gentoo auto-resync : 17:12:2023 - 14:57:38

6 files changed, 225 insertions, 3 deletions

diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index 8c352e2e6b04..f42573d62e87 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -1,6 +1,9 @@
 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 hdf5-1.14.2-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch 852 BLAKE2B 70e31289d44479909f10d38aa1ee83ff8791d37ef33f9ba3d34879b655271d822434c41ec32875cc60154a53eb555b6d73f1a06cb369a1bc8b8a5d698bbbc12c SHA512 34969fdb657c0b7d7d89917eb4adc4479a52efd63c03d243c5e5be1e8db6b1238833ecfd381a7e0b881466905b1464c37689fa4b693c04e9cc2366a0985d25ad
+AUX hdf5-1.14.2-0002-Disable-forced-stripping.patch 832 BLAKE2B 86fe49b93a52d9f538c1359d0e1412a31444dd424607a7a54cf40e55d842550e18a7107d41a1f11d41e7ed0410799d73454826d56bd3401e2eca4e27a9fdd5a1 SHA512 1935b4ff52d7296563b67ef8db694e0996353075a9f2e44cba1992a27c57bf0361d346b9b4489a2d5dbc0b0e6097d421f6b9c52784bfd6562a2f07418a84d515
+AUX hdf5-1.14.2-0003-Drop-broken-Werror-stripping.patch 1280 BLAKE2B 82c563607233aa863e996463a2f6a7a73c8f17aeeba97ad2fd7e04ad400941d8b166e2e845bc051c7f697f6fdf6bba392c01b1e24e65aba74d33f7ce4fcb37bc SHA512 286b3bc5ecb6e0b94880ce65a9f2722e7a72d0ee9b91a4887424e25d89296017f8f2730f66ba24f550276e7df000e7e35e34b468b35f5fa1cb85f02e04ae3a4f
 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
@@ -8,9 +11,11 @@ DIST hdf5-1.10.5.tar.bz2 8706317 BLAKE2B ac326be8fe4ccc4b0153f15bc7d65aa8f1adc2a
 DIST hdf5-1.12.2.tar.bz2 10494264 BLAKE2B 99ca5b57f6f54fa044c909f0773de62b218c1f0ec3c011f88f3c227536dd719e77ddbe42d562b1214e8843e41d8fc56db499d7f122876fdd36ef31b235229cb7 SHA512 cbb4663570de76b11adb6bf62cfdb754371d31eeab04691479a5764a45207a9c1309665ab80f51c63a4b9b87354f9cbe6835cef506a9fd554d142c6d2bec21e5
 DIST hdf5-1.14.1.tar.bz2 16257319 BLAKE2B fbabbe2a61fca3f841d0206e3918390001ec1ec713696b69845eb6390595794a63740db9a7b48fd132814268e216d8fea6288cd23b04b2fa981058b557113e73 SHA512 b4dd3fca88547fdcbb2afcc22cb11bb45b7b15c3c01d9e11b7f06030ffff1a9d5c4995abb6cf27b0c4e748f1a7ca497a7f2d995ba00586f447fcd2fa537e0e16
 DIST hdf5-1.14.2.tar.bz2 16070491 BLAKE2B 04acdc5352f7f0455bf6304ef07ddf51b99125bb585984bd3e27a521a784a6ad6723d64aa3b4179e4bd382334b7e68d06650404d7d4617a696d3f64917487dbc SHA512 1e1bfdff50c2e0e172d399c2d5b79b9ad0c7c72b9b30c4849aad7c5656393e8cf2af788cdf62b51fbe596023483fbc7fa23fdebf37bfe3109dae7f0783ea590f
+DIST hdf5-1.14.3.tar.bz2 16320137 BLAKE2B 4c58edc04788db739c5c74d6edbfb9277011e2d6776862404fc29b30bb2c06a4314eb317393c230ebd2617a9a362ff78183d39ae80ce08f8963bdf6c02e8a865 SHA512 06d51638a56f387f6d0ef484b72e182509c15ab639315052be9821adeed6ad08551c50d7fe84d2b550b64211f68484cf3022a4660c8004cd0afd90eaa83c1bb1
 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 hdf5-1.14.1.ebuild 3078 BLAKE2B 30428ba92c299c92463276e3853c8332efb0904856749f6a6f716b2f07a58a7fc12c62a7298d15067af9b436a5e5f237c322ff30a942337ab9e65a4f1765074f SHA512 076ceaa6f8eb5330e8bf1913ddfc659524a4770e2df0d459b88ce41eec4d99e4e0b9da42f7b690b24bc678f15dd96ba8d20c443bbd9f4afe9c111abe5efc9f10
-EBUILD hdf5-1.14.2.ebuild 3078 BLAKE2B 98535ae991ee7208e307b22f8eb515ee7431c05a59f4fa6d01793d6832899780686e42774cb19f2ce84faecef87cde130c04864ccd68129689030492acf08846 SHA512 14422e163c1985f27c8d106f4c35081c59e953fcb4987fec084eb9d8cedf4be30a67b5bf60e7c8c9f67e5fd6b834f0b286cfc07b1270cbc50b2dfe705ecd4cbc
+EBUILD hdf5-1.14.2.ebuild 3196 BLAKE2B d28620682d589fc2547744be2840f2548c5a4991e0c4eee7fb0fdbd0c25a0320fdd77792a53578f16e2a3426f37649bcb98e8938b14432c6095ca51e762d9382 SHA512 64a97e1175e4bb97cf0d05bd4e84d897de1299a4eaeb7c6e29699e7b6beafde4dec06c64df31cc027930d1ecfe81acac78694006725fbeb99eec272664291ea1
+EBUILD hdf5-1.14.3.ebuild 3244 BLAKE2B 18daf63cef5914b3df1be2ee1c178a48e398307c6c264d550581ac4fb20c6c63e1022cd025f0da719ba771187521002bf046812069a1b4b440a55cf4d66b18bd SHA512 65608f331187e36621174b97b1f42784e1267ac00c110e081be4c86f236228e6c07c69a4673f681a522c051a6607990ed3c04f148930ea0cf89d04494b1f4c35
 MISC metadata.xml 826 BLAKE2B fd131bb207e4ab863ef7c05ab95e5c0254fa08230139a2508ab5f0c363809b0735532498ad26cc39621495a063de86ab5bd97447514ff561a63302e8b1d7d26d SHA512 290883ed9bf3de60bf04e2474c4db50e095b1b87974867e58601a5c5c2f98d6b839ed22d9ce2798bc44f484f1a38ee4b6df99aaea7d134629bd441d34b5a29b5
diff --git a/sci-libs/hdf5/files/hdf5-1.14.2-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch b/sci-libs/hdf5/files/hdf5-1.14.2-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch
new file mode 100644
index 000000000000..91ed578ccc14
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.14.2-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch
@@ -0,0 +1,28 @@
+From 1a5293a30594afbfd3a24899e055429046a47837 Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 17 Dec 2023 09:25:43 +0000
+Subject: [PATCH 1/3] Make sure that during runtime we'll use the same
+ libgfortran as during linking
+
+Bug: https://bugs.gentoo.org/419991
+Bug: https://bugs.gentoo.org/419895
+Signed-off-by: Sam James <sam@gentoo.org>
+---
+ fortran/src/Makefile.am | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/fortran/src/Makefile.am b/fortran/src/Makefile.am
+index d42a41d..2b2a316 100644
+--- a/fortran/src/Makefile.am
++++ b/fortran/src/Makefile.am
+@@ -96,6 +96,7 @@ if BUILD_PARALLEL_CONDITIONAL
+ else
+   H5FC_NAME = h5fc
+ endif
++H5test_kind_LDFLAGS=-static-libgfortran
+ 
+ # Rules for automatically detecting which fortran types are present
+ # and matching them to C types.  This is accomplished using helper
+-- 
+2.43.0
+
diff --git a/sci-libs/hdf5/files/hdf5-1.14.2-0002-Disable-forced-stripping.patch b/sci-libs/hdf5/files/hdf5-1.14.2-0002-Disable-forced-stripping.patch
new file mode 100644
index 000000000000..646950c62167
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.14.2-0002-Disable-forced-stripping.patch
@@ -0,0 +1,31 @@
+From 260c90de63af19ff96fcf735d75d497356747788 Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 17 Dec 2023 09:26:33 +0000
+Subject: [PATCH 2/3] Disable forced stripping
+
+Bug: https://bugs.gentoo.org/665378
+Signed-off-by: Sam James <sam@gentoo.org>
+---
+ configure.ac | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index baad732..8c6b6f4 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -2183,9 +2183,9 @@ case "X-$SYMBOLS" in
+     AC_MSG_RESULT([yes])
+     ;;
+   X-no)
+-    H5_CFLAGS="$H5_CFLAGS $NO_SYMBOLS_CFLAGS"
+-    H5_CXXFLAGS="$H5_CXXFLAGS $NO_SYMBOLS_CXXFLAGS"
+-    H5_FCFLAGS="$H5_FCFLAGS $NO_SYMBOLS_FCFLAGS"
++    H5_CFLAGS="$H5_CFLAGS"
++    H5_CXXFLAGS="$H5_CXXFLAGS"
++    H5_FCFLAGS="$H5_FCFLAGS"
+     AC_MSG_RESULT([no])
+     ;;
+   *)
+-- 
+2.43.0
+
diff --git a/sci-libs/hdf5/files/hdf5-1.14.2-0003-Drop-broken-Werror-stripping.patch b/sci-libs/hdf5/files/hdf5-1.14.2-0003-Drop-broken-Werror-stripping.patch
new file mode 100644
index 000000000000..fbe69dcadb92
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.14.2-0003-Drop-broken-Werror-stripping.patch
@@ -0,0 +1,37 @@
+From 5c87a2125ca2620de633e33a52020d12b7661da8 Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 17 Dec 2023 09:27:18 +0000
+Subject: [PATCH 3/3] Drop broken -Werror stripping
+
+The stripping is broken and mangles -Werror=x -> -x [0].
+
+[0] https://github.com/HDFGroup/hdf5/commit/41526f68f3482f2b3a7aa581288bc86e9c6dcb43#r100076265
+
+Bug: https://bugs.gentoo.org/917448
+Signed-off-by: Sam James <sam@gentoo.org>
+---
+ configure.ac | 8 --------
+ 1 file changed, 8 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 8c6b6f4..a66830e 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -189,14 +189,6 @@ saved_user_JAVAFLAGS="$JAVAFLAGS"
+ saved_user_LDFLAGS="$LDFLAGS"
+ saved_user_CPPFLAGS="$CPPFLAGS"
+ 
+-## Strip out -Werror from CFLAGS since that can cause checks to fail when
+-## compiling the test program fails due to warnings
+-CFLAGS="`echo $CFLAGS | sed -e 's/-Werror//g'`"
+-CXXFLAGS="`echo $CXXFLAGS | sed -e 's/-Werror//g'`"
+-FCFLAGS="`echo $FCFLAGS | sed -e 's/-Werror//g'`"
+-JAVACFLAGS="`echo $JAVACFLAGS | sed -e 's/-Werror//g'`"
+-CPPFLAGS="`echo $CPPFLAGS | sed -e 's/-Werror//g'`"
+-
+ ## Support F9X variable to define Fortran compiler if FC variable is
+ ## not used.  This should be deprecated in the future.
+ if test "x" = "x$FC"; then
+-- 
+2.43.0
+
diff --git a/sci-libs/hdf5/hdf5-1.14.2.ebuild b/sci-libs/hdf5/hdf5-1.14.2.ebuild
index 0cd8c97ec4cf..b40823d3c6b7 100644
--- a/sci-libs/hdf5/hdf5-1.14.2.ebuild
+++ b/sci-libs/hdf5/hdf5-1.14.2.ebuild
@@ -37,8 +37,9 @@ RDEPEND="
 DEPEND="${RDEPEND}"
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch
-	"${FILESDIR}"/${PN}-1.12.2-no-strip-symbols.patch
+	"${FILESDIR}"/hdf5-1.14.2-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch
+	"${FILESDIR}"/hdf5-1.14.2-0002-Disable-forced-stripping.patch
+	"${FILESDIR}"/hdf5-1.14.2-0003-Drop-broken-Werror-stripping.patch
 )
 
 pkg_setup() {
diff --git a/sci-libs/hdf5/hdf5-1.14.3.ebuild b/sci-libs/hdf5/hdf5-1.14.3.ebuild
new file mode 100644
index 000000000000..47b70efe199b
--- /dev/null
+++ b/sci-libs/hdf5/hdf5-1.14.3.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 ~arm64-macos ~x64-macos"
+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:= )
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/hdf5-1.14.2-0001-Make-sure-that-during-runtime-we-ll-use-the-same-lib.patch
+	"${FILESDIR}"/hdf5-1.14.2-0002-Disable-forced-stripping.patch
+	"${FILESDIR}"/hdf5-1.14.2-0003-Drop-broken-Werror-stripping.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) $(find . -name "run*.sh.in") || die
+	sed \
+		-e '/docdir/d' \
+		-i config/commence.am || die
+
+	if ! use examples; then
+		# bug #409091
+		sed -e '/^install:/ s/install-examples//' \
+			-i Makefile.am || die
+	fi
+
+	# Enable shared libs by default for h5cc config utility
+	sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" bin/h5cc.in || die
+	hprefixify m4/libtool.m4
+
+	eautoreconf
+}
+
+src_configure() {
+	# bug #686620
+	use sparc && tc-is-gcc && append-flags -fno-tree-ccp
+
+	local myeconfargs=(
+		--disable-static
+		--disable-doxygen-errors
+		--enable-deprecated-symbols
+		--enable-build-mode=$(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)
+		$(use_with zlib)
+	)
+
+	econf "${myeconfargs[@]}"
+}
+
+src_install() {
+	emake DESTDIR="${D}" EPREFIX="${EPREFIX}" install
+
+	# No static archives
+	find "${ED}" -name '*.la' -delete || die
+}