gentoo resync : 16.06.2019

6 files changed, 4 insertions, 261 deletions

diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index 2f147b790e8a..b6265b919a47 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -1,11 +1,6 @@
 AUX hdf5-1.8.13-no-messing-ldpath.patch 1141 BLAKE2B d7d186e4c00acb9fd3d44beb1d8c3c4da0c373f88b3fdf21e1f89b169b747d49572239385228687cfc10380bdceb9ca6d1ac0d5f5154cb7a328f8a2d509fb28d SHA512 e43021ceb83909ab06ba378363c192aa0f1b34cc7c2b121f5000e215516dbdea1b825a53ac4023073bf4870a5c3452c22f5535391d95af45ad63a309e1ffa5a4
-AUX hdf5-1.8.15-implicits.patch 1050 BLAKE2B 9a019e69e9e02c487c5cf460380aaff08c672354f5d3c623c36daacf2e107a5b9f6fcfc1c380eed6adb62d2e9cdffbe8cbec13928e35ec8e5742e1d26114bcf3 SHA512 e3cfc3e3c01b8eafe426a3ebb87a4880d326b88d15897ce6d50b47456d69c0ef0888ad7f839928eb1fd283eb617f63869c2051d46669986bb5ed30afa6181088
 AUX hdf5-1.8.9-mpicxx.patch 494 BLAKE2B 148d87af064e2ba28c918c8db39ece0782a179803e4c38c5cd5eaba81a673bb8aa3699a48e80a7ae2d4579ac0261cc21d5509e46661ada9a69f444a58eb45ecd SHA512 8b4c39e40591860652547ea8ff205230da7d67488233e911cbcb3416eab561f2529c65bc5e7c9c812bf4298812346f47f9209e5f69f7e8f66ad587306a5b477b
 AUX hdf5-1.8.9-static_libgfortran.patch 429 BLAKE2B 9e1c544a453c09b3498a7d9d3e8090c928571776934c4dd6b426cbdb2783ed8f47185d6ee0c73ede6b4f14e27459ef5e1412112e9d897daa2dc57f1ad5fb0b24 SHA512 af97c54469a90bf3b0e8ec1218d4ca95822ac0cbc7120114979fc467fe3114743c74f4d4e16f0c10b1cd82d40880ef482f6fd34e1effc7c621b981ad466204f9
-DIST hdf5-1.10.1.tar.bz2 11769617 BLAKE2B 66ad762aed90cea9e58a9735bf0e189d78befc40cac0e566586e967f2b3ba6f5bf8a6bfd12a2f4062f8b20900c16d467c34134c17dedfd8f345cb96bd853a2fe SHA512 266b0e2f28c5fd540099a4955244ddb8c03aca3ad40d626358643f033a6ae5e9266a1d6c1d60925c7d42d24d28a1549d3305fe8ddb42cec2379af7231b93e554
 DIST hdf5-1.10.5.tar.bz2 8706317 BLAKE2B ac326be8fe4ccc4b0153f15bc7d65aa8f1adc2ae279d3980f57ed46722b754d3f36ecf1d6273c75e80ed1afd4bbf10c6b1c5d9408e1f83a4b2e397e7902a7d3c SHA512 769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4
-DIST hdf5-1.8.18.tar.bz2 10081294 BLAKE2B cf0d0c8a41576bcf816460eaabcfab29cfffba240721a64fe584c42fbb322470f29fb93c8513f7bbdedeeb392c2fe64cd3261b47b47de5b01828dae0b1929cd3 SHA512 01f6d14bdd3be2ced9c63cc9e1820cd7ea11db649ff9f3a3055c18c4b0fffe777fd23baad536e3bce31c4d76fe17db64a3972762e1bb4d232927c1ca140e72b2
-EBUILD hdf5-1.10.1.ebuild 2808 BLAKE2B 79eb6b5c889d717f6a8391ce334baa0878971256460be4d6bde00726078f4a944c2e4843867c767fa25cf346cca9f7f2cf58f0c918d17bd4cf050a11ba17c396 SHA512 29b39083a7fc5400490c81a5c6ad9bc76485c5ac67f983a45524010b1d72e99cca6e218b1dd052c000bfd7bd7397ec770e6d62ca0d5e313ac3c3c2253387e758
-EBUILD hdf5-1.10.5.ebuild 2653 BLAKE2B 10b4f2bb9ae764ff7e5dc5f13aac456a3a216f47a10f03adf3a6316df1be83d5bb5f127ecba36a7a5bff3306d8084873dd0356cf7b554db22d946a5317db8e82 SHA512 c0ab47c0ba474727105abfa6714dd048771ab69a5a23eed711019049441b940b441013f01e8f1ade3605a706501de41c71627b951746fd46df96dbdf1918849d
-EBUILD hdf5-1.8.18.ebuild 3366 BLAKE2B 5ea79bd8cfd5664c92de2cfb62c826500b1847290684a9ad3a1bda7ac2aa33d2d428b59ce9f7f1bfb17637472742804ddb98f9018386ebfbdff33c2023d942e4 SHA512 54e66dc074fd9b0fe9ad23f23234fc20e79c6ed9e9759d6964cb8e4d3e79321c08b4539a814f2fae2c935bb9358549115a884b8f55719fb77744fd26ad680867
-MISC metadata.xml 822 BLAKE2B ab9bf739575f9758fa521e9640438b345379373884ffd25a021a15589b7016d519f01d4d4d39dc5c8efbd271fbeb89d584b3d627e2b0d90cecf55d36747447cf SHA512 5e6cb47fcf2e704887a375f527b447075a36a51225cc2bdf10892bff5cce548599dd6f04a36ae2e31f691bd635dd6cc5d1455729e05923a8992d95fb27716164
+EBUILD hdf5-1.10.5.ebuild 2652 BLAKE2B d5246ea650a0070769990375325cadd8a57e9815a446b99f27343b7a2c21f23a3cf4579ce9f0c179327cf32e7f68477ea4e0106dd365151e9a18aac10d103ed7 SHA512 fba29598ee82a68adcbfbc8f78849923dbee1cb5f079a670833e7a5c16467396853c7e28761c59bf28783b02377521980c4e61cf79ca698cc37a2303f57da565
+MISC metadata.xml 670 BLAKE2B 6ec39c2c545ea8130677894921b6914d4503199a40f5498b81f1520312a451585276a2192ecb388323574bf0a17acfe798d090bf499f8ef2b6bb7ff831c662ba SHA512 2cbdee7294537d76bee9c72c77c36d0d2aab176dd4588a7b99d16bc3a421b52770bf6d93943c13fb32674f5deb7bbebb94b9e18875b3e473395a9176277fd56a
diff --git a/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch
deleted file mode 100644
index 72e096170975..000000000000
--- a/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- a/hl/src/H5LTanalyze.c
-+++ b/hl/src/H5LTanalyze.c
-@@ -40,6 +40,7 @@
- #include <string.h>
- #include <errno.h>
- #include <stdlib.h>
-+#include <unistd.h>
- 
- /* end standard C headers. */
- 
---- a/hl/src/H5LTanalyze.l
-+++ b/hl/src/H5LTanalyze.l
-@@ -16,6 +16,7 @@
- %{
- #include <stdlib.h>
- #include <string.h>
-+#include <unistd.h>
- #include <hdf5.h>
- #include "H5LTparse.h"
- 
---- a/test/cache_common.h
-+++ b/test/cache_common.h
-@@ -702,5 +702,8 @@ void validate_mdc_config(hid_t file_id,
-                          hbool_t compare_init,
-                          int test_num);
- 
-+hbool_t resize_configs_are_equal(const H5C_auto_size_ctl_t *a,
-+                                 const H5C_auto_size_ctl_t *b,
-+                                 hbool_t compare_init);
- #endif /* _CACHE_COMMON_H */
- 
---- a/testpar/t_span_tree.c
-+++ b/testpar/t_span_tree.c
-@@ -37,6 +37,9 @@
- #include "hdf5.h"
- #include "H5private.h"
- #include "testphdf5.h"
-+#define H5S_PACKAGE
-+#define H5S_TESTING
-+#include "H5Spkg.h"
- 
- 
- static void coll_write_test(int chunk_factor);
diff --git a/sci-libs/hdf5/hdf5-1.10.1.ebuild b/sci-libs/hdf5/hdf5-1.10.1.ebuild
deleted file mode 100644
index 6cf18a83be0f..000000000000
--- a/sci-libs/hdf5/hdf5-1.10.1.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-AUTOTOOLS_AUTORECONF=1
-
-inherit autotools-utils eutils fortran-2 flag-o-matic toolchain-funcs multilib versionator prefix
-
-MY_P=${PN}-${PV/_p/-patch}
-MAJOR_P=${PN}-$(get_version_component_range 1-2 ${PV})
-
-DESCRIPTION="General purpose library and file format for storing scientific data"
-HOMEPAGE="http://www.hdfgroup.org/HDF5/"
-SRC_URI="http://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2"
-
-LICENSE="NCSA-HDF"
-SLOT="0/${PV%%_p*}"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux"
-IUSE="cxx debug examples fortran +hl mpi static-libs szip threads zlib"
-
-REQUIRED_USE="
-	cxx? ( !mpi ) mpi? ( !cxx )
-	threads? ( !cxx !mpi !fortran !hl )"
-
-RDEPEND="
-	mpi? ( virtual/mpi[romio] )
-	szip? ( virtual/szip )
-	zlib? ( sys-libs/zlib:0= )"
-
-DEPEND="${RDEPEND}
-	sys-devel/libtool:2
-	>=sys-devel/autoconf-2.69"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch
-	"${FILESDIR}"/${PN}-1.8.9-mpicxx.patch
-	"${FILESDIR}"/${PN}-1.8.13-no-messing-ldpath.patch
-)
-
-pkg_setup() {
-	tc-export CXX CC AR # workaround for bug 285148
-	use fortran && fortran-2_pkg_setup
-
-	if use mpi; then
-		if has_version 'sci-libs/hdf5[-mpi]'; then
-			ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail."
-			ewarn "Try to uninstall the current hdf5 prior to enabling mpi support."
-		fi
-		export CC=mpicc
-		use fortran && export FC=mpif90
-	elif has_version 'sci-libs/hdf5[mpi]'; then
-		ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail."
-		ewarn "Try to uninstall the current hdf5 prior to disabling mpi support."
-	fi
-}
-
-src_prepare() {
-	# respect gentoo examples directory
-	sed \
-		-e "s:hdf5_examples:doc/${PF}/examples:g" \
-		-i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die
-	sed \
-		-e '/docdir/d' \
-		-i config/commence.am || die
-	if ! use examples; then
-		sed -e '/^install:/ s/install-examples//' \
-			-i Makefile.am || die #409091
-	fi
-	# enable shared libs by default for h5cc config utility
-	sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" tools/src/misc/h5cc.in || die
-	hprefixify m4/libtool.m4
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--docdir="${EPREFIX}"/usr/share/doc/${PF}
-		--enable-deprecated-symbols
-		$(use debug && echo --enable-build-mode=debug || echo --enable-build-mode=production)
-		$(use_enable debug codestack)
-		$(use_enable cxx)
-		$(use_enable fortran)
-		$(use_enable hl)
-		$(use_enable mpi parallel)
-		$(use_enable threads threadsafe)
-		$(use_with szip szlib)
-		$(use_with threads pthread)
-		$(use_with zlib)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/hdf5/hdf5-1.10.5.ebuild b/sci-libs/hdf5/hdf5-1.10.5.ebuild
index b0d3827d079e..b22b8c598250 100644
--- a/sci-libs/hdf5/hdf5-1.10.5.ebuild
+++ b/sci-libs/hdf5/hdf5-1.10.5.ebuild
@@ -16,7 +16,7 @@ SRC_URI="http://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P
 
 LICENSE="NCSA-HDF"
 SLOT="0/${PV%%_p*}"
-KEYWORDS="alpha amd64 ~arm arm64 ia64 ppc ppc64 ~sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux"
+KEYWORDS="alpha amd64 ~arm arm64 ia64 ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux"
 IUSE="cxx debug examples fortran +hl mpi static-libs szip threads zlib"
 
 REQUIRED_USE="
diff --git a/sci-libs/hdf5/hdf5-1.8.18.ebuild b/sci-libs/hdf5/hdf5-1.8.18.ebuild
deleted file mode 100644
index 4057134a614e..000000000000
--- a/sci-libs/hdf5/hdf5-1.8.18.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-AUTOTOOLS_AUTORECONF=1
-
-inherit autotools-utils eutils fortran-2 flag-o-matic toolchain-funcs multilib
-
-MY_P=${PN}-${PV/_p/-patch}
-
-DESCRIPTION="General purpose library and file format for storing scientific data"
-HOMEPAGE="http://www.hdfgroup.org/HDF5/"
-#SRC_URI="https://support.hdfgroup.org/ftp/HDF5/releases/${MY_P}/src/${MY_P}.tar.bz2"
-# TODO: return to proper SRC_URI once upstream fixes their release
-SRC_URI="https://support.hdfgroup.org/ftp/HDF5/current18/src/${MY_P}.tar.bz2"
-
-LICENSE="NCSA-HDF"
-SLOT="0/${PV%%_p*}"
-KEYWORDS="alpha amd64 ~arm ~arm64 ia64 ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux"
-IUSE="cxx debug examples fortran fortran2003 +hl mpi static-libs szip threads zlib"
-
-REQUIRED_USE="
-	threads? ( !cxx !mpi !fortran !hl )
-	fortran2003? ( fortran )"
-
-RDEPEND="
-	mpi? ( virtual/mpi[romio] )
-	szip? ( virtual/szip )
-	zlib? ( sys-libs/zlib:0= )"
-
-DEPEND="${RDEPEND}
-	sys-devel/libtool:2
-	>=sys-devel/autoconf-2.69"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch
-	"${FILESDIR}"/${PN}-1.8.9-mpicxx.patch
-	"${FILESDIR}"/${PN}-1.8.13-no-messing-ldpath.patch
-	"${FILESDIR}"/${PN}-1.8.15-implicits.patch
-)
-
-pkg_setup() {
-	tc-export CXX CC AR # workaround for bug 285148
-	if use fortran; then
-		use fortran2003 && FORTRAN_STANDARD=2003
-		fortran-2_pkg_setup
-	fi
-	if use mpi; then
-		if has_version 'sci-libs/hdf5[-mpi]'; then
-			ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail."
-			ewarn "Try to uninstall the current hdf5 prior to enabling mpi support."
-		fi
-		export CC=mpicc
-		use fortran && export FC=mpif90
-		if use cxx ; then
-			export CXX=mpicxx
-			ewarn "USE='mpi cxx' requires a configuration unsupported by upstream. Use at your own risk."
-			ewarn "In particular, the C++ API is not parallel safe."
-		fi
-	elif has_version 'sci-libs/hdf5[mpi]'; then
-		ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail."
-		ewarn "Try to uninstall the current hdf5 prior to disabling mpi support."
-	fi
-}
-
-src_prepare() {
-	# respect gentoo examples directory
-	sed \
-		-e "s:hdf5_examples:doc/${PF}/examples:g" \
-		-i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die
-	sed \
-		-e '/docdir/d' \
-		-i config/commence.am || die
-	if ! use examples; then
-		sed -e '/^install:/ s/install-examples//' \
-			-i Makefile.am || die #409091
-	fi
-	# enable shared libs by default for h5cc config utility
-	sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" tools/misc/h5cc.in	|| die
-	# bug #419677
-	use prefix && \
-		append-ldflags -Wl,-rpath,"${EPREFIX}"/usr/$(get_libdir) \
-		-Wl,-rpath,"${EPREFIX}"/$(get_libdir)
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--enable-production
-		--docdir="${EPREFIX}"/usr/share/doc/${PF}
-		--enable-deprecated-symbols
-		$(use_enable prefix sharedlib-rpath)
-		$(use_enable debug debug all)
-		$(use_enable debug codestack)
-		$(use_enable cxx)
-		$(use_enable fortran)
-		$(use_enable fortran2003)
-		$(use_enable hl)
-		$(use_enable mpi parallel)
-		$(use_enable threads threadsafe)
-		$(use_with szip szlib)
-		$(use_with threads pthread)
-		$(use_with zlib)
-		$(use mpi && use cxx && echo --enable-unsupported)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-libs/hdf5/metadata.xml b/sci-libs/hdf5/metadata.xml
index 9c9d5071aa84..040542a30ae7 100644
--- a/sci-libs/hdf5/metadata.xml
+++ b/sci-libs/hdf5/metadata.xml
@@ -12,9 +12,6 @@
   than 2 GB, and supports parallel I/O.
 </longdescription>
   <use>
-    <flag name="fortran2003">Enable new features that require Fortran 2003 
-  (http://www.hdfgroup.org/HDF5/doc/fortran/NewFeatures_F2003.pdf)</flag>
-    <flag name="hl">Enable high level API
-  (https://support.hdfgroup.org/HDF5/doc/HL/index.html)</flag>
+    <flag name="hl">Enable high level API (https://support.hdfgroup.org/HDF5/doc/HL/index.html)</flag>
   </use>
 </pkgmetadata>