commit: 5be3396bbda2c7e75d6cc7fb85e359f9576b4e45 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Mon Jan 2 22:19:54 2017 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Mon Jan 2 22:19:54 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5be3396b
sci-libs/hdf5: Drop vulnerable versions for CVE-2016-4330 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 <AT> gentoo.org> sci-libs/hdf5/Manifest | 3 - sci-libs/hdf5/files/hdf5-1.8.10-buildsystem.patch | 33 ------- sci-libs/hdf5/files/hdf5-1.8.10-comments.patch | 42 --------- sci-libs/hdf5/files/hdf5-1.8.10-implicits.patch | 54 ----------- sci-libs/hdf5/files/hdf5-1.8.10_p1-comments.patch | 29 ------ sci-libs/hdf5/files/hdf5-1.8.13-implicits.patch | 35 ------- sci-libs/hdf5/files/hdf5-1.8.14-implicits.patch | 55 ----------- sci-libs/hdf5/files/hdf5-1.8.14-ldflags.patch | 20 ---- sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch | 22 ----- sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch | 33 ------- sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch | 85 ----------------- sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch | 55 ----------- sci-libs/hdf5/files/mpd.conf | 2 - sci-libs/hdf5/hdf5-1.8.14-r1.ebuild | 105 --------------------- sci-libs/hdf5/hdf5-1.8.15_p1.ebuild | 104 -------------------- sci-libs/hdf5/hdf5-1.8.17.ebuild | 110 ---------------------- 16 files changed, 787 deletions(-) diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest index 72b6e9a..a988c49 100644 --- a/sci-libs/hdf5/Manifest +++ b/sci-libs/hdf5/Manifest @@ -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 diff --git a/sci-libs/hdf5/files/hdf5-1.8.10-buildsystem.patch b/sci-libs/hdf5/files/hdf5-1.8.10-buildsystem.patch deleted file mode 100644 index 58bcc50..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.10-buildsystem.patch +++ /dev/null @@ -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) diff --git a/sci-libs/hdf5/files/hdf5-1.8.10-comments.patch b/sci-libs/hdf5/files/hdf5-1.8.10-comments.patch deleted file mode 100644 index 845bd81..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.10-comments.patch +++ /dev/null @@ -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 <[email protected]> ---- 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; */ - } - - /*------------------------------------------------------------------------- diff --git a/sci-libs/hdf5/files/hdf5-1.8.10-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.10-implicits.patch deleted file mode 100644 index a0b59b7..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.10-implicits.patch +++ /dev/null @@ -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"; diff --git a/sci-libs/hdf5/files/hdf5-1.8.10_p1-comments.patch b/sci-libs/hdf5/files/hdf5-1.8.10_p1-comments.patch deleted file mode 100644 index 44af808..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.10_p1-comments.patch +++ /dev/null @@ -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 <[email protected]> ---- 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; */ - } - - /*------------------------------------------------------------------------- diff --git a/sci-libs/hdf5/files/hdf5-1.8.13-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.13-implicits.patch deleted file mode 100644 index 2061d16..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.13-implicits.patch +++ /dev/null @@ -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 $AM_CPPFLAGS" - ;; - esac - diff --git a/sci-libs/hdf5/files/hdf5-1.8.14-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.14-implicits.patch deleted file mode 100644 index 4ee6e83..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.14-implicits.patch +++ /dev/null @@ -1,55 +0,0 @@ ---- a/configure.ac -+++ b/configure.ac -@@ -1522,6 +1522,9 @@ case "$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 $AM_CPPFLAGS" - ;; - esac - ---- a/hl/src/H5LTanalyze.c -+++ b/hl/src/H5LTanalyze.c -@@ -40,6 +40,7 @@ - #include <string.h> - #include <errno.h> - #include <stdlib.h> -+#include <unistd.h> - - /* end standard C headers. */ - ---- a/hl/src/H5LTanalyze.l -+++ b/hl/src/H5LTanalyze.l -@@ -16,6 +16,7 @@ - %{ - #include <stdlib.h> - #include <string.h> -+#include <unistd.h> - #include <hdf5.h> - #include "H5LTparse.h" - ---- a/test/cache_common.h -+++ b/test/cache_common.h -@@ -702,5 +702,8 @@ void validate_mdc_config(hid_t file_id, - hbool_t compare_init, - int test_num); - -+hbool_t resize_configs_are_equal(const H5C_auto_size_ctl_t *a, -+ const H5C_auto_size_ctl_t *b, -+ hbool_t compare_init); - #endif /* _CACHE_COMMON_H */ - ---- a/testpar/t_span_tree.c -+++ b/testpar/t_span_tree.c -@@ -37,6 +37,9 @@ - #include "hdf5.h" - #include "H5private.h" - #include "testphdf5.h" -+#define H5S_PACKAGE -+#define H5S_TESTING -+#include "H5Spkg.h" - - - static void coll_write_test(int chunk_factor); diff --git a/sci-libs/hdf5/files/hdf5-1.8.14-ldflags.patch b/sci-libs/hdf5/files/hdf5-1.8.14-ldflags.patch deleted file mode 100644 index c27800d..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.14-ldflags.patch +++ /dev/null @@ -1,20 +0,0 @@ -Revert changes made to fix HDFFV-8944 - -https://bugs.gentoo.org/show_bug.cgi?id=530746 - ---- a/configure.ac -+++ b/configure.ac -@@ -115,12 +115,7 @@ - AM_CXXFLAGS="${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="${FCFLAGS}" diff --git a/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch b/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch deleted file mode 100644 index 042d012..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.8-array_bounds.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- a/perform/pio_engine.c -+++ b/perform/pio_engine.c -@@ -454,7 +454,7 @@ - subdir = (user ? user : login); - - if (subdir) { -- for (i = 0; i < size && prefix[i]; i++) -+ for (i = 0; i < size-1 && prefix[i]; i++) - fullname[i] = prefix[i]; - - fullname[i++] = '/'; ---- a/perform/sio_engine.c -+++ b/perform/sio_engine.c -@@ -353,7 +353,7 @@ - subdir = (user ? user : login); - - if (subdir) { -- for (i = 0; i < size && prefix[i]; i++) -+ for (i = 0; i < size-1 && prefix[i]; i++) - fullname[i] = prefix[i]; - - fullname[i++] = '/'; diff --git a/sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch b/sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch deleted file mode 100644 index 0f85cf5..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.8-buildsystem.patch +++ /dev/null @@ -1,33 +0,0 @@ -Prevent build system with messing up LD_LIBRARY_PATH - ---- a/configure.in -+++ b/configure.in -@@ -2328,8 +2328,6 @@ - dnl - AC_MSG_CHECKING([how to print long long]) - AC_CACHE_VAL([hdf5_cv_printf_ll], --LD_LIBRARY_PATH="$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) diff --git a/sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch deleted file mode 100644 index d1217e8..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.8-implicits.patch +++ /dev/null @@ -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 - diff --git a/sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch b/sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch deleted file mode 100644 index 43e4f07..00000000 --- a/sci-libs/hdf5/files/hdf5-1.8.9-implicits.patch +++ /dev/null @@ -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 - diff --git a/sci-libs/hdf5/files/mpd.conf b/sci-libs/hdf5/files/mpd.conf deleted file mode 100644 index 07dd982..00000000 --- a/sci-libs/hdf5/files/mpd.conf +++ /dev/null @@ -1,2 +0,0 @@ -secretword=test69hike -MPD_SECRETWORD=test69hike diff --git a/sci-libs/hdf5/hdf5-1.8.14-r1.ebuild b/sci-libs/hdf5/hdf5-1.8.14-r1.ebuild deleted file mode 100644 index cad6c42..00000000 --- a/sci-libs/hdf5/hdf5-1.8.14-r1.ebuild +++ /dev/null @@ -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 -} diff --git a/sci-libs/hdf5/hdf5-1.8.15_p1.ebuild b/sci-libs/hdf5/hdf5-1.8.15_p1.ebuild deleted file mode 100644 index 7ce15e7..00000000 --- a/sci-libs/hdf5/hdf5-1.8.15_p1.ebuild +++ /dev/null @@ -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 -} diff --git a/sci-libs/hdf5/hdf5-1.8.17.ebuild b/sci-libs/hdf5/hdf5-1.8.17.ebuild deleted file mode 100644 index 7b186c5..00000000 --- a/sci-libs/hdf5/hdf5-1.8.17.ebuild +++ /dev/null @@ -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 -}
