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sci-libs/hdf5: Drop vulnerable versions for CVE-2016-4330

Browse Source 
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=604386

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec@gentoo.org>
This commit is contained in:
Justin Lecher
2017-01-02 22:19:54 +00:00
parent f9daab8b0d
commit 5be3396bbd
16 changed files with 0 additions and 787 deletions
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3
sci-libs/hdf5/Manifest
View File

@@ -1,4 +1 @@
DIST hdf5-1.8.14.tar.bz2 9503743 SHA256 53722cb9f5977af2908f92fc1a3f8c597800a5cb448cfe5c75060d6335bb9bab SHA512 c4f0bb01df7bef9cd29c42ec2e27f4bd27c3e059cf18f1285c583e92b94ef799f8a29ec85c17bab12e47a69626851fbda4b8d74543266b01aa2cffc42cde4fea WHIRLPOOL 646d44d446e2bd2855567046ca00f302e02d39880a77f2d75fd6231ad74692c07910c8670ffa5e02f2922e4e28c5a4afd06f907ac5950615dd328c3e7346f578
DIST hdf5-1.8.15-patch1.tar.bz2 10006036 SHA256 a5afc630c4443547fff15e9637b5b10404adbed4c00206d89517d32d6668fb32 SHA512 380c06f3cab469351d6ddc940c7cdffd5bd20a74e69cb4d549989bec5f130dadae11c04928ead7eea0200a175fc45a042d068a752d8a9c19a35c3a6912a147bd WHIRLPOOL 0c4c918eea3b70a2c4dea2098f24ddb612af6bf026749144dae19380f60de9d4123acd3c4bf324a1a313e4fae1d7874de48afd9e6720bbcc3c4f1fb1c1bc0288
DIST hdf5-1.8.17.tar.bz2 10030234 SHA256 fc35dd8fd8d398de6b525b27cc111c21fc79795ad6db1b1f12cb15ed1ee8486a SHA512 b0fe630b98a83470c48443215b7073fd22c4390cc459127a4c9554682ae8aec215017c7f34adb8494da4b31fabe6580e9d1b63eddb949432d595e99705c0bbd1 WHIRLPOOL 64e508df74aca518be918dbac10db653004f254779e413ee501a7d550892e6baaa56a0891af28a88d419fa06aa3b06a3c213f45e99b7e2bafc7a9d98e9fe4337
DIST hdf5-1.8.18.tar.bz2 10081294 SHA256 01c6deadf4211f86922400da82c7a8b5b50dc8fc1ce0b5912de3066af316a48c SHA512 01f6d14bdd3be2ced9c63cc9e1820cd7ea11db649ff9f3a3055c18c4b0fffe777fd23baad536e3bce31c4d76fe17db64a3972762e1bb4d232927c1ca140e72b2 WHIRLPOOL c1ea97aa30ded9f3129edf47cfda3b7e371aa21fcb2fc409005818f69ed0f0ac41a19e28ec38a5da2c417ef98033f197292169c88f7db81dd94244b016ab2595

33
sci-libs/hdf5/files/hdf5-1.8.10-buildsystem.patch
View File

@@ -1,33 +0,0 @@
Prevent build system with messing up LD_LIBRARY_PATH
--- a/configure.ac
+++ b/configure.ac
@@ -2331,8 +2331,6 @@ AC_TRY_COMPILE(,[
##
AC_MSG_CHECKING([how to print long long])
AC_CACHE_VAL([hdf5_cv_printf_ll], [
-LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
-export LD_LIBRARY_PATH
for hdf5_cv_printf_ll in l ll L q unknown; do
AC_TRY_RUN([
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -125,8 +125,6 @@ settings_DATA=libhdf5.settings
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5Tinit.c: H5detect$(EXEEXT)
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)
@@ -137,8 +135,6 @@ H5Tinit.c: H5detect$(EXEEXT)
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5make_libsettings$(EXEEXT) > $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)

42
sci-libs/hdf5/files/hdf5-1.8.10-comments.patch
View File

@@ -1,42 +0,0 @@
Convert // comment marks to /**/ in order to fix FTBS on ia64
https://bugs.gentoo.org/show_bug.cgi?id=447740
Patch written by Kacper Kowalik <xarthisius@gentoo.org>
--- a/test/th5s.c
+++ b/test/th5s.c
@@ -730,8 +730,8 @@ test_h5s_zero_dim(void)
ret = H5Pset_chunk(plist_id, SPACE1_RANK, chunk_dims);
CHECK(ret, FAIL, "H5Pset_chunk");
- // ret = H5Pset_alloc_time(plist_id, alloc_time);
- // CHECK(ret, FAIL, "H5Pset_alloc_time");
+ /* ret = H5Pset_alloc_time(plist_id, alloc_time);
+ CHECK(ret, FAIL, "H5Pset_alloc_time"); */
dset1 = H5Dcreate2(fid1, BASICDATASET1, H5T_NATIVE_INT, sid_chunk, H5P_DEFAULT, plist_id, H5P_DEFAULT);
CHECK(dset1, FAIL, "H5Dcreate2");
--- a/tools/h5dump/h5dump_ddl.c
+++ b/tools/h5dump/h5dump_ddl.c
@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
string_dataformat.do_escape = display_escape;
outputformat = &string_dataformat;
- //attr_name = attr + j + 1;
- // need to replace escape characters
+ /* attr_name = attr + j + 1; */
+ /* need to replace escape characters */
attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/");
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
h5tools_str_append(str, "%s", OPT(info->line_indent, ""));
}
-// ctx->need_prefix = 0;
+ /* ctx->need_prefix = 0; */
}
/*-------------------------------------------------------------------------

54
sci-libs/hdf5/files/hdf5-1.8.10-implicits.patch
View File

@@ -1,54 +0,0 @@
--- a/configure.ac
+++ b/configure.ac
@@ -1494,6 +1494,9 @@ case "$host_cpu-$host_vendor-$host_os" in
## however, we do not do this since it breaks the big test on some
## older platforms.
AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
+
+ dnl _GNU_SOURCE is needed for vasprintf
+ AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
;;
esac
--- a/hl/src/H5LTanalyze.c
+++ b/hl/src/H5LTanalyze.c
@@ -49,6 +49,7 @@
#define YY_FLEX_MINOR_VERSION 5
#include <stdio.h>
+#include "H5pubconf.h"
#ifdef H5_HAVE_UNISTD_H
#include <unistd.h>
#endif
--- a/test/cache_common.h
+++ b/test/cache_common.h
@@ -702,5 +702,9 @@ 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/tools/h5repack/testh5repack_detect_szip.c
+++ b/tools/h5repack/testh5repack_detect_szip.c
@@ -18,6 +18,7 @@
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5test.h"
+#include "h5tools_utils.h"
/* Name of tool */
--- a/tools/misc/talign.c
+++ b/tools/misc/talign.c
@@ -23,6 +23,7 @@
#include "hdf5.h"
#include "H5private.h"
+#include "h5tools.h"
const char *fname = "talign.h5";
const char *setname = "align";

29
sci-libs/hdf5/files/hdf5-1.8.10_p1-comments.patch
View File

@@ -1,29 +0,0 @@
Convert // comment marks to /**/ in order to fix FTBS on ia64
https://bugs.gentoo.org/show_bug.cgi?id=447740
Patch written by Kacper Kowalik <xarthisius@gentoo.org>
--- a/tools/h5dump/h5dump_ddl.c
+++ b/tools/h5dump/h5dump_ddl.c
@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
string_dataformat.do_escape = display_escape;
outputformat = &string_dataformat;
- //attr_name = attr + j + 1;
- // need to replace escape characters
+ /* attr_name = attr + j + 1; */
+ /* need to replace escape characters */
attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/");
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
h5tools_str_append(str, "%s", OPT(info->line_indent, ""));
}
-// ctx->need_prefix = 0;
+ /* ctx->need_prefix = 0; */
}
/*-------------------------------------------------------------------------

35
sci-libs/hdf5/files/hdf5-1.8.13-implicits.patch
View File

@@ -1,35 +0,0 @@
--- 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);
--- a/configure.ac
+++ b/configure.ac
@@ -1504,6 +1504,9 @@ case "$host_cpu-$host_vendor-$host_os" in
## however, we do not do this since it breaks the big test on some
## older platforms.
AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
+
+ ## _GNU_SOURCE is needed for vasprintf
+ AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
;;
esac

55
sci-libs/hdf5/files/hdf5-1.8.14-implicits.patch
View File

@@ -1,55 +0,0 @@
--- a/configure.ac
+++ b/configure.ac
@@ -1522,6 +1522,9 @@ case "$host_cpu-$host_vendor-$host_os" in
## however, we do not do this since it breaks the big test on some
## older platforms.
AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
+
+ ## _GNU_SOURCE is needed for vasprintf
+ AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
;;
esac
--- 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);

20
sci-libs/hdf5/files/hdf5-1.8.14-ldflags.patch
View File

@@ -1,20 +0,0 @@
Revert changes made to fix HDFFV-8944
https://bugs.gentoo.org/show_bug.cgi?id=530746
--- a/configure.ac
+++ b/configure.ac
@@ -115,12 +115,7 @@
AM_CXXFLAGS="${AM_CXXFLAGS}"
AM_FCFLAGS="${AM_FCFLAGS}"
AM_CPPFLAGS="${AM_CPPFLAGS}"
-# Added to address HDFFV-8944
-if test "x$prefix" = xNONE; then
- AM_LDFLAGS="$AM_LDFLAGS -L$ac_default_prefix/lib"
-else
- AM_LDFLAGS="$AM_LDFLAGS -L$prefix/lib"
-fi
+AM_LDFLAGS="${AM_LDFLAGS}"
CFLAGS="${CFLAGS}"
CXXFLAGS="${CXXFLAGS}"
FCFLAGS="${FCFLAGS}"

22
sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch
View File

@@ -1,22 +0,0 @@
--- a/perform/pio_engine.c
+++ b/perform/pio_engine.c
@@ -454,7 +454,7 @@
subdir = (user ? user : login);
if (subdir) {
- for (i = 0; i < size && prefix[i]; i++)
+ for (i = 0; i < size-1 && prefix[i]; i++)
fullname[i] = prefix[i];
fullname[i++] = '/';
--- a/perform/sio_engine.c
+++ b/perform/sio_engine.c
@@ -353,7 +353,7 @@
subdir = (user ? user : login);
if (subdir) {
- for (i = 0; i < size && prefix[i]; i++)
+ for (i = 0; i < size-1 && prefix[i]; i++)
fullname[i] = prefix[i];
fullname[i++] = '/';

33
sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch
View File

@@ -1,33 +0,0 @@
Prevent build system with messing up LD_LIBRARY_PATH
--- a/configure.in
+++ b/configure.in
@@ -2328,8 +2328,6 @@
dnl
AC_MSG_CHECKING([how to print long long])
AC_CACHE_VAL([hdf5_cv_printf_ll],
-LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
-export LD_LIBRARY_PATH
for hdf5_cv_printf_ll in l ll L q unknown; do
AC_TRY_RUN([
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -125,8 +125,6 @@
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5Tinit.c: H5detect$(EXEEXT)
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)
@@ -137,8 +135,6 @@
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5make_libsettings$(EXEEXT) > $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)

85
sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch
View File

@@ -1,85 +0,0 @@
--- b/configure.in
+++ a/configure.in
@@ -1499,6 +1499,9 @@
dnl though we do not do this as it breaks the big test on older versions
dnl of linux (CentOS 4.6) using newer versions of gcc (4.6.2).
AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
+
+ dnl _GNU_SOURCE is needed for vasprintf
+ AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
;;
esac
--- a/test/cache_common.h
+++ b/test/cache_common.h
@@ -702,5 +702,9 @@
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/tools/misc/talign.c
+++ b/tools/misc/talign.c
@@ -23,6 +23,7 @@
#include "hdf5.h"
#include "H5private.h"
+#include "h5tools.h"
const char *fname = "talign.h5";
const char *setname = "align";
--- a/tools/h5repack/testh5repack_detect_szip.c
+++ b/tools/h5repack/testh5repack_detect_szip.c
@@ -17,6 +17,7 @@
#include "h5repack.h"
#include "h5tools.h"
#include "h5test.h"
+#include "h5tools_utils.h"
/* Name of tool */
--- a/tools/h5jam/h5jam.c
+++ b/tools/h5jam/h5jam.c
@@ -15,6 +15,7 @@
#include "hdf5.h"
#include "H5private.h"
+#include "h5tools.h"
#include "h5tools_utils.h"
/* Name of tool */
--- a/tools/h5jam/h5unjam.c
+++ b/tools/h5jam/h5unjam.c
@@ -15,6 +15,7 @@
#include "hdf5.h"
#include "H5private.h"
+#include "h5tools.h"
#include "h5tools_utils.h"
/* Name of tool */
--- a/tools/h5copy/h5copygentest.c
+++ b/tools/h5copy/h5copygentest.c
@@ -20,6 +20,7 @@
#include "hdf5.h"
#include "H5private.h"
#include "h5tools.h"
+#include "h5tools_utils.h"
/* Name of tool */
#define PROGRAMNAME "h5copygentest"
--- a/hl/src/H5LTanalyze.c
+++ b/hl/src/H5LTanalyze.c
@@ -49,7 +49,8 @@
#define YY_FLEX_MINOR_VERSION 5
#include <stdio.h>
+#include "H5pubconf.h"
#ifdef H5_HAVE_UNISTD_H
#include <unistd.h>
#endif

55
sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch
View File

@@ -1,55 +0,0 @@
--- b/configure.in
+++ a/configure.in
@@ -1499,6 +1499,9 @@
dnl though we do not do this as it breaks the big test on older versions
dnl of linux (CentOS 4.6) using newer versions of gcc (4.6.2).
AM_CPPFLAGS="-D_BSD_SOURCE $AM_CPPFLAGS"
+
+ dnl _GNU_SOURCE is needed for vasprintf
+ AM_CPPFLAGS="-D_GNU_SOURCE $AM_CPPFLAGS"
;;
esac
--- a/test/cache_common.h
+++ b/test/cache_common.h
@@ -702,5 +702,9 @@
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/tools/misc/talign.c
+++ b/tools/misc/talign.c
@@ -23,6 +23,7 @@
#include "hdf5.h"
#include "H5private.h"
+#include "h5tools.h"
const char *fname = "talign.h5";
const char *setname = "align";
--- a/tools/h5repack/testh5repack_detect_szip.c
+++ b/tools/h5repack/testh5repack_detect_szip.c
@@ -17,6 +17,7 @@
#include "h5repack.h"
#include "h5tools.h"
#include "h5test.h"
+#include "h5tools_utils.h"
/* Name of tool */
--- a/hl/src/H5LTanalyze.c
+++ b/hl/src/H5LTanalyze.c
@@ -49,7 +49,8 @@
#define YY_FLEX_MINOR_VERSION 5
#include <stdio.h>
+#include "H5pubconf.h"
#ifdef H5_HAVE_UNISTD_H
#include <unistd.h>
#endif

2
sci-libs/hdf5/files/mpd.conf
View File

@@ -1,2 +0,0 @@
secretword=test69hike
MPD_SECRETWORD=test69hike

105
sci-libs/hdf5/hdf5-1.8.14-r1.ebuild
View File

@@ -1,105 +0,0 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
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"
LICENSE="NCSA-HDF"
SLOT="0/${PV%%_p*}"
KEYWORDS="alpha amd64 ~arm ia64 ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux"
IUSE="cxx debug examples fortran fortran2003 mpi static-libs szip threads zlib"
REQUIRED_USE="
cxx? ( !mpi ) mpi? ( !cxx )
threads? ( !cxx !mpi !fortran )
fortran2003? ( fortran )"
RDEPEND="
mpi? ( virtual/mpi[romio] )
szip? ( virtual/szip )
zlib? ( sys-libs/zlib:0= )"
DEPEND="${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}-1.8.14-implicits.patch
"${FILESDIR}"/${PN}-1.8.14-ldflags.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
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 mpi parallel)
$(use_enable threads threadsafe)
$(use_with szip szlib)
$(use_with threads pthread)
$(use_with zlib)
)
autotools-utils_src_configure
}

104
sci-libs/hdf5/hdf5-1.8.15_p1.ebuild
View File

@@ -1,104 +0,0 @@
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
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"
LICENSE="NCSA-HDF"
SLOT="0/${PV%%_p*}"
KEYWORDS="~alpha ~amd64 ~arm ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux"
IUSE="cxx debug examples fortran fortran2003 mpi static-libs szip threads zlib"
REQUIRED_USE="
cxx? ( !mpi ) mpi? ( !cxx )
threads? ( !cxx !mpi !fortran )
fortran2003? ( fortran )"
RDEPEND="
mpi? ( virtual/mpi[romio] )
szip? ( virtual/szip )
zlib? ( sys-libs/zlib:0= )"
DEPEND="${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
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 mpi parallel)
$(use_enable threads threadsafe)
$(use_with szip szlib)
$(use_with threads pthread)
$(use_with zlib)
)
autotools-utils_src_configure
}

110
sci-libs/hdf5/hdf5-1.8.17.ebuild
View File

@@ -1,110 +0,0 @@
# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
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"
LICENSE="NCSA-HDF"
SLOT="0/${PV%%_p*}"
KEYWORDS="~alpha ~amd64 ~arm ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux"
IUSE="cxx debug examples fortran fortran2003 +hl mpi static-libs szip threads zlib"
REQUIRED_USE="
threads? ( !cxx !mpi !fortran !hl )
fortran2003? ( fortran )"
RDEPEND="
mpi? ( virtual/mpi[romio] )
szip? ( virtual/szip )
zlib? ( sys-libs/zlib:0= )"
DEPEND="${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
}