/deap/Manifest b/sci-libs/deap/Manifest new file mode 100644 index 000000000000..5045d695079f --- /dev/null +++ b/sci-libs/deap/Manifest @@ -0,0 +1,9 @@ +DIST deap-0.9.1.tar.gz 968521 SHA256 fc8d8c58718505aad4255ce8c70ae22f25a97d74916fe7a155491a28a2c5f52e SHA512 70786b444a05e4db9c95f132af4308acb058e507a537946979a735025f2ed5bbafe13c3c876d3c73cef6dc034c8e28f4a982afbc4416a4905be5d3b905831107 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73511656968a939f7b2d8c3b997b40dd676c238cc286cdba6c565097360a10693d415d3e55df776d1d809464fabec2559f9075417fffca4c775ffbd21314dd8c WHIRLPOOL 870f01fa2dc4b5a0f26c40caee3c84e56b88113d602d7f08c2a45c422131dd681d8b408ec2fb76c01de0c5471d7e583785768fd1d4f49f3370aafccc723cb597 diff --git a/sci-libs/deap/deap-0.9.1.ebuild b/sci-libs/deap/deap-0.9.1.ebuild new file mode 100644 index 000000000000..ccb293d84705 --- /dev/null +++ b/sci-libs/deap/deap-0.9.1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Novel evolutionary computation framework" +HOMEPAGE="https://code.google.com/p/deap/" +SRC_URI="https://deap.googlecode.com/files/${P}.tar.gz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="" +DEPEND="dev-python/setuptools" diff --git a/sci-libs/deap/deap-1.0.0.ebuild b/sci-libs/deap/deap-1.0.0.ebuild new file mode 100644 index 000000000000..cc81e092bcb0 --- /dev/null +++ b/sci-libs/deap/deap-1.0.0.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python{2_7,3_4} ) +inherit distutils-r1 + +DESCRIPTION="Distributed Evolutionary Algorithms in Python" +HOMEPAGE="https://code.google.com/p/deap/ https://pypi.python.org/pypi/deap/" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="" +DEPEND="dev-python/setuptools" diff --git a/sci-libs/deap/deap-1.0.1.ebuild b/sci-libs/deap/deap-1.0.1.ebuild new file mode 100644 index 000000000000..f961fd5a3b86 --- /dev/null +++ b/sci-libs/deap/deap-1.0.1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" +PYTHON_COMPAT=( python{2_6,2_7,3_1,3_2,3_3} ) + +inherit distutils-r1 + +DESCRIPTION="Novel evolutionary computation framework" +HOMEPAGE="https://github.com/deap/deap" +SRC_URI="https://github.com/DEAP/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="" +DEPEND="dev-python/setuptools" diff --git a/sci-libs/deap/metadata.xml b/sci-libs/deap/metadata.xml new file mode 100644 index 000000000000..0d9686a43e81 --- /dev/null +++ b/sci-libs/deap/metadata.xml @@ -0,0 +1,17 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>slis@gentoo.org</email> + </maintainer> + <longdescription> + DEAP stands for Distributed Evolutionary Algorithm in Python, it is dedicated to people who + wish to learn how to use evolutionary algorithms and to those who wish to + rediscover evolutionary algorithms. DEAP is the proof that evolutionary + algorithms do **not** need to be neither complex or complicated. + </longdescription> + <upstream> + <remote-id type="pypi">deap</remote-id> + <remote-id type="github">DEAP/deap</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/djbfft/Manifest b/sci-libs/djbfft/Manifest new file mode 100644 index 000000000000..ff144c4f78f4 --- /dev/null +++ b/sci-libs/djbfft/Manifest @@ -0,0 +1,8 @@ +AUX djbfft-0.76-gcc3.patch 1176 SHA256 f6b84b582bdb5846f75bdb0def9695884480c062060eaeddd092e7d106256851 SHA512 e7de40d8ecf5447921fd5f9c21a0a44f58c7351457d029d9848514e032e495a13da2f282c6c3d05f00fd85c1af8d0799db64c786b1a0286ab03dc7c2148dd23c WHIRLPOOL 970e5a9d9a69ad3e09740cb4c1e105a28431572cf1f7cdba8a4826069c0f540d39527d99ee5d4ba40b38f20da628bdb1dbcb578d963747fcd81339998163c660 +AUX djbfft-0.76-headers.patch 995 SHA256 783ef6cf4b82af55efc6d038aa0fe2f76c81dcd52393444fa0ca438c9ebee483 SHA512 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flag-o-matic toolchain-funcs multilib multilib-minimal + +DESCRIPTION="Extremely fast library for floating-point convolution" +HOMEPAGE="http://cr.yp.to/djbfft.html" +SRC_URI="http://cr.yp.to/djbfft/${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="alpha amd64 arm ~arm64 ~hppa ppc ppc64 ~sh sparc x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux" +IUSE="" +DOCS=( CHANGES README TODO VERSION ) + +src_prepare() { + SOVER="${PV:0:1}.${PV:2:1}.${PV:3:1}" # a.bc -> a.b.c + # mask out everything, which is not suggested by the author (RTFM)! + ALLOWED_FLAGS="-fstack-protector -march -mcpu -pipe -mpreferred-stack-boundary -ffast-math" + strip-flags + + SONAME="libdjbfft.so.${SOVER}" + + epatch \ + "${FILESDIR}"/${P}-gcc3.patch \ + "${FILESDIR}"/${P}-shared.patch \ + "${FILESDIR}"/${P}-headers.patch + multilib_copy_sources +} + +multilib_src_configure() { + [[ ${ABI} == x86* ]] && append-cflags -malign-double + + sed -i -e "s:\"lib\":\"$(get_libdir)\":" hier.c || die + echo "$(tc-getCC) ${CFLAGS} -fPIC" > "conf-cc" + echo "$(tc-getCC) ${LDFLAGS}" > "conf-ld" + echo "${ED}usr" > "conf-home" + einfo "conf-cc: $(<conf-cc)" +} + +multilib_src_compile() { + emake \ + LIBDJBFFT=${SONAME} \ + LIBPERMS=0755 \ + ${SONAME} + echo "the compile function was:" + cat ./compile + echo "the conf-ld function was:" + cat ./conf-ld +} + +multilib_src_test() { + local t + for t in accuracy accuracy2 speed; do + emake ${t} + einfo "Testing ${t}" + LD_LIBRARY_PATH=. ./${t} > ${t}.out || die "test ${t} failed" + done +} + +multilib_src_install() { + emake LIBDJBFFT=${SONAME} install + ./install || die "install failed" + dosym ${SONAME} /usr/$(get_libdir)/libdjbfft.so + dosym ${SONAME} /usr/$(get_libdir)/libdjbfft.so.${SOVER%%.*} +} diff --git a/sci-libs/djbfft/files/djbfft-0.76-gcc3.patch b/sci-libs/djbfft/files/djbfft-0.76-gcc3.patch new file mode 100644 index 000000000000..6f1a677d6583 --- /dev/null +++ b/sci-libs/djbfft/files/djbfft-0.76-gcc3.patch @@ -0,0 +1,37 @@ +--- djbfft-0.76/install.c.orig 2003-04-25 23:31:34.000000000 +0200 ++++ djbfft-0.76/install.c 2003-04-25 23:29:05.000000000 +0200 +@@ -1,3 +1,4 @@ ++#include <errno.h> + #include "substdio.h" + #include "strerr.h" + #include "error.h" +--- djbfft-0.76/instcheck.c.orig 2003-04-25 23:31:34.000000000 +0200 ++++ djbfft-0.76/instcheck.c 2003-04-25 23:28:11.000000000 +0200 +@@ -1,5 +1,6 @@ + #include <sys/types.h> + #include <sys/stat.h> ++#include <errno.h> + #include "strerr.h" + #include "error.h" + #include "readwrite.h" +--- djbfft-0.76/strerr_sys.c.orig 2003-04-25 23:31:34.000000000 +0200 ++++ djbfft-0.76/strerr_sys.c 2003-04-25 23:28:32.000000000 +0200 +@@ -1,3 +1,4 @@ ++#include <errno.h> + #include "error.h" + #include "strerr.h" + +--- djbfft-0.76/substdi.c.orig 2003-04-25 23:31:34.000000000 +0200 ++++ djbfft-0.76/substdi.c 2003-04-25 23:28:41.000000000 +0200 +@@ -1,3 +1,4 @@ ++#include <errno.h> + #include "substdio.h" + #include "byte.h" + #include "error.h" +--- djbfft-0.76/substdo.c.orig 2003-04-25 23:31:34.000000000 +0200 ++++ djbfft-0.76/substdo.c 2003-04-25 23:28:47.000000000 +0200 +@@ -1,3 +1,4 @@ ++#include <errno.h> + #include "substdio.h" + #include "str.h" + #include "byte.h" diff --git a/sci-libs/djbfft/files/djbfft-0.76-headers.patch b/sci-libs/djbfft/files/djbfft-0.76-headers.patch new file mode 100644 index 000000000000..39fb623f10ef --- /dev/null +++ b/sci-libs/djbfft/files/djbfft-0.76-headers.patch @@ -0,0 +1,38 @@ +--- strerr.h.orig 1999-09-30 23:25:58.000000000 +0300 ++++ strerr.h 2008-09-13 22:14:09.000000000 +0300 +@@ -1,3 +1,5 @@ ++#include <errno.h> ++ + #ifndef STRERR_H + #define STRERR_H + +--- substdio.h.orig 1999-09-30 23:25:58.000000000 +0300 ++++ substdio.h 2008-09-13 22:13:41.000000000 +0300 +@@ -1,3 +1,5 @@ ++#include <errno.h> ++ + #ifndef SUBSTDIO_H + #define SUBSTDIO_H + +--- speed.c.orig 1999-09-30 23:25:58.000000000 +0300 ++++ speed.c 2008-09-13 19:16:20.352525481 +0300 +@@ -1,4 +1,5 @@ + #include <stdio.h> ++#include <stdlib.h> + #include "fftr4.h" + #include "fftr8.h" + #include "fftc4.h" +--- accuracy2.c.orig 2008-10-10 20:51:06.000000000 +0100 ++++ accuracy2.c 2008-10-10 20:51:55.000000000 +0100 +@@ -1,3 +1,4 @@ ++#include <stdlib.h> + #include <stdio.h> + #include <math.h> + #include "fftc4.h" +--- accuracy.c.orig 2008-10-10 21:03:30.000000000 +0100 ++++ accuracy.c 2008-10-10 21:03:43.000000000 +0100 +@@ -1,3 +1,4 @@ ++#include <stdlib.h> + #include <stdio.h> + #include <math.h> + #include "fftc4.h" diff --git a/sci-libs/djbfft/files/djbfft-0.76-shared.patch b/sci-libs/djbfft/files/djbfft-0.76-shared.patch new file mode 100644 index 000000000000..53ce9af6b7a2 --- /dev/null +++ b/sci-libs/djbfft/files/djbfft-0.76-shared.patch @@ -0,0 +1,133 @@ +--- djbfft-0.76/Makefile.orig 1999-09-30 22:25:58.000000000 +0200 ++++ djbfft-0.76/Makefile 2004-01-17 17:21:37.236669242 +0100 +@@ -2,6 +2,9 @@ + + SHELL=/bin/sh + ++LIBPERMS=0644 ++LIBDJBFFT=djbfft.a ++ + default: it + + 4c0.c: \ +@@ -569,8 +572,8 @@ + ./compile 8v5.c + + accuracy: \ +-load accuracy.o djbfft.a math.lib +- ./load accuracy djbfft.a `cat math.lib` ++load accuracy.o $(LIBDJBFFT) math.lib ++ ./load accuracy $(LIBDJBFFT) `cat math.lib` + + accuracy.o: \ + compile accuracy.c fftc4.h complex4.h real4.h fftc8.h complex8.h \ +@@ -578,8 +581,8 @@ + ./compile accuracy.c + + accuracy2: \ +-load accuracy2.o djbfft.a math.lib +- ./load accuracy2 djbfft.a `cat math.lib` ++load accuracy2.o $(LIBDJBFFT) math.lib ++ ./load accuracy2 $(LIBDJBFFT) `cat math.lib` + + accuracy2.o: \ + compile accuracy2.c fftc4.h complex4.h real4.h fftc8.h complex8.h \ +@@ -649,7 +652,7 @@ + ) > compilebase + chmod 755 compilebase + +-djbfft.a: \ ++$(LIBDJBFFT): \ + makelib 8sc.o 8u5.o 8u4.o 8u3.o 8u2.o 8u1.o 8u0.o 8mc.o 8c0.o 8c1.o \ + 8c2.o 8c3.o 8c4.o 8c5.o 8d0.o 8d1.o 8d2.o 8d3.o 8d4.o 8d5.o 8v5.o \ + 8v4.o 8v3.o 8v2.o 8v1.o 8v0.o 8mr.o 8r0.o 8r1.o 8r2.o 8r3.o 8r4.o \ +@@ -657,7 +660,7 @@ + 4c1.o 4c2.o 4c3.o 4c4.o 4c5.o 4d0.o 4d1.o 4d2.o 4d3.o 4d4.o 4d5.o \ + 4v5.o 4v4.o 4v3.o 4v2.o 4v1.o 4v0.o 4mr.o 4r0.o 4r1.o 4r2.o 4r3.o \ + 4r4.o 4r5.o 4sr.o fftfreq.o +- ./makelib djbfft.a 8sc.o 8u5.o 8u4.o 8u3.o 8u2.o 8u1.o \ ++ ./makelib $(LIBDJBFFT) 8sc.o 8u5.o 8u4.o 8u3.o 8u2.o 8u1.o \ + 8u0.o 8mc.o 8c0.o 8c1.o 8c2.o 8c3.o 8c4.o 8c5.o 8d0.o 8d1.o \ + 8d2.o 8d3.o 8d4.o 8d5.o 8v5.o 8v4.o 8v3.o 8v2.o 8v1.o 8v0.o \ + 8mr.o 8r0.o 8r1.o 8r2.o 8r3.o 8r4.o 8r5.o 8sr.o 4sc.o 4u5.o \ +@@ -692,7 +695,7 @@ + + hier.o: \ + compile hier.c auto_home.h +- ./compile hier.c ++ ./compile -DLIBDJBFFT=\"$(LIBDJBFFT)\" -DLIBPERMS=$(LIBPERMS) hier.c + + install: \ + load install.o hier.o auto_home.o strerr.a substdio.a open.a error.a \ +@@ -731,7 +734,9 @@ + ( cat warn-auto.sh; \ + echo 'main="$$1"; shift'; \ + echo 'rm -f "$$main"'; \ +- echo 'ar cr "$$main" $${1+"$$@"}'; \ ++ echo 'if [ "$${main##*.}" = "a" ]'; \ ++ echo 'then'; \ ++ echo ' ar cr "$$main" $${1+"$$@"}'; \ + case "`cat systype`" in \ + sunos-5.*) ;; \ + unix_sv*) ;; \ +@@ -740,8 +745,11 @@ + dgux-*) ;; \ + hp-ux-*) ;; \ + sco*) ;; \ +- *) echo 'ranlib "$$main"' ;; \ +- esac \ ++ *) echo ' ranlib "$$main"' ;; \ ++ esac; \ ++ echo 'else'; \ ++ echo ' exec `head -1 conf-ld` -shared -Wl,-soname,libdjbfft.so.0.7.6 -o "$$main" $${1+"$$@"}'; \ ++ echo 'fi'; \ + ) > makelib + chmod 755 makelib + +@@ -758,15 +766,15 @@ + ./compile open_trunc.c + + prog: \ +-djbfft.a accuracy accuracy2 speed speed.out ++$(LIBDJBFFT) accuracy accuracy2 speed speed.out + + setup: \ + it install + ./install + + speed: \ +-load speed.o djbfft.a math.lib +- ./load speed djbfft.a `cat math.lib` ++load speed.o $(LIBDJBFFT) math.lib ++ ./load speed $(LIBDJBFFT) `cat math.lib` + + speed.o: \ + compile speed.c fftr4.h real4.h fftr8.h real8.h fftc4.h complex4.h \ +@@ -775,7 +783,7 @@ + + speed.out: \ + speed +- ./speed > speed.out ++ LD_LIBRARY_PATH=".:$$LD_LIBRARY_PATH" ./speed > speed.out + + str.a: \ + makelib byte_copy.o byte_cr.o str_len.o +--- djbfft-0.76/hier.c.orig 1999-09-30 22:25:58.000000000 +0200 ++++ djbfft-0.76/hier.c 2004-01-17 16:39:21.312774411 +0100 +@@ -2,12 +2,12 @@ + + void hier() + { +- h(auto_home,-1,-1,02755); ++ h(auto_home,-1,-1,0755); + +- d(auto_home,"lib",-1,-1,02755); +- c(auto_home,"lib","djbfft.a",-1,-1,0644); ++ d(auto_home,"lib",-1,-1,0755); ++ c(auto_home,"lib",LIBDJBFFT,-1,-1,LIBPERMS); + +- d(auto_home,"include",-1,-1,02755); ++ d(auto_home,"include",-1,-1,0755); + c(auto_home,"include","real4.h",-1,-1,0644); + c(auto_home,"include","real8.h",-1,-1,0644); + c(auto_home,"include","complex4.h",-1,-1,0644); diff --git a/sci-libs/djbfft/metadata.xml b/sci-libs/djbfft/metadata.xml new file mode 100644 index 000000000000..bd31424acb95 --- /dev/null +++ b/sci-libs/djbfft/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="project"> + <email>media-video@gentoo.org</email> + <name>Gentoo Video project</name> + </maintainer> + <longdescription lang="en"> + D.J. Bernstein Fast Fourier Transform (djbfft) is an extremely + fast library for floating-point convolution. The current version + holds most of the speed records for double-precision FFTs on + general-purpose computers. + djbfft provides power-of-2 complex FFTs, real FFTs at twice the speed, + and fast multiplication of complex arrays. Single precision and double + precision are equally supported. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/dlib/Manifest b/sci-libs/dlib/Manifest new file mode 100644 index 000000000000..04c2120c7b2d --- /dev/null +++ b/sci-libs/dlib/Manifest @@ -0,0 +1,5 @@ +DIST dlib-19.4.tar.gz 7226923 SHA256 2bed9669f1a5c436579498d0806b27a9b60c42a975a9b6e67b594b40f58b1a88 SHA512 23bf80353f9b6ce07b6a3a7df05016705645c18bcf2b3ead567935008ea12c9f6dc0722d9bbacc009bd26f78eb43c1cbecf776bfed5a3445c1f2e8e208f201e2 WHIRLPOOL 300670d12b306e224fce6d7f22d79690f543876f78d30064ab2f9782a3a79a031a6b048863a5a2b21f27eb2538b9ab42f9d00dc88f144129fa591b4b1387c367 +EBUILD dlib-19.4.ebuild 1797 SHA256 8b3d3603e881faa1c1d621a3c4d0386d067a0f3a486ce1bc85f0917fc3bcede1 SHA512 ef2172c18b446cf98c79e9b6a4dcf622ca62d05cc353d82d35385a16a334a94d5689af5117f9fee26e9e32346da57227beb83ca35b4b216135ad15b214042328 WHIRLPOOL 2dd5b83b0d721525b230eda84316138724082e772d46e26865165d7b6381c9f9630f616cf6a0ece4417a2d4e8880b400d1936aafa85b24be6a75cf6b75190157 +MISC ChangeLog 2501 SHA256 4b1b8653163e2bfa42bbb9c0c28440f33e8e3b4b9dcfed1e62878791348f5258 SHA512 8af6e77f9b18720fea7d5acdad3e8016f5ecd57be420bb7b0a037313ac040a2271daad1a86826a8d6bf284d1d7a489048d8caacc3ed8d1b8a9fb927979ae81a1 WHIRLPOOL 2b0bfd82c5265319d778f0e6df76b97e28a55f033e10942c0be8ebafe308c76f3e4edc7009caeae6cfc9da6def8b002fba36eee3052463fa03a2da79520fdc8c +MISC ChangeLog-2015 1702 SHA256 47ca3c6e624813797d3a4c616e0c05773007de7e7197360f5786420e0cdd7572 SHA512 341bf52c70e19948f7ae992d2ec6b15dca4eb0362dd0ddf07370e90506112bc688bf0845856ecc6c047d4509039131bcbed720552a2996085b30d5ad62af8f45 WHIRLPOOL e8a47afcb071c3c3b763b75bcf288469cf20873759e4da8fdeddd0d79f86f292b090d5d1b3feec23b21540c8a59aebe488e8757ed123e01bd61a2b238fb87605 +MISC metadata.xml 932 SHA256 0918e11904ec20ee27b01f963a5eac4279d321b683f03f31987502adf1155c3b SHA512 38d0f5760d78564c96dd27209468513c89ae9fd87d517dea16f87d4cd110ce25239b6baf07e58f66d871a2a794545e74f9841569bb2ff2b57782722b026a658a WHIRLPOOL a8c6dbae39283ad9c07f397093af2612cc6e442fdf5655ce0737009c38a4324f0c59d6bc2638cce6bf27a752628e77273f716b3a6a56002bb4edeff36bafa16c diff --git a/sci-libs/dlib/dlib-19.4.ebuild b/sci-libs/dlib/dlib-19.4.ebuild new file mode 100644 index 000000000000..c6116343a93b --- /dev/null +++ b/sci-libs/dlib/dlib-19.4.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils cuda + +DESCRIPTION="Numerical and networking C++ library" +HOMEPAGE="http://dlib.net/" +SRC_URI="https://github.com/davisking/dlib/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Boost-1.0" +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cblas debug cuda examples gif jpeg lapack mkl png + sqlite static-libs test X" + +# doc needs a bunch of deps not in portage + +RDEPEND=" + cblas? ( virtual/cblas:= ) + cuda? ( dev-libs/cudnn:= ) + jpeg? ( virtual/jpeg:0= ) + lapack? ( virtual/lapack:= ) + mkl? ( sci-libs/mkl:= ) + png? ( media-libs/libpng:0= ) + sqlite? ( dev-db/sqlite:3= ) + X? ( x11-libs/libX11:= ) +" +DEPEND="test? ( ${RDEPEND} )" + +src_prepare() { + use cuda && cuda_src_prepare + cmake-utils_src_prepare + sed -i -e '/LICENSE.txt/d' dlib/CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -DLIB_INSTALL_DIR="$(get_libdir)" + -DDLIB_ENABLE_ASSERTS="$(usex debug)" + -DDLIB_ENABLE_STACK_TRACE="$(usex debug)" + -DDLIB_GIF_SUPPORT="$(usex gif)" + -DDLIB_JPEG_SUPPORT="$(usex jpeg)" + -DDLIB_PNG_SUPPORT="$(usex png)" + -DDLIB_LINK_WITH_SQLITE3="$(usex sqlite)" + -DDLIB_NO_GUI_SUPPORT="$(usex X OFF ON)" + -DDLIB_USE_BLAS="$(usex cblas)" + -DDLIB_USE_CUDA="$(usex cuda)" + -DDLIB_USE_LAPACK="$(usex lapack)" + ) + cmake-utils_src_configure +} + +src_test() { + mkdir "${BUILD_DIR}"/dlib/test || die + pushd "${BUILD_DIR}"/dlib/test > /dev/null || die + cmake "${S}"/dlib/test && emake + ./dtest --runall || die + popd > /dev/null || die +} + +src_install() { + cmake-utils_src_install + dodoc docs/README.txt + use static-libs || rm -f "${ED}"/usr/$(get_libdir)/*.a + if use examples; then + dodoc -r examples + docompress -x /usr/share/doc/${PF} + fi +} diff --git a/sci-libs/dlib/metadata.xml b/sci-libs/dlib/metadata.xml new file mode 100644 index 000000000000..422f29c52e5a --- /dev/null +++ b/sci-libs/dlib/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + dlib is a C++ library for developing portable applications dealing with + networking, threads, graphical interfaces, data structures, linear + algebra, machine learning, XML and text parsing, numerical + optimization, Bayesian nets, and numerous other tasks. + </longdescription> + <use> + <flag name="cblas">Build with CBLAS <pkg>virtual/cblas</pkg></flag> + <flag name="cuda">Enable support for CUDA for Deep Neural Networks (cuDNN) on GPU (experimental)</flag> + <flag name="mkl">Enable support for Intel FFT <pkg>sci-libs/mkl</pkg></flag> + </use> + <upstream> + <remote-id type="github">davisking/dlib</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/dmlc-core/Manifest b/sci-libs/dmlc-core/Manifest new file mode 100644 index 000000000000..73062bb28bc0 --- /dev/null +++ b/sci-libs/dmlc-core/Manifest @@ -0,0 +1,4 @@ +AUX dmlc-core-install-dirs.patch 1206 SHA256 aaf481d07de2ff8cfdd491acf671f2d1230fcfbc4d8de9e61653f0660412fca2 SHA512 ceee3e6f6f02e4a96167f12ffb50cbbc3bfbf07d025acb002139072ac73cf02adcd9c8f7a7b371055a68a61a104bf16ad95d7a3769edc3ad2dc63be36ff45ff5 WHIRLPOOL a859b3d85dc022450716d09af9171564961f011062ebb9c8ec15916ab131c9baa361e0a275449cbda33340eefb9a12ed2eff0858be4dc48f126357ea45568532 +DIST dmlc-core-0_p20170719.tar.gz 160242 SHA256 7da1167ae29ccfbc0779ada2a00baa6581462dd06d0e6ac2f9eac0173b28dc60 SHA512 2e2d79800839652772f07deb5ea3aa470cc5a18d2d0e480b8f4a1598aca72443546a438f3309708268cc49cf2d65684c3366cfc6c33c085baf1b804b4c04f02e WHIRLPOOL 77bb23c9f3b3ba5cd1041026e2265caba0daea6235da13de4745ff7d3c2c3f71a616023f84629cb5b62f8a73d44099198ca718af556e81d3640d9b5387637e6b +EBUILD dmlc-core-0_p20170719.ebuild 2250 SHA256 26861e3d3e3aebc1749d3fde44b1258bcc84c70bf0c6ce5185609022dc2c1740 SHA512 2e2e067d276fe36d505f89d131ea8b0d935bbb6290c3bb9c93d43d755e985dcc28e8d15a7da6f4e18b8371def749b80d4e06d65a3c1420999d7f7b91e13e79a7 WHIRLPOOL 0f4a5be3a236c501a309bc343fe61bba06f4a97195779df010b498bc412ce02217d5db5bbc1b2f1e773c9d0e00670c425394c5e5d7d2299b687baf0b9bdf300a +MISC metadata.xml 704 SHA256 55195aff5bbf678f072bfd5317c85a9a0259dcf1d13db4840fbfe103e3d5dde1 SHA512 daa2fd03eb40932f9b28fe3e624a44dd16862952d473c6beba4a60dc7ddae17935858191909dddb471830bfb23de1a98887fd2fd401f353e77d3cd8acd690896 WHIRLPOOL 86cc1504ec5e8edb0280168c214ee9c4eea5ae7627edd3315b730bb263f0fe9f89bcf98259e23885c404719cf1d8f0dc3be797cd9f8dee05b00ba096fc470fdb diff --git a/sci-libs/dmlc-core/dmlc-core-0_p20170719.ebuild b/sci-libs/dmlc-core/dmlc-core-0_p20170719.ebuild new file mode 100644 index 000000000000..adf78c827246 --- /dev/null +++ b/sci-libs/dmlc-core/dmlc-core-0_p20170719.ebuild @@ -0,0 +1,97 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs cmake-utils + +DESCRIPTION="Common bricks library for building distributed machine learning." +HOMEPAGE="https://github.com/dmlc/dmlc-core" + +if [[ ${PV} == *9999* ]] ; then + EGIT_REPO_URI="https://github.com/dmlc/${PN}.git" + inherit git-r3 + KEYWORDS="" +else + EGIT_COMMIT="54db57d5d1b2a7b93319053011802888b827a539" + inherit vcs-snapshot + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + SRC_URI="${HOMEPAGE}/archive/${EGIT_COMMIT}.tar.gz -> ${P}.tar.gz" +fi + +LICENSE="Apache-2.0" +SLOT="0" + +# hdfs needs big java hdfs not yet in portage +# azure not yet in portage +IUSE="doc openmp s3 test" + +RDEPEND="net-misc/curl[ssl]" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + test? ( dev-cpp/gtest ) +" + +PATCHES=( "${FILESDIR}"/${PN}-install-dirs.patch ) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +src_prepare() { + cmake-utils_src_prepare + # respect user flags (SSE2 does nothing more than adding -msse2) + # also doc install everything so remove + sed -e '/-O3/d' \ + -e '/check_cxx.*SSE2/d' \ + -i CMakeLists.txt || die + # all these hacks below to allow testing + sed -e 's|-O3||' -e 's|-lm|-lm -L$(LD_LIBRARY_PATH) -ldmlc|g' -i Makefile || die + sed -e "s|libdmlc.a||g" \ + -i test/dmlc_test.mk test/unittest/dmlc_unittest.mk || die + cat <<-EOF > config.mk + USE_SSE=0 + WITH_FPIC=1 + USE_OPENMP=$(use openmp && echo 1 || echo 0) + USE_S3=$(use s3 && echo 1 || echo 0) + BUILD_TEST=$(use test && echo 1 || echo 0) + DMLC_CFLAGS=${CXXFLAGS} + DMLC_LDFLAGS=${LDFLAGS} + EOF +} + +src_configure() { + local mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DUSE_S3="$(usex s3)" + -DUSE_OPENMP="$(usex openmp)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + if use doc; then + doxygen doc/Doxyfile || die + fi +} + +src_test() { + tc-export CXX + export LD_LIBRARY_PATH="${BUILD_DIR}" + emake test + test/unittest/dmlc_unittest || die +} + +src_install() { + cmake-utils_src_install + if use doc; then + insinto /usr/share/doc/${PF} + doins -r doc/doxygen/html + docompress -x /usr/share/doc/${PF}/html + fi +} diff --git a/sci-libs/dmlc-core/files/dmlc-core-install-dirs.patch b/sci-libs/dmlc-core/files/dmlc-core-install-dirs.patch new file mode 100644 index 000000000000..06f87f701754 --- /dev/null +++ b/sci-libs/dmlc-core/files/dmlc-core-install-dirs.patch @@ -0,0 +1,38 @@ +From 536ba11dfdaa7feacc7fe5726a3a50e4d663da13 Mon Sep 17 00:00:00 2001 +From: Maarten de Vries <maarten@de-vri.es> +Date: Fri, 26 May 2017 15:29:29 +0200 +Subject: [PATCH] Use GNUInstallDirs for standard conforming install target. + +--- + CMakeLists.txt | 18 +++++++----------- + 1 file changed, 7 insertions(+), 11 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0b3b3ec..316e2f5 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -121,18 +121,13 @@ endif() + add_library(dmlc ${SOURCE}) + target_link_libraries(dmlc ${dmlccore_LINKER_LIBS}) + +-# ---[ Install Includes +-if(INSTALL_INCLUDE_DIR) +- add_custom_command(TARGET dmlc POST_BUILD +- COMMAND ${CMAKE_COMMAND} -E copy_directory +- ${PROJECT_SOURCE_DIR}/include ${INSTALL_INCLUDE_DIR}/ +- ) +-endif() +- + # ---[ Install the archive static lib and header files +-install(TARGETS dmlc ARCHIVE DESTINATION lib) +-install(DIRECTORY include DESTINATION .) +-install(DIRECTORY doc DESTINATION .) ++include(GNUInstallDirs) ++install(TARGETS dmlc ++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ++) ++install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}) + + # ---[ Linter target + if(MSVC) diff --git a/sci-libs/dmlc-core/metadata.xml b/sci-libs/dmlc-core/metadata.xml new file mode 100644 index 000000000000..7fb45e55273f --- /dev/null +++ b/sci-libs/dmlc-core/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-mathematics@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Distributed Machine Learning Common Codebase Core is the backbone + library to support all DMLC projects, offers the bricks to build + efficient and scalable distributed machine learning libraries. + </longdescription> + <upstream> + <remote-id type="github">dmlc/dmlc-core</remote-id> + </upstream> + <use> + <flag name="s3">Support for the Amazon Simple Storage Service</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/dsdp/Manifest b/sci-libs/dsdp/Manifest new file mode 100644 index 000000000000..af11f7a01bee --- /dev/null +++ b/sci-libs/dsdp/Manifest @@ -0,0 +1,8 @@ +AUX dsdp-5.8-gold.patch 342 SHA256 5547f8feba4b6ceccdd4a3ff596c7a7a08e75d18859e8efdef83e08546e62285 SHA512 e0910628a1676f7a22eff29487a5f732c28a8d7a9f44f55d5b42e9abd8e65e798e577592c933133265a61c1be2df05ef1c019b86ee93aaa34199a7d0d32c7b03 WHIRLPOOL 09abb51a2445e94d168b4581c143368139d11dff55f658fa7bec8b47e8ec471679eebd6a56da5de1ea88fd282150c4b6088f939c9261f8ff5817b58a7dc9eabb +AUX dsdp-5.8-malloc.patch 212 SHA256 2d446f7c5e3f6e2f77a5487dd64a67fcdc9472888e06cf1aba18a4082814d040 SHA512 a4c324beadb7298c9c8709115c83975d10b359b792042047439631f478fc99648b9348715645cd34d893fe9b6b49b6ba8e628771cde0e007eb0b1f474dd1fd7f WHIRLPOOL a03ae6685df10dbc03f11796664cec3795cd493c6877e16001079d5d70e2f46caf234ae6aac2b317514420f60e39522ffb4bcf9b312ab9ea470126ffdda4b06c +AUX dsdp-5.8-readsdpa.patch 495 SHA256 e0cdcbe1e41e3ff05d50e668fc68ea5bd74e01ca9353f553fcbfe68c39df32f2 SHA512 43b329526f3b7d4761f7dfa44d62f94a843491bf9998f2f839edc880cdd8d04d1c8c7187213eda887025a9f3cdbff19afba6720cd2d70580b0e2dcb9512f8f90 WHIRLPOOL 6efa21b49970d2b6afe8526e6490c6af16122054c0786051cc825e63e6bfb31ff5c4fcd84e2f3886fc87542822dfc59b29cd71e03d2c4c2a4ed04967078b0ac1 +DIST DSDP5.8.tar.gz 2608518 SHA256 26aa624525a636de272c0b329e2dfd01a0d5b7827f1c1c76f393d71e37dead70 SHA512 0a32a34e33dcac151e95ed0f8cee62603bbe2b4ba1e448bba35324fe576376cb33c15908cde61ae5a7c0dcdea945f1ec544f19b3dd36524158573260182e080e WHIRLPOOL 63f5ce91d1c624b3c8f4d6ba61f8f386e739c0a5ad97515b4d36bb6026751ff4ca83b6a466deb5983e15eab3c84879bc3d87d7f2613e8070ab989e2607da9ddf +EBUILD dsdp-5.8-r3.ebuild 2303 SHA256 e70a3164404e457f33e4d55f6a020d962793501f8a88a9993180415e25fd8f1d SHA512 1775122978bf6c17390a801656f30863d3e5bd939660aaece391475f67eacea897a0ef8b2fb61e1a8a718adbda9d1c9ac6084d2f0caeaff049f1414fb115b625 WHIRLPOOL da458f856ae1fdd39cf5779e4d16f0d3a3b5e1bdde11170266f4abdcd8a6484f52ac4254e5cef2e0de294f1a1a2cb001da9289dbb94f721fec79371cb61e7dd0 +MISC ChangeLog 3105 SHA256 87b90d0170b0398055889de6aefa26478f9aa3d378ca8ded7d2b190a4efabdb2 SHA512 49930c5573b0c348b0a62d1726d8ef4fb61c9ab3dcb4204211b4e947191fba7f23aa1285f87430e5b38b9160050546d952d6b846f468dd13a9404c83042735c5 WHIRLPOOL 40355ea13dad45195995c7ff767698fa7b6f701b53fad695b84e0daf23525359bd4fe8ef21ec22fd58422bd20b4a99cef5a53ee5a18ebeb340161ca1d8acb20e +MISC ChangeLog-2015 1539 SHA256 420e8c0806187a9f1befdfbdbb76d58e33622d4330d06bd03d1291966207ae20 SHA512 e3979c1499075ca903b977ea420848f49bf1c8c31006b04260b28917308394751c6bef68b1dc54cd870b77b756b0e1cb2a9c0991d796c3de9c061e76880a81c5 WHIRLPOOL 25ed97b99dfa6f6fdf1297bd871dfe1f9da53f1a00182538cdd27a264d25172896b713a7ecc8fabbeb8971a552a78f7452c4c722b1994565e6845c5c06683ba8 +MISC metadata.xml 1244 SHA256 1dc56f6f03a14663e9ebe64dbfb135617b2ba2ee65944906baf3bc86969bc551 SHA512 7dfa5358092109c0441dc9453f9769e6e63ec2525817a7280fa30c68007a3e31f524ec8600f29b21ea28e585c2776d9264918f7e66243d1a8509f42f5339c3da WHIRLPOOL 697eff3e3fd67b1af37042bb839ffe1a5fbe82ad6b0eea08970fa090b16e0dbaa2c876a0e31f06486e0a4373c20218b69fa64f401b30b6b2251daa5b3f2cba31 diff --git a/sci-libs/dsdp/dsdp-5.8-r3.ebuild b/sci-libs/dsdp/dsdp-5.8-r3.ebuild new file mode 100644 index 000000000000..b5304b9065c0 --- /dev/null +++ b/sci-libs/dsdp/dsdp-5.8-r3.ebuild @@ -0,0 +1,79 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit multilib toolchain-funcs versionator + +MY_P="${PN^^}${PV}" + +DESCRIPTION="Software for interior-point for semidefinite programming" +HOMEPAGE="http://www.mcs.anl.gov/hs/software/DSDP/" +SRC_URI="http://www.mcs.anl.gov/hs/software/DSDP/${MY_P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +IUSE="doc examples" + +RDEPEND="virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}"/${P}-readsdpa.patch + "${FILESDIR}"/${P}-malloc.patch + "${FILESDIR}"/${P}-gold.patch +) + +make_shared_lib() { + local soname=$(basename "${1%.a}")$(get_libname $(get_major_version)) + einfo "Making ${soname}" + ${2:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname="${soname}" \ + $([[ ${CHOST} == *-darwin* ]] && echo "-Wl,-install_name -Wl,${EPREFIX}/usr/$(get_libdir)/${soname}") \ + -Wl,--whole-archive "${1}" -Wl,--no-whole-archive \ + -o $(dirname "${1}")/"${soname}" \ + -lm $($(tc-getPKG_CONFIG) --libs blas lapack) || return 1 +} + +src_prepare() { + default + # to do proper parallel compilation + while IFS="" read -d $'\0' -r file; do + sed -i -e 's:make :$(MAKE) :g' "${file}" || die + done < <(find . -name Makefile -print0) + sed -i -e 's:make clean:$(MAKE) clean:g' make.include || die + sed -i \ + -e "s|#\(DSDPROOT[[:space:]]*=\).*|\1${S}|" \ + -e "s|\(CC[[:space:]]*=\).*|\1$(tc-getCC)|" \ + -e "s|\(OPTFLAGS[[:space:]]*=\).*|\1${CFLAGS}|" \ + -e "s|\(CLINKER[[:space:]]*=\).*|\1 \${CC} ${LDFLAGS}|" \ + -e "s|\(LAPACKBLAS[[:space:]]*=\).*|\1 $($(tc-getPKG_CONFIG) --libs blas lapack)|" \ + -e "s|\(^ARCH[[:space:]]*=\).*|\1$(tc-getAR) cr|" \ + -e "s|\(^RANLIB[[:space:]]*=\).*|\1$(tc-getRANLIB)|" \ + make.include || die +} + +src_compile() { + emake OPTFLAGS="${CFLAGS} -fPIC" dsdplibrary + make_shared_lib lib/lib${PN}.a || die "doing shared lib failed" +} + +src_test() { + emake -j1 example test +} + +src_install() { + dolib.so lib/lib${PN}$(get_libname $(get_major_version)) + dosym lib${PN}$(get_libname $(get_major_version)) \ + /usr/$(get_libdir)/lib${PN}$(get_libname) + + doheader include/*.h src/sdp/*.h + + use doc && DOCS+=( docs/*.pdf ) + use examples && DOCS+=( examples/. ) + einstalldocs +} diff --git a/sci-libs/dsdp/files/dsdp-5.8-gold.patch b/sci-libs/dsdp/files/dsdp-5.8-gold.patch new file mode 100644 index 000000000000..ae677820ffc3 --- /dev/null +++ b/sci-libs/dsdp/files/dsdp-5.8-gold.patch @@ -0,0 +1,13 @@ +diff --git a/examples/Makefile b/examples/Makefile +index 8d7d433..11b9c8c 100644 +--- a/examples/Makefile ++++ b/examples/Makefile +@@ -4,7 +4,7 @@ default: + + include ../make.include + +-EXAMPLE_LIBS = ${DSDPLIB} ${LAPACKBLAS} ++EXAMPLE_LIBS = ${DSDPLIB} ${LAPACKBLAS} -lm + + dsdp: exinfo clean + ${MEX} -I${DSDPROOT}/include dsdp.c ${DSDPLIB}; diff --git a/sci-libs/dsdp/files/dsdp-5.8-malloc.patch b/sci-libs/dsdp/files/dsdp-5.8-malloc.patch new file mode 100644 index 000000000000..487c2a67d270 --- /dev/null +++ b/sci-libs/dsdp/files/dsdp-5.8-malloc.patch @@ -0,0 +1,10 @@ +--- a/src/sys/dsdploginfo.c ++++ b/src/sys/dsdploginfo.c +@@ -6,7 +6,6 @@ + #include <stdarg.h> + #include <sys/types.h> + #include <stdlib.h> +-#include <malloc.h> + #include "dsdpsys.h" + #include "dsdpbasictypes.h" + diff --git a/sci-libs/dsdp/files/dsdp-5.8-readsdpa.patch b/sci-libs/dsdp/files/dsdp-5.8-readsdpa.patch new file mode 100644 index 000000000000..799db6afd5ae --- /dev/null +++ b/sci-libs/dsdp/files/dsdp-5.8-readsdpa.patch @@ -0,0 +1,11 @@ +--- a/examples/readsdpa.c ++++ b/examples/readsdpa.c +@@ -87,7 +87,7 @@ + double ddobj,ppobj,scl,dpot; + char problemname[100],thisline[100], filename[300],savefile[100]; + char directory[100]="/home/benson/sdpexamples/sdplib/"; +- char outputfile[50]="",suffix[20]=".dat-s", tablename[20]="results-dsdp-5.8"; ++ char outputfile[50]="",suffix[20]=".dat-s", tablename[100]="results-dsdp-5.8"; + char success='s',sformat; + FILE *fp1=0,*fp2=0,*fout; + DSDPData dddd; diff --git a/sci-libs/dsdp/metadata.xml b/sci-libs/dsdp/metadata.xml new file mode 100644 index 000000000000..c7207ec72d72 --- /dev/null +++ b/sci-libs/dsdp/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The DSDP software is a free open source implementation of an + interior-point method for semidefinite programming. It provides + primal and dual solutions, exploits low-rank structure and sparsity + in the data, and has relatively low memory requirements for an + interior-point method. It allows feasible and infeasible starting + points and provides approximate certificates of infeasibility when + no feasible solution exists. The dual-scaling algorithm implemented + in this package has a convergence proof and worst-case polynomial + complexity under mild assumptions on the data. Furthermore, the + solver offers scalable parallel performance for large problems and a + well documented interface. Some of the most popular applications of + semidefinite programming and linear matrix inequalities (LMI) are + model control, truss topology design, and semidefinite relaxations + of combinatorial and global optimization problems. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/exodusii/Manifest b/sci-libs/exodusii/Manifest new file mode 100644 index 000000000000..609b7f4373e1 --- /dev/null +++ b/sci-libs/exodusii/Manifest @@ -0,0 +1,9 @@ +AUX exodusii-5.26-multilib.patch 3148 SHA256 69e10995b6a34e90d77bcb8351bec236c1c819665a5a3616c65b585b6424f0ea SHA512 f37a2463b7c8a243a6fdd690e8a2b18601188ba144862842833e81120226c6969f4ed815eef89a3b4f47b2fa55dbe3d0799441783f4acc478eaeed4c0217644b WHIRLPOOL 20b3e03195575d700c3a3a842ce2ba0d76f3bc4bfbbcd880e59961116027828d1aa9bf093a40683fa27e7da79ea31281013dc3d0c05949ec754efb4c67f33538 +AUX exodusii-6.09-multilib.patch 3125 SHA256 8972accb022ca6f1991e903db8f700391cb243a133cb9a5c3ac0a412ccc26efe SHA512 7575ea71ed4d21135c6ddeb6932298951ac4d1cdef3b0129104f12c475308bd9224fef4f85233e9ffb644dabba0dec2bdc1819f7d6c0f6b4adb73bc98636f41c WHIRLPOOL 4e4a2a70c30409db2422ba38b5e058e700bcacec61f6409a2362e7ee52cceb48458b6801476db23795320349a6d94244ed3374c0568b6f83324a03816b7be3b3 +DIST exodus-6.02.tar.gz 4735364 SHA256 a3d7ae6ad433bb9655748c0e3e7a95e66c46d9df1e4c3d8d7e125af3fec89193 SHA512 d086464f0af2edd06d6e6a49be28d3bdfe00c0e9a9a09abad7822a49c7a7fbb75b61324ea54d2163c73b45ee90222c22754c804ee6868cdb0f9e4b780d6d5ad0 WHIRLPOOL 53382f9ec4b11197c4b2424a222b4178de73ac233e2e23110070a7a72f150ec8ed2ad024b4ce1bdfed3ab6b3c9dfb040d243c394af2a60e7330a681f8dac58a2 +DIST exodus-6.09.tar.gz 4757028 SHA256 e14db4c1e2ca893c4602055036b827b8332746439f0869489fdc677058faebe8 SHA512 a48c02952b0edfae416e9b3f77471558dd2d60177471eca3de32890d11afabe3cfb64396de83e728327d43bbea83969ebcdd8ea516a3b9a6ed7353d4cc940516 WHIRLPOOL 97426e487c8f6ae31da4be36f3712ade99eb7e31feb67d3989153dadc394b427b8e38976f06e99c153fae3d04b05357b48b0b537ff0c04fb8199b9aaeb27bcc4 +EBUILD exodusii-6.02.ebuild 1156 SHA256 680a4ce737655ef7ea2b1c2ce121fe8dce3b76697e07ede6afadfb7956889e5f SHA512 916371ad1b1d62e046b4f52f9b88b32292fc8cedc456aa3d4a469757bb7eb1ddf7ff1d610ddd466c4745b3cc6b495fb436fe634aab6a025cfffbcadd7f708cd8 WHIRLPOOL 81bea9fcd13a8ad37cfa6dcb9d3921f23914d76643315669975f6184b02a377923442512e68c06082b99db54884c2eb58ac9472c22ce5467b06e1f643f7a1505 +EBUILD exodusii-6.09.ebuild 1200 SHA256 c9b25165cab5449badf7e064b1802fdee8d8c2f40100bf9c2670068bb2d1903d SHA512 891bf37f0810fbde2cfac9e8141971c3feccc43bd42966ed63af01dd09fbd350c24a2abf48550743be291f91f9aa701e0ff1be9ae0d95eb4c09351dc4d1b8788 WHIRLPOOL d1e4156ffb4ba4edc5c8e58985b63dfae3c61e154fc53525af8cf6690a3841f1be48d0c0d6832392c6f0bc18e28f2fa2adc5b4251dfdc764942f51594a143e83 +MISC ChangeLog 3786 SHA256 e47f366d0b32d5f0e51ac8bed0b1a857b60fd68a0a8932f6657c5982b865d9f9 SHA512 5674c15eb8c9436c48add05356d69d9c56ce44846cf6db7f4a5c1156d0a7a0edcca86bdecf9c58de7f897920fbbca74fb370339bd1f1b15ca1b9b969130d3789 WHIRLPOOL 9903c64e2946bef3fd206f2434a9937c7aa665a74c78638a96975afab915aead68679e51ba34d2eb0cfc1856866ad57c2c55831556d7a3b208ec934a1693ac68 +MISC ChangeLog-2015 2048 SHA256 ba1d2e5d8f289ad257e442d5ab8c5fd87c12c619678b3f32cd1e71c8f9bf42d9 SHA512 8ebb0d6b2d22938d5c96e366fbb8901df9281bde96a1e5a39cab7e371abae22adff901c57affd1c0d1c2ae55798b86b26d59ceaf631739c5857824b825f09110 WHIRLPOOL de10fde4501844160c52b1d238a09985ae4b8d5ab41592b59867e553300e250f4035149cd287898977ceb8469b01ca55a666e4a54ded672a3f1cd651f4f241d1 +MISC metadata.xml 603 SHA256 43a6da724808bbbb13b03d3734a5ac595fbdf9bed704dd76650e81a36b685b1c SHA512 9d703efe9fbf4d49438d83bcdca60db2cd9a40f0b853fcf8cd796d9f96d304c84825c9e2cb26ba98f1893e3e85ddd1af8a5e15c4c4e179d6de25b1df98be3a55 WHIRLPOOL 3902716efeec245c337f1ba8e35992db4d6c19175c51cc60467098de7d45d5a4b67a0995645d08ef4f1d44676275f98ffa7e87364fab5d7efacbabffa7567013 diff --git a/sci-libs/exodusii/exodusii-6.02.ebuild b/sci-libs/exodusii/exodusii-6.02.ebuild new file mode 100644 index 000000000000..dcaf91498fb5 --- /dev/null +++ b/sci-libs/exodusii/exodusii-6.02.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED="test" + +inherit cmake-utils fortran-2 multilib + +MY_PN="${PN%ii}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Model developed to store and retrieve transient data for finite element analyses" +HOMEPAGE="https://sourceforge.net/projects/exodusii/" +SRC_URI="mirror://sourceforge/project/${PN}/${MY_P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +IUSE="static-libs test" + +RDEPEND="sci-libs/netcdf[hdf5]" +DEPEND="${RDEPEND} + test? ( app-shells/tcsh ) +" + +S="${WORKDIR}"/${MY_P}/${MY_PN} + +PATCHES=( "${FILESDIR}"/${PN}-5.26-multilib.patch ) + +src_prepare() { + use test || \ + sed \ + -e 's:Fortran::g' \ + -i CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DLIB_INSTALL_DIR=$(get_libdir) + -DNETCDF_DIR="${EPREFIX}/usr/" + $(cmake-utils_use_build !static-libs SHARED) + $(cmake-utils_use_build test TESTING) + ) + cmake-utils_src_configure +} + +src_test() { + cd "${BUILD_DIR}"/cbind/test || die + ctest || die + cd "${BUILD_DIR}"/forbind/test || die + emake f_check +} diff --git a/sci-libs/exodusii/exodusii-6.09.ebuild b/sci-libs/exodusii/exodusii-6.09.ebuild new file mode 100644 index 000000000000..a91a3e96e992 --- /dev/null +++ b/sci-libs/exodusii/exodusii-6.09.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED="test" + +inherit cmake-utils fortran-2 multilib + +MY_PN="${PN%ii}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Model developed to store and retrieve transient data for finite element analyses" +HOMEPAGE="https://sourceforge.net/projects/exodusii/" +SRC_URI="mirror://sourceforge/project/${PN}/${MY_P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs test" + +RDEPEND="sci-libs/netcdf[hdf5]" +DEPEND="${RDEPEND} + test? ( app-shells/tcsh ) +" + +S="${WORKDIR}"/${MY_P}/${MY_PN} + +PATCHES=( "${FILESDIR}"/${P}-multilib.patch ) + +src_prepare() { + use test || \ + sed \ + -e 's:Fortran::g' \ + -i CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DLIB_INSTALL_DIR=$(get_libdir) + -DNETCDF_DIR="${EPREFIX}/usr/" + -DPYTHON_INSTALL="${EPREFIX}/usr/share/${PN}" + $(cmake-utils_use_build !static-libs SHARED) + $(cmake-utils_use_build test TESTING) + ) + cmake-utils_src_configure +} + +src_test() { + cd "${BUILD_DIR}"/cbind/test || die + ctest || die + cd "${BUILD_DIR}"/forbind/test || die + emake f_check +} diff --git a/sci-libs/exodusii/files/exodusii-5.26-multilib.patch b/sci-libs/exodusii/files/exodusii-5.26-multilib.patch new file mode 100644 index 000000000000..1d1c1fca6c2b --- /dev/null +++ b/sci-libs/exodusii/files/exodusii-5.26-multilib.patch @@ -0,0 +1,95 @@ + CMakeLists.txt | 6 +++--- + cbind/CMakeLists.txt | 6 +++--- + forbind/CMakeLists.txt | 12 ++++++------ + 3 files changed, 12 insertions(+), 12 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index ca372f5..a071d99 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -27,7 +27,7 @@ find_path( NETCDF_INCLUDE_DIR netcdf.h + find_library( NETCDF_LIBRARY + NAMES netcdf + PATHS "$ENV{ACCESS}/lib" +- "$ENV{NETCDF_DIR}/lib" ++ "$ENV{NETCDF_DIR}/lib${LIB_SUFFIX}" + "$ENV{NETCDF_DIR}/libsrc/.libs" + ) + +@@ -41,14 +41,14 @@ find_program (NETCDF_NCDUMP ncdump + find_library( HDF5_LIBRARY hdf5 + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/lib${LIB_SUFFIX} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) + find_library( HDF5HL_LIBRARY hdf5_hl + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/lib${LIB_SUFFIX} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) +diff --git a/cbind/CMakeLists.txt b/cbind/CMakeLists.txt +index 083891f..66fd17b 100644 +--- a/cbind/CMakeLists.txt ++++ b/cbind/CMakeLists.txt +@@ -293,9 +293,9 @@ ENDIF(EXODUS_LIBRARY_PROPERTIES) + + IF(NOT EXODUS_INSTALL_NO_LIBRARIES) + INSTALL(TARGETS exoIIv2c +- RUNTIME DESTINATION lib COMPONENT Runtime +- LIBRARY DESTINATION lib COMPONENT Runtime +- ARCHIVE DESTINATION lib COMPONENT Development) ++ RUNTIME DESTINATION lib${LIB_SUFFIX} COMPONENT Runtime ++ LIBRARY DESTINATION lib${LIB_SUFFIX} COMPONENT Runtime ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} COMPONENT Development) + INSTALL(FILES ${cbind_HEADERS} DESTINATION include COMPONENT Development) + ENDIF(NOT EXODUS_INSTALL_NO_LIBRARIES) + +diff --git a/forbind/CMakeLists.txt b/forbind/CMakeLists.txt +index 5ee026c..66ba1b3 100644 +--- a/forbind/CMakeLists.txt ++++ b/forbind/CMakeLists.txt +@@ -14,7 +14,7 @@ find_path( NETCDF_INCLUDE_DIR netcdf.h + find_library( NETCDF_LIBRARY + NAMES netcdf + PATHS "$ENV{ACCESS}/lib" +- "$ENV{NETCDF_DIR}/lib" ++ "$ENV{NETCDF_DIR}/lib${LIB_SUFFIX}" + "$ENV{NETCDF_DIR}/libsrc/.libs" + ) + +@@ -28,14 +28,14 @@ find_program (NETCDF_NCDUMP ncdump + find_library( HDF5_LIBRARY hdf5 + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/lib${LIB_SUFFIX} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) + find_library( HDF5HL_LIBRARY hdf5_hl + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/lib${LIB_SUFFIX} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) +@@ -61,9 +61,9 @@ ENDIF(EXODUS_LIBRARY_PROPERTIES) + + IF(NOT EXODUS_INSTALL_NO_LIBRARIES) + INSTALL(TARGETS exoIIv2for +- RUNTIME DESTINATION lib COMPONENT Runtime +- LIBRARY DESTINATION lib COMPONENT Runtime +- ARCHIVE DESTINATION lib COMPONENT Development) ++ RUNTIME DESTINATION lib${LIB_SUFFIX} COMPONENT Runtime ++ LIBRARY DESTINATION lib${LIB_SUFFIX} COMPONENT Runtime ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} COMPONENT Development) + INSTALL(FILES ${forbind_HEADERS} DESTINATION include COMPONENT Development) + ENDIF(NOT EXODUS_INSTALL_NO_LIBRARIES) + diff --git a/sci-libs/exodusii/files/exodusii-6.09-multilib.patch b/sci-libs/exodusii/files/exodusii-6.09-multilib.patch new file mode 100644 index 000000000000..3b1b5e2ace7f --- /dev/null +++ b/sci-libs/exodusii/files/exodusii-6.09-multilib.patch @@ -0,0 +1,87 @@ +diff -Naur exodus-6.09.orig/exodus/cbind/CMakeLists.txt exodus-6.09/exodus/cbind/CMakeLists.txt +--- exodus-6.09.orig/exodus/cbind/CMakeLists.txt 2016-05-10 13:20:06.408385120 -0600 ++++ exodus-6.09/exodus/cbind/CMakeLists.txt 2016-05-10 13:22:35.378385120 -0600 +@@ -293,9 +293,9 @@ + + IF(NOT EXODUS_INSTALL_NO_LIBRARIES) + INSTALL(TARGETS exodus +- RUNTIME DESTINATION lib COMPONENT Runtime +- LIBRARY DESTINATION lib COMPONENT Runtime +- ARCHIVE DESTINATION lib COMPONENT Development) ++ RUNTIME DESTINATION lib${LIB_SUFFIX} COMPONENT Runtime ++ LIBRARY DESTINATION lib${LIB_SUFFIX} COMPONENT Runtime ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} COMPONENT Development) + INSTALL(FILES ${cbind_HEADERS} DESTINATION include COMPONENT Development) + ENDIF(NOT EXODUS_INSTALL_NO_LIBRARIES) + +diff -Naur exodus-6.09.orig/exodus/CMakeLists.txt exodus-6.09/exodus/CMakeLists.txt +--- exodus-6.09.orig/exodus/CMakeLists.txt 2016-05-10 13:20:06.418385120 -0600 ++++ exodus-6.09/exodus/CMakeLists.txt 2016-05-10 13:21:25.928385120 -0600 +@@ -27,7 +27,7 @@ + find_library( NETCDF_LIBRARY + NAMES netcdf + PATHS "$ENV{ACCESS}/lib" +- "$ENV{NETCDF_DIR}/lib" ++ "$ENV{NETCDF_DIR}/lib${LIB_SUFFIX}" + "$ENV{NETCDF_DIR}/libsrc/.libs" + ) + +@@ -41,14 +41,14 @@ + find_library( HDF5_LIBRARY hdf5 + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/lib${LIB_SUFFIX} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) + find_library( HDF5HL_LIBRARY hdf5_hl + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/lib${LIB_SUFFIX} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) +diff -Naur exodus-6.09.orig/exodus/forbind/CMakeLists.txt exodus-6.09/exodus/forbind/CMakeLists.txt +--- exodus-6.09.orig/exodus/forbind/CMakeLists.txt 2016-05-10 13:20:06.418385120 -0600 ++++ exodus-6.09/exodus/forbind/CMakeLists.txt 2016-05-10 13:21:25.928385120 -0600 +@@ -14,7 +14,7 @@ + find_library( NETCDF_LIBRARY + NAMES netcdf + PATHS "$ENV{ACCESS}/lib" +- "$ENV{NETCDF_DIR}/lib" ++ "$ENV{NETCDF_DIR}/lib${LIB_SUFFIX}" + "$ENV{NETCDF_DIR}/libsrc/.libs" + ) + +@@ -28,14 +28,14 @@ + find_library( HDF5_LIBRARY hdf5 + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/lib${LIB_SUFFIX} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) + find_library( HDF5HL_LIBRARY hdf5_hl + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/lib${LIB_SUFFIX} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) +@@ -61,9 +61,9 @@ + + IF(NOT EXODUS_INSTALL_NO_LIBRARIES) + INSTALL(TARGETS exoIIv2for +- RUNTIME DESTINATION lib COMPONENT Runtime +- LIBRARY DESTINATION lib COMPONENT Runtime +- ARCHIVE DESTINATION lib COMPONENT Development) ++ RUNTIME DESTINATION lib${LIB_SUFFIX} COMPONENT Runtime ++ LIBRARY DESTINATION lib${LIB_SUFFIX} COMPONENT Runtime ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} COMPONENT Development) + INSTALL(FILES ${forbind_HEADERS} DESTINATION include COMPONENT Development) + ENDIF(NOT EXODUS_INSTALL_NO_LIBRARIES) + diff --git a/sci-libs/exodusii/metadata.xml b/sci-libs/exodusii/metadata.xml new file mode 100644 index 000000000000..b6f57a347068 --- /dev/null +++ b/sci-libs/exodusii/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +EXODUS II is a model developed to store and retrieve transient data for +finite element analyses. It is used for preprocessing, postprocessing, +as well as code to code data transfer. ExodusII is based on netcdf. +</longdescription> + <upstream> + <remote-id type="sourceforge">exodusii</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/fcl/Manifest b/sci-libs/fcl/Manifest new file mode 100644 index 000000000000..9d9ae442d68d --- /dev/null +++ b/sci-libs/fcl/Manifest @@ -0,0 +1,10 @@ +DIST fcl-0.3.2.tar.gz 5745349 SHA256 cf914f85b32cf8b63879907726df64e50da33f00d538759d789fe10fc5fbc95b SHA512 799c0f698c9d19ebd72c01b4bd51435feda1792462759249446ab968bf3b2b462537ce20135444c3e555da8564d0c93196f3f3448e2a4282afca710b67eaeb6e WHIRLPOOL 4d0694c7a27f117251709368542a5e7ed8ab3ec6e39e0400027f4409bf1b5cad3ff55c14ff529de19137c5dec6a4222799cc3bf0e1081c13105ea6dbc1e17c90 +DIST fcl-0.4.0.tar.gz 5762341 SHA256 1bea2cd5ee6034166d42860a6c5577f807c81f9f54d09dd680fb9bdf58d46747 SHA512 c565b4018a37449ce05b9189a97f2084a68caaa9247968fecdf933d8f5d87ed629d3fcb6ffccf928c4d339be1b70650b78706cc9d4a0c24864da529b25761684 WHIRLPOOL 2463490135ef16f29f608e68e2b2b0d86a7af59b54360275e73dae8d52aea3c7f9013e7a8be794a3fbb1981cf1470fe55866322aed188dd5c4bec0ba96512fa2 +DIST fcl-0.5.0.tar.gz 5760425 SHA256 8e6c19720e77024c1fbff5a912d81e8f28004208864607447bc90a31f18fb41a SHA512 8741c664720cb32e368e0139881ce69c29e3ccb9633ddc22f47b89918774dbc19541c68e1dbfd78a91f4c8c226ad4c0e1867b6e62111d4311fe907310fc71794 WHIRLPOOL 6e4cd25f162979d977a7c4d20c58bbe56009bda25b66f38873b40369adc9c228e2298d4cc6693c643d76c0a1b01d7dffe1af7819cdcda60f349f733319e91b8e +EBUILD fcl-0.3.2.ebuild 974 SHA256 af902706474cfde2186042c5ac5b6ed8b950660e884291a9bd9b752ee70344bd SHA512 49dc9dda67317b7b58582ad118530a7bd48b9ead2a2fd5ac689b769da7ecd876154cf9dda5646153406ed2b67ea1db8c0faa04bcaa4437ec33a25c54b48094ac WHIRLPOOL 64d5625534a86032b5ea6f9eb499ab7a743441ebbb3a27948919d865d1cf433a009f113da45bb8c93ef33ba3505e321d144866fcda9997510579e3016d5e8b16 +EBUILD fcl-0.4.0.ebuild 856 SHA256 230a2ccb9cf185f9c982edee8f414775d39ccda0d1905607560edc367994ba8a SHA512 a2aed79e23a003c247467a64dd3b052a09a0feda3ee5156f759039614a63f455ea1576dc8b750cb77766687ea8c90d7e3674e864e5a4cf8ae531a49146051c74 WHIRLPOOL 58655b126a2662886b89bb5f73fa038fe94015540a51eb656d639b4f6f0d755f82730845021f19f45e33c2632eabf00589899a01ecc29a5f17a21a4db6b6501b +EBUILD fcl-0.5.0.ebuild 856 SHA256 1be4021de5833ea6b369352e22ddffc2059f1c34f05fad798e5f479950ac3143 SHA512 8e0b0f27862a5a1f621fdae61597bb900defb0e3031004692297393ed18d9654409eb0ef5ca4c4d5d51911eee371dce7f58a18d1a84be282662bd07f31d4dc7f WHIRLPOOL 401d59bb9ef82bd791b8ffbd75d8ea4cc8a0a914f679450586f6e5146bd2e957a4597ce93aec8ef3987df2a2c2189ebaabc4b495c9f47fea66ccdca2ebdd372d +EBUILD fcl-9999.ebuild 856 SHA256 230a2ccb9cf185f9c982edee8f414775d39ccda0d1905607560edc367994ba8a SHA512 a2aed79e23a003c247467a64dd3b052a09a0feda3ee5156f759039614a63f455ea1576dc8b750cb77766687ea8c90d7e3674e864e5a4cf8ae531a49146051c74 WHIRLPOOL 58655b126a2662886b89bb5f73fa038fe94015540a51eb656d639b4f6f0d755f82730845021f19f45e33c2632eabf00589899a01ecc29a5f17a21a4db6b6501b +MISC ChangeLog 2734 SHA256 bc51e6b1231890cc6239a4ed2a0d122fb930a672faa1051518901add0596b5ce SHA512 b29241ad13827e81ac02aa77e0b6c6a183900ae01a7550d36bbb9ce0a69a7655287d6f687f01ddf5ff35592506930bc9c64c706faad2f1c991817ffc242aba6c WHIRLPOOL 925909a98e52637f83fc734742bfb345e9f9dafbb0eb7f60cb73808981d09efa6c14f069bd7fcbc7bdc68f9b8f1bffe38315e3ea061c6a4618856cd21992a708 +MISC ChangeLog-2015 605 SHA256 754012641a935d70861bf05fd3ba9016554319d39017bcca799a7cbb233c4e0e SHA512 3940e766382a1a5562d70a0cab412ca77ed92d0d871b901f39f339e8b84b5355cc9765f5d276ae82305e9f4ac6114d9046b36ae8e6fe6996dd9a9f851afca83f WHIRLPOOL d9c5574f5406fb53ba90e502926fd606d5e41f7ffc022909cdeea1c47492f8b36d03bea311b3a10236c9e68cb6c3c1bea1908de436bb32ea1c8abbcfc2720626 +MISC metadata.xml 344 SHA256 1905e62a7addac42d8a16e1d20f1e6d5cb65d90798b7970c820f5b7339140529 SHA512 d5d4ea55ebdabfcd86a1dce36974d9ca2f2746f2f8fec463486c108d58a6cf53850b511bdeef8546d05ecd7fb165d7c13b51eb834d353c25002acc1473c6b5bf WHIRLPOOL e274fa66f3e03f99c0eb2d1f892479e2ad4129642e9069d430da23a160f4eea21dedfc2e8c480808b6f6a7c5a56c31d63142afc6f3bf9b3051397ffdefad668c diff --git a/sci-libs/fcl/fcl-0.3.2.ebuild b/sci-libs/fcl/fcl-0.3.2.ebuild new file mode 100644 index 000000000000..4d1b793423a5 --- /dev/null +++ b/sci-libs/fcl/fcl-0.3.2.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/flexible-collision-library/fcl" +fi + +inherit ${SCM} cmake-utils + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/flexible-collision-library/fcl/archive/${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="The Flexible Collision Library" +HOMEPAGE="http://gamma.cs.unc.edu/FCL/" +LICENSE="BSD" +SLOT="0" +IUSE="cpu_flags_x86_sse" + +RDEPEND=" + sci-libs/octomap + sci-libs/flann + dev-libs/boost:=[threads] + sci-libs/libccd" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + sed -e 's/DESTINATION lib/DESTINATION ${CMAKE_INSTALL_LIBDIR}/g' \ + -i src/CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + "-DFCL_USE_SSE=$(usex cpu_flags_x86_sse TRUE FALSE)" + ) + cmake-utils_src_configure +} diff --git a/sci-libs/fcl/fcl-0.4.0.ebuild b/sci-libs/fcl/fcl-0.4.0.ebuild new file mode 100644 index 000000000000..6d823b172040 --- /dev/null +++ b/sci-libs/fcl/fcl-0.4.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/flexible-collision-library/fcl" +fi + +inherit ${SCM} cmake-utils + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/flexible-collision-library/fcl/archive/${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="The Flexible Collision Library" +HOMEPAGE="http://gamma.cs.unc.edu/FCL/" +LICENSE="BSD" +SLOT="0" +IUSE="cpu_flags_x86_sse" + +RDEPEND=" + sci-libs/octomap + sci-libs/flann + dev-libs/boost:=[threads] + sci-libs/libccd" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_configure() { + local mycmakeargs=( + "-DFCL_USE_SSE=$(usex cpu_flags_x86_sse TRUE FALSE)" + ) + cmake-utils_src_configure +} diff --git a/sci-libs/fcl/fcl-0.5.0.ebuild b/sci-libs/fcl/fcl-0.5.0.ebuild new file mode 100644 index 000000000000..95a962bfbcf9 --- /dev/null +++ b/sci-libs/fcl/fcl-0.5.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/flexible-collision-library/fcl" +fi + +inherit ${SCM} cmake-utils + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/flexible-collision-library/fcl/archive/${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="The Flexible Collision Library" +HOMEPAGE="http://gamma.cs.unc.edu/FCL/" +LICENSE="BSD" +SLOT="0" +IUSE="cpu_flags_x86_sse" + +RDEPEND=" + sci-libs/octomap + sci-libs/flann + dev-libs/boost:=[threads] + sci-libs/libccd" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_configure() { + local mycmakeargs=( + "-DFCL_USE_SSE=$(usex cpu_flags_x86_sse TRUE FALSE)" + ) + cmake-utils_src_configure +} diff --git a/sci-libs/fcl/fcl-9999.ebuild b/sci-libs/fcl/fcl-9999.ebuild new file mode 100644 index 000000000000..6d823b172040 --- /dev/null +++ b/sci-libs/fcl/fcl-9999.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/flexible-collision-library/fcl" +fi + +inherit ${SCM} cmake-utils + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/flexible-collision-library/fcl/archive/${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="The Flexible Collision Library" +HOMEPAGE="http://gamma.cs.unc.edu/FCL/" +LICENSE="BSD" +SLOT="0" +IUSE="cpu_flags_x86_sse" + +RDEPEND=" + sci-libs/octomap + sci-libs/flann + dev-libs/boost:=[threads] + sci-libs/libccd" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_configure() { + local mycmakeargs=( + "-DFCL_USE_SSE=$(usex cpu_flags_x86_sse TRUE FALSE)" + ) + cmake-utils_src_configure +} diff --git a/sci-libs/fcl/metadata.xml b/sci-libs/fcl/metadata.xml new file mode 100644 index 000000000000..fbedec0d5c16 --- /dev/null +++ b/sci-libs/fcl/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>aballier@gentoo.org</email> + <name>Alexis Ballier</name> + </maintainer> + <upstream> + <remote-id type="github">flexible-collision-library/fcl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/fetk/Manifest b/sci-libs/fetk/Manifest new file mode 100644 index 000000000000..44adfd850b5a --- /dev/null +++ b/sci-libs/fetk/Manifest @@ -0,0 +1,4 @@ +EBUILD fetk-1.5.ebuild 424 SHA256 b8ecfd566117b1fb42eafa3cb01da1f0f56e04febd8d63342fec0de5f53db122 SHA512 df722ecc3865e6fa594d76d784c595038d65c1733837e26a287de62d0554a5f7a808daa85d317f5dbd070eb52fa28621764114ef3e3cab28a034fd1b5b29c439 WHIRLPOOL 9c9c7fc3a7c19c2a460666cdc3e20a1f8d1860f135b351b0238dfc5e39563c1324ba4fbff644e714bfd88935ad4f0463c4984df008001cb56af566974b416e8f +MISC ChangeLog 2554 SHA256 b7edb324003b9430ada56369a525bf60bb10466cc996864b420bff4e49d0559a SHA512 d968d003fbff6e7d9771865bb620f8ee36d49ed1ec8c6a9cfa8a7be42892871343e0bc6b8f6c95a90ed462c033bdaa55233403792cd5c978be1476a675d98b42 WHIRLPOOL b8ee003d47f66ccf20aee6a1ba3f22b66a40d1c50737f5b3a27e394112d65700d389f2701fcc0319d70cedb84670c9ebc31a42bb9e142c399d18df182dd422d9 +MISC ChangeLog-2015 654 SHA256 71dc833d17fb2c11bc9e1538678897a22dcb74e2b18ce27e50c5fb16c8b4c3a2 SHA512 4407b96a8f06ccae2aab5b2016588d13f38b40ef243d014fde545a6fac1eb1ae22e5a7bbeb74746f1bb286b4da45212df13f53ffc070e37fb62b779473a11351 WHIRLPOOL 831d00c971bf51e45f95b2f5355464cc6e351f5e2c19aa7f41c0b7111d260c3976cad596a093372da0ec245b7a0cee865ed2df9032c03b3ade9d3a0d175febe1 +MISC metadata.xml 1202 SHA256 bcb2cfb47a009c9aed6d20025e0bdb856fcf445a5f59e1ac9596981497b2cbe9 SHA512 b3df3f22c8757830cec30e5eeb248f104968b689f7a49524db0f2a5051540580347787a981415045b9661b17f54cdd2dbeb9771d0c710348888e27f1ca9450b1 WHIRLPOOL ddc80752e4cd63d20c09f14c75fc789983ef125927453593d2d2931580db768a8214a7b22106f7f1fb78fe1c208fbfec92feb527f8d52e4ea0aa58ca3afb17cf diff --git a/sci-libs/fetk/fetk-1.5.ebuild b/sci-libs/fetk/fetk-1.5.ebuild new file mode 100644 index 000000000000..96d1ea80984f --- /dev/null +++ b/sci-libs/fetk/fetk-1.5.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="The Finite Element ToolKit - Meta package" +HOMEPAGE="http://fetk.org/" +SRC_URI="" + +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="" + +RDEPEND=" + ~dev-libs/maloc-${PV} + ~media-libs/sg-${PV} + ~sci-libs/gamer-${PV} + ~sci-libs/mc-${PV} + ~sci-libs/punc-${PV} + " +DEPEND="" diff --git a/sci-libs/fetk/metadata.xml b/sci-libs/fetk/metadata.xml new file mode 100644 index 000000000000..d9c1802ed751 --- /dev/null +++ b/sci-libs/fetk/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +The Finite Element ToolKit (FETK) is a collaboratively developed, evolving +collection of adaptive finite element method (AFEM) software libraries and +tools for solving coupled systems of nonlinear geometric partial differential +equations (PDE). The FETK libraries and tools are written in an +object-oriented form of ANSI-C and in C++, and include a common portability +layer (MALOC) for all of FETK, a collection of standard numerical +libraries (PUNC), a stand-alone high-quality surface and volume simplex mesh +generator (GAMer), a stand-alone networked polygon display tool (SG), +a general nonlinear finite element modeling kernel (MC), +and a MATLAB toolkit (MCLite) for protyping finite element methods and +examining simplex meshes using MATLAB. The entire FETK Suite of tools is +highly portable (from iPhone to Blue Gene/L), thanks to use of +a small abstraction layer (MALOC). +</longdescription> +</pkgmetadata> diff --git a/sci-libs/fftw/Manifest b/sci-libs/fftw/Manifest new file mode 100644 index 000000000000..cc919f1cb2a0 --- /dev/null +++ b/sci-libs/fftw/Manifest @@ -0,0 +1,22 @@ +AUX fftw-2.1.5-as-needed.patch 4082 SHA256 ff1e90a0437ced34155708b0e5ceec15ae7546eb3f2fb32e0fcc7815ad2d4380 SHA512 9dc1b911bc8360b43c8b604cb3e823abd7c958e4c0aba596daa5fbd2c79d774f3a925d5fa253361f6b87c0e40be57e615bb47c52766acaf8be4bf1ef0787bc0b WHIRLPOOL 92a049fd4972682e6b44f708f005f7bfb028bb85016de0d7cf7959da43b388666cc36f0faefa8418147b6ff4d99a5a46598fd1229dc66c135cb5c2c341262512 +AUX fftw-2.1.5-cc.patch 546 SHA256 52b2ba8a140e46e9a1f1c71d8e85faaac70e6d783ba8e45f4423ba6f70f04dbe SHA512 f21ba12ec727a023d41df95b24d03273d416888b21f56dde8d2a256d15b9543a091a02f7100e86196bb7a38492d470b58ab293fed58a21e2417e2427f786368a WHIRLPOOL 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( virtual/mpi )" +RDEPEND="${DEPEND}" + +SLOT="2.1" +LICENSE="GPL-2+" +IUSE="doc float fortran mpi openmp threads static-libs" + +KEYWORDS="alpha amd64 arm hppa ia64 ppc ppc64 s390 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" + +pkg_setup() { + use openmp && FORTRAN_NEED_OPENMP="1" + fortran-2_pkg_setup + # this one is reported to cause trouble on pentium4 m series + filter-mfpmath "sse" + + # here I need (surprise) to increase optimization: + # --enable-i386-hacks requires -fomit-frame-pointer to work properly + if use x86; then + is-flag "-fomit-frame-pointer" || append-flags "-fomit-frame-pointer" + fi + if use openmp && [[ $(tc-getCC) == *gcc* ]] && ! tc-has-openmp; then + ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 " + ewarn "If you want to build fftw with OpenMP, abort now," + ewarn "and switch CC to an OpenMP capable compiler" + ewarn "Otherwise the configure script will select POSIX threads." + fi + use openmp && [[ $(tc-getCC)$ == icc* ]] && append-ldflags $(no-as-needed) +} + +src_prepare() { + # doc suggests installing single and double precision versions + # via separate compilations. will do in two separate source trees + # since some sed'ing is done during the build + # (?if --enable-type-prefix is set?) + + epatch \ + "${FILESDIR}"/${P}-as-needed.patch \ + "${FILESDIR}"/${P}-configure.in.patch \ + "${FILESDIR}"/${P}-no-test.patch \ + "${FILESDIR}"/${P}-cc.patch \ + "${FILESDIR}"/${P}-texinfo5.1.patch + + # fix info files + for infofile in doc/fftw*info*; do + cat >> ${infofile} <<-EOF + INFO-DIR-SECTION Libraries + START-INFO-DIR-ENTRY + * fftw: (fftw). ${DESCRIPTION} + END-INFO-DIR-ENTRY + EOF + done + + sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.in || die + + eautoreconf + + cd "${WORKDIR}" + cp -R ${P} ${P}-double + mv ${P} ${P}-single + ln -s ${P}-single ${P} +} + +src_configure() { + local myconf=" + --enable-shared + --enable-type-prefix + --enable-vec-recurse + $(use_enable fortran) + $(use_enable mpi) + $(use_enable static-libs static) + $(use_enable x86 i386-hacks)" + if use openmp; then + myconf="${myconf} + --enable-threads + --with-openmp" + elif use threads; then + myconf="${myconf} + --enable-threads + --without-openmp" + else + myconf="${myconf} + --disable-threads + --without-openmp" + fi + cd "${S}-single" + econf ${myconf} \ + --enable-float \ + --with-gcc=$(tc-getCC) + + cd "${S}-double" + econf ${myconf} \ + --with-gcc=$(tc-getCC) +} + +src_compile() { + local dir + for dir in "${S}-single" "${S}-double" + do + einfo "Running compilation in ${dir}" + emake -C ${dir} + done +} + +src_test() { + local dir + for dir in "${S}-single" "${S}-double" + do + einfo "Running tests in ${dir}" + emake -C ${dir} -j1 check + done +} + +src_install () { + # both builds are installed in the same place + # libs are distinguished by prefix (s or d), see docs for details + + local dir + for dir in "${S}-single" "${S}-double" + do + emake DESTDIR="${D}" -C ${dir} install + done + + insinto /usr/include + doins fortran/fftw_f77.i + dodoc AUTHORS ChangeLog NEWS TODO README README.hacks + use doc && dohtml doc/* + + if use float; then + for f in "${ED}"/usr/{include,$(get_libdir)}/*sfft*; do + ln -s $(basename ${f}) ${f/sfft/fft} + done + for f in "${ED}"/usr/{include,$(get_libdir)}/*srfft*; do + ln -s $(basename ${f}) ${f/srfft/rfft} + done + else + for f in "${ED}"/usr/{include,$(get_libdir)}/*dfft*; do + ln -s $(basename ${f}) ${f/dfft/fft} + done + for f in "${ED}"/usr/{include,$(get_libdir)}/*drfft*; do + ln -s $(basename ${f}) ${f/drfft/rfft} + done + fi +} diff --git a/sci-libs/fftw/fftw-2.1.5-r9.ebuild b/sci-libs/fftw/fftw-2.1.5-r9.ebuild new file mode 100644 index 000000000000..75696fb361ba --- /dev/null +++ b/sci-libs/fftw/fftw-2.1.5-r9.ebuild @@ -0,0 +1,137 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit autotools flag-o-matic fortran-2 multibuild toolchain-funcs + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org" +SRC_URI="http://www.fftw.org/${P}.tar.gz" + +KEYWORDS="alpha amd64 arm hppa ia64 ppc ppc64 ~s390 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" + +LICENSE="GPL-2+" +SLOT="2.1" +IUSE="doc float fortran mpi openmp threads static-libs" + +RDEPEND="mpi? ( virtual/mpi )" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-as-needed.patch + "${FILESDIR}"/${P}-configure.in.patch + "${FILESDIR}"/${P}-no-test.patch + "${FILESDIR}"/${P}-cc.patch + "${FILESDIR}"/${P}-texinfo5.1.patch + "${FILESDIR}"/${P}-parallel-tests.patch +) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + tc-check-openmp + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double ) +} + +src_prepare() { + default + + # fix info files + local infofile + for infofile in doc/fftw*info*; do + cat >> ${infofile} <<-EOF || die + INFO-DIR-SECTION Libraries + START-INFO-DIR-ENTRY + * fftw: (fftw). ${DESCRIPTION} + END-INFO-DIR-ENTRY + EOF + done + + mv configure.{in,ac} || die + sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac || die + + eautoreconf + + # 'FAQ' is actually a dir and causes issues with einstalldocs + rm -r FAQ || die + + multibuild_copy_sources +} + +fftw_src_configure() { + local myconf=( + --with-gcc=$(tc-getCC) + --enable-shared + --enable-type-prefix + --enable-vec-recurse + $(use_enable fortran) + $(use_enable mpi) + $(use_enable static-libs static) + $(use_enable x86 i386-hacks) + $(use_with openmp) + ) + + if use openmp || use threads; then + myconf+=( --enable-threads ) + else + myconf+=( --disable-threads ) + fi + + [[ $MULTIBUILD_VARIANT == single ]] && myconf+=( --enable-float ) + + econf "${myconf[@]}" +} + +src_configure() { + # this one is reported to cause trouble on pentium4 m series + filter-mfpmath sse + + # here I need (surprise) to increase optimization: + # --enable-i386-hacks requires -fomit-frame-pointer to work properly + if use x86; then + is-flag -fomit-frame-pointer || append-flags -fomit-frame-pointer + fi + use openmp && [[ $(tc-getCC)$ == icc* ]] && append-ldflags $(no-as-needed) + + multibuild_foreach_variant run_in_build_dir fftw_src_configure +} + +src_compile() { + multibuild_foreach_variant run_in_build_dir default_src_compile +} + +src_test() { + multibuild_foreach_variant run_in_build_dir default_src_test +} + +src_install () { + use doc && HTML_DOCS=( doc/*.{html,gif} ) + multibuild_foreach_variant run_in_build_dir default_src_install + + doheader fortran/fftw_f77.i + + create_fftw_symlinks() { + local i f letter=$1 + for i in fft rfft; do + for f in "${ED%/}"/usr/{include,$(get_libdir)}/*${letter}${i}*; do + ln -s $(basename ${f}) ${f/${letter}${i}/${i}} || die + done + done + } + create_fftw_symlinks $(usex float s d) + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} diff --git a/sci-libs/fftw/fftw-3.3.4.ebuild b/sci-libs/fftw/fftw-3.3.4.ebuild new file mode 100644 index 000000000000..9174c474ef42 --- /dev/null +++ b/sci-libs/fftw/fftw-3.3.4.ebuild @@ -0,0 +1,162 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit autotools-multilib eutils flag-o-matic fortran-2 multibuild toolchain-funcs versionator + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org/" + +if [[ ${PV} = *9999 ]]; then + inherit git-2 + EGIT_REPO_URI="https://github.com/FFTW/fftw3.git" + KEYWORDS="alpha amd64 arm hppa ia64 ppc ppc64 sparc x86" + AUTOTOOLS_AUTORECONF=1 +else + SRC_URI="http://www.fftw.org/${P}.tar.gz" + KEYWORDS="alpha amd64 arm hppa ia64 ~mips ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +fi + +LICENSE="GPL-2+" +SLOT="3.0/3" +IUSE="altivec cpu_flags_x86_avx doc cpu_flags_x86_fma3 cpu_flags_x86_fma4 fortran mpi neon openmp quad cpu_flags_x86_sse cpu_flags_x86_sse2 static-libs test threads zbus" + +RDEPEND=" + mpi? ( virtual/mpi ) + abi_x86_32? ( !<=app-emulation/emul-linux-x86-soundlibs-20130224-r2 + !app-emulation/emul-linux-x86-soundlibs[-abi_x86_32(-)] )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double longdouble ) + if use quad; then + if [[ $(tc-getCC) == *gcc ]] && ! version_is_at_least 4.6 $(gcc-version); then + ewarn "quad precision only available for gcc >= 4.6" + die "need quad precision capable gcc" + fi + MULTIBUILD_VARIANTS+=( quad ) + fi +} + +src_prepare() { + # fix info file for category directory + [[ ${PV} = *9999 ]] || sed -i \ + -e 's/Texinfo documentation system/Libraries/' \ + doc/fftw3."info" || die "failed to fix info file" + + autotools-utils_src_prepare +} + +src_configure() { + local x + + # filter -Os according to docs + replace-flags -Os -O2 + + my_configure() { + #a bit hacky improve after #483758 is solved + local x=${BUILD_DIR%-*} + x=${x##*-} + # there is no abi_x86_32 port of virtual/mpi right now + local enable_mpi=$(use_enable mpi) + multilib_is_native_abi || enable_mpi="--disable-mpi" + + #jlec reported USE=quad on abi_x86_32 has too less registers + #stub Makefiles + if [[ ${ABI} == x86 && ${x} == quad ]]; then + mkdir -p "${BUILD_DIR}/tests" || die + echo "all: ;" > "${BUILD_DIR}/Makefile" || die + echo "install: ;" >> "${BUILD_DIR}/Makefile" || die + echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die + return 0 + fi + + local myeconfargs=( + $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma) + $(use_enable fortran) + $(use_enable zbus mips-zbus-timer) + $(use_enable threads) + $(use_enable openmp) + ) + if [[ $x == single ]]; then + #altivec, sse, single-paired only work for single + myeconfargs+=( + --enable-single + $(use_enable altivec) + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_sse sse) + ${enable_mpi} + $(use_enable neon) + ) + elif [[ $x == double ]]; then + myeconfargs+=( + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_sse2 sse2) + ${enable_mpi} + ) + elif [[ $x == longdouble ]]; then + myeconfargs+=( + --enable-long-double + ${enable_mpi} + ) + elif [[ $x == quad ]]; then + #quad does not support mpi + myeconfargs+=( --enable-quad-precision ) + else + die "${x} precision not implemented in this ebuild" + fi + + autotools-utils_src_configure + } + + multibuild_foreach_variant multilib_parallel_foreach_abi my_configure +} + +src_compile() { + multibuild_foreach_variant autotools-multilib_src_compile +} + +src_test () { + # We want this to be a reasonably quick test, but that is still hard... + ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine" + # Do not increase the number of threads, it will not help your performance + #local testbase="perl check.pl --nthreads=1 --estimate" + # ${testbase} -${p}d || die "Failure: $n" + multibuild_foreach_variant autotools-multilib_src_compile -C tests smallcheck +} + +src_install () { + local u x + DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS ) + HTML_DOCS=( doc/html/ ) + + multibuild_foreach_variant multilib_foreach_abi autotools-utils_src_install + + if use doc; then + dodoc doc/*.pdf + insinto /usr/share/doc/${PF}/faq + doins -r doc/FAQ/fftw-faq.html/* + else + rm -r "${ED}"/usr/share/doc/${PF}/html + fi + + for x in "${ED}"/usr/lib*/pkgconfig/*.pc; do + for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do + sed -e "s|-lfftw3[flq]\?|&_$u &|" "$x" > "${x%.pc}_$u.pc" || die + done + done +} diff --git a/sci-libs/fftw/fftw-3.3.5-r1.ebuild b/sci-libs/fftw/fftw-3.3.5-r1.ebuild new file mode 100644 index 000000000000..8b95ce8b8ba9 --- /dev/null +++ b/sci-libs/fftw/fftw-3.3.5-r1.ebuild @@ -0,0 +1,193 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit flag-o-matic fortran-2 toolchain-funcs versionator multibuild multilib-minimal + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org/" + +if [[ ${PV} = *9999 ]]; then + inherit autotools git-r3 + EGIT_REPO_URI="https://github.com/FFTW/fftw3.git" +else + SRC_URI="http://www.fftw.org/${P}.tar.gz" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +fi + +LICENSE="GPL-2+" +SLOT="3.0/3" +IUSE="altivec cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_fma3 cpu_flags_x86_fma4 cpu_flags_x86_sse cpu_flags_x86_sse2 doc fortran mpi neon openmp quad static-libs test threads zbus" + +RDEPEND=" + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + + if tc-is-clang; then + ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," + ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\"" + fi + + die "need openmp capable compiler" + fi + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double longdouble ) + if use quad; then + if tc-is-gcc && ! version_is_at_least 4.6 $(gcc-version); then + ewarn "quad precision only available for gcc >= 4.6" + die "need quad precision capable gcc" + fi + MULTIBUILD_VARIANTS+=( quad ) + fi +} + +src_prepare() { + default + + # fix info file for category directory + if [[ ${PV} = *9999 ]]; then + sed -i -e + 's/Texinfo documentation system/Libraries/' \ + doc/fftw3."info" || die "failed to fix info file" + + eautoreconf + fi +} + +multilib_src_configure() { + # there is no abi_x86_32 port of virtual/mpi right now, bug 519700 + local enable_mpi=$(multilib_native_use_enable mpi) + + # jlec reported USE=quad on abi_x86_32 has too few registers + # stub Makefiles + if [[ ${MULTILIB_ABI_FLAG} == abi_x86_32 && ${MULTIBUILD_ID} == quad-* ]]; then + mkdir -p "${BUILD_DIR}/tests" || die + echo "all: ;" > "${BUILD_DIR}/Makefile" || die + echo "install: ;" >> "${BUILD_DIR}/Makefile" || die + echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die + return 0 + fi + + local myconf=( + --enable-shared + $(use_enable static-libs static) + $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma) + $(use_enable fortran) + $(use_enable zbus mips-zbus-timer) + $(use_enable threads) + $(use_enable openmp) + ) + case "${MULTIBUILD_ID}" in + single-*) + #altivec, sse, single-paired only work for single + myconf+=( + --enable-single + $(use_enable altivec) + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse sse) + $(use_enable cpu_flags_x86_sse2 sse2) + $(use_enable neon) + ${enable_mpi} + ) + ;; + + double-*) + myconf+=( + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse2 sse2) + ${enable_mpi} + ) + ;; + + longdouble-*) + myconf+=( + --enable-long-double + ${enable_mpi} + ) + ;; + + quad-*) + #quad does not support mpi + myconf+=( + --enable-quad-precision + ) + ;; + + *) + die "${MULTIBUILD_ID%-*} precision not implemented in this ebuild" + ;; + esac + + ECONF_SOURCE="${S}" econf "${myconf[@]}" +} + +src_configure() { + multibuild_foreach_variant multilib-minimal_src_configure +} + +src_compile() { + multibuild_foreach_variant multilib-minimal_src_compile +} + +multilib_src_test() { + emake -C tests smallcheck +} + +src_test() { + # We want this to be a reasonably quick test, but that is still hard... + ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine" + # Do not increase the number of threads, it will not help your performance + # local testbase="perl check.pl --nthreads=1 --estimate" + # ${testbase} -${p}d || die "Failure: $n" + + multibuild_foreach_variant multilib-minimal_src_test +} + +src_install() { + DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS ) + HTML_DOCS=( doc/html/ ) + + #workaroud for bug #590446 + my_abi_install() { + pushd "${BUILD_DIR}" >/dev/null || die + emake DESTDIR="${D}" install + popd >/dev/null || die + } + multibuild_foreach_variant multilib_foreach_abi my_abi_install + + einstalldocs + + if use doc; then + dodoc doc/*.pdf + docinto faq + dodoc -r doc/FAQ/fftw-faq.html/. + else + rm -r "${ED}"/usr/share/doc/${PF}/html || die + fi + + local x + for x in "${ED}"/usr/lib*/pkgconfig/*.pc; do + local u + for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do + sed -e "s|-lfftw3[flq]\?|&_${u} &|" "$x" > "${x%.pc}_${u}.pc" || die + done + done + + # fftw uses pkg-config to record its private dependencies + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-libs/fftw/fftw-3.3.5-r2.ebuild b/sci-libs/fftw/fftw-3.3.5-r2.ebuild new file mode 100644 index 000000000000..07c2837181f1 --- /dev/null +++ b/sci-libs/fftw/fftw-3.3.5-r2.ebuild @@ -0,0 +1,177 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit flag-o-matic fortran-2 toolchain-funcs versionator multibuild multilib-minimal + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org/" + +if [[ ${PV} = *9999 ]]; then + inherit autotools git-r3 + EGIT_REPO_URI="https://github.com/FFTW/fftw3.git" +else + SRC_URI="http://www.fftw.org/${P}.tar.gz" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +fi + +LICENSE="GPL-2+" +SLOT="3.0/3" +IUSE="altivec cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_fma3 cpu_flags_x86_fma4 cpu_flags_x86_sse cpu_flags_x86_sse2 doc fortran mpi neon openmp quad static-libs test threads zbus" + +RDEPEND=" + mpi? ( >=virtual/mpi-2.0-r4[${MULTILIB_USEDEP}] )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + tc-check-openmp + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double longdouble ) + if use quad; then + if tc-is-gcc && ! version_is_at_least 4.6 $(gcc-version); then + ewarn "quad precision only available for gcc >= 4.6" + die "need quad precision capable gcc" + fi + MULTIBUILD_VARIANTS+=( quad ) + fi +} + +src_prepare() { + default + + # fix info file for category directory + if [[ ${PV} = *9999 ]]; then + sed -i -e + 's/Texinfo documentation system/Libraries/' \ + doc/fftw3."info" || die "failed to fix info file" + + eautoreconf + fi +} + +multilib_src_configure() { + # jlec reported USE=quad on abi_x86_32 has too few registers + # stub Makefiles + if [[ ${MULTILIB_ABI_FLAG} == abi_x86_32 && ${MULTIBUILD_ID} == quad-* ]]; then + mkdir -p "${BUILD_DIR}/tests" || die + echo "all: ;" > "${BUILD_DIR}/Makefile" || die + echo "install: ;" >> "${BUILD_DIR}/Makefile" || die + echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die + return 0 + fi + + local myconf=( + --enable-shared + $(use_enable static-libs static) + $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma) + $(use_enable fortran) + $(use_enable zbus mips-zbus-timer) + $(use_enable threads) + $(use_enable openmp) + ) + case "${MULTIBUILD_ID}" in + single-*) + # altivec, sse, single-paired only work for single + myconf+=( + --enable-single + $(use_enable altivec) + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse sse) + $(use_enable cpu_flags_x86_sse2 sse2) + $(use_enable neon) + $(use_enable mpi) + ) + ;; + + double-*) + myconf+=( + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse2 sse2) + $(use_enable mpi) + ) + ;; + + longdouble-*) + myconf+=( + --enable-long-double + $(use_enable mpi) + ) + ;; + + quad-*) + # quad does not support mpi + myconf+=( + --enable-quad-precision + ) + ;; + + *) + die "${MULTIBUILD_ID%-*} precision not implemented in this ebuild" + ;; + esac + + ECONF_SOURCE="${S}" econf "${myconf[@]}" MPICC="$(tc-getCC -lmpi)" +} + +src_configure() { + multibuild_foreach_variant multilib-minimal_src_configure +} + +src_compile() { + multibuild_foreach_variant multilib-minimal_src_compile +} + +multilib_src_test() { + emake -C tests smallcheck +} + +src_test() { + # We want this to be a reasonably quick test, but that is still hard... + ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine" + # Do not increase the number of threads, it will not help your performance + # local testbase="perl check.pl --nthreads=1 --estimate" + # ${testbase} -${p}d || die "Failure: $n" + + multibuild_foreach_variant multilib-minimal_src_test +} + +src_install() { + DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS ) + HTML_DOCS=( doc/html/ ) + + multibuild_foreach_variant multilib-minimal_src_install + + if use doc; then + dodoc doc/*.pdf + docinto faq + dodoc -r doc/FAQ/fftw-faq.html/. + else + rm -r "${ED}"usr/share/doc/${PF}/html || die + fi + + local x + for x in "${ED}"usr/lib*/pkgconfig/*.pc; do + local u + for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do + sed -e "s|-lfftw3[flq]\?|&_${u} &|" "$x" > "${x%.pc}_${u}.pc" || die + done + done + + # fftw uses pkg-config to record its private dependencies + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-libs/fftw/fftw-3.3.6_p1.ebuild b/sci-libs/fftw/fftw-3.3.6_p1.ebuild new file mode 100644 index 000000000000..5b793c7a5ea2 --- /dev/null +++ b/sci-libs/fftw/fftw-3.3.6_p1.ebuild @@ -0,0 +1,181 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit flag-o-matic fortran-2 toolchain-funcs versionator multibuild multilib-minimal + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org/" + +MY_P=${PN}-${PV/_p/-pl} + +if [[ ${PV} = *9999 ]]; then + inherit autotools git-r3 + EGIT_REPO_URI="https://github.com/FFTW/fftw3.git" +else + SRC_URI="http://www.fftw.org/${PN}-${PV/_p/-pl}.tar.gz" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +fi + +LICENSE="GPL-2+" +SLOT="3.0/3" +IUSE="altivec cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_fma3 cpu_flags_x86_fma4 cpu_flags_x86_sse cpu_flags_x86_sse2 doc fortran mpi neon openmp quad static-libs test threads zbus" + +RDEPEND=" + mpi? ( >=virtual/mpi-2.0-r4[${MULTILIB_USEDEP}] )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +S=${WORKDIR}/${MY_P} + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + tc-check-openmp + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double longdouble ) + if use quad; then + if tc-is-gcc && ! version_is_at_least 4.6 $(gcc-version); then + ewarn "quad precision only available for gcc >= 4.6" + die "need quad precision capable gcc" + fi + MULTIBUILD_VARIANTS+=( quad ) + fi +} + +src_prepare() { + default + + # fix info file for category directory + if [[ ${PV} = *9999 ]]; then + sed -i -e + 's/Texinfo documentation system/Libraries/' \ + doc/fftw3."info" || die "failed to fix info file" + + eautoreconf + fi +} + +multilib_src_configure() { + # jlec reported USE=quad on abi_x86_32 has too few registers + # stub Makefiles + if [[ ${MULTILIB_ABI_FLAG} == abi_x86_32 && ${MULTIBUILD_ID} == quad-* ]]; then + mkdir -p "${BUILD_DIR}/tests" || die + echo "all: ;" > "${BUILD_DIR}/Makefile" || die + echo "install: ;" >> "${BUILD_DIR}/Makefile" || die + echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die + return 0 + fi + + local myconf=( + --enable-shared + $(use_enable static-libs static) + $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma) + $(use_enable fortran) + $(use_enable zbus mips-zbus-timer) + $(use_enable threads) + $(use_enable openmp) + ) + case "${MULTIBUILD_ID}" in + single-*) + # altivec, sse, single-paired only work for single + myconf+=( + --enable-single + $(use_enable altivec) + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse sse) + $(use_enable cpu_flags_x86_sse2 sse2) + $(use_enable neon) + $(use_enable mpi) + ) + ;; + + double-*) + myconf+=( + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse2 sse2) + $(use_enable mpi) + ) + ;; + + longdouble-*) + myconf+=( + --enable-long-double + $(use_enable mpi) + ) + ;; + + quad-*) + # quad does not support mpi + myconf+=( + --enable-quad-precision + ) + ;; + + *) + die "${MULTIBUILD_ID%-*} precision not implemented in this ebuild" + ;; + esac + + ECONF_SOURCE="${S}" econf "${myconf[@]}" MPICC="$(tc-getCC -lmpi)" +} + +src_configure() { + multibuild_foreach_variant multilib-minimal_src_configure +} + +src_compile() { + multibuild_foreach_variant multilib-minimal_src_compile +} + +multilib_src_test() { + emake -C tests smallcheck +} + +src_test() { + # We want this to be a reasonably quick test, but that is still hard... + ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine" + # Do not increase the number of threads, it will not help your performance + # local testbase="perl check.pl --nthreads=1 --estimate" + # ${testbase} -${p}d || die "Failure: $n" + + multibuild_foreach_variant multilib-minimal_src_test +} + +src_install() { + DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS ) + HTML_DOCS=( doc/html/ ) + + multibuild_foreach_variant multilib-minimal_src_install + + if use doc; then + dodoc doc/*.pdf + docinto faq + dodoc -r doc/FAQ/fftw-faq.html/. + else + rm -r "${ED}"usr/share/doc/${PF}/html || die + fi + + local x + for x in "${ED}"usr/lib*/pkgconfig/*.pc; do + local u + for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do + sed -e "s|-lfftw3[flq]\?|&_${u} &|" "$x" > "${x%.pc}_${u}.pc" || die + done + done + + # fftw uses pkg-config to record its private dependencies + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-libs/fftw/fftw-3.3.6_p2.ebuild b/sci-libs/fftw/fftw-3.3.6_p2.ebuild new file mode 100644 index 000000000000..df20a22aee45 --- /dev/null +++ b/sci-libs/fftw/fftw-3.3.6_p2.ebuild @@ -0,0 +1,180 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit flag-o-matic fortran-2 toolchain-funcs versionator multibuild multilib-minimal + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org/" + +MY_P=${PN}-${PV/_p/-pl} + +if [[ ${PV} = *9999 ]]; then + inherit autotools git-r3 + EGIT_REPO_URI="https://github.com/FFTW/fftw3.git" +else + SRC_URI="http://www.fftw.org/${PN}-${PV/_p/-pl}.tar.gz" + KEYWORDS="alpha amd64 ~arm ~arm64 hppa ia64 ~mips ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +fi + +LICENSE="GPL-2+" +SLOT="3.0/3" +IUSE="altivec cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_fma3 cpu_flags_x86_fma4 cpu_flags_x86_sse cpu_flags_x86_sse2 doc fortran mpi neon openmp quad static-libs test threads zbus" + +RDEPEND=" + mpi? ( >=virtual/mpi-2.0-r4[${MULTILIB_USEDEP}] )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +S=${WORKDIR}/${MY_P} +HTML_DOCS=( doc/html/. ) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + tc-check-openmp + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double longdouble ) + if use quad; then + if ! tc-is-gcc; then + ewarn "quad precision only available for gcc >= 4.6" + die "need quad precision capable gcc" + fi + MULTIBUILD_VARIANTS+=( quad ) + fi +} + +src_prepare() { + default + + # fix info file for category directory + if [[ ${PV} = *9999 ]]; then + sed -i -e + 's/Texinfo documentation system/Libraries/' \ + doc/fftw3."info" || die "failed to fix info file" + + eautoreconf + fi +} + +multilib_src_configure() { + # jlec reported USE=quad on abi_x86_32 has too few registers + # stub Makefiles + if [[ ${MULTILIB_ABI_FLAG} == abi_x86_32 && ${MULTIBUILD_ID} == quad-* ]]; then + mkdir -p "${BUILD_DIR}/tests" || die + echo "all: ;" > "${BUILD_DIR}/Makefile" || die + echo "install: ;" >> "${BUILD_DIR}/Makefile" || die + echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die + return 0 + fi + + local myconf=( + --enable-shared + $(use_enable static-libs static) + $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma) + $(use_enable fortran) + $(use_enable zbus mips-zbus-timer) + $(use_enable threads) + $(use_enable openmp) + ) + case "${MULTIBUILD_ID}" in + single-*) + # altivec, sse, single-paired only work for single + myconf+=( + --enable-single + $(use_enable altivec) + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse sse) + $(use_enable cpu_flags_x86_sse2 sse2) + $(use_enable neon) + $(use_enable mpi) + ) + ;; + + double-*) + myconf+=( + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse2 sse2) + $(use_enable mpi) + ) + ;; + + longdouble-*) + myconf+=( + --enable-long-double + $(use_enable mpi) + ) + ;; + + quad-*) + # quad does not support mpi + myconf+=( + --enable-quad-precision + ) + ;; + + *) + die "${MULTIBUILD_ID%-*} precision not implemented in this ebuild" + ;; + esac + + ECONF_SOURCE="${S}" econf "${myconf[@]}" MPICC="$(tc-getCC -lmpi)" +} + +src_configure() { + multibuild_foreach_variant multilib-minimal_src_configure +} + +src_compile() { + multibuild_foreach_variant multilib-minimal_src_compile +} + +multilib_src_test() { + emake -C tests smallcheck +} + +src_test() { + # We want this to be a reasonably quick test, but that is still hard... + ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine" + # Do not increase the number of threads, it will not help your performance + # local testbase="perl check.pl --nthreads=1 --estimate" + # ${testbase} -${p}d || die "Failure: $n" + + multibuild_foreach_variant multilib-minimal_src_test +} + +src_install() { + multibuild_foreach_variant multilib-minimal_src_install + dodoc CONVENTIONS + + if use doc; then + dodoc doc/*.pdf + docinto faq + dodoc -r doc/FAQ/fftw-faq.html/. + else + rm -r "${ED%/}"/usr/share/doc/${PF}/html || die + fi + + local x + for x in "${ED%/}"/usr/lib*/pkgconfig/*.pc; do + local u + for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do + sed -e "s|-lfftw3[flq]\?|&_${u} &|" "$x" > "${x%.pc}_${u}.pc" || die + done + done + + # fftw uses pkg-config to record its private dependencies + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/fftw/fftw-9999.ebuild b/sci-libs/fftw/fftw-9999.ebuild new file mode 100644 index 000000000000..53961f54350e --- /dev/null +++ b/sci-libs/fftw/fftw-9999.ebuild @@ -0,0 +1,185 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit flag-o-matic fortran-2 toolchain-funcs versionator multibuild multilib-minimal + +DESCRIPTION="Fast C library for the Discrete Fourier Transform" +HOMEPAGE="http://www.fftw.org/" + +if [[ ${PV} = *9999 ]]; then + inherit autotools git-r3 + EGIT_REPO_URI="https://github.com/FFTW/fftw3.git" +else + SRC_URI="http://www.fftw.org/${P}.tar.gz" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +fi + +LICENSE="GPL-2+" +SLOT="3.0/3" +IUSE="altivec cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_fma3 cpu_flags_x86_fma4 cpu_flags_x86_sse cpu_flags_x86_sse2 doc fortran mpi neon openmp quad static-libs test threads zbus" + +RDEPEND=" + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + test? ( dev-lang/perl )" + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + + if tc-is-clang; then + ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," + ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\"" + fi + + die "need openmp capable compiler" + fi + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + MULTIBUILD_VARIANTS=( single double longdouble ) + if use quad; then + if tc-is-gcc && ! version_is_at_least 4.6 $(gcc-version); then + ewarn "quad precision only available for gcc >= 4.6" + die "need quad precision capable gcc" + fi + MULTIBUILD_VARIANTS+=( quad ) + fi +} + +src_prepare() { + default + + # fix info file for category directory + if [[ ${PV} = *9999 ]]; then + sed -i -e + 's/Texinfo documentation system/Libraries/' \ + doc/fftw3."info" || die "failed to fix info file" + + eautoreconf + fi +} + +multilib_src_configure() { + # there is no abi_x86_32 port of virtual/mpi right now, bug 519700 + local enable_mpi=$(multilib_native_use_enable mpi) + + # jlec reported USE=quad on abi_x86_32 has too few registers + # stub Makefiles + if [[ ${MULTILIB_ABI_FLAG} == abi_x86_32 && ${MULTIBUILD_ID} == quad-* ]]; then + mkdir -p "${BUILD_DIR}/tests" || die + echo "all: ;" > "${BUILD_DIR}/Makefile" || die + echo "install: ;" >> "${BUILD_DIR}/Makefile" || die + echo "smallcheck: ;" > "${BUILD_DIR}/tests/Makefile" || die + return 0 + fi + + local myconf=( + --enable-shared + $(use_enable static-libs static) + $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma) + $(use_enable fortran) + $(use_enable zbus mips-zbus-timer) + $(use_enable threads) + $(use_enable openmp) + ) + case "${MULTIBUILD_ID}" in + single-*) + #altivec, sse, single-paired only work for single + myconf+=( + --enable-single + $(use_enable altivec) + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse sse) + $(use_enable cpu_flags_x86_sse2 sse2) + $(use_enable neon) + ${enable_mpi} + ) + ;; + + double-*) + myconf+=( + $(use_enable cpu_flags_x86_avx avx) + $(use_enable cpu_flags_x86_avx2 avx2) + $(use_enable cpu_flags_x86_sse2 sse2) + ${enable_mpi} + ) + ;; + + longdouble-*) + myconf+=( + --enable-long-double + ${enable_mpi} + ) + ;; + + quad-*) + #quad does not support mpi + myconf+=( + --enable-quad-precision + ) + ;; + + *) + die "${MULTIBUILD_ID%-*} precision not implemented in this ebuild" + ;; + esac + + ECONF_SOURCE="${S}" econf "${myconf[@]}" +} + +src_configure() { + multibuild_foreach_variant multilib-minimal_src_configure +} + +src_compile() { + multibuild_foreach_variant multilib-minimal_src_compile +} + +multilib_src_test() { + emake -C tests smallcheck +} + +src_test() { + # We want this to be a reasonably quick test, but that is still hard... + ewarn "This test series will take 30 minutes on a modern 2.5Ghz machine" + # Do not increase the number of threads, it will not help your performance + # local testbase="perl check.pl --nthreads=1 --estimate" + # ${testbase} -${p}d || die "Failure: $n" + + multibuild_foreach_variant multilib-minimal_src_test +} + +src_install() { + DOCS=( AUTHORS ChangeLog NEWS README TODO COPYRIGHT CONVENTIONS ) + HTML_DOCS=( doc/html/ ) + + multibuild_foreach_variant multilib-minimal_src_install + + if use doc; then + dodoc doc/*.pdf + docinto faq + dodoc -r doc/FAQ/fftw-faq.html/. + else + rm -r "${ED}"/usr/share/doc/${PF}/html || die + fi + + local x + for x in "${ED}"/usr/lib*/pkgconfig/*.pc; do + local u + for u in $(usev mpi) $(usev threads) $(usex openmp omp ""); do + sed -e "s|-lfftw3[flq]\?|&_${u} &|" "$x" > "${x%.pc}_${u}.pc" || die + done + done + + # fftw uses pkg-config to record its private dependencies + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-libs/fftw/files/fftw-2.1.5-as-needed.patch b/sci-libs/fftw/files/fftw-2.1.5-as-needed.patch new file mode 100644 index 000000000000..63f46dccc4fd --- /dev/null +++ b/sci-libs/fftw/files/fftw-2.1.5-as-needed.patch @@ -0,0 +1,112 @@ +--- a/rfftw/Makefile.am ++++ b/rfftw/Makefile.am +@@ -18,6 +18,7 @@ + rfftw.h + + lib@FFTW_PREFIX@rfftw_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@ ++lib@FFTW_PREFIX@rfftw_la_LIBADD = ../fftw/lib@FFTW_PREFIX@fftw.la + MAINTAINERCLEANFILES = $(CODELETS) rconfig.c + DISTCLEANFILES = srfftw.h drfftw.h + +--- a/threads/Makefile.am ++++ b/threads/Makefile.am +@@ -28,6 +28,10 @@ + -version-info @SHARED_VERSION_INFO@ \ + -rpath $(libdir) + ++lib@FFTW_PREFIX@fftw_threads_la_LIBADD = \ ++ $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la \ ++ @THREADLIBS@ ++ + @FFTW_PREFIX1@fftw_threads.h: fftw_threads.h + rm -f $@ + sed 's/\"fftw/\"@FFTW_PREFIX@fftw/g;s/\"rfftw/\"@FFTW_PREFIX@rfftw/g' $(srcdir)/fftw_threads.h > $@ +@@ -49,6 +53,11 @@ + -version-info @SHARED_VERSION_INFO@ \ + -rpath $(libdir) + ++lib@FFTW_PREFIX@rfftw_threads_la_LIBADD = \ ++ $(RFFTWDIR)/lib@FFTW_PREFIX@rfftw.la \ ++ $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la \ ++ @THREADLIBS@ ++ + @FFTW_PREFIX1@rfftw_threads.h: rfftw_threads.h + rm -f $@ + sed 's/\"fftw/\"@FFTW_PREFIX@fftw/g;s/\"rfftw/\"@FFTW_PREFIX@rfftw/g' $(srcdir)/rfftw_threads.h > $@ +--- a/mpi/Makefile.am ++++ b/mpi/Makefile.am +@@ -28,6 +28,9 @@ + -version-info @SHARED_VERSION_INFO@ \ + -rpath $(libdir) + ++lib@FFTW_PREFIX@fftw_mpi_la_LIBADD = \ ++ @MPILIBS@ $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la ++ + @FFTW_PREFIX1@fftw_mpi.h: fftw_mpi.h + rm -f $@ + sed 's/\"fftw/\"@FFTW_PREFIX@fftw/g;s/\"rfftw/\"@FFTW_PREFIX@rfftw/g' $(srcdir)/fftw_mpi.h > $@ +@@ -39,32 +42,38 @@ + -version-info @SHARED_VERSION_INFO@ \ + -rpath $(libdir) + +-@FFTW_PREFIX1@rfftw_mpi.h: rfftw_mpi.h ++lib@FFTW_PREFIX@rfftw_mpi_la_LIBADD = \ ++ @MPILIBS@ \ ++ $(RFFTWDIR)/lib@FFTW_PREFIX@rfftw.la \ ++ $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la ++ ++@FFTW_PREFIX1@rfftw_mpi.h: rfftw_mpi.h + rm -f $@ + sed 's/\"fftw/\"@FFTW_PREFIX@fftw/g;s/\"rfftw/\"@FFTW_PREFIX@rfftw/g' $(srcdir)/rfftw_mpi.h > $@ + + CLEANFILES = @FFTW_PREFIX1@fftw_mpi.h @FFTW_PREFIX1@rfftw_mpi.h + + test_sched_SOURCES = test_sched.c +-test_sched_LDADD = lib@FFTW_PREFIX@fftw_mpi.la \ +- $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la @MPILIBS@ ++test_sched_LDADD = @MPILIBS@ lib@FFTW_PREFIX@fftw_mpi.la \ ++ $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la + + test_transpose_mpi_SOURCES = test_transpose_mpi.c +-test_transpose_mpi_LDADD = lib@FFTW_PREFIX@fftw_mpi.la \ +- $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la @MPILIBS@ ++test_transpose_mpi_LDADD = @MPILIBS@ lib@FFTW_PREFIX@fftw_mpi.la \ ++ $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la + + fftw_mpi_test_SOURCES = fftw_mpi_test.c + fftw_mpi_test_LDADD = ../tests/test_main.o \ ++ @MPILIBS@ \ + lib@FFTW_PREFIX@fftw_mpi.la \ +- $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la @MPILIBS@ ++ $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la + + rfftw_mpi_test_SOURCES = rfftw_mpi_test.c + rfftw_mpi_test_LDADD = ../tests/test_main.o \ ++ @MPILIBS@ \ + lib@FFTW_PREFIX@rfftw_mpi.la \ + lib@FFTW_PREFIX@fftw_mpi.la \ + $(RFFTWDIR)/lib@FFTW_PREFIX@rfftw.la \ +- $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la \ +- @MPILIBS@ ++ $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la + + # for some reason, automake tries to use autoheader in order to + # generate config.h.in, and fails because config.h.in is GNU-lly +--- a/mpi/test_sched.c ++++ b/mpi/test_sched.c +@@ -27,6 +27,8 @@ + int **sched; + int npes = -1, sortpe = -1, steps; + ++ /* needed to link with proper mpi libs */ ++ MPI_Init(&argc,&argv); + if (argc >= 2) { + npes = atoi(argv[1]); + if (npes <= 0) { +@@ -121,5 +123,6 @@ + } + } + ++ MPI_Finalize(); + return 0; + } diff --git a/sci-libs/fftw/files/fftw-2.1.5-cc.patch b/sci-libs/fftw/files/fftw-2.1.5-cc.patch new file mode 100644 index 000000000000..aa5c6db038c8 --- /dev/null +++ b/sci-libs/fftw/files/fftw-2.1.5-cc.patch @@ -0,0 +1,19 @@ +--- a/configure.in ++++ b/configure.in +@@ -25,6 +25,8 @@ + AC_ARG_WITH(gcc, [ --with-gcc use gcc instead of the native compiler cc], ok=$withval, ok=no) + if test "$ok" = "yes"; then + CC=gcc ++else ++ CC=$withval + fi + + AC_ARG_ENABLE(float, [ --enable-float compile fftw for single precision], enable_float=$enableval, enable_float=no) +@@ -96,6 +96,7 @@ + AM_PROG_LIBTOOL + AC_CHECK_PROG(PERL, perl, perl, echo perl) + AC_SUBST(PERL) ++AC_SUBST(CC) + + dnl ----------------------------------------------------------------------- + diff --git a/sci-libs/fftw/files/fftw-2.1.5-configure.in.patch b/sci-libs/fftw/files/fftw-2.1.5-configure.in.patch new file mode 100644 index 000000000000..7abe3e751d5d --- /dev/null +++ b/sci-libs/fftw/files/fftw-2.1.5-configure.in.patch @@ -0,0 +1,226 @@ +--- a/configure.in ++++ b/configure.in +@@ -1,6 +1,8 @@ ++ + dnl Process this file with autoconf to produce a configure script. + AC_INIT(fftw/planner.c) + AM_INIT_AUTOMAKE(fftw, 2.1.5) ++AM_MAINTAINER_MODE + + dnl This is the version info according to the libtool versioning system. + dnl It does *not* correspond to the release number. +@@ -27,7 +29,7 @@ + + AC_ARG_ENABLE(float, [ --enable-float compile fftw for single precision], enable_float=$enableval, enable_float=no) + if test "$enable_float" = "yes"; then +- AC_DEFINE(FFTW_ENABLE_FLOAT) ++ AC_DEFINE(FFTW_ENABLE_FLOAT,1,[Compile fftw for single precision]) + fi + + FFTW_PREFIX="" +@@ -56,27 +58,27 @@ + + AC_ARG_ENABLE(i386-hacks, [ --enable-i386-hacks enable gcc/x86 specific performance hacks], ok=$enableval, ok=no) + if test "$ok" = "yes"; then +- AC_DEFINE(FFTW_ENABLE_I386_HACKS) ++ AC_DEFINE(FFTW_ENABLE_I386_HACKS,1,[Enable x86 specific performance hacks]) + fi + + AC_ARG_ENABLE(pentium-timer, [ --enable-pentium-timer enable high resolution Pentium timer], ok=$enableval, ok=no) + if test "$ok" = "yes"; then +- AC_DEFINE(FFTW_ENABLE_PENTIUM_TIMER) ++ AC_DEFINE(FFTW_ENABLE_PENTIUM_TIMER,1,[Enable high resolution Pentium timer]) + fi + + AC_ARG_ENABLE(debug, [ --enable-debug compile fftw with extra runtime checks for debugging], ok=$enableval, ok=no) + if test "$ok" = "yes"; then +- AC_DEFINE(FFTW_DEBUG) ++ AC_DEFINE(FFTW_DEBUG,1,[Compile with extra rutime checks for debugging]) + fi + + AC_ARG_ENABLE(debug-alignment, [ --enable-debug-alignment enable runtime checks for alignment on x86], ok=$enableval, ok=no) + if test "$ok" = "yes"; then +- AC_DEFINE(FFTW_DEBUG_ALIGNMENT) ++ AC_DEFINE(FFTW_DEBUG_ALIGNMENT,1,[Enable rutime checks for alignment on x86]) + fi + + AC_ARG_ENABLE(vec-recurse, [ --enable-vec-recurse enable experimental performance hack], ok=$enableval, ok=no) + if test "$ok" = "yes"; then +- AC_DEFINE(FFTW_ENABLE_VECTOR_RECURSE) ++ AC_DEFINE(FFTW_ENABLE_VECTOR_RECURSE,1,[Enable experimental performance hack]) + fi + + dnl ----------------------------------------------------------------------- +@@ -90,7 +92,6 @@ + ACX_PROG_CC_EGCS + AC_PROG_INSTALL + AC_PROG_MAKE_SET +-AC_PROG_RANLIB + AC_PROG_LN_S + AM_PROG_LIBTOOL + AC_CHECK_PROG(PERL, perl, perl, echo perl) +@@ -115,7 +116,7 @@ + dnl ----------------------------------------------------------------------- + + AC_SUBST(SHARED_VERSION_INFO) +-AC_DEFINE_UNQUOTED(FFTW_VERSION, "$VERSION") ++AC_DEFINE_UNQUOTED(FFTW_VERSION, "$VERSION",[Fftw Version]) + + # Get the version number that will be appended to shared libraries: + SHARED_VERSION=`echo $SHARED_VERSION_INFO | awk -F':' '{ print $1 "." $3 "." $2 }'` +@@ -123,7 +124,7 @@ + + ACX_PROG_CC_MAXOPT + +-ACX_GCC_ALIGNS_STACK(AC_DEFINE(FFTW_GCC_ALIGNS_STACK), [ ++ACX_GCC_ALIGNS_STACK(AC_DEFINE(FFTW_GCC_ALIGNS_STACK,1,[Gcc align stack]), [ + if test "$enable_i386_hacks" = yes; then + if test "${acx_gcc_stack_align_bug-no}" = yes; then + # we are using a gcc with a stack alignment bug, and we should +@@ -183,7 +184,7 @@ + AC_TRY_LINK([#include <math.h> + ], if (!isnan(3.14159)) isnan(2.7183);, ok=yes, ok=no) + if test "$ok" = "yes"; then +- AC_DEFINE(HAVE_ISNAN) ++ AC_DEFINE(HAVE_ISNAN,1,[Have isnan]) + fi + AC_MSG_RESULT(${ok}) + +@@ -196,7 +197,7 @@ + #endif + ], [hrtime_t foobar;], ok=yes, ok=no) + if test "$ok" = "yes"; then +- AC_DEFINE(HAVE_HRTIME_T) ++ AC_DEFINE(HAVE_HRTIME_T,1,[Have hrtime_t type]) + fi + AC_MSG_RESULT(${ok}) + +@@ -205,7 +206,7 @@ + + AC_ARG_ENABLE(unsafe-mulmod, [ --enable-unsafe-mulmod risk overflow for large prime sizes], enable_unsafe_mulmod=$enableval, enable_unsafe_mulmod=no) + if test "$enable_unsafe_mulmod" = "yes"; then +- AC_DEFINE(FFTW_ENABLE_UNSAFE_MULMOD) ++ AC_DEFINE(FFTW_ENABLE_UNSAFE_MULMOD,1,[Risk overflow for lar prime sizes]) + fi + + +@@ -221,15 +222,25 @@ + FFTW_THREADS_INCLUDELIST="" + FFTW_THREADS_PROGLIST="" + THREADLIBS="" ++omp_enabler=unknown + if test "$enable_threads" = "yes"; then + if test "$with_openmp"x != nox; then + AC_MSG_CHECKING(how to enable OpenMP) +- omp_enabler=unknown + save_CFLAGS="$CFLAGS" + CFLAGS="$save_CFLAGS -omp" + AC_TRY_LINK_FUNC(omp_set_num_threads,THREADLIBS=" " + omp_enabler="$CC -omp") + if test -z "$THREADLIBS"; then ++ CFLAGS="$save_CFLAGS -fopenmp" ++ AC_TRY_LINK_FUNC(omp_set_num_threads,THREADLIBS="-lgomp" ++ omp_enabler="$CC -fopenmp") ++ fi ++ if test -z "$THREADLIBS"; then ++ CFLAGS="$save_CFLAGS -openmp" ++ AC_TRY_LINK_FUNC(omp_set_num_threads,THREADLIBS=" " ++ omp_enabler="$CC -openmp") ++ fi ++ if test -z "$THREADLIBS"; then + CFLAGS="$save_CFLAGS -mp" + AC_TRY_LINK_FUNC(omp_set_num_threads,THREADLIBS=" " + omp_enabler="$CC -mp") +@@ -240,68 +251,70 @@ + omp_enabler="automatic") + fi + AC_MSG_RESULT($omp_enabler) +- if test -z "$THREADLIBS"; then +- AC_MSG_ERROR([don't know how to enable OpenMP]) ++ if test x"$omp_enabler" != x"unknown"; then ++ AC_DEFINE(FFTW_USING_OPENMP_THREADS,1,[Using OpenMP threads]) ++ else ++ AC_MSG_WARN([don't know how to enable OpenMP, reverting to POSIX threads]) + fi +- AC_DEFINE(FFTW_USING_OPENMP_THREADS) ++ + fi + if test "$with_sgimp"x != nox; then + AC_MSG_CHECKING(how to enable SGI MP) + mp_enabler=unknown + save_CFLAGS="$CFLAGS" + CFLAGS="$save_CFLAGS -mp" +- AC_TRY_LINK_FUNC(mp_set_numthreads,THREADLIBS=" " ++ AC_TRY_LINK_FUNC(mp_set_numthreads,THREADLIBS="" + mp_enabler="$CC -mp") + if test -z "$THREADLIBS"; then + CFLAGS="$save_CFLAGS" +- AC_TRY_LINK_FUNC(mp_numthreads,THREADLIBS=" " ++ AC_TRY_LINK_FUNC(mp_numthreads,THREADLIBS="" + mp_enabler="automatic") + fi + AC_MSG_RESULT($mp_enabler) + if test -z "$THREADLIBS"; then + AC_MSG_ERROR([don't know how to enable SGI MP]) + fi +- AC_DEFINE(FFTW_USING_SGIMP_THREADS) ++ AC_DEFINE(FFTW_USING_SGIMP_THREADS,1,[Using SGIMP Threads]) + fi + + # POSIX threads, the default choice: +- if test -z "$THREADLIBS"; then ++ if test x"$omp_enabler" = x"unknown" ; then + sinclude(acx_pthread.m4) + ACX_PTHREAD([THREADLIBS="$PTHREAD_LIBS " + CFLAGS="$CFLAGS $PTHREAD_CFLAGS" + CC="$PTHREAD_CC" +- AC_DEFINE(FFTW_USING_POSIX_THREADS)]) ++ AC_DEFINE(FFTW_USING_POSIX_THREADS,1,[Using POSIX Threads])]) + fi + # Solaris threads: + if test -z "$THREADLIBS"; then + AC_CHECK_LIB(thread, thr_create, + [THREADLIBS="-lthread" +- AC_DEFINE(FFTW_USING_SOLARIS_THREADS)]) ++ AC_DEFINE(FFTW_USING_SOLARIS_THREADS,1,[Using SOLARIS Threads])]) + fi + # Mach C threads: + if test -z "$THREADLIBS"; then + AC_CHECK_FUNC(cthread_fork, + [THREADLIBS=" " +- AC_DEFINE(FFTW_USING_MACH_THREADS)]) ++ AC_DEFINE(FFTW_USING_MACH_THREADS,1,[Using Mach Threads])]) + AC_CHECK_HEADERS(mach/cthreads.h cthreads.h cthread.h) + fi + if test -z "$THREADLIBS"; then + AC_CHECK_LIB(cthread, cthread_fork, + [THREADLIBS="-lcthread" +- AC_DEFINE(FFTW_USING_MACH_THREADS)]) ++ AC_DEFINE(FFTW_USING_MACH_THREADS,1,[Using Mach Threads])]) + AC_CHECK_HEADERS(mach/cthreads.h cthreads.h cthread.h) + fi + if test -z "$THREADLIBS"; then + AC_CHECK_LIB(cthreads, cthread_fork, + [THREADLIBS="-lcthreads" +- AC_DEFINE(FFTW_USING_MACH_THREADS)]) ++ AC_DEFINE(FFTW_USING_MACH_THREADS,1,[Using Mach Threads])]) + AC_CHECK_HEADERS(mach/cthreads.h cthreads.h cthread.h) + fi + # BeOS threads: + if test -z "$THREADLIBS"; then + AC_CHECK_FUNC(spawn_thread, + [THREADLIBS=" " +- AC_DEFINE(FFTW_USING_BEOS_THREADS)]) ++ AC_DEFINE(FFTW_USING_BEOS_THREADS,1,[Using BEOS Threads])]) + fi + if test -z "$THREADLIBS"; then + AC_MSG_ERROR(couldn't find threads library for --enable-threads) +@@ -334,7 +347,7 @@ + CC="$MPICC" + ok=yes + AC_TRY_LINK([#include <mpi.h> +- ], [MPI_Comm_f2c(0);], [AC_DEFINE(HAVE_MPI_COMM_F2C)], [ok=no]) ++ ], [MPI_Comm_f2c(0);], [AC_DEFINE(HAVE_MPI_COMM_F2C,1,[Has MPI COMM F2C])], [ok=no]) + AC_MSG_RESULT($ok) + CC="$save_CC" + else diff --git a/sci-libs/fftw/files/fftw-2.1.5-no-test.patch b/sci-libs/fftw/files/fftw-2.1.5-no-test.patch new file mode 100644 index 000000000000..cc844a455e66 --- /dev/null +++ b/sci-libs/fftw/files/fftw-2.1.5-no-test.patch @@ -0,0 +1,33 @@ +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -1,4 +1,4 @@ +-noinst_PROGRAMS = fftw_test rfftw_test ++check_PROGRAMS = fftw_test rfftw_test + noinst_HEADERS = test_main.h + + FFTWDIR=../fftw +--- a/mpi/Makefile.am ++++ b/mpi/Makefile.am +@@ -4,8 +4,8 @@ + + lib_LTLIBRARIES = @FFTW_MPI_LIBLIST@ + include_HEADERS = @FFTW_MPI_INCLUDELIST@ +-noinst_PROGRAMS = @FFTW_MPI_PROGLIST@ ++check_PROGRAMS = @FFTW_MPI_PROGLIST@ + + EXTRA_LTLIBRARIES = lib@FFTW_PREFIX@fftw_mpi.la \ + lib@FFTW_PREFIX@rfftw_mpi.la + EXTRA_HEADERS = @FFTW_PREFIX@fftw_mpi.h @FFTW_PREFIX@rfftw_mpi.h +--- a/threads/Makefile.am ++++ b/threads/Makefile.am +@@ -4,9 +4,9 @@ + + lib_LTLIBRARIES = @FFTW_THREADS_LIBLIST@ + include_HEADERS = @FFTW_THREADS_INCLUDELIST@ +-noinst_PROGRAMS = @FFTW_THREADS_PROGLIST@ ++check_PROGRAMS = @FFTW_THREADS_PROGLIST@ + + EXTRA_LTLIBRARIES = lib@FFTW_PREFIX@fftw_threads.la \ + lib@FFTW_PREFIX@rfftw_threads.la + EXTRA_HEADERS = @FFTW_PREFIX@fftw_threads.h \ + @FFTW_PREFIX@rfftw_threads.h diff --git a/sci-libs/fftw/files/fftw-2.1.5-parallel-tests.patch b/sci-libs/fftw/files/fftw-2.1.5-parallel-tests.patch new file mode 100644 index 000000000000..b92e6dad299c --- /dev/null +++ b/sci-libs/fftw/files/fftw-2.1.5-parallel-tests.patch @@ -0,0 +1,105 @@ +Fix failure of parallel test suite. This is due to +misspecification of the test suite, which requires +first compiling $(check_PROGRAMS) and only then +running $(TESTS): + +* check-am: all-am +* $(MAKE) $(AM_MAKEFLAGS) $(check_PROGRAMS) +* $(MAKE) $(AM_MAKEFLAGS) check-TESTS + +The old build system never specified $(TESTS) and +erroneously made the check target depend on the +two tests. +See also: https://bugs.gentoo.org/show_bug.cgi?id=603352 + +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -12,22 +12,7 @@ + rfftw_test_LDADD = $(RFFTWDIR)/lib@FFTW_PREFIX@rfftw.la \ + $(FFTWDIR)/lib@FFTW_PREFIX@fftw.la + +-check: fftw-tests rfftw-tests ++TESTS = myfftwtests.sh myrfftwtests.sh + +-fftw-tests: fftw_test +- ./fftw_test -p 0 +- ./fftw_test -x 128 -a 0 +- ./fftw_test -x 32 -a 2 +- ./fftw_test -x 100 -r 0 +- @echo "--------------------------------------------------------------" +- @echo " FFTW complex-complex transforms passed tests!" +- @echo "--------------------------------------------------------------" +- +-rfftw-tests: rfftw_test +- ./rfftw_test -p 0 +- ./rfftw_test -x 128 -a 0 +- ./rfftw_test -x 32 -a 2 +- ./rfftw_test -x 100 -r 0 +- @echo "--------------------------------------------------------------" +- @echo " RFFTW real-complex transforms passed tests!" +- @echo "--------------------------------------------------------------" ++TEST_EXTENSIONS = .sh ++SH_LOG_COMPILER = $(SHELL) +--- a/tests/myfftwtests.sh ++++ b/tests/myfftwtests.sh +@@ -0,0 +1,4 @@ ++./fftw_test -p 0 && \ ++./fftw_test -x 128 -a 0 && \ ++./fftw_test -x 32 -a 2 && \ ++./fftw_test -x 100 -r 0 +--- a/tests/myrfftwtests.sh ++++ b/tests/myrfftwtests.sh +@@ -0,0 +1,4 @@ ++./rfftw_test -p 0 && \ ++./rfftw_test -x 128 -a 0 && \ ++./rfftw_test -x 32 -a 2 && \ ++./rfftw_test -x 100 -r 0 +--- a/threads/fftw_threads_test_check.sh ++++ b/threads/fftw_threads_test_check.sh +@@ -0,0 +1,4 @@ ++./fftw_threads_test 1 -x 100 -r 0 && \ ++./fftw_threads_test 2 -x 100 -r 0 && \ ++./fftw_threads_test 3 -x 100 -r 0 && \ ++./fftw_threads_test 10 -x 100 -r 0 +--- a/threads/Makefile.am ++++ b/threads/Makefile.am +@@ -78,29 +78,7 @@ + # incorrect. Just disable autoheader + AUTOHEADER=echo + +-check: @FFTW_THREADS_PROGLIST@ +- @set fnord $(MAKEFLAGS); amf=$$2; \ +- list='@FFTW_THREADS_PROGLIST@'; for prog in $$list; do \ +- target="$$prog""-check"; \ +- echo "Making $$target"; \ +- ($(MAKE) $$target) \ +- || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \ +- done && test -z "$$fail" ++TESTS = fftw_threads_test_check.sh rfftw_threads_test_check.sh + +-fftw_threads_test-check: fftw_threads_test +- ./fftw_threads_test 1 -x 100 -r 0 +- ./fftw_threads_test 2 -x 100 -r 0 +- ./fftw_threads_test 3 -x 100 -r 0 +- ./fftw_threads_test 10 -x 100 -r 0 +- @echo "--------------------------------------------------------------" +- @echo " FFTW complex-complex threads transforms passed tests!" +- @echo "--------------------------------------------------------------" +- +-rfftw_threads_test-check: rfftw_threads_test +- ./rfftw_threads_test 1 -x 100 -r 0 +- ./rfftw_threads_test 2 -x 100 -r 0 +- ./rfftw_threads_test 3 -x 100 -r 0 +- ./rfftw_threads_test 10 -x 100 -r 0 +- @echo "--------------------------------------------------------------" +- @echo " RFFTW real-complex threads transforms passed tests!" +- @echo "--------------------------------------------------------------" ++TEST_EXTENSIONS = .sh ++SH_LOG_COMPILER = $(SHELL) +--- a/threads/rfftw_threads_test_check.sh ++++ b/threads/rfftw_threads_test_check.sh +@@ -0,0 +1,4 @@ ++./rfftw_threads_test 1 -x 100 -r 0 && \ ++./rfftw_threads_test 2 -x 100 -r 0 && \ ++./rfftw_threads_test 3 -x 100 -r 0 && \ ++./rfftw_threads_test 10 -x 100 -r 0 diff --git a/sci-libs/fftw/files/fftw-2.1.5-texinfo5.1.patch b/sci-libs/fftw/files/fftw-2.1.5-texinfo5.1.patch new file mode 100644 index 000000000000..1947bef8f21f --- /dev/null +++ b/sci-libs/fftw/files/fftw-2.1.5-texinfo5.1.patch @@ -0,0 +1,21 @@ + doc/fftw.texi | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/doc/fftw.texi b/doc/fftw.texi +index 90e8bb6..85a7a53 100644 +--- a/doc/fftw.texi ++++ b/doc/fftw.texi +@@ -46,10 +46,10 @@ approved by the Free Software Foundation. + @titlepage + @sp 10 + @comment The title is printed in a large font. +-@title{FFTW User's Manual} ++@title FFTW User's Manual + @subtitle For version @value{VERSION}, @value{UPDATED} +-@author{Matteo Frigo} +-@author{Steven G. Johnson} ++@author Matteo Frigo ++@author Steven G. Johnson + + @c The following two commands start the copyright page. + @page diff --git a/sci-libs/fftw/metadata.xml b/sci-libs/fftw/metadata.xml new file mode 100644 index 000000000000..38679de9df3e --- /dev/null +++ b/sci-libs/fftw/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The Fastest Fourier Transform in the West is a C subroutine library + for computing the Discrete Fourier Transform (DFT) in one or more + dimensions, of both real and complex data, and of arbitrary input + size. It is becoming the FFT library of choice for most + applications. Benchmarks, performed on a variety of platforms, show + that FFTW's performance is typically superior to that of other + publicly available FFT software. +</longdescription> + <use> + <flag name="float">Link default library to single precision instead of + double (symlinks only and fftw-2.1)</flag> + <flag name="quad">Build quadruple precision lib</flag> + <flag name="zbus">Adds support for ZBus cycle-counter of mips</flag> + </use> + <upstream> + <remote-id type="freecode">fftw</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/flann/Manifest b/sci-libs/flann/Manifest new file mode 100644 index 000000000000..cbab70163276 --- /dev/null +++ b/sci-libs/flann/Manifest @@ -0,0 +1,15 @@ +AUX flann-1.8.4-CUDA_NVCC_FLAGS.patch 618 SHA256 62e8810e965e57c83b45ab1c2d2f316df7ad8dc898751df8d2fc5204ffc8cfda SHA512 8a6e385b0b36386288861bb795fda34cc636d73862c1321fc4482855dd5032179bf3ea0016bd7c51e8d6abf0da3b70f6d22058d8fd2da414db09b2e2bb662a7b WHIRLPOOL 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--git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt +index 8e72409..a4b35b1 100644 +--- a/src/cpp/CMakeLists.txt ++++ b/src/cpp/CMakeLists.txt +@@ -15,7 +15,7 @@ endif() + set_property(TARGET flann_cpp_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC FLANN_USE_CUDA) + + if (BUILD_CUDA_LIB) +- SET(CUDA_NVCC_FLAGS -DFLANN_USE_CUDA) ++ SET(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};-DFLANN_USE_CUDA") + if(CMAKE_COMPILER_IS_GNUCC) + set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};-Xcompiler;-fPIC;-arch=sm_13" ) + if (NVCC_COMPILER_BINDIR) diff --git a/sci-libs/flann/files/flann-1.8.4-cuda5.5.patch b/sci-libs/flann/files/flann-1.8.4-cuda5.5.patch new file mode 100644 index 000000000000..046b3252c36f --- /dev/null +++ b/sci-libs/flann/files/flann-1.8.4-cuda5.5.patch @@ -0,0 +1,61 @@ + src/cpp/flann/util/cuda/result_set.h | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/src/cpp/flann/util/cuda/result_set.h b/src/cpp/flann/util/cuda/result_set.h +index 9ac8111..324ca1e 100644 +--- a/src/cpp/flann/util/cuda/result_set.h ++++ b/src/cpp/flann/util/cuda/result_set.h +@@ -54,7 +54,7 @@ struct SingleResultSet + DistanceType bestDist; + const DistanceType epsError; + +- __device__ ++ __device__ __host__ + SingleResultSet( DistanceType eps ) : bestIndex(-1),bestDist(INFINITY), epsError(eps){ } + + __device__ +@@ -129,7 +129,7 @@ struct KnnResultSet + const DistanceType epsError; + + +- __device__ ++ __device__ __host__ + KnnResultSet(int knn, bool sortResults, DistanceType eps) : foundNeighbors(0),largestHeapDist(INFINITY),k(knn), sorted(sortResults), epsError(eps){ } + + // __host__ __device__ +@@ -229,7 +229,7 @@ struct CountingRadiusResultSet + DistanceType radius_sq_; + int max_neighbors_; + +- __device__ ++ __device__ __host__ + CountingRadiusResultSet(DistanceType radius, int max_neighbors) : count_(0),radius_sq_(radius), max_neighbors_(max_neighbors){ } + + __device__ +@@ -279,7 +279,7 @@ struct RadiusKnnResultSet + // int count_; + + +- __device__ ++ __device__ __host__ + RadiusKnnResultSet(DistanceType radius, int knn, int* segment_starts, bool sortResults) : foundNeighbors(0),largestHeapDist(radius),k(knn), sorted(sortResults), radius_sq_(radius),segment_starts_(segment_starts) { } + + // __host__ __device__ +@@ -381,7 +381,7 @@ struct KnnRadiusResultSet + const DistanceType radius_sq; + + +- __device__ ++ __device__ __host__ + KnnRadiusResultSet(int knn, bool sortResults, DistanceType eps, DistanceType radius) : foundNeighbors(0),largestHeapDist(radius),k(knn), sorted(sortResults), epsError(eps),radius_sq(radius){ } + + // __host__ __device__ +@@ -484,7 +484,7 @@ struct RadiusResultSet + int count_; + bool sorted_; + +- __device__ ++ __device__ __host__ + RadiusResultSet(DistanceType radius, int* segment_starts, bool sorted) : radius_sq_(radius), segment_starts_(segment_starts), count_(0), sorted_(sorted){ } + + __device__ diff --git a/sci-libs/flann/files/flann-1.8.4-docdir.patch b/sci-libs/flann/files/flann-1.8.4-docdir.patch new file mode 100644 index 000000000000..4b16684de14d --- /dev/null +++ b/sci-libs/flann/files/flann-1.8.4-docdir.patch @@ -0,0 +1,24 @@ + doc/CMakeLists.txt | 6 +++++- + 1 file changed, 5 insertions(+), 1 deletion(-) + +diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt +index 2d8eb24..aeac8ed 100644 +--- a/doc/CMakeLists.txt ++++ b/doc/CMakeLists.txt +@@ -1,4 +1,8 @@ + find_package(LATEX) ++ ++if (NOT DOCDIR) ++ set(DOCDIR share/doc/flann) ++endif () + + if (EXISTS ${PDFLATEX_COMPILER} AND EXISTS ${BIBTEX_COMPILER}) + include(${PROJECT_SOURCE_DIR}/cmake/UseLATEX.cmake) +@@ -14,6 +18,6 @@ endif() + + install( + FILES manual.pdf +- DESTINATION share/doc/flann ++ DESTINATION ${DOCDIR} + OPTIONAL + ) diff --git a/sci-libs/flann/files/flann-1.8.4-examples.patch b/sci-libs/flann/files/flann-1.8.4-examples.patch new file mode 100644 index 000000000000..b3346b35f73c --- /dev/null +++ b/sci-libs/flann/files/flann-1.8.4-examples.patch @@ -0,0 +1,35 @@ +From 3922081fbd6710f4b72421069f6bf24dc37d35a8 Mon Sep 17 00:00:00 2001 +From: Casey Goodlett <casey.goodlett@kitware.com> +Date: Thu, 8 Aug 2013 18:42:45 -0400 +Subject: [PATCH] Option to disable example building + +--- + CMakeLists.txt | 5 ++++- + 1 file changed, 4 insertions(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 5b19367..410a8f9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -53,6 +53,7 @@ option(BUILD_C_BINDINGS "Build C bindings" ON) + option(BUILD_PYTHON_BINDINGS "Build Python bindings" ON) + option(BUILD_MATLAB_BINDINGS "Build Matlab bindings" ON) + option(BUILD_CUDA_LIB "Build CUDA library" OFF) ++option(BUILD_EXAMPLES "Build examples" ON) + option(USE_OPENMP "Use OpenMP multi-threading" ON) + option(USE_MPI "Use MPI" OFF) + +@@ -154,7 +155,9 @@ endif() + + add_subdirectory( cmake ) + add_subdirectory( src ) +-add_subdirectory( examples ) ++if (BUILD_EXAMPLES) ++ add_subdirectory( examples ) ++endif(BUILD_EXAMPLES) + add_subdirectory( test ) + add_subdirectory( doc ) + +-- +1.8.5.1 + diff --git a/sci-libs/flann/files/flann-1.8.4-multilib.patch b/sci-libs/flann/files/flann-1.8.4-multilib.patch new file mode 100644 index 000000000000..17a9d65dd778 --- /dev/null +++ b/sci-libs/flann/files/flann-1.8.4-multilib.patch @@ -0,0 +1,15 @@ + cmake/flann_utils.cmake | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/cmake/flann_utils.cmake b/cmake/flann_utils.cmake +index 1a10939..afe4742 100644 +--- a/cmake/flann_utils.cmake ++++ b/cmake/flann_utils.cmake +@@ -1,6 +1,6 @@ + macro(GET_OS_INFO) + string(REGEX MATCH "Linux" OS_IS_LINUX ${CMAKE_SYSTEM_NAME}) +- set(FLANN_LIB_INSTALL_DIR "lib") ++ set(FLANN_LIB_INSTALL_DIR "lib${LIB_SUFFIX}") + set(FLANN_INCLUDE_INSTALL_DIR + "include/${PROJECT_NAME_LOWER}-${FLANN_MAJOR_VERSION}.${FLANN_MINOR_VERSION}") + endmacro(GET_OS_INFO) diff --git a/sci-libs/flann/files/flann-1.8.4-options.patch b/sci-libs/flann/files/flann-1.8.4-options.patch new file mode 100644 index 000000000000..dd212aca66a4 --- /dev/null +++ b/sci-libs/flann/files/flann-1.8.4-options.patch @@ -0,0 +1,41 @@ + CMakeLists.txt | 13 +++++++++++-- + 1 file changed, 11 insertions(+), 2 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 410a8f9..b6244a4 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -54,6 +54,8 @@ option(BUILD_PYTHON_BINDINGS "Build Python bindings" ON) + option(BUILD_MATLAB_BINDINGS "Build Matlab bindings" ON) + option(BUILD_CUDA_LIB "Build CUDA library" OFF) + option(BUILD_EXAMPLES "Build examples" ON) ++option(BUILD_TESTS "Build tests" ON) ++option(BUILD_DOC "Build documentation" ON) + option(USE_OPENMP "Use OpenMP multi-threading" ON) + option(USE_MPI "Use MPI" OFF) + +@@ -158,8 +160,12 @@ add_subdirectory( src ) + if (BUILD_EXAMPLES) + add_subdirectory( examples ) + endif(BUILD_EXAMPLES) +-add_subdirectory( test ) +-add_subdirectory( doc ) ++if (BUILD_TESTS) ++ add_subdirectory( test ) ++endif (BUILD_TESTS) ++if (BUILD_DOC) ++ add_subdirectory( doc ) ++endif (BUILD_DOC) + + + # CPACK options +@@ -202,6 +208,9 @@ include(CPack) + message(STATUS "Install prefix: ${CMAKE_INSTALL_PREFIX}") + message(STATUS "Build type: ${CMAKE_BUILD_TYPE}") + message(STATUS "Building C bindings: ${BUILD_C_BINDINGS}") ++message(STATUS "Building examples: ${BUILD_EXAMPLES}") ++message(STATUS "Building tests: ${BUILD_TESTS}") ++message(STATUS "Building documentation: ${BUILD_DOC}") + message(STATUS "Building python bindings: ${BUILD_PYTHON_BINDINGS}") + message(STATUS "Building matlab bindings: ${BUILD_MATLAB_BINDINGS}") + message(STATUS "Building CUDA library: ${BUILD_CUDA_LIB}") diff --git a/sci-libs/flann/flann-1.8.4-r1.ebuild b/sci-libs/flann/flann-1.8.4-r1.ebuild new file mode 100644 index 000000000000..00be826a33e5 --- /dev/null +++ b/sci-libs/flann/flann-1.8.4-r1.ebuild @@ -0,0 +1,108 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils cuda eutils multilib toolchain-funcs + +DESCRIPTION="Fast approximate nearest neighbor searches in high dimensional spaces" +HOMEPAGE="http://www.cs.ubc.ca/research/flann/" +SRC_URI=" + http://people.cs.ubc.ca/~mariusm/uploads/FLANN/${P}-src.zip + test? ( https://dev.gentoo.org/~bicatali/distfiles/${P}-testdata.tar.xz )" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~arm ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda doc examples mpi openmp octave static-libs test" + +RDEPEND=" + cuda? ( >=dev-util/nvidia-cuda-toolkit-5.5 ) + mpi? ( + sci-libs/hdf5[mpi] + dev-libs/boost[mpi] + ) + !mpi? ( !sci-libs/hdf5[mpi] ) + octave? ( >=sci-mathematics/octave-3.6.4-r1 )" +DEPEND="${RDEPEND} + app-arch/unzip + doc? ( dev-tex/latex2html ) + test? ( + dev-cpp/gtest + cuda? ( sci-libs/hdf5 ) + ) +" + +PATCHES=( + "${FILESDIR}"/${P}-examples.patch + "${FILESDIR}"/${P}-options.patch + "${FILESDIR}"/${P}-CUDA_NVCC_FLAGS.patch + "${FILESDIR}"/${P}-cuda5.5.patch + "${FILESDIR}"/${P}-multilib.patch + "${FILESDIR}"/${P}-docdir.patch +) + +S="${WORKDIR}"/${P}-src + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp ; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + fi +} + +src_prepare() { + # bug #302621 + use mpi && export CXX=mpicxx + # produce pure octave files + # octave gentoo installation for .m files respected + sed -i \ + -e 's/--mex//' \ + -e 's/\.mex/\.oct/' \ + -e '/FILES/s/${MEX_FILE}//' \ + -e 's:share/flann/octave:share/octave/site/m:' \ + -e "/CUSTOM_TARGET/a\INSTALL(FILES \${MEX_FILE} DESTINATION libexec/octave/site/oct/${CHOST})" \ + src/matlab/CMakeLists.txt || die + use cuda && cuda_src_prepare + + cmake-utils_src_prepare +} + +src_configure() { + # python bindings are split + local mycmakeargs=( + -DBUILD_C_BINDINGS=ON + -DBUILD_PYTHON_BINDINGS=OFF + -DPYTHON_EXECUTABLE= + -DDOCDIR=share/doc/${PF} + $(cmake-utils_use_build cuda CUDA_LIB) + $(cmake-utils_use_build examples) + $(cmake-utils_use_build doc) + $(cmake-utils_use_build test TESTS) + $(cmake-utils_use_build octave MATLAB_BINDINGS) + $(cmake-utils_use_use mpi) + $(cmake-utils_use_use openmp) + ) + use cuda && \ + mycmakeargs+=( + -DCUDA_NVCC_FLAGS="${NVCCFLAGS},-arsch" + ) + cmake-utils_src_configure +} + +src_test() { + ln -s "${WORKDIR}"/testdata/* test/ || die + # -j1 to avoid obversubscribing jobs + LD_LIBRARY_PATH="${BUILD_DIR}/lib" \ + cmake-utils_src_compile -j1 test +} + +src_install() { + cmake-utils_src_install + dodoc README.md + if ! use static-libs; then + find "${ED}" -name 'lib*.a' -exec rm -rf '{}' '+' || die + fi +} diff --git a/sci-libs/flann/flann-1.9.1.ebuild b/sci-libs/flann/flann-1.9.1.ebuild new file mode 100644 index 000000000000..cc7583379a9b --- /dev/null +++ b/sci-libs/flann/flann-1.9.1.ebuild @@ -0,0 +1,86 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils cuda flag-o-matic toolchain-funcs + +DESCRIPTION="Fast approximate nearest neighbor searches in high dimensional spaces" +HOMEPAGE="http://www.cs.ubc.ca/research/flann/" +SRC_URI="https://github.com/mariusmuja/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~arm ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda doc examples mpi openmp octave static-libs" + +RDEPEND=" + cuda? ( >=dev-util/nvidia-cuda-toolkit-5.5 ) + mpi? ( + sci-libs/hdf5[mpi] + dev-libs/boost:=[mpi] + ) + !mpi? ( !sci-libs/hdf5[mpi] ) + octave? ( >=sci-mathematics/octave-3.6.4-r1 )" +DEPEND="${RDEPEND} + app-arch/unzip + doc? ( dev-tex/latex2html )" +# TODO: +# readd dependencies for test suite, +# requires multiple ruby dependencies + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +src_prepare() { + # bug #302621 + use mpi && export CXX=mpicxx + # produce pure octave files + # octave gentoo installation for .m files respected + sed -i \ + -e 's/--mex//' \ + -e 's/\.mex/\.oct/' \ + -e '/FILES/s/${MEX_FILE}//' \ + -e 's:share/flann/octave:share/octave/site/m:' \ + -e "/CUSTOM_TARGET/a\INSTALL(FILES \${MEX_FILE} DESTINATION libexec/octave/site/oct/${CHOST})" \ + src/matlab/CMakeLists.txt || die + use cuda && cuda_src_prepare + + cmake-utils_src_prepare +} + +src_configure() { + append-cxxflags -std=c++11 + + # python bindings are split + # off into dev-python/pyflann + local mycmakeargs=( + -DBUILD_C_BINDINGS=ON + -DBUILD_PYTHON_BINDINGS=OFF + -DPYTHON_EXECUTABLE= + -DDOCDIR=share/doc/${PF} + -DBUILD_CUDA_LIB=$(usex cuda) + -DBUILD_EXAMPLES=$(usex examples) + -DBUILD_DOC=$(usex doc) + -DBUILD_TESTS=OFF + -DBUILD_MATLAB_BINDINGS=$(usex octave) + -DUSE_MPI=$(usex mpi) + -DUSE_OPENMP=$(usex openmp) + ) + use cuda && mycmakeargs+=( + -DCUDA_NVCC_FLAGS="${NVCCFLAGS},-arsch" + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if ! use static-libs; then + find "${D}" -name 'lib*.a' -delete || die + fi +} diff --git a/sci-libs/flann/flann-9999.ebuild b/sci-libs/flann/flann-9999.ebuild new file mode 100644 index 000000000000..2f25498da1dc --- /dev/null +++ b/sci-libs/flann/flann-9999.ebuild @@ -0,0 +1,102 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils cuda eutils git-r3 multilib toolchain-funcs + +DESCRIPTION="Fast approximate nearest neighbor searches in high dimensional spaces" +HOMEPAGE="http://www.cs.ubc.ca/research/flann/" +SRC_URI="test? ( https://dev.gentoo.org/~bicatali/distfiles/${PN}-1.8.4-testdata.tar.xz )" +EGIT_REPO_URI="https://github.com/mariusmuja/flann.git" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="" +IUSE="cuda doc examples mpi openmp octave static-libs test" + +RDEPEND=" + cuda? ( >=dev-util/nvidia-cuda-toolkit-5.5 ) + mpi? ( + sci-libs/hdf5[mpi] + dev-libs/boost[mpi] + ) + !mpi? ( !sci-libs/hdf5[mpi] ) + octave? ( >=sci-mathematics/octave-3.6.4-r1 )" +DEPEND="${RDEPEND} + app-arch/unzip + doc? ( dev-tex/latex2html ) + test? ( + dev-cpp/gtest + cuda? ( sci-libs/hdf5 ) + ) +" + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp ; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + fi +} + +src_unpack() { + default + git-r3_src_unpack +} + +src_prepare() { + # bug #302621 + use mpi && export CXX=mpicxx + + # produce pure octave files + # octave gentoo installation for .m files respected + sed -i \ + -e 's/--mex//' \ + -e 's/\.mex/\.oct/' \ + -e '/FILES/s/${MEX_FILE}//' \ + -e 's:share/flann/octave:share/octave/site/m:' \ + -e "/CUSTOM_TARGET/a\INSTALL(FILES \${MEX_FILE} DESTINATION libexec/octave/site/oct/${CHOST})" \ + src/matlab/CMakeLists.txt || die + use cuda && cuda_src_prepare + + cmake-utils_src_prepare +} + +src_configure() { + # python bindings are split + local mycmakeargs=( + -DBUILD_C_BINDINGS=ON + -DBUILD_PYTHON_BINDINGS=OFF + -DPYTHON_EXECUTABLE= + -DDOCDIR=share/doc/${PF} + $(cmake-utils_use_build cuda CUDA_LIB) + $(cmake-utils_use_build examples) + $(cmake-utils_use_build doc) + $(cmake-utils_use_build test TESTS) + $(cmake-utils_use_build octave MATLAB_BINDINGS) + $(cmake-utils_use_use mpi) + $(cmake-utils_use_use openmp) + ) + use cuda && \ + mycmakeargs+=( + -DCUDA_NVCC_FLAGS="${NVCCFLAGS},-arsch" + ) + cmake-utils_src_configure +} + +src_test() { + ln -s "${WORKDIR}"/testdata/* test/ || die + # -j1 to avoid obversubscribing jobs + LD_LIBRARY_PATH="${BUILD_DIR}/lib" \ + cmake-utils_src_compile -j1 test +} + +src_install() { + cmake-utils_src_install + dodoc README.md + if ! use static-libs; then + find "${ED}" -name 'lib*.a' -exec rm -rf '{}' '+' || die + fi +} diff --git a/sci-libs/flann/metadata.xml b/sci-libs/flann/metadata.xml new file mode 100644 index 000000000000..3238be55ea69 --- /dev/null +++ b/sci-libs/flann/metadata.xml @@ -0,0 +1,25 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + FLANN is a library for performing fast approximate nearest neighbor + searches in high dimensional spaces. It contains a collection of + algorithms we found to work best for nearest neighbor search and a + system for automatically choosing the best algorithm and optimum + parameters depending on the dataset. + FLANN is written in C++ and contains bindings for the following + languages: C, MATLAB and Python. + </longdescription> + <use> + <flag name="octave">Add bindings for + <pkg>sci-mathematics/octave</pkg></flag> + <flag name="cuda">Enable support for nVidia CUDA</flag> + </use> + <upstream> + <remote-id type="github">mariusmuja/flann</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/fplll/Manifest b/sci-libs/fplll/Manifest new file mode 100644 index 000000000000..031e184c6709 --- /dev/null +++ b/sci-libs/fplll/Manifest @@ -0,0 +1,5 @@ +DIST libfplll-4.0.4.tar.gz 413519 SHA256 cba8b0ded43f235003a58bcd4b2973105749b3f69732ae09fa44c7e98f5f71b1 SHA512 81cf61118f0dadca8fd82cc58df2fb5f0dc3ddd15a9b5de95a7777e0ece77d8f6a6d50d14ba7fdd6be6697cf375fac2e60792c94cc65f5a181c427dea84d552d 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+DESCRIPTION="Different implementations of the floating-point LLL reduction algorithm" +HOMEPAGE="http://perso.ens-lyon.fr/damien.stehle/index.html#software" +SRC_URI="http://perso.ens-lyon.fr/damien.stehle/fplll/lib${P}.tar.gz" + +LICENSE="LGPL-2+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=">=dev-libs/gmp-4.2.0:0 + >=dev-libs/mpfr-2.3.0:0" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/lib${P} + +src_configure() { + econf \ + $(use_enable static-libs static) +} + +src_install() { + DOCS="AUTHORS ChangeLog NEWS README" default + dohtml README.html + prune_libtool_files +} diff --git a/sci-libs/fplll/metadata.xml b/sci-libs/fplll/metadata.xml new file mode 100644 index 000000000000..6f49eba8f496 --- /dev/null +++ b/sci-libs/fplll/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<!-- maintainer-needed --> +</pkgmetadata> diff --git a/sci-libs/freesteam/Manifest b/sci-libs/freesteam/Manifest new file mode 100644 index 000000000000..3b9e6662d0ca --- /dev/null +++ b/sci-libs/freesteam/Manifest @@ -0,0 +1,8 @@ +AUX freesteam-flags.patch 726 SHA256 d4eccef5ccf0a345271f912715fc888ac948868c0a9e86a555d2eda25a1b1299 SHA512 08fdb64d64f90e7191732195f5f50515efc0a3838d85a17ad10bd588629091f04fec61c50fc780d6efa9d84e595b5cfba4a0f67b757db10d315eca87c98c323d WHIRLPOOL 10ba7326ea714e21673c61667ee9c5b7bbd84fa2d250713d90817651d197aef6ae6fe42b87726cb97e9d2afa59609af41fc0f687fcfb547a2429b2d90a03f385 +AUX freesteam-soname-symlinks.patch 1473 SHA256 cd05e197249150a156d02b30eb7251e15a2f0e2263a9517e1b22e4b8d845c24c SHA512 8aec90dc35af857286fbb2f53a9a1f2215641a27f16d73b009685036467747e30dd8a7ea37cb4b46f8875ecbe82a7ae5e42627b85edcc17ba61c9e84ffd00b7d WHIRLPOOL c9f02fc58422e03187d457c53120eff829d6ef1494425bb94f628679c02cd5e0c6b8a56257f82a4dbc74e378b21e8a25d1716d6c1dc1c59b5db7198818e030de +DIST freesteam-2.0.tar.bz2 80838 SHA256 9c21768648ec4faffeb536fdcde039f3e02d9e413f85e19234c285c64808ffad SHA512 32c69a5b6665c62c566fb1c6e4b349ec820028a0a431532a39d0f8d07c2a474c1d41b166dff5e05087a94b58066084a0a369a5f3f6531df1021596c6252325f8 WHIRLPOOL 33781bc07e20572de53ad272dc7e5dbc159f9c80fc21845860cf738249167e6e0c03e6c0d8c3e6e9f20dd6cf95a2d246208af3e3895d10313e0bc31df5bb6537 +EBUILD freesteam-2.0.ebuild 788 SHA256 eb7b9edd95fec7bd41780d6e0459f6b819f53ba2a09a872f6212d74cee461742 SHA512 3b4e1994630574c716c69bd7a03333df298bac8b06ffc1c7232178fd435abc0bc72d82c49c2618c5b2688902e5a97b588a0fd02020658a953399c99cb53eb3e1 WHIRLPOOL 45048b054f92ee7c3f0555dc922cd5b24aafac18b12e539327edfcea02c1c0a58fd2f718d05e749126b0ea16b704fceccd9c94fb25badfb4d3987604d4919a52 +EBUILD freesteam-9999.ebuild 808 SHA256 7c77396806a8096543b1e5a1c35edab7a48c87a77f47e1bc41a75be6e4d4d3e4 SHA512 c9ade950e139b984e676b05ead2cad59a8da7d5d2c5d00a97962bcd031f9b4f4a8e63eab8a15641e43da9ae3736d4be4631837d8055c8ea99da095b8273468a2 WHIRLPOOL d5626c9091df58c7e3e4bad3086c39ab77e58469151dd034a8471ac03487f2aacb64e75533dfba5e6d3998f1f5ddcdb9d9543d99fe4b065e41799c72fa12b8a7 +MISC ChangeLog 2989 SHA256 129858e7f006e088ce1fab08a506b0beac9906cd01d36dd97cf6defd9e645f30 SHA512 8705be053dd6ca8007dfc8e6de95ec941009e30f05cbf88b683018f0a639faaa1b9b7d6cd1b738c9411e74025dab4c5123c41968e9a483138cdd9807cd0e3a08 WHIRLPOOL c391e539dcf390e719507c0caf3dab6bf362f3e31fd17196ecde88d32afe6b661c75631ea87e70875c402f35a2a89dfd91cef456079c981a2b6be812506d72b0 +MISC ChangeLog-2015 746 SHA256 3295b86072fdb7bbecf2ec93c3e3bff67cb9a9248c315cac897509bc26886685 SHA512 4715ce0574551bacf9d4caf4af26a860e645656142f739695638d24513f94cf721808b0a3ec7938824992e5b4d1f3fa53942a7d9d977bce2437496bdffd22077 WHIRLPOOL af7733365fe746a1db13525095039beac4191533e43e7dd1dabc842e011bb7a8002c778a71ac4cbf8d7dc71f0266a5f30f7abf021780bfa05cf2a8301729bc4a +MISC metadata.xml 336 SHA256 8547776370893eb7fd146988890905752893c17d1df408c7bab81c6fe761e2e9 SHA512 a0c11e2d2258d3488c185235d362b03bab7cd85fb25b936c078dcd0464abf6c26fd94fe10a4ec267e0ad8eab6c49dbabf1883e5a3d174d03e1fa22c8cdc7dc73 WHIRLPOOL a4539e08943cae54008e20abdab956cb4507720c6e210f955c0c12be3ac6f8e9ca1c9cac73117240338f15fc987f11f1f34200be2a73c8263c9586489eabcce1 diff --git a/sci-libs/freesteam/files/freesteam-flags.patch b/sci-libs/freesteam/files/freesteam-flags.patch new file mode 100644 index 000000000000..615bdc050321 --- /dev/null +++ b/sci-libs/freesteam/files/freesteam-flags.patch @@ -0,0 +1,28 @@ +From 6a68348f4b1fb755724e1df34bff4d6986d07dab Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <gentoo@mgorny.alt.pl> +Date: Sat, 26 Nov 2011 22:30:15 +0100 +Subject: [PATCH] Merge CFLAGS and LDFLAGS from the environment. + +--- + SConstruct | 5 +++++ + 1 files changed, 5 insertions(+), 0 deletions(-) + +diff --git a/SConstruct b/SConstruct +index 9dc17f5..e529e88 100644 +--- a/SConstruct ++++ b/SConstruct +@@ -194,6 +194,11 @@ SConsEnvironment.InstallLibraryAs = lambda env, dest, files: InstallPermAs(env, + + vars.Update(env) + ++# Merge environment CFLAGS & LDFLAGS ++ ++env.MergeFlags([os.environ.get('CFLAGS', ''), ++ os.environ.get('LDFLAGS', '')]) ++ + #---------------- + # SWIG + +-- +1.7.8.rc3.31.g017d.dirty + diff --git a/sci-libs/freesteam/files/freesteam-soname-symlinks.patch b/sci-libs/freesteam/files/freesteam-soname-symlinks.patch new file mode 100644 index 000000000000..dbd8b2a64c26 --- /dev/null +++ b/sci-libs/freesteam/files/freesteam-soname-symlinks.patch @@ -0,0 +1,39 @@ +From dd03d6b29fd29f9978022291f0c023e4fe5dd345 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <gentoo@mgorny.alt.pl> +Date: Sat, 26 Nov 2011 23:18:37 +0100 +Subject: [PATCH] Fix SONAME symlinks - make them relative. + +--- + SConstruct | 6 +++--- + 1 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/SConstruct b/SConstruct +index 1794691..d84a13a 100644 +--- a/SConstruct ++++ b/SConstruct +@@ -5,7 +5,7 @@ + # We don't currently propose to support building freesteam from MSVS but + # that shouldn't be necessary, as you should be able to use the MinGW-generated + # DLL even with MSVS, because it only uses C code. +-import platform, sys, distutils.sysconfig, os ++import platform, sys, distutils.sysconfig, os, os.path + + #version number for this copy of freesteam + version = "2.1" +@@ -436,11 +436,11 @@ else: + + install_link1 = None + if env.subst(link1) != env.subst(libname): +- install_link1 = env.Command("${INSTALL_ROOT}"+link1,install_lib,"ln -s %s $TARGET" % libname) ++ install_link1 = env.Command("${INSTALL_ROOT}"+link1,install_lib,"ln -s %s $TARGET" % os.path.basename(libname)) + + install_link2 = None + if env.get("SONAME_MINOR"): +- install_link2 = env.Command("${INSTALL_ROOT}"+link2,install_lib,"ln -s %s $TARGET"%libname) ++ install_link2 = env.Command("${INSTALL_ROOT}"+link2,install_lib,"ln -s %s $TARGET"%os.path.basename(libname)) + + env['installedfiles'] += [install_link1, install_link2] + +-- +1.7.8.rc3.31.g017d.dirty + diff --git a/sci-libs/freesteam/freesteam-2.0.ebuild b/sci-libs/freesteam/freesteam-2.0.ebuild new file mode 100644 index 000000000000..92f6e685bc00 --- /dev/null +++ b/sci-libs/freesteam/freesteam-2.0.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib scons-utils toolchain-funcs + +DESCRIPTION="Open source implementation of IF97 steam tables" +HOMEPAGE="http://freesteam.sourceforge.net/" +SRC_URI="mirror://sourceforge/freesteam/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="sci-libs/gsl" +DEPEND="${RDEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-flags.patch + "${FILESDIR}"/${PN}-soname-symlinks.patch + epatch_user +} + +src_configure() { + myesconsargs=( + INSTALL_PREFIX=/usr + INSTALL_LIB=/usr/$(get_libdir) + INSTALL_ROOT="${D}" + + CC="$(tc-getCC)" + SWIG=false + ) + + mkdir -p "${D}" || die +} + +src_compile() { + escons +} + +src_install() { + escons install +} diff --git a/sci-libs/freesteam/freesteam-9999.ebuild b/sci-libs/freesteam/freesteam-9999.ebuild new file mode 100644 index 000000000000..939afc9dfe20 --- /dev/null +++ b/sci-libs/freesteam/freesteam-9999.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib scons-utils toolchain-funcs subversion + +DESCRIPTION="Open source implementation of IF97 steam tables" +HOMEPAGE="http://freesteam.sourceforge.net/" +SRC_URI="" +ESVN_REPO_URI="https://svn.code.sf.net/p/freesteam/code/trunk" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +RDEPEND="sci-libs/gsl" +DEPEND="${RDEPEND}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-flags.patch + "${FILESDIR}"/${PN}-soname-symlinks.patch + epatch_user +} + +src_configure() { + myesconsargs=( + INSTALL_PREFIX=/usr + INSTALL_LIB=/usr/$(get_libdir) + INSTALL_ROOT="${D}" + + CC="$(tc-getCC)" + SWIG=false + ) + + mkdir -p "${D}" || die +} + +src_compile() { + escons +} + +src_install() { + escons install +} diff --git a/sci-libs/freesteam/metadata.xml b/sci-libs/freesteam/metadata.xml new file mode 100644 index 000000000000..a8f3c63c1bf6 --- /dev/null +++ b/sci-libs/freesteam/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mgorny@gentoo.org</email> + <name>Michał Górny</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">freesteam</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/galib/Manifest b/sci-libs/galib/Manifest new file mode 100644 index 000000000000..0b49ac0cd072 --- /dev/null +++ b/sci-libs/galib/Manifest @@ -0,0 +1,8 @@ +AUX galib-2.4.7-Wformat-security.patch 1804 SHA256 0fadf7504baa91f699759a8ac9ff739873160cf714bb28a7d370ced4c8b84c3b SHA512 6846b2b15f8b348dfc83a7df6688e0c92ab5aa3eb2a6ff113609756cdcb12a679c82af730aebbdba5f9496c439e1e27cc9549812fd77ff9a6ca55812ff756dfb WHIRLPOOL dfa7978c76657f12727795d35f32d5186997abe4631873d8d7d87d0a4a4486358d4a1539fd3b11bd59ce63a79dc05e49cc567877aa60707c69466735f5363e9b +AUX galib-2.4.7-fix-buildsystem.patch 1576 SHA256 2f0b9cbdf03086aea86e28766777d55460a57a57c2040b44897ae02eebb5a135 SHA512 26c8634664b75ef94028dfbf51dce5417256290703f3717ce2fcf660b166012622db97447a7272781c44d02b3d1728470a0f64d4b1a089ad5e4d44eaebcf3004 WHIRLPOOL 9f999d456f6b444e6f4fe0ff37f44be2fa4c53e339f4e0507f0295ca02912f2229d21a0209b91404af5e4ad9dd5f6fe813dd9460ede783f386196e4f553d2c1b +AUX galib-2.4.7-fix-c++14.patch 3951 SHA256 7c6a7e8b470d69648397520e6c616a69b64eb6457e14a5593f21b3dc5176a88a SHA512 2f843b121c06ee124f13cac106a492f495c2043a54030ebc7d67ccf386ea1eacd72dc14e5a4f925d0c1f345038d8d04ed6de96b0030bcb205714afed1e7103f4 WHIRLPOOL cc44c60680df797257530a95fb8506b102ebc6787d3e2c18bebe220a06c484d10415f42a76b6ac11a5a73e0ba0d86fb83bfe7a16a09eb313f793a1b4c9f82417 +DIST galib247.tgz 374912 SHA256 ea76b66ce4db4db2ed86e20d6d3ff144abaf73e33620104246639d9b2a465329 SHA512 9c2aca29f24d3f8401ba65c246a0ca7d1fa67e4f756a5258cdb0da111842ea2903c2d70cfd9d60823c9703bcb3415ca670a731924e99878d5536c2f7eb0faba4 WHIRLPOOL 027e1d8999bb09e31da717fb3fb84f023d4488cc161c173e55fdc545b58583f386b6bb9cab631c30f84eae8a8b58c4e669049507bc0ca8561a8ecfba2e57f480 +EBUILD galib-2.4.7-r1.ebuild 1147 SHA256 392b533ce8079ffcc9655b0866ae8f66b09e1e357d004d4d1ed96ac03a8a84df SHA512 746a8c18f69f76f64696831bda7bb1759312b541885d0e982db54107ea4d9f6567f7b22cb0b5d3e3a32c7c203371282332656e70492c107f8d18b68b4337c0e6 WHIRLPOOL c2c4a5d56ce7525a81fcdf8b16b4a544ac968564dc37f59a87b2dc06ca3677e1fabd451fb3b5ebf6239500d3ce20c30dd6496ba9b5eeba24e0eb3c0f29f10b10 +MISC ChangeLog 2994 SHA256 441353b17265bf71a110648cd7002055ecfa6f7f57a739c4d038e31ad9549397 SHA512 4490686872587b8b27ee8ebc1f52b563cd9c47285e41afafa6e4fc9060f9655380a4b7769d5fe5f38047f0cbf71174053c0c8e37ea40af67da8b21f60be22188 WHIRLPOOL 5573e74fb9f9d6269747a7054a6cef18e225ffd70214502e5419e9437a5bfa1b3366c4c43755d33c2f6bd27630001e8a6e934bdd6cf57937851d908a01d38103 +MISC ChangeLog-2015 2227 SHA256 89fff5b8f076131ae76cb0127377949a54100eff7e644d87372a0c0d3603340c SHA512 0d2841f7e9de22ef636b75c64a129ef04cf54569a6ab441e3f8e593f29c555e275ed0d0edc0cbddc0da2bd916c943605a32627c0b7b034bcfc6b430700eb0877 WHIRLPOOL ff8abaa66b96a07c450555ed291f4bfd16650223497cf14625eb52831b52f4e4ef4a946fa85ba5ae7d55e3c020f2fcdc382025b7e6892686c38335136992250a +MISC metadata.xml 505 SHA256 b6ea03858b104ea5903f96e3718d6ee5a04d5601a45d1978bf5b0824301a3e73 SHA512 52b06bc61b4bb82f35309d4aae723cd4d1a0acb15204b9f28900b43c2def46f152444d7838eb5b4c5351a8a3a0075559c29e2ef438bc049b7fa3bd3689bd9192 WHIRLPOOL 2c1e03200b33058f288313d4269aee90472134cb41fdd13d7c2e0abf5a1c204cdd0e48703527975bbb4133b4bc67fa7d12f468c982338ed3a679e5173d3f1d86 diff --git a/sci-libs/galib/files/galib-2.4.7-Wformat-security.patch b/sci-libs/galib/files/galib-2.4.7-Wformat-security.patch new file mode 100644 index 000000000000..faa7dcff446d --- /dev/null +++ b/sci-libs/galib/files/galib-2.4.7-Wformat-security.patch @@ -0,0 +1,79 @@ +Fix -Wformat-security issues, as we do not want to install potentially +dangerous example C++ files on user systems: +* ex18.C: In function ‘int main(int, char**)’: +* ex18.C:92:27: warning: format not a string literal and no format arguments [-Wformat-security] +* sprintf(filename, argv[i]); + +--- a/examples/ex18.C ++++ b/examples/ex18.C +@@ -89,7 +89,7 @@ + exit(1); + } + else{ +- sprintf(filename, argv[i]); ++ sprintf(filename, "%s", argv[i]); + continue; + } + } +--- a/examples/ex3.C ++++ b/examples/ex3.C +@@ -71,7 +71,7 @@ + exit(1); + } + else{ +- sprintf(filename, argv[i]); ++ sprintf(filename, "%s", argv[i]); + continue; + } + } +--- a/examples/ex5.C ++++ b/examples/ex5.C +@@ -308,7 +308,7 @@ + exit(1); + } + else{ +- sprintf(filename1, argv[i]); ++ sprintf(filename1, "%s", argv[i]); + continue; + } + } +@@ -318,7 +318,7 @@ + exit(1); + } + else{ +- sprintf(filename2, argv[i]); ++ sprintf(filename2, "%s", argv[i]); + continue; + } + } +--- a/examples/ex7.C ++++ b/examples/ex7.C +@@ -68,7 +68,7 @@ + exit(1); + } + else{ +- sprintf(datafile, argv[i]); ++ sprintf(datafile, "%s", argv[i]); + continue; + } + } +@@ -78,7 +78,7 @@ + exit(1); + } + else{ +- sprintf(parmfile, argv[i]); ++ sprintf(parmfile, "%s", argv[i]); + params.read(parmfile); + continue; + } +--- a/ga/gaerror.C ++++ b/ga/gaerror.C +@@ -21,7 +21,7 @@ + static STD_OSTREAM *__gaErrStream = & STD_CERR; + #endif + static GABoolean __gaErrFlag = gaTrue; +-static char *__gaErrStr[] = { ++static const char *__gaErrStr[] = { + "error reading from file: ", + "error writing to file: ", + "unexpected EOF encountered during read.", diff --git a/sci-libs/galib/files/galib-2.4.7-fix-buildsystem.patch b/sci-libs/galib/files/galib-2.4.7-fix-buildsystem.patch new file mode 100644 index 000000000000..3ed7ad84e6d4 --- /dev/null +++ b/sci-libs/galib/files/galib-2.4.7-fix-buildsystem.patch @@ -0,0 +1,65 @@ +Fix the build system, removing hardcoded values for toolchain variables. + +--- a/examples/makefile ++++ b/examples/makefile +@@ -6,7 +6,6 @@ + # want to compile. See the README for a description of what each example does. + # ----------------------------------------------------------------------------- + +-include ../makevars + + # Set these paths to the location of the GA library and headers. + #GA_INC_DIR= /usr/local/include +@@ -14,8 +13,6 @@ + GA_INC_DIR= .. + GA_LIB_DIR= ../ga + +-INC_DIRS= -I$(GA_INC_DIR) +-LIB_DIRS= -L$(GA_LIB_DIR) + + EXS=randtest\ + ex1 ex2 ex3 ex4 ex5 ex6 ex7 ex8 ex9\ +@@ -24,7 +21,7 @@ + + .SUFFIXES: .C + .C.o: +- $(CXX) $(CXXFLAGS) $(INC_DIRS) -c $< ++ $(CXX) $(CXXFLAGS) -I.. -c $< + + all: $(EXS) + +@@ -34,7 +31,7 @@ + + # Use this for gnu make + $(EXS): %: %.o +- $(CXX) $@.o -o $@ $(LIB_DIRS) -lga -lm $(CXX_LIBS) ++ $(CXX) $@.o -o $@ -L../ga/ -lga -lm $(CXX_LIBS) + + clean: + $(RM) $(EXS) +--- a/ga/makefile ++++ b/ga/makefile +@@ -14,7 +14,7 @@ + + $(LIB): $(OBJS) + $(PRELINK) +- $(AR) $(LIB) $? ++ $(AR) rv $(LIB) $? + $(RANLIB) $(LIB) + echo "$(CXX) $(CXXFLAGS)" > BUILD + @echo $(LIB) is now up-to-date +--- a/makevars ++++ b/makevars +@@ -31,12 +31,7 @@ + # verified 06mar07 on linux-x86 (debian with gcc 3.3.5) + # verified 06mar07 on linux-x86 (ubuntu with gcc 4.0.3) + # verified 06mar07 on macosx-ppc (macosx 10.4.8 with gcc 4.0.1) +-CXX = g++ +-CXXFLAGS = -g -Wall +-LD = g++ -w +-AR = ar rv + INSTALL = install -c +-RANLIB = echo no ranlib + + # gcc2 + # verified 28dec04 on linux-x86 (redhat 6.2 with gcc 2.95.2) diff --git a/sci-libs/galib/files/galib-2.4.7-fix-c++14.patch b/sci-libs/galib/files/galib-2.4.7-fix-c++14.patch new file mode 100644 index 000000000000..babc84b63524 --- /dev/null +++ b/sci-libs/galib/files/galib-2.4.7-fix-c++14.patch @@ -0,0 +1,85 @@ +Fix building with C++14, which errors out due to stricter two-phase lookup. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594504 + +Patch by Peter Levine + +--- a/ga/GA1DArrayGenome.C ++++ b/ga/GA1DArrayGenome.C +@@ -222,8 +222,8 @@ + aset = new GAAlleleSet<T>[1]; + aset[0] = s; + +- initializer(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_INITIALIZER); +- mutator(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_MUTATOR); ++ GAGenome::initializer(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_INITIALIZER); ++ GAGenome::mutator(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_MUTATOR); + comparator(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_COMPARATOR); + crossover(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_CROSSOVER); + } +@@ -238,8 +238,8 @@ + for(int i=0; i<naset; i++) + aset[i] = sa.set(i); + +- initializer(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_INITIALIZER); +- mutator(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_MUTATOR); ++ GAGenome::initializer(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_INITIALIZER); ++ GAGenome::mutator(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_MUTATOR); + comparator(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_COMPARATOR); + crossover(GA1DArrayAlleleGenome<T>::DEFAULT_1DARRAY_ALLELE_CROSSOVER); + } +--- a/ga/GA2DArrayGenome.C ++++ b/ga/GA2DArrayGenome.C +@@ -269,10 +269,10 @@ + aset = new GAAlleleSet<T>[1]; + aset[0] = s; + +- initializer(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_INITIALIZER); +- mutator(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_MUTATOR); +- comparator(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_COMPARATOR); +- crossover(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_CROSSOVER); ++ GAGenome::initializer(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_INITIALIZER); ++ GAGenome::mutator(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_MUTATOR); ++ GAGenome::comparator(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_COMPARATOR); ++ GAGenome::crossover(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_CROSSOVER); + } + + template <class T> +@@ -286,10 +286,10 @@ + for(int i=0; i<naset; i++) + aset[i] = sa.set(i); + +- initializer(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_INITIALIZER); +- mutator(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_MUTATOR); +- comparator(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_COMPARATOR); +- crossover(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_CROSSOVER); ++ GAGenome::initializer(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_INITIALIZER); ++ GAGenome::mutator(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_MUTATOR); ++ GAGenome::comparator(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_COMPARATOR); ++ GAGenome::crossover(GA2DArrayAlleleGenome<T>::DEFAULT_2DARRAY_ALLELE_CROSSOVER); + } + + +--- a/ga/GA3DArrayGenome.C ++++ b/ga/GA3DArrayGenome.C +@@ -322,8 +322,8 @@ + aset = new GAAlleleSet<T>[1]; + aset[0] = s; + +- initializer(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_INITIALIZER); +- mutator(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_MUTATOR); ++ GAGenome::initializer(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_INITIALIZER); ++ GAGenome::mutator(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_MUTATOR); + comparator(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_COMPARATOR); + crossover(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_CROSSOVER); + } +@@ -339,8 +339,8 @@ + for(int i=0; i<naset; i++) + aset[i] = sa.set(i); + +- initializer(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_INITIALIZER); +- mutator(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_MUTATOR); ++ GAGenome::initializer(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_INITIALIZER); ++ GAGenome::mutator(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_MUTATOR); + comparator(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_COMPARATOR); + crossover(GA3DArrayAlleleGenome<T>::DEFAULT_3DARRAY_ALLELE_CROSSOVER); + } diff --git a/sci-libs/galib/galib-2.4.7-r1.ebuild b/sci-libs/galib/galib-2.4.7-r1.ebuild new file mode 100644 index 000000000000..5209af1c4c9d --- /dev/null +++ b/sci-libs/galib/galib-2.4.7-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +MY_PV="${PV//\./}" + +DESCRIPTION="Library for genetic algorithms in C++ programs" +HOMEPAGE="http://lancet.mit.edu/ga/" +SRC_URI="http://lancet.mit.edu/ga/dist/galib${MY_PV}.tgz" + +LICENSE="BSD examples? ( GPL-2 )" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc examples" + +S="${WORKDIR}/${PN}${MY_PV}" + +PATCHES=( + "${FILESDIR}/${PN}-2.4.7-fix-buildsystem.patch" + "${FILESDIR}/${PN}-2.4.7-fix-c++14.patch" + "${FILESDIR}/${PN}-2.4.7-Wformat-security.patch" +) + +src_prepare() { + default + sed -e "s:/include:${EPREFIX}/usr/include:" \ + -e "s:/lib:${EPREFIX}/usr/$(get_libdir):" \ + -i makevars || die +} + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + AR="$(tc-getAR)" \ + RANLIB="$(tc-getRANLIB)" \ + lib + emake -C examples clean +} + +src_install() { + dodir /usr/$(get_libdir) + + use doc && HTML_DOCS+=( doc/. ) + if use examples; then + dodoc -r examples + find "${ED%/}/usr/share/doc/${PF}/examples" -iname 'makefile*' -delete || die + docompress -x /usr/share/doc/${PF}/examples + fi + + default +} diff --git a/sci-libs/galib/metadata.xml b/sci-libs/galib/metadata.xml new file mode 100644 index 000000000000..c5d86554ee6d --- /dev/null +++ b/sci-libs/galib/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + GAlib contains a set of C++ genetic algorithm objects. The library + includes tools for using genetic algorithms to do optimization in + any C++ program using any representation and genetic operators. + </longdescription> +</pkgmetadata> diff --git a/sci-libs/gamer/Manifest b/sci-libs/gamer/Manifest new file mode 100644 index 000000000000..86359b72048a --- /dev/null +++ b/sci-libs/gamer/Manifest @@ -0,0 +1,7 @@ +AUX 1.4-doc.patch 535 SHA256 dadce11b0201712e55bf1ddc095f174b2ea5424ce37c29ac7f815b4211a27a95 SHA512 639f0e80eb116c77d723f707488cd66124f1eaefa2f74c2fff80152ce0cf7f17b9c334f33500eeb0f78f11b0574bb20945dcd9718b1ef5e9a149ccce07981228 WHIRLPOOL aa5b23cf2be9ec818269b5733c7a142972cd95282ebcad46b2bf39b875c59c3961d297413aa1443b4eaa9413f5f0919cfc31a50b9852fa8fa0a47a44e69d7a93 +AUX 1.4-multilib.patch 872 SHA256 caf21218d42403d86662b35c5ceeaaf28040435266af4ae01acebfee90213a98 SHA512 44ac7731277c47b822bbcac11b62d62e397c539d7a9dd32c805ee656ecc2cc4cad2878082212abded212419bf609823c21f9d351ad828a07357c9b2900c112e9 WHIRLPOOL df95ada76b55ad18d676ee9880653f9451f259159ef6c593bf9a56774d9c0f950d8d5ff52c4f9bbf43915d691e5dfac15c613779b5d633fe113606bd04e2cb82 +DIST gamer-1.5.tar.gz 4232061 SHA256 3dce4a5137bf1a2b4ee84bde425ea83937b5f8442f1b95b1d284f07dae933788 SHA512 4911b208ae5cd7be7ef165bac8fc9680ff03c0936881ae3d162205df9ef4f3fb176455e27b2f4ca202c3129352156cf5166b1d7d99fde7b281b404e383f72a44 WHIRLPOOL cc32e8772d32bc11a2bed8f5bad124ff4a1c3fad2e2f15462c9fb710f8de82547ae5db9ad0a87a6469ca9839c4e066c9eadc32c5decdb9c207eead2f8a939eb2 +EBUILD gamer-1.5-r2.ebuild 1046 SHA256 4cc45f02d26884212e848d08cc00ca67016dd1a538b8a4b742c5979b3f8f2ed0 SHA512 121137d107e05365205df6162b3908445c0cac4cb481ed15fde1522c96753dc1fe07f7b4f710063dc9b9146976752661b329f28176900debfd7779a4afdf2a50 WHIRLPOOL 985eb71cc5fa792711a5619b021dcff234dafe50e18af8f183021ad67efde196d612387cc211910674559a7c05ad37f7bc9677ef2a3dc8e8978849d98e8a79f1 +MISC ChangeLog 2645 SHA256 489adc47b07ead7306c4f3f97ca18116daf497f76433f7af6e03dcdee5809516 SHA512 47dae237bac1fb5bf684e105a23146aba598798e14f39735c83098fb1623421fd7869497aabef59a0982c086ea7da67b4bd34ad107dff8b34ddf56f43f77e575 WHIRLPOOL 6855ec3b71c059f403cd630a3120535b6d8046d8c411360c6b01116db27b39338145ca145a3de5fac3a1be7b0d0e5a3582de9f3f0eb3b46dc6c9d97fb19b23b1 +MISC ChangeLog-2015 1552 SHA256 f32bb13124db8ec9136c068d9110192226676eab5bf714b1ac4cfa5719c85382 SHA512 a27ca50bb5c57673a14c56f62a306c39dd2a4adcc429691a466c0d669d6c75eab15ea54ff1e4fe64cb2539406f3cb2fda00312cea4ef1f5f73d885085b49156d WHIRLPOOL 9e4a4ffcc4c94f91c189eed9fe407dd7ea8d911767b9506ea316f14ba51153535b4513c176b25dc8d7d9d526311121ee1978d396424aca0fca020cf203328c7f +MISC metadata.xml 259 SHA256 bbfbeb80ffccffa8e7f837d2c93e994bbe024d565ae3a31d30c6646e80a684c8 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 WHIRLPOOL 75b8dd1a97dde63f9cc9f73b5951eaf54579460763ef7cbe6f3a9a0739070601d762152ea00df8b476b80e92e5c29b611a494bac5ab747298942530cabe0ee84 diff --git a/sci-libs/gamer/files/1.4-doc.patch b/sci-libs/gamer/files/1.4-doc.patch new file mode 100644 index 000000000000..642601bcc17b --- /dev/null +++ b/sci-libs/gamer/files/1.4-doc.patch @@ -0,0 +1,20 @@ +diff --git a/doc/doxygen/Makefile.am b/doc/doxygen/Makefile.am +index 4067c1c..43867e2 100644 +--- a/doc/doxygen/Makefile.am ++++ b/doc/doxygen/Makefile.am +@@ -9,13 +9,11 @@ + ## Author: Michael Holst + ## ########################################################################### + +-docdir = @prefix@/doc/gamer +- + doc_DATA = gamer_doc + + gamer_doc: + $(doxygen_path) $(top_srcdir)/doc/doxygen/gamer.dox + + install-docDATA: +- mkdir -p $(docdir) +- cp -r ../api $(docdir)/ ++ mkdir -p $(DESTDIR)/@docdir@ ++ cp -r ../api $(DESTDIR)/@docdir@ diff --git a/sci-libs/gamer/files/1.4-multilib.patch b/sci-libs/gamer/files/1.4-multilib.patch new file mode 100644 index 000000000000..3ebc8dcd7aab --- /dev/null +++ b/sci-libs/gamer/files/1.4-multilib.patch @@ -0,0 +1,26 @@ +diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am +index de1d7c3..b2420c8 100644 +--- a/src/aaa_lib/Makefile.am ++++ b/src/aaa_lib/Makefile.am +@@ -35,18 +35,17 @@ LIBTETGEN = libtetgen.la + #LIBTETGEN = + #endif + +-libdir = ${prefix}/lib + lib_LTLIBRARIES = libgamer.la ${LIBTRIANGLE} ${LIBTETGEN} + + libgamer_la_SOURCES = +-libgamer_la_LIBADD = ${BASE_LIBS} ${BIOM_LIBS} ++libgamer_la_LIBADD = ${BASE_LIBS} ${BIOM_LIBS} -lm -lstdc++ ../tetgen/libtetgen.la + libgamer_la_LDFLAGS = -version-info ${FETK_VERSION} + + libtriangle_la_SOURCES = +-libtriangle_la_LIBADD = ${TRIANGLE_LIBS} ++libtriangle_la_LIBADD = ${TRIANGLE_LIBS} -lm + libtriangle_la_LDFLAGS = -version-info ${FETK_VERSION} + + libtetgen_la_SOURCES = +-libtetgen_la_LIBADD = ${TETGEN_LIBS} ++libtetgen_la_LIBADD = ${TETGEN_LIBS} -lm -lstdc++ + libtetgen_la_LDFLAGS = -version-info ${FETK_VERSION} + diff --git a/sci-libs/gamer/gamer-1.5-r2.ebuild b/sci-libs/gamer/gamer-1.5-r2.ebuild new file mode 100644 index 000000000000..23cbb8033662 --- /dev/null +++ b/sci-libs/gamer/gamer-1.5-r2.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils multilib + +DESCRIPTION="Geometry-preserving Adaptive MeshER" +HOMEPAGE="http://fetk.org/codes/gamer/index.html" +SRC_URI="http://www.fetk.org/codes/download/${P}.tar.gz" + +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="doc static-libs" + +RDEPEND=">=dev-libs/maloc-1.4" +DEPEND=" + ${RDEPEND} + doc? ( + media-gfx/graphviz + app-doc/doxygen + )" + +S="${WORKDIR}"/${PN} + +PATCHES=( + "${FILESDIR}"/1.4-multilib.patch + "${FILESDIR}"/1.4-doc.patch + ) + +src_configure() { + local fetk_include + local fetk_lib + local myeconfargs + + use doc || myeconfargs+=( ${myconf} --with-doxygen= --with-dot= ) + + fetk_include="${EPREFIX}"/usr/include + fetk_lib="${EPREFIX}"/usr/$(get_libdir) + export FETK_INCLUDE="${fetk_include}" + export FETK_LIBRARY="${fetk_lib}" + + myeconfargs+=( + --docdir="${EPREFIX}"/usr/share/doc/${PF} + --disable-triplet + ) + autotools-utils_src_configure +} diff --git a/sci-libs/gamer/metadata.xml b/sci-libs/gamer/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-libs/gamer/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/gaul-devel/Manifest b/sci-libs/gaul-devel/Manifest new file mode 100644 index 000000000000..e5d5716b62b5 --- /dev/null +++ b/sci-libs/gaul-devel/Manifest @@ -0,0 +1,8 @@ +AUX gaul-devel-0.1849-as-needed.patch 972 SHA256 cfd40dd517fc3bcf93f136c04d4e683fbba69952a2ea2705147ad3da75261e37 SHA512 2f5b17231b3bc1d932389a3c550ab2756c39ce302bee3c1d9d64932dd080fb828a6035000c2b0b1b45815f2377da5e4665738630ea32cb827d63387c26c1ab6c WHIRLPOOL 7666203d6ef036b7703b070062415d5465b2751650ee005c296e0375929814c181350b3dff9372095e2842b1342823f7c3e61a77148f562fce2c64d0a9232c6c +AUX gaul-devel-0.1849-slang2-error.patch 976 SHA256 78a933c7212244c2bc96b27394a9e30a24b402621ed96bd84d54dcd2f7e01eec SHA512 7f31cc6d382122e6610230cfc7541517948a35a499b1334573cd023c9af0148a8b1c37ffaaf5b3ca9facbfce5a5ecceeb9a0d9725719979b7e973fc88a478269 WHIRLPOOL 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+-libgaul_la_LIBFLAGS = -lm ++libgaul_la_LIBADD = $(top_srcdir)/util/libgaul_util.la -lm + libgaul_la_LDFLAGS = -version-info ${GA_MAJOR_VERSION}:${GA_LT_MINOR_VERSION}:0 + + +--- gaul-devel-0.1849-0.orig/util/Makefile.am 2005-04-20 16:25:53.000000000 +0200 ++++ gaul-devel-0.1849-0/util/Makefile.am 2010-02-13 17:00:00.128370192 +0100 +@@ -64,10 +64,10 @@ + gaul/table_util.h \ + gaul/timer_util.h + +-libgaul_util_a_LIBFLAGS = ++libgaul_util_la_LIBADD = -lm + libgaul_util_la_LDFLAGS = -version-info ${GA_MAJOR_VERSION}:${GA_LT_MINOR_VERSION}:0 + +-libnn_util_a_LIBFLAGS = ++libnn_util_la_LIBADD = -lm + libnn_util_la_LDFLAGS = -version-info ${GA_MAJOR_VERSION}:${GA_LT_MINOR_VERSION}:0 + + # Regenerate gaul_config.h with config.status whenever gaul_config.h.in changes. diff --git a/sci-libs/gaul-devel/files/gaul-devel-0.1849-slang2-error.patch b/sci-libs/gaul-devel/files/gaul-devel-0.1849-slang2-error.patch new file mode 100644 index 000000000000..64b3c59a28bb --- /dev/null +++ b/sci-libs/gaul-devel/files/gaul-devel-0.1849-slang2-error.patch @@ -0,0 +1,30 @@ +diff -Naur gaul-devel-0.1849-0/tests/test_slang.c gaul-devel-0.1849-0.new/tests/test_slang.c +--- gaul-devel-0.1849-0/tests/test_slang.c 2003-08-19 17:41:20.000000000 -0400 ++++ gaul-devel-0.1849-0.new/tests/test_slang.c 2008-02-09 10:42:43.000000000 -0500 +@@ -287,10 +287,11 @@ + */ + if (-1 == SLang_load_file(script_fname)) + { ++ int error = SLang_get_error(); + dief("Error %d interpreting the S-Lang script \"%s\".", +- SLang_Error, script_fname); ++ error, script_fname); + SLang_restart(1); /* reset interpreter. */ +- SLang_Error = 0; ++ SLang_set_error(0); + return FALSE; + } + +@@ -315,9 +316,10 @@ + */ + if (-1 == SLang_load_file(NULL)) + { +- dief("Error %d interpreting the SLang script from stdin.", SLang_Error); ++ int error = SLang_get_error(); ++ dief("Error %d interpreting the SLang script from stdin.", error); + SLang_restart(1); +- SLang_Error = 0; ++ SLang_set_error(0); + return FALSE; + } + diff --git a/sci-libs/gaul-devel/gaul-devel-0.1849-r1.ebuild b/sci-libs/gaul-devel/gaul-devel-0.1849-r1.ebuild new file mode 100644 index 000000000000..7c5310e12706 --- /dev/null +++ b/sci-libs/gaul-devel/gaul-devel-0.1849-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit eutils + +DESCRIPTION="Genetic Algorithm Utility Library" +HOMEPAGE="http://GAUL.sourceforge.net/" +SRC_URI="mirror://sourceforge/gaul/${P}-0.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="debug slang" + +DEPEND=" + sys-apps/sed + slang? ( sys-libs/slang )" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${P}-0 + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-slang2-error.patch +} + +src_compile() { + local myconf + use slang || myconf="--enable-slang=no" + if use debug ; then + myconf="${myconf} --enable-debug=yes --enable-memory-debug=yes" + else + myconf="${myconf} --enable-g=no" + fi + econf ${myconf} + emake || die "emake failed" +} + +src_install() { + emake -j1 DESTDIR="${D}" install || die "Install failed" + dodoc README || die +} diff --git a/sci-libs/gaul-devel/gaul-devel-0.1849-r2.ebuild b/sci-libs/gaul-devel/gaul-devel-0.1849-r2.ebuild new file mode 100644 index 000000000000..56d910c69c5a --- /dev/null +++ b/sci-libs/gaul-devel/gaul-devel-0.1849-r2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools eutils + +DESCRIPTION="Genetic Algorithm Utility Library" +HOMEPAGE="http://GAUL.sourceforge.net/" +SRC_URI="mirror://sourceforge/gaul/${P}-0.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug slang static-libs" + +DEPEND=" + sys-apps/sed + slang? ( sys-libs/slang )" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${P}-0 + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-slang2-error.patch \ + "${FILESDIR}"/${P}-as-needed.patch + eautoreconf +} + +src_configure() { + local myconf + use slang || myconf="--enable-slang=no" + if use debug ; then + myconf="${myconf} --enable-debug=yes --enable-memory-debug=yes" + else + myconf="${myconf} --enable-g=no" + fi + econf $(use_enable static-libs static) ${myconf} +} + +src_install() { + MAKEOPTS+=" -j1" + default +} diff --git a/sci-libs/gaul-devel/metadata.xml b/sci-libs/gaul-devel/metadata.xml new file mode 100644 index 000000000000..3bbf26aecb84 --- /dev/null +++ b/sci-libs/gaul-devel/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The Genetic Algorithm Utility Library is a + flexible programming library designed to aid in the development of + applications that use genetic, or evolutionary, algorithms. It + provides data structures and functions for handling and manipulation + of the data required for serial and parallel evolutionary + algorithms. Additional stochastic algorithms are provided for + comparison to the genetic algorithms. Much of the functionality is + also available through a simple S-Lang interface. +</longdescription> + <upstream> + <remote-id type="sourceforge">gaul</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/gdal/Manifest b/sci-libs/gdal/Manifest new file mode 100644 index 000000000000..f33f25fb25cf --- /dev/null +++ b/sci-libs/gdal/Manifest @@ -0,0 +1,14 @@ +AUX gdal-1.5.0-install_name.patch 1731 SHA256 da631282e7ee42b3f9c46a4ce76d7b4905caa4a056c8109fce0f661b9aa58abd SHA512 fa5ecc9e14cbfc282a41d0c55e328c2f56bd92d8fac1897d8e921d59c9705b1291eff66e7f6cf8a1305b2c5f044e0813d28affb398b715d9d207c31af341318e WHIRLPOOL f67a2f307c16d664af34fe26993e74c2a0d1a2b52d43176eb1f03fbd9523533906d1a7df34a0745927f46febdb60e6efe7291bf0e520e0d6c904bcbfe5be928f +AUX gdal-1.5.0-soname-r1.patch 491 SHA256 0745b525d52092c47e5e169bfe9666a6e8efb2c3c153849fe7ef007a1035f608 SHA512 883828de32d55a79a390f4737b640c8d50d174117e86396545d075fb5328a7e5ffffa150c11a6e9a6317b7cfd5458eb5ac543152fc2acafb1abf3688b78a573f 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mode 100644 index 000000000000..e17575267d6e --- /dev/null +++ b/sci-libs/gdal/files/gdal-1.5.0-install_name.patch @@ -0,0 +1,45 @@ +--- GDALmake.opt.in.orig 2008-02-02 18:25:48.000000000 -0800 ++++ GDALmake.opt.in 2008-02-02 18:54:53.000000000 -0800 +@@ -97,6 +97,10 @@ + GDAL_SLIB = $(GDAL_ROOT)/libgdal.$(SO_EXT) + GDAL_SLIB_LINK = -L$(GDAL_ROOT) -lgdal + ++# for building without libtool ++GDAL_SLIB_SO_VER = $(GDAL_VERSION_MAJOR).$(LIBGDAL_CURRENT).$(LIBGDAL_REVISION) ++GDAL_SLIB_SONAME = -install_name $(INST_LIB)/libgdal.$(GDAL_VERSION_MAJOR).$(SO_EXT) ++ + # Mac OS X Framework definition + MACOSX_FRAMEWORK = @MACOSX_FRAMEWORK@ + +--- GNUmakefile.orig 2010-03-09 14:03:08 +0100 ++++ GNUmakefile 2010-03-09 14:05:29 +0100 +@@ -218,7 +218,7 @@ + + ifeq ($(HAVE_LD_SHARED),yes) + +-GDAL_SLIB_B = $(notdir $(GDAL_SLIB)) ++GDAL_SLIB_B = libgdal + + install-lib: + +@@ -226,14 +226,14 @@ + ifeq ($(MACOSX_FRAMEWORK),yes) + $(INSTALL_LIB) $(GDAL_SLIB) $(DESTDIR)$(INST_LIB)/GDAL + else +- rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B) +- rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR) +- rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VER) +- $(INSTALL_LIB) $(GDAL_SLIB) $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VER) ++ rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).dylib ++ rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR).dylib ++ rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VER).dylib ++ $(INSTALL_LIB) $(GDAL_SLIB) $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VER).dylib + (cd $(DESTDIR)$(INST_LIB) ; \ +- ln -s $(GDAL_SLIB_B).$(GDAL_VER) $(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR)) ++ ln -s $(GDAL_SLIB_B).$(GDAL_VER).dylib $(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR).dylib) + (cd $(DESTDIR)$(INST_LIB) ; \ +- ln -s $(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR) $(GDAL_SLIB_B)) ++ ln -s $(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR).dylib $(GDAL_SLIB_B).dylib) + endif + + else diff --git a/sci-libs/gdal/files/gdal-1.5.0-soname-r1.patch b/sci-libs/gdal/files/gdal-1.5.0-soname-r1.patch new file mode 100644 index 000000000000..ec35018868dd --- /dev/null +++ b/sci-libs/gdal/files/gdal-1.5.0-soname-r1.patch @@ -0,0 +1,13 @@ +--- old/GDALmake.opt.in.orig 2008-02-02 18:25:48.000000000 -0800 ++++ new/GDALmake.opt.in 2008-02-02 18:54:53.000000000 -0800 +@@ -97,6 +97,10 @@ + GDAL_SLIB = $(GDAL_ROOT)/libgdal.$(SO_EXT) + GDAL_SLIB_LINK = -L$(GDAL_ROOT) -lgdal + ++# for building without libtool ++GDAL_SLIB_SO_VER = $(GDAL_VERSION_MAJOR).$(LIBGDAL_CURRENT).$(LIBGDAL_REVISION) ++GDAL_SLIB_SONAME = -Wl,-soname,libgdal.$(SO_EXT).$(GDAL_VERSION_MAJOR) ++ + # Mac OS X Framework definition + MACOSX_FRAMEWORK = @MACOSX_FRAMEWORK@ + diff --git a/sci-libs/gdal/files/gdal-1.5.0-soname.patch b/sci-libs/gdal/files/gdal-1.5.0-soname.patch new file mode 100644 index 000000000000..f784536316c2 --- /dev/null +++ b/sci-libs/gdal/files/gdal-1.5.0-soname.patch @@ -0,0 +1,13 @@ +--- GDALmake.opt.in.orig 2008-02-02 18:25:48.000000000 -0800 ++++ GDALmake.opt.in 2008-02-02 18:54:53.000000000 -0800 +@@ -97,6 +97,10 @@ + GDAL_SLIB = $(GDAL_ROOT)/libgdal.$(SO_EXT) + GDAL_SLIB_LINK = -L$(GDAL_ROOT) -lgdal + ++# for building without libtool ++GDAL_SLIB_SO_VER = $(GDAL_VERSION_MAJOR).$(LIBGDAL_CURRENT).$(LIBGDAL_REVISION) ++GDAL_SLIB_SONAME = -Wl,-soname,libgdal.$(SO_EXT).$(GDAL_VERSION_MAJOR) ++ + # Mac OS X Framework definition + MACOSX_FRAMEWORK = @MACOSX_FRAMEWORK@ + diff --git a/sci-libs/gdal/files/gdal-2.0.2-jasper.patch b/sci-libs/gdal/files/gdal-2.0.2-jasper.patch new file mode 100644 index 000000000000..00cf5c16fa4d --- /dev/null +++ b/sci-libs/gdal/files/gdal-2.0.2-jasper.patch @@ -0,0 +1,13 @@ +diff -urpN gdal-2.0.2.orig/frmts/jpeg2000/jpeg2000_vsil_io.h gdal-2.0.2/frmts/jpeg2000/jpeg2000_vsil_io.h +--- gdal-2.0.2.orig/frmts/jpeg2000/jpeg2000_vsil_io.h 2016-01-26 07:21:48.000000000 -0800 ++++ gdal-2.0.2/frmts/jpeg2000/jpeg2000_vsil_io.h 2016-10-31 23:45:28.939407322 -0700 +@@ -29,7 +29,8 @@ +
+ #ifndef JPEG2000_VSIL_IO_H
+ #define JPEG2000_VSIL_IO_H
+-
++
++#include <sys/types.h>
+ #include <jasper/jasper.h>
+
+ jas_stream_t *JPEG2000_VSIL_fopen(const char *filename, const char *mode);
diff --git a/sci-libs/gdal/files/gdal-2.0.2-jasper2.patch b/sci-libs/gdal/files/gdal-2.0.2-jasper2.patch new file mode 100644 index 000000000000..a418e4159c0a --- /dev/null +++ b/sci-libs/gdal/files/gdal-2.0.2-jasper2.patch @@ -0,0 +1,62 @@ +diff -urN orig/frmts/jpeg2000/jpeg2000_vsil_io.cpp dwok/frmts/jpeg2000/jpeg2000_vsil_io.cpp +--- orig/frmts/jpeg2000/jpeg2000_vsil_io.cpp 2016-01-26 16:21:48.000000000 +0100 ++++ dwok/frmts/jpeg2000/jpeg2000_vsil_io.cpp 2016-11-16 21:53:15.280302723 +0100 +@@ -179,40 +179,25 @@ + * Buffer initialization code.
+ \******************************************************************************/
+
+-static void JPEG2000_VSIL_jas_stream_initbuf(jas_stream_t *stream, int bufmode, char *buf,
+- int bufsize)
++static void JPEG2000_VSIL_jas_stream_initbuf(jas_stream_t *stream, int bufmode)
+ {
+ /* If this function is being called, the buffer should not have been
+ initialized yet. */
+ assert(!stream->bufbase_);
+
+ if (bufmode != JAS_STREAM_UNBUF) {
+- /* The full- or line-buffered mode is being employed. */
+- if (!buf) {
+- /* The caller has not specified a buffer to employ, so allocate
+- one. */
+- if ((stream->bufbase_ = (unsigned char*)jas_malloc(JAS_STREAM_BUFSIZE +
+- JAS_STREAM_MAXPUTBACK))) {
+- stream->bufmode_ |= JAS_STREAM_FREEBUF;
+- stream->bufsize_ = JAS_STREAM_BUFSIZE;
+- } else {
+- /* The buffer allocation has failed. Resort to unbuffered
+- operation. */
+- stream->bufbase_ = stream->tinybuf_;
+- stream->bufsize_ = 1;
+- }
++ if ((stream->bufbase_ = (unsigned char*)jas_malloc(JAS_STREAM_BUFSIZE +
++ JAS_STREAM_MAXPUTBACK))) {
++ stream->bufmode_ |= JAS_STREAM_FREEBUF;
++ stream->bufsize_ = JAS_STREAM_BUFSIZE;
+ } else {
+- /* The caller has specified a buffer to employ. */
+- /* The buffer must be large enough to accommodate maximum
+- putback. */
+- assert(bufsize > JAS_STREAM_MAXPUTBACK);
+- stream->bufbase_ = JAS_CAST(uchar *, buf);
+- stream->bufsize_ = bufsize - JAS_STREAM_MAXPUTBACK;
++ /* The buffer allocation has failed. Resort to unbuffered
++ operation. */
++ stream->bufbase_ = stream->tinybuf_;
++ stream->bufsize_ = 1;
+ }
+ } else {
+ /* The unbuffered mode is being employed. */
+- /* A buffer should not have been supplied by the caller. */
+- assert(!buf);
+ /* Use a trivial one-character buffer. */
+ stream->bufbase_ = stream->tinybuf_;
+ stream->bufsize_ = 1;
+@@ -282,7 +267,7 @@ + }
+
+ /* By default, use full buffering for this type of stream. */
+- JPEG2000_VSIL_jas_stream_initbuf(stream, JAS_STREAM_FULLBUF, 0, 0);
++ JPEG2000_VSIL_jas_stream_initbuf(stream, JAS_STREAM_FULLBUF);
+
+ return stream;
+ }
diff --git a/sci-libs/gdal/files/gdal-2.0.3-add-dlopen-support-for-jvm.patch b/sci-libs/gdal/files/gdal-2.0.3-add-dlopen-support-for-jvm.patch new file mode 100644 index 000000000000..7c35d1cb1242 --- /dev/null +++ b/sci-libs/gdal/files/gdal-2.0.3-add-dlopen-support-for-jvm.patch @@ -0,0 +1,232 @@ +From baba2c213770972e79be6be4902716278f351fb4 Mon Sep 17 00:00:00 2001 +From: James Le Cuirot <chewi@gentoo.org> +Date: Wed, 24 Aug 2016 23:32:13 +0100 +Subject: [PATCH 1/2] Allow libjvm.so to be dlopen'd with --with-jvm-lib=dlopen + +Having to set LD_LIBRARY_PATH is a pain and relying on the rpath can +be problematic when libjvm.so lives in a versioned directory. Some +distributions even allow per-user JVM selection so checking the value +of JAVA_HOME at runtime allows this choice to be respected. + +libjvm.so's location is hard to predict (amd64 vs i386, jre or not?) +so ${JAVA_HOME}/bin/java -XshowSettings is executed to find its +location. If JAVA_HOME is not set then java is executed from the PATH +instead. +--- + gdal/configure | 11 +++++- + gdal/configure.in | 7 +++- + gdal/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp | 57 +++++++++++++++++++++++++++-- + gdal/port/cpl_config.h.in | 3 ++ + 4 files changed, 71 insertions(+), 7 deletions(-) + +diff --git a/configure b/configure +index 75e4e279de..acdfa439de 100755 +--- a/configure ++++ b/configure +@@ -1753,7 +1753,7 @@ Optional Packages: + --with-python=ARG Enable python bindings (ARG=yes, no, or path to python binary) + --with-java Include Java support (ARG=yes, no or JDK home path) [default=no] + --with-mdb Include MDB driver +- --with-jvm-lib=ARG ARG points to Java libjvm path ++ --with-jvm-lib=ARG ARG is dlopen or points to Java libjvm path + --with-jvm-lib-add-rpath Add the libjvm path to the RPATH (no by default) + --with-rasdaman=DIR Include rasdaman support (DIR is rasdaman's install dir). + --with-armadillo=ARG Include Armadillo support for faster TPS transform computation (ARG=yes/no/path to armadillo install root) [default=no] +@@ -29491,7 +29491,14 @@ if test "${with_jvm_lib_add_rpath+set}" = set; then : + fi + + +- if test "x$with_jvm_lib" != "x"; then ++ if test "x$with_jvm_lib" = "xdlopen"; then ++ ++cat >>confdefs.h <<_ACEOF ++#define JVM_LIB_DLOPEN 1 ++_ACEOF ++ ++ JVM_LIB="-ldl" ++ elif test "x$with_jvm_lib" != "x"; then + if test -d "$with_jvm_lib"; then + saved_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS -L$with_jvm_lib" +diff --git a/configure.in b/configure.in +index 91efa5a32a..546ff04049 100644 +--- a/configure.in ++++ b/configure.in +@@ -4213,11 +4213,14 @@ if test "$with_mdb" = "yes" ; then + AC_MSG_ERROR("--with-java must be specified.") + fi + +- AC_ARG_WITH(jvm-lib, [ --with-jvm-lib=[ARG] ARG points to Java libjvm path],,) ++ AC_ARG_WITH(jvm-lib, [ --with-jvm-lib=[ARG] ARG is dlopen or points to Java libjvm path],,) + + AC_ARG_WITH(jvm-lib-add-rpath,[ --with-jvm-lib-add-rpath Add the libjvm path to the RPATH (no by default)],,) + +- if test "x$with_jvm_lib" != "x"; then ++ if test "x$with_jvm_lib" = "xdlopen"; then ++ AC_DEFINE_UNQUOTED(JVM_LIB_DLOPEN, 1, [Define to 1 if libjvm.so should be dlopen'd]) ++ JVM_LIB="-ldl" ++ elif test "x$with_jvm_lib" != "x"; then + if test -d "$with_jvm_lib"; then + saved_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS -L$with_jvm_lib" +diff --git a/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp b/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp +index b068adf777..bc54a115df 100644 +--- a/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp ++++ b/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp +@@ -29,6 +29,11 @@ + + #include "ogr_mdb.h" + ++#if JVM_LIB_DLOPEN ++#include <limits.h> ++#include <stdio.h> ++#endif ++ + CPL_CVSID("$Id: ogrmdbjackcess.cpp 27044 2014-03-16 23:41:27Z rouault $"); + + static JavaVM *jvm_static = NULL; +@@ -161,9 +166,41 @@ int OGRMDBJavaEnv::Init() + { + JavaVM* vmBuf[1]; + jsize nVMs; ++ int ret = 0; ++ ++#if JVM_LIB_DLOPEN ++ const char *jvmLibPtr = "libjvm.so"; ++ char jvmLib[PATH_MAX]; ++ ++ FILE *javaCmd = popen("\"${JAVA_HOME}${JAVA_HOME:+/bin/}java\" -XshowSettings 2>&1 | sed -n '/\\bsun\\.boot\\.library\\.path =/s:.* = \\(.*\\):\\1/server/libjvm.so:p'", "r"); ++ ++ if (javaCmd != NULL) ++ { ++ size_t javaCmdRead = fread(jvmLib, 1, PATH_MAX, javaCmd); ++ ret = pclose(javaCmd); ++ ++ if (ret == 0 && javaCmdRead >= 2) ++ { ++ /* Chomp the new line */ ++ jvmLib[javaCmdRead - 1] = '\0'; ++ jvmLibPtr = jvmLib; ++ } ++ } ++ ++ jint (*pfnJNI_GetCreatedJavaVMs)(JavaVM **, jsize, jsize *); ++ pfnJNI_GetCreatedJavaVMs = (jint (*)(JavaVM **, jsize, jsize *)) ++ CPLGetSymbol(jvmLibPtr, "JNI_GetCreatedJavaVMs"); ++ ++ if (pfnJNI_GetCreatedJavaVMs == NULL) ++ return FALSE; ++ else ++ ret = pfnJNI_GetCreatedJavaVMs(vmBuf, 1, &nVMs); ++#else ++ ret = JNI_GetCreatedJavaVMs(vmBuf, 1, &nVMs); ++#endif + + /* Are we already called from Java ? */ +- if (JNI_GetCreatedJavaVMs(vmBuf, 1, &nVMs) == JNI_OK && nVMs == 1) ++ if (ret == JNI_OK && nVMs == 1) + { + jvm = vmBuf[0]; + if (jvm->GetEnv((void **)&env, JNI_VERSION_1_2) == JNI_OK) +@@ -194,8 +231,22 @@ int OGRMDBJavaEnv::Init() + args.nOptions = 0; + args.ignoreUnrecognized = JNI_FALSE; + +- int ret = JNI_CreateJavaVM(&jvm, (void **)&env, &args); +- if (ret != 0 || jvm == NULL || env == NULL) ++#if JVM_LIB_DLOPEN ++ jint (*pfnJNI_CreateJavaVM)(JavaVM **, void **, void *); ++ pfnJNI_CreateJavaVM = (jint (*)(JavaVM **, void **, void *)) ++ CPLGetSymbol(jvmLibPtr, "JNI_CreateJavaVM"); ++ ++ if (pfnJNI_CreateJavaVM == NULL) ++ return FALSE; ++ else ++ ret = pfnJNI_CreateJavaVM(&jvm, (void **)&env, &args); ++#else ++ ret = JNI_CreateJavaVM(&jvm, (void **)&env, &args); ++#endif ++ ++ CPLFree(pszClassPathOption); ++ ++ if (ret != JNI_OK || jvm == NULL || env == NULL) + { + CPLError(CE_Failure, CPLE_AppDefined, "JNI_CreateJavaVM failed (%d)", ret); + return FALSE; +diff --git a/port/cpl_config.h.in b/port/cpl_config.h.in +index 313729fd3e..e8fa21140a 100644 +--- a/port/cpl_config.h.in ++++ b/port/cpl_config.h.in +@@ -161,6 +161,9 @@ + /* For .cpp files, define as const if the declaration of iconv() needs const. */ + #undef ICONV_CPP_CONST + ++/* Define to 1 if libjvm.so should be dlopen'd */ ++#undef JVM_LIB_DLOPEN ++ + /* Define to the sub-directory in which libtool stores uninstalled libraries. + */ + #undef LT_OBJDIR +-- +2.11.0 + + +From cd6bbb60ced62b6176482e86c54ab618e2592ac8 Mon Sep 17 00:00:00 2001 +From: James Le Cuirot <chewi@gentoo.org> +Date: Thu, 25 Aug 2016 21:26:20 +0100 +Subject: [PATCH 2/2] Fetch jackcess classpath using java-config instead of + using CLASSPATH + +--- + gdal/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp | 26 ++++++++++++++++++++++---- + 1 file changed, 22 insertions(+), 4 deletions(-) + +diff --git a/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp b/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp +index bc54a115df..5b0972677e 100644 +--- a/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp ++++ b/ogr/ogrsf_frmts/mdb/ogrmdbjackcess.cpp +@@ -218,19 +218,37 @@ int OGRMDBJavaEnv::Init() + JavaVMInitArgs args; + JavaVMOption options[1]; + args.version = JNI_VERSION_1_2; +- const char* pszClassPath = CPLGetConfigOption("CLASSPATH", NULL); +- CPLString osClassPathOption; ++ ++ FILE *javaCmd = popen("java-config --with-dependencies --classpath=jackcess-1", "r"); ++ ++ const char* pszClassPath = NULL; ++ if (javaCmd != NULL) ++ { ++ pszClassPath = CPLReadLine(javaCmd); ++ ret = pclose(javaCmd); ++ ++ if (ret != 0) ++ pszClassPath = NULL; ++ } ++ ++ if (pszClassPath == NULL) ++ pszClassPath = CPLGetConfigOption("CLASSPATH", NULL); ++ ++ char* pszClassPathOption = NULL; + if (pszClassPath) + { + args.nOptions = 1; +- osClassPathOption.Printf("-Djava.class.path=%s", pszClassPath); +- options[0].optionString = (char*) osClassPathOption.c_str(); ++ pszClassPathOption = CPLStrdup(CPLSPrintf("-Djava.class.path=%s", pszClassPath)); ++ options[0].optionString = pszClassPathOption; + args.options = options; + } + else + args.nOptions = 0; + args.ignoreUnrecognized = JNI_FALSE; + ++ if (javaCmd != NULL) ++ CPLReadLine(NULL); ++ + #if JVM_LIB_DLOPEN + jint (*pfnJNI_CreateJavaVM)(JavaVM **, void **, void *); + pfnJNI_CreateJavaVM = (jint (*)(JavaVM **, void **, void *)) +-- +2.11.0 + diff --git a/sci-libs/gdal/files/gdal-2.0.3-install_name.patch b/sci-libs/gdal/files/gdal-2.0.3-install_name.patch new file mode 100644 index 000000000000..1e83d55ecf7d --- /dev/null +++ b/sci-libs/gdal/files/gdal-2.0.3-install_name.patch @@ -0,0 +1,49 @@ +Unbreak compilation on Darwin + +Author: Fabian Groffen <grobian@gentoo.org> + +--- gdal-2.0.3.old/GDALmake.opt.in ++++ gdal-2.0.3/GDALmake.opt.in +@@ -104,6 +104,10 @@ GDAL_LIB = $(GDAL_ROOT)/libgdal.a + GDAL_SLIB = $(GDAL_ROOT)/libgdal.$(SO_EXT) + GDAL_SLIB_LINK = -L$(GDAL_ROOT) -lgdal + ++# for building without libtool ++GDAL_SLIB_SO_VER = $(GDAL_VERSION_MAJOR).$(LIBGDAL_CURRENT).$(LIBGDAL_REVISION) ++GDAL_SLIB_SONAME = -install_name $(INST_LIB)/libgdal.$(GDAL_VERSION_MAJOR).$(SO_EXT) ++ + # Mac OS X Framework definition + MACOSX_FRAMEWORK = @MACOSX_FRAMEWORK@ + +--- gdal-2.0.3.old/GNUmakefile ++++ gdal-2.0.3/GNUmakefile +@@ -208,7 +208,7 @@ else + + ifeq ($(HAVE_LD_SHARED),yes) + +-GDAL_SLIB_B = $(notdir $(GDAL_SLIB)) ++GDAL_SLIB_B = libgdal + + install-lib: + +@@ -216,14 +216,14 @@ install-lib: + ifeq ($(MACOSX_FRAMEWORK),yes) + $(INSTALL_LIB) $(GDAL_SLIB) $(DESTDIR)$(INST_LIB)/GDAL + else +- rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B) +- rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR) +- rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VER) +- $(INSTALL_LIB) $(GDAL_SLIB) $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VER) ++ rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).dylib ++ rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR).dylib ++ rm -f $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VER).dylib ++ $(INSTALL_LIB) $(GDAL_SLIB) $(DESTDIR)$(INST_LIB)/$(GDAL_SLIB_B).$(GDAL_VER).dylib + (cd $(DESTDIR)$(INST_LIB) ; \ +- ln -s $(GDAL_SLIB_B).$(GDAL_VER) $(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR)) ++ ln -s $(GDAL_SLIB_B).$(GDAL_VER).dylib $(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR).dylib) + (cd $(DESTDIR)$(INST_LIB) ; \ +- ln -s $(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR) $(GDAL_SLIB_B)) ++ ln -s $(GDAL_SLIB_B).$(GDAL_VERSION_MAJOR).dylib $(GDAL_SLIB_B).dylib) + $(INSTALL_DIR) $(DESTDIR)$(INST_LIB)/gdalplugins + endif + diff --git a/sci-libs/gdal/gdal-2.0.2-r3.ebuild b/sci-libs/gdal/gdal-2.0.2-r3.ebuild new file mode 100644 index 000000000000..4a713012e981 --- /dev/null +++ b/sci-libs/gdal/gdal-2.0.2-r3.ebuild @@ -0,0 +1,288 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +WANT_AUTOCONF="2.5" + +GENTOO_DEPEND_ON_PERL="no" +PYTHON_COMPAT=( python2_7 python3_4 ) +DISTUTILS_OPTIONAL=1 + +inherit autotools eutils libtool perl-module distutils-r1 flag-o-matic toolchain-funcs java-pkg-opt-2 + +DESCRIPTION="Translator library for raster geospatial data formats (includes OGR support)" +HOMEPAGE="http://www.gdal.org/" +SRC_URI="http://download.osgeo.org/${PN}/${PV}/${P}.tar.gz" + +SLOT="0/2" +LICENSE="BSD Info-ZIP MIT" +KEYWORDS="amd64 ~arm ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" +IUSE="armadillo +aux_xml curl debug doc fits geos gif gml hdf5 java jpeg jpeg2k mdb mysql netcdf odbc ogdi opencl pdf perl png postgres python spatialite sqlite threads xls" + +RDEPEND=" + dev-libs/expat + dev-libs/json-c + dev-libs/libpcre + dev-libs/libxml2 + media-libs/tiff:0= + sci-libs/libgeotiff + sys-libs/zlib[minizip(+)] + armadillo? ( sci-libs/armadillo[lapack] ) + curl? ( net-misc/curl ) + fits? ( sci-libs/cfitsio ) + geos? ( >=sci-libs/geos-2.2.1 ) + gif? ( media-libs/giflib:= ) + gml? ( >=dev-libs/xerces-c-3 ) + hdf5? ( >=sci-libs/hdf5-1.6.4[szip] ) + java? ( >=virtual/jre-1.6:* ) + jpeg? ( virtual/jpeg:0= ) + jpeg2k? ( media-libs/jasper:= ) + mysql? ( virtual/mysql ) + netcdf? ( sci-libs/netcdf ) + odbc? ( dev-db/unixODBC ) + ogdi? ( sci-libs/ogdi ) + opencl? ( virtual/opencl ) + pdf? ( >=app-text/poppler-0.24.3:= ) + perl? ( dev-lang/perl:= ) + png? ( media-libs/libpng:0= ) + postgres? ( >=dev-db/postgresql-8.4:= ) + python? ( + ${PYTHON_DEPS} + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + ) + sqlite? ( dev-db/sqlite:3 ) + spatialite? ( dev-db/spatialite ) + xls? ( dev-libs/freexl ) +" + +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + java? ( >=virtual/jdk-1.6 ) + perl? ( dev-lang/swig:0 ) + python? ( dev-lang/swig:0 )" + +AT_M4DIR="${S}/m4" + +REQUIRED_USE=" + spatialite? ( sqlite ) + python? ( ${PYTHON_REQUIRED_USE} ) + mdb? ( java ) +" + +pkg_setup() { + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + java-pkg-opt-2_src_prepare + + # fix datadir and docdir placement + sed -i \ + -e "s:@datadir@:@datadir@/gdal:" \ + -e "s:@exec_prefix@/doc:@exec_prefix@/share/doc/${PF}/html:g" \ + "${S}"/GDALmake.opt.in || die + + if use jpeg2k; then + epatch "${FILESDIR}"/${P}-jasper.patch + epatch "${FILESDIR}"/${P}-jasper2.patch #bug 599626 + fi + + # -soname is only accepted by GNU ld/ELF + [[ ${CHOST} == *-darwin* ]] \ + && epatch "${FILESDIR}"/${PN}-1.5.0-install_name.patch \ + || epatch "${FILESDIR}"/${PN}-1.5.0-soname.patch + + # Fix spatialite/sqlite include issue + sed -i \ + -e 's:spatialite/sqlite3.h:sqlite3.h:g' \ + ogr/ogrsf_frmts/sqlite/ogr_sqlite.h || die + + # Fix freexl configure check + sed -i \ + -e 's:FREEXL_LIBS=missing):FREEXL_LIBS=missing,-lm):g' \ + configure.in || die + + sed \ + -e "s: /usr/: \"${EPREFIX}\"/usr/:g" \ + -i configure.in || die + + sed \ + -e 's:^ar:$(AR):g' \ + -i ogr/ogrsf_frmts/sdts/install-libs.sh || die + + # updated for newer swig (must specify the path to input files) + sed -i \ + -e "s: gdal_array.i: ../include/gdal_array.i:" \ + -e "s:\$(DESTDIR)\$(prefix):\$(DESTDIR)\$(INST_PREFIX):g" \ + swig/python/GNUmakefile || die "sed python makefile failed" + sed -i \ + -e "s:library_dirs = :library_dirs = /usr/$(get_libdir):g" \ + swig/python/setup.cfg || die "sed python setup.cfg failed" + + # bug 626844, poppler headers require C++11 + use pdf && append-cxxflags -std=c++11 + + tc-export AR RANLIB + + eautoreconf +} + +src_configure() { + local myopts="" + + if use java; then + myopts+=" + --with-java=$(java-config --jdk-home 2>/dev/null) + $(use_with mdb)" + else + myopts+=" --without-java --without-mdb" + use mdb && ewarn "mdb requires java use enabled. disabling" + fi + + if use sqlite; then + myopts+=" LIBS=-lsqlite3" + fi + + # pcidsk is internal, because there is no such library yet released + # also that thing is developed by the gdal people + # kakadu, mrsid jp2mrsid - another jpeg2k stuff, ignore + # bsb - legal issues + # oracle - disabled, i dont have and can't test + # ingres - same story as oracle oci + # podofo - we use poppler instead they are exclusive for each other + # tiff is a hard dep + ECONF_SOURCE="${S}" econf \ + --includedir="${EPREFIX}/usr/include/${PN}" \ + --disable-static \ + --enable-shared \ + --with-expat \ + --with-geotiff \ + --with-grib \ + --with-libtiff \ + --with-libz="${EPREFIX}/usr/" \ + --with-ogr \ + --without-bsb \ + --without-dods-root \ + --without-dwgdirect \ + --without-epsilon \ + --without-fme \ + --without-grass \ + --without-hdf4 \ + --without-idb \ + --without-ingres \ + --without-jp2mrsid \ + --without-kakadu \ + --without-libtool \ + --without-mrsid \ + --without-msg \ + --without-oci \ + --without-pcraster \ + --without-podofo \ + --without-python \ + --without-sde \ + $(use_enable debug) \ + $(use_with armadillo) \ + $(use_with aux_xml pam) \ + $(use_with curl) \ + --without-ecw \ + $(use_with fits cfitsio) \ + $(use_with geos) \ + $(use_with gif) \ + $(use_with gml xerces) \ + $(use_with hdf5) \ + $(use_with jpeg pcidsk) \ + $(use_with jpeg) \ + $(use_with jpeg2k jasper) \ + $(use_with mysql mysql "${EPREFIX}"/usr/bin/mysql_config) \ + $(use_with netcdf) \ + $(use_with odbc) \ + $(use_with ogdi ogdi "${EPREFIX}"/usr) \ + $(use_with opencl) \ + $(use_with pdf poppler) \ + $(use_with perl) \ + $(use_with png) \ + $(use_with postgres pg) \ + $(use_with spatialite) \ + $(use_with sqlite sqlite3 "${EPREFIX}"/usr) \ + $(use_with threads) \ + $(use_with xls freexl) \ + ${myopts} + + # mysql-config puts this in (and boy is it a PITA to get it out) + if use mysql; then + sed -i \ + -e "s: -rdynamic : :" \ + GDALmake.opt || die "sed LIBS failed" + fi +} + +src_compile() { + if use perl; then + rm "${S}"/swig/perl/*_wrap.cpp || die + emake -C "${S}"/swig/perl generate + fi + + # gdal-config needed before generating Python bindings + default + + if use perl ; then + pushd "${S}"/swig/perl > /dev/null || die + perl-module_src_configure + perl-module_src_compile + popd > /dev/null || die + fi + + if use python; then + rm -f "${S}"swig/python/*_wrap.cpp || die + emake -C "${S}"/swig/python generate + pushd "${S}"/swig/python > /dev/null || die + distutils-r1_src_compile + popd > /dev/null || die + fi + + use doc && emake docs +} + +src_install() { + if use perl ; then + pushd "${S}"/swig/perl > /dev/null || die + perl-module_src_install + popd > /dev/null || die + sed -e 's:BINDINGS = \(.*\) perl:BINDINGS = \1:g' \ + -i GDALmake.opt || die + fi + + default + + use perl && perl_delete_localpod + + dodoc Doxyfile HOWTO-RELEASE NEWS + + use doc && dohtml html/* + + python_install() { + distutils-r1_python_install + python_doscript scripts/*.py + } + if use python; then + pushd "${S}"/swig/python > /dev/null || die + distutils-r1_src_install + popd > /dev/null || die + newdoc swig/python/README.txt README-python.txt + insinto /usr/share/${PN}/samples + doins swig/python/samples/* + fi + + pushd man/man1 > /dev/null || die + for i in * ; do + newman ${i} ${i} + done + popd > /dev/null || die +} + +pkg_postinst() { + elog "Check available image and data formats after building with" + elog "gdalinfo and ogrinfo (using the --formats switch)." +} diff --git a/sci-libs/gdal/gdal-2.0.3.ebuild b/sci-libs/gdal/gdal-2.0.3.ebuild new file mode 100644 index 000000000000..74f1aa7ecb35 --- /dev/null +++ b/sci-libs/gdal/gdal-2.0.3.ebuild @@ -0,0 +1,293 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="6" + +WANT_AUTOCONF="2.5" + +GENTOO_DEPEND_ON_PERL="no" +PYTHON_COMPAT=( python2_7 python3_{4,5} ) +DISTUTILS_OPTIONAL=1 + +inherit autotools perl-module distutils-r1 toolchain-funcs flag-o-matic java-pkg-opt-2 + +DESCRIPTION="Translator library for raster geospatial data formats (includes OGR support)" +HOMEPAGE="http://www.gdal.org/" +SRC_URI="http://download.osgeo.org/${PN}/${PV}/${P}.tar.gz" + +SLOT="0/2" +LICENSE="BSD Info-ZIP MIT" +KEYWORDS="amd64 ~arm ~arm64 ~ia64 ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" +IUSE="armadillo +aux_xml curl debug doc fits geos gif gml hdf5 java jpeg jpeg2k mdb mysql netcdf odbc ogdi opencl oracle pdf perl png postgres python spatialite sqlite threads xls" + +COMMON_DEPEND="dev-libs/expat + dev-libs/json-c:= + dev-libs/libpcre + dev-libs/libxml2:= + media-libs/tiff:0= + sci-libs/libgeotiff + sys-libs/zlib[minizip(+)] + armadillo? ( sci-libs/armadillo:=[lapack] ) + curl? ( net-misc/curl ) + fits? ( sci-libs/cfitsio:= ) + geos? ( >=sci-libs/geos-2.2.1 ) + gif? ( media-libs/giflib:= ) + gml? ( >=dev-libs/xerces-c-3 ) + hdf5? ( >=sci-libs/hdf5-1.6.4:=[szip] ) + jpeg? ( virtual/jpeg:0= ) + jpeg2k? ( media-libs/openjpeg:2= ) + mdb? ( dev-java/jackcess:1 ) + mysql? ( virtual/mysql ) + netcdf? ( sci-libs/netcdf:= ) + odbc? ( dev-db/unixODBC ) + ogdi? ( sci-libs/ogdi ) + opencl? ( virtual/opencl ) + oracle? ( dev-db/oracle-instantclient:= ) + pdf? ( >=app-text/poppler-0.24.3:= ) + perl? ( dev-lang/perl:= ) + png? ( media-libs/libpng:0= ) + postgres? ( >=dev-db/postgresql-8.4:= ) + python? ( + ${PYTHON_DEPS} + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + ) + sqlite? ( dev-db/sqlite:3 ) + spatialite? ( dev-db/spatialite ) + xls? ( dev-libs/freexl )" + +RDEPEND="${COMMON_DEPEND} + java? ( >=virtual/jre-1.7:* )" + +DEPEND="${COMMON_DEPEND} + doc? ( app-doc/doxygen ) + java? ( >=virtual/jdk-1.7:* ) + perl? ( dev-lang/swig:0 ) + python? ( dev-lang/swig:0 )" + +REQUIRED_USE="mdb? ( java ) + python? ( ${PYTHON_REQUIRED_USE} ) + spatialite? ( sqlite ) +" + +src_prepare() { + local PATCHES=() + local PATCHES=( "${FILESDIR}"/gdal-2.0.3-add-dlopen-support-for-jvm.patch ) + + # -soname is only accepted by GNU ld/ELF + if [[ ${CHOST} == *-darwin* ]]; then + PATCHES+=( "${FILESDIR}"/${PN}-2.0.3-install_name.patch ) + else + PATCHES+=( "${FILESDIR}"/${PN}-1.5.0-soname-r1.patch ) + fi + + # fix datadir and docdir placement + sed -i \ + -e "s:@datadir@:@datadir@/gdal:" \ + -e "s:@exec_prefix@/doc:@exec_prefix@/share/doc/${PF}/html:g" \ + "${S}"/GDALmake.opt.in || die + + # the second sed expression should fix bug 371075 + sed -i \ + -e "s:setup.py install:setup.py install --root=\$(DESTDIR):" \ + -e "s:--prefix=\$(DESTDIR):--prefix=:" \ + "${S}"/swig/python/GNUmakefile || die + + # Fix spatialite/sqlite include issue + sed -i \ + -e 's:spatialite/sqlite3.h:sqlite3.h:g' \ + ogr/ogrsf_frmts/sqlite/ogr_sqlite.h || die + + # Fix freexl configure check + sed -i \ + -e 's:FREEXL_LIBS=missing):FREEXL_LIBS=missing,-lm):g' \ + configure.in || die + + sed \ + -e "s: /usr/: \"${EPREFIX}\"/usr/:g" \ + -i configure.in || die + + sed \ + -e 's:^ar:$(AR):g' \ + -i ogr/ogrsf_frmts/sdts/install-libs.sh || die + + # updated for newer swig (must specify the path to input files) + sed -i \ + -e "s: gdal_array.i: ../include/gdal_array.i:" \ + -e "s:\$(DESTDIR)\$(prefix):\$(DESTDIR)\$(INST_PREFIX):g" \ + swig/python/GNUmakefile || die "sed python makefile failed" + sed -i \ + -e "s:library_dirs = :library_dirs = /usr/$(get_libdir):g" \ + swig/python/setup.cfg || die "sed python setup.cfg failed" + + default + + # bug 626844, poppler headers require C++11 + use pdf && append-cxxflags -std=c++11 + + tc-export AR RANLIB + + mv configure.{in,ac} || die + + eautoreconf +} + +src_configure() { + local myopts="" + + if use java; then + myopts+=" + --with-java=$(java-config --jdk-home 2>/dev/null) + --with-jvm-lib=dlopen + $(use_with mdb)" + else + myopts+=" --without-java --without-mdb" + fi + + if use sqlite; then + myopts+=" LIBS=-lsqlite3" + fi + + # pcidsk is internal, because there is no such library yet released + # also that thing is developed by the gdal people + # kakadu, mrsid jp2mrsid - another jpeg2k stuff, ignore + # bsb - legal issues + # ingres - same story as oracle oci + # jasper - disabled because unmaintained and vulnerable; openjpeg will be used as JPEG-2000 provider instead + # podofo - we use poppler instead they are exclusive for each other + # tiff is a hard dep + ECONF_SOURCE="${S}" econf \ + --includedir="${EPREFIX}/usr/include/${PN}" \ + --disable-static \ + --enable-shared \ + --with-expat \ + --with-geotiff \ + --with-grib \ + --with-libtiff \ + --with-libz="${EPREFIX}/usr/" \ + --with-ogr \ + --without-bsb \ + --without-dods-root \ + --without-dwgdirect \ + --without-epsilon \ + --without-fme \ + --without-grass \ + --without-hdf4 \ + --without-idb \ + --without-ingres \ + --without-jasper \ + --without-jp2mrsid \ + --without-kakadu \ + --without-libtool \ + --without-mrsid \ + --without-msg \ + --without-pcraster \ + --without-podofo \ + --without-sde \ + $(use_enable debug) \ + $(use_with armadillo) \ + $(use_with aux_xml pam) \ + $(use_with curl) \ + --without-ecw \ + $(use_with fits cfitsio) \ + $(use_with geos) \ + $(use_with gif) \ + $(use_with gml xerces) \ + $(use_with hdf5) \ + $(use_with jpeg pcidsk) \ + $(use_with jpeg) \ + $(use_with jpeg2k openjpeg) \ + $(use_with mysql mysql "${EPREFIX}"/usr/bin/mysql_config) \ + $(use_with netcdf) \ + $(use_with oracle oci) \ + $(use_with odbc) \ + $(use_with ogdi ogdi "${EPREFIX}"/usr) \ + $(use_with opencl) \ + $(use_with pdf poppler) \ + $(use_with perl) \ + $(use_with png) \ + $(use_with postgres pg) \ + $(use_with python) \ + $(use_with spatialite) \ + $(use_with sqlite sqlite3 "${EPREFIX}"/usr) \ + $(use_with threads) \ + $(use_with xls freexl) \ + ${myopts} + + # mysql-config puts this in (and boy is it a PITA to get it out) + if use mysql; then + sed -i \ + -e "s: -rdynamic : :" \ + GDALmake.opt || die "sed LIBS failed" + fi +} + +src_compile() { + if use perl; then + rm "${S}"/swig/perl/*_wrap.cpp || die + emake -C "${S}"/swig/perl generate + fi + + # gdal-config needed before generating Python bindings + default + + if use perl ; then + pushd "${S}"/swig/perl > /dev/null || die + perl-module_src_configure + perl-module_src_compile + popd > /dev/null || die + fi + + if use python; then + rm -f "${S}"swig/python/*_wrap.cpp || die + emake -C "${S}"/swig/python generate + pushd "${S}"/swig/python > /dev/null || die + distutils-r1_src_compile + popd > /dev/null || die + fi + + use doc && emake docs +} + +src_install() { + if use perl ; then + pushd "${S}"/swig/perl > /dev/null || die + perl-module_src_install + popd > /dev/null || die + sed -e 's:BINDINGS = \(.*\) perl:BINDINGS = \1:g' \ + -i GDALmake.opt || die + fi + + use perl && perl_delete_localpod + + local DOCS=( Doxyfile HOWTO-RELEASE NEWS ) + use doc && HTML_DOCS=( html/. ) + + default + + python_install() { + distutils-r1_python_install + python_doscript scripts/*.py + } + + if use python; then + # Don't clash with gdal's docs + unset DOCS HTML_DOCS + + pushd "${S}"/swig/python > /dev/null || die + distutils-r1_src_install + popd > /dev/null || die + + newdoc swig/python/README.txt README-python.txt + + insinto /usr/share/${PN}/samples + doins swig/python/samples/* + fi + + doman "${S}"/man/man*/* +} + +pkg_postinst() { + elog "Check available image and data formats after building with" + elog "gdalinfo and ogrinfo (using the --formats switch)." +} diff --git a/sci-libs/gdal/metadata.xml b/sci-libs/gdal/metadata.xml new file mode 100644 index 000000000000..7088f71ba0f1 --- /dev/null +++ b/sci-libs/gdal/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-geosciences@gentoo.org</email> + <name>Gentoo Geosciences Project</name> + </maintainer> + <longdescription> + GDAL is the Geospatial Data Abstraction Library, a set of tools for + converting between geospatial raster data formats (includes OGR for + vector data). + </longdescription> + <slots> + <subslots>Reflects ABI compatibility of libgdal.so</subslots> + </slots> + <use> + <flag name="armadillo">Use <pkg>sci-libs/armadillo</pkg> for faster TPS transform computation</flag> + <flag name="aux_xml">Enable Portable Auxilliary Metadata generation</flag> + <flag name="fits">Enable support for NASA's <pkg>sci-libs/cfitsio</pkg> library</flag> + <flag name="geos">Add support for geometry engine (<pkg>sci-libs/geos</pkg>)</flag> + <flag name="gml">Enable support for <pkg>dev-libs/xerces-c</pkg> C++ API</flag> + <flag name="hdf5">Add support for the Hierarchical Data Format v5 (<pkg>sci-libs/hdf5</pkg>)</flag> + <flag name="mdb">Enable support for Microsoft Access database</flag> + <flag name="ogdi">Enable support for the open geographic datastore interface (<pkg>sci-libs/ogdi</pkg>)</flag> + <flag name="opencl">Enable OpenCL support</flag> + <flag name="spatialite">Enable Spatial DBMS over sqlite <pkg>dev-db/spatialite</pkg></flag> + <flag name="xls">Add the <pkg>dev-libs/freexl</pkg> library for xls import support</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/geos/Manifest b/sci-libs/geos/Manifest new file mode 100644 index 000000000000..d33ac62d91e8 --- /dev/null +++ b/sci-libs/geos/Manifest @@ -0,0 +1,12 @@ +AUX 3.4.2-solaris-isnan.patch 575 SHA256 88221c77c0ab08a4c000cede7528ebacc6ec1535ca00a9bcb0a01f11853cad39 SHA512 efa2730f178814e8d98318347e7a8313327679a5c861ef2a844ce821c5854f4dd56e0cc2c52fa5866fb4214b0d9aa8614b1f1ebaa62f0427e69221a93106aa45 WHIRLPOOL bab6b200b942bb83d8a9a298f9c658b48a35b4abd308c6eb77f43359424de029fe2387ab74030b2a5b440a38202e300b0971895535d11b3a8b9158ecf9fc4b42 +AUX geos-3.5.0-autoconf-detect-isnan.patch 743 SHA256 b436c8540c9fa5b517f1fa97b6611fafef44ce03cee115d47d934e19190538cb SHA512 319b853ae42a9ba5ead8854dc2e4005ab1bc644f71f1f05fdbc469e2179a63653226423be0623dcb4499c58a9b1831b2ae7f8f3e8026e1ebe60cc1dde86c8288 WHIRLPOOL d660d6f3cc21a1a1eade93adfef8fef5b9249e420583e33eb8f92807692c2f73a169e40b1418641702797f2dba0de210d49396cb9001b4d5d4bb457db42ca311 +AUX geos-3.5.0-phpconfig-path.patch 1199 SHA256 82f128367477f66d88b9cfb0989d60e18097e82fece4478661c628b05e749bd2 SHA512 7b8b70904b86ad5b677cf3ea43d31e89fcf4bfeab429c8d71e6a96924f1500684c992e3a23dd4b993c9d36e6aa50c38158526c6a78e5e802968b795efcbc9c54 WHIRLPOOL af51b47ce428b43e3fa1dd22daab6d5083a084fd73560d4f2b6241106f84ac115c2de1009a9b209013e60c6aa4205d620c8546dd22e0d0d5b6ee017ee8e4e7cd +AUX geos-3.5.0-std-isnan.patch 799 SHA256 c09fa85543e55ea401994bbeb1863224702a3f891aac0d5d35edfed649d045bf SHA512 786fd52721378481bed7d040d4e3f7ab4be3090982e82839f8993ea63d09ff03ec5df9edb776da0afb43a94c745a52af34517cc264b47f1f57278292bc65e1dc WHIRLPOOL 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cf93ad12e2e2d23ce6b454ae1032e8362beccd952a0f431780467c2985c07fa284edcb10a5d7b61d098a70c097f091a7f771be5a1650c1ed431ba249f73e5b1c WHIRLPOOL 08c68f1b72095471e86966fb518da6d6717b9605339c6f60fece23b402e017a7a7160af7bcb73b71d1987e3ea177ddee875bb2920727adc7d096879904c17958 diff --git a/sci-libs/geos/files/3.4.2-solaris-isnan.patch b/sci-libs/geos/files/3.4.2-solaris-isnan.patch new file mode 100644 index 000000000000..a66d36f6587d --- /dev/null +++ b/sci-libs/geos/files/3.4.2-solaris-isnan.patch @@ -0,0 +1,14 @@ +diff -Naruw geos-3.4.2.orig/include/geos/platform.h.in geos-3.4.2/include/geos/platform.h.in +--- geos-3.4.2.orig/include/geos/platform.h.in 2013-08-25 15:10:32.000000000 +0000 ++++ geos-3.4.2/include/geos/platform.h.in 2013-10-20 23:45:29.891690795 +0000 +@@ -98,8 +98,9 @@ + // It does leave a version in std. + # define ISNAN(x) (std::isnan(x)) + # elif (defined(__sun) || defined(__sun__)) && defined(__SUNPRO_CC) ++# define _XOPEN_SOURCE 600 //force iso/math_c99 + # include <math.h> +-# define ISNAN(x) (::isnan(x)) ++# define ISNAN(x) (std::isnan(x)) + # endif + #endif + diff --git a/sci-libs/geos/files/geos-3.5.0-autoconf-detect-isnan.patch b/sci-libs/geos/files/geos-3.5.0-autoconf-detect-isnan.patch new file mode 100644 index 000000000000..79e319da493e --- /dev/null +++ b/sci-libs/geos/files/geos-3.5.0-autoconf-detect-isnan.patch @@ -0,0 +1,25 @@ +From edbeee650287a4a36837e090eafed90a760bad83 Mon Sep 17 00:00:00 2001 +From: Sandro Santilli <strk@keybit.net> +Date: Mon, 7 Mar 2016 10:21:33 +0000 +Subject: [PATCH] Look for isnan in std:: namespace + +Tested with gcc 4.8.4 + +git-svn-id: http://svn.osgeo.org/geos/trunk@4169 5242fede-7e19-0410-aef8-94bd7d2200fb +--- + configure.ac | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/configure.ac b/configure.ac +index 7fdc579..8976a6a 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -197,7 +197,7 @@ dnl of isnan(). + AC_LANG_PUSH([C++]) + AC_CACHE_CHECK([for isnan], ac_cv_isnan, + [AC_TRY_LINK([#include <cmath>], +- [double x; int y; y = isnan(x);], ++ [double x; int y; y = std::isnan(x);], + ac_cv_isnan=yes, + ac_cv_isnan=no + )]) diff --git a/sci-libs/geos/files/geos-3.5.0-phpconfig-path.patch b/sci-libs/geos/files/geos-3.5.0-phpconfig-path.patch new file mode 100644 index 000000000000..b44eb9da9ea1 --- /dev/null +++ b/sci-libs/geos/files/geos-3.5.0-phpconfig-path.patch @@ -0,0 +1,29 @@ +diff --git a/php/Makefile.am b/php/Makefile.am +index 5b50c0f..fad05c0 100644 +--- a/php/Makefile.am ++++ b/php/Makefile.am +@@ -56,7 +56,7 @@ geos_la_CPPFLAGS = $(AM_CPPFLAGS) \ + -I$(top_srcdir)/include + + install: all +- $(INSTALL) -d "$(DESTDIR)"/`$(PHP_CONFIG) --extension-dir` +- $(INSTALL) -m 755 .libs/geos.so "$(DESTDIR)"/`php-config --extension-dir` ++ $(INSTALL) -d "$(DESTDIR)"`$(PHP_CONFIG) --extension-dir` ++ $(INSTALL) -m 755 .libs/geos.so "$(DESTDIR)"`$(PHP_CONFIG) --extension-dir` + + endif +diff --git a/php/Makefile.in b/php/Makefile.in +index d8c343e..9485d0d 100644 +--- a/php/Makefile.in ++++ b/php/Makefile.in +@@ -877,8 +877,8 @@ uninstall-am: uninstall-pkglibLTLIBRARIES + + + @ENABLE_PHP_TRUE@install: all +-@ENABLE_PHP_TRUE@ $(INSTALL) -d "$(DESTDIR)"/`$(PHP_CONFIG) --extension-dir` +-@ENABLE_PHP_TRUE@ $(INSTALL) -m 755 .libs/geos.so "$(DESTDIR)"/`php-config --extension-dir` ++@ENABLE_PHP_TRUE@ $(INSTALL) -d "$(DESTDIR)"`$(PHP_CONFIG) --extension-dir` ++@ENABLE_PHP_TRUE@ $(INSTALL) -m 755 .libs/geos.so "$(DESTDIR)"`$(PHP_CONFIG) --extension-dir` + + # Tell versions [3.59,3.63) of GNU make to not export all variables. + # Otherwise a system limit (for SysV at least) may be exceeded. diff --git a/sci-libs/geos/files/geos-3.5.0-std-isnan.patch b/sci-libs/geos/files/geos-3.5.0-std-isnan.patch new file mode 100644 index 000000000000..c2b6a996afcd --- /dev/null +++ b/sci-libs/geos/files/geos-3.5.0-std-isnan.patch @@ -0,0 +1,26 @@ +From a9bb3ed34e71f5f9d1d1b0bc3044555a0b3b932c Mon Sep 17 00:00:00 2001 +From: Sandro Santilli <strk@keybit.net> +Date: Thu, 14 Jul 2016 10:38:35 +0000 +Subject: [PATCH] Fully qualify isnan call when HAVE_ISNAN is defined + +Fixes build with GCC-5.3.0 and higher. +Closes #784 + +git-svn-id: http://svn.osgeo.org/geos/trunk@4224 5242fede-7e19-0410-aef8-94bd7d2200fb +--- + include/geos/platform.h.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/geos/platform.h.in b/include/geos/platform.h.in +index d8d4558..c3bc9c8 100644 +--- a/include/geos/platform.h.in ++++ b/include/geos/platform.h.in +@@ -86,7 +86,7 @@ extern "C" + #endif + + #if defined(HAVE_ISNAN) +-# define ISNAN(x) (isnan(x)) ++# define ISNAN(x) (std::isnan(x)) + #else + # if defined(_MSC_VER) + # define ISNAN(x) _isnan(x) diff --git a/sci-libs/geos/geos-3.5.0-r2.ebuild b/sci-libs/geos/geos-3.5.0-r2.ebuild new file mode 100644 index 000000000000..986fa56bbe03 --- /dev/null +++ b/sci-libs/geos/geos-3.5.0-r2.ebuild @@ -0,0 +1,135 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +USE_PHP="php5-4 php5-5 php5-6" +PHP_EXT_NAME="geos" +PHP_EXT_OPTIONAL_USE="php" +PHP_EXT_SKIP_PHPIZE="yes" + +inherit php-ext-source-r2 autotools eutils python-single-r1 + +DESCRIPTION="Geometry engine library for Geographic Information Systems" +HOMEPAGE="http://trac.osgeo.org/geos/" +SRC_URI="http://download.osgeo.org/geos/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris" +IUSE="doc php python ruby static-libs" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + python? ( ${PYTHON_DEPS} ) + ruby? ( dev-lang/ruby:* ) +" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + php? ( + dev-lang/swig + app-admin/chrpath + ) + python? ( dev-lang/swig ) + ruby? ( dev-lang/swig ) +" + +PATCHES=( + "${FILESDIR}"/3.4.2-solaris-isnan.patch + "${FILESDIR}"/${PN}-3.5.0-std-isnan.patch + "${FILESDIR}"/${PN}-3.5.0-autoconf-detect-isnan.patch + "${FILESDIR}"/${P}-phpconfig-path.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +# Call default here to override the php-ext-source-r2_src_unpack +src_unpack() { + default +} + +src_prepare() { + epatch "${PATCHES[@]}" + eautoreconf + echo "#!${EPREFIX}/bin/bash" > py-compile + if use php; then + local php_slot + for php_slot in $(php_get_slots); do + cp -a "${S}" "${WORKDIR}/${php_slot}" || die + done + fi +} + +src_configure() { + # bug 576436 - does not support PHP-7.0 + local PHP_CONFIG + local php_libdir="${EROOT}usr/$(get_libdir)" + + econf \ + $(use_enable python) \ + $(use_enable ruby) \ + --disable-php \ + $(use_enable static-libs static) + + if use php; then + local php_slot + for php_slot in $(php_get_slots); do + PHP_CONFIG="${php_libdir}/${php_slot}/bin/php-config" + [[ -e "${PHP_CONFIG}" ]] && export PHP_CONFIG + pushd "${WORKDIR}/${php_slot}" > /dev/null || die + econf \ + --disable-python \ + --disable-ruby \ + --enable-php \ + --disable-static + popd > /dev/null || die + done + fi +} + +src_compile() { + emake + if use php; then + local php_slot + for php_slot in $(php_get_slots); do + pushd "${WORKDIR}/${php_slot}/php" > /dev/null || die + rm -r ../capi || die + ln -sfr "${S}/capi" ../capi + emake + popd > /dev/null || die + done + fi + + use doc && emake -C "${S}/doc" doxygen-html +} + +src_install() { + emake DESTDIR="${D}" install + + use doc && dohtml -r doc/doxygen_docs/html/* + use python && python_optimize "${D}$(python_get_sitedir)"/geos/ + + if use php; then + local php_slot + local libpath + local php_libdir="${EROOT}usr/$(get_libdir)" + + for php_slot in $(php_get_slots); do + pushd "${WORKDIR}/${php_slot}/php" > /dev/null || die + emake DESTDIR="${D}" install + popd > /dev/null || die + # The libpath will vary by slot as the extension-dir is tied to the API date + libpath="lib/extensions/$(${php_libdir}/${php_slot}/bin/php-config --extension-dir | grep -o '[^/]*$')/geos.so" + local lib="${D}/usr/$(get_libdir)/${php_slot}/${libpath}" + if [[ -e "${lib}" ]]; then + chrpath -d ${lib} || die "Failed cleaning RPATH on '${lib}'" + fi + done + fi + + prune_libtool_files +} diff --git a/sci-libs/geos/geos-3.5.0.ebuild b/sci-libs/geos/geos-3.5.0.ebuild new file mode 100644 index 000000000000..60c7caacb525 --- /dev/null +++ b/sci-libs/geos/geos-3.5.0.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python2_7 ) +inherit autotools eutils python-single-r1 + +DESCRIPTION="Geometry engine library for Geographic Information Systems" +HOMEPAGE="http://trac.osgeo.org/geos/" +SRC_URI="http://download.osgeo.org/geos/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 arm ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris" +IUSE="doc php python ruby static-libs" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + php? ( >=dev-lang/php-5.3:* ) + python? ( ${PYTHON_DEPS} ) + ruby? ( dev-lang/ruby:* ) +" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + php? ( dev-lang/swig ) + python? ( dev-lang/swig ) + ruby? ( dev-lang/swig ) +" + +src_prepare() { + epatch "${FILESDIR}"/3.4.2-solaris-isnan.patch + eautoreconf + echo "#!${EPREFIX}/bin/bash" > py-compile +} + +src_configure() { + econf \ + $(use_enable python) \ + $(use_enable ruby) \ + $(use_enable php) \ + $(use_enable static-libs static) +} + +src_compile() { + emake + + use doc && emake -C "${S}/doc" doxygen-html +} + +src_install() { + emake DESTDIR="${D}" install + + use doc && dohtml -r doc/doxygen_docs/html/* + use python && python_optimize "${D}$(python_get_sitedir)"/geos/ + + find "${ED}" -name '*.la' -exec rm -f {} + +} diff --git a/sci-libs/geos/geos-3.6.1.ebuild b/sci-libs/geos/geos-3.6.1.ebuild new file mode 100644 index 000000000000..b6c6daaabed6 --- /dev/null +++ b/sci-libs/geos/geos-3.6.1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-single-r1 + +DESCRIPTION="Geometry engine library for Geographic Information Systems" +HOMEPAGE="http://trac.osgeo.org/geos/" +SRC_URI="http://download.osgeo.org/geos/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 arm ~arm64 ~ia64 ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris" +IUSE="doc python ruby static-libs" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + python? ( ${PYTHON_DEPS} ) + ruby? ( dev-lang/ruby:* ) +" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + python? ( dev-lang/swig:0 ) + ruby? ( dev-lang/swig:0 ) +" + +PATCHES=( "${FILESDIR}"/3.4.2-solaris-isnan.patch ) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_prepare() { + default + echo "#!${EPREFIX}/bin/bash" > py-compile +} + +src_configure() { + econf \ + $(use_enable python) \ + $(use_enable ruby) \ + $(use_enable static-libs static) +} + +src_compile() { + default + use doc && emake -C "${S}/doc" doxygen-html +} + +src_install() { + use doc && HTML_DOCS=( doc/doxygen_docs/html/. ) + default + use python && python_optimize "${D}$(python_get_sitedir)"/geos/ + + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/geos/metadata.xml b/sci-libs/geos/metadata.xml new file mode 100644 index 000000000000..ff68ab052ff5 --- /dev/null +++ b/sci-libs/geos/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-geosciences@gentoo.org</email> + <name>Gentoo Geosciences Project</name> + </maintainer> + <maintainer type="project"> + <email>pgsql-bugs@gentoo.org</email> + <name>PostgreSQL and Related Package Development</name> + </maintainer> + <longdescription lang="en"> + Geometric Engine Open Source provides a spatial object model and + fundamental geometric functions. It implements the geometry model + defined in the OpenGIS Consortium Simple Features Specification for + SQL. Functions provided include: spatial predicates (based on the + DE-9IM model), overlay functions (intersection, difference, union, + symmetric difference), buffer, convex hull, area and distance + functions, and topological validity checking. + </longdescription> +</pkgmetadata> diff --git a/sci-libs/gerris/Manifest b/sci-libs/gerris/Manifest new file mode 100644 index 000000000000..782a0e9f9e9a --- /dev/null +++ b/sci-libs/gerris/Manifest @@ -0,0 +1,10 @@ +AUX gerris-20130531-hypre-no-mpi.patch 644 SHA256 4d7fab9f49325ded81589242dafe95008fb2fff350bd77870e4118f8de3e7d9c SHA512 01dd5e4c159b81ee47e653173361b41b5ab5ddc05f0595cfad862d40f1d6f041c4de4860b76a1ab691c296cec7c2b4258d7ea269c8c58d37a1c8f6d17f4b0ac5 WHIRLPOOL 0e6d26f2336ad1e606226c196b0bee7157a413a128647eae06a990edad6177f74830ecafe861754692ec9457d9aad65ce91f22af3d797ae43dd13e9c97ea8637 +AUX gerris-20130531-lis-matrix-csr.patch 265 SHA256 8a9e90bff38b0933b5a9f56d7dbb5cad9ec3f7332cd00093949747b995f3ef5e SHA512 1b64fb1847e213829471c0baac812cbc9e1599c202e299a84114db598970fec911cbf6abf2cf158acca1dd472d0d3df0164956b5e41f1411a2be5e19b83d168c WHIRLPOOL 40a1f511926cce03248d6965f38c1a6de7dbfcb02da71342a42f982fe9fad4a003e08f421a43f45f654596a46e9fcbc3b39660eb7770c952a61233e7bd70aa82 +AUX gerris-20130531-use-blas-lapack-system.patch 1466 SHA256 0759033b4c3790879c0a4c161047a490d087ae71cb7cbbce205f04f10cee0d65 SHA512 4ff7f35c1d8698cc6ce2ed31708e0d05fd1cd6c8829d2ab7cc589fb5e4e1ea080df27587a7bf59ec7303c0dcfaa159da625a330a5eb5d1901ecfa45a762d41e4 WHIRLPOOL b68d2f15c1934617b31c9e5571e2e22b34f67429e74b70ae5fc7b3409bb47888f20479c6e9959ae8a7b2ebbcfc2b59b77d78c11ac22db440c89538ef9f3336c7 +AUX gerris-20131206-DEFAULT_SOURCE-replacement.patch 728 SHA256 feb7eb02a40cca753dc096418e2fb9e58edbfb009029ccbdf3e4628e449e3f27 SHA512 b1ca792b4b9ffe88964f58e12a3caff23ec3ba31f8f43136acf9adc106c57d10f75f32d2ec7a6769cdd130324e9de9a1621fc4c90be834eef330690f765159c7 WHIRLPOOL 31d8e57c033f44120bc3592914c9b677de3f4d6046e67d581f5281c049af855fa400a15fec47ba4c8cd8d38c9c91ce04ac867828e4bc65d8cf6bc23a6cf0ad49 +AUX gerris-20131206-lis-api-change.patch 526 SHA256 228d63b8432cb60084c8ba98dd85f1b785924858b99fb72d8da55f9e170ac387 SHA512 bba5cc317e66cbd48e80e2a1ce6cbd1f3688f77e3433c846294c56ba39591a840c2577eaffeed05553f651dc749ceaf751c2451624b71812ea2238014f456b25 WHIRLPOOL 153b70e986af94a071888e8fd51adf11c85594e29f5ed28383baed50ff7c94618f64346c71ae604244d4f50dacd37a3c9d96ebf459a9548ab2cc1e19b2588df1 +DIST gerris-snapshot-131206.tar.gz 2841686 SHA256 d5346a362b104ccc858c4b79938727d56c4654b103c268e54cf3aa56d0b55b39 SHA512 b3855d51eea04c496d2e5f662c148560d9ab8d5dfa97e4f7d1c22c70405b9b801b46f30aa0d159b1bd6a8182f171a1649b5f510f0e13feeb55f29cafe57b45dd WHIRLPOOL 81027d9c4c9bf44b542e1161e3238711f321b5db581b0538d5c7addc4dd5229c90f787216d05a689e287ba511546b4e7cc2fb9664bcfb9098e421722a5d8e0fd +EBUILD gerris-20131206-r1.ebuild 1557 SHA256 b66f7a884a396c5a965b9939c98ce02675729a1cdf4dd5c2768a6bc316a1973b SHA512 9a5a6d041fb41618c13d53fef7b8ad9af3c1753b52d6fd6e0466e9c20c1533dec2d9563d680966adfb01068c533cfebdf1fd18f3befe5361fd1280634b666e09 WHIRLPOOL f953bef13d3dc74c2d235aca16c4850eecf75fd6fcde84cc87768d0cbc0b45ae1933eb1d3d34e8d0db5cac2f1de03ee5d3c86dc99428c63df104b3e9352e70bf +MISC ChangeLog 4230 SHA256 cebad52470a219558efad5341201afd85c9c973340a259fd914fcb4d2ea0fb3d SHA512 029e1a2668bde1a782771d6ea6fafb58fba5e5e6517f337d870758131fbcfdc62531276dc46e849ace501bab184100ba2036fe3055e456f759735f2fc668cf29 WHIRLPOOL a20990d43d120b468e30694e882012f78c2213599806701526eca1e752e422990ecabf7d104723a62af67edee077a99ea7607f12e7a8c6426825a956680af425 +MISC ChangeLog-2015 4293 SHA256 d475e72326324d99d18c1a3407aca918a35e588d6f08622ebd625ddcce7111af SHA512 c47b6eb5c7b27dee3093f600eca7e39a7a234317b6fa1bbb434617ef7fe75acc3f1e7b9a48e76777f99bd6d6c939406081e66ca545f9e268356993c5acbf90fb WHIRLPOOL db2613d68c873e3f3ff26160470405cd91258b2eadf968dcde2a80f9d23e6d28a597e6675d79480756b0baf4ae128e5e1d31ef96904863981b958a8352a31e48 +MISC metadata.xml 510 SHA256 3a00e5b25bd5203e7919c5ccd7a2234b9dafe9c9385578ac8512ddab1b81be7d SHA512 876a9ba57d32d3bcb0071d8644a6d050ef67df1a94b90064bd7f7e45ddf44c3efa220c1c9738279892f2c8327da26043c29f8478cfb5599e3e3eda43d99719e8 WHIRLPOOL c68e847f3791efb370eb8dc7636eb53e09caedcb80a1f9630ee7b65c4f05ea52280b5ffae3875dc2b5d905a1ab45664b3fec2171c3db1ff8b18fbbff72fb38af diff --git a/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch b/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch new file mode 100644 index 000000000000..a52c78bf77c8 --- /dev/null +++ b/sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch @@ -0,0 +1,22 @@ +patch to allow gerris to use hypre without mpi + +--- a/configure.ac ++++ b/configure.ac +@@ -336,7 +336,7 @@ + + # Build hypre module if HYPRE is installed + hypre=no +-if test "x$use_mpicc" = "xyes" ; then # HYPRE needs MPI ++# hypre does not need mpi + AC_CHECK_LIB(HYPRE, HYPRE_IJMatrixCreate, hypre="yes", hypre="no", [-lm]) + if test x$hypre = xyes; then + AC_CHECK_HEADERS(HYPRE.h, hypre="yes", hypre="no") +@@ -344,7 +344,7 @@ + if test x$hypre = xno; then + AC_MSG_WARN([HYPRE not found. hypre Module won't be available.]) + fi +-fi ++ + AM_CONDITIONAL(BUILD_HYPRE, test x$hypre = xyes) + + # Build lis module if lis is installed diff --git a/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch new file mode 100644 index 000000000000..d4c7bfae15bb --- /dev/null +++ b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch @@ -0,0 +1,11 @@ +--- a/modules/lis.c ++++ b/modules/lis.c +@@ -45,7 +45,7 @@ + g_array_index (stencil->coeff, double, j), + A); + } +- lis_matrix_set_type (A, LIS_MATRIX_CRS); ++ lis_matrix_set_type (A, LIS_MATRIX_CSR); + lis_matrix_assemble (A); + + LIS_VECTOR b, x; diff --git a/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch new file mode 100644 index 000000000000..1c25a8f516b6 --- /dev/null +++ b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch @@ -0,0 +1,33 @@ +--- a/modules/Makefile.am ++++ b/modules/Makefile.am +@@ -105,7 +105,7 @@ + libstokes2D_la_LIBADD = $(GFS2D_LIBS) + + libwavewatch2D_la_SOURCES = wavewatch.c +-libwavewatch2D_la_LIBADD = $(GFS2D_LIBS) -Lwavewatch -lwavewatch -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran ++libwavewatch2D_la_LIBADD = $(GFS2D_LIBS) -Lwavewatch -lwavewatch + libwavewatch2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1 \ + -DW3SRCE=`nm wavewatch/libwavewatch.a | grep w3srce | awk '{ if ($$2 == "T") print $$3; }'` \ + -DGFSW3INIT=`nm wavewatch/libwavewatch.a | grep gfsw3_init | awk '{ if ($$2 == "T") print $$3; }'` +@@ -164,17 +164,17 @@ + + liblis3D_la_SOURCES = lis.c + liblis3D_la_CFLAGS = $(AM_CFLAGS) +-liblis3D_la_LIBADD = $(GFS3D_LIBS) -llis -lgfortran -lm ++liblis3D_la_LIBADD = $(GFS3D_LIBS) -llis -lm + liblis2D_la_SOURCES = lis.c + liblis2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1 +-liblis2D_la_LIBADD = $(GFS2D_LIBS) -llis -lgfortran -lm ++liblis2D_la_LIBADD = $(GFS2D_LIBS) -llis -lm + + libagmg3D_la_SOURCES = agmg.c dagmg.f90 + libagmg3D_la_CFLAGS = $(AM_CFLAGS) +-libagmg3D_la_LIBADD = $(GFS3D_LIBS) -llapack -lblas -lgfortran -lm ++libagmg3D_la_LIBADD = $(GFS3D_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) -lm + libagmg2D_la_SOURCES = agmg.c dagmg.f90 + libagmg2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1 +-libagmg2D_la_LIBADD = $(GFS2D_LIBS) -llapack -lblas -lgfortran -lm ++libagmg2D_la_LIBADD = $(GFS2D_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) -lm + + libokada3D_la_SOURCES = okada.c + libokada3D_la_CFLAGS = $(AM_CFLAGS) diff --git a/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch b/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch new file mode 100644 index 000000000000..d20df635512c --- /dev/null +++ b/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch @@ -0,0 +1,16 @@ +Silence warnings due to _BSD_SOURCE being deprecated by glib: +* /usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and +* _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] +* # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + +--- a/configure.ac ++++ b/configure.ac +@@ -108,7 +108,7 @@ + AC_PROG_CC + + # -D_GNU_SOURCE is only necessary for old (< 2.10) glibc implementations of open_memstream() +-CFLAGS="$CFLAGS -D_XOPEN_SOURCE=700 -D_BSD_SOURCE -D_GNU_SOURCE" ++CFLAGS="$CFLAGS -D_XOPEN_SOURCE=700 -D_DEFAULT_SOURCE -D_GNU_SOURCE" + if test x$GCC = xyes ; then + CFLAGS="$CFLAGS -Wall -Werror-implicit-function-declaration -Wmissing-prototypes -Wmissing-declarations -pipe -std=c99" + fi diff --git a/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch b/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch new file mode 100644 index 000000000000..28892ddadedf --- /dev/null +++ b/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch @@ -0,0 +1,18 @@ +sci-libs/lis changed some of its function prototypes by renaming +lis_solver_get_iters to lis_solver_get_iter in version 1.4.43 from 17 July 2014 + +See also: +http://www.ssisc.org/lis/ChangeLog.txt +https://bugs.gentoo.org/show_bug.cgi?id=593282 + +--- a/modules/lis.c ++++ b/modules/lis.c +@@ -67,7 +67,7 @@ + + lis_solve (A, b, x, solver); + int iter; +- lis_solver_get_iters (solver, &iter); ++ lis_solver_get_iter (solver, &iter); + par->niter = iter; + + lis_vector_get_values (x, 0, lp->lhs->len, (double *) lp->lhs->data); diff --git a/sci-libs/gerris/gerris-20131206-r1.ebuild b/sci-libs/gerris/gerris-20131206-r1.ebuild new file mode 100644 index 000000000000..d17000bbe95f --- /dev/null +++ b/sci-libs/gerris/gerris-20131206-r1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools flag-o-matic toolchain-funcs + +MY_P=${P/-20/-snapshot-} + +DESCRIPTION="Gerris Flow Solver" +HOMEPAGE="http://gfs.sourceforge.net/" +SRC_URI="http://gerris.dalembert.upmc.fr/gerris/tarballs/${MY_P}.tar.gz" + +LICENSE="GPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples mpi static-libs" + +# all these deps could be optional +# but the configure.in would have to be modified +# heavily for the automagic +RDEPEND=" + dev-libs/glib:2 + dev-games/ode + sci-libs/netcdf:= + sci-libs/gsl:= + sci-libs/gts + sci-libs/hypre[mpi?] + sci-libs/lis[mpi?] + sci-libs/proj + sci-libs/fftw:3.0= + virtual/lapack + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MY_P}" + +# buggy tests, need extra packages and require gerris to be installed +RESTRICT=test + +PATCHES=( + "${FILESDIR}"/${PN}-20130531-hypre-no-mpi.patch + "${FILESDIR}"/${PN}-20130531-lis-matrix-csr.patch + "${FILESDIR}"/${PN}-20130531-use-blas-lapack-system.patch + "${FILESDIR}"/${PN}-20131206-lis-api-change.patch + "${FILESDIR}"/${PN}-20131206-DEFAULT_SOURCE-replacement.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + append-cppflags "-I${EPREFIX}/usr/include/hypre" + econf \ + --enable-shared \ + $(use_enable static-libs static) \ + $(use_enable mpi) \ + LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" +} + +src_install() { + default + use examples && dodoc -r doc/examples + + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/gerris/metadata.xml b/sci-libs/gerris/metadata.xml new file mode 100644 index 000000000000..cbf216a39022 --- /dev/null +++ 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++++ b/bindings/python/Makefile.am +@@ -35,7 +35,7 @@ LIBS= + + BUILT_SOURCES = pyconstants.c + AM_CFLAGS = ${WALL} -fno-strict-aliasing +-AM_CPPFLAGS = $(CPPFLAGS) $(PYTHON_CPPFLAGS) $(NUMPY_CPPFLAGS) ++AM_CPPFLAGS = $(CPPFLAGS) $(PYTHON_CPPFLAGS) $(NUMPY_CPPFLAGS) -I$(top_srcdir)/src + pygetdata_la_LDFLAGS = -module -avoid-version \ + -export-symbols-regex initpygetdata + pygetdata_la_LIBADD = $(PYTHON_LIBS) ../../src/libgetdata.la diff --git a/sci-libs/getdata/files/getdata-0.8.5-serial-test.patch b/sci-libs/getdata/files/getdata-0.8.5-serial-test.patch new file mode 100644 index 000000000000..976757ea8646 --- /dev/null +++ b/sci-libs/getdata/files/getdata-0.8.5-serial-test.patch @@ -0,0 +1,42 @@ + bindings/Makefile.am | 6 +----- + bindings/python/test/Makefile.am | 3 +-- + 2 files changed, 2 insertions(+), 7 deletions(-) + +diff --git a/bindings/Makefile.am b/bindings/Makefile.am +index df53b0f..ec33316 100644 +--- a/bindings/Makefile.am ++++ b/bindings/Makefile.am +@@ -38,10 +38,6 @@ if MAKE_MATLABBINDINGS + MATLAB_SUBDIR=matlab + endif + +-if MAKE_PYBINDINGS +-PY_SUBDIR=python +-endif +- + if MAKE_PERLBINDINGS + PERL_SUBDIR=perl + endif +@@ -52,7 +48,7 @@ make_parameters_SOURCES = make_parameters.c + nodist_make_parameters_SOURCES = ../src/getdata.h ../src/gd_config.h + + SUBDIRS = . ${F77_SUBDIR} ${CXX_SUBDIR} ${IDL_SUBDIR} ${MATLAB_SUBDIR} \ +- ${PY_SUBDIR} ${PERL_SUBDIR} ++ ${PERL_SUBDIR} + + make_parameters$(EXEEXT): $(make_parameters_SOURCES) \ + $(nodist_make_parameters_SOURCES) +diff --git a/bindings/python/test/Makefile.am b/bindings/python/test/Makefile.am +index d159cad..b793b02 100644 +--- a/bindings/python/test/Makefile.am ++++ b/bindings/python/test/Makefile.am +@@ -18,8 +18,7 @@ + # along with GetData; if not, write to the Free Software Foundation, Inc., + # 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + # +-AUTOMAKE_OPTIONS = foreign +- ++AUTOMAKE_OPTIONS = foreign serial-tests + if TEST_PYTHON + TESTS_ENVIRONMENT=${DL_LIBRARY_PATH}=${${DL_LIBRARY_PATH}}:../../../src/.libs PYTHONPATH=../.libs/ ${PYTHON} + pyTESTS=callback.py big_test.py diff --git a/sci-libs/getdata/files/getdata-0.9.0-remove-python-test.patch b/sci-libs/getdata/files/getdata-0.9.0-remove-python-test.patch new file mode 100644 index 000000000000..98da89dfb8ec --- /dev/null +++ b/sci-libs/getdata/files/getdata-0.9.0-remove-python-test.patch @@ -0,0 +1,13 @@ +Remove python test suite. + +--- getdata-0.9.0/bindings/python/Makefile.am ++++ getdata-0.9.0/bindings/python/Makefile.am +@@ -20,8 +20,6 @@ + # + AUTOMAKE_OPTIONS = foreign + +-SUBDIRS=test +- + nodist_python_SCRIPTS = pygetdata.so + + BUILT_SOURCES = pyconstants.c diff --git a/sci-libs/getdata/files/getdata-0.9.0-serial-test.patch b/sci-libs/getdata/files/getdata-0.9.0-serial-test.patch new file mode 100644 index 000000000000..ea17e548da2f --- /dev/null +++ b/sci-libs/getdata/files/getdata-0.9.0-serial-test.patch @@ -0,0 +1,41 @@ + bindings/Makefile.am | 6 +----- + bindings/python/test/Makefile.am | 2 +- + 2 files changed, 2 insertions(+), 6 deletions(-) + +diff --git a/bindings/Makefile.am b/bindings/Makefile.am +index ad9f0d2..9e333a5 100644 +--- a/bindings/Makefile.am ++++ b/bindings/Makefile.am +@@ -38,10 +38,6 @@ if MAKE_MATLABBINDINGS + MATLAB_SUBDIR=matlab + endif + +-if MAKE_PYBINDINGS +-PY_SUBDIR=python +-endif +- + if MAKE_PERLBINDINGS + PERL_SUBDIR=perl + endif +@@ -55,7 +51,7 @@ noinst_PROGRAMS=make_parameters + make_parameters_SOURCES = make_parameters.c + nodist_make_parameters_SOURCES = ../src/getdata.h ../src/gd_config.h + +-SUBDIRS = . ${F77_SUBDIR} ${CXX_SUBDIR} ${IDL_SUBDIR} ${PY_SUBDIR} \ ++SUBDIRS = . ${F77_SUBDIR} ${CXX_SUBDIR} ${IDL_SUBDIR} \ + ${PERL_SUBDIR} ${MATLAB_SUBDIR} ${PHP_SUBDIR} + + make_parameters$(EXEEXT): $(make_parameters_SOURCES) \ +diff --git a/bindings/python/test/Makefile.am b/bindings/python/test/Makefile.am +index 32d786f..f4be3de 100644 +--- a/bindings/python/test/Makefile.am ++++ b/bindings/python/test/Makefile.am +@@ -18,7 +18,7 @@ + # along with GetData; if not, write to the Free Software Foundation, Inc., + # 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + # +-AUTOMAKE_OPTIONS = foreign serial-tests ++AUTOMAKE_OPTIONS = foreign + + if TEST_PYTHON + TESTS_ENVIRONMENT=${DL_LIBRARY_PATH}=../../../src/.libs:${${DL_LIBRARY_PATH}} PYTHONPATH=..:${PYTHONPATH} ${PYTHON} diff --git a/sci-libs/getdata/getdata-0.8.5.ebuild b/sci-libs/getdata/getdata-0.8.5.ebuild new file mode 100644 index 000000000000..e22e53814e25 --- /dev/null +++ b/sci-libs/getdata/getdata-0.8.5.ebuild @@ -0,0 +1,94 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +AUTOTOOLS_AUTORECONF=true + +FORTRAN_STANDARD="95" +FORTRAN_NEEDED=fortran + +inherit autotools-utils fortran-2 python-single-r1 + +DESCRIPTION="Reference implementation of the Dirfile, format for time-ordered binary data" +HOMEPAGE="http://getdata.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.bz2" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="bzip2 debug fortran lzma python perl static-libs" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS} + bzip2? ( app-arch/bzip2 ) + lzma? ( app-arch/xz-utils ) + perl? ( dev-lang/perl )" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-serial-test.patch + "${FILESDIR}"/${P}-out-of-source.patch + ) + +src_configure() { + local myeconfargs=() + use perl && myeconfargs+=( --with-perl-dir=vendor ) + myeconfargs+=( + --disable-idl + --without-libslim + --with-libz + --docdir="${EPREFIX}/usr/share/doc/${P}" + $(use_enable debug) + $(use_enable fortran) + $(use_enable fortran fortran95) + $(use_enable python) + $(use_enable perl) + $(use_with bzip2 libbz2) + $(use_with lzma liblzma) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + + if use python; then + python_copy_sources + building() { + cd "${BUILD_DIR}"/bindings/python || die + sed "s:-lpython...:$(python_get_LIBS):g" -i Makefile || die + emake \ + PYTHON_VERSION="${EPYTHON#python}" \ + NUMPY_CPPFLAGS="-I${EPREFIX}$(python_get_sitedir)/numpy/core/include" \ + PYTHON_CPPFLAGS="-I${EPREFIX}$(python_get_includedir)" \ + pyexecdir="${EPREFIX}$(python_get_sitedir)" \ + pythondir="${EPREFIX}$(python_get_sitedir)" + } + python_foreach_impl building + fi +} + +src_install() { + autotools-utils_src_install + if use python; then + installation() { + cd "${BUILD_DIR}"/bindings/python || die + emake \ + DESTDIR="${D}" \ + PYTHON_VERSION="${EPYTHON#python}" \ + NUMPY_CPPFLAGS="-I${EPREFIX}$(python_get_sitedir)/numpy/core/include" \ + PYTHON_CPPFLAGS="-I${EPREFIX}$(python_get_includedir)" \ + pyexecdir="${EPREFIX}$(python_get_sitedir)" \ + pythondir="${EPREFIX}$(python_get_sitedir)" \ + install + find \ + "${ED}/$(python_get_sitedir)" \ + -type f \( -name "*.a" -o -name "*.la" \) -delete || die + } + python_foreach_impl installation + fi +} diff --git a/sci-libs/getdata/getdata-0.9.0-r1.ebuild b/sci-libs/getdata/getdata-0.9.0-r1.ebuild new file mode 100644 index 000000000000..9bbc02d66ae9 --- /dev/null +++ b/sci-libs/getdata/getdata-0.9.0-r1.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +FORTRAN_STANDARD="95" +FORTRAN_NEEDED=fortran + +inherit autotools eutils fortran-2 python-single-r1 + +DESCRIPTION="Reference implementation of the Dirfile, format for time-ordered binary data" +HOMEPAGE="http://getdata.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.xz" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="bzip2 cxx debug flac fortran lzma perl python static-libs" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +DEPEND=" + bzip2? ( app-arch/bzip2 ) + lzma? ( app-arch/xz-utils ) + perl? ( dev-lang/perl ) + python? ( dev-python/numpy[${PYTHON_USEDEP}] ${PYTHON_DEPS} )" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-remove-python-test.patch" +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --disable-idl \ + --disable-matlab \ + --disable-php \ + $(use_enable cxx cplusplus) \ + $(use_enable debug) \ + $(use_enable fortran) \ + $(use_enable fortran fortran95) \ + $(use_enable perl) \ + $(use_enable python) \ + $(use_enable static-libs static) \ + --with-libz \ + --without-libslim \ + --without-libzzip \ + $(use_with bzip2 libbz2) \ + $(use_with flac libFLAC) \ + $(use_with lzma liblzma) \ + $(usex perl --with-perl-dir=vendor) +} + +src_install() { + default + prune_libtool_files --all +} diff --git a/sci-libs/getdata/getdata-0.9.0.ebuild b/sci-libs/getdata/getdata-0.9.0.ebuild new file mode 100644 index 000000000000..458e6a8186ac --- /dev/null +++ b/sci-libs/getdata/getdata-0.9.0.ebuild @@ -0,0 +1,94 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +AUTOTOOLS_AUTORECONF=true + +FORTRAN_STANDARD="95" +FORTRAN_NEEDED=fortran + +inherit autotools-utils fortran-2 python-single-r1 + +DESCRIPTION="Reference implementation of the Dirfile, format for time-ordered binary data" +HOMEPAGE="http://getdata.sourceforge.net/" +SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.xz" + +SLOT="0" +LICENSE="LGPL-2.1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="bzip2 debug fortran lzma python perl static-libs" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +DEPEND=" + bzip2? ( app-arch/bzip2 ) + lzma? ( app-arch/xz-utils ) + python? ( ${PYTHON_DEPS} ) + perl? ( dev-lang/perl )" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-serial-test.patch + ) + +src_configure() { + local myeconfargs=() + use perl && myeconfargs+=( --with-perl-dir=vendor ) + myeconfargs+=( + --disable-idl + --without-libslim + --with-libz + --docdir="${EPREFIX}/usr/share/doc/${P}" + $(use_enable debug) + $(use_enable fortran) + $(use_enable fortran fortran95) + $(use_enable python) + $(use_enable perl) + $(use_with bzip2 libbz2) + $(use_with lzma liblzma) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + + if use python; then + python_copy_sources + building() { + cd "${BUILD_DIR}"/bindings/python || die + sed "s:-lpython...:$(python_get_LIBS):g" -i Makefile || die + emake \ + PYTHON_VERSION="${EPYTHON#python}" \ + NUMPY_CPPFLAGS="-I${EPREFIX}$(python_get_sitedir)/numpy/core/include" \ + PYTHON_CPPFLAGS="-I${EPREFIX}$(python_get_includedir)" \ + pyexecdir="${EPREFIX}$(python_get_sitedir)" \ + pythondir="${EPREFIX}$(python_get_sitedir)" + } + python_foreach_impl building + fi +} + +src_install() { + autotools-utils_src_install + if use python; then + installation() { + cd "${BUILD_DIR}"/bindings/python || die + emake \ + DESTDIR="${D}" \ + PYTHON_VERSION="${EPYTHON#python}" \ + NUMPY_CPPFLAGS="-I${EPREFIX}$(python_get_sitedir)/numpy/core/include" \ + PYTHON_CPPFLAGS="-I${EPREFIX}$(python_get_includedir)" \ + pyexecdir="${EPREFIX}$(python_get_sitedir)" \ + pythondir="${EPREFIX}$(python_get_sitedir)" \ + install + find \ + "${ED}/$(python_get_sitedir)" \ + -type f \( -name "*.a" -o -name "*.la" \) -delete || die + } + python_foreach_impl installation + fi +} diff --git a/sci-libs/getdata/metadata.xml b/sci-libs/getdata/metadata.xml new file mode 100644 index 000000000000..7a03fbedeac4 --- /dev/null +++ b/sci-libs/getdata/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The GetData Project is the reference implementation of the Dirfile + Standards, a filesystem-based, column-oriented database format for + time-ordered binary data. The Dirfile database format is designed to + provide a fast, simple format for storing and reading data. +</longdescription> + <upstream> + <remote-id type="sourceforge">getdata</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/gpp4/Manifest b/sci-libs/gpp4/Manifest new file mode 100644 index 000000000000..562d702a2c15 --- /dev/null +++ b/sci-libs/gpp4/Manifest @@ -0,0 +1,5 @@ +DIST gpp4-1.3.1.tar.gz 694533 SHA256 ad18b8771f68b55bcf40a59f2be5489daf6bd97934a181602de7f44fbe27776f SHA512 b24b26ecb38406bf5895f1dd43e847836f9aeecf7b5bc54df602e23e828b5cf8ae4a8902e294065d67edfb3507763e3d7496acbd6373e7dbc5e85d049c044920 WHIRLPOOL 9c55c8da522be0e519caaff076b83fcc415f37bcff6a80ff727067ae9a822d8b573d7103846e2c1859cbc2cfe63af9d6e541853be6f7183f39dae5d21e93092c +EBUILD gpp4-1.3.1.ebuild 586 SHA256 68e36514cc9aa76e2b0c00123d71ea63ac79774c27e7d310465f4dfbd60caa73 SHA512 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+SRC_URI="https://launchpad.net/${PN}/1.3/${PV}/+download/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="fortran static-libs" + +RDEPEND="sci-libs/mmdb:0=" +DEPEND="${RDEPEND}" + +src_configure() { + econf \ + $(use_with fortran fortran-api) \ + $(use_enable static-libs static) +} diff --git a/sci-libs/gpp4/metadata.xml b/sci-libs/gpp4/metadata.xml new file mode 100644 index 000000000000..046af6ea9df6 --- /dev/null +++ b/sci-libs/gpp4/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="launchpad">gpp4</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/grib_api/Manifest b/sci-libs/grib_api/Manifest new file mode 100644 index 000000000000..d9fd9e768491 --- /dev/null +++ b/sci-libs/grib_api/Manifest @@ -0,0 +1,10 @@ +AUX grib_api-1.14.5-add-missing-destdir.patch 1319 SHA256 dbb93b642d4375b6ad19638d0492c304241d99a2461ad9e58a17e56170de2362 SHA512 bb0e2586bb2a2b708c914a952cef499e0fec09ddbd563c7d821ae4ff205ef913a826f3985203b8ef0f766207724d5bd41a19578d6089ecc05ca6afead579a67c WHIRLPOOL 711397b1bdaa94db126a84c44a9e0344550e177d772a5f882cc27261f6efa65ae0d32074a4a15b8326ae6ecc24bf20c77d435a5c1dc89207a87bed5ee5de4375 +AUX grib_api-1.14.5-disable-failing-test.patch 841 SHA256 90078d83b6ffec1d1860da47a1e00556a5382c785c786cd0855a07824db5fcee SHA512 23adfb01f6ee47e9207940468c342588f523f373066f217e018669c5a19d456fab10a986fad5ec9aa2e073f9d9c2305886c3a5b55d63a3017a365c02739232dc WHIRLPOOL ce670bc993bd750a0cee15b93e24b91abe17c91aed98fe7520da0e73de3a9131631f64371898708217ab56380e9eb1eb3893d66548762336e83416aa4ffba2fa +DIST grib_api-1.11.0.tar.gz 14412684 SHA256 7a7ee16c6df1b0dceff3d8b5cd5f614804ca6e49b6aa99892f99fd6d6a2f5b35 SHA512 09c50d194049d2d19686139fb7150bd7399fc05bb5b7e40e8d91ce0301698263c40357b8524f925642ae6f78d9bc61218be26bef7f2dfeb326ccc9e8bc3a49e3 WHIRLPOOL 0e1f3bf8b36c12f12ef04dd653aa9eb024095adaec0a56fae7beb1c666f4410e912f56bbba3a0526e08f78000859b113ffff4a6f3ee11f6fa1944aa249e4289a +DIST grib_api-1.14.5-Source.tar.gz 4530071 SHA256 047029afca9445047f8fce8250146f6b17d1bc4eb9c17fcaa8e74aa173c4ab08 SHA512 ad31dc27adcdeeded1aa3c3620181c0d4a5250734724c242443d19332b84f2297b4dea2aa02027627321fa35822c94865a41f24d03eb1143756621da14a59322 WHIRLPOOL 29b48fb8babe5cca4695480f675eba557d86e26ea1e230e164586b713dfebd9ce4033ae4e72e7cdcce258ed8129860897c66e6acf0393f7ccc710c649b5cc80d +DIST grib_api_test_data.tar.gz 131042849 SHA256 faf56d38c9776c52a48fddaaa3651e25293978e0f8697764b37e36d312877c91 SHA512 25b37c3e725f7a2c18979d96e7d512111ba54f4e448c57e6a8ae913b7f13be25d9e643edb45ebc714daf6de51d85e9a7d252e735299affc562b9911e53a95058 WHIRLPOOL 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dc016ac73ecad055caa5dbb34d7472df6a8a8b92cd5b58f38915b3ca56e3c452e2edec9d2c689bd4a4a834396e9a879d7a8c59bbf91d2f5ea9675270ace3415b diff --git a/sci-libs/grib_api/files/grib_api-1.14.5-add-missing-destdir.patch b/sci-libs/grib_api/files/grib_api-1.14.5-add-missing-destdir.patch new file mode 100644 index 000000000000..6bd6fb53f6e9 --- /dev/null +++ b/sci-libs/grib_api/files/grib_api-1.14.5-add-missing-destdir.patch @@ -0,0 +1,19 @@ +From: Sébastien Fabbro <bicatali@gentoo.org> +Subject: add missing DESTDIR to respect sandbox install + +--- grib_api-1.14.5-Source.orig/fortran/CMakeLists.txt 2016-03-14 22:53:44.310678929 +0000 ++++ grib_api-1.14.5-Source/fortran/CMakeLists.txt 2016-03-14 22:55:42.479193350 +0000 +@@ -55,11 +55,11 @@ + install( CODE + " + if( EXISTS ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR}/GRIB_API.mod ) +- execute_process( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR}/GRIB_API.mod ${CMAKE_INSTALL_PREFIX}/${INSTALL_INCLUDE_DIR}/grib_api.mod ) ++ execute_process( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR}/GRIB_API.mod \$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/${INSTALL_INCLUDE_DIR}/grib_api.mod ) + endif() + + if( EXISTS ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR}/grib_api.mod ) +- execute_process( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR}/grib_api.mod ${CMAKE_INSTALL_PREFIX}/${INSTALL_INCLUDE_DIR}/GRIB_API.mod ) ++ execute_process( COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_Fortran_MODULE_DIRECTORY}/${CMAKE_CFG_INTDIR}/grib_api.mod \$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/${INSTALL_INCLUDE_DIR}/GRIB_API.mod ) + endif() + " ) + diff --git a/sci-libs/grib_api/files/grib_api-1.14.5-disable-failing-test.patch b/sci-libs/grib_api/files/grib_api-1.14.5-disable-failing-test.patch new file mode 100644 index 000000000000..0615edc15420 --- /dev/null +++ b/sci-libs/grib_api/files/grib_api-1.14.5-disable-failing-test.patch @@ -0,0 +1,15 @@ +From: Sébastien Fabbro <bicatali@gentoo.org> +Subject: comment out failing test +https://software.ecmwf.int/issues/browse/SUP-521 +--- grib_api-1.14.5-Source.orig/tests/ls.sh 2016-03-14 21:56:28.933867464 +0000 ++++ grib_api-1.14.5-Source/tests/ls.sh 2016-03-14 21:56:57.103513324 +0000 +@@ -62,7 +62,8 @@ + + # Test for bug GRIB-56 + ${tools_dir}grib_set -s typeOfLevel=depthBelowLandLayer,topLevel=missing regular_latlon_surface.grib1 tmp_rlls.grib1 +-${tools_dir}grib_ls -plevels tmp_rlls.grib1 | grep MISSING>/dev/null ++# disabling because MISSING is not there and fails the test ++#${tools_dir}grib_ls -plevels tmp_rlls.grib1 | grep MISSING>/dev/null + + ${tools_dir}grib_set -s typeOfLevel=depthBelowLandLayer,bottomLevel=missing regular_latlon_surface.grib1 tmp_rlls.grib1 + ${tools_dir}grib_ls -plevels tmp_rlls.grib1 | grep MISSING>/dev/null diff --git a/sci-libs/grib_api/grib_api-1.11.0.ebuild b/sci-libs/grib_api/grib_api-1.11.0.ebuild new file mode 100644 index 000000000000..27686ff47ae3 --- /dev/null +++ b/sci-libs/grib_api/grib_api-1.11.0.ebuild @@ -0,0 +1,88 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +FORTRAN_NEEDED=fortran +FORTRAN_STANDARD="77 90" +PYTHON_COMPAT=( python{2_7,3_4} ) + +inherit autotools-utils toolchain-funcs fortran-2 python-single-r1 + +PID=3473437 + +DESCRIPTION="Library for decoding WMO FM-92 GRIB messages" +HOMEPAGE="https://software.ecmwf.int/wiki/display/GRIB/Home" +SRC_URI="https://software.ecmwf.int/wiki/download/attachments/${PID}/${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="doc examples fortran jasper jpeg2k netcdf openmp png python static-libs threads perl" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + jpeg2k? ( + jasper? ( media-libs/jasper:= ) + !jasper? ( media-libs/openjpeg:0 ) + ) + netcdf? ( sci-libs/netcdf ) + png? ( media-libs/libpng:0= ) + python? ( + ${PYTHON_DEPS} + dev-python/numpy[${PYTHON_USEDEP}] + )" +DEPEND="${RDEPEND} + python? ( dev-lang/swig )" + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + fi + fortran-2_pkg_setup + use python && python-single-r1_pkg_setup +} + +src_prepare() { + # failing test + sed -i \ + -e 's/\(${tools_dir}grib_ls -plevels tmp_rlls.grib1 | grep MISSING\)/#\1/' \ + tests/ls.sh +} + +src_configure() { + # perl module needs serious packaging work from upstream + local myeconfargs=( + --without-perl + $(use_enable jpeg2k jpeg) + $(use_enable fortran) + $(use_enable openmp omp-packing) + $(use_enable python) + $(use_enable python numpy) + $(use_enable threads pthread) + $( + use netcdf && \ + echo --with-netcdf="${EPREFIX}"/usr || \ + echo --with-netcdf=none + ) + $(use_with png png-support) + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + use doc && dohtml -r html/* + if use examples; then + insinto /usr/share/doc/${PF}/examples + emake clean + doins -r * + fi + use python && python_optimize +} diff --git a/sci-libs/grib_api/grib_api-1.14.5.ebuild b/sci-libs/grib_api/grib_api-1.14.5.ebuild new file mode 100644 index 000000000000..8f1103676741 --- /dev/null +++ b/sci-libs/grib_api/grib_api-1.14.5.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran +FORTRAN_STANDARD="77 90" +PYTHON_COMPAT=( python{2_7,3_4,3_5} ) + +inherit cmake-utils toolchain-funcs fortran-2 python-single-r1 + +PID=3473437 + +DESCRIPTION="Library for encoding and decoding WMO FM-92 GRIB messages" +HOMEPAGE="https://software.ecmwf.int/wiki/display/GRIB/Home" +SRC_URI="https://software.ecmwf.int/wiki/download/attachments/${PID}/${P}-Source.tar.gz + test? ( http://download.ecmwf.org/test-data/grib_api/grib_api_test_data.tar.gz )" + +S="${WORKDIR}/${P}-Source" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="aec doc examples fortran jpeg2k netcdf png python static-libs test threads" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + aec? ( sci-libs/libaec:= ) + jpeg2k? ( media-libs/jasper:= ) + netcdf? ( sci-libs/netcdf:= ) + png? ( media-libs/libpng:= ) + python? ( + ${PYTHON_DEPS} + dev-python/numpy[${PYTHON_USEDEP}] + )" + +DEPEND="${RDEPEND} + python? ( dev-lang/swig ) + test? ( dev-libs/boost )" + +PATCHES=( + "${FILESDIR}"/${P}-disable-failing-test.patch + "${FILESDIR}"/${P}-add-missing-destdir.patch +) + +pkg_setup() { + use fortran && fortran-2_pkg_setup + use python && python-single-r1_pkg_setup +} + +src_unpack() { + # only unpack the source and not the test data at this stage + unpack ${P}-Source.tar.gz +} + +src_prepare() { + # remove package build type to allow gentoo one + sed -i -e '/include(ecbuild_define_build_types)/d' cmake/ecbuild_system.cmake || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DDISABLE_OS_CHECK=ON + -DENABLE_EXAMPLES=OFF + -DENABLE_ALIGN_MEMORY=ON + -DENABLE_MEMORY_MANAGEMENT=ON + -DENABLE_GRIB_TIMER=ON + -DENABLE_RELATIVE_RPATHS=OFF + -DENABLE_RPATHS=OFF + -DENABLE_AEC="$(usex aec)" + -DENABLE_FORTRAN="$(usex fortran)" + -DENABLE_GRIB_THREADS="$(usex threads)" + -DENABLE_JPG="$(usex jpeg2k)" + -DENABLE_NETCDF="$(usex netcdf)" + -DENABLE_PNG="$(usex png)" + -DENABLE_PYTHON="$(usex python)" + -DENABLE_TESTS="$(usex test)" + ) + use static-libs && mycmakeargs+=( -DBUILD_SHARED_LIBS=BOTH ) + cmake-utils_src_configure +} + +src_test() { + # unpack here because subdirectory tree + use test && cd "${BUILD_DIR}" && unpack grib_api_test_data.tar.gz || die + cmake-utils_src_test +} + +src_install() { + cmake-utils_src_install + insinto /usr/share/doc/${PF} + use examples && doins -r examples + use doc && doins -r html +} diff --git a/sci-libs/grib_api/metadata.xml b/sci-libs/grib_api/metadata.xml new file mode 100644 index 000000000000..b053bfcb8747 --- /dev/null +++ b/sci-libs/grib_api/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The European Centre for Medium-Range Weather Forecasts GRIdded + Binary (GRIB) API is an application program interface accessible + from C and FORTRAN programs developed for encoding and decoding WMO + FM-92 GRIB edition 1 and edition 2 messages. A useful set of command + line tools is also provided to give quick access to grib messages. +</longdescription> +<use> + <flag name="jasper">Use <pkg>media-libs/jasper</pkg> instead of + <pkg>media-libs/openjpeg</pkg> for JPEG 2000 support</flag> + <flag name="aec">Build with Adaptive Entropy Coding compression, needs <pkg>sci-libs/libaec</pkg></flag> +</use> +</pkgmetadata> diff --git a/sci-libs/gsl/Manifest b/sci-libs/gsl/Manifest new file mode 100644 index 000000000000..82d239affbdd --- /dev/null +++ b/sci-libs/gsl/Manifest @@ -0,0 +1,16 @@ +AUX cblas.pc.in 290 SHA256 f47133de2f49a5ff53c8e295d03fbe8923c79cd0978cedb903cfdf7e57a873a1 SHA512 2a1dc22097e2a50fd4a797c446b32202b74e9d754c8b61c51a3789c3eb42372adcc7fb25901c468d604cc4e7961d7f11e0e5883179894047948e46879fc04719 WHIRLPOOL f8e93aa2c61d3ac08664c3162f0e754c1d6cefca0a4d4ab8ee8f763e6ec46049ff5537c7f9266200856b58ffab88fb9af115eb4be32deb99ed6d2005abcb13ec +AUX eselect.cblas.gsl 216 SHA256 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000000000000..a2580f85e6e8 --- /dev/null +++ b/sci-libs/gsl/files/cblas.pc.in @@ -0,0 +1,12 @@ +prefix=/usr +exec_prefix=${prefix} +libdir=/usr/@LIBDIR@ +includedir=${prefix}/include + +Name: cblas +Description: GSL C Implementation of the Basic Linear Algebra Subprograms +Version: @PV@ +URL: http://www.gnu.org/software/gsl +Libs: -L${libdir} -lcblas +Libs.private: -lm +Cflags: -I${includedir} diff --git a/sci-libs/gsl/files/eselect.cblas.gsl b/sci-libs/gsl/files/eselect.cblas.gsl new file mode 100644 index 000000000000..af6fee51fef9 --- /dev/null +++ b/sci-libs/gsl/files/eselect.cblas.gsl @@ -0,0 +1,5 @@ +libgslcblas.so /usr/@LIBDIR@/libcblas.so +libgslcblas.so.0 /usr/@LIBDIR@/libcblas.so.0 +libgslcblas.a /usr/@LIBDIR@/libcblas.a +../blas/gsl/cblas.pc /usr/@LIBDIR@/pkgconfig/cblas.pc +gsl/gsl_cblas.h /usr/include/cblas.h diff --git a/sci-libs/gsl/files/gsl-1.16-cblas.patch b/sci-libs/gsl/files/gsl-1.16-cblas.patch new file mode 100644 index 000000000000..c29ef5294717 --- /dev/null +++ b/sci-libs/gsl/files/gsl-1.16-cblas.patch @@ -0,0 +1,294 @@ +diff -Nur gsl-1.16.orig/ax_cblas.m4 gsl-1.16/ax_cblas.m4 +--- gsl-1.16.orig/ax_cblas.m4 1969-12-31 16:00:00.000000000 -0800 ++++ gsl-1.16/ax_cblas.m4 2013-08-19 15:48:54.376300825 -0700 +@@ -0,0 +1,69 @@ ++AC_DEFUN([AX_CBLAS],[ ++ ++ ext_cblas=no ++ ext_cblas_libs="-lcblas" ++ ext_cblas_cflags="" ++ ++ AC_ARG_WITH(cblas-external, ++ [AS_HELP_STRING([--with-cblas-external], ++ [Use external CBLAS library (default is no)])], ++ [with_ext_cblas=$withval], ++ [with_ext_cblas=no]) ++ ++ case $with_ext_cblas in ++ no) ext_cblas=no ;; ++ yes) ext_cblas=yes ;; ++ -* | */* | *.a | *.so | *.so.* | *.o) ++ ext_cblas=yes ++ ext_cblas_libs="$with_cblas" ;; ++ *) ext_cblas=yes ++ ext_cblas_libs="-l$with_cblas" ;; ++ esac ++ ++ AC_ARG_WITH(cblas-external-libs, ++ [AS_HELP_STRING([--with-cblas-external-libs=<libs>], ++ [External cblas libraries to link with (default is "$ext_cblas_libs")])], ++ [ext_cblas_libs=$withval], ++ []) ++ ++ AC_ARG_WITH(cblas-external-cflags, ++ [AS_HELP_STRING([--with-cblas-external-cflags=<flags>], ++ [Pre-processing flags to compile with external cblas ("-I<dir>")])], ++ [ext_cblas_cflags=$withval], ++ []) ++ ++ if test x$ext_cblas != xno; then ++ if test "x$CBLAS_LIBS" = x; then ++ CBLAS_LIBS="$ext_cblas_libs" ++ fi ++ if test "x$CBLAS_CFLAGS" = x; then ++ CBLAS_CFLAGS="$ext_cblas_cflags" ++ fi ++ ++ CFLAGS_sav="$CFLAGS" ++ CFLAGS="$CFLAGS $CBLAS_CFLAGS" ++ AC_CHECK_HEADER(cblas.h, , ++ [AC_MSG_ERROR([ ++ *** Header file cblas.h not found. ++ *** If you installed cblas header in a non standard place, ++ *** specify its install prefix using the following option ++ *** --with-cblas-external-cflags="-I<include_dir>"]) ++ ]) ++ CFLAGS="$CFLAGS_sav" ++ ++ LIBS_sav="$LIBS" ++ LIBS="$LIBS $CBLAS_LIBS -lm" ++ AC_MSG_CHECKING([for cblas_sgemm in $CBLAS_LIBS]) ++ AC_TRY_LINK_FUNC(cblas_sgemm, [ext_cblas=yes], ++ [AC_MSG_ERROR([ ++ *** Linking with cblas with $LIBS failed. ++ *** If you installed cblas library in a non standard place, ++ *** specify its install prefix using the following option ++ *** --with-cblas-external-libs="-L<lib_dir> -l<lib>"]) ++ ]) ++ AC_MSG_RESULT($ext_cblas) ++ LIBS="$LIBS_sav" ++ AC_SUBST([CBLAS_CFLAGS]) ++ AC_SUBST([CBLAS_LIBS]) ++ fi ++]) +diff -Nur gsl-1.16.orig/bspline/Makefile.am gsl-1.16/bspline/Makefile.am +--- gsl-1.16.orig/bspline/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/bspline/Makefile.am 2013-08-19 15:25:27.728497742 -0700 +@@ -12,6 +12,6 @@ + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la ++test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la + + test_SOURCES = test.c +diff -Nur gsl-1.16.orig/configure.ac gsl-1.16/configure.ac +--- gsl-1.16.orig/configure.ac 2013-07-19 08:14:45.000000000 -0700 ++++ gsl-1.16/configure.ac 2013-08-19 15:28:24.172640793 -0700 +@@ -191,6 +191,16 @@ + AC_CHECK_LIB(m, cos) + fi + ++sinclude(ax_cblas.m4) ++AX_CBLAS ++if test "x$CBLAS_LIBS" != "x"; then ++ CBLAS_LINK_LIBS="$CBLAS_LIBS" ++else ++ CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la" ++ CBLAS_LIBS="-lgslcblas" ++fi ++AC_SUBST(CBLAS_LINK_LIBS) ++ + dnl Remember to put a definition in acconfig.h for each of these + AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1 + #include <fenv.h>]) +diff -Nur gsl-1.16.orig/eigen/Makefile.am gsl-1.16/eigen/Makefile.am +--- gsl-1.16.orig/eigen/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/eigen/Makefile.am 2013-08-19 15:25:27.728497742 -0700 +@@ -11,7 +11,7 @@ + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la ++test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la + + test_SOURCES = test.c + +diff -Nur gsl-1.16.orig/gsl-config.in gsl-1.16/gsl-config.in +--- gsl-1.16.orig/gsl-config.in 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/gsl-config.in 2013-08-19 15:25:27.728497742 -0700 +@@ -58,11 +58,11 @@ + ;; + + --cflags) +- echo @GSL_CFLAGS@ ++ echo @GSL_CFLAGS@ @CBLAS_CFLAGS@ + ;; + + --libs) +- : ${GSL_CBLAS_LIB=-lgslcblas} ++ : ${GSL_CBLAS_LIB=@CBLAS_LIBS@} + echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@ + ;; + +diff -Nur gsl-1.16.orig/gsl.pc.in gsl-1.16/gsl.pc.in +--- gsl-1.16.orig/gsl.pc.in 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/gsl.pc.in 2013-08-19 15:25:27.728497742 -0700 +@@ -2,7 +2,7 @@ + exec_prefix=@exec_prefix@ + libdir=@libdir@ + includedir=@includedir@ +-GSL_CBLAS_LIB=-lgslcblas ++GSL_CBLAS_LIB=@CBLAS_LIBS@ + + Name: GSL + Description: GNU Scientific Library +diff -Nur gsl-1.16.orig/interpolation/Makefile.am gsl-1.16/interpolation/Makefile.am +--- gsl-1.16.orig/interpolation/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/interpolation/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -10,7 +10,7 @@ + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff -Nur gsl-1.16.orig/linalg/Makefile.am gsl-1.16/linalg/Makefile.am +--- gsl-1.16.orig/linalg/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/linalg/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -12,7 +12,7 @@ + + check_PROGRAMS = test + +-test_LDADD = libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff -Nur gsl-1.16.orig/Makefile.am gsl-1.16/Makefile.am +--- gsl-1.16.orig/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -19,13 +19,12 @@ + + lib_LTLIBRARIES = libgsl.la + libgsl_la_SOURCES = version.c +-libgsl_la_LIBADD = $(SUBLIBS) ++libgsl_la_LIBADD = $(SUBLIBS) @CBLAS_LINK_LIBS@ + libgsl_la_LDFLAGS = -version-info $(GSL_LT_VERSION) + noinst_HEADERS = templates_on.h templates_off.h build.h + + MINGW32_HOST = @MINGW32_HOST@ + if MINGW32_HOST +-libgsl_la_LIBADD += cblas/libgslcblas.la + libgsl_la_LDFLAGS += -no-undefined + endif + +@@ -35,10 +34,10 @@ + bin_PROGRAMS = gsl-randist gsl-histogram + + gsl_randist_SOURCES = gsl-randist.c +-gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la ++gsl_randist_LDADD = libgsl.la + + gsl_histogram_SOURCES = gsl-histogram.c +-gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la ++gsl_histogram_LDADD = libgsl.la + + check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test + TESTS = test_gsl_histogram.sh pkgconfig.test +@@ -57,6 +56,8 @@ + -e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \ + -e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \ + -e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \ ++ -e 's|@CBLAS_CFLAGS[@]|$(CBLAS_CFLAGS)|g' \ ++ -e 's|@CBLAS_LIBS[@]|$(CBLAS_LIBS)|g' \ + -e 's|@LIBS[@]|$(LIBS)|g' \ + -e 's|@VERSION[@]|$(VERSION)|g' + +--- gsl-1.16.orig/multifit/Makefile.am 2013-07-18 06:04:26.000000000 +1000 ++++ gsl-1.16/multifit/Makefile.am 2013-11-22 16:57:26.170330257 +1100 +@@ -13,8 +13,8 @@ + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c +-test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ++test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la + + #demo_SOURCES = demo.c +-#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ++#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la + +diff -Nur gsl-1.16.orig/multimin/Makefile.am gsl-1.16/multimin/Makefile.am +--- gsl-1.16.orig/multimin/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/multimin/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -13,8 +13,8 @@ + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c test_funcs.c test_funcs.h +-test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + #demo_SOURCES = demo.c +-#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + +diff -Nur gsl-1.16.orig/multiroots/Makefile.am gsl-1.16/multiroots/Makefile.am +--- gsl-1.16.orig/multiroots/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/multiroots/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -15,5 +15,5 @@ + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c test_funcs.c test_funcs.h +-test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + +diff -Nur gsl-1.16.orig/ode-initval/Makefile.am gsl-1.16/ode-initval/Makefile.am +--- gsl-1.16.orig/ode-initval/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/ode-initval/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -12,7 +12,7 @@ + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff -Nur gsl-1.16.orig/poly/Makefile.am gsl-1.16/poly/Makefile.am +--- gsl-1.16.orig/poly/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/poly/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -10,7 +10,7 @@ + + TESTS = $(check_PROGRAMS) + +-check_PROGRAMS = test ++#check_PROGRAMS = test + + test_SOURCES = test.c + test_LDADD = libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../sort/libgslsort.la +diff -Nur gsl-1.16.orig/specfunc/Makefile.am gsl-1.16/specfunc/Makefile.am +--- gsl-1.16.orig/specfunc/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/specfunc/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -12,7 +12,7 @@ + + check_PROGRAMS = test + +-test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test_sf.c test_sf.h test_airy.c test_bessel.c test_coulomb.c test_dilog.c test_gamma.c test_hyperg.c test_legendre.c test_mathieu.c + +diff -Nur gsl-1.16.orig/wavelet/Makefile.am gsl-1.16/wavelet/Makefile.am +--- gsl-1.16.orig/wavelet/Makefile.am 2013-07-17 13:04:26.000000000 -0700 ++++ gsl-1.16/wavelet/Makefile.am 2013-08-19 15:25:27.729497736 -0700 +@@ -10,7 +10,7 @@ + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslwavelet.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslwavelet.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + diff --git a/sci-libs/gsl/files/gsl-2.1-cblas.patch b/sci-libs/gsl/files/gsl-2.1-cblas.patch new file mode 100644 index 000000000000..54cc8802c594 --- /dev/null +++ b/sci-libs/gsl/files/gsl-2.1-cblas.patch @@ -0,0 +1,326 @@ + Makefile.am | 8 +++--- + ax_cblas.m4 | 69 +++++++++++++++++++++++++++++++++++++++++++++++ + bspline/Makefile.am | 2 +- + configure.ac | 10 +++++++ + eigen/Makefile.am | 2 +- + gsl-config.in | 4 +-- + gsl.pc.in | 2 +- + interpolation/Makefile.am | 2 +- + linalg/Makefile.am | 2 +- + multifit/Makefile.am | 4 +-- + multimin/Makefile.am | 4 +-- + multiroots/Makefile.am | 2 +- + ode-initval/Makefile.am | 2 +- + poly/Makefile.am | 2 +- + specfunc/Makefile.am | 2 +- + wavelet/Makefile.am | 2 +- + 16 files changed, 100 insertions(+), 19 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 278dcd9..a75418c 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -19,7 +19,7 @@ EXTRA_DIST = autogen.sh gsl-config.in gsl.pc.in configure.ac THANKS BUGS gsl.spe + + lib_LTLIBRARIES = libgsl.la + libgsl_la_SOURCES = version.c +-libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) ++libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) @CBLAS_LINK_LIBS@ + libgsl_la_LDFLAGS = $(GSL_LDFLAGS) -version-info $(GSL_LT_VERSION) + noinst_HEADERS = templates_on.h templates_off.h build.h + +@@ -29,10 +29,10 @@ m4data_DATA = gsl.m4 + bin_PROGRAMS = gsl-randist gsl-histogram + + gsl_randist_SOURCES = gsl-randist.c +-gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la ++gsl_randist_LDADD = libgsl.la + + gsl_histogram_SOURCES = gsl-histogram.c +-gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la ++gsl_histogram_LDADD = libgsl.la + + check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test + TESTS = test_gsl_histogram.sh pkgconfig.test +@@ -51,6 +51,8 @@ edit = $(SED) \ + -e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \ + -e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \ + -e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \ ++ -e 's|@CBLAS_CFLAGS[@]|$(CBLAS_CFLAGS)|g' \ ++ -e 's|@CBLAS_LIBS[@]|$(CBLAS_LIBS)|g' \ + -e 's|@LIBS[@]|$(LIBS)|g' \ + -e 's|@VERSION[@]|$(VERSION)|g' + +diff --git a/ax_cblas.m4 b/ax_cblas.m4 +new file mode 100644 +index 0000000..6ef143a +--- /dev/null ++++ b/ax_cblas.m4 +@@ -0,0 +1,69 @@ ++AC_DEFUN([AX_CBLAS],[ ++ ++ ext_cblas=no ++ ext_cblas_libs="-lcblas" ++ ext_cblas_cflags="" ++ ++ AC_ARG_WITH(cblas-external, ++ [AS_HELP_STRING([--with-cblas-external], ++ [Use external CBLAS library (default is no)])], ++ [with_ext_cblas=$withval], ++ [with_ext_cblas=no]) ++ ++ case $with_ext_cblas in ++ no) ext_cblas=no ;; ++ yes) ext_cblas=yes ;; ++ -* | */* | *.a | *.so | *.so.* | *.o) ++ ext_cblas=yes ++ ext_cblas_libs="$with_cblas" ;; ++ *) ext_cblas=yes ++ ext_cblas_libs="-l$with_cblas" ;; ++ esac ++ ++ AC_ARG_WITH(cblas-external-libs, ++ [AS_HELP_STRING([--with-cblas-external-libs=<libs>], ++ [External cblas libraries to link with (default is "$ext_cblas_libs")])], ++ [ext_cblas_libs=$withval], ++ []) ++ ++ AC_ARG_WITH(cblas-external-cflags, ++ [AS_HELP_STRING([--with-cblas-external-cflags=<flags>], ++ [Pre-processing flags to compile with external cblas ("-I<dir>")])], ++ [ext_cblas_cflags=$withval], ++ []) ++ ++ if test x$ext_cblas != xno; then ++ if test "x$CBLAS_LIBS" = x; then ++ CBLAS_LIBS="$ext_cblas_libs" ++ fi ++ if test "x$CBLAS_CFLAGS" = x; then ++ CBLAS_CFLAGS="$ext_cblas_cflags" ++ fi ++ ++ CFLAGS_sav="$CFLAGS" ++ CFLAGS="$CFLAGS $CBLAS_CFLAGS" ++ AC_CHECK_HEADER(cblas.h, , ++ [AC_MSG_ERROR([ ++ *** Header file cblas.h not found. ++ *** If you installed cblas header in a non standard place, ++ *** specify its install prefix using the following option ++ *** --with-cblas-external-cflags="-I<include_dir>"]) ++ ]) ++ CFLAGS="$CFLAGS_sav" ++ ++ LIBS_sav="$LIBS" ++ LIBS="$LIBS $CBLAS_LIBS -lm" ++ AC_MSG_CHECKING([for cblas_sgemm in $CBLAS_LIBS]) ++ AC_TRY_LINK_FUNC(cblas_sgemm, [ext_cblas=yes], ++ [AC_MSG_ERROR([ ++ *** Linking with cblas with $LIBS failed. ++ *** If you installed cblas library in a non standard place, ++ *** specify its install prefix using the following option ++ *** --with-cblas-external-libs="-L<lib_dir> -l<lib>"]) ++ ]) ++ AC_MSG_RESULT($ext_cblas) ++ LIBS="$LIBS_sav" ++ AC_SUBST([CBLAS_CFLAGS]) ++ AC_SUBST([CBLAS_LIBS]) ++ fi ++]) +diff --git a/bspline/Makefile.am b/bspline/Makefile.am +index 3f4f950..d413036 100644 +--- a/bspline/Makefile.am ++++ b/bspline/Makefile.am +@@ -12,6 +12,6 @@ check_PROGRAMS = test + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la ++test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la + + test_SOURCES = test.c +diff --git a/configure.ac b/configure.ac +index d6b673f..c642454 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -205,6 +205,16 @@ if test "x$LIBS" = "x" ; then + AC_CHECK_LIB(m, cos) + fi + ++sinclude(ax_cblas.m4) ++AX_CBLAS ++if test "x$CBLAS_LIBS" != "x"; then ++ CBLAS_LINK_LIBS="$CBLAS_LIBS" ++else ++ CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la" ++ CBLAS_LIBS="-lgslcblas" ++fi ++AC_SUBST(CBLAS_LINK_LIBS) ++ + dnl Remember to put a definition in acconfig.h for each of these + AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1 + #include <fenv.h>]) +diff --git a/eigen/Makefile.am b/eigen/Makefile.am +index c28bfde..14197a4 100644 +--- a/eigen/Makefile.am ++++ b/eigen/Makefile.am +@@ -11,7 +11,7 @@ noinst_HEADERS = qrstep.c + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la ++test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la + + test_SOURCES = test.c + +diff --git a/gsl-config.in b/gsl-config.in +old mode 100755 +new mode 100644 +index 3f3fa61..c9c4262 +--- a/gsl-config.in ++++ b/gsl-config.in +@@ -58,11 +58,11 @@ while test $# -gt 0; do + ;; + + --cflags) +- echo @GSL_CFLAGS@ ++ echo @GSL_CFLAGS@ @CBLAS_CFLAGS@ + ;; + + --libs) +- : ${GSL_CBLAS_LIB=-lgslcblas} ++ : ${GSL_CBLAS_LIB=@CBLAS_LIBS@} + echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@ + ;; + +diff --git a/gsl.pc.in b/gsl.pc.in +index 5e9ef21..5a7a0f3 100644 +--- a/gsl.pc.in ++++ b/gsl.pc.in +@@ -2,7 +2,7 @@ prefix=@prefix@ + exec_prefix=@exec_prefix@ + libdir=@libdir@ + includedir=@includedir@ +-GSL_CBLAS_LIB=-lgslcblas ++GSL_CBLAS_LIB=@CBLAS_LIBS@ + + Name: GSL + Description: GNU Scientific Library +diff --git a/interpolation/Makefile.am b/interpolation/Makefile.am +index 1d80755..e45bd51 100644 +--- a/interpolation/Makefile.am ++++ b/interpolation/Makefile.am +@@ -12,7 +12,7 @@ AM_CPPFLAGS = -I$(top_srcdir) + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff --git a/linalg/Makefile.am b/linalg/Makefile.am +index 8fb6e7c..90d22e0 100644 +--- a/linalg/Makefile.am ++++ b/linalg/Makefile.am +@@ -12,7 +12,7 @@ TESTS = $(check_PROGRAMS) + + check_PROGRAMS = test + +-test_LDADD = libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff --git a/multifit/Makefile.am b/multifit/Makefile.am +index 891964b..b33f71e 100644 +--- a/multifit/Makefile.am ++++ b/multifit/Makefile.am +@@ -67,8 +67,8 @@ check_PROGRAMS = test #demo + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c +-test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la ++test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la + + #demo_SOURCES = demo.c +-#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ++#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la + +diff --git a/multimin/Makefile.am b/multimin/Makefile.am +index 7071359..65a488a 100644 +--- a/multimin/Makefile.am ++++ b/multimin/Makefile.am +@@ -13,8 +13,8 @@ check_PROGRAMS = test #demo + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c test_funcs.c test_funcs.h +-test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + #demo_SOURCES = demo.c +-#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + +diff --git a/multiroots/Makefile.am b/multiroots/Makefile.am +index a351c3f..6178448 100644 +--- a/multiroots/Makefile.am ++++ b/multiroots/Makefile.am +@@ -15,5 +15,5 @@ check_PROGRAMS = test + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c test_funcs.c test_funcs.h +-test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + +diff --git a/ode-initval/Makefile.am b/ode-initval/Makefile.am +index 9c774b5..346c381 100644 +--- a/ode-initval/Makefile.am ++++ b/ode-initval/Makefile.am +@@ -12,7 +12,7 @@ check_PROGRAMS = test + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff --git a/poly/Makefile.am b/poly/Makefile.am +index f1dae5d..e0f8e83 100644 +--- a/poly/Makefile.am ++++ b/poly/Makefile.am +@@ -10,7 +10,7 @@ noinst_HEADERS = balance.c companion.c qr.c + + TESTS = $(check_PROGRAMS) + +-check_PROGRAMS = test ++#check_PROGRAMS = test + + test_SOURCES = test.c + test_LDADD = libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../sort/libgslsort.la +diff --git a/specfunc/Makefile.am b/specfunc/Makefile.am +index 0a7e672..d1361d0 100644 +--- a/specfunc/Makefile.am ++++ b/specfunc/Makefile.am +@@ -12,7 +12,7 @@ TESTS = $(check_PROGRAMS) + + check_PROGRAMS = test + +-test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test_sf.c test_sf.h test_airy.c test_bessel.c test_coulomb.c test_dilog.c test_gamma.c test_hyperg.c test_legendre.c test_mathieu.c + +diff --git a/wavelet/Makefile.am b/wavelet/Makefile.am +index 9da20d8..8cdbd77 100644 +--- a/wavelet/Makefile.am ++++ b/wavelet/Makefile.am +@@ -10,7 +10,7 @@ check_PROGRAMS = test + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslwavelet.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslwavelet.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + diff --git a/sci-libs/gsl/files/gsl-2.3-cblas.patch b/sci-libs/gsl/files/gsl-2.3-cblas.patch new file mode 100644 index 000000000000..7e12b370b0dc --- /dev/null +++ b/sci-libs/gsl/files/gsl-2.3-cblas.patch @@ -0,0 +1,1485 @@ + Makefile.am | 8 +- + Makefile.am.porig | 66 ++++ + ax_cblas.m4 | 69 +++++ + bspline/Makefile.am | 2 +- + bspline/Makefile.am.porig | 17 ++ + configure.ac | 10 + + configure.ac.porig | 647 ++++++++++++++++++++++++++++++++++++++++ + eigen/Makefile.am | 2 +- + eigen/Makefile.am.porig | 18 ++ + gsl-config.in | 4 +- + gsl-config.in.porig | 80 +++++ + gsl.pc.in | 2 +- + gsl.pc.in.porig | 11 + + interpolation/Makefile.am | 2 +- + interpolation/Makefile.am.porig | 18 ++ + linalg/Makefile.am | 2 +- + linalg/Makefile.am.porig | 16 + + multifit/Makefile.am | 4 +- + multifit/Makefile.am.porig | 74 +++++ + multimin/Makefile.am | 4 +- + multimin/Makefile.am.porig | 20 ++ + multiroots/Makefile.am | 2 +- + multiroots/Makefile.am.porig | 19 ++ + ode-initval/Makefile.am | 2 +- + ode-initval/Makefile.am.porig | 18 ++ + poly/Makefile.am | 2 +- + poly/Makefile.am.porig | 17 ++ + specfunc/Makefile.am | 2 +- + specfunc/Makefile.am.porig | 19 ++ + wavelet/Makefile.am | 2 +- + wavelet/Makefile.am.porig | 17 ++ + 31 files changed, 1157 insertions(+), 19 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index c522001..4513bc8 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -19,7 +19,7 @@ EXTRA_DIST = autogen.sh gsl-config.in gsl.pc.in configure.ac THANKS BUGS gsl.spe + + lib_LTLIBRARIES = libgsl.la + libgsl_la_SOURCES = version.c +-libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) ++libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) @CBLAS_LINK_LIBS@ + libgsl_la_LDFLAGS = $(GSL_LDFLAGS) -version-info $(GSL_LT_VERSION) + noinst_HEADERS = templates_on.h templates_off.h build.h + +@@ -29,10 +29,10 @@ m4data_DATA = gsl.m4 + bin_PROGRAMS = gsl-randist gsl-histogram + + gsl_randist_SOURCES = gsl-randist.c +-gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la ++gsl_randist_LDADD = libgsl.la + + gsl_histogram_SOURCES = gsl-histogram.c +-gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la ++gsl_histogram_LDADD = libgsl.la + + check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test + TESTS = test_gsl_histogram.sh pkgconfig.test +@@ -51,6 +51,8 @@ edit = $(SED) \ + -e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \ + -e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \ + -e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \ ++ -e 's|@CBLAS_CFLAGS[@]|$(CBLAS_CFLAGS)|g' \ ++ -e 's|@CBLAS_LIBS[@]|$(CBLAS_LIBS)|g' \ + -e 's|@LIBS[@]|$(LIBS)|g' \ + -e 's|@VERSION[@]|$(VERSION)|g' + +diff --git a/Makefile.am.porig b/Makefile.am.porig +new file mode 100644 +index 0000000..c522001 +--- /dev/null ++++ b/Makefile.am.porig +@@ -0,0 +1,66 @@ ++## Process this file with automake to produce Makefile.in ++ ++# AUTOMAKE_OPTIONS = readme-alpha ++ ++SUBDIRS = gsl utils sys test err const complex cheb block vector matrix permutation combination multiset sort ieee-utils cblas blas linalg eigen specfunc dht qrng rng randist fft poly fit multifit multifit_nlinear multilarge multilarge_nlinear rstat statistics siman sum integration interpolation histogram ode-initval ode-initval2 roots multiroots min multimin monte ntuple diff deriv cdf wavelet bspline spblas spmatrix splinalg doc ++ ++SUBLIBS = block/libgslblock.la blas/libgslblas.la bspline/libgslbspline.la complex/libgslcomplex.la cheb/libgslcheb.la dht/libgsldht.la diff/libgsldiff.la deriv/libgslderiv.la eigen/libgsleigen.la err/libgslerr.la fft/libgslfft.la fit/libgslfit.la histogram/libgslhistogram.la ieee-utils/libgslieeeutils.la integration/libgslintegration.la interpolation/libgslinterpolation.la linalg/libgsllinalg.la matrix/libgslmatrix.la min/libgslmin.la monte/libgslmonte.la multifit/libgslmultifit.la multifit_nlinear/libgslmultifit_nlinear.la multilarge/libgslmultilarge.la multilarge_nlinear/libgslmultilarge_nlinear.la multimin/libgslmultimin.la multiroots/libgslmultiroots.la ntuple/libgslntuple.la ode-initval/libgslodeiv.la ode-initval2/libgslodeiv2.la permutation/libgslpermutation.la combination/libgslcombination.la multiset/libgslmultiset.la poly/libgslpoly.la qrng/libgslqrng.la randist/libgslrandist.la rng/libgslrng.la roots/libgslroots.la siman/libgslsiman.la sort/libgslsort.la specfunc/libgslspecfunc.la rstat/libgslrstat.la statistics/libgslstatistics.la sum/libgslsum.la sys/libgslsys.la test/libgsltest.la utils/libutils.la vector/libgslvector.la cdf/libgslcdf.la wavelet/libgslwavelet.la spmatrix/libgslspmatrix.la spblas/libgslspblas.la splinalg/libgslsplinalg.la ++ ++pkginclude_HEADERS = gsl_math.h gsl_pow_int.h gsl_nan.h gsl_machine.h gsl_mode.h gsl_precision.h gsl_types.h gsl_version.h gsl_minmax.h gsl_inline.h ++ ++bin_SCRIPTS = gsl-config ++ ++pkgconfigdir = $(libdir)/pkgconfig ++pkgconfig_DATA= gsl.pc ++ ++CLEANFILES = gsl.pc gsl-config ++ ++EXTRA_DIST = autogen.sh gsl-config.in gsl.pc.in configure.ac THANKS BUGS gsl.spec.in gsl.m4 test_gsl_histogram.sh pkgconfig.test ++ ++lib_LTLIBRARIES = libgsl.la ++libgsl_la_SOURCES = version.c ++libgsl_la_LIBADD = $(GSL_LIBADD) $(SUBLIBS) ++libgsl_la_LDFLAGS = $(GSL_LDFLAGS) -version-info $(GSL_LT_VERSION) ++noinst_HEADERS = templates_on.h templates_off.h build.h ++ ++m4datadir = $(datadir)/aclocal ++m4data_DATA = gsl.m4 ++ ++bin_PROGRAMS = gsl-randist gsl-histogram ++ ++gsl_randist_SOURCES = gsl-randist.c ++gsl_randist_LDADD = libgsl.la cblas/libgslcblas.la ++ ++gsl_histogram_SOURCES = gsl-histogram.c ++gsl_histogram_LDADD = libgsl.la cblas/libgslcblas.la ++ ++check_SCRIPTS = test_gsl_histogram.sh pkgconfig.test ++TESTS = test_gsl_histogram.sh pkgconfig.test ++ ++#bin_PROGRAMS = main dummy ++#dummy_SOURCES = version.c ++#dummy_LDADD = $(SUBLIBS) ++#main_SOURCES = version.c env.c ++#main_LDADD = libgsl.la ++ ++edit = $(SED) \ ++ -e 's|@prefix[@]|$(prefix)|g' \ ++ -e 's|@exec_prefix[@]|$(exec_prefix)|g' \ ++ -e 's|@libdir[@]|$(libdir)|g' \ ++ -e 's|@includedir[@]|$(includedir)|g' \ ++ -e 's|@GSL_CFLAGS[@]|$(GSL_CFLAGS)|g' \ ++ -e 's|@GSL_LIBM[@]|$(GSL_LIBM)|g' \ ++ -e 's|@GSL_LIBS[@]|$(GSL_LIBS)|g' \ ++ -e 's|@LIBS[@]|$(LIBS)|g' \ ++ -e 's|@VERSION[@]|$(VERSION)|g' ++ ++gsl-config gsl.pc: Makefile ++ @rm -f $@ $@.tmp ++ @$(edit) '$(srcdir)/$@.in' >>$@.tmp ++ @chmod a-w $@.tmp ++ @mv $@.tmp $@ ++ @echo creating $@ ++ ++gsl-config: $(srcdir)/gsl-config.in ++gsl.pc: $(srcdir)/gsl.pc.in ++ +diff --git a/ax_cblas.m4 b/ax_cblas.m4 +new file mode 100644 +index 0000000..6ef143a +--- /dev/null ++++ b/ax_cblas.m4 +@@ -0,0 +1,69 @@ ++AC_DEFUN([AX_CBLAS],[ ++ ++ ext_cblas=no ++ ext_cblas_libs="-lcblas" ++ ext_cblas_cflags="" ++ ++ AC_ARG_WITH(cblas-external, ++ [AS_HELP_STRING([--with-cblas-external], ++ [Use external CBLAS library (default is no)])], ++ [with_ext_cblas=$withval], ++ [with_ext_cblas=no]) ++ ++ case $with_ext_cblas in ++ no) ext_cblas=no ;; ++ yes) ext_cblas=yes ;; ++ -* | */* | *.a | *.so | *.so.* | *.o) ++ ext_cblas=yes ++ ext_cblas_libs="$with_cblas" ;; ++ *) ext_cblas=yes ++ ext_cblas_libs="-l$with_cblas" ;; ++ esac ++ ++ AC_ARG_WITH(cblas-external-libs, ++ [AS_HELP_STRING([--with-cblas-external-libs=<libs>], ++ [External cblas libraries to link with (default is "$ext_cblas_libs")])], ++ [ext_cblas_libs=$withval], ++ []) ++ ++ AC_ARG_WITH(cblas-external-cflags, ++ [AS_HELP_STRING([--with-cblas-external-cflags=<flags>], ++ [Pre-processing flags to compile with external cblas ("-I<dir>")])], ++ [ext_cblas_cflags=$withval], ++ []) ++ ++ if test x$ext_cblas != xno; then ++ if test "x$CBLAS_LIBS" = x; then ++ CBLAS_LIBS="$ext_cblas_libs" ++ fi ++ if test "x$CBLAS_CFLAGS" = x; then ++ CBLAS_CFLAGS="$ext_cblas_cflags" ++ fi ++ ++ CFLAGS_sav="$CFLAGS" ++ CFLAGS="$CFLAGS $CBLAS_CFLAGS" ++ AC_CHECK_HEADER(cblas.h, , ++ [AC_MSG_ERROR([ ++ *** Header file cblas.h not found. ++ *** If you installed cblas header in a non standard place, ++ *** specify its install prefix using the following option ++ *** --with-cblas-external-cflags="-I<include_dir>"]) ++ ]) ++ CFLAGS="$CFLAGS_sav" ++ ++ LIBS_sav="$LIBS" ++ LIBS="$LIBS $CBLAS_LIBS -lm" ++ AC_MSG_CHECKING([for cblas_sgemm in $CBLAS_LIBS]) ++ AC_TRY_LINK_FUNC(cblas_sgemm, [ext_cblas=yes], ++ [AC_MSG_ERROR([ ++ *** Linking with cblas with $LIBS failed. ++ *** If you installed cblas library in a non standard place, ++ *** specify its install prefix using the following option ++ *** --with-cblas-external-libs="-L<lib_dir> -l<lib>"]) ++ ]) ++ AC_MSG_RESULT($ext_cblas) ++ LIBS="$LIBS_sav" ++ AC_SUBST([CBLAS_CFLAGS]) ++ AC_SUBST([CBLAS_LIBS]) ++ fi ++]) +diff --git a/bspline/Makefile.am b/bspline/Makefile.am +index 3f4f950..d413036 100644 +--- a/bspline/Makefile.am ++++ b/bspline/Makefile.am +@@ -12,6 +12,6 @@ check_PROGRAMS = test + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la ++test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la + + test_SOURCES = test.c +diff --git a/bspline/Makefile.am.porig b/bspline/Makefile.am.porig +new file mode 100644 +index 0000000..3f4f950 +--- /dev/null ++++ b/bspline/Makefile.am.porig +@@ -0,0 +1,17 @@ ++noinst_LTLIBRARIES = libgslbspline.la ++ ++pkginclude_HEADERS = gsl_bspline.h ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgslbspline_la_SOURCES = bspline.c greville.c ++ ++noinst_HEADERS = bspline.h ++ ++check_PROGRAMS = test ++ ++TESTS = $(check_PROGRAMS) ++ ++test_LDADD = libgslbspline.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../statistics/libgslstatistics.la ++ ++test_SOURCES = test.c +diff --git a/configure.ac b/configure.ac +index a26fc1e..564d426 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -208,6 +208,16 @@ if test "x$LIBS" = "x" ; then + AC_CHECK_LIB(m, cos) + fi + ++sinclude(ax_cblas.m4) ++AX_CBLAS ++if test "x$CBLAS_LIBS" != "x"; then ++ CBLAS_LINK_LIBS="$CBLAS_LIBS" ++else ++ CBLAS_LINK_LIBS="\$(top_builddir)/cblas/libgslcblas.la" ++ CBLAS_LIBS="-lgslcblas" ++fi ++AC_SUBST(CBLAS_LINK_LIBS) ++ + dnl Remember to put a definition in acconfig.h for each of these + AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1 + #include <fenv.h>]) +diff --git a/configure.ac.porig b/configure.ac.porig +new file mode 100644 +index 0000000..a26fc1e +--- /dev/null ++++ b/configure.ac.porig +@@ -0,0 +1,647 @@ ++dnl Process this file with autoconf to produce a configure script. ++ ++AC_INIT([gsl],[2.3]) ++AC_CONFIG_SRCDIR(gsl_math.h) ++ ++AM_INIT_AUTOMAKE([gnu]) ++AC_CONFIG_HEADERS([config.h]) ++AM_MAINTAINER_MODE ++ ++dnl Library versioning (C:R:A == current:revision:age) ++dnl See the libtool manual for an explanation of the numbers ++dnl ++dnl gsl-1.0 libgsl 0:0:0 libgslcblas 0:0:0 ++dnl gsl-1.1 libgsl 1:0:1 libgslcblas 0:0:0 ++dnl gsl-1.1.1 libgsl 2:0:2 libgslcblas 0:0:0 ++dnl gsl-1.2 libgsl 3:0:3 libgslcblas 0:0:0 ++dnl gsl-1.3 libgsl 4:0:4 libgslcblas 0:0:0 ++dnl gsl-1.4 libgsl 5:0:5 libgslcblas 0:0:0 ++dnl gsl-1.5 libgsl 6:0:6 libgslcblas 0:0:0 ++dnl gsl-1.6 libgsl 7:0:7 libgslcblas 0:0:0 ++dnl gsl-1.7 libgsl 8:0:8 libgslcblas 0:0:0 ++dnl gsl-1.8 libgsl 9:0:9 libgslcblas 0:0:0 ++dnl gsl-1.9 libgsl 10:0:10 libgslcblas 0:0:0 ++dnl gsl-1.10 libgsl 10:0:10 (*) libgslcblas 0:0:0 ++dnl gsl-1.11 libgsl 12:0:12 libgslcblas 0:0:0 ++dnl gsl-1.12 libgsl 13:0:13 libgslcblas 0:0:0 ++dnl gsl-1.13 libgsl 14:0:14 libgslcblas 0:0:0 ++dnl gsl-1.14 libgsl 15:0:15 libgslcblas 0:0:0 ++dnl gsl-1.15 libgsl 16:0:16 libgslcblas 0:0:0 ++dnl gsl-1.16 libgsl 17:0:17 libgslcblas 0:0:0 ++dnl gsl-2.0 libgsl 18:0:18 (**) libgslcblas 0:0:0 ++dnl gsl-2.1 libgsl 19:0:0 libgslcblas 0:0:0 ++dnl gsl-2.2 libgsl 20:0:1 libgslcblas 0:0:0 ++dnl gsl-2.2.1 libgsl 21:0:2 libgslcblas 0:0:0 ++dnl gsl-2.3 libgsl 22:0:3 libgslcblas 0:0:0 ++dnl ++dnl (*) There was an error on this release. Firstly, the versioning ++dnl numbers were not updated. Secondly, 2 functions were removed, but ++dnl the age not reset--this should have been 11:0:0. However these ++dnl functions were not documented and are regarded as internal, so we ++dnl will assume 11:0:11. ++dnl ++dnl (**) There was an error on this release. Age should have been ++dnl reset to 18:0:0 ++dnl ++dnl How to update library version number ++dnl ==================================== ++dnl ++dnl C: increment if the interface has additions, changes, removals. ++dnl ++dnl R: increment any time the source changes; set to 0 if you ++dnl incremented CURRENT ++dnl ++dnl A: increment if any interfaces have been added; set to 0 if any ++dnl interfaces have been removed. removal has precedence over adding, ++dnl so set to 0 if both happened. ++dnl ++dnl See https://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html ++dnl for more detailed info ++ ++dnl ++GSL_CURRENT=22 ++GSL_REVISION=0 ++GSL_AGE=3 ++dnl ++CBLAS_CURRENT=0 ++CBLAS_REVISION=0 ++CBLAS_AGE=0 ++ ++GSL_LT_VERSION="${GSL_CURRENT}:${GSL_REVISION}:${GSL_AGE}" ++AC_SUBST(GSL_LT_VERSION) ++ ++GSL_LT_CBLAS_VERSION="${CBLAS_CURRENT}:${CBLAS_REVISION}:${CBLAS_AGE}" ++AC_SUBST(GSL_LT_CBLAS_VERSION) ++ ++case "$VERSION" in ++ *+) ++ ;; ++ *) ++ AC_DEFINE(RELEASED,[],[Defined if this is an official release]) ++ ;; ++esac ++ ++dnl Split VERSION into GSL_VERSION_MAJOR and GSL_VERSION_MINOR ++dnl Follows AX_SPLIT_VERSION macro from AC-Archive ++dnl Rhys Ulerich <rhys.ulerich@gmail.com> ++AC_PROG_SED ++GSL_MAJOR_VERSION=`echo "$VERSION" | $SED 's/\([[^.]][[^.]]*\).*/\1/'` ++GSL_MINOR_VERSION=`echo "$VERSION" | $SED 's/[[^.]][[^.]]*.\([[^.]][[^.]]*\).*/\1/'` ++AC_SUBST(GSL_MAJOR_VERSION) ++AC_SUBST(GSL_MINOR_VERSION) ++ ++dnl things required by automake ++dnl AC_ARG_PROGRAM ++AC_PROG_MAKE_SET ++ ++dnl Check for which system. ++AC_CANONICAL_HOST ++ ++dnl Checks for programs. ++AC_LANG(C) ++AC_PROG_CC ++AC_PROG_CPP ++AC_PROG_INSTALL ++AC_PROG_LN_S ++LT_INIT([win32-dll]) ++ ++dnl Check compiler features ++AC_TYPE_SIZE_T ++dnl AC_C_CONST ++AC_C_VOLATILE ++AC_C_INLINE ++AC_C_CHAR_UNSIGNED ++ ++GSL_CFLAGS="-I$includedir" ++GSL_LIBS="-L$libdir -lgsl" ++dnl macro from libtool - can be replaced with LT_LIB_M when we require libtool 2 ++LT_LIB_M ++GSL_LIBM=$LIBM ++ ++AC_SUBST(GSL_CFLAGS) ++AC_SUBST(GSL_LIBS) ++AC_SUBST(GSL_LIBM) ++ ++if test "$ac_cv_c_inline" != no ; then ++dnl Check for "extern inline", using a modified version of the test ++dnl for AC_C_INLINE from acspecific.mt ++dnl ++ AC_CACHE_CHECK([for GNU-style extern inline], ac_cv_c_extern_inline, ++ [ac_cv_c_extern_inline=no ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[extern $ac_cv_c_inline double foo(double x); ++ extern $ac_cv_c_inline double foo(double x) { return x + 1.0 ; } ; ++ double foo (double x) { return x + 1.0 ; };]], [[ foo(1.0) ]])],[ac_cv_c_extern_inline="yes"],[]) ++ ]) ++ ++ if test "$ac_cv_c_extern_inline" != no ; then ++ AC_DEFINE(HAVE_INLINE,[1],[Define if you have inline]) ++ else ++ AC_CACHE_CHECK([for C99-style inline], ac_cv_c_c99inline, ++ [ac_cv_c_c99inline=no ++ dnl next line is a necessary condition ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[extern inline void* foo() { foo(); return &foo ; };]], ++ [[ return foo() != 0 ]])],[ac_cv_c_c99inline="yes"],[]) ++ dnl but not sufficient, extern must work but inline on its own should not ++ if test "$ac_cv_c_c99inline" != no ; then ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[inline void* foo() { foo(); return &foo ; };]], ++ [[ return foo() != 0 ]])],[],ac_cv_c_c99inline="no") ++ fi ++ ]) ++ if test "$ac_cv_c_c99inline" != no ; then ++ AC_DEFINE(HAVE_INLINE,[1],[Define if you have inline]) ++ AC_DEFINE(HAVE_C99_INLINE,[1],[Define if you have inline with C99 behavior]) ++ fi ++ fi ++fi ++ ++dnl Checks for header files. ++AC_CHECK_HEADERS(ieeefp.h) ++ ++dnl Checks for typedefs, structures, and compiler characteristics. ++ ++case $host in ++ *-*-cygwin* | *-*-mingw* ) ++ if test "$enable_shared" = yes; then ++ GSLCBLAS_LDFLAGS="$GSLCBLAS_LDFLAGS -no-undefined" ++ GSL_LDFLAGS="$GSL_LDFLAGS -no-undefined" ++ GSL_LIBADD="cblas/libgslcblas.la" ++ fi ++ ;; ++esac ++ ++AC_SUBST(GSLCBLAS_LDFLAGS) ++AC_SUBST(GSL_LDFLAGS) ++AC_SUBST(GSL_LIBADD) ++ ++dnl Checks for library functions. ++ ++dnl AC_FUNC_ALLOCA ++AC_FUNC_VPRINTF ++ ++dnl strcasecmp, strerror, xmalloc, xrealloc, probably others should be added. ++dnl removed strerror from this list, it's hardcoded in the err/ directory ++dnl Any functions which appear in this list of functions should be provided ++dnl in the utils/ directory ++dnl xmalloc is not used, removed (bjg) ++AC_REPLACE_FUNCS(memcpy memmove strdup strtol strtoul) ++ ++AC_CACHE_CHECK(for EXIT_SUCCESS and EXIT_FAILURE, ++ac_cv_decl_exit_success_and_failure, ++AC_EGREP_CPP(yes, ++[ ++#include <stdlib.h> ++#ifdef EXIT_SUCCESS ++yes ++#endif ++], ++ac_cv_decl_exit_success_and_failure=yes, ++ac_cv_decl_exit_success_and_failure=no) ++) ++ ++if test "$ac_cv_decl_exit_success_and_failure" = yes ; then ++ AC_DEFINE(HAVE_EXIT_SUCCESS_AND_FAILURE,1,[Defined if you have ansi EXIT_SUCCESS and EXIT_FAILURE in stdlib.h]) ++fi ; ++ ++dnl Use alternate libm if specified by user ++ ++if test "x$LIBS" = "x" ; then ++ AC_CHECK_LIB(m, cos) ++fi ++ ++dnl Remember to put a definition in acconfig.h for each of these ++AC_CHECK_DECLS(feenableexcept,,,[#define _GNU_SOURCE 1 ++#include <fenv.h>]) ++AC_CHECK_DECLS(fesettrapenable,,,[#define _GNU_SOURCE 1 ++#include <fenv.h>]) ++AC_CHECK_DECLS(hypot,,,[#include <math.h>]) ++AC_CHECK_DECLS(expm1,,,[#include <math.h>]) ++AC_CHECK_DECLS(acosh,,,[#include <math.h>]) ++AC_CHECK_DECLS(asinh,,,[#include <math.h>]) ++AC_CHECK_DECLS(atanh,,,[#include <math.h>]) ++AC_CHECK_DECLS(ldexp,,,[#include <math.h>]) ++AC_CHECK_DECLS(frexp,,,[#include <math.h>]) ++AC_CHECK_DECLS([fprnd_t],[],[],[[#include <float.h>]]) ++AC_CHECK_DECLS(isinf,,,[#include <math.h>]) ++AC_CHECK_DECLS(isfinite,,,[#include <math.h>]) ++AC_CHECK_DECLS(finite,,,[#include <math.h> ++#if HAVE_IEEEFP_H ++#include <ieeefp.h> ++#endif]) ++AC_CHECK_DECLS(isnan,,,[#include <math.h>]) ++ ++dnl OpenBSD has a broken implementation of log1p. ++case "$host" in ++ *-*-*openbsd*) ++ AC_MSG_RESULT([avoiding OpenBSD system log1p - using gsl version]) ++ ;; ++ *) ++ AC_CHECK_DECLS(log1p,,,[#include <math.h>]) ++ ;; ++esac ++ ++AC_CACHE_CHECK([for long double stdio], ac_cv_func_printf_longdouble, ++[AC_RUN_IFELSE([AC_LANG_SOURCE([[ ++#include <stdlib.h> ++#include <stdio.h> ++int main (void) ++{ ++const char * s = "5678.25"; long double x = 1.234 ; ++fprintf(stderr,"%Lg\n",x) ; ++sscanf(s, "%Lg", &x); ++if (x == 5678.25) {exit (0);} else {exit(1); }; ++}]])],[ac_cv_func_printf_longdouble="yes"],[ac_cv_func_printf_longdouble="no"],[ac_cv_func_printf_longdouble="no"])]) ++ ++if test "$ac_cv_func_printf_longdouble" != no; then ++ AC_DEFINE(HAVE_PRINTF_LONGDOUBLE,1,[Define this if printf can handle %Lf for long double]) ++fi ++ ++AC_CACHE_CHECK([for extended floating point registers],ac_cv_c_extended_fp, ++[case "$host" in ++ *sparc*-*-*) ++ ac_cv_c_extended_fp=no ++ ;; ++ *powerpc*-*-*) ++ ac_cv_c_extended_fp=no ++ ;; ++ *hppa*-*-*) ++ ac_cv_c_extended_fp=no ++ ;; ++ *alpha*-*-*) ++ ac_cv_c_extended_fp=no ++ ;; ++ *68k*-*-*) ++ ac_cv_c_extended_fp=yes ++ ;; ++ *86-*-*) ++ ac_cv_c_extended_fp=yes ++ ;; ++ x86_64-*-*) ++ ac_cv_c_extended_fp=yes ++ ;; ++ *) ++ ac_cv_c_extended_fp=unknown ++ ;; ++esac ++]) ++ ++if test $ac_cv_c_extended_fp != "no" ; then ++ AC_DEFINE(HAVE_EXTENDED_PRECISION_REGISTERS,1,[Defined on architectures with excess floating-point precision]) ++fi ++ ++AC_CACHE_CHECK([for IEEE arithmetic interface type], ac_cv_c_ieee_interface, ++[case "$host" in ++ sparc-*-linux*) ++ ac_cv_c_ieee_interface=gnusparc ++ ;; ++ m68k-*-linux*) ++ ac_cv_c_ieee_interface=gnum68k ++ ;; ++ powerpc-*-linux*) ++ ac_cv_c_ieee_interface=gnuppc ++ ;; ++ *86-*-gnu | *86_64-*-gnu | *86-*-linux* | *86_64-*-linux*) ++ ac_cv_c_ieee_interface=gnux86 ++ ;; ++ *-*-sunos4*) ++ ac_cv_c_ieee_interface=sunos4 ++ ;; ++ *-*-solaris*) ++ ac_cv_c_ieee_interface=solaris ++ ;; ++ *-*-hpux11*) ++ ac_cv_c_ieee_interface=hpux11 ++ ;; ++ *-*-hpux*) ++ ac_cv_c_ieee_interface=hpux ++ ;; ++ *-*-osf*) ++ ac_cv_c_ieee_interface=tru64 ++ ;; ++ *-*-aix*) ++ ac_cv_c_ieee_interface=aix ++ ;; ++ *-*-irix*) ++ ac_cv_c_ieee_interface=irix ++ ;; ++ powerpc-*-*darwin*) ++ ac_cv_c_ieee_interface=darwin ++ ;; ++ *86-*-*darwin*) ++ ac_cv_c_ieee_interface=darwin86 ++ ;; ++ *-*-*netbsd*) ++ ac_cv_c_ieee_interface=netbsd ++ ;; ++ *-*-*openbsd*) ++ ac_cv_c_ieee_interface=openbsd ++ ;; ++ *-*-*bsd*) ++ ac_cv_c_ieee_interface=freebsd ++ ;; ++ *-*-os2*) ++ ac_cv_c_ieee_interface=os2emx ++ ;; ++ *) ++ ac_cv_c_ieee_interface=unknown ++ ;; ++esac ++]) ++ ++if test "$ac_cv_c_ieee_interface" = "gnux86" ; then ++ AC_CACHE_CHECK([for FPU_SETCW], ac_cv_c_fpu_setcw, ++ [ac_cv_c_fpu_setcw=no ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <fpu_control.h> ++#ifndef _FPU_SETCW ++#include <i386/fpu_control.h> ++#define _FPU_SETCW(cw) __setfpucw(cw) ++#endif ++]], [[ unsigned short mode = 0 ; _FPU_SETCW(mode); ]])],[ac_cv_c_fpu_setcw="yes"],[ac_cv_c_ieee_interface=unknown]) ++ ]) ++fi ++ ++if test "$ac_cv_c_ieee_interface" = "gnux86" ; then ++ AC_CACHE_CHECK([for SSE extensions], ac_cv_c_fpu_sse, ++ [ac_cv_c_fpu_sse=no ++ AC_RUN_IFELSE([AC_LANG_PROGRAM([[ ++#include <stdlib.h> ++#define _FPU_SETMXCSR(cw_sse) asm volatile ("ldmxcsr %0" : : "m" (*&cw_sse)) ++]], [[ unsigned int mode = 0x1f80 ; _FPU_SETMXCSR(mode); exit(0); ]])],[ac_cv_c_fpu_sse="yes"],[ac_cv_c_fpu_sse="no"],[ ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ ++#include <stdlib.h> ++#define _FPU_SETMXCSR(cw_sse) asm volatile ("ldmxcsr %0" : : "m" (*&cw_sse)) ++]], [[ unsigned int mode = 0x1f80 ; _FPU_SETMXCSR(mode); exit(0); ]])],[ac_cv_c_fpu_sse="yes"],[ac_cv_c_fpu_sse="no"]) ++])]) ++ ++ if test $ac_cv_c_fpu_sse = yes; then ++ AC_DEFINE([HAVE_FPU_X86_SSE], 1, ++ [Define if x86 processor has sse extensions.]) ++ fi ++fi ++ ++ac_tr_ieee_interface=HAVE_`echo $ac_cv_c_ieee_interface | tr 'abcdefghijklmnopqrstuvwxyz' 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'`_IEEE_INTERFACE ++AC_DEFINE_UNQUOTED($ac_tr_ieee_interface,1,[IEEE Interface Type]) ++ ++AC_SUBST(HAVE_GNUSPARC_IEEE_INTERFACE) ++AC_SUBST(HAVE_GNUM68K_IEEE_INTERFACE) ++AC_SUBST(HAVE_GNUPPC_IEEE_INTERFACE) ++AC_SUBST(HAVE_GNUX86_IEEE_INTERFACE) ++AC_SUBST(HAVE_SUNOS4_IEEE_INTERFACE) ++AC_SUBST(HAVE_SOLARIS_IEEE_INTERFACE) ++AC_SUBST(HAVE_HPUX11_IEEE_INTERFACE) ++AC_SUBST(HAVE_HPUX_IEEE_INTERFACE) ++AC_SUBST(HAVE_TRU64_IEEE_INTERFACE) ++AC_SUBST(HAVE_IRIX_IEEE_INTERFACE) ++AC_SUBST(HAVE_AIX_IEEE_INTERFACE) ++AC_SUBST(HAVE_FREEBSD_IEEE_INTERFACE) ++AC_SUBST(HAVE_OS2EMX_IEEE_INTERFACE) ++AC_SUBST(HAVE_NETBSD_IEEE_INTERFACE) ++AC_SUBST(HAVE_OPENBSD_IEEE_INTERFACE) ++AC_SUBST(HAVE_DARWIN_IEEE_INTERFACE) ++AC_SUBST(HAVE_DARWIN86_IEEE_INTERFACE) ++ ++dnl Check for IEEE control flags ++ ++save_cflags="$CFLAGS" ++AC_CACHE_CHECK([for IEEE compiler flags], ac_cv_c_ieee_flags, ++[ ++case "$host" in ++ alpha*-*-*) ++ if test X"$GCC" = Xyes ; then ++ ieee_flags='-mieee -mfp-rounding-mode=d' ++ else ++ # This assumes Compaq's C compiler. ++ ieee_flags='-ieee -fprm d' ++ fi ++ ;; ++esac ++if test X"$ieee_flags" != X ; then ++ CFLAGS="$ieee_flags $CFLAGS" ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[int foo;]])],[ac_cv_c_ieee_flags="$ieee_flags"],[ac_cv_c_ieee_flags="none"]) ++else ++ ac_cv_c_ieee_flags="none" ++fi]) ++ ++if test "$ac_cv_c_ieee_flags" != "none" ; then ++ CFLAGS="$ac_cv_c_ieee_flags $save_cflags" ++else ++ CFLAGS="$save_cflags" ++fi ++ ++dnl Check IEEE comparisons, whether "x != x" is true for NaNs ++dnl ++AC_CACHE_CHECK([for IEEE comparisons], ac_cv_c_ieee_comparisons, ++[AC_RUN_IFELSE([AC_LANG_SOURCE([[ ++#include <math.h> ++int main (void) ++{ ++ int status; double inf, nan; ++ inf = exp(1.0e10); ++ nan = inf / inf ; ++ status = (nan == nan); ++ exit (status); ++}]])],[ac_cv_c_ieee_comparisons="yes"],[ac_cv_c_ieee_comparisons="no"],[ac_cv_c_ieee_comparisons="yes"]) ++]) ++ ++if test "$ac_cv_c_ieee_comparisons" != no ; then ++ AC_DEFINE(HAVE_IEEE_COMPARISONS,1,[Define this if IEEE comparisons work correctly (e.g. NaN != NaN)]) ++fi ++ ++dnl Check for IEEE denormalized arithmetic ++dnl ++AC_CACHE_CHECK([for IEEE denormalized values], ac_cv_c_ieee_denormals, ++[AC_RUN_IFELSE([AC_LANG_SOURCE([[ ++#include <math.h> ++int main (void) ++{ ++ int i, status; ++ volatile double z = 1e-308; ++ for (i = 0; i < 5; i++) { z = z / 10.0 ; }; ++ for (i = 0; i < 5; i++) { z = z * 10.0 ; }; ++ status = (z == 0.0); ++ exit (status); ++}]])],[ac_cv_c_ieee_denormals="yes"],[ac_cv_c_ieee_denormals="no"],[ac_cv_c_ieee_denormals="yes"]) ++]) ++ ++if test "$ac_cv_c_ieee_denormals" != no ; then ++ AC_DEFINE(HAVE_IEEE_DENORMALS,1,[Define this if IEEE denormalized numbers are available]) ++fi ++ ++AH_TEMPLATE([HIDE_INLINE_STATIC],[Define if you need to hide the static definitions of inline functions]) ++ ++AH_BOTTOM([/* Use 0 and 1 for EXIT_SUCCESS and EXIT_FAILURE if we don't have them */ ++#if !HAVE_EXIT_SUCCESS_AND_FAILURE ++#define EXIT_SUCCESS 0 ++#define EXIT_FAILURE 1 ++#endif]) ++ ++AH_BOTTOM([/* Define one of these if you have a known IEEE arithmetic interface */ ++#undef HAVE_GNUSPARC_IEEE_INTERFACE ++#undef HAVE_GNUM68K_IEEE_INTERFACE ++#undef HAVE_GNUPPC_IEEE_INTERFACE ++#undef HAVE_GNUX86_IEEE_INTERFACE ++#undef HAVE_SUNOS4_IEEE_INTERFACE ++#undef HAVE_SOLARIS_IEEE_INTERFACE ++#undef HAVE_HPUX11_IEEE_INTERFACE ++#undef HAVE_HPUX_IEEE_INTERFACE ++#undef HAVE_TRU64_IEEE_INTERFACE ++#undef HAVE_IRIX_IEEE_INTERFACE ++#undef HAVE_AIX_IEEE_INTERFACE ++#undef HAVE_FREEBSD_IEEE_INTERFACE ++#undef HAVE_OS2EMX_IEEE_INTERFACE ++#undef HAVE_NETBSD_IEEE_INTERFACE ++#undef HAVE_OPENBSD_IEEE_INTERFACE ++#undef HAVE_DARWIN_IEEE_INTERFACE ++#undef HAVE_DARWIN86_IEEE_INTERFACE]) ++ ++AH_BOTTOM([/* Define a rounding function which moves extended precision values ++ out of registers and rounds them to double-precision. This should ++ be used *sparingly*, in places where it is necessary to keep ++ double-precision rounding for critical expressions while running in ++ extended precision. For example, the following code should ensure ++ exact equality, even when extended precision registers are in use, ++ ++ double q = GSL_COERCE_DBL(3.0/7.0) ; ++ if (q == GSL_COERCE_DBL(3.0/7.0)) { ... } ; ++ ++ It carries a penalty even when the program is running in double ++ precision mode unless you compile a separate version of the ++ library with HAVE_EXTENDED_PRECISION_REGISTERS turned off. */ ++ ++#if HAVE_EXTENDED_PRECISION_REGISTERS ++#define GSL_COERCE_DBL(x) (gsl_coerce_double(x)) ++#else ++#define GSL_COERCE_DBL(x) (x) ++#endif]) ++ ++AH_BOTTOM([/* Substitute gsl functions for missing system functions */ ++ ++#if !HAVE_DECL_HYPOT ++#define hypot gsl_hypot ++#endif ++ ++#if !HAVE_DECL_LOG1P ++#define log1p gsl_log1p ++#endif ++ ++#if !HAVE_DECL_EXPM1 ++#define expm1 gsl_expm1 ++#endif ++ ++#if !HAVE_DECL_ACOSH ++#define acosh gsl_acosh ++#endif ++ ++#if !HAVE_DECL_ASINH ++#define asinh gsl_asinh ++#endif ++ ++#if !HAVE_DECL_ATANH ++#define atanh gsl_atanh ++#endif ++ ++#if !HAVE_DECL_LDEXP ++#define ldexp gsl_ldexp ++#endif ++ ++#if !HAVE_DECL_FREXP ++#define frexp gsl_frexp ++#endif ++ ++#if !HAVE_DECL_ISINF ++#define isinf gsl_isinf ++#endif ++ ++#if !HAVE_DECL_ISFINITE ++#define isfinite gsl_finite ++#endif ++ ++#if !HAVE_DECL_FINITE ++#define finite gsl_finite ++#endif ++ ++#if !HAVE_DECL_ISNAN ++#define isnan gsl_isnan ++#endif]) ++ ++AH_BOTTOM([#ifdef __GNUC__ ++#define DISCARD_POINTER(p) do { ; } while(p ? 0 : 0); ++#else ++#define DISCARD_POINTER(p) /* ignoring discarded pointer */ ++#endif]) ++ ++AH_BOTTOM([#if defined(GSL_RANGE_CHECK_OFF) || !defined(GSL_RANGE_CHECK) ++#define GSL_RANGE_CHECK 0 /* turn off range checking by default internally */ ++#endif]) ++ ++AH_BOTTOM([#define RETURN_IF_NULL(x) if (!x) { return ; } ++]) ++ ++AH_VERBATIM([GSL_DISABLE_DEPRECATED], ++[/* Disable deprecated functions and enums while building */ ++#define GSL_DISABLE_DEPRECATED 1]) ++ ++dnl ++AC_CONFIG_FILES([ \ ++Makefile \ ++gsl_version.h \ ++gsl.spec \ ++blas/Makefile \ ++block/Makefile \ ++bspline/Makefile \ ++cblas/Makefile \ ++cdf/Makefile \ ++cheb/Makefile \ ++combination/Makefile \ ++complex/Makefile \ ++const/Makefile \ ++deriv/Makefile \ ++dht/Makefile \ ++diff/Makefile \ ++doc/Makefile \ ++doc/examples/Makefile \ ++eigen/Makefile \ ++err/Makefile \ ++fit/Makefile \ ++fft/Makefile \ ++gsl/Makefile \ ++histogram/Makefile \ ++ieee-utils/Makefile \ ++integration/Makefile \ ++interpolation/Makefile \ ++linalg/Makefile \ ++matrix/Makefile \ ++min/Makefile \ ++monte/Makefile \ ++multifit/Makefile \ ++multifit_nlinear/Makefile \ ++multilarge/Makefile \ ++multilarge_nlinear/Makefile \ ++multimin/Makefile \ ++multiroots/Makefile \ ++multiset/Makefile \ ++ntuple/Makefile \ ++ode-initval/Makefile \ ++ode-initval2/Makefile \ ++permutation/Makefile \ ++poly/Makefile \ ++qrng/Makefile \ ++randist/Makefile \ ++rng/Makefile \ ++roots/Makefile \ ++rstat/Makefile \ ++siman/Makefile \ ++sort/Makefile \ ++spblas/Makefile \ ++splinalg/Makefile \ ++spmatrix/Makefile \ ++specfunc/Makefile \ ++statistics/Makefile \ ++sum/Makefile \ ++sys/Makefile \ ++test/Makefile \ ++utils/Makefile \ ++vector/Makefile \ ++wavelet/Makefile \ ++]) ++ ++AC_OUTPUT +diff --git a/eigen/Makefile.am b/eigen/Makefile.am +index c28bfde..14197a4 100644 +--- a/eigen/Makefile.am ++++ b/eigen/Makefile.am +@@ -11,7 +11,7 @@ noinst_HEADERS = qrstep.c + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la ++test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la + + test_SOURCES = test.c + +diff --git a/eigen/Makefile.am.porig b/eigen/Makefile.am.porig +new file mode 100644 +index 0000000..c28bfde +--- /dev/null ++++ b/eigen/Makefile.am.porig +@@ -0,0 +1,18 @@ ++noinst_LTLIBRARIES = libgsleigen.la ++ ++check_PROGRAMS = test ++ ++pkginclude_HEADERS = gsl_eigen.h ++libgsleigen_la_SOURCES = jacobi.c symm.c symmv.c nonsymm.c nonsymmv.c herm.c hermv.c gensymm.c gensymmv.c genherm.c genhermv.c gen.c genv.c sort.c francis.c schur.c ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++noinst_HEADERS = qrstep.c ++ ++TESTS = $(check_PROGRAMS) ++ ++test_LDADD = libgsleigen.la ../test/libgsltest.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../sys/libgslsys.la ../err/libgslerr.la ../utils/libutils.la ../rng/libgslrng.la ../sort/libgslsort.la ++ ++test_SOURCES = test.c ++ ++ +diff --git a/gsl-config.in b/gsl-config.in +old mode 100755 +new mode 100644 +index 3f3fa61..c9c4262 +--- a/gsl-config.in ++++ b/gsl-config.in +@@ -58,11 +58,11 @@ while test $# -gt 0; do + ;; + + --cflags) +- echo @GSL_CFLAGS@ ++ echo @GSL_CFLAGS@ @CBLAS_CFLAGS@ + ;; + + --libs) +- : ${GSL_CBLAS_LIB=-lgslcblas} ++ : ${GSL_CBLAS_LIB=@CBLAS_LIBS@} + echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@ + ;; + +diff --git a/gsl-config.in.porig b/gsl-config.in.porig +new file mode 100755 +index 0000000..3f3fa61 +--- /dev/null ++++ b/gsl-config.in.porig +@@ -0,0 +1,80 @@ ++#! /bin/sh ++ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++includedir=@includedir@ ++ ++usage() ++{ ++ cat <<EOF ++Usage: gsl-config [OPTION] ++ ++Known values for OPTION are: ++ ++ --prefix show GSL installation prefix ++ --libs print library linking information, with cblas ++ --libs-without-cblas print library linking information, without cblas ++ --cflags print pre-processor and compiler flags ++ --help display this help and exit ++ --version output version information ++ ++An external CBLAS library can be specified using the GSL_CBLAS_LIB ++environment variable. The GSL CBLAS library is used by default. ++ ++EOF ++ ++ exit $1 ++} ++ ++if test $# -eq 0; then ++ usage 1 ++fi ++ ++cflags=false ++libs=false ++ ++while test $# -gt 0; do ++ case "$1" in ++ -*=*) optarg=`echo "$1" | sed 's/[-_a-zA-Z0-9]*=//'` ;; ++ *) optarg= ;; ++ esac ++ ++ case "$1" in ++ --prefix=*) ++ prefix=$optarg ++ ;; ++ ++ --prefix) ++ echo $prefix ++ ;; ++ ++ --version) ++ echo @VERSION@ ++ exit 0 ++ ;; ++ ++ --help) ++ usage 0 ++ ;; ++ ++ --cflags) ++ echo @GSL_CFLAGS@ ++ ;; ++ ++ --libs) ++ : ${GSL_CBLAS_LIB=-lgslcblas} ++ echo @GSL_LIBS@ $GSL_CBLAS_LIB @GSL_LIBM@ ++ ;; ++ ++ --libs-without-cblas) ++ echo @GSL_LIBS@ @GSL_LIBM@ ++ ;; ++ *) ++ usage ++ exit 1 ++ ;; ++ esac ++ shift ++done ++ ++exit 0 +diff --git a/gsl.pc.in b/gsl.pc.in +index 5e9ef21..5a7a0f3 100644 +--- a/gsl.pc.in ++++ b/gsl.pc.in +@@ -2,7 +2,7 @@ prefix=@prefix@ + exec_prefix=@exec_prefix@ + libdir=@libdir@ + includedir=@includedir@ +-GSL_CBLAS_LIB=-lgslcblas ++GSL_CBLAS_LIB=@CBLAS_LIBS@ + + Name: GSL + Description: GNU Scientific Library +diff --git a/gsl.pc.in.porig b/gsl.pc.in.porig +new file mode 100644 +index 0000000..5e9ef21 +--- /dev/null ++++ b/gsl.pc.in.porig +@@ -0,0 +1,11 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++GSL_CBLAS_LIB=-lgslcblas ++ ++Name: GSL ++Description: GNU Scientific Library ++Version: @VERSION@ ++Libs: @GSL_LIBS@ ${GSL_CBLAS_LIB} @GSL_LIBM@ @LIBS@ ++Cflags: @GSL_CFLAGS@ +diff --git a/interpolation/Makefile.am b/interpolation/Makefile.am +index 1d80755..e45bd51 100644 +--- a/interpolation/Makefile.am ++++ b/interpolation/Makefile.am +@@ -12,7 +12,7 @@ AM_CPPFLAGS = -I$(top_srcdir) + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la @CBLAS_LINK_LIBS@ ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff --git a/interpolation/Makefile.am.porig b/interpolation/Makefile.am.porig +new file mode 100644 +index 0000000..1d80755 +--- /dev/null ++++ b/interpolation/Makefile.am.porig +@@ -0,0 +1,18 @@ ++noinst_LTLIBRARIES = libgslinterpolation.la ++ ++check_PROGRAMS = test ++ ++pkginclude_HEADERS = gsl_interp.h gsl_spline.h gsl_interp2d.h gsl_spline2d.h ++ ++libgslinterpolation_la_SOURCES = accel.c akima.c cspline.c interp.c linear.c integ_eval.h spline.c poly.c steffen.c inline.c interp2d.c bilinear.c bicubic.c spline2d.c ++ ++noinst_HEADERS = test2d.c ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++TESTS = $(check_PROGRAMS) ++ ++test_LDADD = libgslinterpolation.la ../poly/libgslpoly.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../cblas/libgslcblas.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++ ++test_SOURCES = test.c ++ +diff --git a/linalg/Makefile.am b/linalg/Makefile.am +index a6c15b0..447ebbe 100644 +--- a/linalg/Makefile.am ++++ b/linalg/Makefile.am +@@ -13,4 +13,4 @@ TESTS = $(check_PROGRAMS) + check_PROGRAMS = test + + test_SOURCES = test.c +-test_LDADD = libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../rng/libgslrng.la ++test_LDADD = libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../rng/libgslrng.la +diff --git a/linalg/Makefile.am.porig b/linalg/Makefile.am.porig +new file mode 100644 +index 0000000..a6c15b0 +--- /dev/null ++++ b/linalg/Makefile.am.porig +@@ -0,0 +1,16 @@ ++noinst_LTLIBRARIES = libgsllinalg.la ++ ++pkginclude_HEADERS = gsl_linalg.h ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgsllinalg_la_SOURCES = cod.c condest.c invtri.c multiply.c exponential.c tridiag.c tridiag.h lu.c luc.c hh.c qr.c qrpt.c lq.c ptlq.c svd.c householder.c householdercomplex.c hessenberg.c hesstri.c cholesky.c choleskyc.c mcholesky.c pcholesky.c symmtd.c hermtd.c bidiag.c balance.c balancemat.c inline.c ++ ++noinst_HEADERS = apply_givens.c cholesky_common.c svdstep.c tridiag.h test_cholesky.c ++ ++TESTS = $(check_PROGRAMS) ++ ++check_PROGRAMS = test ++ ++test_SOURCES = test.c ++test_LDADD = libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../rng/libgslrng.la +diff --git a/multifit/Makefile.am b/multifit/Makefile.am +index 988614e..793b485 100644 +--- a/multifit/Makefile.am ++++ b/multifit/Makefile.am +@@ -67,8 +67,8 @@ check_PROGRAMS = test #demo + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c +-test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la ../min/libgslmin.la ++test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la ../min/libgslmin.la + + #demo_SOURCES = demo.c +-#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ++#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la + +diff --git a/multifit/Makefile.am.porig b/multifit/Makefile.am.porig +new file mode 100644 +index 0000000..988614e +--- /dev/null ++++ b/multifit/Makefile.am.porig +@@ -0,0 +1,74 @@ ++noinst_LTLIBRARIES = libgslmultifit.la ++ ++pkginclude_HEADERS = gsl_multifit.h gsl_multifit_nlin.h ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgslmultifit_la_SOURCES = gcv.c multilinear.c multiwlinear.c work.c lmniel.c lmder.c fsolver.c fdfsolver.c fdfridge.c fdjac.c convergence.c gradient.c covar.c multirobust.c robust_wfun.c multireg.c ++ ++noinst_HEADERS = \ ++linear_common.c \ ++lmutil.c \ ++lmpar.c \ ++lmset.c \ ++lmiterate.c \ ++lmmisc.c \ ++qrsolv.c \ ++test_bard.c \ ++test_beale.c \ ++test_biggs.c \ ++test_box.c \ ++test_boxbod.c \ ++test_brown1.c \ ++test_brown2.c \ ++test_brown3.c \ ++test_eckerle.c \ ++test_enso.c \ ++test_estimator.c \ ++test_exp1.c \ ++test_filip.c \ ++test_gaussian.c \ ++test_hahn1.c \ ++test_helical.c \ ++test_jennrich.c \ ++test_kirby2.c \ ++test_kowalik.c \ ++test_lin1.c \ ++test_lin2.c \ ++test_lin3.c \ ++test_linear.c \ ++test_longley.c \ ++test_meyer.c \ ++test_meyerscal.c \ ++test_nelson.c \ ++test_nonlinear.c \ ++test_osborne.c \ ++test_penalty1.c \ ++test_penalty2.c \ ++test_pontius.c \ ++test_powell1.c \ ++test_powell2.c \ ++test_powell3.c \ ++test_rat42.c \ ++test_rat43.c \ ++test_reg.c \ ++test_rosenbrock.c \ ++test_rosenbrocke.c \ ++test_roth.c \ ++test_shaw.c \ ++test_thurber.c \ ++test_vardim.c \ ++test_watson.c \ ++test_wnlin.c \ ++test_wood.c ++ ++check_PROGRAMS = test #demo ++ ++TESTS = $(check_PROGRAMS) ++ ++test_SOURCES = test.c ++test_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../sort/libgslsort.la ../statistics/libgslstatistics.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ../rng/libgslrng.la ../specfunc/libgslspecfunc.la ../min/libgslmin.la ++ ++#demo_SOURCES = demo.c ++#demo_LDADD = libgslmultifit.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../randist/libgslrandist.la ../rng/libgslrng.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../utils/libutils.la ../sys/libgslsys.la ++ +diff --git a/multimin/Makefile.am b/multimin/Makefile.am +index 7071359..65a488a 100644 +--- a/multimin/Makefile.am ++++ b/multimin/Makefile.am +@@ -13,8 +13,8 @@ check_PROGRAMS = test #demo + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c test_funcs.c test_funcs.h +-test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + #demo_SOURCES = demo.c +-#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + +diff --git a/multimin/Makefile.am.porig b/multimin/Makefile.am.porig +new file mode 100644 +index 0000000..7071359 +--- /dev/null ++++ b/multimin/Makefile.am.porig +@@ -0,0 +1,20 @@ ++noinst_LTLIBRARIES = libgslmultimin.la ++ ++pkginclude_HEADERS = gsl_multimin.h ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgslmultimin_la_SOURCES = fdfminimizer.c steepest_descent.c conjugate_fr.c conjugate_pr.c convergence.c diff.c vector_bfgs.c vector_bfgs2.c fminimizer.c simplex.c simplex2.c ++ ++noinst_HEADERS = directional_minimize.c linear_minimize.c linear_wrapper.c ++ ++check_PROGRAMS = test #demo ++ ++TESTS = $(check_PROGRAMS) ++ ++test_SOURCES = test.c test_funcs.c test_funcs.h ++test_LDADD = libgslmultimin.la ../min/libgslmin.la ../poly/libgslpoly.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++ ++#demo_SOURCES = demo.c ++#demo_LDADD = libgslmultimin.la ../min/libgslmin.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../linalg/libgsllinalg.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++ +diff --git a/multiroots/Makefile.am b/multiroots/Makefile.am +index a351c3f..6178448 100644 +--- a/multiroots/Makefile.am ++++ b/multiroots/Makefile.am +@@ -15,5 +15,5 @@ check_PROGRAMS = test + TESTS = $(check_PROGRAMS) + + test_SOURCES = test.c test_funcs.c test_funcs.h +-test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + +diff --git a/multiroots/Makefile.am.porig b/multiroots/Makefile.am.porig +new file mode 100644 +index 0000000..a351c3f +--- /dev/null ++++ b/multiroots/Makefile.am.porig +@@ -0,0 +1,19 @@ ++# -*-makefile-*- ++ ++noinst_LTLIBRARIES = libgslmultiroots.la ++ ++pkginclude_HEADERS = gsl_multiroots.h ++ ++noinst_HEADERS = enorm.c dogleg.c ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgslmultiroots_la_SOURCES = fdjac.c fsolver.c fdfsolver.c convergence.c newton.c gnewton.c dnewton.c broyden.c hybrid.c hybridj.c ++ ++check_PROGRAMS = test ++ ++TESTS = $(check_PROGRAMS) ++ ++test_SOURCES = test.c test_funcs.c test_funcs.h ++test_LDADD = libgslmultiroots.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../permutation/libgslpermutation.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++ +diff --git a/ode-initval/Makefile.am b/ode-initval/Makefile.am +index 9c774b5..346c381 100644 +--- a/ode-initval/Makefile.am ++++ b/ode-initval/Makefile.am +@@ -12,7 +12,7 @@ check_PROGRAMS = test + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff --git a/ode-initval/Makefile.am.porig b/ode-initval/Makefile.am.porig +new file mode 100644 +index 0000000..9c774b5 +--- /dev/null ++++ b/ode-initval/Makefile.am.porig +@@ -0,0 +1,18 @@ ++noinst_LTLIBRARIES = libgslodeiv.la ++ ++pkginclude_HEADERS = gsl_odeiv.h ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgslodeiv_la_SOURCES = control.c cstd.c cscal.c evolve.c step.c rk2.c rk2imp.c rk2simp.c rk4.c rk4imp.c rkf45.c rk8pd.c rkck.c bsimp.c gear1.c gear2.c ++ ++noinst_HEADERS = odeiv_util.h ++ ++check_PROGRAMS = test ++ ++TESTS = $(check_PROGRAMS) ++ ++test_LDADD = libgslodeiv.la ../linalg/libgsllinalg.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../permutation/libgslpermutation.la ../vector/libgslvector.la ../block/libgslblock.la ../complex/libgslcomplex.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++ ++test_SOURCES = test.c ++ +diff --git a/poly/Makefile.am b/poly/Makefile.am +index f1dae5d..e0f8e83 100644 +--- a/poly/Makefile.am ++++ b/poly/Makefile.am +@@ -10,7 +10,7 @@ noinst_HEADERS = balance.c companion.c qr.c + + TESTS = $(check_PROGRAMS) + +-check_PROGRAMS = test ++#check_PROGRAMS = test + + test_SOURCES = test.c + test_LDADD = libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../sort/libgslsort.la +diff --git a/poly/Makefile.am.porig b/poly/Makefile.am.porig +new file mode 100644 +index 0000000..f1dae5d +--- /dev/null ++++ b/poly/Makefile.am.porig +@@ -0,0 +1,17 @@ ++noinst_LTLIBRARIES = libgslpoly.la ++ ++pkginclude_HEADERS = gsl_poly.h ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgslpoly_la_SOURCES = dd.c eval.c solve_quadratic.c solve_cubic.c zsolve_quadratic.c zsolve_cubic.c zsolve.c zsolve_init.c deriv.c ++ ++noinst_HEADERS = balance.c companion.c qr.c ++ ++TESTS = $(check_PROGRAMS) ++ ++check_PROGRAMS = test ++ ++test_SOURCES = test.c ++test_LDADD = libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ../sort/libgslsort.la ++ +diff --git a/specfunc/Makefile.am b/specfunc/Makefile.am +index eba9ab2..772cc7e 100644 +--- a/specfunc/Makefile.am ++++ b/specfunc/Makefile.am +@@ -12,7 +12,7 @@ TESTS = $(check_PROGRAMS) + + check_PROGRAMS = test + +-test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../complex/libgslcomplex.la ../poly/libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../block/libgslblock.la ../complex/libgslcomplex.la ../poly/libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test_sf.c test_sf.h test_airy.c test_bessel.c test_coulomb.c test_dilog.c test_gamma.c test_hyperg.c test_legendre.c test_mathieu.c + +diff --git a/specfunc/Makefile.am.porig b/specfunc/Makefile.am.porig +new file mode 100644 +index 0000000..eba9ab2 +--- /dev/null ++++ b/specfunc/Makefile.am.porig +@@ -0,0 +1,19 @@ ++noinst_LTLIBRARIES = libgslspecfunc.la ++ ++pkginclude_HEADERS = gsl_sf.h gsl_sf_airy.h gsl_sf_bessel.h gsl_sf_clausen.h gsl_sf_coulomb.h gsl_sf_coupling.h gsl_sf_dawson.h gsl_sf_debye.h gsl_sf_dilog.h gsl_sf_elementary.h gsl_sf_ellint.h gsl_sf_elljac.h gsl_sf_erf.h gsl_sf_exp.h gsl_sf_expint.h gsl_sf_fermi_dirac.h gsl_sf_gamma.h gsl_sf_gegenbauer.h gsl_sf_hyperg.h gsl_sf_laguerre.h gsl_sf_lambert.h gsl_sf_legendre.h gsl_sf_log.h gsl_sf_mathieu.h gsl_sf_pow_int.h gsl_sf_psi.h gsl_sf_result.h gsl_sf_synchrotron.h gsl_sf_transport.h gsl_sf_trig.h gsl_sf_zeta.h gsl_specfunc.h ++ ++noinst_HEADERS = bessel_amp_phase.h bessel_olver.h bessel_temme.h bessel.h hyperg.h legendre.h eval.h chebyshev.h cheb_eval.c cheb_eval_mode.c check.h error.h legendre_source.c ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgslspecfunc_la_SOURCES = airy.c airy_der.c airy_zero.c atanint.c bessel.c bessel.h bessel_I0.c bessel_I1.c bessel_In.c bessel_Inu.c bessel_J0.c bessel_J1.c bessel_Jn.c bessel_Jnu.c bessel_K0.c bessel_K1.c bessel_Kn.c bessel_Knu.c bessel_Y0.c bessel_Y1.c bessel_Yn.c bessel_Ynu.c bessel_amp_phase.c bessel_amp_phase.h bessel_i.c bessel_j.c bessel_k.c bessel_olver.c bessel_temme.c bessel_y.c bessel_zero.c bessel_sequence.c beta.c beta_inc.c clausen.c coulomb.c coupling.c coulomb_bound.c dawson.c debye.c dilog.c elementary.c ellint.c elljac.c erfc.c exp.c expint.c expint3.c fermi_dirac.c gegenbauer.c gamma.c gamma_inc.c hyperg_0F1.c hyperg_2F0.c hyperg_1F1.c hyperg_2F1.c hyperg_U.c hyperg.c laguerre.c lambert.c legendre_H3d.c legendre_P.c legendre_Qn.c legendre_con.c legendre_poly.c log.c mathieu_angfunc.c mathieu_charv.c mathieu_coeff.c mathieu_radfunc.c mathieu_workspace.c poch.c pow_int.c psi.c recurse.h result.c shint.c sinint.c synchrotron.c transport.c trig.c zeta.c ++ ++TESTS = $(check_PROGRAMS) ++ ++check_PROGRAMS = test ++ ++test_LDADD = libgslspecfunc.la ../eigen/libgsleigen.la ../linalg/libgsllinalg.la ../sort/libgslsort.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../block/libgslblock.la ../complex/libgslcomplex.la ../poly/libgslpoly.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++ ++test_SOURCES = test_sf.c test_sf.h test_airy.c test_bessel.c test_coulomb.c test_dilog.c test_gamma.c test_hyperg.c test_legendre.c test_mathieu.c ++ ++ +diff --git a/wavelet/Makefile.am b/wavelet/Makefile.am +index 9da20d8..8cdbd77 100644 +--- a/wavelet/Makefile.am ++++ b/wavelet/Makefile.am +@@ -10,7 +10,7 @@ check_PROGRAMS = test + + TESTS = $(check_PROGRAMS) + +-test_LDADD = libgslwavelet.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++test_LDADD = libgslwavelet.la ../blas/libgslblas.la @CBLAS_LINK_LIBS@ ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la + + test_SOURCES = test.c + +diff --git a/wavelet/Makefile.am.porig b/wavelet/Makefile.am.porig +new file mode 100644 +index 0000000..9da20d8 +--- /dev/null ++++ b/wavelet/Makefile.am.porig +@@ -0,0 +1,17 @@ ++noinst_LTLIBRARIES = libgslwavelet.la ++ ++pkginclude_HEADERS = gsl_wavelet.h gsl_wavelet2d.h ++ ++AM_CPPFLAGS = -I$(top_srcdir) ++ ++libgslwavelet_la_SOURCES = dwt.c wavelet.c bspline.c daubechies.c haar.c ++ ++check_PROGRAMS = test ++ ++TESTS = $(check_PROGRAMS) ++ ++test_LDADD = libgslwavelet.la ../blas/libgslblas.la ../cblas/libgslcblas.la ../matrix/libgslmatrix.la ../vector/libgslvector.la ../block/libgslblock.la ../ieee-utils/libgslieeeutils.la ../err/libgslerr.la ../test/libgsltest.la ../sys/libgslsys.la ../utils/libutils.la ++ ++test_SOURCES = test.c ++ ++ diff --git a/sci-libs/gsl/gsl-1.16.ebuild b/sci-libs/gsl/gsl-1.16.ebuild new file mode 100644 index 000000000000..a26b3b72f776 --- /dev/null +++ b/sci-libs/gsl/gsl-1.16.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic autotools toolchain-funcs + +DESCRIPTION="The GNU Scientific Library" +HOMEPAGE="https://www.gnu.org/software/gsl/" +SRC_URI="mirror://gnu/${PN}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="alpha amd64 arm hppa ia64 ~mips ppc ppc64 ~s390 ~sh sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos ~sparc-solaris ~x86-solaris" +IUSE="cblas-external static-libs" + +RDEPEND="cblas-external? ( virtual/cblas )" +DEPEND="${RDEPEND} + app-eselect/eselect-cblas + virtual/pkgconfig" + +DOCS=( AUTHORS BUGS ChangeLog NEWS README THANKS TODO ) + +pkg_pretend() { + # prevent to use external cblas from a previously installed gsl + local current_lib + if use cblas-external; then + current_lib=$(eselect cblas show | cut -d' ' -f2) + if [[ ${current_lib} == gsl ]]; then + ewarn "USE flag cblas-external is set: linking gsl with an external cblas." + ewarn "However the current selected external cblas is gsl." + ewarn "Please install and/or eselect another cblas" + die "Circular gsl dependency" + fi + fi +} + +src_prepare() { + ESELECT_PROF="gsl" + + # bug 349005 + [[ $(tc-getCC)$ == *gcc* ]] && \ + [[ $(tc-getCC)$ != *apple* ]] && \ + [[ $(gcc-major-version)$(gcc-minor-version) -eq 44 ]] \ + && filter-mfpmath sse + filter-flags -ffast-math + + epatch "${FILESDIR}"/${P}-cblas.patch + eautoreconf + + cp "${FILESDIR}"/eselect.cblas.gsl "${T}"/ || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.cblas.gsl || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.cblas.gsl || die + fi +} + +src_configure() { + if use cblas-external; then + export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)" + export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)" + fi + econf \ + --enable-shared \ + $(use_with cblas-external) \ + $(use_enable static-libs static) +} + +src_test() { + emake -j1 check +} + +src_install() { + default + + find "${ED}" -name '*.la' -exec rm -f {} + || die + + # take care of pkgconfig file for cblas implementation. + sed -e "s/@LIBDIR@/$(get_libdir)/" \ + -e "s/@PV@/${PV}/" \ + -e "/^prefix=/s:=:=${EPREFIX}:" \ + -e "/^libdir=/s:=:=${EPREFIX}:" \ + "${FILESDIR}"/cblas.pc.in > cblas.pc \ + || die "sed cblas.pc failed" + insinto /usr/$(get_libdir)/blas/gsl + doins cblas.pc + eselect cblas add $(get_libdir) "${T}"/eselect.cblas.gsl \ + ${ESELECT_PROF} +} + +pkg_postinst() { + local p=cblas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/gsl/gsl-2.1.ebuild b/sci-libs/gsl/gsl-2.1.ebuild new file mode 100644 index 000000000000..b380fcc5bb81 --- /dev/null +++ b/sci-libs/gsl/gsl-2.1.ebuild @@ -0,0 +1,108 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils flag-o-matic toolchain-funcs + +DESCRIPTION="The GNU Scientific Library" +HOMEPAGE="https://www.gnu.org/software/gsl/" +SRC_URI="mirror://gnu/${PN}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0/19" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos ~sparc-solaris ~x86-solaris" +IUSE="cblas-external static-libs" + +RDEPEND="cblas-external? ( virtual/cblas )" +DEPEND="${RDEPEND} + app-eselect/eselect-cblas + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${P}-cblas.patch ) + +pkg_pretend() { + # prevent to use external cblas from a previously installed gsl + local current_lib + if use cblas-external; then + current_lib=$(eselect cblas show | cut -d' ' -f2) + if [[ ${current_lib} == gsl ]]; then + ewarn "USE flag cblas-external is set: linking gsl with an external cblas." + ewarn "However the current selected external cblas is gsl." + ewarn "Please install and/or eselect another cblas" + die "Circular gsl dependency" + fi + fi +} + +src_prepare() { + ESELECT_PROF="gsl" + + # bug 349005 + [[ $(tc-getCC)$ == *gcc* ]] && \ + [[ $(tc-getCC)$ != *apple* ]] && \ + [[ $(gcc-major-version)$(gcc-minor-version) -eq 44 ]] \ + && filter-mfpmath sse + filter-flags -ffast-math + + default + eautoreconf + + cp "${FILESDIR}"/eselect.cblas.gsl "${T}"/ + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.cblas.gsl || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.cblas.gsl || die + fi +} + +src_configure() { + if use cblas-external; then + export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)" + export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)" + fi + econf \ + --enable-shared \ + $(use_with cblas-external) \ + $(use_enable static-libs static) +} + +src_test() { + local MAKEOPTS="${MAKEOPTS} -j1" + default +} + +src_install() { + default + + find "${ED}" -name '*.la' -exec rm -f {} + + + # take care of pkgconfig file for cblas implementation. + sed \ + -e "s/@LIBDIR@/$(get_libdir)/" \ + -e "s/@PV@/${PV}/" \ + -e "/^prefix=/s:=:=${EPREFIX}:" \ + -e "/^libdir=/s:=:=${EPREFIX}:" \ + "${FILESDIR}"/cblas.pc.in > cblas.pc \ + || die "sed cblas.pc failed" + insinto /usr/$(get_libdir)/blas/gsl + doins cblas.pc + eselect cblas add $(get_libdir) "${T}"/eselect.cblas.gsl \ + ${ESELECT_PROF} +} + +pkg_postinst() { + local p=cblas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/gsl/gsl-2.3.ebuild b/sci-libs/gsl/gsl-2.3.ebuild new file mode 100644 index 000000000000..9e70befa7198 --- /dev/null +++ b/sci-libs/gsl/gsl-2.3.ebuild @@ -0,0 +1,111 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils flag-o-matic toolchain-funcs + +DESCRIPTION="The GNU Scientific Library" +HOMEPAGE="https://www.gnu.org/software/gsl/" +SRC_URI="mirror://gnu/${PN}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0/19.3" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos ~sparc-solaris ~x86-solaris" +IUSE="cblas-external +deprecated static-libs" + +RDEPEND="cblas-external? ( virtual/cblas )" +DEPEND="${RDEPEND} + app-eselect/eselect-cblas + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${P}-cblas.patch ) + +pkg_pretend() { + # prevent to use external cblas from a previously installed gsl + local current_lib + if use cblas-external; then + current_lib=$(eselect cblas show | cut -d' ' -f2) + if [[ ${current_lib} == gsl ]]; then + ewarn "USE flag cblas-external is set: linking gsl with an external cblas." + ewarn "However the current selected external cblas is gsl." + ewarn "Please install and/or eselect another cblas" + die "Circular gsl dependency" + fi + fi +} + +src_prepare() { + ESELECT_PROF="gsl" + + # bug 349005 + [[ $(tc-getCC)$ == *gcc* ]] && \ + [[ $(tc-getCC)$ != *apple* ]] && \ + [[ $(gcc-major-version)$(gcc-minor-version) -eq 44 ]] \ + && filter-mfpmath sse + filter-flags -ffast-math + + default + if use deprecated; then + sed -i -e "/GSL_DISABLE_DEPRECATED/,+2d" configure.ac || die + fi + eautoreconf + + cp "${FILESDIR}"/eselect.cblas.gsl "${T}"/ || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.cblas.gsl || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.cblas.gsl || die + fi +} + +src_configure() { + if use cblas-external; then + export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)" + export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)" + fi + econf \ + --enable-shared \ + $(use_with cblas-external) \ + $(use_enable static-libs static) +} + +src_test() { + local MAKEOPTS="${MAKEOPTS} -j1" + default +} + +src_install() { + default + + find "${ED}" -name '*.la' -exec rm -f {} + + + # take care of pkgconfig file for cblas implementation. + sed \ + -e "s/@LIBDIR@/$(get_libdir)/" \ + -e "s/@PV@/${PV}/" \ + -e "/^prefix=/s:=:=${EPREFIX}:" \ + -e "/^libdir=/s:=:=${EPREFIX}:" \ + "${FILESDIR}"/cblas.pc.in > cblas.pc \ + || die "sed cblas.pc failed" + insinto /usr/$(get_libdir)/blas/gsl + doins cblas.pc + eselect cblas add $(get_libdir) "${T}"/eselect.cblas.gsl \ + ${ESELECT_PROF} +} + +pkg_postinst() { + local p=cblas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/gsl/gsl-2.4.ebuild b/sci-libs/gsl/gsl-2.4.ebuild new file mode 100644 index 000000000000..659ed95f7978 --- /dev/null +++ b/sci-libs/gsl/gsl-2.4.ebuild @@ -0,0 +1,111 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils flag-o-matic toolchain-funcs + +DESCRIPTION="The GNU Scientific Library" +HOMEPAGE="https://www.gnu.org/software/gsl/" +SRC_URI="mirror://gnu/${PN}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0/23" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos ~sparc-solaris ~x86-solaris" +IUSE="cblas-external +deprecated static-libs" + +RDEPEND="cblas-external? ( virtual/cblas:= )" +DEPEND="${RDEPEND} + app-eselect/eselect-cblas + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${PN}-2.3-cblas.patch ) + +pkg_pretend() { + # prevent to use external cblas from a previously installed gsl + local current_lib + if use cblas-external; then + current_lib=$(eselect cblas show | cut -d' ' -f2) + if [[ ${current_lib} == gsl ]]; then + ewarn "USE flag cblas-external is set: linking gsl with an external cblas." + ewarn "However the current selected external cblas is gsl." + ewarn "Please install and/or eselect another cblas" + die "Circular gsl dependency" + fi + fi +} + +src_prepare() { + ESELECT_PROF="gsl" + + # bug 349005 + [[ $(tc-getCC)$ == *gcc* ]] && \ + [[ $(tc-getCC)$ != *apple* ]] && \ + [[ $(gcc-major-version)$(gcc-minor-version) -eq 44 ]] \ + && filter-mfpmath sse + filter-flags -ffast-math + + default + if use deprecated; then + sed -i -e "/GSL_DISABLE_DEPRECATED/,+2d" configure.ac || die + fi + eautoreconf + + cp "${FILESDIR}"/eselect.cblas.gsl "${T}"/ || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.cblas.gsl || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.cblas.gsl || die + fi +} + +src_configure() { + if use cblas-external; then + export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)" + export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)" + fi + econf \ + --enable-shared \ + $(use_with cblas-external) \ + $(use_enable static-libs static) +} + +src_test() { + local MAKEOPTS="${MAKEOPTS} -j1" + default +} + +src_install() { + default + + find "${ED}" -name '*.la' -exec rm -f {} + + + # take care of pkgconfig file for cblas implementation. + sed \ + -e "s/@LIBDIR@/$(get_libdir)/" \ + -e "s/@PV@/${PV}/" \ + -e "/^prefix=/s:=:=${EPREFIX}:" \ + -e "/^libdir=/s:=:=${EPREFIX}:" \ + "${FILESDIR}"/cblas.pc.in > cblas.pc \ + || die "sed cblas.pc failed" + insinto /usr/$(get_libdir)/blas/gsl + doins cblas.pc + eselect cblas add $(get_libdir) "${T}"/eselect.cblas.gsl \ + ${ESELECT_PROF} +} + +pkg_postinst() { + local p=cblas + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/gsl/metadata.xml b/sci-libs/gsl/metadata.xml new file mode 100644 index 000000000000..4a8296b2f944 --- /dev/null +++ b/sci-libs/gsl/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The GNU Scientific Library (GSL) is a collection of routines for + numerical analysis. The routines are written from scratch by the GSL + team in C, and present a modern API for C programmers, while allowing + wrappers to be written for very high level languages. + + GSL includes data types and routines for complex numbers, vectors, + matrices, basic linear algebra subroutines (BLAS), eigensystems, + simulated annealing, minimization, root finding, pseudo-random + numbers, least-squares fitting, fast Fourier transforms (FFT), + differential equations, quadrature, Monte Carlo integration, special + functions, physical constants, and much more. +</longdescription> + <use> + <flag name="cblas-external">Link gsl with external cblas provided by + (<pkg>virtual/cblas</pkg>) instead of shipped internal version</flag> + <flag name="deprecated">Enable deprecated functions</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/gts/Manifest b/sci-libs/gts/Manifest new file mode 100644 index 000000000000..2c6d3887126c --- /dev/null +++ b/sci-libs/gts/Manifest @@ -0,0 +1,6 @@ +AUX gts-20111025-autotools.patch 1475 SHA256 32409693d6ae034666f7f5392b42b06edb117b80be3b458b8958f1101f11c5df SHA512 1be24faff8e81020b1f349360e4654307d3ac2306f2c8ad5d5534946f1c29db862b337732a41d941b5e67a1f0b0dae61d945b52295e7cddbed640d7653a01dd9 WHIRLPOOL d0f751757581c0e2a361d13baa1945773689d64f9d65cfc47c12c9058598d5400f635415f3c5dce4bc1418c63f37d92c76ed31d068cf162c26373efce96bc82f +DIST gts-snapshot-121130.tar.gz 880569 SHA256 c23f72ab74bbf65599f8c0b599d6336fabe1ec2a09c19b70544eeefdc069b73b SHA512 84c38dc345830eea75755d9d55235b6d76786a84c3b9c3b7e057437bf395a9f2687596bbf037afd601b9f31a485d425a371ca5e60680265f10cb414400db4142 WHIRLPOOL 0f0a105877e46b0af4da59d7728d73c7cd03378302fccfdf8ba2336618b8599123793c83f98658a1a88e0a1106679cded61f547e36ef34f8b404685f1dcd964f +EBUILD gts-20121130.ebuild 1058 SHA256 8ab15f372cf641712aac348ddda786945d095351bf535aefe9ba7ed5bf8dcf39 SHA512 c30785c54e3e66a8eed189f9e10cadbf750c3a289a4cf98392b803088a7da18face0367d2ef8a087846a01e3c25f03460120c05bbfc053b5aa701a0c0ba9e52d WHIRLPOOL ee025397e40dbad16b8f1419c33e42521ce038ea7cf274a86394a34f8f5b679e9ddf7fd10019b6eada5b8a7487470e77130a979a7bd19d53beb671309fc342c1 +MISC ChangeLog 4128 SHA256 5d225b3c77b5be12935507377b1130d9928b8c4168b3d6637cea6f8492b3cbff SHA512 7e7652d923d602cce25bbb03d6a675dc00c50e71ea4572bb24a91e837a77f71d78ff80620ff085d3304827d22e2b34e5fc0553e40b9866b80895eae374c1872d WHIRLPOOL 21af2c42e45fe94b2a70839ab62db6d5904d0a20c59d2b94ad803623704788b0bb618bf5f8434557aad09f41a6fdc1082b35ed4996cfdcc3ae0e087b02a1385b +MISC ChangeLog-2015 5637 SHA256 f65d267b441488974519865df3191c97873490f79ae4986f8ce3a03ec5a2b106 SHA512 877068dcece0b951e4472a61b4874f8e976d0ca9713619fd0df285927e40b1b490994ec1c5e5f512425255714393b584c2d33f03b5f338157fdb531531044641 WHIRLPOOL 694a27b1eee961719ed883cb66db7f514a8d92069862af9af5f546b46a427ec2cd89e34ee2897cb7d224716760a2a61dc555a6fd74505162c39edeef37094573 +MISC metadata.xml 510 SHA256 21486a95aa5485eda8240f03c6686b5ef0859fad9680052537ebe82673d5fdac SHA512 12fd9a10b7f46ab73d79c79f4ae31f4f174acddd4a5603a20ae49b0c2d39385b23e70b58389281dbff24a567c2162ea513d505c90c28dbac066b873be60aeea3 WHIRLPOOL c7d88ead146a298835b5aa8eb71f11f39b66d410666188cd5064fdd8a6fa65da6b19596cd4a52c294b7e56e951ca2180d189463e85c5883d067341e3cddb32bb diff --git a/sci-libs/gts/files/gts-20111025-autotools.patch b/sci-libs/gts/files/gts-20111025-autotools.patch new file mode 100644 index 000000000000..7ab3805e2477 --- /dev/null +++ b/sci-libs/gts/files/gts-20111025-autotools.patch @@ -0,0 +1,56 @@ +--- doc/Makefile.am.orig ++++ doc/Makefile.am +@@ -9,7 +9,7 @@ DOC_MODULE=gts + DOC_MAIN_SGML_FILE=gts-docs.sgml + + # The directory containing the source code (if it contains documentation). +-DOC_SOURCE_DIR=../src ++DOC_SOURCE_DIR=$(top_srcdir)/src + + TARGET_DIR=html/$(DOC_MODULE) + +@@ -21,10 +21,10 @@ scan: + templates: scan + gtkdoc-mktmpl --module=$(DOC_MODULE) + +-sgml: ++sgml: scan + gtkdoc-mkdb --module=$(DOC_MODULE) --source-dir=$(DOC_SOURCE_DIR) + +-html: ++html: sgml + if ! test -d html ; then mkdir html ; fi + -cd html && gtkdoc-mkhtml $(DOC_MODULE) ../$(DOC_MAIN_SGML_FILE) + +--- src/Makefile.am.orig ++++ src/Makefile.am +@@ -66,10 +66,10 @@ predicates.o: predicates.c predicates_init.h predicates.h + $(COMPILE) -c $(srcdir)/predicates.c + + predicates_init: predicates_init.c rounding.h +- $(COMPILE) $(srcdir)/predicates_init.c -o $(srcdir)/predicates_init ++ $(COMPILE) $(srcdir)/predicates_init.c -o $(top_builddir)/src/predicates_init + + predicates_init.h: predicates_init +- ./predicates_init > $(srcdir)/predicates_init.h ++ $(top_builddir)/src/predicates_init > $(srcdir)/predicates_init.h + + CLEANFILES = $(BUILT_SOURCES) + +--- examples/Makefile.am.orig 2012-01-20 19:44:46.000000000 +0000 ++++ examples/Makefile.am 2012-01-20 19:45:04.000000000 +0000 +@@ -13,12 +13,10 @@ + NETPBM_EXTRA = happrox + endif + +-bin_PROGRAMS = \ ++check_PROGRAMS = \ + transform \ + delaunay \ +- $(NETPBM_EXTRA) +- +-noinst_PROGRAMS = \ ++ $(NETPBM_EXTRA) \ + set \ + volume \ + cleanup \ diff --git a/sci-libs/gts/gts-20121130.ebuild b/sci-libs/gts/gts-20121130.ebuild new file mode 100644 index 000000000000..33c9796abf2f --- /dev/null +++ b/sci-libs/gts/gts-20121130.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 + +inherit autotools-utils + +MYP=${P/-20/-snapshot-} + +DESCRIPTION="GNU Triangulated Surface Library" +HOMEPAGE="http://gts.sourceforge.net/" +SRC_URI="http://gts.sourceforge.net/tarballs/${MYP}.tar.gz" + +SLOT="0" +LICENSE="LGPL-2" +KEYWORDS="amd64 ~arm64 hppa ppc ppc64 x86 ~amd64-fbsd ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND="dev-libs/glib:2" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( dev-util/gtk-doc ) + test? ( media-libs/netpbm )" + +# buggy +RESTRICT=test + +S="${WORKDIR}/${MYP}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( "${FILESDIR}"/${PN}-20111025-autotools.patch ) + +src_compile() { + autotools-utils_src_compile + use doc && autotools-utils_src_compile -C doc html + chmod +x test/*/*.sh || die +} + +src_install() { + use doc && HTML_DOCS=("${AUTOTOOLS_BUILD_DIR}"/doc/html/) + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins examples/*.c + fi +} diff --git a/sci-libs/gts/metadata.xml b/sci-libs/gts/metadata.xml new file mode 100644 index 000000000000..9980dad1bf17 --- /dev/null +++ b/sci-libs/gts/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Gerris Flow Solver is a software program for the solution of the partial + differential equations describing fluid flow. + </longdescription> + <upstream> + <remote-id type="sourceforge">gts</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/h5hut/Manifest b/sci-libs/h5hut/Manifest new file mode 100644 index 000000000000..ad6e68ddde9c --- /dev/null +++ b/sci-libs/h5hut/Manifest @@ -0,0 +1,5 @@ +AUX h5hut-1.99.13-autotools.patch 2809 SHA256 4a77a7382f240ce79d05ca923c36d58501e70d359bd9c095c46032f02dc3c9eb SHA512 05200ef8073c1c39e322015e9d4b9764c470336f704c8f86e056d1936de669f256c64baf94307d84f4574d1204f914abffa9b134942e354f474c51dc0b78c05c WHIRLPOOL 84766b04f9941e03b680effb63b8ac2fe677d1bdd181b8e2078f8cea4fc0413fe6813f1f7984bfeb50f5ae452843f17be156f92aa020890006e0a6eac070d0c0 +AUX h5hut-1.99.13-mpio.patch 574 SHA256 90b5df7a473edbfa18df17bbbb1c3a75d0c857a2402db037f431bfcef61eccd2 SHA512 9335f2d84c4353123e1c1af5f82a729322cacd6f0bfa95ccbe042b76693f035c5b2860d788d31063299e3705addd6160b4b985be88beba341bee56a397387919 WHIRLPOOL de497c64b08f123488cabb8ec1e377f8084f48b2e33838610688b80a2cacf60241e73dca20df31c26a75caed3b906ab1593bc86fba9b96ceea3406b09002b947 +DIST H5hut-1.99.13.tar.gz 3029357 SHA256 3dc76e00a0cbce718dfde3a59955fa6b69148bfbaac3a500d4a6799db24880c5 SHA512 c2590795c45ecf5e642308f5b36c4e573fdcbb6e985f5867c13fd9e1f0ddd9b48fbc423ad0165b8f047256e42a1eb54d508c9322a593bcfad3a2769547d2887a WHIRLPOOL a4d2f0aa8715010968605e260319a5502bbbaa1df9770100292065af5c2283108a7a3ff397c65595e6b68b1111f8f40715964d6efd1f7f5646734cfa22aeb8d6 +EBUILD h5hut-1.99.13.ebuild 726 SHA256 c5283665724e9d27d3935ab0b943a554cfccad15f9b87289e7878850c736acf5 SHA512 1c89b5d2554f5aa1e0365d1591fcf76632fd965a0db6ca580b1be26f23761f617530fb01d554bcdf27c259858bc02e9cd263a189bf5beebec9b678bc42fa255b WHIRLPOOL e1ceb7d59d47085837af6bf973753222028d072171e675684bd4a3ae7f23ea0602e70976736ea54ea192c3e9c7ddc9b4abe655e1b22ae2309610723c0ec78c55 +MISC metadata.xml 367 SHA256 ac8d9fb591cb385322c5b19e610391ed7c6df9554f4901b3789e0b0410533d37 SHA512 455c79e8837ba1ed980967e3236d4a0ac0edbd1b88b056a06d715894e03e7fc802079440752e60a06c9ce4acb62fd68d4020a7847a154a14065afd995257f685 WHIRLPOOL 7b8aae6b6e9c08408300de466754b331e1ec556f8dc4fcc11c22069e913d2d600c2b7dc2d9a5ee5de84c472540cc78aeac1b4a3b0abbc92a539cdbbb6ca30c37 diff --git a/sci-libs/h5hut/files/h5hut-1.99.13-autotools.patch b/sci-libs/h5hut/files/h5hut-1.99.13-autotools.patch new file mode 100644 index 000000000000..262aa61461a3 --- /dev/null +++ b/sci-libs/h5hut/files/h5hut-1.99.13-autotools.patch @@ -0,0 +1,77 @@ +diff -Naur H5hut-1.99.13.orig/src/Fortran/Makefile.am H5hut-1.99.13/src/Fortran/Makefile.am +--- H5hut-1.99.13.orig/src/Fortran/Makefile.am 2017-07-02 16:46:44.899690038 -0600 ++++ H5hut-1.99.13/src/Fortran/Makefile.am 2017-07-02 16:53:46.414587073 -0600 +@@ -49,9 +49,6 @@ + awk '/INTEGER\*8 :: /{print "\t" $$0}' $^ >$@ + awk '/PARAMETER /{print "\t" $$0}' $^ >> $@ + awk '/INTEGER\*8 FUNCTION/{print "\t" $$1 " " $$3}' $^ >>$@ +- +-all-local: $(top_srcdir)/src/include/H5hutF.h +- $(INSTALL) -m644 .libs/libH5hutF.a $(top_srcdir)/src/lib + endif + + clean: clean-am +diff -Naur H5hut-1.99.13.orig/src/h5core/Makefile.am H5hut-1.99.13/src/h5core/Makefile.am +--- H5hut-1.99.13.orig/src/h5core/Makefile.am 2017-07-02 16:46:44.899690038 -0600 ++++ H5hut-1.99.13/src/h5core/Makefile.am 2017-07-02 16:58:03.017839542 -0600 +@@ -89,15 +89,10 @@ + + libH5hut_la_LDFLAGS = -version-info 2:0:0 + +-all-local: +- $(INSTALL) -m0755 -d $(top_builddir)/src/lib +- $(INSTALL) -m644 .libs/libH5hut.a $(top_builddir)/src/lib +- + install-exec-local: + @$(INSTALL) -d $(DESTDIR)$(includedir)/h5core + @$(INSTALL) -m644 $(top_srcdir)/src/include/h5core/*.h $(DESTDIR)$(includedir)/h5core/ + + clean-local: +- $(RM) -f $(top_srcdir)/src/lib/libH5hut.* + $(RM) -f *~ + +diff -Naur H5hut-1.99.13.orig/test/Makefile.am H5hut-1.99.13/test/Makefile.am +--- H5hut-1.99.13.orig/test/Makefile.am 2017-07-02 16:46:44.919690283 -0600 ++++ H5hut-1.99.13/test/Makefile.am 2017-07-02 16:58:01.297818301 -0600 +@@ -1,10 +1,9 @@ + # test level Makefile.am + + AM_CPPFLAGS += -I$(top_srcdir)/src/include +-AM_LDFLAGS += -L${abs_top_builddir}/src/lib + + LDADD = +-LDADD += -lH5hut ++LDADD += ../src/h5core/libH5hut.la + + noinst_PROGRAMS = + +diff -Naur H5hut-1.99.13.orig/tools/Makefile.am H5hut-1.99.13/tools/Makefile.am +--- H5hut-1.99.13.orig/tools/Makefile.am 2017-07-02 16:46:44.919690283 -0600 ++++ H5hut-1.99.13/tools/Makefile.am 2017-07-02 16:59:30.228916458 -0600 +@@ -8,10 +8,9 @@ + + AM_CPPFLAGS += -I${abs_top_builddir}/src/include -Wno-deprecated + FFLAGS += -cpp $(AM_CPPFLAGS) +-AM_LDFLAGS += -L${abs_top_builddir}/src/lib + + LDADD = +-LDADD += -lH5hut ++LDADD += ../src/h5core/libH5hut.la + + if ENABLE_C + EXTRA_SCRIPTS = # h5hutcc +diff -Naur H5hut-1.99.13.orig/tools/vtk2h5grid/Makefile.am H5hut-1.99.13/tools/vtk2h5grid/Makefile.am +--- H5hut-1.99.13.orig/tools/vtk2h5grid/Makefile.am 2017-07-02 16:46:44.919690283 -0600 ++++ H5hut-1.99.13/tools/vtk2h5grid/Makefile.am 2017-07-02 16:58:58.978530564 -0600 +@@ -1,10 +1,9 @@ + AM_CPPFLAGS = -I${abs_top_srcdir}/src/include -Wno-deprecated + FFLAGS += -cpp $(AM_CPPFLAGS) +-LDFLAGS += -L${abs_top_builddir}/src/lib + + LDADD = + +-LDADD += -lH5hut -lvtkIO -lvtkFiltering -lvtkCommon -lvtksys -lpthread -ldl ++LDADD += ../src/h5core/libH5hut.la -lvtkIO -lvtkFiltering -lvtkCommon -lvtksys -lpthread -ldl + + + bin_PROGRAMS = diff --git a/sci-libs/h5hut/files/h5hut-1.99.13-mpio.patch b/sci-libs/h5hut/files/h5hut-1.99.13-mpio.patch new file mode 100644 index 000000000000..a94c8e59000f --- /dev/null +++ b/sci-libs/h5hut/files/h5hut-1.99.13-mpio.patch @@ -0,0 +1,12 @@ +diff -Naur H5hut-1.99.13.orig/src/h5core/h5_hdf5_private.h H5hut-1.99.13/src/h5core/h5_hdf5_private.h +--- H5hut-1.99.13.orig/src/h5core/h5_hdf5_private.h 2017-07-02 16:46:44.899690038 -0600 ++++ H5hut-1.99.13/src/h5core/h5_hdf5_private.h 2017-07-02 16:47:16.550080867 -0600 +@@ -934,7 +934,7 @@ + HDF5_WRAPPER_ENTER (h5_err_t, + "fapl_id=%d, comm=..., use_gpfs=%d", + fapl_id, (int)use_gpfs); +- if ( H5Pset_fapl_mpiposix (fapl_id, comm, use_gpfs) < 0) ++ if ( H5Pset_fapl_mpio (fapl_id, comm, use_gpfs) < 0) + HDF5_WRAPPER_LEAVE ( + h5_error ( + H5_ERR_HDF5, diff --git a/sci-libs/h5hut/h5hut-1.99.13.ebuild b/sci-libs/h5hut/h5hut-1.99.13.ebuild new file mode 100644 index 000000000000..5eca8e34f1dc --- /dev/null +++ b/sci-libs/h5hut/h5hut-1.99.13.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +MY_P="${P^h}" +DESCRIPTION="High-Performance I/O Library for Particle-based Simulations" +HOMEPAGE="http://www-vis.lbl.gov/Research/H5hut/" +SRC_URI="https://amas.psi.ch/H5hut/raw-attachment/wiki/DownloadSources/${MY_P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + virtual/mpi + sci-libs/hdf5[mpi] + " +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-mpio.patch" + "${FILESDIR}/${P}-autotools.patch" + ) + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf --enable-parallel --enable-shared --disable-static CC=mpicc CXX=mpicxx +} diff --git a/sci-libs/h5hut/metadata.xml b/sci-libs/h5hut/metadata.xml new file mode 100644 index 000000000000..903883b48f16 --- /dev/null +++ b/sci-libs/h5hut/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/h5part/Manifest b/sci-libs/h5part/Manifest new file mode 100644 index 000000000000..f37ddb76381c --- /dev/null +++ b/sci-libs/h5part/Manifest @@ -0,0 +1,5 @@ +AUX h5part-1.6.6-mpio.patch 948 SHA256 3b76db69fb4ebd8a8c1dd73b4bf1fd65198825ceda256defe697fc45f94808b8 SHA512 41ae0a9b9f2ae84b29133879136b392cf58c68ab75195179c7b95600bc693b3f6d2ab74533285a3727590f5aac61db2d9f4c9c732720fba15164fea8f29e7a34 WHIRLPOOL 53c774ab057ceb516658df3c956637e325e00bdc19f46298e30d5832e0b29fb40403dcefc9e8749ad7c6422f17393eb2106bcbb078d61bce0ac5e5bf5f0c6435 +DIST H5Part-1.6.6.tar.gz 441755 SHA256 10347e7535d1afbb08d51be5feb0ae008f73caf889df08e3f7dde717a99c7571 SHA512 0842017bfe1510746e6f9451daaaaff3d9f6eee5209e241bcc8f2d0ce96450b8929f718c41a3434f53c9457adc2547628ad57ac8a0fb1cbfb7c74862aebf996d WHIRLPOOL 0b2cf42ecc50ca157a7a9a4faf781786a765d04b188f4d23b5a388815e6f40de743e28458c24656f48a477fcaf297a62b5132a0aa226ea364974306b0ab6064e +EBUILD h5part-1.6.6.ebuild 622 SHA256 59424d0367e72fa41f627ad4b85079d4fd4225cf8196201f4fb6e608fde5b89d SHA512 fc7dc6445857d9bec9453e0be6e16f0581cb82edc1946a6b798d7a58f8743c7c827687d848bf9bea3ff6b2ebc49f8b85e72c5177da3c45c5aeff24388abf17e5 WHIRLPOOL a94e70b50be1a7777d48792d2498ab61494a9cce741f809c56508b7c058f7679a8f2e3d8da3316794d1c4a3dc07894327dddcf65451ed7eb8a6bc6416fa9af0d +MISC ChangeLog 343 SHA256 dcc0506c7072e5510910c9b7a8eada1be8f4a728cb471e8c3f9c70b0c14f7d52 SHA512 4ca28df7d42e98b8d658883572f1ee06fa44e18236764bef8dfaacf38940389ed74b6701c9a22555a22fc59b84389e41c58af8a7e4cbd2bc3e7360a62d2ca264 WHIRLPOOL 743276cc67d62d82143e14ef4cb95ea269d59a30e1e7bd42533f6e7c6c659a386d5802929f9a8f0d3f2f09409db7fdf8836d07de68b5a40ca06129403f1d377b +MISC metadata.xml 367 SHA256 ac8d9fb591cb385322c5b19e610391ed7c6df9554f4901b3789e0b0410533d37 SHA512 455c79e8837ba1ed980967e3236d4a0ac0edbd1b88b056a06d715894e03e7fc802079440752e60a06c9ce4acb62fd68d4020a7847a154a14065afd995257f685 WHIRLPOOL 7b8aae6b6e9c08408300de466754b331e1ec556f8dc4fcc11c22069e913d2d600c2b7dc2d9a5ee5de84c472540cc78aeac1b4a3b0abbc92a539cdbbb6ca30c37 diff --git a/sci-libs/h5part/files/h5part-1.6.6-mpio.patch b/sci-libs/h5part/files/h5part-1.6.6-mpio.patch new file mode 100644 index 000000000000..152cfec34985 --- /dev/null +++ b/sci-libs/h5part/files/h5part-1.6.6-mpio.patch @@ -0,0 +1,26 @@ +https://github.com/quinoacomputing/H5Part/commit/b8b106c368c3400b4df3d38e97ae2943d37d3c7d.patch + +From b8b106c368c3400b4df3d38e97ae2943d37d3c7d Mon Sep 17 00:00:00 2001 +From: Jozsef Bakosi <jbakosi@lanl.gov> +Date: Thu, 28 Jul 2016 08:37:24 -0600 +Subject: [PATCH] Replace H5Pset_fapl_mpiposix with H5Pset_fapl_mpio + +Based on the advice at +http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2014/msg00188.html. +--- + src/H5Part.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/H5Part.c b/src/H5Part.c +index 433a574..8a1b893 100644 +--- a/src/H5Part.c ++++ b/src/H5Part.c +@@ -246,7 +246,7 @@ _H5Part_open_file ( + /* select the HDF5 VFD */ + if (flags & H5PART_VFD_MPIPOSIX) { + _H5Part_print_info ( "Selecting MPI-POSIX VFD" ); +- if (H5Pset_fapl_mpiposix ( f->access_prop, comm, 0 ) < 0) { ++ if (H5Pset_fapl_mpio ( f->access_prop, comm, 0 ) < 0) { + HANDLE_H5P_SET_FAPL_ERR; + goto error_cleanup; + } diff --git a/sci-libs/h5part/h5part-1.6.6.ebuild b/sci-libs/h5part/h5part-1.6.6.ebuild new file mode 100644 index 000000000000..3e15653d504a --- /dev/null +++ b/sci-libs/h5part/h5part-1.6.6.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_P="${P^^[hp]}" +DESCRIPTION="Portable High Performance Parallel Data Interface to HDF5" +HOMEPAGE="http://vis.lbl.gov/Research/H5Part/" +SRC_URI="https://codeforge.lbl.gov/frs/download.php/latestfile/18/${MY_P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + virtual/mpi + sci-libs/hdf5[mpi] + " +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}/${P}-mpio.patch" ) + +S="${WORKDIR}/${MY_P}" + +src_configure() { + econf --enable-parallel --enable-shared --disable-static CC=mpicc CXX=mpicxx +} diff --git a/sci-libs/h5part/metadata.xml b/sci-libs/h5part/metadata.xml new file mode 100644 index 000000000000..903883b48f16 --- /dev/null +++ b/sci-libs/h5part/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/hdf/Manifest b/sci-libs/hdf/Manifest new file mode 100644 index 000000000000..2385ecf7285a --- /dev/null +++ b/sci-libs/hdf/Manifest @@ -0,0 +1,17 @@ +AUX 4.2.7_p1-autotools.patch 3908 SHA256 1cbe8655274b7c5f5616c80e6b212e59d06205b70e328fae640f0c8b13d10ef5 SHA512 ba33a5a2e182feca790069f730dcc2a67d1ac22985a4e4b484e28b8cff7fe55da9675d8c2c60a2a0c733035b76df9325642e7e71a38d2ba7cc4c5378cc9a133c WHIRLPOOL e29d8ea043b93cee99044cff041c2dd8287acbf8c6f21d98ee1d49963f0e3c0e47eed7554332676eb2f82efe09a6deb3d9bcb90b4ee10e7f60f64563acc271c9 +AUX hdf-4.2.11-enable-fortran-shared.patch 1287 SHA256 ccc9013278d3fa01a8a82da9b5b13c9abb2e667cdb0684d6eefeb2f24c662430 SHA512 787260127abff6695e5cddbbd75290c2349ae150c01dd1c74e83539e78d503bbcb017ea8aba8f808d846e7e291e4cb13ef69d4186ff1e38780c75e0046ca6734 WHIRLPOOL 52de4c1f720bee45c46df77bb312e8be77029854ff1a5c1ddaddf43af20d27cb115634fe2659de100a4f043ddde39befda77620331daf12518dfdfa59a36abaa +AUX hdf-4.2.11-fix-examples-dir.patch 5966 SHA256 ee092a4117cd67a71eeb02b51382c9a3d6cb351e987dac223ab502a1eaf7ec1d SHA512 f33b6e2f5de26687accba8b6ff7c1d50b96f9ad40b84771ea8a361692da88d2f376331cb8a80dc662e3213d6ddc7707ca5fcbfcaf7c1ef7224a534c0a969fabb WHIRLPOOL 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SHA512 ac88c595e369709dc907b5f009429654c59ae1ac31869aace2656511687d0a7093d41af218768cc825181f623d0018991d1e49e0c48329766c01f608873d2ddb WHIRLPOOL 81462bfcf6b11b924a591060fbe0b5f914ab0b69614ba1ce3e39fa768426c79852bc226c21a3ff0c49c23bbab2ecf2702c5d7464423364999e589fda13db05ef +DIST hdf-4.2.11.tar.bz2 3173535 SHA256 bb0e900b8cc6bc89a5730abc97e654e7705e8e1fbc4e0d4477f417822428d99b SHA512 b3be9a91c62fa258c8aa6f97d1ccbd8301225e43938b525a826c639fd8b30b7dd566f58f4d54e365606d861ad01660887163e5ca6521293791080e5ed41ef781 WHIRLPOOL 6168284c0f4cb272cfa14f12779ca2106d86d68d38d85f58ba73c137611acde6ed3d1c32bd5620496b20578de7decae6428654eb6a3afffbf7c11fff1ccebc20 +DIST hdf-4.2.13.tar.bz2 3616255 SHA256 55d3a42313bda0aba7b0463687caf819a970e0ba206f5ed2c23724f80d2ae0f3 SHA512 d7be2b3650255590b72db4a6931325ec0af256db4b846cfe886c76bf24034901b2ba7a7e546566f426d265b1793287ea3f95d8fbd818a3d018fa6813a4541657 WHIRLPOOL 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2012-03-18 03:45:46.000000000 +0000 ++++ hdf-4.2.7-patch1/configure.ac 2012-04-13 03:04:17.000000000 +0100 +@@ -200,20 +200,6 @@ + dnl Build static libraries by default. Furthermore, fortran shared libraries + dnl are unsupported. Disallow a user from enabling both shared libraries and + dnl fortran. +-if test "X${enable_shared}" != "Xyes"; then +- enable_shared="no" +-fi +- +-if test "X${enable_shared}" = "Xyes"; then +- if test "X${BUILD_FORTRAN}" = "Xyes"; then +- AC_MSG_ERROR([Cannot build shared fortran libraries. Please configure with --disable-fortran flag.]) +- fi +-fi +- +-AC_PROG_INSTALL +-AC_PROG_LN_S +- +-AC_CHECK_PROGS([AR], [ar xar], [:], [$PATH]) + + AC_CHECK_PROGS([YACC], ['bison -y' byacc yacc], [none], []) + +@@ -404,6 +390,8 @@ + + if test -z "$HAVE_SZIP"; then + AC_MSG_ERROR([couldn't find szlib library]) ++ else ++ USE_COMP_SZIP="yes" + fi + ;; + no) +@@ -447,7 +435,7 @@ + + AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress],, [unset HAVE_SZIP]) + +- if test -z "$HAVE_SZIP"; then ++ if test "X$HAVE_SZIP" != "Xyes"; then + AC_MSG_ERROR([couldn't find szlib library]) + else + USE_COMP_SZIP="yes" +@@ -703,7 +691,7 @@ + dnl ====================================================================== + dnl Libtool initialization + dnl ====================================================================== +-LT_INIT(dlopen disable-shared) ++LT_INIT(dlopen) + LT_OUTPUT + + dnl ====================================================================== +@@ -781,11 +769,6 @@ + dnl ------------------------------------------------------------------------ + dnl Check to see if libtool has enabled shared libraries. Set a conditional + dnl as some Makefiles will build based on availability of shared libraries. +-if (./libtool --features | grep '^enable shared libraries' > /dev/null); then +- enable_shared=yes +-else +- enable_shared=no +-fi + + dnl ------------------------------------------------------------------------ + dnl Specify shared library extension the host machine should recognize. +@@ -840,23 +823,8 @@ + dnl name of the compiler and the reported version number. + AC_SUBST([F77_VERSION]) + dnl Strip anything that looks like a flag off of $F77 +-F77_NOFLAGS=`echo $F77 | sed 's/ -.*//'` +- +-if `echo $F77_NOFLAGS | grep ^/ >/dev/null 2>&1`; then +- F77_VERSION="$F77" +-else +- F77_VERSION="$F77"; +- for x in `echo $PATH | sed -e 's/:/ /g'`; do +- if test -x $x/$F77_NOFLAGS; then +- F77_VERSION="$x/$F77" +- break +- fi +- done +-fi +-if test -n "$fc_version_info"; then +- F77_VERSION="$F77_VERSION ( $fc_version_info)" +-fi + ++F77_VERSION="$F77"; + + dnl This part doesn't work yet since HDF4 config files do not contain + dnl information for fortran_vendor and fortran_version. +diff -Nur hdf-4.2.7-patch1.orig/hdf/test/fortestF.f hdf-4.2.7-patch1/hdf/test/fortestF.f +--- hdf-4.2.7-patch1.orig/hdf/test/fortestF.f 2012-03-18 03:44:01.000000000 +0000 ++++ hdf-4.2.7-patch1/hdf/test/fortestF.f 2012-04-13 02:20:45.000000000 +0100 +@@ -203,7 +203,7 @@ + + if (cmd .NE. 'Test' .AND. cmd .NE. 'test') then + print *, 'Unknown Command: ', cmd, param +- print *, 'Try one of "Skip", "Test", "Verbosity" or "Cleanup"' ++ print *, 'Try one of Skip, Test, Verbosity or Cleanup' + retcode = -1 + return + endif +diff -Nur hdf-4.2.7-patch1.orig/mfhdf/libsrc/Makefile.am hdf-4.2.7-patch1/mfhdf/libsrc/Makefile.am +--- hdf-4.2.7-patch1.orig/mfhdf/libsrc/Makefile.am 2012-03-18 03:44:00.000000000 +0000 ++++ hdf-4.2.7-patch1/mfhdf/libsrc/Makefile.am 2012-04-13 02:20:45.000000000 +0100 +@@ -32,10 +32,11 @@ + else + libmfhdf_la_SOURCES = $(CSOURCES) + endif ++libmfhdf_la_LIBADD = $(top_builddir)/hdf/src/libdf.la + + if HDF_BUILD_XDR + XDRLIB = ../xdr/libxdr.la +-libmfhdf_la_LIBADD = $(XDRLIB) ++libmfhdf_la_LIBADD += $(XDRLIB) + endif + + if HDF_BUILD_NETCDF diff --git a/sci-libs/hdf/files/hdf-4.2.11-enable-fortran-shared.patch b/sci-libs/hdf/files/hdf-4.2.11-enable-fortran-shared.patch new file mode 100644 index 000000000000..7d48a8a0ca97 --- /dev/null +++ b/sci-libs/hdf/files/hdf-4.2.11-enable-fortran-shared.patch @@ -0,0 +1,35 @@ +--- hdf-4.2.11.orig/configure.ac 2016-03-16 20:07:45.093493050 +0000 ++++ hdf-4.2.11/configure.ac 2016-03-16 20:15:56.767311873 +0000 +@@ -224,20 +224,6 @@ + ## Build static libraries by default. Furthermore, fortran shared libraries + ## are unsupported. Disallow a user from enabling both shared libraries and + ## fortran. +-if test "X${enable_shared}" != "Xyes"; then +- enable_shared="no" +-fi +- +-if test "X${enable_shared}" = "Xyes"; then +- if test "X${BUILD_FORTRAN}" = "Xyes"; then +- AC_MSG_ERROR([Cannot build shared fortran libraries. Please configure with --disable-fortran flag.]) +- fi +-fi +- +-AC_PROG_INSTALL +-AC_PROG_LN_S +- +-AC_CHECK_PROGS([AR], [ar xar], [:], [$PATH]) + + AC_CHECK_PROGS([YACC], ['bison -y' byacc yacc], [none], []) + +@@ -847,11 +833,6 @@ + ## ------------------------------------------------------------------------ + ## Check to see if libtool has enabled shared libraries. Set a conditional + ## as some Makefiles will build based on availability of shared libraries. +-if (./libtool --features | grep '^enable shared libraries' > /dev/null); then +- enable_shared=yes +-else +- enable_shared=no +-fi + + ## ------------------------------------------------------------------------ + ## Specify shared library extension the host machine should recognize. diff --git a/sci-libs/hdf/files/hdf-4.2.11-fix-examples-dir.patch b/sci-libs/hdf/files/hdf-4.2.11-fix-examples-dir.patch new file mode 100644 index 000000000000..f6f15545d66b --- /dev/null +++ b/sci-libs/hdf/files/hdf-4.2.11-fix-examples-dir.patch @@ -0,0 +1,120 @@ +diff -Nur hdf-4.2.11.orig/hdf/examples/Makefile.am hdf-4.2.11/hdf/examples/Makefile.am +--- hdf-4.2.11.orig/hdf/examples/Makefile.am 2016-03-16 20:07:45.103492925 +0000 ++++ hdf-4.2.11/hdf/examples/Makefile.am 2016-03-16 22:16:35.836304451 +0000 +@@ -46,8 +46,8 @@ + INSTALL_TOP_FILES = README + + # Where to install example files +-EXAMPLEDIR=$(prefix)/examples/c +-EXAMPLETOPDIR=$(prefix)/examples ++EXAMPLEDIR=$(docdir)/examples/c ++EXAMPLETOPDIR=$(docdir)/examples + + # How to build C programs using h4cc + $(EXTRA_PROG): $(H4CC) +diff -Nur hdf-4.2.11.orig/hdf/fortran/examples/Makefile.am hdf-4.2.11/hdf/fortran/examples/Makefile.am +--- hdf-4.2.11.orig/hdf/fortran/examples/Makefile.am 2016-03-16 20:07:45.103492925 +0000 ++++ hdf-4.2.11/hdf/fortran/examples/Makefile.am 2016-03-16 22:17:58.775261767 +0000 +@@ -41,7 +41,7 @@ + INSTALL_SCRIPT_FILES = run-fortran-ex.sh + + # Where to install Fortran example files +-EXAMPLEDIR=$(prefix)/examples/fortran ++EXAMPLEDIR=$(docdir)/examples/fortran + + # How to build Fortran programs using h4fc + $(EXTRA_PROG): $(H4FC) +diff -Nur hdf-4.2.11.orig/mfhdf/examples/Makefile.am hdf-4.2.11/mfhdf/examples/Makefile.am +--- hdf-4.2.11.orig/mfhdf/examples/Makefile.am 2016-03-16 20:07:45.183491919 +0000 ++++ hdf-4.2.11/mfhdf/examples/Makefile.am 2016-03-16 22:18:38.304764814 +0000 +@@ -23,7 +23,7 @@ + SD_get_info.c SD_find_sds_by_name.c SD_set_get_dim_info.c \ + SD_dimscale_vs_sds.c SD_set_attr.c SD_get_attr.c SD_chunking_example.c + +-EXAMPLEDIR=$(prefix)/examples/c ++EXAMPLEDIR=$(docdir)/examples/c + + # How to build programs using h4cc + $(EXTRA_PROG): $(H4CC) +diff -Nur hdf-4.2.11.orig/mfhdf/fortran/examples/Makefile.am hdf-4.2.11/mfhdf/fortran/examples/Makefile.am +--- hdf-4.2.11.orig/mfhdf/fortran/examples/Makefile.am 2016-03-16 20:07:45.183491919 +0000 ++++ hdf-4.2.11/mfhdf/fortran/examples/Makefile.am 2016-03-16 22:18:15.075056851 +0000 +@@ -24,7 +24,7 @@ + SD_set_attr.f SD_get_attr.f SD_compress_sds.f SD_chunking_example.f + + # Where to install example files +-EXAMPLEDIR=$(prefix)/examples/fortran ++EXAMPLEDIR=$(docdir)/examples/fortran + + # How to build Fortran programs using h4fc + $(EXTRA_PROG): $(H4FC) +diff -up hdf-4.2.11/config/examples.am.destdir hdf-4.2.11/config/examples.am +--- hdf-4.2.11/config/examples.am.destdir 2015-02-09 09:43:05.000000000 -0700 ++++ hdf-4.2.11/config/examples.am 2015-02-13 13:24:09.008230956 -0700 +@@ -44,7 +44,7 @@ CHECK_CLEANFILES+= *.hdf + CLEANFILES=$(EXAMPLE_PROG) + + # How to create EXAMPLEDIR if it doesn't already exist +-$(EXAMPLEDIR): ++$(DESTDIR)$(EXAMPLEDIR): + mkdir -p $@ + + # Install and uninstall rules. We install the source files, not the +@@ -54,42 +54,42 @@ install-data-local: + uninstall-local: + @$(MAKE) $(AM_MAKEFLAGS) uninstall-examples + +-install-examples: $(EXAMPLEDIR) ++install-examples: $(DESTDIR)$(EXAMPLEDIR) + @for f in X $(INSTALL_FILES); do \ + if test $$f != X; then \ +- (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLEDIR)/. || exit 1); \ +- chmod a-x $(EXAMPLEDIR)/$$f; \ ++ (set -x; $(INSTALL) $(srcdir)/$$f $(DESTDIR)$(EXAMPLEDIR)/. || exit 1); \ ++ chmod a-x $(DESTDIR)$(EXAMPLEDIR)/$$f; \ + fi; \ + done + @for f in X $(INSTALL_SCRIPT_FILES); do \ + if test $$f != X; then \ +- (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLEDIR)/. || exit 1); \ ++ (set -x; $(INSTALL) $(srcdir)/$$f $(DESTDIR)$(EXAMPLEDIR)/. || exit 1); \ + fi; \ + done + @for f in X $(INSTALL_TOP_FILES); do \ + if test $$f != X; then \ +- (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLETOPDIR)/. || exit 1); \ +- chmod a-x $(EXAMPLETOPDIR)/$$f; \ ++ (set -x; $(INSTALL) $(srcdir)/$$f $(DESTDIR)$(EXAMPLETOPDIR)/. || exit 1); \ ++ chmod a-x $(DESTDIR)$(EXAMPLETOPDIR)/$$f; \ + fi; \ + done + @for f in X $(INSTALL_TOP_SCRIPT_FILES); do \ + if test $$f != X; then \ +- (set -x; $(INSTALL) $(srcdir)/$$f $(EXAMPLETOPDIR)/. || exit 1); \ ++ (set -x; $(INSTALL) $(srcdir)/$$f $(DESTDIR)$(EXAMPLETOPDIR)/. || exit 1); \ + fi; \ + done + + uninstall-examples: +- @if test -n "$(INSTALL_FILES)" -a -d $(EXAMPLEDIR); then \ +- set -x; cd $(EXAMPLEDIR) && $(RM) $(INSTALL_FILES); \ ++ @if test -n "$(INSTALL_FILES)" -a -d $(DESTDIR)$(EXAMPLEDIR); then \ ++ set -x; cd $(DESTDIR)$(EXAMPLEDIR) && $(RM) $(INSTALL_FILES); \ + fi +- @if test -n "$(INSTALL_SCRIPT_FILES)" -a -d $(EXAMPLEDIR); then \ +- set -x; cd $(EXAMPLEDIR) && $(RM) $(INSTALL_SCRIPT_FILES); \ ++ @if test -n "$(INSTALL_SCRIPT_FILES)" -a -d $(DESTDIR)$(EXAMPLEDIR); then \ ++ set -x; cd $(DESTDIR)$(EXAMPLEDIR) && $(RM) $(INSTALL_SCRIPT_FILES); \ + fi +- @if test -n "$(INSTALL_TOP_FILES)" -a -d $(EXAMPLETOPDIR); then \ +- set -x; cd $(EXAMPLETOPDIR) && $(RM) $(INSTALL_TOP_FILES); \ ++ @if test -n "$(INSTALL_TOP_FILES)" -a -d $(DESTDIR)$(EXAMPLETOPDIR); then \ ++ set -x; cd $$(DESTDIR)(EXAMPLETOPDIR) && $(RM) $(INSTALL_TOP_FILES); \ + fi +- @if test -n "$(INSTALL_TOP_SCRIPT_FILES)" -a -d $(EXAMPLETOPDIR); then \ +- set -x; cd $(EXAMPLETOPDIR) && $(RM) $(INSTALL_TOP_SCRIPT_FILES); \ ++ @if test -n "$(INSTALL_TOP_SCRIPT_FILES)" -a -d $(DESTDIR)$(EXAMPLETOPDIR); then \ ++ set -x; cd $(DESTDIR)$(EXAMPLETOPDIR) && $(RM) $(INSTALL_TOP_SCRIPT_FILES); \ + fi + + installcheck-local: diff --git a/sci-libs/hdf/files/hdf-4.2.11-fix-szip-detection.patch b/sci-libs/hdf/files/hdf-4.2.11-fix-szip-detection.patch new file mode 100644 index 000000000000..4486eb959b82 --- /dev/null +++ b/sci-libs/hdf/files/hdf-4.2.11-fix-szip-detection.patch @@ -0,0 +1,27 @@ +--- hdf-4.2.11.orig/configure.ac 2016-03-16 20:07:45.093493050 +0000 ++++ hdf-4.2.11/configure.ac 2016-03-16 22:08:06.232711036 +0000 +@@ -473,12 +473,14 @@ + yes) + HAVE_SZIP="yes" + AC_CHECK_HEADERS([szlib.h], [HAVE_SZLIB_H="yes"], [unset HAVE_SZIP]) +- if test "x$HAVE_SZLIB" = "xyes" -a "x$HAVE_SZLIB_H" = "xyes"; then ++ if test "x$HAVE_SZIP" = "xyes" -a "x$HAVE_SZLIB_H" = "xyes"; then + AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress],, [unset HAVE_SZIP]) + fi + + if test -z "$HAVE_SZIP"; then + AC_MSG_ERROR([couldn't find szlib library]) ++ else ++ USE_COMP_SZIP="yes" + fi + ;; + no) +@@ -525,7 +527,7 @@ + AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress],, [unset HAVE_SZIP]) + fi + +- if test -z "$HAVE_SZIP"; then ++ if test "x$HAVE_SZIP" != "xyes"; then + AC_MSG_ERROR([couldn't find szlib library]) + else + USE_COMP_SZIP="yes" diff --git a/sci-libs/hdf/files/hdf-4.2.9-autotools.patch b/sci-libs/hdf/files/hdf-4.2.9-autotools.patch new file mode 100644 index 000000000000..a31946a0dfee --- /dev/null +++ b/sci-libs/hdf/files/hdf-4.2.9-autotools.patch @@ -0,0 +1,112 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -216,20 +216,6 @@ AC_SUBST([BUILD_FORTRAN]) + ## Build static libraries by default. Furthermore, fortran shared libraries + ## are unsupported. Disallow a user from enabling both shared libraries and + ## fortran. +-if test "X${enable_shared}" != "Xyes"; then +- enable_shared="no" +-fi +- +-if test "X${enable_shared}" = "Xyes"; then +- if test "X${BUILD_FORTRAN}" = "Xyes"; then +- AC_MSG_ERROR([Cannot build shared fortran libraries. Please configure with --disable-fortran flag.]) +- fi +-fi +- +-AC_PROG_INSTALL +-AC_PROG_LN_S +- +-AC_CHECK_PROGS([AR], [ar xar], [:], [$PATH]) + + AC_CHECK_PROGS([YACC], ['bison -y' byacc yacc], [none], []) + +@@ -261,7 +247,7 @@ AC_SUBST([LT_STATIC_EXEC]) + ## ====================================================================== + ## Libtool initialization + ## ====================================================================== +-LT_INIT([dlopen disable-shared]) ++LT_INIT([dlopen]) + LT_OUTPUT + + ## ---------------------------------------------------------------------- +@@ -453,6 +439,8 @@ case "$withval" in + + if test -z "$HAVE_SZIP"; then + AC_MSG_ERROR([couldn't find szlib library]) ++ else ++ USE_COMP_SZIP="yes" + fi + ;; + no) +@@ -496,7 +484,7 @@ case "$withval" in + + AC_CHECK_LIB([sz], [SZ_BufftoBuffCompress],, [unset HAVE_SZIP]) + +- if test -z "$HAVE_SZIP"; then ++ if test "X$HAVE_SZIP" != "Xyes"; then + AC_MSG_ERROR([couldn't find szlib library]) + else + USE_COMP_SZIP="yes" +@@ -837,11 +825,6 @@ done + ## ------------------------------------------------------------------------ + ## Check to see if libtool has enabled shared libraries. Set a conditional + ## as some Makefiles will build based on availability of shared libraries. +-if (./libtool --features | grep '^enable shared libraries' > /dev/null); then +- enable_shared=yes +-else +- enable_shared=no +-fi + + ## ------------------------------------------------------------------------ + ## Specify shared library extension the host machine should recognize. +@@ -911,22 +894,7 @@ fi + ## name of the compiler and the reported version number. + AC_SUBST([F77_VERSION]) + ## Strip anything that looks like a flag off of $F77 +-F77_NOFLAGS=`echo $F77 | sed 's/ -.*//'` +- +-if `echo $F77_NOFLAGS | grep ^/ >/dev/null 2>&1`; then +- F77_VERSION="$F77" +-else +- F77_VERSION="$F77"; +- for x in `echo $PATH | sed -e 's/:/ /g'`; do +- if test -x $x/$F77_NOFLAGS; then +- F77_VERSION="$x/$F77" +- break +- fi +- done +-fi +-if test -n "$fc_version_info"; then +- F77_VERSION="$F77_VERSION ( $fc_version_info)" +-fi ++F77_VERSION="$F77" + + ## This part doesn't work yet since HDF4 config files do not contain + ## information for fortran_vendor and fortran_version. +--- a/hdf/test/fortestF.f ++++ b/hdf/test/fortestF.f +@@ -203,7 +203,7 @@ C Skip command + + if (cmd .NE. 'Test' .AND. cmd .NE. 'test') then + print *, 'Unknown Command: ', cmd, param +- print *, 'Try one of "Skip", "Test", "Verbosity" or "Cleanup"' ++ print *, 'Try one of Skip, Test, Verbosity or Cleanup' + retcode = -1 + return + endif +--- a/mfhdf/libsrc/Makefile.am ++++ b/mfhdf/libsrc/Makefile.am +@@ -32,10 +32,11 @@ libmfhdf_la_SOURCES = $(CSOURCES) $(FSOURCES) + else + libmfhdf_la_SOURCES = $(CSOURCES) + endif ++libmfhdf_la_LIBADD = $(top_builddir)/hdf/src/libdf.la + + if HDF_BUILD_XDR + XDRLIB = $(top_builddir)/mfhdf/xdr/libxdr.la +-libmfhdf_la_LIBADD = $(XDRLIB) ++libmfhdf_la_LIBADD += $(XDRLIB) + endif + + if HDF_BUILD_NETCDF diff --git a/sci-libs/hdf/files/hdf-ppc.patch b/sci-libs/hdf/files/hdf-ppc.patch new file mode 100644 index 000000000000..3cf62d09371d --- /dev/null +++ b/sci-libs/hdf/files/hdf-ppc.patch @@ -0,0 +1,214 @@ +Fix FTBS on ppc + +https://bugs.gentoo.org/show_bug.cgi?id=450188 + +Source: http://pkgs.fedoraproject.org/cgit/hdf.git +--- a/hdf/src/hdfi.h ++++ b/hdf/src/hdfi.h +@@ -76,6 +76,7 @@ + #define DFMT_IA64 0x4441 + #define DFMT_LINUX64 0x4441 + #define DFMT_POWERPC64 0x1111 ++#define DFMT_LINUXPPC 0x1111 + + /* I/O library constants */ + #define UNIXUNBUFIO 1 +@@ -1289,6 +1290,57 @@ typedef long hdf_pint_t; + + #endif /*Linux 64 */ + ++/* Linux PPC */ ++#if defined __powerpc__ && !defined __powerpc64__ ++ ++#ifdef GOT_MACHINE ++If you get an error on this line more than one machine type has been defined. ++Please check your Makefile. ++#endif ++#define GOT_MACHINE ++ ++#include <sys/file.h> /* for unbuffered i/o stuff */ ++#include <sys/stat.h> ++#define DF_MT DFMT_LINUXPPC ++typedef void VOID; ++typedef void *VOIDP; ++typedef char *_fcd; ++typedef char char8; ++typedef unsigned char uchar8; ++typedef char int8; ++typedef unsigned char uint8; ++typedef short int int16; ++typedef unsigned short int uint16; ++typedef int int32; ++typedef unsigned int uint32; ++typedef int intn; ++typedef unsigned int uintn; ++typedef int intf; /* size of INTEGERs in Fortran compiler */ ++typedef float float32; ++typedef double float64; ++typedef long hdf_pint_t; /* an integer the same size as a pointer */ ++#define FNAME_POST_UNDERSCORE ++#define _fcdtocp(desc) (desc) ++#ifdef HAVE_FMPOOL ++#define FILELIB PAGEBUFIO /* enable page buffering */ ++#else ++#define FILELIB UNIXBUFIO ++#endif ++ ++/* JPEG #define's - Look in the JPEG docs before changing - (Q) */ ++ ++/* Determine the memory manager we are going to use. Valid values are: */ ++/* MEM_DOS, MEM_ANSI, MEM_NAME, MEM_NOBS. See the JPEG docs for details on */ ++/* what each does */ ++#define JMEMSYS MEM_ANSI ++ ++#ifdef __GNUC__ ++#define HAVE_STDC ++#define INCLUDES_ARE_ANSI ++#endif ++ ++#endif /*Linux PPC */ ++ + /*-----------------------------------------------------*/ + /* 64-bit Free BSD */ + +--- a/mfhdf/fortran/config/jackets-linux.c ++++ b/mfhdf/fortran/config/jackets-linux.c +@@ -34,7 +34,7 @@ + + struct ncfils { /* This will be a common block from Fortran */ + double dd; +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + int ll; + #else + long ll; +@@ -65,7 +65,7 @@ struct ncfils { /* This will be a comm + + struct ncfils { /* This will be a common block from Fortran */ + double dd; +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + int ll; + #else + long ll; +@@ -430,7 +430,7 @@ stoig(shorts, ints, dims, basis, ndims) + } + #endif /* FORTRAN_HAS_NO_SHORT */ + +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + /* + * Convert multi-dimensional array of NCLONGs stored in ints to packed + * array of longs, in malloc'ed space. Returns pointer to longs or NULL +@@ -916,7 +916,7 @@ nncvpt1(cdfid, varid, indices, value, rc + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long longs = *(int *)value; +@@ -1030,7 +1030,7 @@ nncvpt(cdfid, varid, start, count, value + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long *longs = itol (value, ncount, ndims); +@@ -1141,7 +1141,7 @@ nncvptg(cdfid, varid, start, count, stri + tmpbasis = nctypelen(NC_LONG); + else + #endif +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + if (datatype == NC_LONG) + tmpbasis = sizeof(int); + else +@@ -1198,7 +1198,7 @@ nncvptg(cdfid, varid, start, count, stri + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long *longs = itolg (value, ncount, nbasis, ndims); +@@ -1334,7 +1334,7 @@ nncvgt1(cdfid, varid, indices, value, rc + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long longs; +@@ -1476,7 +1476,7 @@ nncvgt(cdfid, varid, start, count, value + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long iocount = dimprod (ncount, ndims); /* product of dimensions */ +@@ -1614,7 +1614,7 @@ nncvgtg(cdfid, varid, start, count, stri + tmpbasis = nctypelen(NC_LONG); + else + #endif +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + if (datatype == NC_LONG) + tmpbasis = sizeof(int); + else +@@ -1685,7 +1685,7 @@ nncvgtg(cdfid, varid, start, count, stri + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long iocount = dimprod (ncount, ndims); /* product of dimensions */ +@@ -1851,7 +1851,7 @@ nncapt(cdfid, varid, attname, datatype, + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + #ifdef HDF + if ((nc_type) *datatype == NC_LONG && handle->file_type!=HDF_FILE) { + long *longs = itol (value, attlen, 1); +@@ -2016,7 +2016,7 @@ nncagt(cdfid, varid, attname, value, rco + return; + } /* else */ + #endif /* FORTRAN_HAS_NO_SHORT */ +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + #ifdef HDF + if ((nc_type) datatype == NC_LONG && handle->file_type!=HDF_FILE) { + /* EIP We need to use int buffer to read data in on the platforms where long is 8 bytes +--- a/mfhdf/libsrc/netcdf.h.in ++++ b/mfhdf/libsrc/netcdf.h.in +@@ -295,7 +295,7 @@ typedef double ncdouble; + */ + #if defined _CRAYMPP + typedef short nclong; +-#elif defined __alpha || (_MIPS_SZLONG == 64) || defined IA64 || (defined __sun__ && defined _LP64) || defined AIX5L64 ++#elif defined __alpha || (_MIPS_SZLONG == 64) || defined IA64 || (defined __sun__ && defined _LP64) || defined AIX5L64 || defined __powerpc64__ + typedef int nclong; + #else + typedef long nclong; /* default, compatible type */ +--- a/mfhdf/ncgen/ncgen.l ++++ b/mfhdf/ncgen/ncgen.l +@@ -134,7 +134,7 @@ FloatInf|Infinity|Inf { /* float miss + yyerror(errstr); + } + +-#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || __powerpc64__ ++#if defined __alpha || (_MIPS_SZLONG == 64) || defined __ia64 || (defined __sun && defined _LP64) || defined AIX5L64 || defined __x86_64__ || defined __powerpc64__ + if (dd < INT_MIN || dd > INT_MAX) + #else + #if defined (_CRAYMPP) diff --git a/sci-libs/hdf/hdf-4.2.11.ebuild b/sci-libs/hdf/hdf-4.2.11.ebuild new file mode 100644 index 000000000000..1d23a4cfe970 --- /dev/null +++ b/sci-libs/hdf/hdf-4.2.11.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit fortran-2 toolchain-funcs autotools flag-o-matic + +MYP=${P/_p/-patch} + +DESCRIPTION="General purpose library and format for storing scientific data" +HOMEPAGE="http://www.hdfgroup.org/hdf4.html" +SRC_URI="http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/${MYP}.tar.bz2" + +SLOT="0" +LICENSE="NCSA-HDF" +KEYWORDS="~amd64 ~ia64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="examples fortran szip static-libs test" +REQUIRED_USE="test? ( szip )" + +RDEPEND=" + sys-libs/zlib + virtual/jpeg:0 + szip? ( virtual/szip )" +DEPEND="${RDEPEND} + test? ( virtual/szip )" + +S="${WORKDIR}/${MYP}" + +PATCHES=( + "${FILESDIR}"/${PN}-4.2.11-fix-szip-detection.patch + "${FILESDIR}"/${PN}-4.2.11-enable-fortran-shared.patch + "${FILESDIR}"/${PN}-4.2.11-fix-examples-dir.patch +) + +src_prepare() { + default + sed -i -e 's/-R/-L/g' config/commence.am || die #rpath + eautoreconf + [[ $(tc-getFC) = *gfortran ]] && append-fflags -fno-range-check +} + +src_configure() { + econf \ + --enable-shared \ + --enable-production=gentoo \ + --disable-netcdf \ + $(use_enable fortran) \ + $(use_enable static-libs static) \ + $(use_with szip szlib) \ + CC="$(tc-getCC)" +} + +src_install() { + default + use static-libs || prune_libtool_files --all + dodoc release_notes/{RELEASE,HISTORY,bugs_fixed,misc_docs}.txt + cd "${ED}"usr + use examples || rm -rf share/doc/${PF}/examples + mv bin/ncgen{,-hdf} || die + mv bin/ncdump{,-hdf} || die + mv share/man/man1/ncgen{,-hdf}.1 || die + mv share/man/man1/ncdump{,-hdf}.1 || die +} diff --git a/sci-libs/hdf/hdf-4.2.13.ebuild b/sci-libs/hdf/hdf-4.2.13.ebuild new file mode 100644 index 000000000000..103ea3b4428a --- /dev/null +++ b/sci-libs/hdf/hdf-4.2.13.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit fortran-2 toolchain-funcs autotools flag-o-matic + +MYP=${P/_p/-patch} + +DESCRIPTION="General purpose library and format for storing scientific data" +HOMEPAGE="http://www.hdfgroup.org/hdf4.html" +SRC_URI="http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/${MYP}.tar.bz2" + +SLOT="0" +LICENSE="NCSA-HDF" +KEYWORDS="~amd64 ~ia64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="examples fortran szip static-libs test" +REQUIRED_USE="test? ( szip )" + +RDEPEND=" + sys-libs/zlib + virtual/jpeg:0 + szip? ( virtual/szip )" +DEPEND="${RDEPEND} + test? ( virtual/szip )" + +S="${WORKDIR}/${MYP}" + +PATCHES=( + "${FILESDIR}"/${PN}-4.2.11-fix-szip-detection.patch + "${FILESDIR}"/${PN}-4.2.11-enable-fortran-shared.patch +) + +src_prepare() { + default + sed -i -e 's/-R/-L/g' config/commence.am || die #rpath + eautoreconf + [[ $(tc-getFC) = *gfortran ]] && append-fflags -fno-range-check +} + +src_configure() { + econf \ + --enable-shared \ + --enable-production=gentoo \ + --disable-netcdf \ + $(use_enable fortran) \ + $(use_enable static-libs static) \ + $(use_with szip szlib) \ + CC="$(tc-getCC)" +} + +src_install() { + default + use static-libs || prune_libtool_files --all + dodoc release_notes/{RELEASE,HISTORY,bugs_fixed,misc_docs}.txt + cd "${ED}"usr + if use examples; then + mv share/hdf4_examples share/doc/${PF}/examples || die + docompress -x /usr/share/doc/${PF}/examples + else + rm -r share/hdf4_examples || die + fi + mv bin/ncgen{,-hdf} || die + mv bin/ncdump{,-hdf} || die + mv share/man/man1/ncgen{,-hdf}.1 || die + mv share/man/man1/ncdump{,-hdf}.1 || die +} diff --git a/sci-libs/hdf/hdf-4.2.8.ebuild b/sci-libs/hdf/hdf-4.2.8.ebuild new file mode 100644 index 000000000000..3561a95953c1 --- /dev/null +++ b/sci-libs/hdf/hdf-4.2.8.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +FORTRAN_NEEDED=fortran + +inherit eutils fortran-2 toolchain-funcs autotools flag-o-matic + +MYP=${P/_p/-patch} + +DESCRIPTION="General purpose library and format for storing scientific data" +HOMEPAGE="http://www.hdfgroup.org/hdf4.html" +SRC_URI="http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/${MYP}.tar.bz2" + +SLOT="0" +LICENSE="NCSA-HDF" +KEYWORDS="amd64 ia64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="fortran szip static-libs" + +RDEPEND=" + sys-libs/zlib + virtual/jpeg + szip? ( virtual/szip )" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${MYP} + +src_prepare() { + epatch "${FILESDIR}"/4.2.7_p1-autotools.patch \ + "${FILESDIR}"/${PN}-ppc.patch + sed -i -e 's/-R/-L/g' config/commence.am || die #rpath + eautoreconf + [[ $(tc-getFC) = *gfortran ]] && append-fflags -fno-range-check +} + +src_configure() { + econf \ + --enable-shared \ + --enable-production=gentoo \ + --disable-netcdf \ + $(use_enable fortran) \ + $(use_enable static-libs static) \ + $(use_with szip szlib) \ + CC="$(tc-getCC)" +} + +src_install() { + default + dodoc release_notes/{RELEASE,HISTORY,bugs_fixed,misc_docs}.txt + cd "${ED}"usr + mv bin/ncgen{,-hdf} || die + mv bin/ncdump{,-hdf} || die + mv share/man/man1/ncgen{,-hdf}.1 || die + mv share/man/man1/ncdump{,-hdf}.1 || die +} diff --git a/sci-libs/hdf/hdf-4.2.9.ebuild b/sci-libs/hdf/hdf-4.2.9.ebuild new file mode 100644 index 000000000000..3d7f73a04cda --- /dev/null +++ b/sci-libs/hdf/hdf-4.2.9.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +FORTRAN_NEEDED=fortran + +inherit eutils fortran-2 toolchain-funcs autotools flag-o-matic + +MYP=${P/_p/-patch} + +DESCRIPTION="General purpose library and format for storing scientific data" +HOMEPAGE="http://www.hdfgroup.org/hdf4.html" +SRC_URI="http://www.hdfgroup.org/ftp/HDF/HDF_Current/src/${MYP}.tar.bz2" + +SLOT="0" +LICENSE="NCSA-HDF" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="fortran szip static-libs" + +RDEPEND=" + sys-libs/zlib + virtual/jpeg + szip? ( virtual/szip )" +DEPEND="${RDEPEND}" + +S=${WORKDIR}/${MYP} + +src_prepare() { + epatch "${FILESDIR}"/${P}-autotools.patch \ + "${FILESDIR}"/${PN}-ppc.patch + sed -i -e 's/-R/-L/g' config/commence.am || die #rpath + eautoreconf + [[ $(tc-getFC) = *gfortran ]] && append-fflags -fno-range-check +} + +src_configure() { + econf \ + --enable-shared \ + --enable-production=gentoo \ + --disable-netcdf \ + $(use_enable fortran) \ + $(use_enable static-libs static) \ + $(use_with szip szlib) \ + CC="$(tc-getCC)" +} + +src_install() { + default + dodoc release_notes/{RELEASE,HISTORY,bugs_fixed,misc_docs}.txt + cd "${ED}"usr + mv bin/ncgen{,-hdf} || die + mv bin/ncdump{,-hdf} || die + mv share/man/man1/ncgen{,-hdf}.1 || die + mv share/man/man1/ncdump{,-hdf}.1 || die +} diff --git a/sci-libs/hdf/metadata.xml b/sci-libs/hdf/metadata.xml new file mode 100644 index 000000000000..396675338791 --- /dev/null +++ b/sci-libs/hdf/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The Hierarchical Data Format is a general purpose library and + file format for storing scientific data. + HDF can store two primary objects: datasets and groups. A dataset is + essentially a multidimensional array of data elements, and a group is + a structure for organizing objects in an HDF file. Using these two basic + objects, one can create and store almost any kind of scientific data + structure, such as images, arrays of vectors, and structured and + unstructured grids. You can also mix and match them in HDF files + according to your needs. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest new file mode 100644 index 000000000000..7d98e0e96c4e --- /dev/null +++ b/sci-libs/hdf5/Manifest @@ -0,0 +1,9 @@ +AUX hdf5-1.8.13-no-messing-ldpath.patch 1141 SHA256 cec0d9c73a0f4611c3453190a2c01ad7dce4c62feea6e0a7cd79a93c84f43e62 SHA512 e43021ceb83909ab06ba378363c192aa0f1b34cc7c2b121f5000e215516dbdea1b825a53ac4023073bf4870a5c3452c22f5535391d95af45ad63a309e1ffa5a4 WHIRLPOOL d0e75d8a05e13385aedd075cf96380a10dfeffaace5d5a8ba4926a5f7ed583bf36e17583dba6110a1ddbcf2652bed15b902a57ec157fb30412a2fd3b87a303a3 +AUX hdf5-1.8.15-implicits.patch 1050 SHA256 2b348408942b14bb272caa94eee07b7b399c6e9396e2afb1dfc51b99ab679cfa SHA512 e3cfc3e3c01b8eafe426a3ebb87a4880d326b88d15897ce6d50b47456d69c0ef0888ad7f839928eb1fd283eb617f63869c2051d46669986bb5ed30afa6181088 WHIRLPOOL b80c2cfcf1a499c7a39a89770c6e5159834f8fd170d812ffed91bb25d49a43f17a9a656659795a0b58f65b9809e22424602de680344694e059b4174970911183 +AUX hdf5-1.8.9-mpicxx.patch 494 SHA256 b8412a94dcc88b520f28ea119694dd3037ab6bd2c2bc064ab0ab868b1eb970bb SHA512 8b4c39e40591860652547ea8ff205230da7d67488233e911cbcb3416eab561f2529c65bc5e7c9c812bf4298812346f47f9209e5f69f7e8f66ad587306a5b477b WHIRLPOOL a345a591813303a0ee87f08de2b9b96a2e80246be671dc7854307767abdc6f6db9684a7c298478090ef4e5bd9d2891e1f097cd77bae736bd39b6353c26bd80ea +AUX hdf5-1.8.9-static_libgfortran.patch 429 SHA256 7802a4535f456c951fb4162850edd53f667ac29fc4838fce960a18f23d2dfc0d SHA512 af97c54469a90bf3b0e8ec1218d4ca95822ac0cbc7120114979fc467fe3114743c74f4d4e16f0c10b1cd82d40880ef482f6fd34e1effc7c621b981ad466204f9 WHIRLPOOL 08e6f90b86ee3020eab9c3e02caf315ff77b57365f96175c1aea6c52b254dd59d2e7bf647a6458ef51147fdb3a20622bd31bdbc82e69b0bbb689178edb6768f4 +DIST hdf5-1.8.18.tar.bz2 10081294 SHA256 01c6deadf4211f86922400da82c7a8b5b50dc8fc1ce0b5912de3066af316a48c SHA512 01f6d14bdd3be2ced9c63cc9e1820cd7ea11db649ff9f3a3055c18c4b0fffe777fd23baad536e3bce31c4d76fe17db64a3972762e1bb4d232927c1ca140e72b2 WHIRLPOOL c1ea97aa30ded9f3129edf47cfda3b7e371aa21fcb2fc409005818f69ed0f0ac41a19e28ec38a5da2c417ef98033f197292169c88f7db81dd94244b016ab2595 +EBUILD hdf5-1.8.18.ebuild 3366 SHA256 4eb3c4384e24d6abc328cea0c85d8e4ad27ca537a7cb43886a03c08ceed0ab71 SHA512 54e66dc074fd9b0fe9ad23f23234fc20e79c6ed9e9759d6964cb8e4d3e79321c08b4539a814f2fae2c935bb9358549115a884b8f55719fb77744fd26ad680867 WHIRLPOOL dc1f99be5353e2933aadcbd6f789db6a5e4f2729d5118793354f21bf0658337f07b6f18be364875af2f64ea3594a298463a11e939b46ed7cfb47698bf1daf027 +MISC ChangeLog 4944 SHA256 d0c84472a1090cd6e3571ab1c2e9a1c6ae6779cb7b95a27870f1d658506ea3ed SHA512 67dac36eac6b8485bad4405fe88b1ace692429ed1b05202cda59439ebad2429f351287559029bdd0aaaeabe59ed83bc31b8313ed2ba78bbbb16769b43ed4d717 WHIRLPOOL e7e5bd3527aa16cef5741cdfe0ea416cdaf7a9e40cb48a6d90ff40db2e825e748e58f8346ab81379678c35a0a47559a0fb813157c2e280a16a0e4e0d00b124ea +MISC ChangeLog-2015 23886 SHA256 8182cdba0602b72a314930a8dc9f76649a065b7e2377461d2db81735b5e5e82c SHA512 538ba6ef68d8af232c03c2fa5e4295bae8bd91678062a31aa0ad802ddc1f9f86c6bd1d0d97ad0ffbc116727e75d2f3f0b27f3b9afada1b51b36b94518b85f9b0 WHIRLPOOL efbfc52b7bf7ba50755ba464a510759bedcdc34164259ed74a11a20de5cabcfce1eb79875c078c4aa75ef2b2f99ecc46816fa2871136892644db6e7b957b0fd1 +MISC metadata.xml 822 SHA256 c44ff6a909f6e7e7b6191574ab7c4352d778052b612ae81f7d19172a8aa87d2e SHA512 5e6cb47fcf2e704887a375f527b447075a36a51225cc2bdf10892bff5cce548599dd6f04a36ae2e31f691bd635dd6cc5d1455729e05923a8992d95fb27716164 WHIRLPOOL a40f07570191840605716769cd5df110594c99378900d1e7902bea63053c9554e1c9f8f674d530d60035726a095637f96efa3cd56199298f0b24508b99213b9b diff --git a/sci-libs/hdf5/files/hdf5-1.8.13-no-messing-ldpath.patch b/sci-libs/hdf5/files/hdf5-1.8.13-no-messing-ldpath.patch new file mode 100644 index 000000000000..82bc5d8b120a --- /dev/null +++ b/sci-libs/hdf5/files/hdf5-1.8.13-no-messing-ldpath.patch @@ -0,0 +1,21 @@ +Prevent build system with messing up LD_LIBRARY_PATH +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -125,8 +125,6 @@ settings_DATA=libhdf5.settings + # Remove the generated .c file if errors occur unless HDF5_Make_Ignore + # is set to ignore the error. + H5Tinit.c: H5detect$(EXEEXT) +- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \ +- sed -e 's/-L/:/g' -e 's/ //g'`" \ + $(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \ + (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \ + ($(RM) $@ ; exit 1) +@@ -137,8 +135,6 @@ H5Tinit.c: H5detect$(EXEEXT) + # Remove the generated .c file if errors occur unless HDF5_Make_Ignore + # is set to ignore the error. + H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings +- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \ +- sed -e 's/-L/:/g' -e 's/ //g'`" \ + $(RUNSERIAL) ./H5make_libsettings$(EXEEXT) > $@ || \ + (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \ + ($(RM) $@ ; exit 1) diff --git a/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch new file mode 100644 index 000000000000..72e096170975 --- /dev/null +++ b/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch @@ -0,0 +1,43 @@ +--- a/hl/src/H5LTanalyze.c ++++ b/hl/src/H5LTanalyze.c +@@ -40,6 +40,7 @@ + #include <string.h> + #include <errno.h> + #include <stdlib.h> ++#include <unistd.h> + + /* end standard C headers. */ + +--- a/hl/src/H5LTanalyze.l ++++ b/hl/src/H5LTanalyze.l +@@ -16,6 +16,7 @@ + %{ + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> + #include <hdf5.h> + #include "H5LTparse.h" + +--- a/test/cache_common.h ++++ b/test/cache_common.h +@@ -702,5 +702,8 @@ void validate_mdc_config(hid_t file_id, + hbool_t compare_init, + int test_num); + ++hbool_t resize_configs_are_equal(const H5C_auto_size_ctl_t *a, ++ const H5C_auto_size_ctl_t *b, ++ hbool_t compare_init); + #endif /* _CACHE_COMMON_H */ + +--- a/testpar/t_span_tree.c ++++ b/testpar/t_span_tree.c +@@ -37,6 +37,9 @@ + #include "hdf5.h" + #include "H5private.h" + #include "testphdf5.h" ++#define H5S_PACKAGE ++#define H5S_TESTING ++#include "H5Spkg.h" + + + static void coll_write_test(int chunk_factor); diff --git a/sci-libs/hdf5/files/hdf5-1.8.9-mpicxx.patch b/sci-libs/hdf5/files/hdf5-1.8.9-mpicxx.patch new file mode 100644 index 000000000000..28f554c0c592 --- /dev/null +++ b/sci-libs/hdf5/files/hdf5-1.8.9-mpicxx.patch @@ -0,0 +1,16 @@ +Prevent accidental inclusion of mpi c++ headers +when hdf5.h is included third party library + +https://bugs.gentoo.org/show_bug.cgi?id=420777 + +--- a/src/H5public.h ++++ b/src/H5public.h +@@ -58,6 +58,8 @@ + # include <stddef.h> + #endif + #ifdef H5_HAVE_PARALLEL ++# define OMPI_SKIP_MPICXX /* Make sure that cxx specific headers are not included */ ++# define MPICH_SKIP_MPICXX + # include <mpi.h> + #ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */ + # include <mpio.h> diff --git a/sci-libs/hdf5/files/hdf5-1.8.9-static_libgfortran.patch b/sci-libs/hdf5/files/hdf5-1.8.9-static_libgfortran.patch new file mode 100644 index 000000000000..f87ccdd08f7a --- /dev/null +++ b/sci-libs/hdf5/files/hdf5-1.8.9-static_libgfortran.patch @@ -0,0 +1,15 @@ +Make sure that during runtime we'll use the same libgfortran as during linking + +https://bugs.gentoo.org/show_bug.cgi?id=419991 +https://bugs.gentoo.org/show_bug.cgi?id=419895 + +--- a/fortran/src/Makefile.am ++++ b/fortran/src/Makefile.am +@@ -181,6 +181,7 @@ + else + H5test_kind_SOURCES = $(srcdir)/H5test_kind.f90 + endif ++H5test_kind_LDFLAGS=-static-libgfortran + + # Mark this directory as part of the Fortran API + FORTRAN_API=yes diff --git a/sci-libs/hdf5/hdf5-1.8.18.ebuild b/sci-libs/hdf5/hdf5-1.8.18.ebuild new file mode 100644 index 000000000000..4057134a614e --- /dev/null +++ b/sci-libs/hdf5/hdf5-1.8.18.ebuild @@ -0,0 +1,111 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED=fortran +AUTOTOOLS_AUTORECONF=1 + +inherit autotools-utils eutils fortran-2 flag-o-matic toolchain-funcs multilib + +MY_P=${PN}-${PV/_p/-patch} + +DESCRIPTION="General purpose library and file format for storing scientific data" +HOMEPAGE="http://www.hdfgroup.org/HDF5/" +#SRC_URI="https://support.hdfgroup.org/ftp/HDF5/releases/${MY_P}/src/${MY_P}.tar.bz2" +# TODO: return to proper SRC_URI once upstream fixes their release +SRC_URI="https://support.hdfgroup.org/ftp/HDF5/current18/src/${MY_P}.tar.bz2" + +LICENSE="NCSA-HDF" +SLOT="0/${PV%%_p*}" +KEYWORDS="alpha amd64 ~arm ~arm64 ia64 ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux" +IUSE="cxx debug examples fortran fortran2003 +hl mpi static-libs szip threads zlib" + +REQUIRED_USE=" + threads? ( !cxx !mpi !fortran !hl ) + fortran2003? ( fortran )" + +RDEPEND=" + mpi? ( virtual/mpi[romio] ) + szip? ( virtual/szip ) + zlib? ( sys-libs/zlib:0= )" + +DEPEND="${RDEPEND} + sys-devel/libtool:2 + >=sys-devel/autoconf-2.69" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch + "${FILESDIR}"/${PN}-1.8.9-mpicxx.patch + "${FILESDIR}"/${PN}-1.8.13-no-messing-ldpath.patch + "${FILESDIR}"/${PN}-1.8.15-implicits.patch +) + +pkg_setup() { + tc-export CXX CC AR # workaround for bug 285148 + if use fortran; then + use fortran2003 && FORTRAN_STANDARD=2003 + fortran-2_pkg_setup + fi + if use mpi; then + if has_version 'sci-libs/hdf5[-mpi]'; then + ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail." + ewarn "Try to uninstall the current hdf5 prior to enabling mpi support." + fi + export CC=mpicc + use fortran && export FC=mpif90 + if use cxx ; then + export CXX=mpicxx + ewarn "USE='mpi cxx' requires a configuration unsupported by upstream. Use at your own risk." + ewarn "In particular, the C++ API is not parallel safe." + fi + elif has_version 'sci-libs/hdf5[mpi]'; then + ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail." + ewarn "Try to uninstall the current hdf5 prior to disabling mpi support." + fi +} + +src_prepare() { + # respect gentoo examples directory + sed \ + -e "s:hdf5_examples:doc/${PF}/examples:g" \ + -i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die + sed \ + -e '/docdir/d' \ + -i config/commence.am || die + if ! use examples; then + sed -e '/^install:/ s/install-examples//' \ + -i Makefile.am || die #409091 + fi + # enable shared libs by default for h5cc config utility + sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" tools/misc/h5cc.in || die + # bug #419677 + use prefix && \ + append-ldflags -Wl,-rpath,"${EPREFIX}"/usr/$(get_libdir) \ + -Wl,-rpath,"${EPREFIX}"/$(get_libdir) + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-production + --docdir="${EPREFIX}"/usr/share/doc/${PF} + --enable-deprecated-symbols + $(use_enable prefix sharedlib-rpath) + $(use_enable debug debug all) + $(use_enable debug codestack) + $(use_enable cxx) + $(use_enable fortran) + $(use_enable fortran2003) + $(use_enable hl) + $(use_enable mpi parallel) + $(use_enable threads threadsafe) + $(use_with szip szlib) + $(use_with threads pthread) + $(use_with zlib) + $(use mpi && use cxx && echo --enable-unsupported) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/hdf5/metadata.xml b/sci-libs/hdf5/metadata.xml new file mode 100644 index 000000000000..9c9d5071aa84 --- /dev/null +++ b/sci-libs/hdf5/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + HDF5 is a file format and library for storing scientific data. HDF5 + was designed and implemented to address the deficiencies of HDF4.x. It + has a more powerful and flexible data model, supports files larger + than 2 GB, and supports parallel I/O. +</longdescription> + <use> + <flag name="fortran2003">Enable new features that require Fortran 2003 + (http://www.hdfgroup.org/HDF5/doc/fortran/NewFeatures_F2003.pdf)</flag> + <flag name="hl">Enable high level API + (https://support.hdfgroup.org/HDF5/doc/HL/index.html)</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest new file mode 100644 index 000000000000..03d729ae2d3b --- /dev/null +++ b/sci-libs/htslib/Manifest @@ -0,0 +1,5 @@ +DIST htslib-1.5.tar.bz2 1051132 SHA256 a02b515ea51d86352b089c63d778fb5e8b9d784937cf157e587189cb97ad922d SHA512 fd58552ddbd178f9797123fdaf47914ccd0e2aefd055fc6557ac8f479c600775616107cfa871c3acd93079f45974a19f443941a79f2acfd2a8c2983ef35b8917 WHIRLPOOL fb7026c26816db6746006d1b5ade235ce10181a633c9bab8ed3d9f72aaa152d0b68fd69d8988d69fef2bd2d57f9676de0761b2577ef0dd1d334da5d028cb64ee +EBUILD htslib-1.5.ebuild 769 SHA256 b6d7dc3d9fc707a1d18f5157d4bb7589e5541424f46460ef9dbc38b7b06822eb SHA512 e5df03c2dfa5088743674af125f7464a6e2add8d9c092060d7ddfc914cac4cff16d65eabb35ca3c199290461b92f7424a4347fded4f76dce763801b2b70f91c2 WHIRLPOOL a099d967b3cf780b3bce8aa8be9a016f2a0cfeae3212c6de37129e56e0ec691a8f825a30081cb4e1dadc99cee954896f34658daafbc354c4f8f1977c1d4737c6 +MISC ChangeLog 2816 SHA256 29bb0a3893413645602a369cae4c5eea0017bb2d8bb145a2debed426f1ed54e3 SHA512 753eccc9e6fbed3655add25379760e605fe280b75fe46ecbb7b59045ef39a225c54d80eb5d4a3d2999db45bad687dfa11769c27e33ae99ae4ebc074deadca18c WHIRLPOOL 979d98bc8e8f68a452451563fed6da037099e75d0dd941bc9d7fb1f7fde6871af69ab5bfab1088a16ad0fb12887eb5b12c6cc0f5ea3bdb1276ef86569f116511 +MISC ChangeLog-2015 1160 SHA256 73ce61e91f307b805648f5a76f694a6be2e4bba9a07d175d80740b5d6d1cc11b SHA512 d35ebd96c9e5279128f823e55a4a7eb027a622c5f73f21cae3b151ea3f7d679ccea22057902dae21558a2ae57fb7aff865dca217b3fae7a6224418c55bbef239 WHIRLPOOL f407acf8a7d7ea3c988f227e871df7e549238d1e3c14f84b9f2672c7274b7142ebc6ee024233bdf4b19f5a8d7e0c41d4331a542899749f1e5b56e34d91628b25 +MISC metadata.xml 349 SHA256 2b207b1089e4524124ade2610609ccb62e9916556681e30816be2977103227c5 SHA512 9108691a0c4c68ececa5e93d1719b4a6fc42c423c0b7dca3c037007873a40c86a44610c54139c6868391bb903d509b0202a87640d7114815d07ef62e478ffce7 WHIRLPOOL f293efbaf02dd19229edb93b9a1de22b9b784402d1070b1da9acef285ff36d82d14785bf13ed3147a10a61f528879371957f1285b60f4613aa49e2839f3c19f0 diff --git a/sci-libs/htslib/htslib-1.5.ebuild b/sci-libs/htslib/htslib-1.5.ebuild new file mode 100644 index 000000000000..d9957ce3a171 --- /dev/null +++ b/sci-libs/htslib/htslib-1.5.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="C library for high-throughput sequencing data formats" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2" + +SLOT="0/2" +LICENSE="MIT" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+bzip2 curl +lzma static-libs" + +RDEPEND=" + bzip2? ( app-arch/bzip2 ) + curl? ( net-misc/curl ) + lzma? ( app-arch/xz-utils )" +DEPEND="${RDEPEND}" + +src_configure() { + econf \ + --disable-gcs \ + --disable-plugins \ + --disable-s3 \ + $(use_enable bzip2 bz2) \ + $(use_enable curl libcurl) \ + $(use_enable lzma) +} + +src_install() { + default + + if ! use static-libs; then + find "${D}" -name '*.a' -delete || die + fi +} diff --git a/sci-libs/htslib/metadata.xml b/sci-libs/htslib/metadata.xml new file mode 100644 index 000000000000..5b953af488ad --- /dev/null +++ b/sci-libs/htslib/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">samtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/hypre/Manifest b/sci-libs/hypre/Manifest new file mode 100644 index 000000000000..7f19c3d2938d --- /dev/null +++ b/sci-libs/hypre/Manifest @@ -0,0 +1,7 @@ +DIST hypre-2.11.1.tar.gz 8054149 SHA256 6bb2ff565ff694596d0e94d0a75f0c3a2cd6715b8b7652bc71feb8698554db93 SHA512 4266c1b5225bcc97781246475100382f4929d7c918c854570a36b90602e8f111a4893cd1c93b95c68305c851898b970dd92ac173efe9211be5bb914d3c3c5d83 WHIRLPOOL b650b51b983d1af9bcec797c4160fc4161936d09534e0b21212b52d34f225fd91bd917eb97d7a92cbd544f9391b00f17337518be9b284e57b04eac80b81b4d59 +DIST hypre-2.9.0b.tar.gz 9053035 SHA256 6568f65e7c3c11531a00c300a059f0b81dcab3b2d038cd1154e1458a73edbe5d SHA512 6856f2c80eaf669258d73a36a59c0fd0f43e20a5b2e633b6aefbccf41f5217ea821a6201dadc0de2b17a039ba9f53d98031f0b091e3db552cc5251a4f766acb8 WHIRLPOOL acc84dec19fca2908170286adc582adb7c6b06d058a5518d87ccb4093a301046f978fea3ede6f854f9fcdf482993612b420bb0391474421b95721a91122b72dd +EBUILD hypre-2.11.1.ebuild 2894 SHA256 676fb076082f2aefe0ad563c84342e9c68abee706ba2b50b5481d3e2c70804a2 SHA512 1ad0f91f45d9aedc2b4e4495d448c4f21ee968158be5529ef07a22bb543a6752119d42099029e8537e870630be29080edc78b8f4d172ecf2b357383cb23a18d7 WHIRLPOOL 488e0b961871ab41bce383e3e1475e0b0e4ff4e1c4b76a0ab0afe4f353ec104787518438a9fb25b31b8a8bbf22e9f95beed0eb03b860b34377669c466008b781 +EBUILD hypre-2.9.0b.ebuild 1826 SHA256 48f58b95bcecf9369921425382574875c24d46b32417d5f95178f99c69f429b1 SHA512 15da19738acd91d284fb7dd936017f963e25edd116da5bb63340766592c2f1413b7340f7c53ebcee3fc676fa37ca750202302f599ebcff260650d07be18b760b WHIRLPOOL f4c0d02bca901ce22f8f27bb4a475b41b491a4aad4977fb07b31323d9569eaf1371b6ef7d4490a3ee96c89d8363e77a65c1c27a598fc95b626d9ab736270ec31 +MISC ChangeLog 2423 SHA256 775a0ab9256d5a59c6fdefbb4f3fed96334b3c314ecf005fb49b4eb57cf3125c SHA512 878b9aaa551c38ed154d872f17e47955d51b933874fa234f68b0b1b19cb522c1c15096edd0238425c0d5c39c2ae795d84184a983b468a495fbefd38d38e94661 WHIRLPOOL 51d73b6828fd1da745097cd2e45436e37e7f2a245c041bcb8ff67a6f043938df3f30e045818db312fca56a35f5325f9c0137a4f9a3c8afd3d74fd5c0ffe43f49 +MISC ChangeLog-2015 2448 SHA256 2b7203c2dc85532f8c7a53e8c603eb850a18694c4f86b6ed5d4bcd51ba83ca7a SHA512 3ba50f8df84f25aa1f55341db22987786f369f411cfbb502bd49cb9fc53e0f802d30bdcf9f9cc855bc4e554621f6de66f2b6b54ea9671c9b9abb247b79caac5b WHIRLPOOL e19b08dfc917f58d46e6201118ba3d13f97d2dae335492145fc30633db86104ed2cf14bc9f3e9c9d8e4fae8206fb4ee0403132e7fb282a90af9f43ad6c2f9435 +MISC metadata.xml 689 SHA256 ce4be07db5ce24ee372f7ba301d079e6ef111c1d0fe2af5953d50a9b43879c87 SHA512 fb10f8f67754f103b109fa7696e66e02f6a66ff74472341f3e2dcb27957646fd4140594c9eee489c3d47f1985bf8a122b48269c6a6168ddbfcdcd0ffe2a415e2 WHIRLPOOL affb892d49f0e6ced33133b135a85ba31cc169951bc7662f64b25f90c047eef10825efbbd3ad599db2f38dc7e805400409d70b389603f8bb0eab3d2c560140cd diff --git a/sci-libs/hypre/hypre-2.11.1.ebuild b/sci-libs/hypre/hypre-2.11.1.ebuild new file mode 100644 index 000000000000..7131f2b2fcec --- /dev/null +++ b/sci-libs/hypre/hypre-2.11.1.ebuild @@ -0,0 +1,107 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit cmake-utils fortran-2 toolchain-funcs flag-o-matic + +DESCRIPTION="Parallel matrix preconditioners library" +HOMEPAGE="http://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods" +SRC_URI="${HOMEPAGE}/download/${P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug doc examples fei fortran int64 openmp mpi" + +RDEPEND=" + sci-libs/superlu:= + virtual/blas + virtual/lapack + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +DOCS=( CHANGELOG COPYRIGHT README ) + +# 2.11.1: fei and mli wrappers still buggy with big integers +REQUIRED_USE="int64? ( !fei )" + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] &&\ + use openmp && [[ $(tc-getCC)$ == *gcc* ]] && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && \ + use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp ; then + ewarn "You are using a non capable gcc compiler ( < 4.2 ? )" + die "Need an OpenMP capable compiler" + fi +} + +src_prepare() { + default + # link with system superlu and propagate LDFLAGS + sed -e "s:@LIBS@:@LIBS@ $($(tc-getPKG_CONFIG) --libs superlu):" \ + -e 's:_SHARED@:_SHARED@ $(LDFLAGS):g' \ + -i src/config/Makefile.config.in || die + sed -e '/HYPRE_ARCH/s: = :=:g' \ + -i src/configure || die + # link with system blas and lapack + sed -e '/^BLASFILES/d' \ + -e '/^LAPACKFILES/d' \ + -i src/lib/Makefile || die +} + +src_configure() { + tc-export CC CXX + append-flags -Dhypre_dgesvd=dgesvd_ + use openmp && [[ $(tc-getCC)$ == *gcc* ]] && \ + append-flags -fopenmp && append-ldflags -fopenmp + use mpi && CC=mpicc FC=mpif77 CXX=mpicxx + + cd src + + # without-superlu: means do not use bundled one + econf \ + --enable-shared \ + --with-blas-libs="$($(tc-getPKG_CONFIG) --libs-only-l blas | sed -e 's/-l//g')" \ + --with-blas-lib-dirs="$($(tc-getPKG_CONFIG) --libs-only-L blas | sed -e 's/-L//g')" \ + --with-lapack-libs="$($(tc-getPKG_CONFIG) --libs-only-l lapack | sed -e 's/-l//g')" \ + --with-lapack-lib-dirs="$($(tc-getPKG_CONFIG) --libs-only-L lapack | sed -e 's/-L//g')" \ + --with-timing \ + --without-superlu \ + $(use_enable debug) \ + $(use_enable openmp hopscotch) \ + $(use_enable int64 bigint) \ + $(use_enable fortran) \ + $(use_with fei) \ + $(use_with fei mli) \ + $(use_with openmp) \ + $(use_with mpi MPI) +} + +src_compile() { + emake -C src +} + +src_test() { + LD_LIBRARY_PATH="${S}/src/lib:${LD_LIBRARY_PATH}" \ + PATH="${S}/src/test:${PATH}" \ + emake -C src check +} + +src_install() { + emake -C src install \ + HYPRE_INSTALL_DIR="${ED}" \ + HYPRE_LIB_INSTALL="${ED}/usr/$(get_libdir)" \ + HYPRE_INC_INSTALL="${ED}$/usr/include/hypre" + use doc && dodoc docs/*.pdf + if use examples; then + insinto /usr/share/doc/${PF} + doins -r src/examples + fi +} diff --git a/sci-libs/hypre/hypre-2.9.0b.ebuild b/sci-libs/hypre/hypre-2.9.0b.ebuild new file mode 100644 index 000000000000..ce42c05cbcbe --- /dev/null +++ b/sci-libs/hypre/hypre-2.9.0b.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="Parallel matrix preconditioners library" +HOMEPAGE="http://acts.nersc.gov/hypre/" +SRC_URI="https://computation.llnl.gov/casc/hypre/download/${P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples fortran mpi" + +RDEPEND=" + sci-libs/superlu:0= + virtual/blas + virtual/lapack + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +DOCS=( "${WORKDIR}"/${P}/{CHANGELOG,COPYRIGHT,README} ) + +S="${WORKDIR}/${P}/src" + +src_prepare() { + # link with system superlu and propagate LDFLAGS + sed -i \ + -e 's:@LIBS@:@LIBS@ -lsuperlu:' \ + -e 's:_SHARED@:_SHARED@ $(LDFLAGS):g' \ + config/Makefile.config.in || die + sed -i \ + -e '/HYPRE_ARCH/s: = :=:g' \ + configure || die + # link with system blas and lapack + sed -i \ + -e '/^BLASFILES/d' \ + -e '/^LAPACKFILES/d' \ + lib/Makefile || die + use mpi && export CC=mpicc CXX=mpicxx FC=mpif77 + tc-export CC CXX +} + +src_configure() { + local myeconfargs=( + --enable-shared + --without-superlu + --with-blas-libs="$($(tc-getPKG_CONFIG) --libs-only-l blas | sed -e 's/-l//g')" + --with-blas-lib-dirs="$($(tc-getPKG_CONFIG) --libs-only-L blas | sed -e 's/-L//g')" + --with-lapack-libs="$($(tc-getPKG_CONFIG) --libs-only-l lapack | sed -e 's/-l//g')" + --with-lapack-lib-dirs="$($(tc-getPKG_CONFIG) --libs-only-L lapack | sed -e 's/-L//g')" + $(use_enable fortran) + $(use_with mpi MPI) + ) + econf "${myeconfargs[@]}" +} + +src_install() { + dolib.so hypre/lib/lib* + insinto /usr/include/hypre + doins -r hypre/include/* + + use doc && dodoc "${WORKDIR}"/${P}/docs/*.pdf + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/hypre/metadata.xml b/sci-libs/hypre/metadata.xml new file mode 100644 index 000000000000..48b9bd61f1b4 --- /dev/null +++ b/sci-libs/hypre/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-mathematics@gentoo.org</email> + <name>Gentoo Mathematics Project</name> + </maintainer> + <longdescription lang="en"> + Hypre is a set of matrix preconditioning libraries to aid in the + solution of large systems of linear equations. + </longdescription> + <upstream> + <remote-id type="github">LLNL/hypre</remote-id> + </upstream> + <use> + <flag name="int64">Build the 64 bits integer library</flag> + <flag name="fei">Build the internal Finite Element Interface routines</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/idlcoyote/Manifest b/sci-libs/idlcoyote/Manifest new file mode 100644 index 000000000000..3655a1708b46 --- /dev/null +++ b/sci-libs/idlcoyote/Manifest @@ -0,0 +1,5 @@ +DIST idlcoyote-20161220.zip 1437560 SHA256 64cf332a6f630f97799837dc0592a28945aa3543bc38976fc1543af22fecbd30 SHA512 2c175cf3a42a0f2915eb8d02884f06892245ee023e6f3f2702b00ced0311dcde504d014fb8936aef7148fe6d91e258e3f6ffeec7d5c0bb22f65962b8ebe3bd8b WHIRLPOOL a4949825fc53d5002af68764df598e914525e853b929c9a686550b33c741466e1aec00b01ed083442c5baebcd89ef2314e0cb103050cfd379e161aaed49fa94d +EBUILD idlcoyote-20161220.ebuild 716 SHA256 8f9cd0c21c5951ecff449f1b3a414bbc9833a3769e5c9a4564c9fd1adc943d0a SHA512 ab15c9d275ff96b99814952ec5a1f6cc5ce079e338908688e97625ebf519d8da474df7188bd8932e1587b92565d965bb77b4c4c7f75983c530ebcd1b23f56979 WHIRLPOOL c0e6eca2848756dcf4b8a7110b9f4af04dcee9249d611f98c4856826eec5a2d6c4c07780e8985df76aab7ce731200db9b29426a2d96ecce986593b1719dfab22 +EBUILD idlcoyote-99999999.ebuild 716 SHA256 8f9cd0c21c5951ecff449f1b3a414bbc9833a3769e5c9a4564c9fd1adc943d0a SHA512 ab15c9d275ff96b99814952ec5a1f6cc5ce079e338908688e97625ebf519d8da474df7188bd8932e1587b92565d965bb77b4c4c7f75983c530ebcd1b23f56979 WHIRLPOOL c0e6eca2848756dcf4b8a7110b9f4af04dcee9249d611f98c4856826eec5a2d6c4c07780e8985df76aab7ce731200db9b29426a2d96ecce986593b1719dfab22 +MISC ChangeLog 395 SHA256 b1eba7fdf87d446ecef0d150f7717d006174dccfc83175cf0026bbc1f87f321f SHA512 7bc4be108b09cebaf2f333c0cdb5bfadc82c8755b1399b05b913958d0e783cf431ccc35cc5b1e7916876c8cc7defee708a8e64460f3efe8e80dcd98218f8f8d1 WHIRLPOOL 226e5aff3fdbfee2296f09bd3cb697362f2a489d28e8b5b01421168d454e127afe187a6c20eee23711e45d266ff4b741dabcda1a726401da409acf7cddbc4055 +MISC metadata.xml 606 SHA256 c3be8b6eb906a1937da691cf9fa05537fcc7a44e47eee09bf31f6929fb6b13c3 SHA512 06b29c96c7e57cf99f22333ba9df18a23fac6659d1ae57fbe9273c0f548cec1f0a18a5500222e4c000cfb3307bdc8c450da7c57e6e4be7143490c3ca282c76cb WHIRLPOOL f9a1f4844ce68356e1d86a9d05a5b7e77596378318bba39a9596a64e2bcedc51a78af3688aa5f693d5305373c078f94b6cdf3bb7977a2ed445b416a904dd5d00 diff --git a/sci-libs/idlcoyote/idlcoyote-20161220.ebuild b/sci-libs/idlcoyote/idlcoyote-20161220.ebuild new file mode 100644 index 000000000000..20857bb5a31f --- /dev/null +++ b/sci-libs/idlcoyote/idlcoyote-20161220.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +if [[ ${PV} != 99999999 ]]; then + SRC_URI="http://www.idlcoyote.com/programs/zip_files/coyoteprograms.zip -> ${P}.zip" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + S="${WORKDIR}/coyote" + DEPEND="app-arch/unzip" +else + inherit git-r3 + GIT_ECLASS="git-r3" + EGIT_REPO_URI="https://github.com/idl-coyote/coyote.git" + KEYWORDS="" +fi + +DESCRIPTION="GDL library from D. Fannings IDL courses" +HOMEPAGE="http://www.idlcoyote.com/" + +LICENSE="BSD GPL-2" +SLOT="0" +IUSE="" + +RDEPEND="dev-lang/gdl" + +src_install() { + dodoc README.txt + rm README.txt || die + insinto /usr/share/gnudatalanguage/coyote + doins -r * +} diff --git a/sci-libs/idlcoyote/idlcoyote-99999999.ebuild b/sci-libs/idlcoyote/idlcoyote-99999999.ebuild new file mode 100644 index 000000000000..20857bb5a31f --- /dev/null +++ b/sci-libs/idlcoyote/idlcoyote-99999999.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +if [[ ${PV} != 99999999 ]]; then + SRC_URI="http://www.idlcoyote.com/programs/zip_files/coyoteprograms.zip -> ${P}.zip" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + S="${WORKDIR}/coyote" + DEPEND="app-arch/unzip" +else + inherit git-r3 + GIT_ECLASS="git-r3" + EGIT_REPO_URI="https://github.com/idl-coyote/coyote.git" + KEYWORDS="" +fi + +DESCRIPTION="GDL library from D. Fannings IDL courses" +HOMEPAGE="http://www.idlcoyote.com/" + +LICENSE="BSD GPL-2" +SLOT="0" +IUSE="" + +RDEPEND="dev-lang/gdl" + +src_install() { + dodoc README.txt + rm README.txt || die + insinto /usr/share/gnudatalanguage/coyote + doins -r * +} diff --git a/sci-libs/idlcoyote/metadata.xml b/sci-libs/idlcoyote/metadata.xml new file mode 100644 index 000000000000..298edd428429 --- /dev/null +++ b/sci-libs/idlcoyote/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-astronomy@gentoo.org</email> + <name>Gentoo Astronomy Project</name> + </maintainer> + <longdescription lang="en"> + The Coyote Library evolved from work David Fanning was doing teaching + IDL courses and answering IDL questions on the IDL newsgroup. It is + meant to be a well-documented library that demonstrates how to write + solid IDL/GDL programs that are easy to maintain and extend. + </longdescription> +</pkgmetadata> diff --git a/sci-libs/idlmarkwardt/Manifest b/sci-libs/idlmarkwardt/Manifest new file mode 100644 index 000000000000..dd175ecef255 --- /dev/null +++ b/sci-libs/idlmarkwardt/Manifest @@ -0,0 +1,7 @@ +DIST idlmarkwardt-20130418.tar.gz 703131 SHA256 b1abe54bf1ca7ce2940abf31ef43cebf838e748be482da1745e2014aa1b94369 SHA512 e93187ffa6c719c9b3b54bf61d5b138abd6c7cc91029b0802b9542c6699c29c3d8ee26e3afeccf10bfabecea36d588cd27031621739ab509e3dfd6c0ade7b4cc WHIRLPOOL b18c5f22a43d270972f1fbfc4b7cd8d7b10a48d3163551015c35a05829adf1d9a6c66fdc88a23331ca4f9b0f0b04a6600ea99bf0828e7d8e5eeccd0860773f8f +DIST idlmarkwardt-20160319.tar.gz 705496 SHA256 ea81dd2b8875647f9717da631b3ae34d0cde129e319224b500b72fc0befa4f47 SHA512 b0eb3ee4cf4ac9450e2557f1ec53660ed6e618a4602f592d551d0a81270aba15cd4eeefb1307b415f2b6f498c192db54ca1ef5e07400260b25a2f7f4b308ecdc WHIRLPOOL 50bd003690ee77179e68ee093786d20da9ac1c27b9ee6fa72860a3b7b140ae0048d7acf876c2b467892d6e85c5e883743f97cc5afd854c95bc2337e8a6702926 +EBUILD idlmarkwardt-20130418.ebuild 552 SHA256 a5d60efed1f79f310abb2007b8b29412e87b58e4c6e40c78155ac6de68f2fe1e SHA512 e785c100df3dddd4751e799a17b3fa404972178198c457fd662eb1780b7b4c084911e4a0fcc08878bf05648f2aa87dc7d8c2633e1184c4c54f3e9c0ef92ade3d WHIRLPOOL 62f5a27188d3743829010662e45f4332cdb07539f5cd9ab993b1d8c31949430d5986325eec747ce6dc00fdd186c932dc43a98acff0966aec4f6dd3e106017ffe +EBUILD idlmarkwardt-20160319.ebuild 552 SHA256 a5d60efed1f79f310abb2007b8b29412e87b58e4c6e40c78155ac6de68f2fe1e SHA512 e785c100df3dddd4751e799a17b3fa404972178198c457fd662eb1780b7b4c084911e4a0fcc08878bf05648f2aa87dc7d8c2633e1184c4c54f3e9c0ef92ade3d WHIRLPOOL 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cffd6b2db81b376426fe6713f6f1b7c25bcf44ccab7248639908af3b93571f4099223ce436248735ffdb3465ef8438867f9a75b81d3e1bffea9a3e795a9c8ea3 WHIRLPOOL a15554a5828b57de315a98ec278bcf7286a6cb24c799fb6382fac8acebae046b59146bece20b6512178a7c6e3a8881f2ef7ca53063828c48be474323384ed2c3 diff --git a/sci-libs/idlmarkwardt/idlmarkwardt-20130418.ebuild b/sci-libs/idlmarkwardt/idlmarkwardt-20130418.ebuild new file mode 100644 index 000000000000..695912942d65 --- /dev/null +++ b/sci-libs/idlmarkwardt/idlmarkwardt-20130418.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Craig Markwardt IDL procedures (MPFIT, CMSVLIB, etc)" +HOMEPAGE="http://cow.physics.wisc.edu/~craigm/idl/idl.html" +SRC_URI="http://www.physics.wisc.edu/~craigm/idl/down/cmtotal.tar.gz -> ${P}.tar.gz" + +LICENSE="Markwardt" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="" +RDEPEND="dev-lang/gdl" + +S="${WORKDIR}" + +src_install() { + insinto /usr/share/gnudatalanguage/${PN} + doins *.pro + dodoc *README +} diff --git a/sci-libs/idlmarkwardt/idlmarkwardt-20160319.ebuild b/sci-libs/idlmarkwardt/idlmarkwardt-20160319.ebuild new file mode 100644 index 000000000000..695912942d65 --- /dev/null +++ b/sci-libs/idlmarkwardt/idlmarkwardt-20160319.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Craig Markwardt IDL procedures (MPFIT, CMSVLIB, etc)" +HOMEPAGE="http://cow.physics.wisc.edu/~craigm/idl/idl.html" +SRC_URI="http://www.physics.wisc.edu/~craigm/idl/down/cmtotal.tar.gz -> ${P}.tar.gz" + +LICENSE="Markwardt" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="" +RDEPEND="dev-lang/gdl" + +S="${WORKDIR}" + +src_install() { + insinto /usr/share/gnudatalanguage/${PN} + doins *.pro + dodoc *README +} diff --git a/sci-libs/idlmarkwardt/metadata.xml b/sci-libs/idlmarkwardt/metadata.xml new file mode 100644 index 000000000000..4e4195583fcb --- /dev/null +++ b/sci-libs/idlmarkwardt/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + Library of IDL software procedures that Craig Markwardt is making + available to the general public. It contains: + * Curve Fitting and Function Minimization + * Read and Write SAVE Files + * Graphics Programs + * Mathematics + * Ephemeris and Timing + * Array / Set Operations + * Input / Output +</longdescription> +</pkgmetadata> diff --git a/sci-libs/ignition-math/Manifest b/sci-libs/ignition-math/Manifest new file mode 100644 index 000000000000..f532025287d0 --- /dev/null +++ b/sci-libs/ignition-math/Manifest @@ -0,0 +1,4 @@ +DIST ignition-math3_3.2.0.tar.bz2 382201 SHA256 929794ababed10c92d7217973e1d268a9de4a51dae80c401c6d1333ff65f7f89 SHA512 ffb5d61105ba0951c6420c53d64b47bdd65bdcac17e8ef2ce7cb83aeb2310280e5acb4d029d1af5c05fb5c40accf05df61d1e04dc990225159f1749284e3dcf1 WHIRLPOOL 300279c839246ab892c79cdf4dbe0a59a188f9e0ca10b0980e0dd3bbcbe11ea776bcfacae3c7c56b0d7d4d991183235db0addd688d5f44129ca216c96e74d451 +EBUILD ignition-math-3.2.0.ebuild 880 SHA256 ce94e09e0717aac949b71a29846851149509820694f87fb571b932556a347b15 SHA512 8c5e7eb0bba7b5c928dd42169a7ffcc594ef338314dfa81373b6ffe3e5d836d944627ae68c342ca01b630c6badb1e094cb680e449fb5d68f160fb9b93bf96a88 WHIRLPOOL 7bcc650651ee183de44a828affbeef7a59c1212c4a509a8e6b808fb87f62940a7ad3762b4255d060ffaf53b70b0ab8f4f5349dc0356071e698f7ae29e0dafd5b +MISC ChangeLog 1987 SHA256 f424ee8c6f10f257435d0b99d0d2554bdeccee62db5966cf8def5a28e05a1779 SHA512 1a73a35e3b2f26998f2505f195ced77d1b2ef93c7b112c3c19b746cd7847df4636a6a8a31174ca25baca8025475aa32bf441a17dde8b28c1b734e0470eaad49e WHIRLPOOL 3c4c2ddc28912aca3c2eb6ff9808481a41881e42a4f95fec8fe346e65fbcd4929f64d98f8b148a940c142580465b4a197f273308ce7cdc1968849a3f1e16e912 +MISC metadata.xml 342 SHA256 f21cd7dd1f0994b6e4a35cc4e60fa40017f50ddb9c29cfa9c5031cd29c329cf9 SHA512 8969e6c2df55cfae7cc21640498871d7049499d146d06b13057701e742e9ef6f2c5124acd144b9e7f0974ea39032e89402252e32192242697555c64d90eb4b4a WHIRLPOOL 5a6f57638a4e971df8698ec5d73bf13f0b4afb48ab0fcc73e060341c2cb499794d44127e1c7c8fcfb51580da84cc0aaa97d0e16bf4bf731dec5ce62af4d451cb diff --git a/sci-libs/ignition-math/ignition-math-3.2.0.ebuild b/sci-libs/ignition-math/ignition-math-3.2.0.ebuild new file mode 100644 index 000000000000..edbe8795a029 --- /dev/null +++ b/sci-libs/ignition-math/ignition-math-3.2.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-multilib vcs-snapshot flag-o-matic + +DESCRIPTION="A small, fast, and high performance math library for robot applications" +HOMEPAGE="http://ignitionrobotics.org/libraries/math" +SRC_URI="https://bitbucket.org/ignitionrobotics/ign-math/get/${PN}3_${PV}.tar.bz2" + +LICENSE="Apache-2.0" +SLOT="3/3" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" +S="${WORKDIR}/${PN}3_${PV}" +CMAKE_BUILD_TYPE=RelWithDebInfo + +src_configure() { + # upstream appends this conditionally... + append-flags "-fPIC" + echo "set (CMAKE_C_FLAGS_ALL \"${CXXFLAGS} \${CMAKE_C_FLAGS_ALL}\")" > "${S}/cmake/HostCFlags.cmake" + sed -i -e "s/LINK_FLAGS_RELWITHDEBINFO \" \"/LINK_FLAGS_RELWITHDEBINFO \" ${LDFLAGS} \"/" cmake/DefaultCFlags.cmake || die + cmake-multilib_src_configure +} diff --git a/sci-libs/ignition-math/metadata.xml b/sci-libs/ignition-math/metadata.xml new file mode 100644 index 000000000000..cd92ae6d0f49 --- /dev/null +++ b/sci-libs/ignition-math/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>aballier@gentoo.org</email> + <name>Alexis Ballier</name> + </maintainer> + <upstream> + <remote-id type="bitbucket">ignitionrobotics/ign-math</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/inchi/Manifest b/sci-libs/inchi/Manifest new file mode 100644 index 000000000000..ceef9ded4824 --- /dev/null +++ b/sci-libs/inchi/Manifest @@ -0,0 +1,8 @@ +AUX inchi-1.03-shared.patch 804 SHA256 bff5e32c125603e02f48f035493a9e5b342c4d0706f95f4c0d79418ff3342007 SHA512 58fef060fd199cd12f62135a139d0e09a5e50c7b0e8e3c992c698ab10ad88f938f18e002b5f590d0f4346b4a801b62906bdb0dd6391ad8e53e9c59f62a465085 WHIRLPOOL 907c2b55f89c22fc16f0a231b02232696c86572e239584156beca4dce45de6590534ee1ef8218bfdf1f62854eb9bb302779412067ed2287382c5a9511f20203b +AUX inchi-1.04-static.patch 570 SHA256 d69d5b5ec0f39ba0f3281ea9604d36a2ed9ab022f30e441fa52f886077391ae2 SHA512 0bc4aaf5ff4565517dbef481ca89069f3e91bd8d2b02f8e2591519183feca8725004a51375bec4560002d35b030483a21d9e36a1eb8202e3692186e23dcb7078 WHIRLPOOL aedda41fa4c38c46f419635a0d2509730ae20cc72e25b58147cf1215548a59dfb08ebd5471358f3268647e475ac5f3e388ba52c4f1dcad2b76a2118c064e858b +DIST inchi-1.04-doc.zip 2128303 SHA256 abede36063e838614aa6ade7f20f386f557a78aefb041e1ba0b736088a6a79bc SHA512 930fe10ac2bae11074b7e47446b5af9c01e2aa55f891d04912c71c76e214871c78cc22b3dafea99b57eede5080ac0cfaa6b6d35a73242c8549bea8ffa86e7df7 WHIRLPOOL 5cb5884dbfc9f2e530deb8be0e35643b0a6af70a5b4e069cd610407fac067261a3282ad9db22651fc2efc313ade78930de10ff165dd709a83880815b89e4a4fd +DIST inchi-1.04.zip 2701930 SHA256 c187573c0f6a1fcd555393315383bd1f69563ee47bd43c898f17c473b7bb690a SHA512 c5a1c2f08d472fcde603acbd898a9a8880407474869eadf0089444503693ae89ff805c579161cb3ee9d7f18e891289a21c4b8a65cc7ece69ee730f7f4e283be4 WHIRLPOOL 89a7ac2f80a9a87a663934bd0f24af6aed77f51115bf0b4858f66c135f932b67dff7bbffa16999ab79f7ca1358ef716fa5f11cb8756011f7622f6440470c59e4 +EBUILD inchi-1.04.ebuild 1866 SHA256 a659274037ee6aeecf7629bbe6d2ec919121c7e7571419a75d5424d7f8abd4b8 SHA512 f1a9bff0cfe54e26d0c0368c539cc66cf0d405c852e7959f07ef9795082b74e1f7866c7c094edd8e83557af293b488f20c8e0adfaa083e5ba176b6aae158f7be WHIRLPOOL c18c8ee2176575f249b4211fd465452f9eb990e8b6c0b030e60f88b7c59dc56c0b0e1d4d1eeaac565b5eaf120d7c6db1bccf1a65bd7119fd862661b81123a33d +MISC ChangeLog 2589 SHA256 ddbae389b130fa7af58e07d833516b2876916a67db5868c389644c4e46c889f7 SHA512 9276192da35219087f8de278be62b91e1cb389c6ebb92b8c895a495fd97d9148fc7927adb357e544e5bad5d0bbd2adb859f867aa1564fe91c63920f856c3624a WHIRLPOOL 93803a6b84d3f03e2d013d98ed365226ac0cfbe18944115f698886c4c0a7ae245a668b23c1901b4c2155cc778d102d2990cd515ea314547e429d615f0183a4a2 +MISC ChangeLog-2015 1702 SHA256 a5bcded51299c1740873451567d165af4c013249c79bc552d7d72e9132beafdc SHA512 12ff775e363978b3d8f3914844247714fff411f40cf895b8cf3a59e285adf3c25c3b7d3053792e75b056f7c0379d6163a87ba95ab8ec33a663d5d205804a28f9 WHIRLPOOL 697dec9225646c02a4df216f16187fd4711415d4d42bc0170be5620dca851bf486daa33a41b7ea093031373891dd64558ccf328a98b554a60a4c32552d7a2e95 +MISC metadata.xml 380 SHA256 2482e06cc13a03e4b3002070dc286a604c5a091013f673d8b096fc08326a6a98 SHA512 04f24f7bca8346ab9b06e3e7edd77e45a38bf48bb2a4592234999cf3f6fccd74851508b892e5d6b33ae9cac00ec7725985924e91c5a6fae3a032e551acfb044e WHIRLPOOL 1cc7f58c0103d3a995f0e7710a5b8d6e4d3573e64119872b8c4cb49c9c2896824f2513056086d7e6cd00dd614c36f5fef13af1e011a016e3bf28bd9122593bc8 diff --git a/sci-libs/inchi/files/inchi-1.03-shared.patch b/sci-libs/inchi/files/inchi-1.03-shared.patch new file mode 100644 index 000000000000..6f4619d86bd9 --- /dev/null +++ b/sci-libs/inchi/files/inchi-1.03-shared.patch @@ -0,0 +1,20 @@ + INCHI_API/gcc_so_makefile/makefile | 4 +++- + 1 files changed, 3 insertions(+), 1 deletions(-) + +diff --git a/INCHI_API/gcc_so_makefile/makefile b/INCHI_API/gcc_so_makefile/makefile +index dd8e53c..cd617ad 100644 +--- a/INCHI_API/gcc_so_makefile/makefile ++++ b/INCHI_API/gcc_so_makefile/makefile +@@ -213,9 +213,11 @@ $(INCHI_LIB_PATHNAME).so$(VERSION): $(INCHI_LIB_OBJS) + $(SHARED_LINK) $(SHARED_LINK_PARM) -o \ + $(INCHI_LIB_PATHNAME).so$(VERSION) \ + $(INCHI_LIB_OBJS) \ +- -Wl$(LINUX_MAP)$(LINUX_Z_RELRO),-soname,$(INCHI_LIB_NAME).so$(MAIN_VERSION) ++ -Wl$(LINUX_MAP)$(LINUX_Z_RELRO),-soname,$(INCHI_LIB_NAME).so$(MAIN_VERSION) -lm + ln -fs $(INCHI_LIB_NAME).so$(VERSION) \ + $(INCHI_LIB_PATHNAME).so$(MAIN_VERSION) ++ ln -fs $(INCHI_LIB_NAME).so$(VERSION) \ ++ $(INCHI_LIB_PATHNAME).so + + endif + diff --git a/sci-libs/inchi/files/inchi-1.04-static.patch b/sci-libs/inchi/files/inchi-1.04-static.patch new file mode 100644 index 000000000000..a367c153824a --- /dev/null +++ b/sci-libs/inchi/files/inchi-1.04-static.patch @@ -0,0 +1,26 @@ +--- INCHI_API/gcc_so_makefile/makefile 2012-05-13 14:52:53.587632989 +0300 ++++ INCHI_API/gcc_so_makefile/makefile 2012-05-13 14:52:11.668635419 +0300 +@@ -209,6 +209,14 @@ + + else + ++ifdef STATIC ++ ++libinchi.a: $(INCHI_LIB_OBJS) ++ $(AR) rcs $(INCHI_LIB_PATHNAME).a $(INCHI_LIB_OBJS) ++ $(RANLIB) $(INCHI_LIB_PATHNAME).a ++ ++else ++ + $(INCHI_LIB_PATHNAME).so$(VERSION): $(INCHI_LIB_OBJS) + $(SHARED_LINK) $(SHARED_LINK_PARM) -o \ + $(INCHI_LIB_PATHNAME).so$(VERSION) \ +@@ -219,6 +226,8 @@ + + endif + ++endif ++ + # === InChI Library compile rule ========= + + %.o: $(P_LIBR)%.c diff --git a/sci-libs/inchi/inchi-1.04.ebuild b/sci-libs/inchi/inchi-1.04.ebuild new file mode 100644 index 000000000000..84ae21c021e9 --- /dev/null +++ b/sci-libs/inchi/inchi-1.04.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="A program and library for generating standard and non-standard InChI and InChIKeys" +HOMEPAGE="http://www.iupac.org/inchi/" +SRC_URI=" + http://www.inchi-trust.org/sites/default/files/inchi-${PV}/INCHI-1-API.ZIP -> ${P}.zip + doc? ( http://www.inchi-trust.org/sites/default/files/inchi-${PV}/INCHI-1-DOC.ZIP -> ${P}-doc.zip )" + +LICENSE="IUPAC-InChi" +SLOT="0" +KEYWORDS="amd64 arm ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +DEPEND="app-arch/unzip" +RDEPEND="" + +S="${WORKDIR}"/INCHI-1-API + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-1.03-shared.patch \ + "${FILESDIR}"/${PN}-1.04-static.patch + tc-export AR RANLIB +} + +src_compile() { + local dir common_opts + common_opts=( + C_COMPILER=$(tc-getCC) + CPP_COMPILER=$(tc-getCXX) + LINKER="$(tc-getCXX) ${LDFLAGS}" + SHARED_LINK="$(tc-getCC) ${LDFLAGS} -shared" + C_COMPILER_OPTIONS="\${P_INCL} -ansi -DCOMPILE_ANSI_ONLY ${CFLAGS} -c " + CPP_COMPILER_OPTIONS="\${P_INCL} -D_LIB -ansi ${CXXFLAGS} -frtti -c " + C_OPTIONS="${CFLAGS} -fPIC -c " + LINKER_OPTIONS="${LDFLAGS}" + CREATE_MAIN= + ISLINUX=1 + ) + for dir in INCHI/gcc/inchi-1 INCHI_API/gcc_so_makefile; do + pushd ${dir} > /dev/null + emake \ + "${common_opts[@]}" + popd > /dev/null + done + if use static-libs ; then + pushd INCHI_API/gcc_so_makefile > /dev/null + emake libinchi.a \ + "${common_opts[@]}" \ + STATIC=1 + popd > /dev/null + fi +} + +src_install() { + dodoc readme*.txt + if use doc ; then + cd "${WORKDIR}/INCHI-1-DOC/" + docinto doc + dodoc *.pdf readme.txt + fi + dobin "${S}"/INCHI/gcc/inchi-1/inchi-1 + cd "${S}/INCHI_API/gcc_so_makefile/result" || die + rm *gz || die + dolib.so lib*so* + use static-libs && dolib.a lib*a + doheader ../../inchi_main/inchi_api.h +} diff --git a/sci-libs/inchi/metadata.xml b/sci-libs/inchi/metadata.xml new file mode 100644 index 000000000000..9b10958b0172 --- /dev/null +++ b/sci-libs/inchi/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Program v1.03 implementing IUPAC (Standard) InChI/InChIKey version 1. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/indilib/Manifest b/sci-libs/indilib/Manifest new file mode 100644 index 000000000000..4d17b8a5cdc6 --- /dev/null +++ b/sci-libs/indilib/Manifest @@ -0,0 +1,7 @@ +DIST indi-1.3.1.zip 20752009 SHA256 a28b3cd578ac6c85bda91ace287f0d37e6e315d1746d55d1623f9094ebf5747b SHA512 80184287aebf1bc8381ba9f36b83f346411348c610c6c06c7b9aeb4a2c9f3a9713e4f043af66cb777d7fa8fe208d98fa1134c1f0935a706d1797eae38f0ef3f0 WHIRLPOOL 7335c2c4ab9da01fddf1c8844500fe0da35d0e139f9ac67ac8133f5d922f8a6a4ec4bf83859f6aa8e9389e4563820a106f3cb3473c7d4e8a2e5efaa658d4b6f1 +DIST indilib-1.4.1.tar.gz 1529660 SHA256 f393faa01d98ead9a4205b567402d37fc48a1e53896ed0caeb0e0567bd3ba2e6 SHA512 b1655070fbc71095215a06edc88b8fff247ed3dcab86c2af058978b209e48ce1701f3a6eef13d0b200be58abfcfdffe7800ecea35d820fc2fb158ea0f899833f WHIRLPOOL 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ChangeLog README TODO ) + +S=${WORKDIR}/${PN/lib/}-${PV}/${MY_PN} + +src_configure() { + local mycmakeargs=( + -INDI_BUILD_UNITTESTS=OFF + -DUDEVRULES_INSTALL_DIR="$(get_udevdir)" + ) + + cmake-utils_src_configure +} diff --git a/sci-libs/indilib/indilib-1.4.1.ebuild b/sci-libs/indilib/indilib-1.4.1.ebuild new file mode 100644 index 000000000000..6ff6dfdaa8c5 --- /dev/null +++ b/sci-libs/indilib/indilib-1.4.1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_PN="lib${PN/lib/}" + +inherit cmake-utils udev + +DESCRIPTION="INDI Astronomical Control Protocol library" +HOMEPAGE="http://www.indilib.org/" +SRC_URI="https://github.com/${PN}/${PN/lib/}/releases/download/v${PV}/${MY_PN}_${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0/1" +KEYWORDS="amd64 ~ppc ~ppc64 x86" +IUSE="" + +RDEPEND=" + net-misc/curl + sci-libs/cfitsio + sci-libs/gsl + sci-libs/libnova + sys-libs/zlib + virtual/jpeg:0 + virtual/libusb:0 +" +DEPEND="${RDEPEND} + sys-kernel/linux-headers +" + +DOCS=( AUTHORS ChangeLog README TODO ) + +S=${WORKDIR}/${MY_PN} + +src_configure() { + local mycmakeargs=( + -INDI_BUILD_UNITTESTS=OFF + -INDI_BUILD_QT5_CLIENT=OFF + -DUDEVRULES_INSTALL_DIR="$(get_udevdir)" + ) + + cmake-utils_src_configure +} diff --git a/sci-libs/indilib/metadata.xml b/sci-libs/indilib/metadata.xml new file mode 100644 index 000000000000..f0a7e60d23ed --- /dev/null +++ b/sci-libs/indilib/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>kde@gentoo.org</email> + <name>Gentoo KDE Project</name> + </maintainer> + <upstream> + <remote-id type="github">indilib/indi</remote-id> + <remote-id type="sourceforge">indi</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/io_lib/Manifest b/sci-libs/io_lib/Manifest new file mode 100644 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(Only +# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.) +DEPEND="!sci-biology/bioperl" +RDEPEND="${DEPEND}" + +src_install() { + make install DESTDIR="${D}" || die + + dodoc CHANGES README || die "Failed to install documentation." +} diff --git a/sci-libs/io_lib/io_lib-1.11.2.1.ebuild b/sci-libs/io_lib/io_lib-1.11.2.1.ebuild new file mode 100644 index 000000000000..b793f7eabbb4 --- /dev/null +++ b/sci-libs/io_lib/io_lib-1.11.2.1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2008 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +DESCRIPTION="A general purpose trace and experiment file reading/writing interface" +HOMEPAGE="http://staden.sourceforge.net/" +SRC_URI="mirror://sourceforge/staden/${P}.tar.gz" +LICENSE="staden" + +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ia64 ~ppc ~sparc ~x86" +IUSE="" + +# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. (Only +# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.) +DEPEND="!sci-biology/bioperl" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${PN}-1.11.2" + +src_install() { + make install DESTDIR="${D}" || die + + dodoc ChangeLog CHANGES README docs/{Hash_File_Format,ZTR_format} || \ + die "Failed to install documentation." +} diff --git a/sci-libs/io_lib/io_lib-1.12.5.ebuild b/sci-libs/io_lib/io_lib-1.12.5.ebuild new file mode 100644 index 000000000000..00ac1a525aff --- /dev/null +++ b/sci-libs/io_lib/io_lib-1.12.5.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +DESCRIPTION="General purpose trace and experiment file reading/writing interface" +HOMEPAGE="http://staden.sourceforge.net/" +SRC_URI="mirror://sourceforge/staden/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +# needs stadden, not in portage +RESTRICT=test +# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. (Only +# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.) +#DEPEND="!sci-biology/bioperl" +DEPEND="net-misc/curl + sys-libs/zlib" +RDEPEND="${DEPEND}" + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + dodoc docs/{Hash_File_Format,ZTR_format} +} diff --git a/sci-libs/io_lib/io_lib-1.13.2.ebuild b/sci-libs/io_lib/io_lib-1.13.2.ebuild new file mode 100644 index 000000000000..cf0f35094a51 --- /dev/null +++ b/sci-libs/io_lib/io_lib-1.13.2.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="General purpose trace and experiment file reading/writing interface" +HOMEPAGE="http://staden.sourceforge.net/" +SRC_URI="mirror://sourceforge/staden/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +# needs stadden, not in portage +RESTRICT=test +# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. (Only +# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.) +#DEPEND="!sci-biology/bioperl" +DEPEND=" + net-misc/curl + sys-libs/zlib" +RDEPEND="${DEPEND}" + +src_install() { + autotools-utils_src_install + dodoc docs/{Hash_File_Format,ZTR_format} +} diff --git a/sci-libs/io_lib/io_lib-1.14.7.ebuild b/sci-libs/io_lib/io_lib-1.14.7.ebuild new file mode 100644 index 000000000000..f1475e779918 --- /dev/null +++ b/sci-libs/io_lib/io_lib-1.14.7.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils + +DESCRIPTION="General purpose trace and experiment file reading/writing interface" +HOMEPAGE="http://staden.sourceforge.net/" +SRC_URI="mirror://sourceforge/staden/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +DEPEND=" + net-misc/curl + sys-libs/zlib" +RDEPEND="${DEPEND}" + +# tests fails and might need sci-biology/staden from +# the science overlay + +RESTRICT="test" + +src_configure() { + econf $(use static-libs static) +} + +src_install() { + default + use static-libs || prune_libtool_files + dodoc docs/{Hash_File_Format,ZTR_format} +} diff --git a/sci-libs/io_lib/metadata.xml b/sci-libs/io_lib/metadata.xml new file mode 100644 index 000000000000..a88279ec5d96 --- /dev/null +++ b/sci-libs/io_lib/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + io_lib is a library of file reading and writing code to provide a + general purpose trace file (and Experiment File) reading interface. The + programmer simply calls the (eg) read_reading to create a "Read" C structure + with the data loaded into memory. +</longdescription> + <upstream> + <remote-id type="sourceforge">staden</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/ipopt/Manifest b/sci-libs/ipopt/Manifest new file mode 100644 index 000000000000..27cbc108af2d --- /dev/null +++ b/sci-libs/ipopt/Manifest @@ -0,0 +1,7 @@ +DIST Ipopt-3.11.7.tgz 4749511 SHA256 c276555cf913cf9cb32d9b0e4faabc2a21d34b52baf8da132d29f3541323739a SHA512 a9edd33b59c9744dc4e09d709519be1fc3d014cc4f50254402784aa8035d21617323f2879c430245886f2a13165cc81d26779331dc1601f0edfc406953dca56f WHIRLPOOL 709eefc5fd6ec43bbb343bc91ba4f0289e9963b931a3d70d36b3b3cadcb41b5ee01da6e6d743d781fb91bb789fcf45a424d5109291074695019027ff76bba9b1 +DIST Ipopt-3.11.8.tgz 4749758 SHA256 9f9b76075fbd9315286ea4d7c159c94cab4a4fb16122fb172b24910af5b5b75b SHA512 1f60ea769dd7305348af3a5d4ed56938f04e59c36fb7a3fa0b808e4788dccee4711f82c3767e2aae87d21618d2a840d0bb22491c21c40bc2f9ebdf4b3a01aeec WHIRLPOOL a8022439d3509a2d1c7cf7c9c1c97d2ddda6baae948c3628c14a1eae622069ca090647c2e4051ca330d767bc09da7d908005bfb5b021e3277ee4bc1294f33019 +EBUILD ipopt-3.11.7.ebuild 2396 SHA256 63de62e5eec9b0680d2e488c69fa6dc0821a242fd185509260969d2e82192ff5 SHA512 6a56ea64340b458b928e6024388b9df26ce8ee881d2dff77e5db4840d16391e1239768b4e18be35bdd911b227615df85b372161a45adc63c14c4ceac8344e593 WHIRLPOOL 10b558c84290f39f90b0e1b6781cade0610d03e29b6d92815bb0396b42fcb419b54c1cc50df299d693fe463054bfd16e356b5be57b9ac77e257af4a940614dd8 +EBUILD ipopt-3.11.8.ebuild 2403 SHA256 7a4e92b6ef023244bf586dfd28c054decd41e87fce8f02bfdb7726e024ec3f20 SHA512 19515a32ac7745199237f185a7bb84155e538be4e9effbd6b01a7571e289d09290215c43b56a12fda9cb43ed69d5a67a8c38815ab66b571be9b99392eadaa5e7 WHIRLPOOL 3cab1525787fdf52f3dbfa99b213a29aeb8a0a0562d998a95c929a9ad5f1274410b61bdd1b3d1a5e8a01e768671ae20dfd7545804442a1987f7ed87fe2d69fce +MISC ChangeLog 2473 SHA256 dafcbef9cac565e3a28bff0f148ab876c0ef6253c6b8a34ca52ffcc8438f5080 SHA512 4bac4fe3e0a47b951e1183a04535672fea0dbafbae46e12b06e5fc1a158999ef38c9874c2119ca0caa056ba45a50cdea2b2b0be65fc02aa9e5d4609a66220b6e WHIRLPOOL 9130597051cff6a22e482508a43fbbe76034154abae7471034173e43dff38227377a5475614d5abfc82800b1a30115b4192881e3655f460157aba536e344ca18 +MISC ChangeLog-2015 673 SHA256 99b2a78c95b29dbc4fe00bf79b73a0ac95fef4733cdabbb5e44d7ee13d32fe1a SHA512 60c51eb5f12ca144c84a8726e1a895a3078ef4047deda460c468771808386af2656fbe3e9b21f6ee447fee2851ee3e1814f25ec66b0b5c33197eca333cd35c29 WHIRLPOOL cd10e7c2f9940b8f1be0e44878e8ab5a7358b27762fa074a8966d384110c2aafd6c2396bc8fcbf14242eae5781098a73639f7826fcac91b850565f2234a1476e +MISC metadata.xml 842 SHA256 8075edf169ffe4558aa305703976888f9a320212fc8922b178c84a1f366e4e5d SHA512 6e18c52fa233ba8c19d3493ceda613b39e310fc32976f289a5f1c9709dac860a0e482390ad601019ea1d9818e5e3499887974466803d8c5800e96e9b0d6c0a72 WHIRLPOOL e50c246305548daa1ffaca7b4c7ed0e698737c0d6ccd074822194a669fac4c61717352efcca5ed44a1512acf52b4f193f2ee2a0082318ac62315cd538528ec37 diff --git a/sci-libs/ipopt/ipopt-3.11.7.ebuild b/sci-libs/ipopt/ipopt-3.11.7.ebuild new file mode 100644 index 000000000000..cf3bf34adda8 --- /dev/null +++ b/sci-libs/ipopt/ipopt-3.11.7.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_IN_SOURCE_BUILD=yes +FORTRAN_NEEDED="mumps" +inherit eutils autotools-utils multilib toolchain-funcs fortran-2 + +MYPN=Ipopt +MYP=${MYPN}-${PV} + +DESCRIPTION="Interior-Point Optimizer for large-scale nonlinear optimization" +HOMEPAGE="https://projects.coin-or.org/Ipopt/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYP}.tgz" + +LICENSE="EPL-1.0 hsl? ( HSL )" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples hsl lapack mpi mumps static-libs test" + +RDEPEND=" + virtual/blas + hsl? ( sci-libs/coinhsl ) + lapack? ( virtual/lapack ) + mumps? ( sci-libs/mumps[mpi=] )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample sci-libs/mumps )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + if use mumps && ! use mpi; then + ln -s "${EPREFIX}"/usr/include/mpiseq/mpi.h \ + src/Algorithm/LinearSolvers/ + elif use mpi; then + export CXX=mpicxx FC=mpif77 F77=mpif77 CC=mpicc + fi + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + # needed for the --with-coin-instdir + dodir /usr + local myeconfargs=( + --enable-dependency-linking + --with-blas-lib="$($(tc-getPKG_CONFIG) --libs blas)" + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + + if use lapack; then + myeconfargs+=( --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" ) + else + myeconfargs+=( --without-lapack ) + fi + if use mumps; then + myeconfargs+=( + --with-mumps-incdir="${EPREFIX}"/usr/include + --with-mumps-lib="-lmumps_common -ldmumps -lzmumps -lsmumps -lcmumps" ) + else + myeconfargs+=( --without-mumps ) + fi + if use hsl; then + myeconfargs+=( + --with-hsl-incdir="${EPREFIX}"/usr/include + --with-hsl-lib="$($(tc-getPKG_CONFIG) --libs coinhsl)" ) + else + myeconfargs+=( --without-hsl ) + fi + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile all $(use doc && echo doxydoc) +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${AUTOTOOLS_BUILD_DIR}/doxydocs/html/") + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/ipopt/ipopt-3.11.8.ebuild b/sci-libs/ipopt/ipopt-3.11.8.ebuild new file mode 100644 index 000000000000..bb3c71daaa61 --- /dev/null +++ b/sci-libs/ipopt/ipopt-3.11.8.ebuild @@ -0,0 +1,97 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_IN_SOURCE_BUILD=yes +FORTRAN_NEEDED="mumps" + +inherit eutils autotools-utils multilib toolchain-funcs fortran-2 + +MYPN=Ipopt +MYP=${MYPN}-${PV} + +DESCRIPTION="Interior-Point Optimizer for large-scale nonlinear optimization" +HOMEPAGE="https://projects.coin-or.org/Ipopt/" +SRC_URI="http://www.coin-or.org/download/source/${MYPN}/${MYP}.tgz" + +LICENSE="EPL-1.0 hsl? ( HSL )" +SLOT="0/1" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples hsl lapack mpi mumps static-libs test" + +RDEPEND=" + virtual/blas + hsl? ( sci-libs/coinhsl:0= ) + lapack? ( virtual/lapack ) + mumps? ( sci-libs/mumps:0=[mpi=] )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen[dot] ) + test? ( sci-libs/coinor-sample sci-libs/mumps )" + +S="${WORKDIR}/${MYPN}-${PV}/${MYPN}" + +src_prepare() { + if use mumps && ! use mpi; then + ln -s "${EPREFIX}"/usr/include/mpiseq/mpi.h \ + src/Algorithm/LinearSolvers/ + elif use mpi; then + export CXX=mpicxx FC=mpif77 F77=mpif77 CC=mpicc + fi + sed -i \ + -e "s:lib/pkgconfig:$(get_libdir)/pkgconfig:g" \ + configure || die + autotools-utils_src_prepare +} + +src_configure() { + # needed for the --with-coin-instdir + dodir /usr + local myeconfargs=( + --enable-dependency-linking + --with-blas-lib="$($(tc-getPKG_CONFIG) --libs blas)" + --with-coin-instdir="${ED}"/usr + $(use_with doc dot) + ) + + if use lapack; then + myeconfargs+=( --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" ) + else + myeconfargs+=( --without-lapack ) + fi + if use mumps; then + myeconfargs+=( + --with-mumps-incdir="${EPREFIX}"/usr/include + --with-mumps-lib="-lmumps_common -ldmumps -lzmumps -lsmumps -lcmumps" ) + else + myeconfargs+=( --without-mumps ) + fi + if use hsl; then + myeconfargs+=( + --with-hsl-incdir="${EPREFIX}"/usr/include + --with-hsl-lib="$($(tc-getPKG_CONFIG) --libs coinhsl)" ) + else + myeconfargs+=( --without-hsl ) + fi + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile all $(use doc && echo doxydoc) +} + +src_test() { + autotools-utils_src_test test +} + +src_install() { + use doc && HTML_DOC=("${AUTOTOOLS_BUILD_DIR}/doxydocs/html/") + autotools-utils_src_install + # already installed + rm "${ED}"/usr/share/coin/doc/${MYPN}/{README,AUTHORS,LICENSE} || die + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/ipopt/metadata.xml b/sci-libs/ipopt/metadata.xml new file mode 100644 index 000000000000..fa265c7e52e5 --- /dev/null +++ b/sci-libs/ipopt/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + Ipopt is a solver for large-scale nonlinear continuous + optimization. It can be used from modeling environments, such as + AMPL, GAMS, or Matlab, and it is also available as a callable library with + interfaces to C++, C, and Fortran. Ipopt uses an interior point + method, together with a filter linear search procedure. Ipopt is + part of the larger COIN-OR initiative (Computational Infrastructure + for Operations Research). +</longdescription> +<use> + <flag name="hsl">hsl</flag> + <flag name="mumps">Enable <pkg>sci-libs/mumps</pkg> support</flag> +</use> +</pkgmetadata> diff --git a/sci-libs/ipp/Manifest b/sci-libs/ipp/Manifest new file mode 100644 index 000000000000..20789b5c4d75 --- /dev/null +++ b/sci-libs/ipp/Manifest @@ -0,0 +1,27 @@ +DIST parallel_studio_xe_2013.tgz 2097190124 SHA256 22ac8d6dd1bf9fd646c1d1322c0a9051b89b6dba975112d492cccd8359f8dc0a SHA512 d49c519c0b2f82e6fc0db6820d5f84999d2a973d8caa0e103c0ad355644f52d209147a2b3a884effad9bbae117bd9ebbad4869f5440009355ffacb65cae274fa WHIRLPOOL bb5f05ceeae39f794dcd6c4fafafb2e5ebf8e5332083f7eaf357dddb9b2a1e94f52f82f850a8b0aefe1920f2fd21be67bfa8aafa9590707e25e84e9f2be07bd5 +DIST parallel_studio_xe_2013_ia32.tgz 1161979592 SHA256 3f0ff2ece4cfc5ec3d7c2fddefeda2b55b1295a0d62440c172a14d8e60b7b551 SHA512 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for multimedia and data processing" +HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" + +IUSE="" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=">=dev-libs/intel-common-13" +DEPEND="" + +CHECKREQS_DISK_BUILD=3000M + +INTEL_BIN_RPMS="ipp ipp-devel" +INTEL_DAT_RPMS="ipp-common" diff --git a/sci-libs/ipp/ipp-7.1.1.117.ebuild b/sci-libs/ipp/ipp-7.1.1.117.ebuild new file mode 100644 index 000000000000..9ed49be71f15 --- /dev/null +++ b/sci-libs/ipp/ipp-7.1.1.117.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +INTEL_DPN=parallel_studio_xe +INTEL_DID=2872 +INTEL_DPV=2013_update1 +INTEL_SUBDIR=composerxe + +inherit intel-sdp + +DESCRIPTION="Intel Integrated Performance Primitive library for multimedia and data processing" +HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" + +IUSE="" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=">=dev-libs/intel-common-13" +DEPEND="" + +CHECKREQS_DISK_BUILD=3000M + +INTEL_BIN_RPMS="ipp ipp-devel" +INTEL_DAT_RPMS="ipp-common" diff --git a/sci-libs/ipp/ipp-7.1.1.146.ebuild b/sci-libs/ipp/ipp-7.1.1.146.ebuild new file mode 100644 index 000000000000..fbc627c795aa --- /dev/null +++ b/sci-libs/ipp/ipp-7.1.1.146.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +INTEL_DPN=parallel_studio_xe +INTEL_DID=2987 +INTEL_DPV=2013_update2 +INTEL_SUBDIR=composerxe + +inherit intel-sdp + +DESCRIPTION="Intel Integrated Performance Primitive library for multimedia and data processing" +HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" + +IUSE="" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=">=dev-libs/intel-common-13.1" +DEPEND="" + +CHECKREQS_DISK_BUILD=3000M + +INTEL_BIN_RPMS="ipp ipp-devel" +INTEL_DAT_RPMS="ipp-common" + +INTEL_SKIP_LICENSE=true diff --git a/sci-libs/ipp/ipp-7.1.1.192.ebuild b/sci-libs/ipp/ipp-7.1.1.192.ebuild new file mode 100644 index 000000000000..f4c227f95669 --- /dev/null +++ b/sci-libs/ipp/ipp-7.1.1.192.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +INTEL_DPN=parallel_studio_xe +INTEL_DID=3266 +INTEL_DPV=2013_update4 +INTEL_SUBDIR=composerxe + +inherit intel-sdp + +DESCRIPTION="Intel Integrated Performance Primitive library for multimedia and data processing" +HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" + +IUSE="" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=">=dev-libs/intel-common-13.1" +DEPEND="" + +CHECKREQS_DISK_BUILD=3000M + +INTEL_BIN_RPMS="ipp ipp-devel" +INTEL_DAT_RPMS="ipp-common" + +INTEL_SKIP_LICENSE=true diff --git a/sci-libs/ipp/ipp-8.0.1.080.ebuild b/sci-libs/ipp/ipp-8.0.1.080.ebuild new file mode 100644 index 000000000000..d277b4b54894 --- /dev/null +++ b/sci-libs/ipp/ipp-8.0.1.080.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +INTEL_DPN=parallel_studio_xe +INTEL_DID=3447 +INTEL_DPV=2013_sp1 +INTEL_SUBDIR=composerxe +INTEL_SINGLE_ARCH=false + +inherit intel-sdp + +DESCRIPTION="Intel Integrated Performance Primitive library for multimedia and data processing" +HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" + +IUSE="" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=">=dev-libs/intel-common-13.1" +DEPEND="" + +CHECKREQS_DISK_BUILD=8000M + +INTEL_BIN_RPMS="ipp-common-devel ipp-mt ipp-mt-devel ipp-perftest ipp-perftest-devel ipp-st ipp-st-devel" +INTEL_DAT_RPMS="ipp-common" + +INTEL_SKIP_LICENSE=true diff --git a/sci-libs/ipp/ipp-8.2.0.090.ebuild b/sci-libs/ipp/ipp-8.2.0.090.ebuild new file mode 100644 index 000000000000..a0d811280079 --- /dev/null +++ b/sci-libs/ipp/ipp-8.2.0.090.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +INTEL_DPN=parallel_studio_xe +INTEL_DID=4584 +INTEL_DPV=2015 +INTEL_SUBDIR=composerxe +INTEL_SINGLE_ARCH=false + +inherit intel-sdp + +DESCRIPTION="Intel Integrated Performance Primitive library for multimedia and data processing" +HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" + +IUSE="" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=">=dev-libs/intel-common-15" +DEPEND="" + +CHECKREQS_DISK_BUILD=6400M + +INTEL_BIN_RPMS=( ipp-{ac,di,gen,jp,mt,mt-devel,mx,rr,sc,st,st-devel,vc} ) +INTEL_DAT_RPMS=( ipp-common ipp-{ac,di,gen,jp,mx,rr,sc,st-devel,vc}-common ) + +INTEL_SKIP_LICENSE=true diff --git a/sci-libs/ipp/ipp-8.2.1.164.ebuild b/sci-libs/ipp/ipp-8.2.1.164.ebuild new file mode 100644 index 000000000000..eaacbe6a2faa --- /dev/null +++ b/sci-libs/ipp/ipp-8.2.1.164.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +INTEL_DPN=parallel_studio_xe +INTEL_DID=5207 +INTEL_DPV=2015_update2 +INTEL_SUBDIR=composerxe +INTEL_SINGLE_ARCH=false + +inherit intel-sdp + +DESCRIPTION="Intel Integrated Performance Primitive library for multimedia and data processing" +HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" + +IUSE="" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=">=dev-libs/intel-common-15" +DEPEND="" + +CHECKREQS_DISK_BUILD=6400M + +INTEL_BIN_RPMS=( ipp-{ac,di,gen,jp,mt,mt-devel,mx,rr,sc,st,st-devel,vc} ) +INTEL_DAT_RPMS=( ipp-common ipp-{ac,di,gen,jp,mx,rr,sc,st-devel,vc}-common ) + +INTEL_SKIP_LICENSE=true diff --git a/sci-libs/ipp/ipp-8.2.2.187.ebuild b/sci-libs/ipp/ipp-8.2.2.187.ebuild new file mode 100644 index 000000000000..1be53f0bef16 --- /dev/null +++ b/sci-libs/ipp/ipp-8.2.2.187.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +INTEL_DPN=parallel_studio_xe +INTEL_DID=7538 +INTEL_DPV=2015_update3 +INTEL_SUBDIR=composerxe +INTEL_SINGLE_ARCH=false + +inherit intel-sdp + +DESCRIPTION="Intel Integrated Performance Primitive library for multimedia and data processing" +HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" + +IUSE="" +KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=">=dev-libs/intel-common-15" +DEPEND="" + +CHECKREQS_DISK_BUILD=6400M + +INTEL_BIN_RPMS=( ipp-{ac,di,gen,jp,mt,mt-devel,mx,rr,sc,st,st-devel,vc} ) +INTEL_DAT_RPMS=( ipp-common ipp-{ac,di,gen,jp,mx,rr,sc,st-devel,vc}-common ) + +INTEL_SKIP_LICENSE=true diff --git a/sci-libs/ipp/metadata.xml b/sci-libs/ipp/metadata.xml new file mode 100644 index 000000000000..b61694fd8092 --- /dev/null +++ b/sci-libs/ipp/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Intel(R) Integrated Performance Primitives (Intel(R) IPP) is a + library of multi-core-ready, optimized software functions for + multimedia data processing, and communications applications. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/itpp/Manifest b/sci-libs/itpp/Manifest new file mode 100644 index 000000000000..81938c85f123 --- /dev/null +++ b/sci-libs/itpp/Manifest @@ -0,0 +1,5 @@ +DIST itpp-4.3.1.tar.bz2 1289687 SHA256 50717621c5dfb5ed22f8492f8af32b17776e6e06641dfe3a3a8f82c8d353b877 SHA512 b46d048fa7f33e80d2291a5e38e205c159791ea200f92c70d69e8ad8447ac2f0c847fece566a99af739853a1643cb16e226b4200c8bf115417f324e6d38c66bd WHIRLPOOL e4791babcdb9e874a29b8f628af000e93fc316a7da0199713e7b840317d1b1109e4350c7582a3f88db3fe8be03ff8ee93b40712b77f61faa155acc668f39c0e0 +EBUILD itpp-4.3.1-r1.ebuild 1313 SHA256 34f9f091e800f9f935963a581cd3574c5fbab9a72cf89f6e761554a401a82e09 SHA512 09e1b8bc70c37b7ea1bd92a280f9b2b880c0fb0b8cb5d55f806b3886ac1ed1923c74580203296261fb99410173a9df7b9c3f755c0df98b4367bc057adea0f464 WHIRLPOOL 90c84e1356f45dab29d6a55f72e885d08d8a721fe6b0300e614c12a17b71ebeb4245c66d52f4b0a2fbe25ee40078a9ae5c237f7863946ee10bd2964429d8521e +MISC ChangeLog 4108 SHA256 9642be080c217aaaf5397c64a84eddd33af6a38783f48c46c99f6fcfb8755d6e SHA512 32bb71df0a1940e8602c4ae93c76a80b7b5a9cf3b786935be453a1ec115793433b45372fd696f0228452b7760552ab6a700ffc07be53ff7fc36e2e91e97768d0 WHIRLPOOL 85c8725ac70cf7d8848f462bf0c28e55fe171ba1ee4920f80be7e8300e5858a42259eda7fe578f22254ff9f9f7f705498234564c3510df5a4d6ca5bca7e63905 +MISC ChangeLog-2015 17860 SHA256 385812077fe6a13c347c8baf0dbcb991f14049c35f8d7b1e813a65d5c8df5a67 SHA512 1d8b51cbfdba67d4266cddb215490ac54c62361d61ac48e350472a67c37d6c00ee0ea8a594be0c43c18ed986162f256bba77b0f3112127506cb0f2c78a059d81 WHIRLPOOL e527c9bd5dbef09915c82487828f7e2321222c3aa0ca20200b4c9b480507769d9faeed7d7d2ee0b515f9839225f5d83d08b560b205ff5629d29892b37783a221 +MISC metadata.xml 778 SHA256 e0533a86039e784b8b9c9106d848818abe7a352c8285337701c3bafcbfe9c92b SHA512 daef37adb619d49abcb70482f581cbf3492f7fc352f0414f5da2f77ca114b45816fd20466e70028030de3f478ca2ebfb2ff576cb231f860be09e5918931860a8 WHIRLPOOL de8db3bf7b2ad6f6521a743d9bf8b2fefdcbb6219518c7fa9d6e2213ac5e8c380d6944ff24259b41654ccd3f9fcde2bebf66ba22842cc2aa59def75a4a6e8b43 diff --git a/sci-libs/itpp/itpp-4.3.1-r1.ebuild b/sci-libs/itpp/itpp-4.3.1-r1.ebuild new file mode 100644 index 000000000000..dab233c0d4cd --- /dev/null +++ b/sci-libs/itpp/itpp-4.3.1-r1.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils multilib + +DESCRIPTION="C++ library of mathematical, signal processing and communication" +HOMEPAGE="http://itpp.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +RDEPEND=" + virtual/blas + virtual/lapack + >=sci-libs/fftw-3" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/doxygen virtual/latex-base )" + +DOCS=(ChangeLog NEWS AUTHORS README) + +src_prepare() { + # gentoo redefines the CMAKE_BUILD_TYPE + sed -i \ + -e 's/CMAKE_BUILD_TYPE STREQUAL Release/NOT CMAKE_BUILD_TYPE STREQUAL Debug/' \ + CMakeLists.txt || die + # respect gentoo doc dir + sed -i \ + -e "s:share/doc/itpp:share/doc/${PF}:" \ + itpp/CMakeLists.txt || die + + # respect gentoo libdir + sed -i "s#/lib#/$(get_libdir)#" itpp-config.cmake.in + sed -i "s#/lib#/$(get_libdir)#" itpp.pc.cmake.in + sed -i \ + -e "s#LIBRARY DESTINATION lib#LIBRARY DESTINATION $(get_libdir)#" \ + -e "s#ARCHIVE DESTINATION lib#ARCHIVE DESTINATION $(get_libdir)#" \ + itpp/CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -DBLA_VENDOR=Generic + $(cmake-utils_use doc HTML_DOCS) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/itpp/metadata.xml b/sci-libs/itpp/metadata.xml new file mode 100644 index 000000000000..6606a6014ad7 --- /dev/null +++ b/sci-libs/itpp/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + IT++ is a C++ library of mathematical, signal processing and + communication classes and functions. Its main use is in simulation + of communication systems and for performing research in the area of + communications. The kernel of the library consists of generic vector + and matrix classes, and a set of accompanying routines. Such a + kernel makes IT++ similar to MATLAB or GNU Octave . +</longdescription> + <upstream> + <remote-id type="sourceforge">itpp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/jama/Manifest b/sci-libs/jama/Manifest new file mode 100644 index 000000000000..06bc32b6e903 --- /dev/null +++ b/sci-libs/jama/Manifest @@ -0,0 +1,6 @@ +DIST jama102doc.zip 61085 SHA256 0175a981cba82b316f17e1066e605a1bc6aa2840edf70b5e1a06305f16e5f7e3 SHA512 0082e632ce0a9e06e225013a8079eb77311f62f7e1b1f2a8d05c18f6e1415dfb1db271bef102aed5ea78b841e8b89e191a452014ee0eed17517d7f45e101d74c WHIRLPOOL 1947fe40531c6249648475c1e8754a0065cc1d9d4057c9e9f2fe0537726d4f644bc94b9d24715737f6a8590b865ef3eaf0293a1478df774a559ae0fe1a9df5ec +DIST jama125.zip 16277 SHA256 7432bf51d7101f63d5880421f940f64cea124f1460ff2fcfb6226e6744d1360c SHA512 773cbf98de2384df5429db3ecc117304934a1de1c24ee1f342ededae8bdc9747e3bb5ec0d3cd7fde62b2ee13ee2e0c6e86f6b30c7082036bd5b224b76592b4f9 WHIRLPOOL 20acceecdeb81fd388baebe0c279b3adfb57b9daeda7e5713a3b85e4d8c0124ed8043e79a2b9dc66b65c03cbe656b3d2bd8fc253bb1342ff2e53647d9fa80895 +EBUILD jama-1.2.5.ebuild 622 SHA256 0aecc9c04c5d9b812051aa0d2f179c54c6ca792d051fe9078846de28674cd018 SHA512 bda3d77977801a312389fae48bff4ce9918cbed51a2c98216bb28947bce32bcd9bec0df5e267847f73259cf2386e41e7f4d3e28f0f61632fc27e1c2d79303dce WHIRLPOOL cb66cf1c2f0b40efcc2e744f6132ff13da83a6b7cf424a2f127bf5955b64e2057ec19b4b67d56446ea2f26b63e8b0368b769361760e467accbf12ba2866d67a0 +MISC ChangeLog 2418 SHA256 490b150b653b7544695c3dfc499fed9e90568f2f11ec47581f9fa33f12c1d001 SHA512 1689cbb0c9634947e1631fe4b560f5666cacad359c95d074d361dda1c21cb0e8572cf0fe4244d5befda3c6ca04f1d6485044d2ab21430326d47c2cab6ac8bcfc WHIRLPOOL f4ee86b7d9bdb7547235a8f4a3410acc77848df14a05587652a92ed063113d7fc3a0bc326fad1373f989d4b52cd447879019e4467c09173bb8b065a72780e6bc +MISC ChangeLog-2015 691 SHA256 0125238dc9f9dd58ef7ef5939b6bc9622d9728df0324e5dbe0288b7464093c57 SHA512 2cf9856553b608b7e1d94c1d20fa286242c1932ca146bd81692462b95be93b0ce8411ef6f50f82b8bcce6faa76cde34e3697cd396c2aa15f4fe52743df18943c WHIRLPOOL 781c8a5e9e6898717a4bbc698063133f3db0d3d71688bd3838bf6157289e8ec5a929fc22c9e4dff4cde5966bc2a4ff6e6031572ab3a32f2e38116371eda23b0b +MISC metadata.xml 581 SHA256 e6cc94ca1565e120e9a7241cedf5f6953dbd4bca4d385eed4dd386803b236d7d SHA512 33822ae3ae80165c7dd5b3e2878fc620f25ebc03bbccad0be4d8a049bdb96f5b01abc22851caed3222a10352848cac9b74ca3e06605391c82fcf4eecbb086530 WHIRLPOOL efcb55484753c06d462d86a782ac165c30ff508e6e1a06de0177125d9d11b1245ad940567700181ac80eb0e83c635bbce99b1b78e3bed3eda54de479cbe3d5b5 diff --git a/sci-libs/jama/jama-1.2.5.ebuild b/sci-libs/jama/jama-1.2.5.ebuild new file mode 100644 index 000000000000..232208b2534d --- /dev/null +++ b/sci-libs/jama/jama-1.2.5.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit versionator + +MYP="${PN}$(replace_all_version_separators '')" +DOCPV=102 + +DESCRIPTION="Java-like matrix C++ templates" +HOMEPAGE="http://math.nist.gov/tnt/" +SRC_URI="http://math.nist.gov/tnt/${MYP}.zip + doc? ( http://math.nist.gov/tnt/${PN}${DOCPV}doc.zip )" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="doc" + +DEPEND="app-arch/unzip" +RDEPEND="sci-libs/tnt" + +S="${WORKDIR}" + +src_install() { + insinto /usr/include + doins *.h || die + use doc && dohtml doxygen/html/* +} diff --git a/sci-libs/jama/metadata.xml b/sci-libs/jama/metadata.xml new file mode 100644 index 000000000000..ba662363459f --- /dev/null +++ b/sci-libs/jama/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + JAMA/C++: a translation of the Java Matrix Library, developed by the + Mathworks and NIST, into C++ . It includes the following routines: + * classical matrix linear algebra + * QR + * SVD + * Cholesky + * Eigenvalue solver + It is based on NIST's Template Numerical Toolkit. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/jmol-acme/Manifest b/sci-libs/jmol-acme/Manifest new file mode 100644 index 000000000000..673b7bf45ab3 --- /dev/null +++ b/sci-libs/jmol-acme/Manifest @@ -0,0 +1,6 @@ +AUX src.list 115 SHA256 14f9bbf65ef25555840c8551df9caba3fe80015bc334e83d178b7296167d3a97 SHA512 3e9a0dc4aa7890554ab66c6e9cbf60287e3c37b45cfc73ccee6f0078cb0f7a267c5eeed07e0bae91fa39759cf15dd794e278058506760ebce4e617963b391f6d WHIRLPOOL 26b40d4aa42f2b049b2bd0efe62601f9ef6528fee4fbed51a15e2d1dfc02b86dd3738667361ae6a11be977474f9ce11e9a3125812b771e4481eaf6005b2a0bac +DIST Acme.tar.gz 478667 SHA256 6becb7e097bc9a3c7b39a42aaf8dd9ce8d35508b5221c3076e0c1e060ecc688c SHA512 cf172ce6d341d9a559ef8db837a7c163fb494d5629d2738279b2b0b68bf8874303e37d72c519171a885efca9a1505345f454e434f6f578d370bef961cb7a4d46 WHIRLPOOL ffca0e40e7070b3d31ba3e519f3d873e7d86604bb9b0af454b11ee3d5b60598ddbe9d38d3d0aa3703c59fbfa4779337927ee105f08fc3f7ea54d4e6354e2954f +EBUILD jmol-acme-1.0.ebuild 873 SHA256 f8ea8d5506c2b955a3b155d24349f8ba387e1270ec336481e306436264e2cd5c SHA512 a04c66a90033b979d17e427689455247b8700a8d1ffb4f13c3f1720e54c90ca2151d32af278568393fe1ddaa2d5b1e96323973bf246788783c17342a27645ca9 WHIRLPOOL b70006146bc258a0fc0dce2ffb022465d2882df48f365f78733f23699de81de4eca16266fd098bfb4e7ea5e0f8314973b6a7060700d5775928491afa146e168e +MISC ChangeLog 2567 SHA256 717a22cfe2162ff1fc793db2c0f3b41e1656d6b1bc3fccf09499f3e09162c084 SHA512 d02af26fe55c49f519c473c6b35c04be13f9a3192a9d0fe94dc3a06a2d49ca33e6800ca48c4a7f2bb670fe3d2cc6c9d70a3a9261b4820dc97cf5d191df2c75e2 WHIRLPOOL b38e8898759c2e4247144f2a1b737e66dddf68d5fa80ab71374044311f8054636bf6bf50f2886a84786c5931b44861325474c848a0da852feed2795b306e5d28 +MISC ChangeLog-2015 838 SHA256 ae6c5315f75c5fea9b5a02af3fc9af3bcdc0d0842d6ed2e530c519cb10117f7d SHA512 5b546bcf16de13d9d05e7c53e5ee9fe70634edce09426ba7d2c3221ae1d507bbdbd786c8d416667599cc31ef07afa1a58ac47a497a1988b8fc9364b123814e19 WHIRLPOOL 03ce518df3d7010063253c090eff4617803a1295808d9e721c59fb0ccf0e87f8b763b1cae92c66b8dc57f79ee4b28080fc64a83f225a60f8be2412e1e3d49686 +MISC metadata.xml 253 SHA256 45344b6a377f639b56950e98338690fa1e0c5b51d2bf174635aff3b025b7e616 SHA512 819062e1ccefa39fc7f577279b08e781b9631eb14b7794db691ab92263c013ca432d279ac08671b19c80f7effb8c67528e5221278c573dd29dc0354bbff4a77e WHIRLPOOL 73680e667729b1d31cac7b2b730a5d94195071c96383438c66c4a94e445fe874e78d3e5e2c9c5a6d77406dc392eab967595402e063e557f9a3680714d709e830 diff --git a/sci-libs/jmol-acme/files/src.list b/sci-libs/jmol-acme/files/src.list new file mode 100644 index 000000000000..14d1fc028561 --- /dev/null +++ b/sci-libs/jmol-acme/files/src.list @@ -0,0 +1,4 @@ +./IntHashtable.java +./JPM/Encoders/GifEncoder.java +./JPM/Encoders/ImageEncoder.java +./JPM/Encoders/PpmEncoder.java diff --git a/sci-libs/jmol-acme/jmol-acme-1.0.ebuild b/sci-libs/jmol-acme/jmol-acme-1.0.ebuild new file mode 100644 index 000000000000..30ad53ef215f --- /dev/null +++ b/sci-libs/jmol-acme/jmol-acme-1.0.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit java-pkg-2 java-ant-2 + +MY_P="Acme" + +# It proved difficult to recompile the whole Acme package, so we'll only take what we need. + +DESCRIPTION="Portions of the Acme collection required for jMol" +HOMEPAGE="http://www.acme.com/" +SRC_URI="http://www.acme.com/resources/classes/${MY_P}.tar.gz" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=">=virtual/jdk-1.4" +RDEPEND=">=virtual/jre-1.4" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + mkdir -p classes + find . -name \*.class -delete + java-pkg_filter-compiler jikes +} + +src_compile() { + cp "${FILESDIR}/src.list" "${T}" || die + ejavac -sourcepath "" -d "${S}/classes" "@${T}/src.list" + jar cf "${PN}.jar" -C classes . || die "failed to create jar" +} + +src_install() { + java-pkg_dojar ${PN}.jar +} diff --git a/sci-libs/jmol-acme/metadata.xml b/sci-libs/jmol-acme/metadata.xml new file mode 100644 index 000000000000..ae9640ffb9f1 --- /dev/null +++ b/sci-libs/jmol-acme/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/kim-api/Manifest b/sci-libs/kim-api/Manifest new file mode 100644 index 000000000000..99b87efcad07 --- /dev/null +++ b/sci-libs/kim-api/Manifest @@ -0,0 +1,3 @@ +DIST kim-api-v1.8.2.tgz 1634997 SHA256 26bf3bf6960290797c0be7a3435b6350e572f7e07ad87e743e5a9c04e074386d SHA512 fed930d147bfbb7936548eb129fcc403df90d1a8010f0fd5b85eaa35c1529d76c9c7c10b098b8eb74d9878e6d3ba0fad3c10d2a3e5bc9b673841a2abc290bac3 WHIRLPOOL cafdff25be9e7186184dbd45f57033542e38e88c9bc62d2a10557924d5bd8763ed92bc63a507f6ed0185174e1747c60ec567dd09899bad315d74fa6b7400c5f2 +EBUILD kim-api-1.8.2.ebuild 642 SHA256 603dad7b7a4eb102e70c78469b243bb7d5d14093e905b91a0686e341ec635134 SHA512 3a6a1f11f40af004330ebb4a55edcd12a93249e8c816f695e5a42044096e864c23154dbdb4d0f024d8882e538ef29269fb0c3ab56f4b516ce79b7f5408530405 WHIRLPOOL bb3c389452544ad60a96f7234c0050cd08526d30aeb770efdb78139bbf868d157fb9378981fd07720b3cfd3eab1b40796a3304696daedb6dfdeb9c6a72a55245 +MISC metadata.xml 367 SHA256 ac8d9fb591cb385322c5b19e610391ed7c6df9554f4901b3789e0b0410533d37 SHA512 455c79e8837ba1ed980967e3236d4a0ac0edbd1b88b056a06d715894e03e7fc802079440752e60a06c9ce4acb62fd68d4020a7847a154a14065afd995257f685 WHIRLPOOL 7b8aae6b6e9c08408300de466754b331e1ec556f8dc4fcc11c22069e913d2d600c2b7dc2d9a5ee5de84c472540cc78aeac1b4a3b0abbc92a539cdbbb6ca30c37 diff --git a/sci-libs/kim-api/kim-api-1.8.2.ebuild b/sci-libs/kim-api/kim-api-1.8.2.ebuild new file mode 100644 index 000000000000..b15535489e2c --- /dev/null +++ b/sci-libs/kim-api/kim-api-1.8.2.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +MY_P="${PN}-v${PV}" +DESCRIPTION="Application Programming Interface for atomistic simulations" +HOMEPAGE="https://openkim.org" +SRC_URI="https://s3.openkim.org/${PN}/${MY_P}.tgz" + +LICENSE="CDDL" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MY_P}" + +MAKEOPTS+=" -j1" + +src_prepare() { + #https://github.com/openkim/kim-api/pull/2 + sed -i 's/libDir/libdir/' configure + default +} + +src_configure() { + #not an Autotools configure + ./configure --prefix=/usr --libdir=/usr/$(get_libdir) || die +} diff --git a/sci-libs/kim-api/metadata.xml b/sci-libs/kim-api/metadata.xml new file mode 100644 index 000000000000..903883b48f16 --- /dev/null +++ b/sci-libs/kim-api/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/klu/Manifest b/sci-libs/klu/Manifest new file mode 100644 index 000000000000..997fba712f68 --- /dev/null +++ b/sci-libs/klu/Manifest @@ -0,0 +1,5 @@ +DIST klu-1.2.1.tar.bz2 612428 SHA256 c61d56f5dd6bff0259a6d082e6a6ca714ceba96521ab88487445f8b77b328494 SHA512 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--- /dev/null +++ b/sci-libs/klu/klu-1.2.1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Sparse LU factorization for circuit simulation" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/klu/" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +RDEPEND=" + >=sci-libs/amd-1.3 + >=sci-libs/btf-1.2 + >=sci-libs/colamd-1.3" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base )" + +src_configure() { + local myeconfargs=( + $(use_with doc) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/klu/metadata.xml b/sci-libs/klu/metadata.xml new file mode 100644 index 000000000000..5d78c49fdc95 --- /dev/null +++ b/sci-libs/klu/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + KLU is a sparse LU factorization algorithm well-suited for use in + circuit simulation. It is also part of the University + of Florida sparse matrix suite. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/lapack-reference/Manifest b/sci-libs/lapack-reference/Manifest new file mode 100644 index 000000000000..8c4643f981e4 --- /dev/null +++ b/sci-libs/lapack-reference/Manifest @@ -0,0 +1,15 @@ +AUX eselect.lapack.reference 237 SHA256 2a72a6a9b49ec944656e164842907ee76d878a6772a7d71c1cb196d8beb6fa13 SHA512 cd0b5c771e552d348ce87192583bed2dbf9f2c61cbaf512b006dd9da3b36d3f0c8ad24129e595f644fc0472f5e60e0c3c0964ec86f9ece1c0f00e942d2515936 WHIRLPOOL 102823a489c08259775505f7e67e41ca0b4dc7dcc50a6a67bcd79d3a0b166439d756659a56df4ee59518888ec68d106865a67aa96ef326478c5ec0c2e56c91f3 +AUX eselect.lapack.reference-r1 237 SHA256 ecde7c9d21dcdddd8d185e35dd077b31357eba98a8d7b87b935c92ed8817ea89 SHA512 f33b5e14184017192a51e6cf9e6c41a55cf79e60f133e1ef552b80fd2c50ad33f8252d20e379e28b283eab3f33c755172e4244bfe7cfbc633db7f8dd8d5537c3 WHIRLPOOL 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b/sci-libs/lapack-reference/files/eselect.lapack.reference-r1 @@ -0,0 +1,4 @@ +lapack/reference/liblapack.so /usr/@LIBDIR@/liblapack.so +lapack/reference/liblapack.so.3 /usr/@LIBDIR@/liblapack.so.3 +lapack/reference/liblapack.a /usr/@LIBDIR@/liblapack.a +../lapack/reference/lapack.pc /usr/@LIBDIR@/pkgconfig/lapack.pc diff --git a/sci-libs/lapack-reference/files/lapack-reference-3.2.1-parallel-make.patch b/sci-libs/lapack-reference/files/lapack-reference-3.2.1-parallel-make.patch new file mode 100644 index 000000000000..72bc71ca2d95 --- /dev/null +++ b/sci-libs/lapack-reference/files/lapack-reference-3.2.1-parallel-make.patch @@ -0,0 +1,112 @@ +diff -Nauru lapack-3.2.1.old/TESTING/EIG/Makefile lapack-3.2.1/TESTING/EIG/Makefile +--- lapack-3.2.1.old/TESTING/EIG/Makefile 2008-11-17 17:51:24.000000000 -0500 ++++ lapack-3.2.1/TESTING/EIG/Makefile 2009-12-12 11:23:22.000000000 -0500 +@@ -126,25 +126,25 @@ + double: ../xeigtstd + complex16: ../xeigtstz + +-../xeigtsts: $(SEIGTST) $(SCIGTST) $(AEIGTST) ; \ +- $(LOADER) $(LOADOPTS) -o xeigtsts \ +- $(SEIGTST) $(SCIGTST) $(AEIGTST) ../../$(TMGLIB) \ +- ../../$(LAPACKLIB) $(BLASLIB) && mv xeigtsts $@ +- +-../xeigtstc: $(CEIGTST) $(SCIGTST) $(AEIGTST) ; \ +- $(LOADER) $(LOADOPTS) -o xeigtstc \ +- $(CEIGTST) $(SCIGTST) $(AEIGTST) ../../$(TMGLIB) \ +- ../../$(LAPACKLIB) $(BLASLIB) && mv xeigtstc $@ +- +-../xeigtstd: $(DEIGTST) $(DZIGTST) $(AEIGTST) ; \ +- $(LOADER) $(LOADOPTS) -o xeigtstd \ +- $(DEIGTST) $(DZIGTST) $(AEIGTST) ../../$(TMGLIB) \ +- ../../$(LAPACKLIB) $(BLASLIB) && mv xeigtstd $@ +- +-../xeigtstz: $(ZEIGTST) $(DZIGTST) $(AEIGTST) ; \ +- $(LOADER) $(LOADOPTS) -o xeigtstz \ +- $(ZEIGTST) $(DZIGTST) $(AEIGTST) ../../$(TMGLIB) \ +- ../../$(LAPACKLIB) $(BLASLIB) && mv xeigtstz $@ ++../xeigtsts: $(SEIGTST) $(SCIGTST) $(AEIGTST) ++ $(LOADER) $(LOADOPTS) \ ++ $(SEIGTST) $(SCIGTST) $(AEIGTST) ../../$(TMGLIB) \ ++ ../../$(LAPACKLIB) $(BLASLIB) -o ../xeigtsts ++ ++../xeigtstc: $(CEIGTST) $(SCIGTST) $(AEIGTST) ++ $(LOADER) $(LOADOPTS) \ ++ $(CEIGTST) $(SCIGTST) $(AEIGTST) ../../$(TMGLIB) \ ++ ../../$(LAPACKLIB) $(BLASLIB) -o ../xeigtstc ++ ++../xeigtstd: $(DEIGTST) $(DZIGTST) $(AEIGTST) ++ $(LOADER) $(LOADOPTS) \ ++ $(DEIGTST) $(DZIGTST) $(AEIGTST) ../../$(TMGLIB) \ ++ ../../$(LAPACKLIB) $(BLASLIB) -o ../xeigtstd ++ ++../xeigtstz: $(ZEIGTST) $(DZIGTST) $(AEIGTST) ++ $(LOADER) $(LOADOPTS) \ ++ $(ZEIGTST) $(DZIGTST) $(AEIGTST) ../../$(TMGLIB) \ ++ ../../$(LAPACKLIB) $(BLASLIB) -o ../xeigtstz + + $(AEIGTST): $(FRC) + $(SCIGTST): $(FRC) +@@ -169,4 +169,5 @@ + zchkee.o: zchkee.f + $(FORTRAN) $(DRVOPTS) -c $< -o $@ + +-.f.o : ; $(FORTRAN) $(OPTS) -c $< -o $@ ++.f.o : ++ $(FORTRAN) $(OPTS) -c $< -o $@ +diff -Nauru lapack-3.2.1.old/TESTING/LIN/Makefile lapack-3.2.1/TESTING/LIN/Makefile +--- lapack-3.2.1.old/TESTING/LIN/Makefile 2009-02-10 12:23:05.000000000 -0500 ++++ lapack-3.2.1/TESTING/LIN/Makefile 2009-12-12 07:22:41.000000000 -0500 +@@ -238,43 +238,43 @@ + + ../xlintsts : $(ALINTST) $(SLINTST) $(SCLNTST) + $(LOADER) $(LOADOPTS) $(ALINTST) $(SCLNTST) $(SLINTST) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(XBLASLIB) $(BLASLIB) -o xlintsts && mv xlintsts $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(XBLASLIB) $(BLASLIB) -o ../xlintsts + + ../xlintstc : $(ALINTST) $(CLINTST) $(SCLNTST) + $(LOADER) $(LOADOPTS) $(ALINTST) $(SCLNTST) $(CLINTST) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(XBLASLIB) $(BLASLIB) -o xlintstc && mv xlintstc $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(XBLASLIB) $(BLASLIB) -o ../xlintstc + + ../xlintstd : $(ALINTST) $(DLINTST) $(DZLNTST) + $(LOADER) $(LOADOPTS) $^ \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(XBLASLIB) $(BLASLIB) -o xlintstd && mv xlintstd $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(XBLASLIB) $(BLASLIB) -o ../xlintstd + + ../xlintstz : $(ALINTST) $(ZLINTST) $(DZLNTST) + $(LOADER) $(LOADOPTS) $(ALINTST) $(DZLNTST) $(ZLINTST) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(XBLASLIB) $(BLASLIB) -o xlintstz && mv xlintstz $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(XBLASLIB) $(BLASLIB) -o ../xlintstz + + ../xlintstds : $(DSLINTST) + $(LOADER) $(LOADOPTS) $(DSLINTST) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o xlintstds && mv xlintstds $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o ../xlintstds + + ../xlintstzc : $(ZCLINTST) + $(LOADER) $(LOADOPTS) $(ZCLINTST) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o xlintstzc && mv xlintstzc $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o ../xlintstzc + + ../xlintstrfs : $(SLINTSTRFP) + $(LOADER) $(LOADOPTS) $(SLINTSTRFP) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o xlintstrfs && mv xlintstrfs $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o ../xlintstrfs + + ../xlintstrfd : $(DLINTSTRFP) + $(LOADER) $(LOADOPTS) $(DLINTSTRFP) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o xlintstrfd && mv xlintstrfd $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o ../xlintstrfd + + ../xlintstrfc : $(CLINTSTRFP) + $(LOADER) $(LOADOPTS) $(CLINTSTRFP) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o xlintstrfc && mv xlintstrfc $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o ../xlintstrfc + + ../xlintstrfz : $(ZLINTSTRFP) + $(LOADER) $(LOADOPTS) $(ZLINTSTRFP) \ +- ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o xlintstrfz && mv xlintstrfz $@ ++ ../../$(TMGLIB) ../../$(LAPACKLIB) $(BLASLIB) -o ../xlintstrfz + + $(ALINTST): $(FRC) + $(SCLNTST): $(FRC) diff --git a/sci-libs/lapack-reference/files/lapack-reference-3.6.0-fix-build-system.patch b/sci-libs/lapack-reference/files/lapack-reference-3.6.0-fix-build-system.patch new file mode 100644 index 000000000000..8661709d369b --- /dev/null +++ b/sci-libs/lapack-reference/files/lapack-reference-3.6.0-fix-build-system.patch @@ -0,0 +1,92 @@ +--- lapack-3.6.0/BLAS/blas.pc.in ++++ lapack-3.6.0/BLAS/blas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: blas + Description: Basic Linear Algebra Subprograms F77 reference implementations +--- lapack-3.6.0/BLAS/CMakeLists.txt ++++ lapack-3.6.0/BLAS/CMakeLists.txt +@@ -2,7 +2,7 @@ + if(BUILD_TESTING) + add_subdirectory(TESTING) + endif(BUILD_TESTING) +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/blas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/blas.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/blas.pc + DESTINATION ${PKG_CONFIG_DIR} +--- lapack-3.6.0/CBLAS/cblas.pc.in ++++ lapack-3.6.0/CBLAS/cblas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: lapacke + Description: C Standard Interface to BLAS Linear Algebra PACKage +--- lapack-3.6.0/CBLAS/CMakeLists.txt ++++ lapack-3.6.0/CBLAS/CMakeLists.txt +@@ -71,7 +71,7 @@ + ${LAPACK_BINARY_DIR}/cblas-config.cmake @ONLY) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cblas.pc.in ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/cblas.pc + DESTINATION ${PKG_CONFIG_DIR} +--- lapack-3.6.0/CMakeLists.txt ++++ lapack-3.6.0/CMakeLists.txt +@@ -333,7 +333,7 @@ + ${LAPACK_BINARY_DIR}/lapack-config.cmake @ONLY) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapack.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/lapack.pc + DESTINATION ${PKG_CONFIG_DIR} +--- lapack-3.6.0/LAPACKE/CMakeLists.txt ++++ lapack-3.6.0/LAPACKE/CMakeLists.txt +@@ -65,7 +65,7 @@ + endif(BUILD_TESTING) + + +-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc) ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/lapacke.pc.in ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc @ONLY) + install(FILES + ${CMAKE_CURRENT_BINARY_DIR}/lapacke.pc + DESTINATION ${PKG_CONFIG_DIR} +--- lapack-3.6.0/LAPACKE/lapacke.pc.in ++++ lapack-3.6.0/LAPACKE/lapacke.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: lapacke + Description: C Standard Interface to LAPACK Linear Algebra PACKage +--- lapack-3.6.0/lapack.pc.in ++++ lapack-3.6.0/lapack.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: lapack + Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage diff --git a/sci-libs/lapack-reference/files/lapack-reference-3.7.0-fix-build-system.patch b/sci-libs/lapack-reference/files/lapack-reference-3.7.0-fix-build-system.patch new file mode 100644 index 000000000000..70f7cb0ee926 --- /dev/null +++ b/sci-libs/lapack-reference/files/lapack-reference-3.7.0-fix-build-system.patch @@ -0,0 +1,56 @@ +diff --git a/BLAS/blas.pc.in b/BLAS/blas.pc.in +index 7fd6f1e..e52f3ad 100644 +--- a/BLAS/blas.pc.in ++++ b/BLAS/blas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: BLAS + Description: FORTRAN reference implementation of BLAS Basic Linear Algebra Subprograms +diff --git a/CBLAS/cblas.pc.in b/CBLAS/cblas.pc.in +index 4a938fe..311aed9 100644 +--- a/CBLAS/cblas.pc.in ++++ b/CBLAS/cblas.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: CBLAS + Description: C Standard Interface to BLAS Basic Linear Algebra Subprograms +diff --git a/LAPACKE/lapacke.pc.in b/LAPACKE/lapacke.pc.in +index 028f8da..dc092b1 100644 +--- a/LAPACKE/lapacke.pc.in ++++ b/LAPACKE/lapacke.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: LAPACKE + Description: C Standard Interface to LAPACK Linear Algebra PACKage +diff --git a/lapack.pc.in b/lapack.pc.in +index 878efc2..2cca4c2 100644 +--- a/lapack.pc.in ++++ b/lapack.pc.in +@@ -1,5 +1,7 @@ +-prefix=@prefix@ +-libdir=@libdir@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ ++includedir=${prefix}/include + + Name: LAPACK + Description: FORTRAN reference implementation of LAPACK Linear Algebra PACKage diff --git a/sci-libs/lapack-reference/lapack-reference-3.2.1-r4.ebuild b/sci-libs/lapack-reference/lapack-reference-3.2.1-r4.ebuild new file mode 100644 index 000000000000..26258bbf0c57 --- /dev/null +++ b/sci-libs/lapack-reference/lapack-reference-3.2.1-r4.ebuild @@ -0,0 +1,100 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils fortran-2 flag-o-matic multilib toolchain-funcs + +MyPN="${PN/-reference/}" +PATCH_V="3.2.1" + +DESCRIPTION="FORTRAN reference implementation of LAPACK Linear Algebra PACKage" +HOMEPAGE="http://www.netlib.org/lapack/index.html" +SRC_URI=" + mirror://gentoo/${MyPN}-${PV}.tgz + mirror://gentoo/${PN}-${PATCH_V}-autotools.patch.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="alpha amd64 arm hppa ia64 ppc ppc64 ~s390 sparc x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos" +IUSE="doc" + +RDEPEND=" + app-eselect/eselect-lapack + virtual/blas" +DEPEND=" + ${RDEPEND} + virtual/pkgconfig + doc? ( app-doc/lapack-docs )" + +S="${WORKDIR}/${MyPN}-${PV}" + +pkg_setup() { + fortran-2_pkg_setup + if [[ $(tc-getFC) =~ if ]]; then + ewarn "Using Intel Fortran at your own risk" + export LDFLAGS="$(raw-ldflags)" + export NOOPT_FFLAGS=-O + fi + ESELECT_PROF=reference +} + +src_prepare() { + epatch \ + "${WORKDIR}"/${PN}-${PATCH_V}-autotools.patch \ + "${FILESDIR}"/${P}-parallel-make.patch + eautoreconf + + # set up the testing routines + sed \ + -e "s:g77:$(tc-getFC):" \ + -e "s:-funroll-all-loops -O3:${FFLAGS} $($(tc-getPKG_CONFIG) --cflags blas):" \ + -e "s:LOADOPTS =:LOADOPTS = ${LDFLAGS} $($(tc-getPKG_CONFIG) --cflags blas):" \ + -e "s:../../blas\$(PLAT).a:$($(tc-getPKG_CONFIG) --libs blas):" \ + -e "s:lapack\$(PLAT).a:SRC/.libs/liblapack.a:" \ + make.inc.example > make.inc \ + || die "Failed to set up make.inc" + + cp "${FILESDIR}"/eselect.lapack.reference "${T}"/eselect.lapack.reference || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.lapack.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.lapack.reference || die + fi + sed \ + -e '/Libs:/s|: |: -L${libdir} |g' \ + -i lapack.pc.in || die +} + +src_configure() { + econf \ + --libdir="${EPREFIX}/usr/$(get_libdir)/lapack/reference" \ + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" +} + +src_install() { + default + eselect lapack add $(get_libdir) "${T}"/eselect.lapack.reference ${ESELECT_PROF} +} + +src_test() { + MAKEOPTS+=" -j1" + cd "${S}"/TESTING/MATGEN && emake || die + cd "${S}"/TESTING && emake || die +} + +pkg_postinst() { + local p=lapack + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/lapack-reference/lapack-reference-3.6.0.ebuild b/sci-libs/lapack-reference/lapack-reference-3.6.0.ebuild new file mode 100644 index 000000000000..f7f204af0676 --- /dev/null +++ b/sci-libs/lapack-reference/lapack-reference-3.6.0.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils fortran-2 cmake-utils multilib flag-o-matic toolchain-funcs + +DESCRIPTION="Reference implementation of LAPACK" +HOMEPAGE="http://www.netlib.org/lapack/" +SRC_URI="http://www.netlib.org/lapack/lapack-${PV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos" +IUSE="+deprecated" + +DEPEND="app-eselect/eselect-lapack + >=virtual/blas-3.6 + virtual/pkgconfig" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/lapack-${PV}" +PATCHES=( "${FILESDIR}/${P}-fix-build-system.patch" ) + +src_prepare() { + epatch "${PATCHES[@]}" + + eapply_user + + ESELECT_PROF=reference + + # some string does not get passed properly + sed -i \ + -e '/lapack_testing.py/d' \ + CTestCustom.cmake.in || die + # separate ebuild to tmglib + sed -i \ + -e '/lapack_install_library(tmglib)/d' \ + TESTING/MATGEN/CMakeLists.txt || die + + cp "${FILESDIR}"/eselect.lapack.reference-r1 "${T}"/eselect.lapack.reference || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.lapack.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.lapack.reference || die + fi +} + +src_configure() { + local mycmakeargs=( + -Wno-dev + -DUSE_OPTIMIZED_BLAS=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + -DBUILD_DEPRECATED=$(usex deprecated) + -DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags blas) $(get_abi_CFLAGS) ${FCFLAGS}" + -DBUILD_STATIC_LIBS=ON + -DBUILD_SHARED_LIBS=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile +} + +src_install() { + cmake-utils_src_install + + mkdir -p "${ED}/usr/$(get_libdir)/lapack/reference" || die + mv "${ED}/usr/$(get_libdir)"/lib* "${ED}/usr/$(get_libdir)/pkgconfig"/* \ + "${ED}/usr/$(get_libdir)/lapack/reference" || die + rmdir "${ED}/usr/$(get_libdir)/pkgconfig" || die + + eselect lapack add $(get_libdir) "${T}"/eselect.lapack.reference ${ESELECT_PROF} +} + +pkg_postinst() { + local p=lapack + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/lapack-reference/lapack-reference-3.7.0.ebuild b/sci-libs/lapack-reference/lapack-reference-3.7.0.ebuild new file mode 100644 index 000000000000..2bc7edc7b4ff --- /dev/null +++ b/sci-libs/lapack-reference/lapack-reference-3.7.0.ebuild @@ -0,0 +1,99 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils fortran-2 cmake-utils multilib flag-o-matic toolchain-funcs + +DESCRIPTION="Reference implementation of LAPACK" +HOMEPAGE="http://www.netlib.org/lapack/" +SRC_URI="http://www.netlib.org/lapack/lapack-${PV}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos" +IUSE="+deprecated" + +DEPEND="app-eselect/eselect-lapack + >=virtual/blas-3.6 + virtual/pkgconfig" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/lapack-${PV}" +PATCHES=( "${FILESDIR}/${P}-fix-build-system.patch" ) + +src_prepare() { + epatch "${PATCHES[@]}" + + eapply_user + + ESELECT_PROF=reference + + # some string does not get passed properly + sed -i \ + -e '/lapack_testing.py/d' \ + CTestCustom.cmake.in || die + # separate ebuild to tmglib + sed -i \ + -e '/lapack_install_library(tmglib)/d' \ + TESTING/MATGEN/CMakeLists.txt || die + + cp "${FILESDIR}"/eselect.lapack.reference-r1 "${T}"/eselect.lapack.reference || die + sed -i -e "s:/usr:${EPREFIX}/usr:" "${T}"/eselect.lapack.reference || die + if [[ ${CHOST} == *-darwin* ]] ; then + sed -i -e 's/\.so\([\.0-9]\+\)\?/\1.dylib/g' \ + "${T}"/eselect.lapack.reference || die + fi +} + +src_configure() { + local mycmakeargs=( + -Wno-dev + -DUSE_OPTIMIZED_BLAS=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + -DBUILD_DEPRECATED=$(usex deprecated) + -DCMAKE_Fortran_FLAGS="$($(tc-getPKG_CONFIG) --cflags blas) $(get_abi_CFLAGS) ${FCFLAGS}" + -DBUILD_STATIC_LIBS=ON + -DBUILD_SHARED_LIBS=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile +} + +src_install() { + cmake-utils_src_install + + mkdir -p "${ED}/usr/$(get_libdir)/lapack/reference" || die + mv "${ED}/usr/$(get_libdir)"/lib* "${ED}/usr/$(get_libdir)/pkgconfig"/* \ + "${ED}/usr/$(get_libdir)/lapack/reference" || die + if [[ ${CHOST} == *-darwin* ]] ; then + # modify install_names accordingly, bug #608266 + local lib + for lib in "${ED}"/usr/$(get_libdir)/lapack/reference/*.dylib ; do + install_name_tool -id "${lib#${D%/}}" "${lib}" + done + fi + rmdir "${ED}/usr/$(get_libdir)/pkgconfig" || die + + eselect lapack add $(get_libdir) "${T}"/eselect.lapack.reference ${ESELECT_PROF} +} + +pkg_postinst() { + local p=lapack + local current_lib=$(eselect ${p} show | cut -d' ' -f2) + if [[ ${current_lib} == ${ESELECT_PROF} || -z ${current_lib} ]]; then + # work around eselect bug #189942 + local configfile="${EROOT}"/etc/env.d/${p}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${p} set ${ESELECT_PROF} + elog "${p} has been eselected to ${ESELECT_PROF}" + else + elog "Current eselected ${p} is ${current_lib}" + elog "To use ${p} ${ESELECT_PROF} implementation, you have to issue (as root):" + elog "\t eselect ${p} set ${ESELECT_PROF}" + fi +} diff --git a/sci-libs/lapack-reference/metadata.xml b/sci-libs/lapack-reference/metadata.xml new file mode 100644 index 000000000000..9bd49b11cd5c --- /dev/null +++ b/sci-libs/lapack-reference/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +LAPACK is a comprehensive library that does linear algebra +operations including matrix inversions, least squared solutions to +linear sets of equations, eigenvector analysis, singular value +decomposition, etc. It is a very comprehensive and reputable package +that has found extensive use in the scientific community. +This package installs the reference FORTRAN 77 implementation from Netlib. + </longdescription> + <use> + <flag name="deprecated">Build deprecated routines</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/ldl/Manifest b/sci-libs/ldl/Manifest new file mode 100644 index 000000000000..ea5d1894d799 --- /dev/null +++ b/sci-libs/ldl/Manifest @@ -0,0 +1,8 @@ +AUX ldl-2.0.3-autotools.patch 2001 SHA256 ee59cb2ded5a7cd167e20993e63659bf31ca515c31d4fe5320dd3336c410ed11 SHA512 5c61ad57d39a91b3327803bf7589497679afb78b7754ab5660e855dbc28f47fe288accd62a35fd4aa318dcf25c36e5066818ed88221863830c1962681359493b WHIRLPOOL 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69a918aa9b28b640fe229aee1bb3f2f727b4d958f0b8f6e8a7a4339c26fe342ac48f37ea8b76ea0e74d7fbb621cbe86527119ca231373cbe192d6c472f88ca81 WHIRLPOOL 6a6318fb7a05c90e8c0143162937705cf3f630827effc033ce76253473919dda5ac8c91d3176db17f711afe9a7ffb4984e4a990e016405c6cf8b989b6be4c9ad +EBUILD ldl-2.1.0.ebuild 688 SHA256 29e7af45d574f3b054fd698a09b847145a69f587c5c69dd1e2591e3bf6bcc1d9 SHA512 f84ac5a1a8377176f9d174852e1885e82ae38a71a6185cd964a29421af8169683faca5a2e801ea6f06152c25730280e0f82f2a0e6ee911cb7bbb01db4d5364c7 WHIRLPOOL 89ffeace6108b06554f509a9d21b11d72715456be5e47c16d7ef560e156e6676711210220bc3401e463fad1e22f45c407ddf8b69bfb074845d060dac2dc024a8 +MISC ChangeLog 2681 SHA256 609c21d63378f0579ecfeb2220ec369bbd0a1ce9f95fd6fbc77d6ea7419829be SHA512 00f5745963abf81b481fed276219a9e92223c9526b883c2874d13f2735026b6847a68a16027cc8dffcaade9b075c5f42dc49e8a2539bad2179d9f9c023b32077 WHIRLPOOL ccccc0c32c3a29cc52c548da847356f888534657369d7624ae1ddd5a7b5ea190bc1ed21b5e6105d65fabe56f78d9e136e52f293bc9ca4edecc487d0721835997 +MISC ChangeLog-2015 1336 SHA256 e37df6f30da5532be4a5eda80af84f2fde5492c6d407864a40a99a347e2f7e56 SHA512 c4d1e578261c14b30b7ec27f2d8311c9f86b1593653d166196b73af50e1740d81c8675a4b3a0ec8530c4a6caaacad5d81a097f58554e7cbc4977f306e2c09165 WHIRLPOOL 7d3d8322c75306c43fe5fdbbd66e697c42c0007b1f8dfbaef5e0dea69750378891ed9af7833155b1df77a572fe3997727e994559690e38b82f483d0fd65036e7 +MISC metadata.xml 885 SHA256 fca11c24fa8e15785c2592dff5d6348651a1b9f4baf9d445a485088165528977 SHA512 bf0ae9850026ae2099aefa1ffea11633f8dfa35f6fc631afa688a12bc018a45a1155c04ac159fc07322324b73da76fcb97d5ce79b999509d91045d6145cbc291 WHIRLPOOL 36daf05dc508858a8a5f0d449e078f0f17b3748149cd47ab200db43afdc525f80706353d581759be20b53a43e3556491be0ae5173fd9f73a5b51946bac00c20f diff --git a/sci-libs/ldl/files/ldl-2.0.3-autotools.patch b/sci-libs/ldl/files/ldl-2.0.3-autotools.patch new file mode 100644 index 000000000000..5e174999a5f3 --- /dev/null +++ b/sci-libs/ldl/files/ldl-2.0.3-autotools.patch @@ -0,0 +1,64 @@ +--- configure.ac 1970-01-01 01:00:00.000000000 +0100 ++++ configure.ac 2008-01-30 12:45:53.174426797 +0000 +@@ -0,0 +1,10 @@ ++# -*- Autoconf -*- ++AC_PREREQ(2.59) ++AC_INIT(ldl, 2.0.3, davis@cise.ufl.edu) ++AM_INIT_AUTOMAKE([foreign]) ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++AC_CHECK_LIB(m, sqrt) ++AC_CHECK_HEADERS(UFconfig.h) ++AC_CONFIG_FILES([Makefile Source/Makefile Demo/Makefile]) ++AC_OUTPUT +--- Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Makefile.am 2008-01-30 15:49:41.835515468 +0000 +@@ -0,0 +1,4 @@ ++SUBDIRS = Source Demo ++EXTRA_DIST = README.txt ++include_HEADERS = Include/ldl.h ++ +--- Source/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Source/Makefile.am 2008-01-30 12:49:25.858546974 +0000 +@@ -0,0 +1,11 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include ++ ++LDLSRC=ldl.c ++lib_LTLIBRARIES = libldl.la ++noinst_LTLIBRARIES = libldli.la libldll.la ++libldli_la_SOURCES = $(LDLSRC) ++libldli_la_CPPFLAGS = $(AM_CPPFLAGS) ++libldll_la_SOURCES = $(LDLSRC) ++libldll_la_CPPFLAGS = $(AM_CPPFLAGS) -DLDL_LONG ++libldl_la_SOURCES = ++libldl_la_LIBADD = libldll.la libldli.la +--- Demo/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Demo/Makefile.am 2008-01-30 15:43:45.603214946 +0000 +@@ -0,0 +1,27 @@ ++LDADD = $(top_builddir)/Source/libldl.la -lm ++AM_CPPFLAGS = -I$(top_srcdir)/Include ++check_PROGRAMS = ldlsimple ldllsimple ldlmain ldllmain ldlamd ldllamd ++ ++ldlmain_SOURCES = ldlmain.c ++ldllmain_SOURCES = ldlmain.c ++ldllmain_CPPFLAGS = $(AM_CPPFLAGS) -DLDL_LONG ++ ++ldlsimple_SOURCES = ldlsimple.c ++ldllsimple_SOURCES = ldlsimple.c ++ldllsimple_CPPFLAGS = $(AM_CPPFLAGS) -DLDL_LONG ++ ++ldlamd_SOURCES = ldlamd.c ++ldllamd_CPPFLAGS = $(AM_CPPFLAGS) -DUSE_AMD ++ldllamd_SOURCES = ldlamd.c ++ldllamd_CPPFLAGS = $(AM_CPPFLAGS) -DUSE_AMD -DLDL_LONG ++ldllamd_LDADD = $(LDADD) -lamd ++ ++check-local: $(check_PROGRAMS) ++ @for i in $(check_PROGRAMS); do \ ++ echo "Testing $$i"; \ ++ ./$$i > my_$$i.out; \ ++ if ! diff $$i.out my_$$i.out; then \ ++ echo "Testing $$i failed"; \ ++ exit 1; \ ++ fi \ ++ done; diff --git a/sci-libs/ldl/ldl-2.0.4.ebuild b/sci-libs/ldl/ldl-2.0.4.ebuild new file mode 100644 index 000000000000..91e5ecea53e8 --- /dev/null +++ b/sci-libs/ldl/ldl-2.0.4.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes +inherit autotools-utils + +MY_PN=LDL + +DESCRIPTION="Simple but educational LDL^T matrix factorization algorithm" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/ldl" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc static-libs" +DEPEND="sci-libs/ufconfig" +RDEPEND="" + +PATCHES=( "${FILESDIR}"/${PN}-2.0.3-autotools.patch ) +DOCS=( README.txt Doc/ChangeLog ) + +S="${WORKDIR}/${MY_PN}" + +src_install() { + autotools-utils_src_install + use doc && dodoc Doc/ldl_userguide.pdf +} diff --git a/sci-libs/ldl/ldl-2.1.0.ebuild b/sci-libs/ldl/ldl-2.1.0.ebuild new file mode 100644 index 000000000000..d356f046a806 --- /dev/null +++ b/sci-libs/ldl/ldl-2.1.0.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Simple but educational LDL^T matrix factorization algorithm" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/ldl" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~arm ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc static-libs" + +RDEPEND="sci-libs/suitesparseconfig" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base )" + +src_configure() { + local myeconfargs=( + $(use_with doc) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/ldl/metadata.xml b/sci-libs/ldl/metadata.xml new file mode 100644 index 000000000000..776f7e760b66 --- /dev/null +++ b/sci-libs/ldl/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + LDL is a set of concise routines for factorizing symmetric + positive-definite sparse matrices, with some applicability to + symmetric indefinite matrices. Its primary purpose is to illustrate + much of the basic theory of sparse matrix algorithms in as concise a + code as possible, including an elegant new method of sparse symmetric + factorization that computes the factorization row-by-row but stores it + column-by-column. The entire symbolic and numeric factorization + consists of a total of only 49 lines of code. The package is written + in C, and includes a MATLAB interface. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/lemon/Manifest b/sci-libs/lemon/Manifest new file mode 100644 index 000000000000..fdaeee51cd1a --- /dev/null +++ b/sci-libs/lemon/Manifest @@ -0,0 +1,7 @@ +AUX lemon-1.3-as-needed.patch 1346 SHA256 4731c61ac838d8eed834ef300b9a6fdff134ee7bb71c446569d19c57c3eb03b7 SHA512 20aef0cfc1b6884604a3cf1f4a60feb688ab4d1a958314c242e965195d6cc950062f67f7ef273fc096fe5fcd7a7ee9acb76215c1a6a173587da3b5e76b163468 WHIRLPOOL 5f8422f9cdb616ffe321d9a16013f65bf2396ecdefaf4bba52a2872cabd18683d02bd2f8bbe0481a464a011578b54cfb7cba2b7ef634b7041420d6d17c566165 +AUX lemon-1.3-multilib.patch 437 SHA256 110fbd9a4e9fd23f6ad2edf89c27002cb0d3ea372e0df399f957963e2467bd19 SHA512 6efd7280070bae7bf7e62b28fb6a99e5f2190ddff75f8dd500a629c2a60908670c3ea19aeaf0086059ba9c3c7439e0c835811684dc1c2525c4f8a304a36bba8c WHIRLPOOL 2feb14b8b7ff54cd33cf5c96372480a5a935287ff673357c3f9e3d1fd7d22e18c9365f717ee3839a8a9945268b587a9479eba4d538631269877267207e4218e5 +DIST lemon-1.3.tar.gz 5454290 SHA256 6c190dbb1e17bdb71597e79c409b2e798ffcbdb7d764ea45d6299339b12d3e05 SHA512 f48c14e42e0a463a3d203a05a012fdf635cf09503a5d18e14e64722e9f7f68d7fc223059e0a6a5d118491a473a25196d531e0a6302552f9fb8c121a4ed70af45 WHIRLPOOL 14325b538a27a8d46bc3840fa5687c8d286e7668e06f06c074417db245bc920b90f48825189b0e20858050b26676151a55bdb279bed4a0bccb133d9439435fad +EBUILD lemon-1.3-r2.ebuild 1822 SHA256 d93bce3fc9d28cbea5402ccc9e6281f4eb390ff1cfa659b2fe13afca2668c169 SHA512 d9fc4a966c4cbfe05f034acc1a3ce8d789aa2b7daeded6bbe95ccc00433ca222e54d78ff9ab6de3b100891058cf3928d7800e27272f80c804c90e99122eb80e8 WHIRLPOOL a615ba1f60f9bc4843d61f7b048bafdaec2e15a891db6606856bc23e9e2052c90c18f461dcbef1b0fdae7a6aded3f862480c17e9d3d2eb18dfbd99c0ac0c7217 +MISC ChangeLog 3027 SHA256 c7ff26fb0bd8041346643e76a3974b784d8db690850b9a70374c5311f9e8a2b8 SHA512 5b47a2bd5a179bf792564384515b12a59275b51e7daa8e27b4c9662c341838ffb08a5431af3264f321456d764a21b1b419a658fd8825e9666ce6a76599a8c377 WHIRLPOOL 0bd39aee330178ea29c214561b4471f680e3e6bbe717839a8c43710e11636de20e698ea2e5ba9b483373bde0df586ae28be0a4fe2fb114e883fc3715c3aa46d6 +MISC ChangeLog-2015 2199 SHA256 e1e4cae254290d2c24109281da3a787370834df68cb8e8b64e51f78108f4e402 SHA512 010e10b12b342fc5d8eeb9178158a7e0e4fecae207a80e746b18cabb55ea8dfb4eaab7e2804fe42119694f8cae3a9f2e4752af228f7776bc824e4baded8a3048 WHIRLPOOL c1b8b8d7309546376001c7b22e61571d6edfac33b3652310d1543322e0a40c70af98f67afb1caf90ffd8829ba2c0bb8b4b37454c910a0088a441e7253c7998f4 +MISC metadata.xml 969 SHA256 ecd901cfe5c6f1b58eaf80431f377be17537d1a8ff6560d2efd664d12d098a4c SHA512 2d83367611c99baa4a589677c752344b4d72ec460456d99ff1cc030f202df32e680b871159532cf5d06472dda596919e8edc23872eb166e25277015c38b9c9e8 WHIRLPOOL 3f9f662e8cd05caa9eb9bfccf77490ba09ff76e3767a32b989ecceb1ac81f13bfb8146d081a910d407fed88c7ec9bfad3c0f62e1d5a709d9774ed3805653078f diff --git a/sci-libs/lemon/files/lemon-1.3-as-needed.patch b/sci-libs/lemon/files/lemon-1.3-as-needed.patch new file mode 100644 index 000000000000..ab205e69a4fa --- /dev/null +++ b/sci-libs/lemon/files/lemon-1.3-as-needed.patch @@ -0,0 +1,47 @@ + CMakeLists.txt | 4 ++++ + lemon/CMakeLists.txt | 2 ++ + 2 files changed, 6 insertions(+) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index b06e5c7..fa68aa8 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -84,21 +84,25 @@ IF(GLPK_FOUND) + SET(LEMON_HAVE_LP TRUE) + SET(LEMON_HAVE_MIP TRUE) + SET(LEMON_HAVE_GLPK TRUE) ++ SET(LEMON_LP_LIBRARIES ${LEMON_LP_LIBRARIES} ${GLPK_LIBRARIES}) + ENDIF(GLPK_FOUND) + IF(ILOG_FOUND) + SET(LEMON_HAVE_LP TRUE) + SET(LEMON_HAVE_MIP TRUE) + SET(LEMON_HAVE_CPLEX TRUE) ++ SET(LEMON_LP_LIBRARIES ${LEMON_LP_LIBRARIES} ${ILOG_LIBRARIES}) + ENDIF(ILOG_FOUND) + IF(COIN_FOUND) + SET(LEMON_HAVE_LP TRUE) + SET(LEMON_HAVE_MIP TRUE) + SET(LEMON_HAVE_CLP TRUE) + SET(LEMON_HAVE_CBC TRUE) ++ SET(LEMON_LP_LIBRARIES ${LEMON_LP_LIBRARIES} ${COIN_LIBRARIES}) + ENDIF(COIN_FOUND) + IF(SOPLEX_FOUND) + SET(LEMON_HAVE_LP TRUE) + SET(LEMON_HAVE_SOPLEX TRUE) ++ SET(LEMON_LP_LIBRARIES ${LEMON_LP_LIBRARIES} ${COIN_LIBRARIES}) + ENDIF(SOPLEX_FOUND) + + IF(ILOG_FOUND) +diff --git a/lemon/CMakeLists.txt b/lemon/CMakeLists.txt +index 8011833..2487345 100644 +--- a/lemon/CMakeLists.txt ++++ b/lemon/CMakeLists.txt +@@ -59,6 +59,8 @@ IF(UNIX) + SET_TARGET_PROPERTIES(lemon PROPERTIES OUTPUT_NAME emon) + ENDIF() + ++TARGET_LINK_LIBRARIES(lemon ${LEMON_LP_LIBRARIES}) ++ + INSTALL( + TARGETS lemon + ARCHIVE DESTINATION lib diff --git a/sci-libs/lemon/files/lemon-1.3-multilib.patch b/sci-libs/lemon/files/lemon-1.3-multilib.patch new file mode 100644 index 000000000000..ee578d4a0f6a --- /dev/null +++ b/sci-libs/lemon/files/lemon-1.3-multilib.patch @@ -0,0 +1,18 @@ + lemon/CMakeLists.txt | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/lemon/CMakeLists.txt b/lemon/CMakeLists.txt +index 8011833..0209acf 100644 +--- a/lemon/CMakeLists.txt ++++ b/lemon/CMakeLists.txt +@@ -61,8 +61,8 @@ ENDIF() + + INSTALL( + TARGETS lemon +- ARCHIVE DESTINATION lib +- LIBRARY DESTINATION lib ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} ++ LIBRARY DESTINATION lib${LIB_SUFFIX} + COMPONENT library + ) + diff --git a/sci-libs/lemon/lemon-1.3-r2.ebuild b/sci-libs/lemon/lemon-1.3-r2.ebuild new file mode 100644 index 000000000000..4ebb5c672099 --- /dev/null +++ b/sci-libs/lemon/lemon-1.3-r2.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="C++ template static library of common data structures and algorithms" +HOMEPAGE="https://lemon.cs.elte.hu/trac/lemon/" +SRC_URI="http://lemon.cs.elte.hu/pub/sources/${P}.tar.gz" + +LICENSE="Boost-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+coin doc glpk static-libs test tools" + +RDEPEND=" + glpk? ( sci-mathematics/glpk:= ) + coin? ( sci-libs/coinor-cbc:= sci-libs/coinor-clp:= )" +DEPEND="${RDEPEND} + doc? ( + app-text/ghostscript-gpl + dev-libs/mathjax + app-doc/doxygen )" + +REQUIRED_USE="|| ( coin glpk )" + +PATCHES=( + "${FILESDIR}"/${P}-multilib.patch + "${FILESDIR}"/${P}-as-needed.patch +) + +src_prepare() { + sed -i \ + -e '/ADD_SUBDIRECTORY(demo)/d' \ + CMakeLists.txt || die + + use doc || sed -i \ + -e '/ADD_SUBDIRECTORY(doc)/d' \ + CMakeLists.txt || die + + use tools || sed -i \ + -e '/ADD_SUBDIRECTORY(tools)/d' \ + CMakeLists.txt || die + + use test || sed -i \ + -e '/ADD_SUBDIRECTORY(test)/d' \ + CMakeLists.txt || die + + for t in \ + max_clique \ + max_flow \ + graph_utils \ + random \ + time_measure \ + tsp; do + sed -i -e "/${t}_test/d" test/CMakeLists.txt || die + done + sed -i \ + -e '/ADD_TEST(lp_test lp_test)/d' \ + -e '/ADD_DEPENDENCIES(check lp_test)/d' \ + test/CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBUILD_SHARED_LIBS=TRUE + -DCOIN_ROOT_DIR="${EPREFIX}/usr" + -DLEMON_DOC_MATHJAX_RELPATH="${EPREFIX}/usr/share/mathjax" + $(cmake-utils_use doc LEMON_DOC_SOURCE_BROWSER) + $(cmake-utils_use doc LEMON_DOC_USE_MATHJAX) + $(cmake-utils_use coin LEMON_ENABLE_COIN) + $(cmake-utils_use glpk LEMON_ENABLE_GLPK) + ) + cmake-utils_src_configure +} + +src_test() { + emake -C "${BUILD_DIR}" check +} diff --git a/sci-libs/lemon/metadata.xml b/sci-libs/lemon/metadata.xml new file mode 100644 index 000000000000..1802bf9066b2 --- /dev/null +++ b/sci-libs/lemon/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="person"> + <email>mmokrejs@gmail.com</email> + <name>Martin Mokrejs</name> +</maintainer> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription> + LEMON stands for Library for Efficient Modeling and Optimization in + Networks. It is a C++ template library providing efficient + implementations of common data structures and algorithms with focus + on combinatorial optimization tasks connected mainly with graphs and + networks. +</longdescription> +<use> + <flag name="coin">Enable the <pkg>sci-libs/coinor-clp</pkg> and + <pkg>sci-libs/coinor-cbc</pkg> graph algorithms</flag> + <flag name="glpk">Enable GNU Linear Programming Kit + <pkg>sci-mathematics/glpk</pkg> support</flag> + <flag name="tools">Build additional tools</flag> +</use> +</pkgmetadata> diff --git a/sci-libs/levmar/Manifest b/sci-libs/levmar/Manifest new file mode 100644 index 000000000000..35ed76e8ff50 --- /dev/null +++ b/sci-libs/levmar/Manifest @@ -0,0 +1,7 @@ +AUX levmar-2.6-demo-underlinking.patch 419 SHA256 a3fa17bc293258ba511f5efd4c3abd991c96400f9cea9dd2d8e97d2e128c694f SHA512 bed5504603e17dcde3c6fc91031f0d221eec3e8da3a75c930e7a113b04162340d5e83593e7ef3d60e17d2df07caff24356a64b95e8842fcbe5b79c26c1ae2c61 WHIRLPOOL 34e1bb19335c063f8956dda47a0175c011d7685ad8606ea6b4398e4d46b5a345c15d2bfd5a48acebfc1b373397925fbcfa5cdefae67fafaa8c7df00c9bebaabe +AUX levmar-2.6-shared.patch 425 SHA256 4656860078a960a86b2bfb69366cc19f29343ab6222d114e3d230d1d08a87963 SHA512 1544ba8d450f383f556f6f140b7b0c15d128bc0e12071f4cd47ae00068d3c67e82c49c4b7525ef3d9af2e3df805f3c749e460c91de652065e2954d6c1ee76109 WHIRLPOOL 02760b358668d8afae7acb7e68aa96d1921b954ea680f3ca6d9858361d1cf386ac017bad2fa00fe2ca3fcde045a90df71ce869a3671410d52b46f2573f090800 +DIST levmar-2.6.tgz 81143 SHA256 3bf4ef1ea4475ded5315e8d8fc992a725f2e7940a74ca3b0f9029d9e6e94bad7 SHA512 5b4c64b63be9b29d6ad2df435af86cd2c2e3216313378561a670ac6a392a51bbf1951e96c6b1afb77c570f23dd8e194017808e46929fec2d8d9a7fe6cf37022b WHIRLPOOL fd9f45474a2fbc57f3a542480271d90a15163edebc6e9b70444f2d9d4c9ad1a3c1301d77cee5c5d41944224c888547c069ee7443a09ff478ea996c3358f81023 +EBUILD levmar-2.6.ebuild 939 SHA256 c3989bc21c9e5b1798e42be4be520a266b9086e20abbf4ad7f356b1a12abdc56 SHA512 268aa14f432988a216333cd8694edf843f0a13e20617c9f6b976bdcde8fa84633c5dff69ff2098db6bb92974d1197a60cdb456fe4fd5aab6d27bf1658f4a6122 WHIRLPOOL 38ee930a7c0cbe6ac2135471e1173bad3ba24f1b28fca1a40e4f7d0c5baba790606f31d1097af4963480e3a1d6467a3647cbcfe64b464580e266be1539ab3cd8 +MISC ChangeLog 2497 SHA256 26b7592b17580034413c34ad32d22d5e864448451658f89d23a111c9c6cb7ebc SHA512 c72da0a33f219a34fb114ff1a64c4d52ab57590b009c6f28b26fecbfffcc2ecd3ab794266b01107581dd42ae7db6be17152d46f9bbe24264c95b5b814cdca31e WHIRLPOOL f57cfe2cef255cebda834fbbb7e90d33a5c170678279352f831405481d40cf8f127081f72f20c054cd7210da0661e3e598c6421f26c64b307b4eb72924634a00 +MISC ChangeLog-2015 524 SHA256 8724f448cd447d112dba936a9bf01daa4a9b498bf858f66224bd1142c9e02777 SHA512 a71692c3a18654017c4298518e0d250946fd35cc9d5a3845a4a7727ae6ed65544414eec90325d56c03b2c8bc9808153e7a66018bed975e3fb713c41458f05f96 WHIRLPOOL ee07b6ba63b984aa3fcfa0a8a26c283e0671203555a5cc5655810791fa312711df006ef84dcc70a8c46b2eca6a39202a349c4488f0d75b5adb451ff4fc201c32 +MISC metadata.xml 756 SHA256 2bf0204ef8a9e17b988571e0017bdc35e60932472eb01e527668643c38f41fae SHA512 df18f711a4d437895201d04e0288d799cc0754d3712e35df19ccb8d79ffa8f5d696467262d7df03f4860786591b14c021ebf6a07c68878f54ff9d48375808099 WHIRLPOOL 5ae57c1ae0d1403a2df4cb844c56ca456a61fe281f64d95ef2fbaf5f5aa0f9285cbf7a39364da74fdf0767f4fcc7964d4cff19d0170c10f9d037062e4ad5a324 diff --git a/sci-libs/levmar/files/levmar-2.6-demo-underlinking.patch b/sci-libs/levmar/files/levmar-2.6-demo-underlinking.patch new file mode 100644 index 000000000000..a6be5587d3e0 --- /dev/null +++ b/sci-libs/levmar/files/levmar-2.6-demo-underlinking.patch @@ -0,0 +1,12 @@ +diff -urN levmar-2.6.old/CMakeLists.txt levmar-2.6/CMakeLists.txt +--- levmar-2.6.old/CMakeLists.txt 2014-08-07 18:22:25.739008113 +0200 ++++ levmar-2.6/CMakeLists.txt 2014-08-07 18:22:36.050014845 +0200 +@@ -67,7 +67,7 @@ +
+ # demo program
+ IF(BUILD_DEMO)
+- SET(LIBS levmar)
++ SET(LIBS levmar m)
+
+ LINK_DIRECTORIES(${CMAKE_BINARY_DIR}) # location of the levmar library
+ LINK_DIRECTORIES(${LAPACKBLAS_DIR})
diff --git a/sci-libs/levmar/files/levmar-2.6-shared.patch b/sci-libs/levmar/files/levmar-2.6-shared.patch new file mode 100644 index 000000000000..e89750cc028f --- /dev/null +++ b/sci-libs/levmar/files/levmar-2.6-shared.patch @@ -0,0 +1,12 @@ +diff -Nur levmar-2.6.orig/CMakeLists.txt levmar-2.6/CMakeLists.txt +--- levmar-2.6.orig/CMakeLists.txt 2012-04-13 04:53:53.000000000 +0100 ++++ levmar-2.6/CMakeLists.txt 2012-04-13 04:54:20.000000000 +0100 +@@ -60,7 +60,7 @@ + ENDIF(HAVE_PLASMA)
+
+ # levmar library source files
+-ADD_LIBRARY(levmar STATIC
++ADD_LIBRARY(levmar SHARED
+ lm.c Axb.c misc.c lmlec.c lmbc.c lmblec.c lmbleic.c
+ levmar.h misc.h compiler.h
+ )
diff --git a/sci-libs/levmar/levmar-2.6.ebuild b/sci-libs/levmar/levmar-2.6.ebuild new file mode 100644 index 000000000000..c79aa78b669c --- /dev/null +++ b/sci-libs/levmar/levmar-2.6.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils eutils toolchain-funcs + +DESCRIPTION="Levenberg-Marquardt nonlinear least squares C library" +HOMEPAGE="https://www.ics.forth.gr/~lourakis/levmar/" +SRC_URI="${HOMEPAGE}/${P}.tgz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}"/${P}-shared.patch + "${FILESDIR}"/${P}-demo-underlinking.patch +) + +src_configure() { + local mycmakeargs+=( + -DNEED_F2C=OFF + -DHAVE_LAPACK=ON + -DLAPACKBLAS_LIB_NAMES="$($(tc-getPKG_CONFIG) --libs blas lapack)" + $(cmake-utils_use test BUILD_DEMO) + ) + cmake-utils_src_configure +} + +src_test() { + cd ${CMAKE_BUILD_DIR} + ./lmdemo || die +} + +src_install() { + dolib.so ${CMAKE_BUILD_DIR}/liblevmar.so + insinto /usr/include + doins levmar.h +} diff --git a/sci-libs/levmar/metadata.xml b/sci-libs/levmar/metadata.xml new file mode 100644 index 000000000000..a1d97390a7a7 --- /dev/null +++ b/sci-libs/levmar/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="person"> + <email>amynka@gentoo.org</email> +</maintainer> +<maintainer type="project"> + <email>3dprint@gentoo.org</email> + <name>Gentoo 3D print</name> +</maintainer> +<longdescription lang="en"> + levmar is a native ANSI C implementation of the Levenberg-Marquardt + optimization algorithm. Both unconstrained and constrained (under + linear equations, inequality and box constraints) + Levenberg-Marquardt variants are included. The LM algorithm is an + iterative technique that finds a local minimum of a function that is + expressed as the sum of squares of nonlinear functions. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/libaec/Manifest b/sci-libs/libaec/Manifest new file mode 100644 index 000000000000..c43a4a66d980 --- /dev/null +++ b/sci-libs/libaec/Manifest @@ -0,0 +1,8 @@ +DIST libaec-0.3.2.tar.gz 353185 SHA256 acb7cbf4e8f3c63a9ea1af1e1a2d0c9658f4831deb7327f110bdd5c187dc3441 SHA512 c3935f7d3e2e289e66f24d5af8f8fe21aab1044adbe883708ed64eb194bf93511fe2a9dd2b1658571ebbcc502123b3a5e6dfaa1bc4a1b85eaeaedc8b43d8085e WHIRLPOOL 56214327aeebcfac3c3e828ceb8187d00b8cebeec3cf10777c25edd69c74fe7c89fca2a42591bddc3aaa14f3d301371664f80627d902709f2b87a6b54de3bcc0 +DIST libaec-1.0.0.tar.gz 3118578 SHA256 3e79e33b380cb2f17323d3de5e70c4e656242a62bfbe72ffcea36adaa344c47d SHA512 112ded6151e46a90adfe230d8298452b2e42105e0e9d40ce10ac49f1e0160a13fa7ddec22e22346f0d5defc397bbba7c12f9d58b08e024da19991108e6e8d8ba WHIRLPOOL 21154d51c02c03c9f93c5873b4b1d5f3a53c393fe10020d8a6d5e34a7640a6d3b5fcecd6e139164ff042369e7649c4e765fedc95cda267862b38133717aee531 +DIST libaec-1.0.1.tar.gz 769507 SHA256 3668eb4ed36724441e488a7aadc197426afef4b1e8bd139af6d3e36023906459 SHA512 e3e38298d8d1fdf86332612c4dd62cafb8fa59ec8de00ed96aabee5bfbb46fd2396fcc0ad7fa2e4f89f9a22de538e58be5017d214b42176c0450dcc7c35bfedb WHIRLPOOL 46130aa95a078f531c3621148494a428be8cfb79a82dde9175ff8dc15c0f0ee9632cdcddefbfb4ee0cf67f83adeb1f994b25a61a26b96d3a3c51cbfc8a4f1cdd +EBUILD libaec-0.3.2.ebuild 861 SHA256 20b11943478970b6a28ddce31e042c250947db24ed7ca3adc0f093cf66368714 SHA512 98665305d25602202a33013af317ce7c12e65a5c37520db0e7f62b57bed70df064356d4a79cdedc7d8c119fec6bad06f327cc9f4ce95b46bf069f15d14dc63f6 WHIRLPOOL 771d1482184bda49191ae8b159b92b9ef41905ef370cedd8efa8c52f43c3fd60143fcae749d9e981ab602952a92feb56fbe481915a177912bf764e3f24197afd +EBUILD libaec-1.0.0.ebuild 867 SHA256 d0007ddfe57bbf564f365628e410bd74d3a37ef6cae6c4e9f8ea039dc086df3d SHA512 14b5bd5e53710b28b53110cf3720754425220d1a58635da560945a3c2c6aec609adcad5bc5992aec1366e14a6ac3a3d1f200e4a7ee3543b1153835dc21ec1c02 WHIRLPOOL fb3e674f594ffb5367f00779d9836b3ae9d03883ad74d01256912f848db867ffb217163d2ade226971df92abe7d864381f458567029038af4bdaf8d1aa4a9cfd +EBUILD libaec-1.0.1.ebuild 727 SHA256 6ecd117f4ac40c653e0768bebba755e2554bb97219e4504004be0d0ed0d56854 SHA512 c265ab4b16211ff6af0b166b070642f6f3c37ef06b48da3d9dc4d1ba16c955909be9c94a1428d9cace53cac3df099bc5a86091ec110b1c1fa9e382d6919095bb WHIRLPOOL ee649a5c946d36682ae38184052d1c5a6a30f410f28471f6e7737fcc74b8726d5c5d99015946a4325f1c26d8957b944443c810f65231653874af9b65722fda89 +MISC ChangeLog 480 SHA256 543c496fe51ea46bfb7c27fd077e688aa68f88dc8a1391a5f6a3a6defabb6990 SHA512 0960d83743f4e1039133b7d2e3b27941ea12836e10b9661c90ec9e33f21a3fce390a4ce2dae048586efec7a9cb84e905990e6126fe7a853e795a6be3659607d9 WHIRLPOOL aecd481615489e135676c7ec515f742cd0bcbe4ce255515f3bfe1769a73232587a8ba7a14471eae13ed6bc57b1aedf00f2f21c6cf123eefc70bb321b8846b63e +MISC metadata.xml 719 SHA256 39d1731451333def53804ec71aac99ccd501eafbdbef905f4114897854ffb38c SHA512 f0197c0cf374cb0771e4b2e3bfcc80f639d3e660943df1cab79eec68b515a605855f792b0b1627d24409cfb6cc2890ca7e96f4aace01639106ee50e14574ccf6 WHIRLPOOL 233f0fd2fb0dabbb07d4cd5bd261adf9a4c1889ae66aebe50eb8e62b3a15902b87c8fac9d926f6034f0b4adf2f1953a7c75c035495f85fe932e28e97d7f9ade6 diff --git a/sci-libs/libaec/libaec-0.3.2.ebuild b/sci-libs/libaec/libaec-0.3.2.ebuild new file mode 100644 index 000000000000..dabdd92993e8 --- /dev/null +++ b/sci-libs/libaec/libaec-0.3.2.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils +# number that might change every version +PID=453 + +DESCRIPTION="Adaptive Entropy Coding library" +HOMEPAGE="https://www.dkrz.de/redmine/projects/aec" +SRC_URI="https://www.dkrz.de/redmine/attachments/download/${PID}/${P}.tar.gz" + +LICENSE="BSD-2" +SLOT="0/2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs +szip" + +DEPEND="" +RDEPEND="szip? ( !sci-libs/szip )" + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + # avoid conflict with szip (easier than to patch autotools) + if ! use szip; then + rm "${ED}"/usr/include/szlib.h || die + rm "${ED}"/usr/$(get_libdir)/libsz* || die + rm "${ED}"/usr/share/doc/${PF}/README.SZIP || die + fi + use static-libs || prune_libtool_files --all +} diff --git a/sci-libs/libaec/libaec-1.0.0.ebuild b/sci-libs/libaec/libaec-1.0.0.ebuild new file mode 100644 index 000000000000..f1d47bb32d3f --- /dev/null +++ b/sci-libs/libaec/libaec-1.0.0.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils +# number that might change every version +PID="631e85bcf877c2dcaca9b2e6d6526339" + +DESCRIPTION="Adaptive Entropy Coding library" +HOMEPAGE="https://gitlab.dkrz.de/k202009/libaec" +SRC_URI="${HOMEPAGE}/uploads/${PID}/${P}.tar.gz" + +LICENSE="BSD-2" +SLOT="0/2" +KEYWORDS="~amd64 ~arm64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs +szip" + +DEPEND="" +RDEPEND="szip? ( !sci-libs/szip )" + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + # avoid conflict with szip (easier than to patch autotools) + if ! use szip; then + rm "${ED}"/usr/include/szlib.h || die + rm "${ED}"/usr/$(get_libdir)/libsz* || die + rm "${ED}"/usr/share/doc/${PF}/README.SZIP || die + fi + use static-libs || prune_libtool_files --all +} diff --git a/sci-libs/libaec/libaec-1.0.1.ebuild b/sci-libs/libaec/libaec-1.0.1.ebuild new file mode 100644 index 000000000000..e6a8588c3d0d --- /dev/null +++ b/sci-libs/libaec/libaec-1.0.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils vcs-snapshot + +DESCRIPTION="Adaptive Entropy Coding library" +HOMEPAGE="https://gitlab.dkrz.de/k202009/libaec" +SRC_URI="${HOMEPAGE}/repository/archive.tar.gz?ref=v${PV} -> ${P}.tar.gz" + +LICENSE="BSD-2" +SLOT="0/2" +KEYWORDS="~amd64 ~arm64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+szip" + +DEPEND="" +RDEPEND="szip? ( !sci-libs/szip )" + +src_install() { + cmake-utils_src_install + # avoid conflict with szip (easier than to patch autotools) + if ! use szip; then + rm "${ED}"/usr/include/szlib.h || die + rm "${ED}"/usr/$(get_libdir)/libsz* || die + rm "${ED}"/usr/share/doc/${PF}/README.SZIP || die + fi +} diff --git a/sci-libs/libaec/metadata.xml b/sci-libs/libaec/metadata.xml new file mode 100644 index 000000000000..6d596231fcd7 --- /dev/null +++ b/sci-libs/libaec/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + Libaec provides fast lossless compression of 1 up to 32 bit wide + signed or unsigned integers (samples). The library achieves best + results for low entropy data as often encountered in space imaging + instrument data or numerical model output from weather or climate + simulations. While floating point representations are not directly + supported, they can also be efficiently coded by grouping exponents + and mantissa. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/libbufr/Manifest b/sci-libs/libbufr/Manifest new file mode 100644 index 000000000000..ed09d49f1688 --- /dev/null +++ b/sci-libs/libbufr/Manifest @@ -0,0 +1,6 @@ +AUX libbufr-000405-makefile.patch 2365 SHA256 e1e2dd553973f6ef9dc55a6208b48345160079c5c6f499592fb7e38606dbbefb SHA512 1a1fb37c5de730c8158572285f5677c61d4bba28da1b9d0651223d0b37b69034f3f2a003c38dc8a0dc96018b2cc476c612379a1d9b58983c83fe8c3600df6569 WHIRLPOOL e3868df7511aaa933a4c11d5c773217b15d21e391ad7fd908f7c6cf55489a29d21a74f5f335b54c5f37d36688a304b5561d86ee98eea3e1e7d4a7a4c06de0086 +DIST bufrdc_000405.tar.gz 11873311 SHA256 0c3ab33bdb3eea600c5af6f1e4064a000ec143f4c96a14b72ca09666ca3c3775 SHA512 3355d6bac54ef152f9feb13ae13f3c94f4e01a665a4b9bc7f85f0c98f9aa37411170668ba9adfb6b62c2fe906d0dff67b03a708cdf1acd21a0037e327c7c6169 WHIRLPOOL f97662c240e40086be2e2f7d33d446280576dd79ff119374d54d02af05bd51c9176a6592d965765baf549043ee80e8bb9e824e3149d4ce85599db1f5e3f42e10 +EBUILD libbufr-000405.ebuild 4876 SHA256 e7671e55cadf84e9c4390b6e9c8390e111d1c04b1ee83cb701d727571e97853b SHA512 7ccad66aa7f1201c1c3322f87cfd8d229846c7449264095de5342fd1e53e67562800ccfaffa5428d50df73a03a09c304b4ad560192785004d9072bfffd9a6acb WHIRLPOOL cd96676607354a28b01225fed16ada8c90e31dd4e5f096b29593b2dbe37d885d4cc38e48baf9dbfbc68ae5799a110b0ab2ee8167ef78d64202ea2b3f335cd834 +MISC ChangeLog 4133 SHA256 edbe76fceb3eaf33bfa8418cde20811c982afce12571cf8b047d30efe048fbc8 SHA512 c5b0d986905932052dffae1b52e5ace2a7a30257e83f00bbd8763c44cb6178626bb057a2925ca6f6a198074d44b57bd23a46c4034eca6acc4d8250de268c703a WHIRLPOOL 8cd7b45b96f4f52c2d42fa89e7e07e5af6ecdf9985c68867a80a8fe230352836de77df0dc3953c5768e48f7cd479d0037c89c06c96b6e11bb7740380fb8f39a3 +MISC ChangeLog-2015 2092 SHA256 c4500ad3614b517640db23e3374fceabb647b891334502ae78af5293579c94be SHA512 50b64126153d965fa0537d51dd28f6ae30221a0145d03048c8fa8e2b1c5646fc027d9704e735c8e6293be6543808f63e14dd1d5cda7e34070a0cb43cfe185a00 WHIRLPOOL 00020f4416e5b4ae0b99f00518e03438f068cdf9d85f5d1ffd113892901046b0e132810c42265aae8f2d17cd21997073cfeece2ce14eaf9e9feb0a571faa5a73 +MISC metadata.xml 413 SHA256 abc95e4aacec10eab01f033f4aa9f89490181883029a44c83ed1113867be3fcc SHA512 215accb7fe4f8e1ad20104ca2205c8eca34a528af360bc6e2325d4f650851b51e80d910688c2b62d6a1d20d556eed5c72bba7045390e5865f49e137c17f66b97 WHIRLPOOL c2a83aea5eba0ba8d3b43348bf35b7add81998fe5c4a85d58bca877cfa04b5f3e3c1dab338b36fd9962f7d0875677af781657da43fad0ddfb059d1b3220d29b0 diff --git a/sci-libs/libbufr/files/libbufr-000405-makefile.patch b/sci-libs/libbufr/files/libbufr-000405-makefile.patch new file mode 100644 index 000000000000..08b30ded8d72 --- /dev/null +++ b/sci-libs/libbufr/files/libbufr-000405-makefile.patch @@ -0,0 +1,80 @@ +--- Makefile.orig 2016-01-04 13:09:58.661150785 -0800 ++++ Makefile 2016-01-04 13:17:12.707621825 -0800 +@@ -1,7 +1,7 @@ + # Makefile for libbufrex + # + R64 = R64 +-TARGETS = all clean ++TARGETS = all clean test + LIBRARY = libbufr$(R64).a + SHELL=/bin/sh + SUBDIRS = fortranC bufrdc pbio bufrtables examples +@@ -11,12 +11,14 @@ + ( echo "*************************"; \ + echo "*** Make in $$name "; \ + echo "*************************"; \ +- cd $$name ; make ; ) done ++ $(MAKE) -C $$name LIB=bufr ; ) done ++ ++test : + ./test.sh + tables_tools/check_tables.sh bufrtables + + clean : + @for name in $(SUBDIRS); do\ +- ( echo "*** Clean in $$name ***" ;cd $$name ; make clean ); \ ++ ( echo "*** Clean in $$name ***" ;$(MAKE) -C $$name clean ); \ + done + rm -f $(LIBRARY) +--- examples/Makefile.in.orig 2016-01-04 13:42:39.790648703 -0800 ++++ examples/Makefile.in 2016-01-04 13:45:02.384967830 -0800 +@@ -16,19 +16,19 @@ + # + # + TARGETS = all clean +-EXECS = decode_bufr decode_bufr_image bufr_decode_all tdexp tdexp create_bufr ++EXECS = decode_bufr decode_bufr_image bufr_decode_all bufr_compress tdexp create_bufr + # + # + all :$(EXECS) + +-decode_bufr: decode_bufr.o ++decode_bufr: decode_bufr.o + $(FC) $(FFLAGS) -o $@ decode_bufr.o -L$(PLACE) -l$(LIB)$(R64) + +-bufr_decode_all: bufr_decode_all.o +- $(FC) $(FFLAGS) -o $@ bufr_decode_all.o -L$(PLACE) -l$(LIB)$(R64) ++bufr_decode_all: bufr_decode_all.o ++ $(FC) $(FFLAGS) -o $@ bufr_decode_all.o -L$(PLACE) -l$(LIB)$(R64) + +-bufr_compress: bufr_compress.o +- $(FC) $(FFLAGS) -o $@ bufr_compress.o -L$(PLACE) -l$(LIB)$(R64) ++bufr_compress: bufr_compress.o ++ $(FC) $(FFLAGS) -o $@ bufr_compress.o -L$(PLACE) -l$(LIB)$(R64) + + bufr2crex : bufr2crex.o + $(FC) $(FFLAGS) -o $@ bufr2crex.o -L$(PLACE) -l$(LIB)$(R64) -lcrex$(R64) +@@ -48,4 +48,4 @@ + clean : + @for name in $(EXECS); do\ + (rm -f $$name *.o ); \ +- done ++ done +--- bufrtables/Makefile.orig 2016-01-04 14:03:47.292850644 -0800 ++++ bufrtables/Makefile 2016-01-04 14:05:22.242500485 -0800 +@@ -25,11 +25,14 @@ + OBJECTS = $(OBJECTS.F) $(OBJECTS.c) + # + # +-all: links ++all: pgms links + + links: + ./clean.sh + ./links.sh ++ ++pgms: bufr2txt_tables bufr_split_tables txt2bufr_tables ++ + bufr2txt_tables: bufr2txt_tables.f + $(FC) $(FFLAGS) -o bufr2txt_tables bufr2txt_tables.f $(LIBRARY) + bufr_split_tables: bufr_split_tables.f diff --git a/sci-libs/libbufr/libbufr-000405.ebuild b/sci-libs/libbufr/libbufr-000405.ebuild new file mode 100644 index 000000000000..a97b5cb6af7d --- /dev/null +++ b/sci-libs/libbufr/libbufr-000405.ebuild @@ -0,0 +1,196 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 toolchain-funcs + +MY_P="${PN/lib/}dc_${PV}" + +DESCRIPTION="ECMWF BUFR library - includes both C and Fortran example utilities" +HOMEPAGE="https://software.ecmwf.int/wiki/display/BUFR/BUFRDC+Home" +SRC_URI="https://software.ecmwf.int/wiki/download/attachments/35752466/${MY_P}.tar.gz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" +# needs someone to test on these: ~alpha ~hppa ~ia64 ~sparc etc ... + +IUSE="debug doc examples" + +RDEPEND=" + virtual/fortran + " + +DEPEND="sys-apps/findutils" + +S=${WORKDIR}/${MY_P} + +pkg_setup() { + fortran-2_pkg_setup + case "$(tc-getFC)" in + *gfortran) + export CNAME="_gfortran" + ;; + *g77) + export CNAME="_gnu" + ;; + *pgf90|*pgf77) + export CNAME="" + ;; + ifc|ifort) + export CNAME="_intel" + ;; + esac + + elog "Note non-GNU compilers are not currently supported on non-x86" + elog "architectures. If you need it, please submit a patch..." + + export target="linux" + export A64="" + export R64="" + case "${ARCH}" in + amd64) + export R64="R64" + export A64="A64" + ;; + ppc64) + export target="ppc_G5" + ;; + ppc) + export target="ppc" + ;; + *) + ;; + esac +} + +src_prepare() { + update_configs + epatch "${FILESDIR}"/${P}-makefile.patch + + local config="config/config.$target$CNAME$R64$A64" + + if [[ "${ARCH}" == "ppc" ]] ; then + sed -i -e "s|= -mcpu=G4 -mtune=G4|= |" ${config} + elif [[ "${ARCH}" == "ppc64" ]] ; then + sed -i -e "s|= -mcpu=G5 -mtune=G5|= |" \ + -e "s|-fdefault-real-8|-fdefault-real-8 -fdefault-double-8|" \ + ${config} + elif [[ "${ARCH}" == "amd64" ]] ; then + cp ${config}.in ${config} + sed -i -e "s|-fdefault-real-8|-fdefault-real-8 -fdefault-double-8|" \ + ${config} + else + cp ${config}.in ${config} || die "Error updating config!" + fi + + sed -i -e "s:DEBUG = -O2:DEBUG = -g:g" ${config} + use debug || sed -i -e "s:DEBUG = -g:DEBUG =:g" ${config} + + # add local CFLAGS to build flags + sed -i -e "s|\$(DEBUG)|${CFLAGS} \$(DEBUG) -fPIC|" \ + -e 's|emos|/usr/share/bufrtables|g' ${config} + + # add local LDFLAGS to bins + sed -i \ + -e "s|-o|${LDFLAGS} -fPIC -o|" \ + examples/Makefile \ + bufrtables/Makefile +} + +src_compile() { + export BUFR_TABLES="${S}"/bufrtables + EBUILD_ARCH="${ARCH}" + EBUILD_CFLAGS="${CFLAGS}" + unset ARCH CFLAGS + + tc-export CC FC AR NM RANLIB + export STRIP="/bin/true" + TC_FLAGS="CC=$CC FC=$FC AR=$AR RANLIB=$RANLIB" + ARFLAGS="rv" + + # emake won't work with this fossil... + BUFRFLAGS="ARCH=$target R64=$R64 CNAME=$CNAME" + make $TC_FLAGS ARFLAGS="${ARFLAGS}" $BUFRFLAGS || die "make failed" + + generate_files + + ARCH="${EBUILD_ARCH}" + CFLAGS="${EBUILD_CFLAGS}" +} + +src_test() { + unset ARCH CFLAGS + BUFRFLAGS="ARCH=$target R64=$R64 CNAME=$CNAME" + make $BUFRFLAGS test || die "make test failed" + + ARCH="${EBUILD_ARCH}" + CFLAGS="${EBUILD_CFLAGS}" +} + +src_install() { + # install library + dolib.a libbufr$R64.a + + dosbin bufrtables/{bufr2txt_tables,bufr_split_tables,txt2bufr_tables} + dobin examples/{bufr_decode_all,create_bufr,decode_bufr,decode_bufr_image,tdexp} + + keepdir /usr/share/bufrtables + insinto /usr/share/bufrtables + doins -r bufrtables/{B,C,D}*.* + + # files generated above + doenvd 20${PN} + + dodoc README + if use doc ; then + insinto /usr/share/doc/${PF} + doins doc/*.pdf + fi + + if use examples ; then + newdoc examples/README README.examples + insinto /usr/share/doc/${PF}/examples + doins examples/{*.F,*.c,Makefile} + fi +} + +pkg_postinst() { + elog + elog "This is the only GPL'd BUFR decoder library written in C/Fortran" + elog "but the build system is an old kluge that pre-dates the discovery" + elog "of fire. File bugs as usual if you have build/runtime problems." + elog "" + elog "The default BUFR tables are stored in /usr/share/bufrtables, so" + elog "add your local tables there if needed. Only a static lib is" + elog "installed currently, as shared lib support is incomplete (feel" + elog "free to submit a patch :)" + elog "" + elog "The installed user-land bufr utilities are just the examples;" + elog "the main library is really all there is (and there are no man" + elog "pages either). Install the examples and use the source, Luke..." + elog +} + +generate_files() { + ## Do not remove blank lines from the response file + cat <<-EOF > 20${PN} + BUFR_TABLES="/usr/share/bufrtables" + EOF +} + +update_configs() { + find . -type f -name \*.distinct -o -name \*.f -o -name \*.in \ + | xargs chmod -x + cp options/options_linux options/options_ppc + cp options/options_linux options/options_ppc_G5 + cp pbio/sources.linux pbio/sources.ppc + cp pbio/sources.linux pbio/sources.ppc_G5 + pushd config > /dev/null + cp config.ppc_gfortran.in config.ppc_gfortran + cp config.ppc_gfortranR64.in config.ppc_gfortranR64 + cp config.ppc_gfortran_G5.in config.ppc_gfortran_G5 + cp config.ppc_gfortranR64_G5.in config.ppc_gfortranR64_G5 + popd > /dev/null +} diff --git a/sci-libs/libbufr/metadata.xml b/sci-libs/libbufr/metadata.xml new file mode 100644 index 000000000000..e6507199b201 --- /dev/null +++ b/sci-libs/libbufr/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>nerdboy@gentoo.org</email> + </maintainer> + <longdescription lang="en"> + This is the only useable open source BUFR library (from ECMWF) + and comes with a few example tools (some of which are built + and installed). + </longdescription> +</pkgmetadata> diff --git a/sci-libs/libccd/Manifest b/sci-libs/libccd/Manifest new file mode 100644 index 000000000000..a42b58d7e2e4 --- /dev/null +++ b/sci-libs/libccd/Manifest @@ -0,0 +1,6 @@ +DIST libccd-2.0.tar.gz 68103 SHA256 513e212fbb22cf720cf16ba911e8a8ccb1050c006789631ff2474ecc2f12b47a SHA512 627426f1acd24779e7d596fd5b18dede4cf3c13d3cceda87a8b2d0195b72d9ada45290fd41baa20d6e3adafda75074db355cb95a60f80023c32b5ad4e72235bf WHIRLPOOL cc83b492855333549e7ab3707f66259191b865e49971a698fa875d44887d00fc9fdad5b5eb014703c8e92f66260c94baafe7f0199f7afdc206b7103b94190488 +EBUILD libccd-2.0.ebuild 1129 SHA256 8ee6ab677581e1706d4e22a0c2dac5b70e24a7bc9543535dbcc15f6ab5fb641f SHA512 bb7d70c13dd6871be004c309c5adb92953ecd4fb73613fe34abad10dc8050dace2169d10f8da49d7ba96edd11153149b1edef5078cebeba4d5fa41e82292c7e3 WHIRLPOOL f3931d45d8cc5d0e87197c533f3c420f1d53e59bfecfb69562110cc0a1f4deee4f4f2e78994b9f663d31beedc3869b72a90fe7b2de75c2a6f059193809924cac +EBUILD libccd-9999.ebuild 1132 SHA256 120901e3b9570de0ae34d3c70cd4960a0d4bc2c53819c17c106001a15ecef273 SHA512 68295196d780ac574edc043165e51683258ad453d28a78a357ceb76a853e6532d653f5a11d39e033d0f24fa9e34f737d4c8c97351a524ae2bba2a196888bfce2 WHIRLPOOL 2b299319f3cb1b46983fc975e1ccfa8e1de7aa40483cc866be79e7767a4fe322d79fd4935310af54eef111f2a439192d6df7569bed7e59f13a7e2251cdd1fc3e +MISC ChangeLog 2625 SHA256 ebd925d28f9ca7bc2e812a388d33798bea05c06eac17305acbfc60dd872dd80c SHA512 57ff4601bf897259f493410c67a63e482a8b2e1973db5796c10b9485e25edbd5e9afa916c269465845bfa26eff5723aa88a56367dd403442b5e13d11f7f99471 WHIRLPOOL 68037caffb49a38dd850e9d2378c15cf3b7aa072d29d91be0fad5e41658d543a6f70e37ff0b3d3d4ef3cec8894e04b8b44e1fb887a265e3ef47edf270fd29e7e +MISC ChangeLog-2015 510 SHA256 7bbac1f292b4321b5f7485af37a72b5c0f08be67dde368695ea5fa3bee47ed2a SHA512 98e4c63a2a43b62505a6c3e72fd53bd295210339ee0aef0a4f4e2fe1fe2dc7477cc7a4af4f951c50a6c02782bc7eb1d0bc235b580294fcf73c7f88c792219f85 WHIRLPOOL c4765893eaa70b841c69cb181d5e280f9ceccf5da31e8c8a3c097829edd58ca4306cf8fc6c08347acad33641a1e503ab874a1c97fa75c076a17b01aa87f0fa50 +MISC metadata.xml 320 SHA256 f4eb568325b4c7738002fc25b0076a0188eb686b8c0eb7024def8d3ee28226f0 SHA512 76ac27595041183f73ae8b7c0a8c653ffd4609bfe780a3931b81a1222f9563b9af0e0c51fab757a16772f3ec285357772c3e5df36fb0058c34f21c8ae1b014bb WHIRLPOOL 4e2e3fcbd604b65d9d3ede6c452a5d0f2b4fcbfa9ba5d03de7905fc6863afbe3def91f555aaa3d28e39e71a40d33294b9c985ed6c00c80250c9104443ea995c1 diff --git a/sci-libs/libccd/libccd-2.0.ebuild b/sci-libs/libccd/libccd-2.0.ebuild new file mode 100644 index 000000000000..894309a26239 --- /dev/null +++ b/sci-libs/libccd/libccd-2.0.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/danfis/libccd" +fi + +inherit ${SCM} cmake-utils toolchain-funcs + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="http://libccd.danfis.cz/files/${P}.tar.gz" +fi + +DESCRIPTION="Library for collision detection between two convex shapes" +HOMEPAGE="http://libccd.danfis.cz/" +LICENSE="BSD" +SLOT="0" +IUSE="double doc" + +RDEPEND="" +DEPEND="${RDEPEND} + doc? ( dev-python/sphinx )" +DOCS=( README ) + +src_configure() { + local mycmakeargs=( + "-DCCD_DOUBLE=$(usex double TRUE FALSE)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + if use doc ; then + cd "${S}/doc" + emake SPHINXBUILD=sphinx-build html + fi +} + +src_test() { + cd src/testsuites + tc-export CC + LDFLAGS="-L${BUILD_DIR} ${LDFLAGS}" \ + LD_LIBRARY_PATH="${BUILD_DIR}:${LD_LIBRARY_PATH}" \ + emake check +} + +src_install() { + cmake-utils_src_install + use doc && dohtml -r "${S}/doc/_build/html/"* +} diff --git a/sci-libs/libccd/libccd-9999.ebuild b/sci-libs/libccd/libccd-9999.ebuild new file mode 100644 index 000000000000..6d2690e84ba0 --- /dev/null +++ b/sci-libs/libccd/libccd-9999.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/danfis/libccd" +fi + +inherit ${SCM} cmake-utils toolchain-funcs + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="http://libccd.danfis.cz/files/${P}.tar.gz" +fi + +DESCRIPTION="Library for collision detection between two convex shapes" +HOMEPAGE="http://libccd.danfis.cz/" +LICENSE="BSD" +SLOT="0" +IUSE="double doc" + +RDEPEND="" +DEPEND="${RDEPEND} + doc? ( dev-python/sphinx )" +DOCS=( README.md ) + +src_configure() { + local mycmakeargs=( + "-DCCD_DOUBLE=$(usex double TRUE FALSE)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + if use doc ; then + cd "${S}/doc" + emake SPHINXBUILD=sphinx-build html + fi +} + +src_test() { + cd src/testsuites + tc-export CC + LDFLAGS="-L${BUILD_DIR} ${LDFLAGS}" \ + LD_LIBRARY_PATH="${BUILD_DIR}:${LD_LIBRARY_PATH}" \ + emake check +} + +src_install() { + cmake-utils_src_install + use doc && dohtml -r "${S}/doc/_build/html/"* +} diff --git a/sci-libs/libccd/metadata.xml b/sci-libs/libccd/metadata.xml new file mode 100644 index 000000000000..20ea537dd9ae --- /dev/null +++ b/sci-libs/libccd/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="person"> +<email>aballier@gentoo.org</email> +<name>Alexis Ballier</name> +</maintainer> + <use> + <flag name="double">Use double precision floats.</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/libccp4/Manifest b/sci-libs/libccp4/Manifest new file mode 100644 index 000000000000..d970927fa68a --- /dev/null +++ b/sci-libs/libccp4/Manifest @@ -0,0 +1,4 @@ +DIST libccp4-6.4.6.tar.gz 934709 SHA256 a51b59c101bd94385408ffd070ec77fcefe43c519e7d6f7ad88d6b204935b8fa SHA512 38893d7c8bec99b6d1245586695d98900284543dfe7f87e0cab81a7f7f93b3dac0780c3ea576fb910fc3712d7b9226814ebe05530948ace136860f398e11daf6 WHIRLPOOL 55c1c02c5e357940da50021e1adaa7018cdf84df6d53f66893fc175afb3458333a92c9542ac6db44faee33f23c39343b5c1703280cee0825fa4f0c28be110074 +EBUILD libccp4-6.4.6.ebuild 597 SHA256 f46ad13d68db5c02c407ffaf0dd6c46678377a2e4a26bbb326e364b7db3a8d4f SHA512 29f519f7ea0ec6c6e9b043523cfe406accbbd0f0c84287085aa9e480ba6fe12b8dfd3646942b9b2af3fae2101165ec90fa257b10441f9ae408817c1361827c85 WHIRLPOOL 226c8c134409d231cdf45aac9c8ffd4948f9221feaf1384c6a5f1417dd67fac864b15b054c7dc2600fb437216c685ebbd31562643eeeaf5ed0fbaca3744b548f +MISC ChangeLog 1022 SHA256 c8a578b635e66b7e4bc1dc7d7c806cd50fc2f8b5e37c2433539cdaa04d568703 SHA512 7ad19bb182a0ad67f7da6accb23f22886bb0add954c1e8671b0bd7fe0c463f9c7263f437929034ab0c28472a4a498765aa5556d152a2b063c09f6b1c0c885650 WHIRLPOOL 6ca6c6b8ceb8df4b7fdc65733b6ed2c8bdc49acfc9621aa22e6f4dabf7e6daf3b9e9eee61f9821d49dd25a687302d4fa9e394e69bbfd0c357ceeaa905c1afa3d +MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d diff --git a/sci-libs/libccp4/libccp4-6.4.6.ebuild b/sci-libs/libccp4/libccp4-6.4.6.ebuild new file mode 100644 index 000000000000..a2f7940a036c --- /dev/null +++ b/sci-libs/libccp4/libccp4-6.4.6.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit autotools-utils fortran-2 + +DESCRIPTION="The CCP4 C and F77 subroutine library" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3 LGPL-3" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="fortran static-libs" + +RDEPEND="sci-libs/mmdb:2" +DEPEND="${RDEPEND} +" +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_configure() { + myeconfargs=( + $(use_enable fortran) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/libccp4/metadata.xml b/sci-libs/libccp4/metadata.xml new file mode 100644 index 000000000000..da36ecbfcd6a --- /dev/null +++ b/sci-libs/libccp4/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libcerf/Manifest b/sci-libs/libcerf/Manifest new file mode 100644 index 000000000000..d5a87d13189d --- /dev/null +++ b/sci-libs/libcerf/Manifest @@ -0,0 +1,8 @@ +AUX libcerf-1.3-autotools.patch 2758 SHA256 a37050253751c640d8b8a657fdd679268670861eb2aba1b94ca7afb4b5a7dd3c SHA512 f4e99359d9ac5719138108c88f9e1b9f88e986df9e024633ca929a7f09dac826022ac1017f67af55115739d2cf0d4e0de56d751b219c3e4f620948df8cfd74fa WHIRLPOOL d7c48b7d431a7eee2ca1f6b9848054e4bcc72b6adc8cd9fa37765aced6bd34054b186bb8329f8642109a3f3597de4b4b74778ff35f6fdf351a4462866557e0e8 +DIST libcerf-1.3.tgz 385600 SHA256 d7059e923d3f370c89fb4d19ed4f827d381bc3f0e36da5595a04aeaaf3e6a859 SHA512 274fa7f3b149bb27582a54a39fe76b478cd5acc6716dd0588a2f637b77c87a6bbc4f467b52bb067ebad2d1ba18750211cc71c6a6feef75fa08d01ac1dbf5dc56 WHIRLPOOL 6f003e26aa76458da620dc4261cfc3b9ec77882a62e5f1a42ffa83c252ae39399e1244c16ad101ff98469ed59970be04b5f901a418e9681f7657adc76e0698f2 +DIST libcerf-1.4.tgz 386065 SHA256 101265dd1e1b10339adb70b22b60e65ef12c4e01c4a3f52e508562eceef62272 SHA512 93d7b03898c0f88e436947b204db7fb5097dc901928aedde48bf0a04552e1c041fdfcdbe6318fdc21508e1349b6c205f557660550e72d6e86b078d9d0dde0faa WHIRLPOOL c2f3093e7a080dde5252fbd91fb62ff3abccbf2d900cd21c6a54821ec8fbc2e4326d1dd60d838111a9d8853e19088453b886a34415e018dd1b5d276d6a86c5ed +EBUILD libcerf-1.3.ebuild 645 SHA256 7372e4a9b2d8f1d6ec362dcea07041f6c925cc4cda3cfbf99a35dda30516b103 SHA512 e5e7d05cd77fecd8bc3edcff851487c7f0d13202c6372cf9fe1a24887a118048a8f8cd6894f5288b97d0743e8abc2e500cf8c94ca35e47e244953c0fb498e15c WHIRLPOOL 74800f8c80e81a96111f9e7f37ef063e4f59070861a2990c9e2413f9f55772ab755dfe83b861c034c0a8739eb63daf99fa4fcc58fe3f7fd6c7fc43f5473903d8 +EBUILD libcerf-1.4.ebuild 739 SHA256 69df4c6edccaa58b2e0b20bb2dd1eec06e463abcb00af3ccaee2061f692441a5 SHA512 00526c5fa222f5a6fe48b790060326aab9ce266b58447ee3eb5bd737f7d142a6602016c77c42fd997ef3576d1a0a011ad049aecd7c3de5cd7f0533f10f0d2332 WHIRLPOOL 7244876493d1bf8661d84aa29364c1d046d6bda165e34f501e02bc1e6da174fe08d3fbcc47f229246b97f5b41fba38fabd32a6f6405c11884edc38e0c2326867 +MISC ChangeLog 4393 SHA256 1e4e3ba4bc1fced456ff206716fd2339ef1ed2f15af1448e2ba93b760205791e SHA512 afd8ffc8f7f43e4608a277deebb25bf5bcd34b996b0f07cbe69aff90ed0df64de1e2291df21bca23f7377ddf2d157bd47a703a22cbeaa2535c18f06b4439f2c5 WHIRLPOOL 285d2e0bd99793d64dcc2ce6544549270b85348db6da5f8171c76c4d86c53a6b1b9c89c638f1cf612036ae8b6f0c9235b0f36bae212110047e8b2871b2cda331 +MISC ChangeLog-2015 1219 SHA256 1194cfe16e6f1c05f05e21d967643e11d038af2272de1ed54c8e5c437420eb9e SHA512 1316b17bd660acc95daef3c43bfce772f939c3eef356face596c1a272bad14866f879608f9f3e200ea681c350aa164d5c59cb53c32ac62118bfaf1eee1ff3b1b WHIRLPOOL 8f83d60721aa0ce4826997fea4ba456ac8bad025598c0216d94af2d3991762d390f692000334f21ac786ae2659767cc319b7caf6cbd4af31979026f43497c42f +MISC metadata.xml 259 SHA256 bbfbeb80ffccffa8e7f837d2c93e994bbe024d565ae3a31d30c6646e80a684c8 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 WHIRLPOOL 75b8dd1a97dde63f9cc9f73b5951eaf54579460763ef7cbe6f3a9a0739070601d762152ea00df8b476b80e92e5c29b611a494bac5ab747298942530cabe0ee84 diff --git a/sci-libs/libcerf/files/libcerf-1.3-autotools.patch b/sci-libs/libcerf/files/libcerf-1.3-autotools.patch new file mode 100644 index 000000000000..caa00dd133ed --- /dev/null +++ b/sci-libs/libcerf/files/libcerf-1.3-autotools.patch @@ -0,0 +1,70 @@ +Send upstream (j.wuttke@fz-juelich.de) 14.07.14 +diff -Naur libcerf-1.3.orig/configure.ac libcerf-1.3/configure.ac +--- libcerf-1.3.orig/configure.ac 2013-07-17 03:49:33.000000000 -0600 ++++ libcerf-1.3/configure.ac 2014-07-21 17:01:15.399324021 -0600 +@@ -19,7 +19,7 @@ + # Website: + # http://apps.jcns.fz-juelich.de/libcerf + +-AC_INIT([cerf],[1:3],[http://apps.jcns.fz-juelich.de/libcerf]) ++AC_INIT([libcerf],[1:3],[http://apps.jcns.fz-juelich.de/libcerf]) + # version is current:revision:age; for simplicity, we always put age=0 + # <- http://www.sourceware.org/autobook/autobook/autobook_91.html + +@@ -31,7 +31,7 @@ + LT_INIT([disable-static]) + + AC_PROG_CC_C99 +-AC_SUBST(AM_CFLAGS,"-pedantic -Wall -Werror") ++AC_SUBST(AM_CFLAGS,"-pedantic -Wall") + AC_CONFIG_HEADERS([config.h]) # to avoid endless -D options + AC_HEADER_STDC + +diff -Naur libcerf-1.3.orig/libcerf.pc.in libcerf-1.3/libcerf.pc.in +--- libcerf-1.3.orig/libcerf.pc.in 2013-07-17 03:51:59.000000000 -0600 ++++ libcerf-1.3/libcerf.pc.in 2014-07-14 11:18:01.646512503 -0600 +@@ -7,4 +7,5 @@ + Description: Complex error function library + Version: @PACKAGE_VERSION@ + Libs: -L${libdir} -lcerf ++Libs.private: -lm + Cflags: -I${includedir} +diff -Naur libcerf-1.3.orig/man/Makefile.am libcerf-1.3/man/Makefile.am +--- libcerf-1.3.orig/man/Makefile.am 2013-02-01 02:00:14.000000000 -0700 ++++ libcerf-1.3/man/Makefile.am 2014-07-14 11:17:36.266182267 -0600 +@@ -19,9 +19,8 @@ + # Website: + # http://apps.jcns.fz-juelich.de/libcerf + +-man_MANS = w_of_z.3 im_w_of_x.3 dawson.3 cdawson.3 cerf.3 cerfc.3 erfcx.3 cerfcx.3 erfi.3 cerfi.3 voigt.3 +-auxdir = $(datadir)/man/html +-aux_DATA = w_of_z.html voigt.html dawson.html cerf.html erfcx.html erfi.html ++man_MANS = w_of_z.3 im_w_of_x.3 dawson.3 cdawson.3 libcerf-cerf.3 cerfc.3 erfcx.3 cerfcx.3 erfi.3 cerfi.3 voigt.3 ++html_DATA = w_of_z.html voigt.html dawson.html cerf.html erfcx.html erfi.html + + w_of_z.3 : w_of_z.pod + pod2man -s 3 -c "libcerf manual" $< > $@ +@@ -35,7 +34,7 @@ + cdawson.3 : dawson.pod + pod2man -s 3 -c "libcerf manual" $< > $@ + +-cerf.3 : cerf.pod ++libcerf-cerf.3 : cerf.pod + pod2man -s 3 -c "libcerf manual" $< > $@ + + cerfc.3 : cerf.pod +diff -Naur libcerf-1.3.orig/test/Makefile.am libcerf-1.3/test/Makefile.am +--- libcerf-1.3.orig/test/Makefile.am 2013-07-17 01:45:37.000000000 -0600 ++++ libcerf-1.3/test/Makefile.am 2014-07-14 11:16:00.204932368 -0600 +@@ -20,8 +20,10 @@ + # http://apps.jcns.fz-juelich.de/libcerf + + AM_CFLAGS += -I$(srcdir)/../lib +-noinst_PROGRAMS = test_libcerf_1 runvoigt run_w_of_z ++noinst_PROGRAMS = runvoigt run_w_of_z + test_libcerf_1_SOURCES = test1.c + runvoigt_SOURCES = runvoigt.c + run_w_of_z_SOURCES = run_w_of_z.c + AM_LDFLAGS = -lm -L../lib -lcerf ++check_PROGRAMS = test_libcerf_1 ++TESTS = test_libcerf_1 diff --git a/sci-libs/libcerf/libcerf-1.3.ebuild b/sci-libs/libcerf/libcerf-1.3.ebuild new file mode 100644 index 000000000000..f67d7d57f041 --- /dev/null +++ b/sci-libs/libcerf/libcerf-1.3.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils multilib + +DESCRIPTION="library that provides an efficient and accurate implementation of complex error functions" +HOMEPAGE="http://apps.jcns.fz-juelich.de/doku/sc/libcerf" +SRC_URI="http://apps.jcns.fz-juelich.de/src/${PN}/${P}.tgz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="alpha ~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +IUSE="doc static-libs test" + +DEPEND="" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}/${P}-autotools.patch" ) +AUTOTOOLS_AUTORECONF=1 diff --git a/sci-libs/libcerf/libcerf-1.4.ebuild b/sci-libs/libcerf/libcerf-1.4.ebuild new file mode 100644 index 000000000000..670cf094a2f9 --- /dev/null +++ b/sci-libs/libcerf/libcerf-1.4.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="library that provides an efficient and accurate implementation of complex error functions" +HOMEPAGE="http://apps.jcns.fz-juelich.de/doku/sc/libcerf" +SRC_URI="http://apps.jcns.fz-juelich.de/src/${PN}/${P}.tgz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="alpha amd64 arm ~arm64 hppa ia64 ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +IUSE="doc static-libs test" + +src_install() { + autotools-utils_src_install + mv "${ED}"/usr/share/man/man3/{,${PN}-}cerf.3 || die #collision with sys-apps/man-pages + use doc || rm "${ED}"/usr/share/doc/${P}/*.html || die +} diff --git a/sci-libs/libcerf/metadata.xml b/sci-libs/libcerf/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-libs/libcerf/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libcmatrix/Manifest b/sci-libs/libcmatrix/Manifest new file mode 100644 index 000000000000..313703c1ce72 --- /dev/null +++ b/sci-libs/libcmatrix/Manifest @@ -0,0 +1,13 @@ +AUX libcmatrix-3.11.0-fix-c++14.patch 1488 SHA256 e4bbb081907f14227446396033f8f72527cea553525431ae86dd11b43db226a9 SHA512 df859444d88b54ad5b8ed19b375d2e77203979e9f979f8cccbc7d4c10d6b76e1852041e2172e3731dd0adb9dca0db49d14a455cd7b6d20766695bd8448839d4c WHIRLPOOL f50e1aa7623b9a997dfb9907f233dd9797f36eb6d7102c3dc30d7cfad63f15e59dad9c0f231da568ec7fb7ba193de99228ec363249f86d858dd42dcfda555cb0 +AUX libcmatrix-3.11.0-gcc5.2.patch 635 SHA256 58a1278a8f1323bd201979cdce8ecdc390ce8825f58a1d143264455d5bc0f80c SHA512 2a07ac76fb7e7e5b6be97ed2d779d2cc1f56c38a2896b586338ace23515e5ea7428264c61faa4457efcd9b8ecdc8d9239beec09b01a8fe989a68b996bf594452 WHIRLPOOL f4e96e888cbc9a55b83ef5b7e3ca4730e73cdba94d7b9d7fff62539f54d68e8b4f94db5c798290322866927f2a587aaa8cba595c0bf7e68bfd1884e1412e3bd8 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0f7dc2eb98a98f1ce6d8ac7cccbe5de8a45121e347ae43ba115bb86eb44afe4b6f202c2758995debfc1a806de46989af40981494e3ab78a3fa58b686450f5f9a +MISC metadata.xml 259 SHA256 bbfbeb80ffccffa8e7f837d2c93e994bbe024d565ae3a31d30c6646e80a684c8 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 WHIRLPOOL 75b8dd1a97dde63f9cc9f73b5951eaf54579460763ef7cbe6f3a9a0739070601d762152ea00df8b476b80e92e5c29b611a494bac5ab747298942530cabe0ee84 diff --git a/sci-libs/libcmatrix/files/libcmatrix-3.11.0-fix-c++14.patch b/sci-libs/libcmatrix/files/libcmatrix-3.11.0-fix-c++14.patch new file mode 100644 index 000000000000..74e49285dd04 --- /dev/null +++ b/sci-libs/libcmatrix/files/libcmatrix-3.11.0-fix-c++14.patch @@ -0,0 +1,40 @@ +Fix building with C++14, which errors out due -Wnarrowing conversions. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594680 + +--- a/include/lcm_ssecomplex.h ++++ b/include/lcm_ssecomplex.h +@@ -151,7 +151,7 @@ + { + static const union { + int i[4]; ssecomplex_t v; +- } signbithigh = {{0,0,0,0x80000000}}; ++ } signbithigh = {{0,0,0,(int)0x80000000}}; + ssecomplex_t b_im = _mm_shuffle_pd(b,b,3); // Imag. part of b in both + const ssecomplex_t b_re = _mm_shuffle_pd(b,b,0); // Real part of b in both + const ssecomplex_t tmp=_mm_mul_pd(a,b_re); +@@ -166,7 +166,7 @@ + ssecomplex_t b_re = _mm_set1_pd(b); + static const union { + int i[4]; ssecomplex_t v; +- } signbithigh = {{0,0,0,0x80000000}}; ++ } signbithigh = {{0,0,0,(int)0x80000000}}; + b_re = _mm_xor_pd(b_re, signbithigh.v); // Change sign of high + return complex(_mm_mul_pd(a.z_, b_re)); + } +@@ -184,14 +184,14 @@ + inline complex operator- (const complex& a) { + static const union { // (signbit,signbit) + int i[4]; ssecomplex_t v; +- } signbits = {{0,0x80000000,0,0x80000000}}; ++ } signbits = {{0,(int)0x80000000,0,(int)0x80000000}}; + return complex(_mm_xor_pd(a, signbits.v)); // Change sign of both elements + } + + inline complex conj(const complex& a) { + static const union { // (signbit,signbit) + int i[4]; ssecomplex_t v; +- } signbithigh = {{0,0,0,0x80000000}}; ++ } signbithigh = {{0,0,0,(int)0x80000000}}; + return complex(_mm_xor_pd(a.z_, signbithigh.v)); // Change sign of imag. part + } + diff --git a/sci-libs/libcmatrix/files/libcmatrix-3.11.0-gcc5.2.patch b/sci-libs/libcmatrix/files/libcmatrix-3.11.0-gcc5.2.patch new file mode 100644 index 000000000000..d5d40246a2f8 --- /dev/null +++ b/sci-libs/libcmatrix/files/libcmatrix-3.11.0-gcc5.2.patch @@ -0,0 +1,16 @@ + include/MultiMatrix.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/MultiMatrix.h b/include/MultiMatrix.h +index 2d54db5..e95ce4c 100755 +--- a/include/MultiMatrix.h ++++ b/include/MultiMatrix.h +@@ -1225,7 +1225,7 @@ template<class T,size_t N> struct new_trait_<T,N,N> { typedef MultiMatrix<T,N> v + #endif + //LCM_SUPPRESS_VIEWS + +- template<size_t N, template<size_t> class CheckClass =LCM_CheckBoundsDefault> ++ template<size_t N, template<size_t> class CheckClass> + class Indexer<N,CheckClass>::permuted_iterator : public ::std::iterator< ::std::bidirectional_iterator_tag,size_t> + { + private: diff --git a/sci-libs/libcmatrix/files/libcmatrix-3.11.0-shared.patch b/sci-libs/libcmatrix/files/libcmatrix-3.11.0-shared.patch new file mode 100644 index 000000000000..6c5c3167619e --- /dev/null +++ b/sci-libs/libcmatrix/files/libcmatrix-3.11.0-shared.patch @@ -0,0 +1,80 @@ +diff --git a/Makefile.in b/Makefile.in +index 1361371..1448e76 100755 +--- a/Makefile.in ++++ b/Makefile.in +@@ -13,8 +13,8 @@ AR=@AR@ + + # You shouldn't need to alter anything below here + +-COMPILE=$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c +-ALLOPTFLAGS=$(OPTFLAGS) -DNDEBUG ++COMPILE=$(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -c ++#ALLOPTFLAGS=$(OPTFLAGS) -DNDEBUG + + LOCALOBJS= local/CrystalSystem.o local/CrystalGeneric.o local/MoleculeStructure.o + COREOBJS= coredefs/complex.o coredefs/common.o coredefs/diagonal.o coredefs/diagonalise.o coredefs/power.o coredefs/invert.o coredefs/transforms.o coredefs/blocking.o coredefs/mixed.o coredefs/realtransforms.o coredefs/Chebyshev.o +@@ -36,7 +36,7 @@ ALLTHROBJS=$(UNSAFEOBJS:.o=_r.o) $(ALLSAFEOBJS) + + ROOT=.. + +-first: lib/libcmatrix.a ++first: lib/libcmatrix.so.3.11.0 + + #%.o: %.f + # @F77@ @FFLAGS@ -c -o $@ $< +@@ -68,25 +68,25 @@ tempclean: + # -cd optim; @CLEAN@ + # -cd local; @CLEAN@ + +-lib/libcmatrix.a: $(ALLNORMOBJS) +- $(AR) $@ $(ALLNORMOBJS) +- chmod a+rx $@ +- $(RANLIB) $@ +- +-lib/libcmatrix_p.a: $(ALLPROFOBJS) +- $(AR) $@ $(ALLPROFOBJS) +- chmod a+rx $@ +- $(RANLIB) $@ +- +-lib/libcmatrix-g.a: $(ALLGOBJS) +- $(AR) $@ $(ALLGOBJS) +- chmod a+rx $@ +- $(RANLIB) $@ +- +-lib/libcmatrix_r.a: $(ALLTHROBJS) +- $(AR) @MTFLAGS@ $@ $(ALLTHROBJS) +- chmod a+rx $@ +- $(RANLIB) $@ ++lib/libcmatrix.so.3.11.0: $(ALLNORMOBJS) ++ $(CXX) $(LDFLAGS) -fPIC -shared -Wl,--soname,libcmatrix.so.3 -o $@ $(ALLNORMOBJS) -lrt @ATLAS_LIBS@ ++ ln -sf libcmatrix.so.3.11.0 lib/libcmatrix.so.3 ++ ln -sf libcmatrix.so.3.11.0 lib/libcmatrix.so ++ ++lib/libcmatrix_p.so.3.11.0: $(ALLPROFOBJS) ++ $(CXX) $(LDFLAGS) -fPIC -shared -Wl,--soname,libcmatrix.so.3 -o $@ $(ALLPROFOBJS) -lrt @ATLAS_LIBS@ ++ ln -sf libcmatrix_p.so.3.11.0 lib/libcmatrix_p.so.3 ++ ln -sf libcmatrix_p.so.3.11.0 lib/libcmatrix_p.so ++ ++lib/libcmatrix-g.so.3.11.0: $(ALLGOBJS) ++ $(CXX) $(LDFLAGS) -fPIC -shared -Wl,--soname,libcmatrix.so.3 -o $@ $(ALLGOBJS) -lrt @ATLAS_LIBS@ ++ ln -sf libcmatrix-g.so.3.11.0 lib/libcmatrix-g.so.3 ++ ln -sf libcmatrix-g.so.3.11.0 lib/libcmatrix-g.so ++ ++lib/libcmatrix.so_r.3.11.0: $(ALLTHROBJS) ++ $(CXX) $(LDFLAGS) -fPIC -shared -Wl,--soname,libcmatrix.so.3 -o $@ $(ALLTHROBJS) -lrt @ATLAS_LIBS@ ++ ln -sf libcmatrix_r.so.3.11.0 lib/libcmatrix_r.so.3 ++ ln -sf libcmatrix_r.so.3.11.0 lib/libcmatrix_r.so + + @CONFIGLEAF@.tar.gz: + cd $(ROOT) ; tar --exclude lib/* --exclude *.o --exclude=*~ --exclude=Makefile --exclude=include/config.h --exclude=config.status -cvf @CONFIGLEAF@.tar @CONFIGLEAF@ +diff --git a/configure.ac b/configure.ac +index c0ae0e1..50dcd5a 100755 +--- a/configure.ac ++++ b/configure.ac +@@ -1,5 +1,6 @@ + AC_INIT(configure.ac) + AC_CONFIG_HEADER(include/config.h) ++LT_INIT + + DEFAR="ar ru" + MAKEEXTRA= diff --git a/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.4.patch b/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.4.patch new file mode 100644 index 000000000000..24c1a89b48d0 --- /dev/null +++ b/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.4.patch @@ -0,0 +1,12 @@ +diff --git a/include/DynamicList.h b/include/DynamicList.h +index f8c1346..05a7b10 100755 +--- a/include/DynamicList.h ++++ b/include/DynamicList.h +@@ -4,6 +4,7 @@ + #include "BaseList.h" + #include "lcm_basethreads.h" + #include "Warnings.h" ++#include <cstdio> + + namespace libcmatrix { + diff --git a/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.6.patch b/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.6.patch new file mode 100644 index 000000000000..b3d8c8d19996 --- /dev/null +++ b/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.6.patch @@ -0,0 +1,16 @@ + NMR/MetaPropagation.cc | 2 +- + 1 files changed, 1 insertions(+), 1 deletions(-) + +diff --git a/NMR/MetaPropagation.cc b/NMR/MetaPropagation.cc +index b7ed98b..ce8c16f 100755 +--- a/NMR/MetaPropagation.cc ++++ b/NMR/MetaPropagation.cc +@@ -2136,7 +2136,7 @@ SpinOpGenerator::add_A0(T& dest,F func, double coup, size_t j, size_t sk, Type2T + { ref_.clear(0); } + const space_T& operator()() const { return ref_; } + ~fudge_isotropic_() { ref_.ensure_rank(0); } +- mutable space_T& ref_; ++ space_T& ref_; + }; + template<> struct fudge_isotropic_<double> { + fudge_isotropic_(double v) : v_(v) {}; diff --git a/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.7.patch b/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.7.patch new file mode 100644 index 000000000000..633c9d50cf94 --- /dev/null +++ b/sci-libs/libcmatrix/files/libcmatrix-3.2.1-gcc4.7.patch @@ -0,0 +1,227 @@ + include/MultiMatrix.h | 14 +++++++------- + include/UnionHolder.h | 40 ++++++++++++++++++++-------------------- + include/basedefs.h | 22 ++++++++++++---------- + utils/Fork_controller.cc | 3 +++ + utils/ttyio.cc | 2 ++ + 5 files changed, 44 insertions(+), 37 deletions(-) + +diff --git a/include/MultiMatrix.h b/include/MultiMatrix.h +index b6fec33..2d54db5 100755 +--- a/include/MultiMatrix.h ++++ b/include/MultiMatrix.h +@@ -254,19 +254,19 @@ namespace libcmatrix { + } + + size_t operator()(size_t r) const +- { check_bounds_open(dim,r); ++ { this->check_bounds_open(dim,r); + return r*mults[0]; } + + size_t operator()(size_t r,size_t s) const +- { check_bounds_open(dim,r,s); ++ { this->check_bounds_open(dim,r,s); + return r*mults[0]+s*mults[1]; } + + size_t operator()(size_t r,size_t s,size_t t) const +- { check_bounds_open(dim,r,s,t); ++ { this->check_bounds_open(dim,r,s,t); + return r*mults[0]+s*mults[1]+t*mults[2]; } + + size_t operator()(size_t r,size_t s,size_t t,size_t u) const +- { check_bounds_open(dim,r,s,t,u); ++ { this->check_bounds_open(dim,r,s,t,u); + return r*mults[0]+s*mults[1]+t*mults[2]+u*mults[3]; } + + size_t index(size_t r) const +@@ -293,14 +293,14 @@ namespace libcmatrix { + + void reverse(size_t& r, size_t& s, size_t ind) const { + LCM_STATIC_CHECK(N==2, Indexer_non2D_object); +- check(ind<size(),"Indexer::reverse"); ++ this->check(ind<size(),"Indexer::reverse"); + r=ind / mults[0]; + s=ind-r*mults[0]; + } + + void reverse(size_t& r, size_t& s, size_t& t, size_t ind) const { + LCM_STATIC_CHECK(N==3, Indexer_non3D_object); +- check(ind<size(),"Indexer::reverse"); ++ this->check(ind<size(),"Indexer::reverse"); + r=ind / mults[0]; + ind-=r*mults[0]; + s=ind / mults[1]; +@@ -309,7 +309,7 @@ namespace libcmatrix { + + void reverse(size_t& r, size_t& s, size_t& t, size_t& u, size_t ind) const { + LCM_STATIC_CHECK(N==4, Indexer_non4D_object); +- check(ind<size(),"Indexer::reverse"); ++ this->check(ind<size(),"Indexer::reverse"); + r=ind / mults[0]; + ind-=r*mults[0]; + s=ind / mults[1]; +diff --git a/include/UnionHolder.h b/include/UnionHolder.h +index f447501..3157330 100755 +--- a/include/UnionHolder.h ++++ b/include/UnionHolder.h +@@ -359,21 +359,21 @@ namespace libcmatrix { + //! overrides ::clear method from ::CommonHolder + void clear() { + switch (type_) { +- case 1: clear_(first_); break; +- case 2: clear_(second_); break; +- case 3: clear_(third_); break; +- case 4: clear_(fourth_); break; +- case 5: clear_(fifth_); break; +- case 6: clear_(sixth_); break; +- case 7: clear_(seventh_); break; +- case 8: clear_(eighth_); break; +- case 9: clear_(nineth_); break; ++ case 1: this->clear_(first_); break; ++ case 2: this->clear_(second_); break; ++ case 3: this->clear_(third_); break; ++ case 4: this->clear_(fourth_); break; ++ case 5: this->clear_(fifth_); break; ++ case 6: this->clear_(sixth_); break; ++ case 7: this->clear_(seventh_); break; ++ case 8: this->clear_(eighth_); break; ++ case 9: this->clear_(nineth_); break; + } + type_=0; + } + + template<class T> UnionHolder& operator= (const T& v) { +- get(Type2Type<T>())=v; ++ this->get(Type2Type<T>())=v; + type(Type2Type<T>()); //only change type if assignment was successful + return *this; + } +@@ -399,12 +399,12 @@ namespace libcmatrix { + + template<class T> T& set(Type2Type<T> in) { + type(in); +- return get(in); ++ return this->get(in); + } + + template<int M> typename reverse<M>::type& set(Int2Type<M> in) { + type(in); +- return get(Type2Type<typename reverse<M>::type>()); ++ return this->get(Type2Type<typename reverse<M>::type>()); + } + + template<class T> T& operator()(Type2Type<T> in) { +@@ -429,12 +429,12 @@ namespace libcmatrix { + + template<int M> typename reverse<M>::type& operator()(Int2Type<M> in) { + verify(in); +- return get(Type2Type<typename reverse<M>::type>()); ++ return this->get(Type2Type<typename reverse<M>::type>()); + } + + template<int M> const typename reverse<M>::type& operator()(Int2Type<M> in) const { + verify(in); +- return get(Type2Type<typename reverse<M>::type>()); ++ return this->get(Type2Type<typename reverse<M>::type>()); + } + }; + +@@ -482,12 +482,12 @@ namespace libcmatrix { + bool iscomplex() const { return (this->type()==COMPLEX); } + bool isreal() const { return (this->type()==REAL); } + +- C& set_complex() { return set(Int2Type<COMPLEX>()); } +- R& set_real() { return set(Int2Type<REAL>()); } +- const C& get_complex() const { return get(Type2Type<C>()); } +- const R& get_real() const { return get(Type2Type<R>()); } +- C& get_complex() { return get(Type2Type<C>()); } +- R& get_real() { return get(Type2Type<R>()); } ++ C& set_complex() { return this->set(Int2Type<COMPLEX>()); } ++ R& set_real() { return this->set(Int2Type<REAL>()); } ++ const C& get_complex() const { return this->get(Type2Type<C>()); } ++ const R& get_real() const { return this->get(Type2Type<R>()); } ++ C& get_complex() { return this->get(Type2Type<C>()); } ++ R& get_real() { return this->get(Type2Type<R>()); } + }; + + } //namespace libcmatrix +diff --git a/include/basedefs.h b/include/basedefs.h +index 420b341..80d47e3 100755 +--- a/include/basedefs.h ++++ b/include/basedefs.h +@@ -13,6 +13,8 @@ + #include <functional> + #include <iterator> + #include <algorithm> ++#include <math.h> ++//#include "BlockedMatrix.h" + //#include <complex> + + // #ifdef LCM_DEBUG_ALLOCATOR +@@ -1703,6 +1705,16 @@ template<size_t N> struct Multiply_<N,N,0> { + } + }; + ++template<size_t,size_t,size_t> struct Mla_ { ++ template<class T1,class T2,class T3> static void func(T1&, const T2&, const T3&) { ++ LCM_STATIC_ERROR( mla_incompatible_dimensionalities ); ++ } ++}; ++ ++template<class T1,class T2,class T3> inline void mla(T1& d,const T2& a,const T3& b) { ++ Mla_<LCM_DIM(T1),LCM_DIM(T2),LCM_DIM(T3)>::func(d,a,b); ++} ++ + template<> struct Multiply_<2,2,2> { + template<class T1,class T2,class T3> static void func(T1& dest,const T2& a,const T3& b) + { +@@ -1875,12 +1887,6 @@ template<> struct Multiply_<0,0,0> { + Multiply_<LCM_DIM(T1),LCM_DIM(T2),LCM_DIM(T3)>::func(d,a,b); + } + +-template<size_t,size_t,size_t> struct Mla_ { +- template<class T1,class T2,class T3> static void func(T1&, const T2&, const T3&) { +- LCM_STATIC_ERROR( mla_incompatible_dimensionalities ); +- } +-}; +- + template<size_t N> struct Mla_<N,0,N> { + template<class T1,class T2,class T3> LCM_INLINE static void func(T1& d, const T2& a, const T3& b) { + if (d.empty()) +@@ -1940,10 +1946,6 @@ template<> struct Mla_<0,0,0> { + } + }; + +-template<class T1,class T2,class T3> inline void mla(T1& d,const T2& a,const T3& b) { +- Mla_<LCM_DIM(T1),LCM_DIM(T2),LCM_DIM(T3)>::func(d,a,b); +-} +- + template<class T,size_t N> struct Print_ { + static void print(const T& a,std::ostream& ostr) { + ostr << '['; +diff --git a/utils/Fork_controller.cc b/utils/Fork_controller.cc +index 5f6b913..08ec942 100755 +--- a/utils/Fork_controller.cc ++++ b/utils/Fork_controller.cc +@@ -3,6 +3,9 @@ + #include <sys/wait.h> + #include <time.h> + #include <cstdio> ++#include <sys/types.h> ++#include <unistd.h> ++ + + namespace libcmatrix { + +diff --git a/utils/ttyio.cc b/utils/ttyio.cc +index 17e4eb3..bbeac81 100755 +--- a/utils/ttyio.cc ++++ b/utils/ttyio.cc +@@ -17,6 +17,8 @@ + #include "args_iter.h" + #endif + ++#include <unistd.h> ++ + namespace libcmatrix { + + namespace { diff --git a/sci-libs/libcmatrix/files/libcmatrix-3.2.1-minuit2.patch b/sci-libs/libcmatrix/files/libcmatrix-3.2.1-minuit2.patch new file mode 100644 index 000000000000..e7a6cec644bf --- /dev/null +++ b/sci-libs/libcmatrix/files/libcmatrix-3.2.1-minuit2.patch @@ -0,0 +1,14 @@ +--- a/configure-libraries.ac ++++ b/configure-libraries.ac +@@ -14,8 +14,8 @@ + fi + if test x$FOUNDMINUIT = xyes; then + AC_CHECK_LIB(lcg_Minuit,main,, +- AC_CHECK_LIB(Minuit,main,,FOUNDMINUIT=no +- AC_MSG_WARN([Minuit library (liblcg_Minuit or libMinuit) not found ++ AC_CHECK_LIB(Minuit2,main,,FOUNDMINUIT=no ++ AC_MSG_WARN([Minuit library (liblcg_Minuit or libMinuit2) not found + Is LDFLAGS is defined to include relevant directory?]))) + if test x$FOUNDMINUIT = xyes; then + AC_DEFINE(HAVE_LIBMINUIT) + diff --git a/sci-libs/libcmatrix/files/libcmatrix-3.9.0-atlas.patch b/sci-libs/libcmatrix/files/libcmatrix-3.9.0-atlas.patch new file mode 100644 index 000000000000..329e794645eb --- /dev/null +++ b/sci-libs/libcmatrix/files/libcmatrix-3.9.0-atlas.patch @@ -0,0 +1,24 @@ + configure-libraries.ac | 3 ++- + 1 files changed, 2 insertions(+), 1 deletions(-) + +diff --git a/configure-libraries.ac b/configure-libraries.ac +index 6e9579d..a919398 100755 +--- a/configure-libraries.ac ++++ b/configure-libraries.ac +@@ -33,6 +33,7 @@ AC_ARG_WITH(atlas, + AS_HELP_STRING([--with-atlas],[use the ATLAS BLAS library (default-use if found)]),,with_atlas=check) + if test x$with_atlas != xno; then + FOUNDATLAS=yes ++ PKG_CHECK_MODULES([ATLAS], [cblas]) + AC_CHECK_HEADERS(cblas.h,,FOUNDATLAS=no + AC_MSG_WARN([ATLAS header files (cblas.h) not found + Is CPPFLAGS is defined to include relevant directory?])) +@@ -40,7 +41,7 @@ Is CPPFLAGS is defined to include relevant directory?])) + AC_MSG_WARN([ATLAS library (libatlas.a) not found + Is LDFLAGS is defined to include relevant directory?])) + if test x$FOUNDATLAS = xyes; then +- LIBS="-lcblas $LIBS" ++ LIBS="$ATLAS_LIBS $LIBS" + CXXFLAGS="$CXXFLAGS -DLCM_USE_EXTERNAL" + else + if test x$with_atlas = xyes; then diff --git a/sci-libs/libcmatrix/libcmatrix-3.11.0-r1.ebuild b/sci-libs/libcmatrix/libcmatrix-3.11.0-r1.ebuild new file mode 100644 index 000000000000..8596928ef6a1 --- /dev/null +++ b/sci-libs/libcmatrix/libcmatrix-3.11.0-r1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +MY_P="${PN}${PV}_lite" + +DESCRIPTION="lite version of pNMRsim" +HOMEPAGE="http://www.dur.ac.uk/paul.hodgkinson/pNMRsim/" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse threads" + +RDEPEND="sci-libs/minuit" +DEPEND="${RDEPEND}" + +RESTRICT=mirror + +S="${WORKDIR}/${PN}R3" + +DOCS=( CHANGES docs/cmatrix.pdf ) +PATCHES=( + "${FILESDIR}/${PN}-3.11.0-shared.patch" + "${FILESDIR}/${PN}-3.2.1-minuit2.patch" + "${FILESDIR}/${PN}-3.2.1-gcc4.4.patch" + "${FILESDIR}/${PN}-3.2.1-gcc4.6.patch" + "${FILESDIR}/${PN}-3.2.1-gcc4.7.patch" + "${FILESDIR}/${PN}-3.9.0-atlas.patch" + "${FILESDIR}/${PN}-3.11.0-gcc5.2.patch" + "${FILESDIR}/${PN}-3.11.0-fix-c++14.patch" +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --with-minuit \ + --without-atlas \ + --with-sysroot="${EROOT}" \ + $(use_with cpu_flags_x86_sse sse) \ + $(use_with threads) +} + +src_install() { + dolib.so lib/*.so* + + insinto /usr/include/${PN}R3 + doins -r include/. + + einstalldocs +} diff --git a/sci-libs/libcmatrix/metadata.xml b/sci-libs/libcmatrix/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-libs/libcmatrix/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libcore/Manifest b/sci-libs/libcore/Manifest new file mode 100644 index 000000000000..4152d064b2bc --- /dev/null +++ b/sci-libs/libcore/Manifest @@ -0,0 +1,7 @@ +AUX 2.1.1-makefiles.patch 4387 SHA256 a3070a003f584766d5214a9aadf9d25e06d79235cfc7388fc4f64508f8b661ce SHA512 586c8b22139f98fd7db1d1cc583eadb7acdc0fada3fbb6df581c71fe8c05c8929438429b6370e67742dfce61efda1b26bd401966388c269b2d4a492636ea6941 WHIRLPOOL d82cb6f199278a31007c401ba4342cb1f04e5f0bdaea500e3f849d22a32362e963e5f515c6d82222e5800745042e0bfde1d6fdb245a3a8b9eabf23b9649daae3 +DIST core-2.1.1.tgz 2759163 SHA256 61b2086563d43f3546ec6de2ddd25ccc0c950c2f0c5f5f13448adf26e3143cbe SHA512 e56e184b8efaee82b737e3947f2934b71983cbf905f05005171d3d5670f326597ff7d25767c00ec18a470eb7306f14b813edf9548869d84054830565c044f6fb WHIRLPOOL 18f28c00fe285c2496f7ac6724179e2f1eb47ba725fc3c8c623aab860b5aca1e611608612649441260323927663f1ee90357800985391e2a896ce7dc5b63dd74 +DIST core-2.1.doc.tgz 657871 SHA256 e2297a2efd2b9b090aac51343a11c38d3b76bfd69784a5152504cea7068d0c9a SHA512 0988640bbc35de675fc536b852371a8f1233ce0d19818b17e540f1238b0e6d1266657ab815604be3a3379e22e7473eb3fbd71ef94ec099255c456307e69f66c7 WHIRLPOOL 82139cb11267140bc13dd8951fc3f64cfd0124082ebbca23ffad793637eacd49718a5300ea2aeca277fefa2b5d7f91fc755ccb305836eee64f6c568c67426c01 +EBUILD libcore-2.1.1-r1.ebuild 1827 SHA256 dcdd4f1574d7783e83756b1e8bc68bc4a5cf296eecd79d7fee9990d35fdc4807 SHA512 805a31c9a1876b7867628b05c8dbffe559095c3d841b175d51ee8b04589db2425f1d39828f59ac5705158ec2c151aff71a26613d7c6882710731ece9aa941e57 WHIRLPOOL 67ea527859c755831abb428255554e4947b4f0198ec42dbb87dfcecd107ddc4f62d4b7f70d65d06948065ba0dee8772758f35b2d4d3e3a7b3545df7adb1353f4 +MISC ChangeLog 2924 SHA256 d64f2cbf1da82669b77ff7c26a3568c9bef1e2f3b1657893f972423dc1b958a2 SHA512 f6a08dc86043bcdfd18df9462298f7865ebba50b88e08dc187d5e8976f9796c8ee757f4c57e7740e3c26ebb146672459c6a35e1e2811b9cca7f37bab91bdd20c WHIRLPOOL 15492910b0905b57aa54dd7296dafae394c93a617e000d9bb05e7e4250bb1933780d7cedd781e0a7ee1cbd79e701531c4372a34159de57e70d35a4f46c429bd8 +MISC ChangeLog-2015 1869 SHA256 aee68afb3ddd9916f21091fc56c38a4375540d6aa1260ba8e5d4d99d54fcff72 SHA512 e448709b71613e6f84fea2c158a348333d28df910ddd96b323a01c732c226d3c42352121b8ca5652a8ebe2c7ff7fb339fa0333a9ce9e3ba4b744006da80c836e WHIRLPOOL b26a622f3a3a273a202f4eecdd5c30fedb6c9ea55c1f5908a81b6d1bf0aeefca5411246479670cfcd24d1f98fe87ff42c366cfadb90d17c021641f4acf6e030c +MISC metadata.xml 673 SHA256 abf175ca98038a3c3e5ab2c4213eeb639a0cc80d71dff764dd3b53c7c83659ed SHA512 e6c9c74d1c85fd21c26bba038a0a17b1bfba0bec3ac350d3c324b355c54bc1f042806d7fbeac1830eff979ec0e0b4b1094d2ea00630266ff242b822446c2c03d WHIRLPOOL 5d6f482443007521b6b991918b1b44cc3c9fa64ac6d95638478a4099fa548fd4df3f0b258c1e8ef5ec3524838934c3e44e489bc56a4dd9e37053f95133686581 diff --git a/sci-libs/libcore/files/2.1.1-makefiles.patch b/sci-libs/libcore/files/2.1.1-makefiles.patch new file mode 100644 index 000000000000..09a8f5be2f38 --- /dev/null +++ b/sci-libs/libcore/files/2.1.1-makefiles.patch @@ -0,0 +1,115 @@ +diff -Nur core-2.1.1.orig/ext/Makefile core-2.1.1/ext/Makefile +--- core-2.1.1.orig/ext/Makefile 2011-08-06 22:53:29.000000000 +0100 ++++ core-2.1.1/ext/Makefile 2011-08-07 00:40:58.000000000 +0100 +@@ -38,16 +38,18 @@ + endif + endif + +-INCLUDE=-I${CORE_PATH}/inc -I${CORE_PATH}/gmp/include \ +- -I${CORE_PATH}/mpfr/include ++INCLUDE=-I${CORE_PATH}/inc + + + COREX_LIB_LEVEL3=${CORE_PATH}/lib/libcorex++$(VAR)_level3.a + COREX_LIB_LEVEL2=${CORE_PATH}/lib/libcorex++$(VAR)_level2.a + COREX_LIB_LEVEL1=${CORE_PATH}/lib/libcorex++$(VAR)_level1.a +-COREX_SHARED_LIB_LEVEL3=${CORE_PATH}/lib/libcorex++$(VAR)_level3.${CORE_DYLIB_EXTENSION} +-COREX_SHARED_LIB_LEVEL2=${CORE_PATH}/lib/libcorex++$(VAR)_level2.${CORE_DYLIB_EXTENSION} +-COREX_SHARED_LIB_LEVEL1=${CORE_PATH}/lib/libcorex++$(VAR)_level1.${CORE_DYLIB_EXTENSION} ++COREX_SHARED_LIB_LEVEL3_NAME=libcorex++$(VAR)_level3.${CORE_DYLIB_EXTENSION}.2 ++COREX_SHARED_LIB_LEVEL2_NAME=libcorex++$(VAR)_level2.${CORE_DYLIB_EXTENSION}.2 ++COREX_SHARED_LIB_LEVEL1_NAME=libcorex++$(VAR)_level1.${CORE_DYLIB_EXTENSION}.2 ++COREX_SHARED_LIB_LEVEL3=${CORE_PATH}/lib/$(COREX_SHARED_LIB_LEVEL3_NAME) ++COREX_SHARED_LIB_LEVEL2=${CORE_PATH}/lib/$(COREX_SHARED_LIB_LEVEL2_NAME) ++COREX_SHARED_LIB_LEVEL1=${CORE_PATH}/lib/$(COREX_SHARED_LIB_LEVEL1_NAME) + + TARGET=${COREX_LIB_LEVEL3} ${COREX_LIB_LEVEL2} ${COREX_LIB_LEVEL1} + +@@ -74,11 +76,11 @@ + -@rm -rf $@ + $(AR) $@ $? + +-COREX_SHARED_DEPS=-L${GMP_PREFIX}/lib -lgmp -L${MPFR_PREFIX}/lib -lmpfr -L${CORE_PATH}/lib -lcore++${VAR} ++COREX_SHARED_DEPS= -lgmp -lmpfr -L${CORE_PATH}/lib -lcore++${VAR} + + ${COREX_SHARED_LIB_LEVEL3}: ${L3_OBJS} + -@rm -rf $@ +- $(CXX) $(COREX_SHARED_DEPS) $(CORE_LDFLAGS) -o $@ $? ++ $(CXX) $(LDFLAGS) $(COREX_SHARED_DEPS) $(CORE_LDFLAGS) -Wl,-soname,$(COREX_SHARED_LIB_LEVEL3_NAME) -o $@ $? + + ${COREX_LIB_LEVEL2}: ${L2_OBJS} + -@rm -rf $@ +@@ -86,7 +88,7 @@ + + ${COREX_SHARED_LIB_LEVEL2}: ${L2_OBJS} + -@rm -rf $@ +- $(CXX) $(COREX_SHARED_DEPS) $(CORE_LDFLAGS) -o $@ $? ++ $(CXX) $(LDFLAGS) $(COREX_SHARED_DEPS) $(CORE_LDFLAGS) -Wl,-soname,$(COREX_SHARED_LIB_LEVEL2_NAME) -o $@ $? + + ${COREX_LIB_LEVEL1}: ${L1_OBJS} + -@rm -rf $@ +@@ -94,7 +96,7 @@ + + ${COREX_SHARED_LIB_LEVEL1}: ${L1_OBJS} + -@rm -rf $@ +- $(CXX) $(COREX_SHARED_DEPS) $(CORE_LDFLAGS) -o $@ $? ++ $(CXX) $(LDFLAGS) $(COREX_SHARED_DEPS) $(CORE_LDFLAGS) -Wl,-soname,$(COREX_SHARED_LIB_LEVEL1_NAME) -o $@ $? + + %_level3.o: %.cpp + ${CXX} $(CORE_CXXFLAGS) -DCORE_LEVEL=3 $(INCLUDE) -c $< -o $@ +diff -Nur core-2.1.1.orig/progs/Make.options core-2.1.1/progs/Make.options +--- core-2.1.1.orig/progs/Make.options 2011-08-06 22:53:29.000000000 +0100 ++++ core-2.1.1/progs/Make.options 2011-08-06 23:31:01.000000000 +0100 +@@ -11,10 +11,8 @@ + + include $(CORE_PATH)/Make.config + +-CORE_INC=-I. -I$(CORE_PATH)/inc -I$(CORE_PATH)/mpfr/include \ +- -I$(CORE_PATH)/gmp/include +-CORE_LIB=-L$(CORE_PATH)/lib -L$(CORE_PATH)/mpfr/lib -L$(CORE_PATH)/gmp/lib \ +- -lcore++$(VAR) -lmpfr -lgmp ++CORE_INC=-I. -I$(CORE_PATH)/inc ++CORE_LIB=-L$(CORE_PATH)/lib -lcore++$(VAR) -lmpfr -lgmp + + COREX_LIB_LEVEL=-lcoreex++$(VAR)_level + +diff -Nur core-2.1.1.orig/src/Makefile core-2.1.1/src/Makefile +--- core-2.1.1.orig/src/Makefile 2011-08-06 22:53:29.000000000 +0100 ++++ core-2.1.1/src/Makefile 2011-08-07 00:24:38.000000000 +0100 +@@ -23,7 +23,7 @@ + endif + endif + +-INCLUDE=-I${CORE_PATH}/inc -I${CORE_PATH}/mpfr/include -I${CORE_PATH}/gmp/include ++INCLUDE=-I${CORE_PATH}/inc + + # VAR indicates variants of the Core library + # E.g., if VAR=(empty) then we compile the release version. +@@ -44,7 +44,8 @@ + + # The following library will be built: + CORE_LIB=$(CORE_PATH)/lib/libcore++${VAR}.a +-CORE_SHARED_LIB=$(CORE_PATH)/lib/libcore++${VAR}.${CORE_DYLIB_EXTENSION} ++CORE_SHARED_LIB_NAME=libcore++${VAR}.${CORE_DYLIB_EXTENSION}.2 ++CORE_SHARED_LIB=$(CORE_PATH)/lib/$(CORE_SHARED_LIB_NAME) + + TARGET=$(CORE_LIB) + +@@ -52,7 +53,7 @@ + TARGET+=$(CORE_SHARED_LIB) + endif + +-DEPS=-L${GMP_PREFIX}/lib -L${MPFR_PREFIX}/lib -lgmp -lmpfr ++DEPS=-lgmp -lmpfr + + # ============================================================= + # RULES ====================================================== +@@ -64,7 +65,7 @@ + $(AR) $@ $^ + + ${CORE_SHARED_LIB}: $(EXPROBJS) +- $(CXX) $(DEPS) $(CORE_LDFLAGS) -o $@ $^ ++ $(CXX) $(LDFLAGS) $(CORE_LDFLAGS) -Wl,-soname,$(CORE_SHARED_LIB_NAME) $(DEPS) -o $@ $^ $(LIBS) + + %${VAR}.o: %.cpp + ${CXX} $(CORE_CXXFLAGS) $(INCLUDE) -c $< -o $@ diff --git a/sci-libs/libcore/libcore-2.1.1-r1.ebuild b/sci-libs/libcore/libcore-2.1.1-r1.ebuild new file mode 100644 index 000000000000..79e8f698f35e --- /dev/null +++ b/sci-libs/libcore/libcore-2.1.1-r1.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 +inherit eutils toolchain-funcs versionator + +MYPN=core +DOCPV="$(get_version_component_range 1-2)" + +DESCRIPTION="Robust numerical and geometric computation library" +HOMEPAGE="http://www.cs.nyu.edu/exact/core_pages/" +SRC_URI="http://cs.nyu.edu/exact/core/download/${MYPN}/${MYPN}-${PV}.tgz + doc? ( http://cs.nyu.edu/exact/core/download/${MYPN}/${MYPN}-${DOCPV}.doc.tgz )" + +LICENSE="QPL-1.0" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +RDEPEND="" +DEPEND="${RDEPEND} + dev-libs/mpfr + dev-libs/gmp + doc? ( app-doc/doxygen[latex] )" + +S="${WORKDIR}/${MYPN}-${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-makefiles.patch + sed -i \ + -e "s/-O2/${CXXFLAGS}/g" \ + -e "s/-shared/-shared ${LDFLAGS}/g" \ + Make.config || die + sed -i -e 's/-lgmp/-lgmp -lgmpxx/g' progs/Make.options || die + # missing input file in gaussian test and buggy test in tutorial + sed -i -e '/gaussian/d' -e '/tutorial/d' progs/Makefile || die +} + +src_compile(){ + emake VAR= LINKAGE=shared corelib corex USE_GMPXX=1 + rm -f src/*.o ext/*.o + use static-libs && emake VAR="" corelib corex USE_GMPXX=1 + if use doc; then + cd "${S}/doc" + export VARTEXFONTS="${T}/fonts" + emake -j1 all + emake -j1 -C doxy/latex pdf + fi +} + +src_test() { + LD_LIBRARY_PATH="${S}/lib" emake \ + VAR= GMP_PREFIX= MPFR_PREFIX= test +} + +src_install(){ + dolib.so lib/*.so* + for i in $(find "${ED}/usr/$(get_libdir)" -name "*so" | sed "s:${ED}::g"); do + dosym $i.2 $i + done + use static-libs && dolib.a lib/*.a + + insinto /usr/include + doins inc/CORE.h + insinto /usr/include/CORE + doins inc/CORE/*.h + + dodoc FAQs README + if use doc; then + dodoc doc/*.txt + dodoc doc/tutorial/tutorial.pdf doc/doxy/latex/*pdf + dohtml -r doc/doxy/html/* + fi +} diff --git a/sci-libs/libcore/metadata.xml b/sci-libs/libcore/metadata.xml new file mode 100644 index 000000000000..9861e117af6a --- /dev/null +++ b/sci-libs/libcore/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-geosciences@gentoo.org</email> + <name>Gentoo Geosciences Project</name> +</maintainer> +<longdescription lang="en"> + The Core Library is a collection of C/C++ classes for exact + computation with real algebraic numbers. + It embodies our precision-driven approach and is + useful for robust numerical (especially geometric) algorithms. + The library supports the Exact Geometric Computation (EGC) + philosophy through its novel and easy-to-use notion of accuracy + levels. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/libctl/Manifest b/sci-libs/libctl/Manifest new file mode 100644 index 000000000000..0fe2091e7928 --- /dev/null +++ b/sci-libs/libctl/Manifest @@ -0,0 +1,7 @@ +DIST libctl-3.1.tar.gz 460108 SHA256 9001f95efa0812b6b76220f2de1edcb512f9c26764df63680fc37c8c9684eee5 SHA512 94e44a0baea067a85c7a8f930545317b1c9f440e18b6ccc59417ed3072652da0ba79f58b469b8d9ba81cd6adae81830566c28aefea18fd76491824dc6c2da067 WHIRLPOOL 12b3f9a079bf415e12485f6c3e5a5ab406fb42968ee160702f89414ec019181e4410738779c3eed1e2a5390318212e275ad89412b01a076676f8623c37b84b14 +DIST libctl-3.2.tar.gz 485681 SHA256 30a4eef0bfde4454941482f859fb738c652750528a30ab240d5ce17faac375cc SHA512 df8701330d3785ff845a065a0d4abb1e7d9167ad7909ff7074a48040092e5bb840f75b3fa90263fe8d29607aeb0b33919be333a619f34a5bac255c0ade4340f5 WHIRLPOOL c3527fa1fe47a087f280f50dfac6f2cf4a9e9448712fe526e4906b435b03f1119bc7faab3f3ba34df804e4e36686835a65c3c84936c8e29c9cbcd484e78e10c5 +EBUILD libctl-3.1.ebuild 730 SHA256 511b2deb1519a8749a67ed8cc4d6e3a3cb6ab10420265a105d1f0c0d20b37683 SHA512 7ddd0d5d118ead986ad401682d1775f45800bfc4499f76219bdc924e34ce0a50817ab0074534bed1f407b7e45988dd46519f02baeb980d73884fcc9fcaf04c3b WHIRLPOOL 372313748e2460d3f845372bf7d36e13eaa5dfde9c11f112c1c22d08f92970c37ab65d8c1b04988b215df5fb49aa0b9eb730fc82b939a9e028698c7fb6df8d9f +EBUILD libctl-3.2.ebuild 744 SHA256 6b0ead4b4b90464b92af2fdd0493fbefd289bd9539411742b0295cc69b435ead SHA512 3026f2c9a8162f03451fb1d4f0dfdd88c21f0485cbfd510ebead32f8727b4eac3091936811af39bea683c4abce26a51483827ba9783a53dbc1d431a35bbb6f8f WHIRLPOOL 0c206942b517cfb971dc51fdf475c406ab9ab4576443d9fcf85dd61814d00ffe3752fbd2b9f99bc341bd14af27c3c06d10a588cb84e8d9bb45c89cdff077d72e +MISC ChangeLog 2466 SHA256 d429d7b0fb82235ff3ad80e1d0b88f617a773e4f24552561b97d2987017835f0 SHA512 1039fa307b9bd9605cecce072b41cf591c73b05fd983df7da3d996ccf7ae76b4a29c5663e06b91111576f2a8b6b219fb9788fcb054319d136715a15ccfd42575 WHIRLPOOL aed7ab7b96905b744adc0b9a56c7a03c5e6ecd284532c196c56f7c2026f6ec7859456d28bdef88ca613e806fb20ac563b3bac1e8729498ed6b146128952bcbe4 +MISC ChangeLog-2015 3476 SHA256 c4b9271c32d33de517ac4aa2bb415d7883bc72ae384a8dea5b6c712b3f003f4a SHA512 dc3d7289b1f1990dea510cebebfb7c5962f51684052f55ac88c66bf4e7925ad0c0f6bd19a83edf2d709bdc472cb552f405de542ef7abc3b4c789812716606399 WHIRLPOOL 5e137fbe01144b7157ca0bcc9270c210ff54ddfc9f4a29975a0df18039ec972d8ffa13a26a9eafc583d00869365a7a75732ef69d6fc26824b7f3b7d78383ee62 +MISC metadata.xml 601 SHA256 27ea3fc6dae5ffa62240d2bd8e9193def31496fd8e71b0ce887c6f88506d594c SHA512 0db88004c480064aa8c97ca9a25265664adb9d7e4cfeaa87a02b81f8aec53b199690fd0ad79dbdad1d27bcf38b5fd614f173cb1caf7db2dd5e6209403506ce06 WHIRLPOOL b9a4322e51cf44ac96ad5b0c405b73c2eeb09062de979e44e6acdeb209850ddcc5ce676d0090e32db5790c57bd928e40a23afdbd76035f5eda3c8eecaf4452c6 diff --git a/sci-libs/libctl/libctl-3.1.ebuild b/sci-libs/libctl/libctl-3.1.ebuild new file mode 100644 index 000000000000..23d9af250871 --- /dev/null +++ b/sci-libs/libctl/libctl-3.1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit fortran-2 autotools-utils + +DESCRIPTION="Guile-based library for scientific simulations" +HOMEPAGE="http://ab-initio.mit.edu/libctl/" +SRC_URI="http://ab-initio.mit.edu/libctl/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="amd64 x86" +IUSE="doc examples static-libs" + +DEPEND=" + dev-scheme/guile[deprecated] + sci-libs/nlopt" +RDEPEND="${DEPEND}" + +src_install() { + autotools-utils_src_install + use doc && dohtml doc/* + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins "${AUTOTOOLS_BUILD_DIR}"/examples/{*.c,*.h,example.scm,Makefile} + doins "${S}"/examples/{README,example.c,run.ctl} + fi +} diff --git a/sci-libs/libctl/libctl-3.2.ebuild b/sci-libs/libctl/libctl-3.2.ebuild new file mode 100644 index 000000000000..14995ee8a35b --- /dev/null +++ b/sci-libs/libctl/libctl-3.2.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit fortran-2 autotools-utils + +DESCRIPTION="Guile-based library for scientific simulations" +HOMEPAGE="http://ab-initio.mit.edu/libctl/" +SRC_URI="http://ab-initio.mit.edu/libctl/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs" + +DEPEND=" + dev-scheme/guile + sci-libs/nlopt" +RDEPEND="${DEPEND}" + +src_install() { + autotools-utils_src_install + use doc && dohtml doc/* + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins "${AUTOTOOLS_BUILD_DIR}"/examples/{*.c,*.h,example.scm,Makefile} + doins "${S}"/examples/{README,example.c,run.ctl} + fi +} diff --git a/sci-libs/libctl/metadata.xml b/sci-libs/libctl/metadata.xml new file mode 100644 index 000000000000..36b9c35b01eb --- /dev/null +++ b/sci-libs/libctl/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + libctl is the Control Language library implementing a control file + structure aimed at simplifying the control file writing in + scientific simulations. The "ctl" in "libctl" stands for Control + Language (by convention, libctl control files end with ".ctl" and + are referred to as ctl files). +</longdescription> +</pkgmetadata> diff --git a/sci-libs/libdap/Manifest b/sci-libs/libdap/Manifest new file mode 100644 index 000000000000..60c54651513e --- /dev/null +++ b/sci-libs/libdap/Manifest @@ -0,0 +1,11 @@ +AUX libdap-3.18.1-disable-broken-tests.patch 719 SHA256 2348872654cb04c2fc551dc7ef04b4611dfd8c5c14e857f92db1cca2f26e66a5 SHA512 11237422b0d129aaa52dc3559e2ffe0d4bcc0562e0acd476290af7a4026a1c7272bc1e0a0ceddcb40250746c0c71e4c6d63a780c5c1635132faf0ee609e3b88c WHIRLPOOL aecd9d89d5a09eb773b930ae9bd5764c4815ab49dfc4cb30ead71e97542449a0fb309bd0bff2781850e4c69184b669ae836236126044f337bfd31982abeee155 +AUX libdap-3.18.1-disable-cache-test.patch 965 SHA256 84d49c91d366d1890fcb82d05e01c9a63a7a26177174944de270cbe11ad47dab SHA512 087dd231f92d4117cbf469077922975029576239e507ef2cd5ae9d5b1f8f38ab3c4a3f32c8e2781a5c299c5e0a29c77cfd7d67ea8bf141058839f2bb4299b187 WHIRLPOOL d89c0ca4c0ee27733eee5ca6241e0110b31cf2ce1223e4ccf20f7b2d3827398ee5ed5d6999c8106c14a4eadf523d4c1035b1fc6e6f9370aaca7713172368ebc1 +AUX libdap-3.18.1-disable-dmr-tests.patch 1241 SHA256 0f7d4f06ed70759fd0dd896b0ab9f5d7f07a100bf8ec75b0ad7aab4cc9064d11 SHA512 5becf972bed0d27b32a67127af5ca2567757c05e04ef13aa3d514212320c552ad91a7b11b5386b73211a72017712b10875931a764f88ba9fa4fba40da453340f WHIRLPOOL 3fb6ef17558f18295f9f9456d06480b32720ecda4b6862b31016a6aafbef5178a7c1c1601353d2b73cc8615c11df08fbe890c096e054e131c1b0510d40b467ee +AUX libdap-3.18.1-disable-net-tests.patch 1281 SHA256 0bcea9e0e9be748410fb1c124dc81748312335fabff5a83e1d0663f5b06ad636 SHA512 91db2d34693eed9a4e4c6f1d138520472c86290de131adaf47b609e3cc2ee7a6806eaf47d7d11a440034c226a18cb7ee1af5efadf08b2c3ba173792b6ee64813 WHIRLPOOL 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a755c472d7c9e54bc3aa6c92a847a69466fbc6cdc56ee912f411802a725d57a4 SHA512 a1d06bbbad654718bbf9980dc0943935089c09772678f6457d4de8a9d37f1ce33c0e1cab4c5eefec6f9e159028b194d6e3a6021597276b233eda52603ae8dd38 WHIRLPOOL 74eb65be375bd81e5d6db9fb93bdd219add79c12fea35eed98445df38f6dc212fc33cc51900ac93657166794b0700ff1be17fd7f41379733de19ad7480f889f0 +EBUILD libdap-3.18.1.ebuild 1095 SHA256 2011c46ff14644b92b1ae83a330edb729381646727593fafba361e0911954ae7 SHA512 10f6e2e7070b7bae860043a15cbb4d570f68a9f0c265eef4416aa4400a8748878773b3d30b3a59f4fdd6bfa9d0cced7064974173d383bdab62334ec01e5216b8 WHIRLPOOL f272edeb731e68907ffa70afd00942428a86fbb65c9f9c321983b4788ee707491ded5c4fc7048c19503d853657e3d91a9acf1815ee2f7f68ba395f06b2fb28c0 +MISC ChangeLog 3424 SHA256 121ea7dff804d7b3553b55751b4284f5f524855b6d540364bd6df39a6fb80f29 SHA512 6abff7d825ddd0098b0932a2ea6c02a046f2581a91c5032f26154950456dcb80e2a7566056f9b0b5415797c84bc50de40836ccbb18a75d318ace1db76c579855 WHIRLPOOL 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b/sci-libs/libdap/files/libdap-3.18.1-disable-broken-tests.patch new file mode 100644 index 000000000000..09c33e6f381a --- /dev/null +++ b/sci-libs/libdap/files/libdap-3.18.1-disable-broken-tests.patch @@ -0,0 +1,18 @@ +Description: D4FilterClauseTest breaks on arm*, powerpc, s390x. +Author: Alastair McKinstry <mckinstry@debian.org> +Last-Updated: 2016-08-31 +Forwarded: no + +Index: libdap-3.18.0/unit-tests/Makefile.am +=================================================================== +--- libdap-3.18.0.orig/unit-tests/Makefile.am ++++ libdap-3.18.0/unit-tests/Makefile.am +@@ -74,7 +74,7 @@ UNIT_TESTS = marshT arrayT attrTableT st + if DAP4_DEFINED + UNIT_TESTS += D4MarshallerTest D4UnMarshallerTest D4DimensionsTest \ + D4EnumDefsTest D4GroupTest D4ParserSax2Test D4AttributesTest D4EnumTest \ +- chunked_iostream_test D4AsyncDocTest DMRTest D4FilterClauseTest \ ++ chunked_iostream_test D4AsyncDocTest DMRTest \ + D4SequenceTest + endif + diff --git a/sci-libs/libdap/files/libdap-3.18.1-disable-cache-test.patch b/sci-libs/libdap/files/libdap-3.18.1-disable-cache-test.patch new file mode 100644 index 000000000000..6ce7ae0c4f6d --- /dev/null +++ b/sci-libs/libdap/files/libdap-3.18.1-disable-cache-test.patch @@ -0,0 +1,22 @@ +Author: Alastair McKinstry <mckinstry@debian.org> +Description: Disable test as website appears to be down +Forwarded: no +Last-Updated: 2015-10-20 + +Index: libdap-3.18.0/unit-tests/Makefile.am +=================================================================== +--- libdap-3.18.0.orig/unit-tests/Makefile.am ++++ libdap-3.18.0/unit-tests/Makefile.am +@@ -67,9 +67,9 @@ D4-xml.tar.gz: D4-xml/DMR_*[0-9].xml + if CPPUNIT + UNIT_TESTS = marshT arrayT attrTableT structT sequenceT ddsT dasT \ + RegexTest ArrayTest AttrTableTest ByteTest MIMEUtilTest ancT DASTest \ +- DDSTest DDXParserTest generalUtilTest HTTPConnectTest parserUtilTest \ +- RCReaderTest SequenceTest SignalHandlerTest MarshallerTest \ +- HTTPCacheTest ServerFunctionsListUnitTest ++ DDSTest DDXParserTest generalUtilTest parserUtilTest \ ++ SequenceTest SignalHandlerTest MarshallerTest \ ++ ServerFunctionsListUnitTest + + if DAP4_DEFINED + UNIT_TESTS += D4MarshallerTest D4UnMarshallerTest D4DimensionsTest \ diff --git a/sci-libs/libdap/files/libdap-3.18.1-disable-dmr-tests.patch b/sci-libs/libdap/files/libdap-3.18.1-disable-dmr-tests.patch new file mode 100644 index 000000000000..d4691f59518f --- /dev/null +++ b/sci-libs/libdap/files/libdap-3.18.1-disable-dmr-tests.patch @@ -0,0 +1,31 @@ +Author: Alastair McKinstry <mckinstry@debian.org> +Description: Disable DMR tests which break on big-endian archs at the moment +Last-Updated: 2015-11-08 +Forwarded: no + +Index: libdap-3.18.0/tests/Makefile.am +=================================================================== +--- libdap-3.18.0.orig/tests/Makefile.am ++++ libdap-3.18.0/tests/Makefile.am +@@ -31,7 +31,7 @@ endif + # TESTS = DASTest DDSTest EXPRTest DMRTest getdapTest + + check_SCRIPTS = $(DASTESTSUITE) $(DDSTESTSUITE) $(EXPRTESTSUITE) \ +- $(DMRTESTSUITE) $(GETDAPTESTSUITE) ++ $(GETDAPTESTSUITE) + + # Build the test drivers. The drivers all use the + # subclassed types in Test*.cc and the TestTypesFactory. +@@ -107,11 +107,10 @@ DMRTESTSUITE = $(srcdir)/DMRTest + GETDAPTESTSUITE = $(srcdir)/getdapTest + + check-local: atconfig atlocal $(DASTESTSUITE) $(DDSTESTSUITE) \ +-$(EXPRTESTSUITE) $(DMRTESTSUITE) $(GETDAPTESTSUITE) ++$(EXPRTESTSUITE) $(GETDAPTESTSUITE) + $(SHELL) '$(DASTESTSUITE)' $(TESTSUITEFLAGS) + $(SHELL) '$(DDSTESTSUITE)' $(TESTSUITEFLAGS) + $(SHELL) '$(EXPRTESTSUITE)' $(TESTSUITEFLAGS) +- $(SHELL) '$(DMRTESTSUITE)' $(TESTSUITEFLAGS) + $(SHELL) '$(GETDAPTESTSUITE)' $(TESTSUITEFLAGS) + + # Make sure there are no spaces after the DASTESTSUITE names. jhrg 3/16/15 diff --git a/sci-libs/libdap/files/libdap-3.18.1-disable-net-tests.patch b/sci-libs/libdap/files/libdap-3.18.1-disable-net-tests.patch new file mode 100644 index 000000000000..7c42ec1199c4 --- /dev/null +++ b/sci-libs/libdap/files/libdap-3.18.1-disable-net-tests.patch @@ -0,0 +1,33 @@ +Author: Alastair McKinstry <mckinstry@debian.org> +Description: Disable network tests, as network not available on + most build systems +Last-Updated: 2016-02-06 +Forwarded: not-needed + +Index: libdap-3.18.0/tests/Makefile.am +=================================================================== +--- libdap-3.18.0.orig/tests/Makefile.am ++++ libdap-3.18.0/tests/Makefile.am +@@ -30,8 +30,7 @@ endif + + # TESTS = DASTest DDSTest EXPRTest DMRTest getdapTest + +-check_SCRIPTS = $(DASTESTSUITE) $(DDSTESTSUITE) $(EXPRTESTSUITE) \ +- $(GETDAPTESTSUITE) ++check_SCRIPTS = $(DASTESTSUITE) $(DDSTESTSUITE) $(EXPRTESTSUITE) + + # Build the test drivers. The drivers all use the + # subclassed types in Test*.cc and the TestTypesFactory. +@@ -107,11 +106,10 @@ DMRTESTSUITE = $(srcdir)/DMRTest + GETDAPTESTSUITE = $(srcdir)/getdapTest + + check-local: atconfig atlocal $(DASTESTSUITE) $(DDSTESTSUITE) \ +-$(EXPRTESTSUITE) $(GETDAPTESTSUITE) ++$(EXPRTESTSUITE) + $(SHELL) '$(DASTESTSUITE)' $(TESTSUITEFLAGS) + $(SHELL) '$(DDSTESTSUITE)' $(TESTSUITEFLAGS) + $(SHELL) '$(EXPRTESTSUITE)' $(TESTSUITEFLAGS) +- $(SHELL) '$(GETDAPTESTSUITE)' $(TESTSUITEFLAGS) + + # Make sure there are no spaces after the DASTESTSUITE names. jhrg 3/16/15 + # Delete the scripts here and not using CLEANFILES because this target is diff --git a/sci-libs/libdap/files/libdap-3.18.1-fix-buildsystem.patch b/sci-libs/libdap/files/libdap-3.18.1-fix-buildsystem.patch new file mode 100644 index 000000000000..f36fdceb1fd0 --- /dev/null +++ b/sci-libs/libdap/files/libdap-3.18.1-fix-buildsystem.patch @@ -0,0 +1,20 @@ +Do not install headers and static library required only for test suite. + +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -36,13 +36,13 @@ + # Build the test drivers. The drivers all use the + # subclassed types in Test*.cc and the TestTypesFactory. + +-lib_LIBRARIES = libtest-types.a ++noinst_LIBRARIES = libtest-types.a + + libtest_types_a_SOURCES = $(TESTSRCS) $(TEST_HDR) + libtest_types_a_CXXFLAGS = -fPIC + + testheadersdir = $(pkgincludedir)/test +-testheaders_HEADERS = $(TEST_HDR) ++noinst_testheaders = $(TEST_HDR) + + das_test_SOURCES = das-test.cc + das_test_LDADD = libtest-types.a ../libdapserver.la ../libdap.la diff --git a/sci-libs/libdap/files/libdap-3.18.1-fix-c++14.patch b/sci-libs/libdap/files/libdap-3.18.1-fix-c++14.patch new file mode 100644 index 000000000000..6b74fa10a240 --- /dev/null +++ b/sci-libs/libdap/files/libdap-3.18.1-fix-c++14.patch @@ -0,0 +1,100 @@ +C++11 changed destructor semantics to be noexcept(true) +by default, leading to potentially changed semantics. + +--- a/HTTPResponse.h ++++ b/HTTPResponse.h +@@ -115,6 +115,9 @@ + temp_file and headers are deleted. If the tmp file name is "", it is + not deleted. */ + virtual ~HTTPResponse() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + DBG(cerr << "Freeing HTTPConnect resources (" + d_file + ")... "); + +--- a/MarshallerThread.cc ++++ b/MarshallerThread.cc +@@ -106,6 +106,9 @@ + * Unlock the mutex + */ + Locker::~Locker() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + DBG(cerr << "Unlocking the mutex! (" << pthread_self() << ")" << endl); + +@@ -140,6 +143,9 @@ + } + + ChildLocker::~ChildLocker() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + DBG(cerr << "Unlocking the mutex! (" << pthread_self() << ")" << endl); + +@@ -164,6 +170,9 @@ + } + + MarshallerThread::~MarshallerThread() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + int status = pthread_mutex_lock(&d_out_mutex); + if (status != 0) throw InternalErr(__FILE__, __LINE__, "Could not lock m_mutex"); +--- a/MarshallerThread.h ++++ b/MarshallerThread.h +@@ -52,7 +52,11 @@ + class Locker { + public: + Locker(pthread_mutex_t &lock, pthread_cond_t &cond, int &count); +- virtual ~Locker(); ++ virtual ~Locker() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ ; + + private: + pthread_mutex_t& m_mutex; +@@ -74,7 +78,11 @@ + class ChildLocker { + public: + ChildLocker(pthread_mutex_t &lock, pthread_cond_t &cond, int &count); +- virtual ~ChildLocker(); ++ virtual ~ChildLocker() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ ; + + private: + pthread_mutex_t& m_mutex; +@@ -144,7 +152,11 @@ + + public: + MarshallerThread(); +- virtual ~MarshallerThread(); ++ virtual ~MarshallerThread() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif ++ ; + + pthread_mutex_t &get_mutex() { return d_out_mutex; } + pthread_cond_t &get_cond() { return d_out_cond; } +--- a/Response.h ++++ b/Response.h +@@ -93,6 +93,9 @@ + + /** Close the stream. */ + virtual ~Response() ++#if __cplusplus >= 201103L ++ noexcept(false) ++#endif + { + if (d_stream) + fclose(d_stream); diff --git a/sci-libs/libdap/libdap-3.18.1.ebuild b/sci-libs/libdap/libdap-3.18.1.ebuild new file mode 100644 index 000000000000..b0a4bfc02ba2 --- /dev/null +++ b/sci-libs/libdap/libdap-3.18.1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Implementation of a C++ SDK for DAP 2.0 and 3.2" +HOMEPAGE="http://opendap.org/" +SRC_URI="http://www.opendap.org/pub/source/${P}.tar.gz" + +LICENSE="|| ( LGPL-2.1 URI )" +SLOT="0" +KEYWORDS="amd64 ~ppc ~ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="static-libs test" + +RDEPEND=" + dev-libs/libxml2:2 + net-misc/curl + sys-libs/zlib" +DEPEND="${RDEPEND} + virtual/pkgconfig + sys-devel/flex + test? ( dev-util/cppunit )" + +PATCHES=( + "${FILESDIR}/${PN}-3.18.1-fix-buildsystem.patch" + "${FILESDIR}/${PN}-3.18.1-fix-c++14.patch" + "${FILESDIR}/${PN}-3.18.1-disable-cache-test.patch" + "${FILESDIR}/${PN}-3.18.1-disable-dmr-tests.patch" + "${FILESDIR}/${PN}-3.18.1-disable-net-tests.patch" + "${FILESDIR}/${PN}-3.18.1-disable-broken-tests.patch" +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable static-libs static) +} + +src_install() { + default + + # package provides .pc files + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/libdap/metadata.xml b/sci-libs/libdap/metadata.xml new file mode 100644 index 000000000000..c1f3d9787739 --- /dev/null +++ b/sci-libs/libdap/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-geosciences@gentoo.org</email> + <name>Gentoo Geosciences Project</name> +</maintainer> +<longdescription> + libdap is a C++ implementation of OPeNDAP which allows access to + data over the internet, from programs that weren't originally + designed for that purpose, as well as some that were. While OPeNDAP + s the original developer of the Data Access Protocol (DAP) which + it's software uses, many other groups have adopted DAP and provide + compatible clients, servers and software development kits. DAP is a + NASA community standard: http://www.esdswg.org/spg/rfc/ese-rfc-004 +</longdescription> +</pkgmetadata> diff --git a/sci-libs/libexcelformat/Manifest b/sci-libs/libexcelformat/Manifest new file mode 100644 index 000000000000..7556cabfbb47 --- /dev/null +++ b/sci-libs/libexcelformat/Manifest @@ -0,0 +1,5 @@ +DIST libexcelformat-101016.tar.bz2 47980 SHA256 b1f552c4f89bb63fe7e46c04ef885a73f7bdd595116a09204a6f807100d55915 SHA512 40d43e7b0c15d00026fde3927b3f6fdf9ea110c43141f1a25f3a8ed9ccf6a2acd1de68e25fc54d0c030364d4a4e300aa267332b9d2ac0fb0a422858715156576 WHIRLPOOL d6d8b410a2de43b32ed8004c73d54108ddb2243500060a0683537443ac87bb55bd5a0a222525a94ddb244addf15cde85e622e6b270bd27b29a33c7a2fd6c7d90 +EBUILD libexcelformat-101016.ebuild 545 SHA256 a5067c9c16e6b09517e1b6fe8eebde33ccd8702861fe1bffd08219afcffe52d3 SHA512 f01ca8a20e2ed4a65cb7adbe308d72e15a532633870627c08fb840359053c85de2dab071acac51b84f0d8b994e24e1aa0fc4d6ecfbe8cdc774edd2b9196fbd14 WHIRLPOOL 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819062e1ccefa39fc7f577279b08e781b9631eb14b7794db691ab92263c013ca432d279ac08671b19c80f7effb8c67528e5221278c573dd29dc0354bbff4a77e WHIRLPOOL 73680e667729b1d31cac7b2b730a5d94195071c96383438c66c4a94e445fe874e78d3e5e2c9c5a6d77406dc392eab967595402e063e557f9a3680714d709e830 diff --git a/sci-libs/libexcelformat/libexcelformat-101016.ebuild b/sci-libs/libexcelformat/libexcelformat-101016.ebuild new file mode 100644 index 000000000000..6b346b4f29f2 --- /dev/null +++ b/sci-libs/libexcelformat/libexcelformat-101016.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="reading, writing, and editing of XLS (BIFF8 format) files using C++" +HOMEPAGE="http://www.codeproject.com/KB/office/ExcelFormat.aspx" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +LICENSE="CPOL" +IUSE="" + +S="${WORKDIR}"/libExcelFormat + +src_prepare() { + default + tc-export CXX +} + +src_install() { + doheader *.h* + + dolib.so libExcelFormat.so* +} diff --git a/sci-libs/libexcelformat/metadata.xml b/sci-libs/libexcelformat/metadata.xml new file mode 100644 index 000000000000..ae9640ffb9f1 --- /dev/null +++ b/sci-libs/libexcelformat/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libgenome/Manifest b/sci-libs/libgenome/Manifest new file mode 100644 index 000000000000..5d3d1b4a9207 --- /dev/null +++ b/sci-libs/libgenome/Manifest @@ -0,0 +1,6 @@ +AUX libgenome-1.3-fix-c++14.patch 979 SHA256 3068c4710c3c3493b356db263660721639dcde86a9c8fd84815c36d6cff66c41 SHA512 9b527401e9d3708adbf5c97727a6c337d776c2a8b097644dc732192e114cfa679413975007aa1c9e2814c27a3617e1e6bb1fc23e6bae30ac146fde1fac6ec6bd WHIRLPOOL d06a58b59cfeada2a327f59e2c1b14e9ea724cd205205153d46ac3b316be549c39f155af6967ffa41fa76514ed9b7ae7e063377458026394f80eb8055a2b3831 +DIST libgenome-1.3-r1.tar.bz2 128503 SHA256 29d62cb367bb498648b6320091fa534b52a8c39fd0bfd495b095706e68bc400d SHA512 0fd1895d9ea1ac75e4efaeae9abd5241193dba17f91426a5be7b244331ac7939c37d51bb08f8378d64a96573ad38b39e2583a928aadf9421e8b5c17fe217dfd4 WHIRLPOOL 97c5be58ce1f2fea3c81159641f8c950845cbb384f0112ce3181bb2f6366b367f0c3b2f998814d2aeac01d14dea1f108d4db60a63acb9044f5094b626a8a91a7 +EBUILD libgenome-1.3-r1.ebuild 692 SHA256 04099f11eb5054ede369590580de2bb0991b6a3fde256e927d46aa5268b62d99 SHA512 e8a0eda85242af55698bb84d442926293886424af20640b78807aa7ac3aef58358aba4ff83351b456b7fa7262a68618a053eb52649fcd4f57681a4e59d8e6912 WHIRLPOOL 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537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8 diff --git a/sci-libs/libgenome/files/libgenome-1.3-fix-c++14.patch b/sci-libs/libgenome/files/libgenome-1.3-fix-c++14.patch new file mode 100644 index 000000000000..ffe30ef91fa2 --- /dev/null +++ b/sci-libs/libgenome/files/libgenome-1.3-fix-c++14.patch @@ -0,0 +1,30 @@ +Fix building with C++14, which errors out due to collisions with internal abs() function. +See also: https://bugs.gentoo.org/show_bug.cgi?id=594372 + +--- a/libGenome/gnDefs.h ++++ b/libGenome/gnDefs.h +@@ -175,13 +175,6 @@ +
+ #define CONTIG_SECTION_SIZE 3
+
+-// some compilers don't have abs() for 64 bit ints
+-#if (defined(__GNUG__) && ( __GNUC__ <= 2 )) || defined(__INTEL_COMPILER) || (defined _MSC_VER && defined __cplusplus)
+-
+-int64 abs( int64 a );
+-
+-#endif
+-
+ #ifdef __cplusplus
+ namespace genome {
+ #endif
+--- a/libGenome/Makefile.am ++++ b/libGenome/Makefile.am +@@ -29,7 +29,7 @@ + gnGenomeSpec.cpp gnLocation.cpp \ + gnRAWSource.cpp gnBaseFeature.cpp gnSEQSource.cpp gnSequence.cpp \ + gnContigSpec.cpp gnSourceHeader.cpp gnException.cpp \ +-gnFastTranslator.cpp gnPosSpecificTranslator.cpp gnDefs.cpp ++gnFastTranslator.cpp gnPosSpecificTranslator.cpp + + library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME) + diff --git a/sci-libs/libgenome/libgenome-1.3-r1.ebuild b/sci-libs/libgenome/libgenome-1.3-r1.ebuild new file mode 100644 index 000000000000..03f05c029ad0 --- /dev/null +++ b/sci-libs/libgenome/libgenome-1.3-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="mirror://gentoo/${PF}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +IUSE="doc static-libs" +KEYWORDS="~amd64 ~x86" + +DEPEND="doc? ( app-doc/doxygen )" +RDEPEND="" + +PATCHES=( "${FILESDIR}/${PN}-1.3-fix-c++14.patch" ) + +src_prepare() { + default + rm libGenome/gnDefs.cpp || die + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable static-libs static) +} + +src_install() { + default + + # package provides .pc files + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/libgenome/metadata.xml b/sci-libs/libgenome/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-libs/libgenome/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libgeodecomp/Manifest b/sci-libs/libgeodecomp/Manifest new file mode 100644 index 000000000000..910acbd2cb89 --- /dev/null +++ b/sci-libs/libgeodecomp/Manifest @@ -0,0 +1,6 @@ +AUX libflatarray.patch 528 SHA256 5858f66ba36289dd0247a70ed2ab26351137f06463ce2331a56a09107a202f12 SHA512 e3b195723999285fa14702e01497485f55e8523883951db16eb883220cb636d3f20f3df776b1a0dff70da221dfd7483a032e08b2996e94fd642fa175f69cc627 WHIRLPOOL d797166bcdbaf987b58288f29ca1f61c7106b6f9a05158a9e2ae7f8dd0a2bc62b0242bddd20a5795d5e4416ea64dcc35cde3881e43b095d4285df18686fe275e +DIST libgeodecomp-0.3.1.tar.bz2 740341 SHA256 3c49a238472a82be3a6e2411a20bda85672aac01d4a87bb0e63ccbff1385ea64 SHA512 28f0ea04e45cb0a5b81b18efd3e3a011d58c077562f8039ff42e701cc362f86dff90bd505690ec22c8a42e9de1236d5b6c61d288ad4c154289e92700a2a7fcc0 WHIRLPOOL 3827974861556ab84a16e81b8cece2cff4d9e88a1559d99192fa47efd571639b252423038b3b579811c7d57452e94ae96b99f7209e87af46b752b5a193dc9994 +EBUILD libgeodecomp-0.3.1.ebuild 1119 SHA256 f028770acd97561b8aa31dea7c5190740f44eb68f4dc4bec0edb0601c8c6995c SHA512 acfa314b68acbad74a88218c01681ac59b5827c3f93bf3d999ab9d45ccbb8072e7eaf7ed4235223266a720bfc1847251c0ff952cbf2b10ce41fa8089430f7cf0 WHIRLPOOL 65e27d0a9877776202b435db60b00f82765edc2e9c7ac66340557a65971338ed0a03dfea91ee2df30291406e7197a670cb84c830c50c7eeac6788d58aaebc740 +MISC ChangeLog 2511 SHA256 5a33add83467c3752615f585c3604cdb166afbd83a3197fa7c26c27fb49a726a SHA512 b1462753b2deeb3b5cd2b033ab3ce5b10758d5bb2ef9f567bd890bee86f7f5ba497a1ecf09fcbd0a710a273639f4a0af971bccb4cf95724f91369b00489fc519 WHIRLPOOL 9ce47507c164e000fe3d5d17f47bd3eb5b2f37cf8f99269e7215bd87df0658836e2958e38980ed4f60f5f6a09e45c9cb04eb803187b60a23c6f83704628c3152 +MISC ChangeLog-2015 509 SHA256 5b81c6d04f6a96e40f434b9378b18ae470f4b5c04ea670d2c67a5a1ec6ebb9ab SHA512 8d1de0c428008effa87f19705f81139bf05dd9c8a4605d98de2274f66f98d99355208f2a303dc6cd65c486f4546864a39db358b7265fd59ffa06ba329e9859b8 WHIRLPOOL 224a8b9d224debff3ed4c80867130a4b4424069623e3ab2d222bb8fba2a56f6e9ab5c418d4e62d8e30bba287b85db3119df95943e07d7c2b18d26753342bfd6d +MISC metadata.xml 219 SHA256 b4761abaa4db71355e68ae61325c38990acb1dc6350e3632aa3ee64bfcd69554 SHA512 b6db740071cb706a6dd7ce9e21ec09a11c9d63752f87e700a5cb58fc100befdfc3c6b16b3065e8a8cb9a8cd3bcae6bd162f3bcd3dfcc592e27b5f738adc71007 WHIRLPOOL a65925ed7d4d3e0ac0530648ec4ca60b6487d124e866ec5c20e75ceceab83949a1af4a9431d07b7a7f966f5b390be01eabd454161fab46d1e39d28ba2c85bbea diff --git a/sci-libs/libgeodecomp/files/libflatarray.patch b/sci-libs/libgeodecomp/files/libflatarray.patch new file mode 100644 index 000000000000..8a109d986577 --- /dev/null +++ b/sci-libs/libgeodecomp/files/libflatarray.patch @@ -0,0 +1,11 @@ +--- src/CMakeLists.txt.orig 2015-05-06 07:03:21.508147301 +0200 ++++ src/CMakeLists.txt 2015-05-06 07:03:27.038147363 +0200 +@@ -439,7 +439,7 @@ + install(FILES ${HEADERS} DESTINATION include/${PACKAGE_NAME}/${dir}) + endforeach(dir) + # install libflatarray, too +-install(FILES ../lib/libflatarray/src/flat_array.hpp DESTINATION include/libflatarray) ++#install(FILES ../lib/libflatarray/src/flat_array.hpp DESTINATION include/libflatarray) + + # link against the libs we need + set(INSTALLER_LINK_FLAGS "-L\${libdir} -lgeodecomp ") diff --git a/sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild b/sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild new file mode 100644 index 000000000000..095cf09eafa5 --- /dev/null +++ b/sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="An auto-parallelizing library to speed up computer simulations" +HOMEPAGE="http://www.libgeodecomp.org" +SRC_URI="http://www.libgeodecomp.org/archive/${P}.tar.bz2" + +SLOT="0" +LICENSE="Boost-1.0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="doc examples" + +RDEPEND=">=dev-libs/boost-1.48" +DEPEND="${RDEPEND} + dev-libs/libflatarray + examples? ( !sys-cluster/mpich2 )" + +S="${WORKDIR}/${P}/src" + +src_prepare() { + epatch "${FILESDIR}/libflatarray.patch" + sed -i 's/libdir=${CMAKE_INSTALL_PREFIX}\/lib/libdir=\/usr\/'$(get_libdir)'/' "${S}/CMakeLists.txt" + sed -i 's/install(TARGETS geodecomp DESTINATION lib)/install(TARGETS geodecomp DESTINATION '$(get_libdir)')/' "${S}/CMakeLists.txt" + + if ! use examples ; then + sed -i 's/examples//g' CMakeLists.txt + fi +} + +src_compile() { + cmake-utils_src_compile + use doc && cmake-utils_src_make doc +} + +src_install() { + DOCS=( ../README ) + use doc && HTML_DOCS=( ../doc/html/* ) + cmake-utils_src_install +} + +src_test() { + cmake-utils_src_make test +} diff --git a/sci-libs/libgeodecomp/metadata.xml b/sci-libs/libgeodecomp/metadata.xml new file mode 100644 index 000000000000..9c43c5cbc14e --- /dev/null +++ b/sci-libs/libgeodecomp/metadata.xml @@ -0,0 +1,7 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>slis@gentoo.org</email> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libgeotiff/Manifest b/sci-libs/libgeotiff/Manifest new file mode 100644 index 000000000000..1b9eda23b850 --- /dev/null +++ b/sci-libs/libgeotiff/Manifest @@ -0,0 +1,8 @@ +AUX Doxyfile 9282 SHA256 9cd2e6d4fb9662ee08c153b8c9b0b35dc81802cb32886c3afc5ee7b2924afbc2 SHA512 cc0324c682d5f45f516f0a71311a9b6527c5c4cd6c1a4113503ad9023b72c64ef9c257008cda95d565723183f932f61f79aab73e123e7b7ecf8b7fdb30457fee WHIRLPOOL 6854c2019d93befd6c5f9e75f09aef84ee725c1f72415f527e25657e3ce0ef653f36e37f0312ce6aa7622b277f2d09a64e5f8907dc3c06a56bb4cb672ebc3e6b +DIST libgeotiff-1.4.0.tar.gz 1517881 SHA256 d0acb8d341fd6a8f2c673456e09fdb8f50f91e3166ac934719fe05b30d328329 SHA512 1336e9b5345d69c47807f350d2f757c753543fecc477a6fc036743e78fbfca7b7f99db1b0fdf03e80418fbd4c66db100d04ac7c3338913f9a2b922b9c9f91f1b WHIRLPOOL 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+OUTPUT_DIRECTORY = +CREATE_SUBDIRS = NO +OUTPUT_LANGUAGE = English +BRIEF_MEMBER_DESC = YES +REPEAT_BRIEF = YES +ABBREVIATE_BRIEF = +ALWAYS_DETAILED_SEC = NO +INLINE_INHERITED_MEMB = NO +FULL_PATH_NAMES = NO +STRIP_FROM_PATH = +STRIP_FROM_INC_PATH = +SHORT_NAMES = NO +JAVADOC_AUTOBRIEF = NO +QT_AUTOBRIEF = NO +MULTILINE_CPP_IS_BRIEF = NO +INHERIT_DOCS = YES +SEPARATE_MEMBER_PAGES = NO +TAB_SIZE = 8 +ALIASES = +OPTIMIZE_OUTPUT_FOR_C = YES +OPTIMIZE_OUTPUT_JAVA = NO +OPTIMIZE_FOR_FORTRAN = NO +OPTIMIZE_OUTPUT_VHDL = NO +EXTENSION_MAPPING = +BUILTIN_STL_SUPPORT = YES +CPP_CLI_SUPPORT = NO +SIP_SUPPORT = NO +IDL_PROPERTY_SUPPORT = YES +DISTRIBUTE_GROUP_DOC = NO +SUBGROUPING = YES +TYPEDEF_HIDES_STRUCT = NO +SYMBOL_CACHE_SIZE = 0 +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- +EXTRACT_ALL = NO +EXTRACT_PRIVATE = NO +EXTRACT_STATIC = NO +EXTRACT_LOCAL_CLASSES = YES +EXTRACT_LOCAL_METHODS = NO +EXTRACT_ANON_NSPACES = NO +HIDE_UNDOC_MEMBERS = YES +HIDE_UNDOC_CLASSES = NO +HIDE_FRIEND_COMPOUNDS = NO +HIDE_IN_BODY_DOCS = NO +INTERNAL_DOCS = NO +CASE_SENSE_NAMES = YES +HIDE_SCOPE_NAMES = NO +SHOW_INCLUDE_FILES = YES +INLINE_INFO = YES +SORT_MEMBER_DOCS = YES +SORT_BRIEF_DOCS = NO +SORT_MEMBERS_CTORS_1ST = NO +SORT_GROUP_NAMES = NO +SORT_BY_SCOPE_NAME = NO +GENERATE_TODOLIST = YES +GENERATE_TESTLIST = YES +GENERATE_BUGLIST = YES +GENERATE_DEPRECATEDLIST= YES +ENABLED_SECTIONS = +MAX_INITIALIZER_LINES = 30 +SHOW_USED_FILES = YES +SHOW_DIRECTORIES = NO +SHOW_FILES = YES +SHOW_NAMESPACES = YES +FILE_VERSION_FILTER = +LAYOUT_FILE = +#--------------------------------------------------------------------------- +# configuration options related to warning and progress messages +#--------------------------------------------------------------------------- +QUIET = NO +WARNINGS = NO +WARN_IF_UNDOCUMENTED = YES +WARN_IF_DOC_ERROR = YES +WARN_NO_PARAMDOC = NO +WARN_FORMAT = "$file:$line: $text" +WARN_LOGFILE = +#--------------------------------------------------------------------------- +# configuration options related to the input files +#--------------------------------------------------------------------------- +INPUT = . \ + libxtiff/xtiff.c +INPUT_ENCODING = UTF-8 +FILE_PATTERNS = *.h \ + *.cpp \ + *.c \ + *.inc +RECURSIVE = NO +EXCLUDE = +EXCLUDE_SYMLINKS = NO +EXCLUDE_PATTERNS = +EXCLUDE_SYMBOLS = +EXAMPLE_PATH = . +EXAMPLE_PATTERNS = +EXAMPLE_RECURSIVE = NO +IMAGE_PATH = +INPUT_FILTER = +FILTER_PATTERNS = +FILTER_SOURCE_FILES = NO +#--------------------------------------------------------------------------- +# configuration options related to source browsing +#--------------------------------------------------------------------------- +SOURCE_BROWSER = NO +INLINE_SOURCES = NO +STRIP_CODE_COMMENTS = YES +REFERENCED_BY_RELATION = NO +REFERENCES_RELATION = NO +REFERENCES_LINK_SOURCE = YES +USE_HTAGS = NO +VERBATIM_HEADERS = YES +#--------------------------------------------------------------------------- +# configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- +ALPHABETICAL_INDEX = NO +COLS_IN_ALPHA_INDEX = 5 +IGNORE_PREFIX = +#--------------------------------------------------------------------------- +# configuration options related to the HTML output +#--------------------------------------------------------------------------- +GENERATE_HTML = YES +HTML_OUTPUT = docs/api +HTML_FILE_EXTENSION = .html +HTML_HEADER = +HTML_FOOTER = +HTML_STYLESHEET = +HTML_ALIGN_MEMBERS = YES +HTML_DYNAMIC_SECTIONS = NO +GENERATE_DOCSET = NO +DOCSET_FEEDNAME = "Doxygen generated docs" +DOCSET_BUNDLE_ID = org.doxygen.Project +GENERATE_HTMLHELP = NO +CHM_FILE = +HHC_LOCATION = +GENERATE_CHI = NO +CHM_INDEX_ENCODING = +BINARY_TOC = NO +TOC_EXPAND = NO +GENERATE_QHP = NO +QCH_FILE = +QHP_NAMESPACE = +QHP_VIRTUAL_FOLDER = doc +QHP_CUST_FILTER_NAME = +QHP_CUST_FILTER_ATTRS = +QHP_SECT_FILTER_ATTRS = +QHG_LOCATION = +DISABLE_INDEX = NO +ENUM_VALUES_PER_LINE = 4 +GENERATE_TREEVIEW = NO +USE_INLINE_TREES = NO +TREEVIEW_WIDTH = 250 +FORMULA_FONTSIZE = 10 +SEARCHENGINE = NO +#--------------------------------------------------------------------------- +# configuration options related to the LaTeX output +#--------------------------------------------------------------------------- +GENERATE_LATEX = NO +LATEX_OUTPUT = +LATEX_CMD_NAME = latex +MAKEINDEX_CMD_NAME = makeindex +COMPACT_LATEX = NO +PAPER_TYPE = a4wide +EXTRA_PACKAGES = +LATEX_HEADER = +PDF_HYPERLINKS = YES +USE_PDFLATEX = YES +LATEX_BATCHMODE = NO +LATEX_HIDE_INDICES = NO +LATEX_SOURCE_CODE = NO +#--------------------------------------------------------------------------- +# configuration options related to the RTF output +#--------------------------------------------------------------------------- +GENERATE_RTF = NO +RTF_OUTPUT = rtf +COMPACT_RTF = NO +RTF_HYPERLINKS = NO +RTF_STYLESHEET_FILE = +RTF_EXTENSIONS_FILE = +#--------------------------------------------------------------------------- +# configuration options related to the man page output +#--------------------------------------------------------------------------- +GENERATE_MAN = NO +MAN_OUTPUT = man +MAN_EXTENSION = .3 +MAN_LINKS = NO +#--------------------------------------------------------------------------- +# configuration options related to the XML output +#--------------------------------------------------------------------------- +GENERATE_XML = NO +XML_OUTPUT = xml +XML_SCHEMA = +XML_DTD = +XML_PROGRAMLISTING = YES +#--------------------------------------------------------------------------- +# configuration options for the AutoGen Definitions output +#--------------------------------------------------------------------------- +GENERATE_AUTOGEN_DEF = NO +#--------------------------------------------------------------------------- +# configuration options related to the Perl module output +#--------------------------------------------------------------------------- +GENERATE_PERLMOD = NO +PERLMOD_LATEX = NO +PERLMOD_PRETTY = YES +PERLMOD_MAKEVAR_PREFIX = +#--------------------------------------------------------------------------- +# Configuration options related to the preprocessor +#--------------------------------------------------------------------------- +ENABLE_PREPROCESSING = YES +MACRO_EXPANSION = NO +EXPAND_ONLY_PREDEF = NO +SEARCH_INCLUDES = YES +INCLUDE_PATH = +INCLUDE_FILE_PATTERNS = +PREDEFINED = +EXPAND_AS_DEFINED = +SKIP_FUNCTION_MACROS = YES +#--------------------------------------------------------------------------- +# Configuration::additions related to external references +#--------------------------------------------------------------------------- +TAGFILES = +GENERATE_TAGFILE = +ALLEXTERNALS = NO +EXTERNAL_GROUPS = YES +PERL_PATH = /usr/local/bin/perl +#--------------------------------------------------------------------------- +# Configuration options related to the dot tool +#--------------------------------------------------------------------------- +CLASS_DIAGRAMS = YES +MSCGEN_PATH = +HIDE_UNDOC_RELATIONS = YES +HAVE_DOT = NO +DOT_FONTNAME = FreeSans +DOT_FONTSIZE = 10 +DOT_FONTPATH = +CLASS_GRAPH = YES +COLLABORATION_GRAPH = YES +GROUP_GRAPHS = YES +UML_LOOK = NO +TEMPLATE_RELATIONS = NO +INCLUDE_GRAPH = YES +INCLUDED_BY_GRAPH = YES +CALL_GRAPH = NO +CALLER_GRAPH = NO +GRAPHICAL_HIERARCHY = YES +DIRECTORY_GRAPH = YES +DOT_IMAGE_FORMAT = png +DOT_PATH = +DOTFILE_DIRS = +DOT_GRAPH_MAX_NODES = 50 +MAX_DOT_GRAPH_DEPTH = 0 +DOT_TRANSPARENT = NO +DOT_MULTI_TARGETS = NO +GENERATE_LEGEND = YES +DOT_CLEANUP = YES diff --git a/sci-libs/libgeotiff/libgeotiff-1.4.0.ebuild b/sci-libs/libgeotiff/libgeotiff-1.4.0.ebuild new file mode 100644 index 000000000000..4b8a64006233 --- /dev/null +++ b/sci-libs/libgeotiff/libgeotiff-1.4.0.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools eutils + +MY_P=${P/_rc/RC} + +DESCRIPTION="Library for reading TIFF files with embedded tags for geographic information" +HOMEPAGE="http://geotiff.osgeo.org/" +SRC_URI="http://download.osgeo.org/geotiff/${PN}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~arm ~mips ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +IUSE="debug doc static-libs" + +RDEPEND=" + virtual/jpeg + >=media-libs/tiff-3.9.1:0 + sci-libs/proj + sys-libs/zlib" + +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +S=${WORKDIR}/${MY_P/RC*/} + +DOCS=( README ChangeLog ) + +src_prepare() { + epatch_user + sed -i \ + -e "s:-O3::g" \ + configure.ac || die + eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + --enable-debug=$(use debug && echo yes || echo no) \ + --with-jpeg="${EPREFIX}"/usr/ \ + --with-zip="${EPREFIX}"/usr/ + +} +src_compile() { + default + + if use doc; then + mkdir -p docs/api + cp "${FILESDIR}"/Doxyfile Doxyfile + doxygen -u Doxyfile || die "updating doxygen config failed" + doxygen Doxyfile || die "docs generation failed" + fi +} + +src_install() { + default + + use doc && dohtml docs/api/* + prune_libtool_files +} + +pkg_postinst() { + echo + ewarn "You should rebuild any packages built against ${PN} by running:" + ewarn "# revdep-rebuild" + ewarn "or using preserved-rebuild features of portage-2.2:" + ewarn "# emerge @preserved-rebuild" + echo +} diff --git a/sci-libs/libgeotiff/libgeotiff-1.4.1.ebuild b/sci-libs/libgeotiff/libgeotiff-1.4.1.ebuild new file mode 100644 index 000000000000..c46ac961cc8f --- /dev/null +++ b/sci-libs/libgeotiff/libgeotiff-1.4.1.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils + +MY_P=${P/_rc/RC} + +DESCRIPTION="Library for reading TIFF files with embedded tags for geographic information" +HOMEPAGE="http://geotiff.osgeo.org/" +SRC_URI="http://download.osgeo.org/geotiff/${PN}/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~arm64 ~ia64 ~mips ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" +IUSE="debug doc static-libs" + +RDEPEND=" + virtual/jpeg:= + >=media-libs/tiff-3.9.1:0 + sci-libs/proj + sys-libs/zlib" + +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +S=${WORKDIR}/${MY_P/RC*/} + +DOCS=( README ChangeLog ) + +src_prepare() { + epatch_user + sed -i \ + -e "s:-O3::g" \ + configure.ac || die + eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + --enable-debug=$(use debug && echo yes || echo no) \ + --with-jpeg="${EPREFIX}"/usr/ \ + --with-zip="${EPREFIX}"/usr/ + +} +src_compile() { + default + + if use doc; then + mkdir -p docs/api + cp "${FILESDIR}"/Doxyfile Doxyfile + doxygen -u Doxyfile || die "updating doxygen config failed" + doxygen Doxyfile || die "docs generation failed" + fi +} + +src_install() { + default + + use doc && dohtml docs/api/* + prune_libtool_files +} + +pkg_postinst() { + echo + ewarn "You should rebuild any packages built against ${PN} by running:" + ewarn "# revdep-rebuild" + ewarn "or using preserved-rebuild features of portage-2.2:" + ewarn "# emerge @preserved-rebuild" + echo +} diff --git a/sci-libs/libgeotiff/metadata.xml b/sci-libs/libgeotiff/metadata.xml new file mode 100644 index 000000000000..d78f80981828 --- /dev/null +++ b/sci-libs/libgeotiff/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-geosciences@gentoo.org</email> + <name>Gentoo Geosciences Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libghemical/Manifest b/sci-libs/libghemical/Manifest new file mode 100644 index 000000000000..1a36d6b7dc0a --- /dev/null +++ b/sci-libs/libghemical/Manifest @@ -0,0 +1,8 @@ +AUX 2.00-really-find-blas-and-lapack.patch 1317 SHA256 4d16fc804523fa24f0eb3fcbe33f3535d0265b6cc858f6291b5304806556d4ff SHA512 5d32b58c62de709ad746e2dfe1ece92ee8985257e95ae9789ea845b758e9ae64072fefe4a563271c5815bd117be175ee5e527c7d9feec2435ac46edfefdd2af6 WHIRLPOOL adffb8c0845d3ef627048c6f3887f5ebc289a759b102b5aaa1d1994eab6fe619740f7de07b48ddd31a2099f3bfc7ff4ee47a1feaecb2029bb0c97fecce431d7b +AUX libghemical-2.98-gl.patch 402 SHA256 f4f8a83120613e2efe95eaf3e57d1bea9a30cce91d19fa7d1105a066d459af72 SHA512 bf0fee685f2f10f467d92f86db3dea47879651335c6966757e69bf7bac1f9a6ee18bd22c9a61f01ca1babc5c7e14cfc3caba382af764fd1a418ee70e32e2b1a6 WHIRLPOOL a0c6e0d838ebf890574bbec0511f91fd962b964f43eb2d106ac4c6e7ce6be3cbf19036bdd3d8a32f338282ac0de832fbbd0c10c6889817986a949dd995efa0b5 +AUX libghemical-2.99.1-gl.patch 785 SHA256 45551c96af992c538c8bc58f7e8d00aa075d7b1007e0e59007d1df61801fb4a4 SHA512 232bcbbcbb4512f9436ad064b7af08decb0bb46955f6a1db1f3830834b73e13db91426d3edea005e1542a0dcad0f580f449a96c59d6a12481360163f8347ba56 WHIRLPOOL 6d327bd0231d9b5dfd75047b156428eee196943755f608c39149f43614c47f2e13d288a02c0a7fd020aa5d6df187c9836a39f7f0a96cb418040b84e363e7f92e +DIST libghemical-3.0.0.tar.gz 787947 SHA256 db8c3add0aa1f94c21016d60fa3f66fb194e56b8e9fceaa3860c603700efc3ac SHA512 71531e7bd72a7fa063dd35536a346f15e3c0fd0284112fa2f304580204b93552bd0c9a426cee22044b5dd1662e34e5d191d20af938e474561fe55f2394e7519e WHIRLPOOL fae8e49a2136460013296e0a23a56513a36941ece73013a1a21b530abdfbabfba2b5098457b70a9cd1694759995ffeae01250d05034e0c1186fd2f47af52af08 +EBUILD libghemical-3.0.0.ebuild 800 SHA256 fd2cebdbe0da745f7d0d63c37efc6b386159f826d9d5e8d76c82f02db1452db0 SHA512 bd1cce3e5dd4f9b4c0e3225e5406da281426381a6e6924a8e6044d4735e1e200d2b4bae48dd14aef3688f53d5e4ffbf58898ac255ca81e46fa3a8c5c86272844 WHIRLPOOL 6c8704254af8618d86ec2ec26f69d30ea307c55d9fe83f7307501f262c4fbeff2e17c25c654a93c0d75872949c62894dac08104c385e9d81dab113877138aa77 +MISC ChangeLog 3146 SHA256 f825e26541fcba9744d429175cf034982b728f894539e063b5652571befce469 SHA512 b27a577086aae9b70110b591b9b721ca02f5ea50dcf18f5efec1e75db7d83a12e9ba8f0f6da7faa8e5a745efb8762cab2448f6224a6c861f2854cff4a22b93c4 WHIRLPOOL 0c409dc12ccc99c905e78217434a4f4aff93783f068dec2be831b5eaacc7ca8a38d6795f5350283c069c8eac393cc65337c4ed8430566073d6d04367787d8206 +MISC ChangeLog-2015 4573 SHA256 27ecb0f40f72d5c04ba7ed220fd40595b74c8ba86be0c9aa25a52fffa8df24e6 SHA512 91b8656dadfbd69fc449cbfff280fb2e4ccd2eadb5408c1a429a36c77c0b944f9250206bb18380eaa4f90530b7b22d1087113cf5113f09bf4dc4ed6b408c9f3e WHIRLPOOL dd3bb16eb4d96f5cd9bb0bbe94a8883472bb21595090ed6199c22f0a81b0a50d0fdb7cff201d82fb4f012598e0c843163ac5ced39ce76c587f5d56414e971123 +MISC metadata.xml 883 SHA256 ef15b4003987162ab6275fdd225c8226cdbb03d3b76c82fc9055a63ef264b869 SHA512 d42e03007ffe7714d44a4729c05096a840f9940ec6a82535967b19279b3c95d78b2373507786c8b6b4a702ceaa4ff0732481e56be64cfc916aeca7375ffc35b0 WHIRLPOOL 1ff8de5ff6d4952bbbc960ad3fffa531d415c873b23a1a46249e7d800cf4c8eee536633c00ef7546bb6766a8a25518dc023a2fef0420fabdff2ee137d36cf37d diff --git a/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch b/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch new file mode 100644 index 000000000000..bef730abbe4c --- /dev/null +++ b/sci-libs/libghemical/files/2.00-really-find-blas-and-lapack.patch @@ -0,0 +1,24 @@ +diff -urN libghemical-2.00.orig/configure.ac libghemical-2.00/configure.ac +--- libghemical-2.00.orig/configure.ac 2006-05-12 23:31:06.000000000 -0700 ++++ libghemical-2.00/configure.ac 2006-05-12 23:54:20.000000000 -0700 +@@ -69,8 +69,18 @@ + AC_CHECK_LIB([m], [acos]) + + if test $WITH_MPQC = yes; then +- AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support])) +- AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support])) ++ AC_CHECK_LIB([blas], [dgemm_], HAVE_BLAS="yes", , -lpthread) ++ AC_CHECK_LIB([blas], [dgemm], HAVE_BLAS="yes", , -lpthread) ++ AC_CHECK_LIB([blas], [dgemm__], HAVE_BLAS="yes", , -lpthread) ++ if test "x${HAVE_BLAS}" = "x"; then ++ AC_MSG_ERROR([Cannot find blas library needed for MPQC support]) ++ fi ++ AC_CHECK_LIB([lapack], [cheev_], HAVE_LAPACK="yes", , -lpthread) ++ AC_CHECK_LIB([lapack], [cheev], HAVE_LAPACK="yes", , -lpthread) ++ AC_CHECK_LIB([lapack], [cheev__], HAVE_LAPACK="yes", , -lpthread) ++ if test "x${HAVE_LAPACK}" = "x"; then ++ AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]) ++ fi + AM_PATH_SC(1.2.5, HAVE_MPQC="yes", HAVE_MPQC="no") + if test "${HAVE_MPQC}" = "yes"; then + AC_DEFINE([ENABLE_MPQC], [], [Define if you are building a version that interfaces directly with MPQC]) diff --git a/sci-libs/libghemical/files/libghemical-2.98-gl.patch b/sci-libs/libghemical/files/libghemical-2.98-gl.patch new file mode 100644 index 000000000000..8cea8aab636e --- /dev/null +++ b/sci-libs/libghemical/files/libghemical-2.98-gl.patch @@ -0,0 +1,13 @@ +diff --git a/src/typedef.h b/src/typedef.h +index 8d2efcc..1e304e8 100644 +--- a/src/typedef.h ++++ b/src/typedef.h +@@ -27,7 +27,7 @@ + + // comment this out if you have no GL/gl.h available... + +-#define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? ++// #define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? + + // added by Robert Williams for Compaq cxx, alpha 11/28/01 + diff --git a/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch b/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch new file mode 100644 index 000000000000..ad46079e945d --- /dev/null +++ b/sci-libs/libghemical/files/libghemical-2.99.1-gl.patch @@ -0,0 +1,26 @@ +diff --git a/configure.ac b/configure.ac +index b01e5fa..943890b 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -151,7 +151,7 @@ fi + # Checks for header files. + # ^^^^^^^^^^^^^^^^^^^^^^^^ + +-AC_CHECK_HEADERS([GL/gl.h]) ++# AC_CHECK_HEADERS([GL/gl.h]) + + # Checks for typedefs, structures, and compiler characteristics. + # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +diff --git a/src/typedef.h b/src/typedef.h +index 8d2efcc..0ba62fe 100644 +--- a/src/typedef.h ++++ b/src/typedef.h +@@ -27,7 +27,7 @@ + + // comment this out if you have no GL/gl.h available... + +-#define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? ++// #define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? + + // added by Robert Williams for Compaq cxx, alpha 11/28/01 + diff --git a/sci-libs/libghemical/libghemical-3.0.0.ebuild b/sci-libs/libghemical/libghemical-3.0.0.ebuild new file mode 100644 index 000000000000..6a3c64969ac5 --- /dev/null +++ b/sci-libs/libghemical/libghemical-3.0.0.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Chemical quantum mechanics and molecular mechanics" +HOMEPAGE="http://bioinformatics.org/ghemical/" +SRC_URI="http://www.bioinformatics.org/ghemical/download/current/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ppc x86" +IUSE="mopac7 mpqc static-libs" + +RDEPEND=" + mopac7? ( >=sci-chemistry/mopac7-1.13-r1 ) + mpqc? ( + >=sci-chemistry/mpqc-2.3.1-r1 + virtual/blas + virtual/lapack + )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${PN}-2.98-gl.patch ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable mopac7) \ + $(use_enable mpqc) \ + $(use_enable static-libs static) +} diff --git a/sci-libs/libghemical/metadata.xml b/sci-libs/libghemical/metadata.xml new file mode 100644 index 000000000000..82a6530d10c8 --- /dev/null +++ b/sci-libs/libghemical/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> +Ghemical supports both quantum-mechanics (semi-empirical and ab initio) models +and molecular mechanics models (there is an experimental Tripos 5.2-like force +field for organic molecules). Also a tool for reduced protein models is +included. Geometry optimization, molecular dynamics and a large set of +visualization tools are currently available. +</longdescription> + <use> + <flag name="mopac7">Use <pkg>sci-chemistry/mopac7</pkg> for semi-empirical + calculations</flag> + <flag name="mpqc">Use <pkg>sci-chemistry/mpqc</pkg> for quantum-mechanical + calculations</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/libh2o/Manifest b/sci-libs/libh2o/Manifest new file mode 100644 index 000000000000..a1e16b103c2a --- /dev/null +++ b/sci-libs/libh2o/Manifest @@ -0,0 +1,6 @@ +DIST libh2o-0.2.1.tar.bz2 290418 SHA256 7a1d0fa5800b8dbc45ac325d4c962b81033359c006eee68c18148bc7900651b7 SHA512 e2fb14171aa401e85edcef6be36bfd2af31a7da2db03bc77c41fd58962a8e2616bbbd43adb268c262b848d044c9d33016c504ce770f5cfe0d585d05dacc63e2a WHIRLPOOL 17c6294f4bf0fa3556ceb7014a13f9df8b39e032b88f02bb09626ea29619c4c09232e359c57c8888d4ee621b4aee2eaee6995af8c3cebef10574af062ccf9570 +EBUILD libh2o-0.2.1.ebuild 528 SHA256 9cc68f133fdafd0d4c8782502446662e141abeead29858831059642bb40e7ea5 SHA512 9f87dbd6f34e2a0a9e2a22ca9f720b0e001584cdc9b388f53a8cda45cdae488993b03fc426bc999bdf01e7c25f95fd46ef68537fd2234df8f18c0965c85277ae WHIRLPOOL 8dcc1912215047384ff12308e7445832e60deb976b91d41757039f55437341d4eb6b9ea46d6ac5f0b8fc41cb3e9479642d36bc678b8639a0dc3470f7c555698a +EBUILD libh2o-9999.ebuild 677 SHA256 4681805577f840efc65b5aca406300d30e5fab5b24fd2c738b5b6683e49994bd SHA512 82685a513e2a3c7e2799bbf3858942997d09bccbc347971227e957e11e8f106d706e3bb224925c5dc8839d3e6267ba548235e2031b2032bd4b6b8310446c3a48 WHIRLPOOL 8d1523fda31f77dfc3035f3f8e9416976f8759b4e5f69227718cc166e5f115028c152b56a41b6d40c7c9379e3f5b10f3b17fc0cae5c90680fe759e485aee2f1b +MISC ChangeLog 2362 SHA256 bb00bab8137a8bc973e6c4893d17cab7e691a38b8414e40dff9b580ad7e0761a SHA512 5e38262399970a21fd3b1f57686a142ffb2daa7d3e1d5440af1e4798a33dfbef0e3ace2b4573763c0ec1068fd157db23fe3db2c66b1744b161db7ec96604330a WHIRLPOOL 0c4ae13f3462462ed93b1ac664245b05471db8ed9c59ff10a490f0062d367e9c272b2a390d6705fe653fc1ad34ff827369ac742e639dbacec58947256e1487dc +MISC ChangeLog-2015 1393 SHA256 6b6dc7d7daae29b7c57e62d9911d9387f2bcef3eedb57b4ed015e55afdc0d154 SHA512 a292814410c6225e97d520dba0b779b3d8d202d1a0f8c471c7df3ba6fcf078cc4537fb9200c02baf80917eeea18c8c1a90faa4c1a4bb36ac4fd4ca5fce11694b WHIRLPOOL 33445ec55cc7e7fb71914da1aa0ada52ecd29ea6b448abdbfe432c411e6d25bf7f9a949fc8f4c512149c3c6060921a87e9da881af28eabedfe2d17f359879349 +MISC metadata.xml 507 SHA256 76ed8501de92f1624ae2c11237bd776b51c221e47372535f9175e1c345aebf09 SHA512 7f7f002eaf1d743555dce80e0c29cc3fb598e784ed76fc3a6e2d807edc1a3858489002cebe07613070d6fd0f4a3293b7e42711cd8c6efe3d5c51a2fb4b0ab427 WHIRLPOOL 343e8f543a936de7dd8ee08ca41a2d9ea11d07eb3f371122828d2e6e40fb803fb15b4759b1da0ca442a26e37c1163d2030a3ea098b33ea311c9cabfd6d316c46 diff --git a/sci-libs/libh2o/libh2o-0.2.1.ebuild b/sci-libs/libh2o/libh2o-0.2.1.ebuild new file mode 100644 index 000000000000..03e9cb7d25c1 --- /dev/null +++ b/sci-libs/libh2o/libh2o-0.2.1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools-utils + +DESCRIPTION="Library of routines for IF97 water & steam properties" +HOMEPAGE="https://bitbucket.org/mgorny/libh2o/" +SRC_URI="https://www.bitbucket.org/mgorny/${PN}/downloads/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug static-libs" + +DEPEND="virtual/pkgconfig" + +src_configure() { + local myeconfargs=( + $(use_enable debug) + ) + + autotools-utils_src_configure +} diff --git a/sci-libs/libh2o/libh2o-9999.ebuild b/sci-libs/libh2o/libh2o-9999.ebuild new file mode 100644 index 000000000000..2413fb4aaf6a --- /dev/null +++ b/sci-libs/libh2o/libh2o-9999.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +#if LIVE +AUTOTOOLS_AUTORECONF=yes +EGIT_REPO_URI="https://bitbucket.org/mgorny/${PN}.git" + +inherit git-r3 +#endif + +inherit autotools-utils + +DESCRIPTION="Library of routines for IF97 water & steam properties" +HOMEPAGE="https://bitbucket.org/mgorny/libh2o/" +SRC_URI="https://www.bitbucket.org/mgorny/${PN}/downloads/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug static-libs" + +DEPEND="virtual/pkgconfig" + +#if LIVE +KEYWORDS= +SRC_URI= +#endif + +src_configure() { + local myeconfargs=( + $(use_enable debug) + ) + + autotools-utils_src_configure +} diff --git a/sci-libs/libh2o/metadata.xml b/sci-libs/libh2o/metadata.xml new file mode 100644 index 000000000000..3b33b5ad848d --- /dev/null +++ b/sci-libs/libh2o/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mgorny@gentoo.org</email> + <name>Michał Górny</name> + </maintainer> + <upstream> + <maintainer status="active"> + <email>mgorny@gentoo.org</email> + <name>Michał Górny</name> + </maintainer> + <bugs-to>https://bitbucket.org/mgorny/libh2o/issues/</bugs-to> + <remote-id type="bitbucket">mgorny/libh2o</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/libh2oxx/Manifest b/sci-libs/libh2oxx/Manifest new file mode 100644 index 000000000000..1f62c342eb7a --- /dev/null +++ b/sci-libs/libh2oxx/Manifest @@ -0,0 +1,6 @@ +DIST libh2oxx-0.2.tar.bz2 266320 SHA256 deb3923f352bb6d80d908d6117a1538f0d8125001f21b2a23d5933f669e0dea5 SHA512 37b5eb713eed9a41f001add0ed3415fb4e1d6a19917de7fe36017f9a8b102394ac86b47fa845b18d7c4c63ad94e270f28e0883c9e9503c1952fdefbfdb6cc3a3 WHIRLPOOL d94d7981887d8671b367e85411a817d43861f975015cf938fd7acaa5f9d17bb6245fbf30a8161dfd0a253fdf907cc5487cc245c2196ead93863ee5a9a7703f29 +EBUILD libh2oxx-0.2.ebuild 525 SHA256 df1c230d2aad26456ebe802c98660af1329907b5ff33d696ad4c6f2f639f4adf SHA512 30dd08bb7ac538a86c653b6150f0c4f5e8e2510016fec6d39dac77cb2b2046972e4436d25f3ddda30865b1eb69b7595e640291b124a5cececcb60040bf7a3e93 WHIRLPOOL fd762049061a6f114a7c394dcff36d2b8a454c172f00897afb92003942810ded4d26cd448f411c5c867de717e83c83159144ccd7fb93c807c4bf9f4f50d4fc1b +EBUILD libh2oxx-9999.ebuild 677 SHA256 56bd593b0ab76fc873b226567b846002d9d22c61d20420cfac946225e20401cb SHA512 50c39a3ca128b6ecfe7e138721f44de46ced4151655e68f7d0275e83780ce58b25002c4fb7cf5954ccf2c6bae99ef201ac20c6b8944593a6e333da725b84fd0e WHIRLPOOL 7c542dbc293c3941dd82fd0a3ff458358afea46b8e1a556ae008e1e1cb42f7fe39ebea797138ea470e475a92ea7d99938a98155063e699c495962001a40e9ca6 +MISC ChangeLog 2370 SHA256 bfde5a5df540241acbdcf907bd801b97c4a847a4d0b6f6b917a82dcf6abae9d8 SHA512 db92c0ba44ecf1d43a91ed62d1a090d94322abb4bcf63d816f5f61cdc3c209b8b0f52a773f2845c255e40f65ef8342d7fef9f603c2b7c0039280cd37a01919f7 WHIRLPOOL 8190339a924567d671a86cb48dd0a9fc6fadc4f01935ba446c65c0ef744419b3af9baeb6561274d1f5927f4dd188366d4dfb407b56649e4e8a57db4afa341649 +MISC ChangeLog-2015 1149 SHA256 5bb56ca62f0fa8d455fe401e65f623a76b23fb01174d7ec9d207fafccbd63131 SHA512 1edbf894c6f94b9a9ad89bd10b21d5149617d29e8ac773cb2266a3d6f414934d9d69a890cf83c8ba781b7301155166f59d50680587077c44e4e06c7003d66f5c WHIRLPOOL b9a7e3bfb9b3024d5aecc7261e0d69742a2a7c7379dfb802543768f13b639beb3157590fb8910deb8a681a715ecb7fa29e81fc71bbaeb6794c1aa03c8dba68a8 +MISC metadata.xml 511 SHA256 dfe94938a577c8dd5f9dd5745278a50add3993a008ca0637f0404a508ba75267 SHA512 3a49f70371effa3cc1935b84e5b4528a4ac106054f713516516c135270323d4fc83cda1b9d50d9c97a3c163d7cedfe7f7cc6711cf7bd8ecc0b5597fb0c32c2df WHIRLPOOL f5e6ddc0fc1ece1ed6b9f3a72420c0b1063396056de57057b282e378c94c5b57890328f2d7140f4965820243b14000ed2232475ee4f79d0c34ce09a968523b73 diff --git a/sci-libs/libh2oxx/libh2oxx-0.2.ebuild b/sci-libs/libh2oxx/libh2oxx-0.2.ebuild new file mode 100644 index 000000000000..5b2383ae7c42 --- /dev/null +++ b/sci-libs/libh2oxx/libh2oxx-0.2.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools-utils + +DESCRIPTION="C++ bindings for libh2o" +HOMEPAGE="https://bitbucket.org/mgorny/libh2oxx/" +SRC_URI="https://www.bitbucket.org/mgorny/${PN}/downloads/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug static-libs" + +RDEPEND=">=sci-libs/libh2o-0.2" +DEPEND="${RDEPEND}" + +src_configure() { + local myeconfargs=( + $(use_enable debug) + ) + + autotools-utils_src_configure +} diff --git a/sci-libs/libh2oxx/libh2oxx-9999.ebuild b/sci-libs/libh2oxx/libh2oxx-9999.ebuild new file mode 100644 index 000000000000..d1de9347c06a --- /dev/null +++ b/sci-libs/libh2oxx/libh2oxx-9999.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +#if LIVE +AUTOTOOLS_AUTORECONF=yes +EGIT_REPO_URI="https://bitbucket.org/mgorny/${PN}.git" + +inherit git-r3 +#endif + +inherit autotools-utils + +DESCRIPTION="C++ bindings for libh2o" +HOMEPAGE="https://bitbucket.org/mgorny/libh2oxx/" +SRC_URI="https://www.bitbucket.org/mgorny/${PN}/downloads/${P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug static-libs" + +RDEPEND=">=sci-libs/libh2o-0.2:0=" +DEPEND="${RDEPEND}" + +#if LIVE +KEYWORDS= +SRC_URI= +#endif + +src_configure() { + local myeconfargs=( + $(use_enable debug) + ) + + autotools-utils_src_configure +} diff --git a/sci-libs/libh2oxx/metadata.xml b/sci-libs/libh2oxx/metadata.xml new file mode 100644 index 000000000000..34c84fc28149 --- /dev/null +++ b/sci-libs/libh2oxx/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mgorny@gentoo.org</email> + <name>Michał Górny</name> + </maintainer> + <upstream> + <maintainer status="active"> + <email>mgorny@gentoo.org</email> + <name>Michał Górny</name> + </maintainer> + <bugs-to>https://bitbucket.org/mgorny/libh2oxx/issues/</bugs-to> + <remote-id type="bitbucket">mgorny/libh2oxx</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/libint/Manifest b/sci-libs/libint/Manifest new file mode 100644 index 000000000000..ec3ebe8e6c5a --- /dev/null +++ b/sci-libs/libint/Manifest @@ -0,0 +1,8 @@ +AUX libint-1.1.6-as-needed.patch 2733 SHA256 d3de3c644d55ae49470491cd1d9e86a9d0b0d8903bc4a2fb9d94a3be3f1aa518 SHA512 69281b26c69f5cae1e33f53c58b8a7b383ae83fa8309db03a505e6df3ca018acdf5e4998b42c9d4d1cfda2eaaf36903c1a39211664358506a90cde7e1012ee8d WHIRLPOOL 271d46cc5f9a292ab0f3fc675f3c86a8f6abe833a0f0cca038e44dfb6ba6c3ccab32b755d68fdd4c4fe7cc28df216025a2b1cb3462160ba8012572c3c8b04b56 +DIST libint-1.1.6.tar.gz 256404 SHA256 f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6 SHA512 cb39d73e89431c324e32d4a71593fe913c7ae2132677d4600e63ce1ed99e8e431758f0aa3d130991da841e98a1064fa931eb0e82dbe80af4c0ece10ee3a4f2d7 WHIRLPOOL ed6e0f850df067da115cdea4e9cff2545ea6ffe4e7b9dea28ef3232adec12d23c6b6709e8a058f78b9764890134440f4869a770b3b4e4934b4571562848fdb6a +DIST libint-2.0.5.tar.gz 3209528 SHA256 f64298bc6513771ffea476a250110b3f488c01d669e05dd309fe4ba6114c5f95 SHA512 d7717a6337b73645dcb77d3c0731df17884b4c662b0d52061b7b80ac0ebd9de344e6c301294f714db09e7b6e3dff5b4b6958ef06122303df52d0ebb6a011cf24 WHIRLPOOL 896269589d6c95f83b5dc0517491d2b07bf60103fb0a11c131681acaa4a83f494ab436647ae7989a1a9e944b0fd59b03d530ab025efbba73efc75e9f1f720653 +EBUILD libint-1.1.6.ebuild 955 SHA256 e25d0e6feb079be67d5e9ba9b9d6e899abf0148e7fd939cc9da0af8a932488d9 SHA512 53f1b0ffc316cb021f05ca6432c24ea8c316bcb87f02149a7a0f8b6401c845d13a5f20b4fa954eee0c25c32b5325bc1f01de8ac183492c9b6f36994c7fddc491 WHIRLPOOL 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7ae90753f1d1f02cf1ed48f4227f309bf2c6c809cb99d4525334026c9d3087d9d1086c2246c942131c6e73143cee8a543a1068c9a223d48be2bdc3d1d334131a WHIRLPOOL 2f051c3ca660133e695153520ab5c644dbdd5efb2957fc90f446de0b9575c24d8059bb10043c86986cab01ad35c0dec9da812241597a12247b04a38fc7419806 +MISC metadata.xml 612 SHA256 8b2436706fca3f92de930e4e98e0c7e89d6e1259e678aa8898b74b6bda1b1fcd SHA512 db9172c0e887d45f42914159eae83c0f11b40fbafac31395c782ff959cdccad8a62a8d468cec66d6e362cd8ea09aa3b05057d19fff8a1f94b9bd472be97d04b0 WHIRLPOOL 29138229f720b0efabcd3c867d0948975e6d272013868ec72797a85c2ba805989dc776d8ce07481a40b0875012aa09a9b4bde1594c48c02b70ab4197f0bcf65e diff --git a/sci-libs/libint/files/libint-1.1.6-as-needed.patch b/sci-libs/libint/files/libint-1.1.6-as-needed.patch new file mode 100644 index 000000000000..c48505314b39 --- /dev/null +++ b/sci-libs/libint/files/libint-1.1.6-as-needed.patch @@ -0,0 +1,77 @@ + configure.ac | 3 +-- + src/bin/MakeRules.in | 2 +- + src/lib/libderiv/Makefile.library | 2 +- + src/lib/libint/Makefile.library | 2 +- + src/lib/libr12/Makefile.library | 2 +- + 5 files changed, 5 insertions(+), 6 deletions(-) + +diff --git a/configure.ac b/configure.ac +index dc86e88..8cc3aac 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -317,12 +317,11 @@ LIBS=$withval + echo Using extra libraries: $withval + ) + +-LDFLAGS= + LIBDIRS= + AC_ARG_WITH(libdirs, + [ --with-libdirs Specifies library directories (-Ldir1 -Ldir2).], + LIBDIRS=$withval +-LDFLAGS=$withval ++LDFLAGS="$LDFLAGS $withval" + echo Using extra library directories: $withval + ) + +diff --git a/src/bin/MakeRules.in b/src/bin/MakeRules.in +index 5b90607..8ea5005 100644 +--- a/src/bin/MakeRules.in ++++ b/src/bin/MakeRules.in +@@ -3,7 +3,7 @@ HAVE_MAKERULES = yes + + BINOBJ = $(BUILD_CSRC:%.c=%.$(OBJSUF)) $(BUILD_CXXSRC:%.cc=%.$(OBJSUF)) + $(BUILD_BINARY): $(BINOBJ) +- $(LD) $^ $(LDFLAGS) $(SYSLIBS) -o $@ ++ $(LD) $(LDFLAGS) $^ $(SYSLIBS) -o $@ + + .PHONY: install install_inc install_target uninstall clean oclean distclean targetclean realclean + install:: +diff --git a/src/lib/libderiv/Makefile.library b/src/lib/libderiv/Makefile.library +index ee152ef..8debfe8 100644 +--- a/src/lib/libderiv/Makefile.library ++++ b/src/lib/libderiv/Makefile.library +@@ -23,7 +23,7 @@ $(TOPDIR)/lib/$(NAME).a: $(LIBOBJ) + + # this is how shared library is made + $(TOPDIR)/lib/$(NAME).la: $(LIBOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS) + + $(TOPDIR)/include/$(NAME)/$(NAME).h: $(NAME).h + $(INSTALL) $(INSTALLDIROPT) $(TOPDIR)/include/$(NAME) +diff --git a/src/lib/libint/Makefile.library b/src/lib/libint/Makefile.library +index 23e2918..01c4225 100644 +--- a/src/lib/libint/Makefile.library ++++ b/src/lib/libint/Makefile.library +@@ -41,7 +41,7 @@ $(TOPDIR)/lib/$(NAME).a: $(LIBOBJ) + + # this is how shared library is made + $(TOPDIR)/lib/$(NAME).la: $(LIBOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS) + + $(TOPDIR)/include/$(NAME)/$(NAME).h: $(NAME).h + $(INSTALL) $(INSTALLDIROPT) $(TOPDIR)/include/$(NAME) +diff --git a/src/lib/libr12/Makefile.library b/src/lib/libr12/Makefile.library +index 1510807..26d47a4 100644 +--- a/src/lib/libr12/Makefile.library ++++ b/src/lib/libr12/Makefile.library +@@ -47,7 +47,7 @@ $(TOPDIR)/lib/$(NAME).a: $(LIBOBJ) + + # this is how shared library is made + $(TOPDIR)/lib/$(NAME).la: $(LIBOBJ) +- $(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS) ++ $(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS) + + $(TOPDIR)/include/$(NAME)/$(NAME).h: $(NAME).h + $(INSTALL) $(INSTALLDIROPT) $(TOPDIR)/include/$(NAME) diff --git a/sci-libs/libint/libint-1.1.6.ebuild b/sci-libs/libint/libint-1.1.6.ebuild new file mode 100644 index 000000000000..760d266a7811 --- /dev/null +++ b/sci-libs/libint/libint-1.1.6.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fortran-2 toolchain-funcs versionator + +MY_PV="$(replace_all_version_separators -)" + +DESCRIPTION="Matrix elements (integrals) evaluation over Cartesian Gaussian functions" +HOMEPAGE="https://github.com/evaleev/libint" +SRC_URI="https://github.com/evaleev/libint/archive/release-${MY_PV}.tar.gz -> ${P}.tar.gz" + +SLOT="1" +LICENSE="GPL-2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +S="${WORKDIR}/${PN}-release-${MY_PV}" + +PATCHES=( "${FILESDIR}"/${P}-as-needed.patch ) + +src_prepare() { + mv configure.{in,ac} || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-deriv + --enable-r12 + --with-cc=$(tc-getCC) + --with-cxx=$(tc-getCXX) + --with-cc-optflags="${CFLAGS}" + --with-cxx-optflags="${CXXFLAGS}" + ) + autotools-utils_src_configure +} diff --git a/sci-libs/libint/libint-2.0.5.ebuild b/sci-libs/libint/libint-2.0.5.ebuild new file mode 100644 index 000000000000..42ac3cfeddf4 --- /dev/null +++ b/sci-libs/libint/libint-2.0.5.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fortran-2 toolchain-funcs versionator + +MY_PV="$(replace_all_version_separators -)" + +DESCRIPTION="Matrix elements (integrals) evaluation over Cartesian Gaussian functions" +HOMEPAGE="https://github.com/evaleev/libint" +SRC_URI="https://github.com/evaleev/libint/archive/release-2-0-5.tar.gz -> ${P}.tar.gz" + +SLOT="2" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs doc" + +S="${WORKDIR}/${PN}-release-${MY_PV}" + +DEPEND=" + dev-libs/boost + dev-libs/gmp[cxx] + doc? ( + dev-texlive/texlive-latex + dev-tex/latex2html + )" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_configure() { + local myeconfargs=( + --with-cxx=$(tc-getCXX) + --with-cxx-optflags="${CXXFLAGS}" + --with-cxxgen-optflags="${CXXFLAGS}" + --with-cxxdepend=$(tc-getCXX) + --with-ranlib=$(tc-getRANLIB) + --with-ar=$(tc-getAR) + --with-ld=$(tc-getLD) + ) + autotools-utils_src_configure +} + +src_compile() { + emake LDFLAGS="${LDFLAGS}" + + use doc && emake html pdf +} + +src_install() { + einstall + + if use doc; then + DOCS=( doc/progman/progman.pdf ) + HTML_DOCS=( doc/progman/progman/*.{html,png,css} ) + einstalldocs + fi +} diff --git a/sci-libs/libint/metadata.xml b/sci-libs/libint/metadata.xml new file mode 100644 index 000000000000..c6610a75fe01 --- /dev/null +++ b/sci-libs/libint/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + libint is two things: + 1. a library of C/C++ functions for efficient evaluation of several + kinds of two-body molecular integrals over Gaussian functions; + 2. the optimizing compiler that generates a Libint library. +</longdescription> + <upstream> + <remote-id type="github">evaleev/libint</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/libmems/Manifest b/sci-libs/libmems/Manifest new file mode 100644 index 000000000000..087631c7c42a --- /dev/null +++ b/sci-libs/libmems/Manifest @@ -0,0 +1,13 @@ +AUX libmems-1.6_p1-boost-1.62-type-traits.patch 537 SHA256 877172cef69d53f5ee3c75f3b8492cc77f0c5da96036dcf28e19bab21cba9a4e SHA512 6f3cd95004fb5a8a8f9649593029ed313b9dde368a8f9c72fed8374ca913303442f6e47519a3163b6a05b4306be888dde1201f51ffb1b244bdd7eebbf5fb2f33 WHIRLPOOL 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9344a745f808f2ab5e36011c545441efecf734da6d1ea57d0b7f3187120d9d1d6e3d9b97aa0136781bc6d1cf389ccb17771db064bf68b5470c61c71f55b1b9ad +AUX libmems-1.6_p1-gcc-4.7.patch 2220 SHA256 624b3e6553075c512540cfae3d4fbaadcc10bcba3bc61d38e288512f8ea8c715 SHA512 685c24779b00c18b08b2d548d03c2412d502dcacc0e14a64ab44c14406293265fb96a33041a7b13d96132cf6372bf8e2a7a0402606055084c1fb37d92dbfa77b WHIRLPOOL 84d46b9d43deec49e18b9c95072efbd19c1f375ed1b76f3c3fe8b89dee808640f56d9dee5ba1f5babd54087d88bbc45f65aa111553dc1bd689df1a9157a71edd +DIST libmems-1.6_p1.tar.xz 226628 SHA256 c692d7d42378e7264d0a39674d1a6072183ee4c073ad90858153986b6a8b4848 SHA512 c6336f69b767bba010617deb2de9bb8fbbbaf516de3b1d293b062c76c6a763166080badd730938c6d849602d64a968edb6d4622b5d3e7ea7a6d8bc38164d3d73 WHIRLPOOL bc216dfb0c24c13b7b770da00100730e0e9b350c7bb6b312a480a83b51bc8c212e6ed73f08a88a7d262da8d4ed9a4c788883cbcfa3f2b2cdc362888e85b7f66a +EBUILD libmems-1.6_p1-r3.ebuild 1082 SHA256 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b/sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch new file mode 100644 index 000000000000..609d0de0c478 --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-boost-1.62-type-traits.patch @@ -0,0 +1,15 @@ +Shuffle around Boost type_traits, which otherwise causes issues with boost 1.62. +See also: https://bugs.gentoo.org/show_bug.cgi?id=595986 + +--- a/libMems/AbstractMatch.h ++++ b/libMems/AbstractMatch.h +@@ -16,8 +16,7 @@ + #include "libGenome/gnClone.h"
+ #include <vector>
+ #include <algorithm>
+-#include <boost/type_traits/remove_pointer.hpp>
+-#include <boost/type_traits/add_pointer.hpp>
++#include <boost/type_traits.hpp>
+ #include <boost/dynamic_bitset.hpp>
+ #include <libMems/SlotAllocator.h>
+ #include <libMems/configuration.h>
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-boost.patch b/sci-libs/libmems/files/libmems-1.6_p1-boost.patch new file mode 100644 index 000000000000..4f0c775a6d9c --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-boost.patch @@ -0,0 +1,120 @@ + libMems/Backbone.cpp | 2 +- + libMems/Files.h | 64 +++++++++++++++++++++--------------------- + libMems/ProgressiveAligner.cpp | 2 +- + 3 files changed, 34 insertions(+), 34 deletions(-) + +diff --git a/libMems/Backbone.cpp b/libMems/Backbone.cpp +index 86698a9..0025cd8 100644 +--- a/libMems/Backbone.cpp ++++ b/libMems/Backbone.cpp +@@ -15,7 +15,7 @@ + #include "libMems/Islands.h"
+ #include "libMems/CompactGappedAlignment.h"
+
+-#include <boost/property_map.hpp>
++#include <boost/property_map/property_map.hpp>
+ #include <boost/graph/graph_traits.hpp>
+ #include <boost/graph/adjacency_list.hpp>
+ #include <boost/graph/topological_sort.hpp>
+diff --git a/libMems/Files.h b/libMems/Files.h +index 8d6e9be..8191065 100644 +--- a/libMems/Files.h ++++ b/libMems/Files.h +@@ -22,44 +22,44 @@ + + #include "boost/filesystem/operations.hpp" + #include "boost/filesystem/exception.hpp" +-#include "boost/algorithm/string.hpp"
++#include "boost/algorithm/string.hpp" + #include <string> + #include <sstream> + #include <iostream> + #include <iomanip> + + +-/**
+- * Register a file name to be deleted before the process exits
+- * When passed an empty string, it does not add to the list of files to delete
+- * @param fname The name of a file to delete, empty strings are ignored
+- * @return A vector of file names registered for deletion
+- */
+-std::vector< std::string >& registerFileToDelete( std::string fname = "" );
+-
+-inline
+-std::vector< std::string >& registerFileToDelete( std::string fname ) {
+- // since this vector is needed when atexit() is called we allocate it
+- // on the heap so its destructor won't get called
+- static std::vector< std::string >* files = new std::vector< std::string >();
+-#pragma omp critical
+-{
+- if( fname != "" )
+- files->push_back( fname );
+-}
+- return *files;
+-}
++/** ++ * Register a file name to be deleted before the process exits ++ * When passed an empty string, it does not add to the list of files to delete ++ * @param fname The name of a file to delete, empty strings are ignored ++ * @return A vector of file names registered for deletion ++ */ ++std::vector< std::string >& registerFileToDelete( std::string fname = "" ); + +-void deleteRegisteredFiles();
+-inline
+-void deleteRegisteredFiles() {
+- // don't be a slob, clean up after yourself:
+- // delete any files that are laying around
+- std::vector< std::string >& del_files = registerFileToDelete();
+- for( int fileI = 0; fileI < del_files.size(); fileI++ )
+- boost::filesystem::remove( del_files[ fileI ] );
+- del_files.clear(); // clear the deleted files from the list
+-}
++inline ++std::vector< std::string >& registerFileToDelete( std::string fname ) { ++ // since this vector is needed when atexit() is called we allocate it ++ // on the heap so its destructor won't get called ++ static std::vector< std::string >* files = new std::vector< std::string >(); ++#pragma omp critical ++{ ++ if( fname != "" ) ++ files->push_back( fname ); ++} ++ return *files; ++} ++ ++void deleteRegisteredFiles(); ++inline ++void deleteRegisteredFiles() { ++ // don't be a slob, clean up after yourself: ++ // delete any files that are laying around ++ std::vector< std::string >& del_files = registerFileToDelete(); ++ for( int fileI = 0; fileI < del_files.size(); fileI++ ) ++ boost::filesystem::remove( del_files[ fileI ] ); ++ del_files.clear(); // clear the deleted files from the list ++} + + + /** +@@ -80,7 +80,7 @@ std::string CreateTempFileName(const std::string& prefix) + #endif + boost::filesystem::path path( prefix ); + dir = path.branch_path().string(); +- name = path.leaf(); ++ name = path.filename().string(); + if( name == "/" ) + { + dir += name; +diff --git a/libMems/ProgressiveAligner.cpp b/libMems/ProgressiveAligner.cpp +index 3be5fe0..5667a9e 100644 +--- a/libMems/ProgressiveAligner.cpp ++++ b/libMems/ProgressiveAligner.cpp +@@ -27,7 +27,7 @@ +
+ #include <boost/dynamic_bitset.hpp>
+ #include <boost/tuple/tuple.hpp>
+-#include <boost/property_map.hpp>
++#include <boost/property_map/property_map.hpp>
+ #include <boost/graph/graph_traits.hpp>
+ #include <boost/graph/adjacency_list.hpp>
+ #include <boost/graph/johnson_all_pairs_shortest.hpp>
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch new file mode 100644 index 000000000000..0bd922c9e111 --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-broken-constness.patch @@ -0,0 +1,24 @@ +Fix bug 529770 caused by non-const copy constructor. + +--- libmems-1.6_p1/libMems/Aligner.cpp ++++ libmems-1.6_p1/libMems/Aligner.cpp +@@ -939,7 +939,7 @@ + MatchLeftEndComparator( unsigned seq = 0 ){
+ m_seq = seq;
+ }
+- MatchLeftEndComparator( MatchLeftEndComparator& msc ){
++ MatchLeftEndComparator( const MatchLeftEndComparator& msc ){
+ m_seq = msc.m_seq;
+ }
+ // TODO?? make this do a wraparound comparison if all is equal?
+--- libmems-1.6_p1/libMems/Aligner.h ++++ libmems-1.6_p1/libMems/Aligner.h +@@ -49,7 +49,7 @@ + LabeledMemComparator( uint seq ){
+ m_seq = seq;
+ }
+- LabeledMemComparator( LabeledMemComparator& lmc ){
++ LabeledMemComparator( const LabeledMemComparator& lmc ){
+ m_seq = lmc.m_seq;
+ }
+ boolean operator()(const LabeledMem& a, const LabeledMem& b) const{
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-build.patch b/sci-libs/libmems/files/libmems-1.6_p1-build.patch new file mode 100644 index 000000000000..04d5dd9c82ac --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-build.patch @@ -0,0 +1,29 @@ + libMems/Makefile.am | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/libMems/Makefile.am b/libMems/Makefile.am +index 6101f71..d66053d 100644 +--- a/libMems/Makefile.am ++++ b/libMems/Makefile.am +@@ -2,10 +2,10 @@ + if DEBUG + D_CXXFLAGS = -Wall -g -D__GNDEBUG__ + endif +-OPTIMIZATION = -O2 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize + AM_CFLAGS = $(OPTIMIZATION) @DEPS_CFLAGS@ -DUSE_POSIX_AIO @OPENMP_CFLAGS@ + AM_CXXFLAGS = $(OPTIMIZATION) @DEPS_CFLAGS@ @BOOST_CPPFLAGS@ $(D_CXXFLAGS) @EXTRA_CXX_FLAGS@ @OPENMP_CXXFLAGS@ + AM_LDFLAGS = $(OPTIMIZATION) ++AM_CPPFLAGS=-I$(top_srcdir) + + LIBMEMS_H = \ + RepeatHash.h MatchHashEntry.h \ +--- a/libMems/dmSML/util.c ++++ b/libMems/dmSML/util.c +@@ -2,6 +2,7 @@ + #include "config.h" + #endif + ++#include <stdlib.h> + #include <stdio.h> + #include "libMems/dmSML/util.h" + diff --git a/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch b/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch new file mode 100644 index 000000000000..bde8efeb4c9c --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-fix-c++14.patch @@ -0,0 +1,18 @@ +Description: Correct compilation with g++-6 +Author: Gert Wollny <gw.fossdev@gmail.com> +Bug-Debian: https://bugs.debian.org/811870 +Forwarded: yes +Bug: https://sourceforge.net/p/mauve/bugs/46/ +Last-Update: 2016-06-30 + +--- a/libMems/ProgressiveAligner.cpp ++++ b/libMems/ProgressiveAligner.cpp +@@ -1599,7 +1599,7 @@ + c.SetLeftEnd(child_1, ancestral_matches[mI]->LeftEnd(1));
+ c.SetOrientation(child_1, ancestral_matches[mI]->Orientation(1));
+ c.SetLength(ancestral_matches[mI]->Length(1), child_1);
+- cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));
++ cga_list.push_back(boost::tuples::make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI]));
+ }
+
+ stack<node_id_t> node_stack;
diff --git a/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch b/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch new file mode 100644 index 000000000000..3ad3da2a8d80 --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-format-security.patch @@ -0,0 +1,16 @@ + libMems/dmSML/dmsort.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/libMems/dmSML/dmsort.c b/libMems/dmSML/dmsort.c +index 4c99215..2cbfa7e 100644 +--- a/libMems/dmSML/dmsort.c ++++ b/libMems/dmSML/dmsort.c +@@ -825,7 +825,7 @@ int InitdmSML( long working_mb, long buffer_size, const char* input_filename, co + if ( fgets(buf, sizeof(buf), fp) ) + { + sscanf(buf, "MemTotal: %ld kB", &memTotal); +- fprintf( stderr, buf ); ++ fprintf( stderr, "%s", buf ); + } + fclose(fp); + // allocate about 6/10 of physical memory diff --git a/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch b/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch new file mode 100644 index 000000000000..ec620ebb35aa --- /dev/null +++ b/sci-libs/libmems/files/libmems-1.6_p1-gcc-4.7.patch @@ -0,0 +1,71 @@ + libMems/CompactGappedAlignment.h | 36 ++++++++++++++++++------------------ + 1 file changed, 18 insertions(+), 18 deletions(-) + +diff --git a/libMems/CompactGappedAlignment.h b/libMems/CompactGappedAlignment.h +index bf78477..942d4aa 100644 +--- a/libMems/CompactGappedAlignment.h ++++ b/libMems/CompactGappedAlignment.h +@@ -13,7 +13,7 @@ + #include "config.h"
+ #endif
+
+-#include "libGenome/gnDebug.h" ++#include "libGenome/gnDebug.h"
+ #include "libGenome/gnFilter.h"
+ #include "libGenome/gnSequence.h"
+ #include "libMems/SparseAbstractMatch.h"
+@@ -103,15 +103,15 @@ public: + /** Eliminates any columns that contain only gap characters */
+ void CondenseGapColumns();
+
+- void swap( CompactGappedAlignment& other ){ swap(&other); } +- +-protected: +- // for use by derived classes in order to swap contents +- void swap( CompactGappedAlignment* other ){ +- std::swap( align_matrix, other->align_matrix ); +- std::swap( bcount, other->bcount ); +- BaseType::swap( other ); +- } ++ void swap( CompactGappedAlignment& other ){ swap(&other); }
++
++protected:
++ // for use by derived classes in order to swap contents
++ void swap( CompactGappedAlignment* other ){
++ std::swap( align_matrix, other->align_matrix );
++ std::swap( bcount, other->bcount );
++ BaseType::swap( other );
++ }
+
+ std::vector< bitset_t > align_matrix; /**< aligned positions have true values, gaps are false */
+ std::vector< std::vector< size_t > > bcount;
+@@ -572,7 +572,7 @@ void CompactGappedAlignment<BaseType>::CropEnd(gnSeqI crop_amount){ + this->SetStart(i, 0);
+ }
+ }
+- SetAlignmentLength( this->AlignmentLength() - crop_amount );
++ this->SetAlignmentLength( this->AlignmentLength() - crop_amount );
+ this->create_bitcount();
+ if( !this->validate() )
+ std::cerr << "CropEnd error\n";
+@@ -806,13 +806,13 @@ void CompactGappedAlignment<BaseType>::CondenseGapColumns() +
+ }
+
+-namespace std { +-template<> inline +-void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b ) +-{ +- a.swap(b); +-} +-} ++namespace std {
++template<> inline
++void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b )
++{
++ a.swap(b);
++}
++}
+
+
+ #endif // __CompactGappedAlignment_h__
diff --git a/sci-libs/libmems/libmems-1.6_p1-r3.ebuild b/sci-libs/libmems/libmems-1.6_p1-r3.ebuild new file mode 100644 index 000000000000..513fd1f3af61 --- /dev/null +++ b/sci-libs/libmems/libmems-1.6_p1-r3.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="GPL-2" +IUSE="doc static-libs" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-libs/boost:= + sci-libs/libgenome + sci-libs/libmuscle" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +PATCHES=( + "${FILESDIR}"/${P}-build.patch + "${FILESDIR}"/${P}-boost.patch + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-broken-constness.patch + "${FILESDIR}"/${P}-format-security.patch + "${FILESDIR}"/${P}-fix-c++14.patch + "${FILESDIR}"/${P}-boost-1.62-type-traits.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable static-libs static) +} + +src_compile() { + default + + if use doc; then + doxygen doxygen.am || die + HTML_DOCS+=( html/. ) + fi +} + +src_install() { + default + + # package provides .pc files + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/libmems/libmems-9999.ebuild b/sci-libs/libmems/libmems-9999.ebuild new file mode 100644 index 000000000000..782686270355 --- /dev/null +++ b/sci-libs/libmems/libmems-9999.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools subversion + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="" +ESVN_REPO_URI="https://svn.code.sf.net/p/mauve/code/libMems/trunk" + +SLOT="0" +LICENSE="GPL-2" +IUSE="doc" +KEYWORDS="" + +CDEPEND=" + dev-libs/boost + sci-libs/libgenome + sci-libs/libmuscle" +DEPEND="${CDEPEND} + doc? ( app-doc/doxygen )" +RDEPEND="${CDEPEND}" + +S="${WORKDIR}" + +src_prepare() { + default + eautoreconf +} diff --git a/sci-libs/libmems/metadata.xml b/sci-libs/libmems/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-libs/libmems/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libmuscle/Manifest b/sci-libs/libmuscle/Manifest new file mode 100644 index 000000000000..12c92ff9ebdd --- /dev/null +++ b/sci-libs/libmuscle/Manifest @@ -0,0 +1,7 @@ +AUX 3.7-bufferoverflow.patch 447 SHA256 cffb273380ae1793dd470b52461bff1475280918e5121927fa5b0fece2bba659 SHA512 09dd1fca3e75eb753a820c2f2957422c9433698af5bcbc572d48e437052d76522bac0b68923d296346d654f5e9130c15839180c4a635d9247e1ddf51993bcce6 WHIRLPOOL 1b7f8ab7fa0f0a03759c85ec6cb61944ff28603ed2dd90b69de0f5ffe609ee4bec65cb9137b0a88ad52c9ddb41b467fa9de1486d1cc1ba0e67459891ae398231 +AUX libmuscle-3.7-fix-build-system.patch 918 SHA256 a1caad44919835c335a4a06185df50512979a8cc80f7ef0f0ec50c7019abe2f0 SHA512 bb1590e8a9980de3a92fba16ce3e45a04a1cdf2f2a7fbbaedeba48f3d08f398e03bb6be7a9c9c0ba39a8772bc24d844480e9b57dce0f391d92b2f595e09677e0 WHIRLPOOL 75f812304ffd7f803281aa20b0f728a402ccc771b428389149d752497536110858f71f447286efe17fddc992fab0b5fe2928a1d3df7140e1b0f4df0596813cd7 +DIST libmuscle-3.7-r1.tar.bz2 458852 SHA256 3c0df6aeb8ea86bcd92e61f509486244176cee22c9bd7239ff16a51e1d046a14 SHA512 3031070dcd888c327b023eeb225a291bf36ec0c6fa8046fb1d945929305692bcdb3bc9623b02dfd753e086d3524bb7f10b9b011f663e38c71b17f6f516c0ac62 WHIRLPOOL d40edcebe7481565cec0efd390c9f545277fcccfc9ef9b3c051c5357bcaa0141c22e7efba794d9ca376724aaf0310c1e75dcd3e3f4bafa983f1692198a6dc51a +EBUILD libmuscle-3.7-r3.ebuild 726 SHA256 c50fb8e9d478960d46d73f7ce4be7078bed506e074bb129df71117e83a035b60 SHA512 97027e93ed6569e302644b76dbdc84cb5d0464b09e3940645a898f779bcead4c9fa029ca2a527623a591f5717442cc505836df2130bfd3bb816a32e262f788ce WHIRLPOOL d7a6aa0b57bd078bdc973fd285cfac88b193eb82765dc54cb101d707bfab428ce2219b2909bbce91799992b40bc72695a47677874aeda70c3cc21cff999c2a5c +MISC ChangeLog 2773 SHA256 e7eda55c3b9c918bb2ea370ac95383a1e91ad2507cb2dbd90799384e1bc13346 SHA512 92c5783a3588662be503cf525659612b1d71449ce425b9474caf47548ff64bf6f17591a84a5b255e0124ce413241d79a871261b830f5d727d410de1ca97b840d WHIRLPOOL c062973779edee12bcd7a0fbaad8653ae4dc1b67dcfcadb82c12fb0f630c253319bd590642135873c6561b9d375f551f29f647a78772de074e0d4d6e830dae76 +MISC ChangeLog-2015 881 SHA256 24dd90b3c5c29f55cf5f32c23012bfec9f11c833738a212aa5774a7a5423c2af SHA512 38106430a2a5c35eee8786a5a4bdf0ae35fd031876a5c7742536078ba9d0793b7b25d55663a6b589b75e0ccdff0629c8389fc833dad4723eb51a99c51d80321d WHIRLPOOL 7ba5b3efcf6aeee8a12c006db5e0a91f1be51aace8e263b3086b628cb5932b0df75f20529d3ac00dd872213e1e99fd3c7af72deac08eb3595c16f94a3af148cc +MISC metadata.xml 261 SHA256 15c95fe0beb2b86b616b7ac1be6f1118bd598d907b441a94d87721c0d6f36855 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8 diff --git a/sci-libs/libmuscle/files/3.7-bufferoverflow.patch b/sci-libs/libmuscle/files/3.7-bufferoverflow.patch new file mode 100644 index 000000000000..384f17acfbf4 --- /dev/null +++ b/sci-libs/libmuscle/files/3.7-bufferoverflow.patch @@ -0,0 +1,22 @@ +--- a/libMUSCLE/globalslinux.cpp ++++ b/libMUSCLE/globalslinux.cpp +@@ -159,7 +159,7 @@ + }
+ return DEFAULT_RAM;
+ }
+- int Bytes = atoi(pMem+9)*1000;
++ long Bytes = atol(pMem+9)*1000;
+ return ((double) Bytes)/1e6;
+ }
+
+--- a/libMUSCLE/progress.cpp ++++ b/libMUSCLE/progress.cpp +@@ -48,7 +48,7 @@ + if (MB < 0)
+ return "";
+
+- static char Str[9];
++ static char Str[11];
+ static double MaxMB = 0;
+ static double RAMMB = 0;
+
diff --git a/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch b/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch new file mode 100644 index 000000000000..2b2c28c8132a --- /dev/null +++ b/sci-libs/libmuscle/files/libmuscle-3.7-fix-build-system.patch @@ -0,0 +1,21 @@ +* Make build system parallel buildable +* Remove -funroll-loops and friends + +--- a/libMUSCLE/Makefile.am ++++ b/libMUSCLE/Makefile.am +@@ -1,6 +1,4 @@ +-OPTIMIZATION = -O2 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations +-AM_CXXFLAGS = $(OPTIMIZATION) -DNDEBUG=1 @OPENMP_CXXFLAGS@ +-AM_LDFLAGS = $(OPTIMIZATION) ++AM_CXXFLAGS = -DNDEBUG=1 @OPENMP_CXXFLAGS@ + + LIBMUSCLE_H = \ + alpha.h cluster.h clust.h clustsetdf.h clustset.h clustsetmsa.h diaglist.h distcalc.h distfunc.h dpregionlist.h dpreglist.h edgelist.h enumopts.h enums.h estring.h gapscoredimer.h gonnet.h intmath.h msadist.h msa.h muscle.h objscore.h params.h profile.h pwpath.h refine.h scorehistory.h seq.h seqvect.h textfile.h timing.h tree.h types.h unixio.h threadstorage.h +@@ -36,6 +34,6 @@ + + + muscle_SOURCES = main.cpp +-muscle_LDADD = $(top_builddir)/libMUSCLE/libMUSCLE-3.7.la ++muscle_LDADD = libMUSCLE-3.7.la + + diff --git a/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild b/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild new file mode 100644 index 000000000000..d3a8107c1052 --- /dev/null +++ b/sci-libs/libmuscle/libmuscle-3.7-r3.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library for sci-biology/mauve" +HOMEPAGE="http://gel.ahabs.wisc.edu/mauve/" +SRC_URI="mirror://gentoo/${P}-r1.tar.bz2" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc static-libs" + +RDEPEND="!sci-biology/muscle" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +PATCHES=( + "${FILESDIR}"/${PV}-bufferoverflow.patch + "${FILESDIR}"/${PN}-3.7-fix-build-system.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + + # package provides .pc file + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/libmuscle/metadata.xml b/sci-libs/libmuscle/metadata.xml new file mode 100644 index 000000000000..8417d1580d40 --- /dev/null +++ b/sci-libs/libmuscle/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libnova/Manifest b/sci-libs/libnova/Manifest new file mode 100644 index 000000000000..9fd9511ce22a --- /dev/null +++ b/sci-libs/libnova/Manifest @@ -0,0 +1,10 @@ +AUX libnova-0.12.1-configure.patch 331 SHA256 7646e2c2c87f56cefb15d9fca2b12a117db4db2f0f398a220b74fa64776d60fb SHA512 fda0ca74341894b544dcf4261bb2abb438dc26c7021c575e45bda0d8215a612a4b3f5456e0f115fd52cbe11c7f79a5cf0f2322bb5f85bd978fffa5c377858f02 WHIRLPOOL 77fc76b4c7cd6ee1a858115d7a2b7f7caea1aba730e857d6e17866b487a2632e8555fcb978fb0ced2a97af6aca073f9284bb8fc7cdb52601c33102c2ac79ee6a +DIST libnova-0.12.3.tar.gz 1505676 SHA256 ac250e678e52c9484629e1e934d0d1276db8b431d338887fb98c41ffd2e9b3a2 SHA512 e39c55c339dc2d7c899ffb7d0a898a5c2d6ebca5cf3a788db21d84f230a7379bfc0dd4736ed7ae66d8a449d1be9d68b8a4382ae55af4aa638bb734402c43bc72 WHIRLPOOL 46761d46202f315d426782354340cf1ed3fe04365b42f42989f18b4c46b6573579f8889cb580bf3fc97c3d3eb9af281fb2ee1947937e6bd77247f3534fa2d340 +DIST libnova-0.14.0.tar.gz 1547373 SHA256 be1b91783310b3803a51d6b224a0eeb171a54e8b0350f7dd0e5ca860484b3145 SHA512 373d32e4f380563f895483d9054cf19bbfc69e32089f75dc91f84daf28610eba94f5615b0eb7004b25b9c702450d594463606b349b93dc9cde46d0d860029da7 WHIRLPOOL 3e45e6449f8fb8d52fdc1dcaa5b62da797f9583dda04c488f5699333b82e918282adf7d92f89d443174395f2001de7ad563dbc172278c4912a5daa5599bc9deb +DIST libnova-0.15.0.tar.gz 1533794 SHA256 7c5aa33e45a3e7118d77df05af7341e61784284f1e8d0d965307f1663f415bb1 SHA512 77ab0ccbfe462c03a21e88656cb4d6389994ea1da0ee8da997f19a83d24ad8fd9e505e70e1580b75332e826e5b7859b5f2af4417f65eb811440493ba586f2574 WHIRLPOOL c4a016dd479852aa977c1ca07354245d0260816adf41992499f1fbef1edf740f30efd3e64739a247139d93156cbf356a409963b9a9f0236726c2a83c2c0c66d7 +EBUILD libnova-0.12.3.ebuild 1127 SHA256 6469c5b5d1e9b5fc3028d96975e6d9c786347d9108907495bc7022df670ecae8 SHA512 d6490764d1558afb0fc4eec5d473e198924e6f983d4439931475f9348427b742fb30a12d9d2a082902a28b042e416acf52c8ec711323f76df42d63e505446a35 WHIRLPOOL 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Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=2 +inherit eutils autotools flag-o-matic + +DESCRIPTION="Celestial Mechanics and Astronomical Calculation Library" +HOMEPAGE="http://libnova.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0" +KEYWORDS="amd64 hppa ppc ppc64 x86" +IUSE="doc examples" + +DEPEND="doc? ( app-doc/doxygen )" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-0.12.1-configure.patch + # 0.12.3 does not pass test with > -02 + replace-flags -O? -O1 + eautoreconf +} + +src_compile() { + emake || die "emake failed" + if use doc; then + cd doc + emake doc || die "emake in doc failed" + fi +} + +src_test() { + emake check || die "emake check failed" + "${S}"/lntest/lntest || die "lntest failed" +} + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" + dodoc AUTHORS ChangeLog NEWS README || die + if use doc; then + dohtml doc/html/* || die "dohtml failed" + fi + if use examples; then + make clean + rm -f examples/Makefile* + insinto /usr/share/doc/${PF} + doins -r examples || die + fi +} diff --git a/sci-libs/libnova/libnova-0.14.0.ebuild b/sci-libs/libnova/libnova-0.14.0.ebuild new file mode 100644 index 000000000000..23a5867f38e0 --- /dev/null +++ b/sci-libs/libnova/libnova-0.14.0.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 +inherit eutils + +DESCRIPTION="Celestial Mechanics and Astronomical Calculation Library" +HOMEPAGE="http://libnova.sourceforge.net/" +SRC_URI="https://dev.gentoo.org/~bicatali/${P}.tar.gz" +# bad tar ball on sf, rebuild it from svn +#SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0" +KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86" +IUSE="doc examples static-libs" + +DEPEND="doc? ( app-doc/doxygen )" +RDEPEND="" + +src_configure() { + econf $(use_enable static-libs static) +} + +src_compile() { + emake + use doc && emake doc +} + +src_install() { + default + use doc && dohtml doc/html/* + if use examples; then + make clean + rm -f examples/Makefile* + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/libnova/libnova-0.15.0.ebuild b/sci-libs/libnova/libnova-0.15.0.ebuild new file mode 100644 index 000000000000..ac3503b00341 --- /dev/null +++ b/sci-libs/libnova/libnova-0.15.0.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 +inherit autotools-utils + +DESCRIPTION="Celestial Mechanics and Astronomical Calculation Library" +HOMEPAGE="http://libnova.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0" +KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs" + +DEPEND="doc? ( app-doc/doxygen )" +RDEPEND="" + +src_prepare() { + sed -i -e '/CFLAGS=-Wall/d' configure.in || die + autotools-utils_src_prepare +} + +src_compile() { + autotools-utils_src_compile + use doc && autotools-utils_src_compile -C doc doc +} + +src_install() { + autotools-utils_src_install + use doc && dohtml doc/html/* + if use examples; then + make clean + rm examples/Makefile* + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/libnova/metadata.xml b/sci-libs/libnova/metadata.xml new file mode 100644 index 000000000000..0c5d20811ad1 --- /dev/null +++ b/sci-libs/libnova/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-astronomy@gentoo.org</email> + <name>Gentoo Astronomy Project</name> + </maintainer> + <longdescription lang="en"> + libnova is a general purpose, double precision, astronomical + calculation library. The intended audience of libnova is C / C++ programmers, + astronomers and anyone else interested in calculating positions of + astronomical objects. +</longdescription> + <upstream> + <remote-id type="sourceforge">libnova</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/liborigin/Manifest b/sci-libs/liborigin/Manifest new file mode 100644 index 000000000000..c89747bd0c21 --- /dev/null +++ b/sci-libs/liborigin/Manifest @@ -0,0 +1,5 @@ +DIST liborigin2-20110829.zip 158364 SHA256 51ebf6de57d2b44cd6f5ab772ed92154eec9598a14a6655967ebcf2d7f8da0a2 SHA512 d0e4013a686fbc61c58b1f39e98aace91978bcadffbb2ef9d32576a3b2f19cc2443d595da2d3ecc19298ec6e29c20717db94e1fda6a64d71f3763841228a01c0 WHIRLPOOL 6828990a46643e7eb838ebda425d2a0d4477945552afe10b18048edaa104b94b43ea428700417c3701251646add3e45a4c4bcd1076b1740e42fa145c816200a2 +EBUILD liborigin-20110829.ebuild 1160 SHA256 b0f12b91b186c24896ce633c4ce0d68bfa6d3f5fb662c9bed21fbdf6476c9db4 SHA512 824731ddab9a30921f862ad847a4ce6519898d884a9662fbe1ed2b7d95d39a8fe79bb0e252c3d80b09558b809884072a314c49d9453b934084af18a1b35d8b49 WHIRLPOOL 38842cbfd9604a4a648d86d6006430d5aa1776591475bf29e57170f377170cb83f5a82cabca291da5336347e94efa42d9cb0f6427ea8bcc2ba954bd9752046b2 +MISC ChangeLog 2468 SHA256 392dbf3352caea176caf1e63fb0b29ae796a0ade6877373f7bb27234eb0bbe8d SHA512 a062ea9b12f92c6acc2e22bae7bc27f4c48f63fc4c12fc5a5f9620123f168719660a1c0fab3a90c53393265efa8a1fe134f7dff9d542fb5118462bae7ad339a3 WHIRLPOOL 7175d9f20a027a917fdd3317426405520fcc867c511d296e0805c2bfcd50d7044fc0d811bd37bf0e4591323be01b03092b8090d6fee48d0fe60ec2b8c72ba64b +MISC ChangeLog-2015 5966 SHA256 1695654cbfcd640b4688235c3709513838311fde99f7cf461de93207e1ddad5e SHA512 1aec897c9bc1b4b53c332a7043e14aef2ca0866c251936aeba3dd715f3b2ae72a1891e9e354c6f8c29195c202b85088a1b30e7887e3f7dc355e77179d777580f WHIRLPOOL 465dd6e70ad59241f6d02d48bf11ae6832f9753ece14f349076b470298485e75195c5c0d15da55e3f8ccbaf83b7874bd7861ba072c195094e5a4705e45a33f98 +MISC metadata.xml 354 SHA256 3f2dadfc648d206b882fe932e43cb8c1fe85487212dd3bf81cb492d3c9fd53db SHA512 22f34d89618d743e35976002620217a1b829a038beede5a7467d62b17e0c70c77fcaa93f9a270ca684eecc15c7f3be98d7683c488de24f0ba27660fa4087934a WHIRLPOOL f88aac3e8231540e6b29ba3f9e756a0b2c182f254e8230c9698dca827a3a2d052fbc5b4bd57b87e0ddd31d93f5767a4c8c118225c440aed5dbef53a10ebdce27 diff --git a/sci-libs/liborigin/liborigin-20110829.ebuild b/sci-libs/liborigin/liborigin-20110829.ebuild new file mode 100644 index 000000000000..801a874105f3 --- /dev/null +++ b/sci-libs/liborigin/liborigin-20110829.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib qt4-r2 + +DESCRIPTION="Library for reading OriginLab OPJ project files" +HOMEPAGE="http://soft.proindependent.com/liborigin2/" +SRC_URI="https://dev.gentoo.org/~dilfridge/distfiles/${PN}2-${PV}.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +RDEPEND=" + dev-libs/boost + dev-qt/qtgui:4" +DEPEND="${RDEPEND} + app-arch/unzip + dev-cpp/tree + doc? ( app-doc/doxygen )" + +S="${WORKDIR}"/${PN}${SLOT} + +src_prepare() { + mv liborigin2.pro liborigin.pro || die + qt4-r2_src_prepare + cat >> liborigin.pro <<-EOF + INCLUDEPATH += "${EPREFIX}/usr/include/tree" + headers.files = \$\$HEADERS + headers.path = "${EPREFIX}/usr/include/liborigin2" + target.path = "${EPREFIX}/usr/$(get_libdir)" + INSTALLS = target headers + EOF + # use system one + rm -f tree.hh || die +} + +src_compile() { + qt4-r2_src_compile + if use doc; then + cd doc && \ + doxygen Doxyfile || die "doc generation failed" + fi +} + +src_install() { + local DOCS="readme FORMAT" + use doc && local HTML_DOCS=( doc/html/. ) + qt4-r2_src_install +} diff --git a/sci-libs/liborigin/metadata.xml b/sci-libs/liborigin/metadata.xml new file mode 100644 index 000000000000..2ad80b902110 --- /dev/null +++ b/sci-libs/liborigin/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + A library providing IO for Microcal Origin files. + </longdescription> +</pkgmetadata> diff --git a/sci-libs/libpdb++/Manifest b/sci-libs/libpdb++/Manifest new file mode 100644 index 000000000000..c80926c80e72 --- /dev/null +++ b/sci-libs/libpdb++/Manifest @@ -0,0 +1,6 @@ +AUX libpdb++-040728-dynlib+flags.patch 1286 SHA256 5a58f060952cba7e91e8e8566e06eb18be795bc49aa87e728cfd919ad977e2c3 SHA512 cd99a481a3e8b50bd414c51b0adb550bf7fe1d54f902a1464432ecdbe978a7ab73d0c9e522b45b34331ceecdfbe8943d0195cc01ec086ae85fb2bd48f720bffb WHIRLPOOL cf8dbadc87b996e5982351b612d68c78df16e39df4dc779129b65243a2193b4e34cf0382acae88af35dc605dfa43b00942007af5bcdbd7a6f270df1404eb3e8b +DIST libpdb++-040728.shar 113174 SHA256 e37fcaa58e04e64a2a1ae6324c699d320c9d6bf07694e29d6bef63c61dd585e7 SHA512 4b3e4b12ea10395ba38fbc12fbb3589bd7b40997e1a0bcb79d3d0a495c361e4dea8dbdc4c434de290b5f62412e297df09742beeea0a8b881dbf92317013aa930 WHIRLPOOL 9bc9ce6861cce47da69609c402759813a050af4849c969b72d27669bd55143be48432e5dcc44d08b04d6f6f0915fdf6ff3860a4652de248d9d13df27ce2b9869 +EBUILD libpdb++-040728-r1.ebuild 822 SHA256 aa47c46bf34c75a095a161fcdbfceadc920d0f4aabb826322a650506df23f7ae SHA512 03eab8f361c34a53c6f90db63d072e2274b1edc95fd45992dab9592f7fcbfe3b6631b9b41cb7a016ac4d9d156a414e253fb47e180ec5d3e91c8fb8e27beb4edf WHIRLPOOL 3270a3a9e720637897a1423745dddb08174e067994e3359284771a9f8378cf320bbe3cba341f4dfea743968a91d105bfaaa5d3515cf8556cceda0238c90543c0 +MISC ChangeLog 2707 SHA256 90835346cd692e549ca93d25f2e89ebc16482a2bb9fe4e2594733b3a0408c081 SHA512 a569ac4bbab0e007259ea5c8fff627ffe7226694c713643ca6cf561a29f863d9db8a7982aea2db1530261d271a50a17d59173731caf457b90e25cd6a0dce1e7e WHIRLPOOL 7dbd62ce1d91efae8fb5cbb582305cc41ee628335aa1e36ee8059d32003913d3930113484a37a5b106108a246bb7ed43c373a371cb40bccbcbaba07ffaee63dd +MISC ChangeLog-2015 775 SHA256 d2e7f2404dfb0041c9a3c44a762b23741705cf213148814ec4b13f9b0b3a008b SHA512 30faf7c1c7fcdd25c3bb14e50211957fb3244953a21d4469372443ad323a482a13f62bff2599a2e68e63e2be046492ad2e1f42ab10addf00dc2ae9338d697f8a WHIRLPOOL 925fd67df4e47e338fb024954671300df6de6288fa047655f4fc9e2dceea2c497914229261da83190dddabc3668dce1230ca77d77a9f594a01e5305ed718fb7b +MISC metadata.xml 253 SHA256 45344b6a377f639b56950e98338690fa1e0c5b51d2bf174635aff3b025b7e616 SHA512 819062e1ccefa39fc7f577279b08e781b9631eb14b7794db691ab92263c013ca432d279ac08671b19c80f7effb8c67528e5221278c573dd29dc0354bbff4a77e WHIRLPOOL 73680e667729b1d31cac7b2b730a5d94195071c96383438c66c4a94e445fe874e78d3e5e2c9c5a6d77406dc392eab967595402e063e557f9a3680714d709e830 diff --git a/sci-libs/libpdb++/files/libpdb++-040728-dynlib+flags.patch b/sci-libs/libpdb++/files/libpdb++-040728-dynlib+flags.patch new file mode 100644 index 000000000000..3600481f4c72 --- /dev/null +++ b/sci-libs/libpdb++/files/libpdb++-040728-dynlib+flags.patch @@ -0,0 +1,54 @@ + Makefile | 20 +++++++++++++------- + 1 file changed, 13 insertions(+), 7 deletions(-) + +diff --git a/Makefile b/Makefile +index bbf0778..1dc6c62 100644 +--- a/Makefile ++++ b/Makefile +@@ -4,22 +4,22 @@ + # On System V machines, RANLIB should be ':' + # + SHELL = /bin/sh +-RANLIB = : ++#RANLIB = : + +-CXX = gcc -felide-constructors ++CXX ?= g++ + #CXX = CC + + .SUFFIXES: .cc + + .cc.o: +- $(CXX) $(CCFLAGS) -c $< -o $@ ++ $(CXX) $(CXXFLAGS) -fPIC -felide-constructors -c $< -o $@ + + OPT = -O + DEBUG = + CCFLAGS = $(OPT) $(DEBUG) + LIBRARY = pdb++ + +-LIBARCH = lib$(LIBRARY).a ++LIBARCH = lib$(LIBRARY) + OBJS = pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_chars.o \ + pdb_type.o pdb++.o pdbinput.o + SRCS = pdb_read.cc pdb_sprntf.cc pdb_sscanf.cc pdb_chars.cc \ +@@ -30,10 +30,16 @@ all: $(LIBARCH) + install: $(LIBARCH) + install -F /usr/local/lib $(LIBARCH) + +-$(LIBARCH): $(OBJS) ++$(LIBARCH).a: $(OBJS) + @echo "Loading $(LIBARCH) ... " +- @ar cru $(LIBARCH) $(OBJS) +- @$(RANLIB) $(LIBARCH) ++ $(AR) cru $@ $(OBJS) ++ $(RANLIB) $@ ++ @echo "done" ++ ++$(LIBARCH).so: $(OBJS) ++ $(CXX) $(LDFLAGS) -shared -Wl,--soname,libpdb++.so.0 -o libpdb++.so.0.1 $(OBJS) ++ ln -sf libpdb++.so.0.1 libpdb++.so.0 ++ ln -sf libpdb++.so.0.1 libpdb++.so + @echo "done" + + clean:; @rm -f $(OBJS) diff --git a/sci-libs/libpdb++/libpdb++-040728-r1.ebuild b/sci-libs/libpdb++/libpdb++-040728-r1.ebuild new file mode 100644 index 000000000000..c4850098afdf --- /dev/null +++ b/sci-libs/libpdb++/libpdb++-040728-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit multilib toolchain-funcs + +DESCRIPTION="PDB Record I/O Libraries -- c++ version" +HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html" +SRC_URI="mirror://gentoo/${P}.shar" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/sharutils" + +S="${WORKDIR}"/${PN} + +PATCHES=( "${FILESDIR}"/${P}-dynlib+flags.patch ) + +src_unpack() { + "${EPREFIX}/usr/bin/unshar" "${DISTDIR}"/${A} || die +} + +src_prepare() { + default + tc-export CXX AR RANLIB +} + +src_compile() { + emake ${PN}.so + use static-libs && emake ${PN}.a +} + +src_install() { + dolib.so ${PN}.so* + use static-libs && dolib.a ${PN}.a + + insinto /usr/include/${PN} + doins *.h +} diff --git a/sci-libs/libpdb++/metadata.xml b/sci-libs/libpdb++/metadata.xml new file mode 100644 index 000000000000..ae9640ffb9f1 --- /dev/null +++ b/sci-libs/libpdb++/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libpdb/Manifest b/sci-libs/libpdb/Manifest new file mode 100644 index 000000000000..e8173d00a763 --- /dev/null +++ b/sci-libs/libpdb/Manifest @@ -0,0 +1,6 @@ +AUX libpdb-991112-dynlib+flags.patch 1142 SHA256 78433bd1ed95852a7fb1e49d84f108ba301c01d3003c1fb9355d1c51c7272b1e SHA512 6d93db5444f4ecb6127afc5cb20e806c4de55c31d909540403ec73a861c09a577a6bb9e55e2f2a0dbfb35c2fe5093776724f5ed735f3519980b8dd87706c3870 WHIRLPOOL 26e60d3a264e0628f5a3e7ab0c21f725143f526630912dbcdf222e9464e316cdbe822a50aa5d363a5d0d1f0e0b5f64373cafb5ba4e9d174a94bc2685534cd722 +DIST libpdb-991112.shar 123895 SHA256 31101a9e6a98a4359241978cb389acc3d0845171209c87e127a7264b21cedcee SHA512 ae356997d11068736bbbd1a57e4e3a28fa54fd396326bc8fea41485186a1c69ce39c7f81195ae65ddc59c017d85dd123614f56f910c8faffd4791fcfd1b064f4 WHIRLPOOL 8017376c127032727b0e115ea240ef084c8a054c4c5be1545152926cb710243e5210a15e191a635df8f7bc6f1fea8422735888b5881efc199176acab85ef2153 +EBUILD libpdb-991112-r1.ebuild 811 SHA256 32d28302d9568ae0be2357d7ad63372128d18af76e9055e34838b38c0b811bce SHA512 7fe2517be72699a94004a16feeab661f68d337e0b64655152aff6337d50d80d12d2ee8a3386bd5933ff742f90f8160b18ebb8bd007f86e14a67f78e8cca7cfb0 WHIRLPOOL b32b16fa0334ffec4948967697b933a2aad46be17665829ee362058efcf89d95d50afe650ddb9c07bf48324c00023a9a36cf478fae46988c0bfe9190cd1519e7 +MISC ChangeLog 2695 SHA256 0ecd1dd07726586c6ae5ee814e9662dfcfc34dff1e6049ff22152919a100ed52 SHA512 2de7fc3c798199686b71e29ea6b0dfe9e25363c5235bfc99bd133bfc8d53795f28a811d3c23e66e931e30b41547bebfd01326a002e0b3f2b8d851a10deb3e428 WHIRLPOOL 83702be4fd8b8bb53eb3f048cf7f255c168ae15833d1298a979beaf815b1e76aa872bb216a1285c5b7afcf6c50fd002d742d524dae3cc889b494f6d0cd0a8f6d +MISC ChangeLog-2015 623 SHA256 15f030797aad1ee5ccbf00fae73bf1e981153a685a9f95f848678b17cec2303f SHA512 edef8996d83ea6866c7ee7f9d9b1d6dc1189ed201a9bc65d3e5b0107abf93eea9380bbd7038ef910236fdc07a4c994c748fe6ad4634a0ea435f2081abba385c0 WHIRLPOOL ea3806e58876b5f51d5927e8492c4709e4c906f9c9746651d228cac7f41279eb3d33b0293c3c74abbf028c06147f865cc4537b22797776a7a2aa12c73022c848 +MISC metadata.xml 253 SHA256 45344b6a377f639b56950e98338690fa1e0c5b51d2bf174635aff3b025b7e616 SHA512 819062e1ccefa39fc7f577279b08e781b9631eb14b7794db691ab92263c013ca432d279ac08671b19c80f7effb8c67528e5221278c573dd29dc0354bbff4a77e WHIRLPOOL 73680e667729b1d31cac7b2b730a5d94195071c96383438c66c4a94e445fe874e78d3e5e2c9c5a6d77406dc392eab967595402e063e557f9a3680714d709e830 diff --git a/sci-libs/libpdb/files/libpdb-991112-dynlib+flags.patch b/sci-libs/libpdb/files/libpdb-991112-dynlib+flags.patch new file mode 100644 index 000000000000..72048b684a93 --- /dev/null +++ b/sci-libs/libpdb/files/libpdb-991112-dynlib+flags.patch @@ -0,0 +1,46 @@ + Makefile | 17 +++++++++++------ + 1 file changed, 11 insertions(+), 6 deletions(-) + +diff --git a/Makefile b/Makefile +index 760a427..de7e724 100644 +--- a/Makefile ++++ b/Makefile +@@ -8,16 +8,16 @@ + # RANLIB should be ':' + # + SHELL = /bin/sh +-RANLIB = : ++#RANLIB = : + NOTHING = + LINTOPT = -o $(NOTHING) + + OPT = -O -g + DEBUG = +-CFLAGS = $(OPT) $(DEBUG) ++CFLAGS += -fPIC + LIBRARY = pdb + +-LIBARCH = lib$(LIBRARY).a ++LIBARCH = lib$(LIBRARY) + LINTLIB = llib-l$(LIBRARY).ln + OBJS = pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o pdbrun.o ms.o + SRCS = pdb_read.c pdb_sprntf.c pdb_sscanf.c pdb_write.c pdbrun.c ms.c +@@ -27,10 +27,15 @@ all: $(LIBARCH) $(LINTLIB) + install: $(LIBARCH) + install -F /usr/local/lib $(LIBARCH) + +-$(LIBARCH): $(OBJS) ++$(LIBARCH).so: $(OBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,libpdb.so.0 -o libpdb.so.0.1 $(OBJS) ++ ln -sf libpdb.so.0.1 libpdb.so.0 ++ ln -sf libpdb.so.0.1 libpdb.so ++ ++$(LIBARCH).a: $(OBJS) + @echo "Loading $(LIBARCH) ... " +- @ar cru $(LIBARCH) $(OBJS) +- @$(RANLIB) $(LIBARCH) ++ $(AR) cru $@ $(OBJS) ++ $(RANLIB) $@ + @echo "done" + + $(LINTLIB): $(SRCS) $(HDRS) diff --git a/sci-libs/libpdb/libpdb-991112-r1.ebuild b/sci-libs/libpdb/libpdb-991112-r1.ebuild new file mode 100644 index 000000000000..d9f08556e58e --- /dev/null +++ b/sci-libs/libpdb/libpdb-991112-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils toolchain-funcs + +DESCRIPTION="PDB Record I/O Libraries -- c version" +HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html" +SRC_URI="mirror://gentoo/${P}.shar" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +RDEPEND="" +DEPEND="${RDEPEND} + app-arch/sharutils" + +S="${WORKDIR}" + +PATCHES=( "${FILESDIR}"/${P}-dynlib+flags.patch ) + +src_unpack() { + "${EPREFIX}/usr/bin/unshar" "${DISTDIR}"/${A} || die +} + +src_prepare() { + default + tc-export CC RANLIB AR +} + +src_compile() { + emake ${PN}.so + use static-libs && emake ${PN}.a +} + +src_install() { + dolib.so ${PN}.so* + use static-libs && dolib.a ${PN}.a + + insinto /usr/include/${PN} + doins *.h +} diff --git a/sci-libs/libpdb/metadata.xml b/sci-libs/libpdb/metadata.xml new file mode 100644 index 000000000000..ae9640ffb9f1 --- /dev/null +++ b/sci-libs/libpdb/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/libqalculate/Manifest b/sci-libs/libqalculate/Manifest new file mode 100644 index 000000000000..11d7714075bf --- /dev/null +++ b/sci-libs/libqalculate/Manifest @@ -0,0 +1,8 @@ +AUX libqalculate-0.9.9-readline.patch 424 SHA256 c3341ad857dadd848425fe03378ef7319e805eb4113034930cc3d4365adae5f2 SHA512 677589db5ce91c8092666f20d54e8f607a4ad06beaddbe8a1b11262d70eb2707cf70a608b797efa20b635e018da082585d74309e6506f78f931c09487b8c9aa2 WHIRLPOOL 829944cac4b29cc7a77047bd93d4f6845d836fce6808cb344dcb46668e4ca7a0d0a9f06e2e4f5c1f313a24f335e0b11e5128ea7e70495e6f6e0f8fa10d17e899 +DIST libqalculate-0.9.7.tar.gz 1256271 SHA256 9a6d97ce3339d104358294242c3ecd5e312446721e93499ff70acc1604607955 SHA512 9aae8540481df4aa1cb24b1c6e8e9424e87758444f0b9689cd809bdf4230c4b5257c74363e6f084cea4e3be1935f45c53e7fc592f76d25d709ad88c97884bc42 WHIRLPOOL 21259323d91a8d7dc746048a3ef52f435ad3ff0450c08238d6a1d246990c5144a3072826ae0d2f656f75fe3c3be51b5c93a90f81eec4c742188bb9e33f5c171f +DIST libqalculate-0.9.9.tar.gz 1509180 SHA256 ca9fe0228b83d8f8398c3aca233691630bf455389e75bffe8164f0f89a208793 SHA512 c7692dcd91e0a7aea8184ca5366a3caf704b6e716c9e8552f4214ce7fc3157cf127daf7a063196383e4d5a99f8703486f2282c7fb01acafee5e1b3d8993de384 WHIRLPOOL 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SHA512 155c9eec94015b8284d2008f03f19337b1cbdd4c24da98ef391dddbb7205bc2d29c899efec30beb3403f3c7176a8007167e4a8aca74f8840119c2f73d9329a32 WHIRLPOOL 7a7d4bfc6f0517093d61eafd7a33a3995dae60721be2b5508a048fe153fc8cb80f7468496a0cafaa3e15565bbcb7989a31bbd7acb7f193506743560d89d1bb6d +MISC ChangeLog-2015 8318 SHA256 8e464f286dce5e8a11f01091b4828df73971b482f119883a9733384d5ba34bb0 SHA512 2dda2a6b478f40b2d3fefe6302ebb07c1d8819cd80f335caa9f14aec006ef34fb12317a46aaa58dcdfb708b629cd57ca37da870bbefbd94efe9b6259832f65d7 WHIRLPOOL 358a21425c44b159ede713b510d05fd37d5ce6a903c1b1b35c74da13dbd218dae6b6c49c9f35ba7aa8667b1d65e5807a4c0cb3b6c6ce204f9896d8cc2a80b5f7 +MISC metadata.xml 412 SHA256 9600fbec6ff67ce8b7ea8323759a6db4d2f5830e57b7d45950f83538b3e3adea SHA512 b6c55b741bda2a497dae278d47c6931611cbda132e08deb16a9c4efef59c7cb18bc464e7d242380b7afde2af4ab6f8e7f72b7db4ed3fd6b8f4cdc9c0359550ce WHIRLPOOL 288788ca9ffe50dc04ea78e572e1c2216c86612a77ddff296abfe953e002e9fa18ed09b5485942e5900c5ad86e1c5611fbc5134341725f2d5a242644ba201170 diff --git a/sci-libs/libqalculate/files/libqalculate-0.9.9-readline.patch b/sci-libs/libqalculate/files/libqalculate-0.9.9-readline.patch new file mode 100644 index 000000000000..ab2a5a0eb3ff --- /dev/null +++ b/sci-libs/libqalculate/files/libqalculate-0.9.9-readline.patch @@ -0,0 +1,13 @@ +diff -ru libqalculate-0.9.9.orig/src/qalc.cc libqalculate-0.9.9/src/qalc.cc +--- libqalculate-0.9.9.orig/src/qalc.cc 2016-07-26 14:41:40.000000000 +0200 ++++ libqalculate-0.9.9/src/qalc.cc 2016-08-04 18:27:36.553906707 +0200 +@@ -3179,7 +3179,9 @@ + if(!file) { + g_free(gstr_file); + g_free(gstr_oldfile); ++#ifdef HAVE_LIBREADLINE + g_free(historyfile); ++#endif + first_time = true; + set_saved_mode(); + return; diff --git a/sci-libs/libqalculate/libqalculate-0.9.7-r1.ebuild b/sci-libs/libqalculate/libqalculate-0.9.7-r1.ebuild new file mode 100644 index 000000000000..1c9d0dc1071a --- /dev/null +++ b/sci-libs/libqalculate/libqalculate-0.9.7-r1.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils + +DESCRIPTION="A modern multi-purpose calculator library" +HOMEPAGE="http://qalculate.sourceforge.net/" +SRC_URI="mirror://sourceforge/${P/lib}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="alpha amd64 ~arm hppa ia64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux" +IUSE="gnuplot readline static-libs" + +COMMON_DEPEND=" + dev-libs/glib:2 + dev-libs/libxml2:2 + >=sci-libs/cln-1.2 + sys-libs/zlib + readline? ( sys-libs/readline:0= )" +DEPEND="${COMMON_DEPEND} + dev-util/intltool + sys-devel/gettext + virtual/pkgconfig" +RDEPEND="${COMMON_DEPEND} + net-misc/wget + gnuplot? ( >=sci-visualization/gnuplot-3.7 )" + +src_prepare() { + cat >po/POTFILES.skip <<-EOF + # Required by make check + data/currencies.xml.in + data/datasets.xml.in + data/elements.xml.in + data/functions.xml.in + data/planets.xml.in + data/units.xml.in + data/variables.xml.in + src/defs2doc.cc + EOF +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_with readline) +} + +src_install() { + # docs/reference/Makefile.am -> referencedir= + emake \ + DESTDIR="${D}" \ + referencedir="${EPREFIX}/usr/share/doc/${PF}/html/reference" \ + install + + dodoc AUTHORS ChangeLog NEWS README* TODO + + prune_libtool_files +} diff --git a/sci-libs/libqalculate/libqalculate-0.9.9.ebuild b/sci-libs/libqalculate/libqalculate-0.9.9.ebuild new file mode 100644 index 000000000000..c4a7b59e1f45 --- /dev/null +++ b/sci-libs/libqalculate/libqalculate-0.9.9.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="A modern multi-purpose calculator library" +HOMEPAGE="https://qalculate.github.io/" +SRC_URI="https://github.com/Qalculate/${PN}/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0/6" +KEYWORDS="alpha amd64 ~arm ~arm64 hppa ia64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux" +IUSE="gnuplot readline static-libs" + +COMMON_DEPEND=" + dev-libs/glib:2 + dev-libs/libxml2:2 + >=sci-libs/cln-1.2 + sys-libs/zlib + readline? ( sys-libs/readline:0= )" +DEPEND="${COMMON_DEPEND} + dev-util/intltool + sys-devel/gettext + virtual/pkgconfig" +RDEPEND="${COMMON_DEPEND} + net-misc/wget + gnuplot? ( >=sci-visualization/gnuplot-3.7 )" + +PATCHES=( + # https://github.com/Qalculate/libqalculate/issues/6 + "${FILESDIR}"/${P}-readline.patch +) + +src_prepare() { + default + + cat >po/POTFILES.skip <<-EOF + # Required by make check + data/currencies.xml.in + data/datasets.xml.in + data/elements.xml.in + data/functions.xml.in + data/planets.xml.in + data/units.xml.in + data/variables.xml.in + src/defs2doc.cc + EOF +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_with readline) +} + +src_install() { + # docs/reference/Makefile.am -> referencedir= + emake \ + DESTDIR="${D}" \ + referencedir="${EPREFIX}/usr/share/doc/${PF}/html" \ + install + + dodoc AUTHORS ChangeLog NEWS README* TODO + + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-libs/libqalculate/metadata.xml b/sci-libs/libqalculate/metadata.xml new file mode 100644 index 000000000000..92e29b80e703 --- /dev/null +++ b/sci-libs/libqalculate/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">qalculate-0.9.7</remote-id> + <remote-id type="github">Qalculate/libqalculate</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/libsc/Manifest b/sci-libs/libsc/Manifest new file mode 100644 index 000000000000..0046fe5d3539 --- /dev/null +++ b/sci-libs/libsc/Manifest @@ -0,0 +1,8 @@ +DIST libsc-1.0.tar.gz 257930 SHA256 a9f8a0f342a4a92c4031735e044e7ee73d9fd7e6df3e50a51c4c5016e27ed1ba SHA512 bf5af600e9cbd4038b1bd40c88776b21be5d474e34f9aacf287b890d262a22dc50ca27982c2eb9adba9735c8d9bb1fc31de2a27b24cdab534e3b2f610d76db7d WHIRLPOOL 56f89fcaf90bc8d4f872cee4fe150f692933b39376758c42b67d2e42659c19a9332a1d5e6d2d81c011dade0c6ab40c526c69ce2168fe41060f5d4be1a6595b1b +DIST libsc-1.1.tar.gz 263643 SHA256 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+DESCRIPTION="Support for parallel scientific applications" +HOMEPAGE="http://www.p4est.org/" +SRC_URI="https://github.com/cburstedde/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="LGPL-2.1+" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug examples mpi romio static-libs" + +REQUIRED_USE="romio? ( mpi )" + +RDEPEND=" + dev-lang/lua:* + sys-apps/util-linux + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[romio?] )" + +DEPEND=" + ${RDEPEND} + virtual/pkgconfig" + +DOCS=( AUTHORS NEWS README ) + +src_prepare() { + default + + # Inject a version number into the build system + echo "${PV}" > ${S}/.tarball-version + eautoreconf +} + +src_configure() { + local myeconfargs=( + $(use_enable debug) + $(use_enable mpi) + $(use_enable romio mpiio) + $(use_enable static-libs static) + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + econf "${myeconfargs[@]}" +} + +src_install() { + default + + if use examples; then + docinto examples + dodoc -r example/* + docompress -x /usr/share/doc/${PF}/examples + else + # Remove compiled example binaries in case of -examples: + rm -r "${ED}"/usr/bin || die "rm failed" + fi + + # Remove ac files, bug #619806 + rm -r "${ED}"/usr/share/aclocal || die "rm failed" + + # Fix wrong installation paths: + dodir /usr/share/libsc + mv "${ED}"/etc/* "${ED}"/usr/share/libsc || die "mv failed" + rmdir "${ED}"/etc/ || die "rmdir failed" +} diff --git a/sci-libs/libsc/libsc-1.1-r1.ebuild b/sci-libs/libsc/libsc-1.1-r1.ebuild new file mode 100644 index 000000000000..6e0d90763200 --- /dev/null +++ b/sci-libs/libsc/libsc-1.1-r1.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils + +DESCRIPTION="Support for parallel scientific applications" +HOMEPAGE="http://www.p4est.org/" +SRC_URI="https://github.com/cburstedde/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="LGPL-2.1+" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug examples mpi romio static-libs" + +REQUIRED_USE="romio? ( mpi )" + +RDEPEND=" + dev-lang/lua:* + sys-apps/util-linux + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[romio?] )" + +DEPEND=" + ${RDEPEND} + virtual/pkgconfig" + +DOCS=( AUTHORS NEWS README ) + +AUTOTOOLS_AUTORECONF=true + +src_prepare() { + default + + # Inject a version number into the build system + echo "${PV}" > ${S}/.tarball-version + eautoreconf +} + +src_configure() { + local myeconfargs=( + $(use_enable debug) + $(use_enable mpi) + $(use_enable romio mpiio) + $(use_enable static-libs static) + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + econf "${myeconfargs[@]}" +} + +src_install() { + default + + if use examples; then + docinto examples + dodoc -r example/* + docompress -x /usr/share/doc/${PF}/examples + else + # Remove compiled example binaries in case of -examples: + rm -r "${ED}"/usr/bin || die "rm failed" + fi + + # Remove ac files, bug #619806 + rm -r "${ED}"/usr/share/aclocal || die "rm failed" + + # Fix wrong installation paths: + dodir /usr/share/libsc + mv "${ED}"/etc/* "${ED}"/usr/share/libsc || die "mv failed" + rmdir "${ED}"/etc/ || die "rmdir failed" +} diff --git a/sci-libs/libsc/libsc-2.0.ebuild b/sci-libs/libsc/libsc-2.0.ebuild new file mode 100644 index 000000000000..229d1ccd05fc --- /dev/null +++ b/sci-libs/libsc/libsc-2.0.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs eutils + +DESCRIPTION="Support for parallel scientific applications" +HOMEPAGE="http://www.p4est.org/" + +if [[ ${PV} = *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/cburstedde/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + SRC_URI="https://github.com/cburstedde/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="LGPL-2.1+" +SLOT="0" +IUSE="debug examples mpi openmp romio static-libs threads" + +REQUIRED_USE="romio? ( mpi )" + +RDEPEND=" + dev-lang/lua:* + sys-apps/util-linux + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[romio?] )" + +DEPEND=" + ${RDEPEND} + virtual/pkgconfig" + +DOCS=( AUTHORS NEWS README ) + +AUTOTOOLS_AUTORECONF=true + +pkg_pretend() { + if [[ ${MERGE_TYPE} != "binary" ]] && use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi +} + +src_prepare() { + default + + # Inject a version number into the build system + echo "${PV}" > ${S}/.tarball-version + eautoreconf +} + +src_configure() { + local myeconfargs=( + $(use_enable debug) + $(use_enable mpi) + $(use_enable openmp openmp) + $(use_enable romio mpiio) + $(use_enable static-libs static) + $(use_enable threads pthread) + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + econf "${myeconfargs[@]}" +} + +src_install() { + default + + if use examples; then + docinto examples + dodoc -r example/* + docompress -x /usr/share/doc/${PF}/examples + else + # Remove compiled example binaries in case of -examples: + rm -r "${ED}"/usr/bin || die "rm failed" + fi + + # Remove ac files, bug #619806 + rm -r "${ED}"/usr/share/aclocal || die "rm failed" + + # Fix wrong installation paths: + dodir /usr/share/libsc + mv "${ED}"/etc/* "${ED}"/usr/share/libsc || die "mv failed" + rmdir "${ED}"/etc/ || die "rmdir failed" + mv "${ED}"/usr/share/ini/* "${ED}"/usr/share/libsc || die "mv failed" + rmdir "${ED}"/usr/share/ini || die "rmdir failed" +} diff --git a/sci-libs/libsc/libsc-9999.ebuild b/sci-libs/libsc/libsc-9999.ebuild new file mode 100644 index 000000000000..229d1ccd05fc --- /dev/null +++ b/sci-libs/libsc/libsc-9999.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs eutils + +DESCRIPTION="Support for parallel scientific applications" +HOMEPAGE="http://www.p4est.org/" + +if [[ ${PV} = *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/cburstedde/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + SRC_URI="https://github.com/cburstedde/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="LGPL-2.1+" +SLOT="0" +IUSE="debug examples mpi openmp romio static-libs threads" + +REQUIRED_USE="romio? ( mpi )" + +RDEPEND=" + dev-lang/lua:* + sys-apps/util-linux + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[romio?] )" + +DEPEND=" + ${RDEPEND} + virtual/pkgconfig" + +DOCS=( AUTHORS NEWS README ) + +AUTOTOOLS_AUTORECONF=true + +pkg_pretend() { + if [[ ${MERGE_TYPE} != "binary" ]] && use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi +} + +src_prepare() { + default + + # Inject a version number into the build system + echo "${PV}" > ${S}/.tarball-version + eautoreconf +} + +src_configure() { + local myeconfargs=( + $(use_enable debug) + $(use_enable mpi) + $(use_enable openmp openmp) + $(use_enable romio mpiio) + $(use_enable static-libs static) + $(use_enable threads pthread) + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + ) + econf "${myeconfargs[@]}" +} + +src_install() { + default + + if use examples; then + docinto examples + dodoc -r example/* + docompress -x /usr/share/doc/${PF}/examples + else + # Remove compiled example binaries in case of -examples: + rm -r "${ED}"/usr/bin || die "rm failed" + fi + + # Remove ac files, bug #619806 + rm -r "${ED}"/usr/share/aclocal || die "rm failed" + + # Fix wrong installation paths: + dodir /usr/share/libsc + mv "${ED}"/etc/* "${ED}"/usr/share/libsc || die "mv failed" + rmdir "${ED}"/etc/ || die "rmdir failed" + mv "${ED}"/usr/share/ini/* "${ED}"/usr/share/libsc || die "mv failed" + rmdir "${ED}"/usr/share/ini || die "rmdir failed" +} diff --git a/sci-libs/libsc/metadata.xml b/sci-libs/libsc/metadata.xml new file mode 100644 index 000000000000..18bfaa1e5479 --- /dev/null +++ b/sci-libs/libsc/metadata.xml @@ -0,0 +1,22 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>tamiko@gentoo.org</email> + <name>Matthias Maier</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +The SC Library provides support for parallel scientific applications. +This support library is primarily used by sci-libs/p4est. + </longdescription> + <use> + <flag name="romio">Build with support for the ROMIO MPI-IO component</flag> + </use> + <upstream> + <remote-id type="github">cburstedde/libsc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/libsigrok/Manifest b/sci-libs/libsigrok/Manifest new file mode 100644 index 000000000000..b8c9985cb076 --- /dev/null +++ b/sci-libs/libsigrok/Manifest @@ -0,0 +1,12 @@ +AUX libsigrok-0.3.0-configure-flags.patch 6291 SHA256 f33627bb98ac855377f20079bd11e3dc067dcb9b15d8b75d455db8729372bf4d SHA512 a7df284a3598dada9ddd63c7fe84b99fdec11a36724656c444a9deb80d0e29c633d85166d926279f3870d800b07816b50198c285a985304041134ad0c84f89c1 WHIRLPOOL 0b12268dd36719fe279478d02e035794551ea900f74ce68898fefa7db07ae507f5c6a8c02eb6a15a82f661b485f0c4f857f0340896b741c3dc50c4bdacd02c0f +AUX libsigrok-0.3.0-no-check-linkage.patch 980 SHA256 3b37d96b0800fbf3da35697c0b504f1bafafeaa1028eaafdda0372f8d1fa6b96 SHA512 45d31733c9942cedd916819baa842ae9b68de7ac9f7fc5d440f93d5eb2ea13975c3a4ac7116d80d669c7f942f5342e616da208b83a98ea005fe6a62fab3db373 WHIRLPOOL 44b41cf0f0d6ed0213954fae51c93094ff886a9c29e6b287c31c92bafe66104f9264aab7a0ea517de512e08c427ec307d21f8e964f833ab065e990dc24bba473 +DIST libsigrok-0.3.0.tar.gz 924503 SHA256 43926907a06f1d7aa73c68ae379d66412ac2728483eed7d20a8cf061f73f7050 SHA512 b94e8a8da1346f9ab267fd693975411243f2cb016e48ec05f4ad88a8a1dfe5ed6f5ad4ac4bf0e94dc551dc92cd70d2719983e21abaa4811693fb28a27bf74550 WHIRLPOOL 709b1e7fd0b3f864129ade9d91cc072cf72675bc10ec053e71cd0e7ce18442d405dc8ab5d435ac59694360a2be4f5a9a2ceb559dd3e6c7a7736dafa7a04ccae7 +DIST libsigrok-0.4.0.tar.gz 1387329 SHA256 5f291f3fee36e6dab1336f1c78596e50588831bc5ebd7cddc2a95fe8c71d669e SHA512 5963c1a44cf351a38d9434f89a15b20d36c7196a78464c302c65ab262bcdb2f26274c7fabf01174757e1f9a367497b9721578ebf802f75ef97ee71ff3dade1e0 WHIRLPOOL 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66db0a2f5de48ec701c30e5c95562ec8508703fecb30a781d05ab74fc5db1e7ea6ff828b43eb68dda16f56833744a55f3f7c7911d889866b098bdcafe5a62f1b WHIRLPOOL daa9978df9729094d3284ecbc51b8982ee27b650c515bb75aad14d0412511e1e3fd89d49bfb6ec3258d4d0b1766a27d88d930faf0bc1206ef93bf128d931806b diff --git a/sci-libs/libsigrok/files/libsigrok-0.3.0-configure-flags.patch b/sci-libs/libsigrok/files/libsigrok-0.3.0-configure-flags.patch new file mode 100644 index 000000000000..16e13349360c --- /dev/null +++ b/sci-libs/libsigrok/files/libsigrok-0.3.0-configure-flags.patch @@ -0,0 +1,169 @@ +https://sourceforge.net/p/sigrok/mailman/message/32459490/ + +From de8690fe8aad81f963f14cf1bd7d6e7013d9d747 Mon Sep 17 00:00:00 2001 +From: Mike Frysinger <vapier@gentoo.org> +Date: Fri, 13 Jun 2014 19:09:35 -0400 +Subject: [PATCH] add explicit configure flags for ftdi/serial/usb libraries + +This makes it a lot easier for distros to control this functionality. +--- + configure.ac | 118 +++++++++++++++++++++++++++++++++++++++-------------------- + 1 file changed, 79 insertions(+), 39 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 496bc7a..f23e630 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -261,6 +261,18 @@ AC_ARG_ENABLE(zeroplus-logic-cube, + [HW_ZEROPLUS_LOGIC_CUBE="$enableval"], + [HW_ZEROPLUS_LOGIC_CUBE=$HW_ENABLED_DEFAULT]) + ++AC_ARG_ENABLE(libserialport, ++ AC_HELP_STRING([--disable-libserialport], ++ [disable libserialport support [default=detect]])) ++ ++AC_ARG_ENABLE(libftdi, ++ AC_HELP_STRING([--disable-libftdi], ++ [disable libftdi support [default=detect]])) ++ ++AC_ARG_ENABLE(libusb, ++ AC_HELP_STRING([--disable-libusb], ++ [disable libusb support [default=detect]])) ++ + # Checks for libraries. + + case "$host" in +@@ -302,19 +314,28 @@ PKG_CHECK_MODULES([libzip], [libzip >= 0.10], + + # libserialport is only needed for some hardware drivers. Disable the + # respective drivers if it is not found. +-PKG_CHECK_MODULES([libserialport], [libserialport >= 0.1.0], +- [have_libserialport="yes"; LIB_CFLAGS="$LIB_CFLAGS $libserialport_CFLAGS"; +- LIBS="$LIBS $libserialport_LIBS"; +- SR_PKGLIBS="$SR_PKGLIBS libserialport"], +- [have_libserialport="no"; HW_AGILENT_DMM="no"; HW_APPA_55II="no"; ++if test "x$enable_libserialport" != "xno"; then ++ PKG_CHECK_MODULES([libserialport], [libserialport >= 0.1.0], ++ [have_libserialport="yes"; LIB_CFLAGS="$LIB_CFLAGS $libserialport_CFLAGS"; ++ LIBS="$LIBS $libserialport_LIBS"; ++ SR_PKGLIBS="$SR_PKGLIBS libserialport"], ++ [have_libserialport="no"]) ++ if test "x$enable_libserialport$have_libserialport" = "xyesno"; then ++ AC_MSG_ERROR([libserialport support requested, but it was not found]) ++ fi ++else ++ have_libserialport="no" ++fi ++ ++# Define HAVE_LIBSERIALPORT in config.h if we found libserialport. ++if test "x$have_libserialport" = "xno"; then ++ HW_AGILENT_DMM="no"; HW_APPA_55II="no"; + HW_ATTEN_PPS3XXX="no"; HW_BRYMEN_DMM="no"; HW_CEM_DT_885X="no"; + HW_CENTER_3XX="no"; HW_COLEAD_SLM="no"; HW_CONRAD_DIGI_35_CPU="no"; + HW_FLUKE_DMM="no"; HW_GMC_MH_1X_2X="no"; HW_HAMEG_HMO="no"; + HW_MIC_985XX="no"; HW_NORMA_DMM="no"; HW_OLS="no"; +- HW_SERIAL_DMM="no"; HW_TELEINFO="no"; HW_TONDAJ_SL_814="no"]) +- +-# Define HAVE_LIBSERIALPORT in config.h if we found libserialport. +-if test "x$have_libserialport" != "xno"; then ++ HW_SERIAL_DMM="no"; HW_TELEINFO="no"; HW_TONDAJ_SL_814="no"; ++else + AC_DEFINE_UNQUOTED(HAVE_LIBSERIALPORT, [1], + [Specifies whether we have libserialport.]) + fi +@@ -340,43 +361,62 @@ fi + + # libusb-1.0 is only needed for some hardware drivers. Disable the respective + # drivers if it is not found. +-case "$host" in +-*freebsd*) +- # FreeBSD comes with an "integrated" libusb-1.0-style USB API. +- # This means libusb-1.0 is always available, no need to check for it, +- # and no need to (potentially) disable any drivers if it's not found. ++if test "x$enable_libusb" != "xno"; then ++ case "$host" in ++ *freebsd*) ++ # FreeBSD comes with an "integrated" libusb-1.0-style USB API. ++ # This means libusb-1.0 is always available, no need to check for it, ++ # and no need to (potentially) disable any drivers if it's not found. ++ have_libusb1_0="yes" ++ ;; ++ *) ++ PKG_CHECK_MODULES([libusb], [libusb-1.0 >= 1.0.16], ++ [have_libusb1_0="yes"; LIB_CFLAGS="$LIB_CFLAGS $libusb_CFLAGS"; ++ LIBS="$LIBS $libusb_LIBS"; ++ SR_PKGLIBS="$SR_PKGLIBS libusb-1.0"], ++ [have_libusb1_0="no"]) ++ if test "x$enable_libusb$have_libusb1_0" = "xyesno"; then ++ AC_MSG_ERROR([libusb support requested, but it was not found]) ++ fi ++ ;; ++ esac ++else ++ have_libusb1_0="no" ++fi ++ ++# Define HAVE_LIBUSB_1_0 in config.h if we found libusb-1.0. ++if test "x$have_libusb1_0" = "xno"; then ++ HW_BRYMEN_BM86X="no"; HW_FX2LAFW="no"; ++ HW_HANTEK_DSO="no"; HW_IKALOGIC_SCANALOGIC2="no"; ++ HW_KECHENG_KC_330B="no"; HW_LASCAR_EL_USB="no"; ++ HW_SYSCLK_LWLA="no"; HW_UNI_T_DMM="no"; ++ HW_UNI_T_UT32X="no"; HW_VICTOR_DMM="no"; ++ HW_ZEROPLUS_LOGIC_CUBE="no"; HW_SALEAE_LOGIC16="no"; ++else + AC_DEFINE_UNQUOTED(HAVE_LIBUSB_1_0, [1], + [Specifies whether we have a libusb.h header.]) +- ;; +-*) +- PKG_CHECK_MODULES([libusb], [libusb-1.0 >= 1.0.16], +- [have_libusb1_0="yes"; LIB_CFLAGS="$LIB_CFLAGS $libusb_CFLAGS"; +- LIBS="$LIBS $libusb_LIBS"; +- SR_PKGLIBS="$SR_PKGLIBS libusb-1.0"], +- [have_libusb1_0="no"; HW_BRYMEN_BM86X="no"; HW_FX2LAFW="no"; +- HW_HANTEK_DSO="no"; HW_IKALOGIC_SCANALOGIC2="no"; +- HW_KECHENG_KC_330B="no"; HW_LASCAR_EL_USB="no"; +- HW_SYSCLK_LWLA="no"; HW_UNI_T_DMM="no"; +- HW_UNI_T_UT32X="no"; HW_VICTOR_DMM="no"; +- HW_ZEROPLUS_LOGIC_CUBE="no"; HW_SALEAE_LOGIC16="no"]) +- +- # Define HAVE_LIBUSB_1_0 in config.h if we found libusb-1.0. +- if test "x$have_libusb1_0" != "xno"; then +- AC_DEFINE_UNQUOTED(HAVE_LIBUSB_1_0, [1], +- [Specifies whether we have a libusb.h header.]) +- fi +- ;; +-esac ++fi + + # USB + FX2 firmware helper code is only compiled in if libusb-1.0 was found. + AM_CONDITIONAL(NEED_USB, test "x$have_libusb1_0" != xno) + + # libftdi is only needed for some hardware drivers. Disable them if not found. +-PKG_CHECK_MODULES([libftdi], [libftdi >= 0.16], +- [LIB_CFLAGS="$LIB_CFLAGS $libftdi_CFLAGS"; +- LIBS="$LIBS $libftdi_LIBS"; +- SR_PKGLIBS="$SR_PKGLIBS libftdi"], +- [HW_ASIX_SIGMA="no"; HW_CHRONOVU_LA="no"; HW_IKALOGIC_SCANAPLUS="no"]) ++if test "x$enable_libftdi" != "xno"; then ++ PKG_CHECK_MODULES([libftdi], [libftdi >= 0.16], ++ [have_libftdi="yes"; LIB_CFLAGS="$LIB_CFLAGS $libftdi_CFLAGS"; ++ LIBS="$LIBS $libftdi_LIBS"; ++ SR_PKGLIBS="$SR_PKGLIBS libftdi"], ++ [have_libftdi="no"]) ++ if test "x$enable_libftdi$have_libftdi" = "xyesno"; then ++ AC_MSG_ERROR([libftdi support requested, but it was not found]) ++ fi ++else ++ have_libftdi="no" ++fi ++ ++if test "x$have_libftdi" = "xno"; then ++ HW_ASIX_SIGMA="no"; HW_CHRONOVU_LA="no"; HW_IKALOGIC_SCANAPLUS="no"; ++fi + + # The Check unit testing framework is optional. Disable if not found. + PKG_CHECK_MODULES([check], [check >= 0.9.4], +-- +2.0.0 + diff --git a/sci-libs/libsigrok/files/libsigrok-0.3.0-no-check-linkage.patch b/sci-libs/libsigrok/files/libsigrok-0.3.0-no-check-linkage.patch new file mode 100644 index 000000000000..f638c47b196e --- /dev/null +++ b/sci-libs/libsigrok/files/libsigrok-0.3.0-no-check-linkage.patch @@ -0,0 +1,30 @@ +https://sourceforge.net/p/sigrok/mailman/message/32459488/ + +From 5326833697a73826babb6a43c74112da7368d2d6 Mon Sep 17 00:00:00 2001 +From: Mike Frysinger <vapier@gentoo.org> +Date: Fri, 13 Jun 2014 21:17:23 -0400 +Subject: [PATCH] do not add check to common cflags/libs + +Only the unittests use these flags, so don't go linking them in for +the main library too. +--- + configure.ac | 3 +-- + 1 file changed, 1 insertion(+), 2 deletions(-) + +diff --git a/configure.ac b/configure.ac +index f23e630..d0654f1 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -420,8 +420,7 @@ fi + + # The Check unit testing framework is optional. Disable if not found. + PKG_CHECK_MODULES([check], [check >= 0.9.4], +- [have_check="yes"; LIB_CFLAGS="$LIB_CFLAGS $check_CFLAGS"; +- LIBS="$LIBS $check_LIBS"], [have_check="no"]) ++ [have_check="yes"], [have_check="no"]) + AM_CONDITIONAL(HAVE_CHECK, test x"$have_check" = "xyes") + + # The OLS driver uses serial port file descriptors directly, and therefore +-- +2.0.0 + diff --git a/sci-libs/libsigrok/libsigrok-0.3.0.ebuild b/sci-libs/libsigrok/libsigrok-0.3.0.ebuild new file mode 100644 index 000000000000..21530e0ef700 --- /dev/null +++ b/sci-libs/libsigrok/libsigrok-0.3.0.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils autotools + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="amd64 x86" +fi + +DESCRIPTION="basic hardware drivers for logic analyzers and input/output file format support" +HOMEPAGE="http://sigrok.org/wiki/Libsigrok" + +LICENSE="GPL-3" +SLOT="0" +IUSE="ftdi serial static-libs test usb" + +# We also support librevisa, but that isn't in the tree ... +LIB_DEPEND=">=dev-libs/glib-2.32.0[static-libs(+)] + >=dev-libs/libzip-0.8:=[static-libs(+)] + ftdi? ( >=dev-embedded/libftdi-0.16:=[static-libs(+)] ) + serial? ( >=dev-libs/libserialport-0.1.0[static-libs(+)] ) + usb? ( virtual/libusb:1[static-libs(+)] )" +RDEPEND="!static-libs? ( ${LIB_DEPEND//\[static-libs(+)]} ) + static-libs? ( ${LIB_DEPEND} )" +DEPEND="${LIB_DEPEND//\[static-libs(+)]} + test? ( >=dev-libs/check-0.9.4 ) + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-0.3.0-configure-flags.patch + epatch "${FILESDIR}"/${PN}-0.3.0-no-check-linkage.patch + eautoreconf + + # Deal with libftdi-0.x & libftdi-1.x changes. + if has_version dev-embedded/libftdi:1 ; then + sed -i 's:libftdi >= 0.16:libftdi1 >= 0.16:g' configure || die + fi + + # Fix implicit decl w/usleep. + sed -i '1i#include <unistd.h>' hardware/asix-sigma/asix-sigma.c || die +} + +src_configure() { + econf \ + $(use_enable ftdi libftdi) \ + $(use_enable serial libserialport) \ + $(use_enable usb libusb) \ + $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrok/libsigrok-0.4.0.ebuild b/sci-libs/libsigrok/libsigrok-0.4.0.ebuild new file mode 100644 index 000000000000..8d30801c1008 --- /dev/null +++ b/sci-libs/libsigrok/libsigrok-0.4.0.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="6" + +PYTHON_COMPAT=( python{2_7,3_{4,5}} ) + +inherit eutils python-single-r1 java-pkg-opt-2 + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="basic hardware drivers for logic analyzers and input/output file format support" +HOMEPAGE="http://sigrok.org/wiki/Libsigrok" + +LICENSE="GPL-3" +SLOT="0" +IUSE="cxx ftdi java parport python serial static-libs test usb" +REQUIRED_USE="java? ( cxx ) python? ( cxx ${PYTHON_REQUIRED_USE} )" + +# We also support librevisa, but that isn't in the tree ... +LIB_DEPEND=">=dev-libs/glib-2.32.0[static-libs(+)] + >=dev-libs/libzip-0.8:=[static-libs(+)] + cxx? ( dev-cpp/glibmm:2[static-libs(+)] ) + python? ( ${PYTHON_DEPS} >=dev-python/pygobject-3.0.0[${PYTHON_USEDEP}] ) + ftdi? ( >=dev-embedded/libftdi-0.16:=[static-libs(+)] ) + parport? ( sys-libs/libieee1284[static-libs(+)] ) + serial? ( >=dev-libs/libserialport-0.1.1[static-libs(+)] ) + usb? ( virtual/libusb:1[static-libs(+)] )" +RDEPEND="!static-libs? ( ${LIB_DEPEND//\[static-libs(+)]} ) + static-libs? ( ${LIB_DEPEND} ) + java? ( >=virtual/jre-1.4 )" +DEPEND="${LIB_DEPEND//\[static-libs(+)]} + test? ( >=dev-libs/check-0.9.4 ) + cxx? ( app-doc/doxygen ) + java? ( + >=dev-lang/swig-3.0.6 + >=virtual/jdk-1.4 + ) + python? ( + >=dev-lang/swig-3.0.6 + ) + virtual/pkgconfig" + +pkg_setup() { + use python && python-single-r1_pkg_setup + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + [[ ${PV} == "9999" ]] && eautoreconf + eapply_user +} + +src_configure() { + econf \ + $(use_with ftdi libftdi) \ + $(use_with parport libieee1284) \ + $(use_with serial libserialport) \ + $(use_with usb libusb) \ + $(use_enable cxx) \ + $(use_enable java) \ + $(use_enable python) \ + --disable-ruby \ + $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrok/libsigrok-0.5.0.ebuild b/sci-libs/libsigrok/libsigrok-0.5.0.ebuild new file mode 100644 index 000000000000..8d30801c1008 --- /dev/null +++ b/sci-libs/libsigrok/libsigrok-0.5.0.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="6" + +PYTHON_COMPAT=( python{2_7,3_{4,5}} ) + +inherit eutils python-single-r1 java-pkg-opt-2 + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="basic hardware drivers for logic analyzers and input/output file format support" +HOMEPAGE="http://sigrok.org/wiki/Libsigrok" + +LICENSE="GPL-3" +SLOT="0" +IUSE="cxx ftdi java parport python serial static-libs test usb" +REQUIRED_USE="java? ( cxx ) python? ( cxx ${PYTHON_REQUIRED_USE} )" + +# We also support librevisa, but that isn't in the tree ... +LIB_DEPEND=">=dev-libs/glib-2.32.0[static-libs(+)] + >=dev-libs/libzip-0.8:=[static-libs(+)] + cxx? ( dev-cpp/glibmm:2[static-libs(+)] ) + python? ( ${PYTHON_DEPS} >=dev-python/pygobject-3.0.0[${PYTHON_USEDEP}] ) + ftdi? ( >=dev-embedded/libftdi-0.16:=[static-libs(+)] ) + parport? ( sys-libs/libieee1284[static-libs(+)] ) + serial? ( >=dev-libs/libserialport-0.1.1[static-libs(+)] ) + usb? ( virtual/libusb:1[static-libs(+)] )" +RDEPEND="!static-libs? ( ${LIB_DEPEND//\[static-libs(+)]} ) + static-libs? ( ${LIB_DEPEND} ) + java? ( >=virtual/jre-1.4 )" +DEPEND="${LIB_DEPEND//\[static-libs(+)]} + test? ( >=dev-libs/check-0.9.4 ) + cxx? ( app-doc/doxygen ) + java? ( + >=dev-lang/swig-3.0.6 + >=virtual/jdk-1.4 + ) + python? ( + >=dev-lang/swig-3.0.6 + ) + virtual/pkgconfig" + +pkg_setup() { + use python && python-single-r1_pkg_setup + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + [[ ${PV} == "9999" ]] && eautoreconf + eapply_user +} + +src_configure() { + econf \ + $(use_with ftdi libftdi) \ + $(use_with parport libieee1284) \ + $(use_with serial libserialport) \ + $(use_with usb libusb) \ + $(use_enable cxx) \ + $(use_enable java) \ + $(use_enable python) \ + --disable-ruby \ + $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrok/libsigrok-9999.ebuild b/sci-libs/libsigrok/libsigrok-9999.ebuild new file mode 100644 index 000000000000..8d30801c1008 --- /dev/null +++ b/sci-libs/libsigrok/libsigrok-9999.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="6" + +PYTHON_COMPAT=( python{2_7,3_{4,5}} ) + +inherit eutils python-single-r1 java-pkg-opt-2 + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="basic hardware drivers for logic analyzers and input/output file format support" +HOMEPAGE="http://sigrok.org/wiki/Libsigrok" + +LICENSE="GPL-3" +SLOT="0" +IUSE="cxx ftdi java parport python serial static-libs test usb" +REQUIRED_USE="java? ( cxx ) python? ( cxx ${PYTHON_REQUIRED_USE} )" + +# We also support librevisa, but that isn't in the tree ... +LIB_DEPEND=">=dev-libs/glib-2.32.0[static-libs(+)] + >=dev-libs/libzip-0.8:=[static-libs(+)] + cxx? ( dev-cpp/glibmm:2[static-libs(+)] ) + python? ( ${PYTHON_DEPS} >=dev-python/pygobject-3.0.0[${PYTHON_USEDEP}] ) + ftdi? ( >=dev-embedded/libftdi-0.16:=[static-libs(+)] ) + parport? ( sys-libs/libieee1284[static-libs(+)] ) + serial? ( >=dev-libs/libserialport-0.1.1[static-libs(+)] ) + usb? ( virtual/libusb:1[static-libs(+)] )" +RDEPEND="!static-libs? ( ${LIB_DEPEND//\[static-libs(+)]} ) + static-libs? ( ${LIB_DEPEND} ) + java? ( >=virtual/jre-1.4 )" +DEPEND="${LIB_DEPEND//\[static-libs(+)]} + test? ( >=dev-libs/check-0.9.4 ) + cxx? ( app-doc/doxygen ) + java? ( + >=dev-lang/swig-3.0.6 + >=virtual/jdk-1.4 + ) + python? ( + >=dev-lang/swig-3.0.6 + ) + virtual/pkgconfig" + +pkg_setup() { + use python && python-single-r1_pkg_setup + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + [[ ${PV} == "9999" ]] && eautoreconf + eapply_user +} + +src_configure() { + econf \ + $(use_with ftdi libftdi) \ + $(use_with parport libieee1284) \ + $(use_with serial libserialport) \ + $(use_with usb libusb) \ + $(use_enable cxx) \ + $(use_enable java) \ + $(use_enable python) \ + --disable-ruby \ + $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrok/metadata.xml b/sci-libs/libsigrok/metadata.xml new file mode 100644 index 000000000000..60598929d67c --- /dev/null +++ b/sci-libs/libsigrok/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>embedded@gentoo.org</email> + <name>Embedded Gentoo</name> +</maintainer> +<longdescription> + libsigrok is a shared library written in C, which provides the basic + hardware access drivers for logic analyzers and other supported devices, + as well as input/output file format support. +</longdescription> +<use> + <flag name="ftdi">Enable drivers that need libftdi</flag> + <flag name="parport">Enable drivers that are parallel (IEEE1284) based</flag> + <flag name="serial">Enable drivers that are serial (RS232) based</flag> +</use> +</pkgmetadata> diff --git a/sci-libs/libsigrokdecode/Manifest b/sci-libs/libsigrokdecode/Manifest new file mode 100644 index 000000000000..8b476f777a8a --- /dev/null +++ b/sci-libs/libsigrokdecode/Manifest @@ -0,0 +1,14 @@ +AUX libsigrokdecode-0.3.0-configure-test.patch 859 SHA256 1cef6c17a6624fe6d56fbeb98d5bde4ee1ec76a684a751b92c4e929a682123ab SHA512 466f21110fa3a8dec268f0b28520fea3497fa36fa7e8a93b98ac9dc8d36ac2172f847a02814625fb2a24740c19dee4ffc06e889727a0385d2a848a72552819ae WHIRLPOOL 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15df289e0f962f564551f61ada3cfef0311f6af639887def780bf5ad3be105515c8d24c950ff340ed35d89b9cd994af3540322b684c5dec3b43ec6bb0041aa4e WHIRLPOOL b6c074cf39f6ec1e2d085151836db47f9a4d71bcc9cc3296889bfa10172c7f07837ca79c8613f9c483b1332683e78eebe88e0a433a7caf801fc7ccac2552cd53 diff --git a/sci-libs/libsigrokdecode/files/libsigrokdecode-0.3.0-configure-test.patch b/sci-libs/libsigrokdecode/files/libsigrokdecode-0.3.0-configure-test.patch new file mode 100644 index 000000000000..8c3b40206040 --- /dev/null +++ b/sci-libs/libsigrokdecode/files/libsigrokdecode-0.3.0-configure-test.patch @@ -0,0 +1,28 @@ +https://sourceforge.net/p/sigrok/mailman/message/32459769/ + +From dc83770847c39934f5cbc63c8652124fafcb8d0b Mon Sep 17 00:00:00 2001 +From: Mike Frysinger <vapier@gentoo.org> +Date: Sat, 14 Jun 2014 01:37:12 -0400 +Subject: [PATCH 1/2] fix test operator + +The == operator is not in POSIX. +--- + configure.ac | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/configure.ac b/configure.ac +index 9527379..3f661ec 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -125,7 +125,7 @@ AC_SUBST(MODNAME_PYTHON) + # We also need to find the name of the python3 executable (for 'make install'). + # Some OSes call this python3, some call it python3.2, etc. etc. + AC_CHECK_PROGS([PYTHON3], [python3.4 python3.3 python3.2 python3]) +-if test "x$PYTHON3" == "x"; then ++if test "x$PYTHON3" = "x"; then + AC_MSG_ERROR([cannot find python3 executable.]) + fi + +-- +2.0.0 + diff --git a/sci-libs/libsigrokdecode/files/libsigrokdecode-0.3.0-no-check-linkage.patch b/sci-libs/libsigrokdecode/files/libsigrokdecode-0.3.0-no-check-linkage.patch new file mode 100644 index 000000000000..a749a0bb64d8 --- /dev/null +++ b/sci-libs/libsigrokdecode/files/libsigrokdecode-0.3.0-no-check-linkage.patch @@ -0,0 +1,30 @@ +https://sourceforge.net/p/sigrok/mailman/message/32459770/ + +From 27ecf0c85482786f7617571c690797ab3f07f795 Mon Sep 17 00:00:00 2001 +From: Mike Frysinger <vapier@gentoo.org> +Date: Sat, 14 Jun 2014 01:38:58 -0400 +Subject: [PATCH 2/2] do not add check to common cflags/libs + +Only the unittests use these flags, so don't go linking them in for +the main library too. +--- + configure.ac | 3 +-- + 1 file changed, 1 insertion(+), 2 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 3f661ec..10213a7 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -134,8 +134,7 @@ AC_SEARCH_LIBS([pow], [m]) + + # The Check unit testing framework is optional. Disable if not found. + PKG_CHECK_MODULES([check], [check >= 0.9.4], +- [have_check="yes"; CFLAGS="$CFLAGS $check_CFLAGS"; +- LIBS="$LIBS $check_LIBS"], [have_check="no"]) ++ [have_check="yes"], [have_check="no"]) + AM_CONDITIONAL(HAVE_CHECK, test x"$have_check" = "xyes") + + # libsigrok is optional (only used for the protocol decoder test framework). +-- +2.0.0 + diff --git a/sci-libs/libsigrokdecode/libsigrokdecode-0.3.0.ebuild b/sci-libs/libsigrokdecode/libsigrokdecode-0.3.0.ebuild new file mode 100644 index 000000000000..7bc6975993c6 --- /dev/null +++ b/sci-libs/libsigrokdecode/libsigrokdecode-0.3.0.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +PYTHON_COMPAT=( python3_4 ) +inherit eutils python-single-r1 autotools + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="provide (streaming) protocol decoding functionality" +HOMEPAGE="http://sigrok.org/wiki/Libsigrokdecode" + +LICENSE="GPL-3" +SLOT="0" +IUSE="static-libs" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=">=dev-libs/glib-2.24.0 + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-0.3.0-configure-test.patch + epatch "${FILESDIR}"/${PN}-0.3.0-no-check-linkage.patch + eautoreconf + + # Only a test program (not installed, and not used by src_test) + # is used by libsigrok, so disable it to avoid the compile. + sed -i \ + -e '/build_runtc=/s:yes:no:' \ + configure || die +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrokdecode/libsigrokdecode-0.4.0.ebuild b/sci-libs/libsigrokdecode/libsigrokdecode-0.4.0.ebuild new file mode 100644 index 000000000000..fdb04d423652 --- /dev/null +++ b/sci-libs/libsigrokdecode/libsigrokdecode-0.4.0.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="6" + +PYTHON_COMPAT=( python3_4 ) + +inherit eutils python-single-r1 + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="provide (streaming) protocol decoding functionality" +HOMEPAGE="http://sigrok.org/wiki/Libsigrokdecode" + +LICENSE="GPL-3" +SLOT="0" +IUSE="static-libs" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=">=dev-libs/glib-2.28.0 + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + [[ ${PV} == "9999" ]] && eautoreconf + + # Only a test program (not installed, and not used by src_test) + # is used by libsigrok, so disable it to avoid the compile. + sed -i \ + -e '/build_runtc=/s:yes:no:' \ + configure || die + + eapply_user +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrokdecode/libsigrokdecode-0.4.1.ebuild b/sci-libs/libsigrokdecode/libsigrokdecode-0.4.1.ebuild new file mode 100644 index 000000000000..b73e6e5f4b7a --- /dev/null +++ b/sci-libs/libsigrokdecode/libsigrokdecode-0.4.1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="6" + +PYTHON_COMPAT=( python3_{4,5,6} ) + +inherit eutils python-single-r1 + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="provide (streaming) protocol decoding functionality" +HOMEPAGE="http://sigrok.org/wiki/Libsigrokdecode" + +LICENSE="GPL-3" +SLOT="0" +IUSE="static-libs" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=">=dev-libs/glib-2.28.0 + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + [[ ${PV} == "9999" ]] && eautoreconf + + # Only a test program (not installed, and not used by src_test) + # is used by libsigrok, so disable it to avoid the compile. + sed -i \ + -e '/build_runtc=/s:yes:no:' \ + configure || die + + eapply_user +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrokdecode/libsigrokdecode-0.5.0.ebuild b/sci-libs/libsigrokdecode/libsigrokdecode-0.5.0.ebuild new file mode 100644 index 000000000000..b73e6e5f4b7a --- /dev/null +++ b/sci-libs/libsigrokdecode/libsigrokdecode-0.5.0.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="6" + +PYTHON_COMPAT=( python3_{4,5,6} ) + +inherit eutils python-single-r1 + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="provide (streaming) protocol decoding functionality" +HOMEPAGE="http://sigrok.org/wiki/Libsigrokdecode" + +LICENSE="GPL-3" +SLOT="0" +IUSE="static-libs" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=">=dev-libs/glib-2.28.0 + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + [[ ${PV} == "9999" ]] && eautoreconf + + # Only a test program (not installed, and not used by src_test) + # is used by libsigrok, so disable it to avoid the compile. + sed -i \ + -e '/build_runtc=/s:yes:no:' \ + configure || die + + eapply_user +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrokdecode/libsigrokdecode-9999.ebuild b/sci-libs/libsigrokdecode/libsigrokdecode-9999.ebuild new file mode 100644 index 000000000000..b73e6e5f4b7a --- /dev/null +++ b/sci-libs/libsigrokdecode/libsigrokdecode-9999.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="6" + +PYTHON_COMPAT=( python3_{4,5,6} ) + +inherit eutils python-single-r1 + +if [[ ${PV} == "9999" ]]; then + EGIT_REPO_URI="git://sigrok.org/${PN}" + inherit git-r3 autotools +else + SRC_URI="http://sigrok.org/download/source/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="provide (streaming) protocol decoding functionality" +HOMEPAGE="http://sigrok.org/wiki/Libsigrokdecode" + +LICENSE="GPL-3" +SLOT="0" +IUSE="static-libs" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=">=dev-libs/glib-2.28.0 + ${PYTHON_DEPS}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + [[ ${PV} == "9999" ]] && eautoreconf + + # Only a test program (not installed, and not used by src_test) + # is used by libsigrok, so disable it to avoid the compile. + sed -i \ + -e '/build_runtc=/s:yes:no:' \ + configure || die + + eapply_user +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_test() { + emake check +} + +src_install() { + default + prune_libtool_files +} diff --git a/sci-libs/libsigrokdecode/metadata.xml b/sci-libs/libsigrokdecode/metadata.xml new file mode 100644 index 000000000000..71b1461e1146 --- /dev/null +++ b/sci-libs/libsigrokdecode/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>embedded@gentoo.org</email> + <name>Embedded Gentoo</name> +</maintainer> +</pkgmetadata> diff --git a/sci-libs/libspatialindex/Manifest b/sci-libs/libspatialindex/Manifest new file mode 100644 index 000000000000..10c21e676890 --- /dev/null +++ b/sci-libs/libspatialindex/Manifest @@ -0,0 +1,9 @@ +AUX libspatialindex-1.8.1-QA.patch 549 SHA256 236e9c3d64a4b680441eb07de8a5a344586f55dd6e0fd936c6e3d2ed6e5b8cc0 SHA512 8dbaa89a8128d1209cb1e4d45f26ebf0ed635e896ee8470ed52eeb121894a0cfa344b888dbac58c96c62137e9750553d892833bdbf76959f9c51219360eb0170 WHIRLPOOL 7b2b40223f043b887d57161cb0b824d7c6c546f2b61ef975e0fe490e4ce522e222fb6d47b1f630759b7d182fa10106ebc5cf7fd45ee8605b0b1db09b9a0b2df2 +AUX libspatialindex-1.8.1-pkgconfig.patch 505 SHA256 7f764e0f46695c7852270de117bc19320dac78e41d6cb826dbc77408667fe801 SHA512 a673e1ea375c4d98a133a80b5d30ef1f0c4bd5ecc6388d50040b46666d8453e70c899f7034fae3977fa399bfec7c26f539dc52d25252cd934f7e295b7d161c09 WHIRLPOOL 459aebc442086673b3f202af5042ac8e470751d30c91e3dac381669e09d6e08b8c1a8a6e9c0e0dbf4f22d455708ba093be558cd783265d1557c16d202ad8f7b5 +DIST spatialindex-src-1.8.1.tar.bz2 368252 SHA256 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spatialindex-src-1.8.0/configure.ac +@@ -49,10 +49,10 @@ + AC_ARG_ENABLE(debug, [ --enable-debug=[no/yes] turn on debugging [default=$debug_default]],, enable_debug=$debug_default) + + if test "x$enable_debug" = "xyes"; then +- CXXFLAGS="$CXXFLAGS -g -DDEBUG" ++ CXXFLAGS="$CXXFLAGS -DDEBUG" + AC_MSG_RESULT(checking wether debug information is enabled... yes) + else +- CXXFLAGS="$CXXFLAGS -O2 -DNDEBUG" ++ CXXFLAGS="$CXXFLAGS -DNDEBUG" + AC_MSG_RESULT(checking wether debug information is enabled... no) + fi + diff --git a/sci-libs/libspatialindex/files/libspatialindex-1.8.1-pkgconfig.patch b/sci-libs/libspatialindex/files/libspatialindex-1.8.1-pkgconfig.patch new file mode 100644 index 000000000000..a17aa80926b1 --- /dev/null +++ b/sci-libs/libspatialindex/files/libspatialindex-1.8.1-pkgconfig.patch @@ -0,0 +1,16 @@ +From: Julian Ospald <hasufell@gentoo.org> +Date: Sun Jun 30 19:10:57 UTC 2013 +Subject: remove LDFLAGS from Libs field + +https://github.com/libspatialindex/libspatialindex/issues/23 + +--- spatialindex-src-1.8.1/src/libspatialindex.pc.in ++++ spatialindex-src-1.8.1/src/libspatialindex.pc.in +@@ -7,6 +7,6 @@ + Description: Generic C/C++ library for spatial indexing + Requires: + Version: @PACKAGE_VERSION@ +-Libs: -L@libdir@ @LDFLAGS@ ++Libs: -L@libdir@ + Cflags: -I${includedir}/spatialindex @CFLAGS@ @CPPFLAGS@ + diff --git a/sci-libs/libspatialindex/libspatialindex-1.8.1.ebuild b/sci-libs/libspatialindex/libspatialindex-1.8.1.ebuild new file mode 100644 index 000000000000..27123fc01822 --- /dev/null +++ b/sci-libs/libspatialindex/libspatialindex-1.8.1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils + +MY_PN="spatialindex-src" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="General framework for developing spatial indices" +HOMEPAGE="https://libspatialindex.github.com/" +SRC_URI="http://download.osgeo.org/libspatialindex/${MY_P}.tar.bz2" +LICENSE="MIT" + +KEYWORDS="amd64 x86" +SLOT="0" +IUSE="debug static-libs" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + epatch "${FILESDIR}"/${P}-{QA,pkgconfig}.patch + eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_enable debug) +} + +src_install() { + default + use static-libs || prune_libtool_files +} diff --git a/sci-libs/libspatialindex/libspatialindex-1.8.5-r1.ebuild b/sci-libs/libspatialindex/libspatialindex-1.8.5-r1.ebuild new file mode 100644 index 000000000000..0327f5819569 --- /dev/null +++ b/sci-libs/libspatialindex/libspatialindex-1.8.5-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils + +MY_PN="spatialindex-src" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="General framework for developing spatial indices" +HOMEPAGE="https://libspatialindex.github.com/" +SRC_URI="http://download.osgeo.org/libspatialindex/${MY_P}.tar.bz2" +LICENSE="MIT" + +KEYWORDS="~amd64 ~x86" +SLOT="0/4" +IUSE="debug static-libs" + +S=${WORKDIR}/${MY_P} + +PATCHES=( + "${FILESDIR}"/${PN}-1.8.1-QA.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_enable debug) +} + +src_install() { + default + use static-libs || prune_libtool_files +} diff --git a/sci-libs/libspatialindex/metadata.xml b/sci-libs/libspatialindex/metadata.xml new file mode 100644 index 000000000000..6f49eba8f496 --- /dev/null +++ b/sci-libs/libspatialindex/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<!-- maintainer-needed --> +</pkgmetadata> diff --git a/sci-libs/libsvm/Manifest b/sci-libs/libsvm/Manifest new file mode 100644 index 000000000000..2b40ffaba4d4 --- /dev/null +++ b/sci-libs/libsvm/Manifest @@ -0,0 +1,9 @@ +AUX 3.11-openmp.patch 943 SHA256 019c9c6d66384367d6d0dd8c1edb12e028a9260dd7268f2214e016b2905eba5a SHA512 17bcea4da6a6aa32192ce7fb66e7eefef5e037ca2afd968e67de385938555975abe2103ee2cc50d02cd21d9783e9334eac93de694d6e685f13af80c49e42af38 WHIRLPOOL 29de725824c2ec2fe55a5e2b272f6953b3b6b348b2e21c3d6ac5766748484f55b6e841e9cffaa4a18fa7f9fb31c562b2bc5bad206f948f4fc37756aefbcd41ec +AUX 3.14-makefile.patch 1634 SHA256 88aea720c824a5910c9bd9cf7e1e8eae8d3f0cbc9d12467734bb1156f7aedfb5 SHA512 f4c2e2f6556604bf3572e341176c855e87caf4c3db8c2b347ce4e7a7948d21b708a7df29d5bf9b741dd3f34e08a0750572b94bd5e94bb4052f1ba4b9ae50e918 WHIRLPOOL d5ada5b43ee143873f0a23d2ea0ecbb160202df29103e37eff93a759ae711c993d485865c16d287a668e002adce3147b51e403705d359fb1871860518417f675 +DIST libsvm-3.21.tar.gz 847291 SHA256 519e0bdc0e31ab8246e9035e7ca91f794c16084f80abe4dffe776261d23c772f SHA512 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start, j; + if((start = cache->get_data(i,&data,len)) < len) + { ++#ifdef OPENMP ++#pragma omp parallel for private(j) ++#endif + for(j=start;j<len;j++) + data[j] = (Qfloat)(y[i]*y[j]*(this->*kernel_function)(i,j)); + } +@@ -2463,7 +2466,10 @@ + model->param.svm_type == NU_SVR) + { + double *sv_coef = model->sv_coef[0]; +- double sum = 0; ++ double sum = 0; int i; ++#ifdef OPENMP ++#pragma omp parallel for private(i) reduction(+:sum) ++#endif + for(i=0;i<model->l;i++) + sum += sv_coef[i] * Kernel::k_function(x,model->SV[i],model->param); + sum -= model->rho[0]; +@@ -2480,6 +2486,9 @@ + int l = model->l; + + double *kvalue = Malloc(double,l); ++#ifdef OPENMP ++#pragma omp parallel for private(i) ++#endif + for(i=0;i<l;i++) + kvalue[i] = Kernel::k_function(x,model->SV[i],model->param); + diff --git a/sci-libs/libsvm/files/3.14-makefile.patch b/sci-libs/libsvm/files/3.14-makefile.patch new file mode 100644 index 000000000000..e38dafc10b20 --- /dev/null +++ b/sci-libs/libsvm/files/3.14-makefile.patch @@ -0,0 +1,51 @@ +* respect CFLAGS and CXXFLAGS from user +* compile with CC for C and CXX for C++ files +* propagate and respect user's LDFLAGS +* PIC only used for the library +* link the shared version library +nov 2012 - bicatali@gentoo.org + +--- a/Makefile.orig 2012-11-29 10:39:07.149421728 -0800 ++++ b/Makefile 2012-11-29 10:57:19.727766521 -0800 +@@ -1,9 +1,12 @@ + CXX ?= g++ +-CFLAGS = -Wall -Wconversion -O3 -fPIC ++CC ?= gcc ++CFLAGS ?= -Wall -Wconversion -O3 ++CXXFLAGS ?= $(CFLAGS) + SHVER = 2 + OS = $(shell uname) ++PICFLAGS ?= -fPIC + +-all: svm-train svm-predict svm-scale ++all: svm-train svm-predict svm-scale lib + + lib: svm.o + if [ "$(OS)" = "Darwin" ]; then \ +@@ -11,15 +14,20 @@ + else \ + SHARED_LIB_FLAG="-shared -Wl,-soname,libsvm.so.$(SHVER)"; \ + fi; \ +- $(CXX) $${SHARED_LIB_FLAG} svm.o -o libsvm.so.$(SHVER) ++ $(CXX) $(LDFLAGS) $${SHARED_LIB_FLAG} svm.o -o libsvm.so.$(SHVER) ; \ ++ ln -s libsvm.so.$(SHVER) libsvm.so + + svm-predict: svm-predict.c svm.o +- $(CXX) $(CFLAGS) svm-predict.c svm.o -o svm-predict -lm ++ $(CC) $(CFLAGS) -c $@.c -o $@.o ++ $(CXX) $(LDFLAGS) $@.o svm.o -lm -o $@ + svm-train: svm-train.c svm.o +- $(CXX) $(CFLAGS) svm-train.c svm.o -o svm-train -lm ++ $(CC) $(CFLAGS) -c $@.c -o $@.o ++ $(CXX) $(LDFLAGS) $@.o svm.o -lm -o $@ + svm-scale: svm-scale.c +- $(CXX) $(CFLAGS) svm-scale.c -o svm-scale ++ $(CC) $(CFLAGS) -c $@.c -o $@.o ++ $(CXX) $(LDFLAGS) $@.o -o $@ ++ + svm.o: svm.cpp svm.h +- $(CXX) $(CFLAGS) -c svm.cpp ++ $(CXX) $(CXXFLAGS) $(PICFLAGS) -c svm.cpp -o $@ + clean: +- rm -f *~ svm.o svm-train svm-predict svm-scale libsvm.so.$(SHVER) ++ rm -f *~ svm.o svm-train svm-predict svm-scale libsvm.so.$(SHVER) libsvm.so diff --git a/sci-libs/libsvm/libsvm-3.21.ebuild b/sci-libs/libsvm/libsvm-3.21.ebuild new file mode 100644 index 000000000000..b36a2fbf3219 --- /dev/null +++ b/sci-libs/libsvm/libsvm-3.21.ebuild @@ -0,0 +1,117 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_4,3_5} ) + +inherit flag-o-matic java-pkg-opt-2 python-r1 toolchain-funcs + +DESCRIPTION="Library for Support Vector Machines" +HOMEPAGE="http://www.csie.ntu.edu.tw/~cjlin/libsvm/" +SRC_URI="http://www.csie.ntu.edu.tw/~cjlin/libsvm/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="java openmp python tools" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +DEPEND=" + java? ( >=virtual/jdk-1.4 ) + python? ( ${PYTHON_DEPS} )" +RDEPEND=" + java? ( >=virtual/jre-1.4 ) + python? ( ${PYTHON_DEPS} ) + tools? ( sci-visualization/gnuplot )" + +PATCHES=( + "${FILESDIR}/3.11-openmp.patch" + "${FILESDIR}/3.14-makefile.patch" +) + +pkg_setup() { + if use openmp; then + if ! tc-has-openmp; then + ewarn "OpenMP is not supported by your currently selected compiler" + + if tc-is-clang; then + ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," + ewarn "which you will need to build ${CATEGORY}/${PN} for USE=\"openmp\"" + fi + + die "need openmp capable compiler" + fi + + append-cflags -fopenmp + append-cxxflags -fopenmp + append-cppflags -DOPENMP + fi +} + +src_prepare() { + default + + sed -i -e "s@\.\./@${EPREFIX}/usr/bin/@g" tools/*.py \ + || die "Failed to fix paths in python files" + sed -i -e "s|./grid.py|${EPREFIX}/usr/bin/svm-grid|g" tools/*.py \ + || die "Failed to fix paths for svm-grid" + sed -i -e 's/grid.py/svm-grid/g' tools/grid.py \ + || die "Failed to rename grid.py to svm-grid" + + if use java; then + local JAVAC_FLAGS="$(java-pkg_javac-args)" + sed -i \ + -e "s/JAVAC_FLAGS =/JAVAC_FLAGS=${JAVAC_FLAGS}/g" \ + java/Makefile || die "Failed to fix java makefile" + fi + tc-export CXX CC +} + +src_compile() { + default + use java && emake -C java +} + +src_install() { + dobin svm-train svm-predict svm-scale + dolib.so *.so* + doheader svm.h + + DOCS=( README ) + + if use tools; then + local t + for t in tools/*.py; do + python_foreach_impl python_newscript ${t} svm-$(basename ${t} .py) + done + + mv tools/README{,.tools} || die + DOCS+=( tools/README.tools ) + + insinto /usr/share/doc/${PF}/examples + docompress -x /usr/share/doc/${PF}/examples + doins heart_scale + doins -r svm-toy + fi + + if use python ; then + installation() { + touch python/__init__.py || die + python_moduleinto libsvm + python_domodule python/*.py + } + python_foreach_impl installation + + mv python/README{,.python} || die + DOCS+=( python/README.python ) + fi + + HTML_DOCS=( FAQ.html ) + if use java; then + java-pkg_dojar java/libsvm.jar + HTML_DOCS+=( java/test_applet.html ) + fi + + einstalldocs +} diff --git a/sci-libs/libsvm/libsvm-3.22.ebuild b/sci-libs/libsvm/libsvm-3.22.ebuild new file mode 100644 index 000000000000..57d4bbb5185f --- /dev/null +++ b/sci-libs/libsvm/libsvm-3.22.ebuild @@ -0,0 +1,117 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} ) + +inherit flag-o-matic java-pkg-opt-2 python-r1 toolchain-funcs + +DESCRIPTION="Library for Support Vector Machines" +HOMEPAGE="http://www.csie.ntu.edu.tw/~cjlin/libsvm/" +SRC_URI="http://www.csie.ntu.edu.tw/~cjlin/libsvm/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0/2" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="java openmp python tools" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +DEPEND=" + java? ( >=virtual/jdk-1.4 ) + python? ( ${PYTHON_DEPS} )" +RDEPEND=" + java? ( >=virtual/jre-1.4 ) + python? ( ${PYTHON_DEPS} ) + tools? ( sci-visualization/gnuplot )" + +PATCHES=( + "${FILESDIR}/3.11-openmp.patch" + "${FILESDIR}/3.14-makefile.patch" +) + +pkg_setup() { + if use openmp; then + if ! tc-has-openmp; then + ewarn "OpenMP is not supported by your currently selected compiler" + + if tc-is-clang; then + ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," + ewarn "which you will need to build ${CATEGORY}/${PN} for USE=\"openmp\"" + fi + + die "need openmp capable compiler" + fi + + append-cflags -fopenmp + append-cxxflags -fopenmp + append-cppflags -DOPENMP + fi +} + +src_prepare() { + default + + sed -i -e "s@\.\./@${EPREFIX}/usr/bin/@g" tools/*.py \ + || die "Failed to fix paths in python files" + sed -i -e "s|./grid.py|${EPREFIX}/usr/bin/svm-grid|g" tools/*.py \ + || die "Failed to fix paths for svm-grid" + sed -i -e 's/grid.py/svm-grid/g' tools/grid.py \ + || die "Failed to rename grid.py to svm-grid" + + if use java; then + local JAVAC_FLAGS="$(java-pkg_javac-args)" + sed -i \ + -e "s/JAVAC_FLAGS =/JAVAC_FLAGS=${JAVAC_FLAGS}/g" \ + java/Makefile || die "Failed to fix java makefile" + fi + tc-export CXX CC +} + +src_compile() { + default + use java && emake -C java +} + +src_install() { + dobin svm-train svm-predict svm-scale + dolib.so *.so* + doheader svm.h + + DOCS=( README ) + + if use tools; then + local t + for t in tools/*.py; do + python_foreach_impl python_newscript ${t} svm-$(basename ${t} .py) + done + + mv tools/README{,.tools} || die + DOCS+=( tools/README.tools ) + + insinto /usr/share/doc/${PF}/examples + docompress -x /usr/share/doc/${PF}/examples + doins heart_scale + doins -r svm-toy + fi + + if use python ; then + installation() { + touch python/__init__.py || die + python_moduleinto libsvm + python_domodule python/*.py + } + python_foreach_impl installation + + mv python/README{,.python} || die + DOCS+=( python/README.python ) + fi + + HTML_DOCS=( FAQ.html ) + if use java; then + java-pkg_dojar java/libsvm.jar + HTML_DOCS+=( java/test_applet.html ) + fi + + einstalldocs +} diff --git a/sci-libs/libsvm/metadata.xml b/sci-libs/libsvm/metadata.xml new file mode 100644 index 000000000000..7ba70023b93f --- /dev/null +++ b/sci-libs/libsvm/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The LIBSVM library is used to calculate Support Vector Machine + optimizations with a great variety of options. It includes + one-class, two-class, multiclass, regression-mode, and probablistic + output functionality. It is primarily of interest to machine-learning + researchers and artificial intelligence application developers. + </longdescription> + <use> + <flag name="tools">Install python based tool scripts for data selection and visualization with <pkg>sci-visualization/gnuplot</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-libs/libticables2/Manifest b/sci-libs/libticables2/Manifest new file mode 100644 index 000000000000..4d7c4490bbd5 --- /dev/null +++ b/sci-libs/libticables2/Manifest @@ -0,0 +1,9 @@ +DIST libticables2-1.3.3.tar.bz2 495883 SHA256 e31ffc2324884aeec37b0cc220e62c78a44c43ab874a933939bfe80c4e84071e SHA512 19c9a6bb8319ccf9e9004e10c4addffbee605c3735e53e4a5628b360b0c2e8575076208d14d00d6304eb894d3c69aede6de00120cd26f8c543c6e6cc4adb21a9 WHIRLPOOL ca916a99942097518fa686b1c68d9260852fa5f88ed4b60649471590c94e84e60ffc2f5cd74c91ec1f11393a0e65a5675ad06ae4d0879c41124f307cb03bb11c +DIST libticables2-1.3.4.tar.bz2 920163 SHA256 45cae91ad9ee1cc2ebc0f5865923ff77f1e0adf0793d3010eeb802efc140e5b0 SHA512 fbea9ed2041a04f79e02045d40e88a3ab20edc8d86ecef4ae6a181063f3609b8b2c3aeb2ce2f4508be56655accba60eab7379116ac341921f233f469eb99b461 WHIRLPOOL 1ce06ad05ffc9919dfc24a6f5ee1f31555d61b1693b994c7b2970d8a8ba551b0744c51d60d8d288c2df607b8961a8826543e2edac17090f692c4d36d7828b05d +DIST libticables2-1.3.5.tar.bz2 187416 SHA256 0c6fb6516e72ccab081ddb3aecceff694ed93aec689ddd2edba9c7c7406c4522 SHA512 171abdf41f496891c62da17a2b84d929ac32021b0f2abc0c37ed73ec93806d4a14df37a8ffbe2b0c172ff3461aa6c639fc1ba23aafb19e024b99448dd66c63bd WHIRLPOOL 9f4c4451035040767f7fff7186978dd69101b311930db88c72291273a45f28809591eff0210296fe016591f81de3424f8979f6469fb1d80656b2d156f5f3f58e +EBUILD libticables2-1.3.3-r1.ebuild 1163 SHA256 4e059a2aa8a853910bb5e885ca0a14010a7477cc956634a30bbd932b640cecb3 SHA512 c0f89f54dfc8c855ca99f453d0ea817f6bcef68566f0afacc7f155b395dbacac4c1d6f4ca52e1e8a9537331b368890a4a0b092fe5fb39090f32088151fa97895 WHIRLPOOL 7dd563ce989d55fa434a7b36576d1e57efa792c6b5b4a522fcd0d620a2e646bc16c2d064f07b4923049b3b4c47ce68e3c682f57e25cb6597ed595d5c10c73713 +EBUILD libticables2-1.3.4.ebuild 1123 SHA256 bff928e6bdfd7600d5eeb37dee69342b67db1a64a62b65b4eea58a78e9a4a5d5 SHA512 72f5a4a4a2b16d2c71d2fe095f858a57bd67a763ce1ca8cdeca2adb24740e803b80cf4afde5fb2f74d57ac09027bf69e4b62db6210098b89dc38652c048a8bdd WHIRLPOOL 7db2777cb5d20bf0f3105bfb7913d24cfda80edf0953fa9da8116ca6c84744222d0d73ce3058f6679ced61010a7ffe353ac462cd223c51a9884eb64282854e6e +EBUILD libticables2-1.3.5.ebuild 1196 SHA256 959a3eeb57eb23561da3584d1844b5d550431c08f1f9f320f385e0e5f92e6c7a SHA512 b0e4f957d5ebc028ba010c3b5613eb0b18398a41706d5cbb73b742441464bbff34134b5a2a34da32ba2cd3bd68a0c402896985d21138ab620dcf55eeec3f1678 WHIRLPOOL db98c740fc281f747aa359002ac852f7ea5d2f05dfe8532b382c1706dd6d9eb86b652db5026acabc35c71b90046f189f223ad0af7849dc91aead21f2e4a1427a +MISC ChangeLog 2552 SHA256 aa9b23d59d566136b43726f94ac65a6cce2a6f5d73a2d885a16bd264a5d60c3b SHA512 cf6c714dabf2e695c3ff5f209be0082a810a026c551960ffcee4f96e1ce83f87b260c7d3cc4488ae01bfc0beb68723d1fccef3b7b57c069f7a98eb0f11a194dd WHIRLPOOL 0a5fd775d57bebe05088e6345805e720531be885c89e1ac895bab86b43dba686ae1734029e4cbb3235e237acedca609e2500262bb2877ecfa4517a7a4e660324 +MISC ChangeLog-2015 3789 SHA256 6d832c16337e4d29e4890680c541d355a8fc4970bb4fd088f77fad228e50616b SHA512 422324c907bee70921174acae9bd222d8505dcfcce7af014d6ea76aaff9248b62788cfcdd66a60e2993f585a671882bd920dada535b77ddc93436a629b7d6d94 WHIRLPOOL 73278e1f386a912c572e65bafe13e27e746ffa393b2079d217029e55e435e9ed275d7662acf24f294ebc8d57d506d2e7652e345b8193fc0d851f5001dc6b1f37 +MISC metadata.xml 606 SHA256 bb54761bda32dbeb4e502a4f10ae37c8a7c782a2965979aef5cf5c2c1fba5f4a SHA512 c26d34796c6d803322c7ac15cc374d12f314a59313c4df26e00b0f3bf972195c106141fb6664f875b89e51a1db1cc2084ecf79ca41b55b68c1eede3262fe8dd7 WHIRLPOOL 77c99743cd649791968042b69509a116c70300cf53ef4739f087216b13914f4bdfb67ac267af44159ba6a7b38d784576eace24bbf7ea1baba4c623d5b62e6810 diff --git a/sci-libs/libticables2/libticables2-1.3.3-r1.ebuild b/sci-libs/libticables2/libticables2-1.3.3-r1.ebuild new file mode 100644 index 000000000000..6696e6c73d35 --- /dev/null +++ b/sci-libs/libticables2/libticables2-1.3.3-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils multilib + +DESCRIPTION="Library to handle different link cables for TI calculators" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="debug doc nls static-libs usb" + +RDEPEND=" + dev-libs/glib:2 + usb? ( virtual/libusb:1 ) + nls? ( virtual/libintl )" + +DEPEND="${RDEPEND} + virtual/pkgconfig + nls? ( sys-devel/gettext )" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_configure() { + # --disable-libusb $(use_enable usb libusb10) would enable virtual/libusb:1 + econf \ + --disable-rpath \ + $(use_enable debug logging) \ + $(use_enable nls) \ + $(use_enable static-libs static) \ + $(use_enable usb libusb) \ + $(use_enable usb libusb10) +} + +src_install() { + default + use doc && dohtml docs/html/* + use static-libs || rm -f "${ED}"/usr/$(get_libdir)/${PN}.la +} + +pkg_postinst() { + elog "Please read README in /usr/share/doc/${PF}" + elog "if you encounter any problem with a link cable" +} diff --git a/sci-libs/libticables2/libticables2-1.3.4.ebuild b/sci-libs/libticables2/libticables2-1.3.4.ebuild new file mode 100644 index 000000000000..3ac960c27d3a --- /dev/null +++ b/sci-libs/libticables2/libticables2-1.3.4.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Library to handle different link cables for TI calculators" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="debug doc nls static-libs usb" + +RDEPEND=" + dev-libs/glib:2 + usb? ( virtual/libusb:1 ) + nls? ( virtual/libintl )" + +DEPEND="${RDEPEND} + virtual/pkgconfig + nls? ( sys-devel/gettext )" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_configure() { + # --disable-libusb $(use_enable usb libusb10) would enable virtual/libusb:1 + local myeconfargs=( + --disable-rpath + $(use_enable debug logging) + $(use_enable nls) + $(use_enable usb libusb) + $(use_enable usb libusb10) + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + use doc && dohtml docs/html/* +} + +pkg_postinst() { + elog "Please read README in /usr/share/doc/${PF}" + elog "if you encounter any problem with a link cable" +} diff --git a/sci-libs/libticables2/libticables2-1.3.5.ebuild b/sci-libs/libticables2/libticables2-1.3.5.ebuild new file mode 100644 index 000000000000..0e42cb2ab1a4 --- /dev/null +++ b/sci-libs/libticables2/libticables2-1.3.5.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library to handle different link cables for TI calculators" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="debug doc nls static-libs usb" + +RDEPEND=" + dev-libs/glib:2 + usb? ( virtual/libusb:1 ) + nls? ( virtual/libintl )" + +DEPEND="${RDEPEND} + virtual/pkgconfig + nls? ( sys-devel/gettext )" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + # --disable-libusb $(use_enable usb libusb10) would enable virtual/libusb:1 + econf \ + --disable-rpath \ + $(use_enable static-libs static) \ + $(use_enable debug logging) \ + $(use_enable nls) \ + $(use_enable usb libusb) \ + $(use_enable usb libusb10) +} + +src_install() { + use doc && HTML_DOCS+=( docs/html/. ) + default + find "${D}" -name '*.la' -delete || die +} + +pkg_postinst() { + elog "Please read README in ${EROOT%/}/usr/share/doc/${PF}" + elog "if you encounter any problem with a link cable" +} diff --git a/sci-libs/libticables2/metadata.xml b/sci-libs/libticables2/metadata.xml new file mode 100644 index 000000000000..913b1258a5b3 --- /dev/null +++ b/sci-libs/libticables2/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + This library provides functions to use Texas Instruments link cables + for TI calculators. It currently supports all cables on i386, + including the USB one. Supported cables may vary depending on your + architecture. +</longdescription> + <upstream> + <remote-id type="sourceforge">tilp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/libticalcs2/Manifest b/sci-libs/libticalcs2/Manifest new file mode 100644 index 000000000000..7c897e777331 --- /dev/null +++ b/sci-libs/libticalcs2/Manifest @@ -0,0 +1,7 @@ +DIST libticalcs2-1.1.8.tar.bz2 524151 SHA256 a8286f8a2552bcad96beab99ce254e67b3dc1a03eb9d82f8de4bdf7b8efc3496 SHA512 0e09148006f5ee227d1b347ef44a6e755cb1dd757b8ff99e0f006aec0bc37c40dc5e293e44a0d91fc966b47da9113b4f00a71d9d9aa5cfbea4b01487232c1c08 WHIRLPOOL 3458fd04e791a174506d21930b1843aa204cf63c504dc93e1f81e8e71e4646fa45493d2056bc6be6b7495f9a9e8afbfe802c3d55c698a70f95d1172dcb73c0c1 +DIST libticalcs2-1.1.9.tar.bz2 269963 SHA256 76780788bc309b647f97513d38dd5f01611c335a72855e0bd10c7bdbf2e38921 SHA512 a55fa92df787929397f4ed3e8f922355f71c7883459ceb98fbb8d39d18f06441147188aaabf7a67083d70549443e439744e68527742e2b7b5d3d2838cc41b4da WHIRLPOOL e965283ac347ea767bcfc6b2b9cc5cf81b45c7d932041370b839f24e2fc57ff18f2f59c4a1b6013cf9f0ae4c8c8219fcb7d4f0779653fb7fdf3ae22b36a47344 +EBUILD libticalcs2-1.1.8.ebuild 872 SHA256 a8e437c65c1eb5c7740689fda71f79c05355d5e7b882d70fcff541b6cb919904 SHA512 5971c7ffe9d8f22c224b967047b4d850d9de590ade19d01254668c851395ec483d4e0e13946cd1cb0adbbda56fcd42f27a05d1a4e7793fefad2014a36e2e47eb WHIRLPOOL 058b54b45f5766dd97cb655e6878e935d203bf11f5e2e1a94c58160bbd84212e9e6ab93031ef1ff49258e9ff8bf7c3cc33fd3e271d758a0ee8de728b0d39b8dc +EBUILD libticalcs2-1.1.9.ebuild 929 SHA256 b0fa1567f6543fbcdcff3677d8801a9d1ebd41e214da57bcae262f8a45407bea SHA512 53bcbcd5017d6ed7c586295774f1a534c3cfa5ce833a282239fbed6a2893ff273760d36a29878e2d35691ad681cfb4be4909d7a9e8cfc233422c3c55a3c6215f WHIRLPOOL 2980b606b53ff757f9b5b356906f885f96370236b8989665db08438384a49fab8ac63cfced85d627428b7fb99e8e8594df6bd8e6753a923cea43a0d89953d5fc +MISC ChangeLog 2540 SHA256 b724d50f062c8751cf13f778aab887ed5d33c448110f0dee83f2ef313ab0bc36 SHA512 296eeed37b6e4eecccbf49e0d6371e41a6fba3bb22979c581a4f9c342ecfe9ecdba26eb23697690eda719335370fb63e561508432998649eebc674d606075929 WHIRLPOOL fe7011294863afb6328310bbedaca8cee1ba04c402afa15f846b733fc91e1238622cd0302f7f83865a158be245a60335347d2b7cae18c1e040b3e6c2df46d240 +MISC ChangeLog-2015 2504 SHA256 2bec2d3f55d2c7db90eca6dc9ffc0769fb94ef0bc0fd059c083982633bfc7127 SHA512 2ba9516e2bef9467ffaa3071d4da2b91543abfdf3b3d9b1fc11c59f80f6de63bbfa29b91ea15a85ac4eefb9a2e1a44e02bf4fe06e41774aa9fa5e48307716c14 WHIRLPOOL bbaa0dcdbf9312b2f06e6c228dbaeffc29d2d871662cadff0f4e649ef80b533934479a1bcbb6baaa17f1bfad0b84afaf149be66357eb386d8ed6ac0b1659377f +MISC metadata.xml 672 SHA256 be13c37828f0d6f6f82d92b69691a1f9580ed391bec7acc07e381b9ba11f05d2 SHA512 7a9782159034bebdad0a67ea352f898a577452ac83f6525f30092cc240a412f938c140da4fad7a254ba5679017de13af5aeeffe5a69c610a01bc882c9ee69d24 WHIRLPOOL f3b4895687cda368d1334f9a4d20c113af0f94b2b5acc06b8c04d38e05ee76169f94e40d7b6e4b25a3981fd71e77a83b17cc0368862a735b2ce9556c42da49a5 diff --git a/sci-libs/libticalcs2/libticalcs2-1.1.8.ebuild b/sci-libs/libticalcs2/libticalcs2-1.1.8.ebuild new file mode 100644 index 000000000000..c40ed386d70d --- /dev/null +++ b/sci-libs/libticalcs2/libticalcs2-1.1.8.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Library for communication with TI calculators" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc nls static-libs" + +RDEPEND=" + dev-libs/glib:2 + >=sci-libs/libticables2-1.3.3 + >=sci-libs/libticonv-1.1.3 + >=sci-libs/libtifiles2-1.1.5 + nls? ( virtual/libintl )" +DEPEND="${RDEPEND} + virtual/pkgconfig + nls? ( sys-devel/gettext )" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_configure() { + local myeconfargs=( + --disable-rpath + $(use_enable nls) + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + use doc && dohtml docs/html/* +} diff --git a/sci-libs/libticalcs2/libticalcs2-1.1.9.ebuild b/sci-libs/libticalcs2/libticalcs2-1.1.9.ebuild new file mode 100644 index 000000000000..fe2478ec3c3a --- /dev/null +++ b/sci-libs/libticalcs2/libticalcs2-1.1.9.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library for communication with TI calculators" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc nls static-libs" + +RDEPEND=" + dev-libs/glib:2 + >=sci-libs/libticables2-1.3.3 + >=sci-libs/libticonv-1.1.3 + >=sci-libs/libtifiles2-1.1.5 + nls? ( virtual/libintl )" +DEPEND="${RDEPEND} + virtual/pkgconfig + nls? ( sys-devel/gettext )" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --disable-rpath \ + $(use_enable static-libs static) \ + $(use_enable nls) +} + +src_install() { + use doc && HTML_DOCS+=( docs/html/. ) + default + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/libticalcs2/metadata.xml b/sci-libs/libticalcs2/metadata.xml new file mode 100644 index 000000000000..1cd5468cfcba --- /dev/null +++ b/sci-libs/libticalcs2/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The libticalcs provides a set of functions to communicate with Texas + Instruments calculators. It implements the TI protocol for each type + of calculator, independently of the link cable used to establish the + link. + All graphing calculators from Texas Instruments are supported +</longdescription> + <upstream> + <remote-id type="sourceforge">tilp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/libticonv/Manifest b/sci-libs/libticonv/Manifest new file mode 100644 index 000000000000..e9f0d5822b90 --- /dev/null +++ b/sci-libs/libticonv/Manifest @@ -0,0 +1,7 @@ +DIST libticonv-1.1.4.tar.bz2 344616 SHA256 1faecc71311bd95c94792cc72dd0844e7881a65156b006f045bb417eddd45183 SHA512 15ceb5acff888c841febc0d3ae96e3df649cce302b4ae2dc4ca150e3cb483337548fff0b32f0308bc759a08e6a167beaa8a2a4349f8ce47a2a7b62755a601018 WHIRLPOOL 7c3b1080809222f98ec519c76cc836c2efde8ada29bcdd26c9b8c2e6dc76b6b8f5aa3850c14f759e01293fb25a2a36676f5ef9662f90c630eab89a55f0d89709 +DIST libticonv-1.1.5.tar.bz2 86036 SHA256 316da6a73bf26b266dd23443882abc4c9fe7013edc3a53e5e301d525c2060878 SHA512 ea589344a656c5c7d28ed45e8da36bf7b746b7a82d77a257ddd305e2ebdc34f0ae14a6090e991f47ef7ad37cdc8d7182181c705fb0814e671ef764ca2a6dc2bf WHIRLPOOL fed46d36f583ac089d37c16be21a45c8d98fd963065f88a1e3f3a5ff46c3b371bec3f9a91c7e235d915ebc4e3616a5ef24aed6914c702e9c793eed9519ae840f +EBUILD libticonv-1.1.4.ebuild 769 SHA256 4cf1aa7975742fef6cc569a859eb4375e12c077b118ffabf6bf50260ee6f43ce SHA512 ea2e7cf0a0d6d049b31c5d58e99a21e6f8d5169d932d70cc5cdeada4c1b99d8838c313f8d1ad025303fd851a968c2fc8f84bcb78e94c6202c161a8a9b9e5a6e5 WHIRLPOOL 5a6a7fe92f0405f177dbbd312bd565884083c847d5114844a47078f5f883edb092fe2c4ccd2e9dd3fc2e97ef73a3572733b5affd1ca050a578f65463b0b6f57f +EBUILD libticonv-1.1.5.ebuild 805 SHA256 e74810d6029144c513f6a7e0b22695fdc2238ac51dd690d4c3868a2d4caaeae3 SHA512 c9da206fb7955d62775f0b960931a9fc73e4970ccbdb3d1344e490154d8e3df11634851113eb62426c6bc115315901da4aa6c778acad51a5431b422d15bd91e7 WHIRLPOOL 4ddd1bb9bafd8ff48a54d79df2fe04b7afec0500627f8e43a934a9eafd45a27fb28d05930b49c73c4a841d6c0248cf097e7dfd204c16202469c04bc1e4cf87c6 +MISC ChangeLog 2489 SHA256 c2c211833c3e609300b1a08212c529aecc72aef9ae0b7d3aa274e9144f1d4751 SHA512 a3bb25d1f1371f63bdd2396293fb141eefe20bc8fb107d27e3c88d10f37abda919c28f9afeda5b0e1c53b5c7193fcf1a017866f702c5e3317c02abc93c9299fd WHIRLPOOL 655fb04b9c66c06c7e80d97a6c7365d29d2bc21d139f97e79ef201102c5238c0c9017e2c5dbbbdf6f596654a9b6574e9393f98f4e2369815d4ff82fb8982b9c4 +MISC ChangeLog-2015 2326 SHA256 ccb1846496c9cee3b7f135f449736b74fab04b84aa636f592e0564c54f2df5cc SHA512 94614426a082bf93412e507e217a01b11ab6876d3c6d5d397d142bd97c0a62c70099734031f636cdd960e5c95fb2013babc1433a70203365e724625bd65c5f35 WHIRLPOOL 2114db016c535168f9f6389a9854da4574e30d68945710b54cb696f0496ab4c2d097bea8a66683d2a2c834b4d5152232b13ff13f1890076d7defd8d7f6639408 +MISC metadata.xml 556 SHA256 08a8a52f22eacc737abe171e31b97f25563a865332edb26f1357c8553fc0ef47 SHA512 da1ed25a63db4e89d62896fe30345739ca77b3f655b9f394a0221126cfb958420728b8d8a1f341012b2f37a3a5709f1704c496d781a3eb2de57ebe76c15dda83 WHIRLPOOL 6a680640fdf6d32fd9a605d636fceda87509a2c5f630dedd1e632e2d51bddba00c4c5f617997f4f63be867cfa82eef369ac78e3fc2f2d978605e41bc14bd07c3 diff --git a/sci-libs/libticonv/libticonv-1.1.4.ebuild b/sci-libs/libticonv/libticonv-1.1.4.ebuild new file mode 100644 index 000000000000..d36975c9db21 --- /dev/null +++ b/sci-libs/libticonv/libticonv-1.1.4.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Charset conversion library for TI calculators" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc iconv static-libs" + +RDEPEND="dev-libs/glib:2" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_configure() { + local myeconfargs=( + $(use_enable iconv) + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + if use doc; then + dohtml docs/html/* + docinto charsets + dohtml docs/charsets/* + fi +} diff --git a/sci-libs/libticonv/libticonv-1.1.5.ebuild b/sci-libs/libticonv/libticonv-1.1.5.ebuild new file mode 100644 index 000000000000..b4bd611bce5c --- /dev/null +++ b/sci-libs/libticonv/libticonv-1.1.5.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Charset conversion library for TI calculators" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc iconv static-libs" + +RDEPEND="dev-libs/glib:2" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_enable iconv) +} + +src_install() { + if use doc; then + HTML_DOCS=( docs/html/. ) + DOCS+=( docs/charsets ) + fi + default + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/libticonv/metadata.xml b/sci-libs/libticonv/metadata.xml new file mode 100644 index 000000000000..e176fa0cacff --- /dev/null +++ b/sci-libs/libticonv/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The libticonv package is a library which handles the various TI + charsets and conversion to/from UTF-8/16 through a set of functions + which constitutes a common API. +</longdescription> + <upstream> + <remote-id type="sourceforge">tilp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/libtifiles2/Manifest b/sci-libs/libtifiles2/Manifest new file mode 100644 index 000000000000..5a6a76625c8a --- /dev/null +++ b/sci-libs/libtifiles2/Manifest @@ -0,0 +1,7 @@ +DIST libtifiles2-1.1.6.tar.bz2 390447 SHA256 ec4d6acd1d135ee04256d04a5e1512c1ccaf82ad01e48f5e24d5c4da31ce898f SHA512 abc40275e7af921a67b658c6b6aa8ec511e965a3e9e00fcdc676c2b85e1d95dbae0f118e127e0806950d26afde9949251e47eb85af04d8f8ecca777dc3afcd23 WHIRLPOOL 40b6973ccdf141f4079790a40731997bd93518284007d16c2fca5e4d54ffab900f72394111471b4174f37fcddefbcff9bde7e0709e19f88c86b9cd8fd5664554 +DIST libtifiles2-1.1.7.tar.bz2 122454 SHA256 9ac63b49e97b09b30b37bbc84aeb15fa7967bceb944e56141c5cd5a528acc982 SHA512 e2ef4de0ce8c78f0da4098ec618a7194f9b94a028f9cb54a0ea1c29c00028d7cf144a067d8aaf8010ad094378b6426d05621d530cfbfa05f793f6c1ed41fcaef WHIRLPOOL ddc3269e7cf9bc1eb45b55f182b94d2c4ea20666455d5280b71b0e4d0f6244c857896234685700228d8c2465ac09074e672e67f102339e4bbda9ceb5893dc14c +EBUILD libtifiles2-1.1.6-r1.ebuild 968 SHA256 7508518f40aae83ddb5acdf52e43d7479afcd23227ef36b0c983b488dc2eff23 SHA512 1d90214dc84adcec0d76c2e9a8f5efb4d517abbba8f35a5ac33e30ca35fda7c4c584cbcb8054959bac05196d7b887796cb0be71e0a09348b7e939f5ed44ebfb2 WHIRLPOOL cdd01a7350501938f5e3715fa06987798ebf5edb1cf50a3e83f660bbb5b07c5063c0a865553da10ac2e39622131b4541c109256f38489d6ba17a979efdeecf22 +EBUILD libtifiles2-1.1.7.ebuild 902 SHA256 f8c3defc42be285d9ba06c992d9b7227ec1c6a7a5fe4d43b9f8c9a0f87a90d05 SHA512 023447c2ab16041bb8c638c17c26ae2ee504869b2d5bcc1a5e5b4b7538bcd8c7484ac79ff5da3495e4f752720479e93558a2659886e9d4b290905d7e75168326 WHIRLPOOL 1b961bff3fb3799eef07bef9ef21945ca27e744f4406ac7ed29b066ca9b3ee50f62e16edd3a964e441a20b0e6f83d5c00ae76d21de239b6bf970e1be6e22256b +MISC ChangeLog 2505 SHA256 790cf53f05524c84744f86bc02597222438581ffacbd179d793809e08711aa1c SHA512 9285ddc455a77e2fce094717f907d13cb81760db51cdc1bf2f9cc5ca19748d4343c19757e20f266b10d49cb9a9180493cf11f391280241a53550319a936cbf15 WHIRLPOOL 493c2d77efb7950c497d1f83097fcc7b9a2ab7e5bad4404df593e6afe6e3ef823fdd765b966ee883557e1d3931e2519f64511243bd3c33bb9f73b0061a76bcb4 +MISC ChangeLog-2015 3104 SHA256 2e1c44616e210ec1faa0dc02213923f26890b4a762aabd3383f3cda8fcfdbfa3 SHA512 6e0df2a20c8b27b5c7a0901cc50d1446aa6889a8cf0ef84d772da88c55f41e3b17c21fbaaf6b6e8ee417370086ae6ba5ca8e7edf6ddce4ec05a237588533b173 WHIRLPOOL 4a28f46524d9700433f9474ff142143638c40643377acfc5d9e155a34b8d80ede24f2ec47e553b8956686c236531204bc75ed03536e8e21986a57fcaa935ab46 +MISC metadata.xml 690 SHA256 b81e01337ef1a13df48a2362a9d34ce819ec5317f8951f2b4d22430b6c90bff2 SHA512 cf23ec955770b70eecd478cc2ddc421185d1dc150062c614387a74d040f01f502f0aecd3e28d3aa61e65c7ce89069db75e99286d9b25498410d83ea5b731b467 WHIRLPOOL 9249e6b889addbdeab01d9015b1a55c88d40c8c6804827ef8cbb4eacc1d8975364f067527a60f8c2f84e7899565b0307cc7e3e5292034f2577ce6d40631085b8 diff --git a/sci-libs/libtifiles2/libtifiles2-1.1.6-r1.ebuild b/sci-libs/libtifiles2/libtifiles2-1.1.6-r1.ebuild new file mode 100644 index 000000000000..6ccf9e28bc6a --- /dev/null +++ b/sci-libs/libtifiles2/libtifiles2-1.1.6-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Library for TI calculator files" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc nls static-libs" + +RDEPEND=" + app-arch/libarchive + dev-libs/glib:2 + >=sci-libs/libticables2-1.3.3 + >=sci-libs/libticonv-1.1.3 + nls? ( virtual/libintl )" + +DEPEND="${RDEPEND} + virtual/pkgconfig + nls? ( sys-devel/gettext )" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_prepare() { + cd src + sed -i -e "s|types\*.h|$(echo types*.h)|" Makefile.in || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-rpath + $(use_enable nls) + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + use doc && dohtml docs/html/* +} diff --git a/sci-libs/libtifiles2/libtifiles2-1.1.7.ebuild b/sci-libs/libtifiles2/libtifiles2-1.1.7.ebuild new file mode 100644 index 000000000000..158a6d79c8b8 --- /dev/null +++ b/sci-libs/libtifiles2/libtifiles2-1.1.7.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library for TI calculator files" +HOMEPAGE="http://lpg.ticalc.org/prj_tilp/" +SRC_URI="mirror://sourceforge/tilp/tilp2-linux/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc nls static-libs" + +RDEPEND=" + app-arch/libarchive + dev-libs/glib:2 + >=sci-libs/libticables2-1.3.3 + >=sci-libs/libticonv-1.1.3 + nls? ( virtual/libintl )" + +DEPEND="${RDEPEND} + virtual/pkgconfig + nls? ( sys-devel/gettext )" + +DOCS=( AUTHORS LOGO NEWS README ChangeLog docs/api.txt ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf --disable-rpath \ + $(use_enable static-libs static) \ + $(use_enable nls) +} + +src_install() { + use doc && HTML_DOCS=( docs/html/. ) + default + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/libtifiles2/metadata.xml b/sci-libs/libtifiles2/metadata.xml new file mode 100644 index 000000000000..95f486416a2c --- /dev/null +++ b/sci-libs/libtifiles2/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The libtifiles is a library providing support for operations on Texas + Instruments calculators files. All formats for all calculators are + supported read/write ; the library is also able to manipulate the + group files, which means it is able to group and ungroup variables + into such group files. +</longdescription> + <upstream> + <remote-id type="sourceforge">tilp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/linux-gpib/Manifest b/sci-libs/linux-gpib/Manifest new file mode 100644 index 000000000000..2d09a7ad0ed1 --- /dev/null +++ b/sci-libs/linux-gpib/Manifest @@ -0,0 +1,14 @@ +AUX linux-gpib-3.2.16-perl.patch 471 SHA256 7393237d7df3bad191d6c6790b87ff6e0b1f5fd006b77c0afeb5e1dcacb744fc SHA512 0ad75078406a8eb6fc09470be108464dcb3e7601d7a3c0813f1c6ba1d9e8f3895dea4da37f5d4928e6ea398a3aeea315a63bb6009a5fa211bba592093a776d10 WHIRLPOOL cd3995233836621a1ce3440a38290ef5162816e9251a5ed6362b9b20ea084cf804d7ad9c246264cfe6246b6e90b7443daa80c7b27225374f2ca97e091456a3d7 +AUX linux-gpib-3.2.21-build.patch 1676 SHA256 f0f2aadc12a7180dc1237f1e991d4a7d0bdde9b1ceca9ecef3e6bad5a2498c25 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dc3581d03a2f9dd5598c8217c04086ea6512ee23a226bd4fb0cdf48d1bf2742e9a5cfb89f7af9f239e93f9ed85188a5c226e6b643a144117c1646df7e17c690f diff --git a/sci-libs/linux-gpib/files/linux-gpib-3.2.16-perl.patch b/sci-libs/linux-gpib/files/linux-gpib-3.2.16-perl.patch new file mode 100644 index 000000000000..16f2f15b0ad7 --- /dev/null +++ b/sci-libs/linux-gpib/files/linux-gpib-3.2.16-perl.patch @@ -0,0 +1,9 @@ +diff -ruN linux-gpib-3.2.16.orig/language/Makefile.am linux-gpib-3.2.16/language/Makefile.am +--- linux-gpib-3.2.16.orig/language/Makefile.am 2009-09-16 19:26:53.000000000 +0200 ++++ linux-gpib-3.2.16/language/Makefile.am 2011-08-14 03:32:53.000000000 +0200 +@@ -67,4 +67,4 @@ + $(RM) perl/Makefile + + perl/Makefile: +- -(cd perl && $(PERL) Makefile.PL) ++ -(cd perl && $(PERL) Makefile.PL PREFIX=$(EPREFIX)/usr INSTALLDIRS=vendor INSTALLMAN3DIR='none' DESTDIR="$(DESTDIR)" ) diff --git a/sci-libs/linux-gpib/files/linux-gpib-3.2.21-build.patch b/sci-libs/linux-gpib/files/linux-gpib-3.2.21-build.patch new file mode 100644 index 000000000000..86ce197ba821 --- /dev/null +++ b/sci-libs/linux-gpib/files/linux-gpib-3.2.21-build.patch @@ -0,0 +1,44 @@ +diff -ruN linux-gpib-3.2.21.orig/drivers/Makefile.am linux-gpib-3.2.21/drivers/Makefile.am +--- linux-gpib-3.2.21.orig/drivers/Makefile.am 2014-12-13 11:27:55.000000000 +0100 ++++ linux-gpib-3.2.21/drivers/Makefile.am 2014-12-17 17:51:47.152588400 +0100 +@@ -28,39 +28,13 @@ + CC="$(LINUX_CC) -I@abs_top_srcdir@ -I@abs_top_srcdir@/drivers/gpib/include -I@abs_top_srcdir@/include" \ + SUBDIRS="$(GPIB_ABS_MODULE_SUBDIR)" + +-install-data-hook: device-file-check /etc/gpib.conf ++install-data-hook: /etc/gpib.conf + $(MAKE) -C $(LINUX_SRCDIR) V=1 modules_install\ + CC="$(LINUX_CC) -I@abs_top_srcdir@ -I@abs_top_srcdir@/driver/include -I@abs_top_srcdir@/include" \ + SUBDIRS="$(GPIB_ABS_MODULE_SUBDIR)" INSTALL_MOD_DIR="gpib" +- $(DEPMOD) -a +- +-/dev/gpib0: +- groupadd gpib || echo "group gpib exists" +- for i in `seq 0 15`; \ +- do \ +- mknod -m u=rw,g=rw,o= /dev/gpib$${i} c $(IBMAJOR) $${i} || exit 1; \ +- chown root:gpib /dev/gpib$${i}; \ +- done +- +-.PHONY : device-file-check +-device-file-check: /dev/gpib0 +- @if [ ! -c /dev/gpib0 ]; then \ +- if [ -a /dev/gpib0 ]; then \ +- echo "A file or directory called /dev/gpib0 exists but it is not" \ +- "a character device. Delete or move it and try again."; \ +- exit 1; \ +- fi; \ +- fi +- @ls -l /dev/gpib0 | grep -q "$(IBMAJOR)"; \ +- if [ $$? != 0 ]; then \ +- echo "/dev/gpib0 has the wrong major number. " \ +- "Delete your /dev/gpibX files and try again."; \ +- exit 1; \ +- fi + + #should move this to util/templates Makefile.am when it exists + /etc/gpib.conf: +- $(INSTALL_DATA) -D $(top_srcdir)/util/templates/gpib.conf /etc/gpib.conf + + #make sure compiled files, etc don't make it into distribution tarballs + dist-hook: diff --git a/sci-libs/linux-gpib/files/linux-gpib-4.0.3-reallydie.patch b/sci-libs/linux-gpib/files/linux-gpib-4.0.3-reallydie.patch new file mode 100644 index 000000000000..e19f8d36755b --- /dev/null +++ b/sci-libs/linux-gpib/files/linux-gpib-4.0.3-reallydie.patch @@ -0,0 +1,16 @@ +Index: drivers/Makefile.am +=================================================================== +--- a/drivers/Makefile.am (revision 1602) ++++ b/drivers/Makefile.am (working copy) +@@ -15,10 +15,8 @@ + + -include $(top_srcdir)/util/linux_flags/flags + +-#ignore errors from kernel's make modules in all-local, to avoid failure of make install +-#on nfs filesystem with root_squash + all-local: +- -$(MAKE) -C $(LINUX_SRCDIR) V=1 modules\ ++ $(MAKE) -C $(LINUX_SRCDIR) V=1 modules\ + CC="$(LINUX_CC) -I@abs_top_srcdir@ -I@abs_top_srcdir@/drivers/gpib/include -I@abs_top_srcdir@/include" \ + SUBDIRS="$(GPIB_ABS_MODULE_SUBDIR)" + diff --git a/sci-libs/linux-gpib/files/linux-gpib-4.0.4_rc2-kernel-4.11.0.patch b/sci-libs/linux-gpib/files/linux-gpib-4.0.4_rc2-kernel-4.11.0.patch new file mode 100644 index 000000000000..c3a9764924c2 --- /dev/null +++ b/sci-libs/linux-gpib/files/linux-gpib-4.0.4_rc2-kernel-4.11.0.patch @@ -0,0 +1,10 @@ +--- linux-gpib-4.0.4rc2.orig/drivers/gpib/lpvo_usb_gpib/lpvo_usb_gpib.c 2016-06-22 09:48:47.000000000 +0100 ++++ linux-gpib-4.0.4rc2/drivers/gpib/lpvo_usb_gpib/lpvo_usb_gpib.c 2017-05-02 00:59:04.509950834 +0100 +@@ -37,6 +37,7 @@ + #include <linux/file.h> + #include <linux/timer.h> + #include <linux/delay.h> ++#include <linux/sched/signal.h> + #include <asm/uaccess.h> + + #include "gpibP.h" diff --git a/sci-libs/linux-gpib/linux-gpib-4.0.3-r1.ebuild b/sci-libs/linux-gpib/linux-gpib-4.0.3-r1.ebuild new file mode 100644 index 000000000000..8e7b27438b4f --- /dev/null +++ b/sci-libs/linux-gpib/linux-gpib-4.0.3-r1.ebuild @@ -0,0 +1,216 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit linux-info readme.gentoo-r1 versionator eutils linux-mod autotools perl-functions python-single-r1 toolchain-funcs udev user + +MY_PV=${PV/_/} + +DESCRIPTION="Kernel module and driver library for GPIB (IEEE 488.2) hardware" +HOMEPAGE="http://linux-gpib.sourceforge.net/" +SRC_URI="mirror://sourceforge/linux-gpib/${PN}-${MY_PV}.tar.gz + firmware? ( http://linux-gpib.sourceforge.net/firmware/gpib_firmware-2006-11-12.tar.gz ) +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~arm ~x86" +IUSE="isa pcmcia static debug guile perl php python tcl doc firmware" + +COMMONDEPEND=" + tcl? ( dev-lang/tcl:0= ) + guile? ( dev-scheme/guile:12 ) + perl? ( dev-lang/perl:= ) + php? ( dev-lang/php:= ) + python? ( ${PYTHON_DEPS} ) + firmware? ( sys-apps/fxload )" +RDEPEND="${COMMONDEPEND}" +DEPEND="${COMMONDEPEND} + virtual/pkgconfig + doc? ( app-text/docbook-sgml-utils ) + perl? ( virtual/perl-ExtUtils-MakeMaker )" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +PATCHES=( + "${FILESDIR}"/${PN}-3.2.21-build.patch + "${FILESDIR}"/${PN}-3.2.16-perl.patch + "${FILESDIR}"/${PN}-4.0.3-reallydie.patch +) + +S=${WORKDIR}/${PN}-${MY_PV} + +pkg_setup () { + use perl && perl_set_version + use python && python_setup + + CONFIG_CHECK="!VMAP_STACK" + linux-mod_pkg_setup + + if kernel_is -lt 2 6 8; then + die "Kernel versions older than 2.6.8 are not supported." + fi + + # https://sourceforge.net/tracker/?func=detail&aid=3285657&group_id=42378&atid=432940 + if use pcmcia && kernel_is -ge 2 6 38; then + die "pcmcia support is broken on kernels newer 2.6.38" + fi +} + +src_prepare () { + default + kernel_is ge 4 11 0 && eapply "${FILESDIR}"/${PN}-4.0.4_rc2-kernel-4.11.0.patch + eautoreconf +} + +src_configure() { + set_arch_to_kernel + econf \ + $(use_enable isa) \ + $(use_enable pcmcia) \ + $(use_enable static) \ + $(use_enable debug driver-debug) \ + $(use_enable guile guile-binding) \ + $(use_enable perl perl-binding) \ + $(use_enable php php-binding) \ + $(use_enable python python-binding) \ + $(use_enable tcl tcl-binding) \ + $(use_enable doc documentation) \ + --with-linux-srcdir=${KV_DIR} +} + +src_compile() { + set_arch_to_kernel + FIRM_DIR=/usr/share/usb + emake \ + DESTDIR="${D}" \ + INSTALL_MOD_PATH="${D}" \ + HOTPLUG_USB_CONF_DIR="${D}"/etc/hotplug/usb \ + UDEV_RULES_DIR="${D}$(get_udevdir)"/rules.d \ + USB_FIRMWARE_DIR="${D}"${FIRM_DIR} \ + docdir=/usr/share/doc/${PF}/html +} + +src_install() { + set_arch_to_kernel + FIRM_DIR=/usr/share/usb + emake \ + DESTDIR="${D}" \ + INSTALL_MOD_PATH="${D}" \ + HOTPLUG_USB_CONF_DIR="${D}"/etc/hotplug/usb \ + UDEV_RULES_DIR="${D}/$(get_udevdir)"/rules.d \ + USB_FIRMWARE_DIR="${D}"${FIRM_DIR} \ + docdir=/usr/share/doc/${PF}/html install + + if use perl; then + einfo "Installing perl module" + cd "${S}"/language/perl || die + DESTDIR=${D} emake install + perl_fix_packlist + perl_delete_emptybsdir + cd "${S}" || die + fi + + echo "KERNEL==\"gpib[0-9]*\", MODE=\"0660\", GROUP=\"gpib\"" >> 99-gpib.rules + udev_dorules 99-gpib.rules + + dodoc doc/linux-gpib.pdf ChangeLog AUTHORS README* NEWS + + insinto /etc + newins util/templates/gpib.conf gpib.conf + newins util/templates/gpib.conf gpib.conf.example + + if use pcmcia; then + dodir /etc/pcmcia + insinto /etc/pcmcia + doins "${S}"/etc/pcmcia/* + fi + + if use firmware; then + insinto "${FIRM_DIR}"/agilent_82357a + doins "${WORKDIR}"/gpib_firmware-2006-11-12/agilent_82357a/* + + insinto "${FIRM_DIR}"/ni_gpib_usb_b + doins "${WORKDIR}"/gpib_firmware-2006-11-12/ni_gpib_usb_b/* + + insinto /usr/share/linux-gpib/hp_82341 + # do not install precompiled generate_firmware + doins "${WORKDIR}"/gpib_firmware-2006-11-12/hp_82341/{*.bin,README} + fi + + # fix rules files + local f + find "${D}$(get_udevdir)"/rules.d -type f -print0 | while read -rd '' f ; do + grep -q "${D}" "${f}" && einfo "File ${f} contains a temporary path, fixing." + sed -i -e "s:${D}:/:g" "${f}" + done + + DOC_CONTENTS=" +You need to run the 'gpib_config' utility to setup the driver before +you can use it. In order to do it automatically you can add to your +start script something like this (supposing the appropriate driver +is loaded on the startup): +\n + gpib_config --minor 0 +\n +To give a user access to the computer's gpib board you will have to add +them to the group 'gpib' or, you could change the permissions on the device +files /dev/gpib[0-15] to something you like better, using 'chmod' +\n +Edit /etc/gpib.conf to match your interface board, and any devices you wish +to open via ibfind(). See the documentation in /usr/share/linux-gpib/html for +more information. +\n +" + + if use pcmcia; then + DOC_CONTENTS+=' +For PCMCIA cards:\n +All files needed for a PCMCIA board were copied to /etc/pcmcia. +You may wish to edit the options passed to the gpib_config call in the +/etc/pcmcia/linux-gpib-pcmcia script. +You may need to send a SIGHUP signal to the cardmgr daemon to force it +to reload the files in /etc/pcmcia \(alternatively you could use your +pcmcia init.d script to restart the cardmgr, or you could just reboot\). +The driver module will be loaded as needed by the cardmgr. + +' + fi + + if use firmware; then + DOC_CONTENTS+=' +For Agilent \(HP\) 82341C and 82341D cards: +The firmware for these boards is uploaded by passing the appropriate +firmware file from /usr/share/linux-gpib/hp_82341 directory to +gpib_config using the -I or --init-data command line option. Example:\n +gpib_config --minor 0 --init-data /usr/share/linux-gpib/hp_82341/hp_82341c_fw.bin +' + fi + + readme.gentoo_create_doc +} + +pkg_preinst () { + linux-mod_pkg_preinst + use perl && perl_set_version + enewgroup gpib +} + +pkg_postinst () { + linux-mod_pkg_postinst + readme.gentoo_print_elog + + local v + for v in ${REPLACING_VERSIONS}; do + if ! version_is_at_least 3.2.21-r1 ${v}; then + ewarn "sci-libs/linux-gpib-3.2.21-r1 introduces incompatible changes to the kernel" + ewarn "interface. You may need to reboot to make sure the newly built driver modules" + ewarn "are used (some of the driver modules cannot be unloaded)." + ewarn "If you do not do this, every gpib call will just result in an error message." + break + fi + done +} diff --git a/sci-libs/linux-gpib/linux-gpib-4.0.4_rc3.ebuild b/sci-libs/linux-gpib/linux-gpib-4.0.4_rc3.ebuild new file mode 100644 index 000000000000..16db1db66082 --- /dev/null +++ b/sci-libs/linux-gpib/linux-gpib-4.0.4_rc3.ebuild @@ -0,0 +1,215 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit linux-info readme.gentoo-r1 versionator eutils linux-mod autotools perl-functions python-single-r1 toolchain-funcs udev user + +MY_PV=${PV/_/} + +DESCRIPTION="Kernel module and driver library for GPIB (IEEE 488.2) hardware" +HOMEPAGE="http://linux-gpib.sourceforge.net/" +SRC_URI="mirror://sourceforge/linux-gpib/${PN}-${MY_PV}.tar.gz + firmware? ( http://linux-gpib.sourceforge.net/firmware/gpib_firmware-2006-11-12.tar.gz ) +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="isa pcmcia static debug guile perl php python tcl doc firmware" + +COMMONDEPEND=" + tcl? ( dev-lang/tcl:0= ) + guile? ( dev-scheme/guile:12 ) + perl? ( dev-lang/perl:= ) + php? ( dev-lang/php:= ) + python? ( ${PYTHON_DEPS} ) + firmware? ( sys-apps/fxload )" +RDEPEND="${COMMONDEPEND}" +DEPEND="${COMMONDEPEND} + virtual/pkgconfig + doc? ( app-text/docbook-sgml-utils ) + perl? ( virtual/perl-ExtUtils-MakeMaker )" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +PATCHES=( + "${FILESDIR}"/${PN}-3.2.21-build.patch + "${FILESDIR}"/${PN}-3.2.16-perl.patch + "${FILESDIR}"/${PN}-4.0.3-reallydie.patch +) + +S=${WORKDIR}/${PN}-${MY_PV} + +pkg_setup () { + use perl && perl_set_version + use python && python_setup + + linux-mod_pkg_setup + + if kernel_is -lt 2 6 8; then + die "Kernel versions older than 2.6.8 are not supported." + fi + + # https://sourceforge.net/tracker/?func=detail&aid=3285657&group_id=42378&atid=432940 + if use pcmcia && kernel_is -ge 2 6 38; then + die "pcmcia support is broken on kernels newer 2.6.38" + fi +} + +src_prepare () { + default + kernel_is ge 4 11 0 && eapply "${FILESDIR}"/${PN}-4.0.4_rc2-kernel-4.11.0.patch + eautoreconf +} + +src_configure() { + set_arch_to_kernel + econf \ + $(use_enable isa) \ + $(use_enable pcmcia) \ + $(use_enable static) \ + $(use_enable debug driver-debug) \ + $(use_enable guile guile-binding) \ + $(use_enable perl perl-binding) \ + $(use_enable php php-binding) \ + $(use_enable python python-binding) \ + $(use_enable tcl tcl-binding) \ + $(use_enable doc documentation) \ + --with-linux-srcdir=${KV_DIR} +} + +src_compile() { + set_arch_to_kernel + FIRM_DIR=/usr/share/usb + emake \ + DESTDIR="${D}" \ + INSTALL_MOD_PATH="${D}" \ + HOTPLUG_USB_CONF_DIR="${D}"/etc/hotplug/usb \ + UDEV_RULES_DIR="${D}$(get_udevdir)"/rules.d \ + USB_FIRMWARE_DIR="${D}"${FIRM_DIR} \ + docdir=/usr/share/doc/${PF}/html +} + +src_install() { + set_arch_to_kernel + FIRM_DIR=/usr/share/usb + emake \ + DESTDIR="${D}" \ + INSTALL_MOD_PATH="${D}" \ + HOTPLUG_USB_CONF_DIR="${D}"/etc/hotplug/usb \ + UDEV_RULES_DIR="${D}/$(get_udevdir)"/rules.d \ + USB_FIRMWARE_DIR="${D}"${FIRM_DIR} \ + docdir=/usr/share/doc/${PF}/html install + + if use perl; then + einfo "Installing perl module" + cd "${S}"/language/perl || die + DESTDIR=${D} emake install + perl_fix_packlist + perl_delete_emptybsdir + cd "${S}" || die + fi + + echo "KERNEL==\"gpib[0-9]*\", MODE=\"0660\", GROUP=\"gpib\"" >> 99-gpib.rules + udev_dorules 99-gpib.rules + + dodoc doc/linux-gpib.pdf ChangeLog AUTHORS README* NEWS + + insinto /etc + newins util/templates/gpib.conf gpib.conf + newins util/templates/gpib.conf gpib.conf.example + + if use pcmcia; then + dodir /etc/pcmcia + insinto /etc/pcmcia + doins "${S}"/etc/pcmcia/* + fi + + if use firmware; then + insinto "${FIRM_DIR}"/agilent_82357a + doins "${WORKDIR}"/gpib_firmware-2006-11-12/agilent_82357a/* + + insinto "${FIRM_DIR}"/ni_gpib_usb_b + doins "${WORKDIR}"/gpib_firmware-2006-11-12/ni_gpib_usb_b/* + + insinto /usr/share/linux-gpib/hp_82341 + # do not install precompiled generate_firmware + doins "${WORKDIR}"/gpib_firmware-2006-11-12/hp_82341/{*.bin,README} + fi + + # fix rules files + local f + find "${D}$(get_udevdir)"/rules.d -type f -print0 | while read -rd '' f ; do + grep -q "${D}" "${f}" && einfo "File ${f} contains a temporary path, fixing." + sed -i -e "s:${D}:/:g" "${f}" + done + + DOC_CONTENTS=" +You need to run the 'gpib_config' utility to setup the driver before +you can use it. In order to do it automatically you can add to your +start script something like this (supposing the appropriate driver +is loaded on the startup): +\n + gpib_config --minor 0 +\n +To give a user access to the computer's gpib board you will have to add +them to the group 'gpib' or, you could change the permissions on the device +files /dev/gpib[0-15] to something you like better, using 'chmod' +\n +Edit /etc/gpib.conf to match your interface board, and any devices you wish +to open via ibfind(). See the documentation in /usr/share/linux-gpib/html for +more information. +\n +" + + if use pcmcia; then + DOC_CONTENTS+=' +For PCMCIA cards:\n +All files needed for a PCMCIA board were copied to /etc/pcmcia. +You may wish to edit the options passed to the gpib_config call in the +/etc/pcmcia/linux-gpib-pcmcia script. +You may need to send a SIGHUP signal to the cardmgr daemon to force it +to reload the files in /etc/pcmcia \(alternatively you could use your +pcmcia init.d script to restart the cardmgr, or you could just reboot\). +The driver module will be loaded as needed by the cardmgr. + +' + fi + + if use firmware; then + DOC_CONTENTS+=' +For Agilent \(HP\) 82341C and 82341D cards: +The firmware for these boards is uploaded by passing the appropriate +firmware file from /usr/share/linux-gpib/hp_82341 directory to +gpib_config using the -I or --init-data command line option. Example:\n +gpib_config --minor 0 --init-data /usr/share/linux-gpib/hp_82341/hp_82341c_fw.bin +' + fi + + readme.gentoo_create_doc +} + +pkg_preinst () { + linux-mod_pkg_preinst + use perl && perl_set_version + enewgroup gpib +} + +pkg_postinst () { + linux-mod_pkg_postinst + readme.gentoo_print_elog + + local v + for v in ${REPLACING_VERSIONS}; do + if ! version_is_at_least 3.2.21-r1 ${v}; then + ewarn "sci-libs/linux-gpib-3.2.21-r1 introduces incompatible changes to the kernel" + ewarn "interface. You may need to reboot to make sure the newly built driver modules" + ewarn "are used (some of the driver modules cannot be unloaded)." + ewarn "If you do not do this, every gpib call will just result in an error message." + break + fi + done +} diff --git a/sci-libs/linux-gpib/linux-gpib-4.1.0.ebuild b/sci-libs/linux-gpib/linux-gpib-4.1.0.ebuild new file mode 100644 index 000000000000..16db1db66082 --- /dev/null +++ b/sci-libs/linux-gpib/linux-gpib-4.1.0.ebuild @@ -0,0 +1,215 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit linux-info readme.gentoo-r1 versionator eutils linux-mod autotools perl-functions python-single-r1 toolchain-funcs udev user + +MY_PV=${PV/_/} + +DESCRIPTION="Kernel module and driver library for GPIB (IEEE 488.2) hardware" +HOMEPAGE="http://linux-gpib.sourceforge.net/" +SRC_URI="mirror://sourceforge/linux-gpib/${PN}-${MY_PV}.tar.gz + firmware? ( http://linux-gpib.sourceforge.net/firmware/gpib_firmware-2006-11-12.tar.gz ) +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="isa pcmcia static debug guile perl php python tcl doc firmware" + +COMMONDEPEND=" + tcl? ( dev-lang/tcl:0= ) + guile? ( dev-scheme/guile:12 ) + perl? ( dev-lang/perl:= ) + php? ( dev-lang/php:= ) + python? ( ${PYTHON_DEPS} ) + firmware? ( sys-apps/fxload )" +RDEPEND="${COMMONDEPEND}" +DEPEND="${COMMONDEPEND} + virtual/pkgconfig + doc? ( app-text/docbook-sgml-utils ) + perl? ( virtual/perl-ExtUtils-MakeMaker )" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +PATCHES=( + "${FILESDIR}"/${PN}-3.2.21-build.patch + "${FILESDIR}"/${PN}-3.2.16-perl.patch + "${FILESDIR}"/${PN}-4.0.3-reallydie.patch +) + +S=${WORKDIR}/${PN}-${MY_PV} + +pkg_setup () { + use perl && perl_set_version + use python && python_setup + + linux-mod_pkg_setup + + if kernel_is -lt 2 6 8; then + die "Kernel versions older than 2.6.8 are not supported." + fi + + # https://sourceforge.net/tracker/?func=detail&aid=3285657&group_id=42378&atid=432940 + if use pcmcia && kernel_is -ge 2 6 38; then + die "pcmcia support is broken on kernels newer 2.6.38" + fi +} + +src_prepare () { + default + kernel_is ge 4 11 0 && eapply "${FILESDIR}"/${PN}-4.0.4_rc2-kernel-4.11.0.patch + eautoreconf +} + +src_configure() { + set_arch_to_kernel + econf \ + $(use_enable isa) \ + $(use_enable pcmcia) \ + $(use_enable static) \ + $(use_enable debug driver-debug) \ + $(use_enable guile guile-binding) \ + $(use_enable perl perl-binding) \ + $(use_enable php php-binding) \ + $(use_enable python python-binding) \ + $(use_enable tcl tcl-binding) \ + $(use_enable doc documentation) \ + --with-linux-srcdir=${KV_DIR} +} + +src_compile() { + set_arch_to_kernel + FIRM_DIR=/usr/share/usb + emake \ + DESTDIR="${D}" \ + INSTALL_MOD_PATH="${D}" \ + HOTPLUG_USB_CONF_DIR="${D}"/etc/hotplug/usb \ + UDEV_RULES_DIR="${D}$(get_udevdir)"/rules.d \ + USB_FIRMWARE_DIR="${D}"${FIRM_DIR} \ + docdir=/usr/share/doc/${PF}/html +} + +src_install() { + set_arch_to_kernel + FIRM_DIR=/usr/share/usb + emake \ + DESTDIR="${D}" \ + INSTALL_MOD_PATH="${D}" \ + HOTPLUG_USB_CONF_DIR="${D}"/etc/hotplug/usb \ + UDEV_RULES_DIR="${D}/$(get_udevdir)"/rules.d \ + USB_FIRMWARE_DIR="${D}"${FIRM_DIR} \ + docdir=/usr/share/doc/${PF}/html install + + if use perl; then + einfo "Installing perl module" + cd "${S}"/language/perl || die + DESTDIR=${D} emake install + perl_fix_packlist + perl_delete_emptybsdir + cd "${S}" || die + fi + + echo "KERNEL==\"gpib[0-9]*\", MODE=\"0660\", GROUP=\"gpib\"" >> 99-gpib.rules + udev_dorules 99-gpib.rules + + dodoc doc/linux-gpib.pdf ChangeLog AUTHORS README* NEWS + + insinto /etc + newins util/templates/gpib.conf gpib.conf + newins util/templates/gpib.conf gpib.conf.example + + if use pcmcia; then + dodir /etc/pcmcia + insinto /etc/pcmcia + doins "${S}"/etc/pcmcia/* + fi + + if use firmware; then + insinto "${FIRM_DIR}"/agilent_82357a + doins "${WORKDIR}"/gpib_firmware-2006-11-12/agilent_82357a/* + + insinto "${FIRM_DIR}"/ni_gpib_usb_b + doins "${WORKDIR}"/gpib_firmware-2006-11-12/ni_gpib_usb_b/* + + insinto /usr/share/linux-gpib/hp_82341 + # do not install precompiled generate_firmware + doins "${WORKDIR}"/gpib_firmware-2006-11-12/hp_82341/{*.bin,README} + fi + + # fix rules files + local f + find "${D}$(get_udevdir)"/rules.d -type f -print0 | while read -rd '' f ; do + grep -q "${D}" "${f}" && einfo "File ${f} contains a temporary path, fixing." + sed -i -e "s:${D}:/:g" "${f}" + done + + DOC_CONTENTS=" +You need to run the 'gpib_config' utility to setup the driver before +you can use it. In order to do it automatically you can add to your +start script something like this (supposing the appropriate driver +is loaded on the startup): +\n + gpib_config --minor 0 +\n +To give a user access to the computer's gpib board you will have to add +them to the group 'gpib' or, you could change the permissions on the device +files /dev/gpib[0-15] to something you like better, using 'chmod' +\n +Edit /etc/gpib.conf to match your interface board, and any devices you wish +to open via ibfind(). See the documentation in /usr/share/linux-gpib/html for +more information. +\n +" + + if use pcmcia; then + DOC_CONTENTS+=' +For PCMCIA cards:\n +All files needed for a PCMCIA board were copied to /etc/pcmcia. +You may wish to edit the options passed to the gpib_config call in the +/etc/pcmcia/linux-gpib-pcmcia script. +You may need to send a SIGHUP signal to the cardmgr daemon to force it +to reload the files in /etc/pcmcia \(alternatively you could use your +pcmcia init.d script to restart the cardmgr, or you could just reboot\). +The driver module will be loaded as needed by the cardmgr. + +' + fi + + if use firmware; then + DOC_CONTENTS+=' +For Agilent \(HP\) 82341C and 82341D cards: +The firmware for these boards is uploaded by passing the appropriate +firmware file from /usr/share/linux-gpib/hp_82341 directory to +gpib_config using the -I or --init-data command line option. Example:\n +gpib_config --minor 0 --init-data /usr/share/linux-gpib/hp_82341/hp_82341c_fw.bin +' + fi + + readme.gentoo_create_doc +} + +pkg_preinst () { + linux-mod_pkg_preinst + use perl && perl_set_version + enewgroup gpib +} + +pkg_postinst () { + linux-mod_pkg_postinst + readme.gentoo_print_elog + + local v + for v in ${REPLACING_VERSIONS}; do + if ! version_is_at_least 3.2.21-r1 ${v}; then + ewarn "sci-libs/linux-gpib-3.2.21-r1 introduces incompatible changes to the kernel" + ewarn "interface. You may need to reboot to make sure the newly built driver modules" + ewarn "are used (some of the driver modules cannot be unloaded)." + ewarn "If you do not do this, every gpib call will just result in an error message." + break + fi + done +} diff --git a/sci-libs/linux-gpib/metadata.xml b/sci-libs/linux-gpib/metadata.xml new file mode 100644 index 000000000000..18c6ece75d7b --- /dev/null +++ b/sci-libs/linux-gpib/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>dilfridge@gentoo.org</email> + <name>Andreas K. Huettel</name> + </maintainer> + <maintainer type="project"> + <email>sci-electronics@gentoo.org</email> + <name>Gentoo Electronics Project</name> + </maintainer> + <use> + <flag name="firmware">Install firmware</flag> + <flag name="isa">Build ISA kernel modules; from 3.12 on the setting is ignored and the decision based on the kernel configuration</flag> + </use> + <upstream> + <remote-id type="sourceforge">linux-gpib</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/lis/Manifest b/sci-libs/lis/Manifest new file mode 100644 index 000000000000..e17b57942381 --- /dev/null +++ b/sci-libs/lis/Manifest @@ -0,0 +1,6 @@ +AUX lis-1.6.2-autotools.patch 14903 SHA256 fa2796e9a51ed75ab130a5a87eb52836d0805a1e49619e851f3407689c63f5a4 SHA512 a9483fac16ab9b384bb06a80ff11fd6cd717100517d9f9af639cb2984a26774fdfe7233b0eb9b2602a8ba0aaf34969c9fa7267d5f4bbc8e11dc872245c74b389 WHIRLPOOL ec8f89b35ec8717fd3fcffb58dead3d96ce0234750d4ba1aad408f41db207a6ceb645625254d62203ce0b582e7c0fe50bd62830b57bd2f6e1588e3ebe1c8e406 +DIST lis-1.6.5.tar.gz 3130045 SHA256 74f9f24308935c2de4f0d8f99d3e36fba4fcc8e40d98e5edb3a5bd47811b6ce3 SHA512 0cd2fc445c6464490f01def99960f33bbde53b45b453e289edbc9f31b7a20f00d70538bd3feb03324b56ddbc5993d8ba3bfbc8a0574809be08a854c05c097f13 WHIRLPOOL 7663a318aa631c1f15a19149e5cb2252a46ebc12c5936d38249de0010c2ae326afecfe24f5cc022c68e1f09d8c7a5f26db80903b4d4612d73b4c9a25ac087ac1 +EBUILD lis-1.6.5.ebuild 1574 SHA256 3d63fc09ee1935946c9becffa037afb60ae70d3c2cdecec294c10a5952e159a0 SHA512 9e1d406279bb7be19a7ab79b36bf1232ed1f31ee21051777a0917d4cbe12834e83b2154379851e56e00d846a638647de2c5ef0074993bac6c7d56e73d6621e87 WHIRLPOOL 8677532778ab1a5b63408ecc99500c523f1cefe67a6780d42c39380dd153b13008440c873c4baa9136740bb305ad3a883b5eb5410051f3a7cc3781bed80159f5 +MISC ChangeLog 3043 SHA256 dec86a63908e9c69970f134dc06b67f2c0d92f8bae8d5911632f30d56743d811 SHA512 0f0417f22f5b4a1e19ef331ad5a2d7547140f87075f60708ec8abd69c7d895836a7392aa50193f7d2575d6576578c2154afa10f0e4222cbb31eacddf396fe3dc WHIRLPOOL 6f07e3ec6092cd110c0e8da696e990d3edff493e4891be09df54d9c32850713ddb2928e743e6d77a2d05db676f2df85871b62c2a035c6742d651cda7893d9e84 +MISC ChangeLog-2015 2417 SHA256 8994dd7a91bf1d0dcdf025d8d42f66698ca23368bdb515ae299586562f653249 SHA512 a729af1ded7cbf24ed243b5633bd7f0cae21e8ee78a534f4612deae0b4c4f140444fff05d18ff5868c34fc7e336ec3f85e804054cc6ae752552b7cec0da6a7f6 WHIRLPOOL 0d7aa36d748381e414e8f099085c5a5b1b901d56154e977e60583286eb14026d955bc590ad58fe61b39285be79696437b3f3435d58cd531cced9686b0846ff4f +MISC metadata.xml 694 SHA256 d7cbc976fd7e6263c70d3baa698f83abb6196e722d8139d949511de8ae13da5b SHA512 16bb9204b7c94ef39884eedf20a392c9ff1205d073662c7d2af960e11ab4ab380bc8107f5274ba6d2a0b417ae875c6b3121b8a418fe218e3951a8226fdb9e60f WHIRLPOOL b516f14544c9a384c3f701612f804f621fbc3caa56ee204b788b40b588132add9dff5cce54fd680cf0c9f7b726502742419161360393c1cf481f1fc2f9d519ae diff --git a/sci-libs/lis/files/lis-1.6.2-autotools.patch b/sci-libs/lis/files/lis-1.6.2-autotools.patch new file mode 100644 index 000000000000..d7e1fa2ad9e9 --- /dev/null +++ b/sci-libs/lis/files/lis-1.6.2-autotools.patch @@ -0,0 +1,378 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -372,26 +372,6 @@ + done + AC_MSG_CHECKING([for C compiler vendor]) + AC_MSG_RESULT($[ax_cv_]_AC_LANG_ABBREV[_compiler_vendor]) +- case $ax_cv_c_compiler_vendor in +- dec) CFLAGS="-newc -w0 -O5 -ansi_alias -ansi_args -fp_reorder -tune host $CFLAGS" ;; +- gnu) CFLAGS="-O3 -fomit-frame-pointer $CFLAGS" ;; +- intel) CFLAGS="-ansi_alias $CFLAGS" ;; +- portland) CFLAGS="-O3 -B -fastsse $CFLAGS" ;; +- pathscale) CFLAGS="-O3 $CFLAGS" ;; +- ibm) CFLAGS="-O3 -qansialias -w -qarch=auto -qtune=auto $CFLAGS" +- AR="ar -X any" +- ;; +- sun) case `(uname -m) 2>/dev/null` in +- "i86pc") CFLAGS="-xtarget=native -xO5 -dalign $CFLAGS" +- LDFLAGS="-xtarget=native -xO5" +- ;; +- *) CFLAGS="-xtarget=native64 -xO5 -dalign $CFLAGS" +- LDFLAGS="-xtarget=native64 -xO5" +- ;; +- esac +- ;; +- hp) CFLAGS="+Oall +Optrs_ansi +DSnative $CFLAGS" ;; +- esac + + AC_DEFUN([_AX_PROG_FC_V_OUTPUT], + [AC_LANG_CONFTEST([AC_LANG_PROGRAM([])]) +@@ -538,6 +518,10 @@ + AC_LANG_PUSH(Fortran 77) + fflags_save="$FFLAGS" + AC_PROG_F77([ifort ifc efc xlf95_r xlf90_r xlf_r xlf95 xlf90 xlf ftn frt pgf95 pgf90 pathf95 pathf90 epcf90 f95 fort lf95 gfortran f90 g77]) ++ ++ AC_F77_LIBRARY_LDFLAGS ++ AC_F77_DUMMY_MAIN ++ + FFLAGS="$fflags_save" + if test "$TARGET" = ""; then + if test "$enable_mpi" = "yes"; then +@@ -582,29 +566,6 @@ + AC_MSG_CHECKING([for Fortran compiler vendor]) + AC_MSG_RESULT($[ax_cv_]_AC_LANG_ABBREV[_compiler_vendor]) + AC_LANG_POP(Fortran 77) +- case $ax_cv_f77_compiler_vendor in +- gnu) FFLAGS="-O3 -fomit-frame-pointer $FFLAGS" +- FCFLAGS="-O3 -fomit-frame-pointer $FCFLAGS" ;; +- intel) FFLAGS="-fpp $FFLAGS" +- FCFLAGS="-fpp $FCFLAGS" +- LDFLAGS="-Vaxlib" +- FCLDFLAGS="-nofor_main" ;; +- portland) FFLAGS="-O3 -fastsse -Mpreprocess $FFLAGS" +- FCFLAGS="-O3 -fastsse -Mpreprocess $FCFLAGS" +- FCLDFLAGS="-Mnomain" ;; +- pathscale) FFLAGS="-O3 $FFLAGS" ;; +- ibm) FFLAGS="-O3 -qsuffix=cpp=F -qfixed=72 -w -qarch=auto -qtune=auto $FFLAGS" +- FCFLAGS="-O3 -qsuffix=cpp=F90 -w -qarch=auto -qtune=auto $FCFLAGS" ;; +- sun) case `(uname -m) 2>/dev/null` in +- "i86pc") FFLAGS="-fpp -xtarget=native -xO5 -dalign $FFLAGS" +- FCFLAGS="-fpp -xtarget=native -xO5 -dalign $FCFLAGS" +- FCLDFLAGS="-xO5" ;; +- *) FFLAGS="-fpp -xtarget=native64 -xO5 -dalign $FFLAGS" +- FCFLAGS="-fpp -xtarget=native64 -xO5 -dalign $FCFLAGS" +- FCLDFLAGS="-xO5" ;; +- esac +- ;; +- esac + + if test x$ax_cv_c_compiler_vendor = x$ax_cv_f77_compiler_vendor; then + CLIBS="" +--- a/src/array/Makefile.am ++++ b/src/array/Makefile.am +@@ -1,16 +1,5 @@ + noinst_LTLIBRARIES = libarray.la + libarray_la_SOURCES = lis_array.c + +-AM_CFLAGS = -I$(top_srcdir)/include $(ILIBS) ++AM_CPPFLAGS = -I$(top_srcdir)/include $(ILIBS) + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/esolver/Makefile.am ++++ b/src/esolver/Makefile.am +@@ -10,16 +10,5 @@ + lis_esolver_rqi.c \ + lis_esolver_si.c + +-AM_CFLAGS = -I$(top_srcdir)/include ++AM_CPPFLAGS = -I$(top_srcdir)/include + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/fortran/amg/Makefile.am ++++ b/src/fortran/amg/Makefile.am +@@ -25,25 +25,6 @@ + + CLEANFILES = *.mod + AM_CPPFLAGS = -I$(top_srcdir)/include +-FCCOMPILE = $(FC) $(AMDEFS) $(AM_FCFLAGS) $(FCFLAGS) +-LTFCCOMPILE = $(LIBTOOL) --mode=compile $(FC) $(AMDEFS) $(AM_FCFLAGS) $(FCFLAGS) +-FCLD = $(FC) +-FCLINK = $(LIBTOOL) --mode=link $(FCLD) $(AM_LDFLAGS) $(LDFLAGS) -o $@ +-PPFCCOMPILE = $(FC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FCFLAGS) $(FCFLAGS) +-LTPPFCCOMPILE = $(LIBTOOL) --mode=compile $(FC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FCFLAGS) $(FCFLAGS) +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) + + .NOTPARALLEL: + .NO_PARALLEL: +--- a/src/fortran/Makefile.am ++++ b/src/fortran/Makefile.am +@@ -12,14 +12,3 @@ + + AM_CPPFLAGS = -I$(top_srcdir)/include + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -23,7 +23,7 @@ + liblis@LIBSUFFIX@_la_LIBADD += fortran/libfortran.la + else + if ENABLE_FORTRAN +- liblis@LIBSUFFIX@_la_LIBADD += fortran/libfortran.la ++ liblis@LIBSUFFIX@_la_LIBADD += fortran/libfortran.la $(FLIBS) + endif + endif + liblis@LIBSUFFIX@_la_SOURCES = +--- a/src/matrix/Makefile.am ++++ b/src/matrix/Makefile.am +@@ -17,16 +17,5 @@ + lis_matrix_rco.c \ + lis_matrix_vbr.c + +-AM_CFLAGS = -I$(top_srcdir)/include $(ILIBS) ++AM_CPPFLAGS = -I$(top_srcdir)/include $(ILIBS) + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/matvec/Makefile.am ++++ b/src/matvec/Makefile.am +@@ -13,16 +13,5 @@ + lis_matvec_vbr.c + + +-AM_CFLAGS = -I$(top_srcdir)/include ++AM_CPPFLAGS = -I$(top_srcdir)/include + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/precision/Makefile.am ++++ b/src/precision/Makefile.am +@@ -4,16 +4,5 @@ + lis_precision_vec.c + + +-AM_CFLAGS = -I$(top_srcdir)/include $(MPFLAG) ++AM_CPPFLAGS = -I$(top_srcdir)/include $(MPFLAG) + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/precon/Makefile.am ++++ b/src/precon/Makefile.am +@@ -12,16 +12,5 @@ + lis_precon_ssor.c + + +-AM_CFLAGS = -I$(top_srcdir)/include ++AM_CPPFLAGS = -I$(top_srcdir)/include + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/solver/Makefile.am ++++ b/src/solver/Makefile.am +@@ -17,16 +17,5 @@ + lis_solver_sor.c + + +-AM_CFLAGS = -I$(top_srcdir)/include ++AM_CPPFLAGS = -I$(top_srcdir)/include + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/system/Makefile.am ++++ b/src/system/Makefile.am +@@ -13,16 +13,5 @@ + mt19937ar.c + + +-AM_CFLAGS = -I$(top_srcdir)/include ++AM_CPPFLAGS = -I$(top_srcdir)/include + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/src/vector/Makefile.am ++++ b/src/vector/Makefile.am +@@ -4,16 +4,5 @@ + lis_vector_opv.c + + +-AM_CFLAGS = -I$(top_srcdir)/include ++AM_CPPFLAGS = -I$(top_srcdir)/include + CLEANFILES = *.il +- +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +--- a/test/Makefile.am ++++ b/test/Makefile.am +@@ -5,21 +5,22 @@ + + EXTRA_DIST = defs test.sh testmat.mtx testmat2.mtx + +-testdir = ${prefix}/share/examples/lis ++testdir = $(prefix)/share/lis/examples + + test_DATA = testmat.mtx testmat2.mtx + + test_SCRIPTS = defs test.sh + +-test_PROGRAMS = etest1 etest2 etest3 etest4 etest5 etest6 etest7 spmvtest1 spmvtest2 spmvtest2b spmvtest3 spmvtest3b spmvtest4 spmvtest5 test1 test2 test2b test3 test3b test4 test5 test6 test7 ++check_PROGRAMS = etest1 etest2 etest3 etest4 etest5 etest6 etest7 spmvtest1 spmvtest2 spmvtest2b spmvtest3 spmvtest3b spmvtest4 spmvtest5 test1 test2 test2b test3 test3b test4 test5 test6 test7 + if ENABLE_FORTRAN +- test_PROGRAMS += etest1f etest4f test1f test4f test7f ++ check_PROGRAMS += etest1f etest4f test1f test4f test7f ++ LDADD += $(FLIBS) + endif + if ENABLE_F90 +- test_PROGRAMS += test2f test6f ++ check_PROGRAMS += test2f test6f + if ENABLE_SAAMG + if ENABLE_MPI +- test_PROGRAMS += test8f ++ check_PROGRAMS += test8f + endif + endif + endif +@@ -60,40 +61,13 @@ + test8f_SOURCES = test8f.F90 + endif + +-bin_PROGRAMS = esolve hpcg_kernel hpcg_spmvtest lsolve spmvtest1 spmvtest2 spmvtest2b spmvtest3 spmvtest3b spmvtest4 spmvtest5 ++noinst_PROGRAMS = esolve hpcg_kernel hpcg_spmvtest lsolve spmvtest1 spmvtest2 spmvtest2b spmvtest3 spmvtest3b spmvtest4 spmvtest5 + + esolve_SOURCES = etest5.c + hpcg_kernel_SOURCES = test3b.c + hpcg_spmvtest_SOURCES = spmvtest3b.c + lsolve_SOURCES = test1.c + +-PPF77COMPILE = $(F77) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ +- $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_FFLAGS) $(FFLAGS) +-LTPPF77COMPILE = $(LIBTOOL) --mode=compile --tag=F77 $(F77) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_FFLAGS) $(FFLAGS) +-COMPILE = $(CC) $(AMDEFS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ +- $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +-LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(AMDEFS) $(DEFS) \ +- $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \ +- $(AM_CFLAGS) $(CFLAGS) +- +-if ENABLE_SAAMG +- LINK = $(LIBTOOL) --mode=link $(FC) \ +- $(AM_LDFLAGS) $(LDFLAGS) $(FCLDFLAGS) -o $@ $(LIBS) $(CLIBS) +- F77LINK = $(LIBTOOL) --mode=link $(FC) \ +- $(AM_LDFLAGS) $(LDFLAGS) -o $@ $(LIBS) $(CLIBS) +-else +-if ENABLE_FORTRAN +- LINK = $(LIBTOOL) --mode=link $(FC) \ +- $(AM_LDFLAGS) $(LDFLAGS) $(FCLDFLAGS) -o $@ $(LIBS) $(CLIBS) +- F77LINK = $(LIBTOOL) --mode=link $(F77) \ +- $(AM_LDFLAGS) $(LDFLAGS) -o $@ $(LIBS) $(CLIBS) +-else +- LINK = $(LIBTOOL) --mode=link $(CC) $(AM_LDFLAGS) $(LDFLAGS) -o $@ $(LIBS) +-endif +-endif +- + CLEANFILES = *.il + + diff --git a/sci-libs/lis/lis-1.6.5.ebuild b/sci-libs/lis/lis-1.6.5.ebuild new file mode 100644 index 000000000000..5cd496ef8d5c --- /dev/null +++ b/sci-libs/lis/lis-1.6.5.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools fortran-2 toolchain-funcs + +DESCRIPTION="Library of Iterative Solvers for Linear Systems" +HOMEPAGE="http://www.ssisc.org/lis/index.en.html" +SRC_URI="http://www.ssisc.org/lis/dl/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_fma3 cpu_flags_x86_fma4 cpu_flags_x86_sse2 doc fortran mpi openmp quad saamg static-libs" + +RDEPEND="mpi? ( virtual/mpi )" +DEPEND="${RDEPEND}" + +PATCHES=( "${FILESDIR}"/${PN}-1.6.2-autotools.patch ) + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + + if tc-is-clang; then + ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," + ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\"" + fi + + die "need openmp capable compiler" + fi + FORTRAN_NEED_OPENMP=1 + fi + + use fortran && fortran-2_pkg_setup +} + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --enable-shared \ + $(use_enable static-libs static) \ + $(use_enable fortran) \ + $(use_enable openmp omp) \ + $(use_enable quad) \ + $(use_enable "cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4)" fma) \ + $(use_enable cpu_flags_x86_sse2 sse2) \ + $(use_enable saamg) \ + $(use_enable mpi) +} + +src_install() { + use doc && DOCS+=( doc/*.pdf ) + default + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} diff --git a/sci-libs/lis/metadata.xml b/sci-libs/lis/metadata.xml new file mode 100644 index 000000000000..e399be309aa6 --- /dev/null +++ b/sci-libs/lis/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Lis, a Library of Iterative Solvers for linear systems, is a + scalable parallel library for solving systems of linear equations + and standard eigenvalue problems with real sparse matrices using + iterative methods. +</longdescription> + <use> + <flag name="saamg">Build the Smoothed Aggregation Algebraic MultiGrid preconditioner</flag> + <flag name="quad">Enable quadruple precision operations</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/lrslib/Manifest b/sci-libs/lrslib/Manifest new file mode 100644 index 000000000000..f937669f0b93 --- /dev/null +++ b/sci-libs/lrslib/Manifest @@ -0,0 +1,10 @@ +DIST lrslib-042c.tar.gz 168765 SHA256 53f99b5271397bb5f317c96fa365edc1ac71fa7cba0295c8bd79e0882f5c3a4a SHA512 a5fdd65b2c4e4cadd5fb9679e0e94ddc6b3564cdb9bdfcb7304351fec943527d2dccf117148d8d418ad8bd4577c9f69dabd6ca07107c1c1555c8c6d17f38fa60 WHIRLPOOL 4c3c1d5a72f8ac91e3d6698a8409578f5c0a940562704adea6631e5f9fb738a24414806a4d4b3aedf4e32de49a8c09ec74058baef61e121ce54db7ef5d2f5c01 +DIST lrslib-051.tar.gz 179396 SHA256 500893df61631944bac14a76c6e13fc08e6e729727443fa5480b2510de0db635 SHA512 65e4752ae75f06bccb74b0e12e0b03943654cba048d54dbcf93a36bea7f73b32826babe066d5fe20d3c6609548dc957063558633affe64d795c240c1fe748927 WHIRLPOOL 54877f0432fef43989b5d7591cef6692dbb555fb0ccb8a634b82eefb06a20d478bbb1a62b2ef241c8cda74328da29bcbcdcf8031640d1e0455a1e57bf839125e +DIST lrslib-062.tar.gz 292745 SHA256 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( dev-libs/gmp )" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -i "s/gcc/$(tc-getCC)/g" makefile || die + sed -i "s/-O3/${CFLAGS} ${LDFLAGS}/g" makefile || die +} + +src_compile () { + if use amd64 ; then + emake all64 || die "make failed" + else + emake || die "make failed" + fi + if use gmp ; then + emake gmp || die "make failed" + fi +} + +src_install() { + dobin lrs redund redund1 || die + # Collides with sys-block/buffer + newbin buffer lrsbuffer || die + if use x86; then + dobin nash setupnash setupnash2 2nash || die + # Prevent clash with cddlib: + newbin fourier lrsfourier || die + fi + if use gmp; then + dobin glrs gredund gfourier || die + # Clash with www-plugins/gnash + newbin gnash lrsgnash || die + fi + dodoc readme || die + dohtml lrslib.html || die +} diff --git a/sci-libs/lrslib/lrslib-042c-r2.ebuild b/sci-libs/lrslib/lrslib-042c-r2.ebuild new file mode 100644 index 000000000000..8fafdff0cba2 --- /dev/null +++ b/sci-libs/lrslib/lrslib-042c-r2.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit toolchain-funcs + +DESCRIPTION="self-contained ANSI C implementation of the reverse search algorithm" +HOMEPAGE="http://cgm.cs.mcgill.ca/~avis/C/lrs.html" +SRC_URI="http://cgm.cs.mcgill.ca/~avis/C/lrslib/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="gmp" + +DEPEND="gmp? ( dev-libs/gmp )" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -i "s/gcc/$(tc-getCC)/g" makefile || die + sed -i "s/-O3/${CFLAGS} ${LDFLAGS}/g" makefile || die + # We don't like static linking to gmp or anywhere. + if use amd64 ; then + # This macro may only change messages that the + # binary outputs, but just in case... (Bug 384195) + sed -i "s/-static/-DB64/g" makefile || die + else + sed -i "s/-static//g" makefile || die + fi +} + +src_compile () { + if use amd64 ; then + emake all64 + else + emake + fi + if use gmp ; then + emake gmp + fi +} + +src_install() { + dobin lrs redund redund1 + # Collides with sys-block/buffer + newbin buffer lrsbuffer + if use x86; then + dobin nash setupnash setupnash2 2nash + # Prevent clash with cddlib: + newbin fourier lrsfourier + fi + if use gmp; then + dobin glrs gredund gfourier + # Clash with www-plugins/gnash + newbin gnash lrsgnash + fi + dodoc readme + dohtml lrslib.html +} diff --git a/sci-libs/lrslib/lrslib-051.ebuild b/sci-libs/lrslib/lrslib-051.ebuild new file mode 100644 index 000000000000..8c8e791b7941 --- /dev/null +++ b/sci-libs/lrslib/lrslib-051.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="self-contained ANSI C implementation of the reverse search algorithm" +HOMEPAGE="http://cgm.cs.mcgill.ca/~avis/C/lrs.html" +SRC_URI="http://cgm.cs.mcgill.ca/~avis/C/lrslib/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86" +IUSE="gmp" + +DEPEND="gmp? ( dev-libs/gmp:0= )" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -i "s/gcc/$(tc-getCC)/g" makefile || die + sed -i "s/-O3/${CFLAGS} ${LDFLAGS}/g" makefile || die + # Prefix for install + sed -i "s,/usr/local,/usr,g" makefile || die +} + +src_compile () { + if use gmp ; then + emake all + emake all-shared + else + emake allmp + fi +} + +src_install() { + dodoc readme + # Library + if use gmp ; then + emake DESTDIR="${D}" install-shared + fi + # Install default set of binaries + emake DESTDIR="${D}" install-common +} diff --git a/sci-libs/lrslib/lrslib-062.ebuild b/sci-libs/lrslib/lrslib-062.ebuild new file mode 100644 index 000000000000..1df9b43c7019 --- /dev/null +++ b/sci-libs/lrslib/lrslib-062.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs eutils + +DESCRIPTION="Self-contained C implementation of the reverse search algorithm" +HOMEPAGE="http://cgm.cs.mcgill.ca/~avis/C/lrs.html" +SRC_URI="http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux" +IUSE="gmp mpi" + +RDEPEND="gmp? ( dev-libs/gmp:0= + mpi? ( virtual/mpi ) )" +DEPEND="${RDEPEND}" + +src_prepare(){ + default + tc-export CC + sed -e "s/gcc/$(tc-getCC)/g" \ + -e "s/g++/$(tc-getCXX)/g" \ + -e "s/-O3/${CFLAGS}/g" \ + -e 's/$(CC) -shared/$(CC) $(LDFLAGS) -shared/' \ + -e "s,/usr/local,${EPREFIX}/usr,g" \ + -e "s,/lib,/$(get_libdir),g" \ + -i makefile || die +} + +src_compile () { + if use gmp ; then + emake + emake all-shared + use mpi && emake mplrs + else + emake allmp + fi +} + +src_install() { + emake DESTDIR="${D}" prefix="${EPREFIX}/usr" install-common + if use gmp; then + emake DESTDIR="${D}" install-shared prefix="${EPREFIX}/usr" + use mpi && dobin mplrs + fi + dodoc README +} diff --git a/sci-libs/lrslib/metadata.xml b/sci-libs/lrslib/metadata.xml new file mode 100644 index 000000000000..8b97646ef0f3 --- /dev/null +++ b/sci-libs/lrslib/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription>lrslib is a self-contained ANSI C implementation as a callable library of the + reverse search algorithm for vertex enumeration/convex hull problems and comes with a choice of + three arithmetic packages. Input file formats are compatible with Komei Fukuda's cdd package. All + computations are done exactly in either multiple precision or fixed integer arithmetic. Output is + not stored in memory, so even problems with very large output sizes can sometimes be + solved.</longdescription> +</pkgmetadata> diff --git a/sci-libs/magma/Manifest b/sci-libs/magma/Manifest new file mode 100644 index 000000000000..1f8df26743f5 --- /dev/null +++ b/sci-libs/magma/Manifest @@ -0,0 +1,7 @@ +DIST magma-1.4.0.tar.gz 3557459 SHA256 bd767d7676c3953722eb75928300c162a2c9e0c35791a5427b58a069241f8a58 SHA512 9857ac544cc1657ab7d2f6e8c9700facb7fa38278dbfbfeecc3656434de4bd5b96c268f1a98c9ffa823775aa64c315bd63e577b4d475e104311e09d3e5c3ca15 WHIRLPOOL 99c16d35f2711b3e5f81f2f5c46e434b6e3d8a0bc0ffe7e63bbfe683d75b2cdd99d3a06fd19b2d61f8d98d0fcdfcfe2e2f7d8ec3d0e918fd31e27aa4c818a196 +DIST magma-1.4.1.tar.gz 3765589 SHA256 f1b87238e0e6f794510538e001be89e6d79198084223ea3024dee438060f065b SHA512 d283b59b75ca35c8206c07eff97caf28f07ab598955c84a90d795d46905d879d0f1d7e6a2cb080dad74710255b28999e5ce9708e4f0f53a4adba50724fc5ef71 WHIRLPOOL c38eddd259788f9c143f8828df8acb12da7c7f571e19b01231b38271c37f2753c245dcca1e9b35e3f3ef5688f738477f22b929dcd01347cd867be04f1de6d481 +EBUILD magma-1.4.0.ebuild 3172 SHA256 d7f1f4e6eb8876d618d159701714175af956acae230ddc0fc54dcb266b7e8195 SHA512 464e3a905cc216908f69384ef4038813bd30be4f06493966bff0cc593d841ca3b3f38e48c51cc03e8efe78e5ccc66a2d04ddefd1a725cabfba48182a8dab161c WHIRLPOOL 85c9fd39798be47adc949ca3bfd1b7f484125cd10fc05a3ede13abe5d95db5c8f37beb9321e0fd5ab357fc0a05a944a5ffcfbb6d56c00a5ff839001f3ca5787b +EBUILD magma-1.4.1.ebuild 3172 SHA256 d7f1f4e6eb8876d618d159701714175af956acae230ddc0fc54dcb266b7e8195 SHA512 464e3a905cc216908f69384ef4038813bd30be4f06493966bff0cc593d841ca3b3f38e48c51cc03e8efe78e5ccc66a2d04ddefd1a725cabfba48182a8dab161c WHIRLPOOL 85c9fd39798be47adc949ca3bfd1b7f484125cd10fc05a3ede13abe5d95db5c8f37beb9321e0fd5ab357fc0a05a944a5ffcfbb6d56c00a5ff839001f3ca5787b +MISC ChangeLog 2870 SHA256 83bc77d53fd7ec73868f6ef720795e175d960b549c9d251f980f40461cbe35b9 SHA512 aaf13117211c1db178456957a99d9fb5d1c584502780acb390cad4e5d63e135ebaa0e216a35691437a7422d64ef2936943786b5e48e8e642adcd6b86c3a7f9f1 WHIRLPOOL 1ad3663d18462af363f95767f39cb3981e7d50467dc5a5ecb881b8db72f61b93a6db70a5161b0eab58dd92733a2fe50fa175004c9d81b5cbbda6bd0bb1c9a484 +MISC ChangeLog-2015 601 SHA256 69771f17e7f193c7b09efec671f2f6a3743d8bddd34afdafb145ee9de6c8ef5a SHA512 6b52d723cfc90e73e1931366e83b7001217ae40c926520536d000f55f88012844f483c672210bcaffc6cda0f446676bf6276b7aa45a644c6627acb7579a7b0b2 WHIRLPOOL 49781d31fe202e2ac518ea03a904a23fe349ff591ca158c4ff47c27c7090759dedee3ffc6624ccc005ae368638af8fcffc1f4823eec6912440bcf3193cdff07e +MISC metadata.xml 712 SHA256 eebe645fa61b4e76ff1a3dfb8d1e3e422ec7c72e7cc8f1a270f5260292432631 SHA512 27a54732753e5a772d40323c4571cbe43b3a9aec5243063e2e37fc9939a0fcf4810e8f91364145ab8982a385bbcdebcb468abbab917a074416fd8818943b5ec0 WHIRLPOOL 42123a2a96cd93f292af642d54944b851ec73cca9d7080a0a70e13e955c5d82306dbfb3d54da3bc84530d7997fe349e2f6a7526067e221b9a44ca0dedd8d5e67 diff --git a/sci-libs/magma/magma-1.4.0.ebuild b/sci-libs/magma/magma-1.4.0.ebuild new file mode 100644 index 000000000000..33d1cd70c243 --- /dev/null +++ b/sci-libs/magma/magma-1.4.0.ebuild @@ -0,0 +1,124 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +FORTRAN_STANDARD="77 90" + +inherit cuda eutils flag-o-matic fortran-2 multilib toolchain-funcs versionator python-any-r1 + +DESCRIPTION="Matrix Algebra on GPU and Multicore Architectures" +HOMEPAGE="http://icl.cs.utk.edu/magma/" +SRC_URI="http://icl.cs.utk.edu/projectsfiles/${PN}/downloads/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" +IUSE="fermi kepler static-libs test" + +REQUIRED_USE="?? ( fermi kepler )" + +RDEPEND=" + dev-util/nvidia-cuda-toolkit + virtual/cblas + virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( ${PYTHON_DEPS} )" + +# We have to have write acccess /dev/nvidia0 and /dev/nvidiactl and the portage +# user is (usually) not in the video group +RESTRICT="userpriv" + +pkg_setup() { + fortran-2_pkg_setup + use test && python-any-r1_pkg_setup +} + +src_prepare() { + # distributed pc file not so useful so replace it + cat <<-EOF > ${PN}.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include/${PN} + Name: ${PN} + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lmagma + Libs.private: -lm -lpthread -ldl -lcublas -lcudart + Cflags: -I\${includedir} + Requires: cblas lapack + EOF + + if [[ $(tc-getCC) =~ gcc ]]; then + local eopenmp=-fopenmp + elif [[ $(tc-getCC) =~ icc ]]; then + local eopenmp=-openmp + else + elog "Cannot detect compiler type so not setting openmp support" + fi + append-flags -fPIC ${eopenmp} + append-ldflags -Wl,-soname,lib${PN}.so.1.4 ${eopenmp} + + cuda_src_prepare +} + +src_configure() { + cat <<-EOF > make.inc + ARCH = $(tc-getAR) + ARCHFLAGS = cr + RANLIB = $(tc-getRANLIB) + NVCC = nvcc + CC = $(tc-getCXX) + FORT = $(tc-getFC) + INC = -I"${EPREFIX}/opt/cuda/include" -DADD_ -DCUBLAS_GFORTRAN + OPTS = ${CFLAGS} -fPIC + FOPTS = ${FFLAGS} -fPIC -x f95-cpp-input + F77OPTS = ${FFLAGS} -fPIC + NVOPTS = -DADD_ -DUNIX ${NVCCFLAGS} + LDOPTS = ${LDFLAGS} + LOADER = $(tc-getFC) + LIBBLAS = $($(tc-getPKG_CONFIG) --libs cblas) + LIBLAPACK = $($(tc-getPKG_CONFIG) --libs lapack) + CUDADIR = ${EPREFIX}/opt/cuda + LIBCUDA = -L\$(CUDADIR)/$(get_libdir) -lcublas -lcudart + LIB = -pthread -lm -ldl \$(LIBCUDA) \$(LIBBLAS) \$(LIBLAPACK) -lstdc++ + EOF + if use kepler; then + echo >> make.inc "GPU_TARGET = Kepler" + elif use fermi; then + echo >> make.inc "GPU_TARGET = Fermi" + else # See http://icl.cs.utk.edu/magma/forum/viewtopic.php?f=2&t=227 + echo >> make.inc "GPU_TARGET = Tesla" + fi +} + +src_compile() { + emake lib + emake shared + mv lib/lib${PN}.so{,.1.4} || die + ln -sf lib${PN}.so.1.4 lib/lib${PN}.so.1 || die + ln -sf lib${PN}.so.1.4 lib/lib${PN}.so || die +} + +src_test() { + emake test lapacktest + cd testing/lin || die + # we need to access this while running the tests + addwrite /dev/nvidiactl + addwrite /dev/nvidia0 + LD_LIBRARY_PATH="${S}"/lib ${EPYTHON} lapack_testing.py || die +} + +src_install() { + dolib.so lib/lib*$(get_libname)* + use static-libs && dolib.a lib/lib*.a + insinto /usr/include/${PN} + doins include/*.h + insinto /usr/$(get_libdir)/pkgconfig + doins ${PN}.pc + dodoc README ReleaseNotes +} diff --git a/sci-libs/magma/magma-1.4.1.ebuild b/sci-libs/magma/magma-1.4.1.ebuild new file mode 100644 index 000000000000..33d1cd70c243 --- /dev/null +++ b/sci-libs/magma/magma-1.4.1.ebuild @@ -0,0 +1,124 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +FORTRAN_STANDARD="77 90" + +inherit cuda eutils flag-o-matic fortran-2 multilib toolchain-funcs versionator python-any-r1 + +DESCRIPTION="Matrix Algebra on GPU and Multicore Architectures" +HOMEPAGE="http://icl.cs.utk.edu/magma/" +SRC_URI="http://icl.cs.utk.edu/projectsfiles/${PN}/downloads/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" +IUSE="fermi kepler static-libs test" + +REQUIRED_USE="?? ( fermi kepler )" + +RDEPEND=" + dev-util/nvidia-cuda-toolkit + virtual/cblas + virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( ${PYTHON_DEPS} )" + +# We have to have write acccess /dev/nvidia0 and /dev/nvidiactl and the portage +# user is (usually) not in the video group +RESTRICT="userpriv" + +pkg_setup() { + fortran-2_pkg_setup + use test && python-any-r1_pkg_setup +} + +src_prepare() { + # distributed pc file not so useful so replace it + cat <<-EOF > ${PN}.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include/${PN} + Name: ${PN} + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lmagma + Libs.private: -lm -lpthread -ldl -lcublas -lcudart + Cflags: -I\${includedir} + Requires: cblas lapack + EOF + + if [[ $(tc-getCC) =~ gcc ]]; then + local eopenmp=-fopenmp + elif [[ $(tc-getCC) =~ icc ]]; then + local eopenmp=-openmp + else + elog "Cannot detect compiler type so not setting openmp support" + fi + append-flags -fPIC ${eopenmp} + append-ldflags -Wl,-soname,lib${PN}.so.1.4 ${eopenmp} + + cuda_src_prepare +} + +src_configure() { + cat <<-EOF > make.inc + ARCH = $(tc-getAR) + ARCHFLAGS = cr + RANLIB = $(tc-getRANLIB) + NVCC = nvcc + CC = $(tc-getCXX) + FORT = $(tc-getFC) + INC = -I"${EPREFIX}/opt/cuda/include" -DADD_ -DCUBLAS_GFORTRAN + OPTS = ${CFLAGS} -fPIC + FOPTS = ${FFLAGS} -fPIC -x f95-cpp-input + F77OPTS = ${FFLAGS} -fPIC + NVOPTS = -DADD_ -DUNIX ${NVCCFLAGS} + LDOPTS = ${LDFLAGS} + LOADER = $(tc-getFC) + LIBBLAS = $($(tc-getPKG_CONFIG) --libs cblas) + LIBLAPACK = $($(tc-getPKG_CONFIG) --libs lapack) + CUDADIR = ${EPREFIX}/opt/cuda + LIBCUDA = -L\$(CUDADIR)/$(get_libdir) -lcublas -lcudart + LIB = -pthread -lm -ldl \$(LIBCUDA) \$(LIBBLAS) \$(LIBLAPACK) -lstdc++ + EOF + if use kepler; then + echo >> make.inc "GPU_TARGET = Kepler" + elif use fermi; then + echo >> make.inc "GPU_TARGET = Fermi" + else # See http://icl.cs.utk.edu/magma/forum/viewtopic.php?f=2&t=227 + echo >> make.inc "GPU_TARGET = Tesla" + fi +} + +src_compile() { + emake lib + emake shared + mv lib/lib${PN}.so{,.1.4} || die + ln -sf lib${PN}.so.1.4 lib/lib${PN}.so.1 || die + ln -sf lib${PN}.so.1.4 lib/lib${PN}.so || die +} + +src_test() { + emake test lapacktest + cd testing/lin || die + # we need to access this while running the tests + addwrite /dev/nvidiactl + addwrite /dev/nvidia0 + LD_LIBRARY_PATH="${S}"/lib ${EPYTHON} lapack_testing.py || die +} + +src_install() { + dolib.so lib/lib*$(get_libname)* + use static-libs && dolib.a lib/lib*.a + insinto /usr/include/${PN} + doins include/*.h + insinto /usr/$(get_libdir)/pkgconfig + doins ${PN}.pc + dodoc README ReleaseNotes +} diff --git a/sci-libs/magma/metadata.xml b/sci-libs/magma/metadata.xml new file mode 100644 index 000000000000..63989ce9caba --- /dev/null +++ b/sci-libs/magma/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The Matrix Algebra on GPU and Multicore Architectures + project aims to develop a dense linear algebra library + similar to LAPACK but for heterogeneous/hybrid architectures, starting + with current "Multicore+GPU" systems. +</longdescription> + <use> + <flag name="fermi">Compile for GPU NVIDIA Fermi family (2.x cards)</flag> + <flag name="kepler">Compile for GPU NVIDIA Kepler family (GF 6xx cards)</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/mathgl/Manifest b/sci-libs/mathgl/Manifest new file mode 100644 index 000000000000..ed1b325d77cf --- /dev/null +++ b/sci-libs/mathgl/Manifest @@ -0,0 +1,6 @@ +DIST STIX_font.tgz 2450541 SHA256 6408290fd4a5267637a88507344a8f07b908ce72f46ef93d09e068fedb67e8fe SHA512 c9124ec552074c98f15d6d3572a063598ca6bc598e3e78dcb5a5d57ae3928b5327a1374635f428ea1cefc9e51ee1d1aa9bd6ba9a306429fc6965140251d368b5 WHIRLPOOL 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in ${LANGS}; do + IUSE+=" linguas_${l}" +done +unset l + +RDEPEND=" + !sci-visualization/udav + virtual/opengl + fltk? ( x11-libs/fltk:1 ) + gif? ( media-libs/giflib ) + glut? ( media-libs/freeglut ) + gsl? ( >=sci-libs/gsl-2 ) + hdf? ( sci-libs/hdf ) + hdf5? ( >=sci-libs/hdf5-1.8[mpi=] ) + jpeg? ( virtual/jpeg:0 ) + lua? ( >=dev-lang/lua-5.1:0 ) + octave? ( >=sci-mathematics/octave-3.4.0 ) + openmp? ( sys-cluster/openmpi ) + pdf? ( media-libs/libharu ) + png? ( media-libs/libpng:0 ) + python? ( dev-python/numpy[${PYTHON_USEDEP}] ${PYTHON_DEPS} ) + qt4? ( dev-qt/qtgui:4 ) + wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] ) + zlib? ( sys-libs/zlib )" + +DEPEND="${RDEPEND} + doc? ( app-text/texi2html virtual/texi2dvi ) + octave? ( dev-lang/swig ) + python? ( dev-lang/swig )" + +REQUIRED_USE=" + mpi? ( hdf5 ) + openmp? ( !threads ) + png? ( zlib ) + pdf? ( png ) + python? ( ${PYTHON_REQUIRED_USE} )" + +pkg_setup() { + use mpi && export CC=mpicc CXX=mpicxx + use python && python-single-r1_pkg_setup +} + +src_unpack() { + default + if ! [[ -d "${S}"/fonts ]]; then + mkdir "${S}"/fonts || die + fi + cd "${S}"/fonts || die + unpack STIX_font.tgz +} + +src_prepare() { + default + + # fix for location of hdf headers + sed -i -e 's:hdf/::g' src/data_io.cpp || die + # bored of reporting bad libdir upstream + sed -i \ + -e '/DESTINATION/s:lib$:lib${LIB_SUFFIX}:g' \ + {src,widgets}/CMakeLists.txt || die + echo "" > lang/install.m || die + # fix desktop file + sed -i -e 's/.png//' udav/udav.desktop || die + # prevent sandbox violation + sed -i -e 's/update-mime-database/true/' udav/CMakeLists.txt || die + sed -i -e 's/update-desktop-database/true/' udav/CMakeLists.txt || die + # fix missing include, bug 564204 + sed \ + -e '/#include <QStringList>/i #include <QObject>' \ + -i json/Backend.hpp || die + + use python && \ + append-cppflags \ + -I"$(${EPYTHON} -c 'import numpy; print(numpy.get_include())')" + use wxwidgets && need-wxwidgets unicode +} + +src_configure() { + local mycmakeargs=( + # No clue about this option: + # option(enable-mgl2 "Use names 'libmgl2-*' instead of 'libmgl-*'") + -DHDF4_INCLUDE_DIR="${EPREFIX}/usr/include" + -DMGL_LIB_INSTALL_DIR="$(get_libdir)" + $(cmake-utils_use doc enable-all-docs) + $(cmake-utils_use fltk enable-fltk) + $(cmake-utils_use gif enable-gif) + $(cmake-utils_use glut enable-glut) + $(cmake-utils_use gsl enable-gsl) + $(cmake-utils_use hdf enable-hdf4) + $(cmake-utils_use hdf5 enable-hdf5_18) + $(cmake-utils_use jpeg enable-jpeg) + $(cmake-utils_use lua enable-lua) + $(cmake-utils_use mpi enable-mpi) + $(cmake-utils_use octave enable-octave) + $(cmake-utils_use opengl enable-opengl) + $(cmake-utils_use openmp enable-openmp) + $(cmake-utils_use pdf enable-pdf) + $(cmake-utils_use png enable-png) + $(cmake-utils_use qt4 enable-qt4) + $(cmake-utils_use qt5 enable-qt5) + $(cmake-utils_use threads enable-pthread) + $(cmake-utils_use threads enable-pthr-widget) + $(cmake-utils_use python enable-python) + $(cmake-utils_use wxwidgets enable-wx) + $(cmake-utils_use zlib enable-zlib) + ) + cmake-utils_src_configure + # to whoever cares: TODO: do for multiple python ABI + if use python; then + sed -i \ + -e "s:--prefix=\(.*\) :--prefix=\$ENV{DESTDIR}\1 :" \ + "${CMAKE_BUILD_DIR}"/lang/cmake_install.cmake || die + fi +} + +src_install() { + cmake-utils_src_install + dodoc README* *.txt AUTHORS + if ! use static-libs; then + rm "${ED}"/usr/$(get_libdir)/*.a || die + fi + if use qt4 ; then + local lang + insinto /usr/share/udav + for lang in ${LANGS} ; do + use linguas_${lang} && doins udav/udav_${lang}.qm + done + fi + if use octave ; then + insinto /usr/share/${PN}/octave + doins "${CMAKE_BUILD_DIR}"/lang/${PN}.tar.gz + fi + use python && python_optimize +} + +pkg_postinst() { + if use octave; then + octave <<-EOF + pkg install ${EROOT}/usr/share/${PN}/octave/${PN}.tar.gz + EOF + fi +} + +pkg_prerm() { + if use octave; then + octave <<-EOF + pkg uninstall ${PN} + EOF + fi +} diff --git a/sci-libs/mathgl/metadata.xml b/sci-libs/mathgl/metadata.xml new file mode 100644 index 000000000000..2ca4b1ae580f --- /dev/null +++ b/sci-libs/mathgl/metadata.xml @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>grozin@gentoo.org</email> + <name>Andrey Grozin</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + MathGL is a library for: + * making high-quality scientific graphics + * the fast data plotting and data processing of large data arrays + * working in window and console modes and for easy embedding into other programs +</longdescription> + <use> + <flag name="hdf">Add support for the Hierarchical Data Format v.4 <pkg>sci-libs/hdf</pkg></flag> + <flag name="octave">Add bindings for <pkg>sci-mathematics/octave</pkg></flag> + </use> + <upstream> + <remote-id type="sourceforge">mathgl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/matio/Manifest b/sci-libs/matio/Manifest new file mode 100644 index 000000000000..1d7baee5e700 --- /dev/null +++ b/sci-libs/matio/Manifest @@ -0,0 +1,10 @@ +AUX matio-1.5.0-asneeded.patch 484 SHA256 45b05c16558619fb814a54eaeafb892e255bcb5d71dbf7c9e5c90a8fae0e88f1 SHA512 4ad49023834a884c095924a179dca7bd90acdafa6d4fa00954d8d1132771349e63ad86bd0c027fc60b01960d7218970162bbf2eac4faa75e5124ccd607353152 WHIRLPOOL 08cc29a4beaff4bcfe6bb52b5f05e7802ad13e16fd67410879c03c7604c3e12e5cc5ab6b00ca0c9a0173fbd106c6f475db5afeb86e258473982bfb970fee71ac +DIST matio-1.5.1.tar.gz 8160893 SHA256 7d94a1433f67ce21f08fbbfc8af677f3838964b2b07565dce6f65e878394cd2f SHA512 bd1e49bcbfe3e073d2339bc3dff803b222c007aad19759ee9b666438fa59ec2b2750b52ffb3b5e911145cf2977538447f5db977fc056a624c5878ddbcf564b26 WHIRLPOOL 54c5191c9b4b15e54f25d435a7ea680c84c94f1f5c9e432e3340a7a0821b743c95a08c4e77d65dece3768147c7b5e9e9057bc7ad9b8cde358951f5728d81879b +DIST matio-1.5.10.tar.gz 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b/sci-libs/matio/matio-1.5.1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 + +inherit autotools-utils eutils + +DESCRIPTION="Library for reading and writing matlab files" +HOMEPAGE="https://sourceforge.net/projects/matio/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples hdf5 sparse static-libs" + +RDEPEND=" + sys-libs/zlib + hdf5? ( sci-libs/hdf5 )" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +PATCHES=( "${FILESDIR}"/${PN}-1.5.0-asneeded.patch ) + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable hdf5 mat73) + $(use_enable sparse extended-sparse) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + use doc && autotools-utils_src_compile -C documentation pdf +} + +src_install() { + use doc && DOCS=( "${BUILD_DIR}"/documentation/matio_user_guide.pdf ) + autotools-utils_src_install + if use examples; then + docinto examples + dodoc test/test* + insinto /usr/share/${PN} + doins share/test* + fi +} diff --git a/sci-libs/matio/matio-1.5.10.ebuild b/sci-libs/matio/matio-1.5.10.ebuild new file mode 100644 index 000000000000..78479eb8ba9c --- /dev/null +++ b/sci-libs/matio/matio-1.5.10.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="Library for reading and writing matlab files" +HOMEPAGE="https://sourceforge.net/projects/matio/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +SLOT="0/4" # subslot = soname version +LICENSE="BSD-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples hdf5 sparse static-libs" + +RDEPEND=" + sys-libs/zlib + hdf5? ( sci-libs/hdf5 )" +DEPEND="${RDEPEND} + sys-devel/libtool + doc? ( virtual/latex-base )" + +src_configure() { + econf \ + $(use_enable hdf5 mat73) \ + $(use_enable sparse extended-sparse) \ + $(use_enable static-libs static) +} + +src_compile() { + default + use doc && emake -C documentation pdf +} + +src_install() { + default + + use doc && dodoc documentation/matio_user_guide.pdf + if use examples; then + docinto examples + dodoc test/test* + insinto /usr/share/${PN} + doins share/test* + fi + + find "${D}" -name "*.la" -delete || die +} diff --git a/sci-libs/matio/matio-1.5.2.ebuild b/sci-libs/matio/matio-1.5.2.ebuild new file mode 100644 index 000000000000..35b0ae903e3d --- /dev/null +++ b/sci-libs/matio/matio-1.5.2.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 + +inherit autotools-utils eutils + +DESCRIPTION="Library for reading and writing matlab files" +HOMEPAGE="https://sourceforge.net/projects/matio/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples hdf5 sparse static-libs" + +RDEPEND=" + sys-libs/zlib + hdf5? ( sci-libs/hdf5 )" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +PATCHES=( "${FILESDIR}"/${PN}-1.5.0-asneeded.patch ) + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable hdf5 mat73) + $(use_enable sparse extended-sparse) + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + use doc && autotools-utils_src_compile -C documentation pdf +} + +src_install() { + use doc && DOCS=( "${BUILD_DIR}"/documentation/matio_user_guide.pdf ) + autotools-utils_src_install + if use examples; then + docinto examples + dodoc test/test* + insinto /usr/share/${PN} + doins share/test* + fi +} diff --git a/sci-libs/matio/metadata.xml b/sci-libs/matio/metadata.xml new file mode 100644 index 000000000000..2bc7cf11270b --- /dev/null +++ b/sci-libs/matio/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + matio is an ISO C library (with a limited Fortran 90 interface) for + reading and writing Matlab MAT files. +</longdescription> + <use> + <flag name="sparse">Extend formats for sparse matrix (not matlab)</flag> + </use> + <upstream> + <remote-id type="sourceforge">matio</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/mc/Manifest b/sci-libs/mc/Manifest new file mode 100644 index 000000000000..bb903d4a5dcc --- /dev/null +++ b/sci-libs/mc/Manifest @@ -0,0 +1,10 @@ +AUX 1.4-doc.patch 526 SHA256 d1459adc32d7a4c987cbba795935e199939c66a81649ca21159c2d632c9cc408 SHA512 079a62088acae2164965f76821399c49c798e1e38b25f54825d16afa4eefcc43fcda10bddb9dca183c0b53e4fb72402a31ec914c0145b62c674a1244f7a1152d WHIRLPOOL d53281044811a136023028baadc96cc25b904d706d5944b92f6563bcb87a7860ff0bf077d6ef7d3f177bea3be504cdf2a70862177cf7031666ed01014e386039 +AUX 1.4-multilib.patch 693 SHA256 c12e7f95d5ecc9d3bdd6b2d25b0660b63b8ed08d557c7653d89f23b576817aa8 SHA512 878d0ff033ae1926fe53c43bb3e6118612e328b395879359c930c10b7699d0180d024693b9bdc9da21a5dd904557101001683079127657122c7140d49ae9b43b WHIRLPOOL f1307329799827307f264f1b8ba9d1ace520e4171a9d96b9d0ac7d7685391a6cb2fa67b87f3de5e6fa1f5fd6e1237f45b5c04e7ac43ce6ed0cff541b047a1492 +AUX 1.4-overflow.patch 426 SHA256 3ea566138dccc904747021f909d553254e9ff0f7064ea5cffd74b20df678c0bd SHA512 8eef4fcacb4c9b676b071483a7ff7c214110e8af1819552dc732919da2b4138754391cf578c90991e0fb36a475446b73bc9e5764b9e83224ab82519084d1aaee WHIRLPOOL e525a4a1808d9dc9a5aff7a268b04ce748963a59bab28ba6e70d03cf421f447b93a2cff0fc6d9fc039224a1bc2b5c852240b6f3fbe99149fc07109c7a101d334 +AUX 1.4-superlu.patch 695 SHA256 df3feabb7b2bb78973b4e0b85b9382e742f69f1966be6d6e61c418047c87d99e SHA512 9ada97571a91a8b4d832c61e373c2f64267ed4f0730a4e8543f388167daafe8800ed95e74e143d1644019f934b1e5b6b658b5ee639e97a01ad0a78bfe653296b WHIRLPOOL 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cc1530fc862fc93fa7932cc6df5f11ca9d6a99a262cab50beaf0eba325666e079529424370b4b80ed7f8dc31826b92458eb17fbdbe53491e5d40a0b19bb662cb WHIRLPOOL d2375fdda0c91b3fb99c5fc3c0c3ba6badf53b41302f24e2d01d7060af28766901b257d85802d403748db21ca79c818272b0678b2e1964a1e72a3b6c578f8d9d +MISC ChangeLog 2684 SHA256 6f4607162bfbabf955f01331690161b24aa87de86cbf46f737ad9055bae9ed0e SHA512 a759780d2946f621116d1df2cd173f59290dc597f6c202b792bc93463317600c27dd43e8c82ebe07c104b08cf52f0b1ac3dedfa7abcfb19a658a309861279036 WHIRLPOOL c0d4876924c56647c256166dfa819f94d1d07052fff9cb4be715d5be82538bb7b020f218627f48aebd177ca6ab6544a81abaa1b3b632dc9aba530830076e5226 +MISC ChangeLog-2015 1622 SHA256 85dfe8d4e75ee17b1920d7c5e4a4477b06159b35f40105c7bee0827c3db267ea SHA512 e4ea104ffba30fb4c93289ffff42b5eb7d541762cd5d87c88b95b24c07b97d92ad9ab8a0d5359f502087e8d15190808c480d43964da110e2a061b4761990a5fb WHIRLPOOL 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@prefix@/doc/mc +- + doc_DATA = mc_doc + + mc_doc: + $(doxygen_path) $(top_srcdir)/doc/doxygen/mc.dox + + install-docDATA: +- mkdir -p $(docdir) +- cp -r ../api $(docdir)/ ++ mkdir -p $(DESTDIR)/@docdir@ ++ cp -r ../api $(DESTDIR)/@docdir@/ diff --git a/sci-libs/mc/files/1.4-multilib.patch b/sci-libs/mc/files/1.4-multilib.patch new file mode 100644 index 000000000000..427cb94f2c8b --- /dev/null +++ b/sci-libs/mc/files/1.4-multilib.patch @@ -0,0 +1,16 @@ +diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am +index d5b8d47..132824b 100644 +--- a/src/aaa_lib/Makefile.am ++++ b/src/aaa_lib/Makefile.am +@@ -47,10 +47,9 @@ NAM_LIBS = ../nam/libnam.la + DYN_LIBS = ../dyn/libdyn.la + PDE_LIBS = ../pde/libpde.la + +-libdir = ${prefix}/lib + lib_LTLIBRARIES = libmc.la + + libmc_la_SOURCES = +-libmc_la_LIBADD = ${BASE_LIBS} ${BAM_LIBS} ${WHB_LIBS} ${APRX_LIBS} ${GEM_LIBS} ${MCSH_LIBS} ${NAM_LIBS} ${DYN_LIBS} ${PDE_LIBS} ++libmc_la_LIBADD = ${BASE_LIBS} ${BAM_LIBS} ${WHB_LIBS} ${APRX_LIBS} ${GEM_LIBS} ${MCSH_LIBS} ${NAM_LIBS} ${DYN_LIBS} ${PDE_LIBS} -lmaloc -lpunc -lumfpack -lamd -lsuperlu + libmc_la_LDFLAGS = -version-info ${FETK_VERSION} + diff --git a/sci-libs/mc/files/1.4-overflow.patch b/sci-libs/mc/files/1.4-overflow.patch new file mode 100644 index 000000000000..78610b0f2210 --- /dev/null +++ b/sci-libs/mc/files/1.4-overflow.patch @@ -0,0 +1,13 @@ +diff --git a/src/gem/gemdisp.c b/src/gem/gemdisp.c +index 01f277f..96d5851 100644 +--- a/src/gem/gemdisp.c ++++ b/src/gem/gemdisp.c +@@ -1631,7 +1631,7 @@ VPUBLIC void Gem_writeDX(Gem *thee, Vio *sock, + VPUBLIC void Gem_writeTEC(Gem *thee, Vio *sock, + int fldKey, double *defX[MAXV]) + { +- char str1[10], str2[10]; ++ char str1[16], str2[16]; + int i, j, vec, dim, dimII, dimVV, numVV, numSS; + VV *vx; + SS *sm; diff --git a/sci-libs/mc/files/1.4-superlu.patch b/sci-libs/mc/files/1.4-superlu.patch new file mode 100644 index 000000000000..cc3ce0a24740 --- /dev/null +++ b/sci-libs/mc/files/1.4-superlu.patch @@ -0,0 +1,21 @@ +diff --git a/src/bam/zslu.c b/src/bam/zslu.c +index 973b911..d82c7fd 100644 +--- a/src/bam/zslu.c ++++ b/src/bam/zslu.c +@@ -401,6 +401,7 @@ VPUBLIC int Zslu_factor(Zslu *thee) + SCformat *Lstore; + SuperMatrix *BB; + superlu_options_t *oopts; ++ SuperLUStat_t stat; + + VASSERT( thee != VNULL ); + +@@ -444,7 +445,7 @@ VPUBLIC int Zslu_factor(Zslu *thee) + Lstore->nnz + Ustore->nnz - thee->n); + printf("L\\U MB %.3f\ttotal MB needed %.3f\texpansions %d\n", + mem_usage.for_lu/1e6, mem_usage.total_needed/1e6, +- mem_usage.expansions); ++ stat.expansions); + fflush(stdout); + + } else if ( info > 0 && thee->lwork == -1 ) { diff --git a/sci-libs/mc/files/mc-1.5-unbundle.patch b/sci-libs/mc/files/mc-1.5-unbundle.patch new file mode 100644 index 000000000000..5a9a97241980 --- /dev/null +++ b/sci-libs/mc/files/mc-1.5-unbundle.patch @@ -0,0 +1,58 @@ + configure.ac | 38 ++++++-------------------------------- + 1 files changed, 6 insertions(+), 32 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 6198ac0..4b1b169 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -191,44 +191,18 @@ dnl # ----------------------- + dnl # HANDLE THE BLAS LIBRARY + dnl # ----------------------- + blas_lib=""; +-AC_MSG_CHECKING([whether your environment defines FETK_BLAS_LIBRARY]) +-if test -n "${FETK_BLAS_LIBRARY}"; then +- AC_MSG_RESULT([yes]) +- blas_lib_path="-L${FETK_BLAS_LIBRARY} "; +-else +- AC_MSG_RESULT([no]) +- blas_lib_path="-L${FETK_LIBRARY} "; +-fi +-LDFLAGS_SAVE=${LDFLAGS}; +-LDFLAGS=${blas_lib_path}; +-blas_use=""; +-AC_CHECK_LIB(blas,dscal_, +- [blas_use="yes";blas_lib="${blas_lib_path}-lblas";AC_DEFINE(HAVE_BLAS)], +- [blas_use="";blas_lib=""], +- [${blas_lib_path}-lblas ${vf2c_lib}]) +-LDFLAGS=${LDFLAGS_SAVE}; ++blas_lib_path=""; ++PKG_CHECK_MODULES([BLAS], [blas]) ++blas_lib="${BLAS_LIBS}"; + AC_SUBST(blas_lib) + + dnl # ------------------------- + dnl # HANDLE THE LAPACK LIBRARY + dnl # ------------------------- + lapack_lib=""; +-AC_MSG_CHECKING([whether your environment defines FETK_LAPACK_LIBRARY]) +-if test -n "${FETK_LAPACK_LIBRARY}"; then +- AC_MSG_RESULT([yes]) +- lapack_lib_path="-L${FETK_LAPACK_LIBRARY} "; +-else +- AC_MSG_RESULT([no]) +- lapack_lib_path="-L${FETK_LIBRARY} "; +-fi +-LDFLAGS_SAVE=${LDFLAGS}; +-LDFLAGS=${lapack_lib_path}; +-lapack_use=""; +-AC_CHECK_LIB(lapack,dsysv_, +- [lapack_use="yes";lapack_lib="${lapack_lib_path}-llapack";AC_DEFINE(HAVE_LAPACK)], +- [lapack_use="";lapack_lib=""], +- [${lapack_lib_path}-llapack ${blas_lib} ${vf2c_lib}]) +-LDFLAGS=${LDFLAGS_SAVE}; ++lapack_lib_path=""; ++PKG_CHECK_MODULES([LAPACK], [lapack]) ++lapack_lib="${LAPACK_LIBS}" + AC_SUBST(lapack_lib) + + dnl # -------------------------- diff --git a/sci-libs/mc/mc-1.5.ebuild b/sci-libs/mc/mc-1.5.ebuild new file mode 100644 index 000000000000..788d5bfc75d4 --- /dev/null +++ b/sci-libs/mc/mc-1.5.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fortran-2 multilib + +DESCRIPTION="2D/3D AFEM code for nonlinear geometric PDE" +HOMEPAGE="http://fetk.org/codes/mc/index.html" +SRC_URI="http://www.fetk.org/codes/download/${P}.tar.gz" + +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="debug doc static-libs" + +RDEPEND=" + dev-libs/maloc + media-libs/sg + sci-libs/amd + sci-libs/gamer + sci-libs/punc + <sci-libs/superlu-5 + sci-libs/umfpack + virtual/blas + virtual/lapack" +DEPEND=" + ${RDEPEND} + doc? ( + media-gfx/graphviz + app-doc/doxygen + )" + +S="${WORKDIR}"/${PN} + +PATCHES=( + "${FILESDIR}"/1.4-superlu.patch + "${FILESDIR}"/1.4-overflow.patch + "${FILESDIR}"/1.4-multilib.patch + "${FILESDIR}"/1.4-doc.patch + "${FILESDIR}"/${P}-unbundle.patch + ) + +src_prepare() { + sed \ + -e 's:AMD_order:amd_order:g' \ + -e 's:UMFPACK_numeric:umfpack_di_numeric:g' \ + -e 's:buildg_:matvec_:g' \ + -i configure.ac || die + autotools-utils_src_prepare +} + +src_configure() { + local fetk_include + local fetk_lib + local myeconfargs + + use doc || myeconfargs+=( --with-doxygen= --with-dot= ) + + fetk_include="${EPREFIX}"/usr/include + fetk_lib="${EPREFIX}"/usr/$(get_libdir) + export FETK_INCLUDE="${fetk_include}" + export FETK_LIBRARY="${fetk_lib}" + export FETK_MPI_LIBRARY="${fetk_lib}" + export FETK_VF2C_LIBRARY="${fetk_lib}" + export FETK_BLAS_LIBRARY="${fetk_lib}" + export FETK_LAPACK_LIBRARY="${fetk_lib}" + export FETK_AMD_LIBRARY="${fetk_lib}" + export FETK_UMFPACK_LIBRARY="${fetk_lib}" + export FETK_SUPERLU_LIBRARY="${fetk_lib}" + export FETK_ARPACK_LIBRARY="${fetk_lib}" + export FETK_CGCODE_LIBRARY="${fetk_lib}" + export FETK_PMG_LIBRARY="${fetk_lib}" + + myeconfargs+=( + --docdir="${EPREFIX}"/usr/share/doc/${PF} + $(use_enable debug vdebug) + --disable-triplet + --enable-shared + ) + autotools-utils_src_configure +} diff --git a/sci-libs/mc/metadata.xml b/sci-libs/mc/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-libs/mc/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/metadata.xml b/sci-libs/metadata.xml new file mode 100644 index 000000000000..de2ee5e82dd2 --- /dev/null +++ b/sci-libs/metadata.xml @@ -0,0 +1,33 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE catmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<catmetadata> + <longdescription lang="en"> + The sci-libs category contains various science-related libraries. + </longdescription> + <longdescription lang="de"> + Die Kategorie sci-libs enthält wissenschaftlich genutzte Bibliotheken. + </longdescription> + <longdescription lang="es"> + La categoría sci-libs contiene librerías relacionadas con la ciencia. + </longdescription> + <longdescription lang="ja"> + sci-libsカテゴリーには様々な科学関連のライブラリが含まれています。 + </longdescription> + <longdescription lang="nl"> + De sci-libs categorie bevat wetenschappelijke bibliotheken. + </longdescription> + <longdescription lang="vi"> + Nhóm sci-libs chứa các thư viện dùng trong khoa học. + </longdescription> + <longdescription lang="it"> + La categoria sci-libs contiene librerie scientifiche. + </longdescription> + <longdescription lang="pt"> + A categoria sci-libs contém várias bibliotecas relacionadas com + ciência. + </longdescription> + <longdescription lang="pl"> + Kategoria sci-libs zawiera biblioteki związane z programami naukowymi. + </longdescription> +</catmetadata> + diff --git a/sci-libs/metis/Manifest b/sci-libs/metis/Manifest new file mode 100644 index 000000000000..efc03a2311f5 --- /dev/null +++ b/sci-libs/metis/Manifest @@ -0,0 +1,12 @@ +AUX metis-4.0.1-autotools.patch 2561 SHA256 6c0ea173891300c152f7762280d33a19c24ccb29aa2960ea774e48aaaa671f39 SHA512 7e3a5137105e2d6343de864e4f21fb1716d03124842b547c8b4b7e33d096db60b47f33a7a040baa2ddeb0d9de03a0bbb249a2af054cc2beeb4e0a8e12531892b WHIRLPOOL 492fd761ac94eab547d0a5064b400a20e04b26df6b5b5760a448d810cd45f1c87831e40bbcf71a4210f64ea5804b09a6ddde1aaafffeada39caba7f615bedfb0 +AUX metis-5.1.0-datatype.patch 388 SHA256 14826c301ff9c87103c30675eaf4c0686db281879958fe5bee7b7740da18702c SHA512 0b7b10b0d0c958573668f847c2765435a1d9da22fe063430f75fb6ea005ce687d1eaa06879f3c494ea96b6877c1a94df5aa9e538bf02832af3a765cd7687a843 WHIRLPOOL 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4304c3b1ef95bd1a517273c3893e27612889c7e1f2941a5039e7c3594601e28d66c72d5071e902440543a215561789937926599db435ee08503830444769a018 WHIRLPOOL cb0c1f055a74b69d75df782dc801d76439d7da4844847cf54af6a77bc3239b4f404208d1135e5c2890d809003b709c99c5044aa1f47ff1daf4e87efdb27a0bf2 +MISC ChangeLog-2015 6232 SHA256 c650f543e7660da3102d0a7fc523fb9fc59f65b3c60d0da730556852758a3927 SHA512 1894ffdedb3c1353d4ea83e809d0750e68705a8c16fd6aafeeac2e40d44d32318cfc0ea520f224b5e41d11a7ba072dd7830e8debd5c47fed9cde0424882315c3 WHIRLPOOL f3444a1f0fcdc550f1c2aea516506eb9310bb9bd3acbf9c52e762ef08050b58225c53363a2510a09a3762275624fef2ba71c475501697080518ea61d19b52887 +MISC metadata.xml 618 SHA256 f37150dca29d469e748bdef98c7f7ef3a5568d3009177e400c99a2c9d7262341 SHA512 7f46d28a97805eddd9d547ba66263cd395be46b495f4a9651312cfb421714b614d2c7415142c929c99386d32799fe78ea10110471b702487be4072b981ca17ee WHIRLPOOL 4922613f34f907ac3bea17f3c9ece3b02684de31f06160667eabf30abbf300bee27b94c6a1692fc3944c47a65de2e7cc7856237c51335d39c8164451988b0d9e diff --git a/sci-libs/metis/files/metis-4.0.1-autotools.patch b/sci-libs/metis/files/metis-4.0.1-autotools.patch new file mode 100644 index 000000000000..f5d3050a2998 --- /dev/null +++ b/sci-libs/metis/files/metis-4.0.1-autotools.patch @@ -0,0 +1,85 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -0,0 +1,15 @@ ++# -*- Autoconf -*- ++AC_PREREQ(2.59) ++AC_INIT(metis, 4.0.1, karypis@cs.umn.edu) ++AM_INIT_AUTOMAKE([foreign]) ++AC_CONFIG_HEADER([config.h]) ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++AC_CHECK_LIB(m, sqrt) ++AC_CONFIG_FILES([ ++ Makefile ++ metis.pc ++ Lib/Makefile ++ Programs/Makefile\ ++ Test/Makefile]) ++AC_OUTPUT +--- a/metis.pc.in ++++ b/metis.pc.in +@@ -0,0 +1,10 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: METIS ++Description: Software for partioning unstructured graphes and meshes ++Version: @VERSION@ ++Libs: -L${libdir} -lmetis ++Cflags: -I${includedir}/metis +--- a/Makefile.am ++++ b/Makefile.am +@@ -0,0 +1,5 @@ ++SUBDIRS = Lib Programs Test ++EXTRA_DIST = CHANGES VERSION metis.pc.in ++ ++pkgconfigdir = $(libdir)/pkgconfig ++pkgconfig_DATA = metis.pc +--- a/Lib/Makefile.am ++++ b/Lib/Makefile.am +@@ -0,0 +1,15 @@ ++pkginclude_HEADERS = defs.h macros.h metis.h proto.h rename.h struct.h ++pkgincludedir = $(includedir)/metis ++lib_LTLIBRARIES = libmetis.la ++libmetis_la_SOURCES = \ ++ coarsen.c fm.c initpart.c match.c ccgraph.c memory.c \ ++ pmetis.c pqueue.c refine.c util.c timing.c debug.c \ ++ bucketsort.c graph.c stat.c kmetis.c kwayrefine.c \ ++ kwayfm.c balance.c ometis.c srefine.c sfm.c separator.c \ ++ mincover.c mmd.c mesh.c meshpart.c frename.c fortran.c \ ++ myqsort.c compress.c parmetis.c estmem.c \ ++ mpmetis.c mcoarsen.c mmatch.c minitpart.c mbalance.c \ ++ mrefine.c mutil.c mfm.c mkmetis.c mkwayrefine.c mkwayfmh.c \ ++ mrefine2.c minitpart2.c mbalance2.c mfm2.c \ ++ kvmetis.c kwayvolrefine.c kwayvolfm.c subdomains.c ++libmetis_la_LDFLAGS = -no-undefined -version-info 4:0:0 +--- a/Programs/Makefile.am ++++ b/Programs/Makefile.am +@@ -0,0 +1,15 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Lib ++LDADD = $(top_builddir)/Lib/libmetis.la -lm ++ ++bin_PROGRAMS = pmetis kmetis oemetis onmetis mesh2dual mesh2nodal \ ++ partdmesh partnmesh graphchk ++ ++pmetis_SOURCES = pmetis.c io.c ++kmetis_SOURCES = kmetis.c io.c ++oemetis_SOURCES = oemetis.c io.c smbfactor.c ++onmetis_SOURCES = onmetis.c io.c smbfactor.c ++mesh2dual_SOURCES = mesh2dual.c io.c ++mesh2nodal_SOURCES = mesh2nodal.c io.c ++partdmesh_SOURCES = partdmesh.c io.c ++partnmesh_SOURCES = partnmesh.c io.c ++graphchk_SOURCES = graphchk.c io.c +--- a/Test/Makefile.am ++++ b/Test/Makefile.am +@@ -0,0 +1,7 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Lib ++LDADD = $(top_builddir)/Lib/libmetis.la -lm ++check_PROGRAMS = mtest ++mtest_SOURCES = mtest.c ../Programs/io.c ++ ++check-local: $(check_PROGRAMS) ++ - ./mtest ../Graphs/4elt.graph diff --git a/sci-libs/metis/files/metis-5.1.0-datatype.patch b/sci-libs/metis/files/metis-5.1.0-datatype.patch new file mode 100644 index 000000000000..cbca8904ff73 --- /dev/null +++ b/sci-libs/metis/files/metis-5.1.0-datatype.patch @@ -0,0 +1,12 @@ +--- a/include/metis.h ++++ b/include/metis.h +@@ -30,7 +30,7 @@ + GCC does provides these definitions in stdint.h, but it may require some + modifications on other architectures. + --------------------------------------------------------------------------*/ +-#define IDXTYPEWIDTH 32 ++#define IDXTYPEWIDTH 64 + + + /*-------------------------------------------------------------------------- + diff --git a/sci-libs/metis/files/metis-5.1.0-multilib.patch b/sci-libs/metis/files/metis-5.1.0-multilib.patch new file mode 100644 index 000000000000..9e72c5b1b2d3 --- /dev/null +++ b/sci-libs/metis/files/metis-5.1.0-multilib.patch @@ -0,0 +1,20 @@ +--- a/libmetis/CMakeLists.txt ++++ b/libmetis/CMakeLists.txt +@@ -4,13 +4,14 @@ + file(GLOB metis_sources *.c) + # Build libmetis. + add_library(metis ${METIS_LIBRARY_TYPE} ${GKlib_sources} ${metis_sources}) ++set_target_properties(metis PROPERTIES SOVERSION 0) + if(UNIX) + target_link_libraries(metis m) + endif() + + if(METIS_INSTALL) + install(TARGETS metis +- LIBRARY DESTINATION lib +- RUNTIME DESTINATION lib +- ARCHIVE DESTINATION lib) ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ RUNTIME DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX}) + endif() diff --git a/sci-libs/metis/files/metis-5.1.0-shared-GKlib.patch b/sci-libs/metis/files/metis-5.1.0-shared-GKlib.patch new file mode 100644 index 000000000000..483820164638 --- /dev/null +++ b/sci-libs/metis/files/metis-5.1.0-shared-GKlib.patch @@ -0,0 +1,21 @@ +--- a/GKlib/CMakeLists.txt ++++ b/GKlib/CMakeLists.txt +@@ -7,7 +7,7 @@ + include(GKlibSystem.cmake) + + include_directories(".") +-add_library(GKlib STATIC ${GKlib_sources}) ++add_library(GKlib SHARED ${GKlib_sources}) + if(UNIX) + target_link_libraries(GKlib m) + endif(UNIX) +@@ -16,6 +16,6 @@ + add_subdirectory("test") + + install(TARGETS GKlib +- ARCHIVE DESTINATION lib +- LIBRARY DESTINATION lib) +-install(FILES ${GKlib_includes} DESTINATION include) ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} ++ LIBRARY DESTINATION lib${LIB_SUFFIX}) ++install(FILES ${GKlib_includes} DESTINATION include/metis) diff --git a/sci-libs/metis/metadata.xml b/sci-libs/metis/metadata.xml new file mode 100644 index 000000000000..142ea93c83ad --- /dev/null +++ b/sci-libs/metis/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + METIS is a set of serial programs for partitioning graphs, + partitioning finite element meshes, and producing fill reducing + orderings for sparse matrices. The algorithms implemented in METIS are + based on the multilevel recursive-bisection, multilevel k-way, and + multi-constraint partitioning schemes. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/metis/metis-4.0.3.ebuild b/sci-libs/metis/metis-4.0.3.ebuild new file mode 100644 index 000000000000..73b9671feace --- /dev/null +++ b/sci-libs/metis/metis-4.0.3.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils fortran-2 + +DESCRIPTION="A package for unstructured serial graph partitioning" +HOMEPAGE="http://www-users.cs.umn.edu/~karypis/metis/metis/" +SRC_URI="http://glaros.dtc.umn.edu/gkhome/fetch/sw/${PN}/OLD/${P}.tar.gz" + +SLOT="0" +KEYWORDS="~alpha amd64 ~arm ~arm64 hppa ~ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux" +LICENSE="free-noncomm" +IUSE="doc static-libs" + +DEPEND="" +RDEPEND="${DEPEND} + !sci-libs/parmetis" + +src_prepare() { + epatch -p1 "${FILESDIR}"/${PN}-4.0.1-autotools.patch + sed -i -e "s/4.0.1/${PV}/" configure.ac || die + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + use doc && dodoc Doc/manual.ps +} diff --git a/sci-libs/metis/metis-5.1.0-r2.ebuild b/sci-libs/metis/metis-5.1.0-r2.ebuild new file mode 100644 index 000000000000..fb332f98d4a9 --- /dev/null +++ b/sci-libs/metis/metis-5.1.0-r2.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils fortran-2 + +DESCRIPTION="A package for unstructured serial graph partitioning" +HOMEPAGE="http://www-users.cs.umn.edu/~karypis/metis/metis/" +SRC_URI="http://glaros.dtc.umn.edu/gkhome/fetch/sw/${PN}/${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux" +LICENSE="Apache-2.0" +IUSE="doc openmp static-libs" + +DEPEND="" +RDEPEND="${DEPEND} + !sci-libs/parmetis" + +DOCS=( manual/manual.pdf ) + +PATCHES=( + "${FILESDIR}"/${P}-datatype.patch + "${FILESDIR}"/${P}-shared-GKlib.patch + "${FILESDIR}"/${P}-multilib.patch +) + +src_prepare() { + sed \ + -e 's:-O3::g' \ + -i GKlib/GKlibSystem.cmake || die + + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DGKLIB_PATH="${S}"/GKlib + -DSHARED=TRUE + -DOPENMP="$(usex openmp)" + ) + cmake-utils_src_configure +} + +src_test() { + cd graphs || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib ndmetis mdual.graph || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib mpmetis metis.mesh 2 || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib gpmetis test.mgraph 4 || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib gpmetis copter2.graph 4 || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib graphchk 4elt.graph || die +} + +src_install() { + cat >> "${T}"/metis.pc <<- EOF + prefix=${EPREFIX}/usr + exec_prefix=\${prefix} + libdir=\${exec_prefix}/$(get_libdir) + includedir=\${prefix}/include + + Name: METIS + Description: Software for partioning unstructured graphes and meshes + Version: ${PV} + Cflags: -I\${includedir}/metis + Libs: -L\${libdir} -lmetis + EOF + + insinto /usr/$(get_libdir)/pkgconfig + doins "${T}"/metis.pc + cmake-utils_src_install +} diff --git a/sci-libs/metis/metis-5.1.0-r3.ebuild b/sci-libs/metis/metis-5.1.0-r3.ebuild new file mode 100644 index 000000000000..307eb0e6a180 --- /dev/null +++ b/sci-libs/metis/metis-5.1.0-r3.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils fortran-2 + +DESCRIPTION="A package for unstructured serial graph partitioning" +HOMEPAGE="http://www-users.cs.umn.edu/~karypis/metis/metis/" +SRC_URI="http://glaros.dtc.umn.edu/gkhome/fetch/sw/${PN}/${P}.tar.gz" + +SLOT="0" +KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux" +LICENSE="Apache-2.0" +IUSE="doc openmp static-libs" + +DEPEND="" +RDEPEND="${DEPEND} + !sci-libs/parmetis" + +DOCS=( manual/manual.pdf ) + +PATCHES=( + "${FILESDIR}"/${P}-datatype.patch + "${FILESDIR}"/${P}-shared-GKlib.patch + "${FILESDIR}"/${P}-multilib.patch +) + +src_prepare() { + sed \ + -e 's:-O3::g' \ + -i GKlib/GKlibSystem.cmake || die + + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DGKLIB_PATH="${S}"/GKlib + -DSHARED="$(usex static-libs no yes)" + -DOPENMP="$(usex openmp)" + ) + cmake-utils_src_configure +} + +src_test() { + cd graphs || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib ndmetis mdual.graph || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib mpmetis metis.mesh 2 || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib gpmetis test.mgraph 4 || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib gpmetis copter2.graph 4 || die + PATH="${BUILD_DIR}"/programs/:${PATH} LD_LIBRARY_PATH="${BUILD_DIR}"/lib graphchk 4elt.graph || die +} + +src_install() { + cat >> "${T}"/metis.pc <<- EOF + prefix=${EPREFIX}/usr + exec_prefix=\${prefix} + libdir=\${exec_prefix}/$(get_libdir) + includedir=\${prefix}/include + + Name: METIS + Description: Software for partioning unstructured graphes and meshes + Version: ${PV} + Cflags: -I\${includedir}/metis + Libs: -L\${libdir} -lmetis + EOF + + insinto /usr/$(get_libdir)/pkgconfig + doins "${T}"/metis.pc + cmake-utils_src_install +} diff --git a/sci-libs/minfx/Manifest b/sci-libs/minfx/Manifest new file mode 100644 index 000000000000..41fb06dd0b88 --- /dev/null +++ b/sci-libs/minfx/Manifest @@ -0,0 +1,17 @@ +DIST 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<email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <longdescription> + The minfx project is a python package for numerical optimisation, + being a large collection of standard minimisation algorithms. The name minfx + is simply a shortening of the mathematical expression min f(x). +</longdescription> +</pkgmetadata> diff --git a/sci-libs/minfx/minfx-1.0.10.ebuild b/sci-libs/minfx/minfx-1.0.10.ebuild new file mode 100644 index 000000000000..8830ec34c629 --- /dev/null +++ b/sci-libs/minfx/minfx-1.0.10.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python{2_7,3_4} pypy ) + +inherit distutils-r1 + +DESCRIPTION="Numerical optimisation library" +HOMEPAGE="http://gna.org/projects/minfx" +SRC_URI="http://download.gna.org/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-libs/minfx/minfx-1.0.11.ebuild b/sci-libs/minfx/minfx-1.0.11.ebuild new file mode 100644 index 000000000000..ac630dd24b45 --- /dev/null +++ b/sci-libs/minfx/minfx-1.0.11.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} pypy ) + +inherit distutils-r1 + +DESCRIPTION="Numerical optimisation library" +HOMEPAGE="http://gna.org/projects/minfx" +SRC_URI="http://download.gna.org/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-libs/minfx/minfx-1.0.3-r1.ebuild b/sci-libs/minfx/minfx-1.0.3-r1.ebuild new file mode 100644 index 000000000000..608d4a2ef76d --- /dev/null +++ b/sci-libs/minfx/minfx-1.0.3-r1.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 pypy ) + +inherit distutils-r1 + +DESCRIPTION="Numerical optimisation library" +HOMEPAGE="http://gna.org/projects/minfx" +SRC_URI="http://download.gna.org/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-libs/minfx/minfx-1.0.4.ebuild b/sci-libs/minfx/minfx-1.0.4.ebuild new file mode 100644 index 000000000000..608d4a2ef76d --- /dev/null +++ b/sci-libs/minfx/minfx-1.0.4.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 pypy ) + +inherit distutils-r1 + +DESCRIPTION="Numerical optimisation library" +HOMEPAGE="http://gna.org/projects/minfx" +SRC_URI="http://download.gna.org/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-libs/minfx/minfx-1.0.4_pre98.ebuild b/sci-libs/minfx/minfx-1.0.4_pre98.ebuild new file mode 100644 index 000000000000..9e9d8b9b6cef --- /dev/null +++ b/sci-libs/minfx/minfx-1.0.4_pre98.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 pypy ) + +inherit distutils-r1 + +DESCRIPTION="Numerical optimisation library" +HOMEPAGE="http://gna.org/projects/minfx" +#SRC_URI="http://download.gna.org/${PN}/${P}.tar.gz" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-libs/minfx/minfx-1.0.5.ebuild b/sci-libs/minfx/minfx-1.0.5.ebuild new file mode 100644 index 000000000000..608d4a2ef76d --- /dev/null +++ b/sci-libs/minfx/minfx-1.0.5.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 pypy ) + +inherit distutils-r1 + +DESCRIPTION="Numerical optimisation library" +HOMEPAGE="http://gna.org/projects/minfx" +SRC_URI="http://download.gna.org/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-libs/minfx/minfx-1.0.6.ebuild b/sci-libs/minfx/minfx-1.0.6.ebuild new file mode 100644 index 000000000000..23872b8a5e79 --- /dev/null +++ b/sci-libs/minfx/minfx-1.0.6.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python{2_7,3_4} pypy ) + +inherit distutils-r1 + +DESCRIPTION="Numerical optimisation library" +HOMEPAGE="http://gna.org/projects/minfx" +SRC_URI="http://download.gna.org/${PN}/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-libs/minuit/Manifest b/sci-libs/minuit/Manifest new file mode 100644 index 000000000000..944e13f5d624 --- /dev/null +++ b/sci-libs/minuit/Manifest @@ -0,0 +1,8 @@ +AUX minuit-5.27.02-asneeded.patch 1180 SHA256 e097534dc55e1725f0e9e48c0904396a61835edc8a8c9b124836a2a6bdf5aebf SHA512 d5be2d60a39f3b7b2bf1afbf29a3fbc2d6d559c2be38141dc4871809a45b53ffbdbc12e39c6f887811c447b0e6c5ef47a32e4976cb78fa00d1b92b3ba3dd0e9a WHIRLPOOL ab103f3d16d7f8689874161896ee823029e570ff9e299e723a82bdb170d39039d0eefa2a7c78fc1497ad86ffe1e6506d7fdd44a674c2ea04da3702687364638e +DIST minuit-5.34.14.tar.gz 510005 SHA256 2ca9a283bbc315064c0a322bc4cb74c7e8fd51f9494f7856e5159d0a0aa8c356 SHA512 96e520e0f9454f57a9529662612f444f60bcf63d21b7950b832cf3c670ee407ae78c9ffaf34eee728c0b68a4e39c347ea69121b4a51f1b2d33fd2176db88f720 WHIRLPOOL 921a290b176de9d53cec4c4aa11f05e1e202af93e2a401099e28234e5fb1204cccd16789428e02b8cbd8e8c4d0b9088d16e4d90708eab92903237cbc6821165e +DIST mntutorial.pdf 263735 SHA256 a72207746c548f4b468b147c27552b4a1bc9762df2a19f9cb0f9ec297899ef07 SHA512 27d6fdc85fa190cd8e4e22d9ccac543005878718e24ececfbc1236266f50759390daf7ff50859dcfae18562a655955846460a56deeb4d44f23e77a629b1cddb1 WHIRLPOOL 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6a67cf4fe872f73730763bda3cceee3762e8c7298dfc8f2728a820f213cc02d337f534e95790b155082dbd9e8fc1343517fd0e5015198fcdc5e96cc1c59c756e WHIRLPOOL 9d4ff3c6fea3bc2264ac3a28df9f73417fde42c0401abf2361012763b8ab2ed49ff105f2ba5bbd445b9206fc29c1873db58c3f96bd80ae2fb6b71b1c50d24006 +MISC ChangeLog-2015 2850 SHA256 c13c913252a6f7cb23b031e34738a49e947fb3c220496d48998ed300388b40a7 SHA512 9299c93d4bb8c2e1b85f79f51e3b70895254a92d897ccdee720304e5df7352b426eb1373239eff725711b4444aaacb01395a978813124b3a9e49d9c34361b47a WHIRLPOOL a7025ad0ed628e750ea6b6ac803b4b3aca88c87fda36d48ef557312c9fd1663305665411d74768366e6a1f550478c1de76b4d3dcd1128abe8c53b70c9abfeeef +MISC metadata.xml 618 SHA256 2c5265727976c0bb4d7b1af6f53cc34df207b6755beeeb4c2da858043f59c05f SHA512 4f0d43ab313f083fb79b4a6fef506caafdad61e09cb321f005b8dc35bde642d44a533e8bab42eb229bb4faf67c12f61deebf2ba1deac855b6a78e7db78c853e8 WHIRLPOOL 0f898c11ab5f10c00fdd31a8980d8eee28b2577a222f5fbf2530a4a93f371d535ccd525d0c57353604bb90a7296f13a79c4d7336424043e17bfe9527eb8c0906 diff --git a/sci-libs/minuit/files/minuit-5.27.02-asneeded.patch b/sci-libs/minuit/files/minuit-5.27.02-asneeded.patch new file mode 100644 index 000000000000..e808a928f5e6 --- /dev/null +++ b/sci-libs/minuit/files/minuit-5.27.02-asneeded.patch @@ -0,0 +1,38 @@ +This OpenMP library finding code is from ImageMagick's configure.ac + +http://bugs.gentoo.org/314095 + +--- a/configure.in ++++ b/configure.in +@@ -44,6 +44,20 @@ + CFLAGS="$CFLAGS $OPENMP_CFLAGS" + CXXFLAGS="$CXXFLAGS $OPENMP_CXXFLAGS" + ++dnl Find OpenMP library ++GOMP_LIBS='' ++if test "$enable_openmp" != 'no'; then ++ if test "${GCC}" = "yes"; then ++ AC_CHECK_LIB(gomp,GOMP_parallel_start,GOMP_LIBS="-lgomp",,) # gcc ++ else ++ AC_CHECK_LIB(mtsk,sunw_mp_register_warn,GOMP_LIBS="-lmtsk",,) # solaris cc ++ AC_CHECK_LIB(xlsmp,_xlsmpFlush,GOMP_LIBS="-lxlsmp",,) # AIX xlc ++ AC_CHECK_LIB(mp,mp_destroy,GOMP_LIBS="-lmp",,) # SGI IRIX 6.5 MIPSpro C/C++ ++ fi ++ LIBS="$GOMP_LIBS $LIBS" ++fi ++AC_SUBST(GOMP_LIBS) ++ + dnl files to be generated + AC_OUTPUT(Makefile inc/Makefile inc/Minuit2/Makefile inc/Math/Makefile src/Makefile + doc/Doxyfile doc/Makefile test/Makefile test/MnSim/Makefile +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -9,6 +9,8 @@ + # The convenience library to be built. + lib_LTLIBRARIES = libMinuit2.la + ++libMinuit2_la_LIBADD = $(GOMP_LIBS) ++ + libMinuit2_la_SOURCES = \ + AnalyticalGradientCalculator.cxx \ + BasicMinimumError.cxx \ diff --git a/sci-libs/minuit/metadata.xml b/sci-libs/minuit/metadata.xml new file mode 100644 index 000000000000..114115b4b53a --- /dev/null +++ b/sci-libs/minuit/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + Minuit provides a C++ library for non-linear optimization, + and parameter error estimation. Widely used in High Energy Physics, + originally as a fortran library, it has been entirely re-written from + scratch in C++. It is now included in ROOT-5 and higher. + This is the stand-alone version, quick to build and use. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/minuit/minuit-5.34.14.ebuild b/sci-libs/minuit/minuit-5.34.14.ebuild new file mode 100644 index 000000000000..433d7e2663a2 --- /dev/null +++ b/sci-libs/minuit/minuit-5.34.14.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="A C++ physics analysis tool for function minimization" +HOMEPAGE="https://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/" +SRC_URI=" + http://www.cern.ch/mathlibs/sw/${PV//./_}/${PN^}2/${PN^}2-5.34.14.tar.gz -> ${P}.tar.gz + doc? ( + http://seal.cern.ch/documents/minuit/mnusersguide.pdf + http://seal.cern.ch/documents/minuit/mntutorial.pdf + )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc openmp static-libs" + +DEPEND="doc? ( app-doc/doxygen )" +RDEPEND="" + +S="${WORKDIR}/${PN^}2-${PV}" + +PATCHES=( "${FILESDIR}"/${PN}-5.27.02-asneeded.patch ) + +src_prepare() { + default + rm config/m4/ac_openmp.m4 || die + mv configure.{in,ac} || die + + AT_M4DIR="config/m4" eautoreconf +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_enable openmp) +} + +src_compile() { + default + use doc && emake docs +} + +src_test() { + emake check + + cd test/MnTutorial || die + local t + for t in test_*; do + ./${t} || die "${t} failed" + done +} + +src_install() { + if use doc; then + # remove doxygen junk + find doc/html \( -iname '*.map' -o -iname '*.md5' \) -delete || die + HTML_DOCS=( doc/html/. ) + dodoc "${DISTDIR}"/mn{usersguide,tutorial}.pdf + fi + default + + docinto examples + dodoc test/MnTutorial/*.{h,cxx} + docompress -x /usr/share/doc/${PF}/examples + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} diff --git a/sci-libs/mkl/Manifest b/sci-libs/mkl/Manifest new file mode 100644 index 000000000000..24e400def8e8 --- /dev/null +++ b/sci-libs/mkl/Manifest @@ -0,0 +1,8 @@ +AUX mkl-10.0.2.018-openmpi.patch 332 SHA256 758c3aef0124932426002aa502c0e7b721a026d6c54c37c679d3ee7eb607b58c SHA512 5efb139622a6f0e8f03c5a76a12298685a9dfe9e816b8eaabd2874fda6c0d468a111a46df8e6885cd62a40ec611c322a99762a805dc74a4c684c85fdf222b530 WHIRLPOOL b846db00af9cf3dcefe0422323a1871f1486ca6f51bd440c829b0c6c8ae6e956f9ca172ba9730560db7ddd204dcf6096ea185736ab10499d3f56cedcb5df7e56 +AUX mkl-10.0.2.018-tests.patch 528 SHA256 f65a074c64a3969b08d41f88874f25fdc06693b5a5aee930bd7ef9763e94e71d SHA512 6dd716f5d6764cd79c6de22703729d77be71f35e5f600a11f01ccff06c87309471ac5289e68ef40ae830d5917cbd20d4b2b9f1b5554384977f1b83c4b3556382 WHIRLPOOL b413212509adf6501f709ab867b17e120a28df8c9e427c22bd7871d9630ff61f0c24e8ffdd06c8c1052101a3cb08be8873a0815bf0874de7ac81545560431b26 +DIST l_mkl_p_10.0.5.025.tgz 230389719 SHA256 c98f2c5c652c02ac7200cba40d996b1f11b567278d849016b7ee3b0320e26e3c SHA512 621c3bfdecb57313e375424e391c0630a29efd70196e3e4bfc5b4ddd03aa45fda4761523652d875f2e60d466a0010c06659306b11f20966fba4943c308fa6f84 WHIRLPOOL 6c96123254aebd897e061ee971f487bd5d51586e74572da18bb5461ab8f7fb2cbb34e5f782c11712a7ece8b58b348554c07a68dd91ff5fc9771894e3aef04352 +EBUILD mkl-10.0.5.025-r1.ebuild 9905 SHA256 5db8bfc0772c924f3eba8714f0c82f35299f3a0180affdd5d4e88b8bff58f55a SHA512 a9c8638edf0472314d87ce6cbcd803fdb4c7f725f06e51868950bd521bf0053789d0ae2b40c6072cc905d4c1d646f783ef09b1dc42b48058ea50c3fa8ef7364b WHIRLPOOL a034c57c0535c9e56901f1f40cba4ffc1b5fc6ea4b89563c1989fe76dca3b3efe6f89351c6c342207964d6869be50597fe2487e3e230270838ebb3e67af4af60 +EBUILD mkl-10.0.5.025.ebuild 10066 SHA256 a3e842f7e9321858fa39bf91a753bca781efa0e4ec440cb2933a9dca6b48805e SHA512 3b79dced34319543dc04804e1df965580471c485aff6282a1b60d7402229c1e4e7dc65f19ad4971a366936ba74fbf75d3f7724f77e0f692a1b2c3c11be1e077f WHIRLPOOL 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8930dec116eac1fe455b4eab4940acf370d6b72f15829bfe18375c5308f69189303753a858433eeb6367381e0601f593474073996d447f11030f718ff1264bb9 WHIRLPOOL b6d1d0961cc896a8e4421fd0f435ed1f146870502b698c2a5727c6b6366593dfd66e50cb672e0f7b3f4b59aee129d6ccaca01e9d7fb20920b4f61ae6c35cd127 diff --git a/sci-libs/mkl/files/mkl-10.0.2.018-openmpi.patch b/sci-libs/mkl/files/mkl-10.0.2.018-openmpi.patch new file mode 100644 index 000000000000..6f7f9edebb0f --- /dev/null +++ b/sci-libs/mkl/files/mkl-10.0.2.018-openmpi.patch @@ -0,0 +1,18 @@ +--- interfaces/fftw2x_cdft/makefile.orig 2008-03-11 23:26:26.287984332 +0000 ++++ interfaces/fftw2x_cdft/makefile 2008-03-13 10:56:44.755095617 +0000 +@@ -172,6 +172,15 @@ + endif + + ++ifeq ($(mpi),openmpi) ++CS = mpicc ++ifdef mpidir ++_CS = $(mpidir)/bin/$(CS) ++else ++_CS = $(CS) ++endif ++endif ++ + vpath %.c wrappers + + $(WRP): %.o: %.c diff --git a/sci-libs/mkl/files/mkl-10.0.2.018-tests.patch b/sci-libs/mkl/files/mkl-10.0.2.018-tests.patch new file mode 100644 index 000000000000..975170f7dbc0 --- /dev/null +++ b/sci-libs/mkl/files/mkl-10.0.2.018-tests.patch @@ -0,0 +1,21 @@ +--- tests/scalapack/make.inc.orig 2008-03-13 22:36:06.119890888 +0000 ++++ tests/scalapack/make.inc 2008-03-13 22:54:58.201781899 +0000 +@@ -59,6 +59,9 @@ + IFACE_PART = _ilp64 + COPTS = -DMKL_ILP64 + FOPTS = -i8 ++ifeq ($(compiler),gnu) ++FOPTS = -fdefault-integer-8 ++endif + else + ADD_IFACE = _lp64 + IFACE_PART = _lp64 +@@ -203,7 +206,7 @@ + # Compiler flags + F77FLAGS=-w -u $(OPTS) + ifeq ($(comp),gnu) +-F77FLAGS=$(OPTS) -ff90 -fno-globals -Wno-globals ++F77FLAGS=$(OPTS) + endif + # Remove objects variable + RMOBJ=rm -f *.o core work.pc* diff --git a/sci-libs/mkl/metadata.xml b/sci-libs/mkl/metadata.xml new file mode 100644 index 000000000000..2504a4ee49a8 --- /dev/null +++ b/sci-libs/mkl/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The Intel(R) Math Kernel Library is a mathematical library mostly + optimized for Intel processors (also works on AMDs). It contains BLAS + and LAPACK implementations, Fast Fourier Transforms, a vector math + library, and random number generators. It also has multiprocessor + capacities. The package is installed as binary and has a restrictive + license. Please see license terms and home page for proper use. +</longdescription> + <use> + <flag name="fortran95">Installs the BLAS/LAPACK FORTRAN95 static libraries</flag> + <flag name="int64">Installs the 64 bits integer libraries</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/mkl/mkl-10.0.5.025-r1.ebuild b/sci-libs/mkl/mkl-10.0.5.025-r1.ebuild new file mode 100644 index 000000000000..ed1c3a7da3f0 --- /dev/null +++ b/sci-libs/mkl/mkl-10.0.5.025-r1.ebuild @@ -0,0 +1,366 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit check-reqs fortran-2 toolchain-funcs + +PID=1232 +PB=${PN} +P_ARCHIVE=l_${PN}_p_${PV} + +DESCRIPTION="Intel(R) Math Kernel Library: linear algebra, fft, math functions" +HOMEPAGE="http://developer.intel.com/software/products/mkl/" +SRC_URI="http://registrationcenter-download.intel.com/irc_nas/${PID}/${P_ARCHIVE}.tgz" + +SLOT="0" +LICENSE="Intel-SDP" +KEYWORDS="-* ~amd64 ~ia64 ~x86" +IUSE="doc fftw fortran95 int64 mpi" + +RESTRICT="strip mirror" + +DEPEND=" + app-eselect/eselect-blas + app-eselect/eselect-cblas + app-eselect/eselect-lapack" +RDEPEND="${DEPEND} + doc? ( app-doc/blas-docs app-doc/lapack-docs ) + mpi? ( virtual/mpi )" + +PATCHES=( + "${FILESDIR}"/${PN}-10.0.2.018-openmpi.patch # allow openmpi to work +) + +MKL_DIR=/opt/intel/${PN}/${PV} +INTEL_LIC_DIR=/opt/intel/licenses + +CHECKREQS_DISK_BUILD=3500M + +QA_PREBUILT="opt/intel/${PN}/${PV}/*" + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + check-reqs_pkg_setup + fortran-2_pkg_setup + # Check the license + if [[ -z ${MKL_LICENSE} ]]; then + MKL_LICENSE="$(grep -ls MKern ${ROOT}${INTEL_LIC_DIR}/* | tail -n 1)" + MKL_LICENSE=${MKL_LICENSE/${ROOT}/} + fi + if [[ -z ${MKL_LICENSE} ]]; then + eerror "Did not find any valid mkl license." + eerror "Register at ${HOMEPAGE} to receive a license" + eerror "and place it in ${INTEL_LIC_DIR} or run:" + eerror "export MKL_LICENSE=/my/license/file emerge mkl" + die "license setup failed" + fi + + # Check if we have enough free diskspace to install + CHECKREQS_DISK_BUILD="1100M" + check-reqs_pkg_setup + + # Check and setup fortran + if use fortran95; then + # blas95 and lapack95 don't compile with gfortran < 4.2 + [[ $(tc-getFC) =~ (gfortran|g77) ]] && [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] && + die "blas95 and lapack95 don't compile with gfortran < 4.2" + fi + MKL_FC="gnu" + [[ $(tc-getFC) =~ if ]] && MKL_FC="intel" + + # build profiles according to what compiler is installed + MKL_CC="gnu" + [[ $(tc-getCC) == icc ]] && MKL_CC="intel" + + if has_version sys-cluster/mpich; then + MKL_MPI=mpich + elif has_version sys-cluster/mpich2; then + MKL_MPI=mpich2 + elif has_version sys-cluster/openmpi; then + MKL_MPI=openmpi + else + MKL_MPI=intelmpi + fi + get_fcomp +} + +src_unpack () { + default + cd "${WORKDIR}/${P_ARCHIVE}"/install || die + + cp ${MKL_LICENSE} "${WORKDIR}"/ || die + MKL_LIC="$(basename ${MKL_LICENSE})" + + # binary blob extractor installs rpm leftovers in /opt/intel + addwrite /opt/intel + # undocumented features: INSTALLMODE_mkl=NONRPM + + # We need to install mkl non-interactively. + # If things change between versions, first do it interactively: + # tar xf l_*; ./install.sh --duplicate mkl.ini; + # The file will be instman/mkl.ini + # Then check it and modify the ebuild-created one below + # --norpm is required to be able to install 10.x + cat > mkl.ini <<-EOF || die + [MKL] + EULA_ACCEPT_REJECT=ACCEPT + FLEXLM_LICENSE_LOCATION=${WORKDIR}/${MKL_LIC} + INSTALLMODE_mkl=NONRPM + INSTALL_DESTINATION=${S} + EOF + einfo "Extracting ..." + ./install \ + --silent ./mkl.ini \ + --installpath "${S}" \ + --log log.txt &> /dev/null \ + || die + + if [[ -z $(find "${S}" -name libmkl.so) ]]; then + eerror "Could not find extracted files" + eerror "See ${PWD}/log.txt to see why" + die "extracting failed" + fi +} + +src_prepare() { + default + + # remove left over + rm -f /opt/intel/.*mkl*.log /opt/intel/intel_sdp_products.db || die + + # remove unused stuff and set up intel names + rm -rf "${WORKDIR}"/l_* || die + + case ${ARCH} in + x86) MKL_ARCH=32 + MKL_KERN=ia32 + rm -rf lib*/{em64t,64} || die + ;; + + amd64) MKL_ARCH=em64t + MKL_KERN=em64t + rm -rf lib*/{32,64} || die + ;; + + ia64) MKL_ARCH=64 + MKL_KERN=ipf + rm -rf lib*/{32,em64t} || die + ;; + esac + MKL_LIBDIR=${MKL_DIR}/lib/${MKL_ARCH} + # fix env scripts + sed -i \ + -e "s:${S}:${MKL_DIR}:g" \ + tools/environment/*sh || die "sed support file failed" +} + +src_compile() { + cd "${S}"/interfaces || die + if use fortran95; then + einfo "Compiling fortan95 static lib wrappers" + local myconf="lib${MKL_ARCH}" + [[ $(tc-getFC) =~ gfortran ]] && \ + myconf="${myconf} FC=gfortran" + if use int64; then + myconf="${myconf} interface=ilp64" + [[ $(tc-getFC) =~ gfortran ]] && \ + myconf="${myconf} FOPTS=-fdefault-integer-8" + fi + local x + for x in blas95 lapack95; do + emake -C ${x} ${myconf} + done + fi + + if use fftw; then + local fftwdirs="fftw2xc fftw2xf fftw3xc fftw3xf" + local myconf="lib${MKL_ARCH} compiler=${MKL_CC}" + if use mpi; then + fftwdirs="${fftwdirs} fftw2x_cdft" + myconf="${myconf} mpi=${MKL_MPI}" + fi + einfo "Compiling fftw static lib wrappers" + local x + for x in ${fftwdirs}; do + emake -C ${x} ${myconf} + done + fi +} + +src_test() { + cd "${S}"/tests + local myconf + local testdirs="blas cblas" + local x + use int64 && myconf="${myconf} interface=ilp64" + # buggy with g77 and gfortran + #if use mpi; then + # testdirs="${testdirs} scalapack" + # myconf="${myconf} mpi=${MKL_MPI}" + #fi + for x in ${testdirs}; do + einfo "Testing ${x}" + emake -C ${x} \ + compiler=${MKL_FC} \ + ${myconf} \ + so${MKL_ARCH} + done +} + +mkl_make_generic_profile() { + cd "${S}" || die + # produce eselect files + # don't make them in FILESDIR, it changes every major version + cat > eselect.blas <<-EOF || die + ${MKL_LIBDIR}/libmkl_${MKL_KERN}.a /usr/@LIBDIR@/libblas.a + ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libblas.so + ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libblas.so.0 + EOF + cat > eselect.cblas <<-EOF || die + ${MKL_LIBDIR}/libmkl_${MKL_KERN}.a /usr/@LIBDIR@/libcblas.a + ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libcblas.so + ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libcblas.so.0 + ${MKL_DIR}/include/mkl_cblas.h /usr/include/cblas.h + EOF + cat > eselect.lapack <<-EOF || die + ${MKL_LIBDIR}/libmkl_lapack.a /usr/@LIBDIR@/liblapack.a + ${MKL_LIBDIR}/libmkl_lapack.so /usr/@LIBDIR@/liblapack.so + ${MKL_LIBDIR}/libmkl_lapack.so /usr/@LIBDIR@/liblapack.so.0 + EOF +} + +# usage: mkl_add_profile <profile> <interface_lib> <thread_lib> <rtl_lib> +mkl_add_profile() { + cd "${S}" || die + local prof=${1} + local x + for x in blas cblas lapack; do + cat > ${x}-${prof}.pc <<-EOF || die + prefix=${MKL_DIR} + libdir=${MKL_LIBDIR} + includedir=\${prefix}/include + Name: ${x} + Description: Intel(R) Math Kernel Library implementation of ${x} + Version: ${PV} + URL: ${HOMEPAGE} + EOF + done + cat >> blas-${prof}.pc <<-EOF || die + Libs: -Wl,--no-as-needed -L\${libdir} ${2} ${3} -lmkl_core ${4} -lpthread + EOF + cat >> cblas-${prof}.pc <<-EOF || die + Requires: blas + Libs: -Wl,--no-as-needed -L\${libdir} ${2} ${3} -lmkl_core ${4} -lpthread + Cflags: -I\${includedir} + EOF + cat >> lapack-${prof}.pc <<-EOF || die + Requires: blas + Libs: -Wl,--no-as-needed -L\${libdir} ${2} ${3} -lmkl_core -lmkl_lapack ${4} -lpthread + EOF + insinto ${MKL_LIBDIR} + for x in blas cblas lapack; do + doins ${x}-${prof}.pc + cp eselect.${x} eselect.${x}.${prof} || die + echo "${MKL_LIBDIR}/${x}-${prof}.pc /usr/@LIBDIR@/pkgconfig/${x}.pc" \ + >> eselect.${x}.${prof} || die + eselect ${x} add $(get_libdir) eselect.${x}.${prof} ${prof} + done +} + +mkl_make_profiles() { + local clib="gf" + has_version 'dev-lang/ifc' && clib+=" intel" + local slib="-lmkl_sequential" + local rlib="-liomp5" + local pbase=${PN} + local c + for c in ${clib}; do + local ilib="-lmkl_${c}_lp64" + use x86 && ilib="-lmkl_${c}" + local tlib="-lmkl_${c/gf/gnu}_thread" + local comp="${c/gf/gfortran}" + comp="${comp/intel/ifort}" + mkl_add_profile ${pbase}-${comp} ${ilib} ${slib} + mkl_add_profile ${pbase}-${comp}-threads ${ilib} ${tlib} ${rlib} + if use int64; then + ilib="-lmkl_${c}_ilp64" + mkl_add_profile ${pbase}-${comp}-int64 ${ilib} ${slib} + mkl_add_profile ${pbase}-${comp}-threads-int64 ${ilib} ${tlib} ${rlib} + fi + done +} + +src_install() { + dodir ${MKL_DIR} + + # install license + if [[ ! -f ${INTEL_LIC_DIR}/${MKL_LIC} ]]; then + insinto ${INTEL_LIC_DIR} + doins "${WORKDIR}"/${MKL_LIC} || die "install license failed" + fi + + # install main stuff: cp faster than doins + einfo "Installing files..." + local cpdirs="benchmarks doc examples include interfaces lib man tests" + local doinsdirs="tools" + cp -pPR ${cpdirs} "${D}"${MKL_DIR} \ + || die "installing mkl failed" + insinto ${MKL_DIR} + doins -r ${doinsdirs} || die "doins ${doinsdirs} failed" + dosym mkl_cblas.h ${MKL_DIR}/include/cblas.h + + # install blas/lapack profiles + mkl_make_generic_profile + mkl_make_profiles + + # install env variables + cat > 35mkl <<-EOF || die + MKLROOT=${MKL_DIR} + LDPATH=${MKL_LIBDIR} + MANPATH=${MKL_DIR}/man + EOF + doenvd 35mkl +} + +pkg_postinst() { + # if blas profile is mkl, set lapack and cblas profiles as mkl + local blas_prof=$(eselect blas show | cut -d' ' -f2) + local def_prof="mkl-gfortran-threads" + local x + has_version 'dev-lang/ifc' && def_prof="mkl-ifort-threads" + use int64 && def_prof="${def_prof}-int64" + for x in blas cblas lapack; do + local cur_prof=$(eselect ${x} show | cut -d' ' -f2) + if [[ -z ${cur_prof} || ${cur_prof} == ${def_prof} ]]; then + # work around eselect bug #189942 + local configfile="${ROOT}"/etc/env.d/${x}/$(get_libdir)/config + rm -f ${configfile} || die + eselect ${x} set ${def_prof} + elog "${x} has been eselected to ${def_prof}" + else + elog "Current eselected ${x} is ${current_lib}" + elog "To use one of mkl profiles, issue (as root):" + elog "\t eselect ${x} set <profile>" + fi + if [[ ${blas_prof} == mkl* && ${cur_prof} != ${blas_prof} ]]; then + eselect blas set ${def_prof} + elog "${x} is now set to ${def_prof} for consistency" + fi + done + if [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]]; then + elog "Multi-threading OpenMP for GNU compilers only available" + elog "with gcc >= 4.2. Make sure you have a compatible version" + elog "and select it with gcc-config before selecting gnu profiles" + fi +} diff --git a/sci-libs/mkl/mkl-10.0.5.025.ebuild b/sci-libs/mkl/mkl-10.0.5.025.ebuild new file mode 100644 index 000000000000..dc66e4a23e98 --- /dev/null +++ b/sci-libs/mkl/mkl-10.0.5.025.ebuild @@ -0,0 +1,368 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit check-reqs eutils fortran-2 multilib toolchain-funcs + +PID=1232 +PB=${PN} +P_ARCHIVE=l_${PN}_p_${PV} + +DESCRIPTION="Intel(R) Math Kernel Library: linear algebra, fft, math functions" +HOMEPAGE="http://developer.intel.com/software/products/mkl/" +SRC_URI="http://registrationcenter-download.intel.com/irc_nas/${PID}/${P_ARCHIVE}.tgz" + +SLOT="0" +LICENSE="Intel-SDP" +KEYWORDS="-* amd64 ~ia64 x86" +IUSE="doc fftw fortran95 int64 mpi" + +RESTRICT="strip mirror" + +DEPEND=" + app-eselect/eselect-blas + app-eselect/eselect-cblas + app-eselect/eselect-lapack" +RDEPEND="${DEPEND} + doc? ( app-doc/blas-docs app-doc/lapack-docs ) + mpi? ( virtual/mpi )" + +MKL_DIR=/opt/intel/${PN}/${PV} +INTEL_LIC_DIR=/opt/intel/licenses + +CHECKREQS_DISK_BUILD=3500M + +QA_PREBUILT="opt/intel/${PN}/${PV}/*" + +get_fcomp() { + case $(tc-getFC) in + *gfortran* ) + FCOMP="gfortran" ;; + ifort ) + FCOMP="ifc" ;; + * ) + FCOMP=$(tc-getFC) ;; + esac +} + +pkg_setup() { + check-reqs_pkg_setup + fortran-2_pkg_setup + # Check the license + if [[ -z ${MKL_LICENSE} ]]; then + MKL_LICENSE="$(grep -ls MKern ${ROOT}${INTEL_LIC_DIR}/* | tail -n 1)" + MKL_LICENSE=${MKL_LICENSE/${ROOT}/} + fi + if [[ -z ${MKL_LICENSE} ]]; then + eerror "Did not find any valid mkl license." + eerror "Register at ${HOMEPAGE} to receive a license" + eerror "and place it in ${INTEL_LIC_DIR} or run:" + eerror "export MKL_LICENSE=/my/license/file emerge mkl" + die "license setup failed" + fi + + # Check if we have enough free diskspace to install + CHECKREQS_DISK_BUILD="1100M" + check-reqs_pkg_setup + + # Check and setup fortran + if use fortran95; then + # blas95 and lapack95 don't compile with gfortran < 4.2 + [[ $(tc-getFC) =~ (gfortran|g77) ]] && [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] && + die "blas95 and lapack95 don't compile with gfortran < 4.2" + fi + MKL_FC="gnu" + [[ $(tc-getFC) =~ if ]] && MKL_FC="intel" + + # build profiles according to what compiler is installed + MKL_CC="gnu" + [[ $(tc-getCC) == icc ]] && MKL_CC="intel" + + if has_version sys-cluster/mpich; then + MKL_MPI=mpich + elif has_version sys-cluster/mpich2; then + MKL_MPI=mpich2 + elif has_version sys-cluster/openmpi; then + MKL_MPI=openmpi + else + MKL_MPI=intelmpi + fi + get_fcomp +} + +src_unpack () { + default + cd "${WORKDIR}/${P_ARCHIVE}"/install || die + + cp ${MKL_LICENSE} "${WORKDIR}"/ || die + MKL_LIC="$(basename ${MKL_LICENSE})" + + # binary blob extractor installs rpm leftovers in /opt/intel + addwrite /opt/intel + # undocumented features: INSTALLMODE_mkl=NONRPM + + # We need to install mkl non-interactively. + # If things change between versions, first do it interactively: + # tar xf l_*; ./install.sh --duplicate mkl.ini; + # The file will be instman/mkl.ini + # Then check it and modify the ebuild-created one below + # --norpm is required to be able to install 10.x + cat > mkl.ini <<-EOF + [MKL] + EULA_ACCEPT_REJECT=ACCEPT + FLEXLM_LICENSE_LOCATION=${WORKDIR}/${MKL_LIC} + INSTALLMODE_mkl=NONRPM + INSTALL_DESTINATION=${S} + EOF + einfo "Extracting ..." + ./install \ + --silent ./mkl.ini \ + --installpath "${S}" \ + --log log.txt &> /dev/null + + if [[ -z $(find "${S}" -name libmkl.so) ]]; then + eerror "Could not find extracted files" + eerror "See ${PWD}/log.txt to see why" + die "extracting failed" + fi +} + +src_prepare() { + # remove left over + rm -f /opt/intel/.*mkl*.log /opt/intel/intel_sdp_products.db || die + + # remove unused stuff and set up intel names + rm -rf "${WORKDIR}"/l_* || die + + # allow openmpi to work + epatch "${FILESDIR}"/${PN}-10.0.2.018-openmpi.patch + # make scalapack tests work for gfortran + #epatch "${FILESDIR}"/${PN}-10.0.2.018-tests.patch + case ${ARCH} in + x86) MKL_ARCH=32 + MKL_KERN=ia32 + rm -rf lib*/{em64t,64} || die + ;; + + amd64) MKL_ARCH=em64t + MKL_KERN=em64t + rm -rf lib*/{32,64} || die + ;; + + ia64) MKL_ARCH=64 + MKL_KERN=ipf + rm -rf lib*/{32,em64t} || die + ;; + esac + MKL_LIBDIR=${MKL_DIR}/lib/${MKL_ARCH} + # fix env scripts + sed -i \ + -e "s:${S}:${MKL_DIR}:g" \ + tools/environment/*sh || die "sed support file failed" +} + +src_compile() { + cd "${S}"/interfaces || die + if use fortran95; then + einfo "Compiling fortan95 static lib wrappers" + local myconf="lib${MKL_ARCH}" + [[ $(tc-getFC) =~ gfortran ]] && \ + myconf="${myconf} FC=gfortran" + if use int64; then + myconf="${myconf} interface=ilp64" + [[ $(tc-getFC) =~ gfortran ]] && \ + myconf="${myconf} FOPTS=-fdefault-integer-8" + fi + local x + for x in blas95 lapack95; do + pushd ${x} > /dev/null || die + emake ${myconf} + popd > /dev/null || die + done + fi + + if use fftw; then + local fftwdirs="fftw2xc fftw2xf fftw3xc fftw3xf" + local myconf="lib${MKL_ARCH} compiler=${MKL_CC}" + if use mpi; then + fftwdirs="${fftwdirs} fftw2x_cdft" + myconf="${myconf} mpi=${MKL_MPI}" + fi + einfo "Compiling fftw static lib wrappers" + local x + for x in ${fftwdirs}; do + pushd ${x} > /dev/null || die + emake ${myconf} + popd > /dev/null || die + done + fi +} + +src_test() { + cd "${S}"/tests + local myconf + local testdirs="blas cblas" + use int64 && myconf="${myconf} interface=ilp64" + # buggy with g77 and gfortran + #if use mpi; then + # testdirs="${testdirs} scalapack" + # myconf="${myconf} mpi=${MKL_MPI}" + #fi + for x in ${testdirs}; do + pushd ${x} + einfo "Testing ${x}" + emake \ + compiler=${MKL_FC} \ + ${myconf} \ + so${MKL_ARCH} \ + || die "emake ${x} failed" + popd + done +} + +mkl_make_generic_profile() { + cd "${S}" || die + # produce eselect files + # don't make them in FILESDIR, it changes every major version + cat > eselect.blas <<-EOF + ${MKL_LIBDIR}/libmkl_${MKL_KERN}.a /usr/@LIBDIR@/libblas.a + ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libblas.so + ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libblas.so.0 + EOF + cat > eselect.cblas <<-EOF + ${MKL_LIBDIR}/libmkl_${MKL_KERN}.a /usr/@LIBDIR@/libcblas.a + ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libcblas.so + ${MKL_LIBDIR}/libmkl.so /usr/@LIBDIR@/libcblas.so.0 + ${MKL_DIR}/include/mkl_cblas.h /usr/include/cblas.h + EOF + cat > eselect.lapack <<-EOF + ${MKL_LIBDIR}/libmkl_lapack.a /usr/@LIBDIR@/liblapack.a + ${MKL_LIBDIR}/libmkl_lapack.so /usr/@LIBDIR@/liblapack.so + ${MKL_LIBDIR}/libmkl_lapack.so /usr/@LIBDIR@/liblapack.so.0 + EOF +} + +# usage: mkl_add_profile <profile> <interface_lib> <thread_lib> <rtl_lib> +mkl_add_profile() { + cd "${S}" || die + local prof=${1} + local x + for x in blas cblas lapack; do + cat > ${x}-${prof}.pc <<-EOF + prefix=${MKL_DIR} + libdir=${MKL_LIBDIR} + includedir=\${prefix}/include + Name: ${x} + Description: Intel(R) Math Kernel Library implementation of ${x} + Version: ${PV} + URL: ${HOMEPAGE} + EOF + done + cat >> blas-${prof}.pc <<-EOF + Libs: -Wl,--no-as-needed -L\${libdir} ${2} ${3} -lmkl_core ${4} -lpthread + EOF + cat >> cblas-${prof}.pc <<-EOF + Requires: blas + Libs: -Wl,--no-as-needed -L\${libdir} ${2} ${3} -lmkl_core ${4} -lpthread + Cflags: -I\${includedir} + EOF + cat >> lapack-${prof}.pc <<-EOF + Requires: blas + Libs: -Wl,--no-as-needed -L\${libdir} ${2} ${3} -lmkl_core -lmkl_lapack ${4} -lpthread + EOF + insinto ${MKL_LIBDIR} + for x in blas cblas lapack; do + doins ${x}-${prof}.pc + cp eselect.${x} eselect.${x}.${prof} || die + echo "${MKL_LIBDIR}/${x}-${prof}.pc /usr/@LIBDIR@/pkgconfig/${x}.pc" \ + >> eselect.${x}.${prof} + eselect ${x} add $(get_libdir) eselect.${x}.${prof} ${prof} + done +} + +mkl_make_profiles() { + local clib="gf" + has_version 'dev-lang/ifc' && clib+=" intel" + local slib="-lmkl_sequential" + local rlib="-liomp5" + local pbase=${PN} + local c + for c in ${clib}; do + local ilib="-lmkl_${c}_lp64" + use x86 && ilib="-lmkl_${c}" + local tlib="-lmkl_${c/gf/gnu}_thread" + local comp="${c/gf/gfortran}" + comp="${comp/intel/ifort}" + mkl_add_profile ${pbase}-${comp} ${ilib} ${slib} + mkl_add_profile ${pbase}-${comp}-threads ${ilib} ${tlib} ${rlib} + if use int64; then + ilib="-lmkl_${c}_ilp64" + mkl_add_profile ${pbase}-${comp}-int64 ${ilib} ${slib} + mkl_add_profile ${pbase}-${comp}-threads-int64 ${ilib} ${tlib} ${rlib} + fi + done +} + +src_install() { + dodir ${MKL_DIR} + + # install license + if [[ ! -f ${INTEL_LIC_DIR}/${MKL_LIC} ]]; then + insinto ${INTEL_LIC_DIR} + doins "${WORKDIR}"/${MKL_LIC} || die "install license failed" + fi + + # install main stuff: cp faster than doins + einfo "Installing files..." + local cpdirs="benchmarks doc examples include interfaces lib man tests" + local doinsdirs="tools" + cp -pPR ${cpdirs} "${D}"${MKL_DIR} \ + || die "installing mkl failed" + insinto ${MKL_DIR} + doins -r ${doinsdirs} || die "doins ${doinsdirs} failed" + dosym mkl_cblas.h ${MKL_DIR}/include/cblas.h + + # install blas/lapack profiles + mkl_make_generic_profile + mkl_make_profiles + + # install env variables + cat > 35mkl <<-EOF + MKLROOT=${MKL_DIR} + LDPATH=${MKL_LIBDIR} + MANPATH=${MKL_DIR}/man + EOF + doenvd 35mkl +} + +pkg_postinst() { + # if blas profile is mkl, set lapack and cblas profiles as mkl + local blas_prof=$(eselect blas show | cut -d' ' -f2) + local def_prof="mkl-gfortran-threads" + has_version 'dev-lang/ifc' && def_prof="mkl-ifort-threads" + use int64 && def_prof="${def_prof}-int64" + for x in blas cblas lapack; do + local cur_prof=$(eselect ${x} show | cut -d' ' -f2) + if [[ -z ${cur_prof} || ${cur_prof} == ${def_prof} ]]; then + # work around eselect bug #189942 + local configfile="${ROOT}"/etc/env.d/${x}/$(get_libdir)/config + [[ -e ${configfile} ]] && rm -f ${configfile} + eselect ${x} set ${def_prof} + elog "${x} has been eselected to ${def_prof}" + else + elog "Current eselected ${x} is ${current_lib}" + elog "To use one of mkl profiles, issue (as root):" + elog "\t eselect ${x} set <profile>" + fi + if [[ ${blas_prof} == mkl* && ${cur_prof} != ${blas_prof} ]]; then + eselect blas set ${def_prof} + elog "${x} is now set to ${def_prof} for consistency" + fi + done + if [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]]; then + elog "Multi-threading OpenMP for GNU compilers only available" + elog "with gcc >= 4.2. Make sure you have a compatible version" + elog "and select it with gcc-config before selecting gnu profiles" + fi +} diff --git a/sci-libs/mmdb/Manifest b/sci-libs/mmdb/Manifest new file mode 100644 index 000000000000..cd89b1d0c589 --- /dev/null +++ b/sci-libs/mmdb/Manifest @@ -0,0 +1,8 @@ +AUX mmdb-1.25.5-include-path.patch 362 SHA256 69b0b3f3006bc6e96c28a1a6ef7414272f174b5d50baad7f5b7645ea4c2385ae SHA512 60b110b173867c4b3eb45ad370141950046e248dd94d6496e8c8a14a72051a24cdfe805a2401083d53b471893d4e528a8f953ed28935393ab40201a973921f3b WHIRLPOOL b59818ba2d8c441d07e781c01851fb06df79e846a9a973344f9d0926bb44a4b396deb51a31f0b67d05593fa9462242becffb16dadf196d6847a22d4f7f3fee9d +DIST mmdb-1.25.5.tar.gz 732911 SHA256 44c614e2fa24aa492f2aa1852d2d12f440f5b1de35441cdba131db941ea3db4d SHA512 19784f119422e176ff97c0f40256815584ddf2156570593047125ffaf509c961840619799ce20c43efb330d22f068f96c061d31aa5bc5851f538da1742152ba0 WHIRLPOOL c6e5792a6f5456771da711a8d6f07d2fbfb6cc6e59aaab01176d63c2e29552e14dd41be85ae29800bbd26fde9ab76ad455a4d95e33c0faf7e5eb1d0f00e76867 +DIST mmdb2-2.0.1.tar.gz 721759 SHA256 6df04205747ae35cd62edc9649ab0187f902a56fb16f355cbdbdc7ca3e14b6bd SHA512 00465204aa2b76867f805259d25653d48e0e4fe5eabb3929b86a9e3ae8d88345737ca187cfd21dc6c2808e6e8da9c9d61c11be2f587e733390bc69e5ef87b7cd WHIRLPOOL ab78e08739467bb62703f91abc37a6583cc189e0b90dca2bef4fa825a3f8544dcad5c914683a2bfa4502b016e6c958e6ca0597ceefddfa5b99078108c920edfa +EBUILD mmdb-1.25.5-r1.ebuild 517 SHA256 9e959b2b6a84f9971e26a97d291fe00f1d031921f5968739ca49f5a1be26e04b SHA512 e95b84254904bbe9aa636bb5c88d8186d1e83e47df5592ff21facbea1c64e6467c62f5ce94a291c291f7c62789bd39bd2de53ea6eb566d492100d0d2eaaccd94 WHIRLPOOL 10115466d8c8527770feb5dd7b7d651251549637c63725424b71a78556ee66313adbee89e698ee6865be2a4b3f058a5af6607ad9c7db6eddf53bf49b78faa27d +EBUILD mmdb-2.0.1.ebuild 514 SHA256 f679e5cd8b399c15c2532398fb86b625c980a1b8e7337449e3864c514c2abcf2 SHA512 f510d64360d06dbc6ade9423022875047ac298eb56ceedc45c13a862ffd53e081bfe63fe2c2ad604d99f1948c7217cc7ed1f3b4af2d1e41c91b5b62e6425440f WHIRLPOOL 1d99dfa5c99044ba191ad11790e83dcab0f693da47d6b9b643787c997e6dc3413d53586b6a2a9b9124d3a78b127499d5c56fc4d02d1a557aed729e44ff0c0894 +MISC ChangeLog 5078 SHA256 88ef6e31ca123c35b85aa0ca35b70c16a49f0bdde4187490663e60123f41ad6f SHA512 771f72179cfa3f7048d5816c1a46355db26c0294bc092a8eb38308334a88b0591addd792ffe4928cf923bd9e84dc2f323daff41c7a43d51e870b7dea25e20fda WHIRLPOOL 2bacf03570babf632da1d13f1e3cb371080ded86407703f1464ada30cf29ebbda7dc0dd3f1199a0d6d6da28488589497560da4d62883f8a4479145cf4e24c463 +MISC ChangeLog-2015 4451 SHA256 7e183769459a3500603f463506b26d7a2547943825c2ebc0121dbf08baa6a294 SHA512 a4186ebacd2f011a8656e06fe63c5eaaefe278531bca7bf81d7fdacdf186eadfcc14f64979ab9a444974f06e1c4318026ad673d746b45a735afd5124c6e64f6d WHIRLPOOL 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libdir=@libdir@ +-includedir=@includedir@ ++includedir=@includedir@/mmdb + + Name: mmdb + Description: Macromolecular coordinate library diff --git a/sci-libs/mmdb/metadata.xml b/sci-libs/mmdb/metadata.xml new file mode 100644 index 000000000000..8f40a97a08ad --- /dev/null +++ b/sci-libs/mmdb/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="launchpad">mmdb</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild new file mode 100644 index 000000000000..5e96460fb6c5 --- /dev/null +++ b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files" +HOMEPAGE="https://launchpad.net/mmdb/" +SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz" + +LICENSE="GPL-2 LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="static-libs" + +PATCHES=( "${FILESDIR}"/${P}-include-path.patch ) diff --git a/sci-libs/mmdb/mmdb-2.0.1.ebuild b/sci-libs/mmdb/mmdb-2.0.1.ebuild new file mode 100644 index 000000000000..d93f9549df5c --- /dev/null +++ b/sci-libs/mmdb/mmdb-2.0.1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +MY_P="${PN}2-${PV}" + +DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files" +HOMEPAGE="https://launchpad.net/mmdb/" +SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${MY_P}.tar.gz" + +LICENSE="GPL-2 LGPL-3" +SLOT="2" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="static-libs" + +S="${WORKDIR}"/${MY_P} diff --git a/sci-libs/mmtk/Manifest b/sci-libs/mmtk/Manifest new file mode 100644 index 000000000000..4759a058df31 --- /dev/null +++ b/sci-libs/mmtk/Manifest @@ -0,0 +1,5 @@ +DIST MMTK-2.7.9.tar.gz 1213599 SHA256 8c53acc12428ca6464e6b7e11fb1587200e16f8a5c92eb56e48ece387b6977ed SHA512 66819048aec4d8bdd370bb063f702c828145ecc9b7cb3247fcdd067486c78e00110a4e316f5c76df0b57a7885e05c347fa1616944daabfaa6d8b35933a79a7d8 WHIRLPOOL 765c9407df5dfa48891cd8b29f0e53196ca8ae20e536bb78b65458832aa342d21d84ef30b4d26c5a25c24126b65fe428f3129942435f6035931b921f1b0ba4d1 +EBUILD mmtk-2.7.9.ebuild 1195 SHA256 8132c79c328320acdac591afef5382fe6f143cefb62847b36622e014699d2fd2 SHA512 5cd7eff1be05dab6da4e7b4f026a80f3c5e88eb8eab6912bd734efbd86ca17f071273076521c89076c4d256bc2b5ddb30e51fefe36d20147f363096584d7a744 WHIRLPOOL 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3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-libs/mmtk/metadata.xml b/sci-libs/mmtk/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/mmtk/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/mmtk/mmtk-2.7.9.ebuild b/sci-libs/mmtk/mmtk-2.7.9.ebuild new file mode 100644 index 000000000000..15a2992306a5 --- /dev/null +++ b/sci-libs/mmtk/mmtk-2.7.9.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +# This number identifies each release on the CRU website. +# Can't figure out how to avoid hardcoding it. +NUMBER="4324" + +MY_PN=${PN/mmtk/MMTK} +MY_P=${MY_PN}-${PV} + +DESCRIPTION="Molecular Modeling ToolKit for Python" +HOMEPAGE="http://dirac.cnrs-orleans.fr/MMTK/" +SRC_URI="http://sourcesup.cru.fr/frs/download.php/${NUMBER}/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="CeCILL-2" +KEYWORDS="~amd64 ~x86 ~ppc ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + <dev-python/numpy-1.9[${PYTHON_USEDEP}] + dev-python/scientificpython[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_P} + +python_prepare_all() { + export MMTK_USE_CYTHON="1" + sed \ + -e "/ext_package/d" \ + -e "/^if sphinx/s|:| == 3:|g" \ + -e "s:import sphinx:sphinx = None:g" \ + -i "${S}"/setup.py || die + distutils-r1_python_prepare_all +} + +python_install_all() { + DOCS=( README* Doc/CHANGELOG ) + HTML_DOCS=( Doc/HTML/. ) + + distutils-r1_python_install_all + + if use examples; then + insinto /usr/share/${P} + doins -r Examples + fi +} diff --git a/sci-libs/monomer-db/Manifest b/sci-libs/monomer-db/Manifest new file mode 100644 index 000000000000..0a7efc40c7e8 --- /dev/null +++ b/sci-libs/monomer-db/Manifest @@ -0,0 +1,5 @@ +DIST refmac_dictionary_v5.41.tar.gz 28087020 SHA256 8cb5ffeb6ae844f76284ee23db4ca0c2455f5f5553e6d60e6a0b6ed558940953 SHA512 4e694c63fb783d998ce30a65f8cd4111a13a9dcb6e45bd29ed4e7ad87d58a11e8004205ab7e108bb52723834bddfaaca1e7d9d7336e17f4d2ea38093cfd1be7c WHIRLPOOL 665a65113aecb392f2b18b34972e824f5e6dd967ce331bbb3099f93a559aff11fd67137b0412f0cd6c3fa0549e66304492efabde2cd7a82d509a28e163ca6754 +EBUILD monomer-db-5.41.ebuild 737 SHA256 6fa968bde8e266485963189c8a17fa4eff3f280fe520a528bbcc971bfac66a03 SHA512 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a/sci-libs/monomer-db/monomer-db-5.41.ebuild b/sci-libs/monomer-db/monomer-db-5.41.ebuild new file mode 100644 index 000000000000..42a0643c4d6c --- /dev/null +++ b/sci-libs/monomer-db/monomer-db-5.41.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +MY_PN="refmac_dictionary" + +DESCRIPTION="Monomer library used for macromolecular structure building and refinement" +HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/" +SRC_URI="http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/${MY_PN}_v${PV}.tar.gz" + +SLOT="0" +LICENSE="LGPL-3" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="" + +RESTRICT="binchecks strip" + +S="${WORKDIR}"/monomers + +src_install() { + insinto /usr/share/data/monomers/ + for i in {a..z} {0..9} *list *.cif *.txt *table *pdb; do + einfo "Installing ${i}** ..." + doins -r ${i} + done + dodoc *.txt +} diff --git a/sci-libs/mpfi/Manifest b/sci-libs/mpfi/Manifest new file mode 100644 index 000000000000..d2eebd9d5fdf --- /dev/null +++ b/sci-libs/mpfi/Manifest @@ -0,0 +1,5 @@ +DIST mpfi-1.5.1.tar.bz2 365467 SHA256 3fcc6536d117a67fbfbb875ab2d2b3d7fe76cdf0ce85a7e707aae1e89893696e SHA512 498f8b2e114e71c0600f601e4bfef21011e46434d6795e3cd999d38ea9a3d4c66cad2d27e7899629ae422a91b6a776dad2fdbd7c93d51a56f5cfc4ab0e3aeca1 WHIRLPOOL 22116a383cde6048e1ba6626f9e6632ffd8ba48aa9d2387c740a75e827432b7b8163fdbe695014cd5158331c9989ad6271be48027c7b38268c1a064cb64c1c63 +EBUILD mpfi-1.5.1.ebuild 527 SHA256 7370ca2027b281bcb28d4aab363a346e1b4a813d2e62ae51cdee13754e5a5d32 SHA512 64043699a92d35aac4f68111ebace7afea870323728fba414d9eb607cbbcc4cc9c3e8350b496e2e59c88678ec7667ff9e667e99b0ce41ff9c6add0c5afdc7643 WHIRLPOOL 102f1142fa44dda4b3cba8bfc41c9994b6ea40f86a14f69707d044caea762bc87a0d5bcb5e151819e0ab208999daf38c6840870a57ff907de2f667e84b19b623 +MISC ChangeLog 2418 SHA256 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4ed7a637b3ac5d666b30d1ea60bd04d288a2a4cd5ae8957669c75d9e336bdbc600a2d7fee6c2c1893f0c614bc3d6d9fa36576802fb20568d5637015d997f1e1e diff --git a/sci-libs/mpfi/metadata.xml b/sci-libs/mpfi/metadata.xml new file mode 100644 index 000000000000..a0c9c3fcbb0c --- /dev/null +++ b/sci-libs/mpfi/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-mathematics@gentoo.org</email> + <name>Gentoo Mathematics Project</name> + </maintainer> + <longdescription lang="en"> + MPFI is intended to be a portable library written in C for arbitrary + precision interval arithmetic with intervals represented using MPFR + reliable floating-point numbers. It is based on the GNU MP library + and on the MPFR library. The purpose of an arbitrary precision + interval arithmetic is on the one hand to get guaranteed results, + thanks to interval computation, and on the other hand to obtain + accurate results, thanks to multiple precision arithmetic. The MPFI + library is built upon MPFR in order to benefit from the correct + roundings provided by MPFR. Further advantages of using MPFR are its + portability and compliance with the IEEE 754 standard for + floating-point arithmetic. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/mpfi/mpfi-1.5.1.ebuild b/sci-libs/mpfi/mpfi-1.5.1.ebuild new file mode 100644 index 000000000000..b448cb8cde86 --- /dev/null +++ b/sci-libs/mpfi/mpfi-1.5.1.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="4" + +inherit autotools-utils + +PID=30129 + +DESCRIPTION="Multiple precision interval arithmetic library based on MPFR" +HOMEPAGE="http://perso.ens-lyon.fr/nathalie.revol/software.html" +SRC_URI="https://gforge.inria.fr/frs/download.php/${PID}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +DEPEND=">=dev-libs/gmp-4.1.2 + >=dev-libs/mpfr-2.4" +RDEPEND="${DEPEND}" diff --git a/sci-libs/mpir/Manifest b/sci-libs/mpir/Manifest new file mode 100644 index 000000000000..d207a623f8e7 --- /dev/null +++ b/sci-libs/mpir/Manifest @@ -0,0 +1,15 @@ +AUX mpir-1.3.0-ABI-multilib.patch 3903 SHA256 3db2dc41f385d6c8ce9da8406a42072c8462e6e15eba0b6ff93664ef31c00957 SHA512 a1b008f7daccb03a5e6c7af6311d96279ff2d052201f54ef32890ad0404e79e179a0a8d60e2adde5a0b487e16325ce2df4d0fd74464411c983e9630833662886 WHIRLPOOL ae123f02a8e2868f19ad27802042ba45d6e40204ecdf982e346e503ef6808d3f6fafd9b4da336db92164327f2af9e59dfd5e51d97876097ba18a60c30a4ef70b +AUX mpir-2.5.1-automake-1.12.patch 3388 SHA256 dc003924094f88d89582a5e4d626e67c6edacf8e81ee5080fff34fae1b9f836a SHA512 d96b238d2a0deaae1d5489121db02766bfde34e602cf137a608a862584192694da6bd61a27dce3294c62cb950fdbc80b71302585f9cf4a2ac0e5f68c48a66846 WHIRLPOOL 949cb479df53d8d643fdefa95199c777516b843368ef7c68e40fc85429c2736a4d62bda469c9b08224016af223617c573795f6d4041045c90997511a0513fd28 +AUX mpir-2.6.0-gcc48.patch 467 SHA256 5e3656543f9a50bbfe063681d1135a33ca2c272bb79c1762a6759d907b601355 SHA512 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SHA512 8436a0123201f9e30130ea340331c5a6445dddb58ce1f6c6a3a8303c310ac5b3c279c83b5c520a757cba82c2b14e92da44583e0eec287090cf69cbb29d516a9c WHIRLPOOL 8c7804b183282b7d804e91233176ce948a2e5e5c83dcefc4eaf31194a59431af55002a8b6a3405ddb45cac89270066c3c0ae2c4adcaa22329f4af06dbdf10ffb +DIST mpir-3.0.0.tar.bz2 2572041 SHA256 52f63459cf3f9478859de29e00357f004050ead70b45913f2c2269d9708675bb SHA512 c735105db8b86db739fd915bf16064e6bc82d0565ad8858059e4e93f62c9d72d9a1c02a5ca9859b184346a8dc64fa714d4d61404cff1e405dc548cbd54d0a88e WHIRLPOOL 7f10d08291f3a47db2d02d1db63fde8a187bd6896d42dfdd45ec9d77dafa35199b87871c53abbd43b22f78f2948e202402100c67f78f73c60a0692e5bdb49753 +EBUILD mpir-2.6.0-r2.ebuild 1713 SHA256 90d99aa37129aa7b2f634f5c5b3ec0f057d5fa225608363b7af029d58d6247be SHA512 0fc862cd24cb1dbb78d54e444b5fdc04a8c2f0f053e78c766c08139b7ea7af88fc172bcd337a5e79de1b867cd29ca71b4eb2e9fbd4a8cd44693c630065f0c647 WHIRLPOOL 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f9c05457cfa28226e7b9ea57d08e96be05ebdcace8a1ec6c578360cb2ff0d6a28e845548e99ae11edd11160a764ac209260797baf88efde4c75162c23e2b6a62 diff --git a/sci-libs/mpir/files/mpir-1.3.0-ABI-multilib.patch b/sci-libs/mpir/files/mpir-1.3.0-ABI-multilib.patch new file mode 100644 index 000000000000..fba6fea2e8f6 --- /dev/null +++ b/sci-libs/mpir/files/mpir-1.3.0-ABI-multilib.patch @@ -0,0 +1,145 @@ +--- configure.in.orig 2009-11-28 10:48:59.196977657 +0000 ++++ configure.in 2009-11-28 10:54:50.717976971 +0000 +@@ -361,7 +361,7 @@ + # hugely bloat the output. + + +-AC_ARG_VAR(ABI, [desired ABI (for processors supporting more than one ABI)]) ++AC_ARG_VAR(MPIRABI, [desired ABI (for processors supporting more than one ABI)]) + + # abilist needs to be non-empty, "standard" is just a generic name here + abilist="standard" +@@ -1590,7 +1590,7 @@ + + cat >&AC_FD_CC <<EOF + User: +-ABI=$ABI ++MPIRABI=$MPIRABI + CC=$CC + CFLAGS=$CFLAGS_or_unset + CPPFLAGS=$CPPFLAGS_or_unset +@@ -1611,22 +1611,22 @@ + # If the user specifies an ABI then it must be in $abilist, after that + # $abilist is restricted to just that choice. + # +-if test -n "$ABI"; then ++if test -n "$MPIRABI"; then + found=no + for abi in $abilist; do +- if test $abi = "$ABI"; then found=yes; break; fi ++ if test $abi = "$MPIRABI"; then found=yes; break; fi + done + if test $found = no; then +- AC_MSG_ERROR([ABI=$ABI is not among the following valid choices: $abilist]) ++ AC_MSG_ERROR([MPIRABI=$MPIRABI is not among the following valid choices: $abilist]) + fi +- abilist="$ABI" ++ abilist="$MPIRABI" + fi + + found_compiler=no + + for abi in $abilist; do + +- echo "checking ABI=$abi" ++ echo "checking MPIRABI=$abi" + + # Suppose abilist="64 32", then for abi=64, will have abi1="_64" and + # abi2="_64". For abi=32, will have abi1="_32" and abi2="". This is how +@@ -1879,7 +1879,7 @@ + done + fi + +- ABI="$abi" ++ MPIRABI="$abi" + CC="$cc" + CFLAGS="$cflags" + CPPFLAGS="$cppflags" +@@ -1895,8 +1895,8 @@ + AC_SUBST(GMP_CFLAGS) + + # Could easily have this in config.h too, if desired. +- ABI_nodots=`echo $ABI | sed 's/\./_/'` +- GMP_DEFINE_RAW("define_not_for_expansion(\`HAVE_ABI_$ABI_nodots')", POST) ++ ABI_nodots=`echo $MPIRABI | sed 's/\./_/'` ++ GMP_DEFINE_RAW("define_not_for_expansion(\`HAVE_ABI_$MPIRABI_nodots')", POST) + + + # GMP_LDFLAGS substitution, selected according to ABI. +@@ -2094,7 +2094,7 @@ + # + case $host in + X86_PATTERN | X86_64_PATTERN) +- if test "$ABI" = 32; then ++ if test "$MPIRABI" = 32; then + case "$path $fat_path" in + *mmx*) GMP_ASM_X86_MMX( , [GMP_STRIP_PATH(*mmx*)]) ;; + esac +@@ -2108,7 +2108,7 @@ + + cat >&AC_FD_CC <<EOF + Decided: +-ABI=$ABI ++MPIRABI=$MPIRABI + CC=$CC + CFLAGS=$CFLAGS + CPPFLAGS=$CPPFLAGS +@@ -2117,7 +2117,7 @@ + CXXFLAGS=$CXXFLAGS + path=$path + EOF +-echo "using ABI=\"$ABI\"" ++echo "using MPIRABI=\"$MPIRABI\"" + echo " CC=\"$CC\"" + echo " CFLAGS=\"$CFLAGS\"" + echo " CPPFLAGS=\"$CPPFLAGS\"" +@@ -2593,7 +2593,7 @@ + + + if test -n "$fat_path"; then +- if test "$ABI" = 64; then ++ if test "$MPIRABI" = 64; then + fat_path="$fat_path_64" + fi + +@@ -3099,19 +3099,19 @@ + GMP_INCLUDE_MPN(powerpc32/powerpc-defs.m4) + case $host in + *-*-aix*) +- case $ABI in ++ case $MPIRABI in + 64 | aix64) GMP_INCLUDE_MPN(powerpc64/aix.m4) ;; + *) GMP_INCLUDE_MPN(powerpc32/aix.m4) ;; + esac + ;; + *-*-linux* | *-*-*bsd*) +- case $ABI in ++ case $MPIRABI in + mode64) GMP_INCLUDE_MPN(powerpc64/elf.m4) ;; + mode32 | 32) GMP_INCLUDE_MPN(powerpc32/elf.m4) ;; + esac + ;; + *-*-darwin*) +- case $ABI in ++ case $MPIRABI in + mode64) GMP_INCLUDE_MPN(powerpc64/darwin.m4) ;; + mode32 | 32) GMP_INCLUDE_MPN(powerpc32/darwin.m4) ;; + esac +@@ -3126,7 +3126,7 @@ + GMP_INCLUDE_MPN(powerpc32/aix.m4) + ;; + sparcv9*-*-* | ultrasparc*-*-* | sparc64-*-*) +- case $ABI in ++ case $MPIRABI in + 64) + GMP_ASM_SPARC_REGISTER + ;; +@@ -3134,7 +3134,7 @@ + ;; + X86_PATTERN | X86_64_PATTERN) + GMP_ASM_ALIGN_FILL_0x90 +- case $ABI in ++ case $MPIRABI in + 32) + GMP_INCLUDE_MPN(x86/x86-defs.m4) + AC_DEFINE(HAVE_HOST_CPU_FAMILY_x86) diff --git a/sci-libs/mpir/files/mpir-2.5.1-automake-1.12.patch b/sci-libs/mpir/files/mpir-2.5.1-automake-1.12.patch new file mode 100644 index 000000000000..684bcbf7d3c1 --- /dev/null +++ b/sci-libs/mpir/files/mpir-2.5.1-automake-1.12.patch @@ -0,0 +1,95 @@ +http://bugs.gentoo.org/423767 + +--- configure.in ++++ configure.in +@@ -69,7 +69,7 @@ + dnl Note that there's a copy of these options in the top-level Makefile.am, + dnl so update there too if changing anything. + dnl +-AM_INIT_AUTOMAKE([1.11 gnu no-dependencies parallel-tests dist-bzip2 no-dist-gzip dist-lzma]) ++AM_INIT_AUTOMAKE([1.11 gnu no-dependencies parallel-tests dist-bzip2 no-dist-gzip dist-xz]) + AM_CONFIG_HEADER(config.h:config.in) + AM_MAINTAINER_MODE + +@@ -208,8 +208,7 @@ + [enable_fat=no]) + + # Work around an autoconf bug +-MKDIR_P=@mkdir_p@ +-AC_SUBST(MKDIR_P) ++AC_PROG_MKDIR_P + + # Table of compilers, options, and mpn paths. This code has various related + # purposes +--- yasm/po/Makefile.in.in ++++ yasm/po/Makefile.in.in +@@ -32,17 +32,17 @@ + INSTALL = @INSTALL@ + INSTALL_DATA = @INSTALL_DATA@ + +-# We use $(mkdir_p). +-# In automake <= 1.9.x, $(mkdir_p) is defined either as "mkdir -p --" or as ++# We use $(MKDIR_P). ++# In automake <= 1.9.x, $(MKDIR_P) is defined either as "mkdir -p --" or as + # "$(mkinstalldirs)" or as "$(install_sh) -d". For these automake versions, + # @install_sh@ does not start with $(SHELL), so we add it. +-# In automake >= 1.10, @mkdir_p@ is derived from ${MKDIR_P}, which is defined ++# In automake >= 1.10, @MKDIR_P@ is derived from ${MKDIR_P}, which is defined + # either as "/path/to/mkdir -p" or ".../install-sh -c -d". For these automake + # versions, $(mkinstalldirs) and $(install_sh) are unused. + mkinstalldirs = $(SHELL) @install_sh@ -d + install_sh = $(SHELL) @install_sh@ + MKDIR_P = @MKDIR_P@ +-mkdir_p = @mkdir_p@ ++MKDIR_P = @MKDIR_P@ + + GMSGFMT_ = @GMSGFMT@ + GMSGFMT_no = @GMSGFMT@ +@@ -204,7 +204,7 @@ + install-exec: + install-data: install-data-@USE_NLS@ + if test "$(PACKAGE)" = "gettext-tools"; then \ +- $(mkdir_p) $(DESTDIR)$(gettextsrcdir); \ ++ $(MKDIR_P) $(DESTDIR)$(gettextsrcdir); \ + for file in $(DISTFILES.common) Makevars.template; do \ + $(INSTALL_DATA) $(srcdir)/$$file \ + $(DESTDIR)$(gettextsrcdir)/$$file; \ +@@ -217,13 +217,13 @@ + fi + install-data-no: all + install-data-yes: all +- $(mkdir_p) $(DESTDIR)$(datadir) ++ $(MKDIR_P) $(DESTDIR)$(datadir) + @catalogs='$(CATALOGS)'; \ + for cat in $$catalogs; do \ + cat=`basename $$cat`; \ + lang=`echo $$cat | sed -e 's/\.gmo$$//'`; \ + dir=$(localedir)/$$lang/LC_MESSAGES; \ +- $(mkdir_p) $(DESTDIR)$$dir; \ ++ $(MKDIR_P) $(DESTDIR)$$dir; \ + if test -r $$cat; then realcat=$$cat; else realcat=$(srcdir)/$$cat; fi; \ + $(INSTALL_DATA) $$realcat $(DESTDIR)$$dir/$(DOMAIN).mo; \ + echo "installing $$realcat as $(DESTDIR)$$dir/$(DOMAIN).mo"; \ +@@ -263,19 +263,19 @@ + installdirs-exec: + installdirs-data: installdirs-data-@USE_NLS@ + if test "$(PACKAGE)" = "gettext-tools"; then \ +- $(mkdir_p) $(DESTDIR)$(gettextsrcdir); \ ++ $(MKDIR_P) $(DESTDIR)$(gettextsrcdir); \ + else \ + : ; \ + fi + installdirs-data-no: + installdirs-data-yes: +- $(mkdir_p) $(DESTDIR)$(datadir) ++ $(MKDIR_P) $(DESTDIR)$(datadir) + @catalogs='$(CATALOGS)'; \ + for cat in $$catalogs; do \ + cat=`basename $$cat`; \ + lang=`echo $$cat | sed -e 's/\.gmo$$//'`; \ + dir=$(localedir)/$$lang/LC_MESSAGES; \ +- $(mkdir_p) $(DESTDIR)$$dir; \ ++ $(MKDIR_P) $(DESTDIR)$$dir; \ + for lc in '' $(EXTRA_LOCALE_CATEGORIES); do \ + if test -n "$$lc"; then \ + if (cd $(DESTDIR)$(localedir)/$$lang && LC_ALL=C ls -l -d $$lc 2>/dev/null) | grep ' -> ' >/dev/null; then \ diff --git a/sci-libs/mpir/files/mpir-2.6.0-gcc48.patch b/sci-libs/mpir/files/mpir-2.6.0-gcc48.patch new file mode 100644 index 000000000000..55cd1a087ed6 --- /dev/null +++ b/sci-libs/mpir/files/mpir-2.6.0-gcc48.patch @@ -0,0 +1,13 @@ +https://bugs.gentoo.org/470838 + +--- a/tests/mpz/t-scan.c ++++ b/tests/mpz/t-scan.c +@@ -84,7 +84,7 @@ check_ref (void) + + for (isize = 0; isize <= size; isize++) + { +- for (oindex = 0; oindex <= numberof (offset); oindex++) ++ for (oindex = 0; oindex < numberof (offset); oindex++) + { + o = offset[oindex]; + if ((int) isize*GMP_NUMB_BITS < -o) diff --git a/sci-libs/mpir/files/mpir-2.6.0-yasm.patch b/sci-libs/mpir/files/mpir-2.6.0-yasm.patch new file mode 100644 index 000000000000..3c6b1881f170 --- /dev/null +++ b/sci-libs/mpir/files/mpir-2.6.0-yasm.patch @@ -0,0 +1,52 @@ +diff -U 3 -dHrN mpir-2.6.0.orig/configure.in mpir-2.6.0/configure.in +--- mpir-2.6.0.orig/configure.in 2013-01-16 10:51:13.141047276 +0100 ++++ mpir-2.6.0/configure.in 2013-01-16 10:51:52.437353115 +0100 +@@ -1295,8 +1295,6 @@ + ;; + esac + +-AM_CONDITIONAL(BUILD_YASM, test "$want_yasm" = "yes") +- + CFLAGS_or_unset=${CFLAGS-'(unset)'} + CPPFLAGS_or_unset=${CPPFLAGS-'(unset)'} + +@@ -1681,7 +1679,7 @@ + GMP_CHECK_LIBM_FOR_BUILD + + +-MPIR_AS="/yasm/yasm" ++MPIR_AS="yasm" + + # How to assemble, used with CFLAGS etc, see mpn/Makeasm.am. + # Using the compiler is a lot easier than figuring out how to invoke the +@@ -2984,7 +2982,6 @@ + # Right now automake isn't accepting the new AC_CONFIG_FILES scheme. + + # allways configure all subdirectorys , even if there are not going to be built , +-AC_CONFIG_SUBDIRS([yasm]) + + case $host in + *-w64-mingw*) +diff -U 3 -dHrN mpir-2.6.0.orig/Makefile.am mpir-2.6.0/Makefile.am +--- mpir-2.6.0.orig/Makefile.am 2013-01-16 10:51:13.121047120 +0100 ++++ mpir-2.6.0/Makefile.am 2013-01-16 10:52:25.675611816 +0100 +@@ -98,10 +98,6 @@ + + SUBDIRS = tests + +-if BUILD_YASM +-SUBDIRS += yasm +-endif +- + SUBDIRS += mpn fft mpz mpq mpf printf scanf cxx tune doc + + EXTRA_DIST = configfsf.guess configfsf.sub .gdbinit INSTALL.autoconf +diff -U 3 -dHrN mpir-2.6.0.orig/mpn/Makeasm.am mpir-2.6.0/mpn/Makeasm.am +--- mpir-2.6.0.orig/mpn/Makeasm.am 2013-01-16 10:51:13.045046528 +0100 ++++ mpir-2.6.0/mpn/Makeasm.am 2013-01-16 10:53:25.333076126 +0100 +@@ -119,4 +119,4 @@ + # .as assembler, assembled with Yasm + + .as.lo: +- $(LIBTOOL) --mode=compile --tag=CC $(top_srcdir)/strip_fPIC.sh $(top_builddir)$(MPIR_AS) -I $(top_builddir) $(OBJECT_FORMAT) $(GSYM_FLAG) -o $@ `test -f '$<' || echo '$(srcdir)/'`$< ++ $(LIBTOOL) --mode=compile --tag=CC $(top_srcdir)/strip_fPIC.sh $(MPIR_AS) -I $(top_builddir) $(OBJECT_FORMAT) $(GSYM_FLAG) -o $@ `test -f '$<' || echo '$(srcdir)/'`$< diff --git a/sci-libs/mpir/files/mpir-2.7.2-ABI-multilib.patch b/sci-libs/mpir/files/mpir-2.7.2-ABI-multilib.patch new file mode 100644 index 000000000000..f02df55ccf98 --- /dev/null +++ b/sci-libs/mpir/files/mpir-2.7.2-ABI-multilib.patch @@ -0,0 +1,145 @@ +--- a/configure.ac 2009-11-28 10:48:59.196977657 +0000 ++++ b/configure.ac 2009-11-28 10:54:50.717976971 +0000 +@@ -361,7 +361,7 @@ + # hugely bloat the output. + + +-AC_ARG_VAR(ABI, [desired ABI (for processors supporting more than one ABI)]) ++AC_ARG_VAR(MPIRABI, [desired ABI (for processors supporting more than one ABI)]) + + # abilist needs to be non-empty, "standard" is just a generic name here + abilist="standard" +@@ -1590,7 +1590,7 @@ + + cat >&AC_FD_CC <<EOF + User: +-ABI=$ABI ++MPIRABI=$MPIRABI + CC=$CC + CFLAGS=$CFLAGS_or_unset + CPPFLAGS=$CPPFLAGS_or_unset +@@ -1611,22 +1611,22 @@ + # If the user specifies an ABI then it must be in $abilist, after that + # $abilist is restricted to just that choice. + # +-if test -n "$ABI"; then ++if test -n "$MPIRABI"; then + found=no + for abi in $abilist; do +- if test $abi = "$ABI"; then found=yes; break; fi ++ if test $abi = "$MPIRABI"; then found=yes; break; fi + done + if test $found = no; then +- AC_MSG_ERROR([ABI=$ABI is not among the following valid choices: $abilist]) ++ AC_MSG_ERROR([MPIRABI=$MPIRABI is not among the following valid choices: $abilist]) + fi +- abilist="$ABI" ++ abilist="$MPIRABI" + fi + + found_compiler=no + + for abi in $abilist; do + +- echo "checking ABI=$abi" ++ echo "checking MPIRABI=$abi" + + # Suppose abilist="64 32", then for abi=64, will have abi1="_64" and + # abi2="_64". For abi=32, will have abi1="_32" and abi2="". This is how +@@ -1879,7 +1879,7 @@ + done + fi + +- ABI="$abi" ++ MPIRABI="$abi" + CC="$cc" + CFLAGS="$cflags" + CPPFLAGS="$cppflags" +@@ -1895,8 +1895,8 @@ + AC_SUBST(GMP_CFLAGS) + + # Could easily have this in config.h too, if desired. +- ABI_nodots=`echo $ABI | sed 's/\./_/'` +- GMP_DEFINE_RAW("define_not_for_expansion(\`HAVE_ABI_$ABI_nodots')", POST) ++ ABI_nodots=`echo $MPIRABI | sed 's/\./_/'` ++ GMP_DEFINE_RAW("define_not_for_expansion(\`HAVE_ABI_$MPIRABI_nodots')", POST) + + + # GMP_LDFLAGS substitution, selected according to ABI. +@@ -2094,7 +2094,7 @@ + # + case $host in + X86_PATTERN | X86_64_PATTERN) +- if test "$ABI" = 32; then ++ if test "$MPIRABI" = 32; then + case "$path $fat_path" in + *mmx*) GMP_ASM_X86_MMX( , [GMP_STRIP_PATH(*mmx*)]) ;; + esac +@@ -2108,7 +2108,7 @@ + + cat >&AC_FD_CC <<EOF + Decided: +-ABI=$ABI ++MPIRABI=$MPIRABI + CC=$CC + CFLAGS=$CFLAGS + CPPFLAGS=$CPPFLAGS +@@ -2117,7 +2117,7 @@ + CXXFLAGS=$CXXFLAGS + path=$path + EOF +-echo "using ABI=\"$ABI\"" ++echo "using MPIRABI=\"$MPIRABI\"" + echo " CC=\"$CC\"" + echo " CFLAGS=\"$CFLAGS\"" + echo " CPPFLAGS=\"$CPPFLAGS\"" +@@ -2593,7 +2593,7 @@ + + + if test -n "$fat_path"; then +- if test "$ABI" = 64; then ++ if test "$MPIRABI" = 64; then + fat_path="$fat_path_64" + fi + +@@ -3099,19 +3099,19 @@ + GMP_INCLUDE_MPN(powerpc32/powerpc-defs.m4) + case $host in + *-*-aix*) +- case $ABI in ++ case $MPIRABI in + 64 | aix64) GMP_INCLUDE_MPN(powerpc64/aix.m4) ;; + *) GMP_INCLUDE_MPN(powerpc32/aix.m4) ;; + esac + ;; + *-*-linux* | *-*-*bsd*) +- case $ABI in ++ case $MPIRABI in + mode64) GMP_INCLUDE_MPN(powerpc64/elf.m4) ;; + mode32 | 32) GMP_INCLUDE_MPN(powerpc32/elf.m4) ;; + esac + ;; + *-*-darwin*) +- case $ABI in ++ case $MPIRABI in + mode64) GMP_INCLUDE_MPN(powerpc64/darwin.m4) ;; + mode32 | 32) GMP_INCLUDE_MPN(powerpc32/darwin.m4) ;; + esac +@@ -3126,7 +3126,7 @@ + GMP_INCLUDE_MPN(powerpc32/aix.m4) + ;; + sparcv9*-*-* | ultrasparc*-*-* | sparc64-*-*) +- case $ABI in ++ case $MPIRABI in + 64) + GMP_ASM_SPARC_REGISTER + ;; +@@ -3134,7 +3134,7 @@ + ;; + X86_PATTERN | X86_64_PATTERN) + GMP_ASM_ALIGN_FILL_0x90 +- case $ABI in ++ case $MPIRABI in + 32) + GMP_INCLUDE_MPN(x86/x86-defs.m4) + AC_DEFINE(HAVE_HOST_CPU_FAMILY_x86) diff --git a/sci-libs/mpir/files/mpir-2.7.2-sed-backport.patch b/sci-libs/mpir/files/mpir-2.7.2-sed-backport.patch new file mode 100644 index 000000000000..897642909ca0 --- /dev/null +++ b/sci-libs/mpir/files/mpir-2.7.2-sed-backport.patch @@ -0,0 +1,16 @@ + configure.ac | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/configure.ac b/configure.ac +index a3821c5..15fa93d 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -2595,7 +2595,7 @@ for tmp_fn in $gmp_mpn_functions; do + sed -n 's/^[ ]*MULFUNC_PROLOGUE(\(.*\))/\1/p' $tmp_file ; + sed -n 's/^[ ]*PROLOGUE(\([^,]*\).*)/\1/p' $tmp_file ; + sed -n 's/^;[ ]*PROLOGUE(\([^,]*\).*)/\1/p' $tmp_file ; +- sed -n 's/[^G]*GLOBAL_FUNC[:space:]*\(.*\)/\1/p' $tmp_file ; ++ sed -n 's/[^G]*GLOBAL_FUNC[[:space:]]*\(.*\)/\1/p' $tmp_file ; + `] + for gmp_tmp in $gmp_ep; do + AC_DEFINE_UNQUOTED(HAVE_NATIVE_$gmp_tmp) diff --git a/sci-libs/mpir/metadata.xml b/sci-libs/mpir/metadata.xml new file mode 100644 index 000000000000..cd50fabad650 --- /dev/null +++ b/sci-libs/mpir/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> +MPIR is an open source multiprecision integer (bignum) library forked +from the GMP (GNU Multi Precision) project. It consists of much code +from past GMP releases, in combination with much original contributed +code. + +MPIR is constructed by a developer and vendor friendly community of +professional and amateur mathematicians, computer scientists and +hobbyists. +</longdescription> + <use> + <flag name="cpudetection">Enables runtime cpudetection (useful for bindist, compatability on other CPUs)</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/mpir/mpir-2.6.0-r2.ebuild b/sci-libs/mpir/mpir-2.6.0-r2.ebuild new file mode 100644 index 000000000000..ee388c74a0e7 --- /dev/null +++ b/sci-libs/mpir/mpir-2.6.0-r2.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils eutils toolchain-funcs + +DESCRIPTION="Library for arbitrary precision integer arithmetic (fork of gmp)" +HOMEPAGE="http://www.mpir.org/" +SRC_URI="http://www.mpir.org/${P}.tar.lzma" + +LICENSE="LGPL-3" +SLOT="0/11" +KEYWORDS="alpha amd64 ~arm ~arm64 ~hppa ia64 ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="+cxx cpudetection static-libs" + +DEPEND="x86? ( dev-lang/yasm ) + amd64? ( dev-lang/yasm )" +RDEPEND="" + +src_prepare() { + tc-export CC + epatch \ + "${FILESDIR}"/${PN}-2.6.0-yasm.patch \ + "${FILESDIR}"/${PN}-1.3.0-ABI-multilib.patch \ + "${FILESDIR}"/${PN}-2.5.1-automake-1.12.patch \ + "${FILESDIR}"/${PN}-2.6.0-gcc48.patch + + # In the same way there was QA regarding executable stacks + # with GMP we have some here as well. We cannot apply the + # GMP solution as yasm is used, at least on x86/amd64. + # Furthermore we are able to patch config.ac. + ebegin "Patching assembler files to remove executable sections" + local i + for i in $(find . -type f -name '*.asm') ; do + cat >> $i <<-EOF + #if defined(__linux__) && defined(__ELF__) + .section .note.GNU-stack,"",%progbits + #endif + EOF + done + + for i in $(find . -type f -name '*.as') ; do + cat >> $i <<-EOF + %ifidn __OUTPUT_FORMAT__,elf + section .note.GNU-stack noalloc noexec nowrite progbits + %endif + EOF + done + eend + eautoreconf +} + +src_configure() { + # beware that cpudetection aka fat binaries is x86/amd64 only. + # Place mpir in profiles/arch/$arch/package.use.mask + # when making it available on $arch. + myeconfargs+=( + $(use_enable cxx) + $(use_enable cpudetection fat) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/mpir/mpir-2.7.2.ebuild b/sci-libs/mpir/mpir-2.7.2.ebuild new file mode 100644 index 000000000000..f3e1deeb567d --- /dev/null +++ b/sci-libs/mpir/mpir-2.7.2.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs + +DESCRIPTION="Library for arbitrary precision integer arithmetic (fork of gmp)" +HOMEPAGE="http://www.mpir.org/" +SRC_URI="http://www.mpir.org/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0/16" +KEYWORDS="~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+cxx cpudetection static-libs" + +DEPEND=" + x86? ( dev-lang/yasm ) + amd64? ( dev-lang/yasm ) +" +RDEPEND="" + +PATCHES=( + "${FILESDIR}"/${P}-ABI-multilib.patch + "${FILESDIR}"/${P}-sed-backport.patch +) + +src_prepare() { + tc-export CC + + default + + # In the same way there was QA regarding executable stacks + # with GMP we have some here as well. We cannot apply the + # GMP solution as yasm is used, at least on x86/amd64. + # Furthermore we are able to patch config.ac. + ebegin "Patching assembler files to remove executable sections" + local i + for i in $(find . -type f -name '*.asm') ; do + cat >> $i <<-EOF + #if defined(__linux__) && defined(__ELF__) + .section .note.GNU-stack,"",%progbits + #endif + EOF + done + + for i in $(find . -type f -name '*.as') ; do + cat >> $i <<-EOF + %ifidn __OUTPUT_FORMAT__,elf + section .note.GNU-stack noalloc noexec nowrite progbits + %endif + EOF + done + eend + eautoreconf +} + +src_configure() { + # beware that cpudetection aka fat binaries is x86/amd64 only. + # Place mpir in profiles/arch/$arch/package.use.mask + # when making it available on $arch. + myeconfargs+=( + --with-system-yasm + $(use_enable cxx) + $(use_enable cpudetection fat) + $(use_enable static-libs static) + ) + econf ${myeconfargs[@]} +} + +src_install() { + default + rm "${ED}"/usr/$(get_libdir)/*la || die +} diff --git a/sci-libs/mpir/mpir-3.0.0.ebuild b/sci-libs/mpir/mpir-3.0.0.ebuild new file mode 100644 index 000000000000..14bfad90ba26 --- /dev/null +++ b/sci-libs/mpir/mpir-3.0.0.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools toolchain-funcs + +DESCRIPTION="Library for arbitrary precision integer arithmetic (fork of gmp)" +HOMEPAGE="http://www.mpir.org/" +SRC_URI="http://www.mpir.org/${P}.tar.bz2" + +LICENSE="LGPL-3" +SLOT="0/23" +KEYWORDS="~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+cxx cpudetection static-libs" + +DEPEND=" + x86? ( dev-lang/yasm ) + amd64? ( dev-lang/yasm ) +" +RDEPEND="" + +PATCHES=( + "${FILESDIR}"/${PN}-2.7.2-ABI-multilib.patch +) + +src_prepare() { + tc-export CC + default + # In the same way there was QA regarding executable stacks + # with GMP we have some here as well. We cannot apply the + # GMP solution as yasm is used, at least on x86/amd64. + # Furthermore we are able to patch config.ac. + ebegin "Patching assembler files to remove executable sections" + local i + for i in $(find . -type f -name '*.asm') ; do + cat >> $i <<-EOF + + #if defined(__linux__) && defined(__ELF__) + .section .note.GNU-stack,"",%progbits + #endif + EOF + done + + for i in $(find . -type f -name '*.as') ; do + cat >> $i <<-EOF + + %ifidn __OUTPUT_FORMAT__,elf + section .note.GNU-stack noalloc noexec nowrite progbits + %endif + EOF + done + eend + eautoreconf +} + +src_configure() { + # beware that cpudetection aka fat binaries is x86/amd64 only. + # Place mpir in profiles/arch/$arch/package.use.mask + # when making it available on $arch. + local myeconfargs+=( + $(use_enable cxx) + $(use_enable cpudetection fat) + $(use_enable static-libs static) + ) + econf ${myeconfargs[@]} +} + +src_install() { + default + use static-libs || rm -f "${ED}"/usr/$(get_libdir)/*la +} diff --git a/sci-libs/mumps/Manifest b/sci-libs/mumps/Manifest new file mode 100644 index 000000000000..4982395d6f53 --- /dev/null +++ b/sci-libs/mumps/Manifest @@ -0,0 +1,5 @@ +DIST MUMPS_4.10.0.tar.gz 2481516 SHA256 d0f86f91a74c51a17a2ff1be9c9cee2338976f13a6d00896ba5b43a5ca05d933 SHA512 348df048618ea2086fbe805a90f2e31f57e0db4aa6f4843a0e3c7142bac80fe45e54768e65921657c970bc286b59c2bca91e5006ed8000678f26ba2efe2bfda8 WHIRLPOOL 268a22811395b0a193eed90798ede8bc1a1478da25354711fbc8a220b5cfc3af78e0aedff787deb1592871ff450835533e1266393592056228fa8685f51f13fd +EBUILD mumps-4.10.0-r1.ebuild 5585 SHA256 b8942239fbb7ee16eea149932368f06a92f06973bd7a82d5fd7617d9df752364 SHA512 578f6584f115e6299bac629073701bd8534864693afa7c70f98ed6b0b4edc466e6f242733ec3baaec9b98c61f796a1d822ab10b2671fc90230fb2d73129310ea WHIRLPOOL b249d0df175ae9a00f764372fbafca4955adc66176868fff8dcc22e4cba106c347caa60c8ba489638b0e8d7f6b0ef527a2d92f0acd280c7ef176469d4f16ef83 +MISC ChangeLog 2822 SHA256 4f47bfea7b7b58a28ddf6e75bf689c7735d9463a89f3ae86e19c178d6a4b39ec SHA512 e0b8ff7a4f05ae2746e36d7c409cde67e1d3b893a69e4d6844a3cebc043bdf2686aef52cebac323b20f1b86fd9eb3ea12c28a7e40b97721cc7947052b80c47fd WHIRLPOOL 55296389a5a7fd37aea8d296f789d4be44f64a253f8fd6967f4e5e427f9d72b0120d8d6c1af886709713fceb7a4c256cbd25132aa1cc7dc66a200a31157e5d70 +MISC ChangeLog-2015 2173 SHA256 6f12d65292f1ed149c6ea606040f5956c9f326649122b4fbd550c846fc3f3ee2 SHA512 984fd66370ab1ba6ffdf3b1be7b1880ba3a9724a42f0849815eb95f82272420460a8257c6fcc15c4ce840d39f63468181b05bd5d1b8901e1d6a6902bd7c2c036 WHIRLPOOL bcc12de0c9841f5b6e7f6d5b27e281c379b460e9be658461c7c2cce9ec835d2a246f1d43a29caebfd57617fc22de963090083cceea2d707125ece879066cbefb +MISC metadata.xml 864 SHA256 5a0c2f8342f12c4ae6101439533ffc80850c5de547100106f4b2a9e289ed3179 SHA512 c285d7ed4bd26bb603f40f9d5e4e7262aea8a2679d14f65a4f8959a9bf2c622310422790e6221708fa227cd2c3bb2f4ba140eb5f23acc71b3f1ca20c04c4711a WHIRLPOOL a7da05ff251587017fc41f162ac74d7ef4cb7569a76f77c2157dc114dbc0b9de278c8938aafb6720fb52bed0fcc540a21acbb69cfacc75f1ca657876bbc7bf7b diff --git a/sci-libs/mumps/metadata.xml b/sci-libs/mumps/metadata.xml new file mode 100644 index 000000000000..6c7bab904ee4 --- /dev/null +++ b/sci-libs/mumps/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + MUltifrontal Massively Parallel sparse direct Solver implements a + direct solver for large sparse linear systems, with a particular + focus on symmetric positive definite matrices. It can operate on + distributed matrices e.g. over a cluster. It has Fortran and C + interfaces, and can interface with ordering tools such + as Scotch or Metis. +</longdescription> +<use> + <flag name="metis">Enable matrix ordering with METIS + (<pkg>sci-libs/metis</pkg>, <pkg>sci-libs/parmetis</pkg>)</flag> + <flag name="scotch">Enable matrix ordering with <pkg>sci-libs/scotch</pkg></flag> +</use> +</pkgmetadata> diff --git a/sci-libs/mumps/mumps-4.10.0-r1.ebuild b/sci-libs/mumps/mumps-4.10.0-r1.ebuild new file mode 100644 index 000000000000..d57d19e1d13d --- /dev/null +++ b/sci-libs/mumps/mumps-4.10.0-r1.ebuild @@ -0,0 +1,184 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs flag-o-matic versionator fortran-2 multilib + +MYP=MUMPS_${PV} + +DESCRIPTION="MUltifrontal Massively Parallel sparse direct matrix Solver" +HOMEPAGE="http://mumps.enseeiht.fr/" +SRC_URI="${HOMEPAGE}${MYP}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples metis mpi +scotch static-libs" + +RDEPEND=" + virtual/blas + metis? ( || ( sci-libs/metis <sci-libs/parmetis-4 ) + mpi? ( <sci-libs/parmetis-4 ) ) + scotch? ( <sci-libs/scotch-6[mpi=] ) + mpi? ( sci-libs/scalapack )" + +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MYP}" + +static_to_shared() { + local libstatic=${1}; shift + local libname=$(basename ${libstatic%.a}) + local soname=${libname}$(get_libname $(get_version_component_range 1-2)) + local libdir=$(dirname ${libstatic}) + + einfo "Making ${soname} from ${libstatic}" + if [[ ${CHOST} == *-darwin* ]] ; then + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ + -Wl,-all_load -Wl,${libstatic} \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + else + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + [[ $(get_version_component_count) -gt 1 ]] && \ + ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) + ln -s ${soname} ${libdir}/${libname}$(get_libname) + fi +} + +src_prepare() { + sed -e "s:^\(CC\s*=\).*:\1$(tc-getCC):" \ + -e "s:^\(FC\s*=\).*:\1$(tc-getFC):" \ + -e "s:^\(FL\s*=\).*:\1$(tc-getFC):" \ + -e "s:^\(AR\s*=\).*:\1$(tc-getAR) cr :" \ + -e "s:^\(RANLIB\s*=\).*:\1$(tc-getRANLIB):" \ + -e "s:^\(LIBBLAS\s*=\).*:\1$($(tc-getPKG_CONFIG) --libs blas):" \ + -e "s:^\(INCPAR\s*=\).*:\1:" \ + -e 's:^\(LIBPAR\s*=\).*:\1$(SCALAP):' \ + -e "s:^\(OPTF\s*=\).*:\1${FFLAGS} -DALLOW_NON_INIT \$(PIC):" \ + -e "s:^\(OPTC\s*=\).*:\1${CFLAGS} \$(PIC):" \ + -e "s:^\(OPTL\s*=\).*:\1${LDFLAGS}:" \ + Make.inc/Makefile.inc.generic > Makefile.inc || die + # fixed a missing copy of libseq to libdir +} + +src_configure() { + LIBADD="$($(tc-getPKG_CONFIG) --libs blas) -Llib -lpord" + local ord="-Dpord" + if use metis && use mpi; then + sed -i \ + -e "s:#\s*\(LMETIS\s*=\).*:\1$($(tc-getPKG_CONFIG) --libs parmetis):" \ + -e "s:#\s*\(IMETIS\s*=\).*:\1$($(tc-getPKG_CONFIG) --cflags parmetis):" \ + Makefile.inc || die + LIBADD="${LIBADD} $($(tc-getPKG_CONFIG) --libs parmetis)" + ord="${ord} -Dparmetis" + elif use metis; then + sed -i \ + -e "s:#\s*\(LMETIS\s*=\).*:\1$($(tc-getPKG_CONFIG) --libs metis):" \ + -e "s:#\s*\(IMETIS\s*=\).*:\1$($(tc-getPKG_CONFIG) --cflags metis):" \ + Makefile.inc || die + LIBADD="${LIBADD} $($(tc-getPKG_CONFIG) --libs metis)" + ord="${ord} -Dmetis" + fi + if use scotch && use mpi; then + sed -i \ + -e "s:#\s*\(LSCOTCH\s*=\).*:\1-lptesmumps -lptscotch -lptscotcherr:" \ + -e "s:#\s*\(ISCOTCH\s*=\).*:\1-I${EROOT}usr/include/scotch:" \ + Makefile.inc || die + LIBADD="${LIBADD} -lptesmumps -lptscotch -lptscotcherr" + ord="${ord} -Dptscotch" + elif use scotch; then + sed -i \ + -e "s:#\s*\(LSCOTCH\s*=\).*:\1-lesmumps -lscotch -lscotcherr:" \ + -e "s:#\s*\(ISCOTCH\s*=\).*:\1-I${EROOT}usr/include/scotch:" \ + Makefile.inc || die + LIBADD="${LIBADD} -lesmumps -lscotch -lscotcherr" + ord="${ord} -Dscotch" + fi + if use mpi; then + sed -i \ + -e "s:^\(CC\s*=\).*:\1mpicc:" \ + -e "s:^\(FC\s*=\).*:\1mpif90:" \ + -e "s:^\(FL\s*=\).*:\1mpif90:" \ + -e "s:^\(SCALAP\s*=\).*:\1$($(tc-getPKG_CONFIG) --libs scalapack):" \ + Makefile.inc || die + export LINK=mpif90 + LIBADD="${LIBADD} $($(tc-getPKG_CONFIG) --libs scalapack)" + else + sed -i \ + -e 's:-Llibseq:-L$(topdir)/libseq:' \ + -e 's:PAR):SEQ):g' \ + -e "s:^\(SCALAP\s*=\).*:\1:" \ + -e 's:^LIBSEQNEEDED =:LIBSEQNEEDED = libseqneeded:g' \ + Makefile.inc || die + export LINK="$(tc-getFC)" + fi + sed -i -e "s:^\s*\(ORDERINGSF\s*=\).*:\1 ${ord}:" Makefile.inc || die +} + +src_compile() { + # Workaround #462602 + export FAKEROOTKEY=1 + + # -j1 because of static archive race + emake -j1 alllib PIC="-fPIC" + if ! use mpi; then + #$(tc-getAR) crs lib/libmumps_common.a libseq/*.o || die + LIBADD+=" -Llibseq -lmpiseq" + static_to_shared libseq/libmpiseq.a + fi + static_to_shared lib/libpord.a ${LIBADD} + static_to_shared lib/libmumps_common.a ${LIBADD} + + local i + for i in c d s z; do + static_to_shared lib/lib${i}mumps.a -Llib -lmumps_common ${LIBADD} + done + if use static-libs; then + emake clean + emake -j1 alllib + fi +} + +src_test() { + emake all + local dotest + if use mpi; then + dotest="mpirun -np 2" + else + export LD_LIBRARY_PATH="${S}/libseq:${LD_LIBRARY_PATH}" + fi + cd examples + ${dotest} ./ssimpletest < input_simpletest_real || die + ${dotest} ./dsimpletest < input_simpletest_real || die + ${dotest} ./csimpletest < input_simpletest_cmplx || die + ${dotest} ./zsimpletest < input_simpletest_cmplx || die + einfo "The solutions should be close to (1,2,3,4,5)" + ${dotest} ./c_example || die + einfo "The solution should be close to (1,2)" + make clean +} + +src_install() { + dolib.so lib/lib*$(get_libname)* + use static-libs && dolib.a lib/lib*.a + insinto /usr + doins -r include + if ! use mpi; then + dolib.so libseq/lib*$(get_libname)* + insinto /usr/include/mpiseq + doins libseq/*.h + use static-libs && dolib.a libseq/libmpiseq.a + fi + dodoc README ChangeLog VERSION + use doc && dodoc doc/*.pdf + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/naga/Manifest b/sci-libs/naga/Manifest new file mode 100644 index 000000000000..d02abf70623a --- /dev/null +++ b/sci-libs/naga/Manifest @@ -0,0 +1,5 @@ +DIST naga-2.1.tar.bz2 22102 SHA256 5ccae8052db24f1265d690ea9fd96005f835c5427a66737922eed188ea2bfd95 SHA512 3f8ca39fa7688f75043989546c9ee17de885e8ba1919e218d6a720f1240155c6eaf4a4d79876c11af2b7d15b510881ba67d33bef4ea30c9c343fc7eeb07478ba WHIRLPOOL 6114b00e824631bedf70e2d1fd8b9ec17bc7303ab21271fc9877b08a43dfb47a506a4c604015065fd2770d62b0209511d06b2cf56146bd467e5b80baad88cd5c +EBUILD naga-2.1.ebuild 556 SHA256 1cd27eff7375f0f233153deda55c35ce74e1c31f0bf606ffde3a20cbec101e20 SHA512 a0714ea3ab0556d0bdd1533d90fa6fe317ede12286d37f841d3723536557958cb6fcaaea18a8f4b5d6c01f65bf505f8456ba002703a268c59bd831d6193916f7 WHIRLPOOL 8dd1c2bdce657d1ae41da61f9960fc8c602385418696613f47c02c90a189eb37bfb44c423571b829d16555f6c152f2f243f0a15d5c0615d92b28464d1e943a93 +MISC ChangeLog 2827 SHA256 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+DESCRIPTION="Simplified Java NIO asynchronous sockets" +HOMEPAGE="https://code.google.com/p/naga/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +DEPEND=">=virtual/jdk-1.5 + dev-java/ant-core" +RDEPEND=">=virtual/jre-1.5" + +src_compile() { + eant build +} + +src_install() { + java-pkg_newjar _DIST/${PN}-${MY_PVR}.jar ${PN}.jar +} diff --git a/sci-libs/nanoflann/Manifest b/sci-libs/nanoflann/Manifest new file mode 100644 index 000000000000..363d831c83b5 --- /dev/null +++ b/sci-libs/nanoflann/Manifest @@ -0,0 +1,4 @@ +DIST nanoflann-1.2.3.tar.gz 1157793 SHA256 5ef4dfb23872379fe9eb306aabd19c9df4cae852b72a923af01aea5e8d7a59c3 SHA512 01d5226fb669c9ef21e1bd36bddb07c7bf8bbbf9798e90bfa7966de4ae01e05c669c33a73d37340c41c79fcab81c91c3991077d799a211985b2d0a2a365a8878 WHIRLPOOL 2a1c9a21dbd7571e4c680a2b5e3636086df4e06142d885b390983228a3cf3d36f01d0389fe712f1d9a9106a55887353a1ea7c057a289c727e98b9bf5308c1b20 +EBUILD nanoflann-1.2.3.ebuild 668 SHA256 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This library is a fork + (and a subset) of the <pkg>sci-libs/flann</pkg> library. + </longdescription> + <upstream> + <remote-id type="github">jlblancoc/nanoflann</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/nanoflann/nanoflann-1.2.3.ebuild b/sci-libs/nanoflann/nanoflann-1.2.3.ebuild new file mode 100644 index 000000000000..e82a84965d8b --- /dev/null +++ b/sci-libs/nanoflann/nanoflann-1.2.3.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +DESCRIPTION="C++ header-only library for Nearest Neighbor (NN) search wih KD-trees" +HOMEPAGE="https://github.com/jlblancoc/nanoflann" +SRC_URI="https://github.com/jlblancoc/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="dev-cpp/eigen:*" +DEPEND="${RDEPEND}" + +src_prepare() { + eapply_user + + # do not compile examples + sed -ie 's/add_subdirectory(examples)//g' CMakeLists.txt || die "sed failed" +} + +src_test() { + cd "${BUILD_DIR}" && emake -j1 test +} + +src_compile() { + : +} diff --git a/sci-libs/nanoflann/nanoflann-9999.ebuild b/sci-libs/nanoflann/nanoflann-9999.ebuild new file mode 100644 index 000000000000..2c8467c00469 --- /dev/null +++ b/sci-libs/nanoflann/nanoflann-9999.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +DESCRIPTION="C++ header-only library for Nearest Neighbor (NN) search wih KD-trees" +HOMEPAGE="https://github.com/jlblancoc/nanoflann" + +if [[ ${PV} = *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="git://github.com/jlblancoc/nanoflann.git" + SRC_URI="" + KEYWORDS="" +else + SRC_URI="https://github.com/jlblancoc/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="BSD" +SLOT="0" +IUSE="" + +RDEPEND="dev-cpp/eigen:*" +DEPEND="${RDEPEND}" + +src_prepare() { + eapply_user + + # do not compile examples + sed -ie 's/add_subdirectory(examples)//g' CMakeLists.txt || die "sed failed" +} + +src_test() { + cd "${BUILD_DIR}" && emake -j1 test +} + +src_compile() { + : +} diff --git a/sci-libs/neartree/Manifest b/sci-libs/neartree/Manifest new file mode 100644 index 000000000000..3b019e3f4604 --- /dev/null +++ b/sci-libs/neartree/Manifest @@ -0,0 +1,6 @@ +AUX CMakeLists.txt 713 SHA256 32ad9057abd52e07eb1d6870467e3903b7c5ba3e99f8a26a05e62d7b9ecb16a1 SHA512 038c8e23c642c6e5f6651b9c2cf29f8764a983294b9add97f9af8ac5d14ee52c1b47afa45791a21e8d783cb0e74801df17a34c1fbb08df1d7dd27ef2b4825b94 WHIRLPOOL 6c7609bf400d471ebf15db701ded2bff6fe30d8fa05bf676a8bb862502ac6e558782967513974a02930c0e45cf053af3f5285752689ed41fc321a2dcc8babf71 +DIST neartree-5.1.1.tar.gz 167695 SHA256 b951eb23bb4235ada82cef85b9f129bf74a14e45d992097431e7bfb6bdca6642 SHA512 36f2ab878319153440914325bed67d111dafcac724cbef73d439285f4ad82979b05d2987fa3802c440aa4a037499bf7961ef9b09fa3658364731b5a405854b00 WHIRLPOOL 1b878510835bd5139483f9ba27a61376bed0640af18e4f9f77f729bb880b7d3cac7d4a473954eb58645faeb512c92529fd9a300dde413b6872415d7ada5db2cd +EBUILD neartree-5.1.1.ebuild 718 SHA256 83c821640b5972ea6a00809647bfc20a29db19b82043c8f5c84b445e12d9a665 SHA512 24378cc8d83400f118dc5f8a56e727b00d3e322051b88db25a317283076f23036e83023c0cc2a2c9807b233c4fbbd380bde95fae29ef6c14229ba91cddeabc8e WHIRLPOOL a7c6d7ae61deaea1f99a4c2fd44694dd3b0efb0dd6708f174c96125de0bcbb9b21b13a42b00ca1733d4f6549d3b4170a682a82664048167ad0e8d705e725cb02 +MISC ChangeLog 3062 SHA256 cc41ad05c5c05baaaf3a2a3ebeb401a4488a161fe8d90da6de9d6567ccb0f83c SHA512 c63a287c3f0893382fe960ab37f3d09071bda189f1768d4e288d61d8d5172bfcb120ea6d3fcc3de27a9e84432123bf5302a71b4d7124e7ad90c370fc7a9080e8 WHIRLPOOL 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000000000000..cb4375da7964 --- /dev/null +++ b/sci-libs/neartree/files/CMakeLists.txt @@ -0,0 +1,21 @@ +cmake_minimum_required(VERSION 2.8) +project (Neartree C) + +SET (LIB_MAJOR 5) +SET (LIB_MINOR 1) +SET (LIB_RELEASE 0) + +SET (_soversion ${LIB_MAJOR}.${LIB_MINOR}.${LIB_RELEASE}) + +include_directories ("${PROJECT_SOURCE_DIR}") + +add_library(CNearTree SHARED CNearTree.c) +target_link_libraries(CNearTree CVector m) + +set_target_properties(CNearTree PROPERTIES SOVERSION ${LIB_MAJOR} VERSION ${_soversion}) + +INSTALL(TARGETS CNearTree DESTINATION ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}) +install(FILES CNearTree.h rhrand.h TNear.h triple.h + DESTINATION ${CMAKE_INSTALL_PREFIX}/include) +install(FILES README_NearTree.txt DESTINATION ${DOC_DIR}) +install(FILES README_NearTree.html index.html DESTINATION ${DOC_DIR}/html) diff --git a/sci-libs/neartree/metadata.xml b/sci-libs/neartree/metadata.xml new file mode 100644 index 000000000000..be72ab17e93d --- /dev/null +++ b/sci-libs/neartree/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">neartree</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/neartree/neartree-5.1.1.ebuild b/sci-libs/neartree/neartree-5.1.1.ebuild new file mode 100644 index 000000000000..b9631c226128 --- /dev/null +++ b/sci-libs/neartree/neartree-5.1.1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils + +MY_PN=NearTree +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Function library efficiently solving the Nearest Neighbor Problem" +HOMEPAGE="http://neartree.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz -> ${P}.tar.gz" +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +RDEPEND="dev-libs/cvector" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + default + cp "${FILESDIR}"/CMakeLists.txt . || die +} + +src_configure() { + local mycmakeargs=( -DDOC_DIR="${EPREFIX}/usr/share/doc/${PF}" ) + cmake-utils_src_configure +} diff --git a/sci-libs/nemesis/Manifest b/sci-libs/nemesis/Manifest new file mode 100644 index 000000000000..f3593a77f5fb --- /dev/null +++ b/sci-libs/nemesis/Manifest @@ -0,0 +1,9 @@ +AUX nemesis-5.22b-multilib.patch 1885 SHA256 54045fa277eb349ae3c308ca10e1c8b358e5c5d95e37132c504ca49fec5b8085 SHA512 d068f9d2f35b306fe9c57b41a065c8c6aea85bfa1f0b4d42c538a17c3563840c014cc0b0f93da79a5bfd98d5c8e6007d6f99d03e92aa534278b90871e7da663d WHIRLPOOL 20269e21e7d7e3f8f0c227d06c4e5a6ee3961b7d0577fd3c736d479494a602a5e679ef472e74392968dc37c7ac67807544bbef92522fd19f4b724da18da710b2 +AUX nemesis-6.09-multilib.patch 1649 SHA256 8f78e764726eab183c86b7f7b23ccb5e29dd7d7b50648977dc9172825b9999b3 SHA512 db01d3afe33bc2f30868e5ceceb4fbe5a0eb10c08b39a72f2d3cb0d363eb837c79bd62e4590a0013602419ecfcb6dcc33eaf656e670d2b25600409e8b07890e7 WHIRLPOOL 9bfb5690fa935aa8fdb4248a54a6952ed35772944fbc802800ba6170a78a30f6635c55bbf36cc6585c80520767b5d8205fee5272313a7ec659dfb5f4947025d2 +DIST exodus-5.24.tar.bz2 4252980 SHA256 c16a70c0572341c7e680f8d6420c79e1fd744ba717dc4f7e023f7421c636515d SHA512 d31cf17d2112b625259a70a7f73609323b94a3eed77be3b09961e67518d1b8caf82617a18f8c651fa6549988aa9a02455aea04402463b4fb7e66dd4e15b7e87e WHIRLPOOL 5a622fce123d55187c0895934db76c2cfb3ab2e83e13d6f5b6655c388e7cac1107acaa786b75be5275de7398035a5604d0be2975c78da05edbdaa4f8efbf9513 +DIST exodus-6.09.tar.gz 4757028 SHA256 e14db4c1e2ca893c4602055036b827b8332746439f0869489fdc677058faebe8 SHA512 a48c02952b0edfae416e9b3f77471558dd2d60177471eca3de32890d11afabe3cfb64396de83e728327d43bbea83969ebcdd8ea516a3b9a6ed7353d4cc940516 WHIRLPOOL 97426e487c8f6ae31da4be36f3712ade99eb7e31feb67d3989153dadc394b427b8e38976f06e99c153fae3d04b05357b48b0b537ff0c04fb8199b9aaeb27bcc4 +EBUILD nemesis-5.24.ebuild 1073 SHA256 c5407e25b2c14df851cfd21e54b5c520f466bf8949f48b94f324919b7e1d8dbc SHA512 181b306208310225bd22dc328f7dc40c49279ff70a8b504063df2031a5e6ce4eae91b68d54699d6d39a8ba4f72738668dad71b17c0977eaa85dd741039e6bab6 WHIRLPOOL 84fe892784426423438905e5e9740c1f9ed8c7f0143e45384c80000e0f6fdfa1f351a430d37cbbf82a3f3570aa370fd991375ad18e4c665e8f756845babd002d +EBUILD nemesis-6.09.ebuild 994 SHA256 a50e104b9c5823b5de38d8088fb5b8f7e390dc826584b69f1efae7c01225b914 SHA512 e9e6e4c3d6c56816144f2d3ef8104a452fa042ec97484b619b0b4c9dee614896a41b89e6625c6c5dbbd57f041ff90ed9e53e3b863417620c7ff5ac0805153ac7 WHIRLPOOL 41a316678822a7547b74ed8f946c2d7f88bd09b3fcbc861104e9752709379956ca4d39bdd1821c307f82c682617322ffc3e24ca9e1aebd8a36cd8079a982ff2c +MISC ChangeLog 3022 SHA256 9bd3e5af3db1ed3d1f9826d975a802dc2234e29ced37ab5e8bb9b5642ef0994c SHA512 2b9787f06ea9ac06bcd08b4358c4968f8ed1f1936e45c6b23bcbb9d0f326e57a49a57d7f7a1bdbecacb0401059283d9625f4240793b229fbaec9d4d6ff99e8aa WHIRLPOOL c5a59700c07f8924dcc4f3bdcf4db02dba0a4a0c2e5c815cf7a5a5098e31e1bccb85aae00a70d98027d4e1eededdaa20dff2c646c5a41cdd6089c5400a885fb1 +MISC ChangeLog-2015 570 SHA256 faedc18241d9a19dfb4acd0d107d51ef9db65690ffbc1f779089330b80d082dd SHA512 f421a7feb70d8fb09e30e9e112d6f238b6f946869f6df4ceb6606c8e950f87a4f73655b0f776ce57170cf7e4e3ebc63ecd52ee8a258b1f54a2ec88a5ccbc87b2 WHIRLPOOL 9c9fcb9df27569588cd5c40f8511c9850d3c0b15c99d84f670be4d849b3d7f477016315dbbef6eccffefbe28994fc928e7ea5a895dd9f2693d8c9673f9f7975f +MISC metadata.xml 1055 SHA256 e0918972f38e9df06449110b1a42c9ab83f3595753b16ed2e14191f416b07769 SHA512 bf7702146727a7449c7a0988d64f0036809e3688801a2cca42a8f7a442e4f1f204c0101e50c3ffc98e4a04ee13cc01105c12bad3a480a0179574ae4d1ff6ac14 WHIRLPOOL 72acbbe7f1dd54facb0d189dc1dac18b5507d4ee7c6ec295d3028fc7663eaef55afbbc23e8b71eced013b7f978e251d0ed7cc3723d41a1306ad44d83e79b09a9 diff --git a/sci-libs/nemesis/files/nemesis-5.22b-multilib.patch b/sci-libs/nemesis/files/nemesis-5.22b-multilib.patch new file mode 100644 index 000000000000..b99add01ea56 --- /dev/null +++ b/sci-libs/nemesis/files/nemesis-5.22b-multilib.patch @@ -0,0 +1,57 @@ + nemesis/CMakeLists.txt | 15 ++++++++------- + 1 file changed, 8 insertions(+), 7 deletions(-) + +diff --git a/nemesis/CMakeLists.txt b/nemesis/CMakeLists.txt +index 64aff5d..bed5ede 100644 +--- a/nemesis/CMakeLists.txt ++++ b/nemesis/CMakeLists.txt +@@ -19,7 +19,7 @@ find_path( NETCDF_INCLUDE_DIR netcdf.h + find_library( NETCDF_LIBRARY netcdf + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/${CMAKE_INSTALL_LIBDIR} + $ENV{NETCDF_DIR}/libsrc/.libs + ) + +@@ -29,16 +29,17 @@ find_program (NETCDF_NCDUMP ncdump + $ENV{NETCDF_DIR}/ncdump + ) + +-find_library( EXODUS_LIBRARY exodus ++find_library( EXODUS_LIBRARY exoIIv2c + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib ++ $ENV{EXODUS_DIR}/${CMAKE_INSTALL_LIBDIR} + ) + + # Hack for HDF5 + find_library( HDF5_LIBRARY hdf5 + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/${CMAKE_INSTALL_LIBDIR} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) +@@ -46,7 +47,7 @@ find_library( HDF5_LIBRARY hdf5 + find_library( HDF5HL_LIBRARY hdf5_hl + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/${CMAKE_INSTALL_LIBDIR} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) +@@ -79,8 +80,8 @@ ADD_EXECUTABLE(ne_test ne_ctest_wrap.c) + TARGET_LINK_LIBRARIES( ne_test nemesis ${EXODUS_LIBRARY} ${NETCDF_LIBRARY} ${HDF5HL_LIBRARY} ${HDF5_LIBRARY} ${Z_LIBRARY} ${MATH_LIBRARY}) + + INSTALL(TARGETS nemesis +- RUNTIME DESTINATION lib COMPONENT Runtime +- LIBRARY DESTINATION lib COMPONENT Runtime +- ARCHIVE DESTINATION lib COMPONENT Development) ++ RUNTIME DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Runtime ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Runtime ++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development) + INSTALL(FILES ${HEADERS} DESTINATION include COMPONENT Development) + diff --git a/sci-libs/nemesis/files/nemesis-6.09-multilib.patch b/sci-libs/nemesis/files/nemesis-6.09-multilib.patch new file mode 100644 index 000000000000..d0f05f23a2d2 --- /dev/null +++ b/sci-libs/nemesis/files/nemesis-6.09-multilib.patch @@ -0,0 +1,53 @@ + nemesis/CMakeLists.txt | 15 ++++++++------- + 1 file changed, 8 insertions(+), 7 deletions(-) + +diff --git a/nemesis/CMakeLists.txt b/nemesis/CMakeLists.txt +index 64aff5d..bed5ede 100644 +--- a/nemesis/CMakeLists.txt ++++ b/nemesis/CMakeLists.txt +@@ -19,7 +19,7 @@ + find_library( NETCDF_LIBRARY netcdf + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/${CMAKE_INSTALL_LIBDIR} + $ENV{NETCDF_DIR}/libsrc/.libs + ) + +@@ -33,13 +33,14 @@ + ../exodusii/cbind/ + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib ++ $ENV{EXODUS_DIR}/${CMAKE_INSTALL_LIBDIR} + ) + + # Hack for HDF5 + find_library( HDF5_LIBRARY hdf5 + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/${CMAKE_INSTALL_LIBDIR} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) +@@ -47,7 +48,7 @@ + find_library( HDF5HL_LIBRARY hdf5_hl + $ENV{ACCESS}/lib/shared + $ENV{ACCESS}/lib +- $ENV{NETCDF_DIR}/lib ++ $ENV{NETCDF_DIR}/${CMAKE_INSTALL_LIBDIR} + $ENV{NETCDF_DIR}/libsrc/.libs + /usr/local/hdf5/lib + ) +@@ -80,8 +81,8 @@ + TARGET_LINK_LIBRARIES( ne_test nemesis ${EXODUS_LIBRARY} ${NETCDF_LIBRARY} ${HDF5HL_LIBRARY} ${HDF5_LIBRARY} ${Z_LIBRARY} ${MATH_LIBRARY}) + + INSTALL(TARGETS nemesis +- RUNTIME DESTINATION lib COMPONENT Runtime +- LIBRARY DESTINATION lib COMPONENT Runtime +- ARCHIVE DESTINATION lib COMPONENT Development) ++ RUNTIME DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Runtime ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Runtime ++ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT Development) + INSTALL(FILES ${HEADERS} DESTINATION include COMPONENT Development) + diff --git a/sci-libs/nemesis/metadata.xml b/sci-libs/nemesis/metadata.xml new file mode 100644 index 000000000000..9599a858f64b --- /dev/null +++ b/sci-libs/nemesis/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +NEMESIS is an enhancement to the EXODUSII finite element database +model used to store and retrieve data for unstructured parallel finite +element analyses. NEMESIS adds data structures which facilitate the +partitioning of a scalar (standard serial) EXODUSII file onto parallel +disk systems found on many parallel computers. Since the NEMESIS +application programming interface (API) can be used to append +information to an existing EXODUSII database, any existing software +that reads EXODUSII files can be used on files which contain NEMESIS +information. The NEMESIS information is written and read via C or C++ +callable functions which compromise the NEMESIS I API. +</longdescription> + <upstream> + <remote-id type="sourceforge">exodusii</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/nemesis/nemesis-5.24.ebuild b/sci-libs/nemesis/nemesis-5.24.ebuild new file mode 100644 index 000000000000..7a5a5b95805c --- /dev/null +++ b/sci-libs/nemesis/nemesis-5.24.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils multilib + +MY_PN="exodus" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Enhancement to the EXODUSII finite element database model" +HOMEPAGE="https://sourceforge.net/projects/exodusii/" +SRC_URI="mirror://sourceforge/project/${MY_PN}ii/${MY_P}.tar.bz2" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs test" + +DEPEND=" + sci-libs/exodusii + sci-libs/netcdf" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${MY_P}/${PN} + +PATCHES=( "${FILESDIR}"/${PN}-5.22b-multilib.patch ) + +src_prepare() { + find ../exodus -delete || die + cmake-utils_src_prepare + sed -i 's/exoIIv2c/NAMES exodus &/' CMakeLists.txt || die +} + +src_configure() { + mycmakeargs="${mycmakeargs} + -DLIB_INSTALL_DIR=$(get_libdir) + -DNETCDF_DIR="${EPREFIX}/usr/" + -DEXODUS_DIR="${EPREFIX}/usr/" + $(cmake-utils_use !static-libs BUILD_SHARED_LIBS) + $(cmake-utils_use test BUILD_TESTING)" + cmake-utils_src_configure +} + +src_test() { + "${BUILD_DIR}"/ne_test || die +} diff --git a/sci-libs/nemesis/nemesis-6.09.ebuild b/sci-libs/nemesis/nemesis-6.09.ebuild new file mode 100644 index 000000000000..4bd332e3b01c --- /dev/null +++ b/sci-libs/nemesis/nemesis-6.09.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils multilib + +MY_PN="exodus" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Enhancement to the EXODUSII finite element database model" +HOMEPAGE="https://sourceforge.net/projects/exodusii/" +SRC_URI="mirror://sourceforge/project/${MY_PN}ii/${MY_P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs test" + +DEPEND=" + sci-libs/exodusii + sci-libs/netcdf" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/${MY_P}/${PN} + +PATCHES=( "${FILESDIR}"/${P}-multilib.patch ) + +src_prepare() { + find ../exodus -delete || die + cmake-utils_src_prepare +} + +src_configure() { + mycmakeargs=( + -DLIB_INSTALL_DIR=$(get_libdir) + -DNETCDF_DIR="${EPREFIX}/usr/" + -DEXODUS_DIR="${EPREFIX}/usr/" + $(cmake-utils_use !static-libs BUILD_SHARED_LIBS) + $(cmake-utils_use test BUILD_TESTING) + ) + cmake-utils_src_configure +} + +src_test() { + "${BUILD_DIR}"/ne_test || die +} diff --git a/sci-libs/netcdf-cxx/Manifest b/sci-libs/netcdf-cxx/Manifest new file mode 100644 index 000000000000..8411225406e1 --- /dev/null +++ b/sci-libs/netcdf-cxx/Manifest @@ -0,0 +1,9 @@ +AUX netcdf-cxx-4.2-config.patch 829 SHA256 ebbd4e5f6dd84b8baf1187aa28983740c9714117469a6d243eb5e705a5b6dcfb SHA512 80d0a436103c8408898c065079f3988f706505bace1567a9eff1f5964cac3a09a97f8449b9dcd5bd994d1e3c6e9dfb646d8fcdfb0c5f659cdc64e0800234810f WHIRLPOOL 569bb744dd90ef7f4e11644791644a3467bb68e9d67fc6f6bca7127e0918f938056050bfdf6c1e6982f90efa27cd6c1654a9ac14d22cca3a27e74ebc1e1ea04a +DIST netcdf-cxx-4.2.1.tar.gz 456547 SHA256 bad56abfc99f321829070c04aebb377fc8942a4d09e5a3c88ad2b6547ed50ebc SHA512 d51ab1cbda74db5f7b074799d2407d0214d1c920af780ae3bb7a47b3708e45f721be7eec61902e035968a9df5019a7b2b5a10f236f6bab4cb47a26e4e7867adb WHIRLPOOL b7787c2529b7a1be2523931fcafdff4f78562fbd11c4ad7e9bc318c1b856235413d8a45c2f58b07ca20a7a22e1e020251b11ac688cddae8cd04766005c4f08c8 +DIST netcdf-cxx-4.2.tar.gz 703482 SHA256 95ed6ab49a0ee001255eac4e44aacb5ca4ea96ba850c08337a3e4c9a0872ccd1 SHA512 347ddbc518ac2186868d69417342e5146e285fc3a88f7c55edc33063f5c9a6647af7e512a03b9b6a8f67a448b85a1edcdde5df707b893f6a1527821cfd78e643 WHIRLPOOL 783120762a26663377684cc7898749073b4431d6aa25fd2ff97b6ac12224dbc5303392fcdfafb2a4d841cd09dd90b723af4ebce1f32f8513bce19990bb9420bc +EBUILD netcdf-cxx-4.2-r300.ebuild 608 SHA256 086bc9eff2eea0d18b781990c9b1a5b8ddaa562bfbe194e6ab6cdd920f9e1c83 SHA512 a916e243fabe91c34acd9db64e650b4ddc0a29c5130245417ba9891c9a25b9d57a591ea6f4c39e0e3baf24fc468329d4523aba751879967b5b5bc1a1826fb300 WHIRLPOOL 11cf64ac55f6f88c3b8e8ff4bca945759e654b64fc115cb4bd30dd12c6aa46073f135d4ad174a4c338bc580f6691a14eb22aa382087dc10dcbf26b5aa96579b4 +EBUILD netcdf-cxx-4.2.1-r1.ebuild 724 SHA256 39315a9d4fde50d256019e31d2fdcde8e0828ce671f321f00209f4ebf2344102 SHA512 f26e47e42927b90eb36a070fe986c4ac07bf0b548c4213adfbdcf0547c5fef3d31f8632629ffb780bd8709c83f1fe03c043d4d3c441112b1174f8db973a0f89d WHIRLPOOL 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netcdf-cxx4-4.2.1/ncxx4-config.in 2013-01-10 10:49:22.856926765 -0800 +@@ -5,7 +5,7 @@ + + prefix=@prefix@ + exec_prefix=${prefix} +-libdir=${exec_prefix}/lib ++libdir=@libdir@ + includedir=${prefix}/include + + cc="@CC@" +@@ -13,7 +13,7 @@ + fc="@FC@" + cflags=" -I${includedir} @CPPFLAGS@" + fflags="@FFLAGS@ @MOD_FLAG@${includedir}" +-libs="-L${libdir} @NC_LIBS@" ++libs="-L${libdir} @NC_LIBS@ -lnetcdf" + flibs="-L${libdir} @NC_FLIBS@" + has_dap="@HAS_DAP@" + has_nc2="@HAS_NC2@" +--- netcdf-cxx4-4.2.1/netcdf-cxx4.pc.in.orig 2013-01-10 10:46:50.995177250 -0800 ++++ netcdf-cxx4-4.2.1/netcdf-cxx4.pc.in 2013-01-10 10:49:45.030036161 -0800 +@@ -10,4 +10,4 @@ + Version: @PACKAGE_VERSION@ + Libs: -L${libdir} @NC_LIBS@ + Cflags: -I${includedir} +- ++Requires: netcdf diff --git a/sci-libs/netcdf-cxx/metadata.xml b/sci-libs/netcdf-cxx/metadata.xml new file mode 100644 index 000000000000..534ebb4466b0 --- /dev/null +++ b/sci-libs/netcdf-cxx/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + NetCDF (network Common Data Form) is an interface for scientific + data access and a freely-distributed software library that provides an + implementation of the interface. The netCDF library also defines a + machine-independent format for representing scientific data. + Together, the interface, library, and format support the creation, + access, and sharing of scientific data. + This is the C++ library which links to the C library. + </longdescription> + <upstream> + <remote-id type="github">Unidata/netcdf-cxx4</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/netcdf-cxx/netcdf-cxx-4.2-r300.ebuild b/sci-libs/netcdf-cxx/netcdf-cxx-4.2-r300.ebuild new file mode 100644 index 000000000000..5e1d1c252b1a --- /dev/null +++ b/sci-libs/netcdf-cxx/netcdf-cxx-4.2-r300.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils versionator + +DESCRIPTION="C++ library for netCDF" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="https://www.unidata.ucar.edu/downloads/netcdf/ftp/${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="3" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +IUSE="examples static-libs" + +RDEPEND=">=sci-libs/netcdf-4.2" +DEPEND="${RDEPEND}" + +src_install() { + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/netcdf-cxx/netcdf-cxx-4.2.1-r1.ebuild b/sci-libs/netcdf-cxx/netcdf-cxx-4.2.1-r1.ebuild new file mode 100644 index 000000000000..5d0ad2c8c24f --- /dev/null +++ b/sci-libs/netcdf-cxx/netcdf-cxx-4.2.1-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils + +MYP=${PN}4-${PV} + +DESCRIPTION="C++ library for netCDF" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="https://github.com/Unidata/netcdf-cxx4/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0/1" +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux" +IUSE="examples static-libs" + +RDEPEND=">=sci-libs/netcdf-4.2:=[hdf5]" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYP}" + +PATCHES=( + "${FILESDIR}/${PN}-4.2-config.patch" +) + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + use examples && dodoc -r examples + prune_libtool_files +} diff --git a/sci-libs/netcdf-cxx/netcdf-cxx-4.2.1.ebuild b/sci-libs/netcdf-cxx/netcdf-cxx-4.2.1.ebuild new file mode 100644 index 000000000000..0cff763395d2 --- /dev/null +++ b/sci-libs/netcdf-cxx/netcdf-cxx-4.2.1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +MYP=${PN}4-${PV} + +DESCRIPTION="C++ library for netCDF" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="https://github.com/Unidata/netcdf-cxx4/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0/1" +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux" +IUSE="examples static-libs" + +RDEPEND=">=sci-libs/netcdf-4.2:=" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/${MYP}" + +PATCHES=( "${FILESDIR}"/${PN}-4.2-config.patch ) + +src_install() { + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} + +src_test() { + autotools-utils_src_test -j1 +} diff --git a/sci-libs/netcdf-fortran/Manifest b/sci-libs/netcdf-fortran/Manifest new file mode 100644 index 000000000000..3649ff88d71e --- /dev/null +++ b/sci-libs/netcdf-fortran/Manifest @@ -0,0 +1,9 @@ +DIST netcdf-fortran-4.2.tar.gz 2479928 SHA256 069e1a0fb50972f28309210987a51563369a6ddb4ac768ef76e599354d384ae9 SHA512 af5d489df7b3ff5c3208115af4abdbf12d74d6bc0b9e3c729cfd24b55efafc3766de21c0f9957e037c25726637e9129a1f7009676e81d7e59650fec56d6e776e WHIRLPOOL 7fd0b2e0025b298a221521987132d389e6fc1bb285318d732b238ebcceedd721741f715848d63266c4a20189f4b0d211585af33e2efed2cac89dd893b07a2418 +DIST netcdf-fortran-4.4.2.tar.gz 1246344 SHA256 f2264174074af0cf332b8dd09e4e184517a2d54f0ca5500e17691152c1ed73aa SHA512 c3f025c0f5a08a0141fa09f570c647fc63992f9fd707969b37c7b0590c3578172200e45ecee497ed054129366fd1c73e3cd069aba879015b13a143e77a181c0f WHIRLPOOL 119345cf7563c15e9d088fc734c3dcbe27c2f76a52ea4479fb771d652815e1cda38914368478f055d2b5d705e7b1779e0954b2f26bb54dab4a995b8c6ebace8a +DIST netcdf-fortran-4.4.3.tar.gz 1286951 SHA256 4170fc018c9ee8222e317215c6a273542623185f5f6ee00d37bbb4e024e4e998 SHA512 94f51b4be889d6a9d6a86e3fcb2639ac58288969160d0f334ed6965e3c9cbacff7289b1fc54ed06e6ec8b845b19f5c409fbdcab432c8edf5c96efde887920924 WHIRLPOOL 941da12bc082ca75e33a1481aeb9992b16f3e95cf3f95bacc8ab1f56b95da7d9bb80d1f36b2a6d478f859d03bec5acec4a12ee13b218dc023ecdab5d0ecef788 +EBUILD netcdf-fortran-4.2.ebuild 807 SHA256 a579e72c8ad0948d8c5e3e37cae60d96105b0eeaf1b3d0e9e3c1519fc68c268e SHA512 994fcb3ae059f99d0276adbc4c9d11e349fc6cf25d9d1c5e9b7a6d8d6143fe413a6aeb9d9ed6101b491c19878a4d744bcde4baa5e36d2e9c0db68657512b9e29 WHIRLPOOL d6b48d4d26cec74eb533401605b037eb3c7fbd71c02ea7a0b24e82a1c38dfd5e75ac90dbaad4d1571f474ec2aba0dcefafe42d5df938f70381a60f58128c6543 +EBUILD netcdf-fortran-4.4.2.ebuild 836 SHA256 63c53b9012b0567b79ee852bb3595a3aec83a25272c70aac541f3ddf96a4864c SHA512 cb81a810b053ecbe2b9c0024c6eda2c694de059f00ec44482cc56a0f9f539ba46275d0a75e380a42d1b800dfe517d8292c14e67c7d7b226bbc75099d659abd7a WHIRLPOOL e0c379528274ac72f7110e81100efab40715268232c1eab2def7a4072b242077805af15c6f37864c55dd56b424c3da051c702e387ed5afc76047d12e924e1c2d +EBUILD netcdf-fortran-4.4.3.ebuild 817 SHA256 6524cb5ed7825669aeae02c315ffc330449603bd26ed6064018a4c6ad1c24c5f SHA512 c83f05cead2c1d483020ab0eb988fe1d73b5fdc0c52c1173232da216b2066e54d6892fcfd13816b114d979297bea857e603c3cd766dbc2fc0de6fd72fef3c2bb WHIRLPOOL d54c2d8febc0daa9bb25ee37a874c1d8f71d1e1f574875874a8ba66e96a033f29b60c449a39c217e4c82f2ef73ab1c74bd00229aa759ce255732536721ab3c32 +MISC ChangeLog 2954 SHA256 fff23f16ae934520cd0ce7fe50e8245b42df00ec390f539d1b355a6853f73572 SHA512 5ae6a68420fe42c8e7ef8b53a4148d4d3219bdb69c596b6bab1a5422616e0cd6f10436e5812da84474fb61ce7081feffff822bfe313d541e14bb38ee05dd5c29 WHIRLPOOL 58cb940be0ebfff15134a5596b6d66ce221486efae2bc56c990b4a225a9473542e57fac744014b17a84211ae0eb450a0c10df8ce50573f6650b5556285decb3f +MISC ChangeLog-2015 1149 SHA256 4724bb08bb60fcb3a404b326ec50fa5d9057a031427357926595c8700ab27666 SHA512 8fe62c63fbf496b605151e9ff16b370c1a867bc00b7997fdcab0023846c6f681e9db139bb706588c44f95182bd3d6f1296e2ed9e62e19af85166a77bbc312e21 WHIRLPOOL 17c3ecf36e30205ebccee2e2c9d56e7e83d6a085ce5bd1f6a4e6fd80e1c6e676ab78572241a6a32315fbf667da17d8e1eb97806c22db2670d4e43ffeb8b2fc81 +MISC metadata.xml 838 SHA256 a9660b1a7c9d074e1b1e1253b587c51712c729f292d57b725488ef35539f09de SHA512 116c648f336eb70783ab9408e9840dba21b00151848c190f38ee7d22a741e4fc16e29e250f0be588064ffc3d0a6f2884efe2c65bf1f719e264ac412fa45844cf WHIRLPOOL 65573a80cf2561d1b7a16f8cafd938a7adacc0de6ead305d8cd785c3268d443f0cc0fe421a016f18716a8721cdf898cf81612b5e930ec25b497e7de88c3e3286 diff --git a/sci-libs/netcdf-fortran/metadata.xml b/sci-libs/netcdf-fortran/metadata.xml new file mode 100644 index 000000000000..a0fc25165a93 --- /dev/null +++ b/sci-libs/netcdf-fortran/metadata.xml @@ -0,0 +1,20 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + NetCDF (network Common Data Form) is an interface for scientific + data access and a freely-distributed software library that provides an + implementation of the interface. The netCDF library also defines a + machine-independent format for representing scientific data. + Together, the interface, library, and format support the creation, + access, and sharing of scientific data. + This is the FORTRAN 77 and 90 library on top of the C library. + </longdescription> + <upstream> + <remote-id type="github">Unidata/netcdf-fortran</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/netcdf-fortran/netcdf-fortran-4.2.ebuild b/sci-libs/netcdf-fortran/netcdf-fortran-4.2.ebuild new file mode 100644 index 000000000000..52eecd25d439 --- /dev/null +++ b/sci-libs/netcdf-fortran/netcdf-fortran-4.2.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_STANDARD="77 90" +AUTOTOOLS_IN_SOURCE_BUILD=1 + +inherit autotools-utils fortran-2 + +DESCRIPTION="Scientific library and interface for array oriented data access" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="ftp://ftp.unidata.ucar.edu/pub/netcdf/${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0/5" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs" + +RDEPEND="sci-libs/netcdf" +DEPEND="${RDEPEND} + dev-lang/cfortran +" + +src_prepare() { + # use system cfortran + rm fortran/cfortran.h || die + autotools-utils_src_prepare +} + +src_install() { + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/netcdf-fortran/netcdf-fortran-4.4.2.ebuild b/sci-libs/netcdf-fortran/netcdf-fortran-4.4.2.ebuild new file mode 100644 index 000000000000..31db078a73a7 --- /dev/null +++ b/sci-libs/netcdf-fortran/netcdf-fortran-4.4.2.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_STANDARD="77 90" +AUTOTOOLS_IN_SOURCE_BUILD=1 + +inherit autotools-utils fortran-2 + +DESCRIPTION="Scientific library and interface for array oriented data access" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="https://github.com/Unidata/netcdf-fortran/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0/6" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs" + +RDEPEND="sci-libs/netcdf" +DEPEND="${RDEPEND} + dev-lang/cfortran +" + +src_prepare() { + # use system cfortran + rm libsrc/cfortran.h || die + + autotools-utils_src_prepare +} + +src_install() { + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/netcdf-fortran/netcdf-fortran-4.4.3.ebuild b/sci-libs/netcdf-fortran/netcdf-fortran-4.4.3.ebuild new file mode 100644 index 000000000000..7539ce517aed --- /dev/null +++ b/sci-libs/netcdf-fortran/netcdf-fortran-4.4.3.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_STANDARD="77 90" + +inherit autotools eutils fortran-2 + +DESCRIPTION="Scientific library and interface for array oriented data access" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="https://github.com/Unidata/netcdf-fortran/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0/6" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples static-libs" + +RDEPEND="sci-libs/netcdf" +DEPEND="${RDEPEND} + dev-lang/cfortran +" + +src_prepare() { + # use system cfortran + rm libsrc/cfortran.h || die + + default + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + use examples && dodoc -r examples + prune_libtool_files +} diff --git a/sci-libs/netcdf/Manifest b/sci-libs/netcdf/Manifest new file mode 100644 index 000000000000..6b2ff6fdd110 --- /dev/null +++ b/sci-libs/netcdf/Manifest @@ -0,0 +1,10 @@ +AUX 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c5cae15e86d11e6434a489bdac39ea498bdca2008ae6732a16603b32d79a9227a168a0fa0174c6d55ced0c92d9b644f60db4d946f695731161572abd6b778fa1 WHIRLPOOL cdbf02533cd3ebaad563d28a853ec43f0297e4a4be2ced0aea2f44aa07768846a1dba98199c961d5674996f96f931a7b39df584836fd3451530e37a73277de2f +DIST netcdf-4.4.1.1.tar.gz 17670828 SHA256 7f040a0542ed3f6d27f3002b074e509614e18d6c515b2005d1537fec01b24909 SHA512 ee23f37d7b40e7b9a115d29bc038c7c654d50dedfcad62617b8dee3efa4668305e6a0656ba655770727ff46f4b6d742869c719267eca3392c94e2488eb902da7 WHIRLPOOL 9cb996847441a4f0a865890637f1a5f54ff3a914918f465edd31811c32218c78fdd27017c6bd50d5b09f95a76ccc0421c5e4801c75c8a6689b390aa9fe6b08a9 +EBUILD netcdf-4.3.2-r1.ebuild 1473 SHA256 f837d3f00cc098b8a1bedd3a60079405ab9eafa27ebebf4f3043b18103fb006c SHA512 4482ff6621ff023a3363e754ce75f3a3fad1f7ef962b809cf0d2bf8e76e6f0d9b54a083a6cf222cefccdb6dc9e75b0d2202959c3be3b15b58945b31ccbee0a91 WHIRLPOOL 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26cd72c62989a77fa34af636735ce55483d87c2b6d411e80d6cfa302c8acb9597e790a314e05c9f3ec59dc9a5d07dc0e8b8168d1904e308a938e2b59a5d2b946 diff --git a/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch b/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch new file mode 100644 index 000000000000..783a5b06e991 --- /dev/null +++ b/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch @@ -0,0 +1,145 @@ +From 435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8 Mon Sep 17 00:00:00 2001 +From: Quincey Koziol <quincey@koziol.cc> +Date: Wed, 7 May 2014 08:45:15 -0500 +Subject: [PATCH] Account for the HDF5 library not having the MPI-POSIX VFD + configured in. + +--- + RELEASE_NOTES.md | 2 ++ + libsrc4/nc4file.c | 40 ++++++++++++++++++++++++++++++++++++++++ + nc_test4/tst_nc4perf.c | 5 +++++ + nc_test4/tst_parallel3.c | 5 +++++ + 4 files changed, 52 insertions(+) + +diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md +index 27f228c..1a69d17 100644 +--- a/RELEASE_NOTES.md ++++ b/RELEASE_NOTES.md +@@ -9,6 +9,8 @@ This file contains a high-level description of this package's evolution. Release + + ### 4.3.3-rc1 Released TBD + ++* When the NC_MPIPOSIX flag is given for parallel I/O access and the HDF5 library does not have the MPI-POSIX VFD configured in, the NC_MPIPOSIX flag is transparently aliased to the NC_MPIIO flag within the netCDF-4 library. ++ + ## 4.3.2 Released 2014-04-23 + + * As part of an ongoing project, the Doxygen-generated netcdf documentation has been reorganized. The goal is to make the documentation easier to parse, and to eliminate redundant material. This project is ongoing. +diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c +index ec3bb0c..5c957be 100644 +--- a/libsrc4/nc4file.c ++++ b/libsrc4/nc4file.c +@@ -308,12 +308,21 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info, + if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) + BAIL(NC_EPARINIT); + } ++#ifdef USE_PARALLEL_POSIX + else /* MPI/POSIX */ + { + LOG((4, "creating parallel file with MPI/posix")); + if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) + BAIL(NC_EPARINIT); + } ++#else /* USE_PARALLEL_POSIX */ ++ /* Should not happen! Code in NC4_create/NC4_open should alias the ++ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not ++ * available in HDF5. -QAK ++ */ ++ else /* MPI/POSIX */ ++ BAIL(NC_EPARINIT); ++#endif /* USE_PARALLEL_POSIX */ + + /* Keep copies of the MPI Comm & Info objects */ + if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) +@@ -465,6 +474,17 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe, + ) + return NC_EINVAL; + ++#ifndef USE_PARALLEL_POSIX ++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias ++ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK ++ */ ++ if(cmode & NC_MPIPOSIX) ++ { ++ cmode &= ~NC_MPIPOSIX; ++ cmode |= NC_MPIIO; ++ } ++#endif /* USE_PARALLEL_POSIX */ ++ + cmode |= NC_NETCDF4; + + /* Apply default create format. */ +@@ -2168,12 +2188,21 @@ nc4_open_file(const char *path, int mode, MPI_Comm comm, + if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) + BAIL(NC_EPARINIT); + } ++#ifdef USE_PARALLEL_POSIX + else /* MPI/POSIX */ + { + LOG((4, "opening parallel file with MPI/posix")); + if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) + BAIL(NC_EPARINIT); + } ++#else /* USE_PARALLEL_POSIX */ ++ /* Should not happen! Code in NC4_create/NC4_open should alias the ++ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not ++ * available in HDF5. -QAK ++ */ ++ else /* MPI/POSIX */ ++ BAIL(NC_EPARINIT); ++#endif /* USE_PARALLEL_POSIX */ + + /* Keep copies of the MPI Comm & Info objects */ + if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) +@@ -2640,6 +2669,17 @@ NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp, + (mode & NC_MPIIO && mode & NC_MPIPOSIX)) + return NC_EINVAL; + ++#ifndef USE_PARALLEL_POSIX ++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias ++ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK ++ */ ++ if(mode & NC_MPIPOSIX) ++ { ++ mode &= ~NC_MPIPOSIX; ++ mode |= NC_MPIIO; ++ } ++#endif /* USE_PARALLEL_POSIX */ ++ + + /* Depending on the type of file, open it. */ + +diff --git a/nc_test4/tst_nc4perf.c b/nc_test4/tst_nc4perf.c +index 47af70e..3528b82 100644 +--- a/nc_test4/tst_nc4perf.c ++++ b/nc_test4/tst_nc4perf.c +@@ -244,6 +244,11 @@ int test_pio_4d(size_t cache_size, int facc_type, int access_flag, MPI_Comm comm + return 0; + } + ++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX ++ * flag will be aliased to the NC_MPIIO flag within the library, and ++ * therefore this test will exercise the aliasing, with the MPI-IO VFD, ++ * under that configuration. -QAK ++ */ + #define NUM_MODES 2 + #define NUM_FACC 2 + #define NUM_CHUNK_COMBOS_2D 3 +diff --git a/nc_test4/tst_parallel3.c b/nc_test4/tst_parallel3.c +index 27f9c98..9fa534f 100644 +--- a/nc_test4/tst_parallel3.c ++++ b/nc_test4/tst_parallel3.c +@@ -129,6 +129,11 @@ int main(int argc, char **argv) + if (mpi_rank == 0) + SUMMARIZE_ERR; + ++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX ++ * flag will be aliased to the NC_MPIIO flag within the library, and ++ * therefore this test will exercise the aliasing, with the MPI-IO VFD, ++ * under that configuration. -QAK ++ */ + if (mpi_rank == 0) + printf("*** Testing parallel IO for raw-data with MPIPOSIX-IO (driver)..."); + facc_type = NC_NETCDF4|NC_MPIPOSIX; +-- +2.0.3 + diff --git a/sci-libs/netcdf/metadata.xml b/sci-libs/netcdf/metadata.xml new file mode 100644 index 000000000000..f2b51139d22c --- /dev/null +++ b/sci-libs/netcdf/metadata.xml @@ -0,0 +1,24 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + NetCDF (network Common Data Form) is an interface for scientific + data access and a freely-distributed software library that provides an + implementation of the interface. The netCDF library also defines a + machine-independent format for representing scientific data. + Together, the interface, library, and format support the creation, + access, and sharing of scientific data. + </longdescription> + <use> + <flag name="dap">Support for remote data access with the built-in OPeNDAP client</flag> + <flag name="hdf">Add support for the Hierarchical Data Format v.4 <pkg>sci-libs/hdf</pkg></flag> + <flag name="tools">Build the utilities nccopy, ncgen and ncdump</flag> + </use> + <upstream> + <remote-id type="github">Unidata/netcdf-c</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/netcdf/netcdf-4.3.2-r1.ebuild b/sci-libs/netcdf/netcdf-4.3.2-r1.ebuild new file mode 100644 index 000000000000..fd351c9fc860 --- /dev/null +++ b/sci-libs/netcdf/netcdf-4.3.2-r1.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Scientific library and interface for array oriented data access" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="ftp://ftp.unidata.ucar.edu/pub/netcdf/${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0/7" +KEYWORDS="amd64 ~arm ia64 ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="+dap examples hdf +hdf5 mpi static-libs szip test tools" + +RDEPEND=" + dap? ( net-misc/curl:0= ) + hdf? ( sci-libs/hdf:0= sci-libs/hdf5:0= ) + hdf5? ( sci-libs/hdf5:0=[hl(+),mpi=,szip=,zlib] )" +DEPEND="${RDEPEND}" +# doc generation is missing many doxygen files in tar ball +# doc? ( app-doc/doxygen[dot] )" + +REQUIRED_USE="test? ( tools ) szip? ( hdf5 ) mpi? ( hdf5 )" + +PATCHES=( "${FILESDIR}/${P}-HDF5-1.8.13+-compat.patch" ) + +src_configure() { + # --docdir="${EPREFIX}"/usr/share/doc/${PF} + # $(use_enable doc doxygen) + local myeconfargs=( + --disable-examples + --disable-dap-remote-tests + $(use_enable dap) + $(use_enable hdf hdf4) + $(use_enable hdf5 netcdf-4) + $(use_enable tools utilities) + ) + if use mpi; then + export CC=mpicc + myeconfargs+=( --enable-parallel ) + use test && myeconfargs+=( --enable-parallel-tests ) + fi + autotools-utils_src_configure +} + +src_test() { + autotools-utils_src_test -j1 +} + +src_install() { + autotools-utils_src_install + if use examples; then + insinto /usr/share/doc/${PF} + doins -r examples + fi +} diff --git a/sci-libs/netcdf/netcdf-4.4.0-r1.ebuild b/sci-libs/netcdf/netcdf-4.4.0-r1.ebuild new file mode 100644 index 000000000000..5a8e696da397 --- /dev/null +++ b/sci-libs/netcdf/netcdf-4.4.0-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils + +DESCRIPTION="Scientific library and interface for array oriented data access" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="https://github.com/Unidata/netcdf-c/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0/11" +KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+dap examples hdf +hdf5 mpi static-libs szip test tools" + +RDEPEND=" + dap? ( net-misc/curl:0= ) + hdf? ( sci-libs/hdf:0= sci-libs/hdf5:0= ) + hdf5? ( sci-libs/hdf5:0=[hl(+),mpi=,szip=,zlib] )" +DEPEND="${RDEPEND}" +# doc generation is missing many doxygen files in tar ball +# doc? ( app-doc/doxygen[dot] )" + +REQUIRED_USE="test? ( tools ) szip? ( hdf5 ) mpi? ( hdf5 )" + +S="${WORKDIR}/${PN}-c-${PV}" + +src_configure() { + local myconf + if use mpi; then + export CC=mpicc + myconf="--enable-parallel" + use test && myconf+=" --enable-parallel-tests" + fi + econf "${myconf}" \ + --disable-examples \ + --disable-dap-remote-tests \ + $(use_enable dap) \ + $(use_enable hdf hdf4) \ + $(use_enable hdf5 netcdf-4) \ + $(use_enable static-libs static) \ + $(use_enable tools utilities) +} + +src_install() { + default + use examples && dodoc -r examples + prune_libtool_files +} diff --git a/sci-libs/netcdf/netcdf-4.4.1.1.ebuild b/sci-libs/netcdf/netcdf-4.4.1.1.ebuild new file mode 100644 index 000000000000..b295062f6d98 --- /dev/null +++ b/sci-libs/netcdf/netcdf-4.4.1.1.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils + +DESCRIPTION="Scientific library and interface for array oriented data access" +HOMEPAGE="http://www.unidata.ucar.edu/software/netcdf/" +SRC_URI="https://github.com/Unidata/netcdf-c/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0/11" +KEYWORDS="~amd64 ~arm ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+dap examples hdf +hdf5 mpi static-libs szip test tools" + +RDEPEND=" + dap? ( net-misc/curl:0= ) + hdf? ( sci-libs/hdf:0= sci-libs/hdf5:0= ) + hdf5? ( sci-libs/hdf5:0=[hl(+),mpi=,szip=,zlib] )" +DEPEND="${RDEPEND}" +# doc generation is missing many doxygen files in tar ball +# doc? ( app-doc/doxygen[dot] )" + +REQUIRED_USE="test? ( tools ) szip? ( hdf5 ) mpi? ( hdf5 )" + +S="${WORKDIR}/${PN}-c-${PV}" + +src_configure() { + local myconf + if use mpi; then + export CC=mpicc + myconf="--enable-parallel" + use test && myconf+=" --enable-parallel-tests" + fi + econf "${myconf}" \ + --disable-examples \ + --disable-dap-remote-tests \ + $(use_enable dap) \ + $(use_enable hdf hdf4) \ + $(use_enable hdf5 netcdf-4) \ + $(use_enable static-libs static) \ + $(use_enable tools utilities) +} + +src_test() { + # fails parallel tests: bug #621486 + emake check -j1 +} + +src_install() { + default + use examples && dodoc -r examples + prune_libtool_files +} diff --git a/sci-libs/nfft/Manifest b/sci-libs/nfft/Manifest new file mode 100644 index 000000000000..a428350cd034 --- /dev/null +++ b/sci-libs/nfft/Manifest @@ -0,0 +1,5 @@ +DIST nfft-3.3.2.tar.gz 2821259 SHA256 9dcebd905a82c4f0a339d0d5e666b68c507169d9173b66d5ac588aae5d50b57c SHA512 66bcd2439c9ba27063aa1db01c526a580c5c67938e2db332068ce20035ede1d8766e8f134a0e5dac5263aca14121573ca4f5a906b452c43f218636f5f6161c02 WHIRLPOOL 9e15d7517d504a37b15b221a850e0b6574aeefc9af70d2a265bd0f2aa37f8a498462697c5ab73c47a4487f58978cf0cdd74d58e3073dc2b54361f0a216aba8c5 +EBUILD nfft-3.3.2.ebuild 1211 SHA256 4d8c61453b7e6663f300c93e067349e767744515303dd406277809475d0cfa34 SHA512 cab2ec8d53fd04221644cecd228b899368ed7863cb8d4228bd021fa47f75ac54129e3decf44b224833960344f18945586d075523952b071c4a2fe07dec673d64 WHIRLPOOL 93a75c259a99e00a6c16b5911bd7eabb6a278e2a67a5ed5cd3733a356bd37af2ab62fb818967ea9ddc3c82966d580749db18eb2a1083e4b84cfe98fdda60520a +MISC ChangeLog 2541 SHA256 8d726b330c5c67a9dab76c0406c4cad0fd9259013d83d664b1db9ea78d986de1 SHA512 c50d89b0d8fdcfab4614654063961429d7b101274c1e5a68d8c6ee17b6ad5327c3794bbbbfecbac8e41e4b8c041dba1644fd335d37be9babd00639516d8dfda4 WHIRLPOOL cc70f030f96b494474840c42e0133b00116af578d350458715a7e095f636b9fb0001025a656d5b189e64c287e2b6f706349b3af52bf61ec2a2f70897738ccead +MISC ChangeLog-2015 452 SHA256 8901f6c0c4b689eca7ef6316e34b15cedc90571af3f3ae9f79d94d0cda32bd4c SHA512 5bc8fb61d7c60403de92ef8636039fd3d6f25db0f025b6a12e4873b7788e84419be12a44e041d78cc2ba82f6e8cca66edf443a3c602f7d27279a379ea8f80f11 WHIRLPOOL 7f0d44271ec284f5773485744b3ce9cb9a2d22b80d75c05216307ae38b490c6c820530a9dfcd2f66001d6dd61e5c1f567c2c2f62dae0db214ac61f5c99072656 +MISC metadata.xml 441 SHA256 fd1b58ecbfbe5c0df8e6771bfaf75d892bb3a604e472f8ee183028ffe62c67ce SHA512 72f45a8c112412d0a1db5265b29d4688263465d0039f3f178d7a44dbfb4c87336339c4517b5a948ba631248a27e0e727e92cb1617dbdfedf39910c0df44c6caa WHIRLPOOL 7ba5209cbf3b607a20cbcde91a625a402d4d2feffbdac3ae6198ab9bed783c844ab3fb0324a556e3587bb90baeb77c80e0f025d350f5cdc49c129ea762dde66c diff --git a/sci-libs/nfft/metadata.xml b/sci-libs/nfft/metadata.xml new file mode 100644 index 000000000000..b759151e3dc4 --- /dev/null +++ b/sci-libs/nfft/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>junghans@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">NFFT/nfft</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/nfft/nfft-3.3.2.ebuild b/sci-libs/nfft/nfft-3.3.2.ebuild new file mode 100644 index 000000000000..8c5f1f54b675 --- /dev/null +++ b/sci-libs/nfft/nfft-3.3.2.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="library for nonequispaced discrete Fourier transformations" +HOMEPAGE="http://www-user.tu-chemnitz.de/~potts/nfft" +SRC_URI="https://github.com/NFFT/nfft/releases/download/${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="doc openmp static-libs" + +RDEPEND="sci-libs/fftw:3.0[threads,openmp?]" +DEPEND="${RDEPEND}" + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + + if tc-is-clang; then + ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," + ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\"" + fi + + die "need openmp capable compiler" + fi + fi +} + +src_configure() { + econf \ + --enable-all \ + --enable-shared \ + $(use_enable openmp) \ + $(use_enable static-libs static) +} + +src_install() { + default + use doc || rm -r "${ED}/usr/share/doc/${P}/html" || die + + # infft uses pkg-config to record its private dependencies + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-libs/nlopt/Manifest b/sci-libs/nlopt/Manifest new file mode 100644 index 000000000000..4a940fa89b36 --- /dev/null +++ b/sci-libs/nlopt/Manifest @@ -0,0 +1,9 @@ +AUX nlopt-2.3-as-needed.patch 1062 SHA256 fdd21b03d1a667b0be4b1ce5b516d9c28ea2b5e116252f2f6fd2fbf0530395f2 SHA512 755e04b0e9d2ab5b1256c14015980b051716756777b910a9273a0dced4108e19a8f3030c1d03c6d96561a7edb3e883fdbc2822e1d6c1b74fa2794c336612cc47 WHIRLPOOL 88d7d978eafb5dc9c2de25e26e515d7ce1eed194da39f4b35f8c61c3588cfca49affc3d31ba0b0f7d25188a80310c8f45b9da3237f415df5a7a38f0e73abed4f +AUX nlopt-2.3-pkgconfig.patch 318 SHA256 d7f9eb5f7912b4722e4f5514f27682ed3e20104076c2dc03d693aef449e4283a SHA512 923b20e177a842643b1022d68168978d5fb35e987c6781d8b0b368a6c707f4b42a4141c4ca7cf33cd7067a39147ae87220adeaaa545a8731bb6a5d2f3d11a5bc WHIRLPOOL 4f9fc1ee7800b48fec6c2f2d41dddee39ea371ea31e08f0b57faffe4bfffa370390d2d20e03bd96aec4e5c57d3a6d57897992557895d4be149fa83bc095cb6f8 +AUX nlopt-2.4.2-fix-dynamic-underlinking.patch 2522 SHA256 725e5f0dc4a1c6963860171af56ec915a059dff02f619d404d8367d864dbacb8 SHA512 bdb07b216ffb68b68cb3f03076336234c558db3953c48b02511883bf9fb12f5915c04950a2e3222577c7af4fb1e288a165af2e8adf211fc853e747c98a65cd19 WHIRLPOOL 051dd3abd6e29b0932a3aca9a8d50d99e5f188d7de82ada856e30aab3fcaaf914821b35b94d0cdd130b95884c2a267f0e4990a67256e969b67547af9868e5497 +AUX nlopt-2.4.2-octave-4-map.patch 1858 SHA256 3be25fff014a9157ae0824c908479e23d23eb382aa21b29fc57b34bdfa9205e7 SHA512 00c45fe04fdc1acf4ccbb77aaf39feab0cb2b811b45edf791db7e87aa9e965c23b6131400eebd68335be8dcb86f346c01892e718f739f07dc0853b3dd9ea5ad4 WHIRLPOOL f45b2ebfab0591fe9fcecd19d17d705f4a47214b7d73a1181cc19236a1086b93ca90e2e897df8678f21af8e451e4456d9ce2f770bdea1c55043be1b135410c9c +DIST nlopt-2.4.2.tar.gz 2361992 SHA256 8099633de9d71cbc06cd435da993eb424bbcdbded8f803cdaa9fb8c6e09c8e89 SHA512 136aacc00a69f77e8a7ce5dc26a5f3f027bc8c01b97aa1f43919462e0a412154eabfb01be258e082dffe61f9b554bb2bfbb550a7b82c7c77c7b22874a64a9703 WHIRLPOOL ec07f402cc1868f05adf1f261aa2e50901448e965ccdee3d249e1447ad0abdff354caf1bafbf0700a25896f9fcee509c916fd5e7bdd768514a55bf6fff40784d +EBUILD nlopt-2.4.2-r1.ebuild 2640 SHA256 4e03c7b2128df6fc829758bef1989e337ad4830c088a37b9cba28063ba688d2b SHA512 c8255cebd138aa4a3236f09b6d27f97781353dccb065652d64130973643dd97866d61cdc8f12c7465f5df0b63fc579864afb71ecff06ebdd31aa991de4ee1745 WHIRLPOOL 31ad319f7ee7c1a051738ad20569c6abc94334dab109f385aca39ee79eafa9a9f4152943dc1317c9ebb8a7646ca5b86405a411ff4322c8dc8cec9d75ec12b953 +MISC ChangeLog 3086 SHA256 0ac60e67c5ef3d848d01003e0a0a1eb0b0cb3666b147d1420efe9a3352f6faaf SHA512 8653458187153580beb70f0ca35bf2c6cfe833f0ee7bb4fbefda7bc51055d39280820268e865a82a4735f0b32fa99269935a07b8eaca60d1639257a910b5e004 WHIRLPOOL f430d06d6c4caa28c824d1b9ffba671e4fba326a22700167ce49d63df6e15778c81b123fd8249d2704656534dc701816b4b9096d53139dd0d16de0ab388f7fcc +MISC ChangeLog-2015 3975 SHA256 c2f0c1e857d519df0d27299fb733252a7aafd218c0727f3bc0efd48cc0356f0e SHA512 cd64130435c8f3ad5bf25983125fb7b843e02ab499b156ce8ffb93cc03a1d23146fa65ab01ef643add3924d1be18cf21788a122d16502e17df0a010df6cb0e7b WHIRLPOOL 18da175a8ff6dae1e90c49f8da27fc5d229603b85c732e4c258b14b2f4ed1d76990fc4729736c2a2b0b97dade0308e27031fb647fe856a99983e318399f11a72 +MISC metadata.xml 1095 SHA256 44a69ac8e3f0af0869f79d77a9d21dfd4d7f895714fcc1582d590b0f6dfdb25d SHA512 74a37bc3e6fa74d0f96c3390fadf16e76caf904f43cf9ac0496f70e3e3bc458727e58d9fc65c39a81302b081575e530c27be3812488df20fab42aff5494437f7 WHIRLPOOL ca2f2b21a46fd5607bd7ef7579e54194651b90b8f3ce39f82c1516da153ec43ee6076e4bfde404c176d21a62ae0e75da8c4ac8f320256baaaf6bdcf4bfcbfdc8 diff --git a/sci-libs/nlopt/files/nlopt-2.3-as-needed.patch b/sci-libs/nlopt/files/nlopt-2.3-as-needed.patch new file mode 100644 index 000000000000..928ec174b771 --- /dev/null +++ b/sci-libs/nlopt/files/nlopt-2.3-as-needed.patch @@ -0,0 +1,23 @@ +diff -Nur nlopt-2.3.orig/Makefile.am nlopt-2.3/Makefile.am +--- nlopt-2.3.orig/Makefile.am 2012-08-03 02:07:09.000000000 +0100 ++++ nlopt-2.3/Makefile.am 2012-08-03 02:13:13.000000000 +0100 +@@ -25,6 +25,7 @@ + + if WITH_CXX + libnlopt@NLOPT_SUFFIX@_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@ ++libnlopt@NLOPT_SUFFIX@_la_LIBADD += -lstdc++ + else + libnlopt@NLOPT_SUFFIX@_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@ + endif +diff -Nur nlopt-2.3.orig/swig/Makefile.am nlopt-2.3/swig/Makefile.am +--- nlopt-2.3.orig/swig/Makefile.am 2012-08-03 02:07:09.000000000 +0100 ++++ nlopt-2.3/swig/Makefile.am 2012-08-03 03:04:30.000000000 +0100 +@@ -9,7 +9,7 @@ + # Guile wrapper + + libnlopt@NLOPT_SUFFIX@_guile_la_SOURCES = nlopt-guile.cpp +-libnlopt@NLOPT_SUFFIX@_guile_la_LIBADD = ../libnlopt@NLOPT_SUFFIX@.la ++libnlopt@NLOPT_SUFFIX@_guile_la_LIBADD = ../libnlopt@NLOPT_SUFFIX@.la @GUILE_LIBS@ + libnlopt@NLOPT_SUFFIX@_guile_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@ + libnlopt@NLOPT_SUFFIX@_guile_la_CPPFLAGS = $(GUILE_CPPFLAGS) -I$(top_builddir)/api + diff --git a/sci-libs/nlopt/files/nlopt-2.3-pkgconfig.patch b/sci-libs/nlopt/files/nlopt-2.3-pkgconfig.patch new file mode 100644 index 000000000000..8a072b15e2e2 --- /dev/null +++ b/sci-libs/nlopt/files/nlopt-2.3-pkgconfig.patch @@ -0,0 +1,10 @@ +--- nlopt.pc.in.orig 2012-08-03 01:41:30.000000000 +0100 ++++ nlopt.pc.in 2012-08-03 01:42:29.000000000 +0100 +@@ -6,5 +6,6 @@ + Name: NLopt + Description: nonlinear optimization libary + Version: @VERSION@ +-Libs: -L${libdir} -lnlopt -lm ++Libs: -L${libdir} -lnlopt@NLOPT_SUFFIX@ ++Libs.private: -lm + Cflags: -I${includedir} diff --git a/sci-libs/nlopt/files/nlopt-2.4.2-fix-dynamic-underlinking.patch b/sci-libs/nlopt/files/nlopt-2.4.2-fix-dynamic-underlinking.patch new file mode 100644 index 000000000000..beb9dd4de815 --- /dev/null +++ b/sci-libs/nlopt/files/nlopt-2.4.2-fix-dynamic-underlinking.patch @@ -0,0 +1,62 @@ +Fix underlinking issues, caused by missing -lpython27 and -lpthread + +--- nlopt-2.4.2/configure.ac ++++ nlopt-2.4.2/configure.ac +@@ -161,33 +161,17 @@ + dnl Python: + AM_PATH_PYTHON([],[have_python=yes],[have_python=no]) + if test $have_python = yes; then +- AC_ARG_VAR([PYTHON_CONFIG], [python-config program]) +- AC_PATH_PROGS([PYTHON_CONFIG], [python$PYTHON_VERSION-config python-config], +- [unknown], [`dirname $PYTHON`:$PATH]) +- AC_MSG_CHECKING([for Python include flags]) +- if test "x$PYTHON_CONFIG" = "xunknown"; then +- pinc=-I`echo "import distutils.sysconfig; print (distutils.sysconfig.get_python_inc())" | $PYTHON - 2>/dev/null` +- test "x$pinc" = "x-I" && pinc="" +- else +- pinc=`$PYTHON_CONFIG --includes 2>/dev/null` +- fi +- AC_MSG_RESULT([${pinc:-unknown}]) +- PYTHON_INCLUDES="$pinc" +- save_CPPFLAGS=$CPPFLAGS +- CPPFLAGS="$CPPFLAGS $PYTHON_INCLUDES" +- AC_CHECK_HEADER([Python.h], [], [AC_MSG_WARN([disabling Python wrappers]) +- have_python=no]) +- if test $have_python = yes; then ++ PKG_CHECK_MODULES([PYTHON], [python-2.7]) ++ CPPFLAGS="$CPPFLAGS $PYTHON_CFLAGS" ++ + AC_MSG_CHECKING([for Numpy include directory]) + pinc=`echo "import numpy; print (numpy.get_include())" | $PYTHON - 2>/dev/null` + AC_MSG_RESULT([${pinc:-unknown}]) +- test -n "$pinc" && PYTHON_INCLUDES="$PYTHON_INCLUDES -I$pinc" ++ test -n "$pinc" && PYTHON_INCLUDES="$PYTHON_CFLAGS -I$pinc" + CPPFLAGS="$save_CPPFLAGS $PYTHON_INCLUDES" + AC_CHECK_HEADER([numpy/arrayobject.h],[],[ + AC_MSG_WARN([disabling Python wrappers]) + have_python=no],[#include <Python.h>]) +- fi +- CPPFLAGS=$save_CPPFLAGS + fi + + fi # with_python +--- nlopt-2.4.2/swig/Makefile.am ++++ nlopt-2.4.2/swig/Makefile.am +@@ -9,7 +9,7 @@ + # Guile wrapper + + libnlopt@NLOPT_SUFFIX@_guile_la_SOURCES = nlopt-guile.cpp +-libnlopt@NLOPT_SUFFIX@_guile_la_LIBADD = ../libnlopt@NLOPT_SUFFIX@.la @GUILE_LIBS@ ++libnlopt@NLOPT_SUFFIX@_guile_la_LIBADD = -lpthread ../libnlopt@NLOPT_SUFFIX@.la @GUILE_LIBS@ + libnlopt@NLOPT_SUFFIX@_guile_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@ + libnlopt@NLOPT_SUFFIX@_guile_la_CPPFLAGS = $(GUILE_CPPFLAGS) -I$(top_srcdir)/api + +@@ -23,7 +23,7 @@ + # Python wrapper + + _nlopt_la_SOURCES = nlopt-python.cpp +-_nlopt_la_LIBADD = ../libnlopt@NLOPT_SUFFIX@.la ++_nlopt_la_LIBADD = ../libnlopt@NLOPT_SUFFIX@.la @PYTHON_LIBS@ + _nlopt_la_LDFLAGS = -module -version-info @SHARED_VERSION_INFO@ + _nlopt_la_CPPFLAGS = $(PYTHON_INCLUDES) -I$(top_srcdir)/api + diff --git a/sci-libs/nlopt/files/nlopt-2.4.2-octave-4-map.patch b/sci-libs/nlopt/files/nlopt-2.4.2-octave-4-map.patch new file mode 100644 index 000000000000..c82d99497e67 --- /dev/null +++ b/sci-libs/nlopt/files/nlopt-2.4.2-octave-4-map.patch @@ -0,0 +1,49 @@ +Fix issues caused by Octave-4 renaming Octave_map to octave_map +See also +https://bugs.gentoo.org/show_bug.cgi?id=569996 +https://github.com/stevengj/nlopt/commit/5326ab410c978f9d8c3cae7e4917f55c10ef2c2e?diff=unified + +--- nlopt-2.4.2_old/octave/nlopt_optimize-oct.cc 2014-05-20 20:35:58.000000000 +0200 ++++ nlopt-2.4.2/octave/nlopt_optimize-oct.cc 2016-01-09 16:10:53.358491776 +0100 +@@ -30,5 +30,5 @@ + #include "nlopt_optimize_usage.h" + +-static int struct_val_default(Octave_map &m, const std::string& k, ++static int struct_val_default(octave_map &m, const std::string& k, + int dflt) + { +@@ -40,5 +40,5 @@ + } + +-static double struct_val_default(Octave_map &m, const std::string& k, ++static double struct_val_default(octave_map &m, const std::string& k, + double dflt) + { +@@ -50,5 +50,5 @@ + } + +-static Matrix struct_val_default(Octave_map &m, const std::string& k, ++static Matrix struct_val_default(octave_map &m, const std::string& k, + Matrix &dflt) + { +@@ -141,5 +141,5 @@ + #define CHECK1(cond, msg) if (!(cond)) { fprintf(stderr, msg "\n\n"); nlopt_destroy(opt); nlopt_destroy(local_opt); return NULL; } + +-nlopt_opt make_opt(Octave_map &opts, int n) ++nlopt_opt make_opt(octave_map &opts, int n) + { + nlopt_opt opt = NULL, local_opt = NULL; +@@ -196,5 +196,5 @@ + && (opts.contents("local_optimizer"))(0).is_map(), + "opt.local_optimizer must be a structure"); +- Octave_map local_opts = (opts.contents("local_optimizer"))(0).map_value(); ++ octave_map local_opts = (opts.contents("local_optimizer"))(0).map_value(); + CHECK1((local_opt = make_opt(local_opts, n)), + "error initializing local optimizer"); +@@ -217,5 +217,5 @@ + + CHECK(args(0).is_map(), "opt must be structure") +- Octave_map opts = args(0).map_value(); ++ octave_map opts = args(0).map_value(); + + CHECK(args(1).is_real_matrix() || args(1).is_real_scalar(), diff --git a/sci-libs/nlopt/metadata.xml b/sci-libs/nlopt/metadata.xml new file mode 100644 index 000000000000..35f045929ff6 --- /dev/null +++ b/sci-libs/nlopt/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + NLopt is a library for nonlinear optimization, + providing a common interface for a number of different free + optimization routines available online as well as original + implementations of various other algorithms. Its features include: + * Callable from variety of languages (C, C++, Fortran, Python, Octave) + * A common interface for many different algorithms—try a different + algorithm just by changing one parameter. + * Both global and local optimization algorithms. + * Both derivative-free and gradient-based optimization algorithms. + * Algorithms for unconstrained optimization, bound-constrained + optimization, and general nonlinear inequality constraints. +</longdescription> + <use> + <flag name="octave">Add plugin for <pkg>sci-mathematics/octave</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-libs/nlopt/nlopt-2.4.2-r1.ebuild b/sci-libs/nlopt/nlopt-2.4.2-r1.ebuild new file mode 100644 index 000000000000..8562dd322d07 --- /dev/null +++ b/sci-libs/nlopt/nlopt-2.4.2-r1.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +AUTOTOOLS_AUTORECONF=1 + +inherit python-r1 autotools-utils + +DESCRIPTION="Non-linear optimization library" +HOMEPAGE="http://ab-initio.mit.edu/nlopt/" +SRC_URI="${HOMEPAGE}/${P}.tar.gz" + +LICENSE="LGPL-2.1 MIT" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +SLOT="0" +IUSE="cxx guile octave python static-libs" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +DEPEND=" + guile? ( dev-scheme/guile:* ) + octave? ( sci-mathematics/octave ) + python? ( + ${PYTHON_DEPS} + dev-python/numpy[${PYTHON_USEDEP}] + )" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.3-pkgconfig.patch + "${FILESDIR}"/${PN}-2.3-as-needed.patch + "${FILESDIR}"/${P}-fix-dynamic-underlinking.patch +) + +src_prepare() { + # fix #569996 due to renaming of Octave_map class + has_version ">=sci-mathematics/octave-4.0" && \ + epatch "${FILESDIR}/${P}-octave-4-map.patch" + autotools-utils_src_prepare + use cxx && BUILD_CXX="${S}_cxx" + use python && python_copy_sources +} + +src_configure() { + local myeconfargs=( + $(use_with octave) + ) + if use octave; then + export OCT_INSTALL_DIR="$(octave-config -p LOCALOCTFILEDIR)" + export M_INSTALL_DIR="$(octave-config -p LOCALFCNFILEDIR)" + else + export MKOCTFILE=None + fi + + myeconfargs+=( + $(use_with guile) + ) + + if use python; then + python_foreach_impl run_in_build_dir autotools-utils_src_configure + else + autotools-utils_src_configure + fi + + if use cxx; then + myeconfargs+=( --with-cxx --without-octave --without-python ) + BUILD_DIR="${BUILD_CXX}" autotools-utils_src_configure + fi +} + +src_compile() { + if use python; then + python_foreach_impl run_in_build_dir autotools-utils_src_compile + else + autotools-utils_src_compile + fi + use cxx && BUILD_DIR="${BUILD_CXX}" autotools-utils_src_compile + #-C "${BUILD_DIR}_cxx" +} + +src_test() { + do_test() { + local a f + cd "${BUILD_DIR}"/test + for a in {1..7}; do + for f in {5..9}; do + ./testopt -a $a -o $f || die "algorithm $a function $f failed" + done + done + } + if use python; then + python_foreach_impl run_in_build_dir do_test + else + do_test + fi + cd "${BUILD_CXX}"/test + for a in {1..9}; do + for f in {5..9}; do + ./testopt -a $a -o $f || die "algorithm $a function $f failed" + done + done +} + +src_install() { + # build cxx first so the c lib overwrites the pc file + use cxx && BUILD_DIR="${BUILD_CXX}" autotools-utils_src_install + if use python; then + python_foreach_impl run_in_build_dir autotools-utils_src_install + else + autotools-utils_src_install + fi + local r + for r in */README; do newdoc ${r} README.$(dirname ${r}); done +} diff --git a/sci-libs/o2scl/Manifest b/sci-libs/o2scl/Manifest new file mode 100644 index 000000000000..5f31e2fc79b0 --- /dev/null +++ b/sci-libs/o2scl/Manifest @@ -0,0 +1,3 @@ +DIST o2scl-0.920.tar.gz 34498666 SHA256 dd08c0cb0ab13b9d63ae0cc83f026f69076166877a76661aa5059b7cce29e712 SHA512 a80c959b76d15473e206f1caac496607af254f0617f7a18d13bd9732861b6c51f5db8ca3ff6866bb8d0ea70865d4ac94cb972e0a0c158f19034667340341467c WHIRLPOOL 625548dd5c954d2227627f6ae0b04ccb81ba55948e5f0b5a8315b491ef45a2648b62c062aadc5c0689ce2c2c404996132d33f3ad924c1a1e5ed68c95554d40dc +EBUILD o2scl-0.920.ebuild 1672 SHA256 5cfd99c2e86d20d3adae7e91017349c7871cf3014e56d67dc2d34d251a7d46db SHA512 10469aa3ce9e07a0f614c214e6356ff29206d48d5d7ffb61ca5f53f7d41a985707b980d9fb58329b7806530d4e02de59c40e094dac29a746330daf755d909f27 WHIRLPOOL c83d875e6de7282dbae210e6fffb216549e4fa6d38c39c90fa116809a33fd4b630e3b55085826aa517137b58c8a9de7c4d1486915d02241000c6f905a51ac2e6 +MISC metadata.xml 916 SHA256 3e15f775463e9f1e04352d59e686cb6bcae038021794a0ca3dee6e1e9d3ba6bc SHA512 63f980730302a7c1ecdc6481da44613779115ea67339b8d29d2dd02bc91330994bf09aa6955fb836b7cdc2906ca5c7168ff34c74f94df7854397e87bec279cd3 WHIRLPOOL 76e1755b0504e2cd3d1d479c16f4f8a5d481ac98266cf6e298c697d81f48a7bdd5a13cc24b7ad921deef49d0ede6c68e0656f78639913a7ffb6dadfc9ee93a0a diff --git a/sci-libs/o2scl/metadata.xml b/sci-libs/o2scl/metadata.xml new file mode 100644 index 000000000000..12a668d82eb1 --- /dev/null +++ b/sci-libs/o2scl/metadata.xml @@ -0,0 +1,22 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + O2scl is a C++ class library for object-oriented numerical + programming. It includes classes based on numerical routines from + GSL and CERNLIB and two sub-libraries: thermodynamics of ideal and + nearly-ideal particles with quantum statistics and e quations of + state for finite density relevant for neutron stars. + </longdescription> + <use> + <flag name="armadillo">Build matrix manipulation with <pkg>sci-libs/armadillo</pkg></flag> + <flag name="eigen">Build matrix manipulation with <pkg>dev-cpp/eigen</pkg></flag> + </use> + <upstream> + <remote-id type="github">awsteiner/o2scl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/o2scl/o2scl-0.920.ebuild b/sci-libs/o2scl/o2scl-0.920.ebuild new file mode 100644 index 000000000000..bf2fa4a38a83 --- /dev/null +++ b/sci-libs/o2scl/o2scl-0.920.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic + +DESCRIPTION="Object-oriented Scientific Computing Library" +HOMEPAGE="http://web.utk.edu/~asteine1/o2scl" +SRC_URI="https://github.com/awsteiner/${PN}/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="armadillo debug doc examples eigen fftw gsl hdf5 openmp readline static-libs" + +RDEPEND=" + dev-libs/boost:0= + >=sci-libs/gsl-2:0= + virtual/cblas:= + eigen? ( dev-cpp/eigen:3 ) + armadillo? ( sci-libs/armadillo[lapack] ) + fftw? ( sci-libs/fftw:3.0= ) + hdf5? ( sci-libs/hdf5:0= ) + readline? ( sys-libs/readline:0= ) +" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp && ! tc-check-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + die "need openmp capable compiler" + fi +} + +src_configure() { + use debug || append-cppflags -DO2SCL_NO_RANGE_CHECK + econf \ + --enable-acol \ + $(use_enable armadillo) \ + $(use_enable eigen) \ + $(use_enable fftw) \ + $(use_enable gsl gsl2) \ + $(use_enable hdf5 hdf) \ + $(use_enable hdf5 partlib) \ + $(use_enable hdf5 eoslib) \ + $(use_enable openmp) \ + $(use_enable static-libs static) +} + +src_install() { + default + use static-libs || prune_libtool_files + rm -r "${ED}"/usr/doc || die + if use doc; then + dodoc -r doc/o2scl/html + docompress -x /usr/share/doc/${PF}/html + fi + if use examples; then + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-libs/oc/Manifest b/sci-libs/oc/Manifest new file mode 100644 index 000000000000..66e7daadcf4f --- /dev/null +++ b/sci-libs/oc/Manifest @@ -0,0 +1,5 @@ +DIST oc-2.0.tar.gz 1104073 SHA256 4ed67dc543a6125731ccfadac14fe8f40cc0e7a74139f4f0612a6a3b1a4a4bab SHA512 e583fbacc8929ef5b2ae0d0f675816b8f46056b11987f8285688a7321d3dfd244a748be00f009f1b2c2b7f95e5a6ecc8eb8e907f81415e849f10a5ff138e82a4 WHIRLPOOL 2dbb286e1e6a711f6ff85956e778ea0dd627e2e67588093ca41ebf3045f97098d9766265769175777066ba2bfd1b88024810ba2c8d883b3bfb86ec8029f1e94e +EBUILD oc-2.0.ebuild 570 SHA256 6a0f3bcd65724b67e2467307b71e2690409d57bdff14b762c7efcd21b862b382 SHA512 5fa7ffd3da5a0a2d92bcf280b2419001f0cd8c4d5f0305ad11ba031703bfeda1d9ebfbf42168001ff33c567e09d1547cb276c9faf87f6eb9c31802de606e48a7 WHIRLPOOL d1f50bd87b45e06c1ea26af7c82bc541d91f4571fce5ca867709ef0ae011a3e5dedc7737aaa5de5286bedc9b5373b40cf2fc712ada0409454005b4df1beaf591 +MISC ChangeLog 2408 SHA256 c2db0d24f0d5a2f461c250d2abad4752b4ac8abbe97d469859e47f87177f14f7 SHA512 9c41c0cd6d2105f4a4ae3107a14ab459d10c5ac2d9cbac8d985ed07919a63e34bcf4dd036884e29eb1dbb56c24ca6e7be9f76597fe0587bd0bd40072e9e56196 WHIRLPOOL 4040dcb8206a91b8db177809c4d238240ad26e2939361bcf2663ab77d7d452ab0100365a79066c9c01fbc3c45590b2c07b4b3cea03eba6d42140044da11d064c +MISC ChangeLog-2015 557 SHA256 034bd2593f073654bba0234f602eb2ae7059ef5c465f13b30617f83c2ffb22e3 SHA512 d5f5fd52d49e1bf8ad6ca7f769e4800ae27240625356b9937e20371030c1f79a0d9c9321c16a2bc4795fa1969aadc9aeda0a0a0901e9f7c60b3e620810502dc7 WHIRLPOOL a466e651bc1d96c4c329f1015240637d8f330f359ccc57dff3ed54b95ba30b6abf1a599dc57eca34c1d40f05d304dfcb757c29b9330795677e2bfe172d46a3fe +MISC metadata.xml 482 SHA256 094bbc86dcd67004e06ec8cfd641fd05e1949f376943f5c99f1332fff590bace SHA512 0dd427f07316d37edd10316fb48baed95cec7b180d29944bc9e1bbb3d3f63f947b4681e0adc9786f88a2df2d80838706ad8a9bda6802012b11c4e0033fff1720 WHIRLPOOL fd8df2f5b92f812d46e3a836c4f3541028da07a3323e311814cfc402adffcb2cfd50b17ebb32eb2ae8b86b2196ecc109660cdf4158f139b4050e2d30e36c0d16 diff --git a/sci-libs/oc/metadata.xml b/sci-libs/oc/metadata.xml new file mode 100644 index 000000000000..fb465d5b6c7d --- /dev/null +++ b/sci-libs/oc/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The New OPeNDAP C API (oc) is an OPeNDAP DAP 2.0 client implementation + written in generic C. This new API allows for more funcionality and + less complexity than the original C API. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/oc/oc-2.0.ebuild b/sci-libs/oc/oc-2.0.ebuild new file mode 100644 index 000000000000..f44b5451489a --- /dev/null +++ b/sci-libs/oc/oc-2.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 +inherit autotools-utils + +DESCRIPTION="Network Data Access Protocol client C library" +HOMEPAGE="http://opendap.org/" +SRC_URI="http://opendap.org/pub/OC/source/${P}.tar.gz" + +LICENSE="LGPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +RDEPEND="net-misc/curl" +DEPEND="${RDEPEND}" + +# tests need network +#PROPERTIES=network + +src_install() { + autotools-utils_src_install + use doc; dodoc docs/oc*html && dohtml docs/html/* +} diff --git a/sci-libs/octomap/Manifest b/sci-libs/octomap/Manifest new file mode 100644 index 000000000000..ab4a68995a3e --- /dev/null +++ b/sci-libs/octomap/Manifest @@ -0,0 +1,6 @@ +DIST octomap-1.8.1.tar.gz 1679526 SHA256 8b18ef7693e87f1400b9a8bc41f86e3b28259ac98c0b458037232652380aa6af SHA512 e35567da0d6741747abbc87de49733d0e92bae8aedfe66a63766740cc6566f3cfdbc3c986369177497cc9a8fb208ed9b727da496cec48e2ad23328df06fbc8d6 WHIRLPOOL 7bad33e4bb01ef0d0599d4e7ea6b323e4aacb06d9f5e8d4a05b52aa0be72d205735402ed25f2ff3fcad6636f838124453f61bff1808fbe75154a4e7d32d1ded3 +EBUILD octomap-1.8.1.ebuild 1839 SHA256 6f52c6363f0f7043ef232a7cbf594e4668df4c65270a849c3b8192e0b792136f SHA512 d5b238fd8dcfa388bf9c8f9a6804766b7433e6e6c79e63846b0890963c994293ea955af6639eaf2cefd16a804a7077c5af36d91fbe50196796fdf6f37d36f74a WHIRLPOOL 0a20cc14f8695ed4b50b4af0ca645e958bf78142b276f1e7bd94ab9f8445177cf74a42580dcffcd8e38269b0feef910533a94e46e7c03410edc3fc12c2b38a5c +EBUILD octomap-9999.ebuild 1839 SHA256 6f52c6363f0f7043ef232a7cbf594e4668df4c65270a849c3b8192e0b792136f SHA512 d5b238fd8dcfa388bf9c8f9a6804766b7433e6e6c79e63846b0890963c994293ea955af6639eaf2cefd16a804a7077c5af36d91fbe50196796fdf6f37d36f74a WHIRLPOOL 0a20cc14f8695ed4b50b4af0ca645e958bf78142b276f1e7bd94ab9f8445177cf74a42580dcffcd8e38269b0feef910533a94e46e7c03410edc3fc12c2b38a5c +MISC ChangeLog 3175 SHA256 08b90583cdf7942c86191479f5d868bf465c8215ef27427e1bca7b651e33a389 SHA512 6789c4dfa7a0af71ca60fb387bcc70a632eab091e251689f39b985601817e1bc0485d627d118cb131f7b8b1466f30237acdc4fdc6c97d3f2043b19678907b5ef WHIRLPOOL a6d5b6af19a8855f356b3d58fe00296e131e5f519941a3edc28dbf5db801c3978c7f7393e04d27d59d6608f37056b5687c8915e6b2e05ed916b694f4ce05773b +MISC ChangeLog-2015 524 SHA256 867586cd4bbef6d254bac6bfb8e1b217ffa8c78823b69f7701ce8ccd1c42acb4 SHA512 e36f8999a813e86442588ce532000f3344086735e87653e8fb444957cb0bea84bcbb860af8298562fb657f4a680dc14b90a94f5b050309c47a894c58cff1ef04 WHIRLPOOL b6c7fa09e5769ee5d5ee839e076318c3d91972c4690d522003a5e8f473d6d25971c9f712e5a1e50cf88b0c92d0fbaef892bc262f509209903ec292a7b0dcc52f +MISC metadata.xml 703 SHA256 30883addc464d666b51aa2e7b2674f7ed2d55a63c891464eb360403fdc8c074f SHA512 66b3c9143aea83a044a719031b4eb0d140e599048885ca6bb02e74ebebbbd2e9abccf11dc0af32e6ce94d3849dcf639ebaf34ff2c8d6e34f32767e08e465c6b0 WHIRLPOOL 8d5e109a0dfbcd32d8810e808b10dcf7dd41a86b913ed492a2726b873916d3e5289da914f766106ef1183feab8a6dd2e1eef8d71f2bda84b472efa51d5d9828d diff --git a/sci-libs/octomap/metadata.xml b/sci-libs/octomap/metadata.xml new file mode 100644 index 000000000000..d6afbe70c1f9 --- /dev/null +++ b/sci-libs/octomap/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>aballier@gentoo.org</email> + <name>Alexis Ballier</name> + </maintainer> + <longdescription lang="en"> + The OctoMap library implements a 3D occupancy grid mapping approach, providing data structures and mapping algorithms in C++ particularly suited for robotics. +</longdescription> + <use> + <flag name="dynamicEDT3D">Build and install dynamicEDT3D library: A library for incrementally updatable Euclidean distance transforms in 3D.</flag> + </use> + <upstream> + <remote-id type="github">OctoMap/octomap</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/octomap/octomap-1.8.1.ebuild b/sci-libs/octomap/octomap-1.8.1.ebuild new file mode 100644 index 000000000000..30141845c394 --- /dev/null +++ b/sci-libs/octomap/octomap-1.8.1.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/OctoMap/octomap" +fi + +inherit ${SCM} cmake-utils + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/OctoMap/octomap/archive/v${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="An Efficient Probabilistic 3D Mapping Framework Based on Octrees" +HOMEPAGE="http://octomap.github.io/" +IUSE="qt4 dynamicEDT3D doc" +LICENSE="BSD qt4? ( GPL-2 )" +SLOT="0" + +RDEPEND=" + qt4? ( + virtual/opengl + dev-qt/qtcore:4 + dev-qt/qtgui:4 + x11-libs/libQGLViewer:= + ) +" +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen + media-gfx/graphviz + ) +" + +src_prepare() { + sed -e 's/DESTINATION lib/DESTINATION ${CMAKE_INSTALL_LIBDIR}/' \ + -i */CMakeLists.txt \ + -i */CMakeModules/InstallPkgConfigFile.cmake || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + "-DBUILD_OCTOVIS_SUBPROJECT=$(usex qt4 ON OFF)" + "-DBUILD_DYNAMICETD3D_SUBPROJECT=$(usex dynamicEDT3D ON OFF)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + if use doc ; then + cd "${BUILD_DIR}/octomap" + emake docs + if use dynamicEDT3D ; then + cd "${BUILD_DIR}/dynamicEDT3D" + emake docs_dynamicEDT3D + fi + fi +} + +src_install() { + cmake-utils_src_install + if use doc ; then + insinto /usr/share/doc/${PF}/html/octomap + doins -r "${S}/octomap/doc/html/"* + if use dynamicEDT3D ; then + insinto /usr/share/doc/${PF}/html/dynamicEDT3D + doins -r "${S}/dynamicEDT3D/doc/html/"* + fi + fi + + insinto /usr/share/ros_packages/${PN} + doins "${ED}/usr/share/${PN}/package.xml" + if use qt4; then + insinto /usr/share/ros_packages/octovis + doins "${ED}/usr/share/octovis/package.xml" + fi +} diff --git a/sci-libs/octomap/octomap-9999.ebuild b/sci-libs/octomap/octomap-9999.ebuild new file mode 100644 index 000000000000..30141845c394 --- /dev/null +++ b/sci-libs/octomap/octomap-9999.ebuild @@ -0,0 +1,87 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/OctoMap/octomap" +fi + +inherit ${SCM} cmake-utils + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/OctoMap/octomap/archive/v${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="An Efficient Probabilistic 3D Mapping Framework Based on Octrees" +HOMEPAGE="http://octomap.github.io/" +IUSE="qt4 dynamicEDT3D doc" +LICENSE="BSD qt4? ( GPL-2 )" +SLOT="0" + +RDEPEND=" + qt4? ( + virtual/opengl + dev-qt/qtcore:4 + dev-qt/qtgui:4 + x11-libs/libQGLViewer:= + ) +" +DEPEND="${RDEPEND} + doc? ( + app-doc/doxygen + media-gfx/graphviz + ) +" + +src_prepare() { + sed -e 's/DESTINATION lib/DESTINATION ${CMAKE_INSTALL_LIBDIR}/' \ + -i */CMakeLists.txt \ + -i */CMakeModules/InstallPkgConfigFile.cmake || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + "-DBUILD_OCTOVIS_SUBPROJECT=$(usex qt4 ON OFF)" + "-DBUILD_DYNAMICETD3D_SUBPROJECT=$(usex dynamicEDT3D ON OFF)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + if use doc ; then + cd "${BUILD_DIR}/octomap" + emake docs + if use dynamicEDT3D ; then + cd "${BUILD_DIR}/dynamicEDT3D" + emake docs_dynamicEDT3D + fi + fi +} + +src_install() { + cmake-utils_src_install + if use doc ; then + insinto /usr/share/doc/${PF}/html/octomap + doins -r "${S}/octomap/doc/html/"* + if use dynamicEDT3D ; then + insinto /usr/share/doc/${PF}/html/dynamicEDT3D + doins -r "${S}/dynamicEDT3D/doc/html/"* + fi + fi + + insinto /usr/share/ros_packages/${PN} + doins "${ED}/usr/share/${PN}/package.xml" + if use qt4; then + insinto /usr/share/ros_packages/octovis + doins "${ED}/usr/share/octovis/package.xml" + fi +} diff --git a/sci-libs/ogdi/Manifest b/sci-libs/ogdi/Manifest new file mode 100644 index 000000000000..f8087142fb84 --- /dev/null +++ b/sci-libs/ogdi/Manifest @@ -0,0 +1,13 @@ +AUX ogdi-3.1.5-fpic.patch 7619 SHA256 4cb6775b0b8af81a7a4a18bbdbac004b64df7661e3ad8fa89c26ef664fca1f46 SHA512 da978d0e38794c4b987e787c3fe2168fa4379e316390d7be7bb0490d0e0bdce54d59c105a03314b8e3f9ba450a2ba62ea07d11d89dc199c5f476da2225462251 WHIRLPOOL f75eca99b55ef9ac89607f07e326882440d88ba4312b037e8881b06f75370fafea54a6b1fe8cf9721b3891055926db34f24f076fd0356607ca09d1f9cd2c57e9 +AUX ogdi-3.1.6-fpic.patch 961 SHA256 ddb4e93c553f703f2a14f0f25a2c092377de4cd692cb73c3ecacce0e1fdd40f2 SHA512 9d5d89d907043b14f5a18b6e036a1784b657ae6dd824d03067ab3e1e4e777ad55286e9addf15c9499523d7b2fdb743d329660f64a54e5140961c567135b40579 WHIRLPOOL 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0cd3a58b95b62af6c618751032d5d84ac0adbc72fc8f582c3bb235d23644d794 SHA512 3ac6c554c8f89252b8ff6f8f9ff3824ec1c453b1ac395d41e395ccd1c15c659dfbb77d0a6110edf2cd20a1c738f70e444a566cd6bee7ead2bc563d773c77c737 WHIRLPOOL d8a63c9d69d4ea4f009e80dae49a9825f877d1a9d8511e90a6286a319beaa274b52bf3f8dcb34c62aea3bcc94aa98b4d37a4be4f1648c27df729aa9da5998936 +AUX ogdi-3.2.0_beta2-subdirs.patch 905 SHA256 081ce1a5b9e649a40611253d12467a2a5402875acddda73ef8b7edd5b7bbca49 SHA512 b6e6f50dafdb6aea991b8ece37953a9910b3fa790dcb68108ba7316c81de3cffae1413afb9d9126457550fa46bded8a7613c8be27fcd9956c8c17b5b64065732 WHIRLPOOL 5fe9b97df36fbdf830619a1c3093af0bfbf9055b18da171876ec7fe1d038b6465418db6196fbf0a5a9efc6f8b9390adddfa277b116b1b9ca6532e25329815f7d +DIST ogdi-3.1.5.tar.gz 913902 SHA256 f9d65312d03ac0b1ba0a0dd05885c41a3995fccfe9cab8d7012300546da3e44b SHA512 fd77106a25b07bbaba23cab2e9e5298d7df62faf50c9ead72c4def683c4097717559b816a476ddfa16823f23d418a474ec49937b961ba06f606880f3338d6cfd WHIRLPOOL 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83e2a3b4e79a178f226a30f5c169ad438c0ff29ad4a3472ec6445aed821b0241 SHA512 f73e49a47290430708e4eabfe5aebf83c12d88b71d9f7c542b0f5b5525eb57533479c9ca2c098ec9c3cdb6681a4ae7b36766737bdedd4ce27cbcdfa7fb114372 WHIRLPOOL 4dbfd3fa1ee4af9913f09004f422b0cab57b13dc5c6d42fa9274e90f705e8dc2f7a233f864eee86e8d96620439af92cf81ed8fb264c39644a90222d606895307 +MISC ChangeLog 2775 SHA256 fcaa7c31edb0c657701478b1ec425fca48be2aa282ed34171b2414f3b9c5e59f SHA512 02f5842d232343dd4e60cdee1afff6a753e293814b8b5aa83042f1b1b3b78e84bbe6ec19b2af79b44194988977061eb70a50b0b3b4de53bc7c278947f00769b1 WHIRLPOOL 07ffcce6cebd5bb3a9aee23ed9f80e56ffa303ee2823b99a94e0950f82ecf832594bb1bfbd4fc9d8817fd59ca59495ff9ba3eefa3a0d73d52146ecbc6ab5ebc6 +MISC ChangeLog-2015 7219 SHA256 35e40d7d737d9cacd6901af4bde139ba2d4f8088bdb41e8273ff9c15e0f89858 SHA512 007a1aa5a58efdba46508a71b3bb8d00cb5933bff950b3ae705be65de553d3de111e0b619b50535f31942a2411efe5bc58c3c5a38e7d1dc07ae723d349471441 WHIRLPOOL fd9d61b96c9d16e31ea8c9ab3d53d8691c9a9ae84c419f54d6fc6f95cb50892cc3a41d3003f815be3ae06bd1e3bc750a180d041a33cda0ad816b3ec40bebe529 +MISC metadata.xml 337 SHA256 a7e73c7860ede062ae0b1a4346a45b03c20dd4236458966b70fd9cc6f798b187 SHA512 958474862734f915497c1e574254cd2152009f436b59dd57be9bcd5ad0ae2949dba1f6275ad3a68b3a6d60863093df2bf2bcfffdea51b591e9c1864231899221 WHIRLPOOL 9ad54255d00f741e01a762ca7a7e5b7c34e3366a6b7bdebce1148b6df6449ba282904075663a0b471fec9a8582fb5ebf7138fcf7625e24034928bc50709fd222 diff --git a/sci-libs/ogdi/files/ogdi-3.1.5-fpic.patch b/sci-libs/ogdi/files/ogdi-3.1.5-fpic.patch new file mode 100644 index 000000000000..33fb56103193 --- /dev/null +++ b/sci-libs/ogdi/files/ogdi-3.1.5-fpic.patch @@ -0,0 +1,177 @@ +Only in ogdi-3.1.5.orig: bin +Only in ogdi-3.1.5.orig/config: Linux.mak +Only in ogdi-3.1.5.orig: config.cache +Only in ogdi-3.1.5.orig: config.log +Only in ogdi-3.1.5.orig: config.status +Only in ogdi-3.1.5.orig/external/expat: OBJ.Linux +diff -ur ogdi-3.1.5/external/expat/makefile ogdi-3.1.5.orig/external/expat/makefile +--- ogdi-3.1.5/external/expat/makefile 2001-08-27 14:11:10.000000000 +0000 ++++ ogdi-3.1.5.orig/external/expat/makefile 2005-08-01 18:57:49.020052368 +0000 +@@ -36,7 +36,7 @@ + # Compilation flags + # + INCLUDES = $(CURRENT_INCLUDE) +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) \ ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC \ + -DVERSION=\"expat_1.95.1\" -DPACKAGE="expat" + + ifeq ($(BIG_ENDIAN),1) +Only in ogdi-3.1.5.orig/external/zlib: OBJ.Linux +diff -ur ogdi-3.1.5/external/zlib/makefile ogdi-3.1.5.orig/external/zlib/makefile +--- ogdi-3.1.5/external/zlib/makefile 2001-04-19 05:26:46.000000000 +0000 ++++ ogdi-3.1.5.orig/external/zlib/makefile 2005-08-01 18:58:47.984088472 +0000 +@@ -46,7 +46,7 @@ + # Compilation flags + # + INCLUDES = $(CURRENT_INCLUDE) +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + # + # Primary target +Only in ogdi-3.1.5.orig/lib: Linux +Only in ogdi-3.1.5.orig/ogdi/c-api: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/c-api/makefile ogdi-3.1.5.orig/ogdi/c-api/makefile +--- ogdi-3.1.5/ogdi/c-api/makefile 2001-04-19 05:29:31.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/c-api/makefile 2005-08-01 18:53:51.936094608 +0000 +@@ -23,7 +23,7 @@ + $(GRASS_INCLUDE) $(ZLIB_INCLUDE) $(PROJ_INCLUDE) \ + $(EXPAT_INCLUDE) + +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= $(RPC_LINKLIB) $(ZLIB_LINKLIB) $(EXPAT_LINKLIB) $(WIN_LINKLIB) \ + $(PROJ_STATICLIB) $(MATH_LINKLIB) +Only in ogdi-3.1.5.orig/ogdi/datum_driver/canada: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/datum_driver/canada/makefile ogdi-3.1.5.orig/ogdi/datum_driver/canada/makefile +--- ogdi-3.1.5/ogdi/datum_driver/canada/makefile 2001-02-19 04:12:21.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/datum_driver/canada/makefile 2005-08-01 19:03:00.932634448 +0000 +@@ -17,7 +17,7 @@ + SOURCES = nadconv.c dtcanada.c + + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(OGDI_INCLUDE) $(PROJ_INCLUDE) +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= + +Only in ogdi-3.1.5.orig/ogdi/datum_driver/usa: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/datum_driver/usa/makefile ogdi-3.1.5.orig/ogdi/datum_driver/usa/makefile +--- ogdi-3.1.5/ogdi/datum_driver/usa/makefile 2001-02-19 04:12:21.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/datum_driver/usa/makefile 2005-08-01 19:03:24.883993288 +0000 +@@ -17,7 +17,7 @@ + SOURCES = dtusa.c + + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(OGDI_INCLUDE) $(PROJ_INCLUDE) +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= $(PROJ_STATICLIB) + +Only in ogdi-3.1.5.orig/ogdi/driver/adrg: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/driver/adrg/makefile ogdi-3.1.5.orig/ogdi/driver/adrg/makefile +--- ogdi-3.1.5/ogdi/driver/adrg/makefile 2001-06-22 16:37:50.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/driver/adrg/makefile 2005-08-01 19:06:07.422283712 +0000 +@@ -18,7 +18,7 @@ + + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(OGDI_INCLUDE) $(PROJ_INCLUDE) + +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= $(OGDI_LINKLIB) $(GLUTIL_STATICLIB) + +Only in ogdi-3.1.5.orig/ogdi/driver/dted: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/driver/dted/makefile ogdi-3.1.5.orig/ogdi/driver/dted/makefile +--- ogdi-3.1.5/ogdi/driver/dted/makefile 2001-02-19 04:12:21.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/driver/dted/makefile 2005-08-01 19:06:31.460629328 +0000 +@@ -17,7 +17,7 @@ + SOURCES = dted.c utils.c object.c + + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(OGDI_INCLUDE) $(PROJ_INCLUDE) +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= $(OGDI_LINKLIB) $(GLUTIL_STATICLIB) + +Only in ogdi-3.1.5.orig/ogdi/driver/network: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/driver/network/makefile ogdi-3.1.5.orig/ogdi/driver/network/makefile +--- ogdi-3.1.5/ogdi/driver/network/makefile 2001-02-19 04:12:21.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/driver/network/makefile 2005-08-01 19:06:52.242470008 +0000 +@@ -17,7 +17,7 @@ + SOURCES = remote.c ecs_clnt.c + + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(OGDI_INCLUDE) $(GRASS_INCLUDE) $(PROJ_INCLUDE) +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= $(OGDI_LINKLIB) $(RPC_LINKLIB) $(WIN_LINKLIB) + +Only in ogdi-3.1.5.orig/ogdi/driver/rpf: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/driver/rpf/makefile ogdi-3.1.5.orig/ogdi/driver/rpf/makefile +--- ogdi-3.1.5/ogdi/driver/rpf/makefile 2001-02-19 04:12:21.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/driver/rpf/makefile 2005-08-01 19:07:39.956216416 +0000 +@@ -19,7 +19,7 @@ + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(OGDI_INCLUDE) \ + $(GRASS_INCLUDE) $(PROJ_INCLUDE) + +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= $(OGDI_LINKLIB) $(VPF_STATICLIB) $(GLUTIL_STATICLIB) $(WIN_LINKLIB) $(MATH_LINKLIB) + +Only in ogdi-3.1.5.orig/ogdi/driver/skeleton: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/driver/skeleton/makefile ogdi-3.1.5.orig/ogdi/driver/skeleton/makefile +--- ogdi-3.1.5/ogdi/driver/skeleton/makefile 2001-02-19 04:12:21.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/driver/skeleton/makefile 2005-08-01 19:07:15.500934184 +0000 +@@ -18,7 +18,7 @@ + + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(OGDI_INCLUDE) $(GLUTIL_INCLUDE) $(PROJ_INCLUDE) + +-CFLAGS = $(INCLUDES) $(MACHINE) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(MACHINE) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= $(OGDI_LINKLIB) $(GLUTIL_STATICLIB) + +Only in ogdi-3.1.5.orig/ogdi/driver/vrf: OBJ.Linux +diff -ur ogdi-3.1.5/ogdi/driver/vrf/makefile ogdi-3.1.5.orig/ogdi/driver/vrf/makefile +--- ogdi-3.1.5/ogdi/driver/vrf/makefile 2001-06-20 21:49:31.000000000 +0000 ++++ ogdi-3.1.5.orig/ogdi/driver/vrf/makefile 2005-08-01 19:08:03.541630888 +0000 +@@ -17,7 +17,7 @@ + SOURCES = vrf.c utils.c feature.c object.c open.c swq.c vrfswq.c + + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(OGDI_INCLUDE) $(VPF_INCLUDE) $(PROJ_INCLUDE) $(GLUTIL_INCLUDE) +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + LINK_LIBS= $(OGDI_LINKLIB) $(WIN_LINKLIB) $(VPF_STATICLIB) $(MATH_LINKLIB) + +Only in ogdi-3.1.5.orig/ogdi/gltpd: OBJ.Linux +Only in ogdi-3.1.5.orig/ogdi/glutil: OBJ.Linux +Only in ogdi-3.1.5.orig/proj: OBJ.Linux +diff -ur ogdi-3.1.5/proj/makefile ogdi-3.1.5.orig/proj/makefile +--- ogdi-3.1.5/proj/makefile 2001-04-09 16:20:08.000000000 +0000 ++++ ogdi-3.1.5.orig/proj/makefile 2005-08-01 19:01:03.573475752 +0000 +@@ -42,7 +42,7 @@ + + INCLUDES = $(CURRENT_INCLUDE) + +-CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) ++CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) -fPIC -DPIC + + include $(TOPDIR)/config/common.mak + +Only in ogdi-3.1.5.orig/vpflib: OBJ.Linux +diff -ur ogdi-3.1.5/vpflib/makefile ogdi-3.1.5.orig/vpflib/makefile +--- ogdi-3.1.5/vpflib/makefile 2001-02-20 04:25:20.000000000 +0000 ++++ ogdi-3.1.5.orig/vpflib/makefile 2005-08-01 19:09:48.072739744 +0000 +@@ -31,7 +31,7 @@ + INCLUDES = $(CURRENT_INCLUDE) $(GENERAL_INCLUDE) $(VPF_INCLUDE) + + CFLAGS = $(INCLUDES) $(COMMON_CFLAGS) $(UNIX_DEFINE) \ +- -DSYS_BIG_ENDIAN=$(BIG_ENDIAN) ++ -DSYS_BIG_ENDIAN=$(BIG_ENDIAN) -fPIC -DPIC + + include $(TOPDIR)/config/common.mak + diff --git a/sci-libs/ogdi/files/ogdi-3.1.6-fpic.patch b/sci-libs/ogdi/files/ogdi-3.1.6-fpic.patch new file mode 100644 index 000000000000..f6fbc85e5ae9 --- /dev/null +++ b/sci-libs/ogdi/files/ogdi-3.1.6-fpic.patch @@ -0,0 +1,38 @@ +diff --git a/config/generic.mak.in b/config/generic.mak.in +index 1cb74f5..2e9cabe 100644 +--- a/config/generic.mak.in ++++ b/config/generic.mak.in +@@ -35,16 +35,16 @@ AR = ar cr + # Compilation and linking flags + # + SHLIB_CFLAGS = @C_PIC@ +-COMMON_CFLAGS = $(OPTIMIZATION) @CFLAGS@ @C_WFLAGS@ -DUNIX=1 ++COMMON_CFLAGS = $(OPTIMIZATION) @CFLAGS@ @C_WFLAGS@ -DUNIX=1 @C_PIC@ + +-SHLIB_LDFLAGS = -shared +-COMMON_LDFLAGS = $(OPTIMIZATION) ++SHLIB_LDFLAGS = -shared -Wl,-soname,$(LIB_PREFIX)$(TOBEGEN).$(SHLIB_EXT).$(OGDI_MAJOR) ++COMMON_LDFLAGS = $(OPTIMIZATION) $(LDFLAGS) + + RPC_INCLUDES = @RPC_INCLUDES@ + + UCB_STATICLIB = + +-TCL_INCLUDE = -I/usr/include/tcl8.3 ++TCL_INCLUDE = -I${prefix}/include + TCL_LINKLIB = + + # +diff --git a/config/unix.mak b/config/unix.mak +index e3af578..927b0fc 100644 +--- a/config/unix.mak ++++ b/config/unix.mak +@@ -55,7 +55,7 @@ LINK_SW = -L + ifeq ($(CFG),debug) + OPTIMIZATION = -g + else +-OPTIMIZATION = -O ++OPTIMIZATION = + endif + + # diff --git a/sci-libs/ogdi/files/ogdi-3.2.0_beta2-64b.patch b/sci-libs/ogdi/files/ogdi-3.2.0_beta2-64b.patch new file mode 100644 index 000000000000..16c40b2ff435 --- /dev/null +++ b/sci-libs/ogdi/files/ogdi-3.2.0_beta2-64b.patch @@ -0,0 +1,11 @@ +--- ogdi.old/ogdi/driver/vrf/feature.c 2007/05/09 20:46:28 1.16 ++++ ogdi/ogdi/driver/vrf/feature.c 2009/05/08 04:15:50 1.17 +@@ -1347,7 +1350,7 @@ + short int temp4; + int temp5; + date_type temp6; +- long count; ++ int32 count; + + if (returnString != NULL) { + free(returnString); diff --git a/sci-libs/ogdi/files/ogdi-3.2.0_beta2-endianess.patch b/sci-libs/ogdi/files/ogdi-3.2.0_beta2-endianess.patch new file mode 100644 index 000000000000..75c85fbb29b5 --- /dev/null +++ b/sci-libs/ogdi/files/ogdi-3.2.0_beta2-endianess.patch @@ -0,0 +1,18 @@ +diff -urNad ogdi-dfsg~/vpflib/include/machine.h ogdi-dfsg/vpflib/include/machine.h +--- ogdi-dfsg~/vpflib/include/machine.h 2007-03-27 17:35:24.000000000 +0200 ++++ ogdi-dfsg/vpflib/include/machine.h 2007-03-27 17:41:16.000000000 +0200 +@@ -15,10 +15,11 @@ + long output; + } xBYTE_ORDER; + +-#if SYS_BIG_ENDIAN == 1 +-#define MACHINE_BYTE_ORDER MOST_SIGNIFICANT +-#else ++#include <endian.h> ++#if __BYTE_ORDER == __LITTLE_ENDIAN + #define MACHINE_BYTE_ORDER LEAST_SIGNIFICANT ++#elif __BYTE_ORDER == __BIG_ENDIAN ++#define MACHINE_BYTE_ORDER MOST_SIGNIFICANT + #endif + + #ifdef _WINDOWS diff --git a/sci-libs/ogdi/files/ogdi-3.2.0_beta2-proj480.patch b/sci-libs/ogdi/files/ogdi-3.2.0_beta2-proj480.patch new file mode 100644 index 000000000000..9380f91ffd3d --- /dev/null +++ b/sci-libs/ogdi/files/ogdi-3.2.0_beta2-proj480.patch @@ -0,0 +1,297 @@ +Index: ogdi-dfsg/configure +=================================================================== +--- ogdi-dfsg.orig/configure ++++ ogdi-dfsg/configure +@@ -3939,7 +3939,7 @@ + fi + + +-for ac_header in projects.h ++for ac_header in proj_api.h + do + as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` + if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then +@@ -4085,8 +4085,8 @@ + { (exit 1); exit 1; }; } + fi + if test "$ac_cv_header_projects_h" = no ; then +- { { echo "$as_me:$LINENO: error: Unable to find external PROJ.4 projects.h file, give path or use default internal library." >&5 +-echo "$as_me: error: Unable to find external PROJ.4 projects.h file, give path or use default internal library." >&2;} ++ { { echo "$as_me:$LINENO: error: Unable to find external PROJ.4 proj_api.h file, give path or use default internal library." >&5 ++echo "$as_me: error: Unable to find external PROJ.4 proj_api.h file, give path or use default internal library." >&2;} + { (exit 1); exit 1; }; } + fi + +@@ -4095,12 +4095,12 @@ + + elif test "$with_proj" != "no" -a "$with_proj" != "" ; then + +- if test -r $with_proj/include/projects.h ; then +- echo "checking for $with_proj/include/projects.h ... found" ++ if test -r $with_proj/include/proj_api.h ; then ++ echo "checking for $with_proj/include/proj_api.h ... found" + PROJ_INCLUDE=-I$with_proj/include + else +- { { echo "$as_me:$LINENO: error: Unable to find $with_proj/include/projects.h" >&5 +-echo "$as_me: error: Unable to find $with_proj/include/projects.h" >&2;} ++ { { echo "$as_me:$LINENO: error: Unable to find $with_proj/include/proj_api.h" >&5 ++echo "$as_me: error: Unable to find $with_proj/include/proj_api.h" >&2;} + { (exit 1); exit 1; }; } + fi + +Index: ogdi-dfsg/configure.in +=================================================================== +--- ogdi-dfsg.orig/configure.in ++++ ogdi-dfsg/configure.in +@@ -81,13 +81,13 @@ + if test "$with_proj" = "yes" ; then + + AC_CHECK_LIB(proj,pj_init,PROJ_SETTING=external,PROJ_SETTING=missing,) +- AC_CHECK_HEADERS(projects.h) ++ AC_CHECK_HEADERS(proj_api.h) + + if test $PROJ_SETTING = missing ; then + AC_MSG_ERROR([Unable to find external PROJ.4 library, give path or use default internal library.]) + fi + if test "$ac_cv_header_projects_h" = no ; then +- AC_MSG_ERROR([Unable to find external PROJ.4 projects.h file, give path or use default internal library.]) ++ AC_MSG_ERROR([Unable to find external PROJ.4 proj_api.h file, give path or use default internal library.]) + fi + + PROJ_SETTING=external +@@ -95,11 +95,11 @@ + + elif test "$with_proj" != "no" -a "$with_proj" != "" ; then + +- if test -r $with_proj/include/projects.h ; then +- echo "checking for $with_proj/include/projects.h ... found" ++ if test -r $with_proj/include/projapi.h ; then ++ echo "checking for $with_proj/include/proj_api.h ... found" + PROJ_INCLUDE=-I$with_proj/include + else +- AC_MSG_ERROR([Unable to find $with_proj/include/projects.h]) ++ AC_MSG_ERROR([Unable to find $with_proj/include/proj_api.h]) + fi + + if test -r $with_proj/lib/libproj.so ; then +Index: ogdi-dfsg/ogdi/c-api/client.c +=================================================================== +--- ogdi-dfsg.orig/ogdi/c-api/client.c ++++ ogdi-dfsg/ogdi/c-api/client.c +@@ -1576,7 +1576,7 @@ + char *error_message; + ecs_CtlPoints *cpts; + ecs_Result *res; +- PJ *tempproj; ++ projPJ tempproj; + + if (multiblock != 0) { + res = &cln_dummy_result; +@@ -1598,7 +1598,7 @@ + /* Check if the projection is valid */ + + if (strncmp(projection,PROJ_LONGLAT,13) != 0) { +- tempproj = (PJ *) cln_ProjInit(projection); ++ tempproj = (projPJ) cln_ProjInit(projection); + if(tempproj == NULL) { + res = &cln_dummy_result; + ecs_SetError(res,1,"This projection string is invalid"); +@@ -1775,7 +1775,7 @@ + ecs_Result *res; + register ecs_Client *cln; + char *server_proj; +- PJ *oldtarget,*oldsource; ++ projPJ oldtarget,oldsource; + ecs_Region oldreg; + int oldisprojequal; + int oldisTargetLL; +@@ -1874,7 +1874,7 @@ + + if (strncmp(projection,PROJ_LONGLAT,13) != 0) { + cln->isTargetLL = FALSE; +- cln->target = (PJ *) cln_ProjInit(projection); ++ cln->target = (projPJ) cln_ProjInit(projection); + if(cln->target == NULL) { + goto setprojerror; + } +@@ -1920,7 +1920,7 @@ + + if (strncmp(server_proj,PROJ_LONGLAT,13) != 0) { + cln->isSourceLL = FALSE; +- cln->source = (PJ *) cln_ProjInit(server_proj); ++ cln->source = (projPJ) cln_ProjInit(server_proj); + if(cln->source == NULL) { + goto setprojerror; + } +@@ -2328,13 +2328,13 @@ + * char *d: Projection name + * + * OUT +- * return PJ *: New projection structure. If NULL, the operation ++ * return projPJ: New projection structure. If NULL, the operation + * is a failure. + * + *---------------------------------------------------------------------- + */ + +-PJ *cln_ProjInit(d) ++projPJ cln_ProjInit(d) + char *d; + { + int i,n; +@@ -2343,7 +2343,7 @@ + char *l; + int longueur; + char *c; +- PJ *retour; ++ projPJ retour; + + if ((c = (char *) malloc(strlen(d)+3)) == NULL) { + return NULL; +@@ -2378,7 +2378,7 @@ + n++; + } + +- retour = (PJ *) pj_init(n, (char **) tableau); ++ retour = (projPJ) pj_init(n, (char **) tableau); + free(c); + free(tableau); + +Index: ogdi-dfsg/ogdi/c-api/ecsgeo.c +=================================================================== +--- ogdi-dfsg.orig/ogdi/c-api/ecsgeo.c ++++ ogdi-dfsg/ogdi/c-api/ecsgeo.c +@@ -310,7 +310,7 @@ + char *projection; + double X1,Y1,X2,Y2; + { +- PJ *proj; ++ projPJ proj; + char **argv; + int argc; + double lon1,lat1,lon2,lat2; +Index: ogdi-dfsg/ogdi/datum_driver/usa/dtusa.c +=================================================================== +--- ogdi-dfsg.orig/ogdi/datum_driver/usa/dtusa.c ++++ ogdi-dfsg/ogdi/datum_driver/usa/dtusa.c +@@ -26,7 +26,12 @@ + ********************************************************************/ + + #include "ecs.h" +-#include "projects.h" ++#include "proj_api.h" ++ ++/* Definition from Proj.4 */ ++projUV nad_cvt(projUV, int, struct CTABLE *); ++struct CTABLE *nad_init(projCtx ctx, char *); ++void nad_free(struct CTABLE *); + + typedef struct { + struct CTABLE *dtptr; +@@ -124,7 +129,7 @@ + strcat(pathfile,"/"); + strcat(pathfile,table); + +- ptr->dtptr = nad_init(pathfile); ++ ptr->dtptr = nad_init(pj_get_default_ctx(), pathfile); + if (ptr->dtptr == NULL) { + ptr->count--; + return FALSE; +Index: ogdi-dfsg/ogdi/include/ecs_util.h +=================================================================== +--- ogdi-dfsg.orig/ogdi/include/ecs_util.h ++++ ogdi-dfsg/ogdi/include/ecs_util.h +@@ -105,12 +105,7 @@ + #include <sys/types.h> + #include <sys/stat.h> + +-#include "projects.h" +- +-/* Ensure we are compatible with PROJ.4.4.x and PROJ.4.3.x */ +-#ifndef USE_PROJUV +-# define projUV UV +-#endif ++#include "proj_api.h" + + #include "ecs.h" + +@@ -1054,8 +1049,8 @@ + ecs_Family currentSelectionFamily: Current layer selection type + char *tclprocname: attribute callback procedure for tcl + char *target_proj: Projection descriptor +- PJ *target: target (c interface) projection descriptors +- PJ *source: source (driver) projection descriptors ++ projPJ target: target (c interface) projection descriptors ++ projPJ source: source (driver) projection descriptors + ecs_Datum targetdatum: target datum information + ecs_Datum sourcedatum: source datum information + void *dthandle: Handle to the datum driver +@@ -1092,8 +1088,8 @@ + ecs_Family currentSelectionFamily; /* Current layer selection type */ + char *tclprocname; /* attribute callback procedure for tcl */ + char *target_proj; +- PJ *target; /* source and target projection descriptors */ +- PJ *source; ++ projPJ target; /* source and target projection descriptors */ ++ projPJ source; + int isSourceLL; /* flags to avoid unnecessary computation */ + int isTargetLL; + int isProjEqual; +@@ -1165,7 +1161,7 @@ + + /* Projection conversion functions */ + +-PJ *cln_ProjInit _ANSI_ARGS_((char *d)); ++projPJ cln_ProjInit _ANSI_ARGS_((char *d)); + int cln_CompareProjections _ANSI_ARGS_((int ClientID)); + int cln_UpdateMaxRegion _ANSI_ARGS_((int ClientID, double x, double y, ecs_Region *gr, int sens, int first)); + int cln_ConvRegion _ANSI_ARGS_((int ClientID, ecs_Region *gr, int sens)); +Index: ogdi-dfsg/contrib/ogdi_import/ogdi_import.c +=================================================================== +--- ogdi-dfsg.orig/contrib/ogdi_import/ogdi_import.c ++++ ogdi-dfsg/contrib/ogdi_import/ogdi_import.c +@@ -63,12 +63,7 @@ + #include "ecs.h" + #include "shapefil.h" + #include <assert.h> +-#include "projects.h" +- +-#ifndef PJ_VERSION +-#define projPJ PJ* +-#define projUV UV +-#endif ++#include "proj_api.h" + + static int ClientID = -1; + static int bNoDict = FALSE; +Index: ogdi-dfsg/contrib/ogdi_info/ogdi_info.c +=================================================================== +--- ogdi-dfsg.orig/contrib/ogdi_info/ogdi_info.c ++++ ogdi-dfsg/contrib/ogdi_info/ogdi_info.c +@@ -63,7 +63,7 @@ + */ + + #include "ecs.h" +-#include "projects.h" ++#include "proj_api.h" + + static int ClientID = -1; + static int bNoDict = FALSE; +@@ -214,7 +214,7 @@ + /* DumpGlobalRegion() */ + /************************************************************************/ + +-static int DumpGlobalRegion( ecs_Region * region, PJ * proj_defn ) ++static int DumpGlobalRegion( ecs_Region * region, projPJ proj_defn ) + + { + ecs_Result *result; +@@ -398,7 +398,7 @@ + + { + ecs_Result *result; +- PJ *proj_defn = NULL; ++ projPJ proj_defn = NULL; + + /* -------------------------------------------------------------------- */ + /* Close old client if there is one active. */ diff --git a/sci-libs/ogdi/files/ogdi-3.2.0_beta2-subdirs.patch b/sci-libs/ogdi/files/ogdi-3.2.0_beta2-subdirs.patch new file mode 100644 index 000000000000..c98390c440de --- /dev/null +++ b/sci-libs/ogdi/files/ogdi-3.2.0_beta2-subdirs.patch @@ -0,0 +1,24 @@ +diff -urN ogdi-3.2.0.beta2.old/makefile ogdi-3.2.0.beta2/makefile +--- ogdi-3.2.0.beta2.old/makefile 2011-06-17 12:45:53.171219473 +0200 ++++ ogdi-3.2.0.beta2/makefile 2011-06-17 12:46:34.013708870 +0200 +@@ -17,7 +17,7 @@ + # + # Sub-directories that need to be built + # +-subdirs = external vpflib ogdi contrib ++subdirs = vpflib ogdi contrib + + ifneq ($(PROJ_SETTING),external) + subdirs := proj $(subdirs) +diff -urN ogdi-3.2.0.beta2.old/ogdi/makefile ogdi-3.2.0.beta2/ogdi/makefile +--- ogdi-3.2.0.beta2.old/ogdi/makefile 2011-06-17 12:45:53.174219434 +0200 ++++ ogdi-3.2.0.beta2/ogdi/makefile 2011-06-17 12:47:38.814898744 +0200 +@@ -15,7 +15,7 @@ + # + # Sub-directories that need to be built + # +-subdirs = include c-api glutil attr_driver datum_driver driver gltpd examples ++subdirs = include c-api glutil attr_driver datum_driver driver gltpd + + # + # Default target to build everything in all sub-directories diff --git a/sci-libs/ogdi/metadata.xml b/sci-libs/ogdi/metadata.xml new file mode 100644 index 000000000000..2dc0ec7a6b9b --- /dev/null +++ b/sci-libs/ogdi/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">ogdi</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/ogdi/ogdi-3.1.5-r1.ebuild b/sci-libs/ogdi/ogdi-3.1.5-r1.ebuild new file mode 100644 index 000000000000..ccda853a4d15 --- /dev/null +++ b/sci-libs/ogdi/ogdi-3.1.5-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit toolchain-funcs eutils + +DESCRIPTION="Open Geographical Datastore Interface, a GIS support library" +HOMEPAGE="http://ogdi.sourceforge.net/" +SRC_URI="mirror://sourceforge/ogdi/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + <sci-libs/proj-4.8.0 + sys-libs/zlib + dev-libs/expat" +RDEPEND="${DEPEND}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${P}-fpic.patch +} + +src_compile() { + export TOPDIR="${S}" + export TARGET=`uname` + export CFG="release" + export LD_LIBRARY_PATH=$TOPDIR/bin/${TARGET} + + econf --with-projlib="-L/usr/$(get_libdir) -lproj" \ + --with-zlib --with-expat + + # bug #299239 + emake -j1 || die "make failed" +} + +src_install() { + mv "${S}"/bin/Linux/*.so "${S}"/lib/Linux/. || die "lib move failed" + dobin "${S}"/bin/Linux/* + insinto /usr/include + doins ogdi/include/ecs.h ogdi/include/ecs_util.h + dolib.so lib/Linux/*.so + dosym libogdi31.so /usr/$(get_libdir)/libogdi.so || die "symlink failed" + dodoc ChangeLog NEWS README VERSION +} diff --git a/sci-libs/ogdi/ogdi-3.2.0_beta2.ebuild b/sci-libs/ogdi/ogdi-3.2.0_beta2.ebuild new file mode 100644 index 000000000000..a9a42137ca12 --- /dev/null +++ b/sci-libs/ogdi/ogdi-3.2.0_beta2.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +MY_P=${P/_/.} +inherit eutils toolchain-funcs + +DESCRIPTION="Open Geographical Datastore Interface, a GIS support library" +HOMEPAGE="http://ogdi.sourceforge.net/" +SRC_URI="mirror://sourceforge/ogdi/${MY_P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="alpha amd64 ~arm ~arm64 ~ia64 ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +DEPEND=" + dev-libs/expat + >=sci-libs/proj-4.8.0 + sys-libs/zlib +" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + rm -rf external + epatch \ + "${FILESDIR}"/${P}-subdirs.patch \ + "${FILESDIR}"/${P}-endianess.patch \ + "${FILESDIR}"/${P}-64b.patch \ + "${FILESDIR}"/${P}-proj480.patch \ + "${FILESDIR}"/${PN}-3.1.6-fpic.patch + sed 's:O2:O9:g' -i configure || die +} + +src_configure() { + export TOPDIR="${S}" + export TARGET=$(uname) + export CFG="release" + export LD_LIBRARY_PATH=$TOPDIR/bin/${TARGET} + + econf \ + --with-projlib="-L${EPREFIX}/usr/$(get_libdir) -lproj" \ + --with-zlib --with-expat +} + +src_compile() { + # bug #299239 + emake -j1 \ + CC="$(tc-getCC)" \ + LD="$(tc-getCC)" \ + SHLIB_LD="$(tc-getCC)" +} + +src_install() { + mv "${S}"/bin/${TARGET}/*.so* "${S}"/lib/Linux/. || die "lib move failed" + dobin "${S}"/bin/${TARGET}/* + insinto /usr/include + doins ogdi/include/ecs.h ogdi/include/ecs_util.h + dolib.so lib/${TARGET}/lib* + use static-libs && dolib.a lib/${TARGET}/static/*.a +# dosym libogdi31.so /usr/$(get_libdir)/libogdi.so || die "symlink failed" + dodoc ChangeLog NEWS README +} diff --git a/sci-libs/opencascade/Manifest b/sci-libs/opencascade/Manifest new file mode 100644 index 000000000000..f56664cdfa5c --- 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5483b31f271b1492f499aec837b18dd4e5abe4e0b4ac8a4e3de17be6bd9467faa0629bd7423c9fad3a6c827eb74ecddaedf61f795a2c05757b69400ad0b68311 WHIRLPOOL 04b93b1e78d244ca3dd658f3ac6b63e519c63d84f9eabe9b9ae905195885e56619f7322e755c9717d02f2636c6dc0bf414348a8a420dd9d8f1d8b97c91134b1b diff --git a/sci-libs/opencascade/files/opencascade-6.5.4-fixed-tbb-VERSION.patch b/sci-libs/opencascade/files/opencascade-6.5.4-fixed-tbb-VERSION.patch new file mode 100644 index 000000000000..88b13acd21c4 --- /dev/null +++ b/sci-libs/opencascade/files/opencascade-6.5.4-fixed-tbb-VERSION.patch @@ -0,0 +1,10 @@ +--- src/Standard/Standard_MMgrTBBalloc.cxx ++++ src/Standard/Standard_MMgrTBBalloc.cxx +@@ -12,6 +12,7 @@ + + // paralleling with Intel TBB + #ifdef HAVE_TBB ++#undef VERSION + #include <tbb/scalable_allocator.h> + using namespace tbb; + #else diff --git a/sci-libs/opencascade/files/opencascade-6.7.0-fixed-DESTDIR.patch b/sci-libs/opencascade/files/opencascade-6.7.0-fixed-DESTDIR.patch new file mode 100644 index 000000000000..3a3f98093443 --- /dev/null +++ b/sci-libs/opencascade/files/opencascade-6.7.0-fixed-DESTDIR.patch @@ -0,0 +1,51 @@ +--- Makefile.am.old 2014-01-13 09:43:18.530500362 +0100 ++++ Makefile.am 2014-01-13 09:45:40.430496833 +0100 +@@ -82,29 +82,29 @@ + cd $(top_builddir)/adm/lin/amk && $(MAKE) $(AM_MAKEFLAGS) Draw + + install-exec-local: +- $(INSTALL) -d $(prefix)/$(platform) +- if [ -e $(prefix)/bin -a ! -e $(prefix)/$(platform)/bin ]; then \ +- cd $(prefix)/$(platform) && ln -s ../bin bin; \ ++ $(INSTALL) -d $(DESTDIR)$(prefix)/$(platform) ++ if [ -e $(DESTDIR)$(prefix)/bin -a ! -e $(DESTDIR)$(prefix)/$(platform)/bin ]; then \ ++ cd $(DESTDIR)$(prefix)/$(platform) && ln -s ../bin bin; \ + fi +- if [ -e $(prefix)/lib -a ! -e $(prefix)/$(platform)/lib ]; then \ +- cd $(prefix)/$(platform) && ln -s ../lib lib; \ ++ if [ -e $(DESTDIR)$(prefix)/lib -a ! -e $(DESTDIR)$(prefix)/$(platform)/lib ]; then \ ++ cd $(DESTDIR)$(prefix)/$(platform) && ln -s ../lib lib; \ + fi +- buildd=`pwd`; cd $(top_srcdir); sourced=`pwd`; cd $(prefix); installd=`pwd`; cd $$buildd; \ ++ buildd=`pwd`; cd $(top_srcdir); sourced=`pwd`; cd $(DESTDIR)$(prefix); installd=`pwd`; cd $$buildd; \ + if [ "$$installd" != "$$sourced" ]; then \ +- $(INSTALL) -d $(prefix)/inc; \ +- cp -frL $(top_srcdir)/inc $(prefix); \ +- cp -frL $$buildd/config.h $(prefix); \ ++ $(INSTALL) -d $(DESTDIR)$(prefix)/inc; \ ++ cp -frL $(top_srcdir)/inc $(DESTDIR)$(prefix); \ ++ cp -frL $$buildd/config.h $(DESTDIR)$(prefix); \ + for d in $(FoundationClasses_DIRS) $(ModelingData_DIRS) $(ModelingAlgorithms_DIRS) $(Visualization_DIRS) $(ApplicationFramework_DIRS) $(DataExchange_DIRS) $(Draw_DIRS); do \ +- $(INSTALL) -d $(prefix)/src/$$d; \ +- cp -frL $(top_srcdir)/src/$$d $(prefix)/src; \ ++ $(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \ ++ cp -frL $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \ + done; \ + fi +- if [ -e $(prefix)/inc/config.h ]; then \ +- rm -f $(prefix)/inc/config.h; \ ++ if [ -e $(DESTDIR)$(prefix)/inc/config.h ]; then \ ++ rm -f $(DESTDIR)$(prefix)/inc/config.h; \ + fi +- cd $(prefix)/inc && ln -s ../config.h config.h +- cd $(top_srcdir) && cp draw.sh $(prefix) +- cd $(top_srcdir) && cp custom.sh $(prefix) +- cd $(top_srcdir) && cp env.sh $(prefix) ++ cd $(DESTDIR)$(prefix)/inc && ln -s ../config.h config.h ++ cd $(top_srcdir) && cp draw.sh $(DESTDIR)$(prefix) ++ cd $(top_srcdir) && cp custom.sh $(DESTDIR)$(prefix) ++ cd $(top_srcdir) && cp env.sh $(DESTDIR)$(prefix) + +-.PHONY: FoundationClasses ModelingData ModelingAlgorithms Visualization ApplicationFramework DataExchange Draw +\ Brak znaku nowej linii na końcu pliku ++.PHONY: FoundationClasses ModelingData ModelingAlgorithms Visualization ApplicationFramework DataExchange Draw diff --git a/sci-libs/opencascade/files/opencascade-6.7.1-deprecated-glx-api.patch b/sci-libs/opencascade/files/opencascade-6.7.1-deprecated-glx-api.patch new file mode 100644 index 000000000000..b3c3629aada1 --- /dev/null +++ b/sci-libs/opencascade/files/opencascade-6.7.1-deprecated-glx-api.patch @@ -0,0 +1,89 @@ +From ba7e14489e14f08aae3e0f48b419b2149290b163 Mon Sep 17 00:00:00 2001 +From: Matthias Maier <tamiko@kyomu.43-1.org> +Date: Tue, 23 Dec 2014 21:15:59 +0100 +Subject: [PATCH] Define GLX_GLXEXT_LEGACY prior to inclusion of GL/glx.h + +--- + inc/InterfaceGraphic_X11.hxx | 1 + + samples/qt/Common/src/View.cxx | 1 + + src/InterfaceGraphic/InterfaceGraphic_X11.hxx | 1 + + src/OpenGl/OpenGl_Context.cxx | 1 + + src/OpenGl/OpenGl_Workspace_Raytrace.cxx | 1 + + src/Xw/Xw_Window.cxx | 1 + + 6 files changed, 6 insertions(+) + +diff --git a/inc/InterfaceGraphic_X11.hxx b/inc/InterfaceGraphic_X11.hxx +index 280bb9b..98d7415 100755 +--- a/inc/InterfaceGraphic_X11.hxx ++++ b/inc/InterfaceGraphic_X11.hxx +@@ -21,6 +21,7 @@ + #include <X11/Xlib.h> + #include <X11/Xutil.h> + #include <X11/Xatom.h> ++#define GLX_GLXEXT_LEGACY + #include <GL/glx.h> + + #if defined (sun) || defined (SUNOS) || defined (__alpha) || defined (DECOSF1) || defined (sgi) || defined (IRIX) || defined (__hpux)|| defined (HPUX) +diff --git a/samples/qt/Common/src/View.cxx b/samples/qt/Common/src/View.cxx +index 77f51b8..9b3f4e2 100755 +--- a/samples/qt/Common/src/View.cxx ++++ b/samples/qt/Common/src/View.cxx +@@ -28,6 +28,7 @@ + #include <Cocoa_Window.hxx> + #else + #include <QX11Info> ++#define GLX_GLXEXT_LEGACY + #include <GL/glx.h> + #include <X11/Xutil.h> + #include <X11/Xatom.h> +diff --git a/src/InterfaceGraphic/InterfaceGraphic_X11.hxx b/src/InterfaceGraphic/InterfaceGraphic_X11.hxx +index 280bb9b..98d7415 100755 +--- a/src/InterfaceGraphic/InterfaceGraphic_X11.hxx ++++ b/src/InterfaceGraphic/InterfaceGraphic_X11.hxx +@@ -21,6 +21,7 @@ + #include <X11/Xlib.h> + #include <X11/Xutil.h> + #include <X11/Xatom.h> ++#define GLX_GLXEXT_LEGACY + #include <GL/glx.h> + + #if defined (sun) || defined (SUNOS) || defined (__alpha) || defined (DECOSF1) || defined (sgi) || defined (IRIX) || defined (__hpux)|| defined (HPUX) +diff --git a/src/OpenGl/OpenGl_Context.cxx b/src/OpenGl/OpenGl_Context.cxx +index 9e2f074..1ddf6a4 100755 +--- a/src/OpenGl/OpenGl_Context.cxx ++++ b/src/OpenGl/OpenGl_Context.cxx +@@ -39,6 +39,7 @@ + #elif defined(__APPLE__) && !defined(MACOSX_USE_GLX) + #include <dlfcn.h> + #else ++ #define GLX_GLXEXT_LEGACY + #include <GL/glx.h> // glXGetProcAddress() + #endif + +diff --git a/src/OpenGl/OpenGl_Workspace_Raytrace.cxx b/src/OpenGl/OpenGl_Workspace_Raytrace.cxx +index f1b5afe..870eb7d 100755 +--- a/src/OpenGl/OpenGl_Workspace_Raytrace.cxx ++++ b/src/OpenGl/OpenGl_Workspace_Raytrace.cxx +@@ -32,6 +32,7 @@ + #elif defined(__APPLE__) && !defined(MACOSX_USE_GLX) + #include <OpenGL/CGLCurrent.h> + #else ++ #define GLX_GLXEXT_LEGACY + #include <GL/glx.h> + #endif + +diff --git a/src/Xw/Xw_Window.cxx b/src/Xw/Xw_Window.cxx +index 5442365..0e80444 100755 +--- a/src/Xw/Xw_Window.cxx ++++ b/src/Xw/Xw_Window.cxx +@@ -20,6 +20,7 @@ + #include <Aspect_Convert.hxx> + #include <Aspect_WindowDefinitionError.hxx> + ++#define GLX_GLXEXT_LEGACY + #include <GL/glx.h> + + namespace +-- +2.0.5 + diff --git a/sci-libs/opencascade/files/opencascade-6.8.0-fixed-DESTDIR.patch b/sci-libs/opencascade/files/opencascade-6.8.0-fixed-DESTDIR.patch new file mode 100644 index 000000000000..1f37eace7602 --- /dev/null +++ b/sci-libs/opencascade/files/opencascade-6.8.0-fixed-DESTDIR.patch @@ -0,0 +1,47 @@ +--- opencascade-6.8.0/Makefile.am ++++ opencascade-6.8.0/Makefile.am +@@ -82,27 +82,27 @@ + cd $(top_builddir)/adm/lin/amk && $(MAKE) $(AM_MAKEFLAGS) Draw + + install-exec-local: +- $(INSTALL) -d $(prefix)/$(platform) +- if [ -e $(prefix)/bin -a ! -e $(prefix)/$(platform)/bin ]; then \ +- cd $(prefix)/$(platform) && ln -s ../bin bin; \ ++ $(INSTALL) -d $(DESTDIR)$(prefix)/$(platform) ++ if [ -e $(DESTDIR)$(prefix)/bin -a ! -e $(DESTDIR)$(prefix)/$(platform)/bin ]; then \ ++ cd $(DESTDIR)$(prefix)/$(platform) && ln -s ../bin bin; \ + fi +- if [ -e $(prefix)/lib -a ! -e $(prefix)/$(platform)/lib ]; then \ +- cd $(prefix)/$(platform) && ln -s ../lib lib; \ ++ if [ -e $(DESTDIR)$(prefix)/lib -a ! -e $(DESTDIR)$(prefix)/$(platform)/lib ]; then \ ++ cd $(DESTDIR)$(prefix)/$(platform) && ln -s ../lib lib; \ + fi +- buildd=`pwd`; cd $(top_srcdir); sourced=`pwd`; cd $(prefix); installd=`pwd`; cd $$buildd; \ ++ buildd=`pwd`; cd $(top_srcdir); sourced=`pwd`; cd $(DESTDIR)$(prefix); installd=`pwd`; cd $$buildd; \ + if [ "$$installd" != "$$sourced" ]; then \ +- $(INSTALL) -d $(prefix)/inc; \ +- cp -frL $(top_srcdir)/inc $(prefix); \ +- cp -frL $$buildd/config.h $(prefix); \ ++ $(INSTALL) -d $(DESTDIR)$(prefix)/inc; \ ++ cp -frL $(top_srcdir)/inc $(DESTDIR)$(prefix); \ ++ cp -frL $$buildd/config.h $(DESTDIR)$(prefix); \ + for d in $(FoundationClasses_DIRS) $(ModelingData_DIRS) $(ModelingAlgorithms_DIRS) $(Visualization_DIRS) $(ApplicationFramework_DIRS) $(DataExchange_DIRS) $(Draw_DIRS); do \ +- $(INSTALL) -d $(prefix)/src/$$d; \ +- cp -frL $(top_srcdir)/src/$$d $(prefix)/src; \ ++ $(INSTALL) -d $(DESTDIR)$(prefix)/src/$$d; \ ++ cp -frL $(top_srcdir)/src/$$d $(DESTDIR)$(prefix)/src; \ + done; \ + fi +- if [ -e $(prefix)/inc/config.h ]; then \ +- rm -f $(prefix)/inc/config.h; \ ++ if [ -e $(DESTDIR)$(prefix)/inc/config.h ]; then \ ++ rm -f $(DESTDIR)$(prefix)/inc/config.h; \ + fi +- cd $(prefix)/inc && ln -s ../config.h config.h +- cd $(top_srcdir) && cp *.sh $(prefix) ++ cd $(DESTDIR)$(prefix)/inc && ln -s ../config.h config.h ++ cd $(top_srcdir) && cp *.sh $(DESTDIR)$(prefix) + +-.PHONY: FoundationClasses ModelingData ModelingAlgorithms Visualization ApplicationFramework DataExchange Draw +\ No newline at end of file ++.PHONY: FoundationClasses ModelingData ModelingAlgorithms Visualization ApplicationFramework DataExchange Draw diff --git a/sci-libs/opencascade/files/opencascade-6.9.1-vtk-6.3.patch b/sci-libs/opencascade/files/opencascade-6.9.1-vtk-6.3.patch new file mode 100644 index 000000000000..8e1d3361dde6 --- /dev/null +++ b/sci-libs/opencascade/files/opencascade-6.9.1-vtk-6.3.patch @@ -0,0 +1,70 @@ +--- opencascade-6.9.1/configure.ac ++++ opencascade-6.9.1/configure.ac +@@ -1044,7 +1044,7 @@ + fi + if test "x$vtk_lib" != "x"; then + CSF_VTK_LIB="-L$vtk_lib -lvtkCommonCore -lvtkCommonDataModel -lvtkCommonExecutionModel -lvtkCommonMath -lvtkCommonTransforms " +- CSF_VTK_LIB="${CSF_VTK_LIB} -lvtkRenderingCore -lvtkRenderingOpenGL -lvtkFiltersGeneral -lvtkIOCore -lvtkIOImage -lvtkImagingCore -lvtkInteractionStyle " ++ CSF_VTK_LIB="${CSF_VTK_LIB} -lvtkRenderingCore -lvtkRenderingOpenGL2 -lvtkFiltersGeneral -lvtkIOCore -lvtkIOImage -lvtkImagingCore -lvtkInteractionStyle " + else + HAVE_VTK=no + fi +--- opencascade-6.9.1/src/IVtkVTK/IVtkVTK_View.cxx ++++ opencascade-6.9.1/src/IVtkVTK/IVtkVTK_View.cxx +@@ -151,7 +151,7 @@ bool IVtkVTK_View::DisplayToWorld (const gp_XY& theDisplayPnt, gp_XYZ& theWorldP + myRenderer->SetDisplayPoint (theDisplayPnt.X(), theDisplayPnt.Y(), 0.0); + myRenderer->DisplayToWorld(); + +- vtkFloatingPointType* const aCoords = myRenderer->GetWorldPoint(); ++ double* const aCoords = myRenderer->GetWorldPoint(); + if (aCoords[3] == 0.0) // Point at infinity in homogeneous coordinates + { + return false; +--- opencascade-6.9.1/src/IVtkTools/IVtkTools_ShapePicker.cxx ++++ opencascade-6.9.1/src/IVtkTools/IVtkTools_ShapePicker.cxx +@@ -73,15 +73,15 @@ float IVtkTools_ShapePicker::GetTolerance( ) const + // Method: convertDisplayToWorld + // Purpose: Convert display coordinates to world coordinates + //============================================================================ +-bool IVtkTools_ShapePicker::convertDisplayToWorld (vtkRenderer *theRenderer, +- vtkFloatingPointType theDisplayCoord[3], +- vtkFloatingPointType theWorldCoord[3]) ++bool IVtkTools_ShapePicker::convertDisplayToWorld (vtkRenderer *theRenderer, ++ double theDisplayCoord[3], ++ double theWorldCoord[3]) + { + // Convert the selection point into world coordinates. + theRenderer->SetDisplayPoint (theDisplayCoord[0], theDisplayCoord[1], theDisplayCoord[2]); + theRenderer->DisplayToWorld(); + +- vtkFloatingPointType* const aCoords = theRenderer->GetWorldPoint(); ++ double* const aCoords = theRenderer->GetWorldPoint(); + if (aCoords[3] == 0.0) + { + return false; +--- opencascade-6.9.1/src/IVtkTools/IVtkTools_ShapePicker.hxx ++++ opencascade-6.9.1/src/IVtkTools/IVtkTools_ShapePicker.hxx +@@ -124,8 +124,8 @@ protected: + + //! Convert display coordinates to world coordinates + static bool convertDisplayToWorld (vtkRenderer *theRenderer, +- vtkFloatingPointType theDisplayCoord[3], +- vtkFloatingPointType theWorldCoord[3] ); ++ double theDisplayCoord[3], ++ double theWorldCoord[3] ); + + private: // not copyable + IVtkTools_ShapePicker (const IVtkTools_ShapePicker&); +--- opencascade-6.9.1/inc/IVtkTools_ShapePicker.hxx ++++ opencascade-6.9.1/inc/IVtkTools_ShapePicker.hxx +@@ -124,8 +124,8 @@ + + //! Convert display coordinates to world coordinates + static bool convertDisplayToWorld (vtkRenderer *theRenderer, +- vtkFloatingPointType theDisplayCoord[3], +- vtkFloatingPointType theWorldCoord[3] ); ++ double theDisplayCoord[3], ++ double theWorldCoord[3] ); + + private: // not copyable + IVtkTools_ShapePicker (const IVtkTools_ShapePicker&); diff --git a/sci-libs/opencascade/files/opencascade-6.9.1-vtk-configure.patch b/sci-libs/opencascade/files/opencascade-6.9.1-vtk-configure.patch new file mode 100644 index 000000000000..3c2711d3813e --- /dev/null +++ b/sci-libs/opencascade/files/opencascade-6.9.1-vtk-configure.patch @@ -0,0 +1,13 @@ +--- opencascade-6.9.1/configure.ac ++++ opencascade-6.9.1/configure.ac +@@ -1043,8 +1043,8 @@ + HAVE_VTK=no + fi + if test "x$vtk_lib" != "x"; then +- CSF_VTK_LIB="-L$vtk_lib -lvtkCommonCore-6.1 -lvtkCommonDataModel-6.1 -lvtkCommonExecutionModel-6.1 -lvtkCommonMath-6.1 -lvtkCommonTransforms-6.1 " +- CSF_VTK_LIB="${CSF_VTK_LIB} -lvtkRenderingCore-6.1 -lvtkRenderingOpenGL-6.1 -lvtkFiltersGeneral-6.1 -lvtkIOCore-6.1 -lvtkIOImage-6.1 -lvtkImagingCore-6.1 -lvtkInteractionStyle-6.1 " ++ CSF_VTK_LIB="-L$vtk_lib -lvtkCommonCore -lvtkCommonDataModel -lvtkCommonExecutionModel -lvtkCommonMath -lvtkCommonTransforms " ++ CSF_VTK_LIB="${CSF_VTK_LIB} -lvtkRenderingCore -lvtkRenderingOpenGL -lvtkFiltersGeneral -lvtkIOCore -lvtkIOImage -lvtkImagingCore -lvtkInteractionStyle " + else + HAVE_VTK=no + fi diff --git a/sci-libs/opencascade/metadata.xml b/sci-libs/opencascade/metadata.xml new file mode 100644 index 000000000000..0dc2b1db4c13 --- /dev/null +++ b/sci-libs/opencascade/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>xmw@gentoo.org</email> + <name>Michael Weber</name> + </maintainer> + <use> + <flag name="freeimage">Enable support for image i/o via media-libs/freeimage</flag> + <flag name="gl2ps">Use gl2ps PostScript printing library</flag> + <flag name="tbb">Enable multithreading with the Intel Threads Building Block dev-cpp/tbb</flag> + <flag name="vtk">Enable Virtualisation Toolkit</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/opencascade/opencascade-6.7.1-r1.ebuild b/sci-libs/opencascade/opencascade-6.7.1-r1.ebuild new file mode 100644 index 000000000000..de1201862abe --- /dev/null +++ b/sci-libs/opencascade/opencascade-6.7.1-r1.ebuild @@ -0,0 +1,161 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils check-reqs multilib java-pkg-opt-2 flag-o-matic + +DESCRIPTION="Development platform for CAD/CAE, 3D surface/solid modeling and data exchange" +HOMEPAGE="http://www.opencascade.org/" +SRC_URI="http://files.opencascade.com/OCCT/OCC_${PV}_release/opencascade-${PV}.tgz" + +LICENSE="|| ( Open-CASCADE-LGPL-2.1-Exception-1.0 LGPL-2.1 )" +SLOT="${PV}" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples freeimage gl2ps java qt4 +tbb" + +DEPEND="app-eselect/eselect-opencascade + dev-lang/tcl:0= + dev-lang/tk:0= + dev-tcltk/itcl + dev-tcltk/itk + dev-tcltk/tix + media-libs/ftgl + virtual/glu + virtual/opengl + x11-libs/libXmu + freeimage? ( media-libs/freeimage ) + gl2ps? ( x11-libs/gl2ps ) + java? ( >=virtual/jdk-0:= ) + tbb? ( dev-cpp/tbb )" +RDEPEND="${DEPEND}" + +CHECKREQS_MEMORY="256M" +CHECKREQS_DISK_BUILD="3584M" + +pkg_setup() { + check-reqs_pkg_setup + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + java-pkg-opt-2_src_prepare + + epatch \ + "${FILESDIR}"/${P}-deprecated-glx-api.patch \ + "${FILESDIR}"/${PN}-6.7.0-fixed-DESTDIR.patch \ + "${FILESDIR}"/${PN}-6.5.4-fixed-tbb-VERSION.patch + + # Feed environment variables used by Opencascade compilation + my_install_dir=${EROOT}usr/$(get_libdir)/${P}/ros + local my_env_install="#!/bin/sh -f +if [ -z \"\$PATH\" ]; then + export PATH=VAR_CASROOT/Linux/bin +else + export PATH=VAR_CASROOT/Linux/bin:\$PATH +fi +if [ -z \"\$LD_LIBRARY_PATH\" ]; then + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib +else + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib:\$LD_LIBRARY_PATH +fi" + local my_sys_lib=${EROOT}usr/$(get_libdir) + local my_env="CASROOT=VAR_CASROOT +CSF_MDTVFontDirectory=VAR_CASROOT/src/FontMFT +CSF_LANGUAGE=us +MMGT_CLEAR=1 +CSF_EXCEPTION_PROMPT=1 +CSF_SHMessage=VAR_CASROOT/src/SHMessage +CSF_MDTVTexturesDirectory=VAR_CASROOT/src/Textures +CSF_XSMessage=VAR_CASROOT/src/XSMessage +CSF_StandardDefaults=VAR_CASROOT/src/StdResource +CSF_PluginDefaults=VAR_CASROOT/src/StdResource +CSF_XCAFDefaults=VAR_CASROOT/src/StdResource +CSF_StandardLiteDefaults=VAR_CASROOT/src/StdResource +CSF_GraphicShr=VAR_CASROOT/Linux/lib/libTKOpenGl.so +CSF_UnitsLexicon=VAR_CASROOT/src/UnitsAPI/Lexi_Expr.dat +CSF_UnitsDefinition=VAR_CASROOT/src/UnitsAPI/Units.dat +CSF_IGESDefaults=VAR_CASROOT/src/XSTEPResource +CSF_STEPDefaults=VAR_CASROOT/src/XSTEPResource +CSF_XmlOcafResource=VAR_CASROOT/src/XmlOcafResource +CSF_MIGRATION_TYPES=VAR_CASROOT/src/StdResource/MigrationSheet.txt +TCLHOME=${EROOT}usr/bin +TCLLIBPATH=${my_sys_lib} +ITK_LIBRARY=${my_sys_lib}/itk$(grep ITK_VER /usr/include/itk.h | sed 's/^.*"\(.*\)".*/\1/') +ITCL_LIBRARY=${my_sys_lib}/itcl$(grep ITCL_VER /usr/include/itcl.h | sed 's/^.*"\(.*\)".*/\1/') +TIX_LIBRARY=${my_sys_lib}/tix$(grep TIX_VER /usr/include/tix.h | sed 's/^.*"\(.*\)".*/\1/') +TK_LIBRARY=${my_sys_lib}/tk$(grep TK_VER /usr/include/tk.h | sed 's/^.*"\(.*\)".*/\1/') +TCL_LIBRARY=${my_sys_lib}/tcl$(grep TCL_VER /usr/include/tcl.h | sed 's/^.*"\(.*\)".*/\1/')" + + ( echo "${my_env_install}" + echo "${my_env}" | sed -e "s:^:export :" ) \ + | sed -e "s:VAR_CASROOT:${S}:g" > env.sh || die + source env.sh + + ( echo "PATH=${my_install_dir}/lin/bin" + echo "LDPATH=${my_install_dir}/lin/$(get_libdir)" + echo "${my_env}" | sed \ + -e "s:VAR_CASROOT:${my_install_dir}/lin:g" \ + -e "s:/Linux/lib/:/$(get_libdir)/:g" || die + ) > 50${PN} + + append-cxxflags "-fpermissive" + + sed -e "/^AM_C_PROTOTYPES$/d" \ + -e "s/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/" \ + -e "s:\$qt/include:\$qt/include/qt4:g"\ + -e "s:\$qt/lib:\$qt/$(get_libdir)/qt4:g"\ + -i configure.ac || die + eautoreconf +} + +src_configure() { + econf \ + --prefix=${my_install_dir}/lin --exec-prefix=${my_install_dir}/lin \ + --with-tcl="${EROOT}usr/$(get_libdir)" --with-tk="${EROOT}usr/$(get_libdir)" \ + --with-freetype="${EROOT}usr" \ + --with-ftgl="${EROOT}usr" \ + $(usex freeimage "--with-freeimage=${EROOT}usr" "") \ + $(usex gl2ps "--with-gl2ps=${EROOT}usr" "") \ + $(usex qt4 "--with-qt=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-include=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-library=${EROOT}usr" "") \ + $(use java && echo "--with-java-include=$(java-config -O)/include" || echo "--without-java-include") \ + $(use_enable debug) \ + $(use_enable !debug production) +} + +src_install() { + emake DESTDIR="${D}" install + + prune_libtool_files + + # Symlinks for keeping original OpenCascade folder structure and + # add a link lib to $(get_libdir) if we are e.g. on amd64 multilib + if [ "$(get_libdir)" != "lib" ]; then + dosym "$(get_libdir)" "${my_install_dir}/lin/lib" + fi + + insinto /etc/env.d/${PN} + newins 50${PN} ${PV} + + #cd "${S}" + if use examples ; then + insinto /usr/share/doc/${PF}/examples + doins -r data + doins -r samples + fi + if use doc; then + insinto /usr/share/doc/${PF} + doins -r doc/{overview,pdf,refman} + fi +} + +pkg_postinst() { + eselect ${PN} set ${PV} + einfo + elog "After upgrading OpenCASCADE you may have to rebuild packages depending on it." + elog "You get a list by running \"equery depends sci-libs/opencascade\"" + elog "revdep-rebuild does NOT suffice." + einfo +} diff --git a/sci-libs/opencascade/opencascade-6.8.0-r1.ebuild b/sci-libs/opencascade/opencascade-6.8.0-r1.ebuild new file mode 100644 index 000000000000..1164f28ccc40 --- /dev/null +++ b/sci-libs/opencascade/opencascade-6.8.0-r1.ebuild @@ -0,0 +1,158 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils check-reqs multilib java-pkg-opt-2 flag-o-matic + +DESCRIPTION="Development platform for CAD/CAE, 3D surface/solid modeling and data exchange" +HOMEPAGE="http://www.opencascade.org/" +SRC_URI="http://files.opencascade.com/OCCT/OCC_${PV}_release/opencascade-${PV}.tgz" + +LICENSE="|| ( Open-CASCADE-LGPL-2.1-Exception-1.0 LGPL-2.1 )" +SLOT="${PV}" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples freeimage gl2ps java qt4 +tbb" + +DEPEND="app-eselect/eselect-opencascade + dev-lang/tcl:0= + dev-lang/tk:0= + dev-tcltk/itcl + dev-tcltk/itk + dev-tcltk/tix + media-libs/ftgl + virtual/glu + virtual/opengl + x11-libs/libXmu + freeimage? ( media-libs/freeimage ) + gl2ps? ( x11-libs/gl2ps ) + java? ( >=virtual/jdk-0:= ) + tbb? ( dev-cpp/tbb )" +RDEPEND="${DEPEND}" + +CHECKREQS_MEMORY="256M" +CHECKREQS_DISK_BUILD="3584M" + +pkg_setup() { + check-reqs_pkg_setup + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + java-pkg-opt-2_src_prepare + + epatch \ + "${FILESDIR}"/${P}-fixed-DESTDIR.patch + + # Feed environment variables used by Opencascade compilation + my_install_dir=${EROOT}usr/$(get_libdir)/${P}/ros + local my_env_install="#!/bin/sh -f +if [ -z \"\$PATH\" ]; then + export PATH=VAR_CASROOT/Linux/bin +else + export PATH=VAR_CASROOT/Linux/bin:\$PATH +fi +if [ -z \"\$LD_LIBRARY_PATH\" ]; then + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib +else + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib:\$LD_LIBRARY_PATH +fi" + local my_sys_lib=${EROOT}usr/$(get_libdir) + local my_env="CASROOT=VAR_CASROOT +CSF_MDTVFontDirectory=VAR_CASROOT/src/FontMFT +CSF_LANGUAGE=us +MMGT_CLEAR=1 +CSF_EXCEPTION_PROMPT=1 +CSF_SHMessage=VAR_CASROOT/src/SHMessage +CSF_MDTVTexturesDirectory=VAR_CASROOT/src/Textures +CSF_XSMessage=VAR_CASROOT/src/XSMessage +CSF_StandardDefaults=VAR_CASROOT/src/StdResource +CSF_PluginDefaults=VAR_CASROOT/src/StdResource +CSF_XCAFDefaults=VAR_CASROOT/src/StdResource +CSF_StandardLiteDefaults=VAR_CASROOT/src/StdResource +CSF_GraphicShr=VAR_CASROOT/Linux/lib/libTKOpenGl.so +CSF_UnitsLexicon=VAR_CASROOT/src/UnitsAPI/Lexi_Expr.dat +CSF_UnitsDefinition=VAR_CASROOT/src/UnitsAPI/Units.dat +CSF_IGESDefaults=VAR_CASROOT/src/XSTEPResource +CSF_STEPDefaults=VAR_CASROOT/src/XSTEPResource +CSF_XmlOcafResource=VAR_CASROOT/src/XmlOcafResource +CSF_MIGRATION_TYPES=VAR_CASROOT/src/StdResource/MigrationSheet.txt +TCLHOME=${EROOT}usr/bin +TCLLIBPATH=${my_sys_lib} +ITK_LIBRARY=${my_sys_lib}/itk$(grep ITK_VER /usr/include/itk.h | sed 's/^.*"\(.*\)".*/\1/') +ITCL_LIBRARY=${my_sys_lib}/itcl$(grep ITCL_VER /usr/include/itcl.h | sed 's/^.*"\(.*\)".*/\1/') +TIX_LIBRARY=${my_sys_lib}/tix$(grep TIX_VER /usr/include/tix.h | sed 's/^.*"\(.*\)".*/\1/') +TK_LIBRARY=${my_sys_lib}/tk$(grep TK_VER /usr/include/tk.h | sed 's/^.*"\(.*\)".*/\1/') +TCL_LIBRARY=${my_sys_lib}/tcl$(grep TCL_VER /usr/include/tcl.h | sed 's/^.*"\(.*\)".*/\1/')" + + ( echo "${my_env_install}" + echo "${my_env}" | sed -e "s:^:export :" ) \ + | sed -e "s:VAR_CASROOT:${S}:g" > env.sh || die + source env.sh + + ( echo "PATH=${my_install_dir}/lin/bin" + echo "LDPATH=${my_install_dir}/lin/$(get_libdir)" + echo "${my_env}" | sed \ + -e "s:VAR_CASROOT:${my_install_dir}/lin:g" \ + -e "s:/Linux/lib/:/$(get_libdir)/:g" || die + ) > 50${PN} + + append-cxxflags "-fpermissive" + + sed -e "/^AM_C_PROTOTYPES$/d" \ + -e "s/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/" \ + -e "s:\$qt/include:\$qt/include/qt4:g"\ + -e "s:\$qt/lib:\$qt/$(get_libdir)/qt4:g"\ + -i configure.ac || die + eautoreconf +} + +src_configure() { + econf \ + --prefix=${my_install_dir}/lin --exec-prefix=${my_install_dir}/lin \ + --with-tcl="${EROOT}usr/$(get_libdir)" --with-tk="${EROOT}usr/$(get_libdir)" \ + --with-freetype="${EROOT}usr" \ + --with-ftgl="${EROOT}usr" \ + $(usex freeimage "--with-freeimage=${EROOT}usr" "") \ + $(usex gl2ps "--with-gl2ps=${EROOT}usr" "") \ + $(usex qt4 "--with-qt=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-include=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-library=${EROOT}usr" "") \ + $(use java && echo "--with-java-include=$(java-config -O)/include" || echo "--without-java-include") \ + $(use_enable debug) \ + $(use_enable !debug production) +} + +src_install() { + emake DESTDIR="${D}" install + + prune_libtool_files + + # Symlinks for keeping original OpenCascade folder structure and + # add a link lib to $(get_libdir) if we are e.g. on amd64 multilib + if [ "$(get_libdir)" != "lib" ]; then + dosym "$(get_libdir)" "${my_install_dir}/lin/lib" + fi + + insinto /etc/env.d/${PN} + newins 50${PN} ${PV} + + if use examples ; then + insinto /usr/share/doc/${PF}/examples + doins -r data + doins -r samples + fi + if use doc; then + insinto /usr/share/doc/${PF} + doins -r doc/{overview,pdf,refman} + fi +} + +pkg_postinst() { + eselect ${PN} set ${PV} + einfo + elog "After upgrading OpenCASCADE you may have to rebuild packages depending on it." + elog "You get a list by running \"equery depends sci-libs/opencascade\"" + elog "revdep-rebuild does NOT suffice." + einfo +} diff --git a/sci-libs/opencascade/opencascade-6.9.0-r1.ebuild b/sci-libs/opencascade/opencascade-6.9.0-r1.ebuild new file mode 100644 index 000000000000..df80ca414820 --- /dev/null +++ b/sci-libs/opencascade/opencascade-6.9.0-r1.ebuild @@ -0,0 +1,163 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils check-reqs multilib java-pkg-opt-2 flag-o-matic + +DESCRIPTION="Development platform for CAD/CAE, 3D surface/solid modeling and data exchange" +HOMEPAGE="http://www.opencascade.org/" +SRC_URI="http://files.opencascade.com/OCCT/OCC_${PV}_release/opencascade-${PV}.tgz" + +LICENSE="|| ( Open-CASCADE-LGPL-2.1-Exception-1.0 LGPL-2.1 )" +SLOT="${PV}" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples freeimage gl2ps java qt4 +tbb +vtk" + +MY_VTK="vtk-6.1" +DEPEND="app-eselect/eselect-opencascade + dev-lang/tcl:0= + dev-lang/tk:0= + dev-tcltk/itcl + dev-tcltk/itk + dev-tcltk/tix + media-libs/ftgl + virtual/glu + virtual/opengl + x11-libs/libXmu + freeimage? ( media-libs/freeimage ) + gl2ps? ( x11-libs/gl2ps ) + java? ( >=virtual/jdk-0:= ) + tbb? ( dev-cpp/tbb ) + vtk? ( || ( =sci-libs/${MY_VTK}*[imaging] =sci-libs/${MY_VTK}*[qt4] =sci-libs/${MY_VTK}*[rendering] =sci-libs/${MY_VTK}*[views] =sci-libs/${MY_VTK}*[all-modules] ) )" +RDEPEND="${DEPEND}" + +CHECKREQS_MEMORY="256M" +CHECKREQS_DISK_BUILD="3584M" + +pkg_setup() { + check-reqs_pkg_setup + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + java-pkg-opt-2_src_prepare + + epatch \ + "${FILESDIR}"/${PN}-6.8.0-fixed-DESTDIR.patch + + # Feed environment variables used by Opencascade compilation + my_install_dir=${EROOT}usr/$(get_libdir)/${P}/ros + local my_env_install="#!/bin/sh -f +if [ -z \"\$PATH\" ]; then + export PATH=VAR_CASROOT/Linux/bin +else + export PATH=VAR_CASROOT/Linux/bin:\$PATH +fi +if [ -z \"\$LD_LIBRARY_PATH\" ]; then + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib +else + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib:\$LD_LIBRARY_PATH +fi" + local my_sys_lib=${EROOT}usr/$(get_libdir) + local my_env="CASROOT=VAR_CASROOT +CSF_MDTVFontDirectory=VAR_CASROOT/src/FontMFT +CSF_LANGUAGE=us +MMGT_CLEAR=1 +CSF_EXCEPTION_PROMPT=1 +CSF_SHMessage=VAR_CASROOT/src/SHMessage +CSF_MDTVTexturesDirectory=VAR_CASROOT/src/Textures +CSF_XSMessage=VAR_CASROOT/src/XSMessage +CSF_StandardDefaults=VAR_CASROOT/src/StdResource +CSF_PluginDefaults=VAR_CASROOT/src/StdResource +CSF_XCAFDefaults=VAR_CASROOT/src/StdResource +CSF_StandardLiteDefaults=VAR_CASROOT/src/StdResource +CSF_GraphicShr=VAR_CASROOT/Linux/lib/libTKOpenGl.so +CSF_UnitsLexicon=VAR_CASROOT/src/UnitsAPI/Lexi_Expr.dat +CSF_UnitsDefinition=VAR_CASROOT/src/UnitsAPI/Units.dat +CSF_IGESDefaults=VAR_CASROOT/src/XSTEPResource +CSF_STEPDefaults=VAR_CASROOT/src/XSTEPResource +CSF_XmlOcafResource=VAR_CASROOT/src/XmlOcafResource +CSF_MIGRATION_TYPES=VAR_CASROOT/src/StdResource/MigrationSheet.txt +TCLHOME=${EROOT}usr/bin +TCLLIBPATH=${my_sys_lib} +ITK_LIBRARY=${my_sys_lib}/itk$(grep ITK_VER /usr/include/itk.h | sed 's/^.*"\(.*\)".*/\1/') +ITCL_LIBRARY=${my_sys_lib}/itcl$(grep ITCL_VER /usr/include/itcl.h | sed 's/^.*"\(.*\)".*/\1/') +TIX_LIBRARY=${my_sys_lib}/tix$(grep TIX_VER /usr/include/tix.h | sed 's/^.*"\(.*\)".*/\1/') +TK_LIBRARY=${my_sys_lib}/tk$(grep TK_VER /usr/include/tk.h | sed 's/^.*"\(.*\)".*/\1/') +TCL_LIBRARY=${my_sys_lib}/tcl$(grep TCL_VER /usr/include/tcl.h | sed 's/^.*"\(.*\)".*/\1/')" + + ( echo "${my_env_install}" + echo "${my_env}" | sed -e "s:^:export :" ) \ + | sed -e "s:VAR_CASROOT:${S}:g" > env.sh || die + source env.sh + + ( echo "PATH=${my_install_dir}/lin/bin" + echo "LDPATH=${my_install_dir}/lin/$(get_libdir)" + echo "${my_env}" | sed \ + -e "s:VAR_CASROOT:${my_install_dir}/lin:g" \ + -e "s:/Linux/lib/:/$(get_libdir)/:g" || die + ) > 50${PN} + + append-cxxflags "-fpermissive" + + sed -e "/^AM_C_PROTOTYPES$/d" \ + -e "s/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/" \ + -e "s:\$qt/include:\$qt/include/qt4:g"\ + -e "s:\$qt/lib:\$qt/$(get_libdir)/qt4:g"\ + -e "/CSF_VTK_LIB=/s:-${MY_VTK/vtk-}::g" \ + -i configure.ac || die + eautoreconf +} + +src_configure() { + econf \ + --prefix=${my_install_dir}/lin --exec-prefix=${my_install_dir}/lin \ + --with-tcl="${EROOT}usr/$(get_libdir)" --with-tk="${EROOT}usr/$(get_libdir)" \ + --with-freetype="${EROOT}usr" \ + --with-ftgl="${EROOT}usr" \ + $(usex freeimage "--with-freeimage=${EROOT}usr" "") \ + $(usex gl2ps "--with-gl2ps=${EROOT}usr" "") \ + $(usex qt4 "--with-qt=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-include=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-library=${EROOT}usr" "") \ + $(use java && echo "--with-java-include=$(java-config -O)/include" || echo "--without-java-include") \ + $(usex vtk "--with-vtk-include=${EROOT}usr/include/${MY_VTK}" "") \ + $(usex vtk "--with-vtk-library=${EROOT}usr/$(get_libdir)" "") \ + $(use_enable debug) \ + $(use_enable !debug production) +} + +src_install() { + emake DESTDIR="${D}" install + + prune_libtool_files + + # Symlinks for keeping original OpenCascade folder structure and + # add a link lib to $(get_libdir) if we are e.g. on amd64 multilib + if [ "$(get_libdir)" != "lib" ]; then + dosym "$(get_libdir)" "${my_install_dir}/lin/lib" + fi + + insinto /etc/env.d/${PN} + newins 50${PN} ${PV} + + if use examples ; then + insinto /usr/share/doc/${PF}/examples + doins -r data + doins -r samples + fi + if use doc; then + insinto /usr/share/doc/${PF} + doins -r doc/{overview,pdf,refman} + fi +} + +pkg_postinst() { + eselect ${PN} set ${PV} + einfo + elog "After upgrading OpenCASCADE you may have to rebuild packages depending on it." + elog "You get a list by running \"equery depends sci-libs/opencascade\"" + elog "revdep-rebuild does NOT suffice." + einfo +} diff --git a/sci-libs/opencascade/opencascade-6.9.1-r1.ebuild b/sci-libs/opencascade/opencascade-6.9.1-r1.ebuild new file mode 100644 index 000000000000..dd0a0cb70c10 --- /dev/null +++ b/sci-libs/opencascade/opencascade-6.9.1-r1.ebuild @@ -0,0 +1,164 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils check-reqs multilib java-pkg-opt-2 flag-o-matic + +DESCRIPTION="Development platform for CAD/CAE, 3D surface/solid modeling and data exchange" +HOMEPAGE="http://www.opencascade.org/" +SRC_URI="http://www.opencascade.com/sites/default/files/private/occt/OCC_${PV}_release/opencascade-${PV}.tgz" + +LICENSE="|| ( Open-CASCADE-LGPL-2.1-Exception-1.0 LGPL-2.1 )" +SLOT="${PV}" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples freeimage gl2ps java qt4 +tbb +vtk" + +MY_VTK="vtk-6.1" +DEPEND="app-eselect/eselect-opencascade + dev-lang/tcl:0= + dev-lang/tk:0= + dev-tcltk/itcl + dev-tcltk/itk + dev-tcltk/tix + media-libs/ftgl + virtual/glu + virtual/opengl + x11-libs/libXmu + freeimage? ( media-libs/freeimage ) + gl2ps? ( x11-libs/gl2ps ) + java? ( >=virtual/jdk-0:= ) + tbb? ( dev-cpp/tbb ) + vtk? ( || ( =sci-libs/${MY_VTK}*[imaging] =sci-libs/${MY_VTK}*[qt4] =sci-libs/${MY_VTK}*[rendering] =sci-libs/${MY_VTK}*[views] =sci-libs/${MY_VTK}*[all-modules] ) )" +RDEPEND="${DEPEND}" + +CHECKREQS_MEMORY="256M" +CHECKREQS_DISK_BUILD="3584M" + +PATCHES=( "${FILESDIR}"/${PN}-6.8.0-fixed-DESTDIR.patch ) + +pkg_setup() { + check-reqs_pkg_setup + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + default + + java-pkg-opt-2_src_prepare + + # Feed environment variables used by Opencascade compilation + my_install_dir=${EROOT}usr/$(get_libdir)/${P}/ros + local my_env_install="#!/bin/sh -f +if [ -z \"\$PATH\" ]; then + export PATH=VAR_CASROOT/Linux/bin +else + export PATH=VAR_CASROOT/Linux/bin:\$PATH +fi +if [ -z \"\$LD_LIBRARY_PATH\" ]; then + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib +else + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib:\$LD_LIBRARY_PATH +fi" + local my_sys_lib=${EROOT}usr/$(get_libdir) + local my_env="CASROOT=VAR_CASROOT +CSF_MDTVFontDirectory=VAR_CASROOT/src/FontMFT +CSF_LANGUAGE=us +MMGT_CLEAR=1 +CSF_EXCEPTION_PROMPT=1 +CSF_SHMessage=VAR_CASROOT/src/SHMessage +CSF_MDTVTexturesDirectory=VAR_CASROOT/src/Textures +CSF_XSMessage=VAR_CASROOT/src/XSMessage +CSF_StandardDefaults=VAR_CASROOT/src/StdResource +CSF_PluginDefaults=VAR_CASROOT/src/StdResource +CSF_XCAFDefaults=VAR_CASROOT/src/StdResource +CSF_StandardLiteDefaults=VAR_CASROOT/src/StdResource +CSF_GraphicShr=VAR_CASROOT/Linux/lib/libTKOpenGl.so +CSF_UnitsLexicon=VAR_CASROOT/src/UnitsAPI/Lexi_Expr.dat +CSF_UnitsDefinition=VAR_CASROOT/src/UnitsAPI/Units.dat +CSF_IGESDefaults=VAR_CASROOT/src/XSTEPResource +CSF_STEPDefaults=VAR_CASROOT/src/XSTEPResource +CSF_XmlOcafResource=VAR_CASROOT/src/XmlOcafResource +CSF_MIGRATION_TYPES=VAR_CASROOT/src/StdResource/MigrationSheet.txt +TCLHOME=${EROOT}usr/bin +TCLLIBPATH=${my_sys_lib} +ITK_LIBRARY=${my_sys_lib}/itk$(grep ITK_VER /usr/include/itk.h | sed 's/^.*"\(.*\)".*/\1/') +ITCL_LIBRARY=${my_sys_lib}/itcl$(grep ITCL_VER /usr/include/itcl.h | sed 's/^.*"\(.*\)".*/\1/') +TIX_LIBRARY=${my_sys_lib}/tix$(grep TIX_VER /usr/include/tix.h | sed 's/^.*"\(.*\)".*/\1/') +TK_LIBRARY=${my_sys_lib}/tk$(grep TK_VER /usr/include/tk.h | sed 's/^.*"\(.*\)".*/\1/') +TCL_LIBRARY=${my_sys_lib}/tcl$(grep TCL_VER /usr/include/tcl.h | sed 's/^.*"\(.*\)".*/\1/')" + + ( echo "${my_env_install}" + echo "${my_env}" | sed -e "s:^:export :" ) \ + | sed -e "s:VAR_CASROOT:${S}:g" > env.sh || die + source env.sh + + ( echo "PATH=${my_install_dir}/lin/bin" + echo "LDPATH=${my_install_dir}/lin/$(get_libdir)" + echo "${my_env}" | sed \ + -e "s:VAR_CASROOT:${my_install_dir}/lin:g" \ + -e "s:/Linux/lib/:/$(get_libdir)/:g" || die + ) > 50${PN} + + append-cxxflags "-fpermissive" + + sed -e "/^AM_C_PROTOTYPES$/d" \ + -e "s/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/" \ + -e "s:\$qt/include:\$qt/include/qt4:g"\ + -e "s:\$qt/lib:\$qt/$(get_libdir)/qt4:g"\ + -e "/CSF_VTK_LIB=/s:-${MY_VTK/vtk-}::g" \ + -i configure.ac || die + eautoreconf +} + +src_configure() { + econf \ + --prefix=${my_install_dir}/lin --exec-prefix=${my_install_dir}/lin \ + --with-tcl="${EROOT}usr/$(get_libdir)" --with-tk="${EROOT}usr/$(get_libdir)" \ + --with-freetype="${EROOT}usr" \ + --with-ftgl="${EROOT}usr" \ + $(usex freeimage "--with-freeimage=${EROOT}usr" "") \ + $(usex gl2ps "--with-gl2ps=${EROOT}usr" "") \ + $(usex qt4 "--with-qt=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-include=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-library=${EROOT}usr" "") \ + $(use java && echo "--with-java-include=$(java-config -O)/include" || echo "--without-java-include") \ + $(usex vtk "--with-vtk-include=${EROOT}usr/include/${MY_VTK}" "") \ + $(usex vtk "--with-vtk-library=${EROOT}usr/$(get_libdir)" "") \ + $(use_enable debug) \ + $(use_enable !debug production) +} + +src_install() { + emake DESTDIR="${D}" install + + prune_libtool_files + + # Symlinks for keeping original OpenCascade folder structure and + # add a link lib to $(get_libdir) if we are e.g. on amd64 multilib + if [ "$(get_libdir)" != "lib" ]; then + dosym "$(get_libdir)" "${my_install_dir}/lin/lib" + fi + + insinto /etc/env.d/${PN} + newins 50${PN} ${PV} + + if use examples ; then + insinto /usr/share/doc/${PF}/examples + doins -r data + doins -r samples + fi + if use doc; then + insinto /usr/share/doc/${PF} + doins -r doc/{overview,pdf,refman} + fi +} + +pkg_postinst() { + eselect ${PN} set ${PV} + einfo + elog "After upgrading OpenCASCADE you may have to rebuild packages depending on it." + elog "You get a list by running \"equery depends sci-libs/opencascade\"" + elog "revdep-rebuild does NOT suffice." + einfo +} diff --git a/sci-libs/opencascade/opencascade-6.9.1-r2.ebuild b/sci-libs/opencascade/opencascade-6.9.1-r2.ebuild new file mode 100644 index 000000000000..3f0de66418db --- /dev/null +++ b/sci-libs/opencascade/opencascade-6.9.1-r2.ebuild @@ -0,0 +1,170 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools eutils check-reqs multilib java-pkg-opt-2 flag-o-matic versionator + +DESCRIPTION="Development platform for CAD/CAE, 3D surface/solid modeling and data exchange" +HOMEPAGE="http://www.opencascade.org/" +SRC_URI="http://www.opencascade.com/sites/default/files/private/occt/OCC_${PV}_release/opencascade-${PV}.tgz" + +LICENSE="|| ( Open-CASCADE-LGPL-2.1-Exception-1.0 LGPL-2.1 )" +SLOT="${PV}" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples freeimage gl2ps java qt4 +tbb +vtk" + +DEPEND="app-eselect/eselect-opencascade + dev-lang/tcl:0= + dev-lang/tk:0= + dev-tcltk/itcl + dev-tcltk/itk + dev-tcltk/tix + media-libs/ftgl + virtual/glu + virtual/opengl + x11-libs/libXmu + freeimage? ( media-libs/freeimage ) + gl2ps? ( x11-libs/gl2ps ) + java? ( >=virtual/jdk-0:= ) + tbb? ( dev-cpp/tbb ) + vtk? ( || ( sci-libs/vtk[imaging] sci-libs/vtk[qt4] sci-libs/vtk[rendering] sci-libs/vtk[views] sci-libs/vtk[all-modules] ) )" +RDEPEND="${DEPEND}" + +CHECKREQS_MEMORY="256M" +CHECKREQS_DISK_BUILD="3584M" + +PATCHES=( "${FILESDIR}"/${PN}-6.8.0-fixed-DESTDIR.patch + "${FILESDIR}"/${PN}-6.9.1-vtk-configure.patch ) + +pkg_setup() { + check-reqs_pkg_setup + java-pkg-opt-2_pkg_setup +} + +src_prepare() { + default + + MY_VTK_P=$(best_version sci-libs/vtk) + MY_VTK_PV=${MY_VTK_P/sci-libs\/vtk-} + MY_VTK_SUB=vtk-$(get_version_component_range 1-2 ${MY_VTK_PV}) + if has_version ">=sci-libs/vtk-6.3" ; then #bug 605304 + epatch "${FILESDIR}"/${PN}-6.9.1-vtk-6.3.patch + fi + + java-pkg-opt-2_src_prepare + + # Feed environment variables used by Opencascade compilation + my_install_dir=${EROOT}usr/$(get_libdir)/${P}/ros + local my_env_install="#!/bin/sh -f +if [ -z \"\$PATH\" ]; then + export PATH=VAR_CASROOT/Linux/bin +else + export PATH=VAR_CASROOT/Linux/bin:\$PATH +fi +if [ -z \"\$LD_LIBRARY_PATH\" ]; then + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib +else + export LD_LIBRARY_PATH=VAR_CASROOT/Linux/lib:\$LD_LIBRARY_PATH +fi" + local my_sys_lib=${EROOT}usr/$(get_libdir) + local my_env="CASROOT=VAR_CASROOT +CSF_MDTVFontDirectory=VAR_CASROOT/src/FontMFT +CSF_LANGUAGE=us +MMGT_CLEAR=1 +CSF_EXCEPTION_PROMPT=1 +CSF_SHMessage=VAR_CASROOT/src/SHMessage +CSF_MDTVTexturesDirectory=VAR_CASROOT/src/Textures +CSF_XSMessage=VAR_CASROOT/src/XSMessage +CSF_StandardDefaults=VAR_CASROOT/src/StdResource +CSF_PluginDefaults=VAR_CASROOT/src/StdResource +CSF_XCAFDefaults=VAR_CASROOT/src/StdResource +CSF_StandardLiteDefaults=VAR_CASROOT/src/StdResource +CSF_GraphicShr=VAR_CASROOT/Linux/lib/libTKOpenGl.so +CSF_UnitsLexicon=VAR_CASROOT/src/UnitsAPI/Lexi_Expr.dat +CSF_UnitsDefinition=VAR_CASROOT/src/UnitsAPI/Units.dat +CSF_IGESDefaults=VAR_CASROOT/src/XSTEPResource +CSF_STEPDefaults=VAR_CASROOT/src/XSTEPResource +CSF_XmlOcafResource=VAR_CASROOT/src/XmlOcafResource +CSF_MIGRATION_TYPES=VAR_CASROOT/src/StdResource/MigrationSheet.txt +TCLHOME=${EROOT}usr/bin +TCLLIBPATH=${my_sys_lib} +ITK_LIBRARY=${my_sys_lib}/itk$(grep ITK_VER /usr/include/itk.h | sed 's/^.*"\(.*\)".*/\1/') +ITCL_LIBRARY=${my_sys_lib}/itcl$(grep ITCL_VER /usr/include/itcl.h | sed 's/^.*"\(.*\)".*/\1/') +TIX_LIBRARY=${my_sys_lib}/tix$(grep TIX_VER /usr/include/tix.h | sed 's/^.*"\(.*\)".*/\1/') +TK_LIBRARY=${my_sys_lib}/tk$(grep TK_VER /usr/include/tk.h | sed 's/^.*"\(.*\)".*/\1/') +TCL_LIBRARY=${my_sys_lib}/tcl$(grep TCL_VER /usr/include/tcl.h | sed 's/^.*"\(.*\)".*/\1/')" + + ( echo "${my_env_install}" + echo "${my_env}" | sed -e "s:^:export :" ) \ + | sed -e "s:VAR_CASROOT:${S}:g" > env.sh || die + source env.sh + + ( echo "PATH=${my_install_dir}/lin/bin" + echo "LDPATH=${my_install_dir}/lin/$(get_libdir)" + echo "${my_env}" | sed \ + -e "s:VAR_CASROOT:${my_install_dir}/lin:g" \ + -e "s:/Linux/lib/:/$(get_libdir)/:g" || die + ) > 50${PN} + + append-cxxflags "-fpermissive" + + sed -e "/^AM_C_PROTOTYPES$/d" \ + -e "s/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/" \ + -e "s:\$qt/include:\$qt/include/qt4:g"\ + -e "s:\$qt/lib:\$qt/$(get_libdir)/qt4:g"\ + -i configure.ac || die + eautoreconf +} + +src_configure() { + econf \ + --prefix=${my_install_dir}/lin --exec-prefix=${my_install_dir}/lin \ + --with-tcl="${EROOT}usr/$(get_libdir)" --with-tk="${EROOT}usr/$(get_libdir)" \ + --with-freetype="${EROOT}usr" \ + --with-ftgl="${EROOT}usr" \ + $(usex freeimage "--with-freeimage=${EROOT}usr" "") \ + $(usex gl2ps "--with-gl2ps=${EROOT}usr" "") \ + $(usex qt4 "--with-qt=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-include=${EROOT}usr" "") \ + $(usex tbb "--with-tbb-library=${EROOT}usr" "") \ + $(use java && echo "--with-java-include=$(java-config -O)/include" || echo "--without-java-include") \ + $(usex vtk "--with-vtk-include=${EROOT}usr/include/${MY_VTK_SUB}" "") \ + $(usex vtk "--with-vtk-library=${EROOT}usr/$(get_libdir)" "") \ + $(use_enable debug) \ + $(use_enable !debug production) +} + +src_install() { + emake DESTDIR="${D}" install + + prune_libtool_files + + # Symlinks for keeping original OpenCascade folder structure and + # add a link lib to $(get_libdir) if we are e.g. on amd64 multilib + if [ "$(get_libdir)" != "lib" ]; then + dosym "$(get_libdir)" "${my_install_dir}/lin/lib" + fi + + insinto /etc/env.d/${PN} + newins 50${PN} ${PV} + + if use examples ; then + insinto /usr/share/doc/${PF}/examples + doins -r data + doins -r samples + fi + if use doc; then + insinto /usr/share/doc/${PF} + doins -r doc/{overview,pdf,refman} + fi +} + +pkg_postinst() { + eselect ${PN} set ${PV} + einfo + elog "After upgrading OpenCASCADE you may have to rebuild packages depending on it." + elog "You get a list by running \"equery depends sci-libs/opencascade\"" + elog "revdep-rebuild does NOT suffice." + einfo +} diff --git a/sci-libs/openfoam-bin/Manifest b/sci-libs/openfoam-bin/Manifest new file mode 100644 index 000000000000..97e6d2359dcb --- /dev/null +++ b/sci-libs/openfoam-bin/Manifest @@ -0,0 +1,8 @@ +DIST OpenFOAM-1.6-compile.patch.bz2 5835 SHA256 633966faf70ffb0acbb1684075630cf9a3028b7099e3fcee549d8c850d55b794 SHA512 625d6b30444bb5cfabd81b94ffcdad082dabafc7ee59eb70ab2f6cf816ee395bc7b9b5697308ed95a83c75cf2778ebd03eaa284fbcc3c17c226ac7443f5e76df WHIRLPOOL 8d0aa38367eadd2e8e028322f38b81800cc2d8a572981e3e228255e41d2ccec7d29220cb1712bf5f78a3a23c361215f0dd329c4f711dcfa81289d8fcc8a527f5 +DIST OpenFOAM-1.6.General.tgz 241760751 SHA256 a752d8e70ad26b84d6939e32e443e341f4cafecaff0068c0cc85c43562d21f9a SHA512 88988426c5cbb980e0df82c0a8b6396490c8ac6f6a3633da9d3629f5a017849b4d8637cc0f5003e33f0dd5825003b9405ede6f868b5f747be5afb6f31c96d128 WHIRLPOOL 903bf633d017bdb4e1f099685befed8ff3b3d9cfc5ff4060cbb8ddf437fd683dd0d417f22a955515fd465e7bfedf803ca7d9df9d9e00db85beeadd2d9a183bd8 +DIST OpenFOAM-1.6.linux64GccDPOpt.tgz 44957838 SHA256 58b825423a3fcc7015aa60905c7e65a344908e7e5f8740baeed6cd17fb5bb14d SHA512 bc9f428d729b918597db5b507cb2d558ce52d3faeb1eabcb9b2382a4d4b937906073d336e98e1b5bc1c5a62d0658603348abd7870695001215e467033a8d8f02 WHIRLPOOL 77d8a336b7aca721fa58d27d229c58357c7069a7b6bad1a5c0726d9852782fddc01f51dd0b34a84b47235b931ffbb16fd7ca596f3bc29ea237dc0cee90946c6b +DIST OpenFOAM-1.6.linuxGccDPOpt.tgz 41587474 SHA256 3c551134c0e1a8700c1257e549820d4cf6cbe50c6435ab5dbddb1e4b6123dac0 SHA512 54c764780d563555766c4c4507b6fdd3f138a1cf7ec29e557a8ebc7040aee8626ce80672cf258196fbbabfedea21916ba5dc9dcab94a54d45fbae90ff0edee4b WHIRLPOOL 12afa98c3f7aa7d4911baeaa739302ef577d1ff99c9704faf83a40d7f9d488827a27296b29e1b3c20207a7135ad065bfe804faa1071fb31120f1c70e9958df27 +EBUILD openfoam-bin-1.6.ebuild 2785 SHA256 2bea80c532d4e26ae900e492f46cb9269e459bd39015593f1b97a2849408e994 SHA512 09b4fb9ecbb8b871f017a28150880cba9e9d163d1f785d5c79c6341122a83214663534cead65c626b5e1ba9fc1ce3b8220e9dc8d7aefbab0a9cd4dccec442b41 WHIRLPOOL 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9476f418d74a2ec01ba8eb2eedb79f0351889f67e36c27b1109882f4953b6379af012dbd922868ad5d1537fad3092c3d2a1741a1e6191bed4a8b10426abe60a4 WHIRLPOOL ee608a66540735fcef691e734c96fe7a1e61559e57d30e16adfd727e2c1fae2715ea7a670cf5a9a3419fc8dd5bb0b47e0bba123f269b7168d0ab223846e5e573 diff --git a/sci-libs/openfoam-bin/metadata.xml b/sci-libs/openfoam-bin/metadata.xml new file mode 100644 index 000000000000..8146f9894c85 --- /dev/null +++ b/sci-libs/openfoam-bin/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>patrick@gentoo.org</email> + <name>Patrick Lauer</name> + </maintainer> + <maintainer type="person"> + <email>oli.borm@web.de</email> + <name>Oliver Borm</name> + </maintainer> + <maintainer type="project"> + <email>proxy-maint@gentoo.org</email> + <name>Proxy Maintainers</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">foam</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/openfoam-bin/openfoam-bin-1.6.ebuild b/sci-libs/openfoam-bin/openfoam-bin-1.6.ebuild new file mode 100644 index 000000000000..bef10456aa1b --- /dev/null +++ b/sci-libs/openfoam-bin/openfoam-bin-1.6.ebuild @@ -0,0 +1,107 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="2" + +inherit eutils versionator multilib toolchain-funcs + +MY_PN="OpenFOAM" +MY_PV=$(get_version_component_range 1-2) +MY_P="${MY_PN}-${MY_PV}" + +DESCRIPTION="Open Field Operation and Manipulation - CFD Simulation Toolbox" +HOMEPAGE="http://www.opencfd.co.uk/openfoam/" +SRC_URI="mirror://sourceforge/foam/${MY_P}.General.gtgz -> ${MY_P}.General.tgz + x86? ( mirror://sourceforge/foam/${MY_P}.linuxGccDPOpt.gtgz -> ${MY_P}.linuxGccDPOpt.tgz ) + amd64? ( mirror://sourceforge/foam/${MY_P}.linux64GccDPOpt.gtgz -> ${MY_P}.linux64GccDPOpt.tgz ) + mirror://gentoo/${MY_P}-compile.patch.bz2" + +LICENSE="GPL-2" +SLOT="1.6" +KEYWORDS="-* ~amd64 ~x86" +IUSE="examples doc" + +DEPEND="!=sci-libs/openfoam-${MY_PV}* + !=sci-libs/openfoam-kernel-${MY_PV}* + !=sci-libs/openfoam-meta-${MY_PV}* + !=sci-libs/openfoam-solvers-${MY_PV}* + !=sci-libs/openfoam-utilities-${MY_PV}* + !=sci-libs/openfoam-wmake-${MY_PV}* + sci-visualization/opendx + virtual/mpi" +RDEPEND="${DEPEND} + =sys-libs/ncurses-5*" + +S=${WORKDIR}/${MY_P} +INSDIR="/usr/$(get_libdir)/${MY_PN}/${MY_P}" + +pkg_setup() { + ## binaries are compiled with gcc-4.3.3 + if ! version_is_at_least 4.3 $(gcc-version) ; then + die "${PN} requires >=sys-devel/gcc-4.3 in order to run." + fi + + elog + elog "In order to use ${MY_PN} you should add the following line to ~/.bashrc :" + elog + elog "alias startOF$(delete_all_version_separators ${MY_PV})='source ${INSDIR}/etc/bashrc'" + elog + elog "And everytime you want to use OpenFOAM you have to execute startOF$(delete_all_version_separators ${MY_PV})" + ewarn + ewarn "FoamX is deprecated since ${MY_PN}-1.5! " + ewarn +} + +src_prepare() { + epatch "${WORKDIR}"/${MY_P}-compile.patch +} + +src_configure() { + if has_version sys-cluster/mpich2 ; then + export WM_MPLIB=MPICH + export MPI_VERSION=mpich + elif has_version sys-cluster/openmpi ; then + export WM_MPLIB=OPENMPI + export MPI_VERSION=openmpi + else + die "You need one of the following mpi implementations: openmpi, mpich2" + fi + + sed -i -e "s|WM_MPLIB:=OPENMPI|WM_MPLIB:="${WM_MPLIB}"|" etc/bashrc + sed -i -e "s|setenv WM_MPLIB OPENMPI|setenv WM_MPLIB "${WM_MPLIB}"|" etc/cshrc + + use x86 && WM_OPTIONS="linuxGccDPOpt" + use amd64 && WM_OPTIONS="linux64GccDPOpt" + + mv lib/${WM_OPTIONS}/$MPI_VERSION* lib/${WM_OPTIONS}/$MPI_VERSION +} + +src_test() { + cd bin + ./foamInstallationTest +} + +src_install() { + insinto ${INSDIR} + doins -r etc + + use examples && doins -r tutorials + + insopts -m0755 + doins -r bin + + insinto ${INSDIR}/applications/bin + doins -r applications/bin/${WM_OPTIONS}/* + + insinto ${INSDIR}/lib + doins -r lib/${WM_OPTIONS}/* + + insinto ${INSDIR}/wmake + doins -r wmake/* + + dodoc {doc/Guides-a4/*.pdf,README} + + if use doc ; then + dohtml -r doc/Doxygen + fi +} diff --git a/sci-libs/openfoam/Manifest b/sci-libs/openfoam/Manifest new file mode 100644 index 000000000000..6a61a2faa5c9 --- /dev/null +++ b/sci-libs/openfoam/Manifest @@ -0,0 +1,13 @@ +DIST OpenFOAM-2.2.1.tgz 37600247 SHA256 92ad3d88470db22799e07ae247aa85da92dabcb7995a17a178f791a7098fa2bb SHA512 1b3afab700ca6e8b328ec76b5d862e67696ad6c622bc1d3a26c3cc87d6ad62f752be72cc0644510b63612fd1441e7a2969e3b53728d30f2a67a2453530fcd286 WHIRLPOOL 4f6a16470be52f7ee442b2e8d37b8b86d8e70b1da326011b9952272f3c754f91894693c1edfe8623b23e6cd20cb7ca905a96ba432b963b082b4f7dad3faf54f9 +DIST OpenFOAM-2.2.2.tgz 32536146 SHA256 097adf813e035d04c9be19ee244632cd76971fde107682d50983f8d5cdcf0210 SHA512 c57128b4a3fea0419118963a0e65dcecb532cb36713a03c3beef027e57f5a48c6839f35286eb9163cceb9e278bef6135bca7ca53990c2dbe4544fb26e82098d0 WHIRLPOOL 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SHA512 1916191d810676145a88492e902840f5cbd839f3b221dcf55c5edc26791b395c1d36fd6ef37e4c1bc1f813357a3b22ce3ec3e1b802ac49157f76d25e6ca53cbe WHIRLPOOL 176992376ca67ff473977a22b2c9dcfb6a7c1c5e05a7ed96f0d54043d96351968b8c550584241f08c1022ff109a2023b220de67dda947e085bf92d4b2b8551d7 +EBUILD openfoam-2.2.1.ebuild 2734 SHA256 ec3caece285fb7455ef2e03df598ece06b1c615de5fb5855ac51d13b4d718fe2 SHA512 840b31b22793d5258e26118049a3c1277fcb22f37511bf71217b006af830fd8b360e09640e5026362e88fdc185d2531e86bb80fa1a0c539957d20707bc303234 WHIRLPOOL 5e3196372f2d589d0ae0444ab31766f63f004ef559bf2a16015aba99f915cc09d45848e7468e9f858c44bca6902d219c2d1280f99ff84ae798271feca66a539d +EBUILD openfoam-2.2.2.ebuild 2734 SHA256 ec3caece285fb7455ef2e03df598ece06b1c615de5fb5855ac51d13b4d718fe2 SHA512 840b31b22793d5258e26118049a3c1277fcb22f37511bf71217b006af830fd8b360e09640e5026362e88fdc185d2531e86bb80fa1a0c539957d20707bc303234 WHIRLPOOL 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<name>Oliver Borm</name> + </maintainer> + <maintainer type="project"> + <email>proxy-maint@gentoo.org</email> + <name>Proxy Maintainers</name> + </maintainer> + <use> + <flag name="opendx"> Install opendx visualisation tool</flag> + <flag name="src"> Install source files</flag> + <flag name="paraview">Enable support for paraview library</flag> + </use> + <upstream> + <remote-id type="sourceforge">downloads</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/openfoam/openfoam-2.2.1.ebuild b/sci-libs/openfoam/openfoam-2.2.1.ebuild new file mode 100644 index 000000000000..711bb0042fcd --- /dev/null +++ b/sci-libs/openfoam/openfoam-2.2.1.ebuild @@ -0,0 +1,108 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils versionator multilib toolchain-funcs multiprocessing + +MY_PN="OpenFOAM" +MY_PV=$(get_version_component_range 1-2) +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Open Field Operation and Manipulation - CFD Simulation Toolbox" +HOMEPAGE="http://www.openfoam.org" +SRC_URI="http://downloads.sourceforge.net/foam/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="2.2" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples opendx src" + +RDEPEND="!=sci-libs/openfoam-bin-${MY_PV}* + !=sci-libs/openfoam-kernel-${MY_PV}* + !=sci-libs/openfoam-meta-${MY_PV}* + !=sci-libs/openfoam-solvers-${MY_PV}* + !=sci-libs/openfoam-utilities-${MY_PV}* + !=sci-libs/openfoam-wmake-${MY_PV}* + sci-libs/parmetis + sci-libs/parmgridgen + sci-libs/scotch + virtual/mpi + opendx? ( sci-visualization/opendx )" +DEPEND="${DEPEND} + doc? ( app-doc/doxygen[dot] )" + +S=${WORKDIR}/${MY_P} +INSDIR="/usr/$(get_libdir)/${MY_PN}/${MY_P}" + +pkg_setup() { + # just to be sure the right profile is selected (gcc-config) + if ! version_is_at_least 4.3 $(gcc-version) ; then + die "${PN} requires >=sys-devel/gcc-4.3 to compile." + fi + + elog + elog "In order to use ${MY_PN} you should add the following line to ~/.bashrc :" + elog + elog "alias startOF$(delete_all_version_separators ${MY_PV})='source ${INSDIR}/etc/bashrc'" + elog + elog "And everytime you want to use OpenFOAM you have to execute startOF$(delete_all_version_separators ${MY_PV})" + ewarn + ewarn "FoamX is deprecated since ${MY_PN}-1.5! " + ewarn +} + +src_configure() { + if has_version sys-cluster/mpich2 ; then + export WM_MPLIB=MPICH + elif has_version sys-cluster/openmpi ; then + export WM_MPLIB=OPENMPI + else + die "You need one of the following mpi implementations: openmpi or mpich2" + fi + + sed -i -e "s|WM_MPLIB:=OPENMPI|WM_MPLIB:="${WM_MPLIB}"|" etc/bashrc + sed -i -e "s|setenv WM_MPLIB OPENMPI|setenv WM_MPLIB "${WM_MPLIB}"|" etc/cshrc + + sed -i -e "s|^foamInstall=\$HOME|foamInstall=/usr/$(get_libdir)|" etc/bashrc + sed -i -e "s|^set foamInstall = \$HOME|set foamInstall = /usr/$(get_libdir)|" etc/cshrc +} + +src_compile() { + export WM_NCOMPPROCS=$(makeopts_jobs) + + export FOAM_INST_DIR=${WORKDIR} + source etc/bashrc + + find wmake -name dirToString -exec rm -rf {} + + find wmake -name wmkdep -exec rm -rf {}+ + + if use doc ; then + ./Allwmake doc || die "could not build" + else + ./Allwmake || die "could not build" + fi +} + +src_test() { + cd bin + ./foamInstallationTest +} + +src_install() { + insinto ${INSDIR} + doins -r etc + + use examples && doins -r tutorials + + use src && doins -r src + + insopts -m0755 + doins -r bin applications platforms wmake + + dodoc README.html doc/Guides-a4/*.pdf + + if use doc ; then + dohtml -r doc/Doxygen + fi +} diff --git a/sci-libs/openfoam/openfoam-2.2.2.ebuild b/sci-libs/openfoam/openfoam-2.2.2.ebuild new file mode 100644 index 000000000000..711bb0042fcd --- /dev/null +++ b/sci-libs/openfoam/openfoam-2.2.2.ebuild @@ -0,0 +1,108 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils versionator multilib toolchain-funcs multiprocessing + +MY_PN="OpenFOAM" +MY_PV=$(get_version_component_range 1-2) +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Open Field Operation and Manipulation - CFD Simulation Toolbox" +HOMEPAGE="http://www.openfoam.org" +SRC_URI="http://downloads.sourceforge.net/foam/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="2.2" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples opendx src" + +RDEPEND="!=sci-libs/openfoam-bin-${MY_PV}* + !=sci-libs/openfoam-kernel-${MY_PV}* + !=sci-libs/openfoam-meta-${MY_PV}* + !=sci-libs/openfoam-solvers-${MY_PV}* + !=sci-libs/openfoam-utilities-${MY_PV}* + !=sci-libs/openfoam-wmake-${MY_PV}* + sci-libs/parmetis + sci-libs/parmgridgen + sci-libs/scotch + virtual/mpi + opendx? ( sci-visualization/opendx )" +DEPEND="${DEPEND} + doc? ( app-doc/doxygen[dot] )" + +S=${WORKDIR}/${MY_P} +INSDIR="/usr/$(get_libdir)/${MY_PN}/${MY_P}" + +pkg_setup() { + # just to be sure the right profile is selected (gcc-config) + if ! version_is_at_least 4.3 $(gcc-version) ; then + die "${PN} requires >=sys-devel/gcc-4.3 to compile." + fi + + elog + elog "In order to use ${MY_PN} you should add the following line to ~/.bashrc :" + elog + elog "alias startOF$(delete_all_version_separators ${MY_PV})='source ${INSDIR}/etc/bashrc'" + elog + elog "And everytime you want to use OpenFOAM you have to execute startOF$(delete_all_version_separators ${MY_PV})" + ewarn + ewarn "FoamX is deprecated since ${MY_PN}-1.5! " + ewarn +} + +src_configure() { + if has_version sys-cluster/mpich2 ; then + export WM_MPLIB=MPICH + elif has_version sys-cluster/openmpi ; then + export WM_MPLIB=OPENMPI + else + die "You need one of the following mpi implementations: openmpi or mpich2" + fi + + sed -i -e "s|WM_MPLIB:=OPENMPI|WM_MPLIB:="${WM_MPLIB}"|" etc/bashrc + sed -i -e "s|setenv WM_MPLIB OPENMPI|setenv WM_MPLIB "${WM_MPLIB}"|" etc/cshrc + + sed -i -e "s|^foamInstall=\$HOME|foamInstall=/usr/$(get_libdir)|" etc/bashrc + sed -i -e "s|^set foamInstall = \$HOME|set foamInstall = /usr/$(get_libdir)|" etc/cshrc +} + +src_compile() { + export WM_NCOMPPROCS=$(makeopts_jobs) + + export FOAM_INST_DIR=${WORKDIR} + source etc/bashrc + + find wmake -name dirToString -exec rm -rf {} + + find wmake -name wmkdep -exec rm -rf {}+ + + if use doc ; then + ./Allwmake doc || die "could not build" + else + ./Allwmake || die "could not build" + fi +} + +src_test() { + cd bin + ./foamInstallationTest +} + +src_install() { + insinto ${INSDIR} + doins -r etc + + use examples && doins -r tutorials + + use src && doins -r src + + insopts -m0755 + doins -r bin applications platforms wmake + + dodoc README.html doc/Guides-a4/*.pdf + + if use doc ; then + dohtml -r doc/Doxygen + fi +} diff --git a/sci-libs/openfoam/openfoam-2.3.0-r1.ebuild b/sci-libs/openfoam/openfoam-2.3.0-r1.ebuild new file mode 100644 index 000000000000..45d328296a54 --- /dev/null +++ b/sci-libs/openfoam/openfoam-2.3.0-r1.ebuild @@ -0,0 +1,112 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils versionator multilib toolchain-funcs multiprocessing + +MY_PN="OpenFOAM" +MY_PV=$(get_version_component_range 1-2) +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Open Field Operation and Manipulation - CFD Simulation Toolbox" +HOMEPAGE="http://www.openfoam.org" +SRC_URI="http://downloads.sourceforge.net/foam/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="2.3" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples opendx src paraview" + +RDEPEND="!=sci-libs/openfoam-bin-${MY_PV}* + !=sci-libs/openfoam-kernel-${MY_PV}* + !=sci-libs/openfoam-meta-${MY_PV}* + !=sci-libs/openfoam-solvers-${MY_PV}* + !=sci-libs/openfoam-utilities-${MY_PV}* + !=sci-libs/openfoam-wmake-${MY_PV}* + sci-libs/parmetis + sci-libs/parmgridgen + sci-libs/scotch + virtual/mpi + opendx? ( sci-visualization/opendx ) + paraview? ( ~sci-visualization/paraview-4.1.0[development] )" +DEPEND="${DEPEND} + doc? ( app-doc/doxygen[dot] )" + +S=${WORKDIR}/${MY_P} +INSDIR="/usr/$(get_libdir)/${MY_PN}/${MY_P}" + +pkg_setup() { + # just to be sure the right profile is selected (gcc-config) + if ! version_is_at_least 4.3 $(gcc-version) ; then + die "${PN} requires >=sys-devel/gcc-4.3 to compile." + fi + + elog + elog "In order to use ${MY_PN} you should add the following line to ~/.bashrc :" + elog + elog "alias startOF$(delete_all_version_separators ${MY_PV})='source ${INSDIR}/etc/bashrc'" + elog + elog "And everytime you want to use OpenFOAM you have to execute startOF$(delete_all_version_separators ${MY_PV})" + ewarn + ewarn "FoamX is deprecated since ${MY_PN}-1.5! " + ewarn +} + +src_configure() { + if has_version sys-cluster/mpich2 ; then + export WM_MPLIB=MPICH + elif has_version sys-cluster/openmpi ; then + export WM_MPLIB=OPENMPI + else + die "You need one of the following mpi implementations: openmpi or mpich2" + fi + + sed -i -e "s|WM_MPLIB:=OPENMPI|WM_MPLIB:="${WM_MPLIB}"|" etc/bashrc + sed -i -e "s|setenv WM_MPLIB OPENMPI|setenv WM_MPLIB "${WM_MPLIB}"|" etc/cshrc + + sed -i -e "s|^foamInstall=\$HOME|foamInstall=/usr/$(get_libdir)|" etc/bashrc + sed -i -e "s|^set foamInstall = \$HOME|set foamInstall = /usr/$(get_libdir)|" etc/cshrc + + sed -i -e 's|^export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName|export ParaView_DIR=/usr|' etc/config/paraview.sh + sed -i -e 's|^setenv ParaView_DIR $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName|setenv ParaView_DIR /usr|' etc/config/paraview.csh +} + +src_compile() { + export WM_NCOMPPROCS=$(makeopts_jobs) + + export FOAM_INST_DIR=${WORKDIR} + source etc/bashrc + + find wmake -name dirToString -exec rm -rf {} + + find wmake -name wmkdep -exec rm -rf {}+ + + ./Allwmake || die "could not build" + if use doc ; then + doc/Allwmake || die "could not build" + fi +} + +# Doesn't do anything sane +#src_test() { +# cd bin +# ./foamInstallationTest +#} + +src_install() { + insinto ${INSDIR} + doins -r etc + + use examples && doins -r tutorials + + use src && doins -r src + + insopts -m0755 + doins -r bin applications platforms wmake + + dodoc README.html doc/Guides-a4/*.pdf + + if use doc ; then + dohtml -r doc/Doxygen + fi +} diff --git a/sci-libs/openfoam/openfoam-2.3.1-r1.ebuild b/sci-libs/openfoam/openfoam-2.3.1-r1.ebuild new file mode 100644 index 000000000000..1e302b58e1e2 --- /dev/null +++ b/sci-libs/openfoam/openfoam-2.3.1-r1.ebuild @@ -0,0 +1,112 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils versionator multilib toolchain-funcs multiprocessing + +MY_PN="OpenFOAM" +MY_PV=$(get_version_component_range 1-2) +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Open Field Operation and Manipulation - CFD Simulation Toolbox" +HOMEPAGE="http://www.openfoam.org" +SRC_URI="http://downloads.sourceforge.net/foam/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="2.3" +KEYWORDS="amd64 x86" +IUSE="doc examples opendx src paraview" + +RDEPEND="!=sci-libs/openfoam-bin-${MY_PV}* + !=sci-libs/openfoam-kernel-${MY_PV}* + !=sci-libs/openfoam-meta-${MY_PV}* + !=sci-libs/openfoam-solvers-${MY_PV}* + !=sci-libs/openfoam-utilities-${MY_PV}* + !=sci-libs/openfoam-wmake-${MY_PV}* + sci-libs/parmetis + sci-libs/parmgridgen + sci-libs/scotch + virtual/mpi + opendx? ( sci-visualization/opendx ) + paraview? ( ~sci-visualization/paraview-4.1.0[development] )" +DEPEND="${DEPEND} + doc? ( app-doc/doxygen[dot] )" + +S=${WORKDIR}/${MY_P} +INSDIR="/usr/$(get_libdir)/${MY_PN}/${MY_P}" + +pkg_setup() { + # just to be sure the right profile is selected (gcc-config) + if ! version_is_at_least 4.3 $(gcc-version) ; then + die "${PN} requires >=sys-devel/gcc-4.3 to compile." + fi + + elog + elog "In order to use ${MY_PN} you should add the following line to ~/.bashrc :" + elog + elog "alias startOF$(delete_all_version_separators ${MY_PV})='source ${INSDIR}/etc/bashrc'" + elog + elog "And everytime you want to use OpenFOAM you have to execute startOF$(delete_all_version_separators ${MY_PV})" + ewarn + ewarn "FoamX is deprecated since ${MY_PN}-1.5! " + ewarn +} + +src_configure() { + if has_version sys-cluster/mpich2 ; then + export WM_MPLIB=MPICH + elif has_version sys-cluster/openmpi ; then + export WM_MPLIB=OPENMPI + else + die "You need one of the following mpi implementations: openmpi or mpich2" + fi + + sed -i -e "s|WM_MPLIB:=OPENMPI|WM_MPLIB:="${WM_MPLIB}"|" etc/bashrc + sed -i -e "s|setenv WM_MPLIB OPENMPI|setenv WM_MPLIB "${WM_MPLIB}"|" etc/cshrc + + sed -i -e "s|^foamInstall=\$HOME|foamInstall=/usr/$(get_libdir)|" etc/bashrc + sed -i -e "s|^set foamInstall = \$HOME|set foamInstall = /usr/$(get_libdir)|" etc/cshrc + + sed -i -e 's|^export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName|export ParaView_DIR=/usr|' etc/config/paraview.sh + sed -i -e 's|^setenv ParaView_DIR $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName|setenv ParaView_DIR /usr|' etc/config/paraview.csh +} + +src_compile() { + export WM_NCOMPPROCS=$(makeopts_jobs) + + export FOAM_INST_DIR=${WORKDIR} + source etc/bashrc + + find wmake -name dirToString -exec rm -rf {} + + find wmake -name wmkdep -exec rm -rf {}+ + + ./Allwmake || die "could not build" + if use doc ; then + doc/Allwmake || die "could not build" + fi +} + +# Doesn't do anything sane +#src_test() { +# cd bin +# ./foamInstallationTest +#} + +src_install() { + insinto ${INSDIR} + doins -r etc + + use examples && doins -r tutorials + + use src && doins -r src + + insopts -m0755 + doins -r bin applications platforms wmake + + dodoc README.html doc/Guides-a4/*.pdf + + if use doc ; then + dohtml -r doc/Doxygen + fi +} diff --git a/sci-libs/openfoam/openfoam-2.4.0-r1.ebuild b/sci-libs/openfoam/openfoam-2.4.0-r1.ebuild new file mode 100644 index 000000000000..67bda192d50c --- /dev/null +++ b/sci-libs/openfoam/openfoam-2.4.0-r1.ebuild @@ -0,0 +1,113 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" + +inherit eutils versionator multilib toolchain-funcs multiprocessing + +MY_PN="OpenFOAM" +MY_PV=$(get_version_component_range 1-2) +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Open Field Operation and Manipulation - CFD Simulation Toolbox" +HOMEPAGE="http://www.openfoam.org" +SRC_URI="http://downloads.sourceforge.net/foam/${MY_P}.tgz" + +LICENSE="GPL-2" +SLOT="2.4" +KEYWORDS="~amd64 ~x86" +IUSE="doc examples opendx src paraview" + +RDEPEND="!=sci-libs/openfoam-bin-${MY_PV}* + !=sci-libs/openfoam-kernel-${MY_PV}* + !=sci-libs/openfoam-meta-${MY_PV}* + !=sci-libs/openfoam-solvers-${MY_PV}* + !=sci-libs/openfoam-utilities-${MY_PV}* + !=sci-libs/openfoam-wmake-${MY_PV}* + sci-mathematics/cgal + sci-libs/parmetis + sci-libs/parmgridgen + sci-libs/scotch + virtual/mpi + opendx? ( sci-visualization/opendx ) + paraview? ( sci-visualization/paraview[development] )" +DEPEND="${DEPEND} + doc? ( app-doc/doxygen[dot] )" + +S=${WORKDIR}/${MY_P} +INSDIR="/usr/$(get_libdir)/${MY_PN}/${MY_P}" + +pkg_setup() { + # just to be sure the right profile is selected (gcc-config) + if ! version_is_at_least 4.3 $(gcc-version) ; then + die "${PN} requires >=sys-devel/gcc-4.3 to compile." + fi + + elog + elog "In order to use ${MY_PN} you should add the following line to ~/.bashrc :" + elog + elog "alias startOF$(delete_all_version_separators ${MY_PV})='source ${INSDIR}/etc/bashrc'" + elog + elog "And everytime you want to use OpenFOAM you have to execute startOF$(delete_all_version_separators ${MY_PV})" + ewarn + ewarn "FoamX is deprecated since ${MY_PN}-1.5! " + ewarn +} + +src_configure() { + if has_version sys-cluster/mpich2 ; then + export WM_MPLIB=MPICH + elif has_version sys-cluster/openmpi ; then + export WM_MPLIB=OPENMPI + else + die "You need one of the following mpi implementations: openmpi or mpich2" + fi + + sed -i -e "s|WM_MPLIB:=OPENMPI|WM_MPLIB:="${WM_MPLIB}"|" etc/bashrc + sed -i -e "s|setenv WM_MPLIB OPENMPI|setenv WM_MPLIB "${WM_MPLIB}"|" etc/cshrc + + sed -i -e "s|^foamInstall=\$HOME|foamInstall=/usr/$(get_libdir)|" etc/bashrc + sed -i -e "s|^set foamInstall = \$HOME|set foamInstall = /usr/$(get_libdir)|" etc/cshrc + + sed -i -e 's|^export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName|export ParaView_DIR=/usr|' etc/config/paraview.sh + sed -i -e 's|^setenv ParaView_DIR $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName|setenv ParaView_DIR /usr|' etc/config/paraview.csh +} + +src_compile() { + export WM_NCOMPPROCS=$(makeopts_jobs) + + export FOAM_INST_DIR=${WORKDIR} + source etc/bashrc + + find wmake -name dirToString -exec rm -rf {} + + find wmake -name wmkdep -exec rm -rf {}+ + + ./Allwmake || die "could not build" + if use doc ; then + doc/Allwmake || die "could not build" + fi +} + +# Doesn't do anything sane +#src_test() { +# cd bin +# ./foamInstallationTest +#} + +src_install() { + insinto ${INSDIR} + doins -r etc + + use examples && doins -r tutorials + + use src && doins -r src + + insopts -m0755 + doins -r bin applications platforms wmake + + dodoc README.html doc/Guides-a4/*.pdf + + if use doc ; then + dohtml -r doc/Doxygen + fi +} diff --git a/sci-libs/openlibm/Manifest b/sci-libs/openlibm/Manifest new file mode 100644 index 000000000000..f759a935fb35 --- /dev/null +++ b/sci-libs/openlibm/Manifest @@ -0,0 +1,5 @@ +DIST openlibm-0.5.4.tar.gz 353072 SHA256 9a8ae1d17825a4a6a4c013d36a7f4348b27c47eedb6549c521ecc9c79d021c13 SHA512 ca74936b9eb7a52566cc509ffb98dd9e1672cd4029ba0193162505e53fe671b8903c37ef4036c15d0872ca246079a792d1630f3a93024010ff0c232f78295192 WHIRLPOOL 98d4b3f5fb5515fc0044bb9a1bdb5f61816efead9df906a2a959063765d0275ab527568a141ac6e9a3dc4124948a6c74d78ffc577f652ac47c7bc6374b84e360 +EBUILD openlibm-0.5.4.ebuild 710 SHA256 fccd96a64afdc8df7cda613f556788dc0bad412c137bcc516cd6a07408642574 SHA512 b3a4226d579f610bfb28ad9c46d5fcd11870afdca0e1d6133f7e891530615b3dd974bd8cd9452e98cf6d9847c106b53e2b629a3c682ef318431cf4d046a25458 WHIRLPOOL c3aa79da7438c0431e15e8bdcc2a4eb79489cd8e6cb65b11020cf1146190396215ae7ad5e17377c0b4b6fed9a46cb1fa94c40f36a5d79201deddd48d7d273f30 +MISC ChangeLog 2519 SHA256 edac5ba6b6955b726b04de6fd71986c864c94d933bed363a15f0629faae0e8e5 SHA512 fc9dbd9b4c8b57b5460e715ab6adcb307cd2710f47008113a173296c980db040de89d0a636851354251e400bd4f9970792af76fbe1f2e1a9871f9f523a1bf1f7 WHIRLPOOL 27df534a6f0cfbf311d34d094e03175a8d4b4b6bb79f05f92f005c1b5b94b791f2e4a2db81ecb9e3e99f194ad826625bb20e63154a9baa4be497af090c4c3db7 +MISC ChangeLog-2015 1263 SHA256 a0576640bb04005dc29c17a8e5fb60d9e78d753885797cf3d6886e011e69eacd SHA512 9eba8af0d142210eb7643a8ffce87ceffb0ea5e7477088da0a3b0a1786219367dba97da9531befc3b62406350e7753c02c2494176c4f9c938b705fefdb486570 WHIRLPOOL 2a458154a26bb7292c4b474ce20194d4a25678eefa9f967f010b4664f33eb401539d5903da9e387fa761d5f768320b44eb78ed62175f33345184a159c158bd08 +MISC metadata.xml 770 SHA256 6b6caf12b0eea6381ca3e548bb91f7da996ed7e1ea667d3b22d013624d9bae49 SHA512 c95d57f8ffc872aa8e0b4433d7b51bdb2c06f57c7ba00a66f7ecce06310db0343ff91081249154e2c1e32c9a90ed510704603c337530c1ee1acf36ce808b7b70 WHIRLPOOL 4de41fd43f604a52370ad1722a574e82384449cd96fc1505529055fc14ecc5be6126230cec59ccd944b35572bf013de9118130737ff49e31012217a4e95acf17 diff --git a/sci-libs/openlibm/metadata.xml b/sci-libs/openlibm/metadata.xml new file mode 100644 index 000000000000..cd02d5ec2882 --- /dev/null +++ b/sci-libs/openlibm/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +OpenLibm is an effort to have a high quality, portable, standalone C +mathematical library (libm). It can be used standalone in applications +and programming language implementations. +The project was born out of a need to have a good libm for the Julia +programming langage that worked consistently across compilers and +operating systems, and in 32-bit and 64-bit environments. +</longdescription> + <upstream> + <remote-id type="github">JuliaLang/openlibm</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/openlibm/openlibm-0.5.4.ebuild b/sci-libs/openlibm/openlibm-0.5.4.ebuild new file mode 100644 index 000000000000..7dbbc695f242 --- /dev/null +++ b/sci-libs/openlibm/openlibm-0.5.4.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils toolchain-funcs fortran-2 + +DESCRIPTION="High quality system independent, open source libm" +HOMEPAGE="https://github.com/JuliaLang/openlibm" +SRC_URI="https://github.com/JuliaLang/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="public-domain MIT ISC BSD-2 LGPL-2.1+" +SLOT="0/${PV}.0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="static-libs" + +src_install() { + emake DESTDIR="${D}" prefix="${EPREFIX}/usr" \ + libdir="${EPREFIX}/usr/$(get_libdir)" install + use static-libs || rm "${D}/${EPREFIX}/usr/$(get_libdir)/libopenlibm.a" || die "rm failed" + dodoc README.md +} diff --git a/sci-libs/orocos-bfl/Manifest b/sci-libs/orocos-bfl/Manifest new file mode 100644 index 000000000000..efc91115aa03 --- /dev/null +++ b/sci-libs/orocos-bfl/Manifest @@ -0,0 +1,5 @@ +DIST orocos-bfl-0.8.0-src.tar.bz2 212899 SHA256 e5e14f8abbc4c38ca51f5ff97b36f66c69da3a706ee6276bcb151ada4c71195c SHA512 045bbc415feec66206774a8bdea3843a7edf233d221bd639b1dcc01906386ff55f114a9685e1008b741ae895e6aef33641a1eab67cb106d23a085d77f1a937d5 WHIRLPOOL ba5ff1ad0ff25cbc45367ed3d0bc1f356ef827f1b0ef6fa3e4c26a0a0da7ef8efc44bb6b0b1a33cbc068f28d079d0f9e096b14efd5df0d54d5dafe80e95c0fec +EBUILD orocos-bfl-0.8.0.ebuild 1255 SHA256 2e5120499bf2392d4d9ead9fc7f1cd31e9d2beec56fcd42bcfae0bf373460b2a SHA512 b2d02482f8c5dfb6a7a98a96654ac97d09590fce90d7d2a427663c364c067d755e7fbf2bec28d117fc869c7f9db16ca16492e9d46c612214f76c4d7468145691 WHIRLPOOL 0d57a5246b0b15ab9c1276bc9d46b956c27380f50903664dea18161b153a53f1bfb662540faa038c23cb08e75ff73d871268404004472aff2a3d86d1913a576e +MISC ChangeLog 2185 SHA256 506afd7a9d8caca0a94190791dfb88da02d71382c437f4053063523c4097ff3a SHA512 ac2e9f6968992028ef5b4cad8c81713dd14c07d444cc891d93c8d08989365fa8aa241f99eaf37b8266a7077712ddacb62166b67ad21a4ee1c7fcc9440ae9e157 WHIRLPOOL 149177a9f86ffed1df53053e537933e6d51ac6e244a4a4e17dbfbab111b2390a2c78dac39b6d7585d93823bbcd37dac3b2d76ab299a18fff66489f5bd8bbef6b +MISC ChangeLog-2015 466 SHA256 48623aaa887a1eee7f4c5e752364eff4df1787ede675a14b96249c6ceca143e3 SHA512 ff69419668b0ad5dbad04bb7b3be64adb728310d04db552960d28b38174dacc75edfdd6b6401f7c289f1d3ac556ee28346268725a9082fa2fc41cfc0027fa704 WHIRLPOOL 43ee17dc2dee6c0af9560c7a2b9d8688b26e826190d32011e5516d3024b86c852408b800fa1616074834c75452aa81e5550d64c7b72adac70e0a7f25c03f61ec +MISC metadata.xml 603 SHA256 b8af614cf3d6360b7fa6e60ddfc63081be3a8308f29e5f8d1d24686290c32611 SHA512 e4c29ba5a7a3cbe373fcbb4b69ca3ce99e6e092585f3d27af31469949f4ca28a6bf2d4b1850271ddc7c7bc2c70b43bf27411e9fcdef2039c3e0f0949523ded6c WHIRLPOOL 948d19710b8bca507531ff575b9f6b1673f30efd9728241b3140b46884e8e419768d33a6fc3a43317208884bbd62982abd8ffad3d8af0c2b29d6b79893228253 diff --git a/sci-libs/orocos-bfl/metadata.xml b/sci-libs/orocos-bfl/metadata.xml new file mode 100644 index 000000000000..0dca5e8d0942 --- /dev/null +++ b/sci-libs/orocos-bfl/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="person"> +<email>aballier@gentoo.org</email> +<name>Alexis Ballier</name> +</maintainer> +<longdescription lang="en"> + The Bayesian Filtering Library (BFL) provides an application independent framework + for inference in Dynamic Bayesian Networks, i.e., recursive information processing + and estimation algorithms based on Bayes' rule, such as (Extended) Kalman Filters, + Particle Filters (or Sequential Monte Carlo methods), etc. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/orocos-bfl/orocos-bfl-0.8.0.ebuild b/sci-libs/orocos-bfl/orocos-bfl-0.8.0.ebuild new file mode 100644 index 000000000000..355ea827ed9e --- /dev/null +++ b/sci-libs/orocos-bfl/orocos-bfl-0.8.0.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Bayesian Filtering Library" +HOMEPAGE="http://orocos.org/bfl" +SRC_URI="http://people.mech.kuleuven.be/~tdelaet/bfl_tar/${P}-src.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~arm" +IUSE="doc examples static-libs test" + +RDEPEND="dev-libs/boost:=" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( + app-doc/doxygen + virtual/latex-base + ) + test? ( dev-util/cppunit )" + +src_prepare() { + sed -e 's:/lib:/${CMAKE_INSTALL_LIBDIR}:' \ + -i "${S}/"{,src/,src/bindings/rtt/}CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + "-DLIBRARY_TYPE=$(usex static-libs both shared)" + "-DBUILD_EXAMPLES=$(usex examples ON OFF)" + "-DBUILD_TESTS=$(usex test ON OFF)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + if use doc ; then + cd "${BUILD_DIR}" + doxygen || die + cd "${S}/docs" || die + pdflatex getting_started_guide || die + pdflatex getting_started_guide || die + fi +} + +src_test() { + cd "${BUILD_DIR}" + emake check +} + +src_install() { + cmake-utils_src_install + if use doc ; then + dohtml -r "${BUILD_DIR}/doc/html/" + dodoc "${S}/docs/getting_started_guide.pdf" + fi +} diff --git a/sci-libs/orocos_kdl/Manifest b/sci-libs/orocos_kdl/Manifest new file mode 100644 index 000000000000..bef19f7eaaeb --- /dev/null +++ b/sci-libs/orocos_kdl/Manifest @@ -0,0 +1,6 @@ +DIST orocos_kinematics_dynamics-1.3.1.tar.gz 202471 SHA256 aff361d2b4e2c6d30ae959308a124022eeef5dc5bea2ce779900f9b36b0537bd SHA512 93abd9dd5aef3710f784f9db8eea4738458bffa5295923993e2d77656c18f7354559412fb7eb5f1e9da7112de19aa36d3f0f68f149852f955bce960fd3b719e7 WHIRLPOOL b7b4d897f4d5f170b73fe5bb48e357051ae37a244b9c44e8c2f120d71fc75c80cc1f69d30cb1463bbe10658ba0af98965f18f3055436910f24ebaab0ce1bd8e7 +EBUILD orocos_kdl-1.3.1-r1.ebuild 1621 SHA256 ab8e369ca5db2930eeb14739cbd4b24b9ff6cb45d6a49d138f59a69cd20cb6ca SHA512 10f3ae388edcbbea0495f742c053a2caa6711e6ba6283896cb032a84cf099b4c700484c2237bea3662a187d357acefa9293dfc00f6ad8c32a6c08bea511c9909 WHIRLPOOL df9d4494df61261bdff70925105e24bdbcd1cefdec03435fe9a55ca7c4a23b673a03d3b87c5f9c179ed777a09b20ac1e43a424a3365a43cdc5aa14d8c5d7be25 +EBUILD orocos_kdl-9999.ebuild 1621 SHA256 ab8e369ca5db2930eeb14739cbd4b24b9ff6cb45d6a49d138f59a69cd20cb6ca SHA512 10f3ae388edcbbea0495f742c053a2caa6711e6ba6283896cb032a84cf099b4c700484c2237bea3662a187d357acefa9293dfc00f6ad8c32a6c08bea511c9909 WHIRLPOOL df9d4494df61261bdff70925105e24bdbcd1cefdec03435fe9a55ca7c4a23b673a03d3b87c5f9c179ed777a09b20ac1e43a424a3365a43cdc5aa14d8c5d7be25 +MISC ChangeLog 2698 SHA256 3c5d5a7e5b9521d744a6b40f2271779dc8adf6221c35c22e908ab647587bd804 SHA512 5392a916cfab978d4d8fc88136b056b39f86d800713dd97377fefd163f139e8cf93437cc225c8275101e4db658548bedb4c474b278fe1d6617f9cf13c9bb00a8 WHIRLPOOL 15675af15d260a10fe3a93d76d65dfcb4de7d2a6933e5f5dc3b23ec4518e26ab72c8cb143209e01b5ebd73862c6f5e33cb0343b3e519c0a1d520d42382dbb8ab +MISC ChangeLog-2015 548 SHA256 da5804c461f390a0c6b93a588ab485597f5d37b7f83b54ec77bb00d372790c9c SHA512 1f2da05d28b6fa19325b6bd1049c241f3d85d9109a3c9252fae7a9fcf37467738e55b16e4caf846a34b480587da9263b7cd6461191cb70c33c1c70dc3d412150 WHIRLPOOL 1ea3640830c000c5b729cbef4c2405a3161d48e0bcab4ed17685b6304de1bc66675e38ca0d397aaa7af7cace8d53019b8bef19f5fc72c750aaa387c39ad5b9cc +MISC metadata.xml 934 SHA256 24269a36e2efe2e918c2a89fa081a52707f27e28d62713d48b9adeb7b0cae98c SHA512 09dc8b8c362da950ea685ee6cb2d7eb3ee400f34fca286fa0bf064f3cc4338a5ad2ca8917c951211e9407122a3bd7a1f23e5d394bfed901d6f69e9caefe5eaed WHIRLPOOL 6d8515e76a9c96ac4b10e1eded5b6afbf4938dde5db266bf39a904d78626a06156eff4db1b34bc2e0df7a368673f2aeae7e603434c704c5ffd3d7ca71752e786 diff --git a/sci-libs/orocos_kdl/metadata.xml b/sci-libs/orocos_kdl/metadata.xml new file mode 100644 index 000000000000..8e818f01bbf4 --- /dev/null +++ b/sci-libs/orocos_kdl/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>aballier@gentoo.org</email> + <name>Alexis Ballier</name> + </maintainer> + <longdescription lang="en"> + The Kinematics and Dynamics Library (KDL) develops an application + independent framework for modelling and computation of kinematic chains, + such as robots, biomechanical human models, computer-animated figures, + machine tools, etc. It provides class libraries for geometrical objects + (point, frame, line,... ), kinematic chains of various families (serial, + humanoid, parallel, mobile,... ), and their motion specification and + interpolation. + </longdescription> + <use> + <flag name="models">Build models for some well known robots.</flag> + </use> + <upstream> + <remote-id type="github">orocos/orocos_kinematics_dynamics</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/orocos_kdl/orocos_kdl-1.3.1-r1.ebuild b/sci-libs/orocos_kdl/orocos_kdl-1.3.1-r1.ebuild new file mode 100644 index 000000000000..e2fe4f9b4756 --- /dev/null +++ b/sci-libs/orocos_kdl/orocos_kdl-1.3.1-r1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/orocos/orocos_kinematics_dynamics" +fi + +inherit ${SCM} cmake-utils + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm ~x86" + SRC_URI="https://github.com/orocos/orocos_kinematics_dynamics/archive/v${PV}.tar.gz -> orocos_kinematics_dynamics-${PV}.tar.gz" +fi + +DESCRIPTION="Kinematics and Dynamics Library (KDL)" +HOMEPAGE="http://www.orocos.org/kdl" +LICENSE="LGPL-2.1" +SLOT="0" +IUSE="doc test examples models" + +RDEPEND="dev-cpp/eigen:3" +DEPEND="${RDEPEND} + test? ( dev-util/cppunit ) + doc? ( app-doc/doxygen )" +REQUIRED_USE="examples? ( models )" + +DOCS=( README ) + +if [ "${PV#9999}" != "${PV}" ] ; then + S=${WORKDIR}/${P}/orocos_kdl +else + S=${WORKDIR}/orocos_kinematics_dynamics-${PV}/orocos_kdl +fi + +src_configure() { + local mycmakeargs=( + "$(cmake-utils_use_enable test TESTS)" + "$(cmake-utils_use_enable examples EXAMPLES)" + "-DBUILD_MODELS=$(usex models ON OFF)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + cd "${BUILD_DIR}" + use doc && emake docs +} + +src_test() { + cd "${BUILD_DIR}" + emake check +} + +src_install() { + cmake-utils_src_install + cd "${BUILD_DIR}" + use doc && dohtml -r doc/api/html/* + use examples && dobin "${BUILD_DIR}/examples/"{geometry,trajectory_example,chainiksolverpos_lma_demo} + + # Need to have package.xml in our custom gentoo path + insinto /usr/share/ros_packages/${PN} + doins "${ED}/usr/share/${PN}/package.xml" +} diff --git a/sci-libs/orocos_kdl/orocos_kdl-9999.ebuild b/sci-libs/orocos_kdl/orocos_kdl-9999.ebuild new file mode 100644 index 000000000000..e2fe4f9b4756 --- /dev/null +++ b/sci-libs/orocos_kdl/orocos_kdl-9999.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/orocos/orocos_kinematics_dynamics" +fi + +inherit ${SCM} cmake-utils + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm ~x86" + SRC_URI="https://github.com/orocos/orocos_kinematics_dynamics/archive/v${PV}.tar.gz -> orocos_kinematics_dynamics-${PV}.tar.gz" +fi + +DESCRIPTION="Kinematics and Dynamics Library (KDL)" +HOMEPAGE="http://www.orocos.org/kdl" +LICENSE="LGPL-2.1" +SLOT="0" +IUSE="doc test examples models" + +RDEPEND="dev-cpp/eigen:3" +DEPEND="${RDEPEND} + test? ( dev-util/cppunit ) + doc? ( app-doc/doxygen )" +REQUIRED_USE="examples? ( models )" + +DOCS=( README ) + +if [ "${PV#9999}" != "${PV}" ] ; then + S=${WORKDIR}/${P}/orocos_kdl +else + S=${WORKDIR}/orocos_kinematics_dynamics-${PV}/orocos_kdl +fi + +src_configure() { + local mycmakeargs=( + "$(cmake-utils_use_enable test TESTS)" + "$(cmake-utils_use_enable examples EXAMPLES)" + "-DBUILD_MODELS=$(usex models ON OFF)" + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + cd "${BUILD_DIR}" + use doc && emake docs +} + +src_test() { + cd "${BUILD_DIR}" + emake check +} + +src_install() { + cmake-utils_src_install + cd "${BUILD_DIR}" + use doc && dohtml -r doc/api/html/* + use examples && dobin "${BUILD_DIR}/examples/"{geometry,trajectory_example,chainiksolverpos_lma_demo} + + # Need to have package.xml in our custom gentoo path + insinto /usr/share/ros_packages/${PN} + doins "${ED}/usr/share/${PN}/package.xml" +} diff --git a/sci-libs/p4est/Manifest b/sci-libs/p4est/Manifest new file mode 100644 index 000000000000..5c314832df45 --- /dev/null +++ b/sci-libs/p4est/Manifest @@ -0,0 +1,11 @@ +DIST libsc-1.0.tar.gz 257930 SHA256 a9f8a0f342a4a92c4031735e044e7ee73d9fd7e6df3e50a51c4c5016e27ed1ba SHA512 bf5af600e9cbd4038b1bd40c88776b21be5d474e34f9aacf287b890d262a22dc50ca27982c2eb9adba9735c8d9bb1fc31de2a27b24cdab534e3b2f610d76db7d WHIRLPOOL 56f89fcaf90bc8d4f872cee4fe150f692933b39376758c42b67d2e42659c19a9332a1d5e6d2d81c011dade0c6ab40c526c69ce2168fe41060f5d4be1a6595b1b +DIST libsc-1.1.tar.gz 263643 SHA256 99c3fb3b7d6514ccaa667bdc848a7308c00f05bf6fdc0561ce286db9644ee03e SHA512 a3d8bea406a1987e68e88dd587aebe28c796f2a5bddfc381b34b5eb1448e0ac23889cc6f97fc1e4010289f83996180db42cbb001d0518360349b993dd37d4579 WHIRLPOOL b6c123cd245e4beb4cd6479e9d781d86784fab6975edc20562c14b5ecc59dbc824aca10fb02e4fa7612f0b2743fd7c7d3799f203546c5859896812a21e1362df +DIST libsc-2.0.tar.gz 296392 SHA256 759c7ed33537fc5eb2fee4c9d90f5d80f7112f13042f4d2d5f34d6c6461cb8e6 SHA512 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<name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +The p4est software library enables the dynamic management of a collection +of adaptive octrees, conveniently called a forest of octrees. p4est is +designed to work in parallel and scale to hundreds of thousands of +processor cores. + </longdescription> + <use> + <flag name="vtk-binary">Enable binary vtk output. If disabled vtk files will be written in ASCII text format.</flag> + <flag name="romio">Build with support for the ROMIO MPI-IO component</flag> + </use> + <upstream> + <remote-id type="github">cburstedde/libsc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/p4est/p4est-1.0.ebuild b/sci-libs/p4est/p4est-1.0.ebuild new file mode 100644 index 000000000000..b76a7efb8f01 --- /dev/null +++ b/sci-libs/p4est/p4est-1.0.ebuild @@ -0,0 +1,99 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +# The build system currently fails with everything newer than 1.11. +WANT_AUTOMAKE=1.11 + +inherit autotools eutils + +DESCRIPTION="Scalable Algorithms for Parallel Adaptive Mesh Refinement on Forests of Octrees" +HOMEPAGE="http://www.p4est.org/" +SRC_URI=" + https://github.com/cburstedde/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz + https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz -> libsc-${PV}.tar.gz" + +KEYWORDS="~amd64 ~x86" + +LICENSE="GPL-2+" +SLOT="0" + +IUSE="debug doc examples mpi romio static-libs +vtk-binary" +REQUIRED_USE="romio? ( mpi )" + +RDEPEND=" + ~sci-libs/libsc-${PV}[mpi=,romio=,static-libs=] + dev-lang/lua:* + sys-apps/util-linux + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[romio=] )" + +DEPEND=" + ${RDEPEND} + sys-devel/automake:1.11 + virtual/pkgconfig" + +DOCS=( AUTHORS NEWS README ) + +src_prepare() { + default + + # Inject libsc to get all parts of the build system... + rmdir "${S}/sc" || die "rmdir failed" + mv "${WORKDIR}/libsc-${PV}" "${S}/sc" || die "mv failed" + + # Inject a version number into the build system + echo "${PV}" > ${S}/.tarball-version + + AT_M4DIR="${WORKDIR}/${P}/config ${WORKDIR}/${P}/sc/config" + eautoreconf + + sed -i \ + "s/P4EST_SC_DIR\/etc/P4EST_SC_DIR\/share\/libsc/" \ + "${S}"/configure || die "sed failed" + + sed -i \ + "s/libsc\.la/libsc\.so/" \ + "${S}"/configure || die "sed failed" +} + +src_configure() { + # avoid underlinkage + LDFLAGS="${LDFLAGS} -lsc" + + local myeconfargs=( + $(use_enable debug) + $(use_enable mpi) + $(use_enable romio mpiio) + $(use_enable static-libs static) + $(use_enable vtk-binary) + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + --with-sc="${EPREFIX}/usr" + ) + econf "${myeconfargs[@]}" +} + +src_install() { + default + + use doc && dodoc -r doc/* + + if use examples + then + docinto examples + dodoc -r example/* + docompress -x /usr/share/doc/${PF}/examples + else + # Remove compiled example binaries in case of -examples: + rm -r "${ED}"/usr/bin || die "rm failed" + fi + + # Fix wrong installation paths: + dodir /usr/share/p4est + mv "${ED}"/usr/share/data "${ED}"/usr/share/p4est/data || die "mv failed" + mv "${ED}"/etc/* "${ED}"/usr/share/p4est || die "mv failed" + rmdir "${ED}"/etc/ || die "rmdir failed" +} diff --git a/sci-libs/p4est/p4est-1.1.ebuild b/sci-libs/p4est/p4est-1.1.ebuild new file mode 100644 index 000000000000..b76a7efb8f01 --- /dev/null +++ b/sci-libs/p4est/p4est-1.1.ebuild @@ -0,0 +1,99 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +# The build system currently fails with everything newer than 1.11. +WANT_AUTOMAKE=1.11 + +inherit autotools eutils + +DESCRIPTION="Scalable Algorithms for Parallel Adaptive Mesh Refinement on Forests of Octrees" +HOMEPAGE="http://www.p4est.org/" +SRC_URI=" + https://github.com/cburstedde/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz + https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz -> libsc-${PV}.tar.gz" + +KEYWORDS="~amd64 ~x86" + +LICENSE="GPL-2+" +SLOT="0" + +IUSE="debug doc examples mpi romio static-libs +vtk-binary" +REQUIRED_USE="romio? ( mpi )" + +RDEPEND=" + ~sci-libs/libsc-${PV}[mpi=,romio=,static-libs=] + dev-lang/lua:* + sys-apps/util-linux + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[romio=] )" + +DEPEND=" + ${RDEPEND} + sys-devel/automake:1.11 + virtual/pkgconfig" + +DOCS=( AUTHORS NEWS README ) + +src_prepare() { + default + + # Inject libsc to get all parts of the build system... + rmdir "${S}/sc" || die "rmdir failed" + mv "${WORKDIR}/libsc-${PV}" "${S}/sc" || die "mv failed" + + # Inject a version number into the build system + echo "${PV}" > ${S}/.tarball-version + + AT_M4DIR="${WORKDIR}/${P}/config ${WORKDIR}/${P}/sc/config" + eautoreconf + + sed -i \ + "s/P4EST_SC_DIR\/etc/P4EST_SC_DIR\/share\/libsc/" \ + "${S}"/configure || die "sed failed" + + sed -i \ + "s/libsc\.la/libsc\.so/" \ + "${S}"/configure || die "sed failed" +} + +src_configure() { + # avoid underlinkage + LDFLAGS="${LDFLAGS} -lsc" + + local myeconfargs=( + $(use_enable debug) + $(use_enable mpi) + $(use_enable romio mpiio) + $(use_enable static-libs static) + $(use_enable vtk-binary) + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + --with-sc="${EPREFIX}/usr" + ) + econf "${myeconfargs[@]}" +} + +src_install() { + default + + use doc && dodoc -r doc/* + + if use examples + then + docinto examples + dodoc -r example/* + docompress -x /usr/share/doc/${PF}/examples + else + # Remove compiled example binaries in case of -examples: + rm -r "${ED}"/usr/bin || die "rm failed" + fi + + # Fix wrong installation paths: + dodir /usr/share/p4est + mv "${ED}"/usr/share/data "${ED}"/usr/share/p4est/data || die "mv failed" + mv "${ED}"/etc/* "${ED}"/usr/share/p4est || die "mv failed" + rmdir "${ED}"/etc/ || die "rmdir failed" +} diff --git a/sci-libs/p4est/p4est-2.0.ebuild b/sci-libs/p4est/p4est-2.0.ebuild new file mode 100644 index 000000000000..a54c8b564e3e --- /dev/null +++ b/sci-libs/p4est/p4est-2.0.ebuild @@ -0,0 +1,120 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +# The build system currently fails with everything newer than 1.11. +WANT_AUTOMAKE=1.11 + +inherit autotools toolchain-funcs eutils + +DESCRIPTION="Scalable Algorithms for Parallel Adaptive Mesh Refinement on Forests of Octrees" +HOMEPAGE="http://www.p4est.org/" + +if [[ ${PV} = *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/cburstedde/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + SRC_URI=" + https://github.com/cburstedde/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz + https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz -> libsc-${PV}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="GPL-2+" +SLOT="0" + +# TODO petsc +IUSE="debug doc examples mpi openmp romio static-libs threads +vtk-binary" +REQUIRED_USE="romio? ( mpi )" + +RDEPEND=" + ~sci-libs/libsc-${PV}[mpi=,openmp=,romio=,static-libs=,threads=] + dev-lang/lua:* + sys-apps/util-linux + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[romio=] )" + +DEPEND=" + ${RDEPEND} + sys-devel/automake:1.11 + virtual/pkgconfig" + +DOCS=( AUTHORS NEWS README ) + +pkg_pretend() { + if [[ ${MERGE_TYPE} != "binary" ]] && use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi +} + +src_prepare() { + default + + # Inject libsc to get all parts of the build system... + if ! [[ ${PV} = *9999* ]]; then + rmdir "${S}/sc" || die "rmdir failed" + mv "${WORKDIR}/libsc-${PV}" "${S}/sc" || die "mv failed" + fi + + # Inject a version number into the build system + echo "${PV}" > ${S}/.tarball-version + + AT_M4DIR="${WORKDIR}/${P}/config ${WORKDIR}/${P}/sc/config" + eautoreconf + + sed -i \ + "s/P4EST_SC_DIR\/etc/P4EST_SC_DIR\/share\/libsc/" \ + "${S}"/configure || die "sed failed" + + sed -i \ + "s/libsc\.la/libsc\.so/" \ + "${S}"/configure || die "sed failed" + +} + +src_configure() { + # avoid underlinkage + LDFLAGS="${LDFLAGS} -lsc" + + local myeconfargs=( + $(use_enable debug) + $(use_enable mpi) + $(use_enable openmp) + $(use_enable romio mpiio) + $(use_enable static-libs static) + $(use_enable threads pthread) + $(use_enable vtk-binary) + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + --with-sc="${EPREFIX}/usr" + ) + econf "${myeconfargs[@]}" +} + +src_install() { + default + + use doc && dodoc -r doc/* + + if use examples + then + docinto examples + dodoc -r example/* + docompress -x /usr/share/doc/${PF}/examples + else + # Remove compiled example binaries in case of -examples: + rm -r "${ED}"/usr/bin || die "rm failed" + fi + + # Fix wrong installation paths: + dodir /usr/share/p4est + mv "${ED}"/usr/share/data "${ED}"/usr/share/p4est/data || die "mv failed" + mv "${ED}"/etc/* "${ED}"/usr/share/p4est || die "mv failed" + rmdir "${ED}"/etc/ || die "rmdir failed" +} diff --git a/sci-libs/p4est/p4est-9999.ebuild b/sci-libs/p4est/p4est-9999.ebuild new file mode 100644 index 000000000000..a54c8b564e3e --- /dev/null +++ b/sci-libs/p4est/p4est-9999.ebuild @@ -0,0 +1,120 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +# The build system currently fails with everything newer than 1.11. +WANT_AUTOMAKE=1.11 + +inherit autotools toolchain-funcs eutils + +DESCRIPTION="Scalable Algorithms for Parallel Adaptive Mesh Refinement on Forests of Octrees" +HOMEPAGE="http://www.p4est.org/" + +if [[ ${PV} = *9999* ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/cburstedde/${PN}.git" + EGIT_BRANCH="develop" + SRC_URI="" + KEYWORDS="" +else + SRC_URI=" + https://github.com/cburstedde/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz + https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz -> libsc-${PV}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="GPL-2+" +SLOT="0" + +# TODO petsc +IUSE="debug doc examples mpi openmp romio static-libs threads +vtk-binary" +REQUIRED_USE="romio? ( mpi )" + +RDEPEND=" + ~sci-libs/libsc-${PV}[mpi=,openmp=,romio=,static-libs=,threads=] + dev-lang/lua:* + sys-apps/util-linux + virtual/blas + virtual/lapack + mpi? ( virtual/mpi[romio=] )" + +DEPEND=" + ${RDEPEND} + sys-devel/automake:1.11 + virtual/pkgconfig" + +DOCS=( AUTHORS NEWS README ) + +pkg_pretend() { + if [[ ${MERGE_TYPE} != "binary" ]] && use openmp; then + tc-has-openmp || \ + die "Please select an openmp capable compiler like gcc[openmp]" + fi +} + +src_prepare() { + default + + # Inject libsc to get all parts of the build system... + if ! [[ ${PV} = *9999* ]]; then + rmdir "${S}/sc" || die "rmdir failed" + mv "${WORKDIR}/libsc-${PV}" "${S}/sc" || die "mv failed" + fi + + # Inject a version number into the build system + echo "${PV}" > ${S}/.tarball-version + + AT_M4DIR="${WORKDIR}/${P}/config ${WORKDIR}/${P}/sc/config" + eautoreconf + + sed -i \ + "s/P4EST_SC_DIR\/etc/P4EST_SC_DIR\/share\/libsc/" \ + "${S}"/configure || die "sed failed" + + sed -i \ + "s/libsc\.la/libsc\.so/" \ + "${S}"/configure || die "sed failed" + +} + +src_configure() { + # avoid underlinkage + LDFLAGS="${LDFLAGS} -lsc" + + local myeconfargs=( + $(use_enable debug) + $(use_enable mpi) + $(use_enable openmp) + $(use_enable romio mpiio) + $(use_enable static-libs static) + $(use_enable threads pthread) + $(use_enable vtk-binary) + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" + --with-sc="${EPREFIX}/usr" + ) + econf "${myeconfargs[@]}" +} + +src_install() { + default + + use doc && dodoc -r doc/* + + if use examples + then + docinto examples + dodoc -r example/* + docompress -x /usr/share/doc/${PF}/examples + else + # Remove compiled example binaries in case of -examples: + rm -r "${ED}"/usr/bin || die "rm failed" + fi + + # Fix wrong installation paths: + dodir /usr/share/p4est + mv "${ED}"/usr/share/data "${ED}"/usr/share/p4est/data || die "mv failed" + mv "${ED}"/etc/* "${ED}"/usr/share/p4est || die "mv failed" + rmdir "${ED}"/etc/ || die "rmdir failed" +} diff --git a/sci-libs/parmetis/Manifest b/sci-libs/parmetis/Manifest new file mode 100644 index 000000000000..951dc05f3126 --- /dev/null +++ b/sci-libs/parmetis/Manifest @@ -0,0 +1,6 @@ +AUX parmetis-3.1.1-autotools.patch 10971 SHA256 a72047b7467f39a2058f29c3f6a7a847c58e7c0a85d6233eda7388dbd139a887 SHA512 4e0de7697391da0a49b7051f8f58d83ce4865a1cfc63dd0f6cb2085224385b2c951d0f9297f7e291a225b91ab7053a10a38f36ad369c81e2100d3298ed7b9a15 WHIRLPOOL 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e38276ab7dfcc8c435125ae4d2152ba913b072d1f7deb9671072f148b1b9076f89b1c33e1b690d73662cad74dd339478e9eea30fb09a220d48204f1bde2cee09 diff --git a/sci-libs/parmetis/files/parmetis-3.1.1-autotools.patch b/sci-libs/parmetis/files/parmetis-3.1.1-autotools.patch new file mode 100644 index 000000000000..d38a2f7575cf --- /dev/null +++ b/sci-libs/parmetis/files/parmetis-3.1.1-autotools.patch @@ -0,0 +1,298 @@ +--- configure.ac 1970-01-01 01:00:00.000000000 +0100 ++++ configure.ac 2009-03-14 11:37:58.804041439 +0000 +@@ -0,0 +1,18 @@ ++# -*- Autoconf -*- ++AC_PREREQ(2.59) ++AC_INIT(parmetis, 3.1.1, karypis@cs.umn.edu) ++AM_INIT_AUTOMAKE([foreign]) ++AC_CONFIG_HEADER([config.h]) ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++AC_CHECK_LIB(m, sqrt) ++sinclude(ax_mpi.m4) ++AC_LANG_PUSH([C]) ++AX_MPI([], AC_MSG_ERROR([could not compile an mpi test program])) ++AC_CONFIG_FILES([Makefile ++ metis.pc ++ parmetis.pc ++ ParMETISLib/Makefile ++ METISLib/Makefile ++ Programs/Makefile]) ++AC_OUTPUT +--- Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Makefile.am 2009-03-14 11:37:15.700900498 +0000 +@@ -0,0 +1,5 @@ ++SUBDIRS = METISLib ParMETISLib Programs ++EXTRA_DIST = CHANGES VERSION parmetis.pc.in metis.pc.in ++include_HEADERS = parmetis.h ++pkgconfigdir = $(libdir)/pkgconfig ++pkgconfig_DATA = metis.pc parmetis.pc +--- METISLib/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ METISLib/Makefile.am 2009-03-14 11:37:15.700900498 +0000 +@@ -0,0 +1,18 @@ ++pkginclude_HEADERS = defs.h macros.h metis.h proto.h rename.h \ ++ stdheaders.h struct.h ++pkgincludedir = $(includedir)/metis ++ ++lib_LTLIBRARIES = libmetis.la ++libmetis_la_SOURCES = \ ++ coarsen.c fm.c initpart.c match.c ccgraph.c \ ++ pmetis.c pqueue.c refine.c util.c timing.c debug.c \ ++ bucketsort.c graph.c stat.c kmetis.c kwayrefine.c \ ++ kwayfm.c balance.c ometis.c srefine.c sfm.c separator.c \ ++ mincover.c mmd.c mesh.c meshpart.c frename.c fortran.c \ ++ myqsort.c compress.c parmetis.c estmem.c \ ++ mpmetis.c mcoarsen.c mmatch.c minitpart.c mbalance.c \ ++ mutil.c mkmetis.c mkwayrefine.c mkwayfmh.c \ ++ mrefine2.c minitpart2.c mbalance2.c mfm2.c \ ++ kvmetis.c kwayvolrefine.c kwayvolfm.c subdomains.c \ ++ mfm.c memory.c mrefine.c checkgraph.c ++libmetis_la_LDFLAGS = -no-undefined -version-info 4:1:0 +--- metis.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ metis.pc.in 2009-03-14 11:37:15.700900498 +0000 +@@ -0,0 +1,10 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: METIS ++Description: Software for unstructured graph partitioning ++Version: @VERSION@ ++Libs: -L${libdir} -lmetis ++Cflags: -I${includedir}/metis +--- ParMETISLib/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMETISLib/Makefile.am 2009-03-14 11:57:08.006017954 +0000 +@@ -0,0 +1,21 @@ ++pkginclude_HEADERS = defs.h macros.h parmetislib.h proto.h \ ++ rename.h stdheaders.h struct.h ++pkgincludedir = $(includedir)/parmetis ++ ++lib_LTLIBRARIES = libparmetis.la ++libparmetis_la_SOURCES = \ ++ comm.c util.c debug.c setup.c grsetup.c timer.c \ ++ node_refine.c initmsection.c order.c \ ++ xyzpart.c pspases.c frename.c \ ++ iintsort.c iidxsort.c ikeysort.c ikeyvalsort.c \ ++ kmetis.c gkmetis.c ometis.c \ ++ initpart.c match.c \ ++ kwayfm.c kwayrefine.c kwaybalance.c \ ++ remap.c stat.c fpqueue.c \ ++ ametis.c rmetis.c lmatch.c initbalance.c \ ++ mdiffusion.c diffutil.c wave.c \ ++ csrmatch.c redomylink.c balancemylink.c \ ++ selectq.c akwayfm.c serial.c move.c \ ++ mmetis.c mesh.c memory.c weird.c backcompat.c ++libparmetis_la_LDFLAGS = -no-undefined -version-info 3:1:1 ++libparmetis_la_LIBADD = @MPILIBS@ $(top_builddir)/METISLib/libmetis.la +--- parmetis.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ parmetis.pc.in 2009-03-14 11:37:15.700900498 +0000 +@@ -0,0 +1,11 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: ParMETIS ++Description: Software for parallel (mpi) unstructured graph partitioning ++Version: @VERSION@ ++Requires: metis ++Libs: -L${libdir} -lparmetis ++Cflags: -I${includedir} +--- Programs/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ Programs/Makefile.am 2009-03-14 11:37:15.700900498 +0000 +@@ -0,0 +1,13 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/ParMETISLib ++LDADD = $(top_builddir)/METISLib/libmetis.la \ ++ $(top_builddir)/ParMETISLib/libparmetis.la ++ ++check_PROGRAMS = ptest mtest ++ptest_SOURCES = ptest.c io.c adaptgraph.c ++mtest_SOURCES = mtest.c io.c ++ ++MPIRUN = mpirun -np 2 ++ ++check-local: $(check_PROGRAMS) ++ $(MPIRUN) ptest ../Graphs/rotor.graph ++ $(MPIRUN) mtest ../Graphs/bricks.hex3d 2 +--- ax_mpi.m4 1970-01-01 01:00:00.000000000 +0100 ++++ ax_mpi.m4 2010-01-20 20:33:15.000000000 +0000 +@@ -0,0 +1,178 @@ ++# =========================================================================== ++# http://www.nongnu.org/autoconf-archive/ax_mpi.html ++# =========================================================================== ++# ++# SYNOPSIS ++# ++# AX_MPI([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]) ++# ++# DESCRIPTION ++# ++# This macro tries to find out how to compile programs that use MPI ++# (Message Passing Interface), a standard API for parallel process ++# communication (see http://www-unix.mcs.anl.gov/mpi/) ++# ++# On success, it sets the MPICC, MPICXX, MPIF77, or MPIFC output variable ++# to the name of the MPI compiler, depending upon the current language. ++# (This may just be $CC/$CXX/$F77/$FC, but is more often something like ++# mpicc/mpiCC/mpif77/mpif90.) It also sets MPILIBS to any libraries that ++# are needed for linking MPI (e.g. -lmpi or -lfmpi, if a special ++# MPICC/MPICXX/MPIF77/MPIFC was not found). ++# ++# If you want to compile everything with MPI, you should set: ++# ++# CC="MPICC" #OR# CXX="MPICXX" #OR# F77="MPIF77" #OR# FC="MPIFC" ++# LIBS="$MPILIBS $LIBS" ++# ++# NOTE: The above assumes that you will use $CC (or whatever) for linking ++# as well as for compiling. (This is the default for automake and most ++# Makefiles.) ++# ++# The user can force a particular library/compiler by setting the ++# MPICC/MPICXX/MPIF77/MPIFC and/or MPILIBS environment variables. ++# ++# ACTION-IF-FOUND is a list of shell commands to run if an MPI library is ++# found, and ACTION-IF-NOT-FOUND is a list of commands to run if it is not ++# found. If ACTION-IF-FOUND is not specified, the default action will ++# define HAVE_MPI. ++# ++# LICENSE ++# ++# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2008 Julian C. Cummings <cummings@cacr.caltech.edu> ++# ++# This program is free software: you can redistribute it and/or modify it ++# under the terms of the GNU General Public License as published by the ++# Free Software Foundation, either version 3 of the License, or (at your ++# option) any later version. ++# ++# This program is distributed in the hope that it will be useful, but ++# WITHOUT ANY WARRANTY; without even the implied warranty of ++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General ++# Public License for more details. ++# ++# You should have received a copy of the GNU General Public License along ++# with this program. If not, see <http://www.gnu.org/licenses/>. ++# ++# As a special exception, the respective Autoconf Macro's copyright owner ++# gives unlimited permission to copy, distribute and modify the configure ++# scripts that are the output of Autoconf when processing the Macro. You ++# need not follow the terms of the GNU General Public License when using ++# or distributing such scripts, even though portions of the text of the ++# Macro appear in them. The GNU General Public License (GPL) does govern ++# all other use of the material that constitutes the Autoconf Macro. ++# ++# This special exception to the GPL applies to versions of the Autoconf ++# Macro released by the Autoconf Archive. When you make and distribute a ++# modified version of the Autoconf Macro, you may extend this special ++# exception to the GPL to apply to your modified version as well. ++ ++AU_ALIAS([ACX_MPI], [AX_MPI]) ++AC_DEFUN([AX_MPI], [ ++AC_PREREQ(2.50) dnl for AC_LANG_CASE ++ ++AC_LANG_CASE([C], [ ++ AC_REQUIRE([AC_PROG_CC]) ++ AC_ARG_VAR(MPICC,[MPI C compiler command]) ++ AC_CHECK_PROGS(MPICC, mpicc hcc mpxlc_r mpxlc mpcc cmpicc, $CC) ++ ax_mpi_save_CC="$CC" ++ CC="$MPICC" ++ AC_SUBST(MPICC) ++], ++[C++], [ ++ AC_REQUIRE([AC_PROG_CXX]) ++ AC_ARG_VAR(MPICXX,[MPI C++ compiler command]) ++ AC_CHECK_PROGS(MPICXX, mpic++ mpicxx mpiCC hcp mpxlC_r mpxlC mpCC cmpic++, $CXX) ++ ax_mpi_save_CXX="$CXX" ++ CXX="$MPICXX" ++ AC_SUBST(MPICXX) ++], ++[Fortran 77], [ ++ AC_REQUIRE([AC_PROG_F77]) ++ AC_ARG_VAR(MPIF77,[MPI Fortran 77 compiler command]) ++ AC_CHECK_PROGS(MPIF77, mpif77 hf77 mpxlf_r mpxlf mpf77 cmpifc, $F77) ++ ax_mpi_save_F77="$F77" ++ F77="$MPIF77" ++ AC_SUBST(MPIF77) ++], ++[Fortran], [ ++ AC_REQUIRE([AC_PROG_FC]) ++ AC_ARG_VAR(MPIFC,[MPI Fortran compiler command]) ++ AC_CHECK_PROGS(MPIFC, mpif90 mpxlf95_r mpxlf90_r mpxlf95 mpxlf90 mpf90 cmpif90c, $FC) ++ ax_mpi_save_FC="$FC" ++ FC="$MPIFC" ++ AC_SUBST(MPIFC) ++]) ++ ++if test x = x"$MPILIBS"; then ++ AC_LANG_CASE([C], [AC_CHECK_FUNC(MPI_Init, [MPILIBS=" "])], ++ [C++], [AC_CHECK_FUNC(MPI_Init, [MPILIBS=" "])], ++ [Fortran 77], [AC_MSG_CHECKING([for MPI_Init]) ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[ call MPI_Init])],[MPILIBS=" " ++ AC_MSG_RESULT(yes)], [AC_MSG_RESULT(no)])], ++ [Fortran], [AC_MSG_CHECKING([for MPI_Init]) ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[ call MPI_Init])],[MPILIBS=" " ++ AC_MSG_RESULT(yes)], [AC_MSG_RESULT(no)])]) ++fi ++AC_LANG_CASE([Fortran 77], [ ++ if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(fmpi, MPI_Init, [MPILIBS="-lfmpi"]) ++ fi ++ if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(fmpich, MPI_Init, [MPILIBS="-lfmpich"]) ++ fi ++], ++[Fortran], [ ++ if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(fmpi, MPI_Init, [MPILIBS="-lfmpi"]) ++ fi ++ if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(mpichf90, MPI_Init, [MPILIBS="-lmpichf90"]) ++ fi ++]) ++if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(mpi, MPI_Init, [MPILIBS="-lmpi"]) ++fi ++if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(mpich, MPI_Init, [MPILIBS="-lmpich"]) ++fi ++ ++dnl We have to use AC_TRY_COMPILE and not AC_CHECK_HEADER because the ++dnl latter uses $CPP, not $CC (which may be mpicc). ++AC_LANG_CASE([C], [if test x != x"$MPILIBS"; then ++ AC_MSG_CHECKING([for mpi.h]) ++ AC_TRY_COMPILE([#include <mpi.h>],[],[AC_MSG_RESULT(yes)], [MPILIBS="" ++ AC_MSG_RESULT(no)]) ++fi], ++[C++], [if test x != x"$MPILIBS"; then ++ AC_MSG_CHECKING([for mpi.h]) ++ AC_TRY_COMPILE([#include <mpi.h>],[],[AC_MSG_RESULT(yes)], [MPILIBS="" ++ AC_MSG_RESULT(no)]) ++fi], ++[Fortran 77], [if test x != x"$MPILIBS"; then ++ AC_MSG_CHECKING([for mpif.h]) ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([],[ include 'mpif.h'])],[AC_MSG_RESULT(yes)], [MPILIBS="" ++ AC_MSG_RESULT(no)]) ++fi], ++[Fortran], [if test x != x"$MPILIBS"; then ++ AC_MSG_CHECKING([for mpif.h]) ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([],[ include 'mpif.h'])],[AC_MSG_RESULT(yes)], [MPILIBS="" ++ AC_MSG_RESULT(no)]) ++fi]) ++ ++AC_LANG_CASE([C], [CC="$ax_mpi_save_CC"], ++ [C++], [CXX="$ax_mpi_save_CXX"], ++ [Fortran 77], [F77="$ax_mpi_save_F77"], ++ [Fortran], [FC="$ax_mpi_save_FC"]) ++ ++AC_SUBST(MPILIBS) ++ ++# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND: ++if test x = x"$MPILIBS"; then ++ $2 ++ : ++else ++ ifelse([$1],,[AC_DEFINE(HAVE_MPI,1,[Define if you have the MPI library.])],[$1]) ++ : ++fi ++])dnl AX_MPI diff --git a/sci-libs/parmetis/metadata.xml b/sci-libs/parmetis/metadata.xml new file mode 100644 index 000000000000..744c4ff57d0c --- /dev/null +++ b/sci-libs/parmetis/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + ParMETIS is an MPI-based parallel library that implements a variety + of algorithms for partitioning unstructured graphs and for computing + fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are + especially suited for parallel AMR computations and large scale + numerical simulations. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/parmetis/parmetis-3.2.0.ebuild b/sci-libs/parmetis/parmetis-3.2.0.ebuild new file mode 100644 index 000000000000..7d656c03b719 --- /dev/null +++ b/sci-libs/parmetis/parmetis-3.2.0.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils autotools + +MYP=ParMetis-${PV} + +DESCRIPTION="Parallel graph partitioner" +HOMEPAGE="http://www-users.cs.umn.edu/~karypis/metis/parmetis/" +SRC_URI="http://glaros.dtc.umn.edu/gkhome/fetch/sw/${PN}/OLD/${MYP}.tar.gz" + +SLOT="0" +LICENSE="free-noncomm" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +DEPEND="virtual/mpi" +RDEPEND="${DEPEND} + !sci-libs/metis" + +S="${WORKDIR}/${MYP}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-3.1.1-autotools.patch + sed -i -e "s/3.1.1/${PV}/" configure.ac || die + sed -i -e 's/order.c//' -e 's/lmatch.c//' ParMETISLib/Makefile.am || die + eautoreconf + export CC=mpicc +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + use doc && dodoc Manual/*.pdf +} diff --git a/sci-libs/parmgridgen/Manifest b/sci-libs/parmgridgen/Manifest new file mode 100644 index 000000000000..72bc50f0a27c --- /dev/null +++ b/sci-libs/parmgridgen/Manifest @@ -0,0 +1,7 @@ +AUX parmgridgen-1.0-as-needed.patch 985 SHA256 65d03d0696d0198f3cc1a60f63be36d76410c2d088adf54cc917fc48c795fefa SHA512 3a7a2e854338253934a9e8a05f157465696b7e0307ea30a5046a710831910087937271a0818df325367d3ad65a544b971cd249f61d59d77c125cb3520934d0b5 WHIRLPOOL f50b96fe198c851a38620d64437c5206c5a46dd229f0be9146cba528c477d565a4b84cba2cef4afd18568edb1110d8a9abb7d3216247f68d7fb45f708d1ec0e1 +AUX parmgridgen-1.0-autotools.patch 14205 SHA256 241765986bc276716ceea19b3d2a23ce6b2218b84687938c5dd283ce4d14cfe0 SHA512 cfb39c82cc40dc034b125201cc75f825ae224eda7a0d3ac2ab460c7bf8fd194cc5a01742f869970d987613a35e327da5a107b161e0bd6c6612f189244bd01da5 WHIRLPOOL 6f52a044675a6c85af1a684f53a42b40cbcf916055ba5af5c2d0a872cd688c01462778fa0fe9afb51985e7e284a17763ffbfb8bed5e319e631fc35783c16f416 +DIST ParMGridGen-1.0.tar.gz 2623528 SHA256 62cdb6e48cfc59124e5d5d360c2841e0fc2feecafe65bda110b74e942740b395 SHA512 e12ea3c923dd900c92ba4f2639daacc6c3596c5ea3c8d366b269c4c21247b10e6400c384321cfc65b486e4f8217dcd43f43eee27570b1fe1375deb02e255cb16 WHIRLPOOL a78187a71e04d15b0260e411c713b190c36a68931442ff04e537f7efbbb01ddfdb58c09835ac341dc6d7f3826fc855f64e8b32ea24d41d40b77c438a57db207e +EBUILD parmgridgen-1.0.ebuild 753 SHA256 ccafbaba05d7a5ba090c7ad0db8b399d2bd51c99441b3932400cbdb04c354d87 SHA512 147c3676e89ebc6b7130e9e74ea3e4bf39f808c6a44d6cc7840d133c704e8fd84b9ee6eb4d7a7faa154512dda7394d6998f5dfde7ca68ebb58ea741444f2778f WHIRLPOOL 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29cf52c16b0cce69899d9c2da8acd9144b7d760442aa323b854dceadb42459e009545193b1df7911ac2241b59f4819b4a6bb1d206d6f57953f770031433bb6b7 WHIRLPOOL a135fa622e99d3dcdb432bc6b3c366076b3d86b4bfd9a76c852d781b8e9152541c7e7a2c7c6d6a3c4d2200dce792847a08166aaf7c17c22b6299dfe868234dec diff --git a/sci-libs/parmgridgen/files/parmgridgen-1.0-as-needed.patch b/sci-libs/parmgridgen/files/parmgridgen-1.0-as-needed.patch new file mode 100644 index 000000000000..4f9addda4228 --- /dev/null +++ b/sci-libs/parmgridgen/files/parmgridgen-1.0-as-needed.patch @@ -0,0 +1,19 @@ +--- MGridGen/Lib/Makefile.am.old 2009-03-10 09:28:13.000000000 +0200 ++++ MGridGen/Lib/Makefile.am 2009-03-10 09:28:07.000000000 +0200 +@@ -8,3 +8,5 @@ + lib_LTLIBRARIES = libMGridGen.la + libMGridGen_la_SOURCES = aratio.c coarsen.c kwayfm.c match.c merge.c mgridgen.c refine.c setup.c + libMGridGen_la_LDFLAGS = -no-undefined -export-dynamic -version-info 1:0:0 ++ ++libMGridGen_la_LIBADD = ../IMlib/libIMlib.la +--- ParMGridGen/ParLib/Makefile.am.old 2009-03-10 09:31:43.000000000 +0200 ++++ ParMGridGen/ParLib/Makefile.am 2009-03-10 09:35:13.000000000 +0200 +@@ -8,3 +8,8 @@ + lib_LTLIBRARIES = libParMGridGen.la + libParMGridGen_la_SOURCES = comm.c debug.c grsetup.c ikeysort.c memory.c move.c parmgridgen.c setup.c util.c + libParMGridGen_la_LDFLAGS = -no-undefined -export-dynamic -version-info 1:0:0 ++ ++libParMGridGen_la_LIBADD = \ ++ $(top_builddir)/MGridGen/IMlib/libIMlib.la \ ++ $(top_builddir)/MGridGen/Lib/libMGridGen.la \ ++ ../IMParMetis-2.0/ParMETISLib/libIMparmetis.la diff --git a/sci-libs/parmgridgen/files/parmgridgen-1.0-autotools.patch b/sci-libs/parmgridgen/files/parmgridgen-1.0-autotools.patch new file mode 100644 index 000000000000..5a5f2369a3a8 --- /dev/null +++ b/sci-libs/parmgridgen/files/parmgridgen-1.0-autotools.patch @@ -0,0 +1,368 @@ +--- ParMGridGen-1.0-src/mgridgen.h 2001-11-09 00:41:22.000000000 +0100 ++++ ParMGridGen-1.0/mgridgen.h 1970-01-01 01:00:00.000000000 +0100 +@@ -1,7 +0,0 @@ +-typedef int idxtype; +-typedef double realtype; +- +- +-void MGridGen(int, idxtype *, realtype *, realtype *, idxtype *, realtype *, +- int, int, int *, int *, int *, idxtype *); +- +--- ParMGridGen-1.0-src/parmgridgen.h 2001-12-06 00:05:37.000000000 +0100 ++++ ParMGridGen-1.0/parmgridgen.h 1970-01-01 01:00:00.000000000 +0100 +@@ -1,5 +0,0 @@ +-typedef int idxtype; +-typedef double realtype; +- +-void ParMGridGen(idxtype *, idxtype *, realtype *, realtype *, idxtype *, +- realtype *, int *, int, int, int *, idxtype *, MPI_Comm *); +--- ParMGridGen-1.0-src/acx_mpi.m4 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/acx_mpi.m4 2008-07-19 22:10:53.000000000 +0200 +@@ -0,0 +1,181 @@ ++# =========================================================================== ++# http://autoconf-archive.cryp.to/acx_mpi.html ++# =========================================================================== ++# ++# SYNOPSIS ++# ++# ACX_MPI([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]) ++# ++# DESCRIPTION ++# ++# This macro tries to find out how to compile programs that use MPI ++# (Message Passing Interface), a standard API for parallel process ++# communication (see http://www-unix.mcs.anl.gov/mpi/) ++# ++# On success, it sets the MPICC, MPICXX, MPIF77, or MPIFC output variable ++# to the name of the MPI compiler, depending upon the current language. ++# (This may just be $CC/$CXX/$F77/$FC, but is more often something like ++# mpicc/mpiCC/mpif77/mpif90.) It also sets MPILIBS to any libraries that ++# are needed for linking MPI (e.g. -lmpi or -lfmpi, if a special ++# MPICC/MPICXX/MPIF77/MPIFC was not found). ++# ++# If you want to compile everything with MPI, you should set: ++# ++# CC="MPICC" #OR# CXX="MPICXX" #OR# F77="MPIF77" #OR# FC="MPIFC" ++# LIBS="$MPILIBS $LIBS" ++# ++# NOTE: The above assumes that you will use $CC (or whatever) for linking ++# as well as for compiling. (This is the default for automake and most ++# Makefiles.) ++# ++# The user can force a particular library/compiler by setting the ++# MPICC/MPICXX/MPIF77/MPIFC and/or MPILIBS environment variables. ++# ++# ACTION-IF-FOUND is a list of shell commands to run if an MPI library is ++# found, and ACTION-IF-NOT-FOUND is a list of commands to run if it is not ++# found. If ACTION-IF-FOUND is not specified, the default action will ++# define HAVE_MPI. ++# ++# LAST MODIFICATION ++# ++# 2008-04-12 ++# ++# COPYLEFT ++# ++# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# Copyright (c) 2008 Julian C. Cummings <cummings@cacr.caltech.edu> ++# ++# This program is free software: you can redistribute it and/or modify it ++# under the terms of the GNU General Public License as published by the ++# Free Software Foundation, either version 3 of the License, or (at your ++# option) any later version. ++# ++# This program is distributed in the hope that it will be useful, but ++# WITHOUT ANY WARRANTY; without even the implied warranty of ++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General ++# Public License for more details. ++# ++# You should have received a copy of the GNU General Public License along ++# with this program. If not, see <http://www.gnu.org/licenses/>. ++# ++# As a special exception, the respective Autoconf Macro's copyright owner ++# gives unlimited permission to copy, distribute and modify the configure ++# scripts that are the output of Autoconf when processing the Macro. You ++# need not follow the terms of the GNU General Public License when using ++# or distributing such scripts, even though portions of the text of the ++# Macro appear in them. The GNU General Public License (GPL) does govern ++# all other use of the material that constitutes the Autoconf Macro. ++# ++# This special exception to the GPL applies to versions of the Autoconf ++# Macro released by the Autoconf Macro Archive. When you make and ++# distribute a modified version of the Autoconf Macro, you may extend this ++# special exception to the GPL to apply to your modified version as well. ++ ++AC_DEFUN([ACX_MPI], [ ++AC_PREREQ(2.50) dnl for AC_LANG_CASE ++ ++AC_LANG_CASE([C], [ ++ AC_REQUIRE([AC_PROG_CC]) ++ AC_ARG_VAR(MPICC,[MPI C compiler command]) ++ AC_CHECK_PROGS(MPICC, mpicc hcc mpxlc_r mpxlc mpcc cmpicc, $CC) ++ acx_mpi_save_CC="$CC" ++ CC="$MPICC" ++ AC_SUBST(MPICC) ++], ++[C++], [ ++ AC_REQUIRE([AC_PROG_CXX]) ++ AC_ARG_VAR(MPICXX,[MPI C++ compiler command]) ++ AC_CHECK_PROGS(MPICXX, mpic++ mpicxx mpiCC hcp mpxlC_r mpxlC mpCC cmpic++, $CXX) ++ acx_mpi_save_CXX="$CXX" ++ CXX="$MPICXX" ++ AC_SUBST(MPICXX) ++], ++[Fortran 77], [ ++ AC_REQUIRE([AC_PROG_F77]) ++ AC_ARG_VAR(MPIF77,[MPI Fortran 77 compiler command]) ++ AC_CHECK_PROGS(MPIF77, mpif77 hf77 mpxlf_r mpxlf mpf77 cmpifc, $F77) ++ acx_mpi_save_F77="$F77" ++ F77="$MPIF77" ++ AC_SUBST(MPIF77) ++], ++[Fortran], [ ++ AC_REQUIRE([AC_PROG_FC]) ++ AC_ARG_VAR(MPIFC,[MPI Fortran compiler command]) ++ AC_CHECK_PROGS(MPIFC, mpif90 mpxlf95_r mpxlf90_r mpxlf95 mpxlf90 mpf90 cmpif90c, $FC) ++ acx_mpi_save_FC="$FC" ++ FC="$MPIFC" ++ AC_SUBST(MPIFC) ++]) ++ ++if test x = x"$MPILIBS"; then ++ AC_LANG_CASE([C], [AC_CHECK_FUNC(MPI_Init, [MPILIBS=" "])], ++ [C++], [AC_CHECK_FUNC(MPI_Init, [MPILIBS=" "])], ++ [Fortran 77], [AC_MSG_CHECKING([for MPI_Init]) ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[ call MPI_Init])],[MPILIBS=" " ++ AC_MSG_RESULT(yes)], [AC_MSG_RESULT(no)])], ++ [Fortran], [AC_MSG_CHECKING([for MPI_Init]) ++ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[ call MPI_Init])],[MPILIBS=" " ++ AC_MSG_RESULT(yes)], [AC_MSG_RESULT(no)])]) ++fi ++AC_LANG_CASE([Fortran 77], [ ++ if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(fmpi, MPI_Init, [MPILIBS="-lfmpi"]) ++ fi ++ if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(fmpich, MPI_Init, [MPILIBS="-lfmpich"]) ++ fi ++], ++[Fortran], [ ++ if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(fmpi, MPI_Init, [MPILIBS="-lfmpi"]) ++ fi ++ if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(mpichf90, MPI_Init, [MPILIBS="-lmpichf90"]) ++ fi ++]) ++if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(mpi, MPI_Init, [MPILIBS="-lmpi"]) ++fi ++if test x = x"$MPILIBS"; then ++ AC_CHECK_LIB(mpich, MPI_Init, [MPILIBS="-lmpich"]) ++fi ++ ++dnl We have to use AC_TRY_COMPILE and not AC_CHECK_HEADER because the ++dnl latter uses $CPP, not $CC (which may be mpicc). ++AC_LANG_CASE([C], [if test x != x"$MPILIBS"; then ++ AC_MSG_CHECKING([for mpi.h]) ++ AC_TRY_COMPILE([#include <mpi.h>],[],[AC_MSG_RESULT(yes)], [MPILIBS="" ++ AC_MSG_RESULT(no)]) ++fi], ++[C++], [if test x != x"$MPILIBS"; then ++ AC_MSG_CHECKING([for mpi.h]) ++ AC_TRY_COMPILE([#include <mpi.h>],[],[AC_MSG_RESULT(yes)], [MPILIBS="" ++ AC_MSG_RESULT(no)]) ++fi], ++[Fortran 77], [if test x != x"$MPILIBS"; then ++ AC_MSG_CHECKING([for mpif.h]) ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([],[ include 'mpif.h'])],[AC_MSG_RESULT(yes)], [MPILIBS="" ++ AC_MSG_RESULT(no)]) ++fi], ++[Fortran], [if test x != x"$MPILIBS"; then ++ AC_MSG_CHECKING([for mpif.h]) ++ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([],[ include 'mpif.h'])],[AC_MSG_RESULT(yes)], [MPILIBS="" ++ AC_MSG_RESULT(no)]) ++fi]) ++ ++AC_LANG_CASE([C], [CC="$acx_mpi_save_CC"], ++ [C++], [CXX="$acx_mpi_save_CXX"], ++ [Fortran 77], [F77="$acx_mpi_save_F77"], ++ [Fortran], [FC="$acx_mpi_save_FC"]) ++ ++AC_SUBST(MPILIBS) ++ ++# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND: ++if test x = x"$MPILIBS"; then ++ $2 ++ : ++else ++ ifelse([$1],,[AC_DEFINE(HAVE_MPI,1,[Define if you have the MPI library.])],[$1]) ++ : ++fi ++])dnl ACX_MPI +--- ParMGridGen-1.0-src/mgridgen.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/mgridgen.pc.in 2008-07-20 15:34:06.000000000 +0200 +@@ -0,0 +1,10 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: MGridGen ++Description: Software for generating coarse grids ++Version: @VERSION@ ++Libs: -L${libdir} -lIMlib -lMGridGen ++Cflags: -I${includedir}/mgridgen +--- ParMGridGen-1.0-src/parmgridgen.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/parmgridgen.pc.in 2008-07-20 15:49:53.000000000 +0200 +@@ -0,0 +1,10 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: ParMGridGen ++Description: Software for parallel (mpi) generating coarse grids ++Version: @VERSION@ ++Libs: -L${libdir} -lIMparmetis -lParMGridGen ++Cflags: -I${includedir}/imparmetis -I${includedir}/parmgridgen +--- ParMGridGen-1.0-src/configure.ac 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/configure.ac 2008-07-20 16:05:45.000000000 +0200 +@@ -0,0 +1,24 @@ ++# -*- Autoconf -*- ++AC_PREREQ(2.61) ++AC_INIT(parmgridgen, 1.0, moulitsa@cs.umn.edu) ++AM_INIT_AUTOMAKE([foreign]) ++AC_CONFIG_HEADER([config.h]) ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++AC_CHECK_LIB(m, sqrt) ++sinclude(acx_mpi.m4) ++AC_LANG_PUSH([C]) ++ACX_MPI([], AC_MSG_ERROR([could not compile an mpi test program])) ++AC_CONFIG_FILES([Makefile ++ mgridgen.pc ++ parmgridgen.pc ++ MGridGen/Makefile ++ MGridGen/IMlib/Makefile ++ MGridGen/Lib/Makefile ++ MGridGen/Programs/Makefile ++ ParMGridGen/Makefile ++ ParMGridGen/IMParMetis-2.0/Makefile ++ ParMGridGen/IMParMetis-2.0/ParMETISLib/Makefile ++ ParMGridGen/ParLib/Makefile ++ ParMGridGen/Programs/Makefile]) ++AC_OUTPUT +--- ParMGridGen-1.0-src/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/Makefile.am 2008-07-20 15:55:52.000000000 +0200 +@@ -0,0 +1,7 @@ ++## top directory ++ ++SUBDIRS = MGridGen ParMGridGen ++EXTRA_DIST = VERSION mgridgen.pc.in parmgridgen.pc.in ++ ++pkgconfigdir = $(libdir)/pkgconfig ++pkgconfig_DATA = mgridgen.pc parmgridgen.pc +--- ParMGridGen-1.0-src/MGridGen/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/MGridGen/Makefile.am 2008-07-19 22:53:47.000000000 +0200 +@@ -0,0 +1,4 @@ ++## middle directory ++ ++#Build in these directories: ++SUBDIRS= IMlib Lib Programs +--- ParMGridGen-1.0-src/MGridGen/IMlib/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/MGridGen/IMlib/Makefile.am 2008-07-19 22:48:10.000000000 +0200 +@@ -0,0 +1,8 @@ ++## Source directory ++ ++pkginclude_HEADERS = IMlib.h ++pkgincludedir = $(includedir)/mgridgen ++ ++lib_LTLIBRARIES = libIMlib.la ++libIMlib_la_SOURCES = blas.c dfkeysort.c dkeysort.c file.c ifkeysort.c ifloatsort.c iintsort.c ikeysort.c memory.c sort.c util.c ++libIMlib_la_LDFLAGS = -no-undefined -export-dynamic -version-info 1:0:0 +--- ParMGridGen-1.0-src/MGridGen/Lib/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/MGridGen/Lib/Makefile.am 2008-07-19 22:43:36.000000000 +0200 +@@ -0,0 +1,10 @@ ++## Source directory ++ ++INCLUDES = -I../IMlib ++ ++pkginclude_HEADERS = defs.h macros.h mgridgen.h proto.h struct.h ++pkgincludedir = $(includedir)/mgridgen ++ ++lib_LTLIBRARIES = libMGridGen.la ++libMGridGen_la_SOURCES = aratio.c coarsen.c kwayfm.c match.c merge.c mgridgen.c refine.c setup.c ++libMGridGen_la_LDFLAGS = -no-undefined -export-dynamic -version-info 1:0:0 +--- ParMGridGen-1.0-src/MGridGen/Programs/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/MGridGen/Programs/Makefile.am 2008-07-19 23:38:41.000000000 +0200 +@@ -0,0 +1,7 @@ ++## Source directory ++ ++INCLUDES = -I../IMlib -I../Lib ++ ++bin_PROGRAMS = mgridgen ++mgridgen_SOURCES = io.c mgridgen.c ++mgridgen_LDADD = ../IMlib/libIMlib.la ../Lib/libMGridGen.la -lm +--- ParMGridGen-1.0-src/ParMGridGen/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/ParMGridGen/Makefile.am 2008-07-20 16:04:31.000000000 +0200 +@@ -0,0 +1,4 @@ ++## middle directory ++ ++#Build in these directories: ++SUBDIRS= IMParMetis-2.0 ParLib Programs +--- ParMGridGen-1.0-src/ParMGridGen/IMParMetis-2.0/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/ParMGridGen/IMParMetis-2.0/Makefile.am 2008-07-20 15:24:55.000000000 +0200 +@@ -0,0 +1,4 @@ ++## middle directory ++ ++#Build in these directories: ++SUBDIRS= ParMETISLib +--- ParMGridGen-1.0-src/ParMGridGen/IMParMetis-2.0/ParMETISLib/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/ParMGridGen/IMParMetis-2.0/ParMETISLib/Makefile.am 2008-07-20 16:18:31.000000000 +0200 +@@ -0,0 +1,8 @@ ++## Source directory ++ ++pkginclude_HEADERS = defs.h macros.h parmetis.h proto.h rename.h struct.h ++pkgincludedir = $(includedir)/imparmetis ++ ++lib_LTLIBRARIES = libIMparmetis.la ++libIMparmetis_la_SOURCES = coarsen.c comm.c debug.c diffuse.c drivers.c edge_refine.c fused.c grsetup.c iidxsort.c ikeysort.c memory.c remap.c setup.c timer.c util.c var.c ++libIMparmetis_la_LDFLAGS = -no-undefined -export-dynamic -version-info 1:0:0 +--- ParMGridGen-1.0-src/ParMGridGen/ParLib/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/ParMGridGen/ParLib/Makefile.am 2008-07-20 15:53:06.000000000 +0200 +@@ -0,0 +1,10 @@ ++## Source directory ++ ++INCLUDES = -I$(top_builddir)/MGridGen/IMlib ++ ++pkginclude_HEADERS = defs.h macros.h parmgridgen.h proto.h rename.h struct.h ++pkgincludedir = $(includedir)/parmgridgen ++ ++lib_LTLIBRARIES = libParMGridGen.la ++libParMGridGen_la_SOURCES = comm.c debug.c grsetup.c ikeysort.c memory.c move.c parmgridgen.c setup.c util.c ++libParMGridGen_la_LDFLAGS = -no-undefined -export-dynamic -version-info 1:0:0 +--- ParMGridGen-1.0-src/ParMGridGen/Programs/Makefile.am 1970-01-01 01:00:00.000000000 +0100 ++++ ParMGridGen-1.0/ParMGridGen/Programs/Makefile.am 2008-07-20 16:24:19.000000000 +0200 +@@ -0,0 +1,21 @@ ++## Source directory ++ ++INCLUDES = -I../ParLib -I$(top_builddir)/MGridGen/IMlib ++ ++bin_PROGRAMS = parmgridgen ++parmgridgen_SOURCES = io.c main.c parmgridgen.c ++parmgridgen_LDADD = ../IMParMetis-2.0/ParMETISLib/libIMparmetis.la ../ParLib/libParMGridGen.la \ ++ $(top_builddir)/MGridGen/IMlib/libIMlib.la $(top_builddir)/MGridGen/Lib/libMGridGen.la @MPILIBS@ ++ ++# AM_CPPFLAGS = -I$(top_srcdir)/ParMETISLib ++# LDADD = $(top_builddir)/METISLib/libmetis.la \ ++# $(top_builddir)/ParMETISLib/libparmetis.la ++ ++# check_PROGRAMS = parmgridgen ++# parmgridgen_SOURCES = io.c main.c parmgridgen.c ++ ++MPIRUN = mpirun -np 4 ++ ++check-local: $(check_PROGRAMS) ++ $(MPIRUN) parmgridgen $(top_builddir)/Graphs/M6.metis 3 4 6 1 4 128 ++ diff --git a/sci-libs/parmgridgen/metadata.xml b/sci-libs/parmgridgen/metadata.xml new file mode 100644 index 000000000000..40aa45df2b01 --- /dev/null +++ b/sci-libs/parmgridgen/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>patrick@gentoo.org</email> + <name>Patrick Lauer</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/parmgridgen/parmgridgen-1.0.ebuild b/sci-libs/parmgridgen/parmgridgen-1.0.ebuild new file mode 100644 index 000000000000..04b93b89793d --- /dev/null +++ b/sci-libs/parmgridgen/parmgridgen-1.0.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=2 + +inherit eutils autotools + +MYP=ParMGridGen-${PV} + +DESCRIPTION="Software for parallel (mpi) generating coarse grids" +HOMEPAGE="http://www-users.cs.umn.edu/~moulitsa/software.html" +SRC_URI="http://www-users.cs.umn.edu/~moulitsa/download/${MYP}.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="amd64 x86" +RESTRICT="mirror bindist" + +DEPEND="virtual/mpi" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${MYP} + +pkg_setup(){ + export CC=mpicc +} + +src_prepare() { + epatch "${FILESDIR}/${P}-autotools.patch" + epatch "${FILESDIR}/${P}-as-needed.patch" + eautoreconf +} + +src_install() { + emake DESTDIR="${D}" install || die + dodoc README Doc/*.pdf || die +} diff --git a/sci-libs/pastix/Manifest b/sci-libs/pastix/Manifest new file mode 100644 index 000000000000..0fecdba24993 --- /dev/null +++ b/sci-libs/pastix/Manifest @@ -0,0 +1,8 @@ +AUX pastix-5.2.2.22-isnan-floating-point-cast.patch 1901 SHA256 aa70627dc18a4898acd64dd2c992884baf22c9e22ab6d0248953a5ed87be4dab SHA512 23b3e4854afb459e0f68c4322bd85db6addc6ec043bb9c404a9a60667de6b01bb17c3d7795f8fd5dacaa0b5db6c45a6f1e1358590c77326610bc271903b920ee WHIRLPOOL 73e475e94bebd21e8aa569a490c1f2f795dc02e86eb10a4df2933ea4d3d800275964d6b65358fd35d1c2f2b422a0ee262f356e37fe3913402c512a6818afb2db +AUX pastix-5.2.2.22-nosmp-undefined-variable.patch 494 SHA256 c8dcfc01012239f781747772379d707253a5534cb210967655d6dd2e2f66163e SHA512 c12719176b352b396cc58d7a4474955df0cb01459edce1b2f220c6352d99bf608d39c3b4d6b54b0ae8b4643879ed79b7a5fbd03b746dba0bf4cc265d81d6d38e WHIRLPOOL 2b5e5223954e4564cdd0c1dfdebd37023cbd7443c95736b24e2c799e988b931548a945fa6fa52ea29508874a13e13ba5324a72152a7e763db4992670ea23083f +DIST pastix_5.2.2.22.tar.bz2 2664470 SHA256 30f771a666719e6b116f549a6e4da451beabab99c2ecabc0745247c3654acbed SHA512 15ecdb10b5229e40f744c1ad54be7cac6560cb92e90df1937c90ca7da290df6bdb6f24a1e1c54197731b9df3e0dcc0b9fa39750479fcf03a0c08c304c5b9df70 WHIRLPOOL 7031f822d3c2f89bd520175a124200303adc2dda56cbae4eb9e011b90d5119c5b96958d648c7e18d034e2845a32ad80385714bfb424260aa62c9f6484a18ce6b +DIST pastix_5.2.3.tar.bz2 2246903 SHA256 641978e6b0607e201a409549adc78d5618ec159f44cafc7bddeaca4f4bee1e47 SHA512 69acffac1be8c756886783c2a6307269ab4d14abfc4a77268b3d14995e53b16084c298446812484233d9d52c317490d6ad67788166adf367075e6c8442147b95 WHIRLPOOL e03c04dcf4b932d284d90a06d5c22fe608fc6953eee40190103ef3269938aa04df3b83f769efb02c5c67237482b98f88bfd4100880908db71a89ab3aafcff0ec +EBUILD pastix-5.2.2.22-r1.ebuild 3652 SHA256 c9d93dbd48be7d6a18796203dd287500d8878e0b983d1e248e70cb7f7ea9a8d1 SHA512 3a89871fdd9caf60528945cd43c129392f8a15b81afe00b92f502183cfac8da1a309dc4dfb44b3796dd3039764853a07dbfdfc87b5df6d511a4a377ecde3e887 WHIRLPOOL 8015a3af317ca051fa2c25f4247e42cb10b1f917137dcac9eb4f30027be51fcf73c086f8c3d2d88fc5373cb2556e205f9a2f0654a991e69c7d0bce93eb7f4472 +EBUILD pastix-5.2.3.ebuild 3335 SHA256 5af10e2e3572415c5fbf149dcc855cad1322707ceb8fddac72f462b37a92c7bb SHA512 982558fcf800fefc8bed61f41f3342355ed4795af3ff31c00eda8bca99c45a9651ff2794ca0caf1e23a9aa73a3e1629c7ce72fd5e31547295ea38c8288b9e18e WHIRLPOOL d7f74e588e20ff97885c5f4cb1b8851206de7da0ef699f15a64e9ec263b2804f152feb4beb6f19c685627a6f2b28fdb13ce28cdd5b9808f87cdc67f41f9f6d1b +MISC ChangeLog 1579 SHA256 37e48d9fef7d6726813676ad23e14b6870ab29087390332f304106034d0dc6b0 SHA512 069ee3e9ab1c26c427cea6ae0ab86f4cbf271c42383a7a7a5c07626df05553ff1cedbe285791c5bb33b31a3eead8aa213f90fc8f3cb0cbdc88cf8b8e5f5f89fa WHIRLPOOL 7490eb389df03b74999a74899e3a482d6d88baea820fa4bb1284ceaf31ee2a14ee6132b743d9fbff6cf447761b645f1179004abf1ee8082d875fbb422a706fa4 +MISC metadata.xml 1055 SHA256 23dd726d5b6258f0b0508a83923d303236aa76f718f54d016706da37a6ba164a SHA512 42f9f1f03c4a2df46918ef461d814ca3c0e80e0fa5420327a45d6ca7ec87dd3f14ad0e5a4384b49aebae971578a425b475fa0e1ed6b73370afb743222765bfde WHIRLPOOL 8e71b7d2b69284d60f3709926445b62e7dbc8835d7992323707eae31a3528618d941c3703889a5743cb6f6530c1378258bc4dd7c742243c00e4b861b520f7d3d diff --git a/sci-libs/pastix/files/pastix-5.2.2.22-isnan-floating-point-cast.patch b/sci-libs/pastix/files/pastix-5.2.2.22-isnan-floating-point-cast.patch new file mode 100644 index 000000000000..8aa7c06e5c93 --- /dev/null +++ b/sci-libs/pastix/files/pastix-5.2.2.22-isnan-floating-point-cast.patch @@ -0,0 +1,47 @@ +Add missing cast to floating-point type: +* sopalin/src/variable_csc.c: In function ‘vcsc_add_node’: +* sopalin/src/variable_csc.c:138:13: error: non-floating-point argument in call to function ‘__builtin_isnan’ +* if (isnan(vcsc->values[COL-1][i*dof2 + ii])) { +See also: +https://bugs.gentoo.org/show_bug.cgi?id=580422 + +--- src/common/src/errors.h ++++ src/common/src/errors.h +@@ -140,7 +140,7 @@ + * expr - The value to check. + */ + #define CHECK_NAN(expr) { \ +- ASSERT_DEBUG(!isnan(expr), DBG_SOPALIN_NAN); \ ++ ASSERT_DEBUG(!isnan(((double) expr)), DBG_SOPALIN_NAN); \ + ASSERT_DEBUG(!isinf(expr), DBG_SOPALIN_INF); \ + } + #else +--- src/sopalin/src/variable_csc.c ++++ src/sopalin/src/variable_csc.c +@@ -135,7 +135,7 @@ + #endif + + for (ii = 0; ii < dof2; ii++) { +- if (isnan(vcsc->values[COL-1][i*dof2 + ii])) { ++ if (isnan(((double) vcsc->values[COL-1][i*dof2 + ii]))) { + vcsc->values[COL-1][i*dof2 + ii] = VALUE[ii]; + } else { + vcsc->values[COL-1][i*dof2 + ii] = op(vcsc->values[COL-1][i*dof2 + ii], +@@ -252,7 +252,7 @@ + vcsc->rows[COL_NODE][i]); + } + #endif +- if (isnan(vcsc->values[COL_NODE][idx])) { ++ if (isnan(((double) vcsc->values[COL_NODE][idx]))) { + vcsc->values[COL_NODE][idx] = VALUE; + } else { + vcsc->values[COL_NODE][idx] = op(vcsc->values[COL_NODE][idx], +@@ -660,7 +660,7 @@ + } else { + INTS iterdof; + for (iterdof = 0; iterdof < dof2; iterdof++) { +- if (!isnan(vcsc->values[MYCOL-1][dof2*iter2+iterdof])) { ++ if (!isnan(((double) vcsc->values[MYCOL-1][dof2*iter2+iterdof]))) { + /* ignore NaN values from VCSC */ + (*values_o)[dof2*iter3+iterdof] = op( + (*values_o)[dof2*iter3+iterdof], diff --git a/sci-libs/pastix/files/pastix-5.2.2.22-nosmp-undefined-variable.patch b/sci-libs/pastix/files/pastix-5.2.2.22-nosmp-undefined-variable.patch new file mode 100644 index 000000000000..c01b02bb8f72 --- /dev/null +++ b/sci-libs/pastix/files/pastix-5.2.2.22-nosmp-undefined-variable.patch @@ -0,0 +1,15 @@ +--- ./sopalin/src/updo.c.orig 2016-02-23 01:42:00.000000000 +0000 ++++ ./sopalin/src/updo.c 2016-02-23 01:42:10.000000000 +0000 +@@ -940,8 +940,10 @@ + i = TASK_CBLKNUM(i); + # define END_LOOP(a) } SMP_END_LOOP(a) + # else /* SMP_SOPALIN */ +-# define START_LOOP for (i=0;i<SYMB_CBLKNBR;i++) +-# define END_LOOP ++# define START_LOOP \ ++ int bubnum = me; \ ++ for (i=0;i<SYMB_CBLKNBR;i++) ++# define END_LOOP(a) a + # endif + + /* Xi=(Dii)-1Xi; */ diff --git a/sci-libs/pastix/metadata.xml b/sci-libs/pastix/metadata.xml new file mode 100644 index 000000000000..387eff2e8edd --- /dev/null +++ b/sci-libs/pastix/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + PaStiX (Parallel Sparse matriX package) is a scientific library that + provides a high performance parallel solver for very large sparse + linear systems based on direct methods. Numerical algorithms are + implemented in single or double precision (real or complex) using + LLt, LDLt and LU with static pivoting (for non symmetric matrices + having a symmetric pattern). This solver provides also an adaptive + blockwise iLU(k) factorization that can be used as a parallel + preconditioner using approximated supernodes to build a coarser + block structure of the incomplete factors. +</longdescription> + <use> + <flag name="int64">Build the 64 bits integer library</flag> + <flag name="starpu">Build and link with <pkg>dev-libs/starpu</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-libs/pastix/pastix-5.2.2.22-r1.ebuild b/sci-libs/pastix/pastix-5.2.2.22-r1.ebuild new file mode 100644 index 000000000000..42f5eecb2ad6 --- /dev/null +++ b/sci-libs/pastix/pastix-5.2.2.22-r1.ebuild @@ -0,0 +1,127 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit fortran-2 toolchain-funcs + +# TODO: +# testing: emake examples? +# better doc instalation and building +# pypastix (separate package?) +# multilib with eselect? +# static libs building without pic +# metis? + +# package id: change every version, see the link on inriaforge +PID=35070 +# commit id: change every version +#CID=351ef60 +# leave empty if this is not a post release bug fix +#PPV=bugfix9_ +#MYPN=pastix_release +#SRC_URI="https://gforge.inria.fr/frs/download.php/${PID}/${MYPN}_${PPV}${CID}.tar.bz2" + +DESCRIPTION="Parallel solver for very large sparse linear systems" +HOMEPAGE="http://pastix.gforge.inria.fr" +SRC_URI="https://gforge.inria.fr/frs/download.php/${PID}/${PN}_${PV}.tar.bz2" + +LICENSE="CeCILL-C" +SLOT="0" +KEYWORDS="~alpha amd64 ~arm ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc int64 mpi +smp starpu static-libs" + +RDEPEND=" + sci-libs/scotch:0=[int64?,mpi?] + sys-apps/hwloc:0= + virtual/blas + mpi? ( virtual/mpi ) + starpu? ( dev-libs/starpu:0= )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( + "${FILESDIR}/${P}-nosmp-undefined-variable.patch" + "${FILESDIR}/${P}-isnan-floating-point-cast.patch" +) +S="${WORKDIR}/${PN}_${PV}/src" + +src_prepare() { + default + sed -e 's/^\(HOSTARCH\s*=\).*/\1 ${HOST}/' \ + -e "s:^\(CCPROG\s*=\).*:\1 $(tc-getCC):" \ + -e "s:^\(CFPROG\s*=\).*:\1 $(tc-getFC):" \ + -e "s:^\(CF90PROG\s*=\).*:\1 $(tc-getFC):" \ + -e "s:^\(ARPROG\s*=\).*:\1 $(tc-getAR):" \ + -e "s:^\(CCFOPT\s*=\).*:\1 ${FFLAGS}:" \ + -e "s:^\(CCFDEB\s*=\).*:\1 ${FFLAGS}:" \ + -e 's:^\(EXTRALIB\s*=\).*:\1 -lm -lrt:' \ + -e "s:^#\s*\(ROOT\s*=\).*:\1 \$(DESTDIR)${EPREFIX%/}/usr:" \ + -e 's:^#\s*\(INCLUDEDIR\s*=\).*:\1 $(ROOT)/include:' \ + -e 's:^#\s*\(BINDIR\s*=\).*:\1 $(ROOT)/bin:' \ + -e "s:^#\s*\(LIBDIR\s*=\).*:\1 \$(ROOT)/$(get_libdir):" \ + -e 's:^#\s*\(SHARED\s*=\).*:\1 1:' \ + -e 's:^#\s*\(SOEXT\s*=\).*:\1 .so:' \ + -e '/fPIC/s/^#//g' \ + -e "s:^#\s*\(SHARED_FLAGS\s*=.*\):\1 ${LDFLAGS}:" \ + -e "s:pkg-config:$(tc-getPKG_CONFIG):g" \ + -e "s:^\(BLASLIB\s*=\).*:\1 $($(tc-getPKG_CONFIG) --libs blas):" \ + -e "s:^\s*\(HWLOC_HOME\s*?=\).*:\1 ${EPREFIX}/usr:" \ + -e "s:-I\$(HWLOC_INC):$($(tc-getPKG_CONFIG) --cflags hwloc):" \ + -e "s:-L\$(HWLOC_LIB) -lhwloc:$($(tc-getPKG_CONFIG) --libs hwloc):" \ + -e "s:^\s*\(SCOTCH_HOME\s*?=\).*:\1 ${EPREFIX}/usr:" \ + -e "s:^\s*\(SCOTCH_INC\s*?=.*\):\1/scotch:" \ + -e "s:^\s*\(SCOTCH_LIB\s*?=.*\)lib:\1$(get_libdir):" \ + config/LINUX-GNU.in > config.in || die + sed -e 's/__SO_NAME__,$@/__SO_NAME__,$(notdir $@)/g' -i Makefile || die +} + +src_configure() { + if use amd64; then + sed -e 's/^\(VERSIONBIT\s*=\).*/\1 _64bit/' \ + -i config.in || die + fi + + if use int64; then + sed -e '/VERSIONINT.*_int64/s/#//' \ + -e '/CCTYPES.*INTSSIZE64/s/#//' \ + -i config.in || die + fi + + if ! use mpi; then + sed -e '/VERSIONMPI.*_nompi/s/#//' \ + -e '/CCTYPES.*NOMPI/s/#//' \ + -e '/MPCCPROG\s*= $(CCPROG)/s/#//' \ + -e '/MCFPROG\s*= $(CFPROG)/s/#//' \ + -e 's/-DDISTRIBUTED//' \ + -e 's/-lptscotch/-lscotch/g' \ + -i config.in || die + fi + + if ! use smp; then + sed -e '/VERSIONSMP.*_nosmp/s/#//' \ + -e '/CCTYPES.*NOSMP/s/#//' \ + -i config.in || die + fi + + if use starpu; then + sed -e '/libstarpu/s/#//g' -i config.in || die + fi +} + +src_compile() { + emake all drivers +} + +src_test() { + # both test and tests targets are defined and do not work + echo +} + +src_install() { + default + sed -e "s:${D}::g" -i "${ED}"/usr/bin/pastix-conf || die + # quick and dirty (static libs should really be built without pic) + cd .. || die + dodoc README.txt doc/refcard/refcard.pdf +} diff --git a/sci-libs/pastix/pastix-5.2.3.ebuild b/sci-libs/pastix/pastix-5.2.3.ebuild new file mode 100644 index 000000000000..c307ed61b06c --- /dev/null +++ b/sci-libs/pastix/pastix-5.2.3.ebuild @@ -0,0 +1,117 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit fortran-2 toolchain-funcs + +# TODO: +# testing: emake examples? +# better doc instalation and building +# pypastix (separate package?) +# multilib with eselect? +# static libs building without pic +# metis? + +# package id: change every version, see the link on inriaforge +PID=218 +DESCRIPTION="Parallel solver for very large sparse linear systems" +HOMEPAGE="http://pastix.gforge.inria.fr" +SRC_URI="https://gforge.inria.fr/frs/download.php/latestfile/${PID}/${PN}_${PV}.tar.bz2" + +LICENSE="CeCILL-C" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc int64 mpi +smp starpu static-libs" + +RDEPEND=" + sci-libs/scotch:0=[int64?,mpi?] + sys-apps/hwloc:0= + virtual/blas + mpi? ( virtual/mpi ) + starpu? ( dev-libs/starpu:0= )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}_${PV}/src" + +src_prepare() { + default + sed -e 's/^\(HOSTARCH\s*=\).*/\1 ${HOST}/' \ + -e "s:^\(CCPROG\s*=\).*:\1 $(tc-getCC):" \ + -e "s:^\(CFPROG\s*=\).*:\1 $(tc-getFC):" \ + -e "s:^\(CF90PROG\s*=\).*:\1 $(tc-getFC):" \ + -e "s:^\(ARPROG\s*=\).*:\1 $(tc-getAR):" \ + -e "s:^\(CCFOPT\s*=\).*:\1 ${FFLAGS}:" \ + -e "s:^\(CCFDEB\s*=\).*:\1 ${FFLAGS}:" \ + -e 's:^\(EXTRALIB\s*=\).*:\1 -lm -lrt:' \ + -e "s:^#\s*\(ROOT\s*=\).*:\1 \$(DESTDIR)${EPREFIX%/}/usr:" \ + -e 's:^#\s*\(INCLUDEDIR\s*=\).*:\1 $(ROOT)/include:' \ + -e 's:^#\s*\(BINDIR\s*=\).*:\1 $(ROOT)/bin:' \ + -e "s:^#\s*\(LIBDIR\s*=\).*:\1 \$(ROOT)/$(get_libdir):" \ + -e 's:^#\s*\(SHARED\s*=\).*:\1 1:' \ + -e 's:^#\s*\(SOEXT\s*=\).*:\1 .so:' \ + -e '/fPIC/s/^#//g' \ + -e "s:^#\s*\(SHARED_FLAGS\s*=.*\):\1 ${LDFLAGS}:" \ + -e "s:pkg-config:$(tc-getPKG_CONFIG):g" \ + -e "s:^\(BLASLIB\s*=\).*:\1 $($(tc-getPKG_CONFIG) --libs blas):" \ + -e "s:^\s*\(HWLOC_HOME\s*?=\).*:\1 ${EPREFIX}/usr:" \ + -e "s:-I\$(HWLOC_INC):$($(tc-getPKG_CONFIG) --cflags hwloc):" \ + -e "s:-L\$(HWLOC_LIB) -lhwloc:$($(tc-getPKG_CONFIG) --libs hwloc):" \ + -e "s:^\s*\(SCOTCH_HOME\s*?=\).*:\1 ${EPREFIX}/usr:" \ + -e "s:^\s*\(SCOTCH_INC\s*?=.*\):\1/scotch:" \ + -e "s:^\s*\(SCOTCH_LIB\s*?=.*\)lib:\1$(get_libdir):" \ + config/LINUX-GNU.in > config.in || die + sed -e 's/__SO_NAME__,$@/__SO_NAME__,$(notdir $@)/g' -i Makefile || die +} + +src_configure() { + if use amd64; then + sed -e 's/^\(VERSIONBIT\s*=\).*/\1 _64bit/' \ + -i config.in || die + fi + + if use int64; then + sed -e '/VERSIONINT.*_int64/s/#//' \ + -e '/CCTYPES.*INTSSIZE64/s/#//' \ + -i config.in || die + fi + + if ! use mpi; then + sed -e '/VERSIONMPI.*_nompi/s/#//' \ + -e '/CCTYPES.*NOMPI/s/#//' \ + -e '/MPCCPROG\s*= $(CCPROG)/s/#//' \ + -e '/MCFPROG\s*= $(CFPROG)/s/#//' \ + -e 's/-DDISTRIBUTED//' \ + -e 's/-lptscotch/-lscotch/g' \ + -i config.in || die + fi + + if ! use smp; then + sed -e '/VERSIONSMP.*_nosmp/s/#//' \ + -e '/CCTYPES.*NOSMP/s/#//' \ + -i config.in || die + fi + + if use starpu; then + sed -e '/libstarpu/s/#//g' -i config.in || die + fi +} + +src_compile() { + emake all drivers +} + +src_test() { + # both test and tests targets are defined and do not work + emake examples + echo +} + +src_install() { + default + sed -e "s:${D}::g" -i "${ED}"/usr/bin/pastix-conf || die + # quick and dirty (static libs should really be built without pic) + cd .. || die + dodoc README.txt doc/refcard/refcard.pdf +} diff --git a/sci-libs/pcl/Manifest b/sci-libs/pcl/Manifest new file mode 100644 index 000000000000..fca83da30013 --- /dev/null +++ b/sci-libs/pcl/Manifest @@ -0,0 +1,8 @@ +DIST pcl-1.8.0.tar.gz 66811948 SHA256 9e54b0c1b59a67a386b9b0f4acb2d764272ff9a0377b825c4ed5eedf46ebfcf4 SHA512 185470e980a208bd7213e1087dbc81b9741ae6e8783984e306d34d3e0e4fa69d42aa9c3a2a276d260d11cb89fff9c6cf324401938a66cd3883bdeaa38994e6a1 WHIRLPOOL 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/dev/null +++ b/sci-libs/pcl/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>aballier@gentoo.org</email> + <name>Alexis Ballier</name> + </maintainer> + <use> + <flag name="cuda">Adds support for NVIDIA CUDA.</flag> + <flag name="openni">Adds support for Kinect-like 3D sensors devices with <pkg>dev-libs/OpenNI</pkg>.</flag> + <flag name="openni2">Adds support for Kinect-like 3D sensors devices with <pkg>dev-libs/OpenNI2</pkg> (should be preferred over openni).</flag> + <flag name="pcap">Adds pcap file capabilities in some drivers.</flag> + <flag name="qhull">Adds convex-hull operation support via <pkg>media-libs/qhull</pkg>.</flag> + <flag name="vtk">Adds support for VTK-Visualizations.</flag> + <flag name="tutorials">Builds and installs tutorials.</flag> + </use> + <longdescription lang="en"> + The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing. +</longdescription> + <upstream> + <remote-id type="github">PointCloudLibrary/pcl</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/pcl/pcl-1.8.0.ebuild b/sci-libs/pcl/pcl-1.8.0.ebuild new file mode 100644 index 000000000000..9475d9da7036 --- /dev/null +++ b/sci-libs/pcl/pcl-1.8.0.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/PointCloudLibrary/pcl" +fi + +inherit ${SCM} cmake-utils multilib + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/PointCloudLibrary/pcl/archive/${P}.tar.gz" + S="${WORKDIR}/${PN}-${P}" +fi + +HOMEPAGE="http://pointclouds.org/" +DESCRIPTION="2D/3D image and point cloud processing" +LICENSE="BSD" +SLOT="0/1.8" +IUSE="cuda doc opengl openni openni2 pcap png +qhull qt5 usb vtk cpu_flags_x86_sse test tutorials" + +RDEPEND=" + >=sci-libs/flann-1.7.1 + dev-libs/boost:=[threads] + dev-cpp/eigen:3 + opengl? ( virtual/opengl media-libs/freeglut ) + openni? ( dev-libs/OpenNI ) + openni2? ( dev-libs/OpenNI2 ) + pcap? ( net-libs/libpcap ) + png? ( media-libs/libpng:0= ) + qhull? ( media-libs/qhull ) + qt5? ( + dev-qt/qtgui:5 + dev-qt/qtcore:5 + dev-qt/qtconcurrent:5 + dev-qt/qtopengl:5 + ) + usb? ( virtual/libusb:1 ) + vtk? ( >=sci-libs/vtk-5.6:=[imaging,rendering] ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4 ) +" +DEPEND="${RDEPEND} + !!dev-cpp/metslib + doc? ( app-doc/doxygen ) + tutorials? ( dev-python/sphinx dev-python/sphinxcontrib-doxylink ) + test? ( >=dev-cpp/gtest-1.6.0 ) + virtual/pkgconfig" + +REQUIRED_USE=" + openni? ( usb ) + openni2? ( usb ) + tutorials? ( doc ) +" + +src_configure() { + local mycmakeargs=( + "-DLIB_INSTALL_DIR=$(get_libdir)" + "-DWITH_CUDA=$(usex cuda TRUE FALSE)" + "-DWITH_LIBUSB=$(usex usb TRUE FALSE)" + "-DWITH_OPENGL=$(usex opengl TRUE FALSE)" + "-DWITH_PNG=$(usex png TRUE FALSE)" + "-DWITH_QHULL=$(usex qhull TRUE FALSE)" + "-DWITH_QT=$(usex qt5 TRUE FALSE)" + "-DWITH_VTK=$(usex vtk TRUE FALSE)" + "-DWITH_PCAP=$(usex pcap TRUE FALSE)" + "-DWITH_OPENNI=$(usex openni TRUE FALSE)" + "-DBUILD_OPENNI=$(usex openni TRUE FALSE)" + "-DWITH_OPENNI2=$(usex openni2 TRUE FALSE)" + "-DBUILD_OPENNI2=$(usex openni2 TRUE FALSE)" + "-DPCL_ENABLE_SSE=$(usex cpu_flags_x86_sse TRUE FALSE)" + "-DWITH_DOCS=$(usex doc TRUE FALSE)" + "-DWITH_TUTORIALS=$(usex tutorials TRUE FALSE)" + "-DBUILD_TESTS=$(usex test TRUE FALSE)" + ) + cmake-utils_src_configure +} diff --git a/sci-libs/pcl/pcl-1.8.1.ebuild b/sci-libs/pcl/pcl-1.8.1.ebuild new file mode 100644 index 000000000000..9475d9da7036 --- /dev/null +++ b/sci-libs/pcl/pcl-1.8.1.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/PointCloudLibrary/pcl" +fi + +inherit ${SCM} cmake-utils multilib + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/PointCloudLibrary/pcl/archive/${P}.tar.gz" + S="${WORKDIR}/${PN}-${P}" +fi + +HOMEPAGE="http://pointclouds.org/" +DESCRIPTION="2D/3D image and point cloud processing" +LICENSE="BSD" +SLOT="0/1.8" +IUSE="cuda doc opengl openni openni2 pcap png +qhull qt5 usb vtk cpu_flags_x86_sse test tutorials" + +RDEPEND=" + >=sci-libs/flann-1.7.1 + dev-libs/boost:=[threads] + dev-cpp/eigen:3 + opengl? ( virtual/opengl media-libs/freeglut ) + openni? ( dev-libs/OpenNI ) + openni2? ( dev-libs/OpenNI2 ) + pcap? ( net-libs/libpcap ) + png? ( media-libs/libpng:0= ) + qhull? ( media-libs/qhull ) + qt5? ( + dev-qt/qtgui:5 + dev-qt/qtcore:5 + dev-qt/qtconcurrent:5 + dev-qt/qtopengl:5 + ) + usb? ( virtual/libusb:1 ) + vtk? ( >=sci-libs/vtk-5.6:=[imaging,rendering] ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4 ) +" +DEPEND="${RDEPEND} + !!dev-cpp/metslib + doc? ( app-doc/doxygen ) + tutorials? ( dev-python/sphinx dev-python/sphinxcontrib-doxylink ) + test? ( >=dev-cpp/gtest-1.6.0 ) + virtual/pkgconfig" + +REQUIRED_USE=" + openni? ( usb ) + openni2? ( usb ) + tutorials? ( doc ) +" + +src_configure() { + local mycmakeargs=( + "-DLIB_INSTALL_DIR=$(get_libdir)" + "-DWITH_CUDA=$(usex cuda TRUE FALSE)" + "-DWITH_LIBUSB=$(usex usb TRUE FALSE)" + "-DWITH_OPENGL=$(usex opengl TRUE FALSE)" + "-DWITH_PNG=$(usex png TRUE FALSE)" + "-DWITH_QHULL=$(usex qhull TRUE FALSE)" + "-DWITH_QT=$(usex qt5 TRUE FALSE)" + "-DWITH_VTK=$(usex vtk TRUE FALSE)" + "-DWITH_PCAP=$(usex pcap TRUE FALSE)" + "-DWITH_OPENNI=$(usex openni TRUE FALSE)" + "-DBUILD_OPENNI=$(usex openni TRUE FALSE)" + "-DWITH_OPENNI2=$(usex openni2 TRUE FALSE)" + "-DBUILD_OPENNI2=$(usex openni2 TRUE FALSE)" + "-DPCL_ENABLE_SSE=$(usex cpu_flags_x86_sse TRUE FALSE)" + "-DWITH_DOCS=$(usex doc TRUE FALSE)" + "-DWITH_TUTORIALS=$(usex tutorials TRUE FALSE)" + "-DBUILD_TESTS=$(usex test TRUE FALSE)" + ) + cmake-utils_src_configure +} diff --git a/sci-libs/pcl/pcl-9999.ebuild b/sci-libs/pcl/pcl-9999.ebuild new file mode 100644 index 000000000000..9475d9da7036 --- /dev/null +++ b/sci-libs/pcl/pcl-9999.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/PointCloudLibrary/pcl" +fi + +inherit ${SCM} cmake-utils multilib + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64 ~arm" + SRC_URI="https://github.com/PointCloudLibrary/pcl/archive/${P}.tar.gz" + S="${WORKDIR}/${PN}-${P}" +fi + +HOMEPAGE="http://pointclouds.org/" +DESCRIPTION="2D/3D image and point cloud processing" +LICENSE="BSD" +SLOT="0/1.8" +IUSE="cuda doc opengl openni openni2 pcap png +qhull qt5 usb vtk cpu_flags_x86_sse test tutorials" + +RDEPEND=" + >=sci-libs/flann-1.7.1 + dev-libs/boost:=[threads] + dev-cpp/eigen:3 + opengl? ( virtual/opengl media-libs/freeglut ) + openni? ( dev-libs/OpenNI ) + openni2? ( dev-libs/OpenNI2 ) + pcap? ( net-libs/libpcap ) + png? ( media-libs/libpng:0= ) + qhull? ( media-libs/qhull ) + qt5? ( + dev-qt/qtgui:5 + dev-qt/qtcore:5 + dev-qt/qtconcurrent:5 + dev-qt/qtopengl:5 + ) + usb? ( virtual/libusb:1 ) + vtk? ( >=sci-libs/vtk-5.6:=[imaging,rendering] ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-4 ) +" +DEPEND="${RDEPEND} + !!dev-cpp/metslib + doc? ( app-doc/doxygen ) + tutorials? ( dev-python/sphinx dev-python/sphinxcontrib-doxylink ) + test? ( >=dev-cpp/gtest-1.6.0 ) + virtual/pkgconfig" + +REQUIRED_USE=" + openni? ( usb ) + openni2? ( usb ) + tutorials? ( doc ) +" + +src_configure() { + local mycmakeargs=( + "-DLIB_INSTALL_DIR=$(get_libdir)" + "-DWITH_CUDA=$(usex cuda TRUE FALSE)" + "-DWITH_LIBUSB=$(usex usb TRUE FALSE)" + "-DWITH_OPENGL=$(usex opengl TRUE FALSE)" + "-DWITH_PNG=$(usex png TRUE FALSE)" + "-DWITH_QHULL=$(usex qhull TRUE FALSE)" + "-DWITH_QT=$(usex qt5 TRUE FALSE)" + "-DWITH_VTK=$(usex vtk TRUE FALSE)" + "-DWITH_PCAP=$(usex pcap TRUE FALSE)" + "-DWITH_OPENNI=$(usex openni TRUE FALSE)" + "-DBUILD_OPENNI=$(usex openni TRUE FALSE)" + "-DWITH_OPENNI2=$(usex openni2 TRUE FALSE)" + "-DBUILD_OPENNI2=$(usex openni2 TRUE FALSE)" + "-DPCL_ENABLE_SSE=$(usex cpu_flags_x86_sse TRUE FALSE)" + "-DWITH_DOCS=$(usex doc TRUE FALSE)" + "-DWITH_TUTORIALS=$(usex tutorials TRUE FALSE)" + "-DBUILD_TESTS=$(usex test TRUE FALSE)" + ) + cmake-utils_src_configure +} diff --git a/sci-libs/pgplot/Manifest b/sci-libs/pgplot/Manifest new file mode 100644 index 000000000000..abc64f889849 --- /dev/null +++ b/sci-libs/pgplot/Manifest @@ -0,0 +1,12 @@ 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2008-10-29 18:30:33.000000000 +0000 +@@ -1,4 +1,4 @@ +-# The GNU g77 FORTRAN compiler and Gnu gcc C compiler on an elf-system. ++# The GNU gfortran FORTRAN compiler and Gnu gcc C compiler on an elf-system. + #----------------------------------------------------------------------- + + # Optional: Needed by XWDRIV (/xwindow and /xserve) and +@@ -23,7 +23,7 @@ + # The arguments needed by the C compiler to locate Tcl, Tk and + # X-window include files. + +- TK_INCL="-I/usr/include $XINCL" ++ TK_INCL="$XINCL" + + # Optional: Needed by RVDRIV (/xrv). + # The arguments needed by the C compiler to locate Rivet, Tcl, Tk and +@@ -34,13 +34,13 @@ + # Mandatory. + # The FORTRAN compiler to use. + +- FCOMPL="g77" ++ FCOMPL="gfortran" + + # Mandatory. + # The FORTRAN compiler flags to use when compiling the pgplot library. + # (NB. makemake prepends -c to $FFLAGC where needed) + +- FFLAGC="-u -Wall -fPIC -O" ++ FFLAGC="-u -Wall" + + # Mandatory. + # The FORTRAN compiler flags to use when compiling fortran demo programs. +@@ -57,12 +57,12 @@ + # Mandatory. + # The C compiler flags to use when compiling the pgplot library. + +- CFLAGC="-Wall -fPIC -DPG_PPU -O" ++ CFLAGC="-Wall -DPG_PPU" + + # Mandatory. + # The C compiler flags to use when compiling C demo programs. + +- CFLAGD="-Wall -O" ++ CFLAGD="-Wall" + + # Optional: Only needed if the cpgplot library is to be compiled. + # The flags to use when running pgbind to create the C pgplot wrapper +@@ -74,7 +74,7 @@ + # The library-specification flags to use when linking normal pgplot + # demo programs. + +- LIBS="-L/usr/X11R6/lib -lX11" ++ LIBS="-lX11" + + # Optional: Needed by XMDRIV (/xmotif). + # The library-specification flags to use when linking motif +@@ -92,7 +92,7 @@ + # The library-specification flags to use when linking Tk demo programs. + # Note that you may need to append version numbers to -ltk and -ltcl. + +- TK_LIBS="-L/usr/lib -ltk -ltcl $LIBS -ldl" ++ TK_LIBS="-ltk -ltcl $LIBS -ldl" + + # Mandatory. + # On systems that have a ranlib utility, put "ranlib" here. On other +@@ -103,12 +103,18 @@ + # Optional: Needed on systems that support shared libraries. + # The name to give the shared pgplot library. + +- SHARED_LIB="libpgplot.so" ++ MV=5 ++ SHARED_LIB="libpgplot.so.$MV" ++ SHARED_CLIB="libcpgplot.so.$MV" + + # Optional: Needed if SHARED_LIB is set. + # How to create a shared library from a trailing list of object files. + +- SHARED_LD="gcc -shared -o $SHARED_LIB" ++ SHARED_LD_PGPLOT_OPTS="$LDFLAGS -Wl,-soname,$SHARED_LIB" ++ ++ SHARED_LD_CPGPLOT_OPTS="$LDFLAGS -Wl,-soname,$SHARED_CLIB" ++ ++ SHARED_LD="$FCOMPL -shared" + + # Optional: + # On systems such as Solaris 2.x, that allow specification of the +@@ -117,7 +123,7 @@ + # library-specification flags used to specify these libraries to + # $SHARED_LD + +- SHARED_LIB_LIBS="" ++ SHARED_LIB_LIBS="-lX11 -lXt -lpng" + + # Optional: + # Compiler name used on Next systems to compile objective-C files. diff --git a/sci-libs/pgplot/files/pgplot-drivers.patch b/sci-libs/pgplot/files/pgplot-drivers.patch new file mode 100644 index 000000000000..c03d7508fc38 --- /dev/null +++ b/sci-libs/pgplot/files/pgplot-drivers.patch @@ -0,0 +1,117 @@ +--- a/drivers.list 2007-03-08 15:56:20.000000000 +0000 ++++ b/drivers.list 2007-03-08 15:59:21.000000000 +0000 +@@ -6,71 +6,71 @@ + !------------------------------------------------------------------------------ + ! File Code Description Restrictions + ! BCDRIV 0 /BCANON Canon Laser printer (bitmap version), landscape +-! CADRIV 0 /CANON Canon Laser printer, LBP-8/A2, landscape ++ CADRIV 0 /CANON Canon Laser printer, LBP-8/A2, landscape + ! CCDRIV 0 /CCP DEC LJ250 Color Companion printer +-! CGDRIV 1 /CGM CGM metafile, indexed colour selection C +-! CGDRIV 2 /CGMD CGM metafile, direct colour selection C +-! CWDRIV 0 /CW6320 Gould/Bryans Colourwriter 6320 pen plotter Std F77 ++ CGDRIV 1 /CGM CGM metafile, indexed colour selection C ++ CGDRIV 2 /CGMD CGM metafile, direct colour selection C ++ CWDRIV 0 /CW6320 Gould/Bryans Colourwriter 6320 pen plotter Std F77 + ! EPDRIV 0 /EPSON Epson FX100 dot matrix printer + ! EXDRIV 1 /EXCL Talaris/EXCL printers, landscape + ! EXDRIV 2 /EXCL Talaris/EXCL printers, portrait + ! GCDRIV 0 /GENICOM Genicom 4410 dot-matrix printer, landscape + ! Caution: use of GIDRIV may require a license from Unisys: +-! GIDRIV 1 /GIF GIF-format file, landscape +-! GIDRIV 2 /VGIF GIF-format file, portrait +-! GLDRIV 1 /HPGL Hewlett-Packard HP-GL plotters, landscape Std F77 +-! GLDRIV 2 /VHPGL Hewlett-Packard HP-GL plotters, portrait Std F77 ++ GIDRIV 1 /GIF GIF-format file, landscape ++ GIDRIV 2 /VGIF GIF-format file, portrait ++ GLDRIV 1 /HPGL Hewlett-Packard HP-GL plotters, landscape Std F77 ++ GLDRIV 2 /VHPGL Hewlett-Packard HP-GL plotters, portrait Std F77 + ! GODRIV 0 /GOC GOC Sigma T5670 terminal VMS + ! GVDRIV 0 /GVENICOM Genicom 4410 dot-matrix printer, portrait +-! HGDRIV 0 /HPGL2 Hewlett-Packard graphics language +-! HIDRIV 0 /HIDMP Houston Instruments HIDMP pen plotter ++ HGDRIV 0 /HPGL2 Hewlett-Packard graphics language ++ HIDRIV 0 /HIDMP Houston Instruments HIDMP pen plotter + ! HJDRIV 0 /HJ Hewlett-Packard Desk/Laserjet printer +-! HPDRIV 0 /HP7221 Hewlett-Packard HP7221 pen plotter Std F77 ++ HPDRIV 0 /HP7221 Hewlett-Packard HP7221 pen plotter Std F77 + ! LADRIV 0 /LA50 Dec LA50 and other sixel printers + ! LJDRIV 0 /LJ Hewlett-Packard LaserJet printers VMS +-! LSDRIV 1 /LIPS2 Canon LaserShot printer (landscape) +-! LSDRIV 2 /VLIPS2 Canon LaserShot printer (portrait) ++ LSDRIV 1 /LIPS2 Canon LaserShot printer (landscape) ++ LSDRIV 2 /VLIPS2 Canon LaserShot printer (portrait) + ! LNDRIV 0 /LN03 Dec LN03-PLUS Laser printer (landscape) VMS + ! LVDRIV 0 /LVN03 Dec LN03-PLUS Laser printer (portrait) VMS +-! LXDRIV 0 /LATEX LaTeX picture environment ++ LXDRIV 0 /LATEX LaTeX picture environment + ! MFDRIV 0 /FILE PGPLOT graphics metafile + ! NEDRIV 0 /NEXT Computers running NeXTstep operating system + NUDRIV 0 /NULL Null device (no output) Std F77 +-! PGDRIV 0 /PGMF PGPLOT metafile (new format, experimental) Std F77 +-! PNDRIV 1 /PNG Portable Network Graphics file C +-! PNDRIV 2 /TPNG Portable Network Graphics file - transparent background C +-! PPDRIV 1 /PPM Portable Pixel Map file, landscape +-! PPDRIV 2 /VPPM Portable PIxel Map file, portrait +-! PSDRIV 1 /PS PostScript printers, monochrome, landscape Std F77 +-! PSDRIV 2 /VPS Postscript printers, monochrome, portrait Std F77 +-! PSDRIV 3 /CPS PostScript printers, color, landscape Std F77 +-! PSDRIV 4 /VCPS PostScript printers, color, portrait Std F77 ++ PGDRIV 0 /PGMF PGPLOT metafile (new format, experimental) Std F77 ++ PNDRIV 1 /PNG Portable Network Graphics file C ++ PNDRIV 2 /TPNG Portable Network Graphics file - transparent background C ++ PPDRIV 1 /PPM Portable Pixel Map file, landscape ++ PPDRIV 2 /VPPM Portable PIxel Map file, portrait ++ PSDRIV 1 /PS PostScript printers, monochrome, landscape Std F77 ++ PSDRIV 2 /VPS Postscript printers, monochrome, portrait Std F77 ++ PSDRIV 3 /CPS PostScript printers, color, landscape Std F77 ++ PSDRIV 4 /VCPS PostScript printers, color, portrait Std F77 + ! PXDRIV 0 /PRINTRONI Printronix P300 or P600 dot-matrix printer +-! QMDRIV 1 /QMS QUIC devices (QMS and Talaris), landscape Std F77 +-! QMDRIV 2 /VQMS QUIC devices (QMS and Talaris), portrait Std F77 ++ QMDRIV 1 /QMS QUIC devices (QMS and Talaris), landscape Std F77 ++ QMDRIV 2 /VQMS QUIC devices (QMS and Talaris), portrait Std F77 + ! TFDRIV 0 /TFILE Tektronix-format disk file VMS + ! TODRIV 0 /TOSHIBA Toshiba "3-in-one" printer, model P351 +-! TTDRIV 1 /TEK4010 Tektronix 4006/4010 storage-tube terminal Std F77 +-! TTDRIV 2 /GF GraphOn terminal Std F77 +-! TTDRIV 3 /RETRO RetroGraphics terminal Std F77 +-! TTDRIV 4 /GTERM GTERM Tektronix terminal emulator Std F77 +-! TTDRIV 5 /XTERM XTERM Tektronix terminal emulator Std F77 +-! TTDRIV 6 /ZSTEM ZSTEM terminal emulator Std F77 +-! TTDRIV 7 /V603 Visual 603 terminal Std F77 ++ TTDRIV 1 /TEK4010 Tektronix 4006/4010 storage-tube terminal Std F77 ++ TTDRIV 2 /GF GraphOn terminal Std F77 ++ TTDRIV 3 /RETRO RetroGraphics terminal Std F77 ++ TTDRIV 4 /GTERM GTERM Tektronix terminal emulator Std F77 ++ TTDRIV 5 /XTERM XTERM Tektronix terminal emulator Std F77 ++ TTDRIV 6 /ZSTEM ZSTEM terminal emulator Std F77 ++ TTDRIV 7 /V603 Visual 603 terminal Std F77 + ! TTDRIV 8 /KRM3 Kermit 3 on IBM-PC Std F77 +-! TTDRIV 9 /TK4100 Tektronix 4100-series terminals Std F77 +-! TTDRIV 10 /VMAC Macintosh VersaTerm-PRO Tektronix-4105 emulator Std F77 ++ TTDRIV 9 /TK4100 Tektronix 4100-series terminals Std F77 ++ TTDRIV 10 /VMAC Macintosh VersaTerm-PRO Tektronix-4105 emulator Std F77 + ! TXDRIV 0 /TX TeX PK Font Output files +-! VADRIV 0 /VCANON Canon Laser printer, LBP-8/A2, portrait +-! VBDRIV 0 /VBCANON Canon Laser printer (bitmap version), portrait +-! VTDRIV 0 /VT125 Dec Regis terminals (VT125 etc.) Std F77 +-! WDDRIV 1 /WD X Window dump file, landscape +-! WDDRIV 2 /VWD X Window dump file, portrait ++ VADRIV 0 /VCANON Canon Laser printer, LBP-8/A2, portrait ++! VBDRIV 0 /VBCANON Canon Laser printer (bitmap version), portrait ++ VTDRIV 0 /VT125 Dec Regis terminals (VT125 etc.) Std F77 ++ WDDRIV 1 /WD X Window dump file, landscape ++ WDDRIV 2 /VWD X Window dump file, portrait + ! WSDRIV 0 /WS VAX workstations running VWS software VMS +-! X2DRIV 0 /XDISP PGDISP or FIGDISP server for X workstations C +-! XWDRIV 1 /XWINDOW Workstations running X Window System C +-! XWDRIV 2 /XSERVE Persistent window on X Window System C +-! ZEDRIV 0 /ZETA Zeta 8 Digital Plotter ++ X2DRIV 0 /XDISP PGDISP or FIGDISP server for X workstations C ++ XWDRIV 1 /XWINDOW Workstations running X Window System C ++ XWDRIV 2 /XSERVE Persistent window on X Window System C ++! ZEDRIV 0 /ZETA Zeta 8 Digital Plotter + ! + ! The following drivers can only be used in PGPLOT installations on MS-DOS + ! systems with appropriate hardware and software. Do not select these diff --git a/sci-libs/pgplot/files/pgplot-headers.patch b/sci-libs/pgplot/files/pgplot-headers.patch new file mode 100644 index 000000000000..c05ca702648e --- /dev/null +++ b/sci-libs/pgplot/files/pgplot-headers.patch @@ -0,0 +1,109 @@ +--- a/sys/grtermio.c 2008-10-29 17:42:48.000000000 +0000 ++++ b/sys/grtermio.c 2008-10-29 19:54:43.000000000 +0000 +@@ -7,6 +7,10 @@ + + #include <stdio.h> + #include <termios.h> ++#include <stdlib.h> ++#include <unistd.h> ++#include <string.h> ++#include <fcntl.h> + + #ifdef PG_PPU + #define GROTER groter_ +--- a/sys/grfileio.c 2008-10-29 15:10:02.000000000 +0000 ++++ b/sys/grfileio.c 2008-10-29 17:56:50.000000000 +0000 +@@ -17,7 +17,9 @@ + */ + + #include <stdlib.h> ++#include <unistd.h> + #include <stdio.h> ++#include <string.h> + #include <sys/types.h> + #include <fcntl.h> + +--- a/drivers/figdisp_comm.c 2008-10-29 15:09:15.000000000 +0000 ++++ b/drivers/figdisp_comm.c 2008-10-29 17:54:08.000000000 +0000 +@@ -17,6 +17,8 @@ + + /* The system include files */ + #include <stdio.h> ++#include <stdlib.h> ++#include <unistd.h> + + /* Get ntohs prototype or macro */ + +--- a/pgdispd/resdb.c 2008-10-29 18:22:41.000000000 +0000 ++++ b/pgdispd/resdb.c 2008-10-29 20:10:22.000000000 +0000 +@@ -47,6 +47,8 @@ + #include <stdio.h> + #include <stdlib.h> + #include <string.h> ++#include <unistd.h> ++ + #ifndef VMS + #include <pwd.h> + #endif +@@ -1042,7 +1044,6 @@ + int uid; + + extern char *getenv(); +- extern int getuid(); + extern struct passwd *getpwuid(); + struct passwd *pw; + register char *ptr; +--- a/pgdispd/proccom.c 2008-10-29 15:03:34.000000000 +0000 ++++ b/pgdispd/proccom.c 2008-10-29 18:15:48.000000000 +0000 +@@ -90,6 +90,7 @@ + + /* The system include files */ + #include <stdio.h> ++#include <stdlib.h> + #include <sys/types.h> + #include <netinet/in.h> + +@@ -163,7 +164,6 @@ + void drawline(); /* draw a line in the bitmap window */ + Pixmap XCreatePixmap(); + +- char *malloc(); + + if (!len & savedshorts) + { /* an incomplete command was sent! */ +--- a/pgdispd/getvisuals.c 2008-10-29 17:59:37.000000000 +0000 ++++ b/pgdispd/getvisuals.c 2008-10-29 18:00:18.000000000 +0000 +@@ -30,6 +30,7 @@ + #include "messages.h" + + #include <stdio.h> ++#include <stdlib.h> + + #define MAX_DEPTH 24 /* the maximum visual depth to use */ + +--- a/pgdispd/figcurs.c 2008-10-29 17:58:22.000000000 +0000 ++++ b/pgdispd/figcurs.c 2008-10-29 18:14:02.000000000 +0000 +@@ -19,6 +19,7 @@ + + /* The standard include files */ + #include <stdio.h> ++#include <stdlib.h> + #include <sys/types.h> + #include <netinet/in.h> + +@@ -113,7 +114,6 @@ + void getbuttonval(); + int getkeyval(); + +- char *malloc(); + + if (event.type == ButtonPress) getbuttonval(event.xbutton.button, &val); + else if (!getkeyval(event, &val)) return(1); +@@ -167,7 +167,6 @@ + void getbuttonval(); + int getkeyval(); + +- char *malloc(); + + if (event.type == ButtonPress) getbuttonval(event.xbutton.button, &val); + else if (!getkeyval(event, &val)) return(1); diff --git a/sci-libs/pgplot/files/pgplot-libpng15.patch b/sci-libs/pgplot/files/pgplot-libpng15.patch new file mode 100644 index 000000000000..a3cefe1dde77 --- /dev/null +++ b/sci-libs/pgplot/files/pgplot-libpng15.patch @@ -0,0 +1,11 @@ +--- a/drivers/pndriv.c ++++ b/drivers/pndriv.c +@@ -222,7 +222,7 @@ + return; + } + +- if (setjmp(png_ptr->jmpbuf)) { /* not really sure what I'm doing here... */ ++ if (setjmp(png_jmpbuf(png_ptr))) { + fprintf(stderr,"%s: error in libpng while writing file %s, plotting disabled\n", png_ident, filename); + png_destroy_write_struct(&png_ptr,&info_ptr); + dev->error = true; diff --git a/sci-libs/pgplot/files/pgplot-makemake.patch b/sci-libs/pgplot/files/pgplot-makemake.patch new file mode 100644 index 000000000000..fafd2f16ea40 --- /dev/null +++ b/sci-libs/pgplot/files/pgplot-makemake.patch @@ -0,0 +1,223 @@ +--- a/makemake 2012-07-05 14:08:30.210815190 -0700 ++++ b/makemake 2012-07-05 14:26:28.353381906 -0700 +@@ -73,7 +73,7 @@ + + # List the default make targets. + +-DEFAULT_TARGETS="lib grfont.dat prog pgplot.doc" ++DEFAULT_TARGETS="lib grfont.dat pgplot.doc" + + # Get the configuration variables. + +@@ -199,18 +199,18 @@ + fi + + if (echo $DRIV_LIST | grep -s xmdriv 2>&1 1>/dev/null); then +- DEFAULT_TARGETS="$DEFAULT_TARGETS libXmPgplot.a pgmdemo" +- INSTALL_LIST="$INSTALL_LIST libXmPgplot.a XmPgplot.h" ++ DEFAULT_TARGETS="$DEFAULT_TARGETS libXmPgplot.a" ++ INSTALL_LIST="$INSTALL_LIST libXmPgplot.a XmPgplot.h" + fi + + if (echo $DRIV_LIST | grep -s xadriv 2>&1 1>/dev/null); then +- DEFAULT_TARGETS="$DEFAULT_TARGETS libXaPgplot.a pgawdemo" ++ DEFAULT_TARGETS="$DEFAULT_TARGETS libXaPgplot.a" + INSTALL_LIST="$INSTALL_LIST libXaPgplot.a XaPgplot.h" + fi + + if (echo $DRIV_LIST | grep -s tkdriv 2>&1 1>/dev/null); then +- DEFAULT_TARGETS="$DEFAULT_TARGETS libtkpgplot.a pgtkdemo pgtkdemo.tcl" +- INSTALL_LIST="$INSTALL_LIST libtkpgplot.a tkpgplot.h" ++ DEFAULT_TARGETS="$DEFAULT_TARGETS libtkpgplot.a" ++ INSTALL_LIST="$INSTALL_LIST libtkpgplot.a tkpgplot.h" + fi + + if (echo $DRIV_LIST | grep -s rvdriv 2>&1 1>/dev/null); then +@@ -622,7 +622,7 @@ + # Fortran compiler and compilation flags + # + FCOMPL=$FCOMPL +-FFLAGC=$FFLAGC ++FFLAGC=$FFLAGC \$(FFLAGS) + FFLAGD=$FFLAGD + # + # C compiler and compilation flags +@@ -633,7 +633,7 @@ + TK_INCL=$TK_INCL + RV_INCL=$RV_INCL + CCOMPL=$CCOMPL +-CFLAGC=$CFLAGC -I. ++CFLAGC=$CFLAGC -I. \$(CFLAGS) + CFLAGD=$CFLAGD + MCOMPL=$MCOMPL + MFLAGC=$MFLAGC +@@ -657,7 +657,10 @@ + # Shared library creation. + # + SHARED_LIB=$SHARED_LIB ++SHARED_CLIB=$SHARED_CLIB + SHARED_LD=$SHARED_LD ++SHARED_LD_PGPLOT_OPTS=$SHARED_LD_PGPLOT_OPTS ++SHARED_LD_CPGPLOT_OPTS=$SHARED_LD_CPGPLOT_OPTS + # + # The libraries that the shared PGPLOT library depends upon. + # This is for systems that allow one to specify what libraries +@@ -806,7 +809,8 @@ + # libraries. + #----------------------------------------------------------------------- + +-lib : libpgplot.a $(SHARED_LIB) ++#lib : libpgplot.a $(SHARED_LIB) ++lib : libpgplot.a + + libpgplot.a : $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \ + $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) +@@ -816,6 +820,16 @@ + $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` + $(RANLIB) libpgplot.a + ++#shared: $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \ ++# $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) ++# $(SHARED_LD) ++ ++shared: $(PG_ROUTINES) $(PG_NON_STANDARD) grfont.dat \ ++ $(GR_ROUTINES) $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) ++ $(SHARED_LD) $(SHARED_LD_PGPLOT_OPTS) `ls $(PG_ROUTINES) \ ++ $(PG_NON_STANDARD) $(GR_ROUTINES) $(DISPATCH_ROUTINE) \ ++ $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` $(SHARED_LIB_LIBS) -o $(SHARED_LIB) ++ ln -s $(SHARED_LIB) libpgplot.so + EOD + + # Emit the shared library dependency if requested. +@@ -824,7 +838,7 @@ + cat >> makefile << \EOD + $(SHARED_LIB): $(PG_ROUTINES) $(PG_NON_STANDARD) \ + $(GR_ROUTINES) $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) +- $(SHARED_LD) `ls $(PG_ROUTINES) \ ++ $(SHARED_LD) $(SHARED_LD_PGPLOT_OPTS) `ls $(PG_ROUTINES) \ + $(PG_NON_STANDARD) $(GR_ROUTINES) $(DISPATCH_ROUTINE) \ + $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` $(SHARED_LIB_LIBS) + EOD +@@ -857,7 +871,7 @@ + + for file in $DEMOS; do + echo "${file}: \$(DEMDIR)/${file}.f $EXTRA_DEPENDENCY" +-echo " \$(FCOMPL) \$(FFLAGD) -o ${file} \$(DEMDIR)/${file}.f \$(PGPLOT_LIB) \$(LIBS)" ++echo " \$(FCOMPL) \$(FFLAGD) \$(DEMDIR)/${file}.f \$(PGPLOT_LIB) \$(LIBS) -o ${file}" + done >> makefile + + cat >> makefile << \EOD +@@ -921,13 +935,13 @@ + # Target "pgxwin_server" is the server program for the XW driver + #----------------------------------------------------------------------- + pgxwin_server: $(DRVDIR)/pgxwin_server.c +- $(CCOMPL) $(CFLAGC) $(XINCL) -o pgxwin_server $(DRVDIR)/pgxwin_server.c $(LIBS) ++ $(CCOMPL) $(CFLAGC) $(LDFLAGS) $(XINCL) $(DRVDIR)/pgxwin_server.c $(LIBS) -o pgxwin_server + + #----------------------------------------------------------------------- + # Target "pgdisp" is the pgdisp server program for /XDISP driver + #----------------------------------------------------------------------- + pgdisp: $(PGDISP_ROUTINES) +- $(CCOMPL) $(CFLAGC) -o pgdisp $(PGDISP_ROUTINES) $(LIBS) ++ $(CCOMPL) $(CFLAGC) $(LDFLAGS) $(PGDISP_ROUTINES) $(LIBS) -o pgdisp + + #----------------------------------------------------------------------- + # Target "libxmpgplot.a" contains the Motif widget driver. +@@ -937,6 +951,10 @@ + ar ru libXmPgplot.a XmPgplot.o + $(RANLIB) libXmPgplot.a + ++libXmPgplot.so: XmPgplot.h XmPgplot.o ++ $(SHARED_LD) $(LDFLAGS) -Wl,-soname,libXmPgplot.so.5 XmPgplot.o -L. -lcpgplot $(MOTIF_LIBS) -o libXmPgplot.so.5 ++ ln -s libXmPgplot.so.5 libXmPgplot.so ++ + XmPgplot.h: $(XMDIR)/XmPgplot.h + cp $(XMDIR)/XmPgplot.h XmPgplot.h + +@@ -965,6 +983,10 @@ + ar ru libtkpgplot.a tkpgplot.o + $(RANLIB) libtkpgplot.a + ++libtkpgplot.so: tkpgplot.h tkpgplot.o ++ $(SHARED_LD) $(LDFLAGS) -Wl,-soname,libtkpgplot.so.5 tkpgplot.o -L. -lcpgplot $(TK_LIBS) -o libtkpgplot.so.5 ++ ln -s libtkpgplot.so.5 libtkpgplot.so ++ + tkpgplot.h: $(TKDIR)/tkpgplot.h + cp $(TKDIR)/tkpgplot.h tkpgplot.h + +@@ -983,7 +1005,7 @@ + cp $(TKDIR)/rvpgplot.h rvpgplot.h + + rvpgplot.o: $(DRVDIR)/pgxwin.h rvpgplot.h $(TKDIR)/tkpgplot.c +- $(CCOMPL) -o $@ -c -DUSE_RIVET $(CFLAGC) -I$(DRVDIR) -I$(TKDIR) $(RV_INCL) $(TKDIR)/tkpgplot.c ++ $(CCOMPL) -c -DUSE_RIVET $(CFLAGC) -I$(DRVDIR) -I$(TKDIR) $(RV_INCL) $(TKDIR)/tkpgplot.c -o $@ + + #----------------------------------------------------------------------- + # Target "install" is required for Figaro. +@@ -1025,12 +1047,12 @@ + grivas.o : $(DRVDIR)/gadef.h + grtv00.o : $(DRVDIR)/imdef.h + pgxwin.o : $(DRVDIR)/pgxwin.h +-pndriv.o : ./png.h ./pngconf.h ./zlib.h ./zconf.h ++pndriv.o : /usr/include/png.h /usr/include/pngconf.h /usr/include/zlib.h /usr/include/zconf.h + + x2driv.o figdisp_comm.o: $(DRVDIR)/commands.h + + +-cpg: libcpgplot.a cpgplot.h cpgdemo ++cpg: cpgplot.h libcpgplot.a + @echo ' ' + @echo '*** Finished compilation of the C PGPLOT wrapper library ***' + @echo ' ' +@@ -1039,24 +1061,36 @@ + @echo 'will be needed.' + @echo ' ' + ++cpg-shared: libcpgplot.so ++ + pgbind: $(SRC)/cpg/pgbind.c + $(CCOMPL) $(CFLAGC) $(SRC)/cpg/pgbind.c -o pgbind + +-libcpgplot.a cpgplot.h: $(PG_SOURCE) pgbind ++cpgplot.h: $(PG_SOURCE) pgbind + ./pgbind $(PGBIND_FLAGS) -h -w $(PG_SOURCE) ++ ++libcpgplot.a: cpgplot.h + $(CCOMPL) -c $(CFLAGC) cpg*.c + rm -f cpg*.c + ar ru libcpgplot.a cpg*.o + $(RANLIB) libcpgplot.a + rm -f cpg*.o + ++libcpgplot.so: cpgplot.h $(PG_SOURCE) pgbind ++ ./pgbind $(PGBIND_FLAGS) -w $(PG_SOURCE) ++ $(CCOMPL) -c $(CFLAGC) cpg*.c ++ rm -f cpg*.c ++ $(SHARED_LD) $(SHARED_LD_CPGPLOT_OPTS) cpg*.o -L. -lpgplot $(SHARED_LIB_LIBS) -o $(SHARED_CLIB) ++ ln -s $(SHARED_CLIB) libcpgplot.so ++ rm -f cpg*.o ++ + cpgdemo: cpgplot.h $(SRC)/cpg/cpgdemo.c libcpgplot.a + $(CCOMPL) $(CFLAGD) -c -I. $(SRC)/cpg/cpgdemo.c +- $(FCOMPL) -o cpgdemo cpgdemo.o $(CPGPLOT_LIB) $(LIBS) ++ $(FCOMPL) cpgdemo.o $(CPGPLOT_LIB) $(LIBS) -o cpgdemo + rm -f cpgdemo.o + +-pgmdemo: pgmdemo.o libXmPgplot.a +- $(FCOMPL) -o pgmdemo pgmdemo.o -L`pwd` -lXmPgplot $(CPGPLOT_LIB) $(MOTIF_LIBS) ++pgmdemo: pgmdemo.o libXmPgplot.so ++ $(FCOMPL) pgmdemo.o -L`pwd` -lXmPgplot $(CPGPLOT_LIB) $(MOTIF_LIBS) -o pgmdemo + + pgmdemo.o: $(XMDIR)/pgmdemo.c XmPgplot.h libcpgplot.a cpgplot.h + $(CCOMPL) $(CFLAGD) -c -I`pwd` $(MOTIF_INCL) $(XMDIR)/pgmdemo.c +@@ -1067,8 +1101,8 @@ + pgawdemo.o: $(XADIR)/pgawdemo.c XaPgplot.h libcpgplot.a cpgplot.h + $(CCOMPL) $(CFLAGD) -c -I`pwd` $(ATHENA_INCL) $(XADIR)/pgawdemo.c + +-pgtkdemo: pgtkdemo.o libtkpgplot.a +- $(FCOMPL) -o pgtkdemo pgtkdemo.o -L`pwd` -ltkpgplot $(CPGPLOT_LIB) $(TK_LIBS) ++pgtkdemo: pgtkdemo.o libtkpgplot.so ++ $(FCOMPL) pgtkdemo.o -L`pwd` -ltkpgplot $(CPGPLOT_LIB) $(TK_LIBS) -o pgtkdemo + + pgtkdemo.tcl: $(TKDIR)/pgtkdemo.tcl + cp $(TKDIR)/pgtkdemo.tcl pgtkdemo.tcl diff --git a/sci-libs/pgplot/files/pgplot-tk86.patch b/sci-libs/pgplot/files/pgplot-tk86.patch new file mode 100644 index 000000000000..3223dc0dac4b --- /dev/null +++ b/sci-libs/pgplot/files/pgplot-tk86.patch @@ -0,0 +1,47 @@ +--- a/drivers/xtk/tkpgplot.c 2000-12-13 03:16:28.000000000 +0100 ++++ b/drivers/xtk/tkpgplot.c 2013-01-15 11:02:27.221231471 +0100 +@@ -417,7 +417,7 @@ + /* + * If Tk_Init() hasn't been called, then there won't be a main window + * yet. In such cases, Tk_MainWindow() places a suitable error message +- * in interp->result. ++ * in Tcl_GetStringResult(interp). + */ + if(!main_w) + return TCL_ERROR; +@@ -2136,7 +2136,7 @@ + tkpg->border = bd; + tkpg_draw_3d_border(tkpg); + } else { +- fprintf(stderr, "Tk_Get3DBorder failed: %s\n", tkpg->interp->result); ++ fprintf(stderr, "Tk_Get3DBorder failed: %s\n", Tcl_GetStringResult(tkpg->interp)); + }; + } + +@@ -2261,7 +2261,7 @@ + * argv char ** The array of 'argc' configuration arguments. + * Output: + * return int TCL_ERROR and the context of the error +- * is recorded in interp->result. ++ * is recorded in Tcl_GetStringResult(result). + */ + static int tkpg_scrollbar_error(TkPgplot *tkpg, Tcl_Interp *interp, + char *widget, char *view, int argc, +@@ -2586,7 +2586,7 @@ + * Output: + * return Tk_Window The top-level window of the path, or NULL if + * it doesn't exist. In the latter case an error +- * message will have been appended to interp->result. ++ * message will have been appended to Tcl_GetStringResult(interp). + */ + static Tk_Window tkpg_toplevel_of_path(Tcl_Interp *interp, Tk_Window main_w, + char *path) +@@ -2630,7 +2630,7 @@ + free(first); + /* + * If the window doesn't exist, Tk_NameToWindow() is documented to place +- * an error message in interp->result, so just return the error condition. ++ * an error message in Tcl_GetStringResult(interp), so just return the error condition. + */ + if(!w) + return NULL; diff --git a/sci-libs/pgplot/metadata.xml b/sci-libs/pgplot/metadata.xml new file mode 100644 index 000000000000..1f8f0d3e10fe --- /dev/null +++ b/sci-libs/pgplot/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + PGPLOT is a Fortran subroutine package for drawing graphs on a variety + of display devices. The CPGPLOT library adds an intermediate level of + wrapper functions between C programs and the PGPLOT library. These + functions hide the system dependencies of calling PGPLOT behind a + system independent interface. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/pgplot/pgplot-5.2.2-r6.ebuild b/sci-libs/pgplot/pgplot-5.2.2-r6.ebuild new file mode 100644 index 000000000000..87dd80c669a9 --- /dev/null +++ b/sci-libs/pgplot/pgplot-5.2.2-r6.ebuild @@ -0,0 +1,180 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs multilib + +MY_P="${PN}${PV//.}" + +DESCRIPTION="FORTRAN/C device-independent scientific graphic library" +HOMEPAGE="http://www.astro.caltech.edu/~tjp/pgplot/" +SRC_URI="ftp://ftp.astro.caltech.edu/pub/pgplot/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="free-noncomm" +KEYWORDS="amd64 ~arm ~ia64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="doc motif static-libs tk" + +RDEPEND=" + media-libs/libpng + x11-libs/libX11 + x11-libs/libXt + motif? ( >=x11-libs/motif-2.3:0 ) + tk? ( dev-lang/tk )" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +S="${WORKDIR}/${PN}" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-drivers.patch \ + "${FILESDIR}"/${PN}-makemake.patch \ + "${FILESDIR}"/${PN}-compile-setup.patch \ + "${FILESDIR}"/${PN}-headers.patch \ + "${FILESDIR}"/${PN}-libpng15.patch \ + "${FILESDIR}"/${PN}-tk86.patch + + # gfortran < 4.3 does not compile gif, pp and wd drivers + if [[ $(tc-getFC) == *gfortran* ]] && + [[ $(gcc-major-version)$(gcc-minor-version) -lt 43 ]] ; then + echo + ewarn "Warning!" + ewarn "gfortran < 4.3 selected: does not compile all drivers" + ewarn "disabling gif, wd, and ppd drivers" + ewarn "if you want more drivers, use gfortran >= 4.3" + echo + sed -i \ + -e 's/GIDRIV/! GIDRIV/g' \ + -e 's/PPDRIV/! GIDRIV/g' \ + -e 's/WDDRIV/! GIDRIV/g' \ + drivers.list || die "sed drivers failed" + fi + + # fix pointers for 64 bits + if use amd64 || use ia64; then + sed -i \ + -e 's/INTEGER PIXMAP/INTEGER*8 PIXMAP/g' \ + drivers/{gi,pp,wd}driv.f || die "sed 64bits failed" + fi + + cp sys_linux/g77_gcc.conf local.conf + + sed -i \ + -e "s:FCOMPL=.*:FCOMPL=\"$(tc-getFC)\":g" \ + -e "s:CCOMPL=.*:CCOMPL=\"$(tc-getCC)\":g" \ + local.conf || die "sed flags failed" + + if [[ "$(tc-getFC)" = if* ]]; then + sed -i \ + -e 's/-Wall//g' \ + -e 's/TK_LIBS="/TK_LIBS="-nofor-main /' \ + local.conf || die "sed drivers failed" + fi + + sed -i \ + -e "s:/usr/local/pgplot:/usr/$(get_libdir)/pgplot:g" \ + -e "s:/usr/local/bin:/usr/bin:g" \ + src/grgfil.f makehtml maketex || die "sed path failed" + + use motif && sed -i -e '/XMDRIV/s/!//' drivers.list + use tk && sed -i -e '/TKDRIV/s/!//' drivers.list +} + +src_configure() { + ./makemake . linux + # post makefile creation prefix hack + sed -i -e "s|/usr|${EROOT}/usr|g" makefile || die +} + +src_compile() { + emake \ + CFLAGS="${CFLAGS} -fPIC" \ + FFLAGS="${FFLAGS} -fPIC" \ + shared cpg-shared pgxwin_server pgdisp pgplot.doc + + use tk && emake CFLAGS="${CFLAGS} -fPIC" libtkpgplot.so + use motif && emake CFLAGS="${CFLAGS} -fPIC" libXmPgplot.so + + emake -j1 clean + use static-libs && emake all cpg + + if use doc; then + export VARTEXFONTS="${T}/fonts" + emake pgplot.html pgplot-routines.tex + pdflatex pgplot-routines.tex + pdflatex pgplot-routines.tex + fi + + # this just cleans out not needed files + emake -j1 clean +} + +src_test() { + # i can go to 16 + local i j + for i in 1 2 3; do + emake pgdemo${i} + # j can also be LATEX CPS... + for j in NULL PNG PS CPS LATEX; do + local testexe=./test_${j}_${i} + echo "LD_LIBRARY_PATH=. ./pgdemo${i} <<EOF" > ${testexe} + echo "/${j}" >> ${testexe} + echo "EOF" >> ${testexe} + sh ${testexe} || die "test ${i} failed" + done + done +} + +src_install() { + insinto /usr/$(get_libdir)/pgplot + doins grfont.dat grexec.f *.inc rgb.txt + echo "PGPLOT_FONT=${EROOT%/}/usr/$(get_libdir)/pgplot/grfont.dat" >> 99pgplot + doenvd 99pgplot + + dolib.so libpgplot.so* + dobin pgxwin_server pgdisp + + # C binding + insinto /usr/include + doins cpgplot.h + dolib.so libcpgplot.so* + + if use motif; then + insinto /usr/include + doins XmPgplot.h + dolib.so libXmPgplot.so* + fi + + if use tk; then + insinto /usr/include + doins tkpgplot.h + dolib.so libtkpgplot.so* + fi + + use static-libs && dolib.a lib*pgplot.a + + # minimal doc + dodoc aaaread.me pgplot.doc + newdoc pgdispd/aaaread.me pgdispd.txt + + if use doc; then + dodoc cpg/cpgplot.doc applications/curvefit/curvefit.doc + dohtml pgplot.html + insinto /usr/share/doc/${PF} + doins pgplot-routines.pdf pgplot-routines.tex + insinto /usr/share/doc/${PF}/examples + doins examples/* cpg/cpgdemo.c + insinto /usr/share/doc/${PF}/applications + doins -r applications/* + if use motif; then + insinto /usr/share/doc/${PF}/pgm + doins pgmf/* drivers/xmotif/pgmdemo.c + fi + if use tk; then + insinto /usr/share/doc/${PF}/pgtk + doins drivers/xtk/pgtkdemo.* + fi + fi +} diff --git a/sci-libs/pgplot/pgplot-5.2.2-r7.ebuild b/sci-libs/pgplot/pgplot-5.2.2-r7.ebuild new file mode 100644 index 000000000000..793ce9da5939 --- /dev/null +++ b/sci-libs/pgplot/pgplot-5.2.2-r7.ebuild @@ -0,0 +1,173 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils fortran-2 toolchain-funcs + +MY_P="${PN}${PV//.}" + +DESCRIPTION="FORTRAN/C device-independent scientific graphic library" +HOMEPAGE="http://www.astro.caltech.edu/~tjp/pgplot/" +SRC_URI="ftp://ftp.astro.caltech.edu/pub/pgplot/${MY_P}.tar.gz" + +SLOT="0" +LICENSE="free-noncomm" +KEYWORDS="~amd64 ~arm ~ia64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="doc motif static-libs tk" + +RDEPEND=" + media-libs/libpng:= + x11-libs/libX11:= + x11-libs/libXt:= + motif? ( x11-libs/motif:= ) + tk? ( dev-lang/tk:= )" +DEPEND="${RDEPEND} + doc? ( virtual/latex-base )" + +S="${WORKDIR}/${PN}" + +PATCHES=( + "${FILESDIR}"/${PN}-drivers.patch + "${FILESDIR}"/${PN}-makemake.patch + "${FILESDIR}"/${PN}-compile-setup.patch + "${FILESDIR}"/${PN}-headers.patch + "${FILESDIR}"/${PN}-libpng15.patch + "${FILESDIR}"/${PN}-tk86.patch +) + +src_prepare() { + default + # gfortran < 4.3 does not compile gif, pp and wd drivers + if [[ $(tc-getFC) == *gfortran* ]] && + [[ $(gcc-major-version)$(gcc-minor-version) -lt 43 ]] ; then + ewarn "Warning!" + ewarn "gfortran < 4.3 selected: does not compile all drivers" + ewarn "disabling gif, wd, and ppd drivers" + ewarn "if you want more drivers, use gfortran >= 4.3" + sed -e 's/GIDRIV/! GIDRIV/g' \ + -e 's/PPDRIV/! GIDRIV/g' \ + -e 's/WDDRIV/! GIDRIV/g' \ + -i drivers.list || die "sed drivers failed" + fi + + # fix pointers for 64 bits + if use amd64 || use ia64; then + sed -e 's/INTEGER PIXMAP/INTEGER*8 PIXMAP/g' \ + -i drivers/{gi,pp,wd}driv.f || die "sed 64bits failed" + fi + + cp sys_linux/g77_gcc.conf local.conf + + sed -e "s:FCOMPL=.*:FCOMPL=\"$(tc-getFC)\":g" \ + -e "s:CCOMPL=.*:CCOMPL=\"$(tc-getCC)\":g" \ + -i local.conf || die "sed flags failed" + + if [[ "$(tc-getFC)" = if* ]]; then + sed -e 's/-Wall//g' \ + -e 's/TK_LIBS="/TK_LIBS="-nofor-main /' \ + -i local.conf || die "sed drivers failed" + fi + + sed -e "s:/usr/local/pgplot:${EPREFIX}/usr/$(get_libdir)/pgplot:g" \ + -e "s:/usr/local/bin:${EPREFIX}/usr/bin:g" \ + -i src/grgfil.f makehtml maketex || die "sed path failed" + + use motif && sed -i -e '/XMDRIV/s/!//' drivers.list + use tk && sed -i -e '/TKDRIV/s/!//' drivers.list +} + +src_configure() { + ./makemake . linux + # post makefile creation prefix hack + sed -i -e "s|/usr|${EPREFIX}/usr|g" makefile || die +} + +src_compile() { + emake \ + CFLAGS="${CFLAGS} -fPIC" \ + FFLAGS="${FFLAGS} -fPIC" \ + shared cpg-shared pgxwin_server pgdisp pgplot.doc + + use tk && emake CFLAGS="${CFLAGS} -fPIC" libtkpgplot.so + use motif && emake CFLAGS="${CFLAGS} -fPIC" libXmPgplot.so + + emake -j1 clean + use static-libs && emake all cpg + + if use doc; then + export VARTEXFONTS="${T}/fonts" + emake pgplot.html pgplot-routines.tex + pdflatex pgplot-routines.tex + pdflatex pgplot-routines.tex + fi + + # this just cleans out not needed files + emake -j1 clean +} + +src_test() { + # i can go to 16 + local i j + for i in 1 2 3; do + emake pgdemo${i} + # j can also be LATEX CPS... + for j in NULL PNG PS CPS LATEX; do + local testexe=./test_${j}_${i} + echo "LD_LIBRARY_PATH=. ./pgdemo${i} <<EOF" > ${testexe} + echo "/${j}" >> ${testexe} + echo "EOF" >> ${testexe} + sh ${testexe} || die "test ${i} failed" + done + done +} + +src_install() { + insinto /usr/$(get_libdir)/pgplot + doins grfont.dat grexec.f *.inc rgb.txt + echo "PGPLOT_FONT=${EPREFIX%/}/usr/$(get_libdir)/pgplot/grfont.dat" >> 99pgplot + doenvd 99pgplot + + dolib.so libpgplot.so* + dobin pgxwin_server pgdisp + + # C binding + insinto /usr/include + doins cpgplot.h + dolib.so libcpgplot.so* + + if use motif; then + insinto /usr/include + doins XmPgplot.h + dolib.so libXmPgplot.so* + fi + + if use tk; then + insinto /usr/include + doins tkpgplot.h + dolib.so libtkpgplot.so* + fi + + use static-libs && dolib.a lib*pgplot.a + + # minimal doc + dodoc aaaread.me pgplot.doc + newdoc pgdispd/aaaread.me pgdispd.txt + + if use doc; then + dodoc cpg/cpgplot.doc applications/curvefit/curvefit.doc pgplot.html + dodoc pgplot-routines.pdf pgplot-routines.tex + insinto /usr/share/doc/${PF}/examples + doins examples/* cpg/cpgdemo.c + insinto /usr/share/doc/${PF}/applications + doins -r applications/* + if use motif; then + insinto /usr/share/doc/${PF}/pgm + doins pgmf/* drivers/xmotif/pgmdemo.c + fi + if use tk; then + insinto /usr/share/doc/${PF}/pgtk + doins drivers/xtk/pgtkdemo.* + fi + fi +} diff --git a/sci-libs/plotmm/Manifest b/sci-libs/plotmm/Manifest new file mode 100644 index 000000000000..323c46e8d585 --- /dev/null +++ b/sci-libs/plotmm/Manifest @@ -0,0 +1,6 @@ +AUX plotmm-0.1.2-libsigc++-2.2.patch 4037 SHA256 6c535a0665d561841dc1fa9fce29eb18735850bea3d7af8b19e1d20050237cc6 SHA512 3327b7fcd0311976bbf1a6990e9cf14c43c85fb4eea2de21501bc79e90ee7bbec9527b35dab8204534f797e318659f0d67faefa047bb6ef2a8b0962588e2b4b2 WHIRLPOOL 797145d4936c30858ecc57c0f96138d2a4f8df82822236a316e73fe8de2f0c3efb545f143cbd1a0cc4b8821f47f6e3ed2e087f11c5f86dadff6443bc2c57d35d +DIST plotmm-0.1.2.tar.gz 473175 SHA256 896bb729eb9cad5f3188d72304789dd7a86fdae66020ac0632fe3bc66abe9653 SHA512 68484d7ed3b4d6520782735e05ad3cf9a5749f723285a2a3d0d1fabe3b23df57856d24addb31c23e3f23174655095f55b9b9a8d10316812d7a80fe13e204fab6 WHIRLPOOL f004f50a7e9dc7cbfe891fe924139d7f75e293889b79c86a84ed3a58e2468ad10051105055c71753b3bb9d25fc50d2a6eae423a18af8e11c56228a988c7460bd +EBUILD plotmm-0.1.2.ebuild 1362 SHA256 b6a2550a36bc81b695d789d309ef3278825977547de816013499bbc765bcd82f SHA512 ca586b8907e2d35fe8a8bd4bc1272eff861065e3d770840b612f855b6ea206f6aed09d0fce980b55319394fd824ed75739eced17daa77bbb2097b5e941c61f1d WHIRLPOOL 28b827b2ec9a95c36dc0f6116d58875f2dbb664d0c206c786864ce442065c3f375b1137e80eaa70ac64fddae5746307c853094952874e3ced813f9c393c95192 +MISC ChangeLog 2709 SHA256 c5a24769001a1f8b34b8001b8d4b493ad1d3c5b2efca03a24ecee357aa4e94d3 SHA512 ebd5e9f91e39e061b445aee8172116779aa0636bba8cf84303f8d079c9f5b5dd2e2ee4355a5335242e67a922f18a54ce035e563edd745f82f92da3e556ed6a7d WHIRLPOOL 127b843036effc5d9d23bddd028f5f9260f3710c7a115a1e359d476b134ec9ac9647c58244b81f39409e6f4ab84dbdce6da378a0ac438b3862e5b8a692388cb1 +MISC ChangeLog-2015 939 SHA256 cb1612bfeef0af9f63c6400d3daf173d34f4dfc50c7d71f0938e79b1884ce9a1 SHA512 f0d9f260fee9ce19f6d4c2bea2a634859863301518da63791e94630d65a9d40ae3e65f01a834931285f857d20b22734cb7521310b5fc6c05c5fd3e6dc1f4f57d WHIRLPOOL 69238d89f69846fbec30b73df70debed121d75dbb0d0af90ac87194b86e9bba83c2a9724e5dbe568b90f93492af3f7feb7ef3aceb94598aebb0989a1fc176152 +MISC metadata.xml 243 SHA256 b4f1219eae9ece17a7aa123288c1afca3bbba6c8386652eeb2224eaaf0c8dc3b SHA512 d9179f9fde1433951047043a7c811ea571511473d16c0c4e2b0655933dd41cc7b0b56edbf3db9ed25037086a676de73ea6886a6935a3c3dff67ad441eaa1304a WHIRLPOOL 470263fcbacc3dad02bf8d02b907c14cd4721e46ecaed068430e0c2c59fb7886dd0d9872bdcb19888f2f0cba253c25eb686baa038f0f41028cf1481aecb43bd2 diff --git a/sci-libs/plotmm/files/plotmm-0.1.2-libsigc++-2.2.patch b/sci-libs/plotmm/files/plotmm-0.1.2-libsigc++-2.2.patch new file mode 100644 index 000000000000..a9aa53190d5f --- /dev/null +++ b/sci-libs/plotmm/files/plotmm-0.1.2-libsigc++-2.2.patch @@ -0,0 +1,100 @@ +diff -ur plotmm-0.1.2-old/plotmm/compat.h plotmm-0.1.2/plotmm/compat.h +--- plotmm-0.1.2-old/plotmm/compat.h 2005-11-09 17:36:02.000000000 +0100 ++++ plotmm-0.1.2/plotmm/compat.h 2008-07-25 00:13:55.000000000 +0200 +@@ -58,7 +58,7 @@ + #else + + namespace PlotMM { +- typedef SigC::ObjectBase ObjectBase; ++ typedef sigc::ObjectBase ObjectBase; + } + + #endif +diff -ur plotmm-0.1.2-old/plotmm/curve.h plotmm-0.1.2/plotmm/curve.h +--- plotmm-0.1.2-old/plotmm/curve.h 2005-11-09 17:47:21.000000000 +0100 ++++ plotmm-0.1.2/plotmm/curve.h 2008-07-25 00:24:02.000000000 +0200 +@@ -140,7 +140,7 @@ + int from = 0, int to = -1); + + //! Signals that this curve has changed in some way or the other +- SigC::Signal0<void> signal_curve_changed; ++ sigc::signal0<void> signal_curve_changed; + + protected: + virtual void init(const Glib::ustring &title); +diff -ur plotmm-0.1.2-old/plotmm/plot.cc plotmm-0.1.2/plotmm/plot.cc +--- plotmm-0.1.2-old/plotmm/plot.cc 2005-11-09 17:59:48.000000000 +0100 ++++ plotmm-0.1.2/plotmm/plot.cc 2008-07-25 00:24:30.000000000 +0200 +@@ -322,7 +322,7 @@ + connect(sigc::mem_fun(*this,&Plot::on_canvas_expose_event)); + #else + canvas_.signal_expose_event(). +- connect(SigC::slot(*this,&Plot::on_canvas_expose_event)); ++ connect(sigc::slot(*this,&Plot::on_canvas_expose_event)); + #endif + + show_all(); +@@ -406,19 +406,19 @@ + } + + //! Return the signal owned by plot canvas +-SigC::Signal3<void,int,int,GdkEventButton*> Plot::signal_plot_mouse_press() ++sigc::signal3<void,int,int,GdkEventButton*> Plot::signal_plot_mouse_press() + { + return canvas_.signal_plot_mouse_press; + } + + //! Return the signal owned by plot canvas +-SigC::Signal3<void,int,int,GdkEventButton*> Plot::signal_plot_mouse_release() ++sigc::signal3<void,int,int,GdkEventButton*> Plot::signal_plot_mouse_release() + { + return canvas_.signal_plot_mouse_release; + } + + //! Return the signal owned by plot canvas +-SigC::Signal3<void,int,int,GdkEventMotion*> Plot::signal_plot_mouse_move() ++sigc::signal3<void,int,int,GdkEventMotion*> Plot::signal_plot_mouse_move() + { + return canvas_.signal_plot_mouse_move; + } +diff -ur plotmm-0.1.2-old/plotmm/plot.h plotmm-0.1.2/plotmm/plot.h +--- plotmm-0.1.2-old/plotmm/plot.h 2004-03-09 10:51:55.000000000 +0100 ++++ plotmm-0.1.2/plotmm/plot.h 2008-07-25 00:25:17.000000000 +0200 +@@ -79,9 +79,9 @@ + virtual void clear(); + virtual void end_replot(); + +- SigC::Signal3<void,int,int,GdkEventButton*> signal_plot_mouse_press; +- SigC::Signal3<void,int,int,GdkEventButton*> signal_plot_mouse_release; +- SigC::Signal3<void,int,int,GdkEventMotion*> signal_plot_mouse_move; ++ sigc::signal3<void,int,int,GdkEventButton*> signal_plot_mouse_press; ++ sigc::signal3<void,int,int,GdkEventButton*> signal_plot_mouse_release; ++ sigc::signal3<void,int,int,GdkEventMotion*> signal_plot_mouse_move; + + protected: + virtual bool on_expose_event(GdkEventExpose* event); +@@ -141,9 +141,9 @@ + Scale *scale(PlotAxisID id) { return tickMark_[id]; } + PlotLabel *label(PlotAxisID id) { return axisLabel_[id]; } + +- SigC::Signal3<void,int,int,GdkEventButton*> signal_plot_mouse_press(); +- SigC::Signal3<void,int,int,GdkEventButton*> signal_plot_mouse_release(); +- SigC::Signal3<void,int,int,GdkEventMotion*> signal_plot_mouse_move(); ++ sigc::signal3<void,int,int,GdkEventButton*> signal_plot_mouse_press(); ++ sigc::signal3<void,int,int,GdkEventButton*> signal_plot_mouse_release(); ++ sigc::signal3<void,int,int,GdkEventMotion*> signal_plot_mouse_move(); + + void set_selection(const Rectangle &r); + Rectangle get_selection() { return select_; } +diff -ur plotmm-0.1.2-old/plotmm/scale.h plotmm-0.1.2/plotmm/scale.h +--- plotmm-0.1.2-old/plotmm/scale.h 2004-03-05 16:25:43.000000000 +0100 ++++ plotmm-0.1.2/plotmm/scale.h 2008-07-25 00:25:30.000000000 +0200 +@@ -133,7 +133,7 @@ + /*! This signal is thrown whenever the scale is enabled or disabled + * \sa set_enabled, enabled + */ +- SigC::Signal1<void,bool> signal_enabled; ++ sigc::signal1<void,bool> signal_enabled; + + protected: + virtual void on_realize(); diff --git a/sci-libs/plotmm/metadata.xml b/sci-libs/plotmm/metadata.xml new file mode 100644 index 000000000000..6907b0a4da6b --- /dev/null +++ b/sci-libs/plotmm/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <!-- maintainer-needed --> + <upstream> + <remote-id type="sourceforge">plotmm</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/plotmm/plotmm-0.1.2.ebuild b/sci-libs/plotmm/plotmm-0.1.2.ebuild new file mode 100644 index 000000000000..e6a0447c3f7f --- /dev/null +++ b/sci-libs/plotmm/plotmm-0.1.2.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 +inherit eutils flag-o-matic + +DESCRIPTION="Plot widget for GTKmm" +HOMEPAGE="http://plotmm.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~ppc ~x86" +IUSE="doc examples" + +RDEPEND="dev-cpp/gtkmm:2.4" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +# NOTES: +# somewhat, there is a dep on libsigc++ but it's much more via gtkmm + +src_prepare() { + epatch "${FILESDIR}/${P}-libsigc++-2.2.patch" + + if ! use examples; then + sed -i -e "s:examples::" Makefile.in || die "sed failed" + fi +} + +src_configure() { + append-cxxflags -std=c++11 + econf \ + --disable-maintainer-mode \ + --enable-fast-install \ + --disable-libtool-lock +} + +src_install() { + default + + if use doc; then + dohtml -r doc/html/* || die "dohtml failed" + fi + + if use examples; then + # rename installed bin files + mv "${D}"/usr/bin/curves "${D}"/usr/bin/${PN}-curves || die "mv failed" + mv "${D}"/usr/bin/simple "${D}"/usr/bin/${PN}-simple || die 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b64dfe179d249df7b05cf19ad0a8d6e8ba622b8de90127e8002f22ff3f90c5819e1177cd3f01492b25917f39ac3f2d4e2efa46bf75108626212dc6db7cf1b483 diff --git a/sci-libs/plplot/files/plplot-5.11.0-multiarch.patch b/sci-libs/plplot/files/plplot-5.11.0-multiarch.patch new file mode 100644 index 000000000000..cb6f7d01cf16 --- /dev/null +++ b/sci-libs/plplot/files/plplot-5.11.0-multiarch.patch @@ -0,0 +1,60 @@ + examples/c++/Makefile.examples.in | 3 --- + examples/c/Makefile.examples.in | 2 -- + examples/f95/Makefile.examples.in | 2 -- + examples/tk/Makefile.examples.in | 2 -- + 4 files changed, 9 deletions(-) + +diff --git a/examples/c++/Makefile.examples.in b/examples/c++/Makefile.examples.in +index bb067e7..176706b 100644 +--- a/examples/c++/Makefile.examples.in ++++ b/examples/c++/Makefile.examples.in +@@ -25,10 +25,7 @@ SHELL = @SH_EXECUTABLE@ + CXX = @CXX@ + EXEEXT = @EXEEXT@ + +-PKG_CONFIG_ENV = @PKG_CONFIG_ENV@ +-RPATHCMD = @RPATHCMD@ + @qt_gui_true@QT_MOC_EXECUTABLE = @QT_MOC_EXECUTABLE@ +-@qt_gui_true@qt_RPATHCMD = @qt_RPATHCMD@ + + @wxwidgets_true@PLPLOTWXWIDGETS_EXECUTABLES_list = \ + @wxwidgets_true@ wxPLplotDemo$(EXEEXT) +diff --git a/examples/c/Makefile.examples.in b/examples/c/Makefile.examples.in +index bc47762..56d1f49 100644 +--- a/examples/c/Makefile.examples.in ++++ b/examples/c/Makefile.examples.in +@@ -25,8 +25,6 @@ SHELL = @SH_EXECUTABLE@ + CC = @CC@ + EXEEXT = @EXEEXT@ + +-PKG_CONFIG_ENV = @PKG_CONFIG_ENV@ +-RPATHCMD = @RPATHCMD@ + + @gcw_true@PLPLOTCANVAS_EXECUTABLES_list = \ + @gcw_true@ plplotcanvas_demo$(EXEEXT) \ +diff --git a/examples/f95/Makefile.examples.in b/examples/f95/Makefile.examples.in +index 29631b7..32823d6 100644 +--- a/examples/f95/Makefile.examples.in ++++ b/examples/f95/Makefile.examples.in +@@ -25,8 +25,6 @@ SHELL = @SH_EXECUTABLE@ + F95 = @FC@ + EXEEXT = @EXEEXT@ + +-PKG_CONFIG_ENV = @PKG_CONFIG_ENV@ +-RPATHCMD = @RPATHCMD@ + + EXECUTABLES_list = \ + x00f$(EXEEXT) \ +diff --git a/examples/tk/Makefile.examples.in b/examples/tk/Makefile.examples.in +index 98407fa..c15c94a 100644 +--- a/examples/tk/Makefile.examples.in ++++ b/examples/tk/Makefile.examples.in +@@ -24,8 +24,6 @@ SHELL = @SH_EXECUTABLE@ + CC = @CC@ + EXEEXT = @EXEEXT@ + +-PKG_CONFIG_ENV = @PKG_CONFIG_ENV@ +-plplottcltk_Main_RPATHCMD = @plplottcltk_Main_RPATHCMD@ + + EXECUTABLES_list = xtk01$(EXEEXT) + # Second and fourth examples depend on itk. diff --git a/sci-libs/plplot/files/plplot-5.11.0-ocaml.patch b/sci-libs/plplot/files/plplot-5.11.0-ocaml.patch new file mode 100644 index 000000000000..32841825f0de --- /dev/null +++ b/sci-libs/plplot/files/plplot-5.11.0-ocaml.patch @@ -0,0 +1,40 @@ + bindings/ocaml/CMakeLists.txt | 4 ++-- + bindings/ocaml/plcairo/CMakeLists.txt | 4 ++-- + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/bindings/ocaml/CMakeLists.txt b/bindings/ocaml/CMakeLists.txt +index 93d073a..d31a64f 100644 +--- a/bindings/ocaml/CMakeLists.txt ++++ b/bindings/ocaml/CMakeLists.txt +@@ -154,11 +154,11 @@ if(ENABLE_ocaml) + DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/plplot.cmo + ) + +- # ocamlc -a -custom builds a *.cma library from *.cmo ++ # ocamlc -a builds a *.cma library from *.cmo + add_custom_command( + OUTPUT + ${CMAKE_CURRENT_BINARY_DIR}/plplot.cma +- COMMAND ${OCAMLC} -a -custom -o ${CMAKE_CURRENT_BINARY_DIR}/plplot.cma ${CMAKE_CURRENT_BINARY_DIR}/plplot_core.cmo ${CMAKE_CURRENT_BINARY_DIR}/plplot.cmo -dllib -lplplot_stubs -ccopt -L${CMAKE_CURRENT_BINARY_DIR} -cclib -lplplot_stubs -ccopt -L${CAMLIDL_LIB_DIR} -cclib -lcamlidl -ccopt -L${CMAKE_BINARY_DIR}/src -cclib -lplplot -dllpath ${CMAKE_BINARY_DIR}/src ${ocaml_STATIC_FLAGS} ++ COMMAND ${OCAMLC} -a -o ${CMAKE_CURRENT_BINARY_DIR}/plplot.cma ${CMAKE_CURRENT_BINARY_DIR}/plplot_core.cmo ${CMAKE_CURRENT_BINARY_DIR}/plplot.cmo -dllib -lplplot_stubs -ccopt -L${CMAKE_CURRENT_BINARY_DIR} -cclib -lplplot_stubs -ccopt -L${CAMLIDL_LIB_DIR} -cclib -lcamlidl -ccopt -L${CMAKE_BINARY_DIR}/src -cclib -lplplot -dllpath ${CMAKE_BINARY_DIR}/src ${ocaml_STATIC_FLAGS} + DEPENDS + ${CMAKE_CURRENT_BINARY_DIR}/plplot_core.cmo + ${CMAKE_CURRENT_BINARY_DIR}/plplot.cmo +diff --git a/bindings/ocaml/plcairo/CMakeLists.txt b/bindings/ocaml/plcairo/CMakeLists.txt +index c4b4a41..ce1dc92 100644 +--- a/bindings/ocaml/plcairo/CMakeLists.txt ++++ b/bindings/ocaml/plcairo/CMakeLists.txt +@@ -84,11 +84,11 @@ if(ENABLE_ocaml AND OCAML_HAS_CAIRO) + DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/plcairo.cmo + ) + +- # ocamlc -a -custom builds a *.cma library from *.cmo ++ # ocamlc -a builds a *.cma library from *.cmo + add_custom_command( + OUTPUT + ${CMAKE_CURRENT_BINARY_DIR}/plcairo.cma +- COMMAND ${OCAMLC} -a -custom -o ${CMAKE_CURRENT_BINARY_DIR}/plcairo.cma -I ${PATH_TO_PLPLOT_CMA} plplot.cma ${CMAKE_CURRENT_BINARY_DIR}/plcairo.cmo -dllib -lplcairo_stubs -ccopt -L${CMAKE_CURRENT_BINARY_DIR} -cclib -lplcairo_stubs -ccopt -L${CMAKE_BINARY_DIR}/src -cclib -lplplot -dllpath ${CMAKE_BINARY_DIR}/src ++ COMMAND ${OCAMLC} -a -o ${CMAKE_CURRENT_BINARY_DIR}/plcairo.cma -I ${PATH_TO_PLPLOT_CMA} plplot.cma ${CMAKE_CURRENT_BINARY_DIR}/plcairo.cmo -dllib -lplcairo_stubs -ccopt -L${CMAKE_CURRENT_BINARY_DIR} -cclib -lplcairo_stubs -ccopt -L${CMAKE_BINARY_DIR}/src -cclib -lplplot -dllpath ${CMAKE_BINARY_DIR}/src + DEPENDS + ${CMAKE_CURRENT_BINARY_DIR}/plcairo.cmo + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} diff --git a/sci-libs/plplot/files/plplot-5.11.0-octave.patch b/sci-libs/plplot/files/plplot-5.11.0-octave.patch new file mode 100644 index 000000000000..a2a41c96da7a --- /dev/null +++ b/sci-libs/plplot/files/plplot-5.11.0-octave.patch @@ -0,0 +1,16 @@ + plplot_test/test_octave.sh.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/plplot_test/test_octave.sh.in b/plplot_test/test_octave.sh.in +index 8a50d8b..8eb35fc 100755 +--- a/plplot_test/test_octave.sh.in ++++ b/plplot_test/test_octave.sh.in +@@ -35,7 +35,7 @@ echo "$TOPDIR" + export LD_LIBRARY_PATH="$TOPDIR"/src:"$TOPDIR"/lib/csa:"$TOPDIR"/lib/nn + + # Launch an Octave script that exercises all the demos +-$octave -f -q <<EOF 2> test.error ++$octave -f -q $octaveopts -p "$octavedir" <<EOF 2> test.error + + # Disable warnings about shadowed functions - PLplot is _supposed_ to shadow the core functions + warning("off","Octave:shadowed-function"); diff --git a/sci-libs/plplot/files/plplot-5.12.0-java-install-path.patch b/sci-libs/plplot/files/plplot-5.12.0-java-install-path.patch new file mode 100644 index 000000000000..2c053a2b1669 --- /dev/null +++ b/sci-libs/plplot/files/plplot-5.12.0-java-install-path.patch @@ -0,0 +1,13 @@ +Java libs are installed into an already prefixed path. + +--- a/bindings/java/CMakeLists.txt ++++ b/bindings/java/CMakeLists.txt +@@ -189,7 +189,7 @@ + ) + endif(APPLE) + +- install(TARGETS plplotjavac_wrap LIBRARY DESTINATION ${JAVAWRAPPER_HARDDIR}) ++ install(TARGETS plplotjavac_wrap LIBRARY DESTINATION ${JAVAWRAPPER_DIR}) + + set(JAVA_CLASSES) + foreach( srcfile ${JAVA_FILES_FULL} ) diff --git a/sci-libs/plplot/files/plplot-5.12.0-multiarch.patch b/sci-libs/plplot/files/plplot-5.12.0-multiarch.patch new file mode 100644 index 000000000000..63e92f5aa5ab --- /dev/null +++ b/sci-libs/plplot/files/plplot-5.12.0-multiarch.patch @@ -0,0 +1,49 @@ +--- a/examples/c/Makefile.examples.in ++++ b/examples/c/Makefile.examples.in +@@ -25,9 +25,6 @@ + CC = @CC@ + EXEEXT = @EXEEXT@ + +-PKG_CONFIG_ENV = @PKG_CONFIG_ENV@ +-RPATHCMD = @RPATHCMD@ +- + @extXdrawable_true@extXdrawable_EXECUTABLES_list = \ + @extXdrawable_true@ extXdrawable_demo$(EXEEXT) + +--- a/examples/c++/Makefile.examples.in ++++ b/examples/c++/Makefile.examples.in +@@ -25,10 +25,7 @@ + CXX = @CXX@ + EXEEXT = @EXEEXT@ + +-PKG_CONFIG_ENV = @PKG_CONFIG_ENV@ +-RPATHCMD = @RPATHCMD@ + @qt_gui_true@QT_MOC_EXECUTABLE = @QT_MOC_EXECUTABLE@ +-@qt_gui_true@qt_RPATHCMD = @qt_RPATHCMD@ + + @wxwidgets_true@PLPLOTWXWIDGETS_EXECUTABLES_list = \ + @wxwidgets_true@ @wxdemo_name@$(EXEEXT) +--- a/examples/f95/Makefile.examples.in ++++ b/examples/f95/Makefile.examples.in +@@ -25,9 +25,6 @@ + F95 = @FC@ + EXEEXT = @EXEEXT@ + +-PKG_CONFIG_ENV = @PKG_CONFIG_ENV@ +-FORTRAN_RPATHCMD = @FORTRAN_RPATHCMD@ +- + EXECUTABLES_list = \ + x00f$(EXEEXT) \ + x01f$(EXEEXT) \ +--- a/examples/tk/Makefile.examples.in ++++ b/examples/tk/Makefile.examples.in +@@ -24,9 +24,6 @@ + CC = @CC@ + EXEEXT = @EXEEXT@ + +-PKG_CONFIG_ENV = @PKG_CONFIG_ENV@ +-plplottcltk_Main_RPATHCMD = @plplottcltk_Main_RPATHCMD@ +- + EXECUTABLES_list = xtk01$(EXEEXT) + # Second and fourth examples depend on itk. + @itk_true@itk_EXECUTABLES_list = xtk02$(EXEEXT) xtk04$(EXEEXT) diff --git a/sci-libs/plplot/files/plplot-5.12.0-ocaml-remove-rpath.patch b/sci-libs/plplot/files/plplot-5.12.0-ocaml-remove-rpath.patch new file mode 100644 index 000000000000..2d18c79736fa --- /dev/null +++ b/sci-libs/plplot/files/plplot-5.12.0-ocaml-remove-rpath.patch @@ -0,0 +1,34 @@ +Fix OCaml's asinine RPATH inserting behaviour. + +--- a/bindings/ocaml/CMakeLists.txt ++++ b/bindings/ocaml/CMakeLists.txt +@@ -97,6 +97,20 @@ + + # ocamlc -c compiles *.c into *.o. + # ocamlmklib links *.o into *.so and *.a ++ ++ # ocamlmklib implicits inserts RPATHs if it is provided with an absolute path to -L, ++ # which is absolutely unacceptable and presents a massive security hazard. The ++ # following statements convert the absolute paths to relative ones to fix this. ++ # See also: ++ # https://caml.inria.fr/mantis/view.php?id=5943 ++ if(CMAKE_SKIP_RPATH) ++ file(RELATIVE_PATH CAMLIDL_LINK_LIB_DIR ${CMAKE_CURRENT_BINARY_DIR} ${CAMLIDL_LIB_DIR}) ++ file(RELATIVE_PATH CMAKE_LINK_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_BINARY_DIR}) ++ else(CMAKE_SKIP_RPATH) ++ set(CAMLIDL_LINK_LIB_DIR ${CAMLIDL_LIB_DIR}) ++ set(CMAKE_LINK_BINARY_DIR ${CMAKE_BINARY_DIR}) ++ endif(CMAKE_SKIP_RPATH) ++ + add_custom_command( + OUTPUT + ${CMAKE_CURRENT_BINARY_DIR}/plplot_core_stubs.o +@@ -105,7 +119,7 @@ + ${CMAKE_CURRENT_BINARY_DIR}/libplplot_stubs.a + COMMAND ${OCAMLC} -ccopt -I${CAMLIDL_LIB_DIR} -c ${CMAKE_CURRENT_BINARY_DIR}/plplot_core_stubs.c + COMMAND ${OCAMLC} -ccopt -I${CMAKE_SOURCE_DIR}/include -ccopt -I${CMAKE_BINARY_DIR}/include -ccopt -I${CMAKE_SOURCE_DIR}/lib/qsastime -ccopt -I${CMAKE_BINARY_DIR} -ccopt -I${CAMLIDL_LIB_DIR} -ccopt -DPLPLOT_HAVE_CONFIG_H -c ${CMAKE_CURRENT_SOURCE_DIR}/plplot_impl.c +- COMMAND ${OCAMLMKLIB} -o plplot_stubs -L${CAMLIDL_LIB_DIR} -lcamlidl -L${CMAKE_BINARY_DIR}/src -lplplot ${CMAKE_CURRENT_BINARY_DIR}/plplot_core_stubs.o ${CMAKE_CURRENT_BINARY_DIR}/plplot_impl.o ${ocaml_STATIC_FLAGS} ++ COMMAND ${OCAMLMKLIB} -o plplot_stubs -L${CAMLIDL_LINK_LIB_DIR} -lcamlidl -L${CMAKE_LINK_BINARY_DIR}/src -lplplot ${CMAKE_CURRENT_BINARY_DIR}/plplot_core_stubs.o ${CMAKE_CURRENT_BINARY_DIR}/plplot_impl.o ${ocaml_STATIC_FLAGS} + DEPENDS + ${CMAKE_CURRENT_BINARY_DIR}/plplot_core_stubs.c + ${CMAKE_CURRENT_SOURCE_DIR}/plplot_impl.c diff --git a/sci-libs/plplot/files/plplot-5.9.6-python.patch b/sci-libs/plplot/files/plplot-5.9.6-python.patch new file mode 100644 index 000000000000..d62ece2ec416 --- /dev/null +++ b/sci-libs/plplot/files/plplot-5.9.6-python.patch @@ -0,0 +1,13 @@ +diff --git a/examples/python/CMakeLists.txt b/examples/python/CMakeLists.txt +index 7599164..8457490 100644 +--- a/examples/python/CMakeLists.txt ++++ b/examples/python/CMakeLists.txt +@@ -214,7 +214,7 @@ if(CORE_BUILD) + @ONLY + ) + +- set(python_location1 ${PYTHON_INSTDIR}) ++ set(python_location1) + set(python_location2) + set(python_location3) + set(python_location4) diff --git a/sci-libs/plplot/metadata.xml b/sci-libs/plplot/metadata.xml new file mode 100644 index 000000000000..7b64efe140a1 --- /dev/null +++ b/sci-libs/plplot/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en">PLplot is a library of functions that are useful for making scientific plots. It can be used from within compiled languages such as C, C++, FORTRAN and Java, as well as interactively from interpreted languages such as Octave, Python, Perl and Tcl. It is capable of producing standard x-y plots, semilog plots, log-log plots, contour plots, 3D surface plots, mesh plots, bar charts and pie charts. Multiple graphs may be composited, and it also supports a large variety of output file devices such as Postscript, PNG, JPEG, LaTeX and others. It is also possible to to use interactive devices such as xwin, tk and xterm as output devices. PLplot also offers support for extended characters inculding the Greek alphabet and a host of mathematical symbols.</longdescription> + <use> + <flag name="dynamic">Build with dynamic drivers</flag> + <flag name="octave">Add bindings for <pkg>sci-mathematics/octave</pkg></flag> + <flag name="pdl">Add bindings for <pkg>dev-perl/PDL</pkg></flag> + <flag name="qhull">Add bindings for <pkg>media-libs/qhull</pkg></flag> + <flag name="shapefile">Enable support for ESRI shapefiles</flag> + </use> + <upstream> + <remote-id type="sourceforge">plplot</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/plplot/plplot-5.11.1-r1.ebuild b/sci-libs/plplot/plplot-5.11.1-r1.ebuild new file mode 100644 index 000000000000..a46a090713e9 --- /dev/null +++ b/sci-libs/plplot/plplot-5.11.1-r1.ebuild @@ -0,0 +1,249 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +WX_GTK_VER="3.0" +FORTRAN_NEEDED=fortran +PYTHON_COMPAT=( python2_7 ) +VIRTUALX_REQUIRED=test + +inherit eutils fortran-2 cmake-utils python-single-r1 toolchain-funcs \ + virtualx wxwidgets java-pkg-opt-2 multilib + +DESCRIPTION="Multi-language scientific plotting library" +HOMEPAGE="http://plplot.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0/12" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="cairo cxx doc +dynamic examples fortran gd java jpeg latex lua + ocaml octave pdf pdl png python qhull qt4 shapefile svg tcl test + threads tk truetype wxwidgets X" + +RDEPEND=" + cairo? ( x11-libs/cairo:0=[svg?,X?] ) + gd? ( media-libs/gd:2=[jpeg?,png?] ) + java? ( >=virtual/jre-1.5:* ) + latex? ( + app-text/ghostscript-gpl + virtual/latex-base + ) + lua? ( dev-lang/lua:0= ) + ocaml? ( + dev-lang/ocaml + dev-ml/camlidl + cairo? ( dev-ml/cairo-ocaml[gtk] ) + ) + octave? ( sci-mathematics/octave:0= ) + pdf? ( media-libs/libharu:0= ) + pdl? ( + dev-perl/PDL + dev-perl/XML-DOM + ) + python? ( + ${PYTHON_DEPS} + dev-python/numpy[${PYTHON_USEDEP}] + qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] ) + ) + qhull? ( media-libs/qhull:0= ) + qt4? ( + dev-qt/qtgui:4= + dev-qt/qtsvg:4= + ) + shapefile? ( sci-libs/shapelib:0= ) + tcl? ( + dev-lang/tcl:0= + dev-tcltk/itcl:0= + tk? ( + dev-lang/tk:0= + dev-tcltk/itk + ) + ) + truetype? ( + media-fonts/freefont + media-libs/lasi:0= + gd? ( media-libs/gd:2=[truetype] ) + ) + wxwidgets? ( + x11-libs/wxGTK:${WX_GTK_VER}=[X] + x11-libs/agg:0=[truetype?] + ) + X? ( + x11-libs/libX11:0= + x11-libs/libXau:0= + x11-libs/libXdmcp:0= + )" + +DEPEND="${RDEPEND} + virtual/pkgconfig + java? ( + >=virtual/jdk-1.5 + dev-lang/swig + ) + ocaml? ( dev-ml/findlib ) + octave? ( >=dev-lang/swig-2.0.12 ) + python? ( dev-lang/swig ) + test? ( + media-fonts/font-misc-misc + media-fonts/font-cursor-misc + )" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} ) qt4? ( dynamic ) test? ( latex ) tk? ( tcl )" + +PATCHES=( + "${FILESDIR}"/${PN}-5.9.6-python.patch + "${FILESDIR}"/${PN}-5.11.0-ocaml.patch + "${FILESDIR}"/${PN}-5.11.0-octave.patch + "${FILESDIR}"/${PN}-5.11.0-multiarch.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup + java-pkg-opt-2_pkg_setup + fortran-2_pkg_setup +} + +src_prepare() { + use wxwidgets && need-wxwidgets unicode + cmake-utils_src_prepare + # avoid installing license + sed -i -e '/COPYING.LIB/d' CMakeLists.txt || die + # prexify hard-coded /usr/include in cmake modules + sed -i \ + -e "s:/usr/include:${EPREFIX}/usr/include:g" \ + -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:/usr/share:${EPREFIX}/usr/share:g" \ + cmake/modules/*.cmake || die + # change default install directories for doc and examples + sed -i \ + -e 's:${DATA_DIR}/examples:${DOC_DIR}/examples:g' \ + $(find "${S}" -name CMakeLists.txt) || die + sed -i \ + -e 's:${VERSION}::g' \ + -e "s:doc/\${PACKAGE}:doc/${PF}:" \ + cmake/modules/instdirs.cmake || die + java-utils-2_src_prepare +} + +src_configure() { + # don't build doc, it brings a whole lot of horrible dependencies + + # -DPLPLOT_USE_QT5=ON + # Not recomended by upstream, check next release + + local mycmakeargs=( + -DPLD_plmeta=ON + -DPLD_cgm=ON + -DTEST_DYNDRIVERS=OFF + -DCMAKE_INSTALL_LIBDIR="${EPREFIX}/usr/$(get_libdir)" + -DENABLE_ada=OFF + -DENABLE_d=OFF + -DBUILD_DVI=OFF + -DDOX_DOC=OFF + -DBUILD_DOC=OFF + -DUSE_RPATH=OFF + -DPLD_wxpng=OFF + $(cmake-utils_use doc PREBUILT_DOC) + $(cmake-utils_use_build test) + $(cmake-utils_use_has python NUMPY) + $(cmake-utils_use_has shapefile SHAPELIB) + $(cmake-utils_use_with truetype FREETYPE) + $(cmake-utils_use_enable cxx) + $(cmake-utils_use_enable dynamic DYNDRIVERS) + $(cmake-utils_use_enable fortran f77) + $(cmake-utils_use_enable java) + $(cmake-utils_use_enable lua) + $(cmake-utils_use_enable ocaml) + $(cmake-utils_use_enable octave) + $(cmake-utils_use_enable pdl) + $(cmake-utils_use_enable python) + $(cmake-utils_use_enable qt4 qt) + $(cmake-utils_use_enable tcl) + $(cmake-utils_use_enable tcl itcl) + $(cmake-utils_use_enable tk) + $(cmake-utils_use_enable tk itk) + $(cmake-utils_use_enable wxwidgets) + $(cmake-utils_use threads PL_HAVE_PTHREAD) + $(cmake-utils_use qhull PL_HAVE_QHULL) + $(cmake-utils_use qt4 PLD_aqt) + $(cmake-utils_use qt4 PLD_bmpqt) + $(cmake-utils_use qt4 PLD_epsqt) + $(cmake-utils_use qt4 PLD_extqt) + $(cmake-utils_use qt4 PLD_jpgqt) + $(cmake-utils_use qt4 PLD_memqt) + $(cmake-utils_use qt4 PLD_pdfqt) + $(cmake-utils_use qt4 PLD_pngqt) + $(cmake-utils_use qt4 PLD_ppmqt) + $(cmake-utils_use qt4 PLD_svgqt) + $(cmake-utils_use qt4 PLD_qtwidget) + $(cmake-utils_use qt4 PLD_tiffqt) + $(cmake-utils_use cairo PLD_extcairo) + $(cmake-utils_use cairo PLD_memcairo) + $(cmake-utils_use cairo PLD_pdfcairo) + $(cmake-utils_use cairo PLD_pngcairo) + $(cmake-utils_use cairo PLD_pscairo) + $(cmake-utils_use cairo PLD_svgcairo) + $(cmake-utils_use cairo PLD_wincairo) + $(cmake-utils_use cairo PLD_xcairo) + $(usex cairo "" "-DDEFAULT_NO_CAIRO_DEVICES=ON") + $(cmake-utils_use tk PLD_ntk) + $(cmake-utils_use tk PLD_tk) + $(cmake-utils_use tk PLD_tkwin) + $(cmake-utils_use gd PLD_gif) + $(cmake-utils_use gd PLD_jpeg) + $(cmake-utils_use gd PLD_png) + $(cmake-utils_use pdf PLD_pdf) + $(cmake-utils_use latex PLD_ps) + $(cmake-utils_use latex PLD_pstex) + $(cmake-utils_use truetype PLD_psttf) + $(cmake-utils_use svg PLD_svg) + $(cmake-utils_use wxwidgets PLD_wxwidgets) + $(cmake-utils_use X PLD_xwin) + ) + + [[ $(tc-getFC) != *g77 ]] && \ + mycmakeargs+=( + $(cmake-utils_use_enable fortran f95) + ) + + use truetype && mycmakeargs+=( + -DPL_FREETYPE_FONT_PATH:PATH="${EPREFIX}/usr/share/fonts/freefont" + ) + use shapefile && mycmakeargs+=( + -DSHAPELIB_INCLUDE_DIR="${EPREFIX}/usr/include/libshp" + ) + use ocaml && mycmakeargs+=( + -DOCAML_INSTALL_DIR="$(ocamlc -where)" + ) + use python && mycmakeargs+=( + $(cmake-utils_use_enable qt4 pyqt4) + ) + + cmake-utils_src_configure + + # clean up bloated pkg-config files (help linking properly on prefix) + sed -i \ + -e "/Cflags/s:-I\(${EPREFIX}\|\)/usr/include[[:space:]]::g" \ + -e "/Libs/s:-L\(${EPREFIX}\|\)/usr/lib\(64\|\)[[:space:]]::g" \ + -e "s:${LDFLAGS}::g" \ + "${BUILD_DIR}"/pkgcfg/*pc || die +} + +src_test() { + virtx cmake-utils_src_test +} + +src_install() { + cmake-utils_src_install + if use examples; then + docompress -x /usr/share/doc/${PF}/examples + else + rm -r "${ED}"/usr/share/doc/${PF}/examples || die + fi + if use java; then + java-pkg_dojar "${BUILD_DIR}"/examples/java/${PN}.jar + java-pkg_regso "${ED}"/usr/$(get_libdir)/jni/plplotjavac_wrap.so + fi +} diff --git a/sci-libs/plplot/plplot-5.12.0-r1.ebuild b/sci-libs/plplot/plplot-5.12.0-r1.ebuild new file mode 100644 index 000000000000..a8582c6ed658 --- /dev/null +++ b/sci-libs/plplot/plplot-5.12.0-r1.ebuild @@ -0,0 +1,282 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +WX_GTK_VER=3.0-gtk3 +FORTRAN_NEEDED=fortran +FORTRAN_STANDARD=95 +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils flag-o-matic fortran-2 java-pkg-opt-2 python-single-r1 toolchain-funcs virtualx wxwidgets + +DESCRIPTION="Multi-language scientific plotting library" +HOMEPAGE="http://plplot.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="LGPL-2" +SLOT="0/14" # SONAME of libplplot.so +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cairo cxx doc +dynamic examples fortran gd java jpeg latex lua ocaml octave pdf + pdl png python qhull qt5 shapefile svg tcl test threads tk truetype wxwidgets X" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} ) qt5? ( dynamic ) test? ( latex ) tk? ( tcl )" +RESTRICT="octave? ( test )" + +RDEPEND=" + cairo? ( x11-libs/cairo:0=[svg?,X] ) + gd? ( media-libs/gd:2=[jpeg?,png?] ) + java? ( >=virtual/jre-1.5:* ) + latex? ( + app-text/ghostscript-gpl + virtual/latex-base + ) + lua? ( dev-lang/lua:0= ) + ocaml? ( + dev-lang/ocaml + dev-ml/camlidl + cairo? ( dev-ml/cairo-ocaml[gtk] ) + ) + octave? ( sci-mathematics/octave:0= ) + pdf? ( media-libs/libharu:0= ) + pdl? ( + dev-perl/PDL + dev-perl/XML-DOM + ) + python? ( + ${PYTHON_DEPS} + dev-python/numpy[${PYTHON_USEDEP}] + qt5? ( dev-python/PyQt5[${PYTHON_USEDEP}] ) + ) + qhull? ( media-libs/qhull:0= ) + qt5? ( + dev-qt/qtgui:5 + dev-qt/qtsvg:5 + dev-qt/qtprintsupport:5 + ) + shapefile? ( sci-libs/shapelib:0= ) + tcl? ( + dev-lang/tcl:0= + dev-tcltk/itcl:0= + tk? ( + dev-lang/tk:0= + dev-tcltk/itk + ) + ) + truetype? ( + media-fonts/freefont + media-libs/lasi:0= + gd? ( media-libs/gd:2=[truetype] ) + ) + wxwidgets? ( + x11-libs/wxGTK:${WX_GTK_VER}=[X] + x11-libs/agg:0=[truetype?] + ) + X? ( + x11-libs/libX11:0= + x11-libs/libXau:0= + x11-libs/libXdmcp:0= + )" + +DEPEND="${RDEPEND} + virtual/pkgconfig + java? ( + >=virtual/jdk-1.5 + dev-lang/swig + ) + ocaml? ( dev-ml/findlib ) + octave? ( >=dev-lang/swig-3.0.12 ) + python? ( dev-lang/swig ) + test? ( + media-fonts/font-misc-misc + media-fonts/font-cursor-misc + )" + +PATCHES=( + "${FILESDIR}"/${PN}-5.9.6-python.patch + "${FILESDIR}"/${PN}-5.11.0-octave.patch + "${FILESDIR}"/${PN}-5.12.0-multiarch.patch + "${FILESDIR}"/${PN}-5.12.0-java-install-path.patch + "${FILESDIR}"/${PN}-5.12.0-ocaml-remove-rpath.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup + use java && java-pkg-opt-2_pkg_setup + use fortran && fortran-2_pkg_setup +} + +src_prepare() { + use wxwidgets && need-wxwidgets unicode + cmake-utils_src_prepare + + # avoid installing license + sed -i -e '/COPYING.LIB/d' CMakeLists.txt || die + + # prexify hard-coded /usr/include in cmake modules + sed -i \ + -e "s:/usr/include:${EPREFIX}/usr/include:g" \ + -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:/usr/share:${EPREFIX}/usr/share:g" \ + cmake/modules/*.cmake || die + + # change default install directories for doc and examples + local f + while IFS="" read -d $'\0' -r f; do + sed -i -e 's:${DATA_DIR}/examples:${DOC_DIR}/examples:g' "${f}" || die + done < <(find "${S}" -name CMakeLists.txt -print0) + + sed -i \ + -e 's:${VERSION}::g' \ + -e "s:doc/\${PACKAGE}:doc/${PF}:" \ + cmake/modules/instdirs.cmake || die + + java-utils-2_src_prepare +} + +src_configure() { + # - don't build doc, it pulls in a whole stack of horrible dependencies + # - Bindings: + # * Ada is a mess in Gentoo, don't use + # * D has been removed from Gentoo, don't use + # * Qt4 has been disabled, as it is deprecated and unsupported upstream + # - DPLD_* drivers need to use ON/OFF instead of the usex defaults yes/no, as + # the testsuite performs a string comparison to determine which tests to run + + # Octave bindings now require C++11 support, #609980 + append-cxxflags -std=c++11 + + local mycmakeargs=( + # The build system does not honour CMAKE_INSTALL_LIBDIR as a + # relative dir, which is against the spirit of GNUInstallDirs, #610066 + -DCMAKE_INSTALL_LIBDIR="${EPREFIX}"/usr/$(get_libdir) + + ## Features + -DBUILD_DOC=OFF + -DBUILD_DOX_DOC=OFF + -DCMAKE_SKIP_RPATH=ON + -DPREBUILT_DOC=$(usex doc) + -DHAVE_SHAPELIB=$(usex shapefile) + -DWITH_FREETYPE=$(usex truetype) + -DPL_HAVE_PTHREAD=$(usex threads) + -DPL_HAVE_QHULL=$(usex qhull) + -DPLPLOT_USE_QT5=$(usex qt5) + + ## Tests + -DTEST_DYNDRIVERS=OFF + -DBUILD_TEST=$(usex test) + + ## Bindings + -DENABLE_ada=OFF + -DENABLE_d=OFF + -DENABLE_ocaml=$(usex ocaml) + -DENABLE_pyqt4=OFF + -DENABLE_cxx=$(usex cxx) + -DENABLE_DYNDRIVERS=$(usex dynamic) + -DENABLE_f95=$(usex fortran) + -DENABLE_java=$(usex java) + -DENABLE_lua=$(usex lua) + -DTRY_OCTAVE4=$(usex octave) + -DENABLE_octave=$(usex octave) + -DENABLE_pdl=$(usex pdl) + -DENABLE_python=$(usex python) + -DENABLE_qt=$(usex qt5) + -DENABLE_tcl=$(usex tcl) + -DENABLE_itcl=$(usex tcl) + -DENABLE_tk=$(usex tk) + -DENABLE_itk=$(usex tk) + -DENABLE_wxwidgets=$(usex wxwidgets) + + ## Drivers + -DPLD_cgm=OFF + -DPLD_gif=OFF + -DPLD_jpeg=OFF + -DPLD_plmeta=OFF + -DPLD_png=OFF + -DPLD_pstex=OFF + -DPLD_wxpng=OFF + -DPLD_mem=ON + -DPLD_null=ON + -DPLD_wingcc=ON + # Cairo + $(usex cairo "" "-DDEFAULT_NO_CAIRO_DEVICES=ON") + -DPLD_epscairo=$(usex cairo ON OFF) + -DPLD_extcairo=$(usex cairo ON OFF) + -DPLD_memcairo=$(usex cairo ON OFF) + -DPLD_pdfcairo=$(usex cairo ON OFF) + -DPLD_pngcairo=$(usex cairo ON OFF) + -DPLD_pscairo=$(usex cairo ON OFF) + -DPLD_svgcairo=$(usex cairo ON OFF) + -DPLD_xcairo=$(usex cairo ON OFF) + # LaTeX + -DPLD_ps=$(usex latex ON OFF) + # PDF + -DPLD_pdf=$(usex pdf ON OFF) + # Qt + -DPLD_aqt=$(usex qt5 ON OFF) + -DPLD_bmpqt=$(usex qt5 ON OFF) + -DPLD_epsqt=$(usex qt5 ON OFF) + -DPLD_extqt=$(usex qt5 ON OFF) + -DPLD_jpgqt=$(usex qt5 ON OFF) + -DPLD_memqt=$(usex qt5 ON OFF) + -DPLD_pdfqt=$(usex qt5 ON OFF) + -DPLD_pngqt=$(usex qt5 ON OFF) + -DPLD_ppmqt=$(usex qt5 ON OFF) + -DPLD_qtwidget=$(usex qt5 ON OFF) + -DPLD_svgqt=$(usex qt5 ON OFF) + -DPLD_tiffqt=$(usex qt5 ON OFF) + # SVG + -DPLD_svg=$(usex svg ON OFF) + # Tk + -DPLD_ntk=$(usex tk ON OFF) + -DPLD_tk=$(usex tk ON OFF) + -DPLD_tkwin=$(usex tk ON OFF) + # Truetype + -DPLD_psttf=$(usex truetype ON OFF) + # Wx + -DPLD_wxwidgets=$(usex wxwidgets ON OFF) + # X + -DPLD_xfig=$(usex X ON OFF) + -DPLD_xwin=$(usex X ON OFF) + ) + + use truetype && mycmakeargs+=( + -DPL_FREETYPE_FONT_PATH="${EPREFIX}"/usr/share/fonts/freefont + ) + use shapefile && mycmakeargs+=( + -DSHAPELIB_INCLUDE_DIR="${EPREFIX}"/usr/include/libshp + ) + use ocaml && mycmakeargs+=( + -DOCAML_INSTALL_DIR="$(ocamlc -where)" + ) + use python && mycmakeargs+=( + -DENABLE_pyqt5=$(usex qt5) + ) + + cmake-utils_src_configure + + # clean up bloated pkg-config files (help linking properly on prefix) + sed -i \ + -e "/Cflags/s:-I\(${EPREFIX}\|\)/usr/include[[:space:]]::g" \ + -e "/Libs/s:-L\(${EPREFIX}\|\)/usr/lib\(64\|\)[[:space:]]::g" \ + -e "s:${LDFLAGS}::g" \ + "${BUILD_DIR}"/pkgcfg/*pc || die +} + +src_test() { + virtx cmake-utils_src_test +} + +src_install() { + cmake-utils_src_install + + if use examples; then + docompress -x /usr/share/doc/${PF}/examples + else + rm -r "${ED%/}"/usr/share/doc/${PF}/examples || die + fi + + if use java; then + java-pkg_dojar "${BUILD_DIR}"/examples/java/${PN}.jar + java-pkg_regso "${EPREFIX}"/usr/$(get_libdir)/jni/plplotjavac_wrap.so + fi +} diff --git a/sci-libs/primegen/Manifest b/sci-libs/primegen/Manifest new file mode 100644 index 000000000000..dcbb75900ccf --- /dev/null +++ b/sci-libs/primegen/Manifest @@ -0,0 +1,8 @@ +AUX primegen-0.97-man.patch 738 SHA256 6246982b1e64c5c5c2fd0e0eb82e66d313277b6c1e7d844b9739934e9173818b SHA512 42b3748fe77eea9af4ffd531c9dabe28a6be49e05afbf705a47f7111c936fb7cb31517df475c04dc4a3157be9b7890bff64e5ae73a49d8c3517ab756d954f0e8 WHIRLPOOL a3cc5b3238ac508610cc5c42fb3b628783c64bd4d0f1f435d968dcc2b493ee26527c8177e821ae24fd6119ec09913534bcb3ccc33d1a024c49544a44960cf97c +AUX primegen-0.97-missing-headers.patch 1282 SHA256 05df7c4d2d96c2adcd7fddd5ccda5e9b2a20da0bc00611f407938eacebf82e47 SHA512 4933f7fd107f8272ae863f4b5ccf976ea29a0f1a7eab7f93160ed8dc188fef3520e2cea62513eb802e51db46190d0199c4e440b770abfed4d39b0dc6cef582c1 WHIRLPOOL 9916f55ea93146c588ed687a03179774cfb336c1372faa4b259781c62f39a83bcca91dcff879f82dfd73c8379ce5d208c8c88d1a829ecc3a2315c498e900a53d +DIST primegen-0.97.tar.gz 31491 SHA256 54285baf8eed9e421ff2220a2112d38cfb20c1ebef6014ef3f0004c22c95f40d SHA512 d6d8de4d9866dbbec20afd4d4b563e3383528138cd3ec849f706211045d735c28bbf7aa6931b8aa54163664e87c2e7ad028c68f407040ac88efce7856bc8b6f4 WHIRLPOOL aa5d65806af4059b3b6a50edf304a7588a5db8dc3a853452abf5348aadaed294d4d84652352bf24921ecebb305a036bf65d8f5ffb80b8fa922e75cf672382258 +EBUILD primegen-0.97-r1.ebuild 1315 SHA256 75599f9e10f8187123cffa21a670feae03a763ec13ee6d52185181dbb0878b8e SHA512 d0f4237601b08f9431af575143b8ff5a7ac471b9f4d40be3f90a32c860c8047f972a47a0f32548c69a252df76ca5f2ac8452bfd506ac9e83391e7d83fe34c4f7 WHIRLPOOL 8da9afaa9a9ab8c6bdd15cfeb8badce97e389a904f2965e6b9927c678322769f2ff4c3d131db75774a2cb5a308dac51779e713360d8cddb8d47819058b917d30 +EBUILD primegen-0.97-r2.ebuild 1385 SHA256 1893cf7a6da030c3de96fcda142db7bd83cb6af365358e04931cdb6b8e73113c SHA512 99222f8bdc801d758c6d98cd3eff24c2bf37dc6bb843b1a63fdf220d949b7c15a6401b3b0ecc85c56a7a69c2115323f676ff00c6304d4b9dcc4bbcd02bc2d3ea WHIRLPOOL 26fbb2a2e6115848a2f174b6ce04bc5b2f2807cfa3c16590cbc74f15617fed630172ea8a98b4ce29c27619e9661ae47f653c9d9bb6d04dbe1bffe89851aec381 +MISC ChangeLog 2860 SHA256 d025ed590a77cf2a8557e67b17c3884374b8c7e1061061c46537c87424935a19 SHA512 835a85c4a77ae0da983525a8784e2a34ed1fc8d6de12ff6664638b46b60197fe0fdcaaa335c15f460c7e6c3e821f95829f2d3967b61243ee13fae974757a6c8c WHIRLPOOL 81bfdea65e8cdcb0142bd80fd1ff42951065b63c29f49ac2d3f9435275d65eb64546d7a2d55ef251c272e68ba6db05682e634c0fb2f74c1d6d1715e9a0b5b483 +MISC ChangeLog-2015 2609 SHA256 5f23d96d2d8bbc78da73a049b73ed45522922be82b7700f95513e5090ede663a SHA512 af0ab3e1f472fb701c0b715b56ffead36fe8cbbbaf19d9df7422ef696da9dcae096b8a7536ed9817959e704336e5b032199588d12a821dc81a030121b83909d9 WHIRLPOOL 5b3edc6b9f3a0c70e10576f6af44a0e71e2030c297e021fe9706a30959fea6091e2d4482ea0c921f288443a3a56993f076ba0ba0c0f7b7ea03198123c51acd3d +MISC metadata.xml 716 SHA256 ddea8d2b181230005d62a0793524c9e1cad4094a3c078ba903993660e42d9a43 SHA512 bd1aeec27107646716ede1bcefdd4b804cb7b30fac8d41251d824bcba0453352e7000cc62fcac6f3bde2d547dfda224baf49a92227c15a7d2f2577579f7589fd WHIRLPOOL 3ce62d574ac8e0b6dd4bc8604ecfa28d79057359f159929291901d943286acdc65155cf7019edaa1685b466ef948829ee5ebcbb58577fe0ca6d35f782b81c959 diff --git a/sci-libs/primegen/files/primegen-0.97-man.patch b/sci-libs/primegen/files/primegen-0.97-man.patch new file mode 100644 index 000000000000..069409f1df76 --- /dev/null +++ b/sci-libs/primegen/files/primegen-0.97-man.patch @@ -0,0 +1,24 @@ +Fix incorrect man page and include mention of the possibility +of linking to a static libary only. +https://bugs.gentoo.org/show_bug.cgi?id=562570 + +--- primegen-0.97/primegen.3 ++++ primegen-0.97/primegen.3 +@@ -14,13 +14,16 @@ + .br + void \fBprimegen_skipto\fP(&\fIpg\fR,\fIbound\fR); + +-struct primegen \fIpg\fR; ++primegen \fIpg\fR; + .br + uint64 \fIbound\fR; + .SH DESCRIPTION + The primegen library generates prime numbers in order: + 2, 3, 5, 7, etc. + It can generate primes as large as 10^15. ++Only a static version of this library is provided, so instead of ++linking your program with -lprimegen you will have to pass the ++full path to the library (e.g. /usr/lib/primegen.a) to the compiler. + + The simplest way to use primegen + is to call diff --git a/sci-libs/primegen/files/primegen-0.97-missing-headers.patch b/sci-libs/primegen/files/primegen-0.97-missing-headers.patch new file mode 100644 index 000000000000..51f1aaac3823 --- /dev/null +++ b/sci-libs/primegen/files/primegen-0.97-missing-headers.patch @@ -0,0 +1,46 @@ +--- primegen-0.97/eratspeed.c.orig 2009-03-27 09:16:52.000000000 -0300 ++++ primegen-0.97/eratspeed.c 2009-03-27 09:18:29.000000000 -0300 +@@ -1,6 +1,8 @@ + #define B32 1001 + #define B (B32 * 32) + ++#include <stdio.h> ++#include <stdlib.h> + #include "timing.h" + #include "uint32.h" + +--- primegen-0.97/primegaps.c.orig 2009-03-27 09:17:07.000000000 -0300 ++++ primegen-0.97/primegaps.c 2009-03-27 09:17:19.000000000 -0300 +@@ -1,4 +1,5 @@ + #include <math.h> ++#include <stdio.h> + #include "primegen.h" + + primegen pg; +--- primegen-0.97/primes.c.orig 2009-03-27 09:19:08.000000000 -0300 ++++ primegen-0.97/primes.c 2009-03-27 09:19:14.000000000 -0300 +@@ -1,4 +1,5 @@ + #include <stdio.h> ++#include <stdlib.h> + #include "primegen.h" + #include "fs64.h" + +--- primegen-0.97/primespeed.c.orig 2009-03-27 09:17:41.000000000 -0300 ++++ primegen-0.97/primespeed.c 2009-03-27 09:18:54.000000000 -0300 +@@ -1,3 +1,5 @@ ++#include <stdio.h> ++#include <stdlib.h> + #include "timing.h" + #include "primegen.h" + #include "primegen_impl.h" +--- primegen-0.97/error.h.orig 2009-09-11 19:40:53.000000000 +0100 ++++ primegen-0.97/error.h 2009-09-11 19:41:02.000000000 +0100 +@@ -1,7 +1,7 @@ + #ifndef ERROR_H + #define ERROR_H + +-extern int errno; ++#include <errno.h> + + extern int error_intr; + extern int error_nomem; diff --git a/sci-libs/primegen/metadata.xml b/sci-libs/primegen/metadata.xml new file mode 100644 index 000000000000..b705e6b87a99 --- /dev/null +++ b/sci-libs/primegen/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-mathematics@gentoo.org</email> + <name>Gentoo Mathematics Project</name> +</maintainer> +<longdescription lang="en"> + primegen is a small, fast library to generate prime numbers in + order. It generates the 50847534 primes up to 1000000000 in just 8 + seconds on a Pentium II-350; it prints them in decimal in just 35 + seconds. + + primegen can generate primes up to 1000000000000000, although it + is not optimized for primes past 32 bits. It uses the Sieve of Atkin + instead of the traditional Sieve of Eratosthenes. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/primegen/primegen-0.97-r1.ebuild b/sci-libs/primegen/primegen-0.97-r1.ebuild new file mode 100644 index 000000000000..4dc121e56cd5 --- /dev/null +++ b/sci-libs/primegen/primegen-0.97-r1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 +inherit eutils flag-o-matic toolchain-funcs + +DESCRIPTION="Small, fast library to generate primes in order" +HOMEPAGE="http://cr.yp.to/primegen.html" +SRC_URI="http://cr.yp.to/primegen/${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}/${P}-man.patch" + epatch "${FILESDIR}/${P}-missing-headers.patch" + find . -type f -exec \ + sed -i -e 's:\(primegen.a\):lib\1:' {} \; + mkdir usr +} + +src_configure() { + # Fixes bug #161015 + append-flags -fsigned-char + echo "$(tc-getCC) ${CFLAGS}" > conf-cc + echo "${S}/usr" > conf-home + echo "$(tc-getCC) ${LDFLAGS}" > conf-ld +} + +src_test() { + [[ $(./primes 1 100000000 | md5sum ) == "4e2b0027288a27e9c99699364877c9db "* ]] || die "test failed" +} + +src_install() { + dobin primegaps primes primespeed + doman primegaps.1 primes.1 primespeed.1 primegen.3 + dolib.a libprimegen.a + # include the 2 typedefs to avoid collision (bug #248327) + sed -i \ + -e "s/#include \"uint32.h\"/$(grep typedef uint32.h)/" \ + -e "s/#include \"uint64.h\"/$(grep typedef uint64.h)/" \ + primegen.h || die + insinto /usr/include + doins primegen.h + dodoc BLURB CHANGES README TODO +} diff --git a/sci-libs/primegen/primegen-0.97-r2.ebuild b/sci-libs/primegen/primegen-0.97-r2.ebuild new file mode 100644 index 000000000000..a71a29ef2560 --- /dev/null +++ b/sci-libs/primegen/primegen-0.97-r2.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Small, fast library to generate primes in order" +HOMEPAGE="http://cr.yp.to/primegen.html" +SRC_URI="http://cr.yp.to/primegen/${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +PATCHES=( + "${FILESDIR}/${P}-man.patch" + "${FILESDIR}/${P}-missing-headers.patch" +) + +src_prepare() { + default + while IFS="" read -d $'\0' -r file + do + sed -i -e 's:\(primegen.a\):lib\1:' "${file}" || die + done < <(find . -type f -print0) + mkdir usr || die +} + +src_configure() { + # Fixes bug #161015 + append-flags -fsigned-char + echo "$(tc-getCC) ${CFLAGS}" > conf-cc || die + echo "${S}/usr" > conf-home || die + echo "$(tc-getCC) ${LDFLAGS}" > conf-ld || die +} + +src_test() { + [[ $(./primes 1 100000000 | md5sum ) == "4e2b0027288a27e9c99699364877c9db "* ]] || die "test failed" +} + +src_install() { + dobin primegaps primes primespeed + doman primegaps.1 primes.1 primespeed.1 primegen.3 + dolib.a libprimegen.a + # include the 2 typedefs to avoid collision (bug #248327) + sed -i \ + -e "s/#include \"uint32.h\"/$(grep typedef uint32.h)/" \ + -e "s/#include \"uint64.h\"/$(grep typedef uint64.h)/" \ + primegen.h || die + insinto /usr/include + doins primegen.h + dodoc BLURB CHANGES README TODO +} diff --git a/sci-libs/profnet/Manifest b/sci-libs/profnet/Manifest new file mode 100644 index 000000000000..6327f654732a --- /dev/null +++ b/sci-libs/profnet/Manifest @@ -0,0 +1,5 @@ +DIST profnet-1.0.22.tar.gz 203676 SHA256 a124bbb7822a22189ddc410032cfd1c1ccd30129eecf4a7cd09608edd3955f18 SHA512 11c6d180219b60df7c5e144719354b7fbd5845e4ab6e52027315ee80d820c89fca9bce5b9e9e49314aa64058f93196f0cd35089604b53721fee3c050e45d9555 WHIRLPOOL 58849038cb6500398cd8f3f312fba97fe0c167bc105cddf31e0135114f8969b3d525d3204c4c41b129b2a1d01e541baef5f072b8f7c64025a0cb194610b01c18 +EBUILD profnet-1.0.22.ebuild 660 SHA256 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a/sci-libs/profnet/profnet-1.0.22.ebuild b/sci-libs/profnet/profnet-1.0.22.ebuild new file mode 100644 index 000000000000..df450e7e8d39 --- /dev/null +++ b/sci-libs/profnet/profnet-1.0.22.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit fortran-2 toolchain-funcs + +DESCRIPTION="Neural network architecture for profacc" +HOMEPAGE="https://rostlab.org/" +SRC_URI="ftp://rostlab.org/profnet/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sys-libs/libunwind" +DEPEND="${RDEPEND}" + +src_prepare() { + sed \ + -e '/$@/s:-o:$(LDFLAGS) -o:g' \ + -i src-phd/Makefile || die +} + +src_compile() { + emake \ + F77=$(tc-getF77) \ + FFLAGS="${FFLAGS}" +} + +src_install() { + emake \ + DESTDIR="${D}" \ + prefix="${EPREFIX}/usr" \ + install +} diff --git a/sci-libs/profphd-utils/Manifest b/sci-libs/profphd-utils/Manifest new file mode 100644 index 000000000000..6821005e543d --- /dev/null +++ b/sci-libs/profphd-utils/Manifest @@ -0,0 +1,6 @@ +DIST profphd-utils-1.0.10.tar.gz 388222 SHA256 7096db3400de5173ccf66e8b7dd058569aa46a2408306e9802a1a3e5ff723f38 SHA512 c8a777e20bd721e53610ec28da01771300b06f3d284d40b0681ac0e38e8e0b3c7507e1aec7ddc627808d6ce7ccf8d3db94bf87449b958647e00a9c9d98a4300c WHIRLPOOL 45db07f97882c3f71ff7b018d543574b8c12d774d07ace4bb2f36e526269b4e87044822aa8afccc37a8703069e95f77014a602aa3e7b719e67cfca2ee900e167 +EBUILD profphd-utils-1.0.10-r1.ebuild 570 SHA256 e870451d0c702b360623108a1e24fbd2fdeec620c3404b004d3f23bad1e797f2 SHA512 9066e8bb37c5b12ed8312e2807470657e63c6b054d3d0f96eb0e52a5fc70c57f836e1f56506ba64123df6c1eda816708f37231c35cd23364599fe027644c8fc8 WHIRLPOOL fd3b3e2972854d9635909345c7e1d9965f93fef5a25d4213dd2e8b7e2316b9da6d9c6b6bef0d6c44776b6b510e0aecf43c076fa74f0030d1051a017b6759f2f1 +EBUILD profphd-utils-1.0.10.ebuild 566 SHA256 2222467505240865f33a5470d991329f7047e1007768f604242dcf4e98475b23 SHA512 319a94522a2d3a8e68aacc7413c3d0d77deb499a2cd29ee2d0bc3d953d36438bcac1a9f99169efd403dae79c331ce4cdad5dc9f2de9a8c4f6461b8d73871d541 WHIRLPOOL d8f08b0ed10dacb1722181f4fc0a6b0419ffa1d9bc889848fd4650d0c0bcd5a354d6142742e5a58fdb3feb7e7b22b45a530091482f2f61d3763f16ffc4618445 +MISC ChangeLog 2519 SHA256 a144d735d7387d11cea03952e981a716836b611b5706aff6cf566f6d2b6e6004 SHA512 ca9369c5540ff8d55ea4ea5c21b22be6ef26934897d9a6f271f9c99139506895a98a557cc9f01f19ab80f905e99851b683d12bba687682bf48a155a351433aa3 WHIRLPOOL b163e8c7a385420548dd82521057258d0967d3aa810e7e7d4802e8cd40455f38bb8b710de948e34325bf8e670f65b43c6bbe564702b5e1a542f623c0e18d4956 +MISC ChangeLog-2015 618 SHA256 8ea3365e774aa15200419e7ae2ade719a8b5b51c957af02de474d211424344ab SHA512 a7f7371aeeded412ee4e239c07d2572e772db23eaee4ef1cda66b9489f7074202a247bba0485dbf1958b5d4deffb78de62c0700c6e07cee7815dddbac95a2839 WHIRLPOOL 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a/sci-libs/profphd-utils/profphd-utils-1.0.10-r1.ebuild b/sci-libs/profphd-utils/profphd-utils-1.0.10-r1.ebuild new file mode 100644 index 000000000000..83d0f8485e02 --- /dev/null +++ b/sci-libs/profphd-utils/profphd-utils-1.0.10-r1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit fortran-2 toolchain-funcs + +DESCRIPTION="Additional utils for profphd" +HOMEPAGE="https://rostlab.org/" +SRC_URI="ftp://rostlab.org/profphd-utils/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="dev-lang/perl" + +src_compile() { + emake \ + F77=$(tc-getF77) \ + AM_FFLAGS="" +} + +src_install() { + emake \ + DESTDIR="${D}" \ + prefix="${EPREFIX}"/usr \ + install + dodoc ChangeLog AUTHORS +} diff --git a/sci-libs/profphd-utils/profphd-utils-1.0.10.ebuild b/sci-libs/profphd-utils/profphd-utils-1.0.10.ebuild new file mode 100644 index 000000000000..49afe145c1e6 --- /dev/null +++ b/sci-libs/profphd-utils/profphd-utils-1.0.10.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit fortran-2 toolchain-funcs + +DESCRIPTION="Additional utils for profphd" +HOMEPAGE="https://rostlab.org/" +SRC_URI="ftp://rostlab.org/profphd-utils/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="" +DEPEND="dev-lang/perl" + +src_compile() { + emake \ + F77=$(tc-getF77) \ + AM_FFLAGS="" +} + +src_install() { + emake \ + DESTDIR="${D}" \ + prefix="${EPREFIX}" \ + install + dodoc ChangeLog AUTHORS +} diff --git a/sci-libs/proj/Manifest b/sci-libs/proj/Manifest new file mode 100644 index 000000000000..aa808f93b83a --- /dev/null +++ b/sci-libs/proj/Manifest @@ -0,0 +1,10 @@ +DIST proj-4.8.0-org_proj4_PJ.h 2960 SHA256 ed16ebaf2806fbd74392939085db17adfdaa71d45e908cda29fbc7dc3e0a613e SHA512 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/dev/null +++ b/sci-libs/proj/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-geosciences@gentoo.org</email> + <name>Gentoo Geosciences Project</name> + </maintainer> + <longdescription>Proj.4 cartograpic projection code for forward and inverse +coordinate and projection transformations.</longdescription> +</pkgmetadata> diff --git a/sci-libs/proj/proj-4.8.0.ebuild b/sci-libs/proj/proj-4.8.0.ebuild new file mode 100644 index 000000000000..3c65b5d9f235 --- /dev/null +++ b/sci-libs/proj/proj-4.8.0.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils java-pkg-opt-2 flag-o-matic + +DESCRIPTION="Proj.4 cartographic projection software with updated NAD27 grids" +HOMEPAGE="http://trac.osgeo.org/proj/" +SRC_URI=" + ftp://ftp.remotesensing.org/pub/proj/${P}.tar.gz + http://download.osgeo.org/proj/${PN}-datumgrid-1.5.zip + http://trac.osgeo.org/proj/export/2190/tags/${PV}/proj/src/org_proj4_PJ.h -> ${P}-org_proj4_PJ.h +" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="alpha amd64 ~arm ~mips ppc ppc64 s390 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" +IUSE="java static-libs" + +RDEPEND="" +DEPEND=" + app-arch/unzip + java? ( >=virtual/jdk-1.5 )" + +src_unpack() { + unpack ${P}.tar.gz + cd "${S}"/nad || die + mv README README.NAD || die + cp "${DISTDIR}/${P}-org_proj4_PJ.h" "${S}/src/org_proj4_PJ.h" || die + unpack ${PN}-datumgrid-1.5.zip +} + +src_configure() { + if use java; then + export JAVACFLAGS="$(java-pkg_javac-args)" + append-cflags "$(java-pkg_get-jni-cflags)" + fi + econf \ + $(use_enable static-libs static) \ + $(use_with java jni) +} + +src_install() { + default + cd nad || die + dodoc README.{NAD,NADUS} + insinto /usr/share/proj + insopts -m 755 + doins test27 test83 + insopts -m 644 + doins pj_out27.dist pj_out83.dist + prune_libtool_files +} diff --git a/sci-libs/proj/proj-4.9.2.ebuild b/sci-libs/proj/proj-4.9.2.ebuild new file mode 100644 index 000000000000..39ea236af1ed --- /dev/null +++ b/sci-libs/proj/proj-4.9.2.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils java-pkg-opt-2 flag-o-matic + +DESCRIPTION="Proj.4 cartographic projection software" +HOMEPAGE="http://trac.osgeo.org/proj/" +SRC_URI=" + http://download.osgeo.org/proj/${P}.tar.gz + http://download.osgeo.org/proj/${PN}-datumgrid-1.5.zip + http://trac.osgeo.org/proj/export/2647/trunk/proj/src/org_proj4_PJ.h -> ${P}-org_proj4_PJ.h +" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~ia64 ~ppc ~ppc64 ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" +IUSE="java static-libs" + +RDEPEND="" +DEPEND=" + app-arch/unzip + java? ( >=virtual/jdk-1.5 )" + +src_unpack() { + unpack ${P}.tar.gz + cd "${S}"/nad || die + mv README README.NAD || die + cp "${DISTDIR}/${P}-org_proj4_PJ.h" "${S}/src/org_proj4_PJ.h" || die + unpack ${PN}-datumgrid-1.5.zip +} + +src_configure() { + if use java; then + export JAVACFLAGS="$(java-pkg_javac-args)" + append-cflags "$(java-pkg_get-jni-cflags)" + fi + econf \ + $(use_enable static-libs static) \ + $(use_with java jni) +} + +src_install() { + default + cd nad || die + dodoc README.{NAD,NADUS} + insinto /usr/share/proj + insopts -m 755 + doins test27 test83 + insopts -m 644 + doins pj_out27.dist pj_out83.dist + prune_libtool_files +} diff --git a/sci-libs/punc/Manifest b/sci-libs/punc/Manifest new file mode 100644 index 000000000000..f17e3b41c174 --- /dev/null +++ b/sci-libs/punc/Manifest @@ -0,0 +1,7 @@ +AUX 1.4-doc.patch 534 SHA256 625da0650f17e89b7be3fff73a10e47a6d9ead1ba7e25644c5c4f54a53c79c40 SHA512 388855f15bd17f5bc42ea3dc1d76d338a5586ed6cdb005442d46d158d36a1ffd32c2b08f10f992de30c44c1f160c005ef7499b6c2a629a0e7fab93f59d15bf65 WHIRLPOOL b18c5fe670e181a2c2012c46631bb4f1b305f2f9802ffd5b434d60242e4c121e038e57eebb8fd892d5fa89d3e3f256c1b45846cde064f87596783e90e54dba08 +AUX 1.5-linking.patch 6247 SHA256 7739c434d7c497c6c01e2b79f5c8f13598fd40f06371ad0137538a1c3b2abf60 SHA512 d7b8f8f99a2d26cb3e0cace7f31c72eff997786fcdca4a80e81493f7e255df0975743870543881348814d777507a96f328bacb1115fdc118c848a3a0be4c833f WHIRLPOOL da189480e20561acc5c1113337ed86137c63d035def2cfbadced2fcdbbf03831a853adea76e332ff6def6b5e5121e1621fb87ea98e74fe8d5da371cb264a893d +DIST punc-1.5.tar.gz 7036275 SHA256 6a63e4caf5dcd0529c09cd429cc94b4443ca4ba893b98b68962c0549c2a8246f SHA512 8b454f5de9cd01e87a30083f975ce8901c5d5a2cac7256cb535c8698221ce6d1ddb93a3663b2e903e5cae93ef76b48932ff7f13a816ba7da6bb07ea25490503b WHIRLPOOL 09af2ae6ae32014b5f946fcaa8035853aae93cd78b948bf934e817b6cb82bfa1fde6be2f6c970070ae870b494f64b4769203b773434f215dab0cafe420950ba6 +EBUILD punc-1.5.ebuild 2180 SHA256 3f9e4b95432149717f5f753f07ec0ab7aecb3a787dd86eb207f352178a1bec97 SHA512 5d292598e039484b5056ba8fd2b53c8b9d458b970c48f233983927b5d96444a254663e43f11d2302bf394a74106d8fbb43ee6c6fbbd14beed41fba617cde184c WHIRLPOOL a283b244f3bb3d0bcacbb80d05a0aabf266e723116467b42569e0ce158ec4abbb5248c79d519160450cf5feeba69f02b0a82be9b727edc5ab02f05b603647979 +MISC ChangeLog 2757 SHA256 afcbd151e19205a79f3927bfa2c70cccec59a2a10e581207f4214ccb89741dae SHA512 e73332dbfb110cbc6b777fdb913f4b1ec83a940db60de4e2940322e4946b9f853b26368f372f56d9e11a08b1ee43a8ea5e6a07eb75ae6efc016c8ec2781d2c60 WHIRLPOOL 264454bda67849c60a8c4f0d1f3bdac8038d9a02eff88f377d282da55e91e85580ef664c580fce413544092870d29f4aefa29506c4183ff51fe1dc9cd594c7fb +MISC ChangeLog-2015 3098 SHA256 995c7c072a08478172d31a34cb5c470c263ebccc3e3aaa8c4906fbac7b7368a9 SHA512 21787481faebcf80881e4db32c56147f1b442674826b9ed0a042842108455ebd9e6ee94606c5ecd120244a349b256a78a6072b4be335325a03d57033bace6a01 WHIRLPOOL 8405ac2143fa8ca826fe06c9680033212ce6b01e9d2ac9df4df1d05b7b9fb81945fe2fbbe6e1273bf55286dcf3d1e6e2f17893d486363551b56280c75f3b047f +MISC metadata.xml 1313 SHA256 1d448aea516d3e83ef9dd07bcfd96621b01ab423e73fd5cdb5369d3e764d6981 SHA512 3356e26af4a0c2c87b0255d084066ff5ce678f76c715b189ae1e18c259b799c40cd040cdeac2a70347c03613cdedec85ff2236130685923f6f1dcafdae9b6cb4 WHIRLPOOL 924e716f445ff6c4c472635765e4e4b04f527dfd2557896597a9622cceb73fece857c127a28da83b05e43ed82cb401476940590baa0c11513c2feda3fd16b6a0 diff --git a/sci-libs/punc/files/1.4-doc.patch b/sci-libs/punc/files/1.4-doc.patch new file mode 100644 index 000000000000..ad17da322f17 --- /dev/null +++ b/sci-libs/punc/files/1.4-doc.patch @@ -0,0 +1,20 @@ +diff --git a/doc/doxygen/Makefile.am b/doc/doxygen/Makefile.am +index ca42fe0..264ba82 100644 +--- a/doc/doxygen/Makefile.am ++++ b/doc/doxygen/Makefile.am +@@ -29,13 +29,11 @@ + ## Author: Michael Holst + ## ########################################################################### + +-docdir = @prefix@/doc/punc +- + doc_DATA = punc_doc + + punc_doc: + $(doxygen_path) $(top_srcdir)/doc/doxygen/punc.dox + + install-docDATA: +- mkdir -p $(docdir) +- cp -r ../api $(docdir)/ ++ mkdir -p $(DESTDIR)/@docdir@ ++ cp -r ../api $(DESTDIR)/@docdir@/ diff --git a/sci-libs/punc/files/1.5-linking.patch b/sci-libs/punc/files/1.5-linking.patch new file mode 100644 index 000000000000..9e5d5a8ced69 --- /dev/null +++ b/sci-libs/punc/files/1.5-linking.patch @@ -0,0 +1,174 @@ + configure.ac | 35 +++++++++++++++++------------------ + src/aaa_lib/Makefile.am | 7 +++---- + src/pmg/Makefile.am | 1 + + 3 files changed, 21 insertions(+), 22 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 1295a9f..f8fd97c 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -49,6 +49,8 @@ AC_LANG_C + AC_PROG_CC + AC_PROG_CPP + AC_DISABLE_STATIC ++AC_PROG_F77 ++AC_F77_LIBRARY_LDFLAGS + AM_PROG_LIBTOOL + + dnl 3. checks for libraries +@@ -341,6 +343,10 @@ if test -n "${blas}"; then + else + AC_MSG_RESULT([no ...poking around]) + ++ PKG_CHECK_MODULES([BLAS],[blas],[ ++ blas_lib=${BLAS_LIBS} ++ blas="" ++ ],[ + dnl # BLAS library location ENV specification + AC_MSG_CHECKING([whether your environment defines FETK_BLAS_LIBRARY]) + if test -n "${FETK_BLAS_LIBRARY}"; then +@@ -358,7 +364,7 @@ else + AC_CHECK_LIB(blas,dscal_, + [blas_use="yes";blas_lib="${blas_lib_path}-lblas"], + [blas_use="";blas_lib=""], +- [${blas_lib_path}-lblas -lvf2c]) ++ [${blas_lib_path} $(BLAS_LIBS)]) + if test -z "${blas_use}"; then + AC_MSG_RESULT([** BLAS library missing ...will BUILD **]) + blas="blas"; +@@ -368,7 +374,7 @@ else + fi + + dnl # Return LDFLAGS to normal +- LDFLAGS=${LDFLAGS_SAVE}; ++ LDFLAGS=${LDFLAGS_SAVE};]) + fi + + dnl # Final decisions on BLAS +@@ -414,7 +420,7 @@ dnl lapack_use=""; + dnl AC_CHECK_LIB(lapack,dsysv_, + dnl [lapack_use="yes";lapack_lib="${lapack_lib_path}-llapack"], + dnl [lapack_use="";lapack_lib=""], +-dnl [${lapack_lib_path}-llapack ${blas_lib} -lvf2c]) ++dnl [${lapack_lib_path}-llapack ${blas_lib}]) + dnl if test -z "${lapack_use}"; then + dnl AC_MSG_RESULT([** LAPACK library missing ...will BUILD **]) + dnl lapack="lapack"; +@@ -466,10 +472,10 @@ else + LDFLAGS_SAVE=${LDFLAGS}; + LDFLAGS=${amd_lib_path}; + amd_use=""; +- AC_CHECK_LIB(amd,AMD_order, ++ AC_CHECK_LIB(amd,amd_order, + [amd_use="yes";amd_lib="${amd_lib_path}-lamd"], + [amd_use="";amd_lib=""], +- [${amd_lib_path}-lamd ${blas_lib} -lvf2c]) ++ [${amd_lib_path}-lamd ${blas_lib}]) + if test -z "${amd_use}"; then + AC_MSG_RESULT([** AMD library missing ...will BUILD **]) + amd="amd"; +@@ -521,10 +527,10 @@ else + LDFLAGS_SAVE=${LDFLAGS}; + LDFLAGS=${umfpack_lib_path}; + umfpack_use=""; +- AC_CHECK_LIB(umfpack,UMFPACK_numeric, ++ AC_CHECK_LIB(umfpack,umfpack_di_numeric, + [umfpack_use="yes";umfpack_lib="${umfpack_lib_path}-lumfpack"], + [umfpack_use="";umfpack_lib=""], +- [${umfpack_lib_path}-lumfpack ${blas_lib} -lvf2c]) ++ [${umfpack_lib_path}-lumfpack ${blas_lib}]) + if test -z "${umfpack_use}"; then + AC_MSG_RESULT([** UMFPACK library missing ...will BUILD **]) + umfpack="umfpack"; +@@ -579,7 +585,7 @@ else + AC_CHECK_LIB(superlu,Destroy_SuperMatrix_Store, + [superlu_use="yes";superlu_lib="${superlu_lib_path}-lsuperlu"], + [superlu_use="";superlu_lib=""], +- [${superlu_lib_path}-lsuperlu ${lapack_lib} ${blas_lib} -lvf2c]) ++ [${superlu_lib_path}-lsuperlu ${lapack_lib} ${blas_lib}]) + if test -z "${superlu_use}"; then + AC_MSG_RESULT([** SUPERLU library missing ...will BUILD **]) + superlu="superlu"; +@@ -635,7 +641,7 @@ dnl arpack_use=""; + dnl AC_CHECK_LIB(arpack,dsgets_, + dnl [arpack_use="yes";arpack_lib="${arpack_lib_path}-larpack"], + dnl [arpack_use="";arpack_lib=""], +-dnl [${arpack_lib_path}-larpack ${blas_lib} -lvf2c]) ++dnl [${arpack_lib_path}-larpack ${blas_lib}]) + dnl if test -z "${arpack_use}"; then + dnl AC_MSG_RESULT([** ARPACK library missing ...will BUILD **]) + dnl arpack="arpack"; +@@ -691,7 +697,7 @@ dnl cgcode_use=""; + dnl AC_CHECK_LIB(cgcode,scgdrv_, + dnl [cgcode_use="yes";cgcode_lib="${cgcode_lib_path}-lcgcode"], + dnl [cgcode_use="";cgcode_lib=""], +-dnl [${cgcode_lib_path}-lcgcode ${blas_lib} -lvf2c]) ++dnl [${cgcode_lib_path}-lcgcode ${blas_lib}]) + dnl if test -z "${cgcode_use}"; then + dnl AC_MSG_RESULT([** CGCODE library missing ...will BUILD **]) + dnl cgcode="cgcode"; +@@ -747,7 +753,7 @@ dnl pmg_use=""; + dnl AC_CHECK_LIB(pmg,buildg_, + dnl [pmg_use="yes";pmg_lib="${pmg_lib_path}-lpmg"], + dnl [pmg_use="";pmg_lib=""], +-dnl [${pmg_lib_path}-lpmg ${blas_lib} -lvf2c]) ++dnl [${pmg_lib_path}-lpmg ${blas_lib}]) + dnl if test -z "${pmg_use}"; then + dnl AC_MSG_RESULT([** PMG library missing ...will BUILD **]) + dnl pmg="pmg"; +@@ -986,13 +992,6 @@ AC_OUTPUT([ + src/base/Makefile + + src/vf2c/Makefile +- src/blas/Makefile +- src/lapack/Makefile +- src/amd/Makefile +- src/umfpack/Makefile +- src/superlu/Makefile +- src/arpack/Makefile +- src/cgcode/Makefile + src/pmg/Makefile + + src/aaa_inc/Makefile +diff --git a/src/aaa_lib/Makefile.am b/src/aaa_lib/Makefile.am +index 2e17d41..3cbb9b5 100644 +--- a/src/aaa_lib/Makefile.am ++++ b/src/aaa_lib/Makefile.am +@@ -102,15 +102,14 @@ else + LIBPMG = + endif + +-libdir = ${prefix}/lib + lib_LTLIBRARIES = libpunc.la ${LIBVF2C} ${LIBBLAS} ${LIBLAPACK} ${LIBAMD} ${LIBUMFPACK} ${LIBSUPERLU} ${LIBARPACK} ${LIBCGCODE} ${LIBPMG} + + libpunc_la_SOURCES = +-libpunc_la_LIBADD = ${BASE_LIBS} ++libpunc_la_LIBADD = ${BASE_LIBS} -lm + libpunc_la_LDFLAGS = -version-info ${FETK_VERSION} + + libvf2c_la_SOURCES = +-libvf2c_la_LIBADD = ${VF2C_LIBS} ++libvf2c_la_LIBADD = ${VF2C_LIBS} -lgfortran -lf2c -lm + libvf2c_la_LDFLAGS = -version-info ${FETK_VERSION} + + libblas_la_SOURCES = +@@ -142,6 +141,6 @@ libcgcode_la_LIBADD = ${CGCODE_LIBS} + libcgcode_la_LDFLAGS = -version-info ${FETK_VERSION} + + libpmg_la_SOURCES = +-libpmg_la_LIBADD = ${PMG_LIBS} ++libpmg_la_LIBADD = ${PMG_LIBS} ${BASE_LIBS} -lgfortran -lf2c -lmaloc -lm + libpmg_la_LDFLAGS = -version-info ${FETK_VERSION} + +diff --git a/src/pmg/Makefile.am b/src/pmg/Makefile.am +index cae9324..b34ace9 100644 +--- a/src/pmg/Makefile.am ++++ b/src/pmg/Makefile.am +@@ -45,6 +45,7 @@ SRC = buildAd.c buildBd.c buildGd.c buildPd.c cgd.c cgmgd.c cgmgdrvd.c gsd.c mat + libpmg_la_SOURCES = ${SRC} + INCLUDES = @maloc_inc@ + AM_CFLAGS = @profile@ @pedantic_ansi@ ++libpmg_la_LIBADD = -lf2c + + all-local: + # -cp -p ${top_srcdir}/src/${THISLIB}/punc/*.h ../aaa_inc/punc/. diff --git a/sci-libs/punc/metadata.xml b/sci-libs/punc/metadata.xml new file mode 100644 index 000000000000..41b1fb0d0281 --- /dev/null +++ b/sci-libs/punc/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + PUNC (Portable Understructure for Numerical Computing) is a small standard + collection of software libraries for numerical computing. The PUNC + collection includes reference implementations of the standard (dense matrix) + linear algebra tools BLAS and LAPACK, and also includes some newer (sparse + matrix) linear algebra tools ARPACK, SuperLU, CgCode, and PMG. PUNC also + provides some additional basic infrastructure such as the standard F2C + header and corresponding library (libF2C), to support the use of F2C'd + FORTRAN codes, and some other standard tools used to build numerical + simulation software, such as the HDF5 library. While most of the libraries + included in PUNC are completely stand-alone, and are the reference + implementations developed by the individual library authors, PUNC also + provides some Object-oriented C wrappers (written by the FETK developers) + for use with Object-oriented C/C++ codes such as FETK . This is accomplished + by building PUNC on top of FETK 's MALOC library. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/punc/punc-1.5.ebuild b/sci-libs/punc/punc-1.5.ebuild new file mode 100644 index 000000000000..ccf2b1cc1733 --- /dev/null +++ b/sci-libs/punc/punc-1.5.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils fortran-2 multilib toolchain-funcs + +DESCRIPTION="Portable Understructure for Numerical Computing" +HOMEPAGE="http://fetk.org/codes/punc/index.html" +SRC_URI="http://www.fetk.org/codes/download/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="debug doc mpi static-libs" + +RDEPEND=" + dev-libs/maloc[mpi=] + dev-libs/libf2c + sci-libs/amd + sci-libs/cgcode + sci-libs/arpack[mpi=] + sci-libs/superlu + sci-libs/umfpack + virtual/blas + virtual/lapack + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( + media-gfx/graphviz + app-doc/doxygen )" + +S="${WORKDIR}/${PN}" + +PATCHES=( + "${FILESDIR}"/${PV}-linking.patch + "${FILESDIR}"/1.4-doc.patch + ) + +src_prepare() { + sed 's:punc/slu_ddefs.h:superlu/slu_ddefs.h:g' src/superlu/punc/vsuperlu.h > vsuperlu.h || die + sed 's:punc/umfpack.h:umfpack.h:g' src/umfpack/punc/vumfpack.h > vumfpack.h || die + rm -rf src/{amd,blas,lapack,arpack,superlu,umfpack} + + cp tools/tests/pmg/*.f src/pmg/ -f || die + cp tools/tests/pmg/*.c src/pmg/ -f || die + cp src/pmg/vpmg.h src/vf2c/punc/vpmg.h || die + + autotools-utils_src_prepare +} + +src_configure() { + local fetk_include + local fetk_lib + local myeconfargs + + use doc || myeconfargs+=( --with-doxygen= --with-dot= ) + + fetk_include="${EPREFIX}"/usr/include + fetk_lib="${EPREFIX}"/usr/$(get_libdir) + export FETK_INCLUDE="${fetk_include}" + export FETK_LIBRARY="${fetk_lib}" + export FETK_LAPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs lapack)" + export FETK_BLAS_LIBRARY="${fetk_lib}" + export FETK_SUPERLU_LIBRARY="$($(tc-getPKG_CONFIG) --libs superlu)" + export FETK_ARPACK_LIBRARY="${fetk_lib}" + export FETK_UMFPACK_LIBRARY="${fetk_lib}" + export FETK_CGCODE_LIBRARY="${fetk_lib}" + export FETK_AMD_LIBRARY="${fetk_lib}" + + myeconfargs+=( + $(use_enable debug vdebug) + --enable-vf2cforce + --docdir="${EPREFIX}"/usr/share/doc/${PF} + --disable-triplet + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + + insinto /usr/include/punc + doins v*.h + + dohtml doc/index.html +} diff --git a/sci-libs/pycifrw/Manifest b/sci-libs/pycifrw/Manifest new file mode 100644 index 000000000000..f2d930639ed8 --- /dev/null +++ b/sci-libs/pycifrw/Manifest @@ -0,0 +1,7 @@ +DIST PyCifRW-3.6.2.tar.gz 356813 SHA256 4d0a67311460e1f9ca65780d6cb34ec07e069d07ac19233dac9a0a6b50d0a0e8 SHA512 21b5738deb54a7293faef2d0cb578047be15feb1e2a0f4e6566777977ec8955c4281e6eddc920c08705f553acec4a574b52ca60b37b8bc0269d6b2cdaec7bf71 WHIRLPOOL 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type="pypi">PyCifRW</remote-id> + <remote-id type="bitbucket">jamesrhester/pycifrw</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/pycifrw/pycifrw-3.6.2.ebuild b/sci-libs/pycifrw/pycifrw-3.6.2.ebuild new file mode 100644 index 000000000000..4221d6ae4322 --- /dev/null +++ b/sci-libs/pycifrw/pycifrw-3.6.2.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_PN="PyCifRW" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Provides support for reading and writing of CIF using python" +HOMEPAGE="https://pypi.python.org/pypi/PyCifRW/ https://bitbucket.org/jamesrhester/pycifrw/wiki/Home" +SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz" + +LICENSE="ASRP" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S="${WORKDIR}/${MY_P}" diff --git a/sci-libs/pycifrw/pycifrw-4.1.1.ebuild b/sci-libs/pycifrw/pycifrw-4.1.1.ebuild new file mode 100644 index 000000000000..e2a8a84b2e99 --- /dev/null +++ b/sci-libs/pycifrw/pycifrw-4.1.1.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_PN="PyCifRW" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Reading and writing CIF (Crystallographic Information Format) files" +HOMEPAGE="https://pypi.python.org/pypi/PyCifRW/ https://bitbucket.org/jamesrhester/pycifrw/wiki/Home" +SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz" + +LICENSE="ASRP" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S="${WORKDIR}/${MY_P}" diff --git a/sci-libs/pymmlib/Manifest b/sci-libs/pymmlib/Manifest new file mode 100644 index 000000000000..6ea18adeb81e --- /dev/null +++ b/sci-libs/pymmlib/Manifest @@ -0,0 +1,5 @@ +DIST pymmlib-1.2.1.tar.gz 37480403 SHA256 58e678be6056e40647fd28fec048571563402802156912bb3481852698179738 SHA512 96328fcb8af70a271c0960be753c677f716d3b15c41519c320a1240fd9ad584fee173ab3a8e528c9ae198efea95d20863f64627e44d1a6726513f2916d93b464 WHIRLPOOL 96ba086514c22c7431739fa50908cc9e7678adf864c1402117e1d852b202e9c1da99c54278bd96861f3f4360ea72c25a04e49c7f4b65621e21ec6ee5f8ded774 +EBUILD pymmlib-1.2.1.ebuild 1036 SHA256 c52456578d505b26f38620892da4142f96ec7fb190cc6fd95757dc493505dd1a SHA512 e4989b361596a94c001bf7f5a356632257f1df5865e153f34e7b095668c96f1fbd999fec737e7842c258ad549a00e548f4cc2572a7750bcd3a28fcb837bc4f5d WHIRLPOOL d3cf99fc8d7839e0c01cfb5eab4b72a7ea6460a7d95fd9def6f4110f9be2b984721194e5cf58f18f508ad7ef10952da9ece8659b5a16ab6109a1357c153e2d33 +MISC ChangeLog 2973 SHA256 8582957b1bc65fea674c7cad87437d2d5d918b0a61c4ebe22207bd5d4dd9e479 SHA512 ef1281806a7c4e4ef219d083cbae64bcd6268323bd4bab8a2c75274242909b3c4a77fb922594c6bb03ed1147272e2564ff5b0d8d9b2d83a3374ae431f10b0b32 WHIRLPOOL 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--- /dev/null +++ b/sci-libs/pymmlib/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">pymmlib</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/pymmlib/pymmlib-1.2.1.ebuild b/sci-libs/pymmlib/pymmlib-1.2.1.ebuild new file mode 100644 index 000000000000..380de4cff761 --- /dev/null +++ b/sci-libs/pymmlib/pymmlib-1.2.1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 multilib + +DESCRIPTION="Toolkit and library for the analysis and manipulation of macromolecular structural models" +HOMEPAGE="http://pymmlib.sourceforge.net/" +SRC_URI="mirror://github/masci/mmLib/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pygtkglext[${PYTHON_USEDEP}] + media-libs/freeglut + virtual/glu + virtual/opengl + x11-libs/libXmu" +DEPEND="${RDEPEND} + doc? ( dev-python/epydoc[${PYTHON_USEDEP}] )" + +python_prepare_all() { + rm mmLib/NumericCompat.py || die + distutils-r1_python_prepare_all +} + +python_compile_all() { + use doc && esetup.py doc +} + +python_install_all() { + DOCS=( "${S}"/README.txt ) + use doc && HTML_DOCS=( "${S}"/doc/. ) + distutils-r1_python_install_all + + python_foreach_impl python_doscript "${S}"/applications/* "${S}"/examples/*.py +} diff --git a/sci-libs/pyshp/Manifest b/sci-libs/pyshp/Manifest new file mode 100644 index 000000000000..e60bc350e696 --- /dev/null +++ b/sci-libs/pyshp/Manifest @@ -0,0 +1,6 @@ +DIST pyshp-1.2.0.tar.gz 58993 SHA256 16e9a9b5caae5b69149c7be09415381b61af4f85f2087d08c0698c75e70000e7 SHA512 c77e19f258ba9d2e2c480b82c342d2bbeae4b5855627aa98777fbf590e904d50045edecaa0e5ec2e03ddaaf49bf7261944fb77bcd26bf6d21e50c90c30cd0b43 WHIRLPOOL d1558ce889b5942dd8da9b61d94c2cd5fcc8e84ca8c70a756997efad2355ea0f97eb849bfd75048b30a7337973dca07dbe1be7ecf0b33a1374637accd6bc00a4 +EBUILD pyshp-1.2.0.ebuild 611 SHA256 e459ee84d01a7faa4d01404b37dc9173edee1e76312ae4ed3e84fa2a747da11a SHA512 070562d18b9919f985d617e3a129b9503e543d502397c3d507ca11ea8ed7d223f5a40a35f38394760c455254dd625bd86ca4861d2e02f68e96ab9446399d9604 WHIRLPOOL 783e9dc669d0c15901d22b27007f56bfdae745f2efff4c6acaf2f293c4e5e63b7879580370b8f4b345da14f3fc65cf214ac21955760f1d638e970347b6e24829 +EBUILD pyshp-9999.ebuild 611 SHA256 e459ee84d01a7faa4d01404b37dc9173edee1e76312ae4ed3e84fa2a747da11a SHA512 070562d18b9919f985d617e3a129b9503e543d502397c3d507ca11ea8ed7d223f5a40a35f38394760c455254dd625bd86ca4861d2e02f68e96ab9446399d9604 WHIRLPOOL 783e9dc669d0c15901d22b27007f56bfdae745f2efff4c6acaf2f293c4e5e63b7879580370b8f4b345da14f3fc65cf214ac21955760f1d638e970347b6e24829 +MISC ChangeLog 2545 SHA256 e24142efb12a35fc856fcb7f58d24d0da641be2e41de04e8bb2f8a54091a18c6 SHA512 feb477d761f78ed82961c509030b29689f6f12a33e35916c128400dcca8bacbb1c08f03ca140d5f66900bbda10b2991b3723a43c4e0b66d896be37dbfbfcc4cb WHIRLPOOL e08504bd40e244c80866ee0ec51918fb3c30ec531e9999ffc2b74aa0f492746122bdb8d147606fa68c9cf50b2e22789f6896635ac9fa8981eef2d8a210248392 +MISC ChangeLog-2015 715 SHA256 f2a73cc626e10b1ddec699aef0db7ca3ec04e88c51e909a2155b3282e2bf1866 SHA512 715c4d750da5afaad3a9a4cbf307af72ea0c98951494c78d7a80ce658fd91fa23360110422b7f39187d86f9417b814833de9a0b5a0f285a8867fde0b95113d8f WHIRLPOOL 7b930902d9c5b3a60baeddb799de58ebe5bf3a89b34ef4cbeb23c4e71b8f7528c177bb262240b4304b5978d7f63481a73652b4b930fc0cd2cb54ed2ec68e1129 +MISC metadata.xml 291 SHA256 fad92e925739b29734c1ad9b93ef8e58b1553d9e2ce9b9c416a2182dc235d4dc SHA512 5f734d7badf75d687d67ecfb97c8a826ab4d57240ca8153e7950c758ec1d77c46ad4910f952155f8c601bb64e6f46e0643b2dd53576cbed5e9dd81e890cd807f WHIRLPOOL 1ef7bfb5cf321c2ce6896ec0424c01e7d2c30bfe59648501026078359eaab189503b4b7e98d5418ea7a38f781cd9cb949721827694fa120e11ba1e3cb6bab3d6 diff --git a/sci-libs/pyshp/metadata.xml b/sci-libs/pyshp/metadata.xml new file mode 100644 index 000000000000..97d8d84efce1 --- /dev/null +++ b/sci-libs/pyshp/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>slis@gentoo.org</email> + </maintainer> + <upstream> + <remote-id type="pypi">pyshp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/pyshp/pyshp-1.2.0.ebuild b/sci-libs/pyshp/pyshp-1.2.0.ebuild new file mode 100644 index 000000000000..40a25c90a67f --- /dev/null +++ b/sci-libs/pyshp/pyshp-1.2.0.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" +PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} ) + +inherit distutils-r1 + +DESCRIPTION="Pure Python read/write support for ESRI Shapefile format" +HOMEPAGE="https://pypi.python.org/pypi/pyshp/" + +if [[ ${PV} == "9999" ]] ; then + SRC_URI="" + ESVN_REPO_URI="https://${PN}.googlecode.com/svn/trunk" + inherit subversion +else + SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}]" diff --git a/sci-libs/pyshp/pyshp-9999.ebuild b/sci-libs/pyshp/pyshp-9999.ebuild new file mode 100644 index 000000000000..40a25c90a67f --- /dev/null +++ b/sci-libs/pyshp/pyshp-9999.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI="5" +PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} ) + +inherit distutils-r1 + +DESCRIPTION="Pure Python read/write support for ESRI Shapefile format" +HOMEPAGE="https://pypi.python.org/pypi/pyshp/" + +if [[ ${PV} == "9999" ]] ; then + SRC_URI="" + ESVN_REPO_URI="https://${PN}.googlecode.com/svn/trunk" + inherit subversion +else + SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" +IUSE="" + +RDEPEND="" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}]" diff --git a/sci-libs/qd/Manifest b/sci-libs/qd/Manifest new file mode 100644 index 000000000000..b798f5341f6d --- /dev/null +++ b/sci-libs/qd/Manifest @@ -0,0 +1,6 @@ +AUX qd-2.3.17-fix-build-system.patch 6245 SHA256 12e7a0da23b764c58ef10b61935dd9a44c29595cb7aaa783168961792ba7f54a SHA512 e7db957d3c2927062637a80644bb5d41739fe5ac31d1a2beb6bee62873d348e2675d720ed5c0a5a0b7d621053e299701724becac5ffeff8efc3d8aa5de339e53 WHIRLPOOL 7cab15021bb9df512e8af0497098db82aa966652751bb80fcbec9a5bc75358d5212cd25b0a22c3160d3ed1899cf33d531d137b566caec10afbf97ca327e0ed7f +DIST qd-2.3.17.tar.gz 1445774 SHA256 c58e276f6fcf5f2f442c525f3de42ea00004734572b29c74028bbda0ad81096d SHA512 9c6f5dc8d5ad7c9c3d0ec626f7089eb760f31fb14b36daee9c6ba403ab146ff7ce99e01a8750960117a34d662c11620db2ec999e9cf44eb0f80e9224e365d496 WHIRLPOOL 855b859d9af1491c4158d772cafb7ac6ef982af769b1b855a01c19e7110d68123814fbda477a4bb72887a9670cf2db61042a100a464de47e948ef0eaf1b677ca +EBUILD qd-2.3.17.ebuild 1115 SHA256 f371251333b1022cea5b98954f3226669ba4bcf630bbf99a230ab4769aa7a5c4 SHA512 75b4f56a31b0f3c3c4e581e7325371f133932b0d9b8d2e26c297f9b05d7c34a1ab51bcbb1be96842094cabf713efb47f8fe197a2d2f91d828c7c2fb1e64015e2 WHIRLPOOL 6c90699bb17606af623413f3e115dc87c0ca2505d026b9acdf0ba3347c22619cb3ca3262d38b38977e36cd07a9c747fc9fe5f199aa63b1a3144972d1b21dea67 +MISC ChangeLog 3555 SHA256 683b084490c72fcaa221ca5b2becb623a934dddcd184e87ad318eae1272744bc SHA512 47fbf2323736dd3bf9b2eb1008c3fc9cd9ca03d50614b220b3702a115636757122a4c4a35145acdcc18d936a46659238be2d880c919b188cc6f5c9f22a013347 WHIRLPOOL 6cc91096e73ea4cc93fc89104b53fdd0061a217e2dd6b9a714211fb3383cfc5a6071ff92d99456220f0c61651245eba980164e3701719777cc7210e58ed63c25 +MISC ChangeLog-2015 2719 SHA256 dfe4f41a2717ff52654f1ff52ed155e4cd86db993e669c879d8c530719045076 SHA512 abc2b38b195c8b76a7df9f044bb67bad6db05b290e3d50260ea73d70d12c183d009eddae8db6ceb352e12f3d8ba9113ac8a25acb94f3dbf7eeb80663d988c090 WHIRLPOOL 5de9dd050c7ec6f35127efd1ea836e3f7d470bef9521e59ce12d857f1a56cd42c6c837314a6daf972be95953022f4d0dfff6f8f6805215f520e1c146fb9a795a +MISC metadata.xml 457 SHA256 3caa31e0d56a863c89157c1ef8ff6f46d414f23b8fd36dc1d561a582ce6c6af7 SHA512 52e6763499001331f98c1901ba883df48d3e6dec66f93014ab66fcf1ffe25aaae72f0597dbb556dc538b1e6a7905657db86c5c7d46dfb551a628a6d71261a438 WHIRLPOOL 76e1013cef8056671d3636655c12d27d2008cc383657b81e7b599693f0893af019a5f09618341b20963020168641d4f1d542f468617baa1edc8ae08e9b25cc1e diff --git a/sci-libs/qd/files/qd-2.3.17-fix-build-system.patch b/sci-libs/qd/files/qd-2.3.17-fix-build-system.patch new file mode 100644 index 000000000000..7fa3af79895d --- /dev/null +++ b/sci-libs/qd/files/qd-2.3.17-fix-build-system.patch @@ -0,0 +1,179 @@ +Fix build system +* --enable options were misspecified +* Targets were missing dependencies +* Disable setting CXXFLAGS + +--- a/configure.ac ++++ b/configure.ac +@@ -18,14 +18,14 @@ + + AC_CONFIG_AUX_DIR(config) + AM_INIT_AUTOMAKE([nostdinc]) +-AM_CONFIG_HEADER([config.h]) +-AM_CONFIG_HEADER([include/qd/qd_config.h]) ++AC_CONFIG_HEADERS([config.h]) ++AC_CONFIG_HEADERS([include/qd/qd_config.h]) + + AC_CANONICAL_HOST + + # Checks for arguments + # --enable-inline +-AC_ARG_ENABLE(enable_inline, AC_HELP_STRING(--enable-inline, [inline commonly used functions. [[default=yes]]])) ++AC_ARG_ENABLE([inline], AS_HELP_STRING(--enable-inline, [inline commonly used functions. [[default=yes]]])) + AC_MSG_CHECKING([if commonly used function is to be inlined]) + if test "$enable_inline" != "no"; then + enable_inline="yes" +@@ -34,7 +34,7 @@ + AC_MSG_RESULT($enable_inline) + + # --enable-ieee-add +-AC_ARG_ENABLE(enable_ieee_add, AC_HELP_STRING(--enable-ieee-add, [use addition that satisfies IEEE-style error bound instead of Cray-style error bound. [[default=no]]])) ++AC_ARG_ENABLE([ieee-add], AS_HELP_STRING(--enable-ieee-add, [use addition that satisfies IEEE-style error bound instead of Cray-style error bound. [[default=no]]])) + AC_MSG_CHECKING([if addition with IEEE-style error bound is to be used]) + if test "$enable_ieee_add" = "yes"; then + AC_DEFINE([QD_IEEE_ADD], [1], [Define to 1 to use additions with IEEE-style error bounds.]) +@@ -44,7 +44,7 @@ + AC_MSG_RESULT($enable_ieee_add) + + # --enable-sloppy-mul +-AC_ARG_ENABLE(enable_sloppy_mul, AC_HELP_STRING(--enable-sloppy-mul, [use fast but slightly inaccurate multiplication. [[default=yes]]])) ++AC_ARG_ENABLE([sloppy-mul], AS_HELP_STRING(--enable-sloppy-mul, [use fast but slightly inaccurate multiplication. [[default=yes]]])) + AC_MSG_CHECKING([if sloppy multiplication is to be used]) + if test "$enable_sloppy_mul" != "no"; then + enable_sloppy_mul="yes" +@@ -53,7 +53,7 @@ + AC_MSG_RESULT($enable_sloppy_mul) + + # --enable-sloppy-div +-AC_ARG_ENABLE(enable_sloppy_div, AC_HELP_STRING(--enable-sloppy-div, [use fast but slightly inaccurate division. [[default=yes]]])) ++AC_ARG_ENABLE([sloppy-div], AS_HELP_STRING(--enable-sloppy-div, [use fast but slightly inaccurate division. [[default=yes]]])) + AC_MSG_CHECKING([if sloppy division is to be used]) + if test "$enable_sloppy_div" != "no"; then + enable_sloppy_div="yes" +@@ -63,7 +63,7 @@ + + + # --enable-debug +-AC_ARG_ENABLE(enable_debug, AC_HELP_STRING(--enable-debug, [enable debugging code. [[default=no]]])) ++AC_ARG_ENABLE([debug], AS_HELP_STRING(--enable-debug, [enable debugging code. [[default=no]]])) + AC_MSG_CHECKING([if debugging code is to be enabled]) + if test "$enable_debug" = "yes"; then + AC_DEFINE([QD_DEBUG], [1], [Define to 1 to enable debugging code.]) +@@ -73,7 +73,7 @@ + AC_MSG_RESULT($enable_debug) + + # --enable-warnings +-AC_ARG_ENABLE(enable_warnings, AC_HELP_STRING(--enable-warnings, [enable compiler warnings. [[default=no]]])) ++AC_ARG_ENABLE([warnings], AS_HELP_STRING(--enable-warnings, [enable compiler warnings. [[default=no]]])) + AC_MSG_CHECKING([if compiler warnings is to be enabled]) + if test "$enable_warnings" != "yes"; then + enable_warnings="no" +@@ -83,13 +83,6 @@ + + # Checks for programs. + AC_LANG(C++) +-if test "$CXXFLAGS" = ""; then +- if test "$enable_debug" = "yes"; then +- CXXFLAGS="-O" +- else +- CXXFLAGS="-O2" +- fi +-fi + + # Set up compiler search list. DUe to possible case insensitive filesystems, + # Cygwin and Apple systems sometimes gets confused between cc and CC. +@@ -106,50 +99,10 @@ + fi + AC_PROG_CC + +- +-CXX_PROG_NAME=`basename $CXX` +-case $host in +- powerpc*-*-*) +- case "$CXX_PROG_NAME" in +- xlC*) +- REQ_CXXFLAGS="$REQ_CXXFLAGS -qstrict" +- ;; +- esac +- ;; +- i?86-*-* | k?*-*-* | athlon-*-* | ia64-*-* | x86_64-*-*) +- case "$CXX_PROG_NAME" in +- icc|icpc|ecc) +- REQ_CXXFLAGS="$REQ_CXXFLAGS -mp" +- if test "$enable_warnings" = "yes"; then +- CXXFLAGS="$CXXFLAGS -wd1572 -wd981 -wd1418 -wd1419" +- fi +- ;; +- esac +- ;; +- alpha*-*-*) +- case "$CXX_PROG_NAME" in +- cxx) +- CXXFLAGS="$CXXFLAGS -std strict_ansi -tweak" +- ;; +- esac +- ;; +-esac +- +-AC_SUBST(REQ_CXXFLAGS) +-CXXFLAGS="$CXXFLAGS $REQ_CXXFLAGS" +- +-if test "$enable_warnings" = "yes"; then +- if test "$GCC" = "yes"; then +- CXXFLAGS="$CXXFLAGS -Wall" +- fi +-fi +- +-if test "$enable_debug" = "yes"; then +- CXXFLAGS="$CXXFLAGS -g" +-fi ++CXXFLAGS="${CXXFLAGS} -Wall" + + # --enable-fma +-AC_ARG_ENABLE(enable_fma, AC_HELP_STRING(--enable-fma, [use fused multiply-add/subtract (auto,gnu,ia64,c99,ibm,compiler). Use this option with care. [[default=auto]]])) ++AC_ARG_ENABLE([fma], AS_HELP_STRING(--enable-fma, [use fused multiply-add/subtract (auto,gnu,ia64,c99,ibm,compiler). Use this option with care. [[default=auto]]])) + if test "x$enable_fma" = "x"; then + enable_fma="auto" + fi +@@ -248,7 +201,7 @@ + FCFLAGS="-O2" + fi + fi +-AC_ARG_ENABLE(enable_fortran, AC_HELP_STRING(--enable-fortran, [build Fortran 77/90 interfaces [[default=auto]]])) ++AC_ARG_ENABLE([fortran], AS_HELP_STRING(--enable-fortran, [build Fortran 77/90 interfaces [[default=auto]]])) + if test "$enable_fortran" != "no"; then + AC_LANG_PUSH(Fortran) + AC_PROG_FC([xlf95 ifort pathf95 f95 gfortran g95 pgf95 lf95 fort ifc efc pathf90 xlf90 pgf90 epcf90 xlf f90]) +@@ -312,8 +265,7 @@ + AC_CHECK_LIB(m,sqrt) + + # libtool stuff +-AC_DISABLE_SHARED +-AC_PROG_LIBTOOL ++LT_INIT + + # Output + AC_CONFIG_FILES([Makefile config/Makefile src/Makefile include/Makefile +--- a/fortran/Makefile.am ++++ b/fortran/Makefile.am +@@ -16,7 +16,9 @@ + + lib_LTLIBRARIES = libqdmod.la libqd_f_main.la + libqdmod_la_SOURCES = ddext.f ddmod.f qdext.f qdmod.f f_dd.cpp f_qd.cpp ++libqdmod_la_LIBADD = $(top_builddir)/src/libqd.la $(FCLIBS) + libqd_f_main_la_SOURCES = main.cpp ++libqd_f_main_la_LIBADD = $(top_builddir)/src/libqd.la libqdmod.la $(FCLIBS) + ddmod.lo: $(DDEXT) ddext.lo + qdmod.lo: ddmod.lo $(DDMOD) qdext.lo + $(QDMOD): qdmod.lo $(DDMOD) +--- a/qd-config.in ++++ b/qd-config.in +@@ -14,7 +14,7 @@ + build_CXXFLAGS="@CXXFLAGS@" + build_LDFLAGS="@LDFLAGS@" + CXX="@CXX@" +-CXXFLAGS="-I$includedir @REQ_CXXFLAGS@" ++CXXFLAGS="-I$includedir" + FC="@FC@" + + LDFLAGS="-L$libdir -lqd @LIBS@" diff --git a/sci-libs/qd/metadata.xml b/sci-libs/qd/metadata.xml new file mode 100644 index 000000000000..93ffba17b790 --- /dev/null +++ b/sci-libs/qd/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>grozin@gentoo.org</email> + <name>Andrey Grozin</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription>Quad-double and double-double float arithmetics</longdescription> +</pkgmetadata> diff --git a/sci-libs/qd/qd-2.3.17.ebuild b/sci-libs/qd/qd-2.3.17.ebuild new file mode 100644 index 000000000000..c63f70cc5236 --- /dev/null +++ b/sci-libs/qd/qd-2.3.17.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran + +inherit autotools fortran-2 + +DESCRIPTION="Quad-double and double-double float arithmetics" +HOMEPAGE="http://crd-legacy.lbl.gov/~dhbailey/mpdist/" +SRC_URI="http://crd.lbl.gov/~dhbailey/mpdist/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_fma3 cpu_flags_x86_fma4 doc fortran static-libs" + +PATCHES=( "${FILESDIR}"/${PN}-2.3.17-fix-build-system.patch ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + econf \ + --disable-ieee-add \ + --disable-sloppy-mul \ + --disable-sloppy-div \ + --enable-inline \ + --enable-shared \ + $(use_enable static-libs static) \ + $(use_enable cpu_flags_x86_fma$(usex cpu_flags_x86_fma3 3 4) fma) \ + $(use_enable fortran) +} + +src_install() { + default + + dosym qd_real.h /usr/include/qd/qd.h + dosym dd_real.h /usr/include/qd/dd.h + + if ! use doc; then + rm "${ED%/}"/usr/share/doc/${PF}/*.pdf || die + fi + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} diff --git a/sci-libs/qfits/Manifest b/sci-libs/qfits/Manifest new file mode 100644 index 000000000000..79de3777f700 --- /dev/null +++ b/sci-libs/qfits/Manifest @@ -0,0 +1,7 @@ +AUX qfits-6.2.0-open.patch 683 SHA256 2f98aef5de1628af3f827d333a31decdcb626806f1974c703027b9c2fb99a6d1 SHA512 3c1303640f3d30340f11be173ebc2ce87b33064912f4fa071c3381519d19eeda1244955d07e850f0a2e54552f6fc83eb5d1fd297199023f7c6084e374f960cb7 WHIRLPOOL 504b2265cd97c5b0c2e8282d916ef59cb1e3c39d9c63cf649a45652cb0c26ab982f89ac2072a11b7d361eb1a2b04e3bba3cf8873d4c26194bc5f4eb36634debd +AUX qfits-6.2.0-ttest.patch 376 SHA256 da394f2977ddaec1d33a1389516c84320c420da90d08d743672c426b22b9860c SHA512 32b822144f7b4a4eaf258078004410c5c7c1cd7117eea678c382b2cd8b08ca855fc3d3f2498383cfafdd57d09dee5b9a2eed2e50b483c28255fab9b8d5b8c243 WHIRLPOOL 1298c97d907c3c9dc7d12677b1477381041105956e062a897a7751542378f2c6f725d57446e386bd532980d36f2c1b61e10bb107cfe30e1254116c2bea0fb8fc +DIST qfits-6.2.0.tar.gz 475191 SHA256 04f628ee966859c2e3c58cd63955544adc31a3b3901bf42c25fbb1feb98f8ed1 SHA512 a0f6863a9e5b26d08de487cfdf468b3d04218a36a01cd9df8b786b1cdf2ffa61acf12b087f4fbd751ba023f02b5a32410949a4ee08432108a7129a283ab3d824 WHIRLPOOL bfd4b8ee50add6bb25aa9e2eec6a6a00bca4deaf7a9d463f6f27a52d2e927db4ea4dd2c2d0c624f572d53d811a3abc0b9ebaa34536aca1daec123c3f39e91050 +EBUILD qfits-6.2.0.ebuild 560 SHA256 f56ec21ffedb1ed11b41696d859ba1fbbbe92c7f2d56bc14d07f7198abcbe335 SHA512 5c1733cbffe81295cea50f3625150f43d741fd9159280444e4e1df358363baaef0536a9cbe52e641a1fc65d16e927b5a1ebac44e81ea95fcf459415dc8a5ff00 WHIRLPOOL 145b2af99b602f4070ca2b73f921963d0ccca8ad1fe5a23a832985e32eceba8956e79b726a8d4dc16df3661e0af454f581947f43c349615061c329890812e4b6 +MISC ChangeLog 2486 SHA256 1dd528d0093288297d53cb5bee59d0816f046e908ff7796eb147a97c36772a1a SHA512 c97a1c0a35e85d0c3581ebe242052f027d4ce00de8789aa4dd2f8290b059e184a1059c8a5cdc496c1ac79a8905c43736b54dc74581e240f4cc832575b125e8f4 WHIRLPOOL f9f5df3844abaf2aa039ff460a3d8a59cd10f57325edc297573e6520b790db5e656015153f370e25b0c2b32c186edd29b6e7090ccf10e174f8ff557aedb5d51c +MISC ChangeLog-2015 1076 SHA256 5ce077431d644630867f9f2ece4b0dcf26275c937a5e4c71c3582a4398188650 SHA512 349ec73e4e0f0fc69a8a8bb7a6624806ea82cdaf1f0a2affe198a3373391bc531258e4bf249df9f23e170fb19514bfaec0328112c8de7ffe48a222ee93be714a WHIRLPOOL 5d69b791946a324935a3909549aa8cec97c5abe7b64551f962fcc8fb76ef14c0e3ff2a5b310b60f510f44a982bbb132b16b14476cbc16b0629911960c7e73f97 +MISC metadata.xml 851 SHA256 66fb6a2a13313d181ab599aaa93aa74b869de5b7f83ebf1bfcf801b1d0f733a1 SHA512 97081bccbae198d305fba171d6969993599b8008d82f28acb7489879013564bc95dd42ad9c8d04d883f442cdf70361f080e9ac8bd770752ea2a9ca87e3478434 WHIRLPOOL 95f9175f41d65543b4e9e6064912b383f5eb4352fcb8690dc478f29f33740ce923262ebb760a8a24385fc2e510ba176126940cf7933f42e5b2719862a904fc18 diff --git a/sci-libs/qfits/files/qfits-6.2.0-open.patch b/sci-libs/qfits/files/qfits-6.2.0-open.patch new file mode 100644 index 000000000000..71d2df1a692a --- /dev/null +++ b/sci-libs/qfits/files/qfits-6.2.0-open.patch @@ -0,0 +1,12 @@ +diff -ur qfits-6.2.0/src/qfits_memory.c qfits-6.2.0.new/src/qfits_memory.c +--- qfits-6.2.0/src/qfits_memory.c 2006-08-24 17:01:56.000000000 +0200 ++++ qfits-6.2.0.new/src/qfits_memory.c 2007-09-21 13:43:19.000000000 +0200 +@@ -308,7 +308,7 @@ + /* Create swap file with rights: rw-rw-rw- */ + swapfileid = ++ qfits_memory_table.file_reg ; + fname = qfits_memory_tmpfilename(swapfileid); +- swapfd = open(fname, O_RDWR | O_CREAT); ++ swapfd = open(fname, O_RDWR | O_CREAT, S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH); + if (swapfd==-1) { + fprintf(stderr, "qfits_mem: cannot create swap file\n"); + exit(-1); diff --git a/sci-libs/qfits/files/qfits-6.2.0-ttest.patch b/sci-libs/qfits/files/qfits-6.2.0-ttest.patch new file mode 100644 index 000000000000..ee87bfc702ca --- /dev/null +++ b/sci-libs/qfits/files/qfits-6.2.0-ttest.patch @@ -0,0 +1,11 @@ +--- test/test_tfits.c 2006-04-27 14:08:43.000000000 +0100 ++++ test/test_tfits.c.new 2007-02-23 00:29:41.000000000 +0000 +@@ -322,7 +322,7 @@ + * Test on BINARY tables + */ + say("Test the BINARY table") ; +- strcat(filename, srcdir) ; ++ strcpy(filename, srcdir) ; + strcat(filename, BIN_TABLE_NAME) ; + err += qfits_test_table(filename, 1) ; + diff --git a/sci-libs/qfits/metadata.xml b/sci-libs/qfits/metadata.xml new file mode 100644 index 000000000000..223e7f7b167c --- /dev/null +++ b/sci-libs/qfits/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci-astronomy@gentoo.org</email> + <name>Gentoo Astronomy Project</name> +</maintainer> +<longdescription lang="en"> +qfits is a stand-alone library written in C to interact with files +complying with the FITS format. It is fast and portable over any kind +of POSIX-compliant platform. +Rather than going through the FITS format specification and trying to +implement some support for everything that is described there, this +library was built day after day upon request. This guarantees that +all the functions you will find in the library have been written for +some purpose in the VLT pipeline context, and all of them are used +daily in a production environment. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/qfits/qfits-6.2.0.ebuild b/sci-libs/qfits/qfits-6.2.0.ebuild new file mode 100644 index 000000000000..e98cd4afcfa2 --- /dev/null +++ b/sci-libs/qfits/qfits-6.2.0.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit autotools-utils + +DESCRIPTION="ESO stand-alone C library offering easy access to FITS files" +HOMEPAGE="http://www.eso.org/projects/aot/qfits/" +SRC_URI="ftp://ftp.hq.eso.org/pub/${PN}/${P}.tar.gz" +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" +DEPEND="" +RDEPEND="" + +PATCHES=( "${FILESDIR}"/${P}-{ttest,open}.patch ) + +src_install() { + autotools-utils_src_install + use doc && dohtml html/* +} diff --git a/sci-libs/qrupdate/Manifest b/sci-libs/qrupdate/Manifest new file mode 100644 index 000000000000..3b8d594782ed --- /dev/null +++ b/sci-libs/qrupdate/Manifest @@ -0,0 +1,7 @@ +AUX qrupdate-1.1.1-Makefiles.patch 2350 SHA256 68f6febb354250ccabf1dbe68e96c834aadbe058987ec20f9095e19d7ed2dfb2 SHA512 40945650175668ab5155c330a5e6be20059e90d8bb5f47173d14b385710703693b1c5fb77bc01f08328e064301e2fc0c90438a9fac7f6f1222e6b35835137682 WHIRLPOOL 9dcdc30fabdf376448b65108ebfcbad5788f9f71a5858e7c42294101d37cf491de1ee373a7513118cfa8c3c3d4d7e6f942d7e75f0b3bf39ff8105204e237b947 +AUX qrupdate-1.1.2-install.patch 1263 SHA256 c794f6935cdcceb23beabbf72786883a76b68c69c6d30303e335cbcdfb76cae8 SHA512 3274d57666b2f453f50f0b5244c9f3dd5ea29a2fc05233dedfd43940945744a675d3bbd50e3a1aef7ec8613df16f97c05e0983c711db63364f8b45125e246bb8 WHIRLPOOL e91449c4bad76d93de841620eb7da8ae504f5d80dbb0ca40461eb3e299e468ae4b6a37b64fe6cc021cf81a372479f1eb046f6e2f06a7ba6486794a4acecad035 +DIST qrupdate-1.1.2.tar.gz 49734 SHA256 e2a1c711dc8ebc418e21195833814cb2f84b878b90a2774365f0166402308e08 SHA512 cc4e466ea91958e15c66be82b0c4c8ad813fbe4643f21259a9cb3ca8e0a411dd764bb2397ece848a7045f322d30316801d1540c4ebf7912030bef6995b44917c WHIRLPOOL 9e6fb1d77c63e209816d42a864e3e9bf7fd6e238f672012a1dfc2235036c482291745e947a74afa316b9ef0e4a054fbcd7759d5620b75ac35fc2e4cfbd6467a9 +EBUILD qrupdate-1.1.2-r1.ebuild 1283 SHA256 2bbb0987c33a719ebf5a1a16aa5637da5ef55653eda6672521f987b21f84d025 SHA512 071a1af0dd4bc75b1813c94decc9e3bd33a49bc58b1b3b8e1fd8118d3e4ec8e24bbb771bdda1a3a4bb5e286eb3f3193eff085ca1770adb2d7f6bb67a57374344 WHIRLPOOL e9c69d36219f7af242167f9e8c4894e2722b2ab52fade855bd5bb920df81636cf1831c8a5e4b347e3202d0f61b69f7f5bebeff1577ed3261178651123d421223 +MISC ChangeLog 4892 SHA256 e27e74219d327bd8887623eed2e3979aa6c7aa01441c3f72d9767d290067876b SHA512 30006883a635328532aab33424b0f0a2d9c880ca0a6fc88c1e23d92a7445a75deb21ccfa5af02e8cb84d537093e57a28dbb8d09b1cd8252fc92e73ef2ec48b47 WHIRLPOOL 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file mode 100644 index 000000000000..9c9ef9317342 --- /dev/null +++ b/sci-libs/qrupdate/files/qrupdate-1.1.1-Makefiles.patch @@ -0,0 +1,88 @@ +diff -Nur qrupdate-1.1.1.orig/Makefile qrupdate-1.1.1/Makefile +--- qrupdate-1.1.1.orig/Makefile 2009-02-06 09:12:00.000000000 +0000 ++++ qrupdate-1.1.1/Makefile 2010-05-13 17:27:15.000000000 +0100 +@@ -32,22 +32,22 @@ + @echo " make install - installs everything" + + lib: +- make -C src/ lib ++ $(MAKE) -C src lib + solib: +- make -C src/ solib ++ $(MAKE) -C src solib + test: lib +- make -C test/ ++ $(MAKE) -C test + + clean: + rm -f libqrupdate.a libqrupdate.so +- make -C src/ clean +- make -C test/ clean ++ $(MAKE) -C src clean ++ $(MAKE) -C test clean + + install: +- make -C src/ install ++ $(MAKE) -C src install + + install-shlib: +- make -C src/ install-shlib ++ $(MAKE) -C src install-shlib + + install-staticlib: +- make -C src/ install-staticlib ++ $(MAKE) -C src install-staticlib +diff -Nur qrupdate-1.1.1.orig/src/Makefile qrupdate-1.1.1/src/Makefile +--- qrupdate-1.1.1.orig/src/Makefile 2010-01-19 11:32:35.000000000 +0000 ++++ qrupdate-1.1.1/src/Makefile 2010-05-13 17:28:30.000000000 +0100 +@@ -34,6 +34,8 @@ + + OBJS = $(SRC:%.f=%.o) + ++PICOBJS = $(SRC:%.f=%.lo) ++ + lib: ../libqrupdate.a + + ifeq ($(shell uname),Darwin) +@@ -46,19 +48,22 @@ + ../libqrupdate.a: $(OBJS) + ar -cr $@ $(OBJS) + +-../libqrupdate.so: $(OBJS) +- $(FC) $(FFLAGS) -shared -o $@ -Wl,-soname=libqrupdate.so.$(MAJOR) $(OBJS) \ ++../libqrupdate.so: $(PICOBJS) ++ $(FC) $(LDFLAGS) -shared -o $@ -Wl,-soname=libqrupdate.so.$(MAJOR) $(PICOBJS) \ + $(BLAS) $(LAPACK) + +-../libqrupdate.dylib: $(OBJS) +- $(FC) $(FFLAGS) $(LDFLAGS) -dynamiclib -o $@ -install_name $(PREFIX)/$(LIBDIR)/libqrupdate.$(MAJOR).dylib $(OBJS) \ ++../libqrupdate.dylib: $(PICOBJS) ++ $(FC) $(LDFLAGS) -dynamiclib -o $@ -install_name $(PREFIX)/$(LIBDIR)/libqrupdate.$(MAJOR).dylib $(PICOBJS) \ + $(BLAS) $(LAPACK) + ++$(PICOBJS): %.lo: %.f ++ $(FC) $(FFLAGS) $(FPICFLAGS) -c $< -o $@ ++ + $(OBJS): %.o: %.f +- $(FC) $(FFLAGS) $(FPICFLAGS) -c $< ++ $(FC) $(FFLAGS) -c $< + + clean: +- rm -f $(OBJS) ++ rm -f $(OBJS) $(PICOBJS) + + install: install-shlib install-staticlib + +diff -Nur qrupdate-1.1.1.orig/test/Makefile qrupdate-1.1.1/test/Makefile +--- qrupdate-1.1.1.orig/test/Makefile 2010-02-11 08:25:37.000000000 +0000 ++++ qrupdate-1.1.1/test/Makefile 2010-05-13 17:15:51.000000000 +0100 +@@ -41,7 +41,7 @@ + $(FC) $(FFLAGS) -c $< + + ../libqrupdate.a: +- make -C ../ lib +- ++ $(MAKE) -C .. lib ++ + clean: + rm -f *.o $(PROGS) $(OUTS) diff --git a/sci-libs/qrupdate/files/qrupdate-1.1.2-install.patch b/sci-libs/qrupdate/files/qrupdate-1.1.2-install.patch new file mode 100644 index 000000000000..0eee49ae68f4 --- /dev/null +++ b/sci-libs/qrupdate/files/qrupdate-1.1.2-install.patch @@ -0,0 +1,23 @@ +--- src/Makefile.orig 2010-02-07 15:58:01 +0100 ++++ src/Makefile 2010-02-07 16:02:18 +0100 +@@ -65,14 +65,17 @@ + install-shlib: ../libqrupdate$(SOEXT) install-lib$(SOEXT) + + install-lib.so: +- install -D -m644 ../libqrupdate.so $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.so.$(VERSION) ++ install -d $(DESTDIR)$(PREFIX)/$(LIBDIR)/ ++ install -m644 ../libqrupdate.so $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.so.$(VERSION) + ln -s libqrupdate.so.$(VERSION) $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.so.$(MAJOR) + ln -s libqrupdate.so.$(VERSION) $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.so + + install-lib.dylib: +- install -D -m644 ../libqrupdate.dylib $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.$(VERSION).dylib ++ install -d $(DESTDIR)$(PREFIX)/$(LIBDIR)/ ++ install -m644 ../libqrupdate.dylib $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.$(VERSION).dylib + ln -s libqrupdate.$(VERSION).dylib $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.$(MAJOR).dylib + ln -s libqrupdate.$(VERSION).dylib $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.dylib + + install-staticlib: ../libqrupdate.a +- install -D -m644 ../libqrupdate.a $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.a ++ install -d $(DESTDIR)$(PREFIX)/$(LIBDIR)/ ++ install -m644 ../libqrupdate.a $(DESTDIR)$(PREFIX)/$(LIBDIR)/libqrupdate.a diff --git a/sci-libs/qrupdate/metadata.xml b/sci-libs/qrupdate/metadata.xml new file mode 100644 index 000000000000..4f893e7adf6b --- /dev/null +++ b/sci-libs/qrupdate/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + qrupdate is a library for fast updating of qr and cholesky decompositions. +</longdescription> + <upstream> + <remote-id type="sourceforge">qrupdate</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/qrupdate/qrupdate-1.1.2-r1.ebuild b/sci-libs/qrupdate/qrupdate-1.1.2-r1.ebuild new file mode 100644 index 000000000000..9ecaa417d02c --- /dev/null +++ b/sci-libs/qrupdate/qrupdate-1.1.2-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 multilib versionator toolchain-funcs + +DESCRIPTION="Library for updating of QR and Cholesky decompositions" +HOMEPAGE="https://sourceforge.net/projects/qrupdate" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="alpha amd64 ~arm hppa ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~ppc-macos" +IUSE="static-libs" + +RDEPEND="virtual/lapack" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-1.1.1-Makefiles.patch \ + "${FILESDIR}"/${PN}-1.1.2-install.patch + sed -i Makeconf \ + -e "s:gfortran:$(tc-getFC):g" \ + -e "s:FFLAGS=.*:FFLAGS=${FFLAGS}:" \ + -e "s:BLAS=.*:BLAS=$($(tc-getPKG_CONFIG) --libs blas):" \ + -e "s:LAPACK=.*:LAPACK=$($(tc-getPKG_CONFIG) --libs lapack):" \ + -e "/^LIBDIR=/a\PREFIX=${EPREFIX}/usr" \ + -e "s:LIBDIR=lib:LIBDIR=$(get_libdir):" \ + || die "Failed to set up Makeconf" +} + +src_compile() { + emake solib + use static-libs && emake lib +} + +src_install() { + emake DESTDIR="${D}" install-shlib + dosym libqrupdate.so.$(get_major_version) /usr/$(get_libdir)/libqrupdate.so + use static-libs && emake DESTDIR="${D}" install-staticlib + dodoc README ChangeLog +} diff --git a/sci-libs/rosetta-db/Manifest b/sci-libs/rosetta-db/Manifest new file mode 100644 index 000000000000..83289f537480 --- /dev/null +++ b/sci-libs/rosetta-db/Manifest @@ -0,0 +1,5 @@ +DIST rosetta3.4_database.tgz 212443671 SHA256 4573c2cb43be0fd805ae9dee6a40948c92e829207a52e419552080400e94b2e4 SHA512 c057cabcc95e6ff2278517e04d0fe8c7968a5c29d17ceb7bc75ac6e655b0a798d4ca819b313616c69b6cc18252c12b9af083d9cab9d4e30dac4c32db2f058b81 WHIRLPOOL e856396bd4fcd937fbb643a59c6689079fc3157c48b47b7848cd954267fa68972ee7dbb05fb9d5ee14fc72b064d4b58ae596d0fa7e3e192b3c7aa0b371dc9b43 +EBUILD rosetta-db-3.4.ebuild 700 SHA256 d36a9bd3b5555de1a024bb7295a504401586a08c18e15aabd3005f112299f71d SHA512 fbf3a3b3b9a1a9fa4ace3fe99e671fb84b3c84612d8cfe9572e93f9946b352a842c22d9b4b87dfa59a42fe8a36a1a054e95e44859a81e0f3b1e0067f9e0678ca WHIRLPOOL f92bc7e4917264807db50e72e9dc61d4318f8594c63f66a8936ef485e316ec2f351d2187feae169c0804a791557434e00a91eff84908fd4d33468f869c61fe91 +MISC ChangeLog 2572 SHA256 5acce1839ab3b99c03b20b02fe5c4f91fbb1fa7e945ba0a8496645114f305734 SHA512 1f5b1b30c13491b57cffdf30bfba4add6d921cdd3cfc1372d67d4bd84a70cf498bdfb8689ab8d5548c08017a680db52d4fbd966cf1c9f2defababdbf50ad3756 WHIRLPOOL 5ee9ab6dfffcda4c9c67c253a986819667876f20340fc35ca3b4aa0464b70908d3b5b64b84ee82cc33f6ae405978311df237629ddfc312085a0438ab1d130070 +MISC ChangeLog-2015 674 SHA256 be559d614bead29a7d1bf9c8eb31828968a1cce2b4c0f9e178c8b1730ad494b1 SHA512 59def62e94f9f76c0c32537714d55e8a15fad96173c0984bde26ba362787f4f4d44bdac16ca0b59211c2a14637d109bde289e67caf2e599c61cc50fa0213ab88 WHIRLPOOL 1c73dbcd9ab3dfe63d6eb11f2380c726ded22362a1dea010a915bf965f220b02ac40be772876311e1cce972a81932d7bcc45ca3eb866efc7946d11a851c156bd +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-libs/rosetta-db/metadata.xml b/sci-libs/rosetta-db/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/rosetta-db/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/rosetta-db/rosetta-db-3.4.ebuild b/sci-libs/rosetta-db/rosetta-db-3.4.ebuild new file mode 100644 index 000000000000..aaaf7603fccd --- /dev/null +++ b/sci-libs/rosetta-db/rosetta-db-3.4.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils + +MY_PN="${PN%-db}" +MY_P="${MY_PN}${PV}_database" + +DESCRIPTION="Essential database for rosetta" +HOMEPAGE="http://www.rosettacommons.org" +SRC_URI="${MY_P}.tgz" + +LICENSE="rosetta" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RESTRICT="fetch binchecks strip" + +S="${WORKDIR}"/${MY_PN}_database + +pkg_nofetch() { + einfo "Go to ${HOMEPAGE} and get ${A}" + einfo "which must be placed in ${DISTDIR}" +} + +src_install() { + esvn_clean + insinto /usr/share/${PN} + doins -r * + + cat >> "${T}"/41rosetta-db <<- EOF + ROSETTA3_DB="${EPREFIX}/usr/share/${PN}" + EOF + doenvd "${T}"/41rosetta-db +} diff --git a/sci-libs/rosetta-fragments/Manifest b/sci-libs/rosetta-fragments/Manifest new file mode 100644 index 000000000000..a4b4008cb433 --- /dev/null +++ b/sci-libs/rosetta-fragments/Manifest @@ -0,0 +1,7 @@ +AUX rosetta-fragments-3.1-chemshift.patch 1721 SHA256 02ab89d1d762c65653c6582481f5ece77c57d79c79bc6b16609c522ceafcbb49 SHA512 3475a4fd7a433d4d380ccd5ab11cf32f326fafc828d1bead0dbb0e03f5e53c613bf57c7950e090d8a2eb34c4ba93ecf25b25afcc9f251ff5f943e6b7e3112bb1 WHIRLPOOL d86a5147f7be585bcae825f0ab03eac84ab173aa781351ac4414cfd9ddc0329815097609beb2fc54a88636e3cb277894fe1ad73d5bda77d6d6cb528365fd594a +AUX rosetta-fragments-3.1-nnmake.patch 7030 SHA256 cfb08b00ee66e4342afda54129c735358b3fbd6a70ef88647b9ca18d96ce33b1 SHA512 de6d41f68911a5beddc8a15c9ce33013b03462642229aaf3b09ae4123c281260fa725bbd55593eea305b05d2ed21e1d17394686ee4e42bda20825d71d9367501 WHIRLPOOL 8ae1e9b64c3842e2091bc0cac434673f40ca8e0512ee417a78eeb4ea11c2c48368aa1bf1547843cb26e41c2c5f1e49e6ce3e4487d1b53e248f496db2a07ef5ed +DIST rosetta3.1_fragments.tgz 221931894 SHA256 2211cab76e4848d80d6fd311e97535de220a865d8afc72d8ca12f90b7d4641bf SHA512 a2b2646c916ea1b98e2c7267c1eadb1fd6cb76d015c24bd4e8318ce127cb5d96ca56bfdd76821e1dd884e03d59631f544e221b9f541ad4063a99e96dbb029da1 WHIRLPOOL 32d0758e6782da8088178e11af5bfe23b457e98a3ab9a8cbb583d4e4aa48e5d1ef9005825ff62944c5c755a0ac99b3ff88fb7c1d1b249940110287969ff0118a +EBUILD rosetta-fragments-3.1-r1.ebuild 1133 SHA256 2447cade451d79957ac718d4abff4c7e266949c2866d3a1506f538e21df30750 SHA512 7d424dcfeed1d073c27c2ba5a86d75877c597bfea95f40ab7acff767d41786b66576dbedb0a626e84d00ca63cd0f9131227d3ff200c35ad6b4d33ff485be5ab7 WHIRLPOOL 1c9b9e8eae47c7bab86c8264b438b3050f0542658eb4dcaeeed2fc09fe303f00f26bc52cf7581836332cf347a8d321676593fe4970494730c1a08f4375f21d19 +MISC ChangeLog 2747 SHA256 f27e11f976b2e5f1e144b14a1cdcd603c97d21ea27919a1a99ab7125dfe499b1 SHA512 62a4ec9d7aa0a05a074083ebf74295be4d608317cd86c66b0b46b7932da02388b1fa095b03472e04432d2993670c8e6e602bea31ecd90ed20037621d328e9172 WHIRLPOOL a57ed1ba5934098532e525b2071bdbf1b9e4c66c0d0099acbfe3dcee4909e0331d75838909e2b4c1f95f9dd5ff4b7f932ba2c43cad708c5931f1acf3612fad7b +MISC ChangeLog-2015 1336 SHA256 83a5ea22bb3a9e8e19728f9c48c63adca8912fd367264f98f1c8ad258b674c92 SHA512 74f65c0d5dd99e7fa1d5b0c569917f7d4b66f169f1dbacbaaf91d3151f46b3befc1d75bbe79f26a1f58f370daedc25f337482c6405f6a4ed77e1708478467a3a WHIRLPOOL 9ab4b9cc9d0246d7433d73b864cfd11536d76543f46fa53cf5c2393e386e1c731c670631cd6491d4ef8d686357bb66c812736f811341c5b37892c9aa32165569 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 diff --git a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch new file mode 100644 index 000000000000..cb8fd9197d1b --- /dev/null +++ b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch @@ -0,0 +1,62 @@ + chemshift/make.system | 24 ++++++++++++------------ + chemshift/makefile | 2 +- + 2 files changed, 13 insertions(+), 13 deletions(-) + +diff --git a/chemshift/make.system b/chemshift/make.system +index 53bbd38..d105802 100644 +--- a/chemshift/make.system ++++ b/chemshift/make.system +@@ -60,18 +60,18 @@ endif + ########## once COMPILER is set, here are the options + + # defaults +-F77=f77 +-FFLAGS= +-FOPTIMFLAGS=-O +-FDEBUGFLAGS=-g ++F77?=f77 ++FFLAGS?= ++FOPTIMFLAGS?= ++FDEBUGFLAGS?= + FPROFILEFLAGS=-P + + ifeq ($(COMPILER),gnu) +- F77 = g77 +- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit +- FOPTIMFLAGS = -O -ffast-math -malign-double +- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W +- FPROFILEFLAGS = -pg ++ F77 ?= g77 ++ FFLAGS += -W -ffixed-line-length-132 -Wimplicit ++ FOPTIMFLAGS += -malign-double ++ FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W ++ FPROFILEFLAGS = + endif + + ifeq ($(COMPILER),pgi) # on mary, good bounds checking +@@ -108,9 +108,9 @@ endif + + # Suse ppc gnu + ifeq ($(COMPILER),ppc) +- F77 = g77 +- FFLAGS = -Wall -finline-functions -funroll-loops -W -ffixed-line-length-132 +- FDEBUGFLAGS = -g -C -Mbounds ++ F77 ?= g77 ++ FFLAGS += -Wall -W -ffixed-line-length-132 ++ FDEBUGFLAGS += -C -Mbounds + FOPTIMFLAGS = + endif + +diff --git a/chemshift/makefile b/chemshift/makefile +index 712e98f..05d3b64 100644 +--- a/chemshift/makefile ++++ b/chemshift/makefile +@@ -64,7 +64,7 @@ regular: compile + # rule to compile executable + compile: $(BASE_NAME).$(COMPILER) + $(BASE_NAME).$(COMPILER) : print ${OBJS} +- $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS) ++ $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS) + + # rule to compile object files: + .$(COMPILER).%.o: %.f diff --git a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch new file mode 100644 index 000000000000..91da48017eff --- /dev/null +++ b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch @@ -0,0 +1,153 @@ + nnmake/dipolar_nn.f | 2 +- + nnmake/make.system | 33 ++++++++++++++++----------------- + nnmake/make_fragments.pl | 36 ++++++++++++++++++------------------ + nnmake/makefile | 2 +- + 4 files changed, 36 insertions(+), 37 deletions(-) + +diff --git a/nnmake/dipolar_nn.f b/nnmake/dipolar_nn.f +index c159888..4412a20 100644 +--- a/nnmake/dipolar_nn.f ++++ b/nnmake/dipolar_nn.f +@@ -1396,7 +1396,7 @@ car pairDipolar(1,i) .le. pairDipolar(1,i+1) + write(0,*)'rejected' + write(0,*)x(1,iset),x(2,iset),x(3,iset),x(4,iset),x(5,iset) + do i=1,maplength(iset) +- write(0,'(i,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5), ++ write(0,'(i6,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5), + # b(i) + enddo + goto 300 +diff --git a/nnmake/make.system b/nnmake/make.system +index 34bea8f..2fbfabf 100644 +--- a/nnmake/make.system ++++ b/nnmake/make.system +@@ -55,18 +55,17 @@ endif + ########## once COMPILER is set, here are the options + + # defaults +-F77=f77 +-FFLAGS= +-FOPTIMFLAGS=-O +-FDEBUGFLAGS=-g +-FPROFILEFLAGS=-P ++F77?=f77 ++FOPTIMFLAGS= ++FDEBUGFLAGS= ++FPROFILEFLAGS= + + ifeq ($(COMPILER),gnu) +- F77 = g77 +- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit +- FOPTIMFLAGS = -O -ffast-math -malign-double +- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W +- FPROFILEFLAGS = -pg ++ F77 ?= g77 ++ FFLAGS += -W -ffixed-line-length-132 -Wimplicit ++ FOPTIMFLAGS += -malign-double ++ FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W ++ FPROFILEFLAGS = + endif + + ifeq ($(COMPILER),pgi) # on mary, good bounds checking +@@ -82,9 +81,9 @@ ifeq ($(COMPILER),pgi) # on mary, good bounds checking + endif + + ifeq ($(COMPILER),absoft) # on mary, fast +- F77 = f77 +- FFLAGS = -N109 -s -W +- LINKFLAGS = -lU77 ++ F77 ?= f77 ++ FFLAGS ?= -N109 -s -W ++ LINKFLAGS += -lU77 + FDEBUGFLAGS = -C -g + FOPTIMFLAGS = -O -N18 + FPROFILEFLAGS = -P -O +@@ -103,10 +102,10 @@ endif + + # Suse ppc gnu + ifeq ($(COMPILER),ppc) +- F77 = g77 +- FFLAGS = -Wall -finline-functions -funroll-loops -W -ffixed-line-length-132 +- FDEBUGFLAGS = -g -C -Mbounds +- FOPTIMFLAGS = ++ F77 ?= g77 ++ FFLAGS += -Wall -W -ffixed-line-length-132 ++ FDEBUGFLAGS += -C -Mbounds ++ FOPTIMFLAGS += + endif + + # alpha flags +diff --git a/nnmake/make_fragments.pl b/nnmake/make_fragments.pl +index 5273685..29619a2 100755 +--- a/nnmake/make_fragments.pl ++++ b/nnmake/make_fragments.pl +@@ -19,38 +19,38 @@ + + my $TAIL = "_v1_3"; + +-$src_dir = '/work/chu/rosetta/rosetta_C++/rosetta-2.2.0/rosetta_fragments'; +-$shareware_dir = '/work/chu/src/shareware'; +-$scratch = "/scratch/shared"; ++$src_dir = '@GENTOO_PORTAGE_EPREFIX@/'; ++$shareware_dir = '$src_dir/usr/share'; ++$scratch = "$src_dir/scratch/shared"; + + # psi-blast + #my $BLAST_BIN_DIR = "$shareware_dir/new_blast/blast-2.2.12/bin"; +-my $PSIBLAST = "$shareware_dir/blast/bin/blastpgp"; # PSI-BLAST (duh.) +-my $NR = "/$scratch/genomes/nr"; # nr blast database filename +-my $VALL_BLAST_DB = "/$scratch/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database') +-my $BLOSUM = "$scratch/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database') ++my $PSIBLAST = "$src_dir/usr/bin/blastpgp"; # PSI-BLAST (duh.) ++my $NR = "$shareware_dir/nr"; # nr blast database filename ++my $VALL_BLAST_DB = "$shareware_dir/rosetta-fragments/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database') ++my $BLOSUM = "$shareware_dir/rosetta-fragments/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database') + + # psipred +-my $FILTNR = "$scratch/genomes/filtnr"; # filtnr blast database filename +-my $MAKEMAT = "$shareware_dir/blast/bin/makemat"; # makemat utility (part of NCBI tools) +-my $PSIPRED = "$shareware_dir/psipred/bin/psipred"; # psipred +-my $PSIPASS2 = "$shareware_dir/psipred/bin/psipass2"; # psipass2 (part of psipred pkg) ++my $FILTNR = "$src_dir/tmp/filtnr"; # filtnr blast database filename ++my $MAKEMAT = "$src_dir/usr/bin/makemat"; # makemat utility (part of NCBI tools) ++my $PSIPRED = "$src_dir/usr/bin/psipred"; # psipred ++my $PSIPASS2 = "$src_dir/usr/bin/psipass2"; # psipass2 (part of psipred pkg) + my $PSIPRED_DATA = "$shareware_dir/psipred/data"; # dir containing psipred data files. + + # prof + #my $PROF = "$shareware_dir/prof/run_prof.py"; +-my $PROF = "$src_dir/nnmake/run_prof.py"; # remember to change prof executable location in run_prof.py ++my $PROF = "$src_dir/usr/bin/run_prof.py"; # remember to change prof executable location in run_prof.py + + # nnmake +-my $VALL = "$scratch/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database') +-my $VALL2 = "$scratch/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database') ++my $VALL = "$shareware_dir/rosetta-fragments/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database') ++my $VALL2 = "$shareware_dir/rosetta-fragments/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database') + my $VALL_NAME = "vall.dat.2006-05-05"; # filename of vall (vall.dat.<id> and vall_cst_coord.dat.<id> must exist) +-my $NNMAKE = "$src_dir/nnmake/pNNMAKE.gnu"; # nnmake binary (cvs respository 'nnmake') +-my $TRIMLOOPS = "$src_dir/nnmake/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake') ++my $NNMAKE = "$src_dir/usr/bin/pNNMAKE"; # nnmake binary (cvs respository 'nnmake') ++my $TRIMLOOPS = "$src_dir/usr/bin/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake') + + # chemshift +-my $CHEMSHIFT = "$src_dir/chemshift/pCHEMSHIFT.gnu"; # chemshift binary (cvs repository 'chemshift') +-my $TALOS_DB = "$scratch/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database') ++my $CHEMSHIFT = "$src_dir/usr/bin/pCHEMSHIFT"; # chemshift binary (cvs repository 'chemshift') ++my $TALOS_DB = "$shareware_dir/rosetta-fragments/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database') + + # jufo (secondary structure prediction software) + my $JUFO = "$shareware_dir/jufo/molecule.exe"; # jufo executable +diff --git a/nnmake/makefile b/nnmake/makefile +index c09ac1c..ebfde68 100644 +--- a/nnmake/makefile ++++ b/nnmake/makefile +@@ -102,7 +102,7 @@ VallCoord: coord_compile + # rule to compile executable + compile: print $(BASE_NAME).$(COMPILER) + $(BASE_NAME).$(COMPILER) : ${OBJS} +- $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS) ++ $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS) + + coord_compile: print $(COORD_BASE_NAME).$(COMPILER) + $(COORD_BASE_NAME).$(COMPILER) : ${COORD_OBJS} diff --git a/sci-libs/rosetta-fragments/metadata.xml b/sci-libs/rosetta-fragments/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-libs/rosetta-fragments/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild new file mode 100644 index 000000000000..055c225edf1d --- /dev/null +++ b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic prefix toolchain-funcs + +DESCRIPTION="Fragment library for rosetta" +HOMEPAGE="http://www.rosettacommons.org" +SRC_URI="rosetta3.1_fragments.tgz" + +LICENSE="rosetta" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="" +RDEPEND=" + sci-biology/ncbi-tools + || ( sci-biology/update-blastdb sci-biology/ncbi-tools++ ) + sci-biology/psipred" + +RESTRICT="fetch" + +S="${WORKDIR}"/${PN/-/_} + +pkg_nofetch() { + einfo "Go to ${HOMEPAGE} and get ${PN}.tgz and rename it to ${A}" + einfo "which must be placed in ${DISTDIR}" +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-nnmake.patch \ + "${FILESDIR}"/${P}-chemshift.patch + tc-export F77 + eprefixify nnmake/*.pl +} + +src_compile() { + emake -C nnmake + emake -C chemshift +} + +src_install() { + esvn_clean . + + newbin nnmake/pNNMAKE.gnu pNNMAKE + newbin chemshift/pCHEMSHIFT.gnu pCHEMSHIFT + + dobin nnmake/*.pl + + insinto /usr/share/${PN} + doins -r *_database + dodoc fragments.README nnmake/{nnmake.README,vall/*.pl} chemshift/chemshift.README +} diff --git a/sci-libs/rtabmap/Manifest b/sci-libs/rtabmap/Manifest new file mode 100644 index 000000000000..5ef917b7dbd7 --- /dev/null +++ b/sci-libs/rtabmap/Manifest @@ -0,0 +1,8 @@ +DIST rtabmap-0.13.2.tar.gz 19488841 SHA256 857cf6a002ae3a499d385d883915fa87705461dab572d1ec92fc10ea3d45430b SHA512 ce80e55271e4b998c0ab11ad7d01c6a5b0df1be72057343ed0f4ffca9a2c95f946ea991c14d023772dee3bceee3ce97946207daf90a69eb6e450017c54495f2e WHIRLPOOL 58b9aba5f73288d1fcfec96776fc846724decdf18863415eafc4929a535334064bb2c8468a95d26de3f7b0807f8267077f13d90e6557b2273fd41e0473b3b74b +DIST rtabmap-0.14.0.tar.gz 19515196 SHA256 8d8dd6175dd7f4b769da91fd583874098fa5ebe99702b7f905678ee2b480a709 SHA512 00e2996b11aef8e0f61dc59ac59626b5b695ac3b5281d7776d73b54edbd90473bfffa1daae148e090b601a4d56d7feff2190f362ea188640b93db06e3760042f WHIRLPOOL 287ac32b49255a43cdc5df30fc8221abac645a230495bbc07cb7279a413bc98f772331a3c23146ca5bd8eac386a40eca8258fd6240527523bf2ef415f7fc4f9d +EBUILD rtabmap-0.13.2.ebuild 1401 SHA256 bac2292d023af4f7714aff7f4a376583f2b754eba02fa83874df7baffeb59fcc SHA512 b47443ccdf33d69e61c6912951f7c816cfaa13ca8076dc627c1814b7bbffc4a2c547296d2995726a6203b3317e568b6df7933918d660594729bf436ef80382b6 WHIRLPOOL c101c850551393442f3e224a9250469ef6696e9fd499c3b3f5eca1deff3613be90d5a435ef3131a706c34b39dc345f7c3435865df1b3f0b11a8669c0b91d8aa5 +EBUILD rtabmap-0.14.0.ebuild 1401 SHA256 bac2292d023af4f7714aff7f4a376583f2b754eba02fa83874df7baffeb59fcc SHA512 b47443ccdf33d69e61c6912951f7c816cfaa13ca8076dc627c1814b7bbffc4a2c547296d2995726a6203b3317e568b6df7933918d660594729bf436ef80382b6 WHIRLPOOL c101c850551393442f3e224a9250469ef6696e9fd499c3b3f5eca1deff3613be90d5a435ef3131a706c34b39dc345f7c3435865df1b3f0b11a8669c0b91d8aa5 +EBUILD rtabmap-9999.ebuild 1401 SHA256 bac2292d023af4f7714aff7f4a376583f2b754eba02fa83874df7baffeb59fcc SHA512 b47443ccdf33d69e61c6912951f7c816cfaa13ca8076dc627c1814b7bbffc4a2c547296d2995726a6203b3317e568b6df7933918d660594729bf436ef80382b6 WHIRLPOOL c101c850551393442f3e224a9250469ef6696e9fd499c3b3f5eca1deff3613be90d5a435ef3131a706c34b39dc345f7c3435865df1b3f0b11a8669c0b91d8aa5 +MISC ChangeLog 2878 SHA256 f5e614d852174ad001266d7f2ad2e0b034a19cf1504844af0a603aff59415527 SHA512 170db8d36db96c1159098e05801d44f80737e1b61f433c719dc5a45f4c2e138be51b9282b37677f66d118335f6988a69bf11b5dfdca8b59655b36e1f8cf4e13e WHIRLPOOL 797443f3e1451194350b07c61e8f67a84c3c419726dd2a1ad8bef0e2ac1748e8e6cf415ad8ab68e885f47928323fe459dd363d8ce6ce2f8eedaf994c9f88123a +MISC ChangeLog-2015 1053 SHA256 f6e96514bdd10853d2f27d8488980c2bd834504bb45a968977c6752f71fb998e SHA512 438383cd08ea2ee419ff529c40db5eeea01f2f523f9c56c777b2167fc8a60910c05e44d21e9659ddc21e0ff7faa2b6f0b6b2b024eb7fe3f90778742d2cccbcce WHIRLPOOL 061911391e5ef465cedc455cb3f755440952982a426c59aa72a43eee84ffbfff5f67bede96c2d4c8eb13fe6ec703dc77438e15a1ad667ad60b8c4195541532b8 +MISC metadata.xml 471 SHA256 e760b7c7f110617eecdd209ff62da45aed30192304e5605852cc91519f70ba0e SHA512 41752dfbb60d49072337438d49c313eec8a13b51bf8d3e65ad26ca519d3d8f105966756495111f01c6b365d57acb4f7be0b4dd017f8b7bfa483c08c354b0ca81 WHIRLPOOL b6f96d57864e109a687b266560655b291e1f1f235e5658dd0442d84a22a7b7274ab8fa496bfa8ad43cccfa133de3e464a32a046e3b18399440288cd450a7c81c diff --git a/sci-libs/rtabmap/metadata.xml b/sci-libs/rtabmap/metadata.xml new file mode 100644 index 000000000000..303a16f5feb3 --- /dev/null +++ b/sci-libs/rtabmap/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>aballier@gentoo.org</email> + <name>Alexis Ballier</name> + </maintainer> + <use> + <flag name="openni2">Adds support for Kinect-like 3D sensors devices with <pkg>dev-libs/OpenNI2</pkg>.</flag> + </use> + <upstream> + <remote-id type="github">introlab/rtabmap</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/rtabmap/rtabmap-0.13.2.ebuild b/sci-libs/rtabmap/rtabmap-0.13.2.ebuild new file mode 100644 index 000000000000..ec181ba72d33 --- /dev/null +++ b/sci-libs/rtabmap/rtabmap-0.13.2.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/introlab/rtabmap" +fi + +inherit ${SCM} cmake-utils multilib + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64" + SRC_URI="https://github.com/introlab/rtabmap/archive/${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="Real-Time Appearance-Based Mapping (RGB-D Graph SLAM)" +HOMEPAGE="http://introlab.github.io/rtabmap/" +LICENSE="BSD" +SLOT="0" +IUSE="examples ieee1394 openni2 qt5" + +RDEPEND=" + media-libs/opencv:=[qt5(-)?] + sci-libs/pcl:=[openni,vtk] + sci-libs/vtk:=[qt5(-)?] + sys-libs/zlib + sci-libs/octomap:= + dev-libs/boost:= + ieee1394? ( media-libs/libdc1394 ) + openni2? ( dev-libs/OpenNI2 ) + qt5? ( + dev-qt/qtwidgets:5 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtsvg:5 + ) +" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_configure() { + local mycmakeargs=( + "-DWITH_QT=$(usex qt5 ON OFF)" + "-DWITH_DC1394=$(usex ieee1394 ON OFF)" + "-DWITH_OPENNI2=$(usex openni2 ON OFF)" + "-DBUILD_EXAMPLES=$(usex examples ON OFF)" + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + # Needed since we force ros crawling to be done only in + # /usr/share/ros_packages/ + insinto /usr/share/ros_packages/${PN} + doins "${ED}/usr/share/${PN}/package.xml" +} diff --git a/sci-libs/rtabmap/rtabmap-0.14.0.ebuild b/sci-libs/rtabmap/rtabmap-0.14.0.ebuild new file mode 100644 index 000000000000..ec181ba72d33 --- /dev/null +++ b/sci-libs/rtabmap/rtabmap-0.14.0.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/introlab/rtabmap" +fi + +inherit ${SCM} cmake-utils multilib + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64" + SRC_URI="https://github.com/introlab/rtabmap/archive/${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="Real-Time Appearance-Based Mapping (RGB-D Graph SLAM)" +HOMEPAGE="http://introlab.github.io/rtabmap/" +LICENSE="BSD" +SLOT="0" +IUSE="examples ieee1394 openni2 qt5" + +RDEPEND=" + media-libs/opencv:=[qt5(-)?] + sci-libs/pcl:=[openni,vtk] + sci-libs/vtk:=[qt5(-)?] + sys-libs/zlib + sci-libs/octomap:= + dev-libs/boost:= + ieee1394? ( media-libs/libdc1394 ) + openni2? ( dev-libs/OpenNI2 ) + qt5? ( + dev-qt/qtwidgets:5 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtsvg:5 + ) +" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_configure() { + local mycmakeargs=( + "-DWITH_QT=$(usex qt5 ON OFF)" + "-DWITH_DC1394=$(usex ieee1394 ON OFF)" + "-DWITH_OPENNI2=$(usex openni2 ON OFF)" + "-DBUILD_EXAMPLES=$(usex examples ON OFF)" + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + # Needed since we force ros crawling to be done only in + # /usr/share/ros_packages/ + insinto /usr/share/ros_packages/${PN} + doins "${ED}/usr/share/${PN}/package.xml" +} diff --git a/sci-libs/rtabmap/rtabmap-9999.ebuild b/sci-libs/rtabmap/rtabmap-9999.ebuild new file mode 100644 index 000000000000..ec181ba72d33 --- /dev/null +++ b/sci-libs/rtabmap/rtabmap-9999.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +SCM="" +if [ "${PV#9999}" != "${PV}" ] ; then + SCM="git-r3" + EGIT_REPO_URI="https://github.com/introlab/rtabmap" +fi + +inherit ${SCM} cmake-utils multilib + +if [ "${PV#9999}" != "${PV}" ] ; then + KEYWORDS="" + SRC_URI="" +else + KEYWORDS="~amd64" + SRC_URI="https://github.com/introlab/rtabmap/archive/${PV}.tar.gz -> ${P}.tar.gz" +fi + +DESCRIPTION="Real-Time Appearance-Based Mapping (RGB-D Graph SLAM)" +HOMEPAGE="http://introlab.github.io/rtabmap/" +LICENSE="BSD" +SLOT="0" +IUSE="examples ieee1394 openni2 qt5" + +RDEPEND=" + media-libs/opencv:=[qt5(-)?] + sci-libs/pcl:=[openni,vtk] + sci-libs/vtk:=[qt5(-)?] + sys-libs/zlib + sci-libs/octomap:= + dev-libs/boost:= + ieee1394? ( media-libs/libdc1394 ) + openni2? ( dev-libs/OpenNI2 ) + qt5? ( + dev-qt/qtwidgets:5 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtsvg:5 + ) +" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_configure() { + local mycmakeargs=( + "-DWITH_QT=$(usex qt5 ON OFF)" + "-DWITH_DC1394=$(usex ieee1394 ON OFF)" + "-DWITH_OPENNI2=$(usex openni2 ON OFF)" + "-DBUILD_EXAMPLES=$(usex examples ON OFF)" + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + # Needed since we force ros crawling to be done only in + # /usr/share/ros_packages/ + insinto /usr/share/ros_packages/${PN} + doins "${ED}/usr/share/${PN}/package.xml" +} diff --git a/sci-libs/scalapack/Manifest b/sci-libs/scalapack/Manifest new file mode 100644 index 000000000000..3bf3213f9b50 --- /dev/null +++ b/sci-libs/scalapack/Manifest @@ -0,0 +1,5 @@ +DIST scalapack-2.0.2.tgz 4779534 SHA256 0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c SHA512 92c71d3de0900955511c527ab3ca57ff69d6d9edc390e69f93ac3769d32ce83a714326bcb6218c8c74b8874be2fdc8aad5e42c912a12581e8d4ce8829ea39248 WHIRLPOOL ca5e9261bb046684ecb820247ae2d9953083f9989b5cdeccd033c67519a5ab1eb3bd3f12d0225767513d5307342ccd96f582dbd264b2decc9033bf1f7f5d7dbc +EBUILD scalapack-2.0.2.ebuild 1514 SHA256 f7e6d27f58f1ef6e24a310dc53beaba1c34ff0949f438f7e41d69597053d8c2d SHA512 9eaf38dcb6e4ddd29b0c4c7b102f0eba96985e2e3b2dbe44790d6c3c39d8d8b8f9afec439de237418ba78dc11c44745b7e046738140a3fa6fe314322350e87ad WHIRLPOOL 85bf9fca09012e6ba52d4dc6b8e914438a4088b6436a70ec4c1cbe8842c9ae929108d5b94649a0de157e104923d2b05ad7183be0e366860b95659504314a3651 +MISC ChangeLog 2433 SHA256 d7b790787fe94b35830012af1fef71e05fb206aef092abb8f84f21a31bdbabbd SHA512 6a6ca0518d5be3291b4fa31777301b9d46428d292dfb12ae55ec2da211c2884cb61c1c27b6b4acaa3e433fdb61df09dfceeb5251e140f5ca8862aedae82575dc WHIRLPOOL b72b6d21869240574e3ce623c5c53399db940a87e55ded5bced999a08e7286b2324026bae81d4fcaf65ad09bf39db73d9f7816a673e2ad23f25bcd267e3176e4 +MISC ChangeLog-2015 1687 SHA256 f5ae5b5a27d6e63f8d829112518e0b643b0362e163a7a945acfbe1f69f3bc4d2 SHA512 11e58a7c94e35f2e3759d895d518a6f610a81beeac86153893710a3328fa2bab41efdaaf8e3e7bdba0452510dd53f9c8f3153358726649b9d27e7cf28a1f09ae WHIRLPOOL c9537f569698c1f9a89f131f1d76b0b6be7653abfa09db86665092cb43b485a1a51f70ff56a2a97323f157141d115f4148b935e4ce55ecfcf30735b9d34df18a +MISC metadata.xml 656 SHA256 3299fbdac46be798a2e2373f1a29f05ecf046e16bce1d19e10c247b13894da87 SHA512 c0ee34b1315583fd3d46f707c56ca1c5d3ff5bc85c2a96c65ca02258d3e6799ed6d9f3e3352d8bacd3053681e7b1b15e55049a62520c933df06ede6022786354 WHIRLPOOL a88416e87d2123853427721d8181ede3f79c96fa16c43e46601d676a9544903e3c57a922849663924d4fb113466f83eded75b81cac77cb5e5a01b797626858ea diff --git a/sci-libs/scalapack/metadata.xml b/sci-libs/scalapack/metadata.xml new file mode 100644 index 000000000000..b538e0aef078 --- /dev/null +++ b/sci-libs/scalapack/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers. It is currently + written in a Single-Program-Multiple-Data style using explicit message + passing for interprocessor communication. It assumes matrices are laid out + in a two-dimensional block cyclic decomposition. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/scalapack/scalapack-2.0.2.ebuild b/sci-libs/scalapack/scalapack-2.0.2.ebuild new file mode 100644 index 000000000000..fadcb6568bd5 --- /dev/null +++ b/sci-libs/scalapack/scalapack-2.0.2.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils eutils fortran-2 + +DESCRIPTION="Subset of LAPACK routines redesigned for heterogenous (MPI) computing" +HOMEPAGE="http://www.netlib.org/scalapack/" +SRC_URI="${HOMEPAGE}/${P}.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs test" + +RDEPEND=" + virtual/lapack + virtual/mpi" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_prepare() { + use static-libs && mkdir "${WORKDIR}/${PN}_static" + # mpi does not have a pc file + sed -i -e 's/mpi//' scalapack.pc.in || die +} + +src_configure() { + scalapack_configure() { + local mycmakeargs=( + -DUSE_OPTIMIZED_LAPACK_BLAS=ON + -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" + -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" + $(cmake-utils_use_build test TESTING) + $@ + ) + cmake-utils_src_configure + } + + scalapack_configure -DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=OFF + use static-libs && \ + CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" scalapack_configure \ + -DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_LIBS=ON +} + +src_compile() { + cmake-utils_src_compile + use static-libs && \ + CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_compile +} + +src_install() { + cmake-utils_src_install + use static-libs && \ + CMAKE_BUILD_DIR="${WORKDIR}/${PN}_static" cmake-utils_src_install + + insinto /usr/include/blacs + doins BLACS/SRC/*.h + + insinto /usr/include/scalapack + doins PBLAS/SRC/*.h +} diff --git a/sci-libs/scikits/Manifest b/sci-libs/scikits/Manifest new file mode 100644 index 000000000000..504a14af6018 --- /dev/null +++ b/sci-libs/scikits/Manifest @@ -0,0 +1,5 @@ +DIST scikits.example-0.1.tar.gz 2401 SHA256 bd3ad5e2481a8d19411bf8c88ff06072cd592368650b4ea90c7dce435916ff3a SHA512 9e5534a9f12f5a11e7f9d7c3d4f16cdbfa34293b29882e6bc9ec597b6e7ac306cc65e2b197da8c0bfc8e319b01db31f34b06018b5420c3ad68e8cc3f490259e1 WHIRLPOOL 83655fef2c4b6d04ee890eb84d5e761a51e26257b8d38500e03fbce198e8e7a951afef050c0cda528dbbadf27ef6bbba2f72405acd33be423b1b429fac63e48e +EBUILD scikits-0.1-r1.ebuild 760 SHA256 a84b94a325c681ef55b925c058ee96fe87c2c8f4c90eddd7a2e04c0f97563c9c SHA512 c1911a565f55f02b88413b63dc69cf3734f2106f8ace8d9c2a060ce7800c73205fe6927fee1f5ab155e537e8bef9e259c3433e1edb0ed00074160460e55fdf69 WHIRLPOOL 75c6fe87226f7d9ed08266ec066c05a551ceeada9240157bd8992724bea9b5007c25a99e99d8e814ad8e7be458514736f5eda3b201d4cbdc3cfbdeded75375d5 +MISC ChangeLog 2698 SHA256 ce3c5d5a3b33e8e545a5157cca8c649a7c137869787f15ac66f8b4e2a04e2cce SHA512 8ef8e10248da459aebc128cfd49a7bb5b664fd2e3f001759fef08072054bc41e04b826698b72d4c834438b4db4e9d7604cbf3176f9d4c7674755878e099375db WHIRLPOOL d065aea7dcbb2ee3279f9e62c7ff599216c677123a0ce7bb2de8c7e93da69f7152ae5efb6457b16ea44308e052c72ddef36cc7ad59151b30a0b1dba9d4d51cb2 +MISC ChangeLog-2015 1434 SHA256 9ecea7f6f1288d7e7e3195d554eae952c7d168cd4f68a7087164dcdb801eff83 SHA512 281ce4933ed622265450b34e5e5ad10ab50d2d30e23e8c8f490ca466b61b3ae2e71940ef87e51c377084740a461f863dc449f13bde0e182f85edbe2a0671fd5c WHIRLPOOL 25b389270cd8b19b1442d3783f8f1152c276570aaa145666098c00df00f1d4fb1a64c4b0762672d79568cf41760bc39bffaa5d3721d1788952a3a6f9e7537988 +MISC metadata.xml 454 SHA256 43239e0b74c1ed8c6c4697ee53a9efb3dff9f2f1b8739a1e7f7fabd488853646 SHA512 b33fed7d1199471c4a86dadf1aa90951035fe49c76df9310de4ed13c391b92782230308a55a33c7fa88f5bd42b8718fe5f6ac88c0a8c1818848a447c4c1d0eb8 WHIRLPOOL 80d8146467941d1fff876da230768bfcf76217dac60709964a410066a09d88187c9b907793149a5ca634fe49f968513f1357d0db8ea7f49c96de9fe4dfb378bd diff --git a/sci-libs/scikits/metadata.xml b/sci-libs/scikits/metadata.xml new file mode 100644 index 000000000000..95dca3798e5a --- /dev/null +++ b/sci-libs/scikits/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en">Meta package for the scikits. Include a standard example as well.</longdescription> + <upstream> + <remote-id type="pypi">scikits.example</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/scikits/scikits-0.1-r1.ebuild b/sci-libs/scikits/scikits-0.1-r1.ebuild new file mode 100644 index 000000000000..17719aed0e3c --- /dev/null +++ b/sci-libs/scikits/scikits-0.1-r1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} pypy ) + +inherit python-r1 + +DESCRIPTION="Common files for python scikits" +HOMEPAGE="http://projects.scipy.org/scipy/scikits" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}.example/${PN}.example-${PV}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS}" +DEPEND="${DEPEND}" + +S="${WORKDIR}" + +src_install() { + python_moduleinto scikits + python_foreach_impl python_domodule scikits.example*/scikits/__init__.py + + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r scikits.example*/* + fi +} diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest new file mode 100644 index 000000000000..edabbf53bea8 --- /dev/null +++ b/sci-libs/scikits_image/Manifest @@ -0,0 +1,10 @@ +AUX scikits_image-0.11.3-adapthist-backport.patch 3489 SHA256 2c5bb038bd05fa5afb50264a497411ee7d1ca7bad98cf27d1af091d65f958722 SHA512 5f4e063bc2456f7e78f8485d8a2d68a19e77ab7a171332f758761173cc7608d64c81e69ea785265b71763ab6a0c43c35b17699b954064a38498ebdf0db92e91b WHIRLPOOL 5f0806074b6cbc37530d049323751cc714263304e76b58d8411c61a4ce8139b4bc6eb5353b09a15920db9f61dd42df036bb40931e3769a8b68cfca68418d22f8 +DIST scikit-image-0.11.3.tar.gz 18589296 SHA256 768e568f3299966c294b7eb8cd114fc648f7bfaef422ee9cc750dd8d9d09e44b SHA512 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+Subject: [PATCH] Fix adapthist mask logic + +Use minlength in bincount + +Fix mask logic +--- + skimage/exposure/_adapthist.py | 8 +++++--- + skimage/exposure/tests/test_exposure.py | 14 +++++++------- + 2 files changed, 12 insertions(+), 10 deletions(-) + +diff --git a/skimage/exposure/_adapthist.py b/skimage/exposure/_adapthist.py +index 343f71b..757daff 100644 +--- a/skimage/exposure/_adapthist.py ++++ b/skimage/exposure/_adapthist.py +@@ -247,12 +247,14 @@ def clip_histogram(hist, clip_limit): + while n_excess > 0: # Redistribute remaining excess + index = 0 + while n_excess > 0 and index < hist.size: ++ under_mask = hist < 0 + step_size = int(hist[hist < clip_limit].size / n_excess) + step_size = max(step_size, 1) + indices = np.arange(index, hist.size, step_size) +- under = hist[indices] < clip_limit +- hist[under] += 1 +- n_excess -= hist[under].size ++ under_mask[indices] = True ++ under_mask = (under_mask) & (hist < clip_limit) ++ hist[under_mask] += 1 ++ n_excess -= under_mask.sum() + index += 1 + + return hist +diff --git a/skimage/exposure/tests/test_exposure.py b/skimage/exposure/tests/test_exposure.py +index 8fb6d62..1b9c778 100644 +--- a/skimage/exposure/tests/test_exposure.py ++++ b/skimage/exposure/tests/test_exposure.py +@@ -199,9 +199,9 @@ def test_adapthist_scalar(): + full_scale = skimage.exposure.rescale_intensity(skimage.img_as_float(img)) + + assert_almost_equal = np.testing.assert_almost_equal +- assert_almost_equal(peak_snr(full_scale, adapted), 101.2295, 3) ++ assert_almost_equal(peak_snr(full_scale, adapted), 102.066, 3) + assert_almost_equal(norm_brightness_err(full_scale, adapted), +- 0.041, 3) ++ 0.038, 3) + return img, adapted + + +@@ -217,8 +217,8 @@ def test_adapthist_grayscale(): + nbins=128) + assert_almost_equal = np.testing.assert_almost_equal + assert img.shape == adapted.shape +- assert_almost_equal(peak_snr(img, adapted), 97.6876, 3) +- assert_almost_equal(norm_brightness_err(img, adapted), 0.0591, 3) ++ assert_almost_equal(peak_snr(img, adapted), 102.078, 3) ++ assert_almost_equal(norm_brightness_err(img, adapted), 0.0529, 3) + return data, adapted + + +@@ -238,7 +238,7 @@ def test_adapthist_color(): + assert adapted.max() == 1.0 + assert img.shape == adapted.shape + full_scale = skimage.exposure.rescale_intensity(img) +- assert_almost_equal(peak_snr(full_scale, adapted), 109.6, 1) ++ assert_almost_equal(peak_snr(full_scale, adapted), 109.393, 1) + assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.02, 2) + return data, adapted + +@@ -256,8 +256,8 @@ def test_adapthist_alpha(): + full_scale = skimage.exposure.rescale_intensity(img) + assert img.shape == adapted.shape + assert_almost_equal = np.testing.assert_almost_equal +- assert_almost_equal(peak_snr(full_scale, adapted), 109.60, 2) +- assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.0235, 3) ++ assert_almost_equal(peak_snr(full_scale, adapted), 109.393, 2) ++ assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.0248, 3) + + + def peak_snr(img1, img2): diff --git a/sci-libs/scikits_image/metadata.xml b/sci-libs/scikits_image/metadata.xml new file mode 100644 index 000000000000..8e05ce3947d6 --- /dev/null +++ b/sci-libs/scikits_image/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + This SciKit (toolkit for SciPy) includes useful image processing + algorithms for use with Python and NumPy. While SciPy’s ndimage + provides low-level manipulation, scikits.image centres around + algorithms and applications. +</longdescription> + <use> + <flag name="freeimage">Enable support for image i/o via + <pkg>media-libs/freeimage</pkg></flag> + <flag name="pyamg">Enable support for algebraic solvers via <pkg>dev-python/pyamg</pkg></flag> + </use> + <upstream> + <remote-id type="pypi">scikit-image</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/scikits_image/scikits_image-0.11.3.ebuild b/sci-libs/scikits_image/scikits_image-0.11.3.ebuild new file mode 100644 index 000000000000..99d76385d71a --- /dev/null +++ b/sci-libs/scikits_image/scikits_image-0.11.3.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_4 ) + +inherit distutils-r1 eutils virtualx + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Image processing routines for SciPy" +HOMEPAGE="http://scikit-image.org/" +SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc freeimage gtk pyamg qt4 test" + +RDEPEND=" + >=dev-python/matplotlib-1.1.0[${PYTHON_USEDEP}] + >=dev-python/networkx-1.8[${PYTHON_USEDEP}] + >=dev-python/numpy-1.6.1[${PYTHON_USEDEP}] + >=dev-python/pillow-1.7.8[${PYTHON_USEDEP}] + >=dev-python/six-1.3[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[sparse,${PYTHON_USEDEP}] + freeimage? ( media-libs/freeimage ) + gtk? ( dev-python/pygtk[$(python_gen_usedep 'python2*')] ) + pyamg? ( dev-python/pyamg[$(python_gen_usedep 'python2*')] ) + qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )" +DEPEND="${RDEPEND} + >=dev-python/cython-0.21[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( + dev-python/nose[${PYTHON_USEDEP}] + )" + +S="${WORKDIR}/${MYP}" + +DOCS=( CONTRIBUTORS.txt CONTRIBUTING.txt DEPENDS.txt RELEASE.txt TASKS.txt TODO.txt ) + +PATCHES=( + "${FILESDIR}"/${P}-adapthist-backport.patch +) + +python_test() { + distutils_install_for_testing + mkdir for_test && cd for_test || die + echo "backend : Agg" > matplotlibrc || die + echo "backend.qt4 : PyQt4" >> matplotlibrc || die + #echo "backend.qt4 : PySide" >> matplotlibrc || die + VIRTUALX_COMMAND=nosetests + MPLCONFIGDIR=. virtualmake --exe -v skimage || die +} + +pkg_postinst() { + optfeature "FITS io capability" dev-python/astropy + #optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk + #optfeature "io plugin providing most standard formats" dev-python/imread +} diff --git a/sci-libs/scikits_image/scikits_image-0.12.3.ebuild b/sci-libs/scikits_image/scikits_image-0.12.3.ebuild new file mode 100644 index 000000000000..ed088bd06527 --- /dev/null +++ b/sci-libs/scikits_image/scikits_image-0.12.3.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5} ) + +inherit distutils-r1 eutils virtualx + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Image processing routines for SciPy" +HOMEPAGE="http://scikit-image.org/" +SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc freeimage pyamg qt4 test" + +RDEPEND=" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + sci-libs/scipy[sparse,${PYTHON_USEDEP}] + freeimage? ( media-libs/freeimage ) + pyamg? ( dev-python/pyamg[${PYTHON_USEDEP}] ) + qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )" +DEPEND="${RDEPEND} + >=dev-python/cython-0.23[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/nose[${PYTHON_USEDEP}] )" + +S="${WORKDIR}/${MYP}" + +DOCS=( CONTRIBUTORS.txt CONTRIBUTING.txt DEPENDS.txt RELEASE.txt TASKS.txt TODO.txt ) + +python_test() { + distutils_install_for_testing + cd "${TEST_DIR}" || die "no ${TEST_DIR} available" + echo "backend : Agg" > matplotlibrc || die + echo "backend.qt4 : PyQt4" >> matplotlibrc || die + #echo "backend.qt4 : PySide" >> matplotlibrc || die + MPLCONFIGDIR=. virtx nosetests --exe -v skimage || die +} + +pkg_postinst() { + optfeature "FITS io capability" dev-python/astropy + optfeature "GTK" dev-python/pygtk + optfeature "Parallel computation" dev-python/dask + # not in portage yet + #optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk + #optfeature "io plugin providing most standard formats" dev-python/imread +} diff --git a/sci-libs/scikits_image/scikits_image-0.13.0.ebuild b/sci-libs/scikits_image/scikits_image-0.13.0.ebuild new file mode 100644 index 000000000000..cc09ed813cb9 --- /dev/null +++ b/sci-libs/scikits_image/scikits_image-0.13.0.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 eutils virtualx + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Image processing routines for SciPy" +HOMEPAGE="http://scikit-image.org/" +SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc freeimage pyamg qt4 test" + +RDEPEND=" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/pywavelets[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + sci-libs/scipy[sparse,${PYTHON_USEDEP}] + freeimage? ( media-libs/freeimage ) + pyamg? ( dev-python/pyamg[${PYTHON_USEDEP}] ) + qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )" +DEPEND="${RDEPEND} + >=dev-python/cython-0.23[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/nose[${PYTHON_USEDEP}] )" + +S="${WORKDIR}/${MYP}" + +DOCS=( CONTRIBUTORS.txt DEPENDS.txt RELEASE.txt TASKS.txt TODO.txt ) + +python_test() { + distutils_install_for_testing + cd "${TEST_DIR}" || die "no ${TEST_DIR} available" + echo "backend : Agg" > matplotlibrc || die + echo "backend.qt4 : PyQt4" >> matplotlibrc || die + #echo "backend.qt4 : PySide" >> matplotlibrc || die + MPLCONFIGDIR=. virtx nosetests --exe -v skimage || die +} + +pkg_postinst() { + optfeature "FITS io capability" dev-python/astropy + optfeature "GTK" dev-python/pygtk + optfeature "Parallel computation" dev-python/dask + # not in portage yet + #optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk + #optfeature "io plugin providing most standard formats" dev-python/imread +} diff --git a/sci-libs/scikits_learn/Manifest b/sci-libs/scikits_learn/Manifest new file mode 100644 index 000000000000..69c199c1b841 --- /dev/null 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b/sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch new file mode 100644 index 000000000000..96c6cc2dbde5 --- /dev/null +++ b/sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch @@ -0,0 +1,28 @@ +--- sklearn/setup.py.orig 2013-08-08 13:54:08.310879167 -0700 ++++ sklearn/setup.py 2013-08-08 13:52:59.808456423 -0700 +@@ -68,14 +68,6 @@ + libraries=libraries, + ) + +- # some libs needs cblas, fortran-compiled BLAS will not be sufficient +- blas_info = get_info('blas_opt', 0) +- if (not blas_info) or ( +- ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])): +- config.add_library('cblas', +- sources=[join('src', 'cblas', '*.c')]) +- warnings.warn(BlasNotFoundError.__doc__) +- + # the following packages depend on cblas, so they have to be build + # after the above. + config.add_subpackage('linear_model') +--- sklearn/_build_utils.py.orig 2013-08-08 14:01:35.994589269 -0700 ++++ sklearn/_build_utils.py 2013-08-08 12:19:41.875967870 -0700 +@@ -23,7 +23,7 @@ + return False + + blas_info = get_info('blas_opt', 0) +- if (not blas_info) or atlas_not_found(blas_info): ++ if (not blas_info): + cblas_libs = ['cblas'] + blas_info.pop('libraries', None) + else: diff --git a/sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch b/sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch new file mode 100644 index 000000000000..42657a7adacc --- /dev/null +++ b/sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch @@ -0,0 +1,30 @@ +diff -Nur scikit-learn-0.17.1.orig/sklearn/_build_utils.py scikit-learn-0.17.1/sklearn/_build_utils.py +--- scikit-learn-0.17.1.orig/sklearn/_build_utils.py 2016-03-09 00:27:54.756813784 +0000 ++++ scikit-learn-0.17.1/sklearn/_build_utils.py 2016-03-09 00:30:09.605118512 +0000 +@@ -23,7 +23,7 @@ + return False + + blas_info = get_info('blas_opt', 0) +- if (not blas_info) or atlas_not_found(blas_info): ++ if (not blas_info): + cblas_libs = ['cblas'] + blas_info.pop('libraries', None) + else: +diff -Nur scikit-learn-0.17.1.orig/sklearn/setup.py scikit-learn-0.17.1/sklearn/setup.py +--- scikit-learn-0.17.1.orig/sklearn/setup.py 2016-03-09 00:27:54.806813156 +0000 ++++ scikit-learn-0.17.1/sklearn/setup.py 2016-03-09 00:29:28.215638848 +0000 +@@ -58,14 +58,6 @@ + libraries=libraries, + ) + +- # some libs needs cblas, fortran-compiled BLAS will not be sufficient +- blas_info = get_info('blas_opt', 0) +- if (not blas_info) or ( +- ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])): +- config.add_library('cblas', +- sources=[join('src', 'cblas', '*.c')]) +- warnings.warn(BlasNotFoundError.__doc__) +- + # the following packages depend on cblas, so they have to be build + # after the above. + config.add_subpackage('linear_model') diff --git a/sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch b/sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch new file mode 100644 index 000000000000..e60f64947b03 --- /dev/null +++ b/sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch @@ -0,0 +1,32 @@ +Index: scikit-learn-0.18.1/sklearn/_build_utils/__init__.py +=================================================================== +--- scikit-learn-0.18.1.orig/sklearn/_build_utils/__init__.py ++++ scikit-learn-0.18.1/sklearn/_build_utils/__init__.py +@@ -31,7 +31,7 @@ def get_blas_info(): + return False + + blas_info = get_info('blas_opt', 0) +- if (not blas_info) or atlas_not_found(blas_info): ++ if (not blas_info): + cblas_libs = ['cblas'] + blas_info.pop('libraries', None) + else: +Index: scikit-learn-0.18.1/sklearn/setup.py +=================================================================== +--- scikit-learn-0.18.1.orig/sklearn/setup.py ++++ scikit-learn-0.18.1/sklearn/setup.py +@@ -63,14 +63,6 @@ def configuration(parent_package='', top + libraries=libraries, + ) + +- # some libs needs cblas, fortran-compiled BLAS will not be sufficient +- blas_info = get_info('blas_opt', 0) +- if (not blas_info) or ( +- ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])): +- config.add_library('cblas', +- sources=[join('src', 'cblas', '*.c')]) +- warnings.warn(BlasNotFoundError.__doc__) +- + # the following packages depend on cblas, so they have to be build + # after the above. + config.add_subpackage('linear_model') diff --git a/sci-libs/scikits_learn/metadata.xml b/sci-libs/scikits_learn/metadata.xml new file mode 100644 index 000000000000..0f62a4aec772 --- /dev/null +++ b/sci-libs/scikits_learn/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + scikits.learn is a python library for machine learning. It aims to + implement classic machine learning algorithms while remaining simple + and efficient. + </longdescription> + <upstream> + <remote-id type="pypi">scikit-learn</remote-id> + <remote-id type="sourceforge">scikit-learn</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/scikits_learn/scikits_learn-0.17.1.ebuild b/sci-libs/scikits_learn/scikits_learn-0.17.1.ebuild new file mode 100644 index 000000000000..052d3210d7e6 --- /dev/null +++ b/sci-libs/scikits_learn/scikits_learn-0.17.1.ebuild @@ -0,0 +1,116 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5} ) + +inherit distutils-r1 flag-o-matic + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Python modules for machine learning and data mining" +HOMEPAGE="http://scikit-learn.org" +SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nose[${PYTHON_USEDEP}] + >=dev-python/numpy-1.6.1[lapack,${PYTHON_USEDEP}] + sci-libs/scikits[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + virtual/blas + virtual/cblas + virtual/python-funcsigs[${PYTHON_USEDEP}] + " +DEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/numpy[lapack,${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + virtual/blas + virtual/cblas + doc? ( + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/sphinx[${PYTHON_USEDEP}] + )" + +S="${WORKDIR}/${MYP}" + +PATCHES=( "${FILESDIR}/${P}-system-cblas.patch" ) + +python_prepare_all() { + # bug #397605 + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + # scikits-learn now uses the horrible numpy.distutils automagic + export SCIPY_FCONFIG="config_fc --noopt --noarch" + + # use system joblib + rm -r sklearn/externals/joblib/* || die + echo "from joblib import *" > sklearn/externals/joblib/__init__.py + sed -i -e '/joblib\/test/d' sklearn/externals/setup.py || die + sed -i -e 's/..externals.joblib/ joblib/g' \ + sklearn/cross_validation.py \ + sklearn/decomposition/tests/test_sparse_pca.py \ + sklearn/metrics/pairwise.py || die + + rm sklearn/externals/funcsigs.py || die + rm sklearn/externals/odict.py || die + sed -e 's:from ..externals.funcsigs import signature:from funcsigs import signature:g' \ + -i sklearn/utils/fixes.py || die + + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile ${SCIPY_FCONFIG} +} + +python_compile_all() { + if use doc; then + cd "${S}/doc" || die + local d="${BUILD_DIR}"/lib + ln -s "${S}"/sklearn/datasets/{data,descr,images} \ + "${d}"/sklearn/datasets || die + VARTEXFONTS="${T}"/fonts \ + MPLCONFIGDIR="${BUILD_DIR}" \ + PYTHONPATH="${d}" \ + emake html + rm -r "${d}"/sklearn/datasets/{data,descr,images} || die + fi +} + +python_test() { + # doc builds and runs tests + use doc && return + distutils_install_for_testing ${SCIPY_FCONFIG} + esetup.py \ + install --root="${T}/test-${EPYTHON}" \ + --no-compile ${SCIPY_FCONFIG} + pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null + nosetests -v sklearn --exe || die + popd > /dev/null +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +python_install_all() { + find "${S}" -name \*LICENSE.txt -delete + insinto /usr/share/doc/${PF} + use doc && doins -r doc/_build/html + use examples && doins -r examples + distutils-r1_python_install_all +} diff --git a/sci-libs/scikits_learn/scikits_learn-0.17.ebuild b/sci-libs/scikits_learn/scikits_learn-0.17.ebuild new file mode 100644 index 000000000000..b2e0f79446eb --- /dev/null +++ b/sci-libs/scikits_learn/scikits_learn-0.17.ebuild @@ -0,0 +1,116 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_4 ) + +inherit distutils-r1 eutils multilib flag-o-matic + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Python modules for machine learning and data mining" +HOMEPAGE="http://scikit-learn.org" +SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nose[${PYTHON_USEDEP}] + >=dev-python/numpy-1.6.1[lapack,${PYTHON_USEDEP}] + sci-libs/scikits[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + virtual/blas + virtual/cblas + virtual/python-funcsigs[${PYTHON_USEDEP}] + " +DEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/numpy[lapack,${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + virtual/blas + virtual/cblas + doc? ( + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/sphinx[${PYTHON_USEDEP}] + )" + +S="${WORKDIR}/${MYP}" + +python_prepare_all() { + # bug #397605 + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + # scikits-learn now uses the horrible numpy.distutils automagic + export SCIPY_FCONFIG="config_fc --noopt --noarch" + + # use system joblib + rm -r sklearn/externals/joblib/* || die + echo "from joblib import *" > sklearn/externals/joblib/__init__.py + sed -i -e '/joblib\/test/d' sklearn/externals/setup.py || die + sed -i -e 's/..externals.joblib/joblib/g' \ + sklearn/decomposition/tests/test_sparse_pca.py \ + sklearn/metrics/pairwise.py || die + + rm sklearn/externals/funcsigs.py || die + rm sklearn/externals/odict.py || die + sed \ + -e 's:from ..externals.funcsigs import signature:from funcsigs import signature:g' \ + -i sklearn/utils/fixes.py || die + + # use gentoo cblas infrastructure + epatch "${FILESDIR}"/${PN}-0.14.1-system-cblas.patch + + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile ${SCIPY_FCONFIG} +} + +python_compile_all() { + if use doc; then + cd "${S}/doc" || die + local d="${BUILD_DIR}"/lib + ln -s "${S}"/sklearn/datasets/{data,descr,images} \ + "${d}"/sklearn/datasets || die + VARTEXFONTS="${T}"/fonts \ + MPLCONFIGDIR="${BUILD_DIR}" \ + PYTHONPATH="${d}" \ + emake html + rm -r "${d}"/sklearn/datasets/{data,descr,images} || die + fi +} + +python_test() { + # doc builds and runs tests + use doc && return + distutils_install_for_testing ${SCIPY_FCONFIG} + esetup.py \ + install --root="${T}/test-${EPYTHON}" \ + --no-compile ${SCIPY_FCONFIG} + pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null + nosetests -v sklearn --exe || die + popd > /dev/null +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +python_install_all() { + find "${S}" -name \*LICENSE.txt -delete + use doc && HTML_DOCS=( doc/_build/html/. ) + use examples && EXAMPLES=( examples/. ) + distutils-r1_python_install_all +} diff --git a/sci-libs/scikits_learn/scikits_learn-0.18.1.ebuild b/sci-libs/scikits_learn/scikits_learn-0.18.1.ebuild new file mode 100644 index 000000000000..69d00a0a7a62 --- /dev/null +++ b/sci-libs/scikits_learn/scikits_learn-0.18.1.ebuild @@ -0,0 +1,119 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5} ) + +inherit distutils-r1 flag-o-matic + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Python modules for machine learning and data mining" +HOMEPAGE="http://scikit-learn.org" +SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nose[${PYTHON_USEDEP}] + >=dev-python/numpy-1.6.1[lapack,${PYTHON_USEDEP}] + sci-libs/scikits[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + virtual/blas + virtual/cblas + virtual/python-funcsigs[${PYTHON_USEDEP}] + " +DEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/numpy[lapack,${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + virtual/blas + virtual/cblas + doc? ( + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/sphinx[${PYTHON_USEDEP}] + )" + +S="${WORKDIR}/${MYP}" + +PATCHES=( "${FILESDIR}/${P}-system-cblas.patch" ) + +python_prepare_all() { + # bug #397605 + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + # scikits-learn now uses the horrible numpy.distutils automagic + export SCIPY_FCONFIG="config_fc --noopt --noarch" + + # remove bundled cblas + rm -r sklearn/src || die + + # use system joblib + rm -r sklearn/externals/joblib || die + sed -i -e '/joblib/d' sklearn/externals/setup.py || die + for f in sklearn/{*/,}*.py; do + sed -r -e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \ + -e 's/from (sklearn|\.|)\.externals import/import/' -i $f || die + done + + rm sklearn/externals/funcsigs.py || die + rm sklearn/externals/odict.py || die + for f in sklearn/{utils/fixes.py,gaussian_process/{tests/test_,}kernels.py}; do + sed -r -e 's/from (sklearn|\.|)\.externals\.funcsigs/from funcsigs/' -i $f || die + done + + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile ${SCIPY_FCONFIG} +} + +python_compile_all() { + if use doc; then + cd "${S}/doc" || die + local d="${BUILD_DIR}"/lib + ln -s "${S}"/sklearn/datasets/{data,descr,images} \ + "${d}"/sklearn/datasets || die + VARTEXFONTS="${T}"/fonts \ + MPLCONFIGDIR="${BUILD_DIR}" \ + PYTHONPATH="${d}" \ + emake html + rm -r "${d}"/sklearn/datasets/{data,descr,images} || die + fi +} + +python_test() { + # doc builds and runs tests + use doc && return + distutils_install_for_testing ${SCIPY_FCONFIG} + esetup.py \ + install --root="${T}/test-${EPYTHON}" \ + --no-compile ${SCIPY_FCONFIG} + pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null + nosetests -v sklearn --exe || die + popd > /dev/null +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +python_install_all() { + find "${S}" -name \*LICENSE.txt -delete + insinto /usr/share/doc/${PF} + use doc && doins -r doc/_build/html + use examples && doins -r examples + distutils-r1_python_install_all +} diff --git a/sci-libs/scikits_learn/scikits_learn-0.18.2-r1.ebuild b/sci-libs/scikits_learn/scikits_learn-0.18.2-r1.ebuild new file mode 100644 index 000000000000..339670ff4d3f --- /dev/null +++ b/sci-libs/scikits_learn/scikits_learn-0.18.2-r1.ebuild @@ -0,0 +1,123 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 flag-o-matic + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Python modules for machine learning and data mining" +HOMEPAGE="http://scikit-learn.org" +SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples test" + +# tried to unbundle virtual/python-funcsigs, funcsigs, odict +# but it is a large mess to maintain + +RDEPEND=" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nose[${PYTHON_USEDEP}] + dev-python/numpy[lapack,${PYTHON_USEDEP}] + sci-libs/scikits[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + virtual/blas:= + virtual/cblas:= +" + +DEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/numpy[lapack,${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + virtual/blas:= + virtual/cblas:= + doc? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/sphinx[${PYTHON_USEDEP}] + ) +" + +S="${WORKDIR}/${MYP}" + +PATCHES=( "${FILESDIR}/${PN}-0.18.1-system-cblas.patch" ) + +python_prepare_all() { + # bug #397605 + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + # scikits-learn now uses the horrible numpy.distutils automagic + export SCIPY_FCONFIG="config_fc --noopt --noarch" + + # remove bundled cblas + rm -r sklearn/src || die + + # commented out, since it is a mess to maintain + # use system joblib + #rm -r sklearn/externals/joblib || die + #sed -i -e '/joblib/d' sklearn/externals/setup.py || die + #for f in sklearn/{*/,}*.py; do + # sed -r -e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \ + # -e 's/from (sklearn|\.|)\.externals import/import/' -i $f || die + #done + + # use system funcsigs and odict + #rm sklearn/externals/funcsigs.py || die + #rm sklearn/externals/odict.py || die + #for f in sklearn/{utils/fixes.py,gaussian_process/{tests/test_,}kernels.py}; do + # sed -r -e 's/from (sklearn|\.|)\.externals\.funcsigs/from funcsigs/' -i $f || die + #done + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile ${SCIPY_FCONFIG} +} + +python_compile_all() { + if use doc; then + cd "${S}/doc" || die + local d="${BUILD_DIR}/lib" + ln -s \ + "${S}"/sklearn/datasets/{data,descr,images} \ + "${d}"/sklearn/datasets || die + VARTEXFONTS="${T}"/fonts \ + MPLCONFIGDIR="${BUILD_DIR}" \ + PYTHONPATH="${d}" \ + emake html + rm -r "${d}"/sklearn/datasets/{data,descr,images} || die + fi +} + +python_test() { + # doc builds and runs tests + use doc && return + distutils_install_for_testing ${SCIPY_FCONFIG} + esetup.py install \ + --root="${T}/test-${EPYTHON}" \ + --no-compile ${SCIPY_FCONFIG} + pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null + JOBLIB_MULTIPROCESSING=2 SKLEARN_SKIP_NETWORK_TESTS=1 nosetests -v sklearn --exe || die + popd > /dev/null +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +python_install_all() { + find "${S}" -name \*LICENSE.txt -delete + insinto /usr/share/doc/${PF} + use doc && doins -r doc/_build/html + use examples && doins -r examples + distutils-r1_python_install_all +} diff --git a/sci-libs/scikits_learn/scikits_learn-0.18.2.ebuild b/sci-libs/scikits_learn/scikits_learn-0.18.2.ebuild new file mode 100644 index 000000000000..7f8aa4ce6687 --- /dev/null +++ b/sci-libs/scikits_learn/scikits_learn-0.18.2.ebuild @@ -0,0 +1,119 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 flag-o-matic + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Python modules for machine learning and data mining" +HOMEPAGE="http://scikit-learn.org" +SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nose[${PYTHON_USEDEP}] + >=dev-python/numpy-1.6.1[lapack,${PYTHON_USEDEP}] + sci-libs/scikits[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.9[${PYTHON_USEDEP}] + virtual/blas + virtual/cblas + virtual/python-funcsigs[${PYTHON_USEDEP}] + " +DEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/numpy[lapack,${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + virtual/blas + virtual/cblas + doc? ( + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/sphinx[${PYTHON_USEDEP}] + )" + +S="${WORKDIR}/${MYP}" + +PATCHES=( "${FILESDIR}/${PN}-0.18.1-system-cblas.patch" ) + +python_prepare_all() { + # bug #397605 + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + # scikits-learn now uses the horrible numpy.distutils automagic + export SCIPY_FCONFIG="config_fc --noopt --noarch" + + # remove bundled cblas + rm -r sklearn/src || die + + # use system joblib + rm -r sklearn/externals/joblib || die + sed -i -e '/joblib/d' sklearn/externals/setup.py || die + for f in sklearn/{*/,}*.py; do + sed -r -e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \ + -e 's/from (sklearn|\.|)\.externals import/import/' -i $f || die + done + + rm sklearn/externals/funcsigs.py || die + rm sklearn/externals/odict.py || die + for f in sklearn/{utils/fixes.py,gaussian_process/{tests/test_,}kernels.py}; do + sed -r -e 's/from (sklearn|\.|)\.externals\.funcsigs/from funcsigs/' -i $f || die + done + + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile ${SCIPY_FCONFIG} +} + +python_compile_all() { + if use doc; then + cd "${S}/doc" || die + local d="${BUILD_DIR}"/lib + ln -s "${S}"/sklearn/datasets/{data,descr,images} \ + "${d}"/sklearn/datasets || die + VARTEXFONTS="${T}"/fonts \ + MPLCONFIGDIR="${BUILD_DIR}" \ + PYTHONPATH="${d}" \ + emake html + rm -r "${d}"/sklearn/datasets/{data,descr,images} || die + fi +} + +python_test() { + # doc builds and runs tests + use doc && return + distutils_install_for_testing ${SCIPY_FCONFIG} + esetup.py \ + install --root="${T}/test-${EPYTHON}" \ + --no-compile ${SCIPY_FCONFIG} + pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null + nosetests -v sklearn --exe || die + popd > /dev/null +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +python_install_all() { + find "${S}" -name \*LICENSE.txt -delete + insinto /usr/share/doc/${PF} + use doc && doins -r doc/_build/html + use examples && doins -r examples + distutils-r1_python_install_all +} diff --git a/sci-libs/scikits_learn/scikits_learn-0.19.0.ebuild b/sci-libs/scikits_learn/scikits_learn-0.19.0.ebuild new file mode 100644 index 000000000000..0b9b744c56a6 --- /dev/null +++ b/sci-libs/scikits_learn/scikits_learn-0.19.0.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 flag-o-matic + +MYPN="${PN/scikits_/scikit-}" +MYP="${MYPN}-${PV}" + +DESCRIPTION="Python modules for machine learning and data mining" +HOMEPAGE="http://scikit-learn.org" +SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples test" + +# tried to unbundle virtual/python-funcsigs, funcsigs, odict +# but it is a large mess to maintain + +RDEPEND=" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nose[${PYTHON_USEDEP}] + dev-python/numpy[lapack,${PYTHON_USEDEP}] + sci-libs/scikits[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + virtual/blas:= + virtual/cblas:= +" + +DEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/numpy[lapack,${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + virtual/blas:= + virtual/cblas:= +" + +S="${WORKDIR}/${MYP}" + +PATCHES=( "${FILESDIR}"/${PN}-0.18.1-system-cblas.patch ) + +python_prepare_all() { + # bug #397605 + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + # scikits-learn now uses the horrible numpy.distutils automagic + export SCIPY_FCONFIG="config_fc --noopt --noarch" + + # remove bundled cblas + rm -r sklearn/src || die + + # commented out, since it is a mess to maintain + # use system joblib + #rm -r sklearn/externals/joblib || die + #sed -i -e '/joblib/d' sklearn/externals/setup.py || die + #for f in sklearn/{*/,}*.py; do + # sed -r -e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \ + # -e 's/from (sklearn|\.|)\.externals import/import/' -i $f || die + #done + + # use system funcsigs and odict + #rm sklearn/externals/funcsigs.py || die + #rm sklearn/externals/odict.py || die + #for f in sklearn/{utils/fixes.py,gaussian_process/{tests/test_,}kernels.py}; do + # sed -r -e 's/from (sklearn|\.|)\.externals\.funcsigs/from funcsigs/' -i $f || die + #done + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile ${SCIPY_FCONFIG} +} + +python_test() { + # doc builds and runs tests + use doc && return + distutils_install_for_testing ${SCIPY_FCONFIG} + esetup.py install \ + --root="${T}/test-${EPYTHON}" \ + --no-compile ${SCIPY_FCONFIG} + pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null + JOBLIB_MULTIPROCESSING=2 SKLEARN_SKIP_NETWORK_TESTS=1 nosetests -v sklearn --exe || die + popd > /dev/null +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +python_install_all() { + find "${S}" -name \*LICENSE.txt -delete + distutils-r1_python_install_all + if use examples; then + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi + +} diff --git a/sci-libs/scikits_optimization/Manifest b/sci-libs/scikits_optimization/Manifest new file mode 100644 index 000000000000..a36d1eaebeae --- /dev/null +++ b/sci-libs/scikits_optimization/Manifest @@ -0,0 +1,5 @@ +DIST scikits.optimization-0.3.tar.gz 25297 SHA256 9e33b1c76feec56dde7495ea4339e661d8d9b018709d82a62ee0332fd24a1c79 SHA512 e8f33f4770d9b0514854e36127c53554823a159363c69d1ca0445a05ca9ebc55bc7105b35b2c615bfbef0c63a2b658d628befccb0ab09bcf98d91f8cb4d8be72 WHIRLPOOL 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+ <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + A Python module for numerical optimization. +</longdescription> + <upstream> + <remote-id type="pypi">scikits.optimization</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/scikits_optimization/scikits_optimization-0.3.ebuild b/sci-libs/scikits_optimization/scikits_optimization-0.3.ebuild new file mode 100644 index 000000000000..aefab9cd031b --- /dev/null +++ b/sci-libs/scikits_optimization/scikits_optimization-0.3.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_P="${P/scikits_/scikits.}" + +DESCRIPTION="Python module for numerical optimization" +HOMEPAGE="http://projects.scipy.org/scipy/scikits" +SRC_URI="mirror://pypi/${PN:0:1}/scikits.optimization/${MY_P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scikits[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}]" + +S="${WORKDIR}/${MY_P}" + +python_test() { + esetup.py test +} diff --git a/sci-libs/scikits_timeseries/Manifest b/sci-libs/scikits_timeseries/Manifest new file mode 100644 index 000000000000..f5f2208bc064 --- /dev/null +++ b/sci-libs/scikits_timeseries/Manifest @@ -0,0 +1,6 @@ +DIST scikits.timeseries-0.91.3-html_docs.zip 907495 SHA256 181db1fa0d4b8eac5235eff79fad393c54ef82163cfcee0d78c550869ad8e11a SHA512 9fb474e2a13dee865801fa5aa5f05bb74ea2387b7e14d716210898d9b338b63b7f1935f7a5514d72ffcd6f4a8552054094244fab199e18c819815d4b19cd3f23 WHIRLPOOL d0dacdd7aa31785b68155f3507e34738d83316e72f5439875c0d641b72a7d600cc8e169fd9c84647fa29f7f4051c83f92884a5d5dd197aec2269093de13a0344 +DIST scikits.timeseries-0.91.3.tar.gz 323771 SHA256 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000000000000..49f91d414312 --- /dev/null +++ b/sci-libs/scikits_timeseries/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + The scikits.timeseries module provides classes and functions for + manipulating, reporting, and plotting time series of various + frequencies. The focus is on convenient data access and manipulation + while leveraging the existing mathematical functionality in numpy + and scipy. +</longdescription> + <upstream> + <remote-id type="sourceforge">pytseries</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/scikits_timeseries/scikits_timeseries-0.91.3-r1.ebuild b/sci-libs/scikits_timeseries/scikits_timeseries-0.91.3-r1.ebuild new file mode 100644 index 000000000000..12d23e7fb048 --- /dev/null +++ b/sci-libs/scikits_timeseries/scikits_timeseries-0.91.3-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +MY_P="${P/scikits_/scikits.}" + +DESCRIPTION="SciPy module for manipulating, reporting, and plotting time series" +HOMEPAGE="http://pytseries.sourceforge.net/index.html" +SRC_URI=" + mirror://sourceforge/pytseries/${MY_P}.tar.gz + doc? ( mirror://sourceforge/pytseries/${MY_P}-html_docs.zip )" + +LICENSE="BSD eGenixPublic-1.1" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc" + +DEPEND=" + dev-python/setuptools[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )" +RDEPEND=" + sci-libs/scipy[${PYTHON_USEDEP}] + sci-libs/scikits[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pytables[${PYTHON_USEDEP}]" + +S="${WORKDIR}/${MY_P}" + +python_test() { + esetup.py test +} + +python_install() { + distutils-r1_python_install + rm "${D}"$(python_get_sitedir)/scikits/__init__.py || die +} + +python_install_all() { + use doc && HTMLDOCS=( "${WORKDIR}/html" ) + distutils-r1_python_install_all +} diff --git a/sci-libs/scipy/Manifest b/sci-libs/scipy/Manifest new file mode 100644 index 000000000000..0fd321616b6b --- /dev/null +++ b/sci-libs/scipy/Manifest @@ -0,0 +1,19 @@ +AUX scipy-0.12.0-blitz.patch 731 SHA256 4f487a746aa62a39cdab9381dd4191cef0ccb912ed2e22065a7de02b85c8a269 SHA512 a788d08d34e13b02a0ec8127fd7918786cd26376ef5160f4acde585c6c1ac018a39652d9174b5e31173aa5c4e0c2f63101549de70806ea7ac56731abe3cb929c WHIRLPOOL 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ae95726c4c661a2e5708a98b347f8ea25708574bbaf8ec86f315069551d6a0d68a43279b214be8b54cd20e5aacea1a9abd40a2de43d51f292a830cab0955d625 WHIRLPOOL fd568a6934a11260b01d919e2e2b10d1e859d9aab14625e6aca65348022d9ebdc6a19038649bb537f15b5ba12a82a79d01f2f8bc8e0dd599edf6a238df023ed4 diff --git a/sci-libs/scipy/files/scipy-0.12.0-blitz.patch b/sci-libs/scipy/files/scipy-0.12.0-blitz.patch new file mode 100644 index 000000000000..2817aa39b871 --- /dev/null +++ b/sci-libs/scipy/files/scipy-0.12.0-blitz.patch @@ -0,0 +1,28 @@ +Description: Fixes scipy.weave.inline compalition with g++ 4.3 and upwards +Author: Sameer Morar <smorar@gmail.com> +Forwarded: http://projects.scipy.org/scipy/scipy/ticket/739 +Bug-Debian: http://bugs.debian.org/598520 +Bug-Ubuntu: https://launchpad.net/bugs/302649 + +--- a/scipy/weave/blitz/blitz/blitz.h ++++ b/scipy/weave/blitz/blitz/blitz.h +@@ -65,6 +65,8 @@ + + #define BZ_THROW // Needed in <blitz/numinquire.h> + ++#include <cstdlib> ++ + BZ_NAMESPACE(blitz) + + #ifdef BZ_HAVE_STD +--- a/scipy/weave/blitz/blitz/prettyprint.h ++++ b/scipy/weave/blitz/blitz/prettyprint.h +@@ -22,6 +22,8 @@ + #ifndef BZ_PRETTYPRINT_H + #define BZ_PRETTYPRINT_H + ++#include <cstdlib> ++ + BZ_NAMESPACE(blitz) + + class prettyPrintFormat { diff --git a/sci-libs/scipy/files/scipy-0.12.0-restore-sys-argv.patch b/sci-libs/scipy/files/scipy-0.12.0-restore-sys-argv.patch new file mode 100644 index 000000000000..3eef739f93a8 --- /dev/null +++ b/sci-libs/scipy/files/scipy-0.12.0-restore-sys-argv.patch @@ -0,0 +1,15 @@ +Description: restore sys.argv in case of exception +Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=500814 + +--- a/scipy/weave/build_tools.py ++++ b/scipy/weave/build_tools.py +@@ -283,6 +283,9 @@ def build_extension(module_path,compiler + configure_python_path(build_dir) + except SyntaxError: #TypeError: + success = 0 ++ except Exception, e: ++ restore_sys_argv() ++ raise e + + # restore argv after our trick... + restore_sys_argv() diff --git a/sci-libs/scipy/files/scipy-0.16.1-glibc-2.22-backport.patch b/sci-libs/scipy/files/scipy-0.16.1-glibc-2.22-backport.patch new file mode 100644 index 000000000000..791d67f32531 --- /dev/null +++ b/sci-libs/scipy/files/scipy-0.16.1-glibc-2.22-backport.patch @@ -0,0 +1,30 @@ +From 1f5ccd5447ed2796bb8e9506cfbfdb4a82cccfc0 Mon Sep 17 00:00:00 2001 +From: Ralf Gommers <ralf.gommers@gmail.com> +Date: Sat, 24 Oct 2015 18:17:04 +0200 +Subject: [PATCH] TST: fix issue with a ctypes test for integrate on Fedora. + Closes gh-5370 + +--- + scipy/integrate/tests/test_quadpack.py | 9 ++++++++- + 1 file changed, 8 insertions(+), 1 deletion(-) + +diff --git a/scipy/integrate/tests/test_quadpack.py b/scipy/integrate/tests/test_quadpack.py +index c3a417c..f384c77 100644 +--- a/scipy/integrate/tests/test_quadpack.py ++++ b/scipy/integrate/tests/test_quadpack.py +@@ -42,7 +42,14 @@ def setUp(self): + file = 'libm.dylib' + else: + file = 'libm.so' +- self.lib = ctypes.CDLL(file) ++ ++ try: ++ self.lib = ctypes.CDLL(file) ++ except OSError: ++ # This test doesn't work on some Linux platforms (Fedora for ++ # example) that put an ld script in libm.so - see gh-5370 ++ self.skipTest("Ctypes can't import libm.so") ++ + restype = ctypes.c_double + argtypes = (ctypes.c_double,) + for name in ['sin', 'cos', 'tan']: diff --git a/sci-libs/scipy/metadata.xml b/sci-libs/scipy/metadata.xml new file mode 100644 index 000000000000..a4d8cf789821 --- /dev/null +++ b/sci-libs/scipy/metadata.xml @@ -0,0 +1,23 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + SciPy is an open source library of scientific tools for Python. SciPy + supplements the popular numpy module, gathering a variety of high level + science and engineering modules together as a single package. + SciPy includes modules for graphics and plotting, optimization, + integration, special functions, signal and image processing, genetic + algorithms, ODE solvers, and others. +</longdescription> + <use> + <flag name="sparse">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag> + </use> + <upstream> + <remote-id type="pypi">scipy</remote-id> + <remote-id type="sourceforge">scipy</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/scipy/scipy-0.16.1.ebuild b/sci-libs/scipy/scipy-0.16.1.ebuild new file mode 100644 index 000000000000..dd5908fb2319 --- /dev/null +++ b/sci-libs/scipy/scipy-0.16.1.ebuild @@ -0,0 +1,148 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) +PYTHON_REQ_USE="threads(+)" + +DOC_PV=${PV} + +inherit eutils fortran-2 distutils-r1 flag-o-matic multilib toolchain-funcs + +DESCRIPTION="Scientific algorithms library for Python" +HOMEPAGE="https://www.scipy.org/" +SRC_URI=" + mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz + doc? ( + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${PV}.zip -> ${PN}-${DOC_PV}-html.zip + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${PV}.pdf -> ${PN}-${DOC_PV}-ref.pdf + )" + +LICENSE="BSD LGPL-2" +SLOT="0" +IUSE="doc sparse test" +KEYWORDS="amd64 ~arm ppc ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" + +CDEPEND=" + >=dev-python/numpy-1.6.2[lapack,${PYTHON_USEDEP}] + sci-libs/arpack:0= + virtual/cblas + virtual/lapack + sparse? ( sci-libs/umfpack:0= )" +DEPEND="${CDEPEND} + dev-lang/swig + >=dev-python/cython-0.22[${PYTHON_USEDEP}] + virtual/pkgconfig + doc? ( app-arch/unzip ) + test? ( dev-python/nose[${PYTHON_USEDEP}] ) + " + +RDEPEND="${CDEPEND} + dev-python/pillow[${PYTHON_USEDEP}]" + +DOCS=( HACKING.rst.txt THANKS.txt ) + +DISTUTILS_IN_SOURCE_BUILD=1 + +src_unpack() { + unpack ${P}.tar.gz + if use doc; then + unzip -qo "${DISTDIR}"/${PN}-${DOC_PV}-html.zip -d html || die + fi +} + +pc_incdir() { + $(tc-getPKG_CONFIG) --cflags-only-I $@ | \ + sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libdir() { + $(tc-getPKG_CONFIG) --libs-only-L $@ | \ + sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libs() { + $(tc-getPKG_CONFIG) --libs-only-l $@ | \ + sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ + -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ + | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' +} + +python_prepare_all() { + # scipy automatically detects libraries by default + export {FFTW,FFTW3,UMFPACK}=None + use sparse && unset UMFPACK + # the missing symbols are in -lpythonX.Y, but since the version can + # differ, we just introduce the same scaryness as on Linux/ELF + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + [[ -z ${FC} ]] && export FC="$(tc-getFC)" + # hack to force F77 to be FC until bug #278772 is fixed + [[ -z ${F77} ]] && export F77="$(tc-getFC)" + export F90="${FC}" + export SCIPY_FCONFIG="config_fc --noopt --noarch" + append-fflags -fPIC + + local libdir="${EPREFIX}"/usr/$(get_libdir) + cat >> site.cfg <<-EOF + [blas] + include_dirs = $(pc_incdir cblas) + library_dirs = $(pc_libdir cblas blas):${libdir} + blas_libs = $(pc_libs cblas blas) + [lapack] + library_dirs = $(pc_libdir lapack):${libdir} + lapack_libs = $(pc_libs lapack) + EOF + + # Drop hashes to force rebuild of cython based .c code + rm cythonize.dat || die + + local PATCHES=( + "${FILESDIR}"/${PN}-0.12.0-blitz.patch + "${FILESDIR}"/${PN}-0.12.0-restore-sys-argv.patch + "${FILESDIR}"/${P}-glibc-2.22-backport.patch + ) + distutils-r1_python_prepare_all +} + +python_compile() { + ${EPYTHON} tools/cythonize.py || die + distutils-r1_python_compile ${SCIPY_FCONFIG} +} + +python_test() { + # fails with bdist_egg. should it be fixed in distutils-r1 eclass? + distutils_install_for_testing ${SCIPY_FCONFIG} + cd "${TEST_DIR}" || die "no ${TEST_DIR} available" + "${PYTHON}" -c \ + 'import numpy as np; print("relaxed strides checking:", np.ones((10,1),order="C").flags.f_contiguous)' \ + || die + # https://github.com/scipy/scipy/issues/5426 + "${EPYTHON}" -c \ + "import scipy, sys; r = scipy.test('fast', verbose=2, raise_warnings='release'); sys.exit(0 if r.wasSuccessful() else 1)" \ + || die "Tests fail with ${EPYTHON}" +# "${EPYTHON}" -c \ +# "import scipy, sys; r = scipy.test('fast',verbose=2); sys.exit(0 if r.wasSuccessful() else 1)" \ +# || die "Tests fail with ${EPYTHON}" +} + +python_install_all() { + if use doc; then + dodoc "${DISTDIR}"/${PN}-${DOC_PV}-ref.pdf + docinto html + dodoc -r "${WORKDIR}"/html/. + fi + distutils-r1_python_install_all +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +pkg_postinst() { + elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER" + elog "to your prefered image viewer. Example:" + elog "\t echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc" +} diff --git a/sci-libs/scipy/scipy-0.18.1.ebuild b/sci-libs/scipy/scipy-0.18.1.ebuild new file mode 100644 index 000000000000..c1d9ea57af22 --- /dev/null +++ b/sci-libs/scipy/scipy-0.18.1.ebuild @@ -0,0 +1,146 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) +PYTHON_REQ_USE="threads(+)" + +DOC_PV=${PV} + +inherit fortran-2 distutils-r1 flag-o-matic multiprocessing toolchain-funcs + +DESCRIPTION="Scientific algorithms library for Python" +HOMEPAGE="https://www.scipy.org/" +SRC_URI=" + mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz + doc? ( + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${PV}.zip -> ${PN}-${DOC_PV}-html.zip + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${PV}.pdf -> ${PN}-${DOC_PV}-ref.pdf + )" + +LICENSE="BSD LGPL-2" +SLOT="0" +IUSE="doc sparse test" +KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" + +CDEPEND=" + >=dev-python/numpy-1.10[lapack,${PYTHON_USEDEP}] + sci-libs/arpack:0= + virtual/cblas + virtual/lapack + sparse? ( sci-libs/umfpack:0= )" +DEPEND="${CDEPEND} + dev-lang/swig + >=dev-python/cython-0.22[${PYTHON_USEDEP}] + virtual/pkgconfig + doc? ( app-arch/unzip ) + test? ( dev-python/nose[${PYTHON_USEDEP}] )" +RDEPEND="${CDEPEND} + dev-python/pillow[${PYTHON_USEDEP}]" + +DOCS=( HACKING.rst.txt THANKS.txt ) + +DISTUTILS_IN_SOURCE_BUILD=1 + +PATCHES=( + "${FILESDIR}"/${PN}-0.12.0-blitz.patch + "${FILESDIR}"/${PN}-0.12.0-restore-sys-argv.patch +) + +src_unpack() { + default + if use doc; then + unzip -qo "${DISTDIR}"/${PN}-${DOC_PV}-html.zip -d html || die + fi +} + +pc_incdir() { + $(tc-getPKG_CONFIG) --cflags-only-I $@ | \ + sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libdir() { + $(tc-getPKG_CONFIG) --libs-only-L $@ | \ + sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libs() { + $(tc-getPKG_CONFIG) --libs-only-l $@ | \ + sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ + -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ + | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' +} + +python_prepare_all() { + # scipy automatically detects libraries by default + export {FFTW,FFTW3,UMFPACK}=None + use sparse && unset UMFPACK + # the missing symbols are in -lpythonX.Y, but since the version can + # differ, we just introduce the same scaryness as on Linux/ELF + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + [[ -z ${FC} ]] && export FC="$(tc-getFC)" + # hack to force F77 to be FC until bug #278772 is fixed + [[ -z ${F77} ]] && export F77="$(tc-getFC)" + export F90="${FC}" + export SCIPY_FCONFIG="config_fc --noopt --noarch" + append-fflags -fPIC + + local libdir="${EPREFIX}"/usr/$(get_libdir) + cat >> site.cfg <<-EOF || die + [blas] + include_dirs = $(pc_incdir cblas) + library_dirs = $(pc_libdir cblas blas):${libdir} + blas_libs = $(pc_libs cblas blas) + [lapack] + library_dirs = $(pc_libdir lapack):${libdir} + lapack_libs = $(pc_libs lapack) + EOF + + # Drop hashes to force rebuild of cython based .c code + rm cythonize.dat || die + + distutils-r1_python_prepare_all +} + +python_compile() { + ${EPYTHON} tools/cythonize.py || die + distutils-r1_python_compile \ + $(usex python_targets_python3_5 "" "-j $(makeopts_jobs)") \ + ${SCIPY_FCONFIG} +} + +python_test() { + # fails with bdist_egg. should it be fixed in distutils-r1 eclass? + distutils_install_for_testing ${SCIPY_FCONFIG} + cd "${TEST_DIR}" || die "no ${TEST_DIR} available" + "${PYTHON}" -c \ + 'import numpy as np; print("relaxed strides checking:", np.ones((10,1),order="C").flags.f_contiguous)' \ + || die + # https://github.com/scipy/scipy/issues/5426 + "${EPYTHON}" -c \ + "import scipy, sys; r = scipy.test('fast', verbose=2, raise_warnings='release'); sys.exit(0 if r.wasSuccessful() else 1)" \ + || die "Tests fail with ${EPYTHON}" +# "${EPYTHON}" -c \ +# "import scipy, sys; r = scipy.test('fast',verbose=2); sys.exit(0 if r.wasSuccessful() else 1)" \ +# || die "Tests fail with ${EPYTHON}" +} + +python_install_all() { + use doc && \ + local DOCS=( "${DISTDIR}"/${PN}-${DOC_PV}-ref.pdf ) \ + local HTML_DOCS=( "${WORKDIR}"/html/. ) + distutils-r1_python_install_all +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +pkg_postinst() { + elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER" + elog "to your prefered image viewer. Example:" + elog "\t echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc" +} diff --git a/sci-libs/scipy/scipy-0.19.1.ebuild b/sci-libs/scipy/scipy-0.19.1.ebuild new file mode 100644 index 000000000000..864285aeeb4f --- /dev/null +++ b/sci-libs/scipy/scipy-0.19.1.ebuild @@ -0,0 +1,142 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) +PYTHON_REQ_USE="threads(+)" + +DOC_PV=${PV} + +inherit fortran-2 distutils-r1 flag-o-matic multiprocessing toolchain-funcs + +DESCRIPTION="Scientific algorithms library for Python" +HOMEPAGE="https://www.scipy.org/" +SRC_URI=" + mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz + doc? ( + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${PV}.zip -> ${PN}-${DOC_PV}-html.zip + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${PV}.pdf -> ${PN}-${DOC_PV}-ref.pdf + )" + +LICENSE="BSD LGPL-2" +SLOT="0" +IUSE="doc sparse test" +KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos" + +CDEPEND=" + >=dev-python/numpy-1.10[lapack,${PYTHON_USEDEP}] + sci-libs/arpack:0= + virtual/cblas + virtual/lapack + sparse? ( sci-libs/umfpack:0= )" +DEPEND="${CDEPEND} + dev-lang/swig + >=dev-python/cython-0.22[${PYTHON_USEDEP}] + >=dev-python/setuptools-36[${PYTHON_USEDEP}] + virtual/pkgconfig + doc? ( app-arch/unzip ) + test? ( dev-python/nose[${PYTHON_USEDEP}] )" +RDEPEND="${CDEPEND} + dev-python/pillow[${PYTHON_USEDEP}]" + +DOCS=( HACKING.rst.txt THANKS.txt ) + +DISTUTILS_IN_SOURCE_BUILD=1 + +src_unpack() { + default + if use doc; then + unzip -qo "${DISTDIR}"/${PN}-${DOC_PV}-html.zip -d html || die + fi +} + +pc_incdir() { + $(tc-getPKG_CONFIG) --cflags-only-I $@ | \ + sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libdir() { + $(tc-getPKG_CONFIG) --libs-only-L $@ | \ + sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libs() { + $(tc-getPKG_CONFIG) --libs-only-l $@ | \ + sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ + -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ + | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' +} + +python_prepare_all() { + # scipy automatically detects libraries by default + export {FFTW,FFTW3,UMFPACK}=None + use sparse && unset UMFPACK + # the missing symbols are in -lpythonX.Y, but since the version can + # differ, we just introduce the same scaryness as on Linux/ELF + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + [[ -z ${FC} ]] && export FC="$(tc-getFC)" + # hack to force F77 to be FC until bug #278772 is fixed + [[ -z ${F77} ]] && export F77="$(tc-getFC)" + export F90="${FC}" + export SCIPY_FCONFIG="config_fc --noopt --noarch" + append-fflags -fPIC + + local libdir="${EPREFIX}"/usr/$(get_libdir) + cat >> site.cfg <<-EOF || die + [blas] + include_dirs = $(pc_incdir cblas) + library_dirs = $(pc_libdir cblas blas):${libdir} + blas_libs = $(pc_libs cblas blas) + [lapack] + library_dirs = $(pc_libdir lapack):${libdir} + lapack_libs = $(pc_libs lapack) + EOF + + # Drop hashes to force rebuild of cython based .c code + rm cythonize.dat || die + + distutils-r1_python_prepare_all +} + +python_compile() { + ${EPYTHON} tools/cythonize.py || die + distutils-r1_python_compile \ + $(usex python_targets_python3_5 "" "-j $(makeopts_jobs)") \ + ${SCIPY_FCONFIG} +} + +python_test() { + # fails with bdist_egg. should it be fixed in distutils-r1 eclass? + distutils_install_for_testing ${SCIPY_FCONFIG} + cd "${TEST_DIR}" || die "no ${TEST_DIR} available" + "${PYTHON}" -c \ + 'import numpy as np; print("relaxed strides checking:", np.ones((10,1),order="C").flags.f_contiguous)' \ + || die + # https://github.com/scipy/scipy/issues/5426 + "${EPYTHON}" -c \ + "import scipy, sys; r = scipy.test('fast', verbose=2, raise_warnings='release'); sys.exit(0 if r.wasSuccessful() else 1)" \ + || die "Tests fail with ${EPYTHON}" +# "${EPYTHON}" -c \ +# "import scipy, sys; r = scipy.test('fast',verbose=2); sys.exit(0 if r.wasSuccessful() else 1)" \ +# || die "Tests fail with ${EPYTHON}" +} + +python_install_all() { + use doc && \ + local DOCS=( "${DISTDIR}"/${PN}-${DOC_PV}-ref.pdf ) \ + local HTML_DOCS=( "${WORKDIR}"/html/. ) + distutils-r1_python_install_all +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +pkg_postinst() { + elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER" + elog "to your prefered image viewer. Example:" + elog "\t echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc" +} diff --git a/sci-libs/scipy/scipy-9999.ebuild b/sci-libs/scipy/scipy-9999.ebuild new file mode 100644 index 000000000000..b25250bfad33 --- /dev/null +++ b/sci-libs/scipy/scipy-9999.ebuild @@ -0,0 +1,125 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) +PYTHON_REQ_USE="threads(+)" + +DOC_PV=${PV} + +inherit fortran-2 distutils-r1 flag-o-matic git-r3 multiprocessing toolchain-funcs + +DESCRIPTION="Scientific algorithms library for Python" +HOMEPAGE="https://www.scipy.org/" +EGIT_REPO_URI="https://github.com/scipy/scipy.git" + +LICENSE="BSD LGPL-2" +SLOT="0" +KEYWORDS="" +IUSE="sparse test" + +CDEPEND=" + >=dev-python/numpy-1.10[lapack,${PYTHON_USEDEP}] + sci-libs/arpack:0= + virtual/cblas + virtual/lapack + sparse? ( sci-libs/umfpack:0= )" +DEPEND="${CDEPEND} + dev-lang/swig + >=dev-python/cython-0.23.4[${PYTHON_USEDEP}] + virtual/pkgconfig + test? ( dev-python/nose[${PYTHON_USEDEP}] ) + " + +RDEPEND="${CDEPEND} + dev-python/pillow[${PYTHON_USEDEP}]" + +DOCS=( HACKING.rst.txt THANKS.txt ) + +DISTUTILS_IN_SOURCE_BUILD=1 + +pc_incdir() { + $(tc-getPKG_CONFIG) --cflags-only-I $@ | \ + sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libdir() { + $(tc-getPKG_CONFIG) --libs-only-L $@ | \ + sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libs() { + $(tc-getPKG_CONFIG) --libs-only-l $@ | \ + sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ + -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ + | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' +} + +python_prepare_all() { + # scipy automatically detects libraries by default + export {FFTW,FFTW3,UMFPACK}=None + use sparse && unset UMFPACK + # the missing symbols are in -lpythonX.Y, but since the version can + # differ, we just introduce the same scaryness as on Linux/ELF + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + [[ -z ${FC} ]] && export FC="$(tc-getFC)" + # hack to force F77 to be FC until bug #278772 is fixed + [[ -z ${F77} ]] && export F77="$(tc-getFC)" + export F90="${FC}" + export SCIPY_FCONFIG="config_fc --noopt --noarch" + append-fflags -fPIC + + local libdir="${EPREFIX}"/usr/$(get_libdir) + cat >> site.cfg <<-EOF || die + [blas] + include_dirs = $(pc_incdir cblas) + library_dirs = $(pc_libdir cblas blas):${libdir} + blas_libs = $(pc_libs cblas blas) + [lapack] + library_dirs = $(pc_libdir lapack):${libdir} + lapack_libs = $(pc_libs lapack) + EOF + + # Drop hashes to force rebuild of cython based .c code + rm cythonize.dat || die + + distutils-r1_python_prepare_all +} + +python_compile() { + ${EPYTHON} tools/cythonize.py || die + distutils-r1_python_compile \ + $(usex python_targets_python3_5 "" "-j $(makeopts_jobs)") \ + ${SCIPY_FCONFIG} +} + +python_test() { + # fails with bdist_egg. should it be fixed in distutils-r1 eclass? + distutils_install_for_testing ${SCIPY_FCONFIG} + cd "${TEST_DIR}" || die "no ${TEST_DIR} available" + einfo "Run test I" + "${PYTHON}" -c \ + 'import numpy as np; print("relaxed strides checking:", np.ones((10,1),order="C").flags.f_contiguous)' \ + || die + einfo "Run test II" + # https://github.com/scipy/scipy/issues/5426 + "${EPYTHON}" -c \ + "import scipy, sys; r = scipy.test('fast', verbose=2, raise_warnings='release'); sys.exit(0 if r.wasSuccessful() else 1)" \ + || die "Tests fail with ${EPYTHON}" +# "${EPYTHON}" -c \ +# "import scipy, sys; r = scipy.test('fast',verbose=2); sys.exit(0 if r.wasSuccessful() else 1)" \ +# || die "Tests fail with ${EPYTHON}" +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} +} + +pkg_postinst() { + elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER" + elog "to your prefered image viewer. Example:" + elog "\t echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc" +} diff --git a/sci-libs/scotch/Manifest b/sci-libs/scotch/Manifest new file mode 100644 index 000000000000..18ca1e967d9c --- /dev/null +++ b/sci-libs/scotch/Manifest @@ -0,0 +1,15 @@ +AUX scotch-5.1.12b-as-needed.patch 4878 SHA256 e9084641e7cea9fdf21293a4ae7dcf65b73837e3ba59881d32dafa08bde88a8a SHA512 9f5bf65999978d851b0c61de2235af982e6d1d057af5906d328f2a4b83775f8dd567f1386eecc186d6ec1287d8e84215a88b879ec77de4ac6de5b129ad263411 WHIRLPOOL 122321a4d85a936aceb96a6a2c522c7ee3493e5b1ec76f30d2815388464f3f7681928c71d11595c983a3825b44bba7e8c54b95af94539041bb1cd7b4c3107c7e +AUX scotch-6.0.0-as-needed.patch 5874 SHA256 b9159d4808c91d8846ce05bfe96cd787d777a7195dfd17bc1f589dbcec22495b SHA512 efb458b53ceaa40c140e0920a3e31ab563f347a3bc21d727c338f4b971e4312ef680bb248e99dd609b5191f9e91460a1aa2149932d4277c5bc6406ef0206c24e WHIRLPOOL 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059e33b0e1021dc07c716e0d04b61fe56e97be1ae26c771c8641ce0a2dac83cdc10b6582730778edcd9bb4a25a050e81ae6d8331451c272b2b3727a03b601712 WHIRLPOOL 4b0d9e7f59f92a46eb85a670b62cedd8ca08291ad4da7208b5fe54543ff64976eee03cb557322d513cb46d372cfad1b38eae09afef76ad93d2d37122a60eccf3 diff --git a/sci-libs/scotch/files/scotch-5.1.12b-as-needed.patch b/sci-libs/scotch/files/scotch-5.1.12b-as-needed.patch new file mode 100644 index 000000000000..73888d8797e7 --- /dev/null +++ b/sci-libs/scotch/files/scotch-5.1.12b-as-needed.patch @@ -0,0 +1,112 @@ +diff -Nur src.orig/esmumps/Makefile src/esmumps/Makefile +--- src.orig/esmumps/Makefile 2012-03-12 00:14:14.536109811 +0000 ++++ src/esmumps/Makefile 2012-03-12 04:26:12.884108074 +0000 +@@ -44,7 +44,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -I$(includedir) -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) $(<) -o $(@) -L$(libdir) $(LDFLAGS) -L. -l$(ESMUMPSLIB) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit ++ $(CC) $(CFLAGS) -I$(includedir) $(<) -L$(libdir) -L. -l$(ESMUMPSLIB) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) -o $(@) + + ## + ## Project rules. +@@ -57,9 +57,9 @@ + libesmumps$(LIB) \ + main_esmumps$(EXE) + +-ptscotch : clean ++ptscotch : clean common.h + $(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC=$(CCP) SCOTCHLIB=ptscotch ESMUMPSLIB=ptesmumps \ +- libesmumps$(LIB) \ ++ libptesmumps$(LIB) \ + main_esmumps$(EXE) + + install : +@@ -142,7 +142,7 @@ + common.h \ + esmumps.h + +-libesmumps$(LIB) : graph_graph$(OBJ) \ ++lib$(ESMUMPSLIB)$(LIB) : graph_graph$(OBJ) \ + order$(OBJ) \ + order_scotch_graph$(OBJ) \ + dof$(OBJ) \ +diff -Nur src.orig/libscotch/Makefile src/libscotch/Makefile +--- src.orig/libscotch/Makefile 2012-03-12 00:14:14.496108751 +0000 ++++ src/libscotch/Makefile 2012-03-12 01:32:28.562403624 +0000 +@@ -43,7 +43,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) -o $(@) $(LDFLAGS) ++ $(CC) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) $(LDFLAGS) -o $(@) + + ## + ## Project rules. +@@ -2543,7 +2543,7 @@ + mapping.h \ + order.h \ + parser.h +- $(CCD) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) -o $(@) $(LDFLAGS) ++ $(CCD) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) $(LDFLAGS) -o $(@) + + scotch.h : dummysizes$(EXE) \ + library.h +diff -Nur src.orig/libscotchmetis/Makefile src/libscotchmetis/Makefile +--- src.orig/libscotchmetis/Makefile 2012-03-12 00:14:14.456107691 +0000 ++++ src/libscotchmetis/Makefile 2012-03-12 01:35:00.166422784 +0000 +@@ -44,7 +44,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -I$(includedir) -I../libscotch -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) $(LDFLAGS) ++ $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) $(LDFLAGS) -o $(@) + + ## + ## Project rules. +diff -Nur src.orig/scotch/Makefile src/scotch/Makefile +--- src.orig/scotch/Makefile 2012-03-12 00:14:14.536109811 +0000 ++++ src/scotch/Makefile 2012-03-12 00:50:22.033571205 +0000 +@@ -41,13 +41,13 @@ + include ../Makefile.inc + + %$(EXE) : %$(OBJ) +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) -o $(@) + + %$(OBJ) : %.c + $(CC) $(CFLAGS) -I$(includedir) -I../libscotch -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) -o $(@) + + ## + ## Project rules. +@@ -205,7 +205,7 @@ + $(libdir)/libptscotch$(LIB) \ + $(libdir)/libptscotcherrexit$(LIB) \ + dgmap.h +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) -o $(@) + + dgscat$(EXE) : dgscat.c \ + ../libscotch/module.h \ +@@ -315,7 +315,7 @@ + gout_o.c \ + $(includedir)/scotch.h \ + $(libdir)/libscotch$(LIB) +- $(CC) $(CFLAGS) -I../libscotch -I$(includedir) gout_c.c gout_o.c -o $(@) -L$(libdir) -lscotch -lscotcherrexit $(LDFLAGS) ++ $(CC) $(CFLAGS) -I../libscotch -I$(includedir) gout_c.c gout_o.c -L$(libdir) -lscotch -lscotcherrexit $(LDFLAGS) -o $(@) + + gpart$(EXE) : gmap.c \ + ../libscotch/module.h \ +@@ -324,7 +324,7 @@ + $(libdir)/libscotch$(LIB) \ + $(libdir)/libscotcherrexit$(LIB) \ + gmap.h +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -o $(@) -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -L$(libdir) -l$(SCOTCHLIB) -l$(SCOTCHLIB)errexit $(LDFLAGS) -o $(@) + + + gscat$(EXE) : gscat.c \ diff --git a/sci-libs/scotch/files/scotch-6.0.0-as-needed.patch b/sci-libs/scotch/files/scotch-6.0.0-as-needed.patch new file mode 100644 index 000000000000..ad41380de884 --- /dev/null +++ b/sci-libs/scotch/files/scotch-6.0.0-as-needed.patch @@ -0,0 +1,128 @@ +diff -Nur src.orig/check/Makefile src/check/Makefile +--- src.orig/check/Makefile 2013-02-07 17:27:00.000000000 +0000 ++++ src/check/Makefile 2013-02-07 17:27:21.000000000 +0000 +@@ -48,7 +48,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -I$(SCOTCHINCLUDEDIR) -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(SCOTCHINCLUDEDIR) -L$(SCOTCHLIBDIR) $(<) -o $(@) $(SCOTCHLIBS) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(SCOTCHINCLUDEDIR) -L$(SCOTCHLIBDIR) $(<) $(SCOTCHLIBS) $(LIBS) -o $(@) + + ## + ## Project rules. +diff -Nur src.orig/esmumps/Makefile src/esmumps/Makefile +--- src.orig/esmumps/Makefile 2013-02-07 17:27:00.000000000 +0000 ++++ src/esmumps/Makefile 2013-02-07 17:28:11.000000000 +0000 +@@ -44,7 +44,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -I$(includedir) -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) $(<) -o $(@) -L$(libdir) $(LDFLAGS) -L. -l$(ESMUMPSLIB) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) $(<) -L$(libdir) -L. -l$(ESMUMPSLIB) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LIBS) -o $(@) + + ## + ## Project rules. +@@ -57,7 +57,7 @@ + libesmumps$(LIB) \ + main_esmumps$(EXE) + +-ptscotch : clean ++ptscotch : clean common.h + $(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC=$(CCP) SCOTCHLIB=ptscotch ESMUMPSLIB=ptesmumps \ + libesmumps$(LIB) \ + main_esmumps$(EXE) +@@ -160,6 +160,6 @@ + order.h \ + symbol.h \ + esmumps.h \ +- lib$(ESMUMPSLIB)$(LIB) \ ++ libesmumps$(LIB) \ + $(libdir)/lib$(SCOTCHLIB)$(LIB) \ + $(libdir)/lib$(SCOTCHLIB)errexit$(LIB) +diff -Nur src.orig/libscotch/Makefile src/libscotch/Makefile +--- src.orig/libscotch/Makefile 2013-02-07 17:27:00.000000000 +0000 ++++ src/libscotch/Makefile 2013-02-07 17:27:21.000000000 +0000 +@@ -43,7 +43,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) -o $(@) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) $(LIBS) -o $(@) + + ## + ## Project rules. +@@ -2908,14 +2908,14 @@ + mapping.h \ + order.h \ + parser.h +- $(CCD) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) -o $(@) $(LDFLAGS) ++ $(CCD) $(CFLAGS) $(LDFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) $(LIBS) -o $(@) + + ptdummysizes$(EXE) : dummysizes.c \ + module.h \ + common.h \ + dgraph.h \ + dorder.h +- $(CCD) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) -o $(@) $(LDFLAGS) ++ $(CCD) $(CFLAGS) $(LDFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) $(LIBS) -o $(@) + + scotch.h : dummysizes$(EXE) \ + library.h +diff -Nur src.orig/libscotchmetis/Makefile src/libscotchmetis/Makefile +--- src.orig/libscotchmetis/Makefile 2013-02-07 17:27:00.000000000 +0000 ++++ src/libscotchmetis/Makefile 2013-02-07 17:27:21.000000000 +0000 +@@ -44,7 +44,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -I$(includedir) -I../libscotch -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) -o $(@) + + ## + ## Project rules. +diff -Nur src.orig/scotch/Makefile src/scotch/Makefile +--- src.orig/scotch/Makefile 2013-02-07 17:27:00.000000000 +0000 ++++ src/scotch/Makefile 2013-02-07 17:27:21.000000000 +0000 +@@ -41,13 +41,13 @@ + include ../Makefile.inc + + %$(EXE) : %$(OBJ) +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LIBS) -o $(@) + + %$(OBJ) : %.c + $(CC) $(CFLAGS) -I$(includedir) -I../libscotch -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LIBS) -o $(@) + + ## + ## Project rules. +@@ -205,7 +205,7 @@ + $(libdir)/libptscotch$(LIB) \ + $(libdir)/libptscotcherrexit$(LIB) \ + dgmap.h +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -o $(@) -L$(libdir) -lptscotch -lscotch -lptscotcherrexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -L$(libdir) -lptscotch -lscotch -lptscotcherrexit $(LIBS) -o $(@) + + dgscat$(EXE) : dgscat.c \ + ../libscotch/module.h \ +@@ -315,7 +315,7 @@ + gout_o.c \ + $(includedir)/scotch.h \ + $(libdir)/libscotch$(LIB) +- $(CC) $(CFLAGS) -I../libscotch -I$(includedir) gout_c.c gout_o.c -o $(@) -L$(libdir) -lscotch -lscotcherrexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I../libscotch -I$(includedir) gout_c.c gout_o.c -L$(libdir) -lscotch -lscotcherrexit $(LIBS) -o $(@) + + gpart$(EXE) : gmap.c \ + ../libscotch/module.h \ +@@ -324,7 +324,7 @@ + $(libdir)/libscotch$(LIB) \ + $(libdir)/libscotcherrexit$(LIB) \ + gmap.h +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -o $(@) -L$(libdir) -lscotch -lscotcherrexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -L$(libdir) -lscotch -lscotcherrexit $(LIBS) -o $(@) + + gscat$(EXE) : gscat.c \ + ../libscotch/module.h \ diff --git a/sci-libs/scotch/files/scotch-6.0.4-as-needed.patch b/sci-libs/scotch/files/scotch-6.0.4-as-needed.patch new file mode 100644 index 000000000000..449449bec073 --- /dev/null +++ b/sci-libs/scotch/files/scotch-6.0.4-as-needed.patch @@ -0,0 +1,128 @@ +diff -Nur scotch_6.0.4/src/check/Makefile scotch_6.0.4_patched/src/check/Makefile +--- scotch_6.0.4/src/check/Makefile 2015-03-01 03:18:02.000000000 -0700 ++++ scotch_6.0.4_patched/src/check/Makefile 2015-07-17 15:15:58.447398954 -0600 +@@ -53,7 +53,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -I$(SCOTCHINCLUDEDIR) -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(SCOTCHINCLUDEDIR) -L$(SCOTCHLIBDIR) $(<) -o $(@) $(SCOTCHLIBS) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(SCOTCHINCLUDEDIR) -L$(SCOTCHLIBDIR) $(<) $(SCOTCHLIBS) $(LIBS) -o $(@) + + ## + ## Project rules. +diff -Nur scotch_6.0.4/src/esmumps/Makefile scotch_6.0.4_patched/src/esmumps/Makefile +--- scotch_6.0.4/src/esmumps/Makefile 2015-03-13 17:32:06.000000000 -0600 ++++ scotch_6.0.4_patched/src/esmumps/Makefile 2015-07-17 15:17:47.389600699 -0600 +@@ -44,7 +44,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -I$(includedir) -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) $(<) -o $(@) -L$(libdir) $(LDFLAGS) -L. -l$(ESMUMPSLIB) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) $(<) -L$(libdir) -L. -l$(ESMUMPSLIB) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LIBS) -o $(@) + + ## + ## Project rules. +@@ -57,7 +57,7 @@ + libesmumps$(LIB) \ + main_esmumps$(EXE) + +-ptscotch : clean ++ptscotch : clean common.h + $(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC="$(CCP)" SCOTCHLIB=ptscotch ESMUMPSLIB=ptesmumps \ + libesmumps$(LIB) \ + main_esmumps$(EXE) +@@ -160,6 +160,6 @@ + order.h \ + symbol.h \ + esmumps.h \ +- lib$(ESMUMPSLIB)$(LIB) \ ++ libesmumps$(LIB) \ + $(libdir)/lib$(SCOTCHLIB)$(LIB) \ + $(libdir)/lib$(SCOTCHLIB)errexit$(LIB) +diff -Nur scotch_6.0.4/src/libscotch/Makefile scotch_6.0.4_patched/src/libscotch/Makefile +--- scotch_6.0.4/src/libscotch/Makefile 2014-09-23 13:28:28.000000000 -0600 ++++ scotch_6.0.4_patched/src/libscotch/Makefile 2015-07-17 15:19:17.320116484 -0600 +@@ -43,7 +43,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) -o $(@) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) $(LIBS) -o $(@) + + ## + ## Project rules. +@@ -2937,14 +2937,14 @@ + mapping.h \ + order.h \ + parser.h +- $(CCD) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) -o $(@) $(LDFLAGS) ++ $(CCD) $(CFLAGS) $(LDFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) $(LIBS) -o $(@) + + ptdummysizes$(EXE) : dummysizes.c \ + module.h \ + common.h \ + dgraph.h \ + dorder.h +- $(CCD) $(CFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) -o $(@) $(LDFLAGS) ++ $(CCD) $(CFLAGS) $(LDFLAGS) -DSCOTCH_VERSION=$(VERSION) -DSCOTCH_RELEASE=$(RELEASE) -DSCOTCH_PATCHLEVEL=$(PATCHLEVEL) $(<) $(LIBS) -o $(@) + + scotch.h : dummysizes$(EXE) \ + library.h +diff -Nur scotch_6.0.4/src/libscotchmetis/Makefile scotch_6.0.4_patched/src/libscotchmetis/Makefile +--- scotch_6.0.4/src/libscotchmetis/Makefile 2011-09-06 10:46:48.000000000 -0600 ++++ scotch_6.0.4_patched/src/libscotchmetis/Makefile 2015-07-17 15:19:42.648698497 -0600 +@@ -44,7 +44,7 @@ + $(CC) $(CFLAGS) $(CLIBFLAGS) -I$(includedir) -I../libscotch -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) -o $(@) + + ## + ## Project rules. +diff -Nur scotch_6.0.4/src/scotch/Makefile scotch_6.0.4_patched/src/scotch/Makefile +--- scotch_6.0.4/src/scotch/Makefile 2015-02-24 15:39:44.000000000 -0700 ++++ scotch_6.0.4_patched/src/scotch/Makefile 2015-07-17 15:22:25.275015105 -0600 +@@ -41,13 +41,13 @@ + include ../Makefile.inc + + %$(EXE) : %$(OBJ) +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LIBS) -o $(@) + + %$(OBJ) : %.c + $(CC) $(CFLAGS) -I$(includedir) -I../libscotch -c $(<) -o $(@) + + %$(EXE) : %.c +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -o $(@) -L$(libdir) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -L$(libdir) -l$(SCOTCHLIB) -lscotch -l$(SCOTCHLIB)errexit $(LIBS) -o $(@) + + ## + ## Project rules. +@@ -209,7 +209,7 @@ + $(libdir)/libptscotch$(LIB) \ + $(libdir)/libptscotcherrexit$(LIB) \ + dgmap.h +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -o $(@) -L$(libdir) -lptscotch -lscotch -lptscotcherrexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -L$(libdir) -lptscotch -lscotch -lptscotcherrexit $(LIBS) -o $(@) + + dgscat$(EXE) : dgscat.c \ + ../libscotch/module.h \ +@@ -321,7 +321,7 @@ + gout_o.c \ + $(includedir)/scotch.h \ + $(libdir)/libscotch$(LIB) +- $(CC) $(CFLAGS) -I../libscotch -I$(includedir) gout_c.c gout_o.c -o $(@) -L$(libdir) -lscotch -lscotcherrexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I../libscotch -I$(includedir) gout_c.c gout_o.c -L$(libdir) -lscotch -lscotcherrexit $(LIBS) -o $(@) + + gpart$(EXE) : gmap.c \ + ../libscotch/module.h \ +@@ -330,7 +330,7 @@ + $(libdir)/libscotch$(LIB) \ + $(libdir)/libscotcherrexit$(LIB) \ + gmap.h +- $(CC) $(CFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -o $(@) -L$(libdir) -lscotch -lscotcherrexit $(LDFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -I$(includedir) -I../libscotch $(<) -DSCOTCH_COMPILE_PART -L$(libdir) -lscotch -lscotcherrexit $(LIBS) -o $(@) + + gscat$(EXE) : gscat.c \ + ../libscotch/module.h \ diff --git a/sci-libs/scotch/files/scotch-6.0.4-flex-2.6.3-fix.patch b/sci-libs/scotch/files/scotch-6.0.4-flex-2.6.3-fix.patch new file mode 100644 index 000000000000..c1301f57076a --- /dev/null +++ b/sci-libs/scotch/files/scotch-6.0.4-flex-2.6.3-fix.patch @@ -0,0 +1,33 @@ +--- scotch_6.0.4/src/libscotch/parser_ll.l.old 2017-01-02 08:42:41.216249106 -0800 ++++ scotch-6.0.4-r1/work/scotch_6.0.4/src/libscotch/parser_ll.l 2017-01-02 09:50:14.572579444 -0800 +@@ -84,20 +84,29 @@ + #endif /* X_OSDOS */ + + #ifdef FLEX_SCANNER + #define YY_ALWAYS_INTERACTIVE 1 /* Set the parser as interactive and read one char at a time */ + #define YY_INPUT(buf,result,max_size) { int c = stratParserInput (); result = (c == 0) ? YY_NULL : ((buf)[0] = c, 1); } ++ ++# if YY_FLEX_MAJOR_VERSION > 2 || \ ++ YY_FLEX_MAJOR_VERSION == 2 && YY_FLEX_MINOR_VERSION > 6 || \ ++ YY_FLEX_MAJOR_VERSION == 2 && YY_FLEX_MINOR_VERSION == 6 && YY_FLEX_SUBMINOR_VERSION >= 3 ++ int yywrap() { return 1; } ++# else ++# define yywrap() (1) /* Always return end-of-file on end-of-string */ ++# endif ++ + #else /* FLEX_SCANNER */ + #undef getc /* Redirect I/O functions */ + #define getc yygetc + #undef yygetc + #define yygetc(stream) stratParserInput () ++#define yywrap() (1) /* Always return end-of-file on end-of-string */ + #endif /* FLEX_SCANNER */ + + #define YY_NO_UNPUT /* No prototype for yyunput as not defined */ + #define YY_SKIP_YYWRAP /* No prototype for yywrap as defined as macro */ +-#define yywrap() (1) /* Always return end-of-file on end-of-string */ + + /* + ** The static variables. + */ + diff --git a/sci-libs/scotch/metadata.xml b/sci-libs/scotch/metadata.xml new file mode 100644 index 000000000000..9b35c1ac8b7f --- /dev/null +++ b/sci-libs/scotch/metadata.xml @@ -0,0 +1,37 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="person"> + <email>patrick@gentoo.org</email> + <name>Patrick Lauer</name> +</maintainer> +<maintainer type="person"> + <email>oli.borm@web.de</email> + <name>Oliver Borm</name> +</maintainer> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<maintainer type="project"> + <email>proxy-maint@gentoo.org</email> + <name>Proxy Maintainers</name> +</maintainer> +<use> + <flag name="int64">Build the 64 bits integer library (needed for > 2^31 vertices)</flag> + <flag name="tools">Build and install extra exec tools</flag> +</use> +<longdescription lang="en"> + SCOTCH is a software package and libraries for graph, mesh and + hypergraph partitioning, static mapping, and sparse matrix block + ordering. + Its purpose of Scotch is to apply graph theory, with a divide and + conquer approach, to scientific computing problems such as graph and + mesh partitioning, static mapping, and sparse matrix ordering, in + application domains ranging from structural mechanics to operating + systems or bio-chemistry. + The SCOTCH distribution is a set of programs and libraries which + implement the static mapping and sparse matrix reordering algorithms + developed within the SCOTCH project. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/scotch/scotch-5.1.12b.ebuild b/sci-libs/scotch/scotch-5.1.12b.ebuild new file mode 100644 index 000000000000..7188b5ab48f2 --- /dev/null +++ b/sci-libs/scotch/scotch-5.1.12b.ebuild @@ -0,0 +1,157 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs versionator flag-o-matic multilib + +# use esmumps version to allow linking with mumps +MYP="${PN}_${PV}_esmumps" +# download id on gforge changes every goddamn release +DID=28978 + +DESCRIPTION="Software for graph, mesh and hypergraph partitioning" +HOMEPAGE="http://www.labri.u-bordeaux.fr/perso/pelegrin/scotch/" +# broken ssl cert, so mirroring +#SRC_URI="http://gforge.inria.fr/frs/download.php/${DID}/${MYP}.tar.gz" +SRC_URI="http://dev.gentooexperimental.org/~patrick/${MYP}.tar.gz" + +LICENSE="CeCILL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples int64 mpi static-libs tools" + +DEPEND="sys-libs/zlib + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MYP/b}" + +static_to_shared() { + local libstatic=${1}; shift + local libname=$(basename ${libstatic%.a}) + local soname=${libname}$(get_libname $(get_version_component_range 1-2)) + local libdir=$(dirname ${libstatic}) + + einfo "Making ${soname} from ${libstatic}" + if [[ ${CHOST} == *-darwin* ]] ; then + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ + -Wl,-all_load -Wl,${libstatic} \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + else + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + [[ $(get_version_component_count) -gt 1 ]] && \ + ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) + ln -s ${soname} ${libdir}/${libname}$(get_libname) + fi +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-as-needed.patch + sed -e "s/gcc/$(tc-getCC)/" \ + -e "s/-O3/${CFLAGS} -pthread/" \ + -e "s/ ar/ $(tc-getAR)/" \ + -e "s/ranlib/$(tc-getRANLIB)/" \ + src/Make.inc/Makefile.inc.i686_pc_linux2 > src/Makefile.inc || die + use int64 && append-cflags -DIDXSIZE64 +} + +src_compile() { + emake -C src CLIBFLAGS=-fPIC + static_to_shared lib/libscotcherr.a + static_to_shared lib/libscotcherrexit.a + static_to_shared lib/libscotch.a -Llib -lz -lm -lrt -lscotcherr + static_to_shared lib/libesmumps.a -Llib -lscotch + static_to_shared lib/libscotchmetis.a -Llib -lscotch + + if use mpi; then + emake -C src CLIBFLAGS=-fPIC ptscotch + export LINK=mpicc + static_to_shared lib/libptscotcherr.a + static_to_shared lib/libptscotcherrexit.a + static_to_shared lib/libptscotch.a -Llib -lptscotcherr -lz -lm -lrt + static_to_shared lib/libptesmumps.a -Llib -lptscotch + static_to_shared lib/libptscotchparmetis.a -Llib -lptscotch + fi + if use static-libs; then + emake -C src clean + emake -C src + use mpi && emake -C src ptscotch + fi +} + +src_install() { + dolib.so lib/lib*$(get_libname)* + use static-libs && dolib.a lib/*.a + + insinto /usr/include/scotch + doins include/* + + cat <<-EOF > scotchmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: scotchmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lscotchmetis -lscotcherr -lscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins scotchmetis.pc + + # not sure it is actually a full replacement of metis + #alternatives_for metis scotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis.pc scotchmetis.pc + + if use mpi; then + cat <<-EOF > ptscotchparmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ptscotchparmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lptscotchparmetis -lptscotcherr -lptscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch + Requires: scotchmetis + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ptscotchparmetis.pc + # not sure it is actually a full replacement of parmetis + #alternatives_for metis-mpi ptscotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis-mpi.pc ptscotchparmetis.pc + fi + + dodoc README.txt + + if use tools; then + local b m + pushd bin > /dev/null + for b in *; do + newbin ${b} scotch_${b} + done + popd > /dev/null + + pushd man/man1 > /dev/null + for m in *; do + newman ${m} scotch_${m} + done + popd > /dev/null + fi + + use doc && dodoc doc/*.pdf + + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r examples/* tgt grf + fi +} diff --git a/sci-libs/scotch/scotch-6.0.0.ebuild b/sci-libs/scotch/scotch-6.0.0.ebuild new file mode 100644 index 000000000000..c88bdc8a91c5 --- /dev/null +++ b/sci-libs/scotch/scotch-6.0.0.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs versionator flag-o-matic multilib + +# use esmumps version to allow linking with mumps +MYP="${PN}_${PV}_esmumps" +# download id on gforge changes every goddamn release +DID=31832 +SOVER=$(get_major_version) + +DESCRIPTION="Software for graph, mesh and hypergraph partitioning" +HOMEPAGE="http://www.labri.u-bordeaux.fr/perso/pelegrin/scotch/" +SRC_URI="http://gforge.inria.fr/frs/download.php/${DID}/${MYP}.tar.gz" + +LICENSE="CeCILL-2" +SLOT="0/${SOVER}" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="doc int64 mpi static-libs tools threads" + +DEPEND=" + sys-libs/zlib + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MYP/b}" + +static_to_shared() { + local libstatic=${1}; shift + local libname=$(basename ${libstatic%.a}) + local soname=${libname}$(get_libname ${SOVER}) + local libdir=$(dirname ${libstatic}) + + einfo "Making ${soname} from ${libstatic}" + if [[ ${CHOST} == *-darwin* ]] ; then + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ + -Wl,-all_load -Wl,${libstatic} \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + else + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + [[ $(get_version_component_count) -gt 1 ]] && \ + ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) + ln -s ${soname} ${libdir}/${libname}$(get_libname) + fi +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-as-needed.patch + use int64 && append-cflags -DIDXSIZE64 + if use threads; then + append-cflags "-DSCOTCH_PTHREAD_NUMBER=$(nproc)" + else + append-cflags "-DSCOTCH_PTHREAD_NUMBER=1" + sed -i \ + -e 's/ -DSCOTCH_PTHREAD//' \ + src/Make.inc/Makefile.inc.i686_pc_linux3 || die + fi + sed -e "s/gcc/$(tc-getCC)/" \ + -e "s/-O3/${CFLAGS} -pthread/" \ + -e "s/ ar/ $(tc-getAR)/" \ + -e "s/ranlib/$(tc-getRANLIB)/" \ + -e "s/LDFLAGS/LIBS/" \ + src/Make.inc/Makefile.inc.i686_pc_linux3 > src/Makefile.inc || die +} + +src_compile() { + emake -C src CLIBFLAGS=-fPIC scotch esmumps + static_to_shared lib/libscotcherr.a + static_to_shared lib/libscotcherrexit.a + static_to_shared lib/libscotch.a -Llib -lz -lm -lrt -lpthread -lscotcherr + static_to_shared lib/libesmumps.a -Llib -lscotch + static_to_shared lib/libscotchmetis.a -Llib -lscotch + + if use mpi; then + emake -C src CLIBFLAGS=-fPIC ptscotch ptesmumps + export LINK=mpicc + static_to_shared lib/libptscotcherr.a + static_to_shared lib/libptscotcherrexit.a + static_to_shared lib/libptscotch.a -Llib -lscotch -lptscotcherr -lz -lm -lrt + static_to_shared lib/libptesmumps.a -Llib -lscotch -lptscotch + static_to_shared lib/libptscotchparmetis.a -Llib -lscotch -lptscotch + fi + if use static-libs; then + emake -C src clean + emake -C src + use mpi && emake -C src ptscotch + fi +} + +src_test() { + LD_LIBRARY_PATH="${S}/lib" emake -C src check +} + +src_install() { + dolib.so lib/lib*$(get_libname)* + use static-libs && dolib.a lib/*.a + + insinto /usr/include/scotch + doins include/* + + cat <<-EOF > scotchmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: scotchmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lscotchmetis -lscotcherr -lscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins scotchmetis.pc + + # not sure it is actually a full replacement of metis + #alternatives_for metis scotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis.pc scotchmetis.pc + + if use mpi; then + cat <<-EOF > ptscotchparmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ptscotchparmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lptscotchparmetis -lptscotcherr -lptscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch + Requires: scotchmetis + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ptscotchparmetis.pc + # not sure it is actually a full replacement of parmetis + #alternatives_for metis-mpi ptscotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis-mpi.pc ptscotchparmetis.pc + fi + + dodoc README.txt + + if use tools; then + local b m + pushd bin > /dev/null + for b in *; do + newbin ${b} scotch_${b} + done + popd > /dev/null + + pushd man/man1 > /dev/null + for m in *; do + newman ${m} scotch_${m} + done + popd > /dev/null + fi + + use doc && dodoc doc/*.pdf +} diff --git a/sci-libs/scotch/scotch-6.0.4-r1.ebuild b/sci-libs/scotch/scotch-6.0.4-r1.ebuild new file mode 100644 index 000000000000..28112e3244c3 --- /dev/null +++ b/sci-libs/scotch/scotch-6.0.4-r1.ebuild @@ -0,0 +1,171 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs versionator flag-o-matic multilib + +# use esmumps version to allow linking with mumps +MYP="${PN}_${PV}_esmumps" +# download id on gforge changes every goddamn release +DID=34618 +SOVER=$(get_major_version) + +DESCRIPTION="Software for graph, mesh and hypergraph partitioning" +HOMEPAGE="http://www.labri.u-bordeaux.fr/perso/pelegrin/scotch/" +SRC_URI="http://gforge.inria.fr/frs/download.php/${DID}/${MYP}.tar.gz" + +LICENSE="CeCILL-2" +SLOT="0/${SOVER}" +KEYWORDS="~alpha ~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc int64 mpi static-libs tools threads" + +DEPEND=" + sys-libs/zlib + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${P/-/_} + +static_to_shared() { + local libstatic=${1}; shift + local libname=$(basename ${libstatic%.a}) + local soname=${libname}$(get_libname ${SOVER}) + local libdir=$(dirname ${libstatic}) + + einfo "Making ${soname} from ${libstatic}" + if [[ ${CHOST} == *-darwin* ]] ; then + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ + -Wl,-all_load -Wl,${libstatic} \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + else + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + [[ $(get_version_component_count) -gt 1 ]] && \ + ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) + ln -s ${soname} ${libdir}/${libname}$(get_libname) + fi +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-as-needed.patch + use int64 && append-cflags -DIDXSIZE64 + if use threads; then + append-cflags "-DSCOTCH_PTHREAD_NUMBER=$(nproc)" + else + append-cflags "-DSCOTCH_PTHREAD_NUMBER=1" + sed -i \ + -e 's/ -DSCOTCH_PTHREAD//' \ + src/Make.inc/Makefile.inc.i686_pc_linux3 || die + fi + sed -e "s/gcc/$(tc-getCC)/" \ + -e "s/-O3/${CFLAGS} -pthread/" \ + -e "s/ ar/ $(tc-getAR)/" \ + -e "s/ranlib/$(tc-getRANLIB)/" \ + -e "s/LDFLAGS/LIBS/" \ + src/Make.inc/Makefile.inc.i686_pc_linux3 > src/Makefile.inc || die +} + +src_compile() { + emake -C src CLIBFLAGS=-fPIC scotch esmumps + static_to_shared lib/libscotcherr.a + static_to_shared lib/libscotcherrexit.a + static_to_shared lib/libscotch.a -Llib -lz -lm -lrt -lpthread -lscotcherr + static_to_shared lib/libesmumps.a -Llib -lscotch + static_to_shared lib/libscotchmetis.a -Llib -lscotch + + if use mpi; then + emake -C src CLIBFLAGS=-fPIC ptscotch ptesmumps + export LINK=mpicc + static_to_shared lib/libptscotcherr.a + static_to_shared lib/libptscotcherrexit.a + static_to_shared lib/libptscotch.a -Llib -lscotch -lptscotcherr -lz -lm -lrt + static_to_shared lib/libptesmumps.a -Llib -lscotch -lptscotch + static_to_shared lib/libptscotchparmetis.a -Llib -lscotch -lptscotch + fi + if use static-libs; then + emake -C src clean + emake -C src + use mpi && emake -C src ptscotch + fi +} + +src_test() { + LD_LIBRARY_PATH="${S}/lib" emake -C src check +} + +src_install() { + dolib.so lib/lib*$(get_libname)* + use static-libs && dolib.a lib/*.a + + #install metis headers into a subdir + #to allow usage of real metis and scotch + #in the same code + insinto /usr/include/scotch/metis + doins include/*metis* + rm include/*metis* + insinto /usr/include/scotch + doins include/* + + cat <<-EOF > scotchmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: scotchmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lscotchmetis -lscotcherr -lscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch/metis + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins scotchmetis.pc + + # not sure it is actually a full replacement of metis + #alternatives_for metis scotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis.pc scotchmetis.pc + + if use mpi; then + cat <<-EOF > ptscotchparmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ptscotchparmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lptscotchparmetis -lptscotcherr -lptscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch/metis + Requires: scotchmetis + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ptscotchparmetis.pc + # not sure it is actually a full replacement of parmetis + #alternatives_for metis-mpi ptscotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis-mpi.pc ptscotchparmetis.pc + fi + + dodoc README.txt + + if use tools; then + local b m + pushd bin > /dev/null + for b in *; do + newbin ${b} scotch_${b} + done + popd > /dev/null + + pushd man/man1 > /dev/null + for m in *; do + newman ${m} scotch_${m} + done + popd > /dev/null + fi + + use doc && dodoc doc/*.pdf +} diff --git a/sci-libs/scotch/scotch-6.0.4-r2.ebuild b/sci-libs/scotch/scotch-6.0.4-r2.ebuild new file mode 100644 index 000000000000..b5daf21f66a8 --- /dev/null +++ b/sci-libs/scotch/scotch-6.0.4-r2.ebuild @@ -0,0 +1,172 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs versionator flag-o-matic multilib + +# use esmumps version to allow linking with mumps +MYP="${PN}_${PV}_esmumps" +# download id on gforge changes every goddamn release +DID=34618 +SOVER=$(get_major_version) + +DESCRIPTION="Software for graph, mesh and hypergraph partitioning" +HOMEPAGE="http://www.labri.u-bordeaux.fr/perso/pelegrin/scotch/" +SRC_URI="http://gforge.inria.fr/frs/download.php/${DID}/${MYP}.tar.gz" + +LICENSE="CeCILL-2" +SLOT="0/${SOVER}" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc int64 mpi static-libs tools threads" + +DEPEND=" + sys-libs/zlib + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${P/-/_} + +static_to_shared() { + local libstatic=${1}; shift + local libname=$(basename ${libstatic%.a}) + local soname=${libname}$(get_libname ${SOVER}) + local libdir=$(dirname ${libstatic}) + + einfo "Making ${soname} from ${libstatic}" + if [[ ${CHOST} == *-darwin* ]] ; then + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ + -Wl,-all_load -Wl,${libstatic} \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + else + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + [[ $(get_version_component_count) -gt 1 ]] && \ + ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) + ln -s ${soname} ${libdir}/${libname}$(get_libname) + fi +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-as-needed.patch + epatch "${FILESDIR}"/${P}-flex-2.6.3-fix.patch + use int64 && append-cflags -DIDXSIZE64 + if use threads; then + append-cflags "-DSCOTCH_PTHREAD_NUMBER=$(nproc)" + else + append-cflags "-DSCOTCH_PTHREAD_NUMBER=1" + sed -i \ + -e 's/ -DSCOTCH_PTHREAD//' \ + src/Make.inc/Makefile.inc.i686_pc_linux3 || die + fi + sed -e "s/gcc/$(tc-getCC)/" \ + -e "s/-O3/${CFLAGS} -pthread/" \ + -e "s/ ar/ $(tc-getAR)/" \ + -e "s/ranlib/$(tc-getRANLIB)/" \ + -e "s/LDFLAGS/LIBS/" \ + src/Make.inc/Makefile.inc.i686_pc_linux3 > src/Makefile.inc || die +} + +src_compile() { + emake -C src CLIBFLAGS=-fPIC scotch esmumps + static_to_shared lib/libscotcherr.a + static_to_shared lib/libscotcherrexit.a + static_to_shared lib/libscotch.a -Llib -lz -lm -lrt -lpthread -lscotcherr + static_to_shared lib/libesmumps.a -Llib -lscotch + static_to_shared lib/libscotchmetis.a -Llib -lscotch + + if use mpi; then + emake -C src CLIBFLAGS=-fPIC ptscotch ptesmumps + export LINK=mpicc + static_to_shared lib/libptscotcherr.a + static_to_shared lib/libptscotcherrexit.a + static_to_shared lib/libptscotch.a -Llib -lscotch -lptscotcherr -lz -lm -lrt + static_to_shared lib/libptesmumps.a -Llib -lscotch -lptscotch + static_to_shared lib/libptscotchparmetis.a -Llib -lscotch -lptscotch + fi + if use static-libs; then + emake -C src clean + emake -C src + use mpi && emake -C src ptscotch + fi +} + +src_test() { + LD_LIBRARY_PATH="${S}/lib" emake -C src check +} + +src_install() { + dolib.so lib/lib*$(get_libname)* + use static-libs && dolib.a lib/*.a + + #install metis headers into a subdir + #to allow usage of real metis and scotch + #in the same code + insinto /usr/include/scotch/metis + doins include/*metis* + rm include/*metis* + insinto /usr/include/scotch + doins include/* + + cat <<-EOF > scotchmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: scotchmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lscotchmetis -lscotcherr -lscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch/metis + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins scotchmetis.pc + + # not sure it is actually a full replacement of metis + #alternatives_for metis scotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis.pc scotchmetis.pc + + if use mpi; then + cat <<-EOF > ptscotchparmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ptscotchparmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lptscotchparmetis -lptscotcherr -lptscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch/metis + Requires: scotchmetis + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ptscotchparmetis.pc + # not sure it is actually a full replacement of parmetis + #alternatives_for metis-mpi ptscotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis-mpi.pc ptscotchparmetis.pc + fi + + dodoc README.txt + + if use tools; then + local b m + pushd bin > /dev/null + for b in *; do + newbin ${b} scotch_${b} + done + popd > /dev/null + + pushd man/man1 > /dev/null + for m in *; do + newman ${m} scotch_${m} + done + popd > /dev/null + fi + + use doc && dodoc doc/*.pdf +} diff --git a/sci-libs/scotch/scotch-6.0.4.ebuild b/sci-libs/scotch/scotch-6.0.4.ebuild new file mode 100644 index 000000000000..9ce7d7b3a14b --- /dev/null +++ b/sci-libs/scotch/scotch-6.0.4.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils toolchain-funcs versionator flag-o-matic multilib + +# use esmumps version to allow linking with mumps +MYP="${PN}_${PV}_esmumps" +# download id on gforge changes every goddamn release +DID=34618 +SOVER=$(get_major_version) + +DESCRIPTION="Software for graph, mesh and hypergraph partitioning" +HOMEPAGE="http://www.labri.u-bordeaux.fr/perso/pelegrin/scotch/" +SRC_URI="http://gforge.inria.fr/frs/download.php/${DID}/${MYP}.tar.gz" + +LICENSE="CeCILL-2" +SLOT="0/${SOVER}" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc int64 mpi static-libs tools threads" + +DEPEND=" + sys-libs/zlib + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${P/-/_} + +static_to_shared() { + local libstatic=${1}; shift + local libname=$(basename ${libstatic%.a}) + local soname=${libname}$(get_libname ${SOVER}) + local libdir=$(dirname ${libstatic}) + + einfo "Making ${soname} from ${libstatic}" + if [[ ${CHOST} == *-darwin* ]] ; then + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ + -Wl,-all_load -Wl,${libstatic} \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + else + ${LINK:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname=${soname} \ + -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ + "$@" -o ${libdir}/${soname} || die "${soname} failed" + [[ $(get_version_component_count) -gt 1 ]] && \ + ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) + ln -s ${soname} ${libdir}/${libname}$(get_libname) + fi +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-as-needed.patch + use int64 && append-cflags -DIDXSIZE64 + if use threads; then + append-cflags "-DSCOTCH_PTHREAD_NUMBER=$(nproc)" + else + append-cflags "-DSCOTCH_PTHREAD_NUMBER=1" + sed -i \ + -e 's/ -DSCOTCH_PTHREAD//' \ + src/Make.inc/Makefile.inc.i686_pc_linux3 || die + fi + sed -e "s/gcc/$(tc-getCC)/" \ + -e "s/-O3/${CFLAGS} -pthread/" \ + -e "s/ ar/ $(tc-getAR)/" \ + -e "s/ranlib/$(tc-getRANLIB)/" \ + -e "s/LDFLAGS/LIBS/" \ + src/Make.inc/Makefile.inc.i686_pc_linux3 > src/Makefile.inc || die +} + +src_compile() { + emake -C src CLIBFLAGS=-fPIC scotch esmumps + static_to_shared lib/libscotcherr.a + static_to_shared lib/libscotcherrexit.a + static_to_shared lib/libscotch.a -Llib -lz -lm -lrt -lpthread -lscotcherr + static_to_shared lib/libesmumps.a -Llib -lscotch + static_to_shared lib/libscotchmetis.a -Llib -lscotch + + if use mpi; then + emake -C src CLIBFLAGS=-fPIC ptscotch ptesmumps + export LINK=mpicc + static_to_shared lib/libptscotcherr.a + static_to_shared lib/libptscotcherrexit.a + static_to_shared lib/libptscotch.a -Llib -lscotch -lptscotcherr -lz -lm -lrt + static_to_shared lib/libptesmumps.a -Llib -lscotch -lptscotch + static_to_shared lib/libptscotchparmetis.a -Llib -lscotch -lptscotch + fi + if use static-libs; then + emake -C src clean + emake -C src + use mpi && emake -C src ptscotch + fi +} + +src_test() { + LD_LIBRARY_PATH="${S}/lib" emake -C src check +} + +src_install() { + dolib.so lib/lib*$(get_libname)* + use static-libs && dolib.a lib/*.a + + insinto /usr/include/scotch + doins include/* + + cat <<-EOF > scotchmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: scotchmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lscotchmetis -lscotcherr -lscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins scotchmetis.pc + + # not sure it is actually a full replacement of metis + #alternatives_for metis scotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis.pc scotchmetis.pc + + if use mpi; then + cat <<-EOF > ptscotchparmetis.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ptscotchparmetis + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -lptscotchparmetis -lptscotcherr -lptscotch + Private: -lm -lz -lrt + Cflags: -I\${includedir}/scotch + Requires: scotchmetis + EOF + insinto /usr/$(get_libdir)/pkgconfig + doins ptscotchparmetis.pc + # not sure it is actually a full replacement of parmetis + #alternatives_for metis-mpi ptscotch 0 \ + # /usr/$(get_libdir)/pkgconfig/metis-mpi.pc ptscotchparmetis.pc + fi + + dodoc README.txt + + if use tools; then + local b m + pushd bin > /dev/null + for b in *; do + newbin ${b} scotch_${b} + done + popd > /dev/null + + pushd man/man1 > /dev/null + for m in *; do + newman ${m} scotch_${m} + done + popd > /dev/null + fi + + use doc && dodoc doc/*.pdf +} diff --git a/sci-libs/shapelib/Manifest b/sci-libs/shapelib/Manifest new file mode 100644 index 000000000000..380eec0e0847 --- /dev/null +++ b/sci-libs/shapelib/Manifest @@ -0,0 +1,5 @@ +DIST shapelib-1.4.0.tar.gz 548990 SHA256 3eddd5f2690f2cf18d8d9798267537a2102a289020b9818f9a31eb626f91a7a1 SHA512 206b81fe859a837e821e449ab1b2dbd5a3aa7abd1871da4aec69e130b6fad6300697429884ce359c90e4b76bca90e2108f32b9fdbd3b92013fa5a39f3bedeeb1 WHIRLPOOL ac411c0a40923aede1236cc5afe77ffc83f2700b95360204f11c9fe0299512728ae8e66017ffb4baa7f9d54f20d7f7e5c0b8a30dc697c611f601fed158dc1557 +EBUILD shapelib-1.4.0-r1.ebuild 739 SHA256 a688aac0a3a5ba934433f649c29be043399fddd8c895f753826678a2072058da SHA512 587239c58c93654f82a4ec81015e92eabcfdb47f82c5b4c4ca32b9e2e91d67de4cc170d2609531cf4e0dc5ca564f40158c3b549de292362234fc8ca1fe64a8ff WHIRLPOOL 210e4d2e60268ded67133371b34352777bf2e5a85bba2b2e95e80839b4f44e9c6bf649553680e16f97606857f5b62992e4f26c4443cda82d964fc6bf7ad5ffd2 +MISC ChangeLog 2573 SHA256 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2d6a6ce894447d4beff7af2959d322ca61ddd5a9c363aa0d5de0da09541565930cd32017c5ab63025b94956d7caacb002b5e601a3bd86b2e08bca35ddb6ca3df diff --git a/sci-libs/shapelib/metadata.xml b/sci-libs/shapelib/metadata.xml new file mode 100644 index 000000000000..e0675810805a --- /dev/null +++ b/sci-libs/shapelib/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-geosciences@gentoo.org</email> + <name>Gentoo Geosciences Project</name> + </maintainer> + <longdescription>Shapelib is for working with ESRI shape files, a format used by the commercial ArcInfo GIS package.</longdescription> +</pkgmetadata> diff --git a/sci-libs/shapelib/shapelib-1.4.0-r1.ebuild b/sci-libs/shapelib/shapelib-1.4.0-r1.ebuild new file mode 100644 index 000000000000..dca20e97ec45 --- /dev/null +++ b/sci-libs/shapelib/shapelib-1.4.0-r1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Library for manipulating ESRI Shapefiles" +HOMEPAGE="http://shapelib.maptools.org/" +SRC_URI="http://download.osgeo.org/${PN}/${P}.tar.gz" + +LICENSE="GPL-2 LGPL-2" +SLOT="0/2" +KEYWORDS="amd64 ~arm ppc ppc64 x86 ~x86-fbsd ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +RDEPEND="sci-libs/proj" +DEPEND="${RDEPEND}" + +src_prepare() { + default + rm -r m4/* || die + eautoreconf +} + +src_configure() { + econf \ + --includedir=/usr/include/libshp +} + +src_install() { + use doc && HTML_DOCS=( web/. ) + default + + if ! use static-libs; then + find "${D}" \( -name '*.la' -o -name '*.a' \) -delete || die + fi +} diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest new file mode 100644 index 000000000000..9464af36d96f --- /dev/null +++ b/sci-libs/shogun/Manifest @@ -0,0 +1,8 @@ +AUX shogun-4.1.0-remove-C-linkage.patch 825 SHA256 30764cbff6d176d96780ffd8366b457081e1b2896f3248a9dbbc0206c94be675 SHA512 96bdedabcf2e5db1d37f87017c0c436acad97f4ba43a9a2f3c2bb920d8d764dfbc6a3825334e90ed19729870a283a658c24bea5f6ca0ac588a3f9b4bfae9a302 WHIRLPOOL 8d281b4f459167f68a30e485856970f67c6b0be19b58a74b9ba95c07aa2c4848ebae17f333a7d5c675fa10c0ac0f5912df5bd269f6d8dea47e2c1c8da6136235 +AUX shogun-5.0.0-fix-buildsystem.patch 2889 SHA256 97a9ebdde016ca2d6b4d0b2dd09f14b2bfc06a265ca679146e09ba7ff4a58a87 SHA512 3119a95e8fe76804eb113361e09260bbb951679faeb3360d378c0a9afcdbf322ac75f02da6e4c799102949abbd97006f2bbb7550b5f5b01fa8b4335ac530f377 WHIRLPOOL 10af9e23e3c0747f7ece19149e91a4b90e7619cd1ec315dbdcc402e778ec7ccad65deceaf6bd705c598fee8887ef6a852e95e02e7736e7e93fd6be0f297dc73d +DIST shogun-5.0.0.tar.bz2 2448509 SHA256 e82c6a58db9db6624192b018750b0e41f793481791fdc9a6d328bf278d0ae70d SHA512 fa8d9dee4596acce12022540a6927cbdb62e08f8468c8be3790de07ebf3a53055032bcc532b28334ca83284c38f2b0153602634f12bafe4019acb9121b9ff236 WHIRLPOOL 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fc01a70c3c89bfb7137f79094e994d1d97a429b7c4fb662f1149548adb6c255524f6582f8fa77ffac4e6f673830135eb48f326f85d4f595122ad76949b871c01 diff --git a/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch b/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch new file mode 100644 index 000000000000..08edcfac97a2 --- /dev/null +++ b/sci-libs/shogun/files/shogun-4.1.0-remove-C-linkage.patch @@ -0,0 +1,24 @@ +Prevent C linkage errors due to templates in extern "C" blocks: +* /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/bits/cpp_type_traits.h:85:3: error: template with C linkage +* template<bool> +* ^ +* /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/include/g++-v5/bits/cpp_type_traits.h:89:3: error: template specialization with C linkage +* template<> +* ^ +extern "C" blocks can be removed in shogun, as R internally correctly protects C symbols + +--- shogun-4.1.0/src/interfaces/r_modular/sg_print_functions.cpp ++++ shogun-4.1.0/src/interfaces/r_modular/sg_print_functions.cpp +@@ -1,4 +1,3 @@ +-extern "C" { + #include <R.h> + #include <Rinternals.h> + #include <Rdefines.h> +@@ -7,7 +6,6 @@ + #include <Rinterface.h> + #include <R_ext/RS.h> + #include <R_ext/Error.h> +-} + + #include <shogun/base/SGObject.h> + #include <stdio.h> diff --git a/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch b/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch new file mode 100644 index 000000000000..1eb7cd075ece --- /dev/null +++ b/sci-libs/shogun/files/shogun-5.0.0-fix-buildsystem.patch @@ -0,0 +1,72 @@ +* Remove setting of user flags +* Remove erroneous bundling of Eigen + +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -33,15 +33,6 @@ + SET(EIGEN_VERSION_MINIMUM 3.1.2) + SET(VIENNACL_VERSION_MINIMUM 1.5.0) + +-# Store system's or distribution's C[XX]FLAGS. +-SET(SYSTEM_C_FLAGS "${CMAKE_C_FLAGS}") +-SET(SYSTEM_CXX_FLAGS "${CMAKE_CXX_FLAGS}") +-STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE_UC) +-IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION")) +- SET(CMAKE_C_FLAGS "") +- SET(CMAKE_CXX_FLAGS "") +-ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION")) +- + # CCACHE + OPTION(ENABLE_CCACHE "Enable ccache for compilation" ON) + FIND_PACKAGE(CCache) +@@ -174,24 +165,6 @@ + SET(COMPILER_WARNINGS "-Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated") + ENDIF() + +-IF(CMAKE_COMPILER_IS_GNUCXX) +- SET(RELEASE_COMPILER_FLAGS "-fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops") +- IF (${MACHINE} MATCHES "x86_64" OR ${MACHINE} MATCHES "i686") +- SET(RELEASE_COMPILER_FLAGS "${RELEASE_COMPILER_FLAGS} -mfpmath=sse") +- ENDIF() +-ELSEIF(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang") +- SET(RELEASE_COMPILER_FLAGS "-funroll-loops") +-ENDIF() +-SET(SWIG_CXX_COMPILER_FLAGS "-O0 -g") +-SET(CMAKE_C_FLAGS "${COMPILER_WARNINGS} ${CMAKE_C_FLAGS}") +-SET(CMAKE_CXX_FLAGS "${COMPILER_WARNINGS} ${CMAKE_CXX_FLAGS}") +-SET(CMAKE_C_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}") +-SET(CMAKE_CXX_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}") +-SET(CMAKE_C_FLAGS_DISTRIBUTION "-O2") +-SET(CMAKE_CXX_FLAGS_DISTRIBUTION "-O2") +-SET(CMAKE_C_FLAGS_DEBUG "-g") +-SET(CMAKE_CXX_FLAGS_DEBUG "-g") +- + OPTION(ENABLE_COVERAGE "Enable code coverage" OFF) + IF(ENABLE_COVERAGE) + IF(NOT CMAKE_COMPILER_IS_GNUCXX) +@@ -617,13 +590,6 @@ + include(external/Eigen3) + LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR}) + ELSE() +- # eigen3 bug related to aliasing operators and self-storing. +- # TODO put in proper reference and version from when this is fixed +- IF(${EIGEN_VERSION} VERSION_GREATER 3.2.90) +- MESSAGE(WARNING "The system Eigen3 version ${EIGEN_VERSION} is buggy, manually bundling.") +- include(external/Eigen3) +- ENDIF() +- + LIST(APPEND SYSTEM_INCLUDES ${EIGEN_INCLUDE_DIR}) + ENDIF() + +@@ -957,11 +923,6 @@ + # Respect system's or distribution's C[XX]FLAGS. + OPTION(SWIG_WITH_SYSTEM_CFLAGS "Enable system's C[XX]FLAGS for compilation of swig-binaries" ON) + +-IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION")) +- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SYSTEM_C_FLAGS}") +- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SYSTEM_CXX_FLAGS}") +-ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION")) +- + IF(SWIG_WITH_SYSTEM_CFLAGS) + SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} ${SYSTEM_CXX_FLAGS}") + ENDIF(SWIG_WITH_SYSTEM_CFLAGS) diff --git a/sci-libs/shogun/metadata.xml b/sci-libs/shogun/metadata.xml new file mode 100644 index 000000000000..88454ce87eb6 --- /dev/null +++ b/sci-libs/shogun/metadata.xml @@ -0,0 +1,32 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + SHOGUN - is a new machine learning toolbox with focus on large + scale kernel methods and especially on Support Vector Machines + (SVM) with focus to bioinformatics. It provides a generic SVM + object interfacing to several different SVM implementations. Each + of the SVMs can be combined with a variety of the many kernels + implemented. It can deal with weighted linear combination of a + number of sub-kernels, each of which not necessarily working on the + same domain, where an optimal sub-kernel weighting can be learned + using Multiple Kernel Learning. Apart from SVM 2-class + classification and regression problems, a number of linear methods + like Linear Discriminant Analysis (LDA), Linear Programming Machine + (LPM), (Kernel) Perceptrons and also algorithms to train hidden + markov models are implemented. The input feature-objects can be + dense, sparse or strings and of type int/short/double/char and can + be converted into different feature types. Chains of preprocessors + (e.g. substracting the mean) can be attached to each feature object + allowing for on-the-fly pre-processing. + </longdescription> + <use> + <flag name="R">Enable support for <pkg>dev-lang/R</pkg></flag> + <flag name="octave">Enable support for <pkg>sci-mathematics/octave</pkg></flag> + <flag name="opencl">Enable support for building against OpenCL</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/shogun/shogun-5.0.0.ebuild b/sci-libs/shogun/shogun-5.0.0.ebuild new file mode 100644 index 000000000000..faf9808fd09f --- /dev/null +++ b/sci-libs/shogun/shogun-5.0.0.ebuild @@ -0,0 +1,162 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5} ) + +inherit cmake-utils flag-o-matic python-single-r1 toolchain-funcs versionator + +MYPV=$(get_version_component_range 1-2) +MYPD=${PN}-data-0.9 + +DESCRIPTION="Large Scale Machine Learning Toolbox" +HOMEPAGE="http://shogun-toolbox.org/" +SRC_URI=" + ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2 + test? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 ) + examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )" + +LICENSE="GPL-3 free-noncomm" +SLOT="0/16" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cpu_flags_x86_sse doc examples lua octave opencl python R ruby static-libs test" + +REQUIRED_USE=" + python? ( ${PYTHON_REQUIRED_USE} ) + test? ( python )" + +RDEPEND=" + app-arch/bzip2 + app-arch/gzip + app-arch/lzma + app-arch/snappy + dev-libs/lzo + dev-cpp/eigen:3 + dev-libs/json-c:= + dev-libs/libxml2 + dev-libs/protobuf:= + net-misc/curl + sci-libs/arpack + sci-libs/arprec + sci-libs/colpack + sci-libs/hdf5:= + sci-libs/nlopt + sci-mathematics/glpk:= + sci-mathematics/lpsolve:= + sys-libs/readline:0= + sys-libs/zlib + virtual/blas + virtual/cblas + virtual/lapack + lua? ( dev-lang/lua:0 ) + octave? ( >=sci-mathematics/octave-4.2.0:=[hdf5] ) + opencl? ( virtual/opencl ) + python? ( + ${PYTHON_DEPS} + dev-python/numpy[${PYTHON_USEDEP}] + ) + R? ( dev-lang/R ) + ruby? ( dev-ruby/narray )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( + >=app-doc/doxygen-1.8.13-r1[dot] + dev-python/sphinx + ) + lua? ( >=dev-lang/swig-3.0.12 ) + octave? ( >=dev-lang/swig-3.0.12 ) + python? ( + >=dev-lang/swig-3.0.12 + test? ( + sci-libs/scipy + ) + ) + R? ( >=dev-lang/swig-3.0.12 ) + ruby? ( >=dev-lang/swig-3.0.12 ) + test? ( + dev-python/jinja[${PYTHON_USEDEP}] + dev-cpp/gmock + )" + +# javamodular needs jblas (painful to package properly) +# permodular work in progress (as 3.2.0) +# could actually support multiple pythons, multiple rubys +# feel free to do work for it + +PATCHES=( + "${FILESDIR}"/${PN}-5.0.0-fix-buildsystem.patch + "${FILESDIR}"/${PN}-4.1.0-remove-C-linkage.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + export ATLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas lapack)" + export CBLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas)" + export ATLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas cblas lapack)" + export LAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" + + append-cppflags "$($(tc-getPKG_CONFIG) --cflags cblas)" + + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DCMAKE_SKIP_INSTALL_RPATH=ON + -DLIB_INSTALL_DIR=$(get_libdir) + -DENABLE_TESTING=$(usex test) + -DBUILD_EXAMPLES=$(usex examples) + -DDISABLE_SSE=$(usex !cpu_flags_x86_sse) + -DCMAKE_DISABLE_FIND_PACKAGE_Pandoc=ON + $(cmake-utils_use_find_package doc Sphinx) + $(cmake-utils_use_find_package doc Doxygen) + + # Features: + -DENABLE_COVERAGE=OFF + -DENABLE_COLPACK=ON + -DENABLE_PROTOBUF=ON + -DENABLE_PYTHON_DEBUG=OFF + -DENABLE_VIENNACL=$(usex opencl) + -DUSE_ARPREC=ON + -DUSE_HDF5=ON + + # Bindings: + -DJavaModular=OFF + -DPerlModular=OFF + -DCSharpModular=OFF + -DLuaModular=$(usex lua) + -DOctaveModular=$(usex octave) + -DPythonModular=$(usex python) + -DRModular=$(usex R) + -DRubyModular=$(usex ruby) + + # Disable bundled libs + -DBUNDLE_COLPACK=OFF + -DBUNDLE_JSON=OFF + -DBUNDLE_NLOPT=OFF + ) + cmake-utils_src_configure + + # gentoo bug #302621 + has_version 'sci-libs/hdf5[mpi]' && export CXX=mpicxx CC=mpicc +} + +src_compile() { + cmake-utils_src_compile + use doc && cmake-utils_src_compile -C doc +} + +src_install() { + cmake-utils_src_install + + if use doc; then + local i + for i in lua octave python R ruby; do + if use $i; then + docinto html/${i,}_modular + dodoc -r "${BUILD_DIR}"/src/interfaces/${i,}_modular/modshogun/doxygen_xml/. + fi + done + fi +} diff --git a/sci-libs/silo/Manifest b/sci-libs/silo/Manifest new file mode 100644 index 000000000000..1fd178ec69fc --- /dev/null +++ b/sci-libs/silo/Manifest @@ -0,0 +1,12 @@ +AUX silo-4.10.2-mpiposix.patch 1902 SHA256 f51fa69dcefc7ab1cf55968a44eeebba00fb4525151443d3308608498e03c420 SHA512 626a7b8084a936b667f704a1a35edb8f6ce9ab42b58857024b87f280364d99b452e3f149b577e45898eb08523f0741eecc1c4ad20a46018dae377ca17adcf97a WHIRLPOOL 960450184593c9b4577b04eceaddc8a13536a9412e19ca5c46f940e9001511c52098864b067674a7d9c334d8a9721b566263c968dbe196ba48e5d9e94cc83a01 +AUX silo-4.10.2-qtlibs.patch 3558 SHA256 db09bb42b74415de96220b2c8e56d6aad4164153b1aca65d135f1ac588f226b9 SHA512 629a16392ce32d7b9d79cd4870f6236e0129bc2ef570afc515b2af698dc67a4a773fc7d1a92c65ea8663ca1f993cac4d81a326ac6f10e474adcb614599863966 WHIRLPOOL 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H5Pclose(retval); ++// return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me); ++//#endif ++// break; ++// } + + case DB_FILE_OPTS_H5_DEFAULT_MPIO: ++ case DB_FILE_OPTS_H5_DEFAULT_MPIP: + { + #ifdef H5_HAVE_PARALLEL + MPI_Info info; +@@ -5069,15 +5070,15 @@ + if ((p = DBGetOption(opts, DBOPT_H5_MPIP_NO_GPFS_HINTS))) + use_gpfs_hints = FALSE; + +- if (vfd == DB_H5VFD_MPIO) ++// if (vfd == DB_H5VFD_MPIO) + { + h5status |= H5Pset_fapl_mpio(retval, mpi_comm, mpi_info); + if (created_info) MPI_Info_free(&mpi_info); + } +- else +- { +- h5status |= H5Pset_fapl_mpiposix(retval, mpi_comm, use_gpfs_hints); +- } ++// else ++// { ++// h5status |= H5Pset_fapl_mpiposix(retval, mpi_comm, use_gpfs_hints); ++// } + #else + H5Pclose(retval); + return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me); diff --git a/sci-libs/silo/files/silo-4.10.2-qtlibs.patch b/sci-libs/silo/files/silo-4.10.2-qtlibs.patch new file mode 100644 index 000000000000..e8fc4284cac0 --- /dev/null +++ b/sci-libs/silo/files/silo-4.10.2-qtlibs.patch @@ -0,0 +1,66 @@ +diff -ru silo-4.9.1-old/configure silo-4.9.1-new/configure +--- silo-4.9.1-old/configure 2014-01-18 23:19:15.755030306 +0100 ++++ silo-4.9.1-new/configure 2014-01-18 23:20:52.595031159 +0100 +@@ -27503,7 +27503,7 @@ + ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | + sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" + fi +- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + else + # Use cached value or do search, starting with suggestions from + # the command line +@@ -27577,7 +27577,7 @@ + ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | + sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" + fi +- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + else + # There is no valid definition for $QTDIR as Trolltech likes to see it + ax_qt_dir= +@@ -27589,7 +27589,7 @@ + ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | + sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" + fi +- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + else + # Normally, when there is no traditional Trolltech installation, + # the library is installed in a place where the linker finds it +@@ -27607,7 +27607,7 @@ + # See if we find the library without any special options. + # Don't add top $LIBS permanently yet + ax_save_LIBS="$LIBS" +- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + ax_qt_LIBS="$LIBS" + ax_save_CXXFLAGS="$CXXFLAGS" + CXXFLAGS="-I$ax_qt_include_dir -I$ax_qt_include_dir/Qt -I$ax_qt_include_dir/QtCore -I$ax_qt_include_dir/QtGui" +@@ -27668,7 +27668,7 @@ + # That did not work. Try the multi-threaded version + echo "Non-critical error, please neglect the above." >&5 + ax_qt_lib=qt-mt +- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ + _ACEOF +@@ -27726,7 +27726,7 @@ + # That did not work. Try the OpenGL version + echo "Non-critical error, please neglect the above." >&5 + ax_qt_lib=qt-gl +- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ + _ACEOF +@@ -27809,7 +27809,7 @@ + fi + done + # Try with that one +- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ + _ACEOF diff --git a/sci-libs/silo/files/silo-4.10.2-tests.patch b/sci-libs/silo/files/silo-4.10.2-tests.patch new file mode 100644 index 000000000000..2e0a52191d0e --- /dev/null +++ b/sci-libs/silo/files/silo-4.10.2-tests.patch @@ -0,0 +1,11 @@ +--- tests/Makefile.in.old 2014-07-24 07:25:53.464381420 +0200 ++++ tests/Makefile.in 2014-07-24 07:26:14.951048323 +0200 +@@ -169,7 +169,7 @@ + $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ + $(ioperf_stdio_la_LDFLAGS) $(LDFLAGS) -o $@ + rocket_silo_la_LIBADD = +-am_rocket_silo_la_OBJECTS = rocket_silo.lo ++am_rocket_silo_la_OBJECTS = rocket_silo.lo ../src/.libs/libsilo.la + rocket_silo_la_OBJECTS = $(am_rocket_silo_la_OBJECTS) + rocket_silo_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \ + $(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \ diff --git a/sci-libs/silo/files/silo-4.9.1-qtlibs.patch b/sci-libs/silo/files/silo-4.9.1-qtlibs.patch new file mode 100644 index 000000000000..e8fc4284cac0 --- /dev/null +++ b/sci-libs/silo/files/silo-4.9.1-qtlibs.patch @@ -0,0 +1,66 @@ +diff -ru silo-4.9.1-old/configure silo-4.9.1-new/configure +--- silo-4.9.1-old/configure 2014-01-18 23:19:15.755030306 +0100 ++++ silo-4.9.1-new/configure 2014-01-18 23:20:52.595031159 +0100 +@@ -27503,7 +27503,7 @@ + ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | + sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" + fi +- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + else + # Use cached value or do search, starting with suggestions from + # the command line +@@ -27577,7 +27577,7 @@ + ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | + sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" + fi +- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + else + # There is no valid definition for $QTDIR as Trolltech likes to see it + ax_qt_dir= +@@ -27589,7 +27589,7 @@ + ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | + sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" + fi +- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + else + # Normally, when there is no traditional Trolltech installation, + # the library is installed in a place where the linker finds it +@@ -27607,7 +27607,7 @@ + # See if we find the library without any special options. + # Don't add top $LIBS permanently yet + ax_save_LIBS="$LIBS" +- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + ax_qt_LIBS="$LIBS" + ax_save_CXXFLAGS="$CXXFLAGS" + CXXFLAGS="-I$ax_qt_include_dir -I$ax_qt_include_dir/Qt -I$ax_qt_include_dir/QtCore -I$ax_qt_include_dir/QtGui" +@@ -27668,7 +27668,7 @@ + # That did not work. Try the multi-threaded version + echo "Non-critical error, please neglect the above." >&5 + ax_qt_lib=qt-mt +- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ + _ACEOF +@@ -27726,7 +27726,7 @@ + # That did not work. Try the OpenGL version + echo "Non-critical error, please neglect the above." >&5 + ax_qt_lib=qt-gl +- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ + _ACEOF +@@ -27809,7 +27809,7 @@ + fi + done + # Try with that one +- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" ++ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" + cat >conftest.$ac_ext <<_ACEOF + /* confdefs.h. */ + _ACEOF diff --git a/sci-libs/silo/files/silo-4.9.1-tests.patch b/sci-libs/silo/files/silo-4.9.1-tests.patch new file mode 100644 index 000000000000..2e0a52191d0e --- /dev/null +++ b/sci-libs/silo/files/silo-4.9.1-tests.patch @@ -0,0 +1,11 @@ +--- tests/Makefile.in.old 2014-07-24 07:25:53.464381420 +0200 ++++ tests/Makefile.in 2014-07-24 07:26:14.951048323 +0200 +@@ -169,7 +169,7 @@ + $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ + $(ioperf_stdio_la_LDFLAGS) $(LDFLAGS) -o $@ + rocket_silo_la_LIBADD = +-am_rocket_silo_la_OBJECTS = rocket_silo.lo ++am_rocket_silo_la_OBJECTS = rocket_silo.lo ../src/.libs/libsilo.la + rocket_silo_la_OBJECTS = $(am_rocket_silo_la_OBJECTS) + rocket_silo_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \ + $(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \ diff --git a/sci-libs/silo/metadata.xml b/sci-libs/silo/metadata.xml new file mode 100644 index 000000000000..6c626818da20 --- /dev/null +++ b/sci-libs/silo/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription> + Silo is a library for reading and writing a wide variety of + scientific data to binary, disk files. The files Silo produces and + the data within them can be easily shared and exchanged between + wholly independently developed applications running on disparate + computing platforms. + </longdescription> + <use> + <flag name="silex">Build silex data browser</flag> + </use> + <maintainer type="person"> + <email>slis@gentoo.org</email> + </maintainer> +<maintainer type="project"> + <email>cluster@gentoo.org</email> + <name>Gentoo Cluster Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/silo/silo-4.10.2.ebuild b/sci-libs/silo/silo-4.10.2.ebuild new file mode 100644 index 000000000000..0c77dba873a7 --- /dev/null +++ b/sci-libs/silo/silo-4.10.2.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils fortran-2 + +DESCRIPTION="A mesh and field I/O library and scientific database" +HOMEPAGE="https://wci.llnl.gov/simulation/computer-codes/silo" +SRC_URI="https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/${PN}/${P}/${P}.tar.gz" +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" +IUSE="hdf5 +silex static-libs qt4 test" + +REQUIRED_USE="silex? ( qt4 )" + +RDEPEND=" + hdf5? ( sci-libs/hdf5 ) + qt4? ( dev-qt/qtgui:4 )" +DEPEND="${RDEPEND}" + +src_prepare() { + epatch "${FILESDIR}/${P}-qtlibs.patch" + epatch "${FILESDIR}/${P}-tests.patch" + epatch "${FILESDIR}/${P}-mpiposix.patch" +} + +src_configure() { + econf \ + --enable-install-lite-headers \ + --enable-shared \ + $(use_enable silex silex ) \ + $(use_enable static-libs static ) \ + $(use_with qt4 Qt-lib-dir "${EPREFIX}"/usr/lib${LIB_LOCATION_SUFFIX}/qt4 ) \ + $(use_with qt4 Qt-include-dir "${EPREFIX}"/usr/include/qt4 ) \ + $(use_with hdf5 hdf5 ${EPREFIX}"/usr/include,${EPREFIX}"/usr/lib${LIB_LOCATION_SUFFIX} ) +} diff --git a/sci-libs/silo/silo-4.9.1.ebuild b/sci-libs/silo/silo-4.9.1.ebuild new file mode 100644 index 000000000000..7c9677f14773 --- /dev/null +++ b/sci-libs/silo/silo-4.9.1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils + +DESCRIPTION="A mesh and field I/O library and scientific database" +HOMEPAGE="https://wci.llnl.gov/codes/${PN}" +SRC_URI="https://wci.llnl.gov/codes/${PN}/${P}/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" +IUSE="hdf5 +silex static-libs qt4 test" + +REQUIRED_USE="silex? ( qt4 )" + +RDEPEND=" + hdf5? ( sci-libs/hdf5 ) + qt4? ( dev-qt/qtgui:4 )" +DEPEND="${RDEPEND}" + +src_prepare() { + epatch "${FILESDIR}/${P}-qtlibs.patch" + epatch "${FILESDIR}/${P}-tests.patch" +} + +src_configure() { + econf \ + --enable-install-lite-headers \ + --enable-shared \ + $(use_enable silex silex ) \ + $(use_enable static-libs static ) \ + $(use_with qt4 Qt-lib-dir "${EPREFIX}"/usr/lib${LIB_LOCATION_SUFFIX}/qt4 ) \ + $(use_with qt4 Qt-include-dir "${EPREFIX}"/usr/include/qt4 ) \ + $(use_with hdf5 hdf5 ${EPREFIX}"/usr/include,${EPREFIX}"/usr/lib${LIB_LOCATION_SUFFIX} ) +} diff --git a/sci-libs/spooles/Manifest b/sci-libs/spooles/Manifest new file mode 100644 index 000000000000..d8c31dc5a409 --- /dev/null +++ b/sci-libs/spooles/Manifest @@ -0,0 +1,9 @@ +AUX Make.inc.in 139 SHA256 696a22b54ed0b0e3d1709d880cddd63a4bdea027a824b281ab57480987645c0b SHA512 919c60ca856e4b46b6211f4ace815b5066609e054152b696733d5120d7769a17c6db92c451772b83b0bea5a3e9a14034009755ffbef0889fefd76bca8f466611 WHIRLPOOL 5ccad0e9f1ad373dc53244c5e7f362ca02c6c5db0846faa3ded22795374730b55b947a7a5fe238527f622225d7e8bbc3770658a6d50729465fdd11e7d5ad53c5 +AUX spooles-2.2-I2Ohash-64bit.patch 1035 SHA256 160545093456f00f1b0363d97514fec747d0c0e85a69539cc8a943dac496fd09 SHA512 825b1a060102799e17ebcfda5025bfbe53555eab3ed32d8c8ba3bfd2f114b9d622763dec78ba311307cab12a93cc6dac363a9237d819830f5ea4c1a6cce7d1f9 WHIRLPOOL f21c4d6d51317656da78814e58611a643ca215ca09486d4980a96699ed817d1d250a1e05fcf9d07c9e01ba6fdf28281536b49fdfb064f7850e188fa38b24d67c +AUX spooles-2.2-formats.patch 654 SHA256 f59cd1eb1f3fc8aa7fe11eff75fcbac8841203150ab8e605e30144ea925f2b0a SHA512 fc4f4dbd4e457f6e162fef5a0d90a153b677205dc9c6c075b47fddc0d8d9c77cda1573d1f9966d5b127084869c797c666fd1e0b579964774020665d988015b86 WHIRLPOOL df5623563db98db0942e9935f2d4124b0641c28f59f2dc2c3916441f94bb388c495128c19aeb1ae54efa33abcd08a63ba96fd8366e9612c93e2a917c84e8c4ad +AUX spooles-2.2-makefiles.patch 1144 SHA256 402028ae9d356c6c345fa15b98afae8ef6129e96289ed340f02a5f2f12c16140 SHA512 29429923b2d5cb5475a2741327a921ff5311f8bc562b357428befa6f7b26660b7ebc2df45bafc2a5f80131a3fe37afba3fe36deb57bdf445a99178bc17faf53a WHIRLPOOL 2b74e16a9da59e64c25484df6f54260ad6a1f01f251d84fc81daa06fd86f067b93c97e991d4daf7f7f73383c0afb3b833265493f0aa0e95dcaff2d60c2c972fc +DIST spooles.2.2.tgz 4510271 SHA256 a84559a0e987a1e423055ef4fdf3035d55b65bbe4bf915efaa1a35bef7f8c5dd SHA512 440146b4abf81d8e66a7c57e839b06b11c7753e16d40ae67f80255d6d5dc9fb43b4fd549326c405a8f3009223fcb0f6997090b3649029c323c732b0759944d19 WHIRLPOOL e0fef7bb5786bd467e07ab3aba4444f2e3da3aa82a6faaf308a340344cf045676cf5b5c339e35510e6306749a5f31f12647e8c9ce888bc2fb20314e2e63f586b +EBUILD spooles-2.2.ebuild 1821 SHA256 61dd8438db1f5107697357cc50cb36d9365c3edb6e0f98f2b64dabed50651eca SHA512 ef21fe915946fad6ffd84d048763426b38eb08171184de4f41ff0ed1e6b47bd7536f1cdcd6b64d11dc5bf5e0347e98e9ac1b788768fc6d62dab5d30f8e6631f9 WHIRLPOOL 1c8709ad3d755b26cb93e0512ed3aad53de989dd7688f3b0ea6e2d67937d6c559c2faf17170df0f6b594a78918e70f05fb6ed1404b1ca077ac6ac9b90c7c8179 +MISC ChangeLog 2948 SHA256 f273b46b0c80509b556eb1a85903c4d998a4de446c1e66b084f4fb8499312ae0 SHA512 a80bd39268bd0abcb9fd84504f9575fb6e623f30119b76151596bd479b2dea81a2f055a17d5798966e5fbbf45c10777d9cf4453557eed02efd08e6822ec03f5c WHIRLPOOL a0c6cdf3be4bb5000a51f0e6b33979f3a8891c562638c568db6730f9290288527ec7015988f2b6e40bb47f0a03847fbd47cb7d0253faea4c587e2c6442dd9208 +MISC ChangeLog-2015 958 SHA256 8b4ace403528f940382181ecefacc45b21f73dcbdab9eadb9120ce3d55dbfc41 SHA512 d0146bc884ea34113fb75bd79cd80fc0cf3e6a2bd4a0b180903f0e55ab8789617e04aa312be45182bcdc0cf71a2908123ca85dc40725311780b7484c3c457340 WHIRLPOOL 1f08acf4327999cc2128a19bd7f1a86af172cb6d220b199ef88443704e9c39ab3976a279364dd65ccfcdc4ae8e8e321736ee50188770ba50e6a3d899168975d0 +MISC metadata.xml 1054 SHA256 43d4bb0a9d9ebc62396133e8bfca2046cfb238e705747df0cf63aeda2662fc8c SHA512 fdd91d4bd8b41d8058e63c65445d2ef9a7d1e5b6888af0f2d2a81469413c2dbcf5801895ee5c96946ba576c4cac49cfbd50f77512084461f1985a71e73f99aad WHIRLPOOL d739765706e91705fe5fdeca2a3cb0df3765f1ded7c6de2ee96eab60473e151fe3c3b75bd9e11284388f12e493c9c8043867fd338a5d82f9459f495e9228e72a diff --git a/sci-libs/spooles/files/Make.inc.in b/sci-libs/spooles/files/Make.inc.in new file mode 100644 index 000000000000..1557f9fe979e --- /dev/null +++ b/sci-libs/spooles/files/Make.inc.in @@ -0,0 +1,9 @@ +.POSIX: +THREAD_LIBS = -lpthread +CC = @CC@ +AR = @AR@ +RANLIB = @RANLIB@ +ARFLAGS = rv +.c.a : + $(CC) $(CFLAGS) -c $< + $(AR) $(ARFLAGS) $@ $*.o diff --git a/sci-libs/spooles/files/spooles-2.2-I2Ohash-64bit.patch b/sci-libs/spooles/files/spooles-2.2-I2Ohash-64bit.patch new file mode 100644 index 000000000000..0f608da2afc8 --- /dev/null +++ b/sci-libs/spooles/files/spooles-2.2-I2Ohash-64bit.patch @@ -0,0 +1,28 @@ +--- spooles-2.2/I2Ohash/src/util.c~ 1998-05-30 18:45:12.000000000 -0400 ++++ spooles-2.2/I2Ohash/src/util.c 2008-06-28 20:56:49.000000000 -0400 +@@ -39,9 +39,10 @@ + */ + loc1 = (key1 + 1) % hashtable->nlist ; + loc2 = (key2 + 1) % hashtable->nlist ; +-loc = (loc1*loc2) % hashtable->nlist ; ++long int loc3 = (long int)loc1*(long int)loc2 % hashtable->nlist ; ++loc =(int) loc3; + #if MYDEBUG > 0 +-fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %d", loc1, loc2, loc) ; ++fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %ld, loc = %d", loc1, loc2, loc3, loc) ; + fflush(stdout) ; + #endif + /* +@@ -158,9 +159,10 @@ + #endif + loc1 = (key1 + 1) % hashtable->nlist ; + loc2 = (key2 + 1) % hashtable->nlist ; +-loc = (loc1*loc2) % hashtable->nlist ; ++long int loc3 = (long int)loc1*(long int)loc2 % hashtable->nlist ; ++loc =(int) loc3; + #if MYDEBUG > 0 +-fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %d", loc1, loc2, loc) ; ++fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %ld, loc = %d", loc1, loc2, loc3, loc) ; + fflush(stdout) ; + #endif + /* diff --git a/sci-libs/spooles/files/spooles-2.2-formats.patch b/sci-libs/spooles/files/spooles-2.2-formats.patch new file mode 100644 index 000000000000..080574e730d0 --- /dev/null +++ b/sci-libs/spooles/files/spooles-2.2-formats.patch @@ -0,0 +1,17 @@ +--- SolveMap/src/setup.c.orig 2011-03-05 18:08:51.000000000 +0000 ++++ SolveMap/src/setup.c 2011-03-05 18:16:50.000000000 +0000 +@@ -28,12 +28,12 @@ + --------------- + */ + if ( solvemap == NULL ) { +- fprintf(stderr, "\n fatal error in SolveMap_forwardSetup(%p,%d)" ++ fprintf(stderr, "\n fatal error in SolveMap_forwardSetup" + "\n solvemap is NULL\n") ; + exit(-1) ; + } + if ( myid < 0 || myid >= solvemap->nproc ) { +- fprintf(stderr, "\n fatal error in SolveMap_forwardSetup(%p,%d)" ++ fprintf(stderr, "\n fatal error in SolveMap_forwardSetup" + "\n myid %d, solvemap->nproc %d\n", myid, solvemap->nproc) ; + exit(-1) ; + } diff --git a/sci-libs/spooles/files/spooles-2.2-makefiles.patch b/sci-libs/spooles/files/spooles-2.2-makefiles.patch new file mode 100644 index 000000000000..4af8e083736c --- /dev/null +++ b/sci-libs/spooles/files/spooles-2.2-makefiles.patch @@ -0,0 +1,47 @@ +--- MPI/makefile~ 1998-12-17 15:47:44.000000000 +0000 ++++ MPI/makefile 2008-02-26 00:10:57.000000000 +0000 +@@ -2,7 +2,7 @@ + cd drivers ; make drivers + + lib : +- cd src ; make spoolesMPI.a ++ cd src ; make makeLib + + clean : + cd src ; make clean +--- MPI/src/makefile~ 1998-12-16 21:54:41.000000000 +0000 ++++ MPI/src/makefile 2008-02-26 00:08:16.000000000 +0000 +@@ -42,3 +42,8 @@ + + clean : + - rm -f *.a *.o ++ ++makeLib : ++ perl ../../makeLib > makeG ++ make -f makeG ++ rm -f makeG +--- MT/makefile~ 1998-12-17 15:47:48.000000000 +0000 ++++ MT/makefile 2008-02-26 00:12:43.000000000 +0000 +@@ -2,7 +2,7 @@ + cd drivers ; make drivers + + lib : +- cd src ; make spoolesMT.a ++ cd src ; make makeLib + + clean : + cd src ; make clean +--- makeLib~ 2011-03-05 16:44:12.000000000 +0000 ++++ makeLib 2011-03-05 17:46:58.000000000 +0000 +@@ -70,8 +70,8 @@ + .c.o : + $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o + +-../../spooles.a : ${OBJ_FILES} +- $(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o ++../../libspooles.a : ${OBJ_FILES} ++ $(AR) $(ARFLAGS) ../../libspooles.a $(OBJ)_*.o + rm -f $(OBJ)_*.o +- $(RANLIB) ../../spooles.a ++ $(RANLIB) ../../libspooles.a + EOF diff --git a/sci-libs/spooles/metadata.xml b/sci-libs/spooles/metadata.xml new file mode 100644 index 000000000000..24aa1634d185 --- /dev/null +++ b/sci-libs/spooles/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + SPOOLES is a library for solving sparse real and complex linear + systems of equations, written in the C language using object + oriented design. At present, there is the following functionality: + 1. Compute multiple minimum degree, generalized nested dissection + and multisection orderings of matrices with symmetric structure. + 2. Factor and solve square linear systems of equations with + symmetric structure, with or without pivoting for stability. + 3. Factor and solve overdetermined full rank systems of equations + using a multifrontal QR factorization. + 4. Solve square linear systems using a variety of Krylov iterative + methods. The preconditioner is a drop tolerance factorization, + with or without pivoting for stability. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/spooles/spooles-2.2.ebuild b/sci-libs/spooles/spooles-2.2.ebuild new file mode 100644 index 000000000000..cd1a944ec56b --- /dev/null +++ b/sci-libs/spooles/spooles-2.2.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 +inherit eutils toolchain-funcs versionator flag-o-matic + +MYP=${PN}.${PV} + +DESCRIPTION="SParse Object Oriented Linear Equations Solver" +HOMEPAGE="http://www.netlib.org/linalg/spooles" +SRC_URI="http://www.netlib.org/linalg/${PN}/${MYP}.tgz" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="mpi static-libs threads" + +RDEPEND="mpi? ( virtual/mpi )" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +make_shared_lib() { + local soname=$(basename "${1%.a}").so.$(get_major_version) + einfo "Making ${soname}" + ${2:-$(tc-getCC)} ${LDFLAGS} \ + -shared -Wl,-soname="${soname}" \ + -Wl,--whole-archive "${1}" -Wl,--no-whole-archive \ + -o $(dirname "${1}")/"${soname}" || return 1 +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-I2Ohash-64bit.patch + epatch "${FILESDIR}"/${P}-makefiles.patch + epatch "${FILESDIR}"/${P}-formats.patch + find . -name makefile -exec \ + sed -i -e 's:make:$(MAKE):g' '{}' \; + sed -e "s/@CC@/$(tc-getCC)/" \ + -e "s/@AR@/$(tc-getAR)/" \ + -e "s/@RANLIB@/$(tc-getRANLIB)/" \ + "${FILESDIR}"/Make.inc.in > Make.inc || die +} + +src_compile () { + append-flags -fPIC + emake lib + use threads && emake -C MT lib + use mpi && emake -C MPI CC=mpicc lib + make_shared_lib libspooles.a $(use mpi && echo mpicc) || die "shared lib failed" + if use static-libs; then + filter-flags -fPIC + emake clean + emake lib + use threads && emake -C MT lib + use mpi && emake -C MPI CC=mpicc lib + fi +} + +src_install () { + dolib.so libspooles.so.2 + dosym libspooles.so.2 /usr/$(get_libdir)/libspooles.so + use static-libs && dolib.a libspooles.a + find . -name '*.h' -print0 | \ + xargs -0 -n1 --replace=headerfile install -D headerfile tmp/headerfile + insinto /usr/include/${PN} + doins -r tmp/* +} diff --git a/sci-libs/spqr/Manifest b/sci-libs/spqr/Manifest new file mode 100644 index 000000000000..6f83f095b781 --- /dev/null +++ b/sci-libs/spqr/Manifest @@ -0,0 +1,8 @@ +AUX spqr-1.2.3-autotools.patch 7204 SHA256 b71dddd62375f29a4a076fc14be9deee03df5ff951878dd2751a138067d48a99 SHA512 23b07ce5bbc993dbb8c7811f04d0c8997c4293ad2ffb6fee07b4fc23d5306499bfe5a84683add88a8d7050cf0ae5ed5e9d5a3d03064ef8a049918b5f2a2d1250 WHIRLPOOL a89b0e99c0aa8a3ef8b49c860b40d49e226979f0c1cc6727ce68d7845f287b541f7aae5ada3ea32757854ce70d1e62ff07c2e788e3c0dbc05b8604d47d831771 +DIST SPQR-1.2.3.tar.gz 1090017 SHA256 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-0400 +@@ -0,0 +1,78 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include ++ ++LDADD = $(top_builddir)/Source/libspqr.la \ ++ $(CHOLMOD_LIBS) $(AMD_LIBS) $(CAMD_LIBS) \ ++ $(COLAMD_LIBS) $(CCOLAMD_LIBS) \ ++ $(METIS_LIBS) $(BLAS_LIBS) $(LAPACK_LIBS) $(TBB_LIBS) ++ ++check_PROGRAMS = \ ++ qrsimple qrsimplec \ ++ qrdemo qrdemoc ++ ++qrsimple_SOURCES = qrsimple.cpp ++qrsimplec = qrsimplec.c ++qrsimplec_CFLAGS = -ansi ++qrdemo_SOURCES = qrdemo.cpp ++qrdemoc_SOURCES = qrdemoc.c ++qrdemoc_CFLAGS = -ansi ++ ++ ++check-local: $(check_PROGRAMS) ++ ./qrsimple < $(top_srcdir)/Matrix/ash219.mtx || exit 1 ++ ./qrsimplec < $(top_srcdir)/Matrix/ash219.mtx || exit 1 ++ ./qrsimple < $(top_srcdir)/Matrix/west0067.mtx || exit 1 ++ ./qrsimplec < $(top_srcdir)/Matrix/west0067.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/a2.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/r2.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/a04.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/a2.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/west0067.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/c2.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/a0.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/lfat5b.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/bfwa62.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/LFAT5.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/b1_ss.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/bcspwr01.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/lpi_galenet.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/lpi_itest6.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/ash219.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/a4.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/s32.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/c32.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/lp_share1b.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/a1.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/GD06_theory.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/GD01_b.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/Tina_AskCal_perm.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/Tina_AskCal.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/GD98_a.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/Ragusa16.mtx || exit 1 ++ ./qrdemo < $(top_srcdir)/Matrix/young1c.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/a2.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/r2.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/a04.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/a2.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/west0067.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/c2.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/a0.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/lfat5b.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/bfwa62.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/LFAT5.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/b1_ss.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/bcspwr01.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/lpi_galenet.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/lpi_itest6.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/ash219.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/a4.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/s32.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/c32.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/lp_share1b.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/a1.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/GD06_theory.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/GD01_b.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/Tina_AskCal_perm.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/Tina_AskCal.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/GD98_a.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/Ragusa16.mtx || exit 1 ++ ./qrdemoc < $(top_srcdir)/Matrix/young1c.mtx || exit 1 +--- Include/Makefile.am 1969-12-31 19:00:00.000000000 -0500 ++++ Include/Makefile.am 2009-10-22 23:42:08.000000000 -0400 +@@ -0,0 +1,5 @@ ++include_HEADERS = \ ++ spqr.hpp \ ++ SuiteSparseQR_C.h \ ++ SuiteSparseQR_definitions.h \ ++ SuiteSparseQR.hpp +--- Makefile.am 1969-12-31 19:00:00.000000000 -0500 ++++ Makefile.am 2009-10-22 23:42:08.000000000 -0400 +@@ -0,0 +1,2 @@ ++SUBDIRS = Include Source Demo ++EXTRA_DIST = README.txt +--- Source/Makefile.am 1969-12-31 19:00:00.000000000 -0500 ++++ Source/Makefile.am 2009-10-22 23:43:03.000000000 -0400 +@@ -0,0 +1,48 @@ ++AM_CPPFLAGS=-I$(top_srcdir)/Include ++ ++lib_LTLIBRARIES = libspqr.la ++ ++libspqr_la_SOURCES = \ ++ spqr_rmap.cpp \ ++ SuiteSparseQR_C.cpp \ ++ SuiteSparseQR_expert.cpp \ ++ spqr_parallel.cpp \ ++ spqr_kernel.cpp \ ++ spqr_analyze.cpp \ ++ spqr_assemble.cpp \ ++ spqr_cpack.cpp \ ++ spqr_csize.cpp \ ++ spqr_fcsize.cpp \ ++ spqr_debug.cpp \ ++ spqr_front.cpp \ ++ spqr_factorize.cpp \ ++ spqr_freenum.cpp \ ++ spqr_freesym.cpp \ ++ spqr_freefac.cpp \ ++ spqr_fsize.cpp \ ++ spqr_maxcolnorm.cpp \ ++ spqr_rconvert.cpp \ ++ spqr_rcount.cpp \ ++ spqr_rhpack.cpp \ ++ spqr_rsolve.cpp \ ++ spqr_stranspose1.cpp \ ++ spqr_stranspose2.cpp \ ++ spqr_hpinv.cpp \ ++ spqr_1fixed.cpp \ ++ spqr_1colamd.cpp \ ++ SuiteSparseQR.cpp \ ++ spqr_1factor.cpp \ ++ spqr_cumsum.cpp \ ++ spqr_shift.cpp \ ++ spqr_happly.cpp \ ++ spqr_panel.cpp \ ++ spqr_happly_work.cpp \ ++ SuiteSparseQR_qmult.cpp \ ++ spqr_trapezoidal.cpp \ ++ spqr_larftb.cpp \ ++ spqr_append.cpp \ ++ spqr_type.cpp \ ++ spqr_tol.cpp ++ ++libspqr_la_CPPFLAGS = $(AM_CPPFLAGS) $(METIS_CFLAGS) $(TBB_CFLAGS) $(LAPACK_CFLAGS) ++libspqr_la_LIBADD = $(METIS_LIBS) $(TBB_LIBS) $(LAPACK_LIBS) +--- configure.ac 1969-12-31 19:00:00.000000000 -0500 ++++ configure.ac 2009-10-22 23:42:32.000000000 -0400 +@@ -0,0 +1,55 @@ ++AC_PREREQ(2.59) ++AC_INIT(spqr, 1.2, davis@cise.ufl.edu) ++AM_INIT_AUTOMAKE([foreign]) ++AC_CONFIG_SRCDIR([Source/spqr_kernel.cpp]) ++AM_INIT_AUTOMAKE([foreign]) ++ ++AC_PROG_LIBTOOL ++AC_PROG_CXX ++AC_LANG(C++) ++ ++AC_CHECK_LIB(m, sqrt) ++AC_CHECK_LIB(lapack,zlarft_) ++AC_CHECK_HEADERS(UFconfig.h) ++AC_CHECK_HEADERS(cholmod.h) ++AC_CHECK_LIB(cholmod, cholmod_solve, [], \ ++ [AC_MSG_ERROR([Cannot find libcholmod])]) ++ ++AC_ARG_WITH(metis, ++ [AC_HELP_STRING([--with-metis], ++ [Use METIS for partitioning])], ++ [with_metis=$withval], ++ [with_metis="yes"]) ++if test x$with_metis = xyes; then ++ PKG_PROG_PKG_CONFIG ++ if test -n "$PKG_CONFIG"; then ++ PKG_CHECK_MODULES([metis], [metis]) ++ else ++ AC_CHECK_HEADERS(metis.h) ++ AC_CHECK_LIB(metis, METIS_NodeND, [METIS_LIBS=-lmetis], \ ++ [AC_MSG_ERROR([Cannot find libmetis])]) ++ fi ++ AC_DEFINE(NPARTITION) ++fi ++AM_CONDITIONAL([METIS], [test x$with_metis = xyes]) ++ ++AC_ARG_WITH(tbb, ++ [AC_HELP_STRING([--with-tbb], ++ [Use Intel Threading Building Block for multithreading])], ++ [with_tbb=$withval], ++ [with_tbb="yes"]) ++if test x$with_tbb = xyes; then ++ AC_CHECK_HEADERS(tbb/task.h) ++ TBB_CFLAGS="" ++ TBB_LIBS="-ltbb" ++ AC_SUBST(TBB_CFLAGS) ++ AC_SUBST(TBB_LIBS) ++ AC_DEFINE(HAVE_TBB) ++fi ++AM_CONDITIONAL([WITH_TBB], [test x$with_tbb = xyes]) ++ ++AC_CONFIG_FILES([Makefile ++ Source/Makefile ++ Include/Makefile ++ Demo/Makefile]) ++AC_OUTPUT diff --git a/sci-libs/spqr/metadata.xml b/sci-libs/spqr/metadata.xml new file mode 100644 index 000000000000..c7ab54f2c476 --- /dev/null +++ b/sci-libs/spqr/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + SuiteSparseQR is an implementation of the multifrontal sparse QR + factorization method. Parallelism is exploited both in the BLAS and + across different frontal matrices using Intel's Threading Building + Blocks. It can obtain a substantial fraction of the theoretical + peak performance of a multicore computer. +</longdescription> +<use> + <flag name="metis">Use <pkg>sci-libs/metis</pkg> or <pkg>sci-libs/parmetis</pkg> for partitioning</flag> + <flag name="tbb">Enable multithreading with the Intel Threads + Building Block <pkg>dev-cpp/tbb</pkg></flag> +</use> +</pkgmetadata> diff --git a/sci-libs/spqr/spqr-1.2.3-r1.ebuild b/sci-libs/spqr/spqr-1.2.3-r1.ebuild new file mode 100644 index 000000000000..9f722944c3d0 --- /dev/null +++ b/sci-libs/spqr/spqr-1.2.3-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 +AUTOTOOLS_AUTORECONF=yes +inherit autotools-utils + +MY_PN=SPQR +DESCRIPTION="Multithreaded multifrontal sparse QR factorization library" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/SPQR" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${MY_PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="amd64 ~x86" +IUSE="doc metis static-libs tbb" +RDEPEND="sci-libs/cholmod[supernodal(+)] + tbb? ( dev-cpp/tbb ) + metis? ( >=sci-libs/cholmod-1.7.0-r1[metis] )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +DOCS=( README.txt Doc/ChangeLog ) +PATCHES=( "${FILESDIR}"/${P}-autotools.patch ) + +S="${WORKDIR}/${MY_PN}" + +src_configure() { + myeconfargs+=( + $(use_with metis) + $(use_with tbb) + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + use doc && doins Doc/*.pdf +} diff --git a/sci-libs/spqr/spqr-1.3.1.ebuild b/sci-libs/spqr/spqr-1.3.1.ebuild new file mode 100644 index 000000000000..9489d6068380 --- /dev/null +++ b/sci-libs/spqr/spqr-1.3.1.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Multithreaded multifrontal sparse QR factorization library" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/SPQR" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc metis static-libs tbb" +RDEPEND=" + virtual/lapack + >=sci-libs/cholmod-2[metis?] + tbb? ( dev-cpp/tbb )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base )" + +src_configure() { + local myeconfargs+=( + $(use_with doc) + $(use_with metis partition) + $(use_with tbb) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/spr/Manifest b/sci-libs/spr/Manifest new file mode 100644 index 000000000000..98bba3da39e4 --- /dev/null +++ b/sci-libs/spr/Manifest @@ -0,0 +1,8 @@ +AUX spr-3.3.2-autotools.patch 6970 SHA256 e7232e62fd8bf50556267a2035ff279ed90e32bcb4c25fd06171e31a1142ade1 SHA512 f3dcd15c9e6cb5638e80a6eaa89b014618be2a78b6fca5ab34092adff73c4262cac17866f7fd0ed3dc5146f2d2d361bca83afdea66ba5936ebe2bbda99f1e64b WHIRLPOOL 63c028d33ea576e76880ec25b28c7344828be982c114ed513102018fc041c8809fd6d9ca64d8f46ad9fa36c691239cb62f9f9532dc09667363f8f5b961733f44 +AUX spr-3.3.2-fix-c++14.patch 2348 SHA256 6475aa679e4d92a8dd611b1215ce12bde9c583ab0c678d3215cae375720ad0bb SHA512 201548823f74904c46e065246762e8bccf29830ec7f83542b567f27b328047faff59d5737b287d40b771afa8989a61a9f5b8f671f1e05f35fa336fa7fda5e25e WHIRLPOOL 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0c2bc7a025af487a5ad43cf312ae203ac140d66ab7a500ed20f405ac090fb5d3261cac4121cedeb47efdaf860e89ec9baa77fe0eff5cc233c697f5edcbab538a WHIRLPOOL 6d45c4c4eefc141beeb00507c3accc5e8b6254c0e3165e73ad709f3de7ed184561d9923fdac9ca1dfd3d17af1e0622c088fd999362a639772fe1497869e4826a +MISC ChangeLog 2683 SHA256 ed165589476758bdfb1cca73d3a4633cd58e40d5e7d8ca8536a5f2989e941c8c SHA512 1dae784f5072f73ce2edfd63745eb15952fd4d7a12008af3cf67d12f545be341de6065ecfab079544195e1331f0c6e03ffb715db0df5c8991871fc3ea4b846fa WHIRLPOOL 0f7d753d424d9e2fe3b90de6d7e98be3e2d516fa7bf967f4bbb5a5ee39f27789dd4c8168b902bd3966d6057458dd3cd83a20dc70c64e8c6984918d30a29b4407 +MISC ChangeLog-2015 674 SHA256 7c8b1409a713889c68ad489bba1822ad8857b7833b4d62ae0be284c3474e3550 SHA512 c825e4f100886e944fe9824f74d0f30d263654d2115d9768c282bcfc52a90de2435bfbcb58e47e81ba17cf6b506e4ca5f205bd2151ab2bcaa1e97d9dc89c5d8a WHIRLPOOL 50f2eee3266eddc7f23fccaac2a8a3659d4682de5b7f81cc587cbb25c2c66bbc55792f5bbece5ff76bba1bbc134d2481e6cd619e36613ad3df715072d428b276 +MISC metadata.xml 756 SHA256 a06cac870a8fe6221e0d6cf43088097316ed9d961d11085deb0e18476ac0733f SHA512 3ff7493b80e3ac11f697c677a05617e85d1966630f208ecc2f7814293d3b0d02964e26cdbfea908e5d18de66e2cb03555bb9c5bb3a20aef6f15afc41cc8befce WHIRLPOOL 4baed189b169eb564f115b5e4195f8289cda05f219f7357e2359b9d0352dff47085457cec86257d084db69a797d8168cb141eb1c763a22126e525ff75701687a diff --git a/sci-libs/spr/files/spr-3.3.2-autotools.patch b/sci-libs/spr/files/spr-3.3.2-autotools.patch new file mode 100644 index 000000000000..d04d1806dda8 --- /dev/null +++ b/sci-libs/spr/files/spr-3.3.2-autotools.patch @@ -0,0 +1,169 @@ +diff -Nur SPR-3.3.2.orig/configure.ac SPR-3.3.2/configure.ac +--- SPR-3.3.2.orig/configure.ac 2011-03-29 05:52:30.000000000 +0100 ++++ SPR-3.3.2/configure.ac 2011-05-04 00:48:43.000000000 +0100 +@@ -35,9 +35,6 @@ + AC_FUNC_STAT + AC_CHECK_FUNCS([gettimeofday pow sqrt]) + +-## Default compiler flags +-DEFAULTCXXFLAGS="-O4" +- + ## ROOT installation + AC_ARG_VAR([ROOTPATH], [path to ROOT installation]) + AC_ARG_WITH([root], AC_HELP_STRING([--with-root], [path to ROOT installation]), +@@ -97,7 +94,6 @@ + ## Test ROOT libs + AC_MSG_CHECKING([ROOT libraries]) + if test -f ${ROOTLIBPATH}/libCore.so; then +- DEFAULTCXXFLAGS="-O2" + AC_MSG_RESULT([using ROOT libraries in $ROOTLIBPATH]) + else + AC_MSG_WARN([ROOT libraries not found under $ROOTLIBPATH... disabling ROOT]) +@@ -117,16 +113,6 @@ + ################################ + + +-## Set default compiler flags if CXXFLAGS not defined +-if test -z "$CXXFLAGS"; then +- CXXFLAGS=$DEFAULTCXXFLAGS +-fi +- +- +-AM_CXXFLAGS="-ansi -pedantic" +-AC_SUBST(AM_CPPFLAGS) +-AC_SUBST(AM_CXXFLAGS) +-AC_SUBST(CXXFLAGS) + + AC_CONFIG_FILES(Makefile) + AC_CONFIG_FILES(math/Makefile) +diff -Nur SPR-3.3.2.orig/data/Makefile.am SPR-3.3.2/data/Makefile.am +--- SPR-3.3.2.orig/data/Makefile.am 2011-03-29 05:52:30.000000000 +0100 ++++ SPR-3.3.2/data/Makefile.am 2011-03-29 05:54:19.000000000 +0100 +@@ -1,4 +1,5 @@ +-dist_data_DATA = \ ++ ++pkgdata_DATA = \ + discrete_square.pat gausscorr_uniform_2d_train.pat \ + gauss2_uniform_2d_train.pat trainRoot.pat \ + gauss2_uniform_2d_valid.pat triangle_square_00_train.pat \ +@@ -9,4 +10,4 @@ + lambda-test.pat cmc.data \ + gauss2_uniform_2d_train_root.pat mlp_root.pat \ + tmva_root.pat cleveland.data \ +-samplematrixindicator.cfg +\ No newline at end of file ++samplematrixindicator.cfg +diff -Nur SPR-3.3.2.orig/src/Makefile.am SPR-3.3.2/src/Makefile.am +--- SPR-3.3.2.orig/src/Makefile.am 2011-03-29 05:52:30.000000000 +0100 ++++ SPR-3.3.2/src/Makefile.am 2011-05-04 00:45:22.000000000 +0100 +@@ -1,20 +1,14 @@ + lib_LTLIBRARIES = libSPR.la + + AM_CPPFLAGS = -I$(top_srcdir)/include -I$(top_srcdir) +-AM_LDFLAGS = -L/usr/lib -L$(top_srcdir)/src +-AM_LIBS = -lSPR +-APPLDADD = -lSPR ++ + if WITH_ROOT +- AM_CXXFLAGS += $(ROOTCXXFLAGS) -O2 ++ AM_CXXFLAGS = $(ROOTCXXFLAGS) + AM_CPPFLAGS += $(ROOTCPPFLAGS) -DSPRROOTTUPLE +- AM_LDFLAGS += $(ROOTLDFLAGS) +- AM_LIBS += $(ROOTLIBS) +- APPLDADD += $(ROOTLIBS) +-else +- AM_CXXFLAGS += -O4 ++ AM_LDFLAGS = $(ROOTLDFLAGS) + endif + +-libSPR_la_LIBADD = $(top_srcdir)/math/libSPRmath.la ++libSPR_la_LIBADD = $(top_srcdir)/math/libSPRmath.la $(ROOTLIBS) + libSPR_la_SOURCES = \ + SprDataMoments.cc SprDecisionTree.cc \ + SprFisher.cc SprFomCalculator.cc \ +@@ -60,81 +54,52 @@ + ##################################################################### + + ++LDADD = libSPR.la + +-noinst_PROGRAMS = exampleBootstrapVarianceEst exampleCorrTest \ ++check_PROGRAMS = exampleBootstrapVarianceEst exampleCorrTest \ + exampleUserCuts exampleMatrixTest + + exampleBootstrapVarianceEst_SOURCES = exampleBootstrapVarianceEst.cc +-exampleBootstrapVarianceEst_LDADD = $(APPLDADD) + exampleCorrTest_SOURCES = exampleCorrTest.cc +-exampleCorrTest_LDADD = $(APPLDADD) + exampleMatrixTest_SOURCES = exampleMatrixTest.cc +-exampleMatrixTest_LDADD = $(APPLDADD) + + bin_PROGRAMS = SprFisherLogitApp SprDecisionTreeApp SprExploratoryAnalysisApp \ + SprMultiClassApp SprGoFDecisionTreeApp SprAdaBoostBinarySplitApp \ + SprRBFNetApp SprAdaBoostDecisionTreeApp SprStdBackpropApp \ + SprCombinerApp SprBaggerDecisionTreeApp SprBumpHunterApp \ + SprInteractiveAnalysisApp SprOutputAnalyzerApp SprOutputWriterApp \ +- SprBoosterApp SprBaggerApp exampleUserCuts \ ++ SprBoosterApp SprBaggerApp \ + SprVariableImportanceApp SprIOTestApp SprAddBaggersApp \ + SprTransformationApp SprSplitterApp SprAddNRemoveRApp \ + SprGEPApp SprCrossValidatorApp SprAddColumnsForMCLApp \ + SprIndicatorMatrixApp + + SprFisherLogitApp_SOURCES = SprFisherLogitApp.cc +-SprFisherLogitApp_LDADD = $(APPLDADD) + SprDecisionTreeApp_SOURCES = SprDecisionTreeApp.cc +-SprDecisionTreeApp_LDADD = $(APPLDADD) + SprExploratoryAnalysisApp_SOURCES = SprExploratoryAnalysisApp.cc +-SprExploratoryAnalysisApp_LDADD = $(APPLDADD) + SprMultiClassApp_SOURCES = SprMultiClassApp.cc +-SprMultiClassApp_LDADD = $(APPLDADD) + SprGoFDecisionTreeApp_SOURCES = SprGoFDecisionTreeApp.cc +-SprGoFDecisionTreeApp_LDADD = $(APPLDADD) + SprAdaBoostBinarySplitApp_SOURCES = SprAdaBoostBinarySplitApp.cc +-SprAdaBoostBinarySplitApp_LDADD = $(APPLDADD) + SprRBFNetApp_SOURCES = SprRBFNetApp.cc +-SprRBFNetApp_LDADD = $(APPLDADD) + SprAdaBoostDecisionTreeApp_SOURCES = SprAdaBoostDecisionTreeApp.cc +-SprAdaBoostDecisionTreeApp_LDADD = $(APPLDADD) + SprStdBackpropApp_SOURCES = SprStdBackpropApp.cc +-SprStdBackpropApp_LDADD = $(APPLDADD) + SprCombinerApp_SOURCES = SprCombinerApp.cc +-SprCombinerApp_LDADD = $(APPLDADD) + SprBaggerDecisionTreeApp_SOURCES = SprBaggerDecisionTreeApp.cc +-SprBaggerDecisionTreeApp_LDADD = $(APPLDADD) + SprBumpHunterApp_SOURCES = SprBumpHunterApp.cc +-SprBumpHunterApp_LDADD = $(APPLDADD) + SprInteractiveAnalysisApp_SOURCES = SprInteractiveAnalysisApp.cc +-SprInteractiveAnalysisApp_LDADD = $(APPLDADD) + SprOutputAnalyzerApp_SOURCES = SprOutputAnalyzerApp.cc +-SprOutputAnalyzerApp_LDADD = $(APPLDADD) + SprOutputWriterApp_SOURCES = SprOutputWriterApp.cc +-SprOutputWriterApp_LDADD = $(APPLDADD) + SprBoosterApp_SOURCES = SprBoosterApp.cc +-SprBoosterApp_LDADD = $(APPLDADD) + SprBaggerApp_SOURCES = SprBaggerApp.cc +-SprBaggerApp_LDADD = $(APPLDADD) + exampleUserCuts_SOURCES = exampleUserCuts.cc +-exampleUserCuts_LDADD = $(APPLDADD) + SprVariableImportanceApp_SOURCES = SprVariableImportanceApp.cc +-SprVariableImportanceApp_LDADD = $(APPLDADD) + SprIOTestApp_SOURCES = SprIOTestApp.cc +-SprIOTestApp_LDADD = $(APPLDADD) + SprAddBaggersApp_SOURCES = SprAddBaggersApp.cc +-SprAddBaggersApp_LDADD = $(APPLDADD) + SprTransformationApp_SOURCES = SprTransformationApp.cc +-SprTransformationApp_LDADD = $(APPLDADD) + SprSplitterApp_SOURCES = SprSplitterApp.cc +-SprSplitterApp_LDADD = $(APPLDADD) + SprAddNRemoveRApp_SOURCES = SprAddNRemoveRApp.cc +-SprAddNRemoveRApp_LDADD = $(APPLDADD) + SprGEPApp_SOURCES = SprGEPApp.cc +-SprGEPApp_LDADD = $(APPLDADD) + SprCrossValidatorApp_SOURCES = SprCrossValidatorApp.cc +-SprCrossValidatorApp_LDADD = $(APPLDADD) + SprAddColumnsForMCLApp_SOURCES = SprAddColumnsForMCLApp.cc +-SprAddColumnsForMCLApp_LDADD = $(APPLDADD) + SprIndicatorMatrixApp_SOURCES = SprIndicatorMatrixApp.cc +-SprIndicatorMatrixApp_LDADD = $(APPLDADD) ++ diff --git a/sci-libs/spr/files/spr-3.3.2-fix-c++14.patch b/sci-libs/spr/files/spr-3.3.2-fix-c++14.patch new file mode 100644 index 000000000000..fc2939281b3f --- /dev/null +++ b/sci-libs/spr/files/spr-3.3.2-fix-c++14.patch @@ -0,0 +1,68 @@ +Fix building with C++14, which errors out due to bool -> T* conversions +See also: https://bugs.gentoo.org/show_bug.cgi?id=594376 + +--- a/src/SprBinaryEncoder.cc ++++ b/src/SprBinaryEncoder.cc +@@ -165,7 +165,7 @@ + if( found != vars.end() ) { + cerr << "Variable " << sclass.c_str() << " is already included " + << "in the input list for SprBinaryEncoder." << endl; +- return false; ++ return NULL; + } + vars.push_back(sclass); + +--- a/src/SprDecisionTree.cc ++++ b/src/SprDecisionTree.cc +@@ -362,7 +362,7 @@ + { + // header + char s [200]; +- sprintf(s,"Trained DecisionTree %-6i signal nodes. Overall FOM=%-10g W0=%-10g W1=%-10g N0=%-10i N1=%-10i Version=%s",nodes1_.size(),fom_,w0_,w1_,n0_,n1_,SprVersion.c_str()); ++ sprintf(s,"Trained DecisionTree %-6lu signal nodes. Overall FOM=%-10g W0=%-10g W1=%-10g N0=%-10i N1=%-10i Version=%s",nodes1_.size(),fom_,w0_,w1_,n0_,n1_,SprVersion.c_str()); + os << s << endl; + os << "-------------------------------------------------------" << endl; + +--- a/src/SprVarTransformerReader.cc ++++ b/src/SprVarTransformerReader.cc +@@ -50,7 +50,7 @@ + nLine++; + if( !getline(is,line) ) { + cerr << "Unable to read VarTransformer from line " << nLine << endl; +- return 0; ++ return NULL; + } + istringstream ist(line); + string dummy, transformerName, version; +@@ -59,9 +59,9 @@ + // decode name + if( transformerName.empty() ) { + cerr << "Unable to read VarTransformer name on line " << nLine << endl; +- return false; ++ return NULL; + } +- SprAbsVarTransformer* t = 0; ++ SprAbsVarTransformer* t = NULL; + if( transformerName == "PCA" ) + t = SprVarTransformerReader::readPCATransformer(is,nLine); + else if( transformerName == "InputNormalizer" ) +@@ -72,16 +72,16 @@ + t = SprVarTransformerReader::readTransformerSequence(is,nLine); + else { + cerr << "Unknown VarTransformer name specified on line " << nLine << endl; +- return 0; ++ return NULL; + } +- if( t == 0 ) return 0; ++ if( t == NULL ) return NULL; + + // read vars + vector<string> oldVars, newVars; + if( !SprVarTransformerReader::readVars(is,nLine,oldVars,newVars) || + oldVars.empty() || newVars.empty() ) { + cerr << "Unable to read VarTransformer variables." << endl; +- return 0; ++ return NULL; + } + t->setOldVars(oldVars); + t->setNewVars(newVars); diff --git a/sci-libs/spr/files/spr-3.3.2-gcc46.patch b/sci-libs/spr/files/spr-3.3.2-gcc46.patch new file mode 100644 index 000000000000..715d2ab21ede --- /dev/null +++ b/sci-libs/spr/files/spr-3.3.2-gcc46.patch @@ -0,0 +1,33 @@ +diff -Nur SPR-3.3.2.orig/src/SprAddBaggersApp.cc SPR-3.3.2/src/SprAddBaggersApp.cc +--- SPR-3.3.2.orig/src/SprAddBaggersApp.cc 2011-03-29 05:52:30.000000000 +0100 ++++ SPR-3.3.2/src/SprAddBaggersApp.cc 2011-05-04 00:58:45.000000000 +0100 +@@ -6,6 +6,7 @@ + #include "StatPatternRecognition/SprClassifierReader.hh" + #include "StatPatternRecognition/SprStringParser.hh" + ++#include <cstdio> + #include <stdlib.h> + #include <unistd.h> + #include <iostream> +diff -Nur SPR-3.3.2.orig/src/SprAddColumnsForMCLApp.cc SPR-3.3.2/src/SprAddColumnsForMCLApp.cc +--- SPR-3.3.2.orig/src/SprAddColumnsForMCLApp.cc 2011-03-29 05:52:30.000000000 +0100 ++++ SPR-3.3.2/src/SprAddColumnsForMCLApp.cc 2011-05-04 00:59:02.000000000 +0100 +@@ -4,6 +4,7 @@ + #include "StatPatternRecognition/SprMultiClassReader.hh" + #include "StatPatternRecognition/SprTrainedMultiClassLearner.hh" + ++#include <cstdio> + #include <stdlib.h> + #include <unistd.h> + #include <iostream> +diff -Nur SPR-3.3.2.orig/src/SprIndicatorMatrixApp.cc SPR-3.3.2/src/SprIndicatorMatrixApp.cc +--- SPR-3.3.2.orig/src/SprIndicatorMatrixApp.cc 2011-03-29 05:52:30.000000000 +0100 ++++ SPR-3.3.2/src/SprIndicatorMatrixApp.cc 2011-05-04 00:59:31.000000000 +0100 +@@ -4,6 +4,7 @@ + #include "StatPatternRecognition/SprIndicatorMatrix.hh" + #include "StatPatternRecognition/SprConfig.hh" + ++#include <cstdio> + #include <iostream> + #include <string> + #include <unistd.h> diff --git a/sci-libs/spr/metadata.xml b/sci-libs/spr/metadata.xml new file mode 100644 index 000000000000..47921e2be92e --- /dev/null +++ b/sci-libs/spr/metadata.xml @@ -0,0 +1,21 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + The package implements a variety of tools for categorization of + multivariate data such as boosted decision trees, bagging and + random forest, bump hunting, a multi-class learner and others. + It is used mostly in High Energy Physics. + </longdescription> + <use> + <flag name="root">Add <pkg>sci-physics/root</pkg> graphics and i/o + support</flag> + </use> + <upstream> + <remote-id type="sourceforge">statpatrec</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/spr/spr-3.3.2.ebuild b/sci-libs/spr/spr-3.3.2.ebuild new file mode 100644 index 000000000000..5c35b6b55302 --- /dev/null +++ b/sci-libs/spr/spr-3.3.2.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="Statistical analysis and machine learning library" +HOMEPAGE="http://statpatrec.sourceforge.net/" +SRC_URI="mirror://sourceforge/statpatrec/${P^^}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="root static-libs" + +DEPEND="root? ( sci-physics/root )" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${P^^} +PATCHES=( + "${FILESDIR}"/${P}-autotools.patch + "${FILESDIR}"/${P}-gcc46.patch + "${FILESDIR}"/${P}-fix-c++14.patch +) + +src_prepare() { + default + rm aclocal.m4 || die + eautoreconf + cp data/gauss* src/ || die +} + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_with root) +} diff --git a/sci-libs/ssm/Manifest b/sci-libs/ssm/Manifest new file mode 100644 index 000000000000..bcd9c7160024 --- /dev/null +++ b/sci-libs/ssm/Manifest @@ -0,0 +1,5 @@ +DIST ssm-1.4.tar.gz 424785 SHA256 ea1a57d019bd69ab04e1b7c4faa2f8451584474a6fc16285c2211ef9f53b2704 SHA512 93b55c544eaf651544bb664b65701c081aa6e77707aaf680c1489b129f89598d9a9c348d2fae86cd6e7b3e97bfd26c3abe16220633da4b570c983dbceec8b15a WHIRLPOOL 1a4c5b49102ac7bab732d17d3381e2f0ecc2e85902121f93e47c4be624e9009dce1f727441229f842267882b042ebe7315a42a7e3ade6d8f67ed8031e65eed92 +EBUILD ssm-1.4.ebuild 575 SHA256 dd9df099788e77d10c9f909c2aa0deab59d195225efccc6d92005a11f80917af SHA512 5f447c8751449830d09223aad5e3892da03b989058b5a8b6d2183360ca6c5005a2ce2606e6d6e9894e2f78091d5ad1ceef935bd3fe47ec02c519ab763a3f475a WHIRLPOOL 4f7fe86f79c6d31dec8ee65262cd799ac83132ef7ce7ba305c497b1585ca2d8be8165a0c1db9ee7c4bee53812935a1d76c99eabb659323769023b7fd0017c3ad +MISC ChangeLog 4674 SHA256 276dd10539b5398c76aa5b6367d65314fdc49b7805f92b2d69984982f6cbcae4 SHA512 7147f9b79cdd3db2a71051c78b722d6785374f000c4a0513a2eb12520545a8187e48e508e3ecb058780bd2e6d1670ddc237e17131f4dbde6d205202abdf88309 WHIRLPOOL da3530de49075f8d1b66da69a9ec3c4bac022121d713920660301cabcb51047eee0488ddbeb547f5de3840ade93e23e2759d368c1e59bfb25469c61191cff61a +MISC ChangeLog-2015 1534 SHA256 77686252b83694a856ad8a7d5bd73ef344761ddd65ee370f61a1a61f7db06ea5 SHA512 ece01327e60b2426e7ea0b02caf96c7f0acd1f08b9bd992ad1119223449c849c6f0da0f10b0ec191b605b371781feae9ae8f7369b1e1a0a1d31c7fa936507b26 WHIRLPOOL 669293bc767e9f6d218e0f83d254d1af51f5cfd380df701cba8cc49dc028c95b6b1c663deb3894c7f007b65b3c788209c04714b7cd39276c40d5e42daa4f0455 +MISC metadata.xml 408 SHA256 36161822812d866354b4416e05f2025a6a5ad1e8041b2cc58eaddc7e33a1eb89 SHA512 2f93da2950c7ad7dcffc1652f67a4744e7507ae26e597f46b38e52587b9f71cfdb9961781b870c28b5ee81f91625381fa64117dfd31fb12652853096b3e55cc2 WHIRLPOOL 74f5ee6a301207de47bac64fdd0ee6637f5042940004d01d8b2a0b74ffd7234a3e8bdf400ec48eb4fe736f9edb78c643e1849d55cf899b57c83e3fad4e0d1a08 diff --git a/sci-libs/ssm/metadata.xml b/sci-libs/ssm/metadata.xml new file mode 100644 index 000000000000..ba579239e43b --- /dev/null +++ b/sci-libs/ssm/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="ccp4">Link superpose with libccp4</flag> + </use> + <upstream> + <remote-id type="launchpad">ssm</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/ssm/ssm-1.4.ebuild b/sci-libs/ssm/ssm-1.4.ebuild new file mode 100644 index 000000000000..abcd8885a76c --- /dev/null +++ b/sci-libs/ssm/ssm-1.4.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="A macromolecular coordinate superposition library" +HOMEPAGE="https://launchpad.net/ssm" +SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz" + +LICENSE="GPL-3 LGPL-2.1" +SLOT="0/2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+ccp4 static-libs" + +DEPEND=" + sci-libs/mmdb:2 + ccp4? ( sci-libs/libccp4 )" +RDEPEND="${DEPEND}" + +src_configure() { + local myeconfargs=( $(use_enable ccp4) ) + autotools-utils_src_configure +} diff --git a/sci-libs/starparse/Manifest b/sci-libs/starparse/Manifest new file mode 100644 index 000000000000..6936531474b2 --- /dev/null +++ b/sci-libs/starparse/Manifest @@ -0,0 +1,6 @@ +AUX starparse-1.0-guile1.8.patch 1598 SHA256 903ef428f181005fecca241203e96df7fbbbeaa6e5308c851b10674d3fccf1e6 SHA512 bc6b7cdc93486e42035ea7e5d8240194e800958b572437c6cf6a38cf0c4a8e928ae44d001560ec27124cbf4a3b71950ad7e65dbfea337a66ead94efab59eb2ef WHIRLPOOL 15f9a493ec3d9db0d644ba37af69261bec0ee5ad18888937f11c9ebc787c286dc3228334d6ff9b85851ac78a83ff9075149339b1d262025c348d59c03a4d2a5b +DIST starparse-1.0.tar.bz2 5466370 SHA256 0ff25bb00c9481136bd060660340a44095902e17d75cc11d749ace597b5f4c61 SHA512 47e862258281a3faa506d4eb573a2819a9f5b1cb16828c4951d5d23bbfa8877d9b737ca0b33136dcf8ae0e96ecc9d310ba65a5b7cf1fe18ab8beb092f2342e9a WHIRLPOOL 6bb9a9c5b60888045d64b8890c278c97f80b4abb95678f6db166d23c744ac106f0db3913f77e4bda958c8edf8a51f0f7bcd6a93790fe2691081ec231b2ff11cb +EBUILD starparse-1.0-r1.ebuild 850 SHA256 fe7fadbadedbd493751746df87aac663337d5f98a15e3d45f2f8bbd5f0d4d130 SHA512 72e4e5ed295768e78aaa2123b6cb8b47dbe5ecce99531fe8c9b39f923e96765b3abda36de7ddb677b8897fd196fb1104fdfac90038fac16c1f366d8e488d0826 WHIRLPOOL 69f51e69a0764e35cf4e10188a93526bf63d3bde9eb733c30f2ad1464f765b1bac2c755420b8bf70b76700ce45ed97552a4f7c692309767328ee9a3345f74a4a +MISC ChangeLog 3020 SHA256 7b59b44f20f28feecf4b29623a388df520870a526631ac8d89590ec964f5c2bd SHA512 112bd84fc80942237bb77db09a70b101bf988bd21b832a10d809b184be2a4d74dd973b4709daadc92a40294b4aacaa3353fc08b9d7f01793910119793f215fdd WHIRLPOOL 6bd0f55036b0bbe0f9f93c616e7ac3352e64a174ea50c9fc96f80e8171bdb3dedc1e69f18eaa477f2fae854cb6c874e13406a00b18fdc1784fbea31e17d68311 +MISC ChangeLog-2015 1476 SHA256 4a41278ce43fcfe07fb58077a0d8a68bf798628270a6fe77a37c65a88c9e04b2 SHA512 36c298fbe6c3ed3769b79e3394fc6e9ebedbbbc49838adf3aac20a100f6d51e24b5f2d7c9a665a37474bedb5af1b43f609fcfe4eac8944977bf80adc24861b35 WHIRLPOOL 7c218ed4b36f53c0c153619824de3a45b6436ed68a8286e528800d80d1aae2f4cd0351c2cbd6b1e6eafb89b94ac93b66f0f75cf31ba81066f6e9d781203a6949 +MISC metadata.xml 354 SHA256 2a9c15bf8db11104a2364b5e3347ff3d001375a17d44f9b5ff83ab5c8fc7fd4c SHA512 08b0512376b310bac7c53e9e5b6a5b2829a9435c8fa49962e3c156d2af7d379ba6b737e6cd40c2d9278a25cd73f8272e34779d734645e20c5da34515a2840232 WHIRLPOOL 0e2e8070262616621ee52ab4c6253fc187efaaa45841742376f997ea51431ffc4ff63b9064835f793c5240247e3e5667af3e82904382c393635067e24293e02d diff --git a/sci-libs/starparse/files/starparse-1.0-guile1.8.patch b/sci-libs/starparse/files/starparse-1.0-guile1.8.patch new file mode 100644 index 000000000000..1d6e176b079e --- /dev/null +++ b/sci-libs/starparse/files/starparse-1.0-guile1.8.patch @@ -0,0 +1,60 @@ +--- src/guile-binding.c ++++ src/guile-binding.c +@@ -61,10 +61,10 @@ + char* filter_string = NULL; + char* fname = "-"; + +- if (SCM_NFALSEP(filter_string_scm)) ++ if (scm_is_true(filter_string_scm)) + filter_string = scm_to_locale_string(filter_string_scm); + +- if (SCM_NFALSEP(fname_scm)) ++ if (scm_is_true(fname_scm)) + fname = scm_to_locale_string(fname_scm); + + ship_item_cb = ship_item_scm; +--- src/Makefile.am ++++ src/Makefile.am +@@ -6,13 +6,10 @@ + libstarparse_la_SOURCES =\ + parser.y lexer.l starparse.h + +-libstarparse_la_CFLAGS = +-libstarparse_la_LDFLAGS = +- + if ENABLE_GUILE + libstarparse_la_SOURCES += guile-binding.c guile-compat.h +-libstarparse_la_CFLAGS += @GUILE_CFLAGS@ +-libstarparse_la_LDFLAGS += @GUILE_LDFLAGS@ -lpthread ++libstarparse_la_CFLAGS = @GUILE_CFLAGS@ ++libstarparse_la_LIBADD = @GUILE_LIBS@ -lpthread + endif + + +--- configure.ac ++++ configure.ac +@@ -10,18 +10,13 @@ + + AM_INIT_AUTOMAKE + +-AC_ARG_ENABLE(guile, ++AC_ARG_ENABLE([guile], + AS_HELP_STRING([--enable-guile], +- [build bindings for guile scheme interpreter]), +- USE_GUILE=$enable_guile, +- USE_GUILE=yes) # default value +- +-if test "x$USE_GUILE" = "xyes"; +-then +- GUILE_FLAGS +-fi +- +-AM_CONDITIONAL(ENABLE_GUILE, test "x$USE_GUILE" = "xyes") ++ [build bindings for guile scheme interpreter])) ++AS_IF([test "x$enable_guile" = "xyes"], [ ++ PKG_CHECK_MODULES([GUILE], [guile-1.8]) ++]) ++AM_CONDITIONAL(ENABLE_GUILE, test "x$enable_guile" = "xyes") + + AC_CONFIG_FILES([Makefile + starparse-env diff --git a/sci-libs/starparse/metadata.xml b/sci-libs/starparse/metadata.xml new file mode 100644 index 000000000000..9fc24da1501f --- /dev/null +++ b/sci-libs/starparse/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">starparse</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/starparse/starparse-1.0-r1.ebuild b/sci-libs/starparse/starparse-1.0-r1.ebuild new file mode 100644 index 000000000000..3d11e67b51fd --- /dev/null +++ b/sci-libs/starparse/starparse-1.0-r1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="Library for parsing NMR star files (peak-list format) and CIF files" +HOMEPAGE="http://burrow-owl.sourceforge.net/" +#SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +# Created from rev 19 @ http://oregonstate.edu/~benisong/software/projects/starparse/releases/1.0 +SRC_URI="http://dev.gentooexperimental.org/~jlec/distfiles/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="guile static-libs test" + +REQUIRED_USE="test? ( guile )" + +RDEPEND="guile? ( dev-scheme/guile:12 )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${P}-guile1.8.patch ) + +src_configure() { + local myeconfargs=( $(use_enable guile) ) + autotools-utils_src_configure +} diff --git a/sci-libs/suitesparse/Manifest b/sci-libs/suitesparse/Manifest new file mode 100644 index 000000000000..41ca814dd707 --- /dev/null +++ b/sci-libs/suitesparse/Manifest @@ -0,0 +1,5 @@ +EBUILD suitesparse-4.0.2.ebuild 762 SHA256 6667958c877f1bd12ae7677d32d162de708e1e255fe66115da00c53a60751358 SHA512 57ac75b2b86bd6f5476144db5561c0d3197ecdfedccdd7673952c928f6d0c85858c348d8e2821384e802a107870157a0fd7aade95ca7d30aea374642af7af3a2 WHIRLPOOL 4f2855b04fa10a7b62c9dfd48539ac244359322c21d21703ae4cad1c25cda7f865b2bf044949d89be620514cd4770df0bd3a38a89f6aad43be53e4db4222fdaf +EBUILD suitesparse-4.2.1.ebuild 762 SHA256 941497cd1a25df046bf89d2fed46fe980b72fa2fe5977d7afc0b9586539c35ee SHA512 7232069fb3d9f5ebc31424d1c88a930b27756a4a111993c8c607b7c5e1df59e089e5c5f578e331f77837c910ad81718166d7c922fe95a571722885c6ff1cc951 WHIRLPOOL 904b1f4882b5a26dfb2dc70f6d384f32aa06e0ba3f1353ec5a043fe4f3996b068c5db519a026876b09d8d80356bd9effa60807fc9ea3cd01aae7b392c64a5909 +MISC ChangeLog 2892 SHA256 15c5363ea900ed9f409460f2be2c8a2db2ad4e8f424c0149a8cb113ad0929e6f SHA512 0a49f42c81a1665ce14b40b079dcce76991870d9f67f87ec2f1e59a1f2390bd9cb36bcef263d32fce1a95b0510413086882add802ee09df804d44457a78c124e WHIRLPOOL ae4d5521e828ab63565714cf90b9d77960963f973690c1390ea6334d27b919c9e14b13d22c5651e6c558bdbecaebb74ab4834e5ed9045964d9293839227cccd1 +MISC ChangeLog-2015 2076 SHA256 9e426927c5e7b0804da95b8250591ab56ea07226ce898d35d93760cb96722cf5 SHA512 e5cb1064b324bb73cdab16b891cd2301300700acd90bc13346c0926bd34db79554cf30c06e4a93c4a729c12976b547d0a3197cf8d98cae4abe22160efcbd74f2 WHIRLPOOL 0aeaf4dd99b86daee6f914c01e46b0ce72e33247bc852bdf29671bf70c9cc52f87ff86be4aea99e1e902ea732d91a6d164feec16c9d723b5ed1b3cf328a84190 +MISC metadata.xml 1796 SHA256 b61a674c9b2cbd3ccb5a47615e87760bae4c6d02f965818bc8ef7cd56320af38 SHA512 43f5cb3b418015616d24602efadd65cac6f1ea68a552c636d6cb032d00ab6d01c64371477c02d0cbc17dba81edace0148abe7b8babe9f56581abac5e13d4e17a WHIRLPOOL aff04d7743a72d9dd5623bde67fa42b5e046c302030d4ed7b7ccb5e03de69656c9ad24de4dadd401ed86e0c9c9b2bdfb0e041cc8f3709354a06ccf3dafd40be6 diff --git a/sci-libs/suitesparse/metadata.xml b/sci-libs/suitesparse/metadata.xml new file mode 100644 index 000000000000..a30fdd382ec1 --- /dev/null +++ b/sci-libs/suitesparse/metadata.xml @@ -0,0 +1,36 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + SuiteSparse is a suite of sparse matrix libraries from University of + Florida Computer Science Department. Currently, this includes: + * AMD: symmetric approximate minimum degree + * BTF: permutation to block triangular form + * CAMD: symmetric approximate minimum degree + * CCOLAMD: constrained column approximate minimum degree + * COLAMD: column approximate minimum degree + * CHOLMOD: sparse supernodal Cholesky factorization and update/downdate + * CSparse: a concise sparse matrix package + * CXSparse: an extended version of CSparse + * KLU: sparse LU factorization, for circuit simulation + * LDL: a simple LDL^T factorization + * SPQR: multifrontal sparse QT factorization + * UMFPACK: sparse multifrontal LU factorization + * SuiteSparse_config: common configuration for all but CSparse + The Gentoo package does not include the suitesparse MATLAB tools from + upstream, from the packages above and the following MATLAB-only packages: + * RBio: MATLAB toolbox for reading/writing sparse matrices + * LINFACTOR: solve Ax=b using LU or CHOL + * MESHND: 2D and 3D mesh generation and nested dissection + * SSMULT: sparse matrix times sparse matrix +</longdescription> +<use> + <flag name="cuda">Enable nvidia cuda toolkit for speeding up computations</flag> + <flag name="metis">Enable the Partition module to cholmod using <pkg>sci-libs/metis</pkg></flag> + <flag name="tbb">Enable multithreading with the Intel Threads Building Block <pkg>dev-cpp/tbb</pkg></flag> +</use> +</pkgmetadata> diff --git a/sci-libs/suitesparse/suitesparse-4.0.2.ebuild b/sci-libs/suitesparse/suitesparse-4.0.2.ebuild new file mode 100644 index 000000000000..6f7a3d86447f --- /dev/null +++ b/sci-libs/suitesparse/suitesparse-4.0.2.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="Meta package for a suite of sparse matrix tools" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/SuiteSparse/" + +LICENSE="LGPL-2.1 GPL-2" +SLOT="0" + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda doc metis tbb lapack" +DEPEND="" +RDEPEND=" + >=sci-libs/suitesparseconfig-${PV} + >=sci-libs/amd-2.3.1[doc?] + >=sci-libs/btf-1.2.0 + >=sci-libs/camd-2.3.1[doc?] + >=sci-libs/ccolamd-2.8.0 + >=sci-libs/cholmod-2.0.1[cuda?,doc?,metis?,lapack?] + >=sci-libs/colamd-2.3.1 + >=sci-libs/cxsparse-3.1.1 + >=sci-libs/klu-1.2.0[doc?] + >=sci-libs/ldl-2.0.4[doc?] + >=sci-libs/spqr-1.3.1[doc?,metis?,tbb?] + >=sci-libs/umfpack-5.6.1[doc?,cholmod]" diff --git a/sci-libs/suitesparse/suitesparse-4.2.1.ebuild b/sci-libs/suitesparse/suitesparse-4.2.1.ebuild new file mode 100644 index 000000000000..844fddcc7de5 --- /dev/null +++ b/sci-libs/suitesparse/suitesparse-4.2.1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +DESCRIPTION="Meta package for a suite of sparse matrix tools" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/SuiteSparse/" + +LICENSE="LGPL-2.1 GPL-2" +SLOT="0" + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda doc metis tbb lapack" +DEPEND="" +RDEPEND=" + >=sci-libs/suitesparseconfig-${PV} + >=sci-libs/amd-2.3.1[doc?] + >=sci-libs/btf-1.2.0 + >=sci-libs/camd-2.3.1[doc?] + >=sci-libs/ccolamd-2.8.0 + >=sci-libs/cholmod-2.1.2[cuda?,doc?,metis?,lapack?] + >=sci-libs/colamd-2.3.1 + >=sci-libs/cxsparse-3.1.2 + >=sci-libs/klu-1.2.0[doc?] + >=sci-libs/ldl-2.0.4[doc?] + >=sci-libs/spqr-1.3.1[doc?,metis?,tbb?] + >=sci-libs/umfpack-5.6.2[doc?,cholmod]" diff --git a/sci-libs/suitesparseconfig/Manifest b/sci-libs/suitesparseconfig/Manifest new file mode 100644 index 000000000000..3d5dad097b65 --- /dev/null +++ b/sci-libs/suitesparseconfig/Manifest @@ -0,0 +1,6 @@ +DIST suitesparseconfig-4.2.1.tar.bz2 256308 SHA256 cccdd13c8ddf8efdbe738ccd147ed16ef73c6e8d327d825714af5b7aca1d7611 SHA512 2363f8adb962d1f932b4390ac54e7203b5eec6005f9275dc155a4b178fd5259ddd42dc34c663a4c82546452c0f1e05619522567a69be1a58efc5d032b6d7a61d WHIRLPOOL 6e26494c6f6d798893cb807e34243d9cd13454a95fcd61fb2c7545ac392a3177d3b01170990f9a749e0d9bebf95ea7476d39b8f9c5d3d0715715e962e26bd771 +EBUILD suitesparseconfig-4.2.1-r1.ebuild 718 SHA256 a8a08c03d2551e2c825ba51bdc3f0ecd0c7f1e4559cc4073840198aa07410ae4 SHA512 121e42d729d160a915d90e3cc05fdc33649137a35707db53b51e0ae81b8e097511a0eab62619e21a6e2a44e8a2786ed38a640b874ebd6231d80da99de12c91e6 WHIRLPOOL b6bdae7a5e999af2a8d84286ff977951ea79c668dfa3bddf42bd87217688922b0a17c9c1d8d1c2edc94f646b7631b491335f2de08c0f9363f33759f0327832ff +EBUILD suitesparseconfig-4.2.1.ebuild 506 SHA256 0ec8b740372b383b27181046dd85cfc26565196bc66b2aedeba21d789497fdc2 SHA512 fe09daebdfd04923666e391fba1517f44ae03db430056a93dc181c5bd2c3653e1bb56fdc3f682af0e6aedc627bc00bac06df2e5e30a6d75c7b2d7d095abd6233 WHIRLPOOL 4285a0851ef5308fc3048180a4da5616a1e876265a37202079a14d1c7b87ba1ed9a9cd633d6c1f8dd09399dd0063092c2696bcdc689edc08a57e1d956e11304e +MISC ChangeLog 2671 SHA256 d7d6a93f7b90628a7b94cef010858d87cf2cc09843540fc54cb4e898ea3d90ea SHA512 61771e958eabc7370dda04a67e64391fa4b9d904ed3199e7443223da11701d29ceb1750d4362f5d90b43690fa690fe879cde1e6fcee367b0a3d385dc106f9587 WHIRLPOOL 376b6f5750a51c5ebb2b791b92eb5556cea3cafa39c9528f301828a6f1e82e65daa60321d1c41c6ac66cd11605835319db87a2051f6ed3608acdc046e1b811e9 +MISC ChangeLog-2015 1693 SHA256 fe2164cf22e23073f82c4cc31f08684115a28a5542f7009192049ef4e751526c SHA512 314ab92a70cd640035bf507551c40057d3748537f6000512cd3aaf4c8bbc83bfe98787057479b7bf75847259910ace637dc5a8323cf409bbe7f53a6c7bd3cffa WHIRLPOOL 6abc966945be883ece65b7d6130c95217bb3300f9889b67d5a77819f3cdb324dad0477696722898593bf793854e8a13eb94e3a7271016908e56a8b8161b53ab4 +MISC metadata.xml 476 SHA256 8db582977958309643a74a87acef45722d86ca5b894c86adc111cfd0ea17534d SHA512 fbbcd2de1d7b23e4eb45d8102fe76aa4251b83ce2b1fd7ef9cb599c7716ff662b8182060ce7b350ed3541b39483cf72c7c9ac810db1fe739f82406606412acb8 WHIRLPOOL 9e1bfd379170c9b7075e0e40debd319bedc8191d10d4c0d7933cec196ad3404f8b529fe204acb7f8634b89c442610e73f8c36e7be63678934a2362ded671fc37 diff --git a/sci-libs/suitesparseconfig/metadata.xml b/sci-libs/suitesparseconfig/metadata.xml new file mode 100644 index 000000000000..0404cd687a13 --- /dev/null +++ b/sci-libs/suitesparseconfig/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + SuiteSparse_config is a set of configuration files for the SuiteSparse matrix libraries + from CISE at University of Florida. It contains some headers and makefiles. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/suitesparseconfig/suitesparseconfig-4.2.1-r1.ebuild b/sci-libs/suitesparseconfig/suitesparseconfig-4.2.1-r1.ebuild new file mode 100644 index 000000000000..a128d96ea42d --- /dev/null +++ b/sci-libs/suitesparseconfig/suitesparseconfig-4.2.1-r1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit multilib-minimal + +DESCRIPTION="Common configurations for all packages in suitesparse" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/SuiteSparse_config" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~alpha amd64 ~arm ~arm64 hppa ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" + +multilib_src_configure() { + ECONF_SOURCE="${S}" \ + econf \ + $(use_enable static-libs static) +} + +multilib_src_install_all() { + if ! use static-libs; then + find "${ED}" -name "*.la" -delete || die + fi +} diff --git a/sci-libs/suitesparseconfig/suitesparseconfig-4.2.1.ebuild b/sci-libs/suitesparseconfig/suitesparseconfig-4.2.1.ebuild new file mode 100644 index 000000000000..b17c23092e2c --- /dev/null +++ b/sci-libs/suitesparseconfig/suitesparseconfig-4.2.1.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Common configurations for all packages in suitesparse" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/SuiteSparse_config" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~alpha amd64 ~arm hppa ~ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" diff --git a/sci-libs/sundials/Manifest b/sci-libs/sundials/Manifest new file mode 100644 index 000000000000..e3d4f86f4312 --- /dev/null +++ b/sci-libs/sundials/Manifest @@ -0,0 +1,4 @@ +AUX sundials-2.7.0-underlinking-libdir.patch 19659 SHA256 22001d428122ea39f4eb071daaaf1ba1442aa171b9e68d0c841478a1ce8c3444 SHA512 95bc36d359b672b725391d75540304fac6b2610960f67a636cf5656e30904a2ed309a75175f4d20b9199d70d45fa817e53e86433ff18dfcf28ef76840b9d0dba WHIRLPOOL b2115e6f99ff3dc9941e3cefad7136762e48c6dff896b8a1d93996849e0f43f618f04107e7702377bad7a590231046c7da7de1af0828549883f678a8f9062e8e +DIST sundials-2.7.0.tar.gz 12258093 SHA256 d39fcac7175d701398e4eb209f7e92a5b30a78358d4a0c0fcc23db23c11ba104 SHA512 c86c167538065a4109b36ae7c8f60f3d92184133cfa661b5acfccee052c38f40be865412a1746bb57907b61602c212c0f15e1e30ef29e8a49db6d46a75a28e69 WHIRLPOOL 3aabd2912e6be7d159d69853ecc76d9549cc6020344083c71cdcf43867e86d95d14862463c201270f9ff5a16536f4341d6e0eb466402870cf7ee6e7a45669667 +EBUILD sundials-2.7.0.ebuild 2063 SHA256 042c26fdcc6d3bebdda0f931ad0fcdbac219f04d2a67970fd2207f841d518967 SHA512 cd92701c6c400fa5c75610c6d35117b182be293821ce7bd0d15fb8c4807ca5359bd5413e36c2cc12af85321a331a90a2d514b1d31409ed70d9203728b61a995f WHIRLPOOL 471afaad9cefde735506609e7bef8874c61d9641bc18ad87bf3d54366b24708cda38b547dcb3de90c0be1ee378df82cc1390ce4c3f017806bb94cfba806db4a4 +MISC metadata.xml 1063 SHA256 550096d3f924297a9939f33c3c0e5d67b35d6239c7f1a2510c90d3a565090fb7 SHA512 d81c64ac7241460ebc7bcd61f1b398ef55a1e9b5a5a9bb0ede400bfe06889d2db781c43853bf33069510f2461140ab8b7a47a4553cdafca64c1ed7bd0f16d742 WHIRLPOOL 40720e90c9c0b67862382e661f03f626ce876fbaba35ca25b8cc8aeca04e3516409a8cab99a7a6000a616603cf30d5f8a84afd60229a50a4c92bcdf75200bdcd diff --git a/sci-libs/sundials/files/sundials-2.7.0-underlinking-libdir.patch b/sci-libs/sundials/files/sundials-2.7.0-underlinking-libdir.patch new file mode 100644 index 000000000000..db47ac3b350d --- /dev/null +++ b/sci-libs/sundials/files/sundials-2.7.0-underlinking-libdir.patch @@ -0,0 +1,395 @@ +diff -Nur sundials-2.7.0.orig/src/arkode/CMakeLists.txt sundials-2.7.0/src/arkode/CMakeLists.txt +--- sundials-2.7.0.orig/src/arkode/CMakeLists.txt 2016-09-26 22:16:52.000000000 +0000 ++++ sundials-2.7.0/src/arkode/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -127,7 +127,7 @@ + PROPERTIES OUTPUT_NAME sundials_arkode CLEAN_DIRECT_OUTPUT 1) + + # Install the ARKODE library +- INSTALL(TARGETS sundials_arkode_static DESTINATION lib) ++ INSTALL(TARGETS sundials_arkode_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_STATIC_LIBS) + +@@ -146,8 +146,10 @@ + SET_TARGET_PROPERTIES(sundials_arkode_shared + PROPERTIES VERSION ${arkodelib_VERSION} SOVERSION ${arkodelib_SOVERSION}) + ++ TARGET_LINK_LIBRARIES(sundials_arkode_shared -lm ${KLU_LIBRARIES} ${SUPERLUMT_LIBRARIES} ${LAPACK_LIBRARIES}) ++ + # Install the ARKODE library +- INSTALL(TARGETS sundials_arkode_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_arkode_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_SHARED_LIBS) + +diff -Nur sundials-2.7.0.orig/src/arkode/fcmix/CMakeLists.txt sundials-2.7.0/src/arkode/fcmix/CMakeLists.txt +--- sundials-2.7.0.orig/src/arkode/fcmix/CMakeLists.txt 2016-09-26 22:16:52.000000000 +0000 ++++ sundials-2.7.0/src/arkode/fcmix/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -70,7 +70,7 @@ + PROPERTIES OUTPUT_NAME sundials_farkode CLEAN_DIRECT_OUTPUT 1) + + # Install the FARKODE library +-INSTALL(TARGETS sundials_farkode_static DESTINATION lib) ++INSTALL(TARGETS sundials_farkode_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + # + MESSAGE(STATUS "Added ARKODE FCMIX module") +diff -Nur sundials-2.7.0.orig/src/cvode/CMakeLists.txt sundials-2.7.0/src/cvode/CMakeLists.txt +--- sundials-2.7.0.orig/src/cvode/CMakeLists.txt 2016-09-26 22:17:07.000000000 +0000 ++++ sundials-2.7.0/src/cvode/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -134,7 +134,7 @@ + PROPERTIES OUTPUT_NAME sundials_cvode CLEAN_DIRECT_OUTPUT 1) + + # Install the CVODE library +- INSTALL(TARGETS sundials_cvode_static DESTINATION lib) ++ INSTALL(TARGETS sundials_cvode_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_STATIC_LIBS) + +@@ -153,8 +153,10 @@ + SET_TARGET_PROPERTIES(sundials_cvode_shared + PROPERTIES VERSION ${cvodelib_VERSION} SOVERSION ${cvodelib_SOVERSION}) + ++ TARGET_LINK_LIBRARIES(sundials_cvode_shared -lm ${KLU_LIBRARIES} ${SUPERLUMT_LIBRARIES} ${LAPACK_LIBRARIES}) ++ + # Install the CVODE library +- INSTALL(TARGETS sundials_cvode_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_cvode_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_SHARED_LIBS) + +diff -Nur sundials-2.7.0.orig/src/cvode/fcmix/CMakeLists.txt sundials-2.7.0/src/cvode/fcmix/CMakeLists.txt +--- sundials-2.7.0.orig/src/cvode/fcmix/CMakeLists.txt 2016-09-26 22:17:07.000000000 +0000 ++++ sundials-2.7.0/src/cvode/fcmix/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -57,7 +57,7 @@ + PROPERTIES OUTPUT_NAME sundials_fcvode CLEAN_DIRECT_OUTPUT 1) + + # Install the FCVODE library +-INSTALL(TARGETS sundials_fcvode_static DESTINATION lib) ++INSTALL(TARGETS sundials_fcvode_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + # + MESSAGE(STATUS "Added CVODE FCMIX module") +diff -Nur sundials-2.7.0.orig/src/cvodes/CMakeLists.txt sundials-2.7.0/src/cvodes/CMakeLists.txt +--- sundials-2.7.0.orig/src/cvodes/CMakeLists.txt 2016-09-26 22:17:15.000000000 +0000 ++++ sundials-2.7.0/src/cvodes/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -121,7 +121,7 @@ + PROPERTIES OUTPUT_NAME sundials_cvodes CLEAN_DIRECT_OUTPUT 1) + + # Install the CVODES library +- INSTALL(TARGETS sundials_cvodes_static DESTINATION lib) ++ INSTALL(TARGETS sundials_cvodes_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_STATIC_LIBS) + +@@ -140,8 +140,9 @@ + SET_TARGET_PROPERTIES(sundials_cvodes_shared + PROPERTIES VERSION ${cvodeslib_VERSION} SOVERSION ${cvodeslib_SOVERSION}) + ++ TARGET_LINK_LIBRARIES(sundials_cvodes_shared -lm ${KLU_LIBRARIES} ${SUPERLUMT_LIBRARIES} ${LAPACK_LIBRARIES}) + # Install the CVODES library +- INSTALL(TARGETS sundials_cvodes_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_cvodes_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_SHARED_LIBS) + +diff -Nur sundials-2.7.0.orig/src/ida/CMakeLists.txt sundials-2.7.0/src/ida/CMakeLists.txt +--- sundials-2.7.0.orig/src/ida/CMakeLists.txt 2016-09-26 22:17:26.000000000 +0000 ++++ sundials-2.7.0/src/ida/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -124,7 +124,7 @@ + PROPERTIES OUTPUT_NAME sundials_ida CLEAN_DIRECT_OUTPUT 1) + + # Install the IDA library +- INSTALL(TARGETS sundials_ida_static DESTINATION lib) ++ INSTALL(TARGETS sundials_ida_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_STATIC_LIBS) + +@@ -143,8 +143,10 @@ + SET_TARGET_PROPERTIES(sundials_ida_shared + PROPERTIES VERSION ${idalib_VERSION} SOVERSION ${idalib_SOVERSION}) + ++ TARGET_LINK_LIBRARIES(sundials_ida_shared -lm ${KLU_LIBRARIES} ${SUPERLUMT_LIBRARIES} ${LAPACK_LIBRARIES}) ++ + # Install the IDA library +- INSTALL(TARGETS sundials_ida_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_ida_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_SHARED_LIBS) + +diff -Nur sundials-2.7.0.orig/src/ida/fcmix/CMakeLists.txt sundials-2.7.0/src/ida/fcmix/CMakeLists.txt +--- sundials-2.7.0.orig/src/ida/fcmix/CMakeLists.txt 2016-09-26 22:17:26.000000000 +0000 ++++ sundials-2.7.0/src/ida/fcmix/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -56,6 +56,6 @@ + PROPERTIES OUTPUT_NAME sundials_fida CLEAN_DIRECT_OUTPUT 1) + + # Install the FIDA library +-INSTALL(TARGETS sundials_fida_static DESTINATION lib) ++INSTALL(TARGETS sundials_fida_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + # + MESSAGE(STATUS "Added IDA FCMIX module") +diff -Nur sundials-2.7.0.orig/src/idas/CMakeLists.txt sundials-2.7.0/src/idas/CMakeLists.txt +--- sundials-2.7.0.orig/src/idas/CMakeLists.txt 2016-09-26 22:17:32.000000000 +0000 ++++ sundials-2.7.0/src/idas/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -126,7 +126,7 @@ + PROPERTIES OUTPUT_NAME sundials_idas CLEAN_DIRECT_OUTPUT 1) + + # Install the IDA library +- INSTALL(TARGETS sundials_idas_static DESTINATION lib) ++ INSTALL(TARGETS sundials_idas_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_STATIC_LIBS) + +@@ -145,8 +145,10 @@ + SET_TARGET_PROPERTIES(sundials_idas_shared + PROPERTIES VERSION ${idaslib_VERSION} SOVERSION ${idaslib_SOVERSION}) + ++ TARGET_LINK_LIBRARIES(sundials_idas_shared -lm ${KLU_LIBRARIES} ${SUPERLUMT_LIBRARIES} ${LAPACK_LIBRARIES}) ++ + # Install the IDAS library +- INSTALL(TARGETS sundials_idas_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_idas_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_SHARED_LIBS) + +diff -Nur sundials-2.7.0.orig/src/kinsol/CMakeLists.txt sundials-2.7.0/src/kinsol/CMakeLists.txt +--- sundials-2.7.0.orig/src/kinsol/CMakeLists.txt 2016-09-26 22:17:39.000000000 +0000 ++++ sundials-2.7.0/src/kinsol/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -134,7 +134,7 @@ + PROPERTIES OUTPUT_NAME sundials_kinsol CLEAN_DIRECT_OUTPUT 1) + + # Install the KINSOL library +- INSTALL(TARGETS sundials_kinsol_static DESTINATION lib) ++ INSTALL(TARGETS sundials_kinsol_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_STATIC_LIBS) + +@@ -153,8 +153,10 @@ + SET_TARGET_PROPERTIES(sundials_kinsol_shared + PROPERTIES VERSION ${kinsollib_VERSION} SOVERSION ${kinsollib_SOVERSION}) + ++ TARGET_LINK_LIBRARIES(sundials_kinsol_shared -lm ${KLU_LIBRARIES} ${SUPERLUMT_LIBRARIES} ${LAPACK_LIBRARIES}) ++ + # Install the KINSOL library +- INSTALL(TARGETS sundials_kinsol_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_kinsol_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + ENDIF(BUILD_SHARED_LIBS) + +diff -Nur sundials-2.7.0.orig/src/kinsol/fcmix/CMakeLists.txt sundials-2.7.0/src/kinsol/fcmix/CMakeLists.txt +--- sundials-2.7.0.orig/src/kinsol/fcmix/CMakeLists.txt 2016-09-26 22:17:39.000000000 +0000 ++++ sundials-2.7.0/src/kinsol/fcmix/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -54,7 +54,7 @@ + PROPERTIES OUTPUT_NAME sundials_fkinsol CLEAN_DIRECT_OUTPUT 1) + + # Install the FKINSOL library +-INSTALL(TARGETS sundials_fkinsol_static DESTINATION lib) ++INSTALL(TARGETS sundials_fkinsol_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + # + MESSAGE(STATUS "Added KINSOL FCMIX module") +diff -Nur sundials-2.7.0.orig/src/nvec_openmp/CMakeLists.txt sundials-2.7.0/src/nvec_openmp/CMakeLists.txt +--- sundials-2.7.0.orig/src/nvec_openmp/CMakeLists.txt 2016-09-26 22:16:50.000000000 +0000 ++++ sundials-2.7.0/src/nvec_openmp/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -51,7 +51,7 @@ + ADD_LIBRARY(sundials_nvecopenmp_static STATIC ${nvecopenmp_SOURCES} ${shared_SOURCES}) + SET_TARGET_PROPERTIES(sundials_nvecopenmp_static + PROPERTIES OUTPUT_NAME sundials_nvecopenmp CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_nvecopenmp_static DESTINATION lib) ++ INSTALL(TARGETS sundials_nvecopenmp_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + + # Rules for building and installing the shared library: +@@ -65,7 +65,8 @@ + PROPERTIES OUTPUT_NAME sundials_nvecopenmp CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_nvecopenmp_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_nvecopenmp_shared DESTINATION lib) ++ TARGET_LINK_LIBRARIES(sundials_nvecopenmp_shared -lm) ++ INSTALL(TARGETS sundials_nvecopenmp_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + + # Install the NVECOPENMP header files +@@ -78,7 +79,7 @@ + ADD_LIBRARY(sundials_fnvecopenmp_static STATIC ${fnvecopenmp_SOURCES}) + SET_TARGET_PROPERTIES(sundials_fnvecopenmp_static + PROPERTIES OUTPUT_NAME sundials_fnvecopenmp CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_fnvecopenmp_static DESTINATION lib) ++ INSTALL(TARGETS sundials_fnvecopenmp_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + IF(BUILD_SHARED_LIBS) + ADD_LIBRARY(sundials_fnvecopenmp_shared ${fnvecopenmp_SOURCES}) +@@ -86,7 +87,8 @@ + PROPERTIES OUTPUT_NAME sundials_fnvecopenmp CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_fnvecopenmp_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_fnvecopenmp_shared DESTINATION lib) ++ TARGET_LINK_LIBRARIES(sundials_fnvecopenmp_shared -lm) ++ INSTALL(TARGETS sundials_fnvecopenmp_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + ENDIF(FCMIX_ENABLE AND F77_FOUND) + +diff -Nur sundials-2.7.0.orig/src/nvec_par/CMakeLists.txt sundials-2.7.0/src/nvec_par/CMakeLists.txt +--- sundials-2.7.0.orig/src/nvec_par/CMakeLists.txt 2016-09-26 22:16:50.000000000 +0000 ++++ sundials-2.7.0/src/nvec_par/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -52,7 +52,7 @@ + ADD_LIBRARY(sundials_nvecparallel_static STATIC ${nvecparallel_SOURCES} ${shared_SOURCES}) + SET_TARGET_PROPERTIES(sundials_nvecparallel_static + PROPERTIES OUTPUT_NAME sundials_nvecparallel CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_nvecparallel_static DESTINATION lib) ++ INSTALL(TARGETS sundials_nvecparallel_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + + # Rules for building and installing the shared library: +@@ -66,7 +66,8 @@ + PROPERTIES OUTPUT_NAME sundials_nvecparallel CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_nvecparallel_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_nvecparallel_shared DESTINATION lib) ++ TARGET_LINK_LIBRARIES(sundials_nvecparallel_shared -lm) ++ INSTALL(TARGETS sundials_nvecparallel_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + + # Install the NVECPARALLEL header files +@@ -79,7 +80,7 @@ + ADD_LIBRARY(sundials_fnvecparallel_static STATIC ${fnvecparallel_SOURCES}) + SET_TARGET_PROPERTIES(sundials_fnvecparallel_static + PROPERTIES OUTPUT_NAME sundials_fnvecparallel CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_fnvecparallel_static DESTINATION lib) ++ INSTALL(TARGETS sundials_fnvecparallel_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + IF(BUILD_SHARED_LIBS) + ADD_LIBRARY(sundials_fnvecparallel_shared SHARED ${fnvecparallel_SOURCES}) +@@ -87,7 +88,7 @@ + PROPERTIES OUTPUT_NAME sundials_fnvecparallel CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_fnvecparallel_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_fnvecparallel_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_fnvecparallel_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + ENDIF(FCMIX_ENABLE AND MPIF_FOUND) + # +diff -Nur sundials-2.7.0.orig/src/nvec_parhyp/CMakeLists.txt sundials-2.7.0/src/nvec_parhyp/CMakeLists.txt +--- sundials-2.7.0.orig/src/nvec_parhyp/CMakeLists.txt 2016-09-26 22:16:50.000000000 +0000 ++++ sundials-2.7.0/src/nvec_parhyp/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -53,7 +53,7 @@ + ADD_LIBRARY(sundials_nvecparhyp_static STATIC ${nvecparhyp_SOURCES} ${shared_SOURCES}) + SET_TARGET_PROPERTIES(sundials_nvecparhyp_static + PROPERTIES OUTPUT_NAME sundials_nvecparhyp CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_nvecparhyp_static DESTINATION lib) ++ INSTALL(TARGETS sundials_nvecparhyp_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + + # Rules for building and installing the shared library: +@@ -67,7 +67,7 @@ + PROPERTIES OUTPUT_NAME sundials_nvecparhyp CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_nvecparhyp_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_nvecparhyp_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_nvecparhyp_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + + # Install the NVECPARHYP header files +diff -Nur sundials-2.7.0.orig/src/nvec_petsc/CMakeLists.txt sundials-2.7.0/src/nvec_petsc/CMakeLists.txt +--- sundials-2.7.0.orig/src/nvec_petsc/CMakeLists.txt 2016-09-26 22:16:50.000000000 +0000 ++++ sundials-2.7.0/src/nvec_petsc/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -53,7 +53,7 @@ + ADD_LIBRARY(sundials_nvecpetsc_static STATIC ${nvecpetsc_SOURCES} ${shared_SOURCES}) + SET_TARGET_PROPERTIES(sundials_nvecpetsc_static + PROPERTIES OUTPUT_NAME sundials_nvecpetsc CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_nvecpetsc_static DESTINATION lib) ++ INSTALL(TARGETS sundials_nvecpetsc_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + + # Rules for building and installing the shared library: +@@ -67,7 +67,7 @@ + PROPERTIES OUTPUT_NAME sundials_nvecpetsc CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_nvecpetsc_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_nvecpetsc_shared DESTINATION lib) ++ INSTALL(TARGETS sundials_nvecpetsc_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + + # Install the NVECPARHYP header files +diff -Nur sundials-2.7.0.orig/src/nvec_pthreads/CMakeLists.txt sundials-2.7.0/src/nvec_pthreads/CMakeLists.txt +--- sundials-2.7.0.orig/src/nvec_pthreads/CMakeLists.txt 2016-09-26 22:16:50.000000000 +0000 ++++ sundials-2.7.0/src/nvec_pthreads/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -44,7 +44,7 @@ + ADD_LIBRARY(sundials_nvecpthreads_static STATIC ${nvecpthreads_SOURCES} ${shared_SOURCES}) + SET_TARGET_PROPERTIES(sundials_nvecpthreads_static + PROPERTIES OUTPUT_NAME sundials_nvecpthreads CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_nvecpthreads_static DESTINATION lib) ++ INSTALL(TARGETS sundials_nvecpthreads_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + + # Rules for building and installing the shared library: +@@ -58,7 +58,8 @@ + PROPERTIES OUTPUT_NAME sundials_nvecpthreads CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_nvecpthreads_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_nvecpthreads_shared DESTINATION lib) ++ TARGET_LINK_LIBRARIES(sundials_nvecpthreads_shared -lm -lpthread) ++ INSTALL(TARGETS sundials_nvecpthreads_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + + # Install the NVECPTHREADS header files +@@ -71,7 +72,7 @@ + ADD_LIBRARY(sundials_fnvecpthreads_static STATIC ${fnvecpthreads_SOURCES}) + SET_TARGET_PROPERTIES(sundials_fnvecpthreads_static + PROPERTIES OUTPUT_NAME sundials_fnvecpthreads CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_fnvecpthreads_static DESTINATION lib) ++ INSTALL(TARGETS sundials_fnvecpthreads_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + IF(BUILD_SHARED_LIBS) + ADD_LIBRARY(sundials_fnvecpthreads_shared ${fnvecpthreads_SOURCES}) +@@ -79,7 +80,8 @@ + PROPERTIES OUTPUT_NAME sundials_fnvecpthreads CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_fnvecpthreads_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_fnvecpthreads_shared DESTINATION lib) ++ TARGET_LINK_LIBRARIES(sundials_fnvecpthreads_shared -lm -lpthread) ++ INSTALL(TARGETS sundials_fnvecpthreads_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + ENDIF(FCMIX_ENABLE AND F77_FOUND) + +diff -Nur sundials-2.7.0.orig/src/nvec_ser/CMakeLists.txt sundials-2.7.0/src/nvec_ser/CMakeLists.txt +--- sundials-2.7.0.orig/src/nvec_ser/CMakeLists.txt 2016-09-26 22:16:49.000000000 +0000 ++++ sundials-2.7.0/src/nvec_ser/CMakeLists.txt 2016-12-30 23:41:54.355840949 +0000 +@@ -44,7 +44,7 @@ + ADD_LIBRARY(sundials_nvecserial_static STATIC ${nvecserial_SOURCES} ${shared_SOURCES}) + SET_TARGET_PROPERTIES(sundials_nvecserial_static + PROPERTIES OUTPUT_NAME sundials_nvecserial CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_nvecserial_static DESTINATION lib) ++ INSTALL(TARGETS sundials_nvecserial_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + + # Rules for building and installing the shared library: +@@ -58,7 +58,8 @@ + PROPERTIES OUTPUT_NAME sundials_nvecserial CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_nvecserial_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_nvecserial_shared DESTINATION lib) ++ TARGET_LINK_LIBRARIES(sundials_nvecserial_shared -lm) ++ INSTALL(TARGETS sundials_nvecserial_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + + # Install the NVECSERIAL header files +@@ -71,7 +72,7 @@ + ADD_LIBRARY(sundials_fnvecserial_static STATIC ${fnvecserial_SOURCES}) + SET_TARGET_PROPERTIES(sundials_fnvecserial_static + PROPERTIES OUTPUT_NAME sundials_fnvecserial CLEAN_DIRECT_OUTPUT 1) +- INSTALL(TARGETS sundials_fnvecserial_static DESTINATION lib) ++ INSTALL(TARGETS sundials_fnvecserial_static DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_STATIC_LIBS) + IF(BUILD_SHARED_LIBS) + ADD_LIBRARY(sundials_fnvecserial_shared ${fnvecserial_SOURCES}) +@@ -79,7 +80,8 @@ + PROPERTIES OUTPUT_NAME sundials_fnvecserial CLEAN_DIRECT_OUTPUT 1) + SET_TARGET_PROPERTIES(sundials_fnvecserial_shared + PROPERTIES VERSION ${nveclib_VERSION} SOVERSION ${nveclib_SOVERSION}) +- INSTALL(TARGETS sundials_fnvecserial_shared DESTINATION lib) ++ TARGET_LINK_LIBRARIES(sundials_fnvecserial_shared -lm) ++ INSTALL(TARGETS sundials_fnvecserial_shared DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ENDIF(BUILD_SHARED_LIBS) + ENDIF(FCMIX_ENABLE AND F77_FOUND) + diff --git a/sci-libs/sundials/metadata.xml b/sci-libs/sundials/metadata.xml new file mode 100644 index 000000000000..b4735cc5086b --- /dev/null +++ b/sci-libs/sundials/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Scientific Project</name> + </maintainer> + <longdescription lang="en"> + SUite of Nonlinear and DIfferential/ALgebraic equation Solvers was + implemented with the goal of providing robust time integrators and + nonlinear solvers that can easily be incorporated into existing + simulation codes. The primary design goals were to require minimal + information from the user, allow users to easily supply their own + data structures underneath the solvers, and allow for easy + incorporation of user-supplied linear solvers and preconditioners. + </longdescription> + <use> + <flag name="hypre">Build with <pkg>sci-libs/hypre</pkg> conditioners</flag> + <flag name="sparse">Enable support for <pkg>sci-libs/klu</pkg> sparse solver</flag> + <flag name="superlumt">Build with <pkg>sci-libs/superlu_mt</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-libs/sundials/sundials-2.7.0.ebuild b/sci-libs/sundials/sundials-2.7.0.ebuild new file mode 100644 index 000000000000..5eb5426e8a50 --- /dev/null +++ b/sci-libs/sundials/sundials-2.7.0.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_NEEDED=fortran +FORTRAN_STANDARD=90 + +inherit cmake-utils toolchain-funcs fortran-2 versionator + +DESCRIPTION="Suite of nonlinear solvers" +HOMEPAGE="http://computation.llnl.gov/projects/sundials" +SRC_URI="http://computation.llnl.gov/projects/sundials/download/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0/$(get_major_version)" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cxx doc examples fortran hypre lapack mpi openmp sparse static-libs superlumt threads" +REQUIRED_USE="hypre? ( mpi )" + +RDEPEND=" + lapack? ( virtual/lapack ) + mpi? ( virtual/mpi sci-libs/hypre:= ) + sparse? ( sci-libs/klu:= ) + superlumt? ( sci-libs/superlu_mt:= ) +" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +PATCHES=( "${FILESDIR}"/${P}-underlinking-libdir.patch ) + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp && [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi +} + +src_configure() { + mycmakeargs+=( + -DBUILD_SHARED_LIBS=ON + -DBUILD_STATIC_LIBS="$(usex static-libs)" + -DCXX_ENABLE="$(usex cxx)" + -DFCMIX_ENABLE="$(usex fortran)" + -DF90_ENABLE="$(usex fortran)" + -DHYPRE_ENABLE="$(usex hypre)" + -DHYPRE_INCLUDE_DIR="${EPREFIX}/usr/include/hypre" + -DHYPRE_LIBRARY="HYPRE" + -DKLU_ENABLE="$(usex sparse)" + -DKLU_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libklu.so" + -DLAPACK_ENABLE="$(usex lapack)" + -DMPI_ENABLE="$(usex mpi)" + -DOPENMP_ENABLE="$(usex openmp)" + -DPTHREAD_ENABLE="$(usex threads)" + -DSUPERLUMT_ENABLE="$(usex superlumt)" + -DSUPERLUMT_INCLUDE_DIR="${EPREFIX}/usr/include/superlu_mt" + -DSUPERLUMT_LIBRARY="superlu_mt" + -DEXAMPLES_ENABLE="$(usex examples)" + -DEXAMPLES_INSTALL=ON + -DEXAMPLES_INSTALL_PATH="/usr/share/doc/${PF}/examples" + -DUSE_GENERIC_MATH=ON + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + use doc && dodoc doc/*/*.pdf + cd src + for r in */README; do + newdoc ${r} README-${r%/*} + done +} diff --git a/sci-libs/superlu/Manifest b/sci-libs/superlu/Manifest new file mode 100644 index 000000000000..1f17b924827a --- /dev/null +++ b/sci-libs/superlu/Manifest @@ -0,0 +1,11 @@ +AUX superlu-4.3-autotools.patch 18676 SHA256 6dea0fca12629825ec729fafa488ff2025cd950e93b768d5636fa4d05c760291 SHA512 62f868126af7acc3658bdff6eda8839d06dd14b5195d23a2b7bbbe1008e9258875ac3c9bc4ed40f4ac58443ac4aeef786499b02ff45f2adb304160f3b25b0bf3 WHIRLPOOL 68082a67aec45d6a94daa15d90727eebf2e2f67f3df85b7f6f08a253179c71d21b364822a15f1d9e2a107d56c1157ce995222ce42b5013d9b109bfa36adf8284 +AUX superlu-4.3-format-security.patch 312 SHA256 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mode 100644 index 000000000000..c5aae0159344 --- /dev/null +++ b/sci-libs/superlu/files/superlu-4.3-autotools.patch @@ -0,0 +1,584 @@ + EXAMPLE/Makefile | 68 +++++++++--------- + FORTRAN/Makefile | 14 ++-- + Makefile.am | 4 + + SRC/Makefile.am | 110 +++++++++++++++++++++++++++++ + ax_blas.m4 | 201 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ + configure.ac | 16 ++++ + superlu.pc.in | 13 ++++ + 7 files changed, 385 insertions(+), 41 deletions(-) + +diff --git a/EXAMPLE/Makefile b/EXAMPLE/Makefile +index c286ded..37950dc 100644 +--- a/EXAMPLE/Makefile ++++ b/EXAMPLE/Makefile +@@ -1,4 +1,3 @@ +-include ../make.inc + + ####################################################################### + # This makefile creates the example programs for the linear equation +@@ -32,7 +31,9 @@ include ../make.inc + # + ####################################################################### + +-HEADER = ../SRC ++HEADER = $(shell pkg-config --cflags superlu) ++LIBS = $(shell pkg-config --libs superlu) ++CDEFS = -DAdd_ + + SLINEXM = slinsol.o + SLINEXM1 = slinsol1.o +@@ -67,7 +68,6 @@ ZLINXEXM2 = zlinsolx2.o + ZITSOL = zitersol.o zfgmr.o + ZITSOL1 = zitersol1.o zfgmr.o + +- + all: single double complex complex16 + + single: slinsol slinsol1 slinsolx slinsolx1 slinsolx2 sitersol sitersol1 +@@ -77,97 +77,97 @@ complex: clinsol clinsol1 clinsolx clinsolx1 clinsolx2 citersol citersol1 + complex16: zlinsol zlinsol1 zlinsolx zlinsolx1 zlinsolx2 zitersol zitersol1 + + slinsol: $(SLINEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(SLINEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(SLINEXM) $(LIBS) -o $@ + + slinsol1: $(SLINEXM1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(SLINEXM1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(SLINEXM1) $(LIBS) -o $@ + + slinsolx: $(SLINXEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(SLINXEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(SLINXEXM) $(LIBS) -o $@ + + slinsolx1: $(SLINXEXM1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(SLINXEXM1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(SLINXEXM1) $(LIBS) -o $@ + + slinsolx2: $(SLINXEXM2) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(SLINXEXM2) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(SLINXEXM2) $(LIBS) -o $@ + + sitersol: $(SITSOL) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(SITSOL) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(SITSOL) $(LIBS) -o $@ + + sitersol1: $(SITSOL1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(SITSOL1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(SITSOL1) $(LIBS) -o $@ + + dlinsol: $(DLINEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(DLINEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(DLINEXM) $(LIBS) -o $@ + + dlinsol1: $(DLINEXM1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(DLINEXM1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(DLINEXM1) $(LIBS) -o $@ + + dlinsolx: $(DLINXEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(DLINXEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(DLINXEXM) $(LIBS) -o $@ + + dlinsolx1: $(DLINXEXM1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(DLINXEXM1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(DLINXEXM1) $(LIBS) -o $@ + + dlinsolx2: $(DLINXEXM2) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(DLINXEXM2) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(DLINXEXM2) $(LIBS) -o $@ + + superlu: $(SUPERLUEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(SUPERLUEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(SUPERLUEXM) $(LIBS) -o $@ + + ditersol: $(DITSOL) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(DITSOL) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(DITSOL) $(LIBS) -o $@ + + ditersol1: $(DITSOL1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(DITSOL1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(DITSOL1) $(LIBS) -o $@ + + clinsol: $(CLINEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(CLINEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(CLINEXM) $(LIBS) -o $@ + + clinsol1: $(CLINEXM1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(CLINEXM1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(CLINEXM1) $(LIBS) -o $@ + + clinsolx: $(CLINXEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(CLINXEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(CLINXEXM) $(LIBS) -o $@ + + clinsolx1: $(CLINXEXM1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(CLINXEXM1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(CLINXEXM1) $(LIBS) -o $@ + + clinsolx2: $(CLINXEXM2) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(CLINXEXM2) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(CLINXEXM2) $(LIBS) -o $@ + + citersol: $(CITSOL) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(CITSOL) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(CITSOL) $(LIBS) -o $@ + + citersol1: $(CITSOL1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(CITSOL1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(CITSOL1) $(LIBS) -o $@ + + zlinsol: $(ZLINEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(ZLINEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(ZLINEXM) $(LIBS) -o $@ + + zlinsol1: $(ZLINEXM1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(ZLINEXM1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(ZLINEXM1) $(LIBS) -o $@ + + zlinsolx: $(ZLINXEXM) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(ZLINXEXM) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(ZLINXEXM) $(LIBS) -o $@ + + zlinsolx1: $(ZLINXEXM1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(ZLINXEXM1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(ZLINXEXM1) $(LIBS) -o $@ + + zlinsolx2: $(ZLINXEXM2) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(ZLINXEXM2) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(ZLINXEXM2) $(LIBS) -o $@ + + zitersol: $(ZITSOL) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(ZITSOL) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAGS) $(ZITSOL) $(LIBS) -o $@ + + zitersol1: $(ZITSOL1) $(SUPERLULIB) +- $(LOADER) $(LOADOPTS) $(ZITSOL1) $(LIBS) -lm -o $@ ++ $(LD) $(LDFLAG) $(ZITSOL1) $(LIBS) -o $@ + + .c.o: +- $(CC) $(CFLAGS) $(CDEFS) -I$(HEADER) -c $< $(VERBOSE) ++ $(CC) $(CFLAGS) $(CDEFS) $(HEADER) -c $< $(VERBOSE) + + .f.o: +- $(FORTRAN) $(FFLAGS) -c $< $(VERBOSE) ++ $(FC) $(FFLAGS) -c $< $(VERBOSE) + + clean: + rm -f *.o *linsol *linsol1 *linsolx *linsolx1 *linsolx2 \ +diff --git a/FORTRAN/Makefile b/FORTRAN/Makefile +index 23671a7..54da751 100644 +--- a/FORTRAN/Makefile ++++ b/FORTRAN/Makefile +@@ -1,12 +1,12 @@ +-include ../make.inc ++#include ../make.inc + + ####################################################################### + # This makefile creates the Fortran example interface to use the + # C routines in SuperLU. + ####################################################################### + +-HEADER = ../SRC +-LIBS = $(SUPERLULIB) $(BLASLIB) -lm ++HEADER = $(shell pkg-config --cflags superlu) ++LIBS = $(shell pkg-config --libs superlu) + + # double real + F77EXM = f77_main.o hbcode1.o c_fortran_dgssv.o +@@ -17,19 +17,19 @@ ZF77EXM = z_f77_main.o zhbcode1.o c_fortran_zgssv.o + all: f77exm zf77exm + + f77exm: $(F77EXM) $(SUPERLULIB) +- $(FORTRAN) $(LOADOPTS) $(F77EXM) $(LIBS) -o $@ ++ $(FC) $(LDFLAGS) $(F77EXM) $(LIBS) -o $@ + + zf77exm: $(ZF77EXM) $(SUPERLULIB) + $(FORTRAN) $(LOADOPTS) $(ZF77EXM) $(LIBS) -o $@ + + c_fortran_zgssv.o: c_fortran_zgssv.c +- $(CC) $(CFLAGS) $(CDEFS) -I$(HEADER) -c $< $(VERBOSE) ++ $(CC) $(CFLAGS) $(CDEFS) $(HEADER) -c $< $(VERBOSE) + + .c.o: +- $(CC) $(CFLAGS) $(CDEFS) -I$(HEADER) -c $< $(VERBOSE) ++ $(CC) $(CFLAGS) $(CDEFS) $(HEADER) -c $< $(VERBOSE) + + .f.o: +- $(FORTRAN) $(FFLAGS) -c $< $(VERBOSE) ++ $(FC) $(FFLAGS) -c $< $(VERBOSE) + + clean: + rm -f *.o f77exm zf77exm +diff --git a/Makefile.am b/Makefile.am +new file mode 100644 +index 0000000..7e51046 +--- /dev/null ++++ b/Makefile.am +@@ -0,0 +1,4 @@ ++SUBDIRS = SRC ++ ++pkgconfigdir = $(libdir)/pkgconfig ++pkgconfig_DATA = superlu.pc +diff --git a/SRC/Makefile.am b/SRC/Makefile.am +new file mode 100644 +index 0000000..748e5e9 +--- /dev/null ++++ b/SRC/Makefile.am +@@ -0,0 +1,110 @@ ++AM_CPPFLAGS = -DAdd_ ++ ++### headers ++noinst_HEADERS = \ ++ colamd.h \ ++ html_mainpage.h ++ ++src_includedir = $(includedir)/superlu ++src_include_HEADERS = \ ++ slu_cdefs.h \ ++ slu_ddefs.h \ ++ slu_sdefs.h \ ++ slu_zdefs.h \ ++ slu_Cnames.h \ ++ slu_dcomplex.h \ ++ slu_scomplex.h \ ++ slu_util.h \ ++ superlu_enum_consts.h \ ++ supermatrix.h ++ ++### LAPACK ++LAAUX = lsame.c xerbla.c ++SLASRC = slacon.c ++DLASRC = dlacon.c ++CLASRC = clacon.c scsum1.c icmax1.c ++ZLASRC = zlacon.c dzsum1.c izmax1.c ++ ++ ++################################## ++# Do not optimize these routines # ++################################## ++CFLAGS_SAV=@CFLAGS@ ++CFLAGS= ++noinst_LTLIBRARIES = libnoopt.la ++libnoopt_la_SOURCES = slamch.c dlamch.c superlu_timer.c ++libnoopt_la_CFLAGS = -O0 ++ ++### SuperLU ++ALLAUX = util.c memory.c get_perm_c.c mmd.c \ ++ sp_coletree.c sp_preorder.c sp_ienv.c relax_snode.c \ ++ heap_relax_snode.c colamd.c \ ++ ilu_relax_snode.c ilu_heap_relax_snode.c mark_relax.c \ ++ mc64ad.f qselect.f ++ ++SLUSRC = \ ++ sgssv.c sgssvx.c \ ++ ssp_blas2.c ssp_blas3.c sgscon.c \ ++ slangs.c sgsequ.c slaqgs.c spivotgrowth.c \ ++ sgsrfs.c sgstrf.c sgstrs.c scopy_to_ucol.c \ ++ ssnode_dfs.c ssnode_bmod.c \ ++ spanel_dfs.c spanel_bmod.c sreadhb.c \ ++ scolumn_dfs.c scolumn_bmod.c spivotL.c spruneL.c \ ++ smemory.c sutil.c smyblas2.c \ ++ sgsisx.c sgsitrf.c sldperm.c \ ++ ilu_sdrop_row.c ilu_ssnode_dfs.c \ ++ ilu_scolumn_dfs.c ilu_spanel_dfs.c ilu_scopy_to_ucol.c \ ++ ilu_spivotL.c sdiagonal.c ++ ++DLUSRC = \ ++ dgssv.c dgssvx.c \ ++ dsp_blas2.c dsp_blas3.c dgscon.c \ ++ dlangs.c dgsequ.c dlaqgs.c dpivotgrowth.c \ ++ dgsrfs.c dgstrf.c dgstrs.c dcopy_to_ucol.c \ ++ dsnode_dfs.c dsnode_bmod.c \ ++ dpanel_dfs.c dpanel_bmod.c dreadhb.c \ ++ dcolumn_dfs.c dcolumn_bmod.c dpivotL.c dpruneL.c \ ++ dmemory.c dutil.c dmyblas2.c \ ++ dgsisx.c dgsitrf.c \ ++ dldperm.c \ ++ ilu_ddrop_row.c ilu_dsnode_dfs.c \ ++ ilu_dcolumn_dfs.c ilu_dpanel_dfs.c ilu_dcopy_to_ucol.c \ ++ ilu_dpivotL.c ddiagonal.c ++ ++CLUSRC = \ ++ scomplex.c cgssv.c cgssvx.c csp_blas2.c csp_blas3.c cgscon.c \ ++ clangs.c cgsequ.c claqgs.c cpivotgrowth.c \ ++ cgsrfs.c cgstrf.c cgstrs.c ccopy_to_ucol.c \ ++ csnode_dfs.c csnode_bmod.c \ ++ cpanel_dfs.c cpanel_bmod.c creadhb.c \ ++ ccolumn_dfs.c ccolumn_bmod.c cpivotL.c cpruneL.c \ ++ cmemory.c cutil.c cmyblas2.c \ ++ cgsisx.c cgsitrf.c cldperm.c \ ++ ilu_cdrop_row.c ilu_csnode_dfs.c \ ++ ilu_ccolumn_dfs.c ilu_cpanel_dfs.c ilu_ccopy_to_ucol.c \ ++ ilu_cpivotL.c cdiagonal.c ++ ++ZLUSRC = \ ++ dcomplex.c zgssv.c zgssvx.c zsp_blas2.c zsp_blas3.c zgscon.c \ ++ zlangs.c zgsequ.c zlaqgs.c zpivotgrowth.c \ ++ zgsrfs.c zgstrf.c zgstrs.c zcopy_to_ucol.c \ ++ zsnode_dfs.c zsnode_bmod.c \ ++ zpanel_dfs.c zpanel_bmod.c zreadhb.c \ ++ zcolumn_dfs.c zcolumn_bmod.c zpivotL.c zpruneL.c \ ++ zmemory.c zutil.c zmyblas2.c \ ++ zgsisx.c zgsitrf.c zldperm.c \ ++ ilu_zdrop_row.c ilu_zsnode_dfs.c \ ++ ilu_zcolumn_dfs.c ilu_zpanel_dfs.c ilu_zcopy_to_ucol.c \ ++ ilu_zpivotL.c zdiagonal.c ++ ++lib_LTLIBRARIES = libsuperlu.la ++libsuperlu_la_SOURCES = \ ++ $(NOOPTAUX) \ ++ $(ALLAUX) $(LAAUX) \ ++ $(SLUSRC) $(SLASRC) \ ++ $(DLUSRC) $(DLASRC) \ ++ $(CLUSRC) $(CLASRC) \ ++ $(ZLUSRC) $(ZLASRC) ++libsuperlu_la_CFLAGS = $(CFLAGS_SAV) ++libsuperlu_la_LIBADD = $(BLAS_LIBS) libnoopt.la ++libsuperlu_la_LDFLAGS = -no-undefined -version-info 4:2:0 +diff --git a/ax_blas.m4 b/ax_blas.m4 +new file mode 100644 +index 0000000..e4f96cb +--- /dev/null ++++ b/ax_blas.m4 +@@ -0,0 +1,201 @@ ++# =========================================================================== ++# http://www.gnu.org/software/autoconf-archive/ax_blas.html ++# =========================================================================== ++# ++# SYNOPSIS ++# ++# AX_BLAS([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]) ++# ++# DESCRIPTION ++# ++# This macro looks for a library that implements the BLAS linear-algebra ++# interface (see http://www.netlib.org/blas/). On success, it sets the ++# BLAS_LIBS output variable to hold the requisite library linkages. ++# ++# To link with BLAS, you should link with: ++# ++# $BLAS_LIBS $LIBS $FLIBS ++# ++# in that order. FLIBS is the output variable of the ++# AC_F77_LIBRARY_LDFLAGS macro (called if necessary by AX_BLAS), and is ++# sometimes necessary in order to link with F77 libraries. Users will also ++# need to use AC_F77_DUMMY_MAIN (see the autoconf manual), for the same ++# reason. ++# ++# Many libraries are searched for, from ATLAS to CXML to ESSL. The user ++# may also use --with-blas=<lib> in order to use some specific BLAS ++# library <lib>. In order to link successfully, however, be aware that you ++# will probably need to use the same Fortran compiler (which can be set ++# via the F77 env. var.) as was used to compile the BLAS library. ++# ++# ACTION-IF-FOUND is a list of shell commands to run if a BLAS library is ++# found, and ACTION-IF-NOT-FOUND is a list of commands to run it if it is ++# not found. If ACTION-IF-FOUND is not specified, the default action will ++# define HAVE_BLAS. ++# ++# LICENSE ++# ++# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu> ++# ++# This program is free software: you can redistribute it and/or modify it ++# under the terms of the GNU General Public License as published by the ++# Free Software Foundation, either version 3 of the License, or (at your ++# option) any later version. ++# ++# This program is distributed in the hope that it will be useful, but ++# WITHOUT ANY WARRANTY; without even the implied warranty of ++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General ++# Public License for more details. ++# ++# You should have received a copy of the GNU General Public License along ++# with this program. If not, see <http://www.gnu.org/licenses/>. ++# ++# As a special exception, the respective Autoconf Macro's copyright owner ++# gives unlimited permission to copy, distribute and modify the configure ++# scripts that are the output of Autoconf when processing the Macro. You ++# need not follow the terms of the GNU General Public License when using ++# or distributing such scripts, even though portions of the text of the ++# Macro appear in them. The GNU General Public License (GPL) does govern ++# all other use of the material that constitutes the Autoconf Macro. ++# ++# This special exception to the GPL applies to versions of the Autoconf ++# Macro released by the Autoconf Archive. When you make and distribute a ++# modified version of the Autoconf Macro, you may extend this special ++# exception to the GPL to apply to your modified version as well. ++ ++#serial 11 ++ ++AU_ALIAS([ACX_BLAS], [AX_BLAS]) ++AC_DEFUN([AX_BLAS], [ ++AC_PREREQ(2.50) ++AC_REQUIRE([AC_F77_LIBRARY_LDFLAGS]) ++ax_blas_ok=no ++ ++AC_ARG_WITH(blas, ++ [AS_HELP_STRING([--with-blas=<lib>], [use BLAS library <lib>])]) ++case $with_blas in ++ yes | "") ;; ++ no) ax_blas_ok=disable ;; ++ -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;; ++ *) BLAS_LIBS="-l$with_blas" ;; ++esac ++ ++# Get fortran linker names of BLAS functions to check for. ++AC_F77_FUNC(sgemm) ++AC_F77_FUNC(dgemm) ++ ++ax_blas_save_LIBS="$LIBS" ++LIBS="$LIBS $FLIBS" ++ ++# First, check BLAS_LIBS environment variable ++if test $ax_blas_ok = no; then ++if test "x$BLAS_LIBS" != x; then ++ save_LIBS="$LIBS"; LIBS="$BLAS_LIBS $LIBS" ++ AC_MSG_CHECKING([for $sgemm in $BLAS_LIBS]) ++ AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes], [BLAS_LIBS=""]) ++ AC_MSG_RESULT($ax_blas_ok) ++ LIBS="$save_LIBS" ++fi ++fi ++ ++# BLAS linked to by default? (happens on some supercomputers) ++if test $ax_blas_ok = no; then ++ save_LIBS="$LIBS"; LIBS="$LIBS" ++ AC_MSG_CHECKING([if $sgemm is being linked in already]) ++ AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes]) ++ AC_MSG_RESULT($ax_blas_ok) ++ LIBS="$save_LIBS" ++fi ++ ++# BLAS in ATLAS library? (http://math-atlas.sourceforge.net/) ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(atlas, ATL_xerbla, ++ [AC_CHECK_LIB(f77blas, $sgemm, ++ [AC_CHECK_LIB(cblas, cblas_dgemm, ++ [ax_blas_ok=yes ++ BLAS_LIBS="-lcblas -lf77blas -latlas"], ++ [], [-lf77blas -latlas])], ++ [], [-latlas])]) ++fi ++ ++# BLAS in PhiPACK libraries? (requires generic BLAS lib, too) ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(blas, $sgemm, ++ [AC_CHECK_LIB(dgemm, $dgemm, ++ [AC_CHECK_LIB(sgemm, $sgemm, ++ [ax_blas_ok=yes; BLAS_LIBS="-lsgemm -ldgemm -lblas"], ++ [], [-lblas])], ++ [], [-lblas])]) ++fi ++ ++# BLAS in Intel MKL library? ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(mkl, $sgemm, [ax_blas_ok=yes;BLAS_LIBS="-lmkl"]) ++fi ++ ++# BLAS in Apple vecLib library? ++if test $ax_blas_ok = no; then ++ save_LIBS="$LIBS"; LIBS="-framework vecLib $LIBS" ++ AC_MSG_CHECKING([for $sgemm in -framework vecLib]) ++ AC_TRY_LINK_FUNC($sgemm, [ax_blas_ok=yes;BLAS_LIBS="-framework vecLib"]) ++ AC_MSG_RESULT($ax_blas_ok) ++ LIBS="$save_LIBS" ++fi ++ ++# BLAS in Alpha CXML library? ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(cxml, $sgemm, [ax_blas_ok=yes;BLAS_LIBS="-lcxml"]) ++fi ++ ++# BLAS in Alpha DXML library? (now called CXML, see above) ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(dxml, $sgemm, [ax_blas_ok=yes;BLAS_LIBS="-ldxml"]) ++fi ++ ++# BLAS in Sun Performance library? ++if test $ax_blas_ok = no; then ++ if test "x$GCC" != xyes; then # only works with Sun CC ++ AC_CHECK_LIB(sunmath, acosp, ++ [AC_CHECK_LIB(sunperf, $sgemm, ++ [BLAS_LIBS="-xlic_lib=sunperf -lsunmath" ++ ax_blas_ok=yes],[],[-lsunmath])]) ++ fi ++fi ++ ++# BLAS in SCSL library? (SGI/Cray Scientific Library) ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(scs, $sgemm, [ax_blas_ok=yes; BLAS_LIBS="-lscs"]) ++fi ++ ++# BLAS in SGIMATH library? ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(complib.sgimath, $sgemm, ++ [ax_blas_ok=yes; BLAS_LIBS="-lcomplib.sgimath"]) ++fi ++ ++# BLAS in IBM ESSL library? (requires generic BLAS lib, too) ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(blas, $sgemm, ++ [AC_CHECK_LIB(essl, $sgemm, ++ [ax_blas_ok=yes; BLAS_LIBS="-lessl -lblas"], ++ [], [-lblas $FLIBS])]) ++fi ++ ++# Generic BLAS library? ++if test $ax_blas_ok = no; then ++ AC_CHECK_LIB(blas, $sgemm, [ax_blas_ok=yes; BLAS_LIBS="-lblas"]) ++fi ++ ++AC_SUBST(BLAS_LIBS) ++ ++LIBS="$ax_blas_save_LIBS" ++ ++# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND: ++if test x"$ax_blas_ok" = xyes; then ++ ifelse([$1],,AC_DEFINE(HAVE_BLAS,1,[Define if you have a BLAS library.]),[$1]) ++ : ++else ++ ax_blas_ok=no ++ $2 ++fi ++])dnl AX_BLAS +diff --git a/configure.ac b/configure.ac +new file mode 100644 +index 0000000..f6707be +--- /dev/null ++++ b/configure.ac +@@ -0,0 +1,16 @@ ++# -*- Autoconf -*- ++AC_PREREQ(2.59) ++AC_INIT(superlu, 4.3, xsli@lbl.gov) ++AM_INIT_AUTOMAKE([foreign]) ++AC_CONFIG_HEADER([config.h]) ++AC_PROG_INSTALL ++AC_PROG_LIBTOOL ++AC_PROG_F77 ++sinclude(ax_blas.m4) ++AX_BLAS ++if test x"$BLAS_LIBS" = x; then ++ AC_MSG_ERROR([Cannot find blas libraries]) ++fi ++AC_CHECK_LIB([m], [floor]) ++AC_CONFIG_FILES([Makefile SRC/Makefile superlu.pc]) ++AC_OUTPUT +diff --git a/superlu.pc.in b/superlu.pc.in +new file mode 100644 +index 0000000..7bf9942 +--- /dev/null ++++ b/superlu.pc.in +@@ -0,0 +1,13 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: @PACKAGE_NAME@ ++Description: Sparse LU factorization library ++Version: @PACKAGE_VERSION@ ++URL: http://crd.lbl.gov/~xiaoye/SuperLU/ ++Libs: -L${libdir} -lsuperlu ++Libs.private: -lm @FLIBS@ ++Requires: blas ++Cflags: -I${includedir}/superlu diff --git a/sci-libs/superlu/files/superlu-4.3-format-security.patch b/sci-libs/superlu/files/superlu-4.3-format-security.patch new file mode 100644 index 000000000000..809408a166ab --- /dev/null +++ b/sci-libs/superlu/files/superlu-4.3-format-security.patch @@ -0,0 +1,16 @@ + SRC/util.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/SRC/util.c b/SRC/util.c +index 858fbbc..c038ccf 100644 +--- a/SRC/util.c ++++ b/SRC/util.c +@@ -29,7 +29,7 @@ + + void superlu_abort_and_exit(char* msg) + { +- fprintf(stderr, msg); ++ fprintf(stderr, "%s", msg); + exit (-1); + } + diff --git a/sci-libs/superlu/files/superlu-5.2.1-no-implicits.patch b/sci-libs/superlu/files/superlu-5.2.1-no-implicits.patch new file mode 100644 index 000000000000..587380ce2e35 --- /dev/null +++ b/sci-libs/superlu/files/superlu-5.2.1-no-implicits.patch @@ -0,0 +1,153 @@ +diff --git a/SRC/clacon2.c b/SRC/clacon2.c +index 107bb64..39deb83 100644 +--- a/SRC/clacon2.c ++++ b/SRC/clacon2.c +@@ -106,6 +106,11 @@ clacon2_(int *n, complex *v, complex *x, float *est, int *kase, int isave[3]) + extern float smach(char *); + extern int icmax1_slu(int *, complex *, int *); + extern double scsum1_slu(int *, complex *, int *); ++#ifdef _CRAY ++ extern int CCOPY(int *, complex *, int *, complex [], int *); ++#else ++ extern int ccopy_(int *, complex *, int *, complex [], int *); ++#endif + + safmin = smach("Safe minimum"); /* lamch_("Safe minimum"); */ + if ( *kase == 0 ) { +diff --git a/SRC/dmach.c b/SRC/dmach.c +index 73beacb..cafdf1c 100644 +--- a/SRC/dmach.c ++++ b/SRC/dmach.c +@@ -11,6 +11,7 @@ at the top-level directory. + #include <float.h> + #include <math.h> + #include <stdio.h> ++#include <string.h> + + double dmach(char *cmach) + { +diff --git a/SRC/ilu_cdrop_row.c b/SRC/ilu_cdrop_row.c +index 4987548..09b8a93 100644 +--- a/SRC/ilu_cdrop_row.c ++++ b/SRC/ilu_cdrop_row.c +@@ -28,6 +28,7 @@ extern void caxpy_(int *, complex *, complex [], int *, complex [], int *); + extern void ccopy_(int *, complex [], int *, complex [], int *); + extern float scasum_(int *, complex *, int *); + extern float scnrm2_(int *, complex *, int *); ++extern void scopy_(int *, float [], int *, float [], int *); + extern double dnrm2_(int *, double [], int *); + extern int icamax_(int *, complex [], int *); + +diff --git a/SRC/ilu_zdrop_row.c b/SRC/ilu_zdrop_row.c +index f434dd9..2de1226 100644 +--- a/SRC/ilu_zdrop_row.c ++++ b/SRC/ilu_zdrop_row.c +@@ -29,6 +29,7 @@ extern void zcopy_(int *, doublecomplex [], int *, doublecomplex [], int *); + extern double dzasum_(int *, doublecomplex *, int *); + extern double dznrm2_(int *, doublecomplex *, int *); + extern double dnrm2_(int *, double [], int *); ++extern void dcopy_(int *, double [], int *, double [], int *); + extern int izamax_(int *, doublecomplex [], int *); + + static double *A; /* used in _compare_ only */ +diff --git a/SRC/slacon2.c b/SRC/slacon2.c +index 7c93341..50efe78 100644 +--- a/SRC/slacon2.c ++++ b/SRC/slacon2.c +@@ -157,7 +157,7 @@ L40: + #ifdef _CRAY + isave[1] = ISAMAX(n, &x[0], &c__1); /* j */ + #else +- isave[1] = idamax_(n, &x[0], &c__1); /* j */ ++ isave[1] = isamax_(n, &x[0], &c__1); /* j */ + #endif + --isave[1]; /* --j; */ + isave[2] = 2; /* iter = 2; */ +diff --git a/SRC/smach.c b/SRC/smach.c +index fff6c5f..0b69991 100644 +--- a/SRC/smach.c ++++ b/SRC/smach.c +@@ -11,6 +11,7 @@ at the top-level directory. + #include <float.h> + #include <math.h> + #include <stdio.h> ++#include <string.h> + + float smach(char *cmach) + { +diff --git a/SRC/sp_ienv.c b/SRC/sp_ienv.c +index 855d901..ce2865e 100644 +--- a/SRC/sp_ienv.c ++++ b/SRC/sp_ienv.c +@@ -24,6 +24,7 @@ at the top-level directory. + * History: Modified from lapack routine ILAENV + */ + #include "slu_Cnames.h" ++extern int input_error(char *, int *); + + /*! \brief + +diff --git a/SRC/zlacon2.c b/SRC/zlacon2.c +index b43c619..ed5f2b7 100644 +--- a/SRC/zlacon2.c ++++ b/SRC/zlacon2.c +@@ -106,6 +106,11 @@ zlacon2_(int *n, doublecomplex *v, doublecomplex *x, double *est, int *kase, int + extern double dmach(char *); + extern int izmax1_slu(int *, doublecomplex *, int *); + extern double dzsum1_slu(int *, doublecomplex *, int *); ++#ifdef _CRAY ++ extern int CCOPY(int *, doublecomplex *, int *, doublecomplex *, int *); ++#else ++ extern int zcopy_(int *, doublecomplex *, int *, doublecomplex *, int *); ++#endif + + safmin = dmach("Safe minimum"); /* lamch_("Safe minimum"); */ + if ( *kase == 0 ) { +diff --git a/TESTING/zdrive.c b/TESTING/zdrive.c +index 23e96fc..1e7d0aa 100644 +--- a/TESTING/zdrive.c ++++ b/TESTING/zdrive.c +@@ -21,6 +21,7 @@ at the top-level directory. + * Purpose: MAIN test program + */ + #include <string.h> ++#include <unistd.h> + #include "slu_zdefs.h" + + #define NTESTS 5 /* Number of test types */ +diff --git a/TESTING/cdrive.c b/TESTING/cdrive.c +index 8bc8d10..00fe0d8 100644 +--- a/TESTING/cdrive.c ++++ b/TESTING/cdrive.c +@@ -21,6 +21,7 @@ at the top-level directory. + * Purpose: MAIN test program + */ + #include <string.h> ++#include <unistd.h> + #include "slu_cdefs.h" + + #define NTESTS 5 /* Number of test types */ +diff --git a/TESTING/sdrive.c b/TESTING/sdrive.c +index 5b98038..cba0c83 100644 +--- a/TESTING/sdrive.c ++++ b/TESTING/sdrive.c +@@ -21,6 +21,7 @@ at the top-level directory. + * Purpose: MAIN test program + */ + #include <string.h> ++#include <unistd.h> + #include "slu_sdefs.h" + + #define NTESTS 5 /* Number of test types */ +diff --git a/TESTING/ddrive.c b/TESTING/ddrive.c +index 2c3f6fe..35685c5 100644 +--- a/TESTING/ddrive.c ++++ b/TESTING/ddrive.c +@@ -21,6 +21,7 @@ at the top-level directory. + * Purpose: MAIN test program + */ + #include <string.h> ++#include <unistd.h> + #include "slu_ddefs.h" + + #define NTESTS 5 /* Number of test types */ diff --git a/sci-libs/superlu/files/superlu-5.2.1-pkgconfig.patch b/sci-libs/superlu/files/superlu-5.2.1-pkgconfig.patch new file mode 100644 index 000000000000..63252dffdb57 --- /dev/null +++ b/sci-libs/superlu/files/superlu-5.2.1-pkgconfig.patch @@ -0,0 +1,29 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index d8abc1b..5883b34 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -143,3 +143,6 @@ endif() + # ${CMAKE_C_COMPILER} ) + configure_file(${CMAKE_SOURCE_DIR}/make.inc.in ${CMAKE_SOURCE_DIR}/make.inc) + ++configure_file(${CMAKE_CURRENT_SOURCE_DIR}/superlu.pc.in ${CMAKE_CURRENT_BINARY_DIR}/superlu.pc @ONLY) ++install(FILES ${CMAKE_CURRENT_BINARY_DIR}/superlu.pc ++ DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) +diff --git a/superlu.pc.in b/superlu.pc.in +new file mode 100644 +index 0000000..09b1fff +--- /dev/null ++++ b/superlu.pc.in +@@ -0,0 +1,12 @@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++libdir=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@ ++includedir=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_INCLUDEDIR@ ++ ++Name: @CMAKE_PROJECT_NAME@ ++Description: Direct solution of large, sparse systems of linear equations ++Version: @PROJECT_VERSION@ ++URL: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ ++ ++Libs: -L${libdir} -lsuperlu ++Libs.private: @BLAS_LIB@ -lm ++Cflags: -I${includedir} diff --git a/sci-libs/superlu/metadata.xml b/sci-libs/superlu/metadata.xml new file mode 100644 index 000000000000..01512c58f866 --- /dev/null +++ b/sci-libs/superlu/metadata.xml @@ -0,0 +1,28 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + SuperLU is a general purpose library for the direct solution of large, + sparse, nonsymmetric systems of linear equations on high performance + machines. The library is written in C and is callable from either C or + Fortran. The library routines will perform an LU decomposition with + partial pivoting and triangular system solves through forward and back + substitution. The LU factorization routines can handle non-square + matrices but the triangular solves are performed only for square + matrices. The matrix columns may be preordered (before factorization) + either through library or user supplied routines. This preordering for + sparsity is completely separate from the factorization. Working + precision iterative refinement subroutines are provided for improved + backward stability. Routines are also provided to equilibrate the + system, estimate the condition number, calculate the relative backward + error, and estimate error bounds for the refined solutions. + </longdescription> + <upstream> + <remote-id type="github">xiaoyeli/superlu</remote-id> + </upstream> + +</pkgmetadata> diff --git a/sci-libs/superlu/superlu-4.3-r1.ebuild b/sci-libs/superlu/superlu-4.3-r1.ebuild new file mode 100644 index 000000000000..27da140292af --- /dev/null +++ b/sci-libs/superlu/superlu-4.3-r1.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true +AUTOTOOLS_IN_SOURCE_BUILD=1 + +inherit autotools-utils fortran-2 toolchain-funcs multilib + +MY_PN=SuperLU + +DESCRIPTION="Sparse LU factorization library" +HOMEPAGE="http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" +SRC_URI="${HOMEPAGE}/${PN}_${PV}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha amd64 ~arm ~hppa ppc ppc64 x86 ~amd64-linux ~x86-linux" +IUSE="doc examples static-libs test" + +RDEPEND=" + virtual/blas" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( app-shells/tcsh )" + +S="${WORKDIR}/${MY_PN}_${PV}" + +PATCHES=( + "${FILESDIR}"/${P}-autotools.patch + "${FILESDIR}"/${P}-format-security.patch + ) + +src_prepare() { + unset VERBOSE + sed \ + -e "s:= ar:= $(tc-getAR):g" \ + -e "s:= ranlib:= $(tc-getRANLIB):g" \ + -i make.inc || die + + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" ) + autotools-utils_src_configure + rm EXAMPLE/*itersol1 || die +} + +src_test() { + cd "${BUILD_DIR}"/TESTING + emake -j1 \ + CC="$(tc-getCC)" \ + FORTRAN="$(tc-getFC)" \ + LOADER="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" \ + FFLAGS="${FFLAGS}" \ + LOADOPTS="${LDFLAGS}" \ + BLASLIB="$($(tc-getPKG_CONFIG) --libs blas)" \ + SUPERLULIB="${S}/SRC/.libs/libsuperlu$(get_libname)" \ + LD_LIBRARY_PATH="${S}/SRC/.libs" \ + DYLD_LIBRARY_PATH="${S}/SRC/.libs" +} + +src_install() { + autotools-utils_src_install + use doc && dodoc DOC/ug.pdf && dohtml DOC/html/* + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r EXAMPLE FORTRAN + fi +} diff --git a/sci-libs/superlu/superlu-5.2.1-r1.ebuild b/sci-libs/superlu/superlu-5.2.1-r1.ebuild new file mode 100644 index 000000000000..8f2fa083bb98 --- /dev/null +++ b/sci-libs/superlu/superlu-5.2.1-r1.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +FORTRAN_STANDARD=77 + +inherit cmake-utils fortran-2 + +MY_PN=SuperLU + +if [[ ${PV} != *9999* ]]; then + inherit versionator + SRC_URI="http://crd-legacy.lbl.gov/~xiaoye/SuperLU//${PN}_${PV}.tar.gz" + KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" + SLOT="0/$(get_major_version)" + S="${WORKDIR}/SuperLU_${PV}" +else + inherit git-r3 + GIT_ECLASS="git-r3" + EGIT_REPO_URI="https://github.com/xiaoyeli/${PN}" + SLOT="0/9999" + KEYWORDS="~arm64 ~hppa ~ia64" +fi + +DESCRIPTION="Sparse LU factorization library" +HOMEPAGE="http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" +LICENSE="BSD" + +IUSE="doc examples test" + +RDEPEND="virtual/blas" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( app-shells/tcsh )" + +PATCHES=( + "${FILESDIR}"/${P}-no-implicits.patch + "${FILESDIR}"/${P}-pkgconfig.patch +) + +S="${WORKDIR}/${MY_PN}_${PV}" + +src_prepare() { + default + # respect user's CFLAGS + sed -i -e 's/O3//' CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs+=( + -DCMAKE_INSTALL_INCLUDEDIR="include/superlu" + -DBUILD_SHARED_LIBS=ON + -Denable_blaslib=OFF + -Denable_tests=$(usex test) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + use doc && dodoc -r DOC/html + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r EXAMPLE FORTRAN + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-libs/superlu_mt/Manifest b/sci-libs/superlu_mt/Manifest new file mode 100644 index 000000000000..040ef8c443ce --- /dev/null +++ b/sci-libs/superlu_mt/Manifest @@ -0,0 +1,4 @@ +AUX superlu_mt-3.1-duplicate-symbols.patch 7284 SHA256 d10bdc176b68d6903feea629fbe1d919c8a68261375f4b6b62644c7d86070a12 SHA512 b233677071ce175116454614b6289faa80f60ef0dfeee728bc4a1a7603ce8490c93e63ba635d1db231c92a055dee5cdbeff2793a2e138fa688efc18bd72b693f WHIRLPOOL c2297c1a25743db2acadb27a7f25062d79750e35fc7a83be4f2ff9c2a3a534f4c4d924cb37920d1c16abf071b5d364f4c6f33beb19e20a799bd23dbc0e77f25b +DIST superlu_mt_3.1.tar.gz 1824440 SHA256 407b544b9a92b2ed536b1e713e80f986824cf3016657a4bfc2f3e7d2a76ecab6 SHA512 41b8d9808f6a9c3f8d9e983ab253b0c5aec486df1cc419d043a201bd950034fa4bdd5465410e1198a2314d072b92cb388fc117165a06f820922f04060c755971 WHIRLPOOL 4ab6ec9dc9080d6bbd0096514794d0e4c2fcf31a1a7d85865516c3afc028d693baafd06967f777d336e34668678bd8aa390680b742abccbca1f347fffe08d3c5 +EBUILD superlu_mt-3.1.ebuild 2548 SHA256 bb044fd8b0feb83b65a329a12b674b90a2e9ec8ca297c0e397c2fb949b57f7e1 SHA512 ebd183c356861a83f06dc487ca404809cc1546a4bd9341fdebcc03d4fd502dea20da72ee1f0c33ea0a407e432e75a733ac68fa4ea38ab9f41c0b49317af87b04 WHIRLPOOL 2594e14db169123f980342969d2a4ee090ad2e6bccc1a7e61768b7ebe5f48813af4ec86cebe7f216efcb8f06e06322e29d14822aa8cec9b1c92307c4596f98ad +MISC metadata.xml 1471 SHA256 d2ee8efd522809012cb3b43fac28f61ab567d9c2b76d2b473e2445173590fcdb SHA512 1f4ab676f807e3211c894cd5ae692987c419937a0f0aa2bae46b72d029ad843f3d4415ee9ce3876b6d19e8446e3d6c5085b1671f0b7b73329696d9c231540e76 WHIRLPOOL 7bf9e3f6209bf461db0f4c18053c4f2460e7274c5ba0fc684dbcc12c32d9c72caf45ebb84b64f2dbedda8031baf4fc8599e1526d427b2d4ec155f88bea61afe7 diff --git a/sci-libs/superlu_mt/files/superlu_mt-3.1-duplicate-symbols.patch b/sci-libs/superlu_mt/files/superlu_mt-3.1-duplicate-symbols.patch new file mode 100644 index 000000000000..cc82c2692b5c --- /dev/null +++ b/sci-libs/superlu_mt/files/superlu_mt-3.1-duplicate-symbols.patch @@ -0,0 +1,240 @@ +--- a/SRC/smatgen.c 2016-12-28 01:06:35.529467943 +0000 ++++ b/SRC/smatgen.c 2016-12-28 01:06:06.949710330 +0000 +@@ -102,77 +102,3 @@ + + xa[n] = lasta; + } +- +-double dlaran_(int *iseed) +-{ +-/* -- LAPACK auxiliary routine (version 2.0) -- +- Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +- Courant Institute, Argonne National Lab, and Rice University +- February 29, 1992 +- +- Purpose +- ======= +- +- DLARAN returns a random real number from a uniform (0,1) +- distribution. +- +- Arguments +- ========= +- +- ISEED (input/output) INT array, dimension (4) +- On entry, the seed of the random number generator; the array +- +- elements must be between 0 and 4095, and ISEED(4) must be +- odd. +- On exit, the seed is updated. +- +- Further Details +- =============== +- +- This routine uses a multiplicative congruential method with modulus +- 2**48 and multiplier 33952834046453 (see G.S.Fishman, +- 'Multiplicative congruential random number generators with modulus +- 2**b: an exhaustive analysis for b = 32 and a partial analysis for +- b = 48', Math. Comp. 189, pp 331-344, 1990). +- +- 48-bit integers are stored in 4 integer array elements with 12 bits +- per element. Hence the routine is portable across machines with +- integers of 32 bits or more. +- +- ===================================================================== +-*/ +- +- /* Local variables */ +- int it1, it2, it3, it4; +- +- --iseed; +- +- /* multiply the seed by the multiplier modulo 2**48 */ +- it4 = iseed[4] * 2549; +- it3 = it4 / 4096; +- it4 -= it3 << 12; +- it3 = it3 + iseed[3] * 2549 + iseed[4] * 2508; +- it2 = it3 / 4096; +- it3 -= it2 << 12; +- it2 = it2 + iseed[2] * 2549 + iseed[3] * 2508 + iseed[4] * 322; +- it1 = it2 / 4096; +- it2 -= it1 << 12; +- it1 = it1 + iseed[1] * 2549 + iseed[2] * 2508 + iseed[3] * 322 + iseed[4] +- * 494; +- it1 %= 4096; +- +- /* return updated seed */ +- +- iseed[1] = it1; +- iseed[2] = it2; +- iseed[3] = it3; +- iseed[4] = it4; +- +- /* convert 48-bit integer to a real number in the interval (0,1) */ +- +- return ((double) it1 + +- ((double) it2 + ((double) it3 + (double) it4 * 2.44140625e-4) * +- 2.44140625e-4) * 2.44140625e-4) * 2.44140625e-4; +- +-} /* dlaran_ */ +- +--- a/SRC/zmatgen.c 2016-12-28 01:07:05.819211056 +0000 ++++ b/SRC/zmatgen.c 2016-12-28 01:07:26.329037112 +0000 +@@ -102,77 +102,3 @@ + + xa[n] = lasta; + } +- +-double dlaran_(int *iseed) +-{ +-/* -- LAPACK auxiliary routine (version 2.0) -- +- Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +- Courant Institute, Argonne National Lab, and Rice University +- February 29, 1992 +- +- Purpose +- ======= +- +- DLARAN returns a random real number from a uniform (0,1) +- distribution. +- +- Arguments +- ========= +- +- ISEED (input/output) INT array, dimension (4) +- On entry, the seed of the random number generator; the array +- +- elements must be between 0 and 4095, and ISEED(4) must be +- odd. +- On exit, the seed is updated. +- +- Further Details +- =============== +- +- This routine uses a multiplicative congruential method with modulus +- 2**48 and multiplier 33952834046453 (see G.S.Fishman, +- 'Multiplicative congruential random number generators with modulus +- 2**b: an exhaustive analysis for b = 32 and a partial analysis for +- b = 48', Math. Comp. 189, pp 331-344, 1990). +- +- 48-bit integers are stored in 4 integer array elements with 12 bits +- per element. Hence the routine is portable across machines with +- integers of 32 bits or more. +- +- ===================================================================== +-*/ +- +- /* Local variables */ +- int it1, it2, it3, it4; +- +- --iseed; +- +- /* multiply the seed by the multiplier modulo 2**48 */ +- it4 = iseed[4] * 2549; +- it3 = it4 / 4096; +- it4 -= it3 << 12; +- it3 = it3 + iseed[3] * 2549 + iseed[4] * 2508; +- it2 = it3 / 4096; +- it3 -= it2 << 12; +- it2 = it2 + iseed[2] * 2549 + iseed[3] * 2508 + iseed[4] * 322; +- it1 = it2 / 4096; +- it2 -= it1 << 12; +- it1 = it1 + iseed[1] * 2549 + iseed[2] * 2508 + iseed[3] * 322 + iseed[4] +- * 494; +- it1 %= 4096; +- +- /* return updated seed */ +- +- iseed[1] = it1; +- iseed[2] = it2; +- iseed[3] = it3; +- iseed[4] = it4; +- +- /* convert 48-bit integer to a real number in the interval (0,1) */ +- +- return ((double) it1 + +- ((double) it2 + ((double) it3 + (double) it4 * 2.44140625e-4) * +- 2.44140625e-4) * 2.44140625e-4) * 2.44140625e-4; +- +-} /* dlaran_ */ +- +--- a/SRC/cmatgen.c 2016-12-28 00:57:45.513963020 +0000 ++++ b/SRC/cmatgen.c 2016-12-28 00:58:46.413446529 +0000 +@@ -102,77 +102,3 @@ + + xa[n] = lasta; + } +- +-double dlaran_(int *iseed) +-{ +-/* -- LAPACK auxiliary routine (version 2.0) -- +- Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., +- Courant Institute, Argonne National Lab, and Rice University +- February 29, 1992 +- +- Purpose +- ======= +- +- DLARAN returns a random real number from a uniform (0,1) +- distribution. +- +- Arguments +- ========= +- +- ISEED (input/output) INT array, dimension (4) +- On entry, the seed of the random number generator; the array +- +- elements must be between 0 and 4095, and ISEED(4) must be +- odd. +- On exit, the seed is updated. +- +- Further Details +- =============== +- +- This routine uses a multiplicative congruential method with modulus +- 2**48 and multiplier 33952834046453 (see G.S.Fishman, +- 'Multiplicative congruential random number generators with modulus +- 2**b: an exhaustive analysis for b = 32 and a partial analysis for +- b = 48', Math. Comp. 189, pp 331-344, 1990). +- +- 48-bit integers are stored in 4 integer array elements with 12 bits +- per element. Hence the routine is portable across machines with +- integers of 32 bits or more. +- +- ===================================================================== +-*/ +- +- /* Local variables */ +- int it1, it2, it3, it4; +- +- --iseed; +- +- /* multiply the seed by the multiplier modulo 2**48 */ +- it4 = iseed[4] * 2549; +- it3 = it4 / 4096; +- it4 -= it3 << 12; +- it3 = it3 + iseed[3] * 2549 + iseed[4] * 2508; +- it2 = it3 / 4096; +- it3 -= it2 << 12; +- it2 = it2 + iseed[2] * 2549 + iseed[3] * 2508 + iseed[4] * 322; +- it1 = it2 / 4096; +- it2 -= it1 << 12; +- it1 = it1 + iseed[1] * 2549 + iseed[2] * 2508 + iseed[3] * 322 + iseed[4] +- * 494; +- it1 %= 4096; +- +- /* return updated seed */ +- +- iseed[1] = it1; +- iseed[2] = it2; +- iseed[3] = it3; +- iseed[4] = it4; +- +- /* convert 48-bit integer to a real number in the interval (0,1) */ +- +- return ((double) it1 + +- ((double) it2 + ((double) it3 + (double) it4 * 2.44140625e-4) * +- 2.44140625e-4) * 2.44140625e-4) * 2.44140625e-4; +- +-} /* dlaran_ */ +- diff --git a/sci-libs/superlu_mt/metadata.xml b/sci-libs/superlu_mt/metadata.xml new file mode 100644 index 000000000000..5e07f8c182bc --- /dev/null +++ b/sci-libs/superlu_mt/metadata.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + SuperLU is a general purpose library for the direct solution of + large, sparse, nonsymmetric systems of linear equations on high + performance machines. The library is written in C and is callable + from either C or Fortran. The library routines will perform an LU + decomposition with partial pivoting and triangular system solves + through forward and back substitution. The LU factorization routines + can handle non-square matrices but the triangular solves are + performed only for square matrices. The matrix columns may be + preordered (before factorization) either through library or user + supplied routines. This preordering for sparsity is completely + separate from the factorization. Working precision iterative + refinement subroutines are provided for improved backward + stability. Routines are also provided to equilibrate the system, + estimate the condition number, calculate the relative backward + error, and estimate error bounds for the refined solutions. + This is the multi-threaded version (POSIX threads or OpenMP). + </longdescription> + <use> + <flag name="int64">Build the 64 bits integer library</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/superlu_mt/superlu_mt-3.1.ebuild b/sci-libs/superlu_mt/superlu_mt-3.1.ebuild new file mode 100644 index 000000000000..2322df8507e6 --- /dev/null +++ b/sci-libs/superlu_mt/superlu_mt-3.1.ebuild @@ -0,0 +1,102 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils toolchain-funcs versionator + +MYPN=SuperLU_MT +SOVERSION=$(get_major_version) + +DESCRIPTION="Multithreaded sparse LU factorization library" +HOMEPAGE="http://crd.lbl.gov/~xiaoye/SuperLU/" +SRC_URI="${HOMEPAGE}/${PN}_${PV}.tar.gz" + +LICENSE="BSD" +SLOT="0/${SOVERSION}" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples int64 openmp static-libs test threads" +REQUIRED_USE="|| ( openmp threads )" + +RDEPEND="virtual/blas" +DEPEND="${RDEPEND} + virtual/pkgconfig + test? ( app-shells/tcsh )" + +S="${WORKDIR}/${MYPN}_${PV}" + +PATCHES=( "${FILESDIR}"/${P}-duplicate-symbols.patch ) + +pkg_setup() { + if use openmp && ! use threads; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + CTHREADS="-D__OPENMP" + [[ $(tc-getCC) == *gcc ]] && LDTHREADS="-fopenmp" + else + CTHREADS="-D__PTHREAD" + LDTHREADS="-pthread" + fi +} + +src_prepare() { + default + cat <<-EOF > make.inc + CC=$(tc-getCC) + LOADER=$(tc-getCC) + ARCH=$(tc-getAR) + RANLIB=$(tc-getRANLIB) + PREDEFS=${CPPFLAGS} -DUSE_VENDOR_BLAS -DPRNTlevel=0 -DDEBUGlevel=0 $(use int64 && echo -D_LONGINT) + CDEFS=-DAdd_ + CFLAGS=${CFLAGS} ${CTHREADS} \$(PIC) + BLASLIB=$($(tc-getPKG_CONFIG) --libs blas) + MATHLIB=-lm + NOOPTS=-O0 \$(PIC) + ARCHFLAGS=cr + LOADOPTS=${LDFLAGS} ${LDTHREADS} + SUPERLULIB=lib${PN}.a + TMGLIB=libtmglib.a + EOF + SONAME=lib${PN}.so.${SOVERSION} + sed -e 's|../make.inc|make.inc|' \ + -e "s|../SRC|${EPREFIX}/usr/include/${PN}|" \ + -e '/:.*$(SUPERLULIB)/s|../lib/$(SUPERLULIB)||g' \ + -e 's|../lib/$(SUPERLULIB)|-lsuperlu_mt|g' \ + -i EXAMPLE/Makefile || die +} + +src_compile() { + # shared library + emake PIC="-fPIC" \ + ARCH="echo" \ + ARCHFLAGS="" \ + RANLIB="echo" \ + superlulib + $(tc-getCC) ${LDFLAGS} ${LDTHREADS} -shared -Wl,-soname=${SONAME} SRC/*.o \ + $($(tc-getPKG_CONFIG) --libs blas) -lm -o lib/${SONAME} || die + ln -s ${SONAME} lib/libsuperlu_mt.so || die + + use static-libs && rm -f SRC/*.o && \ + emake PIC="" superlulib +} + +src_test() { + emake -j1 tmglib + LD_LIBRARY_PATH="${S}/lib:${LD_LIBRARY_PATH}" \ + emake SUPERLULIB="${SONAME}" testing +} + +src_install() { + dolib.so lib/*so* + use static-libs && dolib.a lib/*.a + insinto /usr/include/${PN} + doins SRC/*h + dodoc README + use doc && dodoc DOC/ug.pdf + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r EXAMPLE/* make.inc + fi +} diff --git a/sci-libs/symengine/Manifest b/sci-libs/symengine/Manifest new file mode 100644 index 000000000000..8ba823459670 --- /dev/null +++ b/sci-libs/symengine/Manifest @@ -0,0 +1,3 @@ +DIST symengine-0.3.0.tar.gz 629813 SHA256 591463cb9e741d59f6dfd39a7943e3865d3afe9eac47d1a9cbf5ca74b9c49476 SHA512 e4a906bb1cc5159003969871711f40b3c6bfb9e38ac25258dc5797933d55374a2f201c8a89e9af48821b24cc54408d4feb70f6de421e0a9fbf766d2b35846b83 WHIRLPOOL c910a8d00edeb686c94b5ec473d69a6da4e4e33e7d126b2ccc9eef4c0dbf04b7e277c63020067fed66cb30e4b00a32c9384feca204054e142835710c70be0bd8 +EBUILD symengine-0.3.0-r1.ebuild 2074 SHA256 b59937015985eccb4a6a290febd48e122d4221e81c7cddac485f7a58e6530d13 SHA512 e60602366c3c14046f7aa5131e884663f5fbbdf216b41b8824d0017ef96f7a8c9307bcf6da0eccfec9fcdf06ad3952153142bb5ea10d18bfc1f64230cc27835d WHIRLPOOL e74f349b82c99a63cb6e04bb61a34e1dfb69ae5516c2d59d60bf824b55dbb40031cac51acece285d0e189a0d668dc95d8a0af343f18b903a100f2c381c3c8e49 +MISC metadata.xml 1150 SHA256 963a25e5aa0fe932fbcde62f95f1de5a9324c81bdcdfd0ca91132397a08187e2 SHA512 33f04c5f8b7eaeb25dfe712582fec5cbc6a17a4d2f90c96eea84c43025af0be6eb8f3d6ce4a9904a46e4d36374d651a15e539ebf09f16ba9bfd2c4a61cd7e911 WHIRLPOOL 8a2af9d0f43c6210f91f23cb3f92a51fe91802d2e67437775adbc530aa66d795ef396774e47dda115db4a8e86c26c599b4741af6ab14e549980f07cb9da74c0f diff --git a/sci-libs/symengine/metadata.xml b/sci-libs/symengine/metadata.xml new file mode 100644 index 000000000000..63672cfa6a09 --- /dev/null +++ b/sci-libs/symengine/metadata.xml @@ -0,0 +1,25 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-mathematics@gentoo.org</email> + <name>Gentoo Mathematics Project</name> + </maintainer> + <longdescription> + SymEngine is a standalone fast C++ symbolic manipulation + library. Optional thin wrappers allow usage of the library from R, + Python, Julia, Ruby, Haskell. + </longdescription> + <upstream> + <remote-id type="github">sympy/symengine</remote-id> + </upstream> + <use> + <flag name="arb">Add support for arb (<pkg>sci-mathematics/arb</pkg>)</flag> + <flag name="benchmarks">Build benchmarks</flag> + <flag name="boost">Add support for boost integers(<pkg>dev-libs/boost</pkg>)</flag> + <flag name="flint">Add support for (<pkg>sci-mathematics/flint</pkg>)</flag> + <flag name="llvm">Build with LLVM</flag> + <flag name="mpc">Add support for multiprecision complex arithmetic(<pkg>dev-libs/mpc</pkg>)</flag> + <flag name="mpfr">Add support for multiprecision floating point rouding(<pkg>dev-libs/mpfr</pkg>)</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/symengine/symengine-0.3.0-r1.ebuild b/sci-libs/symengine/symengine-0.3.0-r1.ebuild new file mode 100644 index 000000000000..c493c94e39e8 --- /dev/null +++ b/sci-libs/symengine/symengine-0.3.0-r1.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils flag-o-matic + +DESCRIPTION="Fast symbolic manipulation library, written in C++" +HOMEPAGE="https://github.com/sympy/symengine" +SRC_URI="https://github.com/sympy/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0/0.3" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="arb benchmarks boost debug doc flint llvm mpc mpfr openmp test tcmalloc threads" + +RDEPEND=" + dev-libs/gmp:= + sys-libs/binutils-libs:= + arb? ( sci-mathematics/arb:= ) + boost? ( dev-libs/boost:= ) + mpc? ( dev-libs/mpc:= ) + tcmalloc? ( dev-util/google-perftools ) +" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen[dot] ) +" + +pkg_pretend() { + use openmp && [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp +} + +src_prepare() { + cmake-utils_src_prepare + sed -e "s|DESTINATION doc| DESTINATION share/doc/${PF}/html|" \ + -e "s|/lib|/$(get_libdir)|g" \ + -e "s|lib/|$(get_libdir)/|g" \ + -e "/DESTINATION/s|lib|$(get_libdir)|g" \ + -i CMakeLists.txt symengine/CMakeLists.txt \ + symengine/utilities/teuchos/CMakeLists.txt || die +} + +src_configure() { + # not in portage yet: piranha, ecm + local int_class + if use arb || use flint; then + int_class=flint + elif use mpfr; then + int_class=gmpxx + elif use boost; then + int_class=boostmp + else + int_class=gmp + fi + local mycmakeargs=( + -DARB_INCLUDE_DIR="${EPREFIX}/usr/include" + -DINTEGER_CLASS="${int_class}" + -DBUILD_SHARED_LIBS=ON + -DBUILD_BENCHMARKS="$(usex benchmarks)" + -DBUILD_DOXYGEN="$(usex doc)" + -DBUILD_TESTS="$(usex test)" + -DWITH_ARB="$(usex arb)" + -DWITH_BFD="$(usex debug)" + -DWITH_SYMENGINE_ASSERT="$(usex debug)" + -DWITH_SYMENGINE_THREAD_SAFE="$(usex threads)" + -DWITH_FLINT="$(usex flint)" + -DWITH_OPENMP="$(usex openmp)" + -DWITH_MPFR="$(usex mpfr)" + -DWITH_MPC="$(usex mpc)" + -DWITH_LLVM="$(usex llvm)" + -DWITH_PTHREAD="$(usex threads)" + -DWITH_TCMALLOC="$(usex tcmalloc)" + ) + test-flag-CXX -std=c++11 && append-cxxflags -std=c++11 + CMAKE_BUILD_TYPE=Release cmake-utils_src_configure +} diff --git a/sci-libs/szip/Manifest b/sci-libs/szip/Manifest new file mode 100644 index 000000000000..b05972905a59 --- /dev/null +++ b/sci-libs/szip/Manifest @@ -0,0 +1,6 @@ +DIST szip-2.1.tar.gz 383219 SHA256 9c03d79597f4c25a4a5fc10dbe912e4112394f805f8d9af52fc5c9fe15dbbdc7 SHA512 bb7e0af6dfaaaaa85013ef52e6901d5b7b6159795338d285c2e843bd2879230a6397fb072662fdfeda5690981db4e9af94782c057bf993f92516d92a8934cb75 WHIRLPOOL 1bf2ab42195da950624a751f17d5398aeea8589dff139f377cc1f0bbfdf59b5a2da6a3adaf1641a5a0aeded1c67651aead1c338517c36faa5877d9775b795a24 +EBUILD szip-2.1-r2.ebuild 719 SHA256 268ae77e224c12d08632ab2c63efe60a05a629cb0bc68c55e883f7554819eece SHA512 1fc06ec85db407b0efc297ac504b79984f3164d66be465657be209247326a0f077dd671f76ba547bd62806109ebe83f870e6206103ef056cb896413ee2ff1b0b WHIRLPOOL 63ef852f76e7260f2b761e27a56f261702898efdd7199bc019efe8fd8c4f458946d214bfe36b8873485afaeb1910cabcb95d4d6638540f91fea093fb5dd6b746 +EBUILD szip-2.1.ebuild 649 SHA256 c61741db74187e4e5de1d0d6727742685ce4a6fbfb2b78c3cbea4a680cf0f990 SHA512 fbcaffb62c0827464c812a577e9b828f54f7cab5de9bce1d189a4deb5eab0980142b3d48b20ff263cd40a0c07dc0baaa89d608fa331e2bc71a89532618140890 WHIRLPOOL 4aa66f6128bb812c2f0c03a1d6d64e430ab751e3423cd661bf1e7943f5b0a5e44f657f07d86813a81c76ccc1a412a90c770e309f256c7ab8f0792eccddb6174d +MISC ChangeLog 2794 SHA256 15041c95030b7bd117ebf611c7c24931a146ef40efee97e482ca66ece06d4227 SHA512 86da3d66a6c7e8196add7c3089c388d59fd9df30f53eb577a7f952b44ecd36f8f1c99bf97613b6a7e819a31ccad6075c271577bcb7e4cd2378c062c0160687ac WHIRLPOOL bfd940d52bbfe0f74a299e8a17725ced1b1d35768f559b6ac45c0dba338a00f5bfd18434b67043acfaa153c699a68b2b146b4c18fe3907925aef079b6b8753aa +MISC ChangeLog-2015 3609 SHA256 e9cb4ca1c85fc6c32b7ce5a00e53a9c810a408166d15a020c274d8f14f8d95b4 SHA512 4ac58e1feb478526684254a46d6906df570d322983fb17e8618ec831433b4ed1db3ae8678d13511708dac13301b45d63ed574c965f327e7f464d3fc1424d0fa0 WHIRLPOOL 182067a49d89eb2086ebf98bd8268c8d1fe6266cb8b7c285b428a00fbc6e398c12dacf9e74c8ec69e6e742b7bbec0a7a027881c83a5dbc30fc6121fa435496eb +MISC metadata.xml 759 SHA256 12022ba7930ca9de2b1aa1add94e809cc4d12a3275a62aea9a576c1be36f091d SHA512 8105dd780203cbd43cbeb175215fe2ea57311cb23d378bd6265de24772040d88d59b07c4af4faa6a60f5812e3bad9efae7d3777732ed123e284ba0c068a653c9 WHIRLPOOL 760f354d7f8b85c2197cf8e7d906867b833a5e1f4107b7a7305f2c228da3b0d629182c58100e99ebc446938512aa8894f94d9f0c7ec6fc85ab537c6a028d58d2 diff --git a/sci-libs/szip/metadata.xml b/sci-libs/szip/metadata.xml new file mode 100644 index 000000000000..3e97c9268b83 --- /dev/null +++ b/sci-libs/szip/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The Consultative Committee on Space Data Systems (CCSDS) has adopted + the extended-Rice algorithm for international standards for space + applications. Szip is reported to provide fast and effective + compression, specifically for the EOS data generated by the NASA + Earth Observatory System (EOS). It was originally developed at + University of New Mexico (UNM) and integrated with HDF4 by UNM + researchers and developers. It can be used for HDF 5 as well. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/szip/szip-2.1-r2.ebuild b/sci-libs/szip/szip-2.1-r2.ebuild new file mode 100644 index 000000000000..86f9bc1b2151 --- /dev/null +++ b/sci-libs/szip/szip-2.1-r2.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils + +DESCRIPTION="Extended-Rice lossless compression algorithm implementation" +HOMEPAGE="http://www.hdfgroup.org/doc_resource/SZIP/" +SRC_URI="ftp://ftp.hdfgroup.org/lib-external/${PN}/${PV}/src/${P}.tar.gz" +LICENSE="szip" + +SLOT="0/2" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux" + +IUSE="static-libs" +RDEPEND="!sci-libs/libaec[szip]" +DEPEND="" + +DOCS=( RELEASE.txt HISTORY.txt examples/example.c ) + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + use static-libs || prune_libtool_files --all +} diff --git a/sci-libs/szip/szip-2.1.ebuild b/sci-libs/szip/szip-2.1.ebuild new file mode 100644 index 000000000000..d9bbe95a2464 --- /dev/null +++ b/sci-libs/szip/szip-2.1.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit eutils + +DESCRIPTION="Implementation of the extended-Rice lossless compression algorithm" +HOMEPAGE="http://www.hdfgroup.org/doc_resource/SZIP/" +SRC_URI="ftp://ftp.hdfgroup.org/lib-external/${PN}/${PV}/src/${P}.tar.gz" +LICENSE="szip" + +SLOT="0" +KEYWORDS="alpha amd64 hppa ia64 ppc ppc64 sparc x86" + +IUSE="" +DEPEND="" +RDEPEND="!sci-libs/libaec" + +src_install() { + emake DESTDIR="${D}" install || die "emake install failed" + dodoc RELEASE.txt HISTORY.txt + insinto /usr/share/doc/${PF}/ + emake -C examples clean || die + doins -r examples +} diff --git a/sci-libs/ta-lib/Manifest b/sci-libs/ta-lib/Manifest new file mode 100644 index 000000000000..d8357205522e --- /dev/null +++ b/sci-libs/ta-lib/Manifest @@ -0,0 +1,6 @@ +AUX ta-lib-0.4.0-asneeded.patch 3304 SHA256 ec37136e33dfecec74ba89759b77bb45bfdabe5ea1514a3f8875da80a9120d16 SHA512 aa43a9cd5382eb43cce2dd64325a36fd88bdae7969c3c191ddbbc7ed726145d7cd1cca17196093c7b4af63a95d3a118d6f2e93ff5d021105091056a325042123 WHIRLPOOL 7d8a46da426f376e2a909efcd34bbe76c8e1d6d4b1dac00007b2b662eab4755fef676b7e095177b2b3ca9c9782dae66415b9cfbf6fa4157bf2cb2dd5fd261dff +DIST ta-lib-0.4.0-src.tar.gz 1330299 SHA256 9ff41efcb1c011a4b4b6dfc91610b06e39b1d7973ed5d4dee55029a0ac4dc651 SHA512 d7ae2acd830cd23b58bded8a90759edfabc73923fbed3cc09501c121cc937caf728c29678f456c2dc7e72fabb52166bccc19ab51ab1131c7d8d35c201c94ed4c WHIRLPOOL e939c2f758502b6056e61d7bbd248a10ed7cfe17ff1766ba0bf77270a9a54c0411da1f15f23b4f82a253a54745286a5f36e5867c725033b5f210feb7dd4a1c72 +EBUILD ta-lib-0.4.0.ebuild 661 SHA256 39f18cdc8f92952973f437ce617368a6f6d3643e1fdc442775bcbb3f09a179af SHA512 018cc046768f40cdc719c494168abb7379da2d4b7b0f4abc3d14ad0003d4a50358a5bc9baf40497e6a6a3e28031db09f1372deeb4af02cc98777bf0c79852a27 WHIRLPOOL 1282033b660e9a63d4341fa019e1a83fd7eb322607e769629c6ec9101912233ae3c9304d0adf04fa7f8e00657469afd6187cc03f03700a6e64f42a058a5388e6 +MISC ChangeLog 2555 SHA256 76c241e056572347b09c93527d854b4031ece799fd81ff09ae0b13d7caa4cace SHA512 b2759dd9fc748d6f3cb17e6a9eb82b2107af2cef30d861e5db8cf69d59304a62764125e6451bb2f1674a43523e2771135f59cb61e9d1b93870fa7332e92766dd WHIRLPOOL 9b259b5dcdbd86fdb8935734dc72ce26fca740e157aa7a498ff14fd63c91f925fab99c4e2bafe814c3fe5ddc3b3b5602f56b49c56b6a9b7853afcc5f7ee6b25d +MISC ChangeLog-2015 1433 SHA256 02f6f9e8ec933c5e44cd8a0bbbbc5b1f2a7035ca33151d2e33542359503275b1 SHA512 d44ace198f71ef08b00a5118226fc56c06c2808e695eb363d13ff988a4e9e91cf44a03017821733b8ffa0c8b4cf7405884d39fe86e525d304a8a229bcc816aff WHIRLPOOL 0d5287ef5a1e89c72a046c93fc6b9063c41b602b7010d380cdd6b1a3f20a3a1208a9fc22dff0cbbaacbd2ad62cb8168fc248fd62c085d8090a9168d63565ccbe +MISC metadata.xml 243 SHA256 c10b11196a9b4adc5b802d68627bcbac0a97e65551413892dfe3b37726e0a244 SHA512 7ce6628e1ef9623673a4981aaaca3a1a3e9f030b6826929de1307bc1ea6d18b31bb5f14e8aefa60a6ecf34c874b4cb18ba8d64e869e151cf750b79e76e394bcf WHIRLPOOL a1ad51bb2a7ebabce86ea08039a05e6ea954cbe5fd287b3c9f5e5032caa7418a4cf0046c7bbafe513b7df74734e9f092ccdacd08892cd2f3ece62c44043aeb85 diff --git a/sci-libs/ta-lib/files/ta-lib-0.4.0-asneeded.patch b/sci-libs/ta-lib/files/ta-lib-0.4.0-asneeded.patch new file mode 100644 index 000000000000..10183938e667 --- /dev/null +++ b/sci-libs/ta-lib/files/ta-lib-0.4.0-asneeded.patch @@ -0,0 +1,83 @@ + src/Makefile.am | 2 +- + src/Makefile.in | 2 +- + src/ta_abstract/Makefile.am | 8 ++++---- + src/ta_common/Makefile.am | 6 +++--- + src/ta_func/Makefile.am | 6 +++--- + 5 files changed, 12 insertions(+), 12 deletions(-) + +diff --git a/src/Makefile.am b/src/Makefile.am +index 12bc5b6..b1a0c6b 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -8,7 +8,7 @@ libta_lib_la_SOURCES = + libta_lib_la_LIBADD = \ + ta_abstract/libta_abstract.la \ + ta_func/libta_func.la \ +- ta_common/libta_common.la ++ ta_common/libta_common.la -lm + + libta_lib_la_LDFLAGS = -version-info $(TALIB_LIBRARY_VERSION) + +diff --git a/src/Makefile.in b/src/Makefile.in +index 489b44a..ef1f506 100644 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -56,7 +56,7 @@ am_libta_lib_la_OBJECTS = + libta_lib_la_OBJECTS = $(am_libta_lib_la_OBJECTS) + libta_lib_la_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ + $(LIBTOOLFLAGS) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ +- $(libta_lib_la_LDFLAGS) $(LDFLAGS) -o $@ ++ $(libta_lib_la_LDFLAGS) $(LDFLAGS) -lm -o $@ + DEFAULT_INCLUDES = -I. -I$(top_builddir)/include@am__isrc@ + COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ + $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +diff --git a/src/ta_abstract/Makefile.am b/src/ta_abstract/Makefile.am +index cba69bb..4411234 100644 +--- a/src/ta_abstract/Makefile.am ++++ b/src/ta_abstract/Makefile.am +@@ -38,12 +38,12 @@ libta_abstract_gc_la_SOURCES = $(libta_abstract_la_SOURCES) + libta_abstract_la_LDFLAGS = -version-info $(TALIB_LIBRARY_VERSION) + libta_abstract_gc_la_LDFLAGS = $(libta_abstract_la_LDFLAGS) + +-libta_abstract_la_CPPFLAGS = -I../ta_common/ -Iframes/ ++libta_abstract_la_CPPFLAGS = -I$(top_srcdir)/src/ta_common/ -Iframes/ + + # The 'gc' version is a minimal version used to just to compile gen_code + libta_abstract_gc_la_CPPFLAGS = -DTA_GEN_CODE $(libta_abstract_la_CPPFLAGS) + + libta_abstractdir=$(includedir)/ta-lib/ +-libta_abstract_HEADERS = ../../include/ta_defs.h \ +- ../../include/ta_libc.h \ +- ../../include/ta_abstract.h ++libta_abstract_HEADERS = $(top_srcdir)/include/ta_defs.h \ ++ $(top_srcdir)/include/ta_libc.h \ ++ $(top_srcdir)/include/ta_abstract.h +diff --git a/src/ta_common/Makefile.am b/src/ta_common/Makefile.am +index 9454490..3e59bd8 100644 +--- a/src/ta_common/Makefile.am ++++ b/src/ta_common/Makefile.am +@@ -9,7 +9,7 @@ libta_common_la_SOURCES = ta_global.c \ + libta_common_la_LDFLAGS = -version-info $(TALIB_LIBRARY_VERSION) + + libta_commondir=$(includedir)/ta-lib/ +-libta_common_HEADERS = ../../include/ta_defs.h \ +- ../../include/ta_libc.h \ +- ../../include/ta_common.h ++libta_common_HEADERS = $(top_builddir)/include/ta_defs.h \ ++ $(top_builddir)/include/ta_libc.h \ ++ $(top_builddir)/include/ta_common.h + +diff --git a/src/ta_func/Makefile.am b/src/ta_func/Makefile.am +index 030a516..299baf9 100644 +--- a/src/ta_func/Makefile.am ++++ b/src/ta_func/Makefile.am +@@ -165,6 +165,6 @@ libta_func_la_SOURCES = ta_utility.c \ + libta_func_la_LDFLAGS = -version-info $(TALIB_LIBRARY_VERSION) + + libta_funcdir=$(includedir)/ta-lib/ +-libta_func_HEADERS = ../../include/ta_defs.h \ +- ../../include/ta_libc.h \ +- ../../include/ta_func.h ++libta_func_HEADERS = $(top_builddir)/include/ta_defs.h \ ++ $(top_builddir)/include/ta_libc.h \ ++ $(top_builddir)/include/ta_func.h diff --git a/sci-libs/ta-lib/metadata.xml b/sci-libs/ta-lib/metadata.xml new file mode 100644 index 000000000000..75af09f93bb4 --- /dev/null +++ b/sci-libs/ta-lib/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <!-- maintainer-needed --> + <upstream> + <remote-id type="sourceforge">ta-lib</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/ta-lib/ta-lib-0.4.0.ebuild b/sci-libs/ta-lib/ta-lib-0.4.0.ebuild new file mode 100644 index 000000000000..99cb7258bb33 --- /dev/null +++ b/sci-libs/ta-lib/ta-lib-0.4.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="Technical Analysis Library for analyzing financial markets trends" +HOMEPAGE="http://www.ta-lib.org/" +SRC_URI="mirror://sourceforge/ta-lib/${P}-src.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +S="${WORKDIR}"/${PN} + +PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +src_test() { + ewarn "Note: this testsuite will fail without an active internet connection." + "${S}"/src/tools/ta_regtest/ta_regtest || die "Failed testsuite." +} diff --git a/sci-libs/tamu_anova/Manifest b/sci-libs/tamu_anova/Manifest new file mode 100644 index 000000000000..6e8c3b0036f9 --- /dev/null +++ b/sci-libs/tamu_anova/Manifest @@ -0,0 +1,7 @@ +AUX 0.2.1-gentoo.patch 913 SHA256 74ddea2e1aa8c7e6bb8bf4719a7e5ba9a74e8ad763663b9941b52c9f012c4f57 SHA512 898ce24ac70b51d865f5e304c17fd663c254c971dea144cf9a1eccce7e6b75e5e60a84dd0e653915aa52e87dcf1687efed542a3b11aff27287ce3efe2ce0b81b WHIRLPOOL de32042743d27c9d591bbbbb068e09f99bfba734f81d1ddebc6fac9ccf65c621fa1ff4ea6dc2b656e368191bccd123ebbe13e653e790d95dd4632a31a3801b13 +AUX tamu_anova-0.2.1-texinfo5.1.patch 1414 SHA256 4be5f9cdc9fd4ae408e51d56e4620672326c49c91cd14af6f55a20d2531b18bf SHA512 f221b19b238f6df374a3d256c7ab594c7e00f0c3c2959c88eeeb8ff1bc8dd7cb22ba60b3a0456f2da834242129a688b2feff781668ec920dff5779d31c31faa7 WHIRLPOOL e02e5868d51016f541f965919f946ab8dd7f22e2fd0c7125d5f574cf8836037a79bf72575b8816a6ffa51f7c1522a73b1c658eb1c3f0edd4591f22b0745b391f +DIST tamu_anova-0.2.1.tar.gz 220803 SHA256 2583bd33bb9243709a5f44ad07677a8362bcca8816bd19f452eb4e3e375c213a SHA512 e4e65997d8ca57b5ad1c0001abbe41652fa86f8b8e9e00aa53d8079062e028baee67436408997d96d87c85801c48e1c87f40dfe291d387cd94dcefd61a52c477 WHIRLPOOL 56367f9fb331ff4502850ecafa99b331f8298859aa7dbf5a30c5d7ddbc5a900692c2fd454493de5601f60f0b9545c3c3fed04869e85667859cc84ba1fa8e345e +EBUILD tamu_anova-0.2.1.ebuild 611 SHA256 b501c4ab37c80b5b5dfbad48e78872a01280fc723e0e2f31d23807af5636e827 SHA512 d0b9ed81a39abfbaac75c3be51eed156c3e5fc7305047cd915a043e294a20e006726ead448299c0fbd6de299655ba686df8b5f9dcc6e7e6fd9feb221c9dec5bd WHIRLPOOL 461a7e574a8b4a14c91ea8c556855857cacd015f4e87a65a09d052f802144cb9b1a817c2daeaa938d605f5372054a3ad64d1ef33b41cdf5ac81dd15136601800 +MISC ChangeLog 2647 SHA256 77f17a98639bad5ee93c5384ce5a6585ddc5c71a4931e3aa4b9ff695b9eae0b4 SHA512 68e739c22511ec1922731e33751a7e7b6e6bf8f7e2aae1b098137c3bc1d9e46dd1a7c17956fa4fd4825f617d88b13f959436e5febdf1e09f4f223a7ba70c84c9 WHIRLPOOL e1227e96bafb99a1a97128342db8ebcf1417700b2bff50fdc388c8e05893bbfbfaa2f7f941f90f6dfa864b5d8ff61041ca7ff1db5e3288b3d69be34b212ebf54 +MISC ChangeLog-2015 912 SHA256 6901d00a47fc83fdb6122c12a6adf21661bae13d433918e799a95b9ed7bb093d SHA512 bf34873f2489e07259d4176f7becdaa609c58a6ffe58257924000aa39cd7779ca774d7afdcc30467131ef0b09fcb25322217615d393aac4abce84283dfc1d4f3 WHIRLPOOL 18dae3dff3ac27f7e5369b9e4cad1e07ab783055834aead888a2efd0786b5b454820011d65a3ceb453e03795c1bf8485627dd353376d851823769dcb5a1a75dc +MISC metadata.xml 259 SHA256 bbfbeb80ffccffa8e7f837d2c93e994bbe024d565ae3a31d30c6646e80a684c8 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 WHIRLPOOL 75b8dd1a97dde63f9cc9f73b5951eaf54579460763ef7cbe6f3a9a0739070601d762152ea00df8b476b80e92e5c29b611a494bac5ab747298942530cabe0ee84 diff --git a/sci-libs/tamu_anova/files/0.2.1-gentoo.patch b/sci-libs/tamu_anova/files/0.2.1-gentoo.patch new file mode 100644 index 000000000000..4d4c1f4a0af1 --- /dev/null +++ b/sci-libs/tamu_anova/files/0.2.1-gentoo.patch @@ -0,0 +1,35 @@ +diff --git a/Makefile.am b/Makefile.am +index 6b11b79..ba5fac3 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,11 +1,11 @@ +-inst_LIBRARIES = libtamuanova.a ++lib_LTLIBRARIES = libtamuanova.la + pkginclude_HEADERS = tamu_anova.h +-libtamuanova_a_SOURCES = anova_1.c anova_2.c +-instdir = /usr/lib/ ++libtamuanova_la_SOURCES = anova_1.c anova_2.c ++libtamuanova_la_LIBADD = $(GSL_LIBS) + + TESTS = $(check_PROGRAMS) + check_PROGRAMS = test +-test_LDADD = libtamuanova.a -lgsl -lgslcblas -lm ++test_LDADD = libtamuanova.la $(GSL_LIBS) -lm + test_SOURCES = test.c + + CLEANFILES = test.dat +diff --git a/configure.ac b/configure.ac +index 7008594..1f161c3 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -7,6 +7,10 @@ AM_INIT_AUTOMAKE([gnu no-dependencies]) + AC_CONFIG_HEADER([config.h]) + + AC_PROG_MAKE_SET ++AC_PROG_LIBTOOL ++PKG_PROG_PKG_CONFIG ++ ++PKG_CHECK_MODULES(GSL, [ gsl ]) + + dnl Check for which system. + AC_CANONICAL_HOST diff --git a/sci-libs/tamu_anova/files/tamu_anova-0.2.1-texinfo5.1.patch b/sci-libs/tamu_anova/files/tamu_anova-0.2.1-texinfo5.1.patch new file mode 100644 index 000000000000..f0c0570fc46d --- /dev/null +++ b/sci-libs/tamu_anova/files/tamu_anova-0.2.1-texinfo5.1.patch @@ -0,0 +1,39 @@ + fdl.texi | 2 +- + tamu_anova.texi | 4 ++-- + 2 files changed, 3 insertions(+), 3 deletions(-) + +diff --git a/fdl.texi b/fdl.texi +index 006dec7..6d8114a 100644 +--- a/fdl.texi ++++ b/fdl.texi +@@ -403,7 +403,7 @@ number of this License, you may choose any version ever published (not + as a draft) by the Free Software Foundation. + @end enumerate + +-@unnumberedsubsec ADDENDUM: How to use this License for your documents ++@unnumberedsec ADDENDUM: How to use this License for your documents + + To use this License in a document you have written, include a copy of + the License in the document and put the following copyright and +diff --git a/tamu_anova.texi b/tamu_anova.texi +index 8d4cd5b..5fba0e5 100644 +--- a/tamu_anova.texi ++++ b/tamu_anova.texi +@@ -177,7 +177,7 @@ that the first effect is the fixed effect, while the second effect is the random + @section Structures + @b{One way table} + +-@deftypefn {struct tamu_anova_table} ++@deftypefn {Structures} struct tamu_anova_table + @code{struct tamu_anova_table@{ + long df_tr, df_err, df_tot; + double SSTr, SSE, SST, MSTr, MSE, F, p;@}; +@@ -185,7 +185,7 @@ that the first effect is the fixed effect, while the second effect is the random + @end deftypefn + @* + @b{Two way table} +-@deftypefn {struct tamu_anova_table_twoway} ++@deftypefn {Structures} struct tamu_anova_table_twoway + @code{struct tamu_anova_table_twoway @{ + long + dfA, dfB, dfAB, dfT, dfE; diff --git a/sci-libs/tamu_anova/metadata.xml b/sci-libs/tamu_anova/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-libs/tamu_anova/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/tamu_anova/tamu_anova-0.2.1.ebuild b/sci-libs/tamu_anova/tamu_anova-0.2.1.ebuild new file mode 100644 index 000000000000..5ae7872d14fe --- /dev/null +++ b/sci-libs/tamu_anova/tamu_anova-0.2.1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils + +DESCRIPTION="ANOVA Extensions to the GNU Scientific Library" +HOMEPAGE="http://www.stat.tamu.edu/~aredd/tamuanova/" +SRC_URI="http://www.stat.tamu.edu/~aredd/tamuanova/${PN}-0.2.tar.gz -> ${P}.tar.gz" + +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +LICENSE="GPL-2" +IUSE="static-libs" + +RDEPEND="sci-libs/gsl" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${PN}-0.2 + +PATCHES=( + "${FILESDIR}"/${PV}-gentoo.patch + "${FILESDIR}"/${P}-texinfo5.1.patch + ) diff --git a/sci-libs/taucs/Manifest b/sci-libs/taucs/Manifest new file mode 100644 index 000000000000..a8e0b7044b8b --- /dev/null +++ b/sci-libs/taucs/Manifest @@ -0,0 +1,6 @@ +AUX taucs-2.2-no-test-cilk.patch 816 SHA256 7803d2d35b4a4648c0b6856ada62175551c6db08fa3e7801565f887994cc6211 SHA512 04b580315d600eb68d908e10aaf5c600e03d7ec51437cf814dad6eed1eecd09e7b9c1d770e8c9c13e6ec268202c3335805dc32a68b9e5164cf038cd31acbcc95 WHIRLPOOL 5461d2b6e6dd39435541c8dfb2db633b9ba2d0301ce6626a203a02bb4a20dd606d8144548252627d5b87d1e60c34f56afd689dc8ed5f9ee66ba90f62ef82eabf +DIST taucs-2.2.tgz 1573863 SHA256 fc13dae767db5e9035b1ce63036a16d3a260aad784f461e073f1150a078a77e4 SHA512 d8652de2da343dfd19c4278ac99313bcb577d976decdd3bd3875f0c9576832605b787feaef916eb4e82f22907c8bd029125c2ae56c827639e4d535ad62f20fcf WHIRLPOOL 6c789d98e0919a0e9fb4e7f002e16c8af8006ede9d25fc4a8416c5f7dd3f4bfcce7159edac6febba975d286c87d5564e551df9aa495ce253f450631210c499ab +EBUILD taucs-2.2.ebuild 2351 SHA256 a2e15451652f4a20d828c403df6de1275a7200dd90ebb047aea9b55b74581792 SHA512 eb276dd7eded2f3b4df30cfe8734ebb7f75013d6e759ec7a299890739a2dafdca98e82ee74b32f873c57540988ad55acb8a733e4dfc24d12d05e04b15089301b WHIRLPOOL cb868841270daf805f00809c8dd6bd273d58fd45a1f7b6ac32bd52b56bce0ef897d86660d0c0d4888cdd598e03fb4cd9e8a5998fd05346415cdc3af8286757a0 +MISC ChangeLog 2454 SHA256 b3bf9ec52d12c431abbd3579f3de5c795f3102a95255c31042f1c0df123a6ca2 SHA512 2db76e976bee2bbd94460049a1e67b1ee977f2a46e723391d99af045d1eda281d11c8f0f49e8fc9623b55581101e901d8ccc65b9c914e54ecd64d572f7f5374c WHIRLPOOL 1738df7c3eee0ba1d7d656759dff0296b462369926ecab57296b44246c85966394d5059be90cf7d3f4dca00db976168eb3a571841441e4df8ddeb5581089f91d +MISC ChangeLog-2015 1720 SHA256 2ede54bcbf0a691bf5a492b040a48e12e525d4e8d7f38e982dd01137d3cad7da SHA512 2412a607adb11a9f278b3777a7ae081a75c11092e8cba108aafb1e71ec8501a570b06cb9f96cad4a6cbea47aa7634a9b09c733875d4f64db40ac2176d4a7966c WHIRLPOOL 1be9129d57aa40bab3d3516bb655d4ef96abf3b27942ac7737b631c92e1579b02cd51bdb8cbf05367f3031bbb9a7f736b605b464b827b42f1a30b56f3dddd6d5 +MISC metadata.xml 1175 SHA256 231a382f04da00ce658ae3703480be7a42713d33cb3d6493701906cd8c65c01f SHA512 8f768378475ce4364a51fbef44315a2c34cedf4db9aae4cbbebc5e487eb193693320ae56e3464b7a14f38adec41ef5e06d940890a5b55c1ef541acaf95b4e693 WHIRLPOOL 52ae0c9262fb05cb7002bde8a3f51557e4877766834fd1051e3a71f7fe3c0064ec2fb73271e8105b9c3c9a663d2dd42c7d192b9624f034287e9f2ff1e42e1550 diff --git a/sci-libs/taucs/files/taucs-2.2-no-test-cilk.patch b/sci-libs/taucs/files/taucs-2.2-no-test-cilk.patch new file mode 100644 index 000000000000..68ecc3bf94b6 --- /dev/null +++ b/sci-libs/taucs/files/taucs-2.2-no-test-cilk.patch @@ -0,0 +1,20 @@ +--- testscript.orig 2012-07-06 19:42:51.000000000 +0100 ++++ testscript 2012-07-06 19:43:17.000000000 +0100 +@@ -12,17 +12,6 @@ + ulimit -s >> testscript.log + echo '==============' >> testscript.log + echo =============== >> testscript.log +-echo = test_cilk_snmf = >> testscript.log +-. ./configure in=progs/test_cilk_snmf.c $* +-echo last conf is $TAUCS_LASTCONF >> testscript.log +-make -f build/${TAUCS_LASTCONF}/makefile +-if bin/${TAUCS_LASTCONF}/test_cilk_snmf >> testscript.log ; then +-echo = TEST PASSED test_cilk_snmf >> testscript.log +-else +-echo = TEST FAILED test_cilk_snmf >> testscript.log +-fi +-echo =============== >> testscript.log +-echo =============== >> testscript.log + echo = test_complex = >> testscript.log + . ./configure in=progs/test_complex.c $* + echo last conf is $TAUCS_LASTCONF >> testscript.log diff --git a/sci-libs/taucs/metadata.xml b/sci-libs/taucs/metadata.xml new file mode 100644 index 000000000000..b1b1d0e9c3fd --- /dev/null +++ b/sci-libs/taucs/metadata.xml @@ -0,0 +1,32 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + TAUCS is a C library of sparse linear solvers. + The current version of the library (1.0) includes the following + functionality: + + * Multifrontal Supernodal Cholesky Factorization. + * Left-Looking Supernodal Cholesky Factorization. + * Drop-Tolerance Incomplete-Cholesky Factorization. + * Out-of-Core, Left-Looking Supernodal Sparse Cholesky Factorization. + * Out-of-Core Sparse LU with Partial Pivoting Factor and Solve. + * Ordering Codes and Interfaces to Existing Ordering Codes. + * Multilevel-Support-Graph Preconditioners. + * Matrix Operations. + * Matrix Input/Output. + * Matrix Generators. + * Iterative Solvers. + * Vaidya's Preconditioners. + * Recursive Vaidya's Preconditioners. + * Multilevel-Support-Graph Preconditioners. + * Utility Routines +</longdescription> + <use> + <flag name="cilk">Enable multithreading using <pkg>dev-lang/cilk</pkg></flag> + </use> +</pkgmetadata> diff --git a/sci-libs/taucs/taucs-2.2.ebuild b/sci-libs/taucs/taucs-2.2.ebuild new file mode 100644 index 000000000000..c3da7a074eb5 --- /dev/null +++ b/sci-libs/taucs/taucs-2.2.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs + +DESCRIPTION="C library of sparse linear solvers" +HOMEPAGE="http://www.tau.ac.il/~stoledo/taucs/" +SRC_URI="http://www.tau.ac.il/~stoledo/${PN}/${PV}/${PN}.tgz -> ${P}.tgz" + +SLOT="0" +LICENSE="LGPL-2.1" +IUSE="cilk doc static-libs" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + virtual/blas + virtual/lapack + || ( sci-libs/metis sci-libs/parmetis ) + cilk? ( dev-lang/cilk )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}" + +src_prepare() { + # test with cilk has memory leaks + epatch "${FILESDIR}"/${P}-no-test-cilk.patch +} + +src_configure() { + cat > config/linux_shared.mk <<-EOF + FC=$(tc-getFC) + CC=$(tc-getCC) + LD=$(tc-getFC) + CFLAGS=${CFLAGS} -fPIC + FFLAGS=${FFLAGS} -fPIC + LDFLAGS=${LDFLAGS} -fPIC + LIBBLAS=$($(tc-getPKG_CONFIG) --libs blas) + LIBLAPACK=$($(tc-getPKG_CONFIG) --libs lapack) + LIBF77= + EOF + + echo "LIBMETIS=$($(tc-getPKG_CONFIG) --libs metis)" >> config/linux_shared.mk + # no cat <<EOF because -o has a trailing space + if use cilk; then + echo "CILKC=cilkc" >> config/linux_shared.mk + echo "CILKFLAGS=-O2 -I${EPREFIX}/usr/include/cilk -fPIC" >> config/linux_shared.mk + echo "CILKOUTFLG=-o " >> config/linux_shared.mk + fi + sed -e 's/ -fPIC//g' \ + config/linux_shared.mk \ + > config/linux_static.mk || die +} + +src_compile() { + # not autotools configure + if use static-libs; then + ./configure variant=_static || die + emake + fi + ./configure variant=_shared || die + emake + + cd lib/linux_shared + $(tc-getFC) ${LDFLAGS} -shared -Wl,-soname=libtaucs.so.1 \ + -Wl,--whole-archive libtaucs.a -Wl,--no-whole-archive \ + $($(tc-getPKG_CONFIG) --libs blas lapack metis) \ + -o libtaucs.so.1.0.0 \ + || die "shared lib linking failed" +} + +src_test() { + LD_LIBRARY_PATH=lib/linux_shared \ + ./testscript variant=_shared || die "compile test failed" + if grep -q FAILED testscript.log; then + eerror "Test failed. See ${S}/testscript.log" + die "test failed" + fi +} + +src_install() { + use static-libs && dolib.a lib/linux_static/libtaucs.a + ln -s libtaucs.so.1.0.0 lib/linux_shared/libtaucs.so.1 + ln -s libtaucs.so.1 lib/linux_shared/libtaucs.so + dolib.so lib/linux_shared/libtaucs.so* + + insinto /usr/include + doins build/*/*.h src/*.h + + use doc && dodoc doc/*.pdf +} diff --git a/sci-libs/tnt/Manifest b/sci-libs/tnt/Manifest new file mode 100644 index 000000000000..947e5f747af2 --- /dev/null +++ b/sci-libs/tnt/Manifest @@ -0,0 +1,8 @@ +DIST tnt120doc.zip 115063 SHA256 a3ca1327815c79cf9c12d432120d2cb2100748c18aac55e58338b8b8e56116c8 SHA512 c18677ea319bb5485b91c4bcaa09a26bc00a83f0d41b6e1028e57d4924a4524fb7a818169e591c04d71eb03787fc8e4895d76b49721ae8efa4309e3a6be19385 WHIRLPOOL 5add455340f0e77d6981414c73a416e01c467aa924e4e7fab1aeae7508feac7f5f72494308d3c93ed6307659eb8208b4e905859bd258b48c549a7d74eec3d582 +DIST tnt126.zip 28784 SHA256 93c7cdd116a6faeb679890a52d5b513055388c7faaac74beea570f8f2edbd7e4 SHA512 09e4c27cdd0619b25c02dfed6ab8a2f121d002949dee4d1303968df4688196395871ad2ade9e4010cef72f9c6b5c9c02888566d44454949121ad3094e06651f6 WHIRLPOOL d26339211e34f13a020e692179fa0fa64f0405426e021ab8233f9764f5c42e03f713b76c18f57e44a3ab641f2c37927328800518b5aae16aca45ab67b08937d4 +DIST tnt_3_0_12.zip 50166 SHA256 479609bbc249e91c00392597fc48387fed8431471615c02826a8a0545673f3af SHA512 3be00d37880ffc191022db13993c3946e913e92409cef1ff5f53b74cab5ea09782d131056d89bcbd0990939967b5d93ebe93e8a7db956be2fb9e8a7356dafbfd WHIRLPOOL 10050d4eb1869e74779bc3aeee0000c1847e89cbb42f480fc479c280657d734c892429245d5ff271785dd656778c2c3bc0a762b9c92b137f60bd5ea6c094a89f +EBUILD tnt-1.2.6.ebuild 635 SHA256 a1304bff2b6570da79d6a02bb226b81bb01b553e146d6586d48d26cf3733ef0b SHA512 fd35902adf25e42f09207559fbc1bebf415b609130d63adcc71ef9e2dcc69fb3fe8a034dc3cafcc76dbf07d15125ab0cc79c64785795f7ec4c141dcbff7e5186 WHIRLPOOL 6a5f35e0c3e58e3e525ac9f3be2d8fc8549c8995bdf0132eb7e2df9dd09e9e89767469a4cd130c2564913b85cb117faff9f0951eaf9940e1da5dd21375a4f695 +EBUILD tnt-3.0.12.ebuild 548 SHA256 f7fdaecaaf886d1aed2b0eae433e58a81adbf37fbe4a296e7768860bce6ac451 SHA512 10300c5eb64ac9603a2aee519d2542f7ad7236b414c4b2377561baf397a1059bd8fcd03d663191fa4def3a962b998da3b9b24ef34eba466a519319eb4e0c699b WHIRLPOOL 20b139ee724af16ab211f93cba3c9b6c0943cf3fad5e304d9e4f64b77057ea410614b70ebf66cc972417ea5367123e85a460be46f71cb9b28ba5dfc1beea9e41 +MISC ChangeLog 2461 SHA256 7ddcac4ca9329fd75913c9e3602f88bb698c0a7b465ded1a699a4b80e6f587bd SHA512 aa66a90efac12103978ff9a7f404ad8496218cd4bf4cfd89610059ebeace3e3a7f92ba49ff054d5eeb92d03b3763459823f9f33b2c3382b042b3f9e88b541ef0 WHIRLPOOL 1fb3d1aaa3c667347baf4a77b4c504c739682b3d0bb84212241c29a1b195c5909849ef53b06f0715584dc8b17182a821efe1b32f88a8b08b64b2074ab1d787b2 +MISC ChangeLog-2015 935 SHA256 d12b7c205c3410e348775be9470d7e32a7ef2f78fc5554d2b36769a89fc0ed24 SHA512 c12d29c4e673768751eee8db1fa72ae5d524c24399a290db2fd6dcbcded720507c4fbf9f5fb3db44fa68da6a1d7f7a97d177c8989e1380faf71370016b176b98 WHIRLPOOL f1327beea0958ffe37f444d0ee0a2ec26847837e31600edb87705741ad1ccba10f802bbe0ac03254e6c9747d7be6f21afd8a285702c8146392f6eedbbc14a9e9 +MISC metadata.xml 771 SHA256 7b50c1b6aeb083688a8517650d9028dabda886a3c4ef7c5fa6bc478bc3a9b095 SHA512 6a48d29540ae6882d09112d13bf3697bb9310dcc2a848539ea2811e4cc1c4b6af83f52e59ad0e753a037f4d984e2a8a05252c13972d113988037a7fc2f218324 WHIRLPOOL 000bc69c50b14af31acd2d488b1787377718ec596e17cdbebd86ed5f7d1df80fd2ab550e8ea676e3a47e1386670ab414753fa226b43a679f98e1be1868d4f383 diff --git a/sci-libs/tnt/metadata.xml b/sci-libs/tnt/metadata.xml new file mode 100644 index 000000000000..b7be80dbecea --- /dev/null +++ b/sci-libs/tnt/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + The Template Numerical Toolkit (TNT) is a collection of interfaces and + reference implementations of numerical objects useful for scientific + computing in C++. The toolkit defines interfaces for basic data + structures, such as multidimensional arrays and sparse matrices, commonly + used in numerical applications. The goal of this package is to provide + reusable software components that address many of the portability and + maintenance problems with C++ codes. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/tnt/tnt-1.2.6.ebuild b/sci-libs/tnt/tnt-1.2.6.ebuild new file mode 100644 index 000000000000..344b36833caa --- /dev/null +++ b/sci-libs/tnt/tnt-1.2.6.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit versionator + +MYP="${PN}$(replace_all_version_separators '')" +DOCPV=120 + +DESCRIPTION="Template Numerical Toolkit: C++ headers for array and matrices" +HOMEPAGE="http://math.nist.gov/tnt/" +SRC_URI="http://math.nist.gov/tnt/${MYP}.zip + doc? ( http://math.nist.gov/tnt/${PN}${DOCPV}doc.zip )" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="doc" + +DEPEND="app-arch/unzip" +RDEPEND="" + +S="${WORKDIR}" + +src_install() { + insinto /usr/include + doins *.h + use doc && dohtml html/* +} diff --git a/sci-libs/tnt/tnt-3.0.12.ebuild b/sci-libs/tnt/tnt-3.0.12.ebuild new file mode 100644 index 000000000000..2a622ddfa0c2 --- /dev/null +++ b/sci-libs/tnt/tnt-3.0.12.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit versionator + +MYP="${PN}_$(replace_all_version_separators '_')" + +DESCRIPTION="Template Numerical Toolkit: C++ headers for array and matrices" +HOMEPAGE="http://math.nist.gov/tnt/" +SRC_URI="http://math.nist.gov/tnt/${MYP}.zip" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="" + +DEPEND="app-arch/unzip" +RDEPEND="" + +S="${WORKDIR}/${PN}" + +src_install() { + insinto /usr/include + doins *.h +} diff --git a/sci-libs/udunits/Manifest b/sci-libs/udunits/Manifest new file mode 100644 index 000000000000..51935a4fbffd --- /dev/null +++ b/sci-libs/udunits/Manifest @@ -0,0 +1,8 @@ +AUX udunits-2.1.15-autotools.patch 1850 SHA256 c4ea7d50d51cfc19be9719cd62d153f74d29c565e17fd969dc69a64096599972 SHA512 bd4371d0ac9c54d2d4e8a3a0e908b38350bcb729c364de6da93da2fa580abd0f7e48cb3b902a67a9ab84fcff043dad554529cbfb5b26f48eb1f8ba87c43236db WHIRLPOOL 5f110e85ea7433087e546e65dec1ab98748945bbb94191b5e7cff447aa807541a6caf7aa180409b6898c6682a00df46cfb581af210d4d9af70c697bbfb4153fe +DIST udunits-2.1.24.tar.gz 1059344 SHA256 2e5fa4583031b26404a68167b38a11773872486f3c342fdde1e48c52a86e0ed0 SHA512 71af2aa62300dd6a2c58318d75cb9182433a208e28446725334a3a80195ebdae77aebe66e6c4e12b53b675501cf3295de2960d1e8beb1496a547d4eed0cde98e WHIRLPOOL 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b7d12a839a770a53c48195939db5996ffae2487cb479f6ddad859e2bc972dbb1 SHA512 0c5936d30b028be8f4f7e19b6c06000447e90df7f0e3e72c48c61e2c80bb5c49b74e2c8e4a85738ed4c6f3798d86a30ffe3aaf4b02fef9b2f0bd271d6eec800d WHIRLPOOL 1b19cb2de2abf9369b77ffe54c240a7543d71a1625aaf8109cb530c87c752ec2095ff839ef69ef7e8f96b4a907bdbd65f17889db3fc664148c12ffad9fd7635c +MISC ChangeLog 4849 SHA256 db6ca9839471f0b4e1f5a9f7dafee3bc55e141b7f4cd9a5059320689622ad629 SHA512 9198df658064538d633756bd043bae21d38dd84c713992e4ed8b138b7dd78f7ebaeb429eba9487be4a7685426f21294ee2c7e5fb1cbc843c0263aff6859249ff WHIRLPOOL a61346bff8e9bfba115a1e78c0f9d8f0a79aa5c6c9840f936de3828491df74f3da51305122d2dce0b90ee85304149cc02967012910ef781f9c79386d304aeced +MISC ChangeLog-2015 5892 SHA256 e6aa744a9dc71d6cbff9aba65995f66963e1e94d0a4c5b2024246f8127e99352 SHA512 135c54f571cf65ca1b80c84833e1a9a5a7f2168cf6a94fe5de57bab5e0b6f27c644e978ead251f286e86acca7dfc44b09d2bfc741ac24307ed85ce319bc3dd8d WHIRLPOOL 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prog ++ SUBDIRS = lib prog + else + SUBDIRS = lib prog + endif +-DIST_SUBDIRS = expat lib prog test ++DIST_SUBDIRS = lib prog test + info_TEXINFOS = udunits2.texi + udunits2_TEXINFOS = success.texi failure.texi make.texi + EXTRA_DIST = \ +diff --git a/configure.ac b/configure.ac +index 097f6eb..091e673 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -13,7 +13,7 @@ AC_INIT(UDUNITS, 2.1.15, support-udunits@unidata.ucar.edu) + AC_CONFIG_SRCDIR([lib/converter.c]) + AC_CONFIG_AUX_DIR([.]) + AM_INIT_AUTOMAKE([foreign subdir-objects]) +-AC_CONFIG_HEADERS([config.h expat/expat_config.h]) ++AC_CONFIG_HEADERS([config.h]) + + CFLAGS_COVERAGE='' + LIBS_COVERAGE='' +@@ -37,7 +37,7 @@ AC_ARG_ENABLE([debug], + CFLAGS="-g${CFLAGS:+ $CFLAGS}" + debug=true ;; + no) +- CFLAGS="-O${CFLAGS:+ $CFLAGS}" ++ CFLAGS="${CFLAGS:+ $CFLAGS}" + debug=false ;; + *) AC_MSG_ERROR([bad value ${enableval} for --enable-debug]) ;; + esac], +@@ -110,20 +110,12 @@ AM_CONDITIONAL([HAVE_CUNIT], [test "$LD_CUNIT"]) + AC_C_CONST + AC_TYPE_SIZE_T + +-# Needed for the Expat subpackage: +-AC_C_BIGENDIAN([byteorder=4321], [byteorder=1234]) +-AC_DEFINE_UNQUOTED([BYTEORDER], [$byteorder], +- [Define to 4321 for big-endian and 1234 for little-endian]) +-AC_DEFINE([XML_CONTEXT_BYTES], 1024, +- [How much context to retain around the current parse point.]) +- + # Checks for library functions. + AC_CHECK_FUNCS([floor memmove memset modf pow strcasecmp strdup strpbrk]) + + AC_PROG_LIBTOOL + + AC_CONFIG_FILES([Makefile +- expat/Makefile + lib/Makefile + lib/xmlFailures/Makefile + lib/xmlSuccesses/Makefile diff --git a/sci-libs/udunits/metadata.xml b/sci-libs/udunits/metadata.xml new file mode 100644 index 000000000000..1edb232766dd --- /dev/null +++ b/sci-libs/udunits/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription> + This is the Unidata Units library, which supports conversion of unit + specifications between formatted and binary forms, arithmetic + manipulation of unit specifications, and conversion of values between + compatible scales of measurement. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/udunits/udunits-2.1.24-r1.ebuild b/sci-libs/udunits/udunits-2.1.24-r1.ebuild new file mode 100644 index 000000000000..5f2aee130be0 --- /dev/null +++ b/sci-libs/udunits/udunits-2.1.24-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools eutils fortran-2 + +DESCRIPTION="Library for manipulating units of physical quantities" +HOMEPAGE="https://www.unidata.ucar.edu/software/udunits/" +SRC_URI="ftp://ftp.unidata.ucar.edu/pub/udunits/${P}.tar.gz" + +SLOT="0" +LICENSE="UCAR-Unidata" +KEYWORDS="alpha amd64 ~hppa ~mips ppc ~sparc x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +RDEPEND="dev-libs/expat" +DEPEND="${RDEPEND}" + +src_prepare() { + # respect user's flags, compile with system libexpat + epatch "${FILESDIR}"/${PN}-2.1.15-autotools.patch + rm -rf expat || die + eautoreconf +} + +src_configure() { + econf \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + $(use_enable static-libs static) +} + +src_install() { + default + doinfo udunits2.info prog/udunits2prog.info + dodoc CHANGE_LOG ANNOUNCEMENT + dodoc udunits2.pdf prog/udunits2prog.pdf + docinto html + dodoc udunits2.html prog/udunits2prog.html +} diff --git a/sci-libs/udunits/udunits-2.2.20.ebuild b/sci-libs/udunits/udunits-2.2.20.ebuild new file mode 100644 index 000000000000..dc56fc673720 --- /dev/null +++ b/sci-libs/udunits/udunits-2.2.20.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit fortran-2 + +DESCRIPTION="Library for manipulating units of physical quantities" +HOMEPAGE="https://www.unidata.ucar.edu/software/udunits/" +SRC_URI="ftp://ftp.unidata.ucar.edu/pub/udunits/${P}.tar.gz" + +SLOT="0" +LICENSE="UCAR-BSD" +KEYWORDS="~alpha ~amd64 ~hppa ~mips ~ppc ~sparc ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +RDEPEND="dev-libs/expat" +DEPEND="${RDEPEND}" + +src_configure() { + econf \ + $(use_enable static-libs static) +} + +src_install() { + default + doinfo udunits2.info prog/udunits2prog.info + dodoc CHANGE_LOG ANNOUNCEMENT + dodoc udunits2.pdf prog/udunits2prog.pdf + docinto html + dodoc udunits2.html prog/udunits2prog.html +} diff --git a/sci-libs/ufconfig/Manifest b/sci-libs/ufconfig/Manifest new file mode 100644 index 000000000000..804b96dc15ea --- /dev/null +++ b/sci-libs/ufconfig/Manifest @@ -0,0 +1,11 @@ +DIST UFconfig-3.5.0.tar.gz 8001 SHA256 32614de9acc4aec534e41d61201d805e4c353cb23cce9c715f8cf2cb078378c1 SHA512 d9edd64d6f7c0a48c149990f55f7d0684459205b2a5a029f50412310db580d28f6336164c96784be5bd7441e175c33f6689a752b50d6af5c168d44b7b51f6d37 WHIRLPOOL b3b17d28749973c680c4d9fead01b68b159bc4c0041428ec71d58c53024d24858830ff8fc6d1135f376ee859f0389ee09055b3b520c225601c695a1f3c344d9a +DIST UFconfig-3.6.1.tar.gz 8163 SHA256 7640438363114c250ed24bc5d7afa9810f4b082b3f1a02bb445d2e4cafc6b3bf SHA512 b4b4af9f460f8aea4de7dcd1dcc1ee1aea319bd05de1781ffc2217d0ed1264a6cebcc4139b62fbcc2a6b1f614ff89eb6f277176a59a17b237729ec9822a93920 WHIRLPOOL cf8b6d4154369e9b3ed9ccd4c6f1f4a96f1c8d86ae1468af7c6493f23de42abd708ea60eb861ebdec050366a1eaa70c5383af9e1860c9a008040ffc3b3369a53 +DIST UFconfig-3.7.0.tar.gz 8557 SHA256 2f6b7bd0d01502586d11cc1f262ba41599b33eeb070dd637a53ec600a3e98215 SHA512 f5aa3723484e05a889434e12fc85521d378430b18d707d7d8807c755ea7046aa28854f8bcb459a42e8764a82f07597b73183a9c7ef070a4b376e76b475cb8d24 WHIRLPOOL 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e5e8a1c204cb3651501705adcd10789c9a1e093ade44625745f0c40244f6fab7c7774da47d23a7eb0f7aa23adb1074bcc80335385567cd41ffee0c130a14900d WHIRLPOOL a2c6b3dd493235dc5313dad99a4e582a6f4c8f6e62cac62de383c23e5221fca3cd094235bf838100b1b2482b61633cd1507ac0b33555bdca233775053630097e diff --git a/sci-libs/ufconfig/metadata.xml b/sci-libs/ufconfig/metadata.xml new file mode 100644 index 000000000000..c1011111c9d8 --- /dev/null +++ b/sci-libs/ufconfig/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> +UFconfig is a set of configuration files for the SuiteSparse matrix libraries +from CISE at University of Florida. It contains some headers and +makefiles. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/ufconfig/ufconfig-3.5.0.ebuild b/sci-libs/ufconfig/ufconfig-3.5.0.ebuild new file mode 100644 index 000000000000..34ee0b91f921 --- /dev/null +++ b/sci-libs/ufconfig/ufconfig-3.5.0.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +inherit multilib toolchain-funcs + +MY_PN=UFconfig +DESCRIPTION="Common configuration scripts for the SuiteSparse libraries" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/UFconfig" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${MY_PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="alpha amd64 hppa ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" +DEPEND="" + +S="${WORKDIR}/${MY_PN}" + +src_compile() { + echo "$(tc-getCC) ${CFLAGS} -fPIC -c UFconfig.c -o UFconfig.lo" + $(tc-getCC) ${CFLAGS} -fPIC -c UFconfig.c -o UFconfig.lo || die + echo "$(tc-getCC) ${LDFLAGS} -shared -Wl,-soname,libufconfig.so.${PV} -o libufconfig.so.${PV} UFconfig.lo" + $(tc-getCC) ${LDFLAGS} -shared -Wl,-soname,libufconfig.so.${PV} -o libufconfig.so.${PV} UFconfig.lo || die + if use static-libs; then + echo "$(tc-getCC) ${CFLAGS} -c UFconfig.c -o UFconfig.o" + $(tc-getCC) ${CFLAGS} -c UFconfig.c -o UFconfig.o || die + echo "$(tc-getAR) libufconfig.a UFconfig.o" + $(tc-getAR) cr libufconfig.a UFconfig.o + fi +} + +src_install() { + dolib.so libufconfig.so.${PV} || die + dosym libufconfig.so.${PV} /usr/$(get_libdir)/libufconfig.so + if use static-libs; then + dolib.a libufconfig.a || die + fi + insinto /usr/include + doins UFconfig.h || die + dodoc README.txt || die +} diff --git a/sci-libs/ufconfig/ufconfig-3.6.1.ebuild b/sci-libs/ufconfig/ufconfig-3.6.1.ebuild new file mode 100644 index 000000000000..0d9d8fc82870 --- /dev/null +++ b/sci-libs/ufconfig/ufconfig-3.6.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 +inherit multilib toolchain-funcs + +MY_PN=UFconfig +DESCRIPTION="Common configuration scripts for the SuiteSparse libraries" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/UFconfig" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${MY_PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" +IUSE="static-libs" +DEPEND="" + +S="${WORKDIR}/${MY_PN}" + +src_compile() { + echo "$(tc-getCC) ${CFLAGS} -fPIC -c UFconfig.c -o UFconfig.lo" + $(tc-getCC) ${CFLAGS} -fPIC -c UFconfig.c -o UFconfig.lo || die + echo "$(tc-getCC) ${LDFLAGS} -shared -Wl,-soname,libufconfig.so.${PV} -o libufconfig.so.${PV} UFconfig.lo" + $(tc-getCC) ${LDFLAGS} -shared -Wl,-soname,libufconfig.so.${PV} -o libufconfig.so.${PV} UFconfig.lo || die + if use static-libs; then + echo "$(tc-getCC) ${CFLAGS} -c UFconfig.c -o UFconfig.o" + $(tc-getCC) ${CFLAGS} -c UFconfig.c -o UFconfig.o || die + echo "$(tc-getAR) libufconfig.a UFconfig.o" + $(tc-getAR) cr libufconfig.a UFconfig.o + fi +} + +src_install() { + dolib.so libufconfig.so.${PV} + dosym libufconfig.so.${PV} /usr/$(get_libdir)/libufconfig.so + use static-libs && dolib.a libufconfig.a + insinto /usr/include + doins UFconfig.h + dodoc README.txt +} diff --git a/sci-libs/ufconfig/ufconfig-3.7.0.ebuild b/sci-libs/ufconfig/ufconfig-3.7.0.ebuild new file mode 100644 index 000000000000..03ac70185036 --- /dev/null +++ b/sci-libs/ufconfig/ufconfig-3.7.0.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 +inherit multilib toolchain-funcs + +MY_PN=UFconfig +DESCRIPTION="Common configuration scripts for the SuiteSparse libraries" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/UFconfig" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${MY_PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="static-libs" +DEPEND="" + +S="${WORKDIR}/${MY_PN}" + +src_compile() { + echo "$(tc-getCC) ${CFLAGS} -fPIC -c UFconfig.c -o UFconfig.lo" + $(tc-getCC) ${CFLAGS} -fPIC -c UFconfig.c -o UFconfig.lo || die + local sharedlink="-shared -Wl,-soname,libufconfig$(get_libname ${PV})" + [[ ${CHOST} == *-darwin* ]] && \ + sharedlink="-dynamiclib -install_name ${EPREFIX}/usr/$(get_libdir)/libufconfig$(get_libname ${PV})" + echo "$(tc-getCC) ${LDFLAGS} ${sharedlink} -o libufconfig$(get_libname ${PV}) UFconfig.lo" + $(tc-getCC) ${LDFLAGS} ${sharedlink} -o libufconfig$(get_libname ${PV}) UFconfig.lo || die + if use static-libs; then + echo "$(tc-getCC) ${CFLAGS} -c UFconfig.c -o UFconfig.o" + $(tc-getCC) ${CFLAGS} -c UFconfig.c -o UFconfig.o || die + echo "$(tc-getAR) libufconfig.a UFconfig.o" + $(tc-getAR) cr libufconfig.a UFconfig.o + fi +} + +src_install() { + dolib.so libufconfig$(get_libname ${PV}) + dosym libufconfig$(get_libname ${PV}) /usr/$(get_libdir)/libufconfig$(get_libname) + use static-libs && dolib.a libufconfig.a + insinto /usr/include + doins UFconfig.h + dodoc README.txt +} diff --git a/sci-libs/ufconfig/ufconfig-3.7.1.ebuild b/sci-libs/ufconfig/ufconfig-3.7.1.ebuild new file mode 100644 index 000000000000..f7b2aa3063ed --- /dev/null +++ b/sci-libs/ufconfig/ufconfig-3.7.1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 +inherit multilib toolchain-funcs + +MY_PN=UFconfig +DESCRIPTION="Common configuration scripts for the SuiteSparse libraries" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/UFconfig" +SRC_URI="http://www.cise.ufl.edu/research/sparse/${MY_PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="static-libs" +DEPEND="" + +S="${WORKDIR}/${MY_PN}" + +src_compile() { + echo "$(tc-getCC) ${CFLAGS} -fPIC -c UFconfig.c -o UFconfig.lo" + $(tc-getCC) ${CFLAGS} -fPIC -c UFconfig.c -o UFconfig.lo || die + local sharedlink="-shared -Wl,-soname,libufconfig$(get_libname ${PV})" + [[ ${CHOST} == *-darwin* ]] && \ + sharedlink="-dynamiclib -install_name ${EPREFIX}/usr/$(get_libdir)/libufconfig$(get_libname ${PV})" + echo "$(tc-getCC) ${LDFLAGS} ${sharedlink} -o libufconfig$(get_libname ${PV}) UFconfig.lo" + $(tc-getCC) ${LDFLAGS} ${sharedlink} -o libufconfig$(get_libname ${PV}) UFconfig.lo || die + if use static-libs; then + echo "$(tc-getCC) ${CFLAGS} -c UFconfig.c -o UFconfig.o" + $(tc-getCC) ${CFLAGS} -c UFconfig.c -o UFconfig.o || die + echo "$(tc-getAR) libufconfig.a UFconfig.o" + $(tc-getAR) cr libufconfig.a UFconfig.o + fi +} + +src_install() { + dolib.so libufconfig$(get_libname ${PV}) + dosym libufconfig$(get_libname ${PV}) /usr/$(get_libdir)/libufconfig$(get_libname) + use static-libs && dolib.a libufconfig.a + insinto /usr/include + doins UFconfig.h + dodoc README.txt +} diff --git a/sci-libs/umfpack/Manifest b/sci-libs/umfpack/Manifest new file mode 100644 index 000000000000..e7ece6efd917 --- /dev/null +++ b/sci-libs/umfpack/Manifest @@ -0,0 +1,5 @@ +DIST umfpack-5.6.2.tar.bz2 780204 SHA256 bac722dd5e715c3312ebe7927c05df2e19bc2a29d7e4ab57d0a98330d03164ed SHA512 7b206235e837e84885c871322c1f0d4378a048008d9c110bd96204e9bc1bd9c72c6909da513fd78b6225fddc7b91e1ceebf1a5147e99943b3f0fff48682403dc WHIRLPOOL fe5069dbbd4b21a3569ae8d81d55feb789b06f7afb4c39be67101fca65e601ac49a4ed455c7e85d7a5504d2f50ff18ec67c3bc02dd3d9635dea4200ffcaad4f5 +EBUILD umfpack-5.6.2.ebuild 895 SHA256 c4c594a86f76dcbf387922fcfd6775138f4ea91f937f2c2facc264fb8be8b158 SHA512 c57ce9c3d4f1e651bc6934db872d535bf86e3ad240e01ce0fe16085901ec444e1d1a42b8ae93ff401e9b7a7aa274a3056d5266f30b7001742c79204e53a22d36 WHIRLPOOL ccbef7e3d1c80f1277fa59bd71be1c6242eb5741f1d2b42e59dd7e3dd022b8d59acf47a7969a4c1d46d8f662e631e202188dca26add937e57e9bc4d8390c1195 +MISC ChangeLog 2711 SHA256 7697526822636c80c7b648a0dd8e71cc0b70c253a777bfeafa83117456a72c5e SHA512 df81b9a44ec678a56f09e124fcd84bc12c93999feb8a10c346cdb9cb6369ccb7f407d08e89a9f3d00ae89a751e32c55e3d599a800211284042913f8c5a6d2f1f WHIRLPOOL ad5c285d6a864eec8bb4bf05f11cf517cebb56c2e7b5492c606951f0edcec8b1a2a59a0dfdffb8fc7d4ece5c4bede4e2460ef2601acda19fbd94611733ae2894 +MISC ChangeLog-2015 8366 SHA256 2c7687a3d56f754d3d9977fd68374f90884a289915962c1b5c874d7a6af9d8ca SHA512 64f4595c61141ae7f3b4524ce033e02acef29918fb9d1b87cab404d85c58a404227d8bf3285509148c72732aa38d804fa6c42d241510b2349f2a30e371497c15 WHIRLPOOL 156be3e429d4c7d3a3330f2b159466466eac24d556546137910fb79ed7fdaddac27d603cdd42eeb2f78d54540bf010cde8f98bae69f9e2a040961e430146bb36 +MISC metadata.xml 667 SHA256 2332ad59738236692f1f467d4fdd5ad602828b7e61d718091008874763589800 SHA512 c204d7f86f2338f9571a46773c251dab31caa3d5bfbe4ae87326466026616d80737435d8cdbf0ae8cb5e109d8b52a5b6ccba09f8b52f38dfe9058049ef541007 WHIRLPOOL de76a2c239fa9f5a3a5194d956cfd56c9e701b233ca87024297011247f107c94f7df7c1fa28a97dbefc7aaba34df4dd3dd76b419df3ff678eb0f69f15e5d9bd7 diff --git a/sci-libs/umfpack/metadata.xml b/sci-libs/umfpack/metadata.xml new file mode 100644 index 000000000000..412bad8f33e1 --- /dev/null +++ b/sci-libs/umfpack/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + UMFPACK is a set of routines for solving unsymmetric sparse linear + systems, Ax=b, using the Unsymmetric MultiFrontal method. + Includes a C-callable interface, and a Fortran-callable interface. + MATLAB routines are not included in the Gentoo package. +</longdescription> + <use> + <flag name="cholmod">Use <pkg>sci-libs/cholmod</pkg> for matrix + ordering</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/umfpack/umfpack-5.6.2.ebuild b/sci-libs/umfpack/umfpack-5.6.2.ebuild new file mode 100644 index 000000000000..a554bfb1cddb --- /dev/null +++ b/sci-libs/umfpack/umfpack-5.6.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils toolchain-funcs + +DESCRIPTION="Unsymmetric multifrontal sparse LU factorization library" +HOMEPAGE="http://www.cise.ufl.edu/research/sparse/umfpack" +SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~alpha amd64 ~arm ~arm64 hppa ~ia64 ~mips ppc ppc64 sparc x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~x86-macos" +IUSE="doc +cholmod static-libs" + +RDEPEND=" + >=sci-libs/amd-1.3 + sci-libs/suitesparseconfig + virtual/blas + cholmod? ( >=sci-libs/cholmod-2[-minimal] )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base )" + +src_configure() { + local myeconfargs=( + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" + $(use_with doc) + $(use_with cholmod) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/vecmath-objectclub/Manifest b/sci-libs/vecmath-objectclub/Manifest new file mode 100644 index 000000000000..dffd4a25a83c --- /dev/null +++ b/sci-libs/vecmath-objectclub/Manifest @@ -0,0 +1,5 @@ +DIST vecmath1.2-1.14.tar.gz 75291 SHA256 d32c53e48471d7de1d097fe199a3df765472cc8d872315d4caf9934833573c93 SHA512 b61c60c4c8341327a7494475da380685220a6ecf193f4005bbe9ac2b9c98b5f587607c136ac8ba19425ba57c9d19d2994c1f474ca4cfa3f5a06cebb7d1c5c020 WHIRLPOOL 0139c64265398e8a603b05fe255c791265c401e0e7477d9690346fb784b6e04b86b051d39559ea7beaadbe1d097cf0579b2fb7952466948c84833c0a5e110160 +EBUILD vecmath-objectclub-1.14.ebuild 825 SHA256 2e29fb85ec53ed3b75c470063841525880e73f3d7a50316672411e0a42c1f814 SHA512 b646d86f84f5c893af3a277017b956e0e9fe23c7ff82aa3d790b93beb03e93db017353e852024903215730321fef99c4b3769f3f8743943c7b547eea2b795260 WHIRLPOOL 5a85591e96bda969c86a189e8f2a0f21886cde3a5d3caff9e4e7a1e58501b0709f13122cb98f3b611bbba39c9c4e5ea6abd53c7c57fdde5ff9df366aaaa5bb83 +MISC ChangeLog 2972 SHA256 1ecba88371f75634c6c31eb8b1f0f10f1a618cef625500ca938739c4ced64551 SHA512 7637f33828adf2d4b5731823234435589d14cd64bad6925d1646ac7e18b58e219a20bd3b9c1e48bcf82d83329e473211e317a054905697fa366cccd2a80450b6 WHIRLPOOL f66b2ad0ef0c11cb893a4e3cee2ae0c6f0ce3076ffa1757233cdc7a523621bf288a0bf140ca02591c6ea0353b1441768d81407b0b90a1dc4520ff71a2ab2a398 +MISC ChangeLog-2015 764 SHA256 5da5cd65a675bdd8c349af504ba1bf4d5a813b01f6e5a60149b60ead2f67feb0 SHA512 6d0094e98c764953f206dde2aa6fc81c8f21a58d3d95e44e4764050d691ffad9292089528fc80842c8bf6e0e11f08d8add7e409ff246d6e49b513c87ebfe32d1 WHIRLPOOL 5eccd17c2c4a4ce06541869f41f32960d50089aebb72544c26f01d291a5ccc94b70055d75807aa65836dd44682a525f5f86e0ae0edc19f78d4aa8e62afa39173 +MISC metadata.xml 743 SHA256 ae403dd5897ed7a39be5101be39edb3a884dbea5e2b5e538ca62fa3f378c25c4 SHA512 77534c2084b740b4cdbe6ce6cdb9c8f9a57d95324a2a0e2240c5a0b9edf34d7292b047b5c0509135d56a583cf41d0370342c646aaf4275bb66443d6f2a4cf2e2 WHIRLPOOL 6d4109af1be1d48ff2312c26ed4db2a6e1f983ceb9aaa29678f00f0431b2dd4982828712a620a7024f1023c13413a3226a1412ce560e794d146996df79b250c9 diff --git a/sci-libs/vecmath-objectclub/metadata.xml b/sci-libs/vecmath-objectclub/metadata.xml new file mode 100644 index 000000000000..6eb27f16c309 --- /dev/null +++ b/sci-libs/vecmath-objectclub/metadata.xml @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> +</maintainer> +<longdescription lang="en"> + This is unofficial implementation(java source code) of the + javax.vecmath package specified in the Java(TM) 3D API 1.2 + The package includes classes for 3-space vector/point, 4-space vector, + 4x4, 3x3 matrix, quaternion, axis-angle combination and etc. which are + often utilized for computer graphics mathematics. Most of the classes + have single and double precision versions. Generic matrices' LU and SV + decomposition are also there. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/vecmath-objectclub/vecmath-objectclub-1.14.ebuild b/sci-libs/vecmath-objectclub/vecmath-objectclub-1.14.ebuild new file mode 100644 index 000000000000..8d0a0986818f --- /dev/null +++ b/sci-libs/vecmath-objectclub/vecmath-objectclub-1.14.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit java-pkg-2 + +MY_PN="${PN/-objectclub/1.2}" + +DESCRIPTION="Unofficial free implementation of Sun javax.vecmath by Kenji Hiranabe" +HOMEPAGE="http://www.objectclub.jp/download/vecmath_e" +SRC_URI="http://www.objectclub.jp/download/files/vecmath/${MY_PN}-${PV}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND=">=virtual/jdk-1.4" +RDEPEND=">=virtual/jre-1.4" + +S="${WORKDIR}/${MY_PN}-${PV}" + +src_prepare() { + mkdir classes +} + +src_compile() { + find javax/ -name "*.java" > "${T}/src.list" + ejavac -d "${S}/classes" "@${T}/src.list" + + cd classes + jar -cf "${S}"/${PN}.jar * || die "failed to create jar" +} + +src_install() { + java-pkg_dojar ${PN}.jar + dodoc README +} diff --git a/sci-libs/voro++/Manifest b/sci-libs/voro++/Manifest new file mode 100644 index 000000000000..a8273aba6a23 --- /dev/null +++ b/sci-libs/voro++/Manifest @@ -0,0 +1,6 @@ +AUX voro++-0.4.6-cmake.patch 5803 SHA256 55936494100a4d4538795164f26ccaf12e585763bae6cc8f74415acbc76371e4 SHA512 547e63a20f9dacf946a927f932150e61fc4a08e22f605dedaf9a1d7c2a24583119d61daadb7a657f0bbfbea121687e185ebd1f300abc08c9290ee45a342bd3f1 WHIRLPOOL f01eb17544c62c7d35907d22668b9bd05925d012b1ebeb7a0ea0f61d92766b36c59c3ca080022ee4d7f9d844d7777027959f437404589eaaedcb6622e73d4862 +DIST voro++-0.4.6.tar.gz 809124 SHA256 ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e SHA512 aa8c73d7634bb4ec4c0a7d4d18c0df07511ef975338f2517e6f0ec65de56bac10397adccf1c0e13439d29d096b7cb9b4540d7cfc191a1662f15dc0c3c1ff77c1 WHIRLPOOL 120643681c2def042f8446b8da1fa674a4e94354e830f7867a92d3ecdcdf00ede8aacdf8a015717583fdfd3054abcb861cdd12c182a94756000828a514673c79 +EBUILD voro++-0.4.6-r1.ebuild 494 SHA256 e4a9026210f05f8c356a66b75a43c784e309b16d3a4aebe32b48b586ec91a308 SHA512 ad52da9b5e67151d5d1ab8ff3e9fac5c295a51f114a0cd42d88811fb4e5a5ca9bc56b88d093a28dc972b0624f89cc7390ad65ea9cc13020b07302903692ea409 WHIRLPOOL a9c5407ec194229e78a35cfbb9cbb3070e8e8ff9639e5d673b456ae866f79f1d8d050975b173b8e6740593494682fdde9d7c2d4ae1a03d307faac1ca0d1a3a97 +MISC ChangeLog 2463 SHA256 7152875ffd4d0f5827b3e43ab5c06309ff30d4de21976864706e177f6f4c2d1d SHA512 5b6454baf82ca6f0fb839c575b50d7e464b677118ff3148dab013667326dcf706a3ab2c62453e285b93feb8f6ba379a52857b24b530f552798c9befa5c69bb88 WHIRLPOOL 1557a042de02d9c754070828f98ff72161dc29e99ff7a439693ce70679020f698d7f90c9dae3906856db78c082ccea0b5766e4b5d7017db1464c9451c2f6d77d +MISC ChangeLog-2015 875 SHA256 225965a7e4252660b4675e1baeefa28bfd2d099b530f30a8de6159f09719c944 SHA512 a51fe8666ec03446b273fd5115fee590c4032848a3a25eb8257150f71353b0ff6f86e4a5c790f9641b85d35e6846bcb2f4bfa196b848214b7bcba1757f6854e1 WHIRLPOOL 79db61d0c39edc430e754db6ddfe102a4697295a5311241d7b80ad335e05de49ea6938d5f072b45bac4580edf01fd91ed57fb960db2fae040a0d94794c37c1b0 +MISC metadata.xml 259 SHA256 bbfbeb80ffccffa8e7f837d2c93e994bbe024d565ae3a31d30c6646e80a684c8 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 WHIRLPOOL 75b8dd1a97dde63f9cc9f73b5951eaf54579460763ef7cbe6f3a9a0739070601d762152ea00df8b476b80e92e5c29b611a494bac5ab747298942530cabe0ee84 diff --git a/sci-libs/voro++/files/voro++-0.4.6-cmake.patch b/sci-libs/voro++/files/voro++-0.4.6-cmake.patch new file mode 100644 index 000000000000..375d58f6474e --- /dev/null +++ b/sci-libs/voro++/files/voro++-0.4.6-cmake.patch @@ -0,0 +1,141 @@ +Index: CMakeLists.txt +=================================================================== +--- CMakeLists.txt (revision 0) ++++ CMakeLists.txt (working copy) +@@ -0,0 +1,109 @@ ++cmake_minimum_required(VERSION 2.6) ++ ++project(voro++) ++ ++set(PROJECT_VERSION "0.4.6") ++set(SOVERSION 0) ++ ++# Cmake modules/macros are in a subdirectory to keep this file cleaner ++set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules) ++ ++if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) ++ #release comes with -O3 by default ++ set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) ++endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) ++ ++enable_language(CXX) ++ ++###################################################################### ++# compiler tests ++# these need ot be done early (before further tests). ++##################################################################### ++ ++include(CheckCXXCompilerFlag) ++ ++######################################################################## ++# User input options # ++######################################################################## ++option(BUILD_SHARED_LIBS "Build shared libs" ON) ++if (NOT DEFINED LIB) ++ set(LIB "lib") ++endif(NOT DEFINED LIB) ++if (NOT DEFINED MAN) ++ set(MAN "share/man") ++endif(NOT DEFINED MAN) ++if (NOT DEFINED DATA) ++ set(DATA "share/voro++") ++endif(NOT DEFINED DATA) ++ ++######################################################################## ++#Find external packages ++######################################################################## ++find_package(Doxygen) ++ ++######################################################################## ++# Basic system tests (standard libraries, headers, functions, types) # ++######################################################################## ++include(CheckIncludeFileCXX) ++foreach(HEADER cmath cstdio cstdlib cstring ctime fstream iostream queue vector) ++ check_include_file_cxx(${HEADER} FOUND_${HEADER}) ++ if(NOT FOUND_${HEADER}) ++ message(FATAL_ERROR "Could not find needed header - ${HEADER}") ++ endif(NOT FOUND_${HEADER}) ++endforeach(HEADER) ++ ++set(MATH_LIBRARIES "m" CACHE STRING "math library") ++mark_as_advanced( MATH_LIBRARIES ) ++include(CheckLibraryExists) ++foreach(FUNC sqrt) ++ check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES}) ++ if(NOT FOUND_${FUNC}_${MATH_LIBRARIES}) ++ message(FATAL_ERROR "Could not find needed math function - ${FUNC}") ++ endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES}) ++endforeach(FUNC) ++ ++###################################### ++# Include the following subdirectory # ++###################################### ++ ++file(GLOB VORO_SOURCES src/*.cc) ++file(GLOB NOT_VORO_SOURCES src/v_base_wl.cc src/cmd_line.cc src/voro++.cc) ++list(REMOVE_ITEM VORO_SOURCES ${NOT_VORO_SOURCES}) ++add_library(voro++ ${VORO_SOURCES}) ++set_target_properties(voro++ PROPERTIES ++ LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/src" ++ SOVERSION ${SOVERSION}) ++install(TARGETS voro++ LIBRARY DESTINATION ${LIB} ARCHIVE DESTINATION ${LIB}) ++ ++add_executable(cmd_line src/cmd_line.cc) ++target_link_libraries(cmd_line voro++) ++#cannot have two target with the same name ++set_target_properties(cmd_line PROPERTIES OUTPUT_NAME voro++ ++ RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/src") ++install(TARGETS cmd_line RUNTIME DESTINATION bin) ++ ++#for voto++.hh ++include_directories(${CMAKE_SOURCE_DIR}/src) ++file(GLOB EXAMPLE_SOURCES examples/*/*.cc) ++foreach(SOURCE ${EXAMPLE_SOURCES}) ++ string(REGEX REPLACE "^.*/([^/]*)\\.cc$" "\\1" PROGNAME "${SOURCE}") ++ if (NOT PROGNAME STREQUAL ellipsoid) #ellipsoid is broken ++ string(REGEX REPLACE "^.*/(examples/.*)/${PROGNAME}\\.cc$" "\\1" DIRNAME "${SOURCE}") ++ add_executable(${PROGNAME} ${SOURCE}) ++ target_link_libraries(${PROGNAME} voro++) ++ set_target_properties(${PROGNAME} PROPERTIES ++ RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${DIRNAME}" ) ++ endif() ++endforeach(SOURCE) ++ ++file(GLOB_RECURSE VORO_HEADERS src/*.hh) ++install(FILES ${VORO_HEADERS} DESTINATION include/voro++) ++install(FILES ${CMAKE_SOURCE_DIR}/man/voro++.1 DESTINATION ${MAN}/man1) ++ ++if (DOXYGEN_FOUND) ++ add_custom_target(help COMMAND ${DOXYGEN_EXECUTABLE} src/Doxyfile ++ COMMENT "Build doxygen documentation") ++endif (DOXYGEN_FOUND) ++ ++configure_file(${CMAKE_MODULE_PATH}/cmake_uninstall.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake IMMEDIATE @ONLY) ++add_custom_target(uninstall COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake) +Index: CMakeModules/cmake_uninstall.cmake.in +=================================================================== +--- CMakeModules/cmake_uninstall.cmake.in (revision 0) ++++ CMakeModules/cmake_uninstall.cmake.in (working copy) +@@ -0,0 +1,22 @@ ++IF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt") ++ MESSAGE(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"") ++ENDIF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt") ++ ++FILE(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files) ++STRING(REGEX REPLACE "\n" ";" files "${files}") ++FOREACH(file ${files}) ++ MESSAGE(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"") ++ IF(EXISTS "$ENV{DESTDIR}${file}") ++ EXEC_PROGRAM( ++ "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\"" ++ OUTPUT_VARIABLE rm_out ++ RETURN_VALUE rm_retval ++ ) ++ IF(NOT "${rm_retval}" STREQUAL 0) ++ MESSAGE(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"") ++ ENDIF(NOT "${rm_retval}" STREQUAL 0) ++ ELSE(EXISTS "$ENV{DESTDIR}${file}") ++ MESSAGE(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.") ++ ENDIF(EXISTS "$ENV{DESTDIR}${file}") ++ENDFOREACH(file) ++ diff --git a/sci-libs/voro++/metadata.xml b/sci-libs/voro++/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-libs/voro++/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/voro++/voro++-0.4.6-r1.ebuild b/sci-libs/voro++/voro++-0.4.6-r1.ebuild new file mode 100644 index 000000000000..1f1aa5a860ae --- /dev/null +++ b/sci-libs/voro++/voro++-0.4.6-r1.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils multilib + +DESCRIPTION="A 3D Voronoi cell software library" +HOMEPAGE="http://math.lbl.gov/voro++/" +SRC_URI="${HOMEPAGE}/download/dir/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}/${P}-cmake.patch" ) + +src_configure() { + mycmakeargs=( -DLIB=$(get_libdir) ) + cmake-utils_src_configure +} diff --git a/sci-libs/votca-moo/Manifest b/sci-libs/votca-moo/Manifest new file mode 100644 index 000000000000..3097792b9d59 --- /dev/null +++ b/sci-libs/votca-moo/Manifest @@ -0,0 +1,2 @@ +EBUILD votca-moo-9999.ebuild 786 SHA256 0798f65e0c2b1f75d6f5a46d8268460b41c4305cb5802ed38c79622b612a24b0 SHA512 0501489fbb54a8f0255f1807331bdbf7e3c9204fff3f86a106f11de6a6da2414eeb54f454bea0d3380056399b82d348f015905bd7f001bd094fa64cfde39a5e4 WHIRLPOOL da23390a3d30fe1e492bf855279f28c31a4f451aa983cac07be53ff0e3a1285770ddb293f17e98a47aed5df369d7ece206338115ed49102b498417f599ac2975 +MISC metadata.xml 453 SHA256 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+</pkgmetadata> diff --git a/sci-libs/votca-moo/votca-moo-9999.ebuild b/sci-libs/votca-moo/votca-moo-9999.ebuild new file mode 100644 index 000000000000..01f3524290df --- /dev/null +++ b/sci-libs/votca-moo/votca-moo-9999.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils multilib + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Votca Molecular orbital library" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="" + +RDEPEND=" + dev-libs/boost:= + =sci-libs/votca-tools-${PV}[sqlite] + dev-db/sqlite:3" + +DEPEND="${RDEPEND}" + +DOCS=( NOTICE README ) + +src_configure() { + mycmakeargs=( + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/votca-tools/Manifest b/sci-libs/votca-tools/Manifest new file mode 100644 index 000000000000..0dfa36d49ecf --- /dev/null +++ b/sci-libs/votca-tools/Manifest @@ -0,0 +1,8 @@ +DIST votca-tools-1.4.1.tar.gz 103152 SHA256 c33a1e7cda3a53d51188d6f0452ddbd9a84141df0a1645c99cfebd3694646b26 SHA512 19165be7c9903cb664051a6556f9fd689b02af71156f040960008e8d74e4a32adfe283c67eb7b53c8bdc6ae6f72516ad0b674d9f2b3354ca50f082b1651dafef WHIRLPOOL 5996c3d264964b8347a057d5ac11a782ebd5bfaf513f9a4e196b957bed01c08993ca12b3a11a1a4b21f4a1600861c6101dade39575c06265d40cfe400e424d01 +DIST votca-tools-1.4.tar.gz 103102 SHA256 df0f96e81a1639eba9e4dce61c28bb08e69c371fb727b4d14c66f5771f22e2fb SHA512 7c4bf2e2ba8cf795f03879138787db3875f48db56b88394c98b18cef0ae90e636d8aafff42eb62a408df06a91583e37e59b33440e83de9f4338295e9ccfc9be5 WHIRLPOOL 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<email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <upstream> + <remote-id type="github">votca/tools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/votca-tools/votca-tools-1.4.1.ebuild b/sci-libs/votca-tools/votca-tools-1.4.1.ebuild new file mode 100644 index 000000000000..2a2c4d6860c4 --- /dev/null +++ b/sci-libs/votca-tools/votca-tools-1.4.1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils eutils multilib + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="Votca tools library" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="doc +fftw +gsl sqlite" + +RDEPEND=" + dev-libs/boost:= + dev-libs/expat + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + sqlite? ( dev-db/sqlite:3 )" + +DEPEND="${RDEPEND} + doc? ( >=app-doc/doxygen-1.7.6.1[dot] ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( NOTICE ) + +src_configure() { + mycmakeargs=( + -DWITH_GSL=$(usex gsl) + -DWITH_FFTW=$(usex fftw) + -DWITH_SQLITE3=$(usex sqlite) + -DWITH_RC_FILES=OFF + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if use doc; then + cd "${CMAKE_BUILD_DIR}" + cmake-utils_src_make html + dodoc -r share/doc/html + fi +} diff --git a/sci-libs/votca-tools/votca-tools-1.4.ebuild b/sci-libs/votca-tools/votca-tools-1.4.ebuild new file mode 100644 index 000000000000..ae9aec9e652e --- /dev/null +++ b/sci-libs/votca-tools/votca-tools-1.4.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils eutils multilib + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="amd64 x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="amd64 x86" +fi + +DESCRIPTION="Votca tools library" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="doc +fftw +gsl sqlite" + +RDEPEND=" + dev-libs/boost:= + dev-libs/expat + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + sqlite? ( dev-db/sqlite:3 )" + +DEPEND="${RDEPEND} + doc? ( >=app-doc/doxygen-1.7.6.1[dot] ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( NOTICE ) + +src_configure() { + mycmakeargs=( + -DWITH_GSL=$(usex gsl) + -DWITH_FFTW=$(usex fftw) + -DWITH_SQLITE3=$(usex sqlite) + -DWITH_RC_FILES=OFF + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if use doc; then + cd "${CMAKE_BUILD_DIR}" + cmake-utils_src_make html + dodoc -r share/doc/html + fi +} diff --git a/sci-libs/votca-tools/votca-tools-9999.ebuild b/sci-libs/votca-tools/votca-tools-9999.ebuild new file mode 100644 index 000000000000..1902116de670 --- /dev/null +++ b/sci-libs/votca-tools/votca-tools-9999.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils eutils multilib + +if [ "${PV}" != "9999" ]; then + SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" + S="${WORKDIR}/${P#votca-}" +else + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN/-//}.git" + KEYWORDS="" +fi + +DESCRIPTION="Votca tools library" +HOMEPAGE="http://www.votca.org" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="doc +fftw +gsl sqlite" + +RDEPEND=" + dev-libs/boost:= + dev-libs/expat + fftw? ( sci-libs/fftw:3.0 ) + gsl? ( sci-libs/gsl ) + sqlite? ( dev-db/sqlite:3 )" + +DEPEND="${RDEPEND} + doc? ( >=app-doc/doxygen-1.7.6.1[dot] ) + >=app-text/txt2tags-2.5 + virtual/pkgconfig" + +DOCS=( NOTICE ) + +src_configure() { + mycmakeargs=( + -DWITH_GSL=$(usex gsl) + -DWITH_FFTW=$(usex fftw) + -DWITH_SQLITE3=$(usex sqlite) + -DWITH_RC_FILES=OFF + -DLIB=$(get_libdir) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + if use doc; then + cd "${CMAKE_BUILD_DIR}" + cmake-utils_src_make html + dodoc -r share/doc/html + fi +} diff --git a/sci-libs/vtk/Manifest b/sci-libs/vtk/Manifest new file mode 100644 index 000000000000..15c63a0919de --- /dev/null +++ b/sci-libs/vtk/Manifest @@ -0,0 +1,29 @@ +AUX vtk-6.1.0-freetype.patch 1159 SHA256 ab95039cf8f39d1dcdf97a3ae62c4aa47f6daad4defdb5be842719102036c452 SHA512 c4e0328d1c7c1a1842de0f70ec93fe28e5537d9add29d4e76243f91138b97e993d5ef02a80fece8cc3476086772bb2f3e97ff6c8ce18a4ffedced90ad98199e0 WHIRLPOOL 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d21bc8590d9535538ff06fd1c7d816aaec5fc50b7f63af1ff3c682b0edabc4403ccb7dff1045de0de89e7454dd673bb46f09b48f5a9c7230f3861c584ba7b47c +MISC ChangeLog 4690 SHA256 281e510f5535b633cd766240f70f68441ff6aa47d08521dc52e362349b01a8df SHA512 c4346e9b89ffc0ac165076102606c5efaa76d925b12f6ca8f8a4c17a0d3324362cad370ae9e825051698d9eecc67ff898411a676f83e989ddd9696c920b5e963 WHIRLPOOL d74fdde3e300ad54cb54d4500ecda9c98d5e266dda6cd65754611f8cc154e8178c71a4dd773d9901be9d4412b3beddc4e8db16d83e570519f22feab8e93686c3 +MISC ChangeLog-2015 21566 SHA256 4bb98b748cdb1c325606e1e71d0c012acfaea25d97e45adcb9f9fa9136152e19 SHA512 2b92f32b8bfa30ebbcee8962dbbdb033f4120e58074d12c81dff492c15fa0aa8da3a6ef4a4947e50e9a87958f4668e8baa65972c2b490c47bc754e0bbd222232 WHIRLPOOL e87ba49915e30ec0a6ec85d0fd4bf47f14ed0e4b728a6d03cead683d928dd40f9d604b1e0091e5c59f83ed2426249d82bb041937a4f185903671b177fc3e0208 +MISC metadata.xml 1120 SHA256 116b3855df2f1366cf28d8a328499ce8f606c6a0dd97dde035784834b12e8e9d SHA512 d0d9ccd1922afe496e24d38fee05793fdf3983f798bef817a00c77bb632f2cabe3d2be554d0e979c223fd4005f3186b9ef78d394050539bd21cba5c2b6e56143 WHIRLPOOL 77458d78ad2bbd73c3b419b109def1e5982002ee29f7c5c66251931da2e48bc49b520d699141ab9b8c447730161fcc29e20c8fe68f24dc44ca6845cbff5714dd diff --git a/sci-libs/vtk/files/vtk-6.1.0-freetype.patch b/sci-libs/vtk/files/vtk-6.1.0-freetype.patch new file mode 100644 index 000000000000..b7d3e409cde1 --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-freetype.patch @@ -0,0 +1,22 @@ +--- a/ParaView-v4.2.0-source/VTK/Rendering/FreeType/vtkFreeTypeTools.cxx_orig 2014-12-23 09:25:35.000000000 +0100 ++++ b/ParaView-v4.2.0-source/VTK/Rendering/FreeType/vtkFreeTypeTools.cxx 2014-12-24 09:40:31.886953389 +0100 +@@ -1185,7 +1185,7 @@ + if (bitmap) + { + metaData.ascent = std::max(bitmapGlyph->top - 1, metaData.ascent); +- metaData.descent = std::min(-(bitmap->rows - (bitmapGlyph->top - 1)), ++ metaData.descent = std::min(-(static_cast<int>(bitmap->rows) - (bitmapGlyph->top - 1)), + metaData.descent); + } + ++heightString; +@@ -1952,8 +1952,8 @@ + if (bitmap) + { + bbox[0] = std::min(bbox[0], pen[0] + bitmapGlyph->left); +- bbox[1] = std::max(bbox[1], pen[0] + bitmapGlyph->left + bitmap->width); +- bbox[2] = std::min(bbox[2], pen[1] + bitmapGlyph->top - 1 - bitmap->rows); ++ bbox[1] = std::max(bbox[1], pen[0] + bitmapGlyph->left + static_cast<int>(bitmap->width)); ++ bbox[2] = std::min(bbox[2], pen[1] + bitmapGlyph->top - 1 - static_cast<int>(bitmap->rows)); + bbox[3] = std::max(bbox[3], pen[1] + bitmapGlyph->top - 1); + } + else diff --git a/sci-libs/vtk/files/vtk-6.1.0-gcc67.patch b/sci-libs/vtk/files/vtk-6.1.0-gcc67.patch new file mode 100644 index 000000000000..83d1ae18f213 --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-gcc67.patch @@ -0,0 +1,26 @@ +diff --git a/old/vtkCompilerExtras.cmake b/CMake/vtkCompilerExtras.cmake +index 05b2db9..92c2c4c 100644 +--- a/old/vtkCompilerExtras.cmake ++++ b/CMake/vtkCompilerExtras.cmake +@@ -27,7 +27,7 @@ if(CMAKE_COMPILER_IS_GNUCXX) + OUTPUT_VARIABLE _gcc_version_info + ERROR_VARIABLE _gcc_version_info) + +- string (REGEX MATCH "[345]\\.[0-9]\\.[0-9]" ++ string (REGEX MATCH "[0-9]\\.[0-9]\\.[0-9]" + _gcc_version "${_gcc_version_info}") + if(NOT _gcc_version) + string (REGEX REPLACE ".*\\(GCC\\).* ([34]\\.[0-9]) .*" "\\1.0" +diff --git a/old/GenerateExportHeader.cmake b/CMake/GenerateExportHeader.cmake +index 3cc12dd..b7a47df 100644 +--- a/old/GenerateExportHeader.cmake ++++ b/CMake/GenerateExportHeader.cmake +@@ -166,7 +166,7 @@ macro(_test_compiler_hidden_visibility) + execute_process(COMMAND ${CMAKE_C_COMPILER} --version + OUTPUT_VARIABLE _gcc_version_info + ERROR_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" ++ string(REGEX MATCH "[0-9]\\.[0-9]\\.[0-9]" + _gcc_version "${_gcc_version_info}") + # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the + # patch level, handle this here: diff --git a/sci-libs/vtk/files/vtk-6.1.0-gdal2.patch b/sci-libs/vtk/files/vtk-6.1.0-gdal2.patch new file mode 100644 index 000000000000..c21864102278 --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-gdal2.patch @@ -0,0 +1,33 @@ +diff --git a/IO/GDAL/vtkGDALVectorReader.cxx b/IO/GDAL/vtkGDALVectorReader.cxx +index 86854a0..a0e234a 100644 +--- a/IO/GDAL/vtkGDALVectorReader.cxx ++++ b/IO/GDAL/vtkGDALVectorReader.cxx +# Patch to build against newer GDAL per upstream commit +# https://projects.archlinux.org/svntogit/community.git/tree/trunk/gdal2.patch?h=packages/vtk&id=43307598a98872fd4ce7739e47f5bb4cfcb5372d +@@ -44,7 +44,7 @@ class vtkGDALVectorReader::Internal + public: + Internal( const char* srcName, int srcMode, int appendFeatures, int addFeatIds ) + { +- this->Source = OGRSFDriverRegistrar::Open( srcName, srcMode, &this->Driver ); ++ this->Source = (GDALDataset*) OGROpen( srcName, srcMode, NULL ); + if ( ! this->Source ) + { + this->LastError = CPLGetLastErrorMsg(); +@@ -61,7 +61,7 @@ public: + { + if ( this->Source ) + { +- OGRDataSource::DestroyDataSource( this->Source ); ++ GDALClose( (GDALDatasetH) this->Source ); + } + } + +@@ -304,7 +304,7 @@ public: + return nCells; + } + +- OGRDataSource* Source; ++ GDALDataset* Source; + OGRSFDriver* Driver; + const char* LastError; + int LayerIdx; diff --git a/sci-libs/vtk/files/vtk-6.1.0-glext.patch b/sci-libs/vtk/files/vtk-6.1.0-glext.patch new file mode 100644 index 000000000000..b5529a5fc3d5 --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-glext.patch @@ -0,0 +1,13 @@ +diff -up VTK-6.1.0/Rendering/OpenGL/vtkOpenGL.h.glext VTK-6.1.0/Rendering/OpenGL/vtkOpenGL.h +--- VTK-6.1.0/Rendering/OpenGL/vtkOpenGL.h.glext 2014-01-22 08:55:41.000000000 -0700 ++++ VTK-6.1.0/Rendering/OpenGL/vtkOpenGL.h 2014-11-19 10:27:12.349345199 -0700 +@@ -19,7 +19,8 @@ + #include "vtkConfigure.h" + + // To prevent gl.h to include glext.h provided by the system +-#define GL_GLEXT_LEGACY ++// https://bugzilla.redhat.com/show_bug.cgi?id=1138466 ++// #define GL_GLEXT_LEGACY + #if defined(__APPLE__) && (defined(VTK_USE_CARBON) || defined(VTK_USE_COCOA)) + # include <OpenGL/gl.h> // Include OpenGL API. + #else diff --git a/sci-libs/vtk/files/vtk-6.1.0-install.patch b/sci-libs/vtk/files/vtk-6.1.0-install.patch new file mode 100644 index 000000000000..27c6c3adfee9 --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-install.patch @@ -0,0 +1,19 @@ +diff -up VTK-6.1.0/CMake/vtkModuleTop.cmake.install VTK-6.1.0/CMake/vtkModuleTop.cmake +--- VTK-6.1.0/CMake/vtkModuleTop.cmake.install 2014-01-23 19:12:04.922871103 -0700 ++++ VTK-6.1.0/CMake/vtkModuleTop.cmake 2014-01-23 19:14:33.002645155 -0700 +@@ -330,11 +330,15 @@ if (NOT VTK_INSTALL_NO_DEVELOPMENT) + CMake/pythonmodules.h.in + CMake/UseVTK.cmake + CMake/FindTCL.cmake ++ CMake/TopologicalSort.cmake + CMake/vtkTclTkMacros.cmake + CMake/vtk-forward.c.in ++ CMake/vtkGroups.cmake + CMake/vtkForwardingExecutable.cmake + CMake/vtkJavaWrapping.cmake + CMake/vtkMakeInstantiator.cmake ++ CMake/vtkMakeInstantiator.cxx.in ++ CMake/vtkMakeInstantiator.h.in + CMake/vtkModuleAPI.cmake + CMake/vtkModuleHeaders.cmake.in + CMake/vtkModuleInfo.cmake.in diff --git a/sci-libs/vtk/files/vtk-6.1.0-memset.patch b/sci-libs/vtk/files/vtk-6.1.0-memset.patch new file mode 100644 index 000000000000..362022edf16d --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-memset.patch @@ -0,0 +1,147 @@ +From ef22d3d69421581b33bc0cd94b647da73b61ba96 Mon Sep 17 00:00:00 2001 +From: Anton Gladky <gladk@debian.org> +Date: Fri, 30 May 2014 23:16:26 +0200 +Subject: [PATCH] Fix compilation by gcc-4.9 + +VTK fails to build during compilation by gcc-4.9 with the +following message: + +CMakeFiles/vtkFiltersParallelMPI.dir/vtkDistributedDataFilter.cxx.o: In +function `memset': +/usr/include/x86_64-linux-gnu/bits/string3.h:81: warning: memset used +with constant zero length parameter; this could be due to transposed +parameters +collect2: error: ld returned 1 exit status + +This patch sets if-condition before all "memsets" in +vtkDistributedDataFilter and checkes, whether the number +of bytes to be set by memset is more than 0 to escape this +error. +--- + Filters/ParallelMPI/vtkDistributedDataFilter.cxx | 48 ++++++++++++++++++------ + 1 file changed, 37 insertions(+), 11 deletions(-) + +diff --git a/Filters/ParallelMPI/vtkDistributedDataFilter.cxx b/Filters/ParallelMPI/vtkDistributedDataFilter.cxx +index 3c1ff30..df4b5d3 100644 +--- a/Filters/ParallelMPI/vtkDistributedDataFilter.cxx ++++ b/Filters/ParallelMPI/vtkDistributedDataFilter.cxx +@@ -1091,7 +1091,10 @@ vtkDataSet *vtkDistributedDataFilter::TestFixTooFewInputFiles(vtkDataSet *input) + vtkIdType cellsPerNode = numTotalCells / nprocs; + + vtkIdList **sendCells = new vtkIdList * [ nprocs ]; +- memset(sendCells, 0, sizeof(vtkIdList *) * nprocs); ++ ++ if (sizeof(vtkIdList *) * nprocs > 0) { ++ memset(sendCells, 0, sizeof(vtkIdList *) * nprocs); ++ } + + if (numConsumers == nprocs - 1) + { +@@ -1582,7 +1585,9 @@ vtkFloatArray ** + // Exchange int arrays + + float **recvArrays = new float * [nprocs]; +- memset(recvArrays, 0, sizeof(float *) * nprocs); ++ if (sizeof(float *) * nprocs > 0) { ++ memset(recvArrays, 0, sizeof(float *) * nprocs); ++ } + + if (sendSize[me] > 0) // sent myself an array + { +@@ -1703,7 +1708,9 @@ vtkIdTypeArray ** + // Exchange int arrays + + vtkIdType **recvArrays = new vtkIdType * [nprocs]; +- memset(recvArrays, 0, sizeof(vtkIdType *) * nprocs); ++ if (sizeof(vtkIdType *) * nprocs > 0) { ++ memset(recvArrays, 0, sizeof(vtkIdType *) * nprocs); ++ } + + if (sendSize[me] > 0) // sent myself an array + { +@@ -2807,7 +2814,9 @@ void vtkDistributedDataFilter::AddConstantUnsignedCharPointArray( + + unsigned char *vals = new unsigned char [npoints]; + +- memset(vals, val, npoints); ++ if (npoints > 0) { ++ memset(vals, val, npoints); ++ } + + vtkUnsignedCharArray *Array = vtkUnsignedCharArray::New(); + Array->SetName(arrayName); +@@ -2827,7 +2836,9 @@ void vtkDistributedDataFilter::AddConstantUnsignedCharCellArray( + + unsigned char *vals = new unsigned char [ncells]; + +- memset(vals, val, ncells); ++ if (ncells > 0) { ++ memset(vals, val, ncells); ++ } + + vtkUnsignedCharArray *Array = vtkUnsignedCharArray::New(); + Array->SetName(arrayName); +@@ -3026,7 +3037,9 @@ int vtkDistributedDataFilter::AssignGlobalNodeIds(vtkUnstructuredGrid *grid) + vtkIdType nGridPoints = grid->GetNumberOfPoints(); + + vtkIdType *numPointsOutside = new vtkIdType [nprocs]; +- memset(numPointsOutside, 0, sizeof(vtkIdType) * nprocs); ++ if (sizeof(vtkIdType) * nprocs > 0) { ++ memset(numPointsOutside, 0, sizeof(vtkIdType) * nprocs); ++ } + + vtkIdTypeArray *globalIds = vtkIdTypeArray::New(); + globalIds->SetNumberOfValues(nGridPoints); +@@ -3108,10 +3121,16 @@ int vtkDistributedDataFilter::AssignGlobalNodeIds(vtkUnstructuredGrid *grid) + // global ID back? + + vtkFloatArray **ptarrayOut = new vtkFloatArray * [nprocs]; +- memset(ptarrayOut, 0, sizeof(vtkFloatArray *) * nprocs); ++ ++ if (sizeof(vtkFloatArray *) * nprocs > 0) { ++ memset(ptarrayOut, 0, sizeof(vtkFloatArray *) * nprocs); ++ } + + vtkIdTypeArray **localIds = new vtkIdTypeArray * [nprocs]; +- memset(localIds, 0, sizeof(vtkIdTypeArray *) * nprocs); ++ ++ if (sizeof(vtkIdTypeArray *) * nprocs > 0) { ++ memset(localIds, 0, sizeof(vtkIdTypeArray *) * nprocs); ++ } + + vtkIdType *next = new vtkIdType [nprocs]; + vtkIdType *next3 = new vtkIdType [nprocs]; +@@ -3286,7 +3305,9 @@ vtkIdTypeArray **vtkDistributedDataFilter::FindGlobalPointIds( + { + // There are no cells in my assigned region + +- memset(gids, 0, sizeof(vtkIdTypeArray *) * nprocs); ++ if (sizeof(vtkIdTypeArray *) * nprocs > 0) { ++ memset(gids, 0, sizeof(vtkIdTypeArray *) * nprocs); ++ } + + return gids; + } +@@ -3491,7 +3512,10 @@ vtkIdTypeArray **vtkDistributedDataFilter::MakeProcessLists( + std::multimap<int, int>::iterator mapIt; + + vtkIdTypeArray **processList = new vtkIdTypeArray * [nprocs]; +- memset(processList, 0, sizeof (vtkIdTypeArray *) * nprocs); ++ ++ if (sizeof (vtkIdTypeArray *) * nprocs > 0) { ++ memset(processList, 0, sizeof (vtkIdTypeArray *) * nprocs); ++ } + + for (int i=0; i<nprocs; i++) + { +@@ -3581,7 +3605,9 @@ vtkIdTypeArray **vtkDistributedDataFilter::GetGhostPointIds( + vtkIdType numPoints = grid->GetNumberOfPoints(); + + vtkIdTypeArray **ghostPtIds = new vtkIdTypeArray * [nprocs]; +- memset(ghostPtIds, 0, sizeof(vtkIdTypeArray *) * nprocs); ++ if (sizeof(vtkIdTypeArray *) * nprocs) { ++ memset(ghostPtIds, 0, sizeof(vtkIdTypeArray *) * nprocs); ++ } + + if (numPoints < 1) + { diff --git a/sci-libs/vtk/files/vtk-6.1.0-netcdf.patch b/sci-libs/vtk/files/vtk-6.1.0-netcdf.patch new file mode 100644 index 000000000000..e6f8b6431720 --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-netcdf.patch @@ -0,0 +1,29 @@ +diff -up VTK/ThirdParty/netcdf/CMakeLists.txt.netcdf VTK/ThirdParty/netcdf/CMakeLists.txt +--- VTK/ThirdParty/netcdf/CMakeLists.txt.netcdf 2013-12-27 20:29:11.644289659 -0700 ++++ VTK/ThirdParty/netcdf/CMakeLists.txt 2013-12-27 20:33:48.071895769 -0700 +@@ -1,10 +1,18 @@ +-vtk_module_third_party(NetCDF +- LIBRARIES vtkNetCDF vtkNetCDF_cxx +- INCLUDE_DIRS +- ${CMAKE_CURRENT_SOURCE_DIR}/vtknetcdf/include +- ${CMAKE_CURRENT_BINARY_DIR}/vtknetcdf +- COMPONENTS C CXX +- ) ++if(NOT VTK_USE_SYSTEM_NETCDF) ++ vtk_module_third_party(NetCDF ++ LIBRARIES vtkNetCDF vtkNetCDF_cxx ++ INCLUDE_DIRS ++ ${CMAKE_CURRENT_SOURCE_DIR}/vtknetcdf/include ++ ${CMAKE_CURRENT_BINARY_DIR}/vtknetcdf ++ COMPONENTS C CXX ++ ) ++else(NOT VTK_USE_SYSTEM_NETCDF) ++ vtk_module_third_party(NetCDF ++ LIBRARIES vtkNetCDF netcdf ++ COMPONENTS C CXX ++ ) ++endif() ++ + + #Configure the top cpp header to switch between system and internal + #netcdf just like vtk_module_third_party does for the c header. diff --git a/sci-libs/vtk/files/vtk-6.1.0-system.patch b/sci-libs/vtk/files/vtk-6.1.0-system.patch new file mode 100644 index 000000000000..c75d544447ea --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-system.patch @@ -0,0 +1,27 @@ +diff -up VTK/CMake/vtkModuleMacros.cmake.system VTK/CMake/vtkModuleMacros.cmake +--- VTK/CMake/vtkModuleMacros.cmake.system 2013-12-24 19:17:43.000000000 -0700 ++++ VTK/CMake/vtkModuleMacros.cmake 2013-12-27 20:28:22.375573277 -0700 +@@ -682,7 +682,7 @@ macro(vtk_module_third_party _pkg) + message(FATAL_ERROR "Cannot specify both LIBRARIES and NO_LIBRARIES") + endif() + +- option(VTK_USE_SYSTEM_${_upper} "Use system-installed ${_pkg}" OFF) ++ option(VTK_USE_SYSTEM_${_upper} "Use system-installed ${_pkg}" ${VTK_USE_SYSTEM_LIBRARIES}) + mark_as_advanced(VTK_USE_SYSTEM_${_upper}) + + if(VTK_USE_SYSTEM_${_upper}) +diff -up VTK/CMakeLists.txt.system VTK/CMakeLists.txt +--- VTK/CMakeLists.txt.system 2013-12-27 20:28:22.374573241 -0700 ++++ VTK/CMakeLists.txt 2013-12-27 20:28:48.118669708 -0700 +@@ -132,6 +132,11 @@ if (CMAKE_CROSSCOMPILING AND NOT COMPILE + endif() + + #----------------------------------------------------------------------------- ++# Do we try to use system libraries by default? ++OPTION(VTK_USE_SYSTEM_LIBRARIES "Use the system's libraries by default." OFF) ++MARK_AS_ADVANCED(VTK_USE_SYSTEM_LIBRARIES) ++ ++#----------------------------------------------------------------------------- + # The third party macros are still used in one or two third party builds. + include(vtkThirdParty) + diff --git a/sci-libs/vtk/files/vtk-6.1.0-web.patch b/sci-libs/vtk/files/vtk-6.1.0-web.patch new file mode 100644 index 000000000000..a85f2cd99640 --- /dev/null +++ b/sci-libs/vtk/files/vtk-6.1.0-web.patch @@ -0,0 +1,25 @@ +From 58373b120db6d51c6d5eace38447cdb45ff858d1 Mon Sep 17 00:00:00 2001 +From: Patric Schmitz <patric.schmitz@rwth-aachen.de> +Date: Tue, 28 Oct 2014 16:24:22 +0100 +Subject: [PATCH] Include vtkPythonPackages in Web/JavaScript/CMakeLists.txt + +Change-Id: Ie7bffa19bdaa78c5b090c886e50c1af76e2aadee +--- + Web/Applications/CMakeLists.txt | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/Web/Applications/CMakeLists.txt b/Web/Applications/CMakeLists.txt +index c9e7ad3..b4c9a60 100644 +--- a/Web/Applications/CMakeLists.txt ++++ b/Web/Applications/CMakeLists.txt +@@ -12,6 +12,7 @@ set(WEB_APPLICATIONS + + set(WEB_APPS_DEPENDS) + ++include(vtkPythonPackages) # for copy_files_recursive + foreach(_app ${WEB_APPLICATIONS}) + file(MAKE_DIRECTORY "${VTK_WWW_DIR}/apps/${_app}") + +-- +2.2.1 + diff --git a/sci-libs/vtk/files/vtk-7.0.0-glext.patch b/sci-libs/vtk/files/vtk-7.0.0-glext.patch new file mode 100644 index 000000000000..5c321340ed6a --- /dev/null +++ b/sci-libs/vtk/files/vtk-7.0.0-glext.patch @@ -0,0 +1,12 @@ +--- a/Rendering/OpenGL/vtkOpenGL.h ++++ b/Rendering/OpenGL/vtkOpenGL.h +@@ -19,7 +19,8 @@ + #include "vtkConfigure.h" + + // To prevent gl.h to include glext.h provided by the system +-#define GL_GLEXT_LEGACY ++// https://bugzilla.redhat.com/show_bug.cgi?id=1138466 ++// #define GL_GLEXT_LEGACY + #if defined(__APPLE__) && defined(VTK_USE_COCOA) + # include <OpenGL/gl.h> // Include OpenGL API. + #else diff --git a/sci-libs/vtk/metadata.xml b/sci-libs/vtk/metadata.xml new file mode 100644 index 000000000000..dbcdc25b2345 --- /dev/null +++ b/sci-libs/vtk/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="all-modules">Build all modules</flag> + <flag name="boost">Add support for boost</flag> + <flag name="cg">Use nvidia's cg shaders</flag> + <flag name="gdal">Support for gdal formated data</flag> + <flag name="imaging">Building Imaging modules</flag> + <flag name="json">Support for json formated data</flag> + <flag name="kaapi">Use <pkg>sci-libs/xkaapi</pkg> to handle smp support</flag> + <flag name="offscreen">Offscreen rendering through OSMesa</flag> + <flag name="rendering">Building Redering modules</flag> + <flag name="tbb">Use <pkg>dev-cpp/tbb</pkg> to handle smp support</flag> + <flag name="views">Building Views modules</flag> + <flag name="web">Install web component</flag> + <flag name="xdmf2">Support for xdmf2 formated data</flag> + <flag name="R">Enable support for dev-lang/R</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/vtk/vtk-6.1.0-r3.ebuild b/sci-libs/vtk/vtk-6.1.0-r3.ebuild new file mode 100644 index 000000000000..1345bde683ec --- /dev/null +++ b/sci-libs/vtk/vtk-6.1.0-r3.ebuild @@ -0,0 +1,390 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +CMAKE_MAKEFILE_GENERATOR=ninja +WEBAPP_OPTIONAL=yes +WEBAPP_MANUAL_SLOT=yes + +inherit eutils flag-o-matic java-pkg-opt-2 python-single-r1 qmake-utils versionator toolchain-funcs cmake-utils virtualx webapp + +# Short package version +SPV="$(get_version_component_range 1-2)" + +DESCRIPTION="The Visualization Toolkit" +HOMEPAGE="http://www.vtk.org/" +SRC_URI=" + http://www.${PN}.org/files/release/${SPV}/VTK-${PV}.tar.gz + doc? ( http://www.${PN}.org/files/release/${SPV}/${PN}DocHtml-${PV}.tar.gz ) + test? ( + http://www.${PN}.org/files/release/${SPV}/VTKData-${PV}.tar.gz + http://www.${PN}.org/files/release/${SPV}/VTKLargeData-${PV}.tar.gz + ) + " + +LICENSE="BSD LGPL-2" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +SLOT="0" +IUSE=" + all-modules aqua boost cg doc examples imaging ffmpeg gdal java json kaapi mpi + mysql odbc offscreen postgres python qt4 rendering smp tbb test theora tk tcl + video_cards_nvidia views web xdmf2 R +X" + +REQUIRED_USE=" + all-modules? ( python xdmf2 ) + java? ( qt4 ) + python? ( ${PYTHON_REQUIRED_USE} ) + tcl? ( rendering ) + smp? ( ^^ ( kaapi tbb ) ) + test? ( python ) + tk? ( tcl ) + web? ( python ) + ^^ ( X aqua offscreen ) + " + +RDEPEND=" + dev-libs/expat + dev-libs/jsoncpp + dev-libs/libxml2:2 + >=media-libs/freetype-2.5.4 + media-libs/libpng:0 + media-libs/mesa + media-libs/libtheora + media-libs/tiff:0 + sci-libs/exodusii + sci-libs/hdf5:= + sci-libs/netcdf-cxx:3 + sys-libs/zlib + virtual/jpeg:0 + virtual/opengl + >=x11-libs/gl2ps-1.3.8 + x11-libs/libX11 + x11-libs/libXmu + x11-libs/libXt + boost? ( >=dev-libs/boost-1.40.0[mpi?] ) + cg? ( media-gfx/nvidia-cg-toolkit ) + examples? ( + dev-qt/qtcore:4 + dev-qt/qtgui:4 + sci-libs/vtkdata + ) + ffmpeg? ( virtual/ffmpeg ) + gdal? ( sci-libs/gdal ) + java? ( >=virtual/jre-1.5:* ) + kaapi? ( <sci-libs/xkaapi-3 ) + mpi? ( + virtual/mpi[cxx,romio] + python? ( dev-python/mpi4py[${PYTHON_USEDEP}] ) + mysql? ( virtual/mysql ) + odbc? ( dev-db/unixODBC ) + offscreen? ( media-libs/mesa[osmesa] ) + postgres? ( dev-db/postgresql:= ) + python? ( + ${PYTHON_DEPS} + dev-python/sip[${PYTHON_USEDEP}] + ) + ) + qt4? ( + dev-qt/designer:4 + dev-qt/qtcore:4 + dev-qt/qtgui:4 + dev-qt/qtopengl:4 + dev-qt/qtsql:4 + dev-qt/qtwebkit:4 + python? ( dev-python/PyQt4[${PYTHON_USEDEP}] ) + ) + tbb? ( dev-cpp/tbb ) + tcl? ( dev-lang/tcl:0= ) + tk? ( dev-lang/tk:0= ) + video_cards_nvidia? ( || ( x11-drivers/nvidia-drivers[tools,static-libs] media-video/nvidia-settings ) ) + web? ( + ${WEBAPP_DEPEND} + python? ( + dev-python/autobahn[${PYTHON_USEDEP}] + dev-python/twisted-core[${PYTHON_USEDEP}] + dev-python/zope-interface[${PYTHON_USEDEP}] + ) + ) + xdmf2? ( sci-libs/xdmf2 ) + R? ( dev-lang/R )" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + java? ( >=virtual/jdk-1.5 )" + +S="${WORKDIR}"/VTK-${PV} + +PATCHES=( + "${FILESDIR}"/${P}-freetype.patch + "${FILESDIR}"/${P}-install.patch + "${FILESDIR}"/${P}-system.patch + "${FILESDIR}"/${P}-netcdf.patch + "${FILESDIR}"/${P}-web.patch + "${FILESDIR}"/${P}-glext.patch + "${FILESDIR}"/${P}-memset.patch + "${FILESDIR}"/${P}-gdal2.patch + "${FILESDIR}"/${P}-gcc67.patch + ) + +RESTRICT=test + +pkg_setup() { + use java && java-pkg-opt-2_pkg_setup + use python && python-single-r1_pkg_setup + use web && webapp_pkg_setup + + append-cppflags -D__STDC_CONSTANT_MACROS -D_UNICODE +} + +src_prepare() { + sed \ + -e 's:libproj4:libproj:g' \ + -e 's:lib_proj.h:lib_abi.h:g' \ + -i CMake/FindLIBPROJ4.cmake || die + + local x + # missing: VPIC alglib exodusII freerange ftgl libproj4 mrmpi sqlite utf8 verdict xmdf2 xmdf3 + for x in expat freetype gl2ps hdf5 jpeg jsoncpp libxml2 netcdf oggtheora png tiff zlib; do + ebegin "Dropping bundled ${x}" + rm -r ThirdParty/${x}/vtk${x} || die + eend $? + done + rm -r \ + ThirdParty/AutobahnPython/autobahn \ + ThirdParty/Twisted/twisted \ + ThirdParty/ZopeInterface/zope \ + || die + + use java && export JAVA_HOME="${EPREFIX}/etc/java-config-2/current-system-vm" + + if use mpi; then + export CC=mpicc + export CXX=mpicxx + export FC=mpif90 + export F90=mpif90 + export F77=mpif77 + fi + + cmake-utils_src_prepare +} + +src_configure() { + # general configuration + local mycmakeargs=( + -Wno-dev +# -DCMAKE_SKIP_RPATH=YES + -DVTK_DIR="${S}" + -DVTK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DVTK_DATA_ROOT:PATH="${EPREFIX}/usr/share/${PN}/data" + -DCMAKE_INSTALL_PREFIX="${EPREFIX}/usr" + -DVTK_CUSTOM_LIBRARY_SUFFIX="" + -DBUILD_SHARED_LIBS=ON + -DVTK_USE_SYSTEM_AUTOBAHN=ON + -DVTK_USE_SYSTEM_EXPAT=ON + -DVTK_USE_SYSTEM_FREETYPE=ON + -DVTK_USE_SYSTEM_FreeType=ON + -DVTK_USE_SYSTEM_GL2PS=ON + -DVTK_USE_SYSTEM_HDF5=ON + -DVTK_USE_SYSTEM_JPEG=ON + -DVTK_USE_SYSTEM_LIBPROJ4=OFF +# -DLIBPROJ4_DIR="${EPREFIX}/usr" + -DVTK_USE_SYSTEM_LIBXML2=ON + -DVTK_USE_SYSTEM_LibXml2=ON + -DVTK_USE_SYSTEM_NETCDF=ON + -DVTK_USE_SYSTEM_OGGTHEORA=ON + -DVTK_USE_SYSTEM_PNG=ON + -DVTK_USE_SYSTEM_TIFF=ON + -DVTK_USE_SYSTEM_TWISTED=ON + -DVTK_USE_SYSTEM_XDMF2=OFF + -DVTK_USE_SYSTEM_XDMF3=OFF + -DVTK_USE_SYSTEM_ZLIB=ON + -DVTK_USE_SYSTEM_ZOPE=ON + -DVTK_USE_SYSTEM_LIBRARIES=ON + -DVTK_USE_GL2PS=ON + -DVTK_USE_LARGE_DATA=ON + -DVTK_USE_PARALLEL=ON + ) + + mycmakeargs+=( + -DVTK_EXTRA_COMPILER_WARNINGS=ON + -DVTK_Group_StandAlone=ON + ) + + mycmakeargs+=( + $(cmake-utils_use_build doc DOCUMENTATION) + $(cmake-utils_use_build examples EXAMPLES) + $(cmake-utils_use_build test VTK_BUILD_ALL_MODULES_FOR_TESTS) + $(cmake-utils_use all-modules VTK_BUILD_ALL_MODULES) + $(cmake-utils_use doc DOCUMENTATION_HTML_HELP) + $(cmake-utils_use imaging VTK_Group_Imaging) + $(cmake-utils_use mpi VTK_Group_MPI) + $(cmake-utils_use qt4 VTK_Group_Qt) + $(cmake-utils_use rendering VTK_Group_Rendering) + $(cmake-utils_use tk VTK_Group_Tk) + $(cmake-utils_use views VTK_Group_Views) + $(cmake-utils_use web VTK_Group_Web) + $(cmake-utils_use web VTK_WWW_DIR="${ED}/${MY_HTDOCSDIR}") + $(cmake-utils_use java VTK_WRAP_JAVA) + $(cmake-utils_use python VTK_WRAP_PYTHON) + $(cmake-utils_use python VTK_WRAP_PYTHON_SIP) + $(cmake-utils_use tcl VTK_WRAP_TCL) + ) + + mycmakeargs+=( + $(cmake-utils_use boost VTK_USE_BOOST) + $(cmake-utils_use cg VTK_USE_CG_SHADERS) + $(cmake-utils_use odbc VTK_USE_ODBC) + $(cmake-utils_use offscreen VTK_USE_OFFSCREEN) + $(cmake-utils_use offscreen VTK_OPENGL_HAS_OSMESA) + $(cmake-utils_use smp vtkFiltersSMP) + $(cmake-utils_use theora VTK_USE_OGGTHEORA_ENCODER) + $(cmake-utils_use video_cards_nvidia VTK_USE_NVCONTROL) + $(cmake-utils_use R Module_vtkFiltersStatisticsGnuR) + $(cmake-utils_use X VTK_USE_X) + ) + + # IO + mycmakeargs+=( + $(cmake-utils_use ffmpeg VTK_USE_FFMPEG_ENCODER) + $(cmake-utils_use gdal Module_vtkIOGDAL) + $(cmake-utils_use json Module_vtkIOGeoJSON) + $(cmake-utils_use xdmf2 Module_vtkIOXdmf2) + ) + # Apple stuff, does it really work? + mycmakeargs+=( $(cmake-utils_use aqua VTK_USE_COCOA) ) + + if use examples || use test; then + mycmakeargs+=( -DBUILD_TESTING=ON ) + fi + + if use kaapi; then + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Kaapi" ) + elif use tbb; then + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="TBB" ) + else + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Sequential" ) + fi + + if use java; then +# local _ejavahome=${EPREFIX}/etc/java-config-2/current-system-vm +# +# mycmakeargs+=( +# -DJAVAC=${EPREFIX}/usr/bin/javac +# -DJAVAC=$(java-config -c) +# -DJAVA_AWT_INCLUDE_PATH=${JAVA_HOME}/include +# -DJAVA_INCLUDE_PATH:PATH=${JAVA_HOME}/include +# -DJAVA_INCLUDE_PATH2:PATH=${JAVA_HOME}/include/linux +# ) +# + if [ "${ARCH}" == "amd64" ]; then + mycmakeargs+=( -DJAVA_AWT_LIBRARY="${JAVA_HOME}/jre/lib/${ARCH}/libjawt.so;${JAVA_HOME}/jre/lib/${ARCH}/xawt/libmawt.so" ) + else + mycmakeargs+=( -DJAVA_AWT_LIBRARY="${JAVA_HOME}/jre/lib/i386/libjawt.so;${JAVA_HOME}/jre/lib/i386/xawt/libmawt.so" ) + fi + fi + if use python; then + mycmakeargs+=( + -DVTK_INSTALL_PYTHON_MODULE_DIR="$(python_get_sitedir)" + -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DPYTHON_LIBRARY="$(python_get_library_path)" + -DSIP_PYQT_DIR="${EPREFIX}/usr/share/sip" + -DSIP_INCLUDE_DIR="$(python_get_includedir)" + -DVTK_PYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DVTK_PYTHON_LIBRARY="$(python_get_library_path)" + -DVTK_PYTHON_SETUP_ARGS:STRING="--prefix=${EPREFIX}/usr --root=${D}" + ) + fi + + if use qt4; then + mycmakeargs+=( + -DVTK_USE_QVTK=ON + -DVTK_USE_QVTK_OPENGL=ON + -DVTK_USE_QVTK_QTOPENGL=ON + -DQT_WRAP_CPP=ON + -DQT_WRAP_UI=ON + -DVTK_INSTALL_QT_DIR=/$(get_libdir)/qt4/plugins/designer + -DDESIRED_QT_VERSION=4 + -DVTK_QT_VERSION=4 + -DQT_MOC_EXECUTABLE="$(qt4_get_bindir)/moc" + -DQT_UIC_EXECUTABLE="$(qt4_get_bindir)/uic" + -DQT_INCLUDE_DIR="${EPREFIX}/usr/include/qt4" + -DQT_QMAKE_EXECUTABLE="$(qt4_get_bindir)/qmake" + ) + fi + + if use R; then + mycmakeargs+=( +# -DR_LIBRARY_BLAS=$($(tc-getPKG_CONFIG) --libs blas) +# -DR_LIBRARY_LAPACK=$($(tc-getPKG_CONFIG) --libs lapack) + -DR_LIBRARY_BLAS=/usr/$(get_libdir)/R/lib/libR.so + -DR_LIBRARY_LAPACK=/usr/$(get_libdir)/R/lib/libR.so + ) + fi + + cmake-utils_src_configure +} + +src_test() { + local tcllib + ln -sf "${BUILD_DIR}"/lib "${BUILD_DIR}"/lib/Release || die + for tcllib in "${BUILD_DIR}"/lib/lib*TCL*so; do + ln -sf $(basename "${tcllib}").1 "${tcllib/.so/-${SPV}.so}" || die + done + export LD_LIBRARY_PATH="${BUILD_DIR}"/lib:"${JAVA_HOME}"/jre/lib/${ARCH}/:"${JAVA_HOME}"/jre/lib/${ARCH}/xawt/ + local VIRTUALX_COMMAND="cmake-utils_src_test" +# local VIRTUALX_COMMAND="cmake-utils_src_test -R Java" +# local VIRTUALX_COMMAND="cmake-utils_src_test -I 364,365" + virtualmake +} + +src_install() { + use web && webapp_src_preinst + # install docs + HTML_DOCS=( "${S}"/README.html ) + + cmake-utils_src_install + + use java && java-pkg_regjar "${ED}"/usr/$(get_libdir)/${PN}.jar + + if use tcl; then + # install Tcl docs + docinto vtk_tcl + dodoc "${S}"/Wrapping/Tcl/README + fi + + # install examples + if use examples; then + insinto /usr/share/${PN} + mv -v Examples examples || die + doins -r examples + fi + + #install big docs + if use doc; then + cd "${WORKDIR}"/html || die + rm -f *.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + docinto html + dodoc -r ./* + fi + + # environment + cat >> "${T}"/40${PN} <<- EOF + VTK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data + VTK_DIR=${EPREFIX}/usr/$(get_libdir)/${PN}-${SPV} + VTKHOME=${EPREFIX}/usr + EOF + doenvd "${T}"/40${PN} + + use web && webapp_src_install +} + +# webapp.eclass exports these but we want it optional #534036 +pkg_postinst() { + use web && webapp_pkg_postinst +} + +pkg_prerm() { + use web && webapp_pkg_prerm +} diff --git a/sci-libs/vtk/vtk-6.1.0-r4.ebuild b/sci-libs/vtk/vtk-6.1.0-r4.ebuild new file mode 100644 index 000000000000..409b62823c89 --- /dev/null +++ b/sci-libs/vtk/vtk-6.1.0-r4.ebuild @@ -0,0 +1,390 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +CMAKE_MAKEFILE_GENERATOR=ninja +WEBAPP_OPTIONAL=yes +WEBAPP_MANUAL_SLOT=yes + +inherit eutils flag-o-matic java-pkg-opt-2 python-single-r1 qmake-utils versionator toolchain-funcs cmake-utils virtualx webapp + +# Short package version +SPV="$(get_version_component_range 1-2)" + +DESCRIPTION="The Visualization Toolkit" +HOMEPAGE="http://www.vtk.org/" +SRC_URI=" + http://www.${PN}.org/files/release/${SPV}/VTK-${PV}.tar.gz + doc? ( http://www.${PN}.org/files/release/${SPV}/${PN}DocHtml-${PV}.tar.gz ) + test? ( + http://www.${PN}.org/files/release/${SPV}/VTKData-${PV}.tar.gz + http://www.${PN}.org/files/release/${SPV}/VTKLargeData-${PV}.tar.gz + ) + " + +LICENSE="BSD LGPL-2" +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux" +SLOT="0" +IUSE=" + all-modules aqua boost cg doc examples imaging ffmpeg gdal java json kaapi mpi + mysql odbc offscreen postgres python qt5 rendering smp tbb test theora tk tcl + video_cards_nvidia views web xdmf2 R +X" + +REQUIRED_USE=" + all-modules? ( python xdmf2 ) + java? ( qt5 ) + python? ( ${PYTHON_REQUIRED_USE} ) + tcl? ( rendering ) + smp? ( ^^ ( kaapi tbb ) ) + test? ( python ) + tk? ( tcl ) + web? ( python ) + ^^ ( X aqua offscreen ) + " + +RDEPEND=" + dev-libs/expat + dev-libs/jsoncpp + dev-libs/libxml2:2 + >=media-libs/freetype-2.5.4 + media-libs/libpng:0 + media-libs/mesa + media-libs/libtheora + media-libs/tiff:0 + sci-libs/exodusii + sci-libs/hdf5:= + sci-libs/netcdf-cxx:3 + sys-libs/zlib + virtual/jpeg:0 + virtual/opengl + >=x11-libs/gl2ps-1.3.8 + x11-libs/libX11 + x11-libs/libXmu + x11-libs/libXt + boost? ( >=dev-libs/boost-1.40.0[mpi?] ) + cg? ( media-gfx/nvidia-cg-toolkit ) + examples? ( + dev-qt/qtcore:5 + dev-qt/qtgui:5 + sci-libs/vtkdata + ) + ffmpeg? ( virtual/ffmpeg ) + gdal? ( sci-libs/gdal ) + java? ( >=virtual/jre-1.5:* ) + kaapi? ( <sci-libs/xkaapi-3 ) + mpi? ( + virtual/mpi[cxx,romio] + python? ( dev-python/mpi4py[${PYTHON_USEDEP}] ) + mysql? ( virtual/mysql ) + odbc? ( dev-db/unixODBC ) + offscreen? ( media-libs/mesa[osmesa] ) + postgres? ( dev-db/postgresql:= ) + python? ( + ${PYTHON_DEPS} + dev-python/sip[${PYTHON_USEDEP}] + ) + ) + qt5? ( + dev-qt/designer:5 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtopengl:5 + dev-qt/qtsql:5 + dev-qt/qtwebkit:5 + python? ( dev-python/PyQt5[${PYTHON_USEDEP}] ) + ) + tbb? ( dev-cpp/tbb ) + tcl? ( dev-lang/tcl:0= ) + tk? ( dev-lang/tk:0= ) + video_cards_nvidia? ( || ( x11-drivers/nvidia-drivers[tools,static-libs] media-video/nvidia-settings ) ) + web? ( + ${WEBAPP_DEPEND} + python? ( + dev-python/autobahn[${PYTHON_USEDEP}] + dev-python/twisted-core[${PYTHON_USEDEP}] + dev-python/zope-interface[${PYTHON_USEDEP}] + ) + ) + xdmf2? ( sci-libs/xdmf2 ) + R? ( dev-lang/R )" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + java? ( >=virtual/jdk-1.5 )" + +S="${WORKDIR}"/VTK-${PV} + +PATCHES=( + "${FILESDIR}"/${P}-freetype.patch + "${FILESDIR}"/${P}-install.patch + "${FILESDIR}"/${P}-system.patch + "${FILESDIR}"/${P}-netcdf.patch + "${FILESDIR}"/${P}-web.patch + "${FILESDIR}"/${P}-glext.patch + "${FILESDIR}"/${P}-memset.patch + "${FILESDIR}"/${P}-gdal2.patch + "${FILESDIR}"/${P}-gcc67.patch + ) + +RESTRICT=test + +pkg_setup() { + use java && java-pkg-opt-2_pkg_setup + use python && python-single-r1_pkg_setup + use web && webapp_pkg_setup + + append-cppflags -D__STDC_CONSTANT_MACROS -D_UNICODE +} + +src_prepare() { + sed \ + -e 's:libproj4:libproj:g' \ + -e 's:lib_proj.h:lib_abi.h:g' \ + -i CMake/FindLIBPROJ4.cmake || die + + local x + # missing: VPIC alglib exodusII freerange ftgl libproj4 mrmpi sqlite utf8 verdict xmdf2 xmdf3 + for x in expat freetype gl2ps hdf5 jpeg jsoncpp libxml2 netcdf oggtheora png tiff zlib; do + ebegin "Dropping bundled ${x}" + rm -r ThirdParty/${x}/vtk${x} || die + eend $? + done + rm -r \ + ThirdParty/AutobahnPython/autobahn \ + ThirdParty/Twisted/twisted \ + ThirdParty/ZopeInterface/zope \ + || die + + use java && export JAVA_HOME="${EPREFIX}/etc/java-config-2/current-system-vm" + + if use mpi; then + export CC=mpicc + export CXX=mpicxx + export FC=mpif90 + export F90=mpif90 + export F77=mpif77 + fi + + cmake-utils_src_prepare +} + +src_configure() { + # general configuration + local mycmakeargs=( + -Wno-dev +# -DCMAKE_SKIP_RPATH=YES + -DVTK_DIR="${S}" + -DVTK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DVTK_DATA_ROOT:PATH="${EPREFIX}/usr/share/${PN}/data" + -DCMAKE_INSTALL_PREFIX="${EPREFIX}/usr" + -DVTK_CUSTOM_LIBRARY_SUFFIX="" + -DBUILD_SHARED_LIBS=ON + -DVTK_USE_SYSTEM_AUTOBAHN=ON + -DVTK_USE_SYSTEM_EXPAT=ON + -DVTK_USE_SYSTEM_FREETYPE=ON + -DVTK_USE_SYSTEM_FreeType=ON + -DVTK_USE_SYSTEM_GL2PS=ON + -DVTK_USE_SYSTEM_HDF5=ON + -DVTK_USE_SYSTEM_JPEG=ON + -DVTK_USE_SYSTEM_LIBPROJ4=OFF +# -DLIBPROJ4_DIR="${EPREFIX}/usr" + -DVTK_USE_SYSTEM_LIBXML2=ON + -DVTK_USE_SYSTEM_LibXml2=ON + -DVTK_USE_SYSTEM_NETCDF=ON + -DVTK_USE_SYSTEM_OGGTHEORA=ON + -DVTK_USE_SYSTEM_PNG=ON + -DVTK_USE_SYSTEM_TIFF=ON + -DVTK_USE_SYSTEM_TWISTED=ON + -DVTK_USE_SYSTEM_XDMF2=OFF + -DVTK_USE_SYSTEM_XDMF3=OFF + -DVTK_USE_SYSTEM_ZLIB=ON + -DVTK_USE_SYSTEM_ZOPE=ON + -DVTK_USE_SYSTEM_LIBRARIES=ON + -DVTK_USE_GL2PS=ON + -DVTK_USE_LARGE_DATA=ON + -DVTK_USE_PARALLEL=ON + ) + + mycmakeargs+=( + -DVTK_EXTRA_COMPILER_WARNINGS=ON + -DVTK_Group_StandAlone=ON + ) + + mycmakeargs+=( + $(cmake-utils_use_build doc DOCUMENTATION) + $(cmake-utils_use_build examples EXAMPLES) + $(cmake-utils_use_build test VTK_BUILD_ALL_MODULES_FOR_TESTS) + $(cmake-utils_use all-modules VTK_BUILD_ALL_MODULES) + $(cmake-utils_use doc DOCUMENTATION_HTML_HELP) + $(cmake-utils_use imaging VTK_Group_Imaging) + $(cmake-utils_use mpi VTK_Group_MPI) + $(cmake-utils_use rendering VTK_Group_Rendering) + $(cmake-utils_use tk VTK_Group_Tk) + $(cmake-utils_use views VTK_Group_Views) + $(cmake-utils_use web VTK_Group_Web) + $(cmake-utils_use web VTK_WWW_DIR="${ED}/${MY_HTDOCSDIR}") + $(cmake-utils_use java VTK_WRAP_JAVA) + $(cmake-utils_use python VTK_WRAP_PYTHON) + $(cmake-utils_use python VTK_WRAP_PYTHON_SIP) + $(cmake-utils_use tcl VTK_WRAP_TCL) + ) + + mycmakeargs+=( + $(cmake-utils_use boost VTK_USE_BOOST) + $(cmake-utils_use cg VTK_USE_CG_SHADERS) + $(cmake-utils_use odbc VTK_USE_ODBC) + $(cmake-utils_use offscreen VTK_USE_OFFSCREEN) + $(cmake-utils_use offscreen VTK_OPENGL_HAS_OSMESA) + $(cmake-utils_use smp vtkFiltersSMP) + $(cmake-utils_use theora VTK_USE_OGGTHEORA_ENCODER) + $(cmake-utils_use video_cards_nvidia VTK_USE_NVCONTROL) + $(cmake-utils_use R Module_vtkFiltersStatisticsGnuR) + $(cmake-utils_use X VTK_USE_X) + ) + + # IO + mycmakeargs+=( + $(cmake-utils_use ffmpeg VTK_USE_FFMPEG_ENCODER) + $(cmake-utils_use gdal Module_vtkIOGDAL) + $(cmake-utils_use json Module_vtkIOGeoJSON) + $(cmake-utils_use xdmf2 Module_vtkIOXdmf2) + ) + # Apple stuff, does it really work? + mycmakeargs+=( $(cmake-utils_use aqua VTK_USE_COCOA) ) + + if use examples || use test; then + mycmakeargs+=( -DBUILD_TESTING=ON ) + fi + + if use kaapi; then + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Kaapi" ) + elif use tbb; then + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="TBB" ) + else + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Sequential" ) + fi + + if use java; then +# local _ejavahome=${EPREFIX}/etc/java-config-2/current-system-vm +# +# mycmakeargs+=( +# -DJAVAC=${EPREFIX}/usr/bin/javac +# -DJAVAC=$(java-config -c) +# -DJAVA_AWT_INCLUDE_PATH=${JAVA_HOME}/include +# -DJAVA_INCLUDE_PATH:PATH=${JAVA_HOME}/include +# -DJAVA_INCLUDE_PATH2:PATH=${JAVA_HOME}/include/linux +# ) +# + if [ "${ARCH}" == "amd64" ]; then + mycmakeargs+=( -DJAVA_AWT_LIBRARY="${JAVA_HOME}/jre/lib/${ARCH}/libjawt.so;${JAVA_HOME}/jre/lib/${ARCH}/xawt/libmawt.so" ) + else + mycmakeargs+=( -DJAVA_AWT_LIBRARY="${JAVA_HOME}/jre/lib/i386/libjawt.so;${JAVA_HOME}/jre/lib/i386/xawt/libmawt.so" ) + fi + fi + if use python; then + mycmakeargs+=( + -DVTK_INSTALL_PYTHON_MODULE_DIR="$(python_get_sitedir)" + -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DPYTHON_LIBRARY="$(python_get_library_path)" + -DSIP_PYQT_DIR="${EPREFIX}/usr/share/sip" + -DSIP_INCLUDE_DIR="$(python_get_includedir)" + -DVTK_PYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DVTK_PYTHON_LIBRARY="$(python_get_library_path)" + -DVTK_PYTHON_SETUP_ARGS:STRING="--prefix=${EPREFIX}/usr --root=${D}" + ) + fi + + if use qt5; then + mycmakeargs+=( + -DVTK_USE_QVTK=ON + -DVTK_USE_QVTK_OPENGL=ON + -DVTK_USE_QVTK_QTOPENGL=ON + -DQT_WRAP_CPP=ON + -DQT_WRAP_UI=ON + -DVTK_INSTALL_QT_DIR=/$(get_libdir)/qt5/plugins/designer + -DDESIRED_QT_VERSION=5 + -DVTK_QT_VERSION=5 + -DQT_MOC_EXECUTABLE="$(qt5_get_bindir)/moc" + -DQT_UIC_EXECUTABLE="$(qt5_get_bindir)/uic" + -DQT_INCLUDE_DIR="${EPREFIX}/usr/include/qt5" + -DQT_QMAKE_EXECUTABLE="$(qt5_get_bindir)/qmake" + -DVTK_Group_Qt:BOOL=ON + ) + fi + + if use R; then + mycmakeargs+=( +# -DR_LIBRARY_BLAS=$($(tc-getPKG_CONFIG) --libs blas) +# -DR_LIBRARY_LAPACK=$($(tc-getPKG_CONFIG) --libs lapack) + -DR_LIBRARY_BLAS=/usr/$(get_libdir)/R/lib/libR.so + -DR_LIBRARY_LAPACK=/usr/$(get_libdir)/R/lib/libR.so + ) + fi + + cmake-utils_src_configure +} + +src_test() { + local tcllib + ln -sf "${BUILD_DIR}"/lib "${BUILD_DIR}"/lib/Release || die + for tcllib in "${BUILD_DIR}"/lib/lib*TCL*so; do + ln -sf $(basename "${tcllib}").1 "${tcllib/.so/-${SPV}.so}" || die + done + export LD_LIBRARY_PATH="${BUILD_DIR}"/lib:"${JAVA_HOME}"/jre/lib/${ARCH}/:"${JAVA_HOME}"/jre/lib/${ARCH}/xawt/ + local VIRTUALX_COMMAND="cmake-utils_src_test" +# local VIRTUALX_COMMAND="cmake-utils_src_test -R Java" +# local VIRTUALX_COMMAND="cmake-utils_src_test -I 364,365" + virtualmake +} + +src_install() { + use web && webapp_src_preinst + # install docs + HTML_DOCS=( "${S}"/README.html ) + + cmake-utils_src_install + + use java && java-pkg_regjar "${ED}"/usr/$(get_libdir)/${PN}.jar + + if use tcl; then + # install Tcl docs + docinto vtk_tcl + dodoc "${S}"/Wrapping/Tcl/README + fi + + # install examples + if use examples; then + insinto /usr/share/${PN} + mv -v Examples examples || die + doins -r examples + fi + + #install big docs + if use doc; then + cd "${WORKDIR}"/html || die + rm -f *.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + docinto html + dodoc -r ./* + fi + + # environment + cat >> "${T}"/40${PN} <<- EOF + VTK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data + VTK_DIR=${EPREFIX}/usr/$(get_libdir)/${PN}-${SPV} + VTKHOME=${EPREFIX}/usr + EOF + doenvd "${T}"/40${PN} + + use web && webapp_src_install +} + +# webapp.eclass exports these but we want it optional #534036 +pkg_postinst() { + use web && webapp_pkg_postinst +} + +pkg_prerm() { + use web && webapp_pkg_prerm +} diff --git a/sci-libs/vtk/vtk-7.0.0.ebuild b/sci-libs/vtk/vtk-7.0.0.ebuild new file mode 100644 index 000000000000..b6db179c4bb1 --- /dev/null +++ b/sci-libs/vtk/vtk-7.0.0.ebuild @@ -0,0 +1,348 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) +WEBAPP_OPTIONAL=yes +WEBAPP_MANUAL_SLOT=yes + +inherit flag-o-matic java-pkg-opt-2 python-single-r1 qmake-utils versionator toolchain-funcs cmake-utils virtualx webapp + +# Short package version +SPV="$(get_version_component_range 1-2)" + +DESCRIPTION="The Visualization Toolkit" +HOMEPAGE="http://www.vtk.org/" +SRC_URI=" + http://www.vtk.org/files/release/${SPV}/VTK-${PV}.tar.gz + doc? ( http://www.vtk.org/files/release/${SPV}/vtkDocHtml-${PV}.tar.gz ) + test? ( + http://www.vtk.org/files/release/${SPV}/VTKData-${PV}.tar.gz + http://www.vtk.org/files/release/${SPV}/VTKLargeData-${PV}.tar.gz + ) + " + +LICENSE="BSD LGPL-2" +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux" +SLOT="0" +IUSE=" + all-modules aqua boost doc examples imaging ffmpeg gdal java json kaapi mpi + mysql odbc offscreen postgres python qt5 rendering tbb test theora tk tcl + video_cards_nvidia views web xdmf2 R +X" + +REQUIRED_USE=" + all-modules? ( python xdmf2 boost ) + java? ( qt5 ) + python? ( ${PYTHON_REQUIRED_USE} ) + tcl? ( rendering ) + test? ( python ) + tk? ( tcl ) + web? ( python ) + ^^ ( X aqua offscreen ) + " + +RDEPEND=" + boost? ( dev-libs/boost:=[mpi?] ) + dev-libs/expat + dev-libs/jsoncpp:= + dev-libs/libxml2:2 + examples? ( + dev-qt/qtcore:5 + dev-qt/qtgui:5 + sci-libs/vtkdata + ) + ffmpeg? ( virtual/ffmpeg ) + gdal? ( sci-libs/gdal ) + java? ( >=virtual/jdk-1.7:* ) + kaapi? ( <sci-libs/xkaapi-3 ) + >=media-libs/freetype-2.5.4 + media-libs/libpng:0= + media-libs/mesa + media-libs/libtheora + media-libs/tiff:0 + mpi? ( + virtual/mpi[cxx,romio] + python? ( dev-python/mpi4py[${PYTHON_USEDEP}] ) + ) + mysql? ( virtual/mysql ) + odbc? ( dev-db/unixODBC ) + offscreen? ( media-libs/mesa[osmesa] ) + postgres? ( dev-db/postgresql:= ) + python? ( + ${PYTHON_DEPS} + dev-python/sip[${PYTHON_USEDEP}] + ) + qt5? ( + dev-qt/designer:5 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtopengl:5 + dev-qt/qtsql:5 + dev-qt/qtwebkit:5 + python? ( dev-python/PyQt5[${PYTHON_USEDEP}] ) + ) + R? ( dev-lang/R ) + sci-libs/exodusii + sci-libs/hdf5:= + sci-libs/netcdf-cxx:0= + sys-libs/zlib + tbb? ( dev-cpp/tbb ) + tcl? ( dev-lang/tcl:0= ) + tk? ( dev-lang/tk:0= ) + video_cards_nvidia? ( || ( x11-drivers/nvidia-drivers[tools,static-libs] media-video/nvidia-settings ) ) + virtual/jpeg:0 + virtual/opengl + web? ( + ${WEBAPP_DEPEND} + dev-python/autobahn[${PYTHON_USEDEP}] + dev-python/twisted-core[${PYTHON_USEDEP}] + dev-python/zope-interface[${PYTHON_USEDEP}] + ) + xdmf2? ( sci-libs/xdmf2 ) + >=x11-libs/gl2ps-1.3.8 + x11-libs/libX11 + x11-libs/libXmu + x11-libs/libXt" + +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +S="${WORKDIR}"/VTK-${PV} + +PATCHES=( + "${FILESDIR}"/${P}-glext.patch + "${FILESDIR}"/${PN}-6.1.0-memset.patch + "${FILESDIR}"/${PN}-6.1.0-gdal2.patch + ) + +RESTRICT=test + +pkg_setup() { + use java && java-pkg-opt-2_pkg_setup + use python && python-single-r1_pkg_setup + use web && webapp_pkg_setup +} + +src_prepare() { + sed \ + -e 's:libproj4:libproj:g' \ + -e 's:lib_proj.h:lib_abi.h:g' \ + -i CMake/FindLIBPROJ4.cmake || die + + local x + # missing: VPIC alglib exodusII freerange ftgl libproj4 mrmpi sqlite utf8 verdict xmdf2 xmdf3 + for x in expat freetype gl2ps hdf5 jpeg jsoncpp libxml2 netcdf oggtheora png tiff zlib; do + ebegin "Dropping bundled ${x}" + rm -r ThirdParty/${x}/vtk${x} || die + eend $? + done + rm -r \ + ThirdParty/AutobahnPython/autobahn \ + ThirdParty/Twisted/twisted \ + ThirdParty/ZopeInterface/zope \ + || die + + cmake-utils_src_prepare +} + +src_configure() { + # general configuration + local mycmakeargs=( + -Wno-dev + -DVTK_DIR="${S}" + -DVTK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DVTK_INSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}" + -DVTK_DATA_ROOT="${EPREFIX}/usr/share/${PN}/data" + -DVTK_CUSTOM_LIBRARY_SUFFIX="" + -DBUILD_SHARED_LIBS=ON + -DVTK_USE_SYSTEM_AUTOBAHN=ON + -DVTK_USE_SYSTEM_EXPAT=ON + -DVTK_USE_SYSTEM_FREETYPE=ON + -DVTK_USE_SYSTEM_FreeType=ON + -DVTK_USE_SYSTEM_GL2PS=ON + -DVTK_USE_SYSTEM_HDF5=ON + -DVTK_USE_SYSTEM_JPEG=ON + -DVTK_USE_SYSTEM_LIBPROJ4=OFF + -DVTK_USE_SYSTEM_LIBXML2=ON + -DVTK_USE_SYSTEM_LibXml2=ON + -DVTK_USE_SYSTEM_NETCDF=ON + -DVTK_USE_SYSTEM_OGGTHEORA=ON + -DVTK_USE_SYSTEM_PNG=ON + -DVTK_USE_SYSTEM_TIFF=ON + -DVTK_USE_SYSTEM_TWISTED=ON + -DVTK_USE_SYSTEM_XDMF2=OFF + -DVTK_USE_SYSTEM_XDMF3=OFF + -DVTK_USE_SYSTEM_ZLIB=ON + -DVTK_USE_SYSTEM_ZOPE=ON + -DVTK_USE_SYSTEM_LIBRARIES=ON + -DVTK_USE_GL2PS=ON + -DVTK_USE_LARGE_DATA=ON + -DVTK_USE_PARALLEL=ON + -DVTK_EXTRA_COMPILER_WARNINGS=ON + -DVTK_Group_StandAlone=ON + -DBUILD_DOCUMENTATION=$(usex doc) + -DBUILD_EXAMPLES=$(usex examples) + -DBUILD_VTK_BUILD_ALL_MODULES_FOR_TESTS=$(usex test) + -DVTK_BUILD_ALL_MODULES=$(usex all-modules) + -DUSE_DOCUMENTATION_HTML_HELP=$(usex doc) + -DVTK_Group_Imaging=$(usex imaging) + -DVTK_Group_MPI=$(usex mpi) + -DVTK_Group_Rendering=$(usex rendering) + -DVTK_Group_Tk=$(usex tk) + -DVTK_Group_Views=$(usex views) + -DVTK_Group_Web=$(usex web) + -DVTK_WWW_DIR="${ED%/}/${MY_HTDOCSDIR}" + -DVTK_WRAP_JAVA=$(usex java) + -DVTK_WRAP_PYTHON=$(usex python) + -DVTK_WRAP_PYTHON_SIP=$(usex python) + -DVTK_WRAP_TCL=$(usex tcl) + -DVTK_USE_BOOST=$(usex boost) + -DUSE_VTK_USE_BOOST=$(usex boost) + -DModule_vtkInfovisBoost=$(usex boost) + -DModule_vtkInfovisBoostGraphAlgorithms=$(usex boost) + -DVTK_USE_ODBC=$(usex odbc) + -DModule_vtkIOODBC=$(usex odbc) + -DVTK_USE_OFFSCREEN=$(usex offscreen) + -DVTK_OPENGL_HAS_OSMESA=$(usex offscreen) + -DVTK_USE_OGGTHEORA_ENCODER=$(usex theora) + -DVTK_USE_NVCONTROL=$(usex video_cards_nvidia) + -DModule_vtkFiltersStatisticsGnuR=$(usex R) + -DVTK_USE_X=$(usex X) + # IO + -DVTK_USE_FFMPEG_ENCODER=$(usex ffmpeg) + -DModule_vtkIOGDAL=$(usex gdal) + -DModule_vtkIOGeoJSON=$(usex json) + -DModule_vtkIOXdmf2=$(usex xdmf2) + # Apple stuff, does it really work? + -DVTK_USE_COCOA=$(usex aqua) + ) + + if use examples || use test; then + mycmakeargs+=( -DBUILD_TESTING=ON ) + fi + + if use java; then + local javacargs=$(java-pkg_javac-args) + mycmakeargs+=( -DJAVAC_OPTIONS=${javacargs// /;} ) + fi + + if use kaapi; then + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Kaapi" ) + elif use tbb; then + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="TBB" ) + else + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Sequential" ) + fi + + if use python; then + mycmakeargs+=( + -DVTK_INSTALL_PYTHON_MODULE_DIR="$(python_get_sitedir)" + -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DPYTHON_LIBRARY="$(python_get_library_path)" + -DSIP_PYQT_DIR="${EPREFIX}/usr/share/sip" + -DSIP_INCLUDE_DIR="$(python_get_includedir)" + -DVTK_PYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DVTK_PYTHON_LIBRARY="$(python_get_library_path)" + -DVTK_PYTHON_SETUP_ARGS:STRING="--prefix=${EPREFIX} --root=${D}" + ) + fi + + if use qt5; then + mycmakeargs+=( + -DVTK_USE_QVTK=ON + -DVTK_USE_QVTK_OPENGL=ON + -DVTK_USE_QVTK_QTOPENGL=ON + -DQT_WRAP_CPP=ON + -DQT_WRAP_UI=ON + -DVTK_INSTALL_QT_DIR="$(qt5_get_libdir)/qt5/plugins/designer" + -DDESIRED_QT_VERSION=5 + -DVTK_QT_VERSION=5 + -DQT_MOC_EXECUTABLE="$(qt5_get_bindir)/moc" + -DQT_UIC_EXECUTABLE="$(qt5_get_bindir)/uic" + -DQT_INCLUDE_DIR="${EPREFIX}/usr/include/qt5" + -DQT_QMAKE_EXECUTABLE="$(qt5_get_bindir)/qmake" + -DVTK_Group_Qt:BOOL=ON + ) + fi + + if use R; then + mycmakeargs+=( + -DR_LIBRARY_BLAS=/usr/$(get_libdir)/R/lib/libR.so + -DR_LIBRARY_LAPACK=/usr/$(get_libdir)/R/lib/libR.so + ) + fi + + append-cppflags -D__STDC_CONSTANT_MACROS -D_UNICODE + + use java && export JAVA_HOME="${EPREFIX}/etc/java-config-2/current-system-vm" + + if use mpi; then + export CC=mpicc + export CXX=mpicxx + export FC=mpif90 + export F90=mpif90 + export F77=mpif77 + fi + + cmake-utils_src_configure +} + +src_test() { + local tcllib + ln -sf "${BUILD_DIR}"/lib "${BUILD_DIR}"/lib/Release || die + for tcllib in "${BUILD_DIR}"/lib/lib*TCL*so; do + ln -sf ${tcllib##*/}.1 "${tcllib/.so/-${SPV}.so}" || die + done + export LD_LIBRARY_PATH="${BUILD_DIR}"/lib:"${JAVA_HOME}"/jre/lib/${ARCH}/:"${JAVA_HOME}"/jre/lib/${ARCH}/xawt/ + virtx cmake-utils_src_test +} + +src_install() { + use web && webapp_src_preinst + + cmake-utils_src_install + + use java && java-pkg_regjar "${ED%/}"/usr/$(get_libdir)/${PN}.jar + + if use tcl; then + # install Tcl docs + docinto vtk_tcl + dodoc Wrapping/Tcl/README + docinto . + fi + + # install examples + if use examples; then + einfo "Installing examples" + mv -v {E,e}xamples || die + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi + + #install big docs + if use doc; then + rm -f "${WORKDIR}"/html/*.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + dodoc -r "${WORKDIR}"/html + fi + + # environment + cat >> "${T}"/40${PN} <<- EOF || die + VTK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data + VTK_DIR=${EPREFIX}/usr/$(get_libdir)/${PN}-${SPV} + VTKHOME=${EPREFIX}/usr + EOF + doenvd "${T}"/40${PN} + + use web && webapp_src_install +} + +# webapp.eclass exports these but we want it optional #534036 +pkg_postinst() { + use web && webapp_pkg_postinst +} + +pkg_prerm() { + use web && webapp_pkg_prerm +} diff --git a/sci-libs/vtk/vtk-7.1.0.ebuild b/sci-libs/vtk/vtk-7.1.0.ebuild new file mode 100644 index 000000000000..b3324b6d7d74 --- /dev/null +++ b/sci-libs/vtk/vtk-7.1.0.ebuild @@ -0,0 +1,349 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) +WEBAPP_OPTIONAL=yes +WEBAPP_MANUAL_SLOT=yes + +inherit flag-o-matic java-pkg-opt-2 python-single-r1 qmake-utils versionator toolchain-funcs cmake-utils virtualx webapp + +# Short package version +SPV="$(get_version_component_range 1-2)" + +DESCRIPTION="The Visualization Toolkit" +HOMEPAGE="http://www.vtk.org/" +SRC_URI=" + http://www.vtk.org/files/release/${SPV}/VTK-${PV}.tar.gz + doc? ( http://www.vtk.org/files/release/${SPV}/vtkDocHtml-${PV}.tar.gz ) + test? ( + http://www.vtk.org/files/release/${SPV}/VTKData-${PV}.tar.gz + http://www.vtk.org/files/release/${SPV}/VTKLargeData-${PV}.tar.gz + ) + " + +LICENSE="BSD LGPL-2" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +SLOT="0" +IUSE=" + all-modules aqua boost doc examples imaging ffmpeg gdal java json kaapi mpi + mysql odbc offscreen postgres python qt5 rendering tbb test theora tk tcl + video_cards_nvidia views web R +X xdmf2" + +REQUIRED_USE=" + all-modules? ( python xdmf2 boost ) + java? ( qt5 ) + python? ( ${PYTHON_REQUIRED_USE} ) + tcl? ( rendering ) + test? ( python ) + tk? ( tcl ) + web? ( python ) + ^^ ( X aqua offscreen ) + " + +RDEPEND=" + boost? ( dev-libs/boost:=[mpi?] ) + dev-libs/expat + dev-libs/jsoncpp:= + dev-libs/libxml2:2 + examples? ( + dev-qt/qtcore:5 + dev-qt/qtgui:5 + sci-libs/vtkdata + ) + ffmpeg? ( virtual/ffmpeg ) + gdal? ( sci-libs/gdal ) + java? ( >=virtual/jdk-1.7:* ) + kaapi? ( <sci-libs/xkaapi-3 ) + >=media-libs/freetype-2.5.4 + media-libs/libpng:0= + media-libs/mesa + media-libs/libtheora + media-libs/tiff:0 + mpi? ( + virtual/mpi[cxx,romio] + python? ( dev-python/mpi4py[${PYTHON_USEDEP}] ) + ) + mysql? ( virtual/mysql ) + odbc? ( dev-db/unixODBC ) + offscreen? ( media-libs/mesa[osmesa] ) + postgres? ( dev-db/postgresql:= ) + python? ( + ${PYTHON_DEPS} + dev-python/sip[${PYTHON_USEDEP}] + ) + qt5? ( + dev-qt/designer:5 + dev-qt/qtcore:5 + dev-qt/qtgui:5 + dev-qt/qtopengl:5 + dev-qt/qtsql:5 + dev-qt/qtwebkit:5 + python? ( dev-python/PyQt5[${PYTHON_USEDEP}] ) + ) + R? ( dev-lang/R ) + sci-libs/exodusii + sci-libs/hdf5:= + sci-libs/netcdf-cxx:3 + sys-libs/zlib + tbb? ( dev-cpp/tbb ) + tcl? ( dev-lang/tcl:0= ) + tk? ( dev-lang/tk:0= ) + video_cards_nvidia? ( || ( x11-drivers/nvidia-drivers[tools,static-libs] media-video/nvidia-settings ) ) + virtual/jpeg:0 + virtual/opengl + web? ( + ${WEBAPP_DEPEND} + dev-python/autobahn[${PYTHON_USEDEP}] + dev-python/twisted-core[${PYTHON_USEDEP}] + dev-python/zope-interface[${PYTHON_USEDEP}] + ) + xdmf2? ( sci-libs/xdmf2 ) + x11-libs/libX11 + x11-libs/libXmu + x11-libs/libXt" + +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +S="${WORKDIR}"/VTK-${PV} + +PATCHES=( + "${FILESDIR}"/${PN}-7.0.0-glext.patch + "${FILESDIR}"/${PN}-6.1.0-memset.patch + ) + +RESTRICT=test + +pkg_setup() { + use java && java-pkg-opt-2_pkg_setup + use python && python-single-r1_pkg_setup + use web && webapp_pkg_setup +} + +src_prepare() { + sed \ + -e 's:libproj4:libproj:g' \ + -e 's:lib_proj.h:lib_abi.h:g' \ + -i CMake/FindLIBPROJ4.cmake || die + + local x + # missing: VPIC alglib exodusII freerange ftgl libproj4 mrmpi sqlite utf8 verdict xmdf2 xmdf3 + for x in expat freetype hdf5 jpeg jsoncpp libxml2 netcdf oggtheora png tiff zlib; do + ebegin "Dropping bundled ${x}" + rm -r ThirdParty/${x}/vtk${x} || die + eend $? + done + rm -r \ + ThirdParty/AutobahnPython/autobahn \ + ThirdParty/Twisted/twisted \ + ThirdParty/ZopeInterface/zope \ + || die + + cmake-utils_src_prepare +} + +src_configure() { + # general configuration + local mycmakeargs=( + -Wno-dev + -DVTK_DIR="${S}" + -DVTK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DVTK_INSTALL_DOC_DIR="${EPREFIX}/usr/share/doc/${PF}" + -DVTK_DATA_ROOT="${EPREFIX}/usr/share/${PN}/data" + -DVTK_CUSTOM_LIBRARY_SUFFIX="" + -DBUILD_SHARED_LIBS=ON + -DVTK_USE_SYSTEM_AUTOBAHN=ON + -DVTK_USE_SYSTEM_EXPAT=ON + -DVTK_USE_SYSTEM_FREETYPE=ON + -DVTK_USE_SYSTEM_FreeType=ON + # Use bundled gl2ps (bundled version is a patched version of 1.3.9. Post 1.3.9 versions should be compatible) + -DVTK_USE_SYSTEM_GL2PS=OFF + -DVTK_USE_SYSTEM_HDF5=ON + -DVTK_USE_SYSTEM_JPEG=ON + -DVTK_USE_SYSTEM_LIBPROJ4=OFF + -DVTK_USE_SYSTEM_LIBXML2=ON + -DVTK_USE_SYSTEM_LibXml2=ON + -DVTK_USE_SYSTEM_NETCDF=ON + -DVTK_USE_SYSTEM_OGGTHEORA=ON + -DVTK_USE_SYSTEM_PNG=ON + -DVTK_USE_SYSTEM_TIFF=ON + -DVTK_USE_SYSTEM_TWISTED=ON + -DVTK_USE_SYSTEM_XDMF2=OFF + -DVTK_USE_SYSTEM_XDMF3=OFF + -DVTK_USE_SYSTEM_ZLIB=ON + -DVTK_USE_SYSTEM_ZOPE=ON + -DVTK_USE_SYSTEM_LIBRARIES=ON + # Use bundled diy2 (no gentoo package / upstream does not provide a Finddiy2.cmake or diy2Config.cmake / diy2-config.cmake) + -DVTK_USE_SYSTEM_DIY2=OFF + -DVTK_USE_GL2PS=ON + -DVTK_USE_LARGE_DATA=ON + -DVTK_USE_PARALLEL=ON + -DVTK_EXTRA_COMPILER_WARNINGS=ON + -DVTK_Group_StandAlone=ON + -DBUILD_DOCUMENTATION=$(usex doc) + -DBUILD_EXAMPLES=$(usex examples) + -DBUILD_VTK_BUILD_ALL_MODULES_FOR_TESTS=$(usex test) + -DVTK_BUILD_ALL_MODULES=$(usex all-modules) + -DUSE_DOCUMENTATION_HTML_HELP=$(usex doc) + -DVTK_Group_Imaging=$(usex imaging) + -DVTK_Group_MPI=$(usex mpi) + -DVTK_Group_Rendering=$(usex rendering) + -DVTK_Group_Tk=$(usex tk) + -DVTK_Group_Views=$(usex views) + -DVTK_Group_Web=$(usex web) + -DVTK_WWW_DIR="${ED%/}/${MY_HTDOCSDIR}" + -DVTK_WRAP_JAVA=$(usex java) + -DVTK_WRAP_PYTHON=$(usex python) + -DVTK_WRAP_PYTHON_SIP=$(usex python) + -DVTK_WRAP_TCL=$(usex tcl) + -DVTK_USE_BOOST=$(usex boost) + -DUSE_VTK_USE_BOOST=$(usex boost) + -DModule_vtkInfovisBoost=$(usex boost) + -DModule_vtkInfovisBoostGraphAlgorithms=$(usex boost) + -DVTK_USE_ODBC=$(usex odbc) + -DModule_vtkIOODBC=$(usex odbc) + -DVTK_USE_OFFSCREEN=$(usex offscreen) + -DVTK_OPENGL_HAS_OSMESA=$(usex offscreen) + -DVTK_USE_OGGTHEORA_ENCODER=$(usex theora) + -DVTK_USE_NVCONTROL=$(usex video_cards_nvidia) + -DModule_vtkFiltersStatisticsGnuR=$(usex R) + -DVTK_USE_X=$(usex X) + # IO + -DVTK_USE_FFMPEG_ENCODER=$(usex ffmpeg) + -DModule_vtkIOGDAL=$(usex gdal) + -DModule_vtkIOGeoJSON=$(usex json) + -DModule_vtkIOXdmf2=$(usex xdmf2) + # Apple stuff, does it really work? + -DVTK_USE_COCOA=$(usex aqua) + ) + + if use examples || use test; then + mycmakeargs+=( -DBUILD_TESTING=ON ) + fi + + if use java; then + local javacargs=$(java-pkg_javac-args) + mycmakeargs+=( -DJAVAC_OPTIONS=${javacargs// /;} ) + fi + + if use kaapi; then + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Kaapi" ) + elif use tbb; then + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="TBB" ) + else + mycmakeargs+=( -DVTK_SMP_IMPLEMENTATION_TYPE="Sequential" ) + fi + + if use python; then + mycmakeargs+=( + -DVTK_INSTALL_PYTHON_MODULE_DIR="$(python_get_sitedir)" + -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DPYTHON_LIBRARY="$(python_get_library_path)" + -DSIP_PYQT_DIR="${EPREFIX}/usr/share/sip" + -DSIP_INCLUDE_DIR="$(python_get_includedir)" + -DVTK_PYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DVTK_PYTHON_LIBRARY="$(python_get_library_path)" + -DVTK_PYTHON_SETUP_ARGS:STRING="--prefix=${EPREFIX} --root=${D}" + ) + fi + + if use qt5; then + mycmakeargs+=( + -DVTK_USE_QVTK=ON + -DVTK_USE_QVTK_OPENGL=ON + -DVTK_USE_QVTK_QTOPENGL=ON + -DQT_WRAP_CPP=ON + -DQT_WRAP_UI=ON + -DVTK_INSTALL_QT_DIR="$(qt5_get_libdir)/qt5/plugins/designer" + -DDESIRED_QT_VERSION=5 + -DVTK_QT_VERSION=5 + -DQT_MOC_EXECUTABLE="$(qt5_get_bindir)/moc" + -DQT_UIC_EXECUTABLE="$(qt5_get_bindir)/uic" + -DQT_INCLUDE_DIR="${EPREFIX}/usr/include/qt5" + -DQT_QMAKE_EXECUTABLE="$(qt5_get_bindir)/qmake" + -DVTK_Group_Qt:BOOL=ON + ) + fi + + if use R; then + mycmakeargs+=( + -DR_LIBRARY_BLAS=/usr/$(get_libdir)/R/lib/libR.so + -DR_LIBRARY_LAPACK=/usr/$(get_libdir)/R/lib/libR.so + ) + fi + + append-cppflags -D__STDC_CONSTANT_MACROS -D_UNICODE + + use java && export JAVA_HOME="${EPREFIX}/etc/java-config-2/current-system-vm" + + if use mpi; then + export CC=mpicc + export CXX=mpicxx + export FC=mpif90 + export F90=mpif90 + export F77=mpif77 + fi + + cmake-utils_src_configure +} + +src_test() { + local tcllib + ln -sf "${BUILD_DIR}"/lib "${BUILD_DIR}"/lib/Release || die + for tcllib in "${BUILD_DIR}"/lib/lib*TCL*so; do + ln -sf ${tcllib##*/}.1 "${tcllib/.so/-${SPV}.so}" || die + done + export LD_LIBRARY_PATH="${BUILD_DIR}"/lib:"${JAVA_HOME}"/jre/lib/${ARCH}/:"${JAVA_HOME}"/jre/lib/${ARCH}/xawt/ + virtx cmake-utils_src_test +} + +src_install() { + use web && webapp_src_preinst + + cmake-utils_src_install + + use java && java-pkg_regjar "${ED%/}"/usr/$(get_libdir)/${PN}.jar + + if use tcl; then + # install Tcl docs + docinto vtk_tcl + dodoc Wrapping/Tcl/README + docinto . + fi + + # install examples + if use examples; then + einfo "Installing examples" + mv -v {E,e}xamples || die + dodoc -r examples + docompress -x /usr/share/doc/${PF}/examples + fi + + #install big docs + if use doc; then + rm -f "${WORKDIR}"/html/*.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + dodoc -r "${WORKDIR}"/html + fi + + # environment + cat >> "${T}"/40${PN} <<- EOF || die + VTK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data + VTK_DIR=${EPREFIX}/usr/$(get_libdir)/${PN}-${SPV} + VTKHOME=${EPREFIX}/usr + EOF + doenvd "${T}"/40${PN} + + use web && webapp_src_install +} + +# webapp.eclass exports these but we want it optional #534036 +pkg_postinst() { + use web && webapp_pkg_postinst +} + +pkg_prerm() { + use web && webapp_pkg_prerm +} diff --git a/sci-libs/vtkdata/Manifest b/sci-libs/vtkdata/Manifest new file mode 100644 index 000000000000..1124b3dc4255 --- /dev/null +++ b/sci-libs/vtkdata/Manifest @@ -0,0 +1,7 @@ +DIST VTKData-6.1.0.tar.gz 94452190 SHA256 aba27ac05d721e36b9424131f1d0f673448f2b31aac34e9e74590fdf208ad0c7 SHA512 4e23cc3de3b81a852458849f2bd4dfe2e84e9df4f77f5f0d4ac249b04a7f74144a483a91876bd748bb90685d1943071e9b36fce8dd618376621bc37e63365e65 WHIRLPOOL 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a/sci-libs/vtkdata/vtkdata-6.0.0.ebuild b/sci-libs/vtkdata/vtkdata-6.0.0.ebuild new file mode 100644 index 000000000000..0ecf958ee161 --- /dev/null +++ b/sci-libs/vtkdata/vtkdata-6.0.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit versionator + +DESCRIPTION="Example data file for VTK" +HOMEPAGE="http://www.vtk.org" +SRC_URI="http://www.vtk.org/files/release/$(get_version_component_range 1-2)/${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RESTRICT="binchecks strip" + +RDEPEND="!<sci-libs/vtk-6" + +S="${WORKDIR}"/VTKDATA${PV} + +src_install() { + insinto /usr/share/vtk/data + doins -r * +} diff --git a/sci-libs/vtkdata/vtkdata-6.1.0.ebuild b/sci-libs/vtkdata/vtkdata-6.1.0.ebuild new file mode 100644 index 000000000000..551014f6949d --- /dev/null +++ b/sci-libs/vtkdata/vtkdata-6.1.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit versionator + +DESCRIPTION="Example data file for VTK" +HOMEPAGE="http://www.vtk.org" +SRC_URI="http://www.vtk.org/files/release/$(get_version_component_range 1-2)/VTKData-${PV}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +IUSE="" + +RESTRICT="binchecks strip" + +RDEPEND="!<sci-libs/vtk-6" + +S="${WORKDIR}"/VTK-${PV} + +src_install() { + insinto /usr/share/vtk/data + doins -r .ExternalData +} diff --git a/sci-libs/xdmf2/Manifest b/sci-libs/xdmf2/Manifest new file mode 100644 index 000000000000..08f5f43bd7cb --- /dev/null +++ b/sci-libs/xdmf2/Manifest @@ -0,0 +1,8 @@ +AUX xdmf2-1.0_p141226-cannot-find-hdf5-bug-591302.patch 1675 SHA256 01b185da444db8b553a42457fd18a4f3d1153dcdb077396df606c2602925aabb SHA512 c2a8a2e5f39b86cd083211f5e14188e8f63822d24b1b0d8a8beb485f0a0766894b4dcd717f6cc57c6352e46b4c69574b5c05ec318b7d6819d03fa68fbcd2e5ea WHIRLPOOL 4eb90fb0597fb4820d18c2d54162403c3c15f421a7c7b333c27632715964f169d17bf3adaf110e33c78764a0d4c4d50c022564eef9b13aa2a4b6026ae00ff9b1 +AUX xdmf2-1.0_p141226-module.patch 452 SHA256 8e254633cab00c1835e0c594c90ae89b405ecb703fffe8a501c487fc0b39f4b2 SHA512 9a9e05001f1d8ea8250a7bb9231a43e8cceeface61fb125330b6255a1ba452650a80cb6592a69fdecc04212752c0d1fa195151b13c88262c40a36ca566a33dcd WHIRLPOOL 476e0b4ac6e216fd678f24f78c4c534d81cd7ff28a3163aa6a4b6bc5b99344f0e5c6c9356cedbf2871d272a6b4e1d1d37cb6365c58286a36838f0433a8328ebf +DIST xdmf2-1.0_p141226.tar.xz 267096 SHA256 9738bfb5d9ae92b885d1543f02ca4ad34f8eb71e6a697980465f40bba7dcf7c5 SHA512 031b947ccd942c39cb40504e939f03bc9e3190ae1a7baf8325809decf70a040e860b43d5bc9debfcf2f3838f5f0d7a9c77c92561c89fc0d632306e140b136db9 WHIRLPOOL f6698badae43d1710ee4642139ff6bc3ecd11424c1d1b72a09a4de2c10edaafd213f0b0773fba133067607c6eba08b39f38d82eef3bf94e709c8dd3257ca09ab +EBUILD xdmf2-1.0_p141226-r1.ebuild 1484 SHA256 0a7d8a6388b12d93857fdd2c857659abe04d557697fedf2b44aba669f1e08b1e SHA512 c43c846d550da9c12834f00325c3d8d1f8f2511ec58ef04036d855fd643c6c5c27d1b8cec5b88f5275904959fcce6a2cb2e0df96d474ffc2db8affce69d7ca6d WHIRLPOOL ebd960775133b3e35ede42863703e6f626534d8bb9b6fc78467b3e75cf162bccddc374ca476984466ef2a0926772b7837c6e2fbf9401a3eaf3270699b7794eb6 +EBUILD xdmf2-1.0_p141226-r2.ebuild 1710 SHA256 44a21e0f56e553224d5e17af502d0957969072dd1643c3c15419be1cd93faa57 SHA512 1795253fc018b7e135691fee4cb19a8750cedba50bca4d3acc92bf490093b87a903d5a41c3d2fa18afbe9bee10f03cbfe0784a0302f84f1afd4fccb3e9c5eac4 WHIRLPOOL b738a948e7feac176594057de2081442126fe6442a7a8f5204f9c0be6361f28851f5f2ac57e0f823ab9f109a9d1e1b36b1ad72181565364e0dff03d5a27f0582 +MISC ChangeLog 3351 SHA256 cb0fe4f26e9e771163d76690e4555eb5b1981094e5864b35d79823f60edf89c8 SHA512 1ba673d9ea4529fb80ab1e015ed5a7f7a947b25c9bc857fdb75288cb5e6037f768072c0401fc5d5ec322156266e9b5edab761f8a9ea6d068af2dae2f6dceef9a WHIRLPOOL 1b6ade6c428a8ebd2e4757438b85e1ecf90a54c44fdc86d0e9ebf6770e1c27ae7f4ab0e9f5dcaf528b79dafffb3d1ac146271990e7921b22b6a9dd25014ef1df +MISC ChangeLog-2015 965 SHA256 9ea2fa40fe9b63352c4bf894530c247371d587b2b9a3af77a9459223772138d6 SHA512 1b6bbb22c7686249f21d51ceb9eb9193d5fd3856fd400b0e40f5c42c985d842c21ed751fa600159b1a75e1c9dde83480c622b282ac6caa921d9408c0fd0feba3 WHIRLPOOL 411f4524935da04e315416c92d89cd3a01ecfc5b6a7133d8eff49a6e284edecd680597b6e8e5611c76a1c732091862bbee6327d3a6bcfef557b815845e78ae8b +MISC metadata.xml 259 SHA256 bbfbeb80ffccffa8e7f837d2c93e994bbe024d565ae3a31d30c6646e80a684c8 SHA512 19fb78cf4029c154954a40df40e28fc8d98a8b7e6b42f97259f664d44c29b284feffb9d073cadc7f90b5654a64b2466e186cb677d3a11830206f173eb9057706 WHIRLPOOL 75b8dd1a97dde63f9cc9f73b5951eaf54579460763ef7cbe6f3a9a0739070601d762152ea00df8b476b80e92e5c29b611a494bac5ab747298942530cabe0ee84 diff --git a/sci-libs/xdmf2/files/xdmf2-1.0_p141226-cannot-find-hdf5-bug-591302.patch b/sci-libs/xdmf2/files/xdmf2-1.0_p141226-cannot-find-hdf5-bug-591302.patch new file mode 100644 index 000000000000..99735a480c67 --- /dev/null +++ b/sci-libs/xdmf2/files/xdmf2-1.0_p141226-cannot-find-hdf5-bug-591302.patch @@ -0,0 +1,41 @@ +Too much automagic trying to find the correct prefix +of HDF5. Remove all the pointless heuristics. +See also: https://bugs.gentoo.org/show_bug.cgi?id=591302 + +* CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:148 (message): +* Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS +* HDF5_HL_LIBRARIES) + +--- xdmf2-1.0_p141226/core/CMakeLists.txt ++++ xdmf2-1.0_p141226/core/CMakeLists.txt +@@ -35,19 +35,7 @@ + mark_as_advanced(FORCE Boost_INCLUDE_DIR) + endif(Boost_FOUND) + +-# Find HDF5_ROOT if not set +-if ("$ENV{HDF5_ROOT}" STREQUAL "") +- find_file (HDF5_LIB libhdf5.so HINTS ENV LD_LIBRARY_PATH) +- if (NOT "${HDF5_LIB}" STREQUAL "") +- get_filename_component(HDF5_LIBRARY_DIR "${HDF5_LIB}" PATH) +- get_filename_component(HDF5_ROOT "${HDF5_LIBRARY_DIR}/../" ABSOLUTE) +- set(ENV{HDF5_ROOT} ${HDF5_ROOT}) +- endif (NOT "${HDF5_LIB}" STREQUAL "") +-endif ("$ENV{HDF5_ROOT}" STREQUAL "") +- +-mark_as_advanced(CLEAR HDF5_C_INCLUDE_DIR) +-mark_as_advanced(CLEAR HDF5_hdf5_LIBRARY_DEBUG) +-mark_as_advanced(CLEAR HDF5_hdf5_LIBRARY_RELEASE) ++# Find HDF5 + find_package(HDF5 REQUIRED) + if(HDF5_FOUND) + mark_as_advanced(FORCE HDF5_C_INCLUDE_DIR) +@@ -73,9 +61,6 @@ + endif(HDF5_IS_PARALLEL) + get_filename_component(HDF5_ROOT "${HDF5_INCLUDE_DIR}/../" REALPATH) + set(HDF5_BINARY_DIRS ${HDF5_ROOT}/bin ${HDF5_ROOT}/dll) +- if (NOT HDF5_LIBRARIES) +- find_library (HDF5_LIBRARIES hdf5 HINTS ${HDF5_ROOT} ENV LD_LIBRARY_PATH) +- endif (NOT HDF5_LIBRARIES) + set(XDMF_LIBRARIES ${XDMF_LIBRARIES} ${HDF5_LIBRARIES}) + set(XDMF_HDF5_BINARY_DIRS ${HDF5_BINARY_DIRS} PARENT_SCOPE) + set(XDMF_BINARIES ${XDMF_BINARIES} ${HDF5_BINARY_DIRS}) diff --git a/sci-libs/xdmf2/files/xdmf2-1.0_p141226-module.patch b/sci-libs/xdmf2/files/xdmf2-1.0_p141226-module.patch new file mode 100644 index 000000000000..c337ca62f73a --- /dev/null +++ b/sci-libs/xdmf2/files/xdmf2-1.0_p141226-module.patch @@ -0,0 +1,13 @@ + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index cef5909..46bcb88 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -346,4 +346,4 @@ endif(NOT XDMF_BUILD_CORE_ONLY) + + xdmf_create_config_file(${PROJECT_NAME}) + install(FILES "${PROJECT_BINARY_DIR}/${PROJECT_NAME}Config.cmake" +- DESTINATION ${CMAKE_INSTALL_PREFIX}) ++ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/cmake/Modules/) diff --git a/sci-libs/xdmf2/metadata.xml b/sci-libs/xdmf2/metadata.xml new file mode 100644 index 000000000000..8425c0d53cb0 --- /dev/null +++ b/sci-libs/xdmf2/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/xdmf2/xdmf2-1.0_p141226-r1.ebuild b/sci-libs/xdmf2/xdmf2-1.0_p141226-r1.ebuild new file mode 100644 index 000000000000..fc04d4922d93 --- /dev/null +++ b/sci-libs/xdmf2/xdmf2-1.0_p141226-r1.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils multilib python-single-r1 + +DESCRIPTION="eXtensible Data Model and Format" +HOMEPAGE="http://xdmf.org/index.php/Main_Page" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="VTK" +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +IUSE="doc python test" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + sci-libs/hdf5:= + dev-libs/libxml2:2 + python? ( ${PYTHON_DEPS} ) + " +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + python? ( dev-lang/swig:0 ) +" + +PATCHES=( "${FILESDIR}"/${P}-module.patch ) + +pkg_setup() { + use python && python-single-r1_pkg_setup && python_export +} + +src_prepare() { + if use python; then + local _site=$(python_get_sitedir) + sed \ + -e "/DESTINATION/s:python:${_site##${EPREFIX}/usr/$(get_libdir)/}:g" \ + -i CMakeLists.txt || die + fi + + sed \ + -e "/DESTINATION/s:lib:$(get_libdir):g" \ + -e "/INSTALL/s:lib:$(get_libdir):g" \ + -i CMakeLists.txt core/CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use doc XDMF_BUILD_DOCUMENTATION) + $(cmake-utils_use_build test TESTING) + $(cmake-utils_use python XDMF_WRAP_PYTHON) +# $(cmake-utils_use java XDMF_WRAP_JAVA) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + dosym XdmfConfig.cmake /usr/share/cmake/Modules/${PN}Config.cmake +} diff --git a/sci-libs/xdmf2/xdmf2-1.0_p141226-r2.ebuild b/sci-libs/xdmf2/xdmf2-1.0_p141226-r2.ebuild new file mode 100644 index 000000000000..c7d39a5b0c8c --- /dev/null +++ b/sci-libs/xdmf2/xdmf2-1.0_p141226-r2.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils python-single-r1 + +DESCRIPTION="eXtensible Data Model and Format" +HOMEPAGE="http://xdmf.org/index.php/Main_Page" +SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" + +SLOT="0" +LICENSE="VTK" +KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux" +IUSE="doc python test" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + dev-libs/boost:= + sci-libs/hdf5:= + dev-libs/libxml2:2 + python? ( ${PYTHON_DEPS} ) + " +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen ) + python? ( dev-lang/swig:0 ) +" + +PATCHES=( + "${FILESDIR}"/${P}-module.patch + "${FILESDIR}"/${P}-cannot-find-hdf5-bug-591302.patch +) + +pkg_setup() { + use python && python-single-r1_pkg_setup && python_export +} + +src_prepare() { + if use python; then + local _site=$(python_get_sitedir) + sed \ + -e "/DESTINATION/s:python:${_site##${EPREFIX}/usr/$(get_libdir)/}:g" \ + -i CMakeLists.txt || die + fi + + sed \ + -e "/DESTINATION/s:lib:$(get_libdir):g" \ + -e "/INSTALL/s:lib:$(get_libdir):g" \ + -i CMakeLists.txt core/CMakeLists.txt || die + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBUILD_SHARED_LIBS=1 + -DXDMF_BUILD_DOCUMENTATION=$(usex doc) + -DBUILD_TESTING=$(usex test) + -DXDMF_WRAP_PYTHON=$(usex python) +# -DXDMF_WRAP_JAVA=$(usex java) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + dosym XdmfConfig.cmake /usr/share/cmake/Modules/${PN}Config.cmake + + # need to byte-compile 'XdmfCore.py' and 'Xdmf.py' + # as the CMake build system does not compile them itself + use python && python_optimize "${D%/}$(python_get_sitedir)" +} diff --git a/sci-libs/xdrfile/Manifest b/sci-libs/xdrfile/Manifest new file mode 100644 index 000000000000..4802cf139806 --- /dev/null +++ b/sci-libs/xdrfile/Manifest @@ -0,0 +1,5 @@ +DIST xdrfile-1.1.1.tar.gz 378942 SHA256 4a2c8c7626dc3bdce45a6165d15d092cea85f39dfce0d176695d98ab3e6b4047 SHA512 bff06b08e547b956825f9b16a55fe93d07ff0c529426b892fd4b39be538774aa06facffc68994215e22e36edfa5642674653022da0762ca7cd1b7bc654112868 WHIRLPOOL d71a6a33334dfed2cd9e6036128cced52afbc215d608263086f50484a1dd4571568d66cd3d81e509ea5e1e55940755cb90846fc9f359035be6cfd13d46f3b8d4 +EBUILD xdrfile-1.1.1.ebuild 597 SHA256 0227e4157268cf45035c3c120b0c9f1a911ade2af77b256013295fb138173a9e SHA512 ab0156c4e760395f0320e640e5f452edab209da13abcb496717bfabaa03c86d001e30bdc4e1365eb18ed58dc287199b724635c304a72d5b6763df826dc37dae6 WHIRLPOOL d741bd218e7b789ebc66382c4a48e4b6cd8742db8d00bfed75f9b9aebc1fa41f7c19a60a5d25282f15f6d7c0f1592153f5c8bb01e0b7db600a91951fa8614d37 +MISC ChangeLog 2596 SHA256 526043d41b3d708add31e0668eff06b7795e1364744b6140e7a72f322c695506 SHA512 0e744abce57986ad2be4d2aa7b8ef09c838732eb31162f8033e63a7fe6dd5f7fa310d17bece5fbb92f7caf640c9a1b71283252cdfedaae6c98a951380c0d821b WHIRLPOOL 02f1f51ab32c65c6b5d744d41f9cc10dffe317cc6f8840cfb61919cbebd6c326fef9ff682cc16593666ec57b3d5fce0691d2e0918400a761e8f467efaeffa4da +MISC ChangeLog-2015 881 SHA256 643f86080b530cb5ddc6f0a52daf84e173fca1f994cb2f772f793dc6b2675687 SHA512 49021901c1da0425ddc2ff7df54e271d7daf7e14c6f80e19a3cf48eebf95abd0185d5c98ae7065a5c809e2a7d869abc996a90e7c968ec07b50cbe96a7dd52429 WHIRLPOOL f9533615db216085c88f7849467f92ae8ccfc7c5b91c87f38f518bb751ba131c85dffddb4ba454d67960b50ebbe85b359ee4f8fc3a14c8833883dd9393ab76c0 +MISC metadata.xml 373 SHA256 ad66cf348026ca024cbe0171448bf41fec6f3db6546cb5f2a5176f135c22699b SHA512 e8817074c54b6f66a21bbb69f4c5cc51e28282dd23e10f322b6e676a1859d47fbef3baea4b55d4f343517ae4de9bda3a009ed76b49ebdf898d875f29b13083ac WHIRLPOOL 3edbba9d57d652ae5dc63f9f8a9fcafd09e6409278482f2a13770827eec7885a961bb02ae2219df2af965f5ef02d68b99968270297cce2979caf83a677a6184b diff --git a/sci-libs/xdrfile/metadata.xml b/sci-libs/xdrfile/metadata.xml new file mode 100644 index 000000000000..c2dc1568a734 --- /dev/null +++ b/sci-libs/xdrfile/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> +<maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/xdrfile/xdrfile-1.1.1.ebuild b/sci-libs/xdrfile/xdrfile-1.1.1.ebuild new file mode 100644 index 000000000000..8994b56ef506 --- /dev/null +++ b/sci-libs/xdrfile/xdrfile-1.1.1.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED="fortran" + +inherit autotools-multilib fortran-2 + +DESCRIPTION="Library to read gromacs trajectory and topology files" +HOMEPAGE="http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library" +SRC_URI="ftp://ftp.gromacs.org/pub/contrib/${P}.tar.gz" + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="fortran static-libs" + +src_configure() { + local myeconfargs=( $(use_enable fortran) ) + + autotools-multilib_src_configure +} diff --git a/sci-libs/xgks-pmel/Manifest b/sci-libs/xgks-pmel/Manifest new file mode 100644 index 000000000000..6827aa562f8c --- /dev/null +++ b/sci-libs/xgks-pmel/Manifest @@ -0,0 +1,6 @@ +AUX aclocal.patch 3851 SHA256 88f8ed94483883af584167a0fb942ddd6b95062cc86020b425aa938cf93cdf24 SHA512 f926c8f1b30dc7f960442f53b9f5facf8d9083e378c896e765284565e9b871434967a77b82303e5bbdbb62ca140cccf65f9a8e5e07a2cfc726a7317eb7706b45 WHIRLPOOL 175410552feaf3e625433d0b37374261cedbcd402e5e75bc3c483eb5be72753b578e7d9a2374ed14e863c0f6c5cb858fc8aa6fd172e8d3ca764773399dcfdfdc +DIST xgks-pmel-2.5.5.tar.gz 1006581 SHA256 43a198aaa4d9497597e9253be19afc60d9dedda63a1fbcd718f77454d27adbb4 SHA512 001ef5742ebd93534569d650833ef04a82b01de819ceb2c3d3c750df58fd5bf9bbd538a79370b1d553db54477f409f6ab24958d3708260fb9ba7c8894ceb91c8 WHIRLPOOL 46e2e1b310edb102c0a47cbc5370d6f37f851e613b66753757648d26a07e89288a2d3f32186ff4438c20ac98cc3432b15b36fa2d92e6fc3b77cbcde7476a30f8 +EBUILD xgks-pmel-2.5.5.ebuild 1749 SHA256 32b52eac811e8ad902e07e472092ad9121a6b1e0841e31cf18500c1704196d93 SHA512 9644d831b3d1ccba28389ded8716580e659008de0306ca4d2e2a70775dfc7219e2b02f33d41fc7112de18b7b872931212b36a86fe80383fb308c7819feddbe00 WHIRLPOOL 0a79ed6ca9f579a505b295f647aac166f80c11723abaed1d121dc0a2d76daca86015523719f3f5620f6cd1aba9ae44c44e2774fee6494b02b02c6f64ae37737c +MISC ChangeLog 2455 SHA256 2b89ff5230b1c58a3d21635f6ee1d8b49ad87d4814d6a916b37329e46f948e38 SHA512 e55d5fd6847763b87c419e8bd729f05feaae30f3650ab2224081b9401b7986eba5a3e98d16ebf9341bcda6dfd12db81f3bfe645e9dc213f724ebde39b556beae WHIRLPOOL f5590d1084766418a24d9b8c9c03da0ca323ff801db67d841b115c9cc71ab10186d8d9bc1de6f72eb1be7f97eb6c53fdb934d144d4920024f458b53360d3eaf6 +MISC ChangeLog-2015 1801 SHA256 5065e9c96f9c8eda24dafd7aed76d3bf852bca4a21b02401f8be9396a4f566f8 SHA512 5d322fed2b090ab0147a894bcbdb167c782ca58b88e212bf19202ecfaba38181c14d78cbc4916e35986c441eabaef273889a336e7920a983507c1b67a6e12c07 WHIRLPOOL a2d923e078ed40470f216c7dc5070029483c03636ecd55c3b2c6d9203df0a23fc4ea410bda13f7555a8991d1ee1f15e8bb794dc80a17197132bd88d971ee004e +MISC metadata.xml 495 SHA256 ebb361a5cdb30156a16bc6e06cbdb4bd64777309085fda56cf7c742705615dd9 SHA512 2adc6d6866325d603ad8e0cf2b4f0175f0dbaefbdffd1081b5742f2a5951c342ab5031e01cf29f52e4d090f0bb0d495eb4c289e21116caec377de62878df50dc WHIRLPOOL 82a28e26314290124eb661df2d479b610023dcfb8fd3b4311e3585bba275a56409e75baf8079bd98bd9cc44f1d335dd9263b837379df7da329f9e8df794fa8de diff --git a/sci-libs/xgks-pmel/files/aclocal.patch b/sci-libs/xgks-pmel/files/aclocal.patch new file mode 100644 index 000000000000..48d44d747647 --- /dev/null +++ b/sci-libs/xgks-pmel/files/aclocal.patch @@ -0,0 +1,146 @@ +--- port/aclocal.m4.orig 2009-04-26 13:33:51.434402251 -0700 ++++ port/aclocal.m4 2009-04-26 13:43:33.466651210 -0700 +@@ -582,26 +582,6 @@ + ])]) + + +-# Check for ncdump(1) +-# +-define([UC_PROG_NCDUMP], [dnl +-AC_PROGRAM_CHECK(NCDUMP, ncdump, ncdump, UC_ABSPATH($exec_prefix)/ncdump)dnl +-if test `which "$NCDUMP" | wc -w` != 1; then +- UC_NEED_VALUE(NCDUMP, [netCDF lister], /usr/local/unidata/bin/ncdump)dnl +-fi +-]) +- +- +-# Check for ncgen(1) +-# +-define([UC_PROG_NCGEN], [dnl +-AC_PROGRAM_CHECK(NCGEN, ncgen, ncgen, UC_ABSPATH($exec_prefix)/ncgen)dnl +-if test `which "$NCGEN" | wc -w` != 1; then +- UC_NEED_VALUE(NCGEN, [netCDF generator], /usr/local/unidata/bin/ncgen)dnl +-fi +-]) +- +- + # Test a script. + # + define([UC_TEST_SCRIPT], +@@ -719,16 +699,6 @@ + ]) + + +-# Check for McIDAS library. +-# +-define([UC_LIB_MCIDAS], [dnl +-echo checking for MCIDAS library +-UC_TEST_LIB(LD_MCIDAS, /home/mcidas/lib /home/mcidasd/lib, mcidas, McIDAS, dnl +- -L/home/mcidas/lib -lmcidas)dnl +-AC_PROVIDE([$0])dnl +-]) +- +- + # Check for X11 library. + # + define([UC_LIB_X11], [dnl +@@ -745,77 +715,6 @@ + define([UC_X11], [AC_REQUIRE([UC_CPP_X11])AC_REQUIRE([UC_LIB_X11])]) + + +-# Check for netCDF header-file directory. +-# +-define([UC_CPP_NETCDF], [dnl +-echo checking for netCDF header-file +-UC_TEST_DIR(CPP_NETCDF, UC_ABSPATH($prefix/[[[include]]]), netcdf.h, +- [netCDF [[include]]-directory], [-I/usr/local/unidata/[[include]]])dnl +-CPP_NETCDF=`case ${CPP_NETCDF} in -I*) echo ${CPP_NETCDF};; *) echo -I${CPP_NETCDF-};; esac` +-AC_PROVIDE([$0])dnl +-]) +- +- +-# Check for netCDF library. +-# +-define([UC_LIB_NETCDF], [dnl +-echo checking for netCDF library +-UC_TEST_LIB(LD_NETCDF, UC_ABSPATH($prefix/lib), netcdf, +- netCDF, -L/usr/local/unidata/lib -lnetcdf)dnl +-AC_PROVIDE([$0])dnl +-]) +- +- +-# Check for netCDF implementation (header file and library). +-# +-define([UC_NETCDF], [AC_REQUIRE([UC_CPP_NETCDF])AC_REQUIRE([UC_LIB_NETCDF])]) +- +- +-# Check for netCDF operators library. +-# +-define([UC_LIB_NCOPERS], [dnl +-echo checking for netCDF operators library +-UC_TEST_LIB(LD_NCOPERS, UC_ABSPATH($prefix/lib), ncopers, +- netCDF-operators, [-L/usr/local/unidata/lib -lncopers])dnl +-AC_PROVIDE([$0])dnl +-]) +- +- +-# Check for LDM header-file directory. +-# +-define([UC_CPP_LDM], [dnl +-echo checking for LDM header-file +-UC_TEST_DIR(CPP_LDM, UC_ABSPATH($prefix/[[[include]]]) dnl +- UC_ABSPATH($prefix/../[[[include]]]) dnl +- UC_ABSPATH($prefix/../ldm/[[[include]]]), ldm.h, +- [LDM [[include]]-directory], [-I/usr/local/unidata/[[include]]])dnl +-CPP_LDM=`case ${CPP_LDM} in -I*) echo ${CPP_LDM};; *) echo -I${CPP_LDM-};; esac` +-if test -z "$CPP_LDM"; then +- UC_NEED_VALUE(CPP_LDM, [LDM include directory], -I/home/ldm/include)dnl +-fi +-AC_PROVIDE([$0])dnl +-]) +- +- +-# Check for LDM library. +-# +-define([UC_LIB_LDM], [dnl +-echo checking for LDM library +-UC_TEST_LIB(LD_LDM, UC_ABSPATH($prefix/lib) dnl +- UC_ABSPATH($prefix/../lib) UC_ABSPATH($prefix/../ldm/lib), ldm, +- LDM, -L/usr/local/unidata/lib -lldm)dnl +-if test -z "$LD_LDM"; then +- UC_NEED_VALUE(LD_LDM, [LDM library], -L/home/ldm/lib -lldm)dnl +-fi +-AC_PROVIDE([$0])dnl +-]) +- +- +-# Check for LDM implementation (header file and library). +-# +-define([UC_LDM], [AC_REQUIRE([UC_CPP_LDM])AC_REQUIRE([UC_LIB_LDM])]) +- +- + # Check for udres(3) library. + # + define([UC_LIB_UDRES], [dnl +--- port/configure.in.orig 2009-04-26 13:34:08.430308009 -0700 ++++ port/configure.in 2009-04-26 13:44:26.218430537 -0700 +@@ -24,8 +24,6 @@ + UC_PROG_FORTC + UC_PROG_NEQN + UC_PROG_TBL +-UC_PROG_NCDUMP +-UC_PROG_NCGEN + UC_PROG_INSTALL + + UC_UDPOSIX +--- port/master.mk.in.orig 2009-04-26 13:34:18.848400960 -0700 ++++ port/master.mk.in 2009-04-26 13:45:03.187651071 -0700 +@@ -19,8 +19,6 @@ + INSTALL_DATA = @INSTALL_DATA@ + INSTALL_PROGRAM = @INSTALL_PROGRAM@ + FC = @FC@ +-NCDUMP = @NCDUMP@ +-NCGEN = @NCGEN@ + NEQN = @NEQN@ + OS = @OS@ + SHELL = /bin/sh diff --git a/sci-libs/xgks-pmel/metadata.xml b/sci-libs/xgks-pmel/metadata.xml new file mode 100644 index 000000000000..446c65af5a70 --- /dev/null +++ b/sci-libs/xgks-pmel/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-geosciences@gentoo.org</email> + <name>Gentoo Geosciences Project</name> + </maintainer> + <longdescription> +XGKS is a level 2C implementation of the ANSI Graphical Kernel System (GKS) for +X-windows, with a C and Fortran interface. This version has support for PMEL's +Ferret visualization tool. +</longdescription> +</pkgmetadata> diff --git a/sci-libs/xgks-pmel/xgks-pmel-2.5.5.ebuild b/sci-libs/xgks-pmel/xgks-pmel-2.5.5.ebuild new file mode 100644 index 000000000000..a329866fa003 --- /dev/null +++ b/sci-libs/xgks-pmel/xgks-pmel-2.5.5.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils fortran-2 toolchain-funcs multilib + +DESCRIPTION="PMEL fork of XGKS, an X11-based version of the ANSI Graphical Kernel System" +HOMEPAGE="http://www.gentoogeek.org/viewvc/Linux/xgks-pmel/" +SRC_URI="http://www.gentoogeek.org/files/${P}.tar.gz" + +LICENSE="UCAR-Unidata" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" +IUSE="doc" + +RDEPEND=" + x11-libs/libX11" +DEPEND="${RDEPEND} + sys-devel/flex + sys-apps/groff" + +src_prepare() { + epatch "${FILESDIR}"/aclocal.patch +} + +src_configure() { + sed -i -e "s:lib64:$(get_libdir):g" port/master.mk.in \ + fontdb/Makefile.in || die + + CFLAGS=${CFLAGS} LD_X11='-L/usr/$(get_libdir) -lX11' \ + FC=$(tc-getFC) CC=$(tc-getCC) OS=linux \ + ./configure --prefix=/usr --exec_prefix=/usr/bin \ + || die +} + +src_compile() { + sed -i -e "s:port/all port/install:port/all:g" Makefile \ + || die + + # Fails parallel build, bug #295724 + emake -j1 + + cd src/fortran + emake -j1 +} + +src_install() { + cd "${S}"/progs + + for tool in {defcolors,font,mi,pline,pmark}; do + newbin ${tool} xgks-${tool} + done + + cd "${S}" + dolib.a src/lib/libxgks.a + + dodoc COPYRIGHT HISTORY INSTALL README + doman doc/{xgks.3,xgks_synop.3} + if use doc; then + newdoc doc/binding/cbinding.me cbinding + newdoc doc/userdoc/userdoc.me userdoc + insinto /usr/share/doc/${P}/examples + doins progs/{hanoi.c,star.c} + fi + + insinto /usr/include/xgks + doins src/lib/gks*.h + doins src/lib/gksm/gksm*.h + doins src/fortran/f*.h + doins src/lib/w*.h + doins src/lib/{input.h,metafile.h,polylines.h,polymarkers.h,text.h} + + insinto /usr/include + doins src/lib/xgks.h + doins port/udposix.h + + insinto /usr/share/xgksfonts + doins fontdb/{[1-9],*.gksfont} +} diff --git a/sci-libs/xkaapi/Manifest b/sci-libs/xkaapi/Manifest new file mode 100644 index 000000000000..ebef6c670718 --- /dev/null +++ b/sci-libs/xkaapi/Manifest @@ -0,0 +1,12 @@ +AUX xkaapi-2.1-ffi.patch 794 SHA256 2b06dd7aa0abb307c706cc3d61af19595ab8dd05a9512210bdb6674a3edcbf13 SHA512 7e99e72fa025659b5598583c4cad556888ca5424b3f41409b07aa1b4268a33cc379748f3181788ff9695433af16c21d69dca6dfddc15fb6071321f21bc80b9eb WHIRLPOOL a73409f9c8fe07c0efc3b4758bd74eb1ee4a0cbefcf4b20a0486322d909001a9e23801742b496d2f9db8041ebcde72282607097473316e171dc5f23debd4ce1c +AUX xkaapi-2.1-flags.patch 1324 SHA256 968793a742cd0170622275cff9a6892b8aec1564791fa29df9977550437691d0 SHA512 cc812130893bcf39e9c20f641e7744be7caa6e6918d195ca5d3b69b10d2a518e6b30e969e4cf6e8b6735e033858b33fc6fb1bbd347c67b87cd436980a0dead0f 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a2f7e17abfad3a9fe4a48ff49e9f88ca6c995924bdccddc085f6fdb7a289a578 SHA512 1be98c4e3c50cf198ec3522c7ccbe7757464889b32fb39e53447548fc2975e727fb2b68b25ae99c367b155588b1ab2181e3280d099ceb991929aa2f0e9c83f0c WHIRLPOOL 737c05986cc0c2139e3ecb9763edfe39084416f44db5579e8047d4a9134dc45fdeae134885cd88077299d180bdba111197baa50f7965a768aa8b6dab0a48a77c +DIST xkaapi-3.0.3.tar.gz 1535482 SHA256 4f37264a1e1fc21249b48923a49debcb88078034364b29996f28be1cc42588e5 SHA512 28fb02a73269e55eec90b5c2c82e4ade3bfb24d55a1f61ac6bf47da4c7e2d864cfa1389772baca9ebef4f24b3373fb6971f3fe98a4d232187e9d29a88110eda1 WHIRLPOOL 0e64d51710eada51912bbc48620fdec2e242b1de5803877ae6f22d8790b3dbc2cd3cf3a27d07489a6e10737a9e35724cc6f304973c79a14d6a4082037f50f7ab +EBUILD xkaapi-2.1.ebuild 1220 SHA256 86fa979fc3d4fac1f3483968759ebb6eb2bd6c6df28766daa410c5aa7bec1ac7 SHA512 7908a3968fa205434e2b3d504324c19800a39ce9e7294ae50d0e7a9f94a35bf678fa3111b451429bb2641f9444ffbe13f91700f139cd11e4bfe91fc4e1e358df WHIRLPOOL 49a0fc08065ed1446ff1a3d98ce463167ff48436e5bd6617c27f02b4de41c365c23d2b216191fcdef9d4908c3cd65dfde304e1b2bb730a60ea137bdd1bb481a1 +EBUILD xkaapi-2.2.ebuild 1228 SHA256 a2bee9a63a2d021e520080be3440a7c565d9c75a5c48fae6b1623cf90a09ca6e SHA512 b2889520f2f91275c58708c74bf5b668789e93367a377b058b5ac15c061a1073c03a44243b1b36a5d4ab3898316d6f2a767b952c9b678b6a624e4980f2383e04 WHIRLPOOL 9de9ccf0f84e729a134dd258215455f64e865244498583173c2af428d3654254e4cd35db90219be1b935951ca8b0a851afcda4a592e810bda91fa3d65262c40a +EBUILD xkaapi-3.0.3.ebuild 1046 SHA256 3399eefa4000a1a625782c564803fd137dbe9373491337e7e60215c563032657 SHA512 934874ca878fb774e417a212a044c6d6e08937925c6c357639fed361135902eb4cdff161f0f08c40dbb7625c625e04c32b1238871b61120f13556931e4fb17ae WHIRLPOOL f81c4d884c8e2d1968b3049f3c6cd9a830294df3b0f12b866192e944164a78ebe8735e633a6f90c216506bf99cbc1e6eaaf2a05a17e6c7ea209274bd25117827 +MISC ChangeLog 2753 SHA256 22621d3bbed9ed4919ee09bec83601e8d4265f0db7319f486a3a82a2220ca550 SHA512 1a9adf7d60fc647c13e936b98541c3e67c661f323f63d52d71379666ae1e168f81d34fd1ddacb9edff8623d8989248ca5cd29578786693975f44f0c526802228 WHIRLPOOL 88a818855e0969fb8e4c999df565d910c03f911c2e3e3d33506c796ac3a98ee1e15808243e4a78bd9ef9d406b6d69d0afa62a24fb65acfe5c8c34d4a72482fd8 +MISC ChangeLog-2015 1110 SHA256 dd93d9671c59b958f6d1413181588c727b654b1f7d85ec5b75f8012c18992892 SHA512 b15aecc1e7a6939a40d99eed090afda906fd6a6fad0fc0d72026a3cfd4929e8b702fcdfd4eb0a46c6a0766b586c7a4ea2c529b17403ef962b8576bd80226e1a9 WHIRLPOOL d5ac6a31db2b6089ff94c6677ddf58de011736281cfd4a31319761ac39e011c3cf4ff98d3d7c2f8f44b5a3a6ba048fa44bc20a8f0456119d48401d3ca7efedcf +MISC metadata.xml 393 SHA256 7e08f0d5fc9ff7d6ae0788f39601808090da50d5a3df295be256341cd8107d78 SHA512 a0fd2c3db31172b8cf83e02118bff28776e8c33dff45a46db79499f9dd57162d37e75982022618b1f505d260276ad5b3f74dbc8ed8db0be330a321ba8fe25e87 WHIRLPOOL 05b7dcfb91138c63ea23534b77d69c4076c56f84e86b27e9f204b0d48c80db2d49dd29003388924dbc95cca06585f370e81c0af62bc1496ab84ca39d530e4ab4 diff --git a/sci-libs/xkaapi/files/xkaapi-2.1-ffi.patch b/sci-libs/xkaapi/files/xkaapi-2.1-ffi.patch new file mode 100644 index 000000000000..485b6c21a969 --- /dev/null +++ b/sci-libs/xkaapi/files/xkaapi-2.1-ffi.patch @@ -0,0 +1,24 @@ + configure.ac | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 2be95ec..13e876b 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -1034,12 +1034,12 @@ dnl ----------------------------------------------------------------------- + + dnl we need to always configure imported-soft/libffi in order to be able + dnl to run "make dist" +-#if test x"$use_ffi" = xinternal; then ++if test x"$use_ffi" = xinternal; then + mkdir -p "imported-soft/libffi" + AC_CONFIG_SUBDIRS([imported-soft/libffi]) +-#else +-# AC_MSG_NOTICE([Not compiling embedded copy of libffi]) +-#fi ++else ++ AC_MSG_NOTICE([Not compiling embedded copy of libffi]) ++fi + + dnl ----------------------------------------------------------------------- + dnl Dependencies between libs diff --git a/sci-libs/xkaapi/files/xkaapi-2.1-flags.patch b/sci-libs/xkaapi/files/xkaapi-2.1-flags.patch new file mode 100644 index 000000000000..a22cabf9e4dd --- /dev/null +++ b/sci-libs/xkaapi/files/xkaapi-2.1-flags.patch @@ -0,0 +1,39 @@ + configure.ac | 11 ++++++++++- + 1 file changed, 10 insertions(+), 1 deletion(-) + +diff --git a/configure.ac b/configure.ac +index c3364aa..2a734fe 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -82,6 +82,9 @@ AC_PROG_F77 + dnl ---------------------------------------------------------------- + dnl Disable default flag for compilation + dnl ---------------------------------------------------------------- ++CPPFLAGS_gentoo="${CPPFLAGS}" ++CFLAGS_gentoo="${CFLAGS}" ++CXXFLAGS_gentoo="${CXXFLAGS}" + CPPFLAGS="" + CFLAGS="" + CXXFLAGS="" +@@ -407,7 +410,7 @@ AC_ARG_ENABLE([mode],[AS_HELP_STRING([--enable-mode], + [choose special compilation mode (debug, release)])],[], + [enable_mode=default] + ) +-clean_default_flags ++clean_default_flags=no + AS_CASE([$enable_mode], + [default], [dnl + AM_CPPFLAGS="$AM_CPPFLAGS" +@@ -428,6 +431,12 @@ AS_CASE([$enable_mode], + AM_CFLAGS="$AM_CFLAGS -O3 -DNDEBUG" + AM_CXXFLAGS="$AM_CXXFLAGS -O3 -DNDEBUG" + clean_default_flags=yes ++ ], [gentoo], [dnl ++ AC_MSG_NOTICE([Using gentoo compile mode]) ++ AM_CPPFLAGS="$AM_CPPFLAGS ${CPPFLAGS_gentoo}" ++ AM_CFLAGS="$AM_CFLAGS -DNDEBUG ${CFLAGS_gentoo}" ++ AM_CXXFLAGS="$AM_CXXFLAGS -DNDEBUG ${CXXFLAGS_gentoo}" ++ clean_default_flags=yes + ], [dnl + AC_MSG_ERROR([Unknown compilation mode '$enable_mode'. Aborting.]) + ]) diff --git a/sci-libs/xkaapi/files/xkaapi-3.0.3-flags.patch b/sci-libs/xkaapi/files/xkaapi-3.0.3-flags.patch new file mode 100644 index 000000000000..0fdad94cb9b9 --- /dev/null +++ b/sci-libs/xkaapi/files/xkaapi-3.0.3-flags.patch @@ -0,0 +1,31 @@ + configure.ac | 11 ++++++++++- + 1 file changed, 10 insertions(+), 1 deletion(-) + +diff --git a/configure.ac b/configure.ac +index c3364aa..2a734fe 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -82,6 +82,9 @@ AC_PROG_F77 + dnl ---------------------------------------------------------------- + dnl Disable default flag for compilation + dnl ---------------------------------------------------------------- ++CPPFLAGS_gentoo="${CPPFLAGS}" ++CFLAGS_gentoo="${CFLAGS}" ++CXXFLAGS_gentoo="${CXXFLAGS}" + CPPFLAGS="" + CFLAGS="" + CXXFLAGS="" +@@ -428,6 +431,13 @@ AS_CASE([$enable_mode], + AM_CXXFLAGS="$AM_CXXFLAGS -O3 -DNDEBUG" + clean_default_flags=yes + AM_CONDITIONAL([KAAPI_USE_DEBUG], [test "$enable_mode" = truc ]) ++ ], [gentoo], [dnl ++ AC_MSG_NOTICE([Using gentoo compile mode]) ++ AM_CPPFLAGS="$AM_CPPFLAGS ${CPPFLAGS_gentoo}" ++ AM_CFLAGS="$AM_CFLAGS -DNDEBUG ${CFLAGS_gentoo}" ++ AM_CXXFLAGS="$AM_CXXFLAGS -DNDEBUG ${CXXFLAGS_gentoo}" ++ clean_default_flags=yes ++ AM_CONDITIONAL([KAAPI_USE_DEBUG], [test "$enable_mode" = gentoo ]) + ], [dnl + AC_MSG_ERROR([Unknown compilation mode '$enable_mode'. Aborting.]) + ]) diff --git a/sci-libs/xkaapi/metadata.xml b/sci-libs/xkaapi/metadata.xml new file mode 100644 index 000000000000..80199bef1f06 --- /dev/null +++ b/sci-libs/xkaapi/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="blas">Kaapi BLAS tasks for PLASMA</flag> + <flag name="gpu">Build library for gpu threading</flag> + </use> +</pkgmetadata> diff --git a/sci-libs/xkaapi/xkaapi-2.1.ebuild b/sci-libs/xkaapi/xkaapi-2.1.ebuild new file mode 100644 index 000000000000..8fda1c5d4b41 --- /dev/null +++ b/sci-libs/xkaapi/xkaapi-2.1.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED=fortran +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fortran-2 + +UPSTREAM_NO=32735 + +DESCRIPTION="Kernel for Adaptative, Asynchronous Parallel and Interactive programming" +HOMEPAGE="http://kaapi.gforge.inria.fr" +SRC_URI="https://gforge.inria.fr/frs/download.php/${UPSTREAM_NO}/${P}.tar.gz" + +SLOT="0" +LICENSE="CeCILL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="blas cxx fortran gpu openmp static-libs" + +RDEPEND=" + sys-apps/hwloc + virtual/libffi +" +DEPEND="${RDEPEND} +" + +PATCHES=( + "${FILESDIR}"/${P}-flags.patch + "${FILESDIR}"/${P}-ffi.patch + ) + +src_prepare() { + sed \ + -e 's:-Werror::g' \ + -i tests/testsuite* tests/*/*.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-mode=gentoo + --enable-api-kaapic + --enable-api-quark + --with-ccache=no + --enable-hwloc + --with-libffi="${EPREFIX}"/usr + --enable-target$(usex gpu gpu mt) + $(use_enable fortran api-kaapif) + $(use_enable cxx api-kaapixx) + $(use_enable blas kblas) + $(use_enable openmp libkomp) +# $(use_with plasma "${EPREFIX}"/usr) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/xkaapi/xkaapi-2.2.ebuild b/sci-libs/xkaapi/xkaapi-2.2.ebuild new file mode 100644 index 000000000000..2481baec666d --- /dev/null +++ b/sci-libs/xkaapi/xkaapi-2.2.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED=fortran +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fortran-2 + +UPSTREAM_NO=33666 + +DESCRIPTION="Kernel for Adaptative, Asynchronous Parallel and Interactive programming" +HOMEPAGE="http://kaapi.gforge.inria.fr" +SRC_URI="https://gforge.inria.fr/frs/download.php/${UPSTREAM_NO}/${P}.tar.gz" + +SLOT="0" +LICENSE="CeCILL-2" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +IUSE="blas cxx fortran gpu openmp static-libs" + +RDEPEND=" + sys-apps/hwloc + virtual/libffi +" +DEPEND="${RDEPEND} +" + +PATCHES=( + "${FILESDIR}"/${PN}-2.1-flags.patch + "${FILESDIR}"/${PN}-2.1-ffi.patch + ) + +src_prepare() { + sed \ + -e 's:-Werror::g' \ + -i tests/testsuite* tests/*/*.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-mode=gentoo + --enable-api-kaapic + --enable-api-quark + --with-ccache=no + --enable-hwloc + --with-libffi="${EPREFIX}"/usr + --enable-target$(usex gpu gpu mt) + $(use_enable fortran api-kaapif) + $(use_enable cxx api-kaapixx) + $(use_enable blas kblas) + $(use_enable openmp libkomp) +# $(use_with plasma "${EPREFIX}"/usr) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/xkaapi/xkaapi-3.0.3.ebuild b/sci-libs/xkaapi/xkaapi-3.0.3.ebuild new file mode 100644 index 000000000000..738863617afd --- /dev/null +++ b/sci-libs/xkaapi/xkaapi-3.0.3.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +FORTRAN_NEEDED=fortran +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils fortran-2 + +UPSTREAM_NO=34360 + +DESCRIPTION="Kernel for Adaptative, Asynchronous Parallel and Interactive programming" +HOMEPAGE="http://kaapi.gforge.inria.fr" +SRC_URI="https://gforge.inria.fr/frs/download.php/${UPSTREAM_NO}/${P}.tar.gz" + +SLOT="0" +LICENSE="CeCILL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cxx fortran openmp static-libs" + +RDEPEND=" + sys-apps/hwloc + virtual/libffi +" +DEPEND="${RDEPEND} +" + +PATCHES=( + "${FILESDIR}"/${P}-flags.patch + ) + +src_prepare() { + sed \ + -e 's:-Werror::g' \ + -i tests/testsuite* tests/*/*.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --enable-mode=gentoo + --enable-api-quark + --with-ccache=no + $(use_enable fortran api-kaapif) + $(use_enable cxx api-kaapixx) + $(use_enable openmp libkomp) +# $(use_with plasma "${EPREFIX}"/usr) + ) + autotools-utils_src_configure +} diff --git a/sci-libs/xylib/Manifest b/sci-libs/xylib/Manifest new file mode 100644 index 000000000000..c028de266167 --- /dev/null +++ b/sci-libs/xylib/Manifest @@ -0,0 +1,7 @@ +DIST xylib-1.1.tar.bz2 288366 SHA256 eb201ec9eca9ba84547fb590839e6e9177ca252eb8edb4b10785ff506c27bddb SHA512 d9952274fc4adb62aa7dab0d86dbb702d907caa954c68db1924284cc0304066ad8dac94571ecd1b764587655d30ac3fb1cae2307bb9e102ca564594a597a9c3f WHIRLPOOL feeb1a3383307daf191620efd7865a8e7370a4cdb118e96652e3fbcba0cdd74c38922a9a708994830d1aa317181a4c21fd98b9a04cd1a680710c264cede0aae2 +DIST xylib-1.2.tar.bz2 297167 SHA256 8a32a0f201e47c8f0665da44af6a1eac0aa06aa9bb61a7bd226bb723e9aebebf SHA512 16eaa4b37014914c75ca3d0188aaf236c342887c03e233a9bb770412b3bb16da6779ab82c8acd66677d98ada75537c77d1abad723defd33dbe6eda78c6c88b91 WHIRLPOOL 4e7f0edf250767c9f5dc1cbec5a9a09f9b56097f872e37af444c3401fd78788b8b1674a01517c509fb7ce4a8813a520a8cb4759427d8be53cdb5c2d4d3554d03 +EBUILD xylib-1.1.ebuild 590 SHA256 ccb6edb3e7d60fb2f1c1b907831f11abe309e48d7f71c7b56d280134f525ccea SHA512 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/dev/null +++ b/sci-libs/xylib/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + xylib is a portable C++ library for reading files that contain x-y + data from powder diffraction, spectroscopy or other experimental + methods. It supports many formats. +</longdescription> + <upstream> + <remote-id type="sourceforge">xylib</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/xylib/xylib-1.1.ebuild b/sci-libs/xylib/xylib-1.1.ebuild new file mode 100644 index 000000000000..6db5c710a483 --- /dev/null +++ b/sci-libs/xylib/xylib-1.1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +DESCRIPTION="Experimental x-y data reading library" +HOMEPAGE="http://www.unipress.waw.pl/fityk/xylib/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="bzip2 static-libs zlib" + +RDEPEND=" + dev-libs/boost + bzip2? ( app-arch/bzip2 ) + zlib? ( sys-libs/zlib )" +DEPEND="${RDEPEND}" + +src_configure() { + econf \ + $(use_enable static-libs static) \ + $(use_with bzip2 bzlib) \ + $(use_with zlib) +} diff --git a/sci-libs/xylib/xylib-1.2.ebuild b/sci-libs/xylib/xylib-1.2.ebuild new file mode 100644 index 000000000000..ed9ee753d6c8 --- /dev/null +++ b/sci-libs/xylib/xylib-1.2.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Experimental x-y data reading library" +HOMEPAGE="http://www.unipress.waw.pl/fityk/xylib/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="LGPL-2.1" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="bzip2 static-libs zlib" + +RDEPEND=" + dev-libs/boost + bzip2? ( app-arch/bzip2 ) + zlib? ( sys-libs/zlib )" +DEPEND="${RDEPEND}" + +src_configure() { + local myeconfargs=( + $(use_with bzip2 bzlib) + $(use_with zlib) + ) + autotools-utils_src_configure +} |