diff options
| author | V3n3RiX <venerix@koprulu.sector> | 2022-07-09 15:43:36 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@koprulu.sector> | 2022-07-09 15:43:36 +0100 |
| commit | 2719f73b6813d11d13a9650cdd2ab8ec6e69385d (patch) | |
| tree | 8c816148bcbd22757d892089c989ae614eae4f5a /sci-biology | |
| parent | 0f558761aa2dee1017b4751e4017205e015a9560 (diff) | |
gentoo resync : 09.07.2022
Diffstat (limited to 'sci-biology')
108 files changed, 1367 insertions, 704 deletions
diff --git a/sci-biology/HTSeq/HTSeq-0.12.4.ebuild b/sci-biology/HTSeq/HTSeq-0.12.4.ebuild deleted file mode 100644 index 548684fd531b..000000000000 --- a/sci-biology/HTSeq/HTSeq-0.12.4.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" -HOMEPAGE="https://htseq.readthedocs.io/" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/htseq/htseq.git" -else - SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz" - - S="${WORKDIR}"/htseq-release_${PV} - KEYWORDS="~amd64" -fi - -LICENSE="GPL-3+" -SLOT="0" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" -BDEPEND=" - >=dev-lang/swig-3.0.8 - dev-python/cython[${PYTHON_USEDEP}]" diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild new file mode 100644 index 000000000000..678968788ff7 --- /dev/null +++ b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_IN_SOURCE_BUILD=1 +PYTHON_COMPAT=( python3_{8..10} ) + +inherit distutils-r1 flag-o-matic + +DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" +HOMEPAGE="https://htseq.readthedocs.io/" + +if [[ ${PV} == *9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/htseq/htseq.git" +else + SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz" + + S="${WORKDIR}"/htseq-release_${PV} + KEYWORDS="~amd64" +fi + +LICENSE="GPL-3+" +SLOT="0" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-biology/pysam[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + test? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + )" +BDEPEND=" + >=dev-lang/swig-3.0.8 + dev-python/cython[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest + +src_configure() { + # mask broken asserts in src/step_vector.h:72 + append-cppflags -DNDEBUG + + distutils-r1_src_configure +} + +python_test() { + distutils_install_for_testing + + # Due to the build directories creating a competing + # hierarchy, we move to the test/ dir to avoid implicitly + # injecting the root HTSeq/ dir into the PYTHONPATH, + # which leads the python module lookup astray: + # ${PWD} + # ├── build + # │ ├── lib + # │ │ └── HTSeq + # │ [...] + # ├── HTSeq + # └── test + cd test/ || die + ln -s ../example_data || die + epytest +} diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild index 548684fd531b..678968788ff7 100644 --- a/sci-biology/HTSeq/HTSeq-9999.ebuild +++ b/sci-biology/HTSeq/HTSeq-9999.ebuild @@ -1,11 +1,12 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +DISTUTILS_IN_SOURCE_BUILD=1 +PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 +inherit distutils-r1 flag-o-matic DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" HOMEPAGE="https://htseq.readthedocs.io/" @@ -14,7 +15,7 @@ if [[ ${PV} == *9999 ]]; then inherit git-r3 EGIT_REPO_URI="https://github.com/htseq/htseq.git" else - SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz" + SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz" S="${WORKDIR}"/htseq-release_${PV} KEYWORDS="~amd64" @@ -22,12 +23,46 @@ fi LICENSE="GPL-3+" SLOT="0" +IUSE="test" +RESTRICT="!test? ( test )" RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" +DEPEND="${RDEPEND} + test? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + )" BDEPEND=" >=dev-lang/swig-3.0.8 dev-python/cython[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest + +src_configure() { + # mask broken asserts in src/step_vector.h:72 + append-cppflags -DNDEBUG + + distutils-r1_src_configure +} + +python_test() { + distutils_install_for_testing + + # Due to the build directories creating a competing + # hierarchy, we move to the test/ dir to avoid implicitly + # injecting the root HTSeq/ dir into the PYTHONPATH, + # which leads the python module lookup astray: + # ${PWD} + # ├── build + # │ ├── lib + # │ │ └── HTSeq + # │ [...] + # ├── HTSeq + # └── test + cd test/ || die + ln -s ../example_data || die + epytest +} diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest index a6845ab37446..5e3f78918536 100644 --- a/sci-biology/HTSeq/Manifest +++ b/sci-biology/HTSeq/Manifest @@ -1,4 +1,4 @@ -DIST HTSeq-0.12.4.tar.gz 36187218 BLAKE2B 27be4e8783f9e32c10e23ae812069b489eb11dfa4058db43b5db4b8089792351901255103e4d4de1bcf866da3acd13e742adf8d35a9b70305aa156c70dde0837 SHA512 ec4a1a7e9177f103465840ffa9f936a5e887ffd17760b99d4cbdfd5a88e2ab44275fadfcbee153aadc6e828de7be205ed7a07f3a0548457b7c66826341c3ca64 -EBUILD HTSeq-0.12.4.ebuild 773 BLAKE2B 78db5ac231e751e473d4e7e94aeeb86995fbf77b7576b404040e1383c99dbfa8fbcedeebdef803944cf542dbc022f95815de340e7a9b4cc3348a444a7f9818a1 SHA512 70fe71d67fd00635025efa19bcdf852da23412d2010057362b389ae67f52bebb83910e7c93f128932d00ed2db1f9c29b3b77cdaf5ce3230a135f9b3cad8d16e2 -EBUILD HTSeq-9999.ebuild 773 BLAKE2B 78db5ac231e751e473d4e7e94aeeb86995fbf77b7576b404040e1383c99dbfa8fbcedeebdef803944cf542dbc022f95815de340e7a9b4cc3348a444a7f9818a1 SHA512 70fe71d67fd00635025efa19bcdf852da23412d2010057362b389ae67f52bebb83910e7c93f128932d00ed2db1f9c29b3b77cdaf5ce3230a135f9b3cad8d16e2 +DIST HTSeq-2.0.2.gh.tar.gz 48468261 BLAKE2B c68ec67906f3cf78954e94214b82fd51bc19e0c505f994a3df4bfc682d804fa26f4883e9a8fa1e8ddf1e4f8ba8690d605705ebdd2d1695470984c2f04b6a19ce SHA512 96c0b4de6c9cfa9e405f02e366ecfed63bb0dba0ab76fe872f6f48b52a4956b08fa75efa4b1e4c6e4560e34b4e2921bf1ec9671831226ad415ed421a88ec3f6d +EBUILD HTSeq-2.0.2.ebuild 1569 BLAKE2B 2a2b83903f275ad6f64da5611958f6e208293def1b2a99e16d505b7de24514b3aae090882263596727650c19f126a2707ef3fa1d17aa58fb9179ff399d62d4c5 SHA512 1ae7790220702b063c6e059459846b8eae4db76cf091651f9a3723bc27fdadf132916f2b7574e45b58af62976a0f67d007046be8ae84e0cc95c25aa95c342b1b +EBUILD HTSeq-9999.ebuild 1569 BLAKE2B 2a2b83903f275ad6f64da5611958f6e208293def1b2a99e16d505b7de24514b3aae090882263596727650c19f126a2707ef3fa1d17aa58fb9179ff399d62d4c5 SHA512 1ae7790220702b063c6e059459846b8eae4db76cf091651f9a3723bc27fdadf132916f2b7574e45b58af62976a0f67d007046be8ae84e0cc95c25aa95c342b1b MISC metadata.xml 330 BLAKE2B 0710ed510732fd584ecbee4d193bf2cccf72af692cc5ce7243ab7864f00ba23d22fca0c4b06213d7e40697c0e469c29f36d988c7fa0d8ab6ea985f8df7255388 SHA512 481004c3e6ba51f4e983e265b7a3f9e4281e27c95ea894eb7f166a339059507cb947eddba1d8642d952289936c8145fc20fa26ed11522535d4c097cc6a3cb018 diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex abaa252910a4..da0f930bf8e8 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest index 30aa4d674f8a..c97246215a2f 100644 --- a/sci-biology/amap/Manifest +++ b/sci-biology/amap/Manifest @@ -1,5 +1,5 @@ AUX amap-2.2-includes.patch 1088 BLAKE2B 3b870c229f3efb9819d9f176b59b014ad4bae3034ed4fe9f8c8474ebf8ce7c8373efef66c3c61c8f6fe04a645243f09639aa4a4c95ee75f692e504f4478fcf77 SHA512 e9c2ae7ea75f059b816a8562c9ac79e343d73b9a3d63ac1182fe41b3634bf0b949738a4bdd90c09f61bb4505a721e2faa98334b81ad17c0d7360a2e3f37f9044 -AUX amap-2.2-makefile.patch 1201 BLAKE2B e404de0909f501dbf5005d6c995fbb6ecf588fe06798483703c25d29c070faa6ce5eb06e98e35b8deeeddbeb309eb6560d13af6a0fa64ec9435d00e41f2bfad2 SHA512 8cd43b70299e12f32dd6b46a73e6ef10c7e85b5ec6d152aef69f54954a1083c92570c40bf35ea363084a3626161c3e28d214bb2c5fb76bb396d9be2edaa869a3 +AUX amap-2.2-makefile.patch 1089 BLAKE2B 5ed09060ebc9c0c5748d1bdd1517bc6d5e7989d8125db1dff13a221f13e69e717508ac30410ae0c38a4e126f490179ac68ee7e501f7c7d61888993c850f6fbf8 SHA512 cd08a7a71eb85521c60e522d3a8ea0b2bbe4dfb93c0f4d6f0e2e4c35787a0836f23f51f50c4c9344eeda6533a7d689c4b246c700f7d37b8b3666f4904bd625d6 DIST amap.2.2.tar.gz 102861 BLAKE2B 7f9b1cb747946232db0b5b469896cc4f83ef78d190e929e28f37df790dfac342e6e7f913797bc9ff00191253318db2d42f79577dc72128d62a21d0e241bfb0e1 SHA512 a297b6eb1b52d5deab65db5bb1344b06a85c7ef6fa4b550798501041091357e605543eaadd85c053a74e857ebdd7b846dca4b226c5c61bedc329bf93c886c18f -EBUILD amap-2.2-r4.ebuild 1142 BLAKE2B c4bf57de7f838559bb4fc5c1b6358802fb54dd2a1d5ef401218ce4c2efaf829f8a0c05a45333b81747539d286bb2e5d0233ea19177aa7ef59b691581c27f3ad9 SHA512 22230076080ef49996c9cc8adea62b488a877f95832d88f53094b71ba868b33c5bc5bee170a444f4a4a928e152b1fa8f348fecfbc37600f02db4a79bc4722e8f +EBUILD amap-2.2-r5.ebuild 1104 BLAKE2B 120ae0dd66942b77dc7acc28d05b6f76c9dc1152dea85b419f2a84cab1a7ef2be373575bdd0f0edabfba1765c3a4db83b699c25ae0855c7e162d19d13f6b404f SHA512 60ad29cc9bb1698ff04eec6fa719f66a9fe0ebc57698f6986abc7b401a4781248140a73d36828d9592dae3176148fc0ee27e6baf0d302e461387b13b98ff9530 MISC metadata.xml 258 BLAKE2B 51009df26b3682090e316b4cf4a3afad84001705063be6c74a28fb11bacde48b758dc280bf9d4d049c69e728d9660e737072674ad5ff8068da4f6a49f1f4e203 SHA512 05153e39b77e8b1437a0ba80b66b6bb1b4837d719765cb157b23d5425a625ddb4056422dcbf28d182e039583a0b3863e8429efe80da85a035c96f4c4788ced6d diff --git a/sci-biology/amap/amap-2.2-r4.ebuild b/sci-biology/amap/amap-2.2-r5.ebuild index df3b16efba30..949749969c27 100644 --- a/sci-biology/amap/amap-2.2-r4.ebuild +++ b/sci-biology/amap/amap-2.2-r5.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit java-pkg-opt-2 java-ant-2 toolchain-funcs @@ -10,6 +10,7 @@ MY_P=${PN}.${PV} DESCRIPTION="Protein multiple-alignment-based sequence annealing" HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage" SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz" +S="${WORKDIR}/${PN}-align" LICENSE="GPL-2" SLOT="0" @@ -17,9 +18,7 @@ KEYWORDS="~amd64 ~x86" IUSE="java" RDEPEND="java? ( >=virtual/jre-1.8:* )" -DEPEND="java? ( >=virtual/jdk-1.8:* )" - -S=${WORKDIR}/${PN}-align +BDEPEND="${RDEPEND}" PATCHES=( "${FILESDIR}"/${P}-makefile.patch @@ -31,8 +30,12 @@ src_prepare() { java-pkg-opt-2_src_prepare } +src_configure() { + tc-export CXX +} + src_compile() { - emake -C align CXX="$(tc-getCXX)" OPT_CXXFLAGS="${CXXFLAGS}" + emake -C align if use java; then pushd display >/dev/null || die @@ -46,8 +49,8 @@ src_install() { dodoc align/{README,PROBCONS.README} - insinto /usr/share/${PN}/examples - doins -r examples/. + insinto /usr/share/${PN} + doins -r examples if use java; then java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch index 5a9841c98255..3749fa58682c 100644 --- a/sci-biology/amap/files/amap-2.2-makefile.patch +++ b/sci-biology/amap/files/amap-2.2-makefile.patch @@ -2,28 +2,25 @@ Respect {CXX,LD}FLAGS http://bugs.gentoo.org/332009 ---- amap-align/align/Makefile -+++ amap-align/align/Makefile -@@ -15,6 +15,8 @@ - # c) RELEASE mode +--- a/align/Makefile ++++ b/align/Makefile +@@ -6,7 +6,6 @@ + # 1) Choose C++ compiler. ################################################################################ -+OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops -+ - OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' +-CXX = g++ - # debug mode -@@ -26,8 +28,7 @@ + ################################################################################ + # 2) Set C++ flags. +@@ -26,7 +25,7 @@ # release mode #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer -CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops -- -+CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) ++CXXFLAGS += -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) + ################################################################################ # 3) Dependencies - ################################################################################ - @@ -38,7 +37,7 @@ all : $(TARGETS) diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index c806da84e07a..94d013ad869a 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,5 +1,5 @@ AUX bedtools-2.29.2-buildsystem.patch 2002 BLAKE2B 7925c788858515ec4454ece3823680e99053790aeb30b2dcab06a52f6827c3cca85543c899fbabcc75ac5872cdfe632c9c5bf8b5dc24146c50a00dbd4ea56a1d SHA512 a76ec350aedfce4926f8fbaed742a992f81b2280727383f7aefd7f3629f7e04f300f9d3d9cce2a98c6fe2767cb6d2261074bd6242d6d5ae26a5095730c054a85 AUX bedtools-2.29.2-python.patch 1235 BLAKE2B 34381a33be915f983b2c93f04954486e7611f56b1bc3259887e5ac3aa54107e3392a784980779948136f97424485a31a53959f2f76b573cb44b7d83023c69005 SHA512 8c22230e3bc1eaeb7d85379eab402eb1e95443f88f60a9c04f628cd38a96b91d138149a1a46d941189a8cd6097e075a8bde8d4ad883757ec7b2c129268cdb37f DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9 -EBUILD bedtools-2.30.0.ebuild 1184 BLAKE2B 128c85d2fae5a45068f3c6f0c64b93902dcfaf0eb1464fbc8546ac7b62827d62fbd01cab422e23153cc9e2975f3d43f628305a3986caf6df36923059f45d6a6c SHA512 77c36f5abcf230a4eff2f7215998ed8188d0e6dda8c1c1de94c16e6dd3b7b480bb6abed0d6bcf0baec2ebbb1d678c51a0c1b16aebc34785e49245e5d30b0626a +EBUILD bedtools-2.30.0.ebuild 1187 BLAKE2B c24ffd5edda4c21dae3640accbf5010105486186f7a6789adfef5f2c0c21234d9e85bb2954feeb01a1b519ad7936a19893f391a6fcf738bfb6cda68ce82bdcfa SHA512 c7038e7139e2ba4e9f39dbd7d606b7de95c105044b6d0307c3560010c9129f91137055dd63e5b29c590405ac384adb805cfcc2d20ed7aa3872c6fab128df4a53 MISC metadata.xml 407 BLAKE2B f3c2890ef1648dcfc7ae92c56fec8c111de2cb82ba4c8f7402756fa9db6f2ee43fa3ccb9a75db5d1e2ca7893ed3041efc22452814944e0e56f1a589353b47774 SHA512 925406053fd5c1aecb5ef26c522b3f410c6f9a639dc1ab7790a4124513c870af5b818adc53875c93ab19a36d444b8fb23c5ef10cc11ed50080785bbe60d1eb98 diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild index 3647f43dabe5..3e0d51b0711b 100644 --- a/sci-biology/bedtools/bedtools-2.30.0.ebuild +++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild @@ -1,15 +1,16 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{8..11} ) inherit python-any-r1 toolchain-funcs DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" HOMEPAGE="https://bedtools.readthedocs.io/" SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" +S="${WORKDIR}/${PN}2" LICENSE="GPL-2" SLOT="0" @@ -26,8 +27,6 @@ BDEPEND=" ${PYTHON_DEPS} test? ( >=sci-biology/samtools-1.10:0 )" -S="${WORKDIR}"/${PN}2 - # bedtools2 has a *terrible* build system and development practices. # Upstream has forked htslib 1.9 and extended it by adding clever callbacks # that make unbundling it nigh impossible. There are no signs of upstream porting @@ -44,6 +43,6 @@ src_configure() { src_install() { default - insinto /usr/share/${PN} + insinto /usr/share/bedtools doins -r genomes } diff --git a/sci-biology/biogrep/Manifest b/sci-biology/biogrep/Manifest index cedc556cfcda..4b2c5540ecc5 100644 --- a/sci-biology/biogrep/Manifest +++ b/sci-biology/biogrep/Manifest @@ -1,4 +1,4 @@ DIST biogrep-1.0.pdf 22179 BLAKE2B 9a401b50480ae8fe903b96082b8011cc02d8f65d97cdcc2659e835d8fc01969f756d33e14428aeee802f5dd994e3b5277b6e705ec73f92c0fb2be255e5a1588f SHA512 b0430bded7529a14e3e551e4c7deeffdbdbbe674b5a4bd68afa359b2a4e9f0b8fb4a6474673d298508fa728cf83a328327860e60b3777e92afb15fa87f076411 DIST biogrep-1.0.tar.gz 71867 BLAKE2B 48baf2b13f65e3b2d79fabccf978c8a3b275e6b915fed56a2fa9a0cd98ab36ff3810dbe9be1447a32b5f95b5ed006cc19dbd0673ec9e617e4a9115dcddf240a4 SHA512 da07ea6f5f6fd601a94dc1b9495b204affcdc4d5e7fedfebbb65d6382ef0573e43b4ebd081c24909b2790ec2ae532505604112d4943c3e4e6575e13bdcdf1ae3 -EBUILD biogrep-1.0-r2.ebuild 866 BLAKE2B 76ffe1136628b52524a32e67c4e739f635609fb6411e1397b478b473aec3a75c4dac60def3dc40ce9c6989fca62736006f706be0a834ad4a228677a137499235 SHA512 224009fb74306670ecff19a0c9d271608aadb20fea285ff9146c8e45c08918629c3ab0176388b6dfadbbd07fb462e1b4d8cc5f1dff93957dfdefde0f4e780fb9 +EBUILD biogrep-1.0-r3.ebuild 831 BLAKE2B fbe6724b5e6e0d5a260a5be5ab85d9e96c80dee7ff48d1baef0ee02cdec91aab34fdb667284a220f753fe0544ce3b0e3f5530cc3fb0a9398138add22b5600074 SHA512 3dcc3a215b1d2ec1403c511d01c9bcda951d973161443d5992d8e848df561f2d4ef0c35bfb26d58e9ae9d46632af6140fadec135f5059ecd8723e971b450f619 MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f diff --git a/sci-biology/biogrep/biogrep-1.0-r2.ebuild b/sci-biology/biogrep/biogrep-1.0-r3.ebuild index 55c780b9ddef..74019b09fb6b 100644 --- a/sci-biology/biogrep/biogrep-1.0-r2.ebuild +++ b/sci-biology/biogrep/biogrep-1.0-r3.ebuild @@ -1,13 +1,14 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools DESCRIPTION="Multithreaded tool for matching large sets of patterns against biosequence DBs" HOMEPAGE="http://stephanopoulos.openwetware.org/BIOGREP.html" -SRC_URI="http://www.openwetware.org/images/3/3d/${P^}.tar.gz -> ${P}.tar.gz +SRC_URI=" + http://www.openwetware.org/images/3/3d/${P^}.tar.gz -> ${P}.tar.gz doc? ( http://www.openwetware.org/images/4/49/${PN^}.pdf -> ${P}.pdf )" LICENSE="GPL-2" @@ -17,19 +18,18 @@ IUSE="doc examples" src_prepare() { default - mv configure.{in,ac} || die eautoreconf } src_install() { - use doc && DOCS+=( "${DISTDIR}"/${P}.pdf ) + default + + use doc && dodoc "${DISTDIR}"/${P}.pdf if use examples; then # remove cruft before installing examples find examples/ \( -name 'CVS' -o -name '*~' \) -exec rm -rf '{}' + || die - DOCS+=( examples ) + dodoc -r examples docompress -x /usr/share/doc/${PF}/examples fi - - default } diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest index bd7eb9ad377c..d030108aa0ab 100644 --- a/sci-biology/biopandas/Manifest +++ b/sci-biology/biopandas/Manifest @@ -1,3 +1,3 @@ DIST biopandas-0.2.7.tar.gz 255846 BLAKE2B b8c6a66f51a00266bc1a271ecfe00b4cfddd24b9766e63e2ad4187048ddd8f985d70eb8083b1be3887a0fd9b666c97553029ecd90c7b73ae882e5347bbc54d2e SHA512 cf4f12601b7f63ca3d5e9a17c6628e4975968f722c9db72e32c00e80ec335c5bf6a928a5f887b16ecd316c49b298d77634cbe1c4ef1ca505379b1de5335e2569 -EBUILD biopandas-0.2.7.ebuild 1029 BLAKE2B 49b93e7b34244beead930e791edc37b7fa11e160a3c21b9260b86e13455d3698da8ea51eba8140ea4bb1abb92901af1764c43360a10d6cc5b8c48cf86f40dbb0 SHA512 e2d99ec571d6758e86bf5149dafec4829857b36a0048599fde3b72ba9a1bf344fda4f54b31ab25e30e44509c1cf8f11cb0c14e20c3770fc025f3ab2e6092b26c +EBUILD biopandas-0.2.7.ebuild 1030 BLAKE2B 9a6dcabb0c7b929d6d4af0aa3fb34e3005d9b3012ef0ecd855c8aff38cb17c47292d04735658eab4b64bae06bf81c468b675982b7cfd7871fec398481d2d9fd7 SHA512 93041ec2e08d416e2fcf1c10de3f749a01e4a09687594d0f823b8243ed841e3ccbfb28a9dbff7c360e017abfae5bd0388aa85d6f3efb46b3d437a9777d12f048 MISC metadata.xml 537 BLAKE2B 3a84070766aa469d204a25e3dec6864db46db27a681327124b208f64b782b598d3b46b4495e08c3e9fd0484980ce1966b498cfd74d81f8d20849f6e531e0bc3e SHA512 13055720124f4586a2949140068976090fe90d997035a8426ee0833c0df9eb082abe838312d44df78c2b28ab16a9cd48df181a2082496278243e4b0e5f8fd25a diff --git a/sci-biology/biopandas/biopandas-0.2.7.ebuild b/sci-biology/biopandas/biopandas-0.2.7.ebuild index 0609b4149e11..7b1d22c8781a 100644 --- a/sci-biology/biopandas/biopandas-0.2.7.ebuild +++ b/sci-biology/biopandas/biopandas-0.2.7.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{8..10} ) inherit distutils-r1 diff --git a/sci-biology/bioperl-db/Manifest b/sci-biology/bioperl-db/Manifest index 4a69d8ed75c3..c9a9fdd4e8f8 100644 --- a/sci-biology/bioperl-db/Manifest +++ b/sci-biology/bioperl-db/Manifest @@ -1,4 +1,4 @@ AUX bioperl-db-1.6.9-db.patch 1567 BLAKE2B 40a1ba874e745630d886d0531ab90385bb2207073bebc823c52f595fa4752b0b9bf310adf7148ba4c7c5c1ec19ddec226d28a34311c932a0f37da6af1c0dd422 SHA512 a0a2ca951645b70b2e4eb3390598b2a42d6631109500238d6fc482d97a616ec1881738e5dc9af118d37fdf50657916ff275124f409510cf15515dfbc829766c0 DIST BioPerl-DB-1.006900.tar.gz 492799 BLAKE2B fb923533ecdb74e868a3aef0c0c6ba8da419ae3c0e9d2e8c55297aad15563b135b6b00fd158481b31dcacd1125f7e10a557052bd4b04eed3a400c972653ff757 SHA512 e06b8b9aa4188a83128f910d7b4a031f69d36f75e4f2d7210357366379024ef39b58eca97112b5b419f141c82b7518086273cc97c9637382ee5e0ddb9ce28746 -EBUILD bioperl-db-1.6.9-r1.ebuild 2337 BLAKE2B 1280789bf53691480419a2cac16eebef3dcce19e98b4216660fba58c582c82b30848f01e47e9adf85a5a1288e0da0114ae12eec29ef05fc680f9ffb3188703e1 SHA512 c954983c93fdd76aa5faa600c1d855d7f4e98da88adc63d93a7d6e7c795a14ab75bc073ae6452570d6042f8dca1927b8dc6b23554fb86be367b2368556631e36 +EBUILD bioperl-db-1.6.9-r2.ebuild 2351 BLAKE2B 338fef5e883902619f1c369fa2ca450711aefe5ac49d16e210242703fe665ee0e7ed9b13e50f02a1d7e866b39bc954f6e163f549f5d4966ee389c320ee550047 SHA512 b481726e1b72f3874449b3a97f9309839658f825ecf39eff4f2f019efa62f696b73e878aceec99fc4e434446f8a92cb4e9267d82f631b301ab4c399fcecf2b08 MISC metadata.xml 345 BLAKE2B 3bc3614e7030d42358f8c616b364d20788507eb62fdb72b9c581bf6ae7629bd1d258a8ff97de8e09e28e83217d88cecb53744c1d36892da04ec264db93287d12 SHA512 e543c3388ae8594a533eb55919e4cff9fbcefef82b043c151c9c1d0732918803a2811c0c3352684483fa0e5494f6559f864a9d453300c790fb4cafc765a418d5 diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild index b36c22532f35..6359865b90e0 100644 --- a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild @@ -1,13 +1,14 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 BIOPERL_RELEASE=1.6.9 DIST_NAME=BioPerl-DB DIST_AUTHOR=CJFIELDS DIST_VERSION=1.006900 +DIST_TEST="do" # Parallelism probably bad inherit perl-module DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" @@ -15,34 +16,32 @@ HOMEPAGE="http://www.bioperl.org/" SLOT="0" KEYWORDS="amd64 x86" -RESTRICT="test" IUSE="test" +RESTRICT="test" -DIST_TEST="do" # Parallelism probably bad -PATCHES=( "${FILESDIR}/${PN}-1.6.9-db.patch" ) RDEPEND=" >=sci-biology/bioperl-${PV} dev-perl/DBD-mysql dev-perl/DBI sci-biology/biosql" -DEPEND="${RDEPEND} - dev-perl/Module-Build +DEPEND=" + ${RDEPEND} test? ( dev-perl/Data-Stag dev-perl/Sub-Uplevel dev-perl/Test-Warn dev-perl/Test-Exception virtual/perl-Test-Simple - ) -" + )" +BDEPEND="dev-perl/Module-Build" + +PATCHES=( "${FILESDIR}"/${PN}-1.6.9-db.patch ) + src_prepare() { export GENTOO_DB_HOSTNAME=localhost perl-module_src_prepare } -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install -} + src_test() { einfo "Removing bundled test libraries t/lib" rm -r "${S}/t/lib" || die "Cannot remove t/lib" @@ -97,3 +96,8 @@ src_test() { pkill -F "${pidfile}" eend $? } + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/biosql/Manifest b/sci-biology/biosql/Manifest index ba740f75612d..126b5f822610 100644 --- a/sci-biology/biosql/Manifest +++ b/sci-biology/biosql/Manifest @@ -1,3 +1,3 @@ DIST biosql-1.0.1.tar.bz2 253516 BLAKE2B d2b0d6c3f03389fbcf9dfca823b02c611b63d4c1ee1356150f92bb8c14c534d988644253fd1a6ed6522b8d2d06cacf7b21d7a9e9fe7b9464704497e7f976b283 SHA512 2e1fef6ab9b4386f146910937700f9108f8ef266161b7adfbbc52c0011eebc84716637c897a01a399ff39b066ff0a5905ba3fa27e7b41f53a87baf58d5b32695 -EBUILD biosql-1.0.1-r1.ebuild 989 BLAKE2B a035872d282e58e54b472e70618bb340de900e2d49c7abf4893d82160ef8dc321caa640f1e0599b6b6d2f834159642dfa1c005bc5e1837dff769b418c04f33f3 SHA512 874448ac12a4e0331ec7b7b5ce8843928f92a6b42987975380715d39f7d0fc5c0cf688c4a596963ae5b008b55367fab3db317a8d17a19230d113e4d8e142c37f +EBUILD biosql-1.0.1-r2.ebuild 985 BLAKE2B 84dddadc810143f3a756d32f5ff881686cf6fdb3f3811b2a75257e6bdfeb95199cccad2e5bd328c7aacdd6c31476504a58d5f299fb1d6343a8fe05ff07c541f7 SHA512 5b7508456174d5893af2a6eb4a794542aa5ba02a3359aa7f93e73deb8ff9146a4a9264b66ff586ceea19d2fb5c31ef180c2ce2a022f83067eb5e070e995782d4 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/biosql/biosql-1.0.1-r1.ebuild b/sci-biology/biosql/biosql-1.0.1-r2.ebuild index 6508d6a3a2e8..c32ff970f9af 100644 --- a/sci-biology/biosql/biosql-1.0.1-r1.ebuild +++ b/sci-biology/biosql/biosql-1.0.1-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="A generic bioinformatics relational database model" HOMEPAGE="http://www.biosql.org/" @@ -22,7 +22,7 @@ RDEPEND=" dev-lang/perl" src_install() { - insinto /usr/share/${PN} + insinto /usr/share/biosql doins -r sql scripts/. dodoc Changes README Release.txt doc/*.pdf @@ -38,6 +38,6 @@ src_install() { pkg_postinst() { elog elog "Please read the BioSQL schema installation instructions in" - elog "${EROOT%/}/usr/share/doc/${PF} to begin using the schema." + elog "${EROOT}/usr/share/doc/${PF} to begin using the schema." elog } diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest index 6b189cb879cb..7121f15e1aec 100644 --- a/sci-biology/blat/Manifest +++ b/sci-biology/blat/Manifest @@ -1,5 +1,5 @@ -AUX blat-34-fix-build-system.patch 5249 BLAKE2B d32fcb326cd204c847a678cabd3fc666ed9285876ec4a3f3dc1873b9b8c83042eb705cf62e63d00b6f388540571d4ebadc497eef51827a30443d3a2aebed9420 SHA512 1c4b592ef1b45ea19d84a798f4d526c43851bf8545d4a9aaaa8842c76eff1e0e31a179d1cd914e44f67c1d5ac709b97a73a5b7e66fa680f6531efe50b6dc6246 +AUX blat-34-fix-build-system.patch 10498 BLAKE2B e2aaf5173b8b6d33733c8c16b3cc5a45d9dd431e77cdd272336baef9265b6da93e0c36b24e64127887224102309e82eda7538fa64747445b3ebdbca2cbc73a44 SHA512 60a07f9c71cfee31f2107b0b87e63f8b845f00f9f39d93f0c9b71f3e228c40c068507b352b1804d95cd049e71252e36a972bf1ebc639a040b22ad26e14ebb42e AUX blat-34-fno-common.patch 466 BLAKE2B 51dd1778f09e51ce1e345ae9474d3aaeb8535b739bc6d46e5d9271204b7043e1c5da0865ed3392b62d85b75c4d6c6611015042d359a113a9b0540c9ae1f6e448 SHA512 fa0b327f212137afa41d8d21717b02c77cf7e8228fe6b104af4a9a430fb0ed11a49be1ae38e8b51016ed5b6c43073c6cbbf27cd8b6f8396d39e623039d700abf DIST blatSrc34.zip 2142975 BLAKE2B 88a2da3b1551d5d50aaa507978c17cbe34de5a27efee9405829aea51b0950b748775f21e8d806470ba5ee7831fe71d6d87cd126c38727f25306a0f793543912e SHA512 67a1dc9a93d8ddee0fca7ce94096ecfffc71d4e0697afb285f4b64205e9eb62150a145375c29dd1ccb3cea8e8a7a71a817c8e73d7aba3e97616f1606b751afe8 -EBUILD blat-34-r2.ebuild 845 BLAKE2B feb7d63cdcf1e1a7b3bb9829fa1d918d26ece463fd4bf58e338b4a31f8ad6e3424c7995c3d6a7f6367ef2744d0c136b5a8513acb61f021c97ddedf3ab2337d19 SHA512 b19c81da2e15b7b39d22a612df4fd23754f3a63ca2290d9d2c8701f77acb15748bcd72187f70157d3538a622e29c50fa30a2ab1814d2d5bc3df477f7c0bb14c4 +EBUILD blat-34-r3.ebuild 835 BLAKE2B 4ee22000d73ec11b3f3f48db343e0d6088958c82baa193a7a45747c1ff2d72bb9a0ebfa5dd3a2f17a4508ea84a9f298d51b022d87d50d6df19780653d61d1bf3 SHA512 5c4effb62bc3c94c8fc34a2a08ace02f47d67d3facfe962e4fe36619c801748a71cdc7e3f78dc1a784dcc6e5b539b6b54a7c87559c39e68646cd62407b3d2a2b MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r3.ebuild index 7c7004cf950e..18c4128ec578 100644 --- a/sci-biology/blat/blat-34-r2.ebuild +++ b/sci-biology/blat/blat-34-r3.ebuild @@ -1,25 +1,22 @@ -# Copyright 2022 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs -MY_PN=${PN}Src +MY_PN="${PN}Src" DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" HOMEPAGE="http://www.cse.ucsc.edu/~kent/" SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" +S="${WORKDIR}/${MY_PN}" LICENSE="blat" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" -RDEPEND="" -DEPEND="app-arch/unzip" - -S=${WORKDIR}/${MY_PN} +BDEPEND="app-arch/unzip" PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch diff --git a/sci-biology/blat/files/blat-34-fix-build-system.patch b/sci-biology/blat/files/blat-34-fix-build-system.patch index 361149cc1211..9aca3f841315 100644 --- a/sci-biology/blat/files/blat-34-fix-build-system.patch +++ b/sci-biology/blat/files/blat-34-fix-build-system.patch @@ -1,34 +1,36 @@ --- a/blat/makefile +++ b/blat/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ O = blat.o blat: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/blat${EXE} +- ${STRIP} ${BINDIR}/blat${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L all: + cd ../lib && ${MAKE} --- a/gfClient/makefile +++ b/gfClient/makefile -@@ -8,5 +8,5 @@ +@@ -8,5 +8,4 @@ X = gfClient gfClient: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/$X${EXE} +- ${STRIP} ${BINDIR}/$X${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L --- a/gfServer/makefile +++ b/gfServer/makefile -@@ -8,7 +8,7 @@ +@@ -8,8 +8,7 @@ X = gfServer gfServer: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L - ${STRIP} ${BINDIR}/$X${EXE} +- ${STRIP} ${BINDIR}/$X${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L test: + ${MKDIR} tests/output --- a/hg/pslPretty/makefile +++ b/hg/pslPretty/makefile @@ -8,7 +8,7 @@ @@ -36,7 +38,7 @@ pslPretty: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L test:: testRna testDnax @@ -47,7 +49,7 @@ pslReps: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L lib: cd ../../lib && ${MAKE} @@ -58,10 +60,20 @@ pslSort: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L lib: +--- a/inc/cgi_build_rules.mk ++++ b/inc/cgi_build_rules.mk +@@ -12,7 +12,6 @@ + mv $A${EXE} ${CGI_BIN}-beta/$A + + strip:: compile +- ${STRIP} $A${EXE} + chmod g+w $A${EXE} + chmod a+rx $A${EXE} + --- a/inc/common.mk +++ b/inc/common.mk @@ -1,20 +1,15 @@ @@ -87,15 +99,24 @@ endif endif # Apply the stronger checks to all code on our development machine: -@@ -37,7 +32,7 @@ +@@ -36,9 +31,6 @@ + BINDIR = ${HOME}/bin/${MACHTYPE} endif MKDIR=mkdir -p - ifeq (${STRIP},) +-ifeq (${STRIP},) - STRIP=strip -+ STRIP=true - endif +-endif CVS=cvs + # portable naming of compiled executables: add ".exe" if compiled on +@@ -55,6 +47,6 @@ + STRINGIFY = ${BINDIR}/stringify + + %.o: %.c +- ${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $< ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $< + + --- a/jkOwnLib/makefile +++ b/jkOwnLib/makefile @@ -9,7 +9,7 @@ @@ -107,6 +128,15 @@ ../lib/$(MACHTYPE): mkdir ../lib/$(MACHTYPE) +--- a/jkOwnLib/tests/freen/makefile ++++ b/jkOwnLib/tests/freen/makefile +@@ -7,5 +7,5 @@ + O = freen.o + + hello: freen.o +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/freen $O $(MYLIBS) $L + --- a/lib/makefile +++ b/lib/makefile @@ -32,7 +32,7 @@ @@ -118,6 +148,102 @@ $(MACHTYPE): mkdir $(MACHTYPE) +--- a/lib/tests/makefile ++++ b/lib/tests/makefile +@@ -14,22 +14,19 @@ + ${MKDIR} output ${BIN_DIR} + + errCatchTest: errCatchTest.o ${MYLIBS} mkdirs +- ${CC} ${COPT} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L +- ${STRIP} ${BIN_DIR}/errCatchTest${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/errCatchTest errCatchTest.o ${MYLIBS} $L + ${BIN_DIR}/errCatchTest secret > output/errCatch.good + diff expected/errCatch.good output/errCatch.good + ${BIN_DIR}/errCatchTest bad > output/errCatch.bad + diff expected/errCatch.bad output/errCatch.bad + + htmlExpandUrlTest: htmlExpandUrlTest.o ${MYLIBS} mkdirs +- ${CC} ${COPT} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L +- ${STRIP} ${BIN_DIR}/htmlExpandUrlTest${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlExpandUrlTest htmlExpandUrlTest.o ${MYLIBS} $L + ${BIN_DIR}/htmlExpandUrlTest > output/htmlExpandUrlTest 2>&1 + diff expected/htmlExpandUrlTest output/htmlExpandUrlTest + + htmlPageTest: htmlPageTest.o ${MYLIBS} mkdirs +- ${CC} ${COPT} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L +- ${STRIP} ${BIN_DIR}/htmlPageTest${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlPageTest htmlPageTest.o ${MYLIBS} $L + ${BIN_DIR}/htmlPageTest input/google.html > output/google.out + diff expected/google.out output/google.out + +@@ -86,20 +83,20 @@ + diff -b expected/$@.err output/$@.err + + ${BIN_DIR}/pipelineTester: mkdirs pipelineTester.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/pipelineTester pipelineTester.o ${MYLIBS} $L + + + dyStringTest: ${BIN_DIR}/dyStringTester mkdirs + ${BIN_DIR}/dyStringTester + + ${BIN_DIR}/dyStringTester: mkdirs dyStringTester.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/dyStringTester dyStringTester.o ${MYLIBS} $L + + + mimeTests: mime1 mime2 mime3 mime4 mimeBin mime5 mimeAltHead mimeAutoBoundary mimeBlat + + ${BIN_DIR}/mimeTester: mkdirs mimeTester.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeTester mimeTester.o ${MYLIBS} $L + + + mime1: ${BIN_DIR}/mimeTester mkdirs +@@ -142,7 +139,7 @@ + ${BIN_DIR}/mimeTester -sizeSeries=3000 + + ${BIN_DIR}/htmlMimeTest: mkdirs htmlMimeTest.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} $L + + htmlMime1: ${BIN_DIR}/htmlMimeTest mkdirs + ${BIN_DIR}/htmlMimeTest http://hgwdev.cse.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 3490 3502 > output/$@.out +@@ -152,7 +149,7 @@ + base64Tests: base64Encode base64Decode + + ${BIN_DIR}/testBase64: mkdirs testBase64.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testBase64 testBase64.o ${MYLIBS} $L + + base64Encode: ${BIN_DIR}/testBase64 mkdirs + ${BIN_DIR}/testBase64 'My Test String' > output/$@.out +@@ -167,7 +164,7 @@ + quotedPTests: quotedPEncode quotedPDecode + + ${BIN_DIR}/testQuotedP: mkdirs testQuotedP.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/testQuotedP testQuotedP.o ${MYLIBS} $L + + quotedPEncode: ${BIN_DIR}/testQuotedP mkdirs + ${BIN_DIR}/testQuotedP 'taxes are quite high ' > output/$@.out +@@ -178,14 +175,14 @@ + diff expected/$@.out output/$@.out + + ${BIN_DIR}/mimeDecodeTest: mkdirs mimeDecodeTest.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/mimeDecodeTest mimeDecodeTest.o ${MYLIBS} $L + + mimeDecodeTest: ${BIN_DIR}/mimeDecodeTest mkdirs + ${BIN_DIR}/mimeDecodeTest -cid -autoBoundary output < input/$@.txt + diff expected/noName1.html output/noName1.html + + ${BIN_DIR}/safeTester: mkdirs safeTester.o ${MYLIBS} +- ${CC} ${COPT} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BIN_DIR}/safeTester safeTester.o ${MYLIBS} $L + + safeTest: ${BIN_DIR}/safeTester mkdirs + ${BIN_DIR}/safeTester --- a/makefile +++ b/makefile @@ -1,18 +1,18 @@ @@ -160,18 +286,19 @@ faToNib: $O $(MYLIBS) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L --- a/utils/faToTwoBit/makefile +++ b/utils/faToTwoBit/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ O = faToTwoBit.o faToTwoBit: $O ${MYLIBS} - ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L - ${STRIP} ${BINDIR}/faToTwoBit${EXE} +- ${STRIP} ${BINDIR}/faToTwoBit${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L clean: + rm -f $O --- a/utils/nibFrag/makefile +++ b/utils/nibFrag/makefile @@ -4,7 +4,7 @@ @@ -179,29 +306,43 @@ nibFrag: $(O) - ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a -+ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a --- a/utils/twoBitInfo/makefile +++ b/utils/twoBitInfo/makefile -@@ -7,7 +7,7 @@ +@@ -7,8 +7,7 @@ O = twoBitInfo.o twoBitInfo: $O ${MYLIBS} - ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L - ${STRIP} ${BINDIR}/twoBitInfo${EXE} +- ${STRIP} ${BINDIR}/twoBitInfo${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L clean: + rm -f $O --- a/utils/twoBitToFa/makefile +++ b/utils/twoBitToFa/makefile -@@ -8,7 +8,7 @@ +@@ -8,8 +8,7 @@ O = twoBitToFa.o twoBitToFa: $O ${MYLIBS} - ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L -+ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L - #${STRIP} ${BINDIR}/twoBitToFa${EXE} +- #${STRIP} ${BINDIR}/twoBitToFa${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L clean: + rm -f $O +--- a/webBlat/makefile ++++ b/webBlat/makefile +@@ -7,8 +7,7 @@ + O = webBlat.o + + webBlat: $O ${MYLIBS} +- ${CC} ${COPT} -o webBlat $O ${MYLIBS} $L +- ${STRIP} webBlat${EXE} ++ ${CC} ${LDFLAGS} ${CFLAGS} -o webBlat $O ${MYLIBS} $L + + installOsX: webBlat + cp webBlat /Library/WebServer/CGI-Executables diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest index d061ecefb980..9b41dfd6d142 100644 --- a/sci-biology/cd-hit/Manifest +++ b/sci-biology/cd-hit/Manifest @@ -1,5 +1,5 @@ AUX cd-hit-4.6.6-fix-build-system.patch 4006 BLAKE2B 28e19d8dbcf2072c1e348c0f4d1784f8ee0375b58fb6233f6bc2a7634c046694b0add6910b513b089b4eaf0fcc0c7c43d91534583d2b0e45a7c7396ff9fff24f SHA512 84aadb9967ad65d04127468edb161b8725a5b1468586320eb89d4b4f5f97ad7b60da9728fa1088ecf4aff179a6bda36675add9a255631cf9359c991b61451c6d AUX cd-hit-4.6.6-fix-perl-shebangs.patch 4909 BLAKE2B 2bf82ee2713206d4782143fc04f2a924b742cb50ee9b1c99aab3a3f6d1265dee78009106970329146f068544caa4edf5878bd9ee3aaaf69ea8e418702ef1e069 SHA512 3ded78d991ee922761a3a7395b4d422ff29c6fe1c0657b61ad74bc6f9253c7dc82414f8d71cfffae37cac192e96ab03f711257d3091cdd0c9444202bdf5967f5 DIST cd-hit-4.6.6.tar.gz 1152570 BLAKE2B 6a7cf99be947376af19172739626b571e06936b7b0bc8c5cb52069c63e98f0949a44edf7560fa50810d2d96e310df87dcf2e3ebf5a3856ada46dcdcd3595b6c0 SHA512 8241d6674fb041559792dbbb58c12b41302d2275d3bacb1362946094b48a0b8e1236e71b5dc77d13405220b60f8253e6f996753a8b051995a72c8353d4333c51 -EBUILD cd-hit-4.6.6.ebuild 997 BLAKE2B 1305388e83140df2e024bc64546b96e849a9f70095dabc29c79ab0a078dff9fd33a091d05df3f07323391e627f28877ad77f52fdf890d20cef5832df0e3053a9 SHA512 fe17e01fc04944df9b86b98dc73a4be2f14300938e3e926f56c952eddad62caf846f0051a7c3a66dbca3132f3a79a8bc21d7a43206bd6d9d784b24c94c3204b8 +EBUILD cd-hit-4.6.6-r1.ebuild 980 BLAKE2B 2eb0e8eee5bcb8174eab19c682aff8e0d0c05737745668bae53bbffd2fab70e348521181aaa4f63854279e50a96588b3e389662c638629344e3b8f70993e5350 SHA512 1f4d334f08da0a7315e109878543522455b91a7cf11104997ab124b15563182920b5e89bfb773fa4915df1805e0777a317dfba4ad6020ecbc14a024aadef222c MISC metadata.xml 1352 BLAKE2B e0549ee891c9d8fb014740930ac5b45817aa5b77cf5d46d48ea7e4992d9c9185b1789afc1b0cb3af66307ef4b183897c707bbc2287f1e1ccdbff0090dd06dd1f SHA512 4bd77a842ab77168c35c5d9a58452e6d1fae5d03cfc0c900ce3b3d5cc1accd2d2dd90924a495b493c69282af455d28dcd97c050fb334c5646b611ff0d63307bf diff --git a/sci-biology/cd-hit/cd-hit-4.6.6.ebuild b/sci-biology/cd-hit/cd-hit-4.6.6-r1.ebuild index ebe345f15245..20e7e2d784fe 100644 --- a/sci-biology/cd-hit/cd-hit-4.6.6.ebuild +++ b/sci-biology/cd-hit/cd-hit-4.6.6-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit flag-o-matic toolchain-funcs +inherit toolchain-funcs RELDATE="2016-0711" RELEASE="${PN}-v${PV}-${RELDATE}" @@ -11,6 +11,7 @@ RELEASE="${PN}-v${PV}-${RELDATE}" DESCRIPTION="Clustering Database at High Identity with Tolerance" HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" SRC_URI="https://github.com/weizhongli/cdhit/releases/download/V${PV}/${RELEASE}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}"/${RELEASE} LICENSE="GPL-2" SLOT="0" @@ -19,8 +20,6 @@ IUSE="openmp" RDEPEND="dev-lang/perl" -S="${WORKDIR}"/${RELEASE} - PATCHES=( "${FILESDIR}"/${PN}-4.6.6-fix-perl-shebangs.patch "${FILESDIR}"/${PN}-4.6.6-fix-build-system.patch diff --git a/sci-biology/clustal-omega/Manifest b/sci-biology/clustal-omega/Manifest index fde021267efa..8318d11f103d 100644 --- a/sci-biology/clustal-omega/Manifest +++ b/sci-biology/clustal-omega/Manifest @@ -1,3 +1,3 @@ DIST clustal-omega-1.2.4.tar.gz 1170516 BLAKE2B 0751a30a8d7bab2bac01980b84a28720e127dfeeec5b72f1826c8d9da4e84d5d9434b0f138b600155cc76f4385320913edb9bbdeb463ed757364feb3538f325b SHA512 b31514c30b412d731ee22c9020156b65a6a6cbc6fd51edc195d17b560935184bc070feeb58964c54df9eecdefb00e5a21ce859cb0ea69d92917f6bd8e93b819e -EBUILD clustal-omega-1.2.4.ebuild 649 BLAKE2B c3cf4ed978a758f0f274fff4469c8ea51567f51619121b00bcaca3777ee6f7e3ca67d117437e99f839fb68aa4be6b98383a5a883ffd854f7525586017e787cde SHA512 61ce83c18a97f09dc0750a2da7179aece9c788eb2792fac799a343e219d11f11d7a60980f791313b0963a7aed720d076e55e05c6134155be07e61e18b382c6d8 +EBUILD clustal-omega-1.2.4-r1.ebuild 543 BLAKE2B 23d251225ea265bf6407ca8fb6d87cae12ec3c564961241385b62e503294a6f112e33497a054d3578402395502fa64802d4a9556fa5fd29cc84e240477501bed SHA512 d139dca41c6b25c8e2c91ef29938b4d80e75e486ce967376cc77225424a3006c42c89bccabe6cd71fc57e62d8bc10c258e660cf663d66929229d278680c8d54e MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.4.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild index 1e7e1f8b166d..2a4a2c108fed 100644 --- a/sci-biology/clustal-omega/clustal-omega-1.2.4.ebuild +++ b/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -12,7 +12,6 @@ SRC_URI="http://www.clustal.org/omega/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="amd64 x86" -IUSE="static-libs" DEPEND="dev-libs/argtable" RDEPEND="${DEPEND}" @@ -25,13 +24,7 @@ src_prepare() { eautoreconf } -src_configure() { - econf \ - --enable-shared \ - $(use_enable static-libs static) -} - src_install() { default - find "${D}" -name '*.la' -delete || die + find "${ED}" -name '*.la' -delete || die } diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest index f642140dff2e..d26b15faea9f 100644 --- a/sci-biology/clustalw/Manifest +++ b/sci-biology/clustalw/Manifest @@ -1,6 +1,7 @@ -AUX 1.83-as-needed.patch 388 BLAKE2B 8da98e05dcdc74ee41ff7a3d75b11590507bc769df0adb181f7c2d0a656f80d15b7363723bd760c359efb666cf962f5cf8c055abc1b7181d37203b0bfe659717 SHA512 1f66a0b539f9101a52b4117d0369294f706a048464d1908ae457def27d33ace0e5c5f9ba507f82a1406bb78ff51896ac6bb76cb03dfe8ff6bbb8ed182dc0f5ea +AUX 1.83-as-needed.patch 800 BLAKE2B 37db9a8c0f7b5db47065f5c6e01cefc095363e30a5f07a95bc7b71af80f12c59b8f70bc898b77ab40ab13120c7d2a851eb177543c5a1d58f24cb2d9b8921993c SHA512 42d4982cb1f2070c9c09312ec9ffadfa274740e2dcaa688f7d1314aa47b88f9e59a6a452cb3481a64f57816786523352a10deb498c7235e2bc1b5999858e0201 +AUX 1.83-clang.patch 162 BLAKE2B b4ed2add1aaf33ef3d3138124377ed88bbe030b2e50f24e7dc87717fd06e3f76c6660c518d60083520f13b2349a1051a3981605e6130e0632e112212af345f51 SHA512 0e9aa3e61194f6d35449544c31693ee9f23ced8460b6ef4eca45b7f969867a6de04b898531e2749e65ee353547bd6fd3f19b7ee29d202ca30b5043567bf045bd DIST clustalw-2.1.tar.gz 350761 BLAKE2B 479acb42ec0b0adee8e04e99132a782c947a1261f48e674c6a11e4f38e44e5709d03f0c864f0cd3cf7eb4faf76a36b6121c3e3d3573c86ee3895971df07f1a58 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921 DIST clustalw1.83.UNIX.tar.gz 166863 BLAKE2B a3b1eabad8bc736cde4655f13fa8544759b7b5c50ea97fd45ee0be45ac6c361db5ced8ad21622ac2530b57c37c77dfd67657afd2c411acbfb7ff2a3ba014637e SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a -EBUILD clustalw-1.83-r4.ebuild 816 BLAKE2B 216e179d5da96bb16b46b64366c54f0482863ebcbb983c19cedadb7d898ed512b9ac679d696f8f74966fc3b24560951674b8eb09c97010c8300785cec01bc887 SHA512 3c013eaabd1f1f951067d6494c03b70913263d71f62fea4669f30dad3d18d52c02b9e8614854350ac8da2b033a7257d708e637e4ac89247a37be492b5d79e87d -EBUILD clustalw-2.1-r1.ebuild 489 BLAKE2B af8ab15dcb6e2fb20199c7054940eaf53bbbcc72ec1fd7c37fc0aa3f3c28e7a23c640e70eb33956367a12ecc04990a3d6b63ad2b3d8bdf35396debff35dc6da6 SHA512 ad9b200b16d55df114440a44f8d771a406e518a49ca140de106ee38b4e8afc7f0acc7ccb18d81ea90f541637013915c6e793832d26a8b4465925fa101747498c +EBUILD clustalw-1.83-r4.ebuild 824 BLAKE2B fbe940a15f3649f3e89bec7fdeed8b2a51b16441c449cfda705a43a632e4125f8ca2aec47efd3dc6c191c9ed4053a82026b3ec6c4a4ef43289ef357bdd9ec277 SHA512 0a5dd3fef90b72aa869104686af477297cbd9dc8c32bd13b2a8f330f161679d41add9ff94198189f32188b82bd9efad74456f0a1b472b323eded33985785f216 +EBUILD clustalw-2.1-r2.ebuild 479 BLAKE2B 2b8cdab7e004824ca9e515d114e49f21abed58bed18229a407e861f4756377771345c9971e5945c258a5d7891f052245443b1f731fc231cc7fe7154f38ab1422 SHA512 16d6478b5ed34f0aa7ac3441cf8b49820ef74e46315363078f82227c865067d950c24c41d309192520adae15b72916fbc3a3e5a12e439d4437effcb9f0d43b7d MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild index 076f16300b3a..62c59747adf3 100644 --- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild +++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild @@ -1,34 +1,35 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="General purpose multiple alignment program for DNA and proteins" HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/" SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz" +S="${WORKDIR}/${PN}${PV}" LICENSE="clustalw" SLOT="1" KEYWORDS="amd64 ~ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" -IUSE="" -S="${WORKDIR}"/${PN}${PV} - -PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch ) +PATCHES=( + "${FILESDIR}"/${PV}-as-needed.patch + "${FILESDIR}"/${PV}-clang.patch +) src_prepare() { default - - sed \ - -e "/^CC/s:cc:$(tc-getCC):g" \ - -i makefile || die sed \ - -e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" \ + -e "s|clustalw_help|${EPREFIX}/usr/share/doc/${PF}/clustalw_help|" \ -i clustalw.c || die } +src_configure() { + tc-export CC +} + src_install() { dobin clustalw dodoc README clustalv.doc clustalw{.doc,.ms,_help} diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r2.ebuild index f42f1ed031b0..58a28e3ef7a5 100644 --- a/sci-biology/clustalw/clustalw-2.1-r1.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="General purpose multiple alignment program for DNA and proteins" HOMEPAGE="http://www.clustal.org/" @@ -10,9 +10,8 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" LICENSE="GPL-3 LGPL-3" SLOT="2" KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" -IUSE="" src_install() { default - rmdir "${ED%/}"/usr/share/aclocal || die + rmdir "${ED}"/usr/share/aclocal || die } diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch index 9bb35b43f24a..54b78b0811e0 100644 --- a/sci-biology/clustalw/files/1.83-as-needed.patch +++ b/sci-biology/clustalw/files/1.83-as-needed.patch @@ -1,17 +1,36 @@ --- a/makefile +++ b/makefile -@@ -11,11 +11,11 @@ +@@ -10,25 +10,22 @@ + HEADERS = general.h clustalw.h - CC = cc +-CC = cc -CFLAGS = -c -O -LFLAGS = -O -lm -+CFLAGS += -c -+LIBS = -lm ++# C99 for gets() ++CFLAGS += -std=gnu99 ++LIBS += -lm clustalw : $(OBJECTS) amenu.o clustalw.o - $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS) -+ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS) interface.o : interface.c $(HEADERS) param.h - $(CC) $(CFLAGS) $*.c +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + amenu.o : amenu.c $(HEADERS) param.h +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + readmat.o : readmat.c $(HEADERS) matrices.h +- $(CC) $(CFLAGS) $*.c ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + + trees.o : trees.c $(HEADERS) dayhoff.h +- $(CC) $(CFLAGS) $*.c +- +-.c.o : +- $(CC) $(CFLAGS) $? ++ $(CC) $(CFLAGS) $(CPPFLAGS) -c $< + diff --git a/sci-biology/clustalw/files/1.83-clang.patch b/sci-biology/clustalw/files/1.83-clang.patch new file mode 100644 index 000000000000..ea1202079d9e --- /dev/null +++ b/sci-biology/clustalw/files/1.83-clang.patch @@ -0,0 +1,11 @@ +--- a/interface.c ++++ b/interface.c +@@ -210,7 +210,7 @@ + Boolean name1 = FALSE; + sint ajb; + +- if(args[0]==NULL) return; ++ if(args[0]==NULL) return 0; + + + diff --git a/sci-biology/dialign2/Manifest b/sci-biology/dialign2/Manifest index 137467c1ad2b..4e0d01571cdf 100644 --- a/sci-biology/dialign2/Manifest +++ b/sci-biology/dialign2/Manifest @@ -1,4 +1,5 @@ -AUX dialign2-2.2.1-fix-build-system.patch 819 BLAKE2B c639532a8bc95744c91f07f0e672255110b31e2964bb8bfbacaa6b401dcee6a10e29199d9a19614f690a610109c2a5f0ab785b66c144373ceb4724112182cab2 SHA512 8a85911d1743c186f3dea402333e502cfd4f7807065277a2657d790ab9cf1c8d535fbb25abf994f83cdab9849d4ec203d8db8198cf10fa91996d61b63d98f807 +AUX dialign2-2.2.1-Wimplicit.patch 5674 BLAKE2B e6af3beda47e2c0e3c73434c6aac27fc8c4ce3ca3a3f1b09f2719672270717235274886afd2c0e8b2f1eb76ae1f9ddf6f9cd66e6cc5d4a3794190dce2b72d676 SHA512 c6fccdfa3c6a373dcee9ea734085b2c4f5e9ee4a0218b91500cdcc52b429b9e787a8cb9c25cf96b589b9f95c57ffa522a4a75cca5b17064b2bfc21827269b962 +AUX dialign2-2.2.1-fix-build-system.patch 845 BLAKE2B bbc4dbfcae56bd463253b61a437f9dce0101b5bc3b70504408df3a37ca74f3e95ce450d42c4c49ea92eedbcb400b39905fe8650b37e2e93c5cfc21ae36e560c5 SHA512 dee19a8c430b79bbfc6c89bc6fe4cd0b300c24f4351cadaffd17cfaad71c38944f28f805efb46d0d66ea512005e47b838ceb85189bd4b8bd107db070ff0d0cb9 DIST dialign-2.2.1-src.tar.gz 209015 BLAKE2B daf903b735e164879a8ceb998ca5ea0c5243927d9b88b4041633af06da7d1f608d58933ee098393e99093b7d11587a59277d9d0927214df0341a8a623b0d5608 SHA512 eb51fbc8d81e384ac19e9cc957be233287a1d81a7f020d77ab16ee6943382bd4e81099c0c9028fcff130def62cdf19de59e9a9c08ea4cb67b9d8f1939eb3bc45 -EBUILD dialign2-2.2.1.ebuild 836 BLAKE2B abb98cbbfcfe09ead711558bb07b41dcd79aa706793d1aadff9eb258daac8bd42ccbef2fbb74602b0e71bc99aa863a749b0239d63c23edc78982116e4febcf0e SHA512 6714a835544683e1b135ee65aa0728e1f2943349358b4d1505c583f1beba3b4210f3fdec01625ef8bf7a92605274f47233e7ce630cd9a2996e77a098d1990e51 +EBUILD dialign2-2.2.1-r1.ebuild 817 BLAKE2B 2e34fd2980597cf20ad1e4a37c3ae4fed42cc0b50f728d6a1e90d4343eed8ad36b8675fdf32af4c0d00ceb57173ca27f3112149290bf94a294b522e3c350a8fc SHA512 2bafe6011fc6835275f4a16dc3d11a3ad964bf032df5adfd56d2d37f58071543a05e7766a0915806802950735115a5a2c836874e62557936e690e9a57cf98f6c MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/dialign2/dialign2-2.2.1.ebuild b/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild index db310e3fe8d3..13b56b66c37b 100644 --- a/sci-biology/dialign2/dialign2-2.2.1.ebuild +++ b/sci-biology/dialign2/dialign2-2.2.1-r1.ebuild @@ -1,24 +1,26 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit flag-o-matic toolchain-funcs +inherit toolchain-funcs DESCRIPTION="Multiple sequence alignment" HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/dialign" SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/dialign/resources/downloads/dialign-${PV}-src.tar.gz" +S="${WORKDIR}/dialign_package" LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -S=${WORKDIR}/dialign_package -PATCHES=( "${FILESDIR}"/${PN}-2.2.1-fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-2.2.1-fix-build-system.patch + "${FILESDIR}"/${PN}-2.2.1-Wimplicit.patch +) src_configure() { tc-export CC - append-cppflags -I. -DCONS } src_compile() { @@ -26,12 +28,12 @@ src_compile() { } src_install() { - dobin src/${PN}-2 - insinto /usr/share/${PN} + dobin src/dialign2-2 + + insinto /usr/share/dialign2 doins -r dialign2_dir/. - cat >> "${T}"/80${PN} <<- EOF || die - DIALIGN2_DIR="${EPREFIX}/usr/share/${PN}" + newenvd - 80dialign2 <<- EOF + DIALIGN2_DIR="${EPREFIX}/usr/share/dialign2" EOF - doenvd "${T}"/80${PN} } diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch b/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch new file mode 100644 index 000000000000..3f886171b070 --- /dev/null +++ b/sci-biology/dialign2/files/dialign2-2.2.1-Wimplicit.patch @@ -0,0 +1,205 @@ +--- a/src/alig_graph_closure.c ++++ b/src/alig_graph_closure.c +@@ -27,7 +27,7 @@ + void init_seq(CLOSURE *clos, int nbreseq, int *longseq); + void desinit_seq(CLOSURE *clos); + +-int print_aligSets(CLOSURE *clos, int nseq, int i); ++void print_aligSets(CLOSURE *clos, int nseq, int i); + + char DEBUG=0; + +@@ -309,7 +309,7 @@ + } + + +-int print_aligSets(CLOSURE *clos, int nseq, int i) ++void print_aligSets(CLOSURE *clos, int nseq, int i) + { + char nouveau_, terminer; + int n, ng, nd, nn, k; +@@ -395,7 +395,7 @@ + liberer(clos); + } + +-int addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j) ++void addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j) + { + char nouveau_, terminer; + int n, n1, n2, ng1, ng2, nd1, nd2, nn, k; +@@ -623,7 +623,7 @@ + return(!path(clos, y, j, x, i)); + } + +-int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l) ++void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l) + { + int k; + +--- a/src/alig_graph_closure.h ++++ b/src/alig_graph_closure.h +@@ -43,13 +43,13 @@ + + void freeAligGraphClosure(CLOSURE *clos); + +-int addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j); ++void addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j); + + int alignablePositions(CLOSURE *clos, int x, int i, int y, int j); + + int alignedPositions(CLOSURE *clos, int x, int i, int y, int j); + +-int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l); ++void addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l); + + int alignableSegments(CLOSURE *clos, int x, int i, int y, int j, int l); + +--- a/src/anchor.c ++++ b/src/anchor.c +@@ -17,6 +17,7 @@ + #include "define.h" + #include "dialign.h" + #include "alig_graph_closure.h" ++#include "pratique.h" + + + extern int anc_num, *seqlen ; +@@ -24,6 +25,8 @@ + extern char *seq[MAX_SEQNUM]; + extern struct multi_frag *anchor_frg ; + ++extern int word_count( char *seq ); ++ + void anchor_check( int s1, int s2, int b1, int b2, int l , float scr ) { + + if( +@@ -101,7 +104,7 @@ + } + + +-int multi_anc_read( char *file_name ) { ++void multi_anc_read( char *file_name ) { + + char anc_file_name[ NAME_LEN ] ; + FILE *fp; +--- a/src/dialign.c ++++ b/src/dialign.c +@@ -218,7 +218,7 @@ + extern void subst_mat(char *file_name, int fragno , struct multi_frag *smp ); + extern int seq_read( char *in_file , char *sq[MAX_SEQNUM] , char **sqn , char **fsqn) ; + extern int anc_read( char *file_name ) ; +- extern int multi_anc_read( char *file_name ) ; ++ extern void multi_anc_read( char *file_name ) ; + extern void randomize( int r_numb , FILE *fp1 ); + extern int mini2(int a, int b); + extern int maxi2(int a, int b); +@@ -250,6 +250,9 @@ + extern void av_tree_print(); + extern void matrix_read( FILE *fp_mat ) ; + extern void mem_alloc( ) ; ++ extern void regex_parse( char *mot_regex ) ; ++ extern void seq_parse( char *mot_regex ) ; ++ extern void exclude_frg_read( char *file_name , int ***exclude_list) ; + + + /******************************/ +@@ -258,7 +261,7 @@ + + + +-main(int argc, char **argv) ++int main(int argc, char **argv) + { + int k, anc1, dia_counter, tmpi1, tmpi2 ; + +--- a/src/functions.c ++++ b/src/functions.c +@@ -853,7 +853,7 @@ + } + } + +-wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, ++void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, + int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) { + + int i, dc, pc, s1, pos; +@@ -882,7 +882,7 @@ + + + +-plot_calc( int num , int e_len, float *w_count, float *pl, ++void plot_calc( int num , int e_len, float *w_count, float *pl, + struct multi_frag *dia , FILE *fp_csc ) + { + int i, dc, pc, s1, pos; +--- a/src/input.c ++++ b/src/input.c +@@ -17,6 +17,7 @@ + #include "define.h" + #include "dialign.h" + #include "alig_graph_closure.h" ++#include "pratique.h" + + extern int max_dia , self_comparison ; + extern int sim_score[21][21]; +@@ -370,8 +371,11 @@ + } + + +- if ( fgets( line , MLINE , fp ) == NULL ) +- erreur("\n\n problem with file %s \n\n", file_name ); ++ if ( fgets( line , MLINE , fp ) == NULL ) { ++ char buffer [500]; ++ snprintf ( buffer, 500, "\n\n problem with file %s \n\n", file_name ); ++ erreur( buffer ); ++ } + else + if( w_type % 2 ) + av_sim_score_nuc = atof( line ); +--- a/src/output.c ++++ b/src/output.c +@@ -61,9 +61,9 @@ + extern void mini(int *a, int b); + extern void maxi(int *a, int b); + extern int int_test(float f); +- extern plot_calc( int num , int e_len, float *w_count, float *pl, ++ extern void plot_calc( int num , int e_len, float *w_count, float *pl, + struct multi_frag *dia , FILE *fp_csc ) ; +- extern wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, ++ extern void wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt, + int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) ; + + +--- a/src/pratique.c ++++ b/src/pratique.c +@@ -4,7 +4,7 @@ + + /* ------------------------------------------------------------*/ + +-void erreur(char *message) ++_Noreturn void erreur(char *message) + { + printf("%s\n", message); + exit(1); +--- a/src/pratique.h ++++ b/src/pratique.h +@@ -12,7 +12,7 @@ + + #define TAILLE_MAX_LIGNE_FICHIER 10000 + +-void erreur(char *message); ++_Noreturn void erreur(char *message); + + void *allouer(size_t taille); + void *reallouer(void *pointeur, size_t taille); +--- a/src/regex.c ++++ b/src/regex.c +@@ -151,7 +151,7 @@ + + } + +-seq_parse( char *mot_regex ) { ++void seq_parse( char *mot_regex ) { + int sn, ok , i ; + int sp, ap, rp, hv, match; + max_mot_offset = sqrt ( - log ( 0.1 ) * 10 / mot_factor ) * mot_offset_factor; diff --git a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch index 45365c56e3a4..a4940ee867ee 100644 --- a/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch +++ b/sci-biology/dialign2/files/dialign2-2.2.1-fix-build-system.patch @@ -1,14 +1,16 @@ --- a/src/makefile +++ b/src/makefile -@@ -10,8 +10,6 @@ +@@ -10,9 +10,7 @@ ############################### -CC = gcc -CFLAGS = -c -O -I$ -DCONS - #CFLAGS = -g -c -I$ -DCONS +-#CFLAGS = -g -c -I$ -DCONS ++CPPFLAGS += -I. -DCONS LIBS = -lm # + @@ -23,33 +21,4 @@ # diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest index 8ae7c859a192..0cd0952651bd 100644 --- a/sci-biology/elph/Manifest +++ b/sci-biology/elph/Manifest @@ -1,4 +1,4 @@ AUX elph-1.0.1-fix-build-system.patch 1303 BLAKE2B 66103bd295fddd45f90734a49a8b673efcd91234abb4355408bca284d1d498bb98a9392b8467117e4ae034780579573a2cf26c78bef245cea8d0dac01c759322 SHA512 d39611f80cd2e67e94f3d1dd7eb1dfe59ac3b221956ab72f3951b5716825387e7d3ed04608e75abfc43ae2cbc53ace474e602ddbd93441c2da74f04516ba2ba5 DIST ELPH-1.0.1.tar.gz 113476 BLAKE2B 7c34e9f847560bf46d1bc6bbb720a0cd0afd91b29c23dac98056d2b9eea39146dda72468cad96892eb551cdfb03b224ea22b8e4cee40f19774e24fa843f55192 SHA512 a76cdcdaa1dc406fb0f1204b6a40ffc9f4c0840611b960a3d4299d447446e5bbf941abe7f70cee38f69a64862e186133fd60c1aac18b4b58d86f2ed5c4dd7d72 -EBUILD elph-1.0.1-r1.ebuild 658 BLAKE2B 420e613f10a35ff0b4963488dff3bfa14a5e352d14ad8be580f1079fd986fa0bc23f5eb41d6b7eab4f25674d2893bce2bde2c26cf886883be2f6fa53c07354a6 SHA512 ae25927fb71058c7543083735082e025defb746ea89f633e0bfa99291507e3a59ccdb05f51924b62a393dbaa40e727e83e83dc6e88b3acbe8e368cd856bd4121 +EBUILD elph-1.0.1-r2.ebuild 648 BLAKE2B 9d7f03f660318cb8c774cd6cb40dafc747319f6fbed2816b800e1c26f6d7cfb020e1e10daa57debd12adc6ad9a69c1988ceaee2a718785222a1794fb988a8a31 SHA512 f29f0e8ee451d4c0781c4d745c5d2e930b27a8bf520d169e1c0090ca983745475deaded45af8360cb198d257aae025723cadcc112cf560eac880d486eb528358 MISC metadata.xml 618 BLAKE2B 4c12f3466489b131857dca3df864faa163d047d038aee453a02a4ab436c742e6df4f93b437643f6b4f449fcbc657dfd0d8a12b3e7ec7f90faa50ffd745dfe7bb SHA512 a19d27931ae95a971d786ff739807ce36f40a05122b1cd454f46a75f3a506b17206bf90516f9eda3aef4c1820026413aef88c3fa9bfc15516ec9c859c8b6bce7 diff --git a/sci-biology/elph/elph-1.0.1-r1.ebuild b/sci-biology/elph/elph-1.0.1-r2.ebuild index c166dd93e41d..66309522b312 100644 --- a/sci-biology/elph/elph-1.0.1-r1.ebuild +++ b/sci-biology/elph/elph-1.0.1-r2.ebuild @@ -1,22 +1,20 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program" -LICENSE="Artistic" HOMEPAGE="http://cbcb.umd.edu/software/ELPH/" SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz" +S="${WORKDIR}/${PN^^}/sources" +LICENSE="Artistic" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -S=${WORKDIR}/${PN^^}/sources - -PATCHES=( "${FILESDIR}/${PN}-1.0.1-fix-build-system.patch" ) +PATCHES=( "${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch ) src_configure() { tc-export CC CXX diff --git a/sci-biology/embassy/Manifest b/sci-biology/embassy/Manifest index e3671c22a4f9..91ad15d2b95c 100644 --- a/sci-biology/embassy/Manifest +++ b/sci-biology/embassy/Manifest @@ -1,2 +1,2 @@ -EBUILD embassy-6.6.0-r2.ebuild 929 BLAKE2B 378e0757280f2e0bc04d673892f79ce0139100790e84618697c4e55d23f4bcb193c075cca1a5ca9aa67eacb0412250be1186e3b32eeff28306358b753852e32d SHA512 1f17adca5f631bea36776135ae545411a35f3d575eb4e059bde004fa3616447ee3eb5f1b867c5c4debfc95a5d6d476b3d2c1a80b2a8bb429c3ce4db83b0f1e4d +EBUILD embassy-6.6.0-r3.ebuild 929 BLAKE2B 6b3be36e0cbf5ca429f20288d275fdeb7d25b7df2458f61e9251aabfdb4658c6bfaf87a063d324f452137908c9565d4146746c8849c65c726de88737905d987d SHA512 b4101e1daa43261c4ce37f2b18ccaee018e8083adf469e6580e096300e5672c2c94e8ff1eafc71d5c1682c99d59395b0915eb9541c3a3159ac340d1fcf682ddf MISC metadata.xml 348 BLAKE2B d71aba38f248b80e63e5805f1c0f710815220774a8a514f69a708666c647f061a3f295196da119cec9b5681648a54a1915073039302586d17540296855a255df SHA512 4f8c9238704b81e38abad62bc92e67ad08fe30907277794ee5a4265f4dd8e69fb1b4cabead1fc45c48888c3dbe30496b2c7df3b1c8fa2662f87a4deef32661cd diff --git a/sci-biology/embassy/embassy-6.6.0-r2.ebuild b/sci-biology/embassy/embassy-6.6.0-r3.ebuild index c0777d1aac70..63feacc58663 100644 --- a/sci-biology/embassy/embassy-6.6.0-r2.ebuild +++ b/sci-biology/embassy/embassy-6.6.0-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" HOMEPAGE="http://emboss.sourceforge.net/embassy/" diff --git a/sci-biology/eugene/Manifest b/sci-biology/eugene/Manifest index ad0cf62db829..78dd82270c34 100644 --- a/sci-biology/eugene/Manifest +++ b/sci-biology/eugene/Manifest @@ -1,8 +1,9 @@ AUX eugene-3.6-overflow.patch 252 BLAKE2B 83b82992d734996b2878028329642ec015a53f6b281255637e5b99eb1d69eea0a6d44b03a2f24959eebc426553835142b479636a629023731d5a2d05ad2b5064 SHA512 ed39c8d4aa73ba9e378a025e740c50f1b431fbb4590e3e9204f789081c8b22aef05fb4ce9ac7a0f22015ee03f73392730894a8dea5f6f16cd4533172e46776ce -AUX eugene-3.6-plugins.patch 1784 BLAKE2B 88ab82e4a1f351587108371ef545ae630277ddb1d4d5bdd31dfa58bc705ec2f06b92723622c37b7f2ac917bc18f089060d2a4c0f2ea3a6e3aa4af288429e13f9 SHA512 300601ee6abe469460ebbe29c45468d516e5e781ad4b0542e9590de38ba6e98e3697c5f6f92f83212a1aa6da5e0650636af279d82241277c0b43fb5472028fcc +AUX eugene-3.6-plugins.patch 1843 BLAKE2B 8bf8f09a43ec35838058094188973f985f69992e7f273b5c40f71abf39b498ec9bad1f8c8db9f0b1f5ec77796abefbf150afa9dc3a6764d33d16c3bdc175f87d SHA512 66d9191656821ec958804462aec83885560dfa35f075e1b012401d9ee4b86368b83005353d0093af0b95dc313b1fee6995f981504737242820125c5ead20ae9c AUX eugene-4.1-format-security.patch 609 BLAKE2B 1571c5c3af87e5ea49fa1f5b5ce19487c1493aa85e8f7782645874abf62c9e5d09e2e8c4c6aa2c5f44aedba257859d0245fcbbd28ae57d24dae118c562561a3a SHA512 f4eedd5b70309d4b8eedce8f3a4f79b65e595d407e88fd79e7f4f2f8c98880432366124b7f0a34c9032c9a498a1db607b0cac20304e84ec01f736589924ff362 AUX eugene-4.1d-Wformat.patch 2719 BLAKE2B 6dbdcb4e9946d0245eeeca1ff23b5d52ff3b37a64cbd88838229836323959325c7f54c9b00dec0abc02c218c4761ddef00def7f111c41df628af6d06f2147a6e SHA512 b235c11791caea63109009b858cde7ec179166640f009bf58caf33a8502345360efb71208a330572d7f870c468810bb9ab54db3e2af187a0d2baba7e12c6ff96 AUX eugene-4.1d-fix-c++14.patch 635 BLAKE2B d6e72bd7e4b80f21ebbc78cfc5f791fa23b0c22cd3414a5ecaaf50c54e1789625901bd0f9a5357f523de5dbca02d75229557d8a032f2e7cdd345e7dae3dbe19d SHA512 8ff6a8a2ee4b70b14d0fa9984c057307fe5b7d22e8a26969d82fb1ab7ee30a90cb3520ea8d3e16a59f09dfc46a3310cb43c621fabb31a39216209a4c3523e718 +AUX eugene-4.1d-portable-getopt.patch 1433 BLAKE2B 8de256a490936a6c893c055917919a7cfc6a510675b4c12021d7cedb8a6cdf4aa73fb60d6ae4186b1df7abb784da09a9dc440464d8cbd90ac5d9ea758262391e SHA512 6a365eed393a27c080ec6f0eaa288a88e7909daa657637cb819aeb3e908934f8f228bd1026205402bc180e54c4ffe56be5ff5eedc95d3817b65da08774c9496c DIST eugene-4.1d.tar.gz 7473965 BLAKE2B 537ba871b701a5c199791809f76ea883ff77fe768e27a69b95186ef82ab32cab9b5761405a9fadfeea9f58fe88cadce83bba4b1fa6cba5f4ede2347a516d1df0 SHA512 dab37930e211b3783954f6e4a762450760201b77e0b4214f16724516d9be583d0a7ec44a2f510e73f4370e9c2dc67a425456a057fdba8f51cb72386e16a26ef5 -EBUILD eugene-4.1d.ebuild 893 BLAKE2B 5aec582935c0e5e2c6ea9a14ed06a14d65c2759a3bfa1fda5fa940f1f700fc0bcf198bb65d47996afa4adc719bf9d40613bb635089e59cddea566518702d4f77 SHA512 9db8db10b469392a9a124f02dcf1272307c6c44b9734d5f101dd13092701a16f64394408200731a63a14d5ff9e2f3ca83b2391b762b312f1a4d163dffa0b0822 +EBUILD eugene-4.1d-r1.ebuild 950 BLAKE2B 33eeae7972f006763a905f06542482714564d8b46d05485886f9441520a3ec9e39620a583ec66d097bc2a26b62ccf953fcc2699075426b8b855541c0af26fd48 SHA512 95ef458f3af2b1ab478d239ebb83cf64105c3b9128e06e72642d0e559ef405beb7e6b2b494320a7a866a108498715408ee693111a0b3ebd5e02297c156811cd0 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d-r1.ebuild index dbf8139e9e20..b1d9f409c096 100644 --- a/sci-biology/eugene/eugene-4.1d.ebuild +++ b/sci-biology/eugene/eugene-4.1d-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -12,16 +12,13 @@ SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz" LICENSE="Artistic" SLOT="0" KEYWORDS="amd64 x86" -IUSE="" +RESTRICT="test" DEPEND=" media-libs/gd[png] - media-libs/libpng:0= - " + media-libs/libpng:=" RDEPEND="${DEPEND}" -RESTRICT="test" - PATCHES=( # https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170 "${FILESDIR}"/${PN}-3.6-overflow.patch @@ -29,6 +26,7 @@ PATCHES=( "${FILESDIR}"/${PN}-4.1-format-security.patch "${FILESDIR}"/${PN}-4.1d-fix-c++14.patch "${FILESDIR}"/${PN}-4.1d-Wformat.patch + "${FILESDIR}"/${PN}-4.1d-portable-getopt.patch ) src_prepare() { @@ -37,5 +35,6 @@ src_prepare() { -e '/SUBDIRS/ s/doc//' \ -e '/INSTALL.*doc/ s/\(.*\)//' \ -i Makefile.am || die + rm src/getopt.h || die eautoreconf } diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch index 1e910a13d5b1..e7424f73fc63 100644 --- a/sci-biology/eugene/files/eugene-3.6-plugins.patch +++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch @@ -1,7 +1,36 @@ -http://bugs.gentoo.org/show_bug.cgi?id=297536 +https://bugs.gentoo.org/297536 ---- eugene-3.6/src/Makefile.am -+++ eugene-3.6/src/Makefile.am +--- a/configure.ac ++++ b/configure.ac +@@ -28,6 +28,7 @@ + AC_PROG_CC + AC_PROG_AWK + AC_PROG_LN_S ++AM_PROG_AR + AC_PROG_RANLIB + + +--- a/Makefile.am ++++ b/Makefile.am +@@ -137,7 +137,7 @@ + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images +- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins ++ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models + $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM +@@ -160,6 +160,6 @@ + $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images + $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg + $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg +- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins ++ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins + $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval + $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get +--- a/src/Makefile.am ++++ b/src/Makefile.am @@ -20,7 +20,7 @@ SUBDIRS = Parametrization GDIF . SensorPlugins @@ -11,8 +40,8 @@ http://bugs.gentoo.org/show_bug.cgi?id=297536 AM_CFLAGS = bin_PROGRAMS = eugene ---- eugene-3.6/src/MSensor.cc -+++ eugene-3.6/src/MSensor.cc +--- a/src/MSensor.cc ++++ b/src/MSensor.cc @@ -97,7 +97,7 @@ std::string use_name; @@ -22,22 +51,3 @@ http://bugs.gentoo.org/show_bug.cgi?id=297536 // On récupère les couples nom de sensor/priorité du .par PAR.ResetIter(); ---- eugene-3.6/Makefile.am -+++ eugene-3.6/Makefile.am -@@ -125,7 +125,7 @@ - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images -- $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins -+ $(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models - $(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM -@@ -144,6 +144,6 @@ - $(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images - $(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg - $(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg -- $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(pkgdatadir)/plugins -+ $(INSTALL) src/SensorPlugins/*/*.so $(DESTDIR)/$(libdir)/eugene/plugins - $(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval - $(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get diff --git a/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch new file mode 100644 index 000000000000..156cb4bbdfac --- /dev/null +++ b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch @@ -0,0 +1,74 @@ +--- a/src/Param.h ++++ b/src/Param.h +@@ -28,26 +28,14 @@ + #include <vector> + #include <string> + #include <string.h> ++#include <unistd.h> + #ifdef HAVE_STRINGS_H + #include <strings.h> + #endif +-// MacOS-X has getopt() defined is stdlib and the library in the libSystem +-#ifndef __APPLE__ +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "getopt.h" +-#endif +-#endif +-#endif + + #include "Const.h" + #include "System.h" + +-extern char *optarg; +-extern int optind; +- + + class ltstr + { +--- a/src/SensorPlugins/MarkovIMM/GetData/CEM.cc ++++ b/src/SensorPlugins/MarkovIMM/GetData/CEM.cc +@@ -22,18 +22,11 @@ + #include "../../../../config.h" + #endif + +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "../../../getopt.h" +-#endif +-#endif +- + #include "../../../System.cc" + #include "../../../Const.h" + #include "../../0_SensorTk/EndianConv.h" + #include "strarray.h" ++#include "unistd.h" + #include <vector> + + // Constantes +--- a/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc ++++ b/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc +@@ -22,18 +22,11 @@ + #include "../../../../config.h" + #endif + +-#ifdef HAVE_GETOPT_H +-#include <getopt.h> +-#else +-#ifndef HAVE_GETOPT +-#include "../../../getopt.h" +-#endif +-#endif +- + #include "../../../System.cc" + #include "../../../Const.h" + #include "../../0_SensorTk/EndianConv.h" + #include "strarray.h" ++#include "unistd.h" + + + // Constantes diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest index a265c7bd94a4..5474f7a87784 100644 --- a/sci-biology/exonerate/Manifest +++ b/sci-biology/exonerate/Manifest @@ -1,4 +1,4 @@ -AUX exonerate-2.2.0-asneeded.patch 362 BLAKE2B 57bb7d7d57bf2347fc0cb20f650cd0a452bd70ed8ed46a87d132cf8d68e152438ec2c4e877129feb91748f5ca43021cc0010cf2f50b3bdb8eed60218d904eb27 SHA512 7c08fe7ee520ab7198557f5ac7f99f0bae53da77d46949d6bac78a3330fc9023a4aece085e060ad6a40303475999654dcfe5311d3a78f1d1be0d461cefbfcfb0 +AUX exonerate-2.2.0-autotools.patch 1407 BLAKE2B b34e8c4d8301d4f416b44f4516154917943e17d30b548c7710e097706ce2c9123770d97d3ae962a268c6253a83ab60159f9285fadab1328be4ad5dc48249ee3f SHA512 f34c35228d23a8fd9402c514312c58bd877a7844487ade7f9f8d545d66c5d350f3f82f1aab1862a7b647b7f7aaaa0dbd8100d34bc0ef7d79969063c30a8558d0 DIST exonerate-2.2.0.tar.gz 509870 BLAKE2B 58b12338ef7d819a8e33ab87d72afe807ca219581a8f35ae38951860915a676bb9ba34a481f685e970948d9272be3e5f28d6b63c14f4d5facf35c4be52530d3b SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c -EBUILD exonerate-2.2.0-r2.ebuild 967 BLAKE2B 27a48f5dc4e1040f4296152ae445ba6bb2dc29132605b6cce240c40d2719d16c0c7d80103d2b9f8440fb7d5bb8fec3e8ba0385f6f87b9196b443dd14ae1a6310 SHA512 1d5be70396afabf08489501cba460bb47a7bfe9efead75226b07707ed00813f0dcd69611b75e3135444ee100ceeaf2cd492cd79ffc5f3d01e6f5d808ce84f2e1 -MISC metadata.xml 327 BLAKE2B 6aaa3e563d3d8f980c3f42b7e5aa1f8cd5e67e5dcea0f467e6698731480ae7cb587b75516931c351f0e562ddebc4811f359f9ec9fb9c16cb93bc0842bd24d2d7 SHA512 82cd2f3b95540ef6132985b835bf482498f60495c7e4718aaae3bfb500a017bc367cd844992b6b3a3f68be276183f62c91ee517f6a72a19d058775f40a95eb0f +EBUILD exonerate-2.2.0-r3.ebuild 945 BLAKE2B 5df41a4c19730cb7b342dcae7875fba40b7c7404ceb85f4568f55f0eaf9d8446195e922c709ae09a62f4a5c0a35b581ef86f03c3a58ead41b0d70313ec7da76f SHA512 f928328f1cb14719343df4c4d7df4fc834b59a3909c6f47ca9d1358d4d2d1d6d31c404074e45e747b3e5736040897861c00bb9e0974582f3472639638cc4c80d +MISC metadata.xml 654 BLAKE2B c84cf7eb3eed086e51e990906b2ea2645160683ba9314d2d15790e03d077714c1592bd4f305a8f3ed9109e376292118b44a1d10ea9ad1118139874a4e451bf6b SHA512 820b824d3d2a05feee023573580135fa2895832dd1b602c35253c1b8ee46aafdd0e010b5e8a77ce1805058264e3110821d27533a1dfe9d30799a5e63ea1551f1 diff --git a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild index 53ae5a97c6ae..73fa9eca83e5 100644 --- a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild +++ b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools toolchain-funcs @@ -12,33 +12,30 @@ SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" -IUSE="test threads utils" -RESTRICT="!test? ( test )" +IUSE="test utils" REQUIRED_USE="test? ( utils )" +RESTRICT="!test? ( test )" DEPEND="dev-libs/glib:2" RDEPEND="${DEPEND}" -PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) +PATCHES=( "${FILESDIR}"/${P}-autotools.patch ) src_prepare() { default - sed \ - -e 's: -O3 -finline-functions::g' \ - -i configure.in || die - mv configure.{in,ac} || die - eautoreconf } src_configure() { - tc-export CC + # the bootstrapping code loads AR and CC from the environment + tc-export CC RANLIB + export C4_AR="$(tc-getAR)" econf \ --enable-glib2 \ --enable-largefile \ - $(use_enable utils utilities) \ - $(use_enable threads pthreads) + --enable-pthreads \ + $(use_enable utils utilities) } src_install() { diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch deleted file mode 100644 index 5c428979a1af..000000000000 --- a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch +++ /dev/null @@ -1,15 +0,0 @@ -Fix build with --as-needed - -https://bugs.gentoo.org/268094 - ---- a/configure.in -+++ b/configure.in -@@ -289,7 +289,7 @@ - if test "$enable_pthreads" = yes; then - echo "Using PTHREADS" - CFLAGS="$CFLAGS -DUSE_PTHREADS" -- LDFLAGS="$LDFLAGS -lpthread" -+ LIBS="$LIBS -lpthread" - elif test "$enable_pthreads" = no; then - echo "Not using pthreads" - else diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch new file mode 100644 index 000000000000..af95b5c8f77a --- /dev/null +++ b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch @@ -0,0 +1,43 @@ +Fix build with --as-needed + +https://bugs.gentoo.org/268094 + +--- a/configure.in ++++ b/configure.in +@@ -144,11 +145,6 @@ + elif test "$enable_assert" = no; then + CFLAGS="$CFLAGS -DG_DISABLE_ASSERT" + echo "Turning assertions off" +- if test "$GCC" = "yes"; then +- # Not currently using -fomit-frame-pointer as clashes with -pg +- # CFLAGS="$CFLAGS -O3 -fomit-frame-pointer -finline-functions" +- CFLAGS="$CFLAGS -O3 -finline-functions" +- fi + else + echo "error: must be yes or no: --enable-assert:[$enable_assert]" + exit 1 +@@ -289,7 +285,7 @@ + if test "$enable_pthreads" = yes; then + echo "Using PTHREADS" + CFLAGS="$CFLAGS -DUSE_PTHREADS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + elif test "$enable_pthreads" = no; then + echo "Not using pthreads" + else +--- a/src/model/bootstrapper.c ++++ b/src/model/bootstrapper.c +@@ -146,8 +146,12 @@ + + static void Bootstrapper_index_archive(Bootstrapper *bs){ + register gchar *command; ++ register gchar *ranlib = "ranlib"; ++ register gchar *tmp = (gchar*)g_getenv("RANLIB"); ++ if(tmp) ++ ranlib = tmp; + register gint ret_val; +- command = g_strdup_printf("ranlib %s", bs->archive_path); ++ command = g_strdup_printf("%s %s", ranlib, bs->archive_path); + g_message("Indexing archive [%s]", bs->archive_path); + g_print("%s\n", command); + ret_val = system(command); diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml index 110611751dc3..421b8ef55beb 100644 --- a/sci-biology/exonerate/metadata.xml +++ b/sci-biology/exonerate/metadata.xml @@ -6,6 +6,6 @@ <name>Gentoo Biology Project</name> </maintainer> <use> - <flag name="utils">Install all utilities</flag> + <flag name="utils">Install the follow binaries: esd2esi, fasta2esd, fastaannotatecdna, fastachecksum, fastaclean, fastaclip, fastacomposition, fastadiff, fastaexplode, fastafetch, fastahardmask, fastaindex, fastalength, fastanrdb, fastaoverlap, fastareformat, fastaremove, fastarevcomp, fastasoftmask, fastasort, fastasplit, fastasubseq, fastatranslate, fastavalidcds</flag> </use> </pkgmetadata> diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest index e041a677a3af..3e02058f5767 100644 --- a/sci-biology/hmmer/Manifest +++ b/sci-biology/hmmer/Manifest @@ -1,9 +1,9 @@ AUX hmmer-2.3.2-fix-build-system-destdir.patch 825 BLAKE2B 46264f43ed43a567c1f650710e1485942eb48a0b7ed3860424f00ca06cf04f9e923318c5df3d56eb312ed773bf2d42e22880b4ac6c2f81ac6c65bf2cebf44008 SHA512 f7eb3de5cbb1bf58b4ae4514e020ea059ad6a267e6f425494d8b444ac1bab056bc4709fed7f2793e68720b057ca1ac8c6dbca907125712d18dc05b77e37b1c3f AUX hmmer-2.3.2-fix-perl-shebangs.patch 2457 BLAKE2B 1afca014901d79416dac2c1d41e20371ef970aa3691a6b414e9a96adf8331c619753df7a42e1d9af63aab12a3fc8b8c7d2251129dd581bfb33a0d7c3e50970b2 SHA512 9597d77b3101c091bb1d005f36229cb6bedaf496a15da472495bb688fdb2750c94a38adc1236f3d90b0085caa78f61bddb350d51e0d3cc8dfa96edcdd5e2e5b9 -AUX hmmer-3.1_beta2-fix-header-install-path.patch 3202 BLAKE2B e6f8050c2edd11c890dc53bd6ba4cfaf6b537ab11ba45b88f497c0b62200029839df5f2adfa54612805ea87a5e252c9c198a52c1ba793a1c612ca99c3f8edb0b SHA512 ccaaff25a50a60526d0a16196b2b1d8cd57a7e9d016ce2b6b36ba1c0123966113b10965303dceb494810cd17a802514bba3a49d010ee6bbdc039715b84524d9a AUX hmmer-3.1_beta2-fix-perl-shebangs.patch 8605 BLAKE2B c0c78fed780b43df960dc24914e5dabe161243cec015deaf058d7eebf79c5e1633ded4f1305bb37b9766d74588009142fd58886e67810940e9601ef138647c21 SHA512 ce2c91c2d34d49dd5082a97ca0543bf3a176c792b4efd0cb37561114fc572b41d6cd546e16267283d33138ad54e2bb0c9c912c8fa1142e558a5452e9e72da2ff +AUX hmmer-3.1_beta2-makefile.patch 3679 BLAKE2B e258b23bda9d0515891f1d571b94f9ef48499f25ce6cb52c3d1bcd0a28bc527f335cb25ece944afb33e4824438315cc9986243fb13e07eb128d7859e0a77f4b1 SHA512 bebd36deee48d4a043a1d84233ccbc93de8e44b5f7f57bf24a551b53a6f3dbfb3166861555755744d0abb4fce871d7c19fa8887c08115b7d8f61ca5ad38c3cc6 DIST hmmer-2.3.2.tar.gz 1024933 BLAKE2B 34fdc7b24b28d653022c80a63b2fd8376c15c961e1550a04cb310943d165575a2721cc5e4cb516335f57414f8621b7e62c4e30ee1f107bb714e40c59ed37d418 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7 DIST hmmer-3.1b2.tar.gz 5965253 BLAKE2B 38d1d6fb43aa814c0e3ddc551469ebd6b967f181c45df3802598f31abef10998595218167555a8862c0d2caa9118d9a7f1c22b673b6d596665f797ba903093f5 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771 -EBUILD hmmer-2.3.2-r4.ebuild 1655 BLAKE2B ffc67289bc761e07d60df1d87e11abcc311b1fccc1652d542b71e0914660f3ed03e4a6e540d76d2c38e0d5cb43c606496da34fcac48bb84ee08c2a4822f0c562 SHA512 f07e067a72e388ebaff6c4712173bd6e68004a778c36823bcc685c7727a81ca77b448d046f2dec599b9c760b0c45fc379971beef227d2f6d43917a13e75b6abb -EBUILD hmmer-3.1_beta2.ebuild 1063 BLAKE2B a3469ebea515d16eb960fb5021ae7374b8736dbc0e0e933146f570478bf24cbfcee2eef59008126315669ab67cd70b569ddf401e07dd78b15a96e8d6b4329296 SHA512 fa75524ced910f633735ab72a1eb8d0ae0fd3ccc88dc12f98995b546fdd5084158509c8c99fe231450f5151dacc2b9477ee35090d9657401e47f8bd1dd0240b6 +EBUILD hmmer-2.3.2-r5.ebuild 1736 BLAKE2B 9ab5016f9a29c9d2dc22ed0456a064f14ea91c22d7a226aeeec02ad2c6766effb4a9933487aed37b335a113ab012829eb8aa583770e2ff01e934347445060a90 SHA512 18eb7ecb918ce4786ee1556fc641d1ca89c9255aa6009ea8b5d524752bad5046eeb50de9b0d5637b4c59cec624879d0c0f07698f5fe370aed7a25610aa377cca +EBUILD hmmer-3.1_beta2-r1.ebuild 1140 BLAKE2B a5a0a26f2461edc08101505fa600383952501083111e828b4a0484a2c895acb63b3784247ea3a9b4fb10a13089a84f09f9721b4835cbb7b5479f0877e62c84aa SHA512 65889b5afe47d60abdd7ebb4d098510e8f25979e442df2a88d6327ab2fffc6d056fa6f96f32c0d37614473bc961c1e60fc3e194e535c5b6816b3c420816c5ea9 MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch index b9ff5b92b8f9..1c08d67e7bdd 100644 --- a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch +++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-makefile.patch @@ -1,4 +1,5 @@ -Install headers into 'hmmer3' subdir and not into global includedir. +* Install headers into 'hmmer3' subdir and not into global includedir +* Respect AR --- a/easel/Makefile.in +++ b/easel/Makefile.in @@ -17,6 +18,26 @@ Install headers into 'hmmer3' subdir and not into global includedir. ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} install # "make uninstall" reverses the steps of "make install" +--- a/libdivsufsort/Makefile.in ++++ b/libdivsufsort/Makefile.in +@@ -16,7 +16,7 @@ + CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@ + CPPFLAGS = @CPPFLAGS@ + MPILIBS = @MPILIBS@ +-AR = @AR@ rc ++AR = @AR@ + RANLIB = @RANLIB@ + INSTALL = @INSTALL@ + +@@ -43,7 +43,7 @@ + + + libdivsufsort.a: $(OBJS) +- ${QUIET_AR}${AR} libdivsufsort.a $(OBJS) ++ ${QUIET_AR}${AR} rc libdivsufsort.a $(OBJS) + @${RANLIB} libdivsufsort.a + @chmod 644 libdivsufsort.a + --- a/Makefile.in +++ b/Makefile.in @@ -143,6 +143,7 @@ diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild index a58b60f93288..b9f77b9dfce8 100644 --- a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild +++ b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild @@ -1,20 +1,21 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 + +inherit toolchain-funcs DESCRIPTION="Sequence analysis using profile hidden Markov models" -LICENSE="GPL-2" HOMEPAGE="http://hmmer.org/" SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz" +LICENSE="GPL-2" SLOT="2" -IUSE="altivec test threads" -RESTRICT="!test? ( test )" KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_ppc_altivec test" +RESTRICT="!test? ( test )" -DEPEND="test? ( dev-lang/perl )" -RDEPEND="" +BDEPEND="test? ( dev-lang/perl )" PATCHES=( "${FILESDIR}/${P}-fix-perl-shebangs.patch" @@ -28,8 +29,12 @@ src_configure() { econf \ --enable-lfs \ - $(use_enable altivec) \ - $(use_enable threads) + --enable-threads \ + $(use_enable cpu_flags_ppc_altivec altivec) +} + +src_compile() { + emake AR="$(tc-getAR) rcs" } src_install() { @@ -52,14 +57,14 @@ src_install() { local i # first rename man pages... - pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die + pushd "${ED}"/usr/share/man/man1/ >/dev/null || die for i in hmm*.1; do mv ${i%.1}{,2}.1 || die done popd >/dev/null || die # ... then rename binaries - pushd "${ED%/}"/usr/bin/ >/dev/null || die + pushd "${ED}"/usr/bin/ >/dev/null || die for i in hmm*; do mv ${i}{,2} || die done diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild index b65fa0824f9b..666d21cd5532 100644 --- a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild +++ b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild @@ -1,49 +1,55 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 + +inherit toolchain-funcs MY_PV="${PV/_beta/b}" DESCRIPTION="Sequence analysis using profile hidden Markov models" HOMEPAGE="http://hmmer.org/" SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz" +S="${WORKDIR}/${PN}-${MY_PV}" LICENSE="GPL-3" SLOT="0" -IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads" -RESTRICT="!test? ( test )" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="cpu_flags_ppc_altivec cpu_flags_x86_sse gsl mpi test" +RESTRICT="!test? ( test )" RDEPEND=" mpi? ( virtual/mpi ) gsl? ( sci-libs/gsl:= )" -DEPEND="${RDEPEND} - test? ( dev-lang/perl )" +DEPEND="${RDEPEND}" +BDEPEND="test? ( dev-lang/perl )" -S="${WORKDIR}/${PN}-${MY_PV}" PATCHES=( - "${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch" - "${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch" + "${FILESDIR}"/${PN}-3.1_beta2-fix-perl-shebangs.patch + "${FILESDIR}"/${PN}-3.1_beta2-makefile.patch ) src_configure() { - # make build verbose, bug 429308 + # make build verbose, bug #429308 export V=1 econf \ --disable-pic \ - $(use_enable altivec vmx) \ + --enable-threads \ + $(use_enable cpu_flags_ppc_altivec vmx) \ $(use_enable cpu_flags_x86_sse sse) \ $(use_enable mpi) \ - $(use_enable threads) \ $(use_with gsl) } +src_compile() { + emake AR="$(tc-getAR)" +} + src_install() { default dodoc Userguide.pdf - insinto /usr/share/${PN} + insinto /usr/share/hmmer doins -r tutorial } diff --git a/sci-biology/iedera/Manifest b/sci-biology/iedera/Manifest index b94ed1791e05..3edddb50dc42 100644 --- a/sci-biology/iedera/Manifest +++ b/sci-biology/iedera/Manifest @@ -1,4 +1,4 @@ -AUX iedera-1.05-fix-buildsystem.patch 385 BLAKE2B ee7ccb9bd08a8be617e0165a4ee6c6f899ef03e297a9839bfa1982960f0e2f132fb8a444d1bdb74c12b55a66068577dd7be127311b71d21b599a4cabe0b3c79e SHA512 7f20d78fce1ab3a9d30290675a6893a73e2935a8842e8ac8a3d4268a0ccd2a3f165ac0201b6bb13978621230f0042460e704f706d6b3e3ee9457d6a4b6417741 +AUX iedera-1.05-fix-buildsystem.patch 385 BLAKE2B 84865e3a1714e4ef67db70f5d144eb82426abf56c22391f576a783c9d237e6c64c2613a5034c7157007679d2456510b84f31bebc1c2d758c98822a1373cf0792 SHA512 5c36266426ac3c51fed5a738d688b23932b3d28de7affa942781beab2460cbff0add6f452b034fcca9733469deb493357ce3865181e71e6721a642667d69486f DIST iedera-1.05.tar.gz 129163 BLAKE2B fe499276da7571be83b847ab98bbe4878470b07fb13ee80ffb55bff1b5674b54fd4bf5e21fa34e10b8296d9c6aad298dbde79910cfa45670ea8afe047de1a979 SHA512 60d35227d5479fea693e8a3c0e629aae9e21f3c7e2be7b2f10aaddcade70cc6525fa18dea1851f73d6c1aadbb5e8776dd4a146b1a81ecfe8c910729a2300066f -EBUILD iedera-1.05-r1.ebuild 490 BLAKE2B a343877f79ccc0678765b4548add19e02aa13aa8d434933e7f0218896e838c25ca668d47ab5d9fe3966eaf995f05857b8ab7b4a28bdf568fda0cef917bfd6aa1 SHA512 2d30e9a6a88e085fc1acad0d5b56eb3bf590f26208b56dc195dec84bf7c946cc5d9ae0d36c147b43b812f16c71ddccdb11db28e2c1263ee46be6dd5659ef8754 +EBUILD iedera-1.05-r2.ebuild 449 BLAKE2B 30d93b6df82103d33135b04d44ebc9587ca30337ce0e5838ec6965081a890f79dc8882827a92b69053a3396056d8bc0c113081bdcab8644daa89d651a945e808 SHA512 6c9bd21c13d202fb7bcd36f37bfae83291d8aec90700fad0f4763cb24e870170217f4f70d00e528c4258ea057430d7486d40725a7403dec2b03de6638e094979 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch b/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch index f232d7de162b..8803ab64b4e1 100644 --- a/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch +++ b/sci-biology/iedera/files/iedera-1.05-fix-buildsystem.patch @@ -1,7 +1,7 @@ iedera sets default flags that override user {C,CXX,LD}FLAGS ---- iedera-1.05/configure.ac -+++ iedera-1.05/configure.ac +--- iedera-1.05/configure.in ++++ iedera-1.05/configure.in @@ -4,11 +4,5 @@ AC_PROG_INSTALL AC_PROG_CXX diff --git a/sci-biology/iedera/iedera-1.05-r1.ebuild b/sci-biology/iedera/iedera-1.05-r2.ebuild index 115b5495f617..96734c6ef1c4 100644 --- a/sci-biology/iedera/iedera-1.05-r1.ebuild +++ b/sci-biology/iedera/iedera-1.05-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -11,15 +11,11 @@ SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" -PATCHES=( - "${FILESDIR}/${P}-fix-buildsystem.patch" -) +PATCHES=( "${FILESDIR}"/${P}-fix-buildsystem.patch ) src_prepare() { - mv configure.{in,ac} || die default eautoreconf } diff --git a/sci-biology/iqpnni/Manifest b/sci-biology/iqpnni/Manifest index f35d0da4a9a7..f6093a3a6cb2 100644 --- a/sci-biology/iqpnni/Manifest +++ b/sci-biology/iqpnni/Manifest @@ -1,4 +1,4 @@ AUX iqpnni-3.3.2-cpp14.patch 1240 BLAKE2B e45efc553f7b0779c5b63639363f2040883f9568cc4bb36fcea8945d8d9855fb57801d8244185f9109781187ee2ea3edf111d2e16240c8f1834042e37ba6b150 SHA512 64cba6133a64fdceff3c7c5ae7f2108e7115718609122fa4b647a6b48cd966774c20e2d9cbb4e8c4c1377de94bd57e07ef40b25692c4ee6d2282f8d4e04ddb78 DIST iqpnni-3.3.2.tar.gz 646603 BLAKE2B 9e4b281b148518b367d9aa7f1cfcc76f032657ac8ae480b84276c16d05afe64845ebfcea33d0325cfb1048d06713a5eb7ed4d9993abed4b739a700e57b849d33 SHA512 6e603117b746956ad0c3b140968abf2b3b3065a18dc78cee4975f1d2e7971334fdde15e2e8d2fd7435b9490aaaffaf17a38f72a3897c951f493d866e21d94156 -EBUILD iqpnni-3.3.2-r1.ebuild 582 BLAKE2B e25b9846e1402d50670d6d0874dc7fcf38d61a63340924fc0709f1e973dece08908f6de1a5c79e8ade5d9655e397e41bfa2311d5805040eaf89e72aed3bb01e6 SHA512 ffaf3eb0c9384c52859bb598247850fa6b38dff9a1b75220b9596a10c5af1dd506edd66af0051cf7799003569665c7ec7c6dda02554e0757c57961988bf4afc2 +EBUILD iqpnni-3.3.2-r2.ebuild 547 BLAKE2B 7d4e5aa9db13cc6a1dfe591c141ce351c354dc5ea9c9ec86af0439ac1050153c42ab0f0c13a55c950a48bc5cdcdbe485fd4a2162fa3b5faab014be5739ff711a SHA512 093890fb933e27b4ce1122dd778e47c15bfa5000a16bbdb280b15a3ff8322a3ca47039c587615b2597bbc51dc8920790ff35a43464f544ede9e823aedd03fbdc MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/iqpnni/iqpnni-3.3.2-r1.ebuild b/sci-biology/iqpnni/iqpnni-3.3.2-r2.ebuild index 1edeeada187b..4175330026a1 100644 --- a/sci-biology/iqpnni/iqpnni-3.3.2-r1.ebuild +++ b/sci-biology/iqpnni/iqpnni-3.3.2-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="Important Quartet Puzzling and NNI Operation" HOMEPAGE="http://www.cibiv.at/software/iqpnni/" @@ -12,18 +12,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc" -DEPEND="" -RDEPEND="${DEPEND}" - PATCHES=( - "${FILESDIR}/${P}-cpp14.patch" # bug #594332 + "${FILESDIR}"/${P}-cpp14.patch # bug #594332 ) src_install() { dobin src/iqpnni if use doc ; then - HTML_DOCS+=( manual/iqpnni-manual.html ) + HTML_DOCS=( manual/iqpnni-manual.html ) dodoc manual/iqpnni-manual.pdf fi einstalldocs diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest index 62fab70bdcdb..ca16027a136e 100644 --- a/sci-biology/kalign/Manifest +++ b/sci-biology/kalign/Manifest @@ -1,3 +1,4 @@ +AUX kalign-2.03-makefile.patch 1115 BLAKE2B 12fb13e6644a81ce4977a134d594b1bc5fa1c4da90a78e905c8aa607d490a1968daf65e5f59c4d8adbb42a5cac1854610c88f8036448f456659505d1c191dbea SHA512 4d41f4c18864b697ef6e54f176ded2a74c44e943d4956617c273655121df70dd1cc8d9a723dda3aa92428a6a9356863f5bd8558411d86827c2fcd2386212938e DIST kalign_2.03.orig.tar.gz 114022 BLAKE2B 3637bde4e9b900def668043e75b2a52ed17a8aed6f894e323b1b76f216ad50784fb2ee352389f8888b5365efd5681361af3818ba0ca593721b19c497ffb83930 SHA512 d60152bd7124f77ea972ea7dac19f47eb731646a12ecafbee8a99335c20a36fb3ce2bdc633b346e4da1016d8e56a0f297f9b33c9b6285197946f404dbc390b0a -EBUILD kalign-2.03-r2.ebuild 601 BLAKE2B 4d988368b81b04012c426de46f87d8287a685617eee1c727a899a9c1a5165130970d08efb5f48b1afadb947ec4a6a0effabf56de00c9eeeb08ec40cc482e58a2 SHA512 f19df61247a35a5a03164ad1a01968a078be043e53f53ff62ea35ba20787d84067fb4cd9212a9294a26270f95c7702ffdf571691df0311856f1de1973d6012ff +EBUILD kalign-2.03-r3.ebuild 397 BLAKE2B ca5aa8d8d0e4ed29ce2480373e7155da54a41377e773e93f0a48cfb53cb489d916e98feceac74d1cc728da634aea81005fbf71ec2ff91b61c7bf4b2bc7aff0fe SHA512 8bd596122b0fb5ba2c4b9664b5e99984f9e52e3ea457bc39d0f3aff4e97d26e56c32e32f228292d4e25422eca59186c46525c84d9a6a1488deaa1114cee4129a MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/kalign/files/kalign-2.03-makefile.patch b/sci-biology/kalign/files/kalign-2.03-makefile.patch new file mode 100644 index 000000000000..61e65c0b73ce --- /dev/null +++ b/sci-biology/kalign/files/kalign-2.03-makefile.patch @@ -0,0 +1,39 @@ +--- a/Makefile.in ++++ b/Makefile.in +@@ -1,7 +1,11 @@ +-PREFIX = /usr/local/bin ++prefix = @prefix@ ++exec_prefix = @exec_prefix@ ++bindir = @bindir@ + TEST = test/ +-CC = gcc +-CFLAGS = -O9 -Wall ++CC = @CC@ ++CFLAGS = @CFLAGS@ ++CPPFLAGS = @CPPFLAGS@ ++LDFLAGS = @LDFLAGS@ + DEBUGFLAGS = -ggdb -Wall + + SOURCES = kalign2_distance_calculation.c kalign2_dp.c kalign2_input.c kalign2_main.c kalign2_mem.c kalign2_inferface.c kalign2_misc.c kalign2_tree.c kalign2_profile.c kalign2_alignment_types.c kalign2_feature.c kalign2_hirschberg.c kalign2_advanced_gaps.c kalign2_hirschberg_dna.c kalign2_output.c kalign2_string_matching.c kalign2_profile_alignment.c +@@ -16,10 +20,7 @@ + .PHONY: clean + + all: $(OBJECTS) +- $(CC) $(CFLAGS) $(OBJECTS) -o $(PROGS) +- +-%.o: %.c +- $(CC) $(CFLAGS) -c $< ++ $(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTS) -o $(PROGS) + + debug: $(DEBUGOBJECTS) + $(CC) $(DEBUGFLAGS) $(DEBUGOBJECTS) -o $(DEBUGPROGS) +@@ -29,7 +30,8 @@ + + + install: +- cp $(PROGS) /usr/local/bin/ ++ mkdir -p $(DESTDIR)$(bindir) ++ cp $(PROGS) $(DESTDIR)$(bindir) + + clean: + rm -f $(PROGS) $(OBJECTS) diff --git a/sci-biology/kalign/kalign-2.03-r2.ebuild b/sci-biology/kalign/kalign-2.03-r2.ebuild deleted file mode 100644 index 53b4490bef71..000000000000 --- a/sci-biology/kalign/kalign-2.03-r2.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Global and progressive multiple sequence alignment" -HOMEPAGE="http://msa.cgb.ki.se/" -SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -S=${WORKDIR}/${PN} - -src_prepare() { - default - sed \ - -e "s/\$(CFLAGS) \$(OBJECTS)/\$(LDFLAGS) &/" \ - -i Makefile.in || die -} - -src_compile() { - emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}" -} - -src_install() { - dobin ${PN} - einstalldocs -} diff --git a/sci-biology/kalign/kalign-2.03-r3.ebuild b/sci-biology/kalign/kalign-2.03-r3.ebuild new file mode 100644 index 000000000000..22d92963a0ea --- /dev/null +++ b/sci-biology/kalign/kalign-2.03-r3.ebuild @@ -0,0 +1,15 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Global and progressive multiple sequence alignment" +HOMEPAGE="http://msa.cgb.ki.se/" +SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz" +S="${WORKDIR}/${PN}" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest index 8119c259e7be..56728e9a4ce6 100644 --- a/sci-biology/maq/Manifest +++ b/sci-biology/maq/Manifest @@ -4,5 +4,5 @@ AUX maq-0.7.1-gcc-4.7.patch 1429 BLAKE2B af81651b07186eed305d70534e9f7c41375f60a AUX maq-0.7.1-remove-64bit-flag.patch 787 BLAKE2B 2e94066962194133ccdae4095d3d6bf6f058f7a7d5d04f8737e03fc725508b3e291c76554418c6ff9a15969e332d340b86e11ae3cab90406ec60e9ea63361f5e SHA512 4864453afa79679c253b17a2b125bf0b44c1a05a6ae6341821382991217026b599437288a1c96625cdc2a1fad2cf73c79798a230bbfccef46e1c92012a6c3df1 DIST calib-36.dat.gz 196371 BLAKE2B e4dab71e0830603a7c25bb4c8e15f92e4a5068eeeece451a3e0a2a9e2c4f65b87325e7ff4e4e5543b79f2c3d9dd43c9398cdb32241535bf44e66705bfdf683f7 SHA512 1033ad47b31882823f71f16054f366a6853b4b5e1fb286ab2c5f62c1409ed20e6dc0faec7e356350e91c71d25a198d8e0d7a521b3662b5e2fae22af44098e8b7 DIST maq-0.7.1.tar.bz2 368645 BLAKE2B a7989ae2348a7332f17a75c6fccba55deb8bd9330863d0c5ab3bf997f2f07abd1ca89ebb41d034902f6571ee36365f63db9c8c84c1e5d3d788236279581b989e SHA512 acaba2d172f8f4ef7a2b1254bd220f134a5eb8e4936af16bf7fa6695d016e6b6fa9a5b00d073ec1ecc0ecc39dfb1c9700c38fd017edb5bd49a83de383cb0d30c -EBUILD maq-0.7.1-r2.ebuild 799 BLAKE2B ea3f9417c26dd0926866436bc00e6f071d1c08d121c820affe7d4af42a55b3d2a356949415bd4e8ddc11d4eb3ab1dff330aead0dfa03f3236a93087fa3b666b5 SHA512 5e52158937efbb822f9e521ec19b76a3dab1d6823da94cc154947d1024d2aa59bab00b111eb9d3d3e23a59782f2069ff4aa079133fa4608a4aa37e623e14c265 +EBUILD maq-0.7.1-r3.ebuild 784 BLAKE2B 092e9683af6c7a9248c7336da930947168e937df9bc80829a5a5d7a07046acd9f1d2c6667cfb4d0a62c8f616802c607db8f6926d26166abe8bca5345318bd855 SHA512 52d16dcffa83aba11f6d1a50a0520252ac410b697793dc6f42ca8459d4ae47b56f22fbafe8af8a75a7f522f1e0b94507d1ac6397f19837fc101f8fb866dc3746 MISC metadata.xml 345 BLAKE2B 3f590b0bf8c9f9fa9470f6b8ed3b20643c84fc92839740e6aebe720edd0a6e0b8bb5d2b74d4dcd8cf80a89c2769308b89e21f2f386a62fc28686f883eff56bbf SHA512 244600e6c19400a837eb859a09582fa78a670d81a58e6a461689d2695273b450df999334ffc44eecdfbed9232784af84e7cdcabe7ee045ae51a24509f2aabdcc diff --git a/sci-biology/maq/maq-0.7.1-r2.ebuild b/sci-biology/maq/maq-0.7.1-r3.ebuild index 14b0284b7f58..a64b2b6f4e81 100644 --- a/sci-biology/maq/maq-0.7.1-r2.ebuild +++ b/sci-biology/maq/maq-0.7.1-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -13,7 +13,6 @@ SRC_URI=" LICENSE="GPL-3" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" RDEPEND="sys-libs/zlib" @@ -34,9 +33,9 @@ src_prepare() { src_install() { default - insinto /usr/share/${PN} + insinto /usr/share/maq doins "${WORKDIR}"/*.dat doman maq.1 - dodoc ${PN}.pdf + dodoc maq.pdf } diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest index 6fbb33162603..250be2139824 100644 --- a/sci-biology/maqview/Manifest +++ b/sci-biology/maqview/Manifest @@ -2,5 +2,5 @@ AUX 0.2.5-ldflags.patch 1335 BLAKE2B 537a13dc3248efae0573a527cb40565081114886478 AUX 0.2.5-zlib.patch 1437 BLAKE2B c8a8908ca6586f3fdff730c2eca39e54b3d08e8fe07fd6dc7ee6676f8a21c0943d939c937f47e3920286acec94b51daec64bf1e500661c661e054315de8d7e36 SHA512 7925f70d1f68bfa4fa87134d8ef20b05a6f022b1a9478a8e594e7b655852d858c0928b101f7eafd4e1ef44a17f8d353d49a6d1ede4072ac85ec452f75bd06c03 AUX maqview-0.2.5-gcc4.7.patch 575 BLAKE2B 8e461d07e0421e5dc1e209e83ed3fccfdcd541954481bbbb1f478cddb9ff045c3704a086a18d6e7a8b255d226a24eca7d791cde9e59673c842a4094d56f03ba0 SHA512 277086e1d6d536ae368083032421029d64d5173e643edaafbad2833d56e8ec283152a49d9874a7142333e0fee976d3600ed118b6beb0482ec7e0e95f4a36fba4 DIST maqview-0.2.5.tar.gz 383410 BLAKE2B 7058f32e49267dfcc8b25da2ca2bbbd5134f66f0f9cbd10de7e876365d955d2e51cbab342af817f13018b7b1903872033c363fe077f10ce76e5fcc87da568dc1 SHA512 40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6 -EBUILD maqview-0.2.5-r3.ebuild 608 BLAKE2B e5ace31c7344228551c0889fd091a78c5d727fb1f3222d5dde51c011fd223741fcbd3954ee92c1b12406a7783bb952c6c49a5fdd154e11e1ecef17058b3983c3 SHA512 71d33765c88d05e9d2c9c24c7d3bed6cefc194bbb4844a274ccb5b16380d8e1608acfb929b9dd8631adf9542ee3af5bcfd1cfed50f420b2d352d9b0d31eaf7bf +EBUILD maqview-0.2.5-r4.ebuild 596 BLAKE2B 4d0efd2a53413b64f88e3831df0262503dc525be738ffbd498e988153524f0fed26ae810b9764dc3eaa83514cc627b6bf035c1baf478c76eb181c7bd781eb718 SHA512 398bc583d66e545dea4cb6194cb757acec65289c6e55099a24f3c51cf3cd3a5d9c1e505fd277612f50fe772c25d7e77ca99f11ecaf8de375db1dbe897be03c52 MISC metadata.xml 345 BLAKE2B 3f590b0bf8c9f9fa9470f6b8ed3b20643c84fc92839740e6aebe720edd0a6e0b8bb5d2b74d4dcd8cf80a89c2769308b89e21f2f386a62fc28686f883eff56bbf SHA512 244600e6c19400a837eb859a09582fa78a670d81a58e6a461689d2695273b450df999334ffc44eecdfbed9232784af84e7cdcabe7ee045ae51a24509f2aabdcc diff --git a/sci-biology/maqview/maqview-0.2.5-r3.ebuild b/sci-biology/maqview/maqview-0.2.5-r4.ebuild index 2d6574217029..80cf5c0f9410 100644 --- a/sci-biology/maqview/maqview-0.2.5-r3.ebuild +++ b/sci-biology/maqview/maqview-0.2.5-r4.ebuild @@ -1,17 +1,17 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler" HOMEPAGE="http://maq.sourceforge.net/" SRC_URI="mirror://sourceforge/maq/${P}.tar.gz" +S="${WORKDIR}/${PN}" LICENSE="GPL-3" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" DEPEND=" @@ -20,8 +20,6 @@ DEPEND=" RDEPEND="${DEPEND} sci-biology/maq" -S="${WORKDIR}/${PN}" - PATCHES=( "${FILESDIR}"/${PV}-ldflags.patch "${FILESDIR}"/${PV}-zlib.patch diff --git a/sci-biology/mummer/Manifest b/sci-biology/mummer/Manifest index 52c9f3976850..449d54fecfea 100644 --- a/sci-biology/mummer/Manifest +++ b/sci-biology/mummer/Manifest @@ -2,5 +2,5 @@ AUX mummer-3.23-fix-build-system.patch 10130 BLAKE2B 1c11e08dcc21daf26b14e13dac8 AUX mummer-3.23-fix-c++-qa.patch 2615 BLAKE2B c4af27ae72445836a71ef6417f56b2feaf10483da70d38ff3cbda80d95db0947eb183ef3f34c3922397c759a7e424b1674b193495199c0f5b942af5c9efd77f8 SHA512 ca1a8156ecac367817f4678ed9fd0dd7e5f31cce0d8d167dd9245ea1e2ad4b4acad254277483f99764891a0cbad8ca6f879acc731b8e3e306e5644739c0f82d2 AUX mummer-3.23-fix-shebangs.patch 2357 BLAKE2B 1a244047f55483240bc257892f2a607ab695624152613d665be5abecd85e02484a251e33f411fc67377dad3c49eb5ac32624acefa5cabeaadc8b5e3506dbb21c SHA512 d0ac58170232244385328d3a23e6b8203593d32dda30d75915b4da8ad935fc1dc447b2a7c7d982b0a86c9fe4ca6f8c2031fe7f81af8a72bfba4d56ae6d246235 DIST MUMmer3.23.tar.gz 3160143 BLAKE2B 5be613e0b7bcdbd0c38bb6dd7ff8d5c220ceb596582d89e0c1b62bbb2b289ce3a1842cd7e335a62d612af55388e21b6f780254de06f59e9e49a7eeadd04b6d8e SHA512 f31d36ef3e07fa4ac017c76c1c8d5f53882a59b061742d201f1f7aafb29d16af8268985285398dd90e98d276b2513d2c611f9876069b23fe82b5da1d3ebc04d3 -EBUILD mummer-3.23.ebuild 1133 BLAKE2B 9777159545c4cf807670d87fe2b4e2db2fd1fcfd9ac5139dc7cc3314cdeb17b03d505d4e7b3cf0995f082782d1ad1c488536df5e50d377b1c7dd3733e9af781e SHA512 a25b94cb5e7a8261178d0a503c33812f106dde277c94a8525a0a8fcd6c120ec6b0d5cb80f26f0710245f89251ad4ac6e4fe86af42f31b31f37ab9eca6afc3b79 +EBUILD mummer-3.23-r1.ebuild 1122 BLAKE2B 3cc8490dabdfd892868789447d811b522fe2efca8ae30e73e43ba3be1d1af3affae47e10740c4ff941176ec99a0b37f67405efaa4043c32092ae0ca4c92bb27a SHA512 6f6ebee7bc3cbc8c69643dd25433ef270de2d99bafb11cf06ec325beaf408cdcb0efdd744474689fdad8cf2c288162e85e4f785362f1bc27935584e75e7e3465 MISC metadata.xml 348 BLAKE2B 4f2a263ee7069564001bbbd3d68c710f9bb1dd0f34c2cd9ad2459b483c942bb4cf0785f57c60fa1a27b57a90b5f445fad1422025e424e70b596bb90fe4f64857 SHA512 17850f7126f24e9d1ae26c3034e679881686f775afddf916905da3108bc2d5e3ce0e6b2aa3f63427c62cd76f7cf232c4e9b24077e5341e9f022ebe1c7e6ee1d5 diff --git a/sci-biology/mummer/mummer-3.23.ebuild b/sci-biology/mummer/mummer-3.23-r1.ebuild index 4839053f4191..59a66abe2f04 100644 --- a/sci-biology/mummer/mummer-3.23.ebuild +++ b/sci-biology/mummer/mummer-3.23-r1.ebuild @@ -1,26 +1,24 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit flag-o-matic toolchain-funcs DESCRIPTION="A rapid whole genome aligner" HOMEPAGE="http://mummer.sourceforge.net/" SRC_URI="mirror://sourceforge/mummer/MUMmer${PV}.tar.gz" +S="${WORKDIR}/MUMmer${PV}" LICENSE="Artistic" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc" -DEPEND="" RDEPEND=" app-shells/tcsh dev-lang/perl" -S=${WORKDIR}/MUMmer${PV} - PATCHES=( "${FILESDIR}"/${PN}-3.23-fix-build-system.patch "${FILESDIR}"/${PN}-3.23-fix-c++-qa.patch @@ -38,7 +36,7 @@ src_install() { dobin scripts/{exact-tandems,mapview,mummerplot,dnadiff,nucmer,promer,run-mummer1,run-mummer3,nucmer2xfig} newbin src/tigr/annotate mummer-annotate - insinto /usr/share/${PN}/lib + insinto /usr/share/mummer/lib doins scripts/Foundation.pm einstalldocs diff --git a/sci-biology/pals/Manifest b/sci-biology/pals/Manifest index 744a9e62e165..860bd22b0564 100644 --- a/sci-biology/pals/Manifest +++ b/sci-biology/pals/Manifest @@ -1,4 +1,4 @@ AUX pals-1.0-fix-build-system.patch 681 BLAKE2B 8460ce718ce1a1a57970ecab525aa798e033c496a0108f44457155312653ce180ee700c76b1cf3a7b9f099a924cd7a8c0f027ba1cd65d96b688a67b97fe247a7 SHA512 bd95517d72cf567a4608878d556919396c9dd1cd77a4e49f2f8604f058c76a1f26c31760ad6ef6048ec12b76de46a6f4c56b5cb27b4aa1f91339c8f14bd963ac DIST pals-1.0.tar.gz 24895 BLAKE2B 09a24b3a2e99471378f33a84c447dea9153ddedd502de4e6b771c85ef99df5ca30f687b58d1d9d4726b29345215b617f1dc93a71b8be417d8c0c03e8ecd71015 SHA512 655e3311c63709dab1f8a13b193ed30a5ee97c04757a1e8408a74f6110ff3bdd96ba9eb07f4987ed5b83790ffa8cec67f722fee783c4ab4120483a683ebb9b8f -EBUILD pals-1.0-r1.ebuild 537 BLAKE2B fd3a09ff6d4e619fd902a67504a5130656412ad9bc8201c549a5b98f8eb7711816b18b72414aeb89a4f24926db8d41457061b045aaa3bdba0cdac1bf3ce1e633 SHA512 666542e4faefb47a94ab6f7cc3be531f39e2ca3f68324a80bafbccc6c0de162d2a20dbda507709cfd2f207b61734aa21211a93bd597b02599d9648ca557d4b4e +EBUILD pals-1.0-r2.ebuild 495 BLAKE2B c056df63e24b170b20bfd958ce6e67f447a028a2199724740d8ca6ea4af20302a33fc46ba40e3b5533b1e8c0ebb6681b4d1db44730aae40c17860a49118e9cdd SHA512 8d7027e01db3f11ebb7c8030c5711ca53af100e0de40510faa4a8ef11f6a08884e88507682d7d72bf36ac39912bfa68299a21455ed1682f9a2874471a66525eb MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/pals/pals-1.0-r1.ebuild b/sci-biology/pals/pals-1.0-r2.ebuild index 32579b9d0757..8f251d2b82ab 100644 --- a/sci-biology/pals/pals-1.0-r1.ebuild +++ b/sci-biology/pals/pals-1.0-r2.ebuild @@ -1,23 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Pairwise Aligner for Long Sequences" HOMEPAGE="http://www.drive5.com/pals/" SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}" LICENSE="public-domain" SLOT="0" KEYWORDS="amd64 x86" -IUSE="" - -RDEPEND="" -DEPEND="${RDEPEND}" - -S=${WORKDIR} PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch ) diff --git a/sci-biology/phred/Manifest b/sci-biology/phred/Manifest index 161f89dffb9d..7fc9ef8e7c6a 100644 --- a/sci-biology/phred/Manifest +++ b/sci-biology/phred/Manifest @@ -1,5 +1,5 @@ AUX phred-071220-fix-build-system.patch 1981 BLAKE2B 0c9ae75ecf54eadd1d6cd3cfeed5d2f949f234b77d4f329133e2c176207410e93a35341c43636c5b2f742a2ee2d20825cf79bb65d5dac43ba28fc07f7c6bb69b SHA512 7647f6f6e9a1ae51cbf1aa3e39b337288e22fc26a95fdd88f92ce43fc6c0ef6ff59ec26919d14dfefff70be48e4a5604ddefef98bddf5d1d14d1e656665c878d AUX phred-071220-fix-qa.patch 787 BLAKE2B 79f687dc1e51dd51e9f97886e0ada9b515d7e4255dff0ec3e81dccb2103ba8b4bee691c8a5b9a321cbdde5576fe8d80dbadafdb740c2cdee81fe9748255084ab SHA512 27811a834358d0e1bf8281882e0420e0eb6bd9586871c8c72a4de79badc9539ea8e9258b9c3a3bf8ca1d3f6924d61abce2dcc0c0ed3b64e5fa53d4548109f5bc DIST phred-dist-071220.b-acd.tar.gz 357767 BLAKE2B ae1180f54eaa3631a4e32c2ffe388b35745302e3d014c8fa893119e7e488d4bb4316f7ee0588cd12db5cbbc23033f689f4a0a487cdc7fe42e8c7a67ceb3c43ae SHA512 0a6b0a733e6dcc0495eaab720b75f8e5815df494d0a773b8b8336d5208321c2ba475921084835a769367ec51aed156585ab97346a510100d4337e3215ec75276 -EBUILD phred-071220-r1.ebuild 978 BLAKE2B c2262024808c5f0fe203ff301964ae0b546de279199cdc1ed9c7ab3ee89e5d68f6285e4726bb9a28f8e22091c177918103dc06cde7501e7ce2b4ee5b78f313c6 SHA512 f66790ce585e4747c4db2eab8cb4c2be63da903510d64bb395ec74173a8b150524ed7ae1149ccd78876dfafb59bbcf2572cbff3bd5b4cab8642112b26a151482 +EBUILD phred-071220-r2.ebuild 942 BLAKE2B 0036b7fbe0891c0a153713fb7a17a12aff626a50ecd1609d6bde5e4788eca5e9d9a13aade9c43e22edcb3796ca4b9ef427e258eded270db7dec532f202986a63 SHA512 beec976e7dfdac8b7f539b680a6240b9a8489d8f35e23f831816be1df356cedf28f0c21109eb605a6e81827aa69298d0b18e3e2bea129ee9d552bb100240246f MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/phred/phred-071220-r1.ebuild b/sci-biology/phred/phred-071220-r2.ebuild index bf7a0c7338cb..9d7ff9a1f6c8 100644 --- a/sci-biology/phred/phred-071220-r1.ebuild +++ b/sci-biology/phred/phred-071220-r2.ebuild @@ -1,28 +1,23 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="A base caller for Sanger DNA sequencing" HOMEPAGE="http://phrap.org/phredphrapconsed.html" SRC_URI="phred-dist-071220.b-acd.tar.gz" +S="${WORKDIR}" LICENSE="phrap" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}" - RESTRICT="fetch" + PATCHES=( - "${FILESDIR}/${PN}-071220-fix-build-system.patch" - "${FILESDIR}/${PN}-071220-fix-qa.patch" + "${FILESDIR}"/${PN}-071220-fix-build-system.patch + "${FILESDIR}"/${PN}-071220-fix-qa.patch ) pkg_nofetch() { @@ -39,11 +34,12 @@ src_compile() { src_install() { dobin phred daev - insinto /usr/share/${PN} + insinto /usr/share/phred doins phredpar.dat - echo "PHRED_PARAMETER_FILE=${EPREFIX}/usr/share/${PN}/phredpar.dat" > 99phred || die - doenvd 99phred + newenvd - 99phred <<- EOF + PHRED_PARAMETER_FILE="${EPREFIX}/usr/share/phred/phredpar.dat" + EOF newdoc DAEV.DOC DAEV.DOC.txt newdoc PHRED.DOC PHRED.DOC.txt diff --git a/sci-biology/phyml/Manifest b/sci-biology/phyml/Manifest index e9c019c5258b..e5a4c6a54843 100644 --- a/sci-biology/phyml/Manifest +++ b/sci-biology/phyml/Manifest @@ -1,4 +1,4 @@ AUX phyml-2.4.5-fix-build-system.patch 1735 BLAKE2B 2ba677db3b00cc1ede4701652cd854aa8f92bc545668fae50add726fc5ddcc0694dbac7189216816026433d5c25864c819c77a887a03f6a75f111084611b6689 SHA512 95079d00d4a7373f9b6f9b17b707ae999db38a341e03f96b5f1b023ea4fd76a4027f6a46c6e33ecf7902ab4dcbc22d199b5c0f75a7b0059c90f7c11fbc9146cf DIST phyml_v2.4.5.tar.gz 92143 BLAKE2B f95b6b5023cd9b68e92e600edd9ee404bdec717d0b1e748c9e4f4667d732a23469762b847e4aa3c36e5cea7ce1d663ade031ec996cd6449ef1cf2fd55b96b2c8 SHA512 119716290eca0de4da05b0bacbec96139f4c89f6a033b861d1cb2655a620766bd0bea0675c4d7722a31d888652a28bf3544a643f39f11682982ede80dc5928c3 -EBUILD phyml-2.4.5-r3.ebuild 536 BLAKE2B 07640b2fdb404b127af7e8f9bcfab6d7571b9a80405cd793bc0c632bfb5642ae8da116bc983b8f6eb248ce23ac10cf4d3625943c3a943baceeb4b58267866222 SHA512 4294fd9067a16934306108c60a078ce8b9987c43d465203aa0f3a801f1359956bc4ac715863581e2d7af616244860e549c5cc9a6f28bbc3d9f5c4be6e23e6ddf +EBUILD phyml-2.4.5-r4.ebuild 524 BLAKE2B bc347c764d77c74c0af028a7334897ca43c73607f77d713e2aad98c0d15655b39cfb5d17f50e3cfbf9f026e5168ac810affe15e71713d2a2c81b7fe99eba3eaa SHA512 d12bc078bf9f3592b2c44f09b3f5c9456d8d1574df0d98ba998cab21af68dae60dc910d90dcc736c1fe83f0e082ba4e88363d8fde3e79cd7eaf287c3c077f641 MISC metadata.xml 564 BLAKE2B 449bbc55fcabbe9a9fea66017ff48bdf5075345496d6cc9abc6a53966245c00894093b0852eaf1a74f6746db4093d8a3be36a4f9e00b6a245d38716b146247a2 SHA512 89b24d285a76e7826563f631b991ea871c7f4e5c2048ab47cb8d1d028abcf817b5e582bf93d3ea122b019e4b4a49f386f3d95f6103bf39c0979b5f6a3c19b791 diff --git a/sci-biology/phyml/phyml-2.4.5-r3.ebuild b/sci-biology/phyml/phyml-2.4.5-r4.ebuild index ef9696573577..d256370553ab 100644 --- a/sci-biology/phyml/phyml-2.4.5-r3.ebuild +++ b/sci-biology/phyml/phyml-2.4.5-r4.ebuild @@ -1,27 +1,24 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs -MY_P=${PN}_v${PV} +MY_P="${PN}_v${PV}" DESCRIPTION="Estimation of large phylogenies by maximum likelihood" HOMEPAGE="http://atgc.lirmm.fr/phyml/" SRC_URI="http://www.lirmm.fr/~guindon/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" LICENSE="GPL-2" SLOT="0" KEYWORDS="amd64 ~ppc x86" -IUSE="" - -S=${WORKDIR}/${MY_P} PATCHES=( "${FILESDIR}"/${PN}-2.4.5-fix-build-system.patch ) -src_prepare() { - default +src_configure() { tc-export CC } diff --git a/sci-biology/piler/Manifest b/sci-biology/piler/Manifest index c25e1ad20625..6fc587829cfc 100644 --- a/sci-biology/piler/Manifest +++ b/sci-biology/piler/Manifest @@ -1,5 +1,5 @@ AUX piler-1.0-fix-build-system.patch 685 BLAKE2B 8df7772012b8809599d0c80d52ec60884ee086f69b6b9f185cfd8b9026d4e047bd7cdd8e4eebea0e5fe991434ebc146cba92721fa9ab0238803c69e2d2ed06da SHA512 e8a618615ce62aa6b4d7e5d0a4ec3facd13b6baf2573323a2f9c03d81171f1c32686bd7b82c4576e0b38cc3b30b201750034ab160cdb9170215ff480eb72a3a2 AUX piler-1.0-glibc-2.10.patch 386 BLAKE2B 758ba0e13cf114998a78866ae4ba3b11cc27aad09f17db84ed7b295c14ccbc15e8446b49bfc425f0ed92c694e16dfbee33ffe9cc0618bbb92c142d4d0c1628eb SHA512 0773c9b6c2eb289c8dee3cc8db6ec0250cd8df3b9e5e729305b58b28db64f486571f2f54041c84d178bf984cedfb4d9941c5abd47f772ecdf29e9ec0bdb55fcc DIST piler-1.0.tar.gz 35220 BLAKE2B a3a5d9ab6885e0900c523db9d1248888cd3de50b18c2c4ae110a13d792a0faa60eefffbac4526df96b482b4fe6ed8bd19299eb96380332a57f2d60330ca40037 SHA512 35be1b445f1eaf26f96d0356a04d985fb528754677403df2061c0872107d31819c5fb355e7f616e953a997e67ce781846acaf3cc2a016097aca785b6a26de3d4 -EBUILD piler-1.0-r1.ebuild 660 BLAKE2B b05e0c65d483624d517ac6155087435cac128c088c14ed7df6091423c88353209acb96c258033bf43bf5983d51ab88aabec78dd9b955646a325a482ee7f28197 SHA512 7a8b1c64559477101989e3a97eb8d0aa3b6e520df66b0f43a97f2531a2de7fa77acb6b9e6066ab0ac46668cd23bfa9357cebbeb5c610e67f3d757e53e5ce97cf +EBUILD piler-1.0-r2.ebuild 640 BLAKE2B 30477b8cee6c18196e5f71db6a5ee4c786b1e84fdb8bc01768f03b3eacb765c3fb500bd8b1901f56a1046fda6f78c220d3b0658c02f82beeeff954e7fca72576 SHA512 88e1e8d19be93fa2325670e8c42c16b3bc19c193af20116e9bd60b8a00968c90088531e345ea1d9f6b9b54b72f021f10cd44387bf10dbdf17b4bba8ae7391fdd MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/piler/piler-1.0-r1.ebuild b/sci-biology/piler/piler-1.0-r2.ebuild index 276ee9bc873e..845be78e1fe0 100644 --- a/sci-biology/piler/piler-1.0-r1.ebuild +++ b/sci-biology/piler/piler-1.0-r2.ebuild @@ -1,20 +1,19 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Analysis of repetitive DNA found in genome sequences" HOMEPAGE="http://www.drive5.com/piler/" SRC_URI="http://www.drive5.com/piler/piler_source.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}" LICENSE="public-domain" SLOT="0" KEYWORDS="amd64 x86" -IUSE="" -DEPEND="" RDEPEND=" || ( sci-biology/muscle @@ -22,8 +21,6 @@ RDEPEND=" ) sci-biology/pals" -S=${WORKDIR} - PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch "${FILESDIR}"/${PN}-1.0-glibc-2.10.patch diff --git a/sci-biology/pilercr/Manifest b/sci-biology/pilercr/Manifest index 51b2db624bb0..bda424303fd2 100644 --- a/sci-biology/pilercr/Manifest +++ b/sci-biology/pilercr/Manifest @@ -1,5 +1,5 @@ AUX pilercr-1.0-fix-build-system.patch 673 BLAKE2B 53bbafb9d1433e78edb3568db8e1a810ba1cd1b08f3f1b53719b1b98483825a50ef5daf06226a4ad72e577e50d3e034f6c2bad6b53fa098c89cb7635166c8223 SHA512 b744c3fdc6e1ec152a27592ce8036de080c113b6385c5743dfca325ae8e0435d34418ca9f51830c540cf8efae710d842b89dd1b2b7b772379a4f527a72ff2c06 AUX pilercr-1.0-gcc43.patch 854 BLAKE2B 2e3ffba380df1522f28eab7e48103d6c56d1548db3eb8622e9e5f77c098d420858b1f9ba656593f949454b43f2cee5d7a79cd9d2fe712749cc481f4f1dad61d9 SHA512 7e83a1c29f2b6b11e101ffebf99516c9da06f7fa7645aa619a89c365dc89d6ea2659d4610eea25b6e260328b56320e6d720f3d0d67a01aae450104fc9513d58e DIST pilercr-1.0.tar.gz 1709144 BLAKE2B 59aef12a10d168c8cbf4d3b3eec95dd4cd47b0ba073f19bd9f3954e6fab088af1c9f0328b0120c219034be07e4d13af4df17ca3eb7f40c19ff2a13d72000251a SHA512 c262ceef1d1af9e71f454809e940c2ad6d835a8404daa51ccef698b8348a504c697f5b5c268ec24df611f5adda2932e4982bcdabe4fbdf99d8c204f0f77f1be5 -EBUILD pilercr-1.0-r1.ebuild 594 BLAKE2B 591e2bdd45588279fc347ac5a31519b3e108bb29bc548b42a432e8f3c8fc73d09f195a5cfe66bac80ac825767a81a8e20814a9e867fbcad35e082383a107ef41 SHA512 5841ff12c7fa7d2290b2310aaba5fd0ec2688e5364e0f973314d9eeb6641fe43d0ff30374bc327f3d6152fd81476424f423841adac6d52656690d0a12090119c +EBUILD pilercr-1.0-r2.ebuild 586 BLAKE2B 56782b41777a8e3bedb47e2dccf4c4f5d1e92bd0287b1100011b3e5b6aa56b02dbb8e5ca463aea9041256c4a808f8963fe7a68427ad079f6841b4183c424b194 SHA512 c999f02d8e05561918a19428ef66894117dbdb99bbae6c722bb90211fafec4401667b756f139926b78bcd30d05492e0f05ffd4f77fc3c5c337340e255ca09e7f MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/pilercr/pilercr-1.0-r1.ebuild b/sci-biology/pilercr/pilercr-1.0-r2.ebuild index 8b1abd5de7d7..819fb3fbb03e 100644 --- a/sci-biology/pilercr/pilercr-1.0-r1.ebuild +++ b/sci-biology/pilercr/pilercr-1.0-r2.ebuild @@ -1,20 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)" HOMEPAGE="http://www.drive5.com/pilercr/" SRC_URI="http://www.drive5.com/pilercr/pilercr1.06.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}" LICENSE="public-domain" SLOT="0" KEYWORDS="amd64 x86" -IUSE="" - -S=${WORKDIR} PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch @@ -26,5 +24,5 @@ src_configure() { } src_install() { - dobin ${PN} + dobin pilercr } diff --git a/sci-biology/prank/Manifest b/sci-biology/prank/Manifest index 4427ad05c7e0..792703ee68e0 100644 --- a/sci-biology/prank/Manifest +++ b/sci-biology/prank/Manifest @@ -1,4 +1,5 @@ -AUX prank-140603-fix-c++14.patch 395 BLAKE2B 9b0242c22bbe87b39da73aaa3639c286601f96b06a75b8bacd7a305dbbf9dc0a5cc6b054ccb05984313ac14c7e9852d2dcbe36150ab4d224e48aa6e72b88bdad SHA512 a7ac7e9e8a138a2ce103302a92e936ab1c0b15c72ac8cdb2aae26c8767e764b42b048d40c436cfd21b372ae471706852ca23b41150578bb83ebbb13a7b7ac014 +AUX prank-140603-fix-c++14.patch 383 BLAKE2B 7894b9020e1156e2a40ac0043534b27890a0628469058959504f4c582ec7262b8a1fb4ef6dac1b0bbd02354633a06fcf95d87c9e11e91b568bb1c78fae80a133 SHA512 0f843c9a1c11f555b2b87c7d5df29a25144c8e11d5e98f79c2d2bb30423d2ec39441c7b9247daaf1afcbbed97bff1ab52298506fe38048273e4ee2823e081276 +AUX prank-140603-makefile.patch 683 BLAKE2B aeb8c4c52691912782268ff9908fe3390ba22ffa6b44fa38da6d28842d2b313b9223c3f7cdefbe7a53c89d306be730eaa9eab8820c20a81a32b74afe4c1a1274 SHA512 eaf27afad46df929add912fde3f632291b3835be13c29a5e185b3abddc6aaf67fb1473c958b36de55fcba845946118940e128614d8785bfc7d221bf0c2546e13 DIST prank.source.140603.tgz 150346 BLAKE2B 4bd5ba1d2f5106a20f51be359ddfc2421ef6c5ae235bf14dddf6fe82745d3375074ee213e957ef290edeae124c070cf14d6674765ebebdafc0a726a037ed269f SHA512 25e5f99a3822ff31436406f9ba1c781ba375959e1ed452c1e7416898d5246183510ec6d2bc715ff1495a779e42d7bd1d49ad1c332e1bd5982dad8c744ad999c7 -EBUILD prank-140603.ebuild 739 BLAKE2B d12e2aae28462ed6682d92ec36852e1ef137578119dcc4b2e0933f90b0dabb12c2ce35a55895049cb6aecdf4b4afad5b8446562c93db977b5197fff2daa1a16a SHA512 81240472088098b2f2685e8a433a527d06a1efdb51edadc17380738700c1202097e5392ad06c13dfef2b554f08bb5a54b0b3008bd9329edb4f363e2688e62dd5 +EBUILD prank-140603-r1.ebuild 527 BLAKE2B e46b41e7745afa4d37083c205c1f2209cff7fc24c208907750ba4e703dc720490184c0d1c931c04b88cd60e77606181669c46c03661caea6be79c1aedbd11162 SHA512 d5fd45de5775337cae1d2f5af7c8edc350c5c82bd2e2e7dfb89d901b3bf0ffb9a4d7a41e4c049c0cda6877d291cb8ef77bfdd135bb52e9ba66dc1e31ec4d7fdd MISC metadata.xml 351 BLAKE2B 836bd7063926bfd74a99679e881df736111f366adc3a2970631be11139148a619911ad5850acd3103ee2cc2441a35e00c2e8665d68653aa1a9ee85fd1f065ec1 SHA512 9ed02c4c733d0fcd6d1bda34272ce06d502e5a20bbd62b718a59e3043fbf8e5002606537b3eaf07d056545633449b78d334795a0a9828747e56934f3f9d96f79 diff --git a/sci-biology/prank/files/prank-140603-fix-c++14.patch b/sci-biology/prank/files/prank-140603-fix-c++14.patch index 5779207e294f..211e377d798a 100644 --- a/sci-biology/prank/files/prank-140603-fix-c++14.patch +++ b/sci-biology/prank/files/prank-140603-fix-c++14.patch @@ -8,7 +8,7 @@ See also: https://bugs.gentoo.org/show_bug.cgi?id=594060 else { - cout<<"HMModel::alignmentModel: impossible 'as'"<<cout; -+ cout<<"HMModel::alignmentModel: impossible 'as'"<<bool(cout); ++ cout<<"HMModel::alignmentModel: impossible 'as'"; exit(-1); } diff --git a/sci-biology/prank/files/prank-140603-makefile.patch b/sci-biology/prank/files/prank-140603-makefile.patch new file mode 100644 index 000000000000..eeb74df89b4c --- /dev/null +++ b/sci-biology/prank/files/prank-140603-makefile.patch @@ -0,0 +1,28 @@ +--- a/Makefile ++++ b/Makefile +@@ -4,14 +4,8 @@ + + ####### Compiler, tools and options + +-CC = gcc +-CXX = g++ +-DEFINES = +-CFLAGS = -m64 -pipe -O3 $(DEFINES) +-CXXFLAGS = -m64 -pipe -O3 $(DEFINES) +-INCPATH = -I. -I/usr/include +-LINK = g++ +-LFLAGS = -m64 ++INCPATH = $(CPPFLAGS) -I. ++LINK = $(CXX) + LIBS = $(SUBLIBS) + AR = ar cqs + RANLIB = +@@ -136,7 +130,7 @@ + all: Makefile $(TARGET) $(MANPAGES) + + $(TARGET): $(OBJECTS) +- $(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS) ++ $(LINK) $(LDFLAGS) -o $(TARGET) $(OBJECTS) $(OBJCOMP) $(LIBS) + + + clean:compiler_clean diff --git a/sci-biology/prank/prank-140603-r1.ebuild b/sci-biology/prank/prank-140603-r1.ebuild new file mode 100644 index 000000000000..9128cf9cf99b --- /dev/null +++ b/sci-biology/prank/prank-140603-r1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Probabilistic Alignment Kit" +HOMEPAGE="http://wasabiapp.org/software/prank/" +SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz" +S="${WORKDIR}/${PN}-msa/src" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-fix-c++14.patch +) + +src_configure() { + tc-export CXX +} + +src_install() { + dobin prank +} diff --git a/sci-biology/prank/prank-140603.ebuild b/sci-biology/prank/prank-140603.ebuild deleted file mode 100644 index a29e425f43bf..000000000000 --- a/sci-biology/prank/prank-140603.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Probabilistic Alignment Kit" -HOMEPAGE="http://wasabiapp.org/software/prank/" -SRC_URI="http://wasabiapp.org/download/${PN}/${PN}.source.${PV}.tgz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -S="${WORKDIR}/${PN}-msa/src" -PATCHES=( "${FILESDIR}/${PN}-140603-fix-c++14.patch" ) - -src_prepare() { - sed \ - -e "s/\$(LINK)/& \$(LDFLAGS)/" \ - -e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \ - -i Makefile || die - default -} - -src_compile() { - emake \ - LINK="$(tc-getCXX)" \ - CXX="$(tc-getCXX)" \ - CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" -} - -src_install() { - dobin ${PN} -} diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest index be235d3110bd..add34be6e72f 100644 --- a/sci-biology/prodigal/Manifest +++ b/sci-biology/prodigal/Manifest @@ -1,4 +1,4 @@ AUX prodigal-2.6.3-fix-build-system.patch 1004 BLAKE2B 5a0323f6f4440e5f45805e8eabc32374f7d47760fa62c426a776a6f5bb573f356241618fbb231522c05ad950b3de71f38787bf848049f4c6fa174726c9134ee8 SHA512 c96e93cbe344bbab43b03b0046b1bca5030f4a731a0b43ea4d4ee87d303502d172fc93975a9d7b907d6ea6beeb865113122e0e2cbca7d660290994bb8214a17b DIST prodigal-2.6.3.tar.gz 610934 BLAKE2B 54a75a694aec216da411717c29c8e896f064b4893d74fa1c736fdea3cd7bff98cb8d597cdbb96dd4cb2f0e82972c99b43eee8f2ddd8678535dc68c831dfd4e08 SHA512 6d6ec310143c50c0d65dbdbd26d6d271839bb23b1da376ecef20059731a9e643d631613eccaac2eb548b295264b9fe58c21b083f1511a6554912cb7d5351d541 -EBUILD prodigal-2.6.3.ebuild 518 BLAKE2B 80e85e8507eed4b64fecf813c54f2fac707cb8aec21182f40ffebbe83ab867eab3243af5618eeb01fbcf1ac33ff06f3bc060ec78f245da1afa30475b2d4220d8 SHA512 44048cc1a61e2e7decd5b4dda026e4b89ba54decfb1f63ad3d378c3b8ebef707b3e3c2338108186be9a3f9400bca165f3331a1f1dd668345716b15c01189a0e1 +EBUILD prodigal-2.6.3-r1.ebuild 486 BLAKE2B 44f22716c8f9bc1e4583a1b4ccb984314d0922162bbf9cddf9012eb8ac988e5f741ba3f1dc8f2194a31e9b7e9ced0bfa9a9e7fb532cdea0024c4b5ff0cd2c2e4 SHA512 e467a9b202296bb7f992d0ab138b4d70d8f2eb3dbdb75408d336f7c10bd5d61b728f5b249b013c7f4d76550c5183a371acf0341ecf2d98b41aba65e4b1d96040 MISC metadata.xml 396 BLAKE2B 1055ca10c3eafe54022acbe3f9d6304d64e56938e7e2ffcdb6d1055b7b687ad1ef38240588bc524eabfd3971e7b5e21eaafc971cdfcb9c9c1e3a798dea6f20ff SHA512 ed9530c82222c10dcbe345636e9208f232d130e693efa9695979980c4a2dd0bac3f006b32d86f3cca1c925c00b1cd5607846bf94532919258f4ee80cefc450fb diff --git a/sci-biology/prodigal/prodigal-2.6.3.ebuild b/sci-biology/prodigal/prodigal-2.6.3-r1.ebuild index db8382982284..8428da82c5e7 100644 --- a/sci-biology/prodigal/prodigal-2.6.3.ebuild +++ b/sci-biology/prodigal/prodigal-2.6.3-r1.ebuild @@ -1,23 +1,18 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm" HOMEPAGE="http://prodigal.ornl.gov/" SRC_URI="https://github.com/hyattpd/${PN^}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${P^}" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" -IUSE="" - -DEPEND="" -RDEPEND="" - -S=${WORKDIR}/${P^} PATCHES=( "${FILESDIR}"/${PN}-2.6.3-fix-build-system.patch ) diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest index f7450ce0bedb..b768a55b1b99 100644 --- a/sci-biology/rebase/Manifest +++ b/sci-biology/rebase/Manifest @@ -1,3 +1,3 @@ DIST rebase-1901.tar.xz 182532548 BLAKE2B 5ac8d26ab057bcd21dc9c57abeb226ac70cfabb156b48a51f820789626257be55bb21c9eb2099e6e55b1cfe3691480df0ec9b3f4b18b50ba2712b986c6d057b4 SHA512 1e3553e59c3520190754cb40bb0900e466d9ffd206e6460d3262a7d7d2af8aab0e28f3e60187665362824fa3730211c0e2119016ce5fed49095f9de46c7f25d4 -EBUILD rebase-1901-r1.ebuild 1082 BLAKE2B 664fe7c05d97d493ed451965467fbcf3a644cca64229c96a8f186e66382de36433c4dbd77430e94ec6a65e3dd411bd5e53562ced6aa386f3b6b2e6b4b6129e67 SHA512 b801b2b467b8107a6e37bc2356ea9f1ef9b8216dd5d10b7f9fe5630eff2aaa900507aaf3a14111c44786d7d4a84bbe7a2d4028c15c378b9a8d600d31c2b46b98 +EBUILD rebase-1901-r2.ebuild 1083 BLAKE2B f9a069d5c66b77b05c72022533ea6b014d99467f44b94667dd16d49507c47a37c414784307cdbbe20fa8540b28f1e9f9c3bd6a61700edff7cddba7db7a91c2d4 SHA512 c1cad2fffbf05027094a9a2d8a2f58b0d749400c69ac6660e7e4ed24fb906c2c5d05214be0626adb318d22b3e44b4bdbf487c8a9b4e83ed7850e8e7e8dc591f8 MISC metadata.xml 908 BLAKE2B c5b8a6f961e426788c9a6b84d01c468fa7613b52da52bf4ba4d057f0c1966ac1092acd219160e96bc2778673ebe82398471044a34e775ded0a5d72221adf363b SHA512 0c9bc87df88e5485350071b4b219dbf90958de0394444fda093fdef18ede4378c0463b6e81bd48c5c162ae0c581d186c693d3474f895a4e4de59d36c3f5a0588 diff --git a/sci-biology/rebase/rebase-1901-r1.ebuild b/sci-biology/rebase/rebase-1901-r2.ebuild index a993a8c2c44a..1b4b75407947 100644 --- a/sci-biology/rebase/rebase-1901-r1.ebuild +++ b/sci-biology/rebase/rebase-1901-r2.ebuild @@ -16,7 +16,7 @@ IUSE="emboss minimal" RESTRICT="binchecks strip" BDEPEND="emboss? ( sci-biology/emboss )" -REPEND="${BDEPEND}" +RDEPEND="${BDEPEND}" src_compile() { if use emboss; then diff --git a/sci-biology/recon/Manifest b/sci-biology/recon/Manifest index 2f04c00a5925..ca9fce3cc629 100644 --- a/sci-biology/recon/Manifest +++ b/sci-biology/recon/Manifest @@ -1,5 +1,6 @@ +AUX recon-1.08-Wimplicit-function-declaration.patch 319 BLAKE2B 7d0eb6bb94d02637d3bf3dd04a22fb0073e41ab772f377157c968a28956234f51fccc00651776dfef149b2b90d47072d0c60f00dcd1e3825ad6aa28726604105 SHA512 8f2bfd1f39886a787ea58f735b7db6abac32c1ad49e2e5da693d05d17761bd2a20ede0746e85ab99cae6b95a4fdc415e01c587e1bae8ccb72e7ef75a1d59a3c1 AUX recon-1.08-buffer-overflow.patch 290 BLAKE2B 3fb3bf31f7975d9c0610e53d56b6e232dcd123df57f1f7fb19efdc260b1fa0e3619eb582650b8cb84cf0e1a855b5192015400b7672cfcbd23b5c34d1ba8bcadb SHA512 d903e6a8e4b61e5f91a318313203890242aa9badbf6af69009b5a3ef6351ba6984e00cdaa7aaf744095fd79557c1a5ad96a80119248cddfde9874f4b763df11b AUX recon-1.08-perl-shebangs.patch 420 BLAKE2B 7ff36e0d6fcd96d7345167880e82ab325f4ab09bdfc37bac2f8949158abf48eba9e8fb64976322d3a3056d50e5c3900bf885049662db1375cd3c2cb9e6b10f47 SHA512 b681a0f911268ab39bc64cc35f4647a71696f3cbc4610f6fb7c061ca70406934ca2f85525578c28530431725ae9399c327a7551eb19dd46552ce5e65b2399a88 DIST RECON-1.08.tar.gz 108477 BLAKE2B 155a740056e876f5aa2279ca0572fe151a52a2db5ac43af9b902ea4c099727f3274dd58abec59b74c13605ccd37ad9b3cd80379f79cb976c4bb677f661fd6273 SHA512 68672312f31751fa93250bbe337ae57f11dc4b1994c7dd5249dca916012c2df83a03c925cb631709e081c72055ef5bffd0846bc252d8c3c6247ae5ef61b160c9 -EBUILD recon-1.08.ebuild 964 BLAKE2B 19ef960784329b03bdcb1d2eb46223b40bfb6dc8e617b06ae526b0690ae6d6ea444e9db1d6c466c1a3f62db0e773de349d4c338a0c9e9182d2803342b35fc6a9 SHA512 39805629341d019e769ff796f9ef12aedaadcc431904a6bd0b6e48b145a3631a1f7ebbccdff6fc23cdaf75e55ee909ea5fc7969b35082fcec0b963e48baf3215 +EBUILD recon-1.08-r1.ebuild 1025 BLAKE2B 9e82d4be8c3d6f20db01dde74f6edcb792a175c94bb4c8fa5da5ce625baeb5236610fd4a7741ca52e37ce21f0bbfe5e21d65370e3f31c16eccc5a02a3f6c4823 SHA512 096e93f4f4a4420c616b52701b6c67792431219a13e4bec7afc840bc6e57ed3a167c484a5752a4703a0c68aaa117176b7900d2b2e434d370ae4e0ce8fa2f32c9 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch new file mode 100644 index 000000000000..9eba16e4a410 --- /dev/null +++ b/sci-biology/recon/files/recon-1.08-Wimplicit-function-declaration.patch @@ -0,0 +1,20 @@ +--- a/src/bolts.h ++++ b/src/bolts.h +@@ -3,6 +3,7 @@ + #include <stdio.h> + #include <math.h> + #include <stdlib.h> ++#include <stdint.h> + + + #define NAME_LEN 50 +--- a/src/seqlist.h ++++ b/src/seqlist.h +@@ -1,6 +1,7 @@ + + #include "bolts.h" + #include "string.h" ++#include <ctype.h> + + #ifndef _seqlist_h + #define _seqlist_h diff --git a/sci-biology/recon/recon-1.08.ebuild b/sci-biology/recon/recon-1.08-r1.ebuild index a96403c812be..dd79dd43c496 100644 --- a/sci-biology/recon/recon-1.08.ebuild +++ b/sci-biology/recon/recon-1.08-r1.ebuild @@ -1,31 +1,31 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs DESCRIPTION="Automated de novo identification of repeat families from genomic sequences" HOMEPAGE="http://www.repeatmasker.org/RepeatModeler.html" SRC_URI="http://www.repeatmasker.org/${P^^}.tar.gz" +S="${WORKDIR}/${P^^}" LICENSE="GPL-2" SLOT="0" -IUSE="examples" KEYWORDS="~amd64 ~x86" +IUSE="examples" RDEPEND="dev-lang/perl" -S=${WORKDIR}/${P^^} - PATCHES=( "${FILESDIR}"/${PN}-1.08-buffer-overflow.patch "${FILESDIR}"/${PN}-1.08-perl-shebangs.patch + "${FILESDIR}"/${PN}-1.08-Wimplicit-function-declaration.patch ) src_prepare() { default - sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/${PN}\";|" scripts/recon.pl || die + sed -i "s|$path = \"\";|$path = \"${EPREFIX}/usr/libexec/recon\";|" scripts/recon.pl || die } src_compile() { @@ -35,13 +35,13 @@ src_compile() { src_install() { dobin scripts/* - exeinto /usr/libexec/${PN} + exeinto /usr/libexec/recon doexe src/{edgeredef,eledef,eleredef,famdef,imagespread} newdoc {00,}README if use examples; then - insinto /usr/share/${PN} + insinto /usr/share/recon doins -r Demos fi } diff --git a/sci-biology/rnaview/Manifest b/sci-biology/rnaview/Manifest index 20f865ebf762..67679a127284 100644 --- a/sci-biology/rnaview/Manifest +++ b/sci-biology/rnaview/Manifest @@ -1,5 +1,5 @@ AUX rnaview-20040713-implicit.patch 347 BLAKE2B fc12a2d06bfdb88889e3b2af1b207b1e46b2733074b6a6ea31a98759cedd63e55cea50ae5a9f31d91a251791a3a48ceb387c8def4531d7fefd2757d4b671b0dc SHA512 698369b7640a36c26970649a8e0fd240c3177b3a3f7d9b8059fb6c294c39ad61389ba8a6eb3d465c3a999981fff47e2aa175ea52b38068145e2941c5934c4a0b AUX rnaview-20040713-makefile.patch 2131 BLAKE2B 502f4eaf2f0f4a82b6a85ad17804d2f2a675e3d28873cb13873aa9cb450e29c51f44685e9c20dda0525a7ea2aab4005f0e5dfce919c03c47ea3489fb981a88ac SHA512 9cde6186c0865405546bbee68ec64bd11cdfe91747b90739b237368b2724763ac4dd9206defec7f00a918449fc2a8451c3a5e447cfddfb7ca5c5fed00bb29de6 DIST rnaview-20040713.tar.bz2 433916 BLAKE2B e6f52fbb90a11290728c0a67b8ccde42c1c20967c8b9810c0c1103a300d1cf1a4ee1c9e501c203ae3f3dfda29fb5851603f095931c3efedd86143793115e633b SHA512 c63bb728bad0f358ab36f4ca18f4f9ef046811f21d3b8f3c6fdd3e6e6fcb367a9a52710476c5daea001f8f3262f72b64f0c0546f0c1423f463f2e0d288809e8e -EBUILD rnaview-20040713-r4.ebuild 657 BLAKE2B d840990168b0e5583ca730daadbbf3ad77b9e3fba023388c508edd65f48d883c7c904840f75f070f9b004b7e08e80f4a17a7c02b261c8cc1febf43bca399b10c SHA512 20ed56130c1a2cdd18cfc0717cdaca75030bdc2315343b390d0f01aa7ee9fc760734c9ec692bbe13c0930007dd47bfefea13b0d0c205bf1ee6850221e8df96c8 +EBUILD rnaview-20040713-r5.ebuild 620 BLAKE2B 7b4df9c2f19a328fdb37a8a49d08333cfc0f3a00f266fd9cdccbeec42dc168da4d35a65fd8d67f5e7e9625ec9569f792c4356e14f650f67617a8b6ba6c5aa209 SHA512 86782af8724b11e1356cd141dd3c8cfc291939a1ec74f82b89e6d95434e058b43d3387f46495d9fbe85eaee1d4443ff714d66272c68e072f6b71943d6099557b MISC metadata.xml 667 BLAKE2B f88e229df64f58024cfd40ef2a6f8acb976f7ff1335080d1de1934a984c709cdf8e32a1831a8c62b1729e83f6a95f97abefc2d2fdcf870e66d704accb9d4cedc SHA512 9984f82b1ee7322822a022724c7c9d8920915fc2d70440a89aa611910b92ac74d1c8a22cf31a9b67d7d51c708319b17bd7e060bc22ea603958223d45ed186a3c diff --git a/sci-biology/rnaview/rnaview-20040713-r4.ebuild b/sci-biology/rnaview/rnaview-20040713-r5.ebuild index 729095be063c..c0c4289ba24b 100644 --- a/sci-biology/rnaview/rnaview-20040713-r4.ebuild +++ b/sci-biology/rnaview/rnaview-20040713-r5.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit toolchain-funcs @@ -12,23 +12,20 @@ SRC_URI="mirror://gentoo/${P}.tar.bz2" LICENSE="public-domain" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" PATCHES=( "${FILESDIR}"/${P}-makefile.patch "${FILESDIR}"/${P}-implicit.patch ) -src_prepare() { - default +src_configure() { tc-export CC } src_install() { default - cat > 22rnaview <<- EOF || die - RNAVIEW="${EPREFIX}/usr/share/${PN}" + newenvd - 22rnaview <<- EOF + RNAVIEW="${EPREFIX}/usr/share/rnaview" EOF - doenvd 22rnaview } diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest index 304c7aff815b..b05e783d9260 100644 --- a/sci-biology/t-coffee/Manifest +++ b/sci-biology/t-coffee/Manifest @@ -1,7 +1,8 @@ AUX t-coffee-11.00-cxx11.patch 988 BLAKE2B 03caf7bf7a10b22f8dc7e98f672564d4346123f04f8505f4fca040c10cb36031b8891dbe3f661b18f61520ebf48e2c8cc2a53d11b21c44d7d6c06728950e3eba SHA512 d97320c97467b64399ffe5917cbae4e7bac37c57f66eedbaad889f5db60b1da0d57bb4ced716dd97e907f4569789183175e531b10e7577560e18050584dd1598 AUX t-coffee-11.00-gcc7.patch 864 BLAKE2B a5f18fc86764d69cf584e976e88e4ce08f5299bfa4410ebff5ebf97dd29e8d4995076d921517d05138dbc37525d2e5f370194c0f6962cd4e2ff43bdee7c3f7c1 SHA512 d96c61f5efb1e89750a2fbb2369fdb6d831ad7c093eb2b4237af1ff21528990578399ecc1bb0f1668086084427902922003407eb1bb19f43fa25c0bcc01789a6 +AUX t-coffee-11.00-makefile.patch 535 BLAKE2B 676bec20031cad8076f31593c106df55eb910c9eb403f680da6eedce3699ce4dddb27a61f9c7e6a80a1136a097eeece3eefc2108216e3af8dd5e722c4f0baffd SHA512 2973276751dc12b7141197861db577b3eedfff01409ebf384cb2001fe53efeb87cb2c5092ef11041dfd5de9d9b12bb4b6c7b0fa5309e54d2e3e7a13274d0d412 AUX t-coffee-11.00-mayhem.patch 1230 BLAKE2B cd54632fb5760f9d76d9e72d69c2d893e0812277c6de7414546a699cf8d98b497273f9ce3f61407181d6c7f0ea0d7720b1de10c02304b92a7d76db3e2732b023 SHA512 b2c232f3e517c9c944c3d13a96b8383f8875e2e968ed16df25e37c6bfeee106cf82f9107187081753fbcaba6e27713fe5f4ca51d2f859ea7e8744f3b2b41f035 AUX t-coffee-11.00-set_proper_dir_permissions.patch 1203 BLAKE2B 220f1932cfab4f3d39cfcf3191754c2a2705c75c9cce8f11d04fb3fe8e3c3e60a10251b01c2109faad2fda4a5ce57ee5e5e598a0ec841c3bb0fa19d0e8e4d636 SHA512 fb19aae00ccc0824bcb757d32ee921159e9ece9c0336b3d663e0140ccfca77bf3fcce0eeb304517e41dc1dd4c9469c345c0c35fe8e7fdf120c6fddba4a4e1524 DIST T-COFFEE_distribution_Version_11.00.4466924.tar.gz 3502302 BLAKE2B 0d8087eb219ff72e6f478a779ccdb51e7aee861236c522dec5391e854b0b0bf6eab324009686237e6d334d2e13e17700f6692333060a2ed55711380ef2ab2cdb SHA512 c6c1a7b768156f8457dc4c53a77b14ce0b85e591d60762faf6e6f6f3b60dab75e99449d55b42ef3af1c90e244f735e19abb72d0ce871bb9fbfbb8d1641531293 -EBUILD t-coffee-11.00-r2.ebuild 1163 BLAKE2B 7b7dd0de076fa4bb9ac5b59d55df39a118b19f333851beccceeb511f3a780f5bfc2128b29cabd0304320810ea373ed15971eb061604da87d8aeae427876d9167 SHA512 7701957be90259bc4cac73bd3a280d5181432a1d6d30c4223fa4b1c6e497b50ec60b605a5a609068d9139bc3bf3183cf1d1860ece76542952dd3a289996d2b87 +EBUILD t-coffee-11.00-r3.ebuild 1045 BLAKE2B 3d546cc0e5981945c34eefe22d0be93e5ff5ad4bbf06ee742271a7648a8a03310158f286f7b334c30546bfa24b1bd2cb1857f1c6a563be2b4a16c6996194faa5 SHA512 9dba70d4c88ea4490235101ae852b036e2ab5e095e3dfe49efb0be91382fb9b90b5920c55889eb466db35b492f24f4cbde5361478c835c47fa5fc17006304408 MISC metadata.xml 763 BLAKE2B d7fd6d3ee9aba1f0b2bebf30b80682da45e3032ebf4edec325ecf372be119a046c32ee2780e646b4fe7aa83ec5930f74e33361b18be2efe794bdb273b7e3df0d SHA512 20b588201c48e90cac001b26dbb780eb70204f876a603f43cef5a7ff75c0f1431de5982dd5c1be8047a00fbd9edee9d433d808c2c6c193cd2a9fe4d5c64e8459 diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch new file mode 100644 index 000000000000..b7a6d9e17a5e --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-makefile.patch @@ -0,0 +1,19 @@ +--- a/t_coffee_source/makefile ++++ b/t_coffee_source/makefile +@@ -1,14 +1,12 @@ +-CC=g++ +-CFLAGS=-O3 -Wno-write-strings + SOURCES := $(shell find . -type f -name *.c) + OBJECTS := $(SOURCES:.c=.o) + DEPS := $(OBJECTS:.o=.deps) + + t_coffee: $(OBJECTS) +- @echo " Linking..."; $(CC) $^ -o t_coffee -lm ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o t_coffee -lm $(LIBS) + + %.o: %.c +- @echo " CC $<"; $(CC) $(CFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $< ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -I. -MD -MF $(@:.o=.deps) -c -o $@ $< + + -include $(DEPS) + diff --git a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild index df1859afb208..0064cc319f47 100644 --- a/sci-biology/t-coffee/t-coffee-11.00-r2.ebuild +++ b/sci-biology/t-coffee/t-coffee-11.00-r3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 -inherit toolchain-funcs +inherit flag-o-matic toolchain-funcs MY_HASH="4466924" MY_PV="${PV}.${MY_HASH}" @@ -12,6 +12,7 @@ MY_P="${PN^^}_distribution_Version_${MY_PV}" DESCRIPTION="A multiple sequence alignment package" HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html" SRC_URI="http://www.tcoffee.org/Packages/Beta/Latest/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" LICENSE="GPL-2" SLOT="0" @@ -20,35 +21,27 @@ KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" RDEPEND=" sci-biology/clustalw sci-chemistry/tm-align" -DEPEND="" -S="${WORKDIR}/${MY_P}" PATCHES=( "${FILESDIR}"/${P}-mayhem.patch "${FILESDIR}"/${P}-set_proper_dir_permissions.patch "${FILESDIR}"/${P}-cxx11.patch "${FILESDIR}"/${P}-gcc7.patch + "${FILESDIR}"/${P}-makefile.patch ) -src_prepare() { - default - sed \ - -e '/@/s:.*;:\t:g' \ - -e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \ - -i t_coffee_source/makefile || die +src_configure() { + tc-export CXX + append-cxxflags -Wno-write-strings -Wno-unused-result } src_compile() { - emake \ - V=1 \ - CC="$(tc-getCXX)" \ - CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \ - -C t_coffee_source t_coffee + emake -C t_coffee_source t_coffee } src_install() { dobin t_coffee_source/t_coffee - insinto /usr/share/${PN} + insinto /usr/share/t-coffee doins -r example } diff --git a/sci-biology/transfac/Manifest b/sci-biology/transfac/Manifest index c4eeebdb8540..7f05368bd6ca 100644 --- a/sci-biology/transfac/Manifest +++ b/sci-biology/transfac/Manifest @@ -1,3 +1,3 @@ DIST transfac32.tar.Z 3346266 BLAKE2B 3bd6cfacd7e4ea75946dce5e77bae84a7d199daa84750fe21cd3c393fa66cdf09518a4043ac15f2fbe7bc19f001482e14b65743f1a89aec34bcb28409277370e SHA512 d7004f90e57fa2b8839714e50b9ce1f67357db404adc1a5caddd1e9b86c8e3e9f4e85bbda15c4d6afed85da82ae8615f63260f9a3df9cfd79897d38896893b9f -EBUILD transfac-3.2-r1.ebuild 999 BLAKE2B 58cbaa6a935993519549d6dfe768fa5f5a5a8eaf70ce0d42e03d3dcc72a25067a81f8b695a0a001f8c698f7132cda44a1761a975a081409a6edd8f8feae986b1 SHA512 7b3680b0fa6887ea1214f7f90e5bd979f8111f995e037fd0eb7ec8d129117bb5721c2aa185301ad0b57c2f83d2abf4bdc2d478be726d54ddd0d09ab8c969dc80 +EBUILD transfac-3.2-r2.ebuild 1002 BLAKE2B 1fbb9b280ffe7afdf5809a312ba1ea8944b2ca16a57d3c3a74593c41e0ef3e8f826e139dd3a40c684634f56f2eff2569dcfca52a6e7b5f00f42d20c56435e59a SHA512 131b794d586366ca5441e364087a413d72cb8c66d550bf13cca522fa2c1851a47064064c9d22870b627931ec46778fb1a03309fe39843b9b3d518507ed423c75 MISC metadata.xml 697 BLAKE2B cfcb8ec7dfc62e50cbec8a92bb511e39577203ca2743a6e9b845a257553428cfb0ef4b5793309c59dae581e0faa58f077a19aee9c8036dc16dccaf01dddeb32a SHA512 0cf54f59885bff6391873c4db379f321c08e0357e24335fe18debcb52c6126ba44feb03fb3a1edd7731460395601b3eaa4e9a79f7faca2f018892831672c0587 diff --git a/sci-biology/transfac/transfac-3.2-r1.ebuild b/sci-biology/transfac/transfac-3.2-r2.ebuild index 91b16f4b4fe4..2fce474da2ad 100644 --- a/sci-biology/transfac/transfac-3.2-r1.ebuild +++ b/sci-biology/transfac/transfac-3.2-r2.ebuild @@ -1,11 +1,12 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 DESCRIPTION="A database of eucaryotic transcription factors" HOMEPAGE="http://www.gene-regulation.com/pub/databases.html" SRC_URI="ftp://ftp.ebi.ac.uk/pub/databases/${PN}/${PN}32.tar.Z" +S="${WORKDIR}" LICENSE="public-domain" SLOT="3" @@ -14,10 +15,8 @@ SLOT="3" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="emboss minimal" -DEPEND="emboss? ( sci-biology/emboss )" -RDEPEND="${DEPEND}" - -S=${WORKDIR} +BDEPEND="emboss? ( sci-biology/emboss )" +RDEPEND="${BDEPEND}" src_compile() { if use emboss; then @@ -32,7 +31,7 @@ src_install() { newdoc readme.txt README if ! use minimal; then - insinto /usr/share/${PN}-${SLOT} + insinto /usr/share/transfac-${SLOT} doins *.dat fi diff --git a/sci-biology/trf/Manifest b/sci-biology/trf/Manifest index 431866ac4fd4..f8a92cfd3364 100644 --- a/sci-biology/trf/Manifest +++ b/sci-biology/trf/Manifest @@ -1,3 +1,3 @@ DIST trf404.linux 89853 BLAKE2B 36abf95c88a5b8793e875a276f1494af4df48ff3b3f095e07683589d84eaadfb54099c1764dcd437158c356dcd9d55dd274e7e41515ef098ee2a929493cc0d83 SHA512 c1aa05e394d47ea153df3082258f9a089aa59976963e9ac5d5816ef9dcd95c47e2e46861d1b2aae52b5ea9950a823a2449dd0d8426b04f2b738f5552c319393e -EBUILD trf-4.04-r1.ebuild 623 BLAKE2B 10cf833dad7e73bb63485452cc6cf0f16517dc859eb37da8a366e5c877bf71469193527dccfc43d6fc090916b09e62eac04323a26a6bb57e6d611c2e201fc8e7 SHA512 a879d5171ebbb5fff9157d05c7f8413044758be60a5d4d790d779f65d3c8b16ac72a9a942f12f651576bd5082e1cb1171471f9886e5eba459903b473a7b07af1 +EBUILD trf-4.04-r2.ebuild 613 BLAKE2B 4c9dc62a46b3278d29a154028d74c070f66e98534f6cbbc207b95e277fefcac5f59ba170abfbc89cbe616764f3a6b9386ec9a54481b75dbd217ab57642f927c6 SHA512 98ac0a58b6c24dc45b62310cd4d5bfd06f1c25cfae2855a0853c801211efec4d44a2b9cdf5b9236355dfbb956dbd0fa6c3a158f4c21910b82a49e900aa56a124 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de diff --git a/sci-biology/trf/trf-4.04-r1.ebuild b/sci-biology/trf/trf-4.04-r2.ebuild index 3b906fb31aaf..c534b74988bd 100644 --- a/sci-biology/trf/trf-4.04-r1.ebuild +++ b/sci-biology/trf/trf-4.04-r2.ebuild @@ -1,29 +1,28 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 MY_P="${PN}404" DESCRIPTION="Tandem Repeats Finder" HOMEPAGE="http://tandem.bu.edu/trf/trf.html" SRC_URI="http://tandem.bu.edu/trf/downloads/${MY_P}.linux" +S="${WORKDIR}" LICENSE="trf" # http://tandem.bu.edu/trf/trf.license.html SLOT="0" KEYWORDS="amd64 x86" RESTRICT="mirror bindist" -S=${WORKDIR} - -QA_PREBUILT="opt/${PN}/.*" +QA_PREBUILT="opt/trf/.*" src_unpack() { - cp "${DISTDIR}/${MY_P}.linux" "${S}/${MY_P}.linux.exe" || die + cp "${DISTDIR}"/${MY_P}.linux "${S}"/${MY_P}.linux.exe || die } src_install() { - exeinto /opt/${PN} + exeinto /opt/trf doexe trf404.linux.exe - dosym /opt/${PN}/${MY_P}.linux.exe /opt/bin/trf + dosym ../trf/${MY_P}.linux.exe /opt/bin/trf } diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest index 5f9151c72b1e..3fb1acc44f13 100644 --- a/sci-biology/trnascan-se/Manifest +++ b/sci-biology/trnascan-se/Manifest @@ -1,4 +1,5 @@ -AUX trnascan-se-1.31-ldflags.patch 973 BLAKE2B 1aeae4e2e5a513caea6eced215e891a42e3ed650d02cf68f3874e20bc5b6b833cb4041ee3cc8fb4fba774143e247908e68f53d4a2b65bd77c32f857366be9621 SHA512 ff677ce9ac3ed9299f6a3bf977642e2a6c300a1b801436bb5d3787968cfe28357a0ec23d0438f0b15c06324cd7e1bbbda590c8fb5574577a3f653779316931df +AUX trnascan-se-1.31-makefile.patch 5126 BLAKE2B 792cbd1226966c9f518672a730e8476f65cb0b4056b52e5416d43a6a1b5264666ae22fce88e4d7bfcf48d537ac4ec4d26ba8e737e60d31fbbc867de98d4315f2 SHA512 543ea32ed47279f5930485f5406d3b2912cba1df99681b2eb7e5d6df28579f48a07c9aba9ffe46819990543f5dbe69de6b086b8f86ed67de76e174dcc80563c4 +AUX trnascan-se-1.31-portable-perl-shebangs.patch 634 BLAKE2B 8089d6320bce63e560791c62a9baecea1dd1f8e54c618360072463507c73087a6412742669624db0539ec4b1cf2a4db0b6edb9b064eaf67e8ad1c3b77643004e SHA512 a910b02e35cb9dcc94f6f9ec3c44936e0f7faa1ec81d9bf6f397cb516b3bd20ba7cd8e334e452e94302b4254876187c36ec8f94ebb2bd8039c8fc3e1a2b5720f DIST trnascan-se-1.31.tar.gz 740960 BLAKE2B 995bfb7ad9f9d46543f15a36134aaec6c27921144c8900a323dbd6152f25e1faa587b5c817dcb8cb838dc1fde8ec7537e5fd6ca8930a4dd1aaadce41c575d651 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d -EBUILD trnascan-se-1.31.ebuild 1191 BLAKE2B 8d492f11917a53e478d1f146bd55ee57b2c1ede4b1206fc419f86fd9acc1f73c30459b159836f8b0c946161cee16ba0cf0131d2635ce67708bd70c56c682f194 SHA512 d79fa9d244d4f3ab98fff94aca074bd23cc953c0b812a270daca2e80c440fcdcfd38e92cba2eea6ccd2ad9873c8fb898f46b9f4356c638d01fa0f2b21e23c55b +EBUILD trnascan-se-1.31-r2.ebuild 925 BLAKE2B c3903dc93120d03a61d02efaae2ba9fff10cc0e804ea70f03b9ac86b9935b58721a319c0e51a452190444b91942192415d8c2406883aaca6fa07881d628b1f55 SHA512 fe165c6732fe579e739fdff25738ea8996974ef41cf927452aa51a91cfba1dc7485b6172adc81bb583fef442d44f5414c4ac2608b214dfc1c315c97799eb140f MISC metadata.xml 602 BLAKE2B 8f0a2a924d5e25b00f3850b903de327eff6811931047cd282386837db9d7905fa0a384b36821aea7c869d5da38969a6efbb43c3f1fd1d82dba50919bdda64172 SHA512 ace918d99f937c74013b854b34eaaeb0404dab2e5e9c21bcf876b471a617db7008cd1a7062a83dd00ba3e69027391a0b81915be8560a10d3ff9062c21862c0c2 diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch deleted file mode 100644 index f28b1e8f6bb0..000000000000 --- a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git a/Makefile b/Makefile -index 53e5c5b..a2d3feb 100644 ---- a/Makefile -+++ b/Makefile -@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o - all: $(PROGS) tRNAscan-SE setpaths - - covels-SE: $(OBJ) scan_main.o -- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) - - coves-SE: $(OBJ) score_main.o -- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) - - eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o -- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -o eufindtRNA eufind_main.o \ - pavesi.o $(SQUIDOBJ) $(LIBS) - - trnascan-1.4: trnascan.o -- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c -+ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c - - tRNAscan-SE: - $(PERLDIR)/$(PERLBIN) checkversion.pl diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch new file mode 100644 index 000000000000..acf3c2a6d862 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-makefile.patch @@ -0,0 +1,140 @@ +--- a/Makefile ++++ b/Makefile +@@ -20,9 +20,9 @@ + PERLBIN = perl + + ## where you want things installed +-BINDIR = $(HOME)/bin +-LIBDIR = $(HOME)/lib/tRNAscan-SE +-MANDIR = $(HOME)/man ++BINDIR = $(EPREFIX)/usr/bin ++LIBDIR = $(EPREFIX)/usr/share/trnascan-se ++MANDIR = $(EPREFIX)/usr/share/man + + ## NOTE !! If you later manually move the location of + ## binaries or data files in the BINDIR or LIBDIR directories, +@@ -33,10 +33,8 @@ + TEMPDIR = /tmp + + ## your compiler +-CC = gcc # GNU cc (if available) otherwise use vendor's cc + + ## any special compiler flags you want +-CFLAGS = -O # ok for most machines (remove -O for DEC OSF/1 cc compiler) + + ## machine specific definitions + # You shouldn't need any. The specific #define's in squid are historical. +@@ -58,7 +56,7 @@ + ####### + + SHELL = /bin/sh +-LIBS = -lm ++LIBS += -lm + .SUFFIXES : .c .o + + DOCS = README MANUAL INSTALL COPYING GNULICENSE FILES Release.history +@@ -109,20 +107,20 @@ + all: $(PROGS) tRNAscan-SE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o +- $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA eufind_main.o \ + pavesi.o $(SQUIDOBJ) $(LIBS) + +-trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++trnascan-1.4: trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c + + tRNAscan-SE: +- $(PERLDIR)/$(PERLBIN) checkversion.pl ++ $(PERLBIN) checkversion.pl + sed 's#/tmp#$(TEMPDIR)#g' tRNAscan-SE.src | \ + sed 's#bindir = ""#bindir =\"$(BINDIR)/"#g' | \ + sed 's#/usr/local/lib/tRNAscanSE#$(LIBDIR)#g' | \ +@@ -200,11 +198,11 @@ + noambig: trnascan-1.4-NA eufindtRNA-NA + + trnascan-1.4-NA: trnascan.o +- $(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c ++ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c + + eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o +- $(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c +- $(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ ++ $(CC) $(CFLAGS) $(CPPFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c ++ $(CC) $(LDFLAGS) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ + pavesi-NA.o $(SQUIDOBJ) $(LIBS) + + +@@ -220,7 +218,7 @@ + rmdir -ps $(MANDIR) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(MDEFS) -c $< + + ## programs from Sean Eddy's sequence i/o function library not + ## needed for tRNAscan-SE but included for their utility +@@ -233,16 +231,16 @@ + cp $(UTILS) $(BINDIR)/. + + reformat: $(SQUIDOBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) + + revcomp: $(SQUIDOBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) + + seqstat: $(SQUIDOBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) + + shuffle: $(SQUIDOBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) + + ## other programs in Cove package (below) not needed for + ## tRNAscan-SE, but are included for users who wish to apply +@@ -255,25 +253,25 @@ + cp $(COVE_SUITE) $(BINDIR)/. + + covea: $(OBJ) align_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) + + coveb: $(OBJ) build_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) + + covee: $(OBJ) emit_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) + + covet: $(OBJ) train_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) + + covels: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) + + coves: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) + + structcheck: $(OBJ) structcheck_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) + + + ## Maspar memory limits diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch new file mode 100644 index 000000000000..187705e8b3a0 --- /dev/null +++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-portable-perl-shebangs.patch @@ -0,0 +1,32 @@ +--- a/fasta2gsi.pl ++++ b/fasta2gsi.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Usage: fasta2gsi.perl <seqfile> + # Creates seqfile.gsi +--- a/instman.pl ++++ b/instman.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Sean Eddy, Wed Jul 29 15:24:43 1992 + +--- a/sstofa.pl ++++ b/sstofa.pl +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + + if ($#ARGV < 0) { +--- a/tRNAscan-SE.src ++++ b/tRNAscan-SE.src +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + # + # -------------------------------------------------------------------- + # tRNAscan-SE: a program for improved detection of transfer RNA diff --git a/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild new file mode 100644 index 000000000000..f35c31b22798 --- /dev/null +++ b/sci-biology/trnascan-se/trnascan-se-1.31-r2.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit perl-functions toolchain-funcs + +DESCRIPTION="tRNA detection in large-scale genome sequences" +HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" +SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}"/tRNAscan-SE-1.3.1/ + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-lang/perl:=" +BDEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-portable-perl-shebangs.patch +) + +src_configure() { + tc-export CC +} + +src_test() { + emake PATH="${S}:${PATH}" testrun +} + +src_install() { + dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 + + newman tRNAscan-SE.man tRNAscan-SE.man.1 + dodoc MANUAL Manual.ps README Release.history + + insinto /usr/share/trnascan-se + doins *.cm gcode.* Dsignal TPCsignal + + perl_domodule -r tRNAscanSE +} diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild deleted file mode 100644 index cd8dc152d6d2..000000000000 --- a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit perl-functions toolchain-funcs - -DESCRIPTION="tRNA detection in large-scale genome sequences" -HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/" -SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 x86" -IUSE="" - -S="${WORKDIR}"/tRNAscan-SE-1.3.1/ - -PATCHES=( - "${FILESDIR}"/${P}-ldflags.patch -) - -src_prepare() { - default - sed \ - -e "s:BINDIR = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \ - -e "s:LIBDIR = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \ - -e "s:MANDIR = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \ - -i Makefile || die - - perl_set_version -} - -src_test() { - emake PATH="${S}:${PATH}" testrun -} - -src_install() { - dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4 - - newman tRNAscan-SE.man tRNAscan-SE.man.1 - - dodoc MANUAL README Release.history - - insinto /usr/share/${PN}/ - doins *.cm gcode.* Dsignal TPCsignal - - dodoc Manual.ps - - insinto ${VENDOR_LIB} - doins -r tRNAscanSE -} diff --git a/sci-biology/vcftools/Manifest b/sci-biology/vcftools/Manifest index 6495838a7c8d..f19cddac8f1e 100644 --- a/sci-biology/vcftools/Manifest +++ b/sci-biology/vcftools/Manifest @@ -1,6 +1,3 @@ -AUX vcftools-0.1.14-buildsystem.patch 1159 BLAKE2B 9eaa626c82b4d23e75f2d31ce31c6161996eb743efbdcb81ad4c3ba306b76a710c4b22670d68178da1b7d2e048d02aea44132f3009d5792dcf248368b53c3482 SHA512 838cade29bbeeee090ea52f546c37b68eee868f3329ceccb710da0dbcf0f14e1b18dcc7b05ceefdbf72d400f450374389649f56fc6981bd86f6e176469b054ea -DIST vcftools-0.1.14.tar.gz 342369 BLAKE2B 14be867c0be41767e2c97c8be212f3cff495c1cb6699294fb8a26ac491901599cd1e400cb80c6d609dce36584ee5defdb3b3652657bd127e0c67c5b29a842cc5 SHA512 863a16b3b20d392deba7f04310af95f1ab21be537273692aa104e22d737af2eb1bc54a768af954f06188e0500e4f7a032d1189886eb3a439b108cb8189b14eb7 DIST vcftools-0.1.16.tar.gz 480575 BLAKE2B 5c0bf67aef8ef4705f621485df4c556f6bace190311c308f0364f3e274cf4818f56f2186905fdfb7459dc4be9664a8b1ff631e2cecd03abd7aa82dcfc7e5aa64 SHA512 c4dd5ceb3ad0512e839154d8a05ef3e7a03cbe52c3099df48775b35460fce7ef10102819c2d1cefa33b98ad09e7bd1608e871978860ec9c0b0c2e781892b22e6 -EBUILD vcftools-0.1.14.ebuild 867 BLAKE2B f25ccc182927cd888c548f4eeb120c526716fc759dc7b8081baf76b9f4cd3a404a2828168577000ff816b02aa8d3e6fec52d883fdc2e6f2ec40f1a9712d024d1 SHA512 260555d8964cf329fe3710547b6ddb5600674525703d0b802d18c2a41d02271ff77c56c4d49bf9fb67966bce76a3d6addc88c5a1e86859425bf0574beecc2c34 EBUILD vcftools-0.1.16.ebuild 818 BLAKE2B 7809d2b55b8e93fea1f4e32a302018e9d2f4b8f289f413be6ea0b34471e639e6f5857f9aeeda1de790abbf773881b63a8c8a31c4f40ba0d83a02363f6a534600 SHA512 e56916000bdcae78e7fd312f078020f2c1e8f007df842d2a0396f15b546dcd945e457fc1771495c7cc242a7c7e938302a9e25c56c884b7722889aa03b54ee550 MISC metadata.xml 409 BLAKE2B 8b6096c95135edaa86244af0fa6c7da5eb131092dc6ff25108723c64183275727c49d9c1fd0f2c4805a3daebc780833e0d03127e58bb5cde3c6ee999b2fca68e SHA512 276a72290a191a7661f130b941ce81dd017242fad97f67efbbf84d9586d097bf5131b12f6fb4bf5f8dc18ee0babcd89d836692b2d912fea5bf90fed18e16885f diff --git a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch b/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch deleted file mode 100644 index 126a709385db..000000000000 --- a/sci-biology/vcftools/files/vcftools-0.1.14-buildsystem.patch +++ /dev/null @@ -1,50 +0,0 @@ -* Add prefix in Makefiles, not the configure script -* Use AC_SEARCH_LIBS instead of AC_CHECK_LIB, - as it is more flexible and helps us with LAPACK -* Use correct ZLIB_CFLAGS instead of non-existent ZLIB_CPPFLAGS - ---- a/configure.ac -+++ b/configure.ac -@@ -34,7 +34,7 @@ - [--with-pmdir=DIR], - [install Perl modules in DIR]), - [PMDIR=${withval}], -- [PMDIR='${prefix}'/"$pmdir_relative_path"]) -+ [PMDIR="$pmdir_relative_path"]) - - AC_SUBST([PMDIR]) - -@@ -73,9 +73,9 @@ - [pca=${enableval}], - [pca=no]) - --if test "x${pca}" = "xyes" ; then -- AC_CHECK_LIB(lapack, dgeev_) --fi -+AS_IF([test "x${pca}" = "xyes"],[ -+ AC_SEARCH_LIBS([dgeev_], [lapack]) -+]) - - # Generate output. - AC_CONFIG_FILES([Makefile ---- a/src/cpp/Makefile.am -+++ b/src/cpp/Makefile.am -@@ -1,6 +1,6 @@ - bin_PROGRAMS = vcftools - --vcftools_CPPFLAGS = $(ZLIB_CPPFLAGS) -+vcftools_CPPFLAGS = $(ZLIB_CFLAGS) - vcftools_LDADD = $(ZLIB_LIBS) - - vcftools_SOURCES = \ ---- a/src/perl/Makefile.am -+++ b/src/perl/Makefile.am -@@ -24,7 +24,7 @@ - vcf-tstv \ - vcf-validator - --pmdir = $(PMDIR) -+pmdir = $(exec_prefix)/$(PMDIR) - - dist_pm_DATA = \ - FaSlice.pm \ diff --git a/sci-biology/vcftools/vcftools-0.1.14.ebuild b/sci-biology/vcftools/vcftools-0.1.14.ebuild deleted file mode 100644 index 7b386453ae25..000000000000 --- a/sci-biology/vcftools/vcftools-0.1.14.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools flag-o-matic perl-functions toolchain-funcs - -DESCRIPTION="Tools for working with VCF (Variant Call Format) files" -HOMEPAGE="http://vcftools.sourceforge.net/" -SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="lapack" - -RDEPEND="sys-libs/zlib - dev-lang/perl:= - lapack? ( virtual/lapack )" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}/${PN}-0.1.14-buildsystem.patch" ) - -src_prepare() { - default - eautoreconf -} - -src_configure() { - perl_set_version - - append-flags $($(tc-getPKG_CONFIG) --cflags lapack) - append-libs $($(tc-getPKG_CONFIG) --libs lapack) - - econf \ - $(use_enable lapack pca) \ - --with-pmdir="${VENDOR_LIB#${EPREFIX}/usr}" -} diff --git a/sci-biology/yass/Manifest b/sci-biology/yass/Manifest index 323e43bd2db0..67d63f2524db 100644 --- a/sci-biology/yass/Manifest +++ b/sci-biology/yass/Manifest @@ -1,4 +1,4 @@ AUX 1.14-as-needed.patch 6046 BLAKE2B d2d7d5f71a4db2780d1485fc9074caac6916428e3b3e28fc9553e0be29b0a58182b2af325b577934b94d831b81d1731226000cad4bdbdc297c6cd3dbf627b94e SHA512 4b9227bb16556084121336b01d6d02257ccf7e35765db53b4a6ba2b0a41946a6b600a9dd05156b763b4b37f18d30d2c9111eeca79a1656f757199ba1cda5b3dd DIST yass-1.14.tar.gz 235530 BLAKE2B 55b7e8e7834f3a76a09e5e509884b391053fe97a7d5aeb3132009c8050014fb6dae92f7b246c85646a872fd5bde7a4b8c3bd0124fb38c7d0f648b85c63d99ad7 SHA512 fdfac6f391848d0bd35829a966721a242697b0832803092bd7ea2116149332642ddf3bf5f095fe707f6edbbb9454efe068852fe6d5cdfe937445d9d32a521fa2 -EBUILD yass-1.14-r2.ebuild 663 BLAKE2B 04803df835cd4cfa8ccf32e82c9c639d61f5e7dc8ac03d508ce4246eaa7db5dac055ecae954fe42dc849dead9c784777d3cb1f1d2f19cc9272dacc494729e823 SHA512 ac373f6d89d678ca71d0e84d76965cc2d3eed9ccf51d33c799613bcdb588f5adfc7ca588b823a92ea6bb12c39bb91fca6cdd685af3a8ec943a43192b633246cc +EBUILD yass-1.14-r3.ebuild 660 BLAKE2B 33b1797f007496be23a552c8c0884379ea4cd7877e81533a982fe33e0c900787f7824bd21c9720ffc2538b3cb8f28921b64d7d3988a176d29cc914d8fa0578b1 SHA512 92c0ca3b5f81598fd4735c0e2251668d1fda7f0a202b0ab685846737db644d78c638b5c6a4ef012b2ea28321b9a39f544f92ddf7939cb44e371e60b44f3cc4e1 MISC metadata.xml 440 BLAKE2B 8dbb90197bbabba0844a01d338185dceecf8dc7925cbbe89f14a394df0e2f328aa600f99576a4fe08e71735d9c190e9278d3f71be3cbbb624d3e9e72e27b668c SHA512 d0912b9e3b46bb9315c830fb998173db9db6ce4ded0f2806c3af78749a4e1477eccc8a4200f71bd6de4eeb43c9dd462d44632eeafd58cca7a811751257d4df14 diff --git a/sci-biology/yass/yass-1.14-r2.ebuild b/sci-biology/yass/yass-1.14-r3.ebuild index cdbe54f0bef6..3913c44f4580 100644 --- a/sci-biology/yass/yass-1.14-r2.ebuild +++ b/sci-biology/yass/yass-1.14-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools @@ -11,8 +11,8 @@ SRC_URI="http://bioinfo.lifl.fr/yass/files/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -IUSE="dmalloc lowmem threads" KEYWORDS="~amd64 ~x86" +IUSE="dmalloc lowmem threads" DEPEND="dmalloc? ( dev-libs/dmalloc )" RDEPEND="${DEPEND}" |