From d33b3cf6cff9fdbfc8362bf854c3c34b2c28d518 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Fri, 21 Apr 2023 00:01:06 +0100 Subject: gentoo auto-resync : 21:04:2023 - 00:01:05 --- sci-libs/hdf5/Manifest | 3 +- .../hdf5/files/hdf5-1.14.0-fix-include-path.patch | 34 ++++++ sci-libs/hdf5/hdf5-1.14.0-r1.ebuild | 120 +++++++++++++++++++++ sci-libs/hdf5/hdf5-1.14.0.ebuild | 119 -------------------- 4 files changed, 156 insertions(+), 120 deletions(-) create mode 100644 sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch create mode 100644 sci-libs/hdf5/hdf5-1.14.0-r1.ebuild delete mode 100644 sci-libs/hdf5/hdf5-1.14.0.ebuild (limited to 'sci-libs/hdf5') diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest index e17f9d4e79bf..080254f61d96 100644 --- a/sci-libs/hdf5/Manifest +++ b/sci-libs/hdf5/Manifest @@ -1,6 +1,7 @@ AUX hdf5-1.12.2-configure-clang16.patch 1239 BLAKE2B 76641263e8cdf1f694a0b23c9787e9c1a0e86e30079507beb25caf2c1b89a2e431f7456321e89a39a6ec1d06c5a51a941f9ae5c85a7e3e24462c0eabd41911e3 SHA512 b664f6e464ec824bad46a8e58b571a46b10bcdcc8eae39b878d239b169685b2d1bba6c0ce295f8a690b94f016731176f500b568ef9f0cd2fe0df290ffb6dc298 AUX hdf5-1.12.2-no-messing-ldpath.patch 1086 BLAKE2B 77aba02cd8f3663883fa5cf91b3f77067163f58ec4270d22e2c4e1a5b9b1cc138a2e9dd1c7a44331165c69d6c7a0427fe2708bae63958b416a9f26c799de7443 SHA512 8b8aa080cb6feded376900cf9f4b1f1bbe98550b37e9ae8ad660419f732e686aae2ff6eac37e7810ee438a0e9c1b7a37d24f5db8590cce0c91f482ec7b873527 AUX hdf5-1.12.2-no-strip-symbols.patch 434 BLAKE2B c8d96cb95d3444c18349d72b7fd59f76b4af3d0c5422a7c31161b8f98afacb322b042b8f5751b581565b351148fd0f4003379349b6ca964f5957cd9e19ebdebc SHA512 6b593a8bbbd4a4e9b97e8b3324ad90024b2c09c669d2f6e21a0d23adb66bbbec34afc5961bf97bc6f913492e33610a4b5aeca6a7a4ef9f7605ce5b69fbba6527 +AUX hdf5-1.14.0-fix-include-path.patch 1319 BLAKE2B b9be1c2c8675feb1dd202849ae1d38bc9d62aec11bbd207d4fff6670a50eecc670b481edd840fe9281a1b54b3cda40917717a3ccd913a843d119f5ebcbca9870 SHA512 e0eaedf03edb1add0fbd55a105d7731a98762ae09ec5c2e3d861fdfddd51292b979d54be54eaed1d7ae7806cfcbaac80bf208fa8a3d01c7ad18d5ddd4f585792 AUX hdf5-1.8.13-no-messing-ldpath.patch 1141 BLAKE2B d7d186e4c00acb9fd3d44beb1d8c3c4da0c373f88b3fdf21e1f89b169b747d49572239385228687cfc10380bdceb9ca6d1ac0d5f5154cb7a328f8a2d509fb28d SHA512 e43021ceb83909ab06ba378363c192aa0f1b34cc7c2b121f5000e215516dbdea1b825a53ac4023073bf4870a5c3452c22f5535391d95af45ad63a309e1ffa5a4 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 @@ -10,5 +11,5 @@ DIST hdf5-1.14.0.tar.bz2 15709493 BLAKE2B c86bc91da66d0136870ef9a63edfb7b3591592 EBUILD hdf5-1.10.5-r1.ebuild 2940 BLAKE2B 45e4cf6004cb70667829844ddf37f2c4f96d6b5c92a8eb9b3c757ea47e6d9f98e28f906c7d2c6a33efd95328bc0b6358d640da36c82fc5408bbb968c38b95115 SHA512 04ac047f56128f41f4cdc8b07caa0d656f31d34200961a1ee525583263dc338abff7860158f9549ddf31bf0563ed963fbd5dff4ee212d85443aff599e5d2c25a EBUILD hdf5-1.12.2-r4.ebuild 3209 BLAKE2B eb7b30bee62cbad778b07f089026395d70046e3845b636bdb526e0960e4ae3789f2e5d1c9eac6fc213b755809c42946cf332446582d032d04900cfd80b57b06a SHA512 e6c2c24f9558c381b8ae5da8f0967635c64b02ad5f8288d5a08841c7637f8de7b72229f89d8be2cff5cd0c8c4482b404db3a7d41aeeaa927157c257f91fb62a3 EBUILD hdf5-1.12.2-r6.ebuild 3341 BLAKE2B c574efa933f240fae23049007c320138ea43354ddd78194d74e6b27f630a6ad0fa2a1bc083b563006eb7dd7e36ee00a77a6f684ad42bee383372a79750726d9a SHA512 0385774ab2be1abeec7467886f8900b514d8c1410c531dac7753570cb9e47d35750cd8ddfe92a0df524ecae8889602cc27caa15a52d8e94aa10455e50cf18df3 -EBUILD hdf5-1.14.0.ebuild 3305 BLAKE2B fb75bf2d922a4c0816c9fc13aaec52d11acb3e319881d0921f68386304132536e5e20aba9fe7a47a67a55ef395dbaea13018abc4303c6e36bb8bdb4ab2d842b9 SHA512 c32d23e533a2b718fe10a99cd8f30df5831f7ff2182fc869da3ec5f7bc515f160c6ffd95dea2bb8781d3de2e02b9a95b46648817f5a3e8c72fdcb0bbfa1f2b28 +EBUILD hdf5-1.14.0-r1.ebuild 3356 BLAKE2B 4da4c8c781b42e5969373c20ba101710caa98cee8fde5eba9c0447ca7ea0246214df531ee9151ed30cb941569bd95ff8705db1e65edc385a2531be3d5d8faa02 SHA512 a608d08e71270fdcf970664bf83ed7361ea7f7532ae5572d252df765e6a2e2f2a827e299adb7d5e8472169e112c9b163f7dc2c3999717a24be8c3bfa3731c350 MISC metadata.xml 826 BLAKE2B fd131bb207e4ab863ef7c05ab95e5c0254fa08230139a2508ab5f0c363809b0735532498ad26cc39621495a063de86ab5bd97447514ff561a63302e8b1d7d26d SHA512 290883ed9bf3de60bf04e2474c4db50e095b1b87974867e58601a5c5c2f98d6b839ed22d9ce2798bc44f484f1a38ee4b6df99aaea7d134629bd441d34b5a29b5 diff --git a/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch b/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch new file mode 100644 index 000000000000..4530f1fa6d2e --- /dev/null +++ b/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch @@ -0,0 +1,34 @@ +https://bugs.gentoo.org/904515 +https://github.com/HDFGroup/hdf5/issues/2422 +https://github.com/HDFGroup/hdf5/issues/2621 +https://github.com/HDFGroup/hdf5/pull/2667 +https://github.com/HDFGroup/hdf5/commit/b77cb393b884c1dbdaffb300aa8c4967d9ba7fb0 + +From b77cb393b884c1dbdaffb300aa8c4967d9ba7fb0 Mon Sep 17 00:00:00 2001 +From: jhendersonHDF +Date: Tue, 11 Apr 2023 14:31:25 -0500 +Subject: [PATCH] Fix improper include of build directory (#2422, #2621) + (#2667) + +--- a/configure.ac ++++ b/configure.ac +@@ -3012,8 +3012,7 @@ SUBFILING_VFD=no + HAVE_MERCURY="no" + + ## Always include subfiling directory so public header files are available +-CPPFLAGS="$CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling" +-AM_CPPFLAGS="$AM_CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling" ++H5_CPPFLAGS="$H5_CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling" + + AC_MSG_CHECKING([if the subfiling I/O virtual file driver (VFD) is enabled]) + +@@ -3061,8 +3060,7 @@ if test "X$SUBFILING_VFD" = "Xyes"; then + mercury_dir="$ac_abs_confdir/src/H5FDsubfiling/mercury" + mercury_inc="$mercury_dir/src/util" + +- CPPFLAGS="$CPPFLAGS -I$mercury_inc" +- AM_CPPFLAGS="$AM_CPPFLAGS -I$mercury_inc" ++ H5_CPPFLAGS="$H5_CPPFLAGS -I$mercury_inc" + + HAVE_STDATOMIC_H="yes" + AC_CHECK_HEADERS([stdatomic.h],,[HAVE_STDATOMIC_H="no"]) diff --git a/sci-libs/hdf5/hdf5-1.14.0-r1.ebuild b/sci-libs/hdf5/hdf5-1.14.0-r1.ebuild new file mode 100644 index 000000000000..8d4d4bf40680 --- /dev/null +++ b/sci-libs/hdf5/hdf5-1.14.0-r1.ebuild @@ -0,0 +1,120 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +FORTRAN_NEEDED=fortran + +# We've reverted *back* to autotools from CMake because of +# https://github.com/HDFGroup/hdf5/issues/1814. +inherit autotools fortran-2 flag-o-matic toolchain-funcs prefix + +MY_P=${PN}-${PV/_p/-patch} +MAJOR_P=${PN}-$(ver_cut 1-2) + +DESCRIPTION="General purpose library and file format for storing scientific data" +HOMEPAGE="https://www.hdfgroup.org/HDF5/" +SRC_URI="https://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2" +S="${WORKDIR}/${MY_P}" + +LICENSE="NCSA-HDF" +SLOT="0/${PV%%_p*}" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~loong ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux" +IUSE="cxx debug examples fortran +hl mpi szip test threads unsupported zlib" +RESTRICT="!test? ( test )" +REQUIRED_USE=" + !unsupported? ( + cxx? ( !mpi ) mpi? ( !cxx ) + threads? ( !cxx !mpi !fortran !hl ) + ) +" + +RDEPEND=" + mpi? ( virtual/mpi[romio] ) + szip? ( virtual/szip ) + zlib? ( sys-libs/zlib:0= )" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch + "${FILESDIR}"/${PN}-1.12.2-no-strip-symbols.patch + "${FILESDIR}"/${PN}-1.14.0-fix-include-path.patch +) + +pkg_setup() { + # Workaround for bug 285148 + tc-export CXX CC AR + + 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() { + default + + # Respect Gentoo examples directory + sed \ + -e "s:hdf5_examples:doc/${PF}/examples:g" \ + -i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die + sed \ + -e '/docdir/d' \ + -i config/commence.am || die + + if ! use examples; then + # bug #409091 + sed -e '/^install:/ s/install-examples//' \ + -i Makefile.am || die + fi + + # Enable shared libs by default for h5cc config utility + sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" bin/h5cc.in || die + hprefixify m4/libtool.m4 + + eautoreconf +} + +src_configure() { + # bug #686620 + use sparc && tc-is-gcc && append-flags -fno-tree-ccp + + econf \ + --disable-static \ + --enable-deprecated-symbols \ + --enable-build-mode=$(usex debug debug production) \ + --with-default-plugindir="${EPREFIX}/usr/$(get_libdir)/${PN}/plugin" \ + $(use_enable cxx) \ + $(use_enable debug codestack) \ + $(use_enable fortran) \ + $(use_enable hl) \ + $(use_enable mpi parallel) \ + $(use_enable test tests) \ + $(use_enable threads threadsafe) \ + $(use_enable unsupported) \ + $(use_with szip szlib) \ + $(use_with threads pthread) \ + $(use_with zlib) +} + +src_install() { + emake DESTDIR="${D}" EPREFIX="${EPREFIX}" install + + # No static archives + find "${ED}" -name '*.la' -delete || die + + # Remove "perf" executable due to file collisions with dev-util/perf. + # Previously with the CMake build system we only installed h5perf, so + # let's simply remove the file for now. + use mpi && { rm "${ED}"/usr/bin/perf || die "rm failed" ; } +} diff --git a/sci-libs/hdf5/hdf5-1.14.0.ebuild b/sci-libs/hdf5/hdf5-1.14.0.ebuild deleted file mode 100644 index d69a56ff0f16..000000000000 --- a/sci-libs/hdf5/hdf5-1.14.0.ebuild +++ /dev/null @@ -1,119 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -FORTRAN_NEEDED=fortran - -# We've reverted *back* to autotools from CMake because of -# https://github.com/HDFGroup/hdf5/issues/1814. -inherit autotools fortran-2 flag-o-matic toolchain-funcs prefix - -MY_P=${PN}-${PV/_p/-patch} -MAJOR_P=${PN}-$(ver_cut 1-2) - -DESCRIPTION="General purpose library and file format for storing scientific data" -HOMEPAGE="https://www.hdfgroup.org/HDF5/" -SRC_URI="https://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2" -S="${WORKDIR}/${MY_P}" - -LICENSE="NCSA-HDF" -SLOT="0/${PV%%_p*}" -KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~loong ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux" -IUSE="cxx debug examples fortran +hl mpi szip test threads unsupported zlib" -RESTRICT="!test? ( test )" -REQUIRED_USE=" - !unsupported? ( - cxx? ( !mpi ) mpi? ( !cxx ) - threads? ( !cxx !mpi !fortran !hl ) - ) -" - -RDEPEND=" - mpi? ( virtual/mpi[romio] ) - szip? ( virtual/szip ) - zlib? ( sys-libs/zlib:0= )" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch - "${FILESDIR}"/${PN}-1.12.2-no-strip-symbols.patch -) - -pkg_setup() { - # Workaround for bug 285148 - tc-export CXX CC AR - - 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() { - default - - # Respect Gentoo examples directory - sed \ - -e "s:hdf5_examples:doc/${PF}/examples:g" \ - -i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die - sed \ - -e '/docdir/d' \ - -i config/commence.am || die - - if ! use examples; then - # bug #409091 - sed -e '/^install:/ s/install-examples//' \ - -i Makefile.am || die - fi - - # Enable shared libs by default for h5cc config utility - sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" bin/h5cc.in || die - hprefixify m4/libtool.m4 - - eautoreconf -} - -src_configure() { - # bug #686620 - use sparc && tc-is-gcc && append-flags -fno-tree-ccp - - econf \ - --disable-static \ - --enable-deprecated-symbols \ - --enable-build-mode=$(usex debug debug production) \ - --with-default-plugindir="${EPREFIX}/usr/$(get_libdir)/${PN}/plugin" \ - $(use_enable cxx) \ - $(use_enable debug codestack) \ - $(use_enable fortran) \ - $(use_enable hl) \ - $(use_enable mpi parallel) \ - $(use_enable test tests) \ - $(use_enable threads threadsafe) \ - $(use_enable unsupported) \ - $(use_with szip szlib) \ - $(use_with threads pthread) \ - $(use_with zlib) -} - -src_install() { - emake DESTDIR="${D}" EPREFIX="${EPREFIX}" install - - # No static archives - find "${ED}" -name '*.la' -delete || die - - # Remove "perf" executable due to file collisions with dev-util/perf. - # Previously with the CMake build system we only installed h5perf, so - # let's simply remove the file for now. - use mpi && { rm "${ED}"/usr/bin/perf || die "rm failed" ; } -} -- cgit v1.2.3