Version bump ahead of main tree
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Horea Christian
parent
ae13bb52d5
commit
85a72199ee
1
sci-libs/hdf5/Manifest
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1
sci-libs/hdf5/Manifest
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DIST hdf5-1.10.5.tar.bz2 8706317 SHA256 68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44 SHA512 769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4 WHIRLPOOL 29eb782010dc03310e623cacf3aa71b0b9bf3abc01170a870ed62f6a767784513f4757d447e8a9b1ab9d833f4a799a39551d9bd8a78873dd43da31b274435b4c
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21
sci-libs/hdf5/files/hdf5-1.8.13-no-messing-ldpath.patch
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21
sci-libs/hdf5/files/hdf5-1.8.13-no-messing-ldpath.patch
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Prevent build system with messing up LD_LIBRARY_PATH
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--- a/src/Makefile.am
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+++ b/src/Makefile.am
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@@ -125,8 +125,6 @@ settings_DATA=libhdf5.settings
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# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
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# is set to ignore the error.
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H5Tinit.c: H5detect$(EXEEXT)
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- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
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- sed -e 's/-L/:/g' -e 's/ //g'`" \
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$(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \
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(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
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($(RM) $@ ; exit 1)
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@@ -137,8 +135,6 @@ H5Tinit.c: H5detect$(EXEEXT)
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# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
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# is set to ignore the error.
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H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
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- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
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- sed -e 's/-L/:/g' -e 's/ //g'`" \
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$(RUNSERIAL) ./H5make_libsettings$(EXEEXT) > $@ || \
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(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
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($(RM) $@ ; exit 1)
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43
sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch
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sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch
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--- a/hl/src/H5LTanalyze.c
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+++ b/hl/src/H5LTanalyze.c
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@@ -40,6 +40,7 @@
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#include <string.h>
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#include <errno.h>
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#include <stdlib.h>
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+#include <unistd.h>
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/* end standard C headers. */
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--- a/hl/src/H5LTanalyze.l
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+++ b/hl/src/H5LTanalyze.l
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@@ -16,6 +16,7 @@
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%{
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#include <stdlib.h>
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#include <string.h>
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+#include <unistd.h>
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#include <hdf5.h>
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#include "H5LTparse.h"
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--- a/test/cache_common.h
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+++ b/test/cache_common.h
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@@ -702,5 +702,8 @@ void validate_mdc_config(hid_t file_id,
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hbool_t compare_init,
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int test_num);
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+hbool_t resize_configs_are_equal(const H5C_auto_size_ctl_t *a,
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+ const H5C_auto_size_ctl_t *b,
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+ hbool_t compare_init);
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#endif /* _CACHE_COMMON_H */
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--- a/testpar/t_span_tree.c
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+++ b/testpar/t_span_tree.c
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@@ -37,6 +37,9 @@
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#include "hdf5.h"
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#include "H5private.h"
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#include "testphdf5.h"
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+#define H5S_PACKAGE
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+#define H5S_TESTING
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+#include "H5Spkg.h"
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static void coll_write_test(int chunk_factor);
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16
sci-libs/hdf5/files/hdf5-1.8.9-mpicxx.patch
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sci-libs/hdf5/files/hdf5-1.8.9-mpicxx.patch
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Prevent accidental inclusion of mpi c++ headers
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when hdf5.h is included third party library
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https://bugs.gentoo.org/show_bug.cgi?id=420777
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--- a/src/H5public.h
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+++ b/src/H5public.h
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@@ -58,6 +58,8 @@
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# include <stddef.h>
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#endif
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#ifdef H5_HAVE_PARALLEL
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+# define OMPI_SKIP_MPICXX /* Make sure that cxx specific headers are not included */
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+# define MPICH_SKIP_MPICXX
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# include <mpi.h>
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#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */
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# include <mpio.h>
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15
sci-libs/hdf5/files/hdf5-1.8.9-static_libgfortran.patch
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sci-libs/hdf5/files/hdf5-1.8.9-static_libgfortran.patch
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Make sure that during runtime we'll use the same libgfortran as during linking
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https://bugs.gentoo.org/show_bug.cgi?id=419991
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https://bugs.gentoo.org/show_bug.cgi?id=419895
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--- a/fortran/src/Makefile.am
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+++ b/fortran/src/Makefile.am
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@@ -181,6 +181,7 @@
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else
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H5test_kind_SOURCES = $(srcdir)/H5test_kind.f90
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endif
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+H5test_kind_LDFLAGS=-static-libgfortran
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# Mark this directory as part of the Fortran API
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FORTRAN_API=yes
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sci-libs/hdf5/hdf5-1.10.5.ebuild
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sci-libs/hdf5/hdf5-1.10.5.ebuild
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# Copyright 1999-2017 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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EAPI=5
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FORTRAN_NEEDED=fortran
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AUTOTOOLS_AUTORECONF=1
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inherit autotools-utils eutils fortran-2 flag-o-matic toolchain-funcs multilib versionator prefix
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MY_P=${PN}-${PV/_p/-patch}
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MAJOR_P=${PN}-$(get_version_component_range 1-2 ${PV})
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DESCRIPTION="General purpose library and file format for storing scientific data"
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HOMEPAGE="http://www.hdfgroup.org/HDF5/"
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SRC_URI="http://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2"
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LICENSE="NCSA-HDF"
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SLOT="0/${PV%%_p*}"
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KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux"
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IUSE="cxx debug examples fortran +hl mpi static-libs szip threads zlib"
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REQUIRED_USE="
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cxx? ( !mpi ) mpi? ( !cxx )
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threads? ( !cxx !mpi !fortran !hl )"
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RDEPEND="
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mpi? ( virtual/mpi[romio] )
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szip? ( virtual/szip )
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zlib? ( sys-libs/zlib:0= )"
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DEPEND="${RDEPEND}
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sys-devel/libtool:2
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>=sys-devel/autoconf-2.69"
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S="${WORKDIR}/${MY_P}"
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PATCHES=(
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"${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch
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"${FILESDIR}"/${PN}-1.8.9-mpicxx.patch
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"${FILESDIR}"/${PN}-1.8.13-no-messing-ldpath.patch
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)
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pkg_setup() {
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tc-export CXX CC AR # workaround for bug 285148
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use fortran && fortran-2_pkg_setup
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if use mpi; then
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if has_version 'sci-libs/hdf5[-mpi]'; then
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ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail."
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ewarn "Try to uninstall the current hdf5 prior to enabling mpi support."
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fi
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export CC=mpicc
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use fortran && export FC=mpif90
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elif has_version 'sci-libs/hdf5[mpi]'; then
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ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail."
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ewarn "Try to uninstall the current hdf5 prior to disabling mpi support."
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fi
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}
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src_prepare() {
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# respect gentoo examples directory
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sed \
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-e "s:hdf5_examples:doc/${PF}/examples:g" \
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-i $(find . -name Makefile.am) $(find . -name "run*.sh.in") || die
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sed \
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-e '/docdir/d' \
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-i config/commence.am || die
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if ! use examples; then
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sed -e '/^install:/ s/install-examples//' \
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-i Makefile.am || die #409091
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fi
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# enable shared libs by default for h5cc config utility
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sed -i -e "s/SHLIB:-no/SHLIB:-yes/g" tools/src/misc/h5cc.in || die
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hprefixify m4/libtool.m4
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autotools-utils_src_prepare
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}
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src_configure() {
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local myeconfargs=(
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--docdir="${EPREFIX}"/usr/share/doc/${PF}
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--enable-deprecated-symbols
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$(use debug && echo --enable-build-mode=debug || echo --enable-build-mode=production)
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$(use_enable debug codestack)
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$(use_enable cxx)
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$(use_enable fortran)
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$(use_enable hl)
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$(use_enable mpi parallel)
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$(use_enable threads threadsafe)
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$(use_with szip szlib)
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$(use_with threads pthread)
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$(use_with zlib)
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)
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autotools-utils_src_configure
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}
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20
sci-libs/hdf5/metadata.xml
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sci-libs/hdf5/metadata.xml
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="project">
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<email>sci@gentoo.org</email>
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<name>Gentoo Science Project</name>
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</maintainer>
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<longdescription>
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HDF5 is a file format and library for storing scientific data. HDF5
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was designed and implemented to address the deficiencies of HDF4.x. It
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has a more powerful and flexible data model, supports files larger
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than 2 GB, and supports parallel I/O.
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</longdescription>
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<use>
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<flag name="fortran2003">Enable new features that require Fortran 2003
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(http://www.hdfgroup.org/HDF5/doc/fortran/NewFeatures_F2003.pdf)</flag>
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<flag name="hl">Enable high level API
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(https://support.hdfgroup.org/HDF5/doc/HL/index.html)</flag>
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</use>
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</pkgmetadata>
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