Accepting request 848498 from science
OBS-URL: https://build.opensuse.org/request/show/848498 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/hdf5?expand=0&rev=70
This commit is contained in:
Dominique Leuenberger
Git OBS Bridge
commit
84e3f0b775
@ -12,9 +12,9 @@ Index: hdf5-1.10.5/testpar/CMakeTests.cmake
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===================================================================
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--- hdf5-1.10.5.orig/testpar/CMakeTests.cmake
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+++ hdf5-1.10.5/testpar/CMakeTests.cmake
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@@ -30,7 +30,7 @@ set (SKIP_testphdf5 "")
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# set (SKIP_testphdf5 "${SKIP_testphdf5};-x;ecdsetw")
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#endif ()
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@@ -43,7 +43,7 @@
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set (SKIP_testphdf5 "${SKIP_testphdf5};-x;${skiptest}")
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endforeach ()
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-add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
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+##add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
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@ -11,10 +11,10 @@ Signed-off-by: Egbert Eich <eich@suse.com>
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hdf5-1.10.1/test/dt_arith.c | 26 ++++++++++++++++++++++++--
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2 files changed, 40 insertions(+), 2 deletions(-)
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Index: hdf5-1.10.5/config/cmake/ConversionTests.c
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Index: hdf5-1.10.7/config/cmake/ConversionTests.c
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===================================================================
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--- hdf5-1.10.5.orig/config/cmake/ConversionTests.c
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+++ hdf5-1.10.5/config/cmake/ConversionTests.c
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--- hdf5-1.10.7.orig/config/cmake/ConversionTests.c
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+++ hdf5-1.10.7/config/cmake/ConversionTests.c
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@@ -34,6 +34,14 @@ int HDF_NO_UBSAN main(void)
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unsigned char s2[8];
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int ret = 1;
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@ -45,11 +45,11 @@ Index: hdf5-1.10.5/config/cmake/ConversionTests.c
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if(sizeof(long double) == 16) {
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/*make sure the long double type is the same as the failing type
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*which has 16 bytes in size and 11 bits of exponent. If it is,
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Index: hdf5-1.10.5/test/dt_arith.c
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Index: hdf5-1.10.7/test/dt_arith.c
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===================================================================
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--- hdf5-1.10.5.orig/test/dt_arith.c
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+++ hdf5-1.10.5/test/dt_arith.c
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@@ -3051,7 +3051,18 @@ test_conv_flt_1 (const char *name, int r
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--- hdf5-1.10.7.orig/test/dt_arith.c
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+++ hdf5-1.10.7/test/dt_arith.c
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@@ -3045,7 +3045,18 @@ test_conv_flt_1 (const char *name, int r
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buf, saved, nelmts);
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#if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0
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} else if(src_type == FLT_LDOUBLE) {
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@ -69,7 +69,7 @@ Index: hdf5-1.10.5/test/dt_arith.c
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buf, saved, nelmts);
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#endif
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} else
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@@ -3711,7 +3722,18 @@ test_conv_int_fp(const char *name, int r
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@@ -3705,7 +3716,18 @@ test_conv_int_fp(const char *name, int r
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INIT_FP_DENORM(long double, LDBL_MANT_DIG, src_size, src_nbits, sendian, dst_size,
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buf, saved, nelmts);
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} else {
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@ -1,3 +0,0 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44
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size 8706317
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3
hdf5-1.10.7.tar.bz2
Normal file
3
hdf5-1.10.7.tar.bz2
Normal file
@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:02018fac7e5efc496d9539a303cfb41924a5dadffab05df9812096e273efa55e
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size 8957844
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@ -2,7 +2,7 @@ Index: configure
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===================================================================
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--- configure.orig
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+++ configure
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@@ -4097,6 +4097,8 @@ done
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@@ -4160,6 +4160,8 @@ done
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if test "X$host_config" != "Xnone"; then
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CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
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. $host_config
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@ -15,7 +15,7 @@ Index: configure.ac
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===================================================================
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--- configure.ac.orig
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+++ configure.ac
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@@ -263,6 +263,8 @@ done
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@@ -271,6 +271,8 @@ done
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if test "X$host_config" != "Xnone"; then
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CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
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. $host_config
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@ -1,8 +1,8 @@
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Index: hdf5-1.10.5/src/Makefile.in
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Index: hdf5-1.10.7/src/Makefile.in
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===================================================================
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--- hdf5-1.10.5.orig/src/Makefile.in
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+++ hdf5-1.10.5/src/Makefile.in
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@@ -1873,8 +1873,6 @@ help:
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--- hdf5-1.10.7.orig/src/Makefile.in
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+++ hdf5-1.10.7/src/Makefile.in
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@@ -1941,8 +1941,6 @@ help:
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# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
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# is set to ignore the error.
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H5Tinit.c: H5detect$(EXEEXT)
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@ -11,7 +11,7 @@ Index: hdf5-1.10.5/src/Makefile.in
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$(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \
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(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
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($(RM) $@ ; exit 1)
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@@ -1885,8 +1883,6 @@ H5Tinit.c: H5detect$(EXEEXT)
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@@ -1953,8 +1951,6 @@ 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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@ -10,11 +10,11 @@ Signed-off-by: Egbert Eich <eich@suse.de>
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---
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src/H5detect.c | 15 ---------------
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1 file changed, 15 deletions(-)
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Index: hdf5-1.10.5/src/H5detect.c
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Index: hdf5-1.10.7/src/H5detect.c
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===================================================================
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--- hdf5-1.10.5.orig/src/H5detect.c
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+++ hdf5-1.10.5/src/H5detect.c
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@@ -1245,21 +1245,6 @@ bit.\n";
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--- hdf5-1.10.7.orig/src/H5detect.c
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+++ hdf5-1.10.7/src/H5detect.c
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@@ -1234,21 +1234,6 @@ bit.\n";
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fprintf(rawoutstream, "/* Generated automatically by H5detect -- do not edit */\n\n\n");
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HDfputs(FileHeader, rawoutstream); /*the copyright notice--see top of this file */
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50
hdf5.changes
50
hdf5.changes
@ -1,3 +1,25 @@
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-------------------------------------------------------------------
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Fri Nov 6 10:41:02 UTC 2020 - Ana Guerrero Lopez <aguerrero@suse.com>
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- Update to version 1.10.7
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* https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6-RELEASE.txt
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* https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7-RELEASE.txt
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- Security bugs fixed:
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* CVE-2018-13870: heap-based buffer over-read in the function
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H5O_link_decode in H5Olink.c (bsc#1101493)
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* CVE-2018-13869: memcpy parameter overlap in the function
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H5O_link_decode in H5Olink.c (bsc#1101495)
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* CVE-2018-17438: A SIGFPE signal is raised in the function
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H5D__select_io() of H5Dselect.c in the HDF HDF5 through 1.10.3
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library during an attempted parse of a crafted HDF file,
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because of incorrect protection against division
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(bsc#1109570)
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* CVE-2018-17435: A heap-based buffer over-read in H5O_attr_decode()
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in H5Oattr.c in the HDF HDF5 through 1.10.3 library allows
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attackers to cause a denial of service via a crafted HDF5 file.
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(bsc#1109567)
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- Refresh patches
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-------------------------------------------------------------------
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Thu Jul 23 16:33:58 UTC 2020 - Egbert Eich <eich@suse.com>
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@ -71,6 +93,13 @@ Fri Aug 23 09:58:01 UTC 2019 - Ana Guerrero Lopez <aguerrero@suse.com>
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- Update to version 1.10.5: (jsc#SLE-8501)
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* https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5-RELEASE.txt
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- Security bugs fixed:
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* CVE-2018-17233: A SIGFPE signal is raised in the function
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H5D__create_chunk_file_map_hyper. (bsc#1109166)
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* CVE-2018-17434: Memory leak in the H5O__chunk_deserialize()
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function in H5Ocache.c (bsc#1109167)
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* CVE-2018-17437: A SIGFPE signal is raised in the function
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H5D__chunk_set_info_real. (bsc#1109168)
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- Bump fortran library soname, sonum_F from 100 to 102.
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- Adjust library installation path, use %hpc_prefix/lib64 in x86_64
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and %hpc_libdir in all other cases
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@ -86,7 +115,6 @@ Fri Aug 23 09:58:01 UTC 2019 - Ana Guerrero Lopez <aguerrero@suse.com>
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- Patch removed, merged upstream
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* 0001-Fix-return-value-in-test_libver_bounds_open.patch
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-------------------------------------------------------------------
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Thu Jul 4 11:45:55 UTC 2019 - Egbert Eich <eich@suse.com>
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@ -202,6 +230,26 @@ Fri Sep 21 14:50:12 UTC 2018 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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* hdf5-buildcompare.patch
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* hdf5-mpi.patch
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- Rebase Disable-phdf5-tests.patch
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- Security bugs fixed:
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* CVE-2017-17505: NULL pointer dereference in the function
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H5O_pline_decode allowing for DoS via crafted file (bsc#1072087)
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* CVE-2017-17506: Out of bounds read in the function
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H5Opline_pline_decode (bsc#1072090)
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* CVE-2017-17508: divide-by-zero vulnerability in function
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H5T_set_loc (bsc#1072108)
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* CVE-2017-17509: out of bounds write vulnerability in function
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H5G__ent_decode_vec (bsc#1072111)
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* CVE-2018-11202: NULL pointer dereference in H5S_hyper_make_spans
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in H5Shyper.c allows a remote denial of service attack (bsc#1093641)
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* CVE-2018-11203: division by zero in H5D__btree_decode_key in H5Dbtree.c
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It could allow a remote denial of service attack (bsc#1093649)
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* CVE-2018-11204: A NULL pointer dereference was discovered in
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H5O__chunk_deserialize in H5Ocache.c (bsc#1093655)
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* CVE-2018-11206: A out of bounds read was discovered
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in H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c
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(bsc#1093657)
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* CVE-2018-11207: division by zero was discovered in H5D__chunk_init
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in H5Dchunk.c (bsc#1093653)
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-------------------------------------------------------------------
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Tue Jun 19 06:15:06 UTC 2018 - eich@suse.com
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29
hdf5.spec
29
hdf5.spec
@ -34,8 +34,8 @@
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%define use_sz2 0
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%define vers 1.10.5
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%define _vers 1_10_5
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%define vers 1.10.7
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%define _vers 1_10_7
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%define short_ver 1.10
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%define src_ver %{version}
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%define pname hdf5
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@ -785,13 +785,13 @@ make install DESTDIR=%{buildroot}
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find %{buildroot} -type f -name "*.la" -delete -print
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%if %{without mpi}
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find %{buildroot}%{_prefix}/share/hdf5_examples -type f \
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| grep -v ".sh$" | xargs chmod 644
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%if %{with hpc}
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# copy to versioned subdir
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install -m 755 -d %{buildroot}%{_prefix}/share/%{version}
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mv %{buildroot}%{_prefix}/share/hdf5_examples/* \
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%{buildroot}%{_prefix}/share/%{version}
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install -m 755 -d %{buildroot}%{_prefix}/share/hdf5_examples
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mv %{buildroot}%{_prefix}/lib/hpc/*/hdf5/*/share/hdf5_examples/* \
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%{buildroot}%{_prefix}/share/%{version}/
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mv %{buildroot}%{_prefix}/share/%{version} \
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%{buildroot}%{_prefix}/share/hdf5_examples
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%else
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@ -805,9 +805,10 @@ cat > %{buildroot}%{_rpmconfigdir}/macros.d/macros.hdf5 <<EOF
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%_hdf5_version %{version}
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EOF
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%endif
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%else
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# delete examples from parallel builds
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rm -rf %{buildroot}%{_prefix}/share/hdf5_examples
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find %{buildroot} -type d -name "hdf5_examples" -exec rm -rf {} +;
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%endif
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%fdupes -s %{buildroot}/%{_datadir}
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@ -906,19 +907,16 @@ export HDF5_Make_Ignore=yes
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%if %{without mpi}
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%files -n %{vname}-examples
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%defattr(-,root,root)
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%{?with_hpc:%dir %{_prefix}/share/hdf5_examples}
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%{_prefix}/share/hdf5_examples%{?with_hpc:/%{version}}
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%if %{without hpc}
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%files -n %{pname}-devel-data
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%defattr(-,root,root,-)
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%{_rpmconfigdir}/macros.d/macros.hdf5
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%endif
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%endif # ?mpi
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%files -n %{name}
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%defattr(-,root,root)
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%{?with_hpc:%dir %my_bindir}
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%{my_bindir}/gif2h5
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%{my_bindir}/h52gif
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@ -943,9 +941,10 @@ export HDF5_Make_Ignore=yes
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%{my_bindir}/h5stat
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%{my_bindir}/h5unjam
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%{my_bindir}/h5watch
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%{my_bindir}/mirror_server
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%{my_bindir}/mirror_server_stop
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%files -n %{libname -s %{sonum}}
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%defattr(-,root,root)
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%doc ACKNOWLEDGMENTS README.txt
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%mylicense COPYING
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##
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@ -959,7 +958,6 @@ export HDF5_Make_Ignore=yes
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%{my_libdir}/libhdf5.so.%{sonum}.*
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%files -n %{libname -l _hl -s %{sonum_HL}}
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%defattr(-,root,root)
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%mylicense COPYING
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%defattr(0755,root,root)
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%{?with_hpc:%hpc_dirs}
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@ -967,7 +965,6 @@ export HDF5_Make_Ignore=yes
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%{my_libdir}/libhdf5_hl.so.%{sonum_HL}.*
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%files -n %{libname -l _cpp -s %{sonum_CXX}}
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%defattr(-,root,root)
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%mylicense COPYING
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%defattr(0755,root,root)
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%{?with_hpc:%hpc_dirs}
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@ -975,7 +972,6 @@ export HDF5_Make_Ignore=yes
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%{my_libdir}/libhdf5_cpp.so.%{sonum_CXX}.*
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%files -n %{libname -l _hl_cpp -s %{sonum_HL_CXX}}
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%defattr(-,root,root)
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%mylicense COPYING
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%defattr(0755,root,root)
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%{?with_hpc:%hpc_dirs}
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@ -983,7 +979,6 @@ export HDF5_Make_Ignore=yes
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%{my_libdir}/libhdf5_hl_cpp.so.%{sonum_HL_CXX}.*
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%files -n %{libname -l _fortran -s %{sonum_F}}
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%defattr(-,root,root)
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%mylicense COPYING
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%defattr(0755,root,root)
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%{?with_hpc:%hpc_dirs}
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@ -991,7 +986,6 @@ export HDF5_Make_Ignore=yes
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%{my_libdir}/libhdf5_fortran.so.%{sonum_F}.*
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%files -n %{libname -l hl_fortran -s %{sonum_HL_F}}
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%defattr(-,root,root)
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%mylicense COPYING
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%defattr(0755,root,root)
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%{?with_hpc:%hpc_dirs}
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@ -1000,12 +994,10 @@ export HDF5_Make_Ignore=yes
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%if %{with hpc}
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%files module
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%defattr(-,root,root)
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%hpc_modules_files
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%endif
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%files devel
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%defattr(-,root,root)
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##
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%{?with_hpc:%dir %{my_incdir}}
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%doc release_docs/HISTORY-1_0-1_8_0_rc3.txt
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@ -1031,7 +1023,6 @@ export HDF5_Make_Ignore=yes
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%{my_incdir}/*.mod
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%files devel-static
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%defattr(-,root,root)
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%{my_libdir}/*.a
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|
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%changelog
|
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|
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