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Accepting request 848496 from home:anag:branches:science

Browse Source 
- Update to version 1.10.7
  * https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6-RELEASE.txt
  * https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7-RELEASE.txt
- Security bugs fixed: 
  * CVE-2018-13870: heap-based buffer over-read in the function 
    H5O_link_decode in H5Olink.c  (bsc#1101493)
  * CVE-2018-13869: memcpy parameter overlap in the function 
    H5O_link_decode in H5Olink.c (bsc#1101495)
  * CVE-2018-17438:  A SIGFPE signal is raised in the function 
    H5D__select_io() of H5Dselect.c in the HDF HDF5 through 1.10.3 
    library during an attempted parse of a crafted HDF file, 
    because of incorrect protection against division
    (bsc#1109570)
  * CVE-2018-17435: A heap-based buffer over-read in H5O_attr_decode() 
    in H5Oattr.c in the HDF HDF5 through 1.10.3 library allows 
    attackers to cause a denial of service via a crafted HDF5 file. 
    (bsc#1109567)
- Refresh patches

- Security bugs fixed: 
  * CVE-2018-17233: A SIGFPE signal is raised in the function 
  H5D__create_chunk_file_map_hyper. (bsc#1109166)
  * CVE-2018-17434: Memory leak in the H5O__chunk_deserialize() 
  function in H5Ocache.c (bsc#1109167)
  * CVE-2018-17437: A SIGFPE signal is raised in the function 
  H5D__chunk_set_info_real. (bsc#1109168)
- Security bugs fixed: 
  * CVE-2017-17505: NULL pointer dereference in the function
    H5O_pline_decode allowing for DoS via crafted file (bsc#1072087)
  * CVE-2017-17506: Out of bounds read in the function

OBS-URL: https://build.opensuse.org/request/show/848496
OBS-URL: https://build.opensuse.org/package/show/science/hdf5?expand=0&rev=139
This commit is contained in:
Ana Guerrero 2020-11-14 11:11:35 +00:00 committed by Git OBS Bridge
parent 6eaaf55460
commit f7f6dfb4d4
9 changed files with 85 additions and 46 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
Disable-phdf5-tests.patch
View File

@ -12,9 +12,9 @@ Index: hdf5-1.10.5/testpar/CMakeTests.cmake
===================================================================
--- hdf5-1.10.5.orig/testpar/CMakeTests.cmake
+++ hdf5-1.10.5/testpar/CMakeTests.cmake
@@ -30,7 +30,7 @@ set (SKIP_testphdf5 "")
# set (SKIP_testphdf5 "${SKIP_testphdf5};-x;ecdsetw")
#endif ()
@@ -43,7 +43,7 @@
set (SKIP_testphdf5 "${SKIP_testphdf5};-x;${skiptest}")
endforeach ()
-add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
+##add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})

16
PPC64LE-Fix-long-double-handling.patch
View File

@ -11,10 +11,10 @@ Signed-off-by: Egbert Eich <eich@suse.com>
hdf5-1.10.1/test/dt_arith.c | 26 ++++++++++++++++++++++++--
2 files changed, 40 insertions(+), 2 deletions(-)
Index: hdf5-1.10.5/config/cmake/ConversionTests.c
Index: hdf5-1.10.7/config/cmake/ConversionTests.c
===================================================================
--- hdf5-1.10.5.orig/config/cmake/ConversionTests.c
+++ hdf5-1.10.5/config/cmake/ConversionTests.c
--- hdf5-1.10.7.orig/config/cmake/ConversionTests.c
+++ hdf5-1.10.7/config/cmake/ConversionTests.c
@@ -34,6 +34,14 @@ int HDF_NO_UBSAN main(void)
unsigned char s2[8];
int ret = 1;
@ -45,11 +45,11 @@ Index: hdf5-1.10.5/config/cmake/ConversionTests.c
if(sizeof(long double) == 16) {
/*make sure the long double type is the same as the failing type
*which has 16 bytes in size and 11 bits of exponent. If it is,
Index: hdf5-1.10.5/test/dt_arith.c
Index: hdf5-1.10.7/test/dt_arith.c
===================================================================
--- hdf5-1.10.5.orig/test/dt_arith.c
+++ hdf5-1.10.5/test/dt_arith.c
@@ -3051,7 +3051,18 @@ test_conv_flt_1 (const char *name, int r
--- hdf5-1.10.7.orig/test/dt_arith.c
+++ hdf5-1.10.7/test/dt_arith.c
@@ -3045,7 +3045,18 @@ test_conv_flt_1 (const char *name, int r
buf, saved, nelmts);
#if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0
} else if(src_type == FLT_LDOUBLE) {
@ -69,7 +69,7 @@ Index: hdf5-1.10.5/test/dt_arith.c
buf, saved, nelmts);
#endif
} else
@@ -3711,7 +3722,18 @@ test_conv_int_fp(const char *name, int r
@@ -3705,7 +3716,18 @@ test_conv_int_fp(const char *name, int r
INIT_FP_DENORM(long double, LDBL_MANT_DIG, src_size, src_nbits, sendian, dst_size,
buf, saved, nelmts);
} else {

3
hdf5-1.10.5.tar.bz2
View File

@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44
size 8706317

3
hdf5-1.10.7.tar.bz2 Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:02018fac7e5efc496d9539a303cfb41924a5dadffab05df9812096e273efa55e
size 8957844

4
hdf5-1.8.11-abort_unknown_host_config.patch
View File

@ -2,7 +2,7 @@ Index: configure
===================================================================
--- configure.orig
+++ configure
@@ -4097,6 +4097,8 @@ done
@@ -4160,6 +4160,8 @@ done
if test "X$host_config" != "Xnone"; then
CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
. $host_config
@ -15,7 +15,7 @@ Index: configure.ac
===================================================================
--- configure.ac.orig
+++ configure.ac
@@ -263,6 +263,8 @@ done
@@ -271,6 +271,8 @@ done
if test "X$host_config" != "Xnone"; then
CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
. $host_config

10
hdf5-LD_LIBRARY_PATH.patch
View File

@ -1,8 +1,8 @@
Index: hdf5-1.10.5/src/Makefile.in
Index: hdf5-1.10.7/src/Makefile.in
===================================================================
--- hdf5-1.10.5.orig/src/Makefile.in
+++ hdf5-1.10.5/src/Makefile.in
@@ -1873,8 +1873,6 @@ help:
--- hdf5-1.10.7.orig/src/Makefile.in
+++ hdf5-1.10.7/src/Makefile.in
@@ -1941,8 +1941,6 @@ help:
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5Tinit.c: H5detect$(EXEEXT)
@ -11,7 +11,7 @@ Index: hdf5-1.10.5/src/Makefile.in
$(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)
@@ -1885,8 +1883,6 @@ H5Tinit.c: H5detect$(EXEEXT)
@@ -1953,8 +1951,6 @@ 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

8
hdf5-Remove-timestamps-from-binaries.patch
View File

@ -10,11 +10,11 @@ Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5detect.c | 15 ---------------
1 file changed, 15 deletions(-)
Index: hdf5-1.10.5/src/H5detect.c
Index: hdf5-1.10.7/src/H5detect.c
===================================================================
--- hdf5-1.10.5.orig/src/H5detect.c
+++ hdf5-1.10.5/src/H5detect.c
@@ -1245,21 +1245,6 @@ bit.\n";
--- hdf5-1.10.7.orig/src/H5detect.c
+++ hdf5-1.10.7/src/H5detect.c
@@ -1234,21 +1234,6 @@ bit.\n";
fprintf(rawoutstream, "/* Generated automatically by H5detect -- do not edit */\n\n\n");
HDfputs(FileHeader, rawoutstream); /*the copyright notice--see top of this file */

50
hdf5.changes
View File

@ -1,3 +1,25 @@
-------------------------------------------------------------------
Fri Nov 6 10:41:02 UTC 2020 - Ana Guerrero Lopez <aguerrero@suse.com>
- Update to version 1.10.7
* https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6-RELEASE.txt
* https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7-RELEASE.txt
- Security bugs fixed:
* CVE-2018-13870: heap-based buffer over-read in the function
H5O_link_decode in H5Olink.c (bsc#1101493)
* CVE-2018-13869: memcpy parameter overlap in the function
H5O_link_decode in H5Olink.c (bsc#1101495)
* CVE-2018-17438: A SIGFPE signal is raised in the function
H5D__select_io() of H5Dselect.c in the HDF HDF5 through 1.10.3
library during an attempted parse of a crafted HDF file,
because of incorrect protection against division
(bsc#1109570)
* CVE-2018-17435: A heap-based buffer over-read in H5O_attr_decode()
in H5Oattr.c in the HDF HDF5 through 1.10.3 library allows
attackers to cause a denial of service via a crafted HDF5 file.
(bsc#1109567)
- Refresh patches
-------------------------------------------------------------------
Thu Jul 23 16:33:58 UTC 2020 - Egbert Eich <eich@suse.com>
@ -71,6 +93,13 @@ Fri Aug 23 09:58:01 UTC 2019 - Ana Guerrero Lopez <aguerrero@suse.com>
- Update to version 1.10.5: (jsc#SLE-8501)
* https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5-RELEASE.txt
- Security bugs fixed:
* CVE-2018-17233: A SIGFPE signal is raised in the function
H5D__create_chunk_file_map_hyper. (bsc#1109166)
* CVE-2018-17434: Memory leak in the H5O__chunk_deserialize()
function in H5Ocache.c (bsc#1109167)
* CVE-2018-17437: A SIGFPE signal is raised in the function
H5D__chunk_set_info_real. (bsc#1109168)
- Bump fortran library soname, sonum_F from 100 to 102.
- Adjust library installation path, use %hpc_prefix/lib64 in x86_64
and %hpc_libdir in all other cases
@ -86,7 +115,6 @@ Fri Aug 23 09:58:01 UTC 2019 - Ana Guerrero Lopez <aguerrero@suse.com>
- Patch removed, merged upstream
* 0001-Fix-return-value-in-test_libver_bounds_open.patch
-------------------------------------------------------------------
Thu Jul 4 11:45:55 UTC 2019 - Egbert Eich <eich@suse.com>
@ -202,6 +230,26 @@ Fri Sep 21 14:50:12 UTC 2018 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
* hdf5-buildcompare.patch
* hdf5-mpi.patch
- Rebase Disable-phdf5-tests.patch
- Security bugs fixed:
* CVE-2017-17505: NULL pointer dereference in the function
H5O_pline_decode allowing for DoS via crafted file (bsc#1072087)
* CVE-2017-17506: Out of bounds read in the function
H5Opline_pline_decode (bsc#1072090)
* CVE-2017-17508: divide-by-zero vulnerability in function
H5T_set_loc (bsc#1072108)
* CVE-2017-17509: out of bounds write vulnerability in function
H5G__ent_decode_vec (bsc#1072111)
* CVE-2018-11202: NULL pointer dereference in H5S_hyper_make_spans
in H5Shyper.c allows a remote denial of service attack (bsc#1093641)
* CVE-2018-11203: division by zero in H5D__btree_decode_key in H5Dbtree.c
It could allow a remote denial of service attack (bsc#1093649)
* CVE-2018-11204: A NULL pointer dereference was discovered in
H5O__chunk_deserialize in H5Ocache.c (bsc#1093655)
* CVE-2018-11206: A out of bounds read was discovered
in H5O_fill_new_decode and H5O_fill_old_decode in H5Ofill.c
(bsc#1093657)
* CVE-2018-11207: division by zero was discovered in H5D__chunk_init
in H5Dchunk.c (bsc#1093653)
-------------------------------------------------------------------
Tue Jun 19 06:15:06 UTC 2018 - eich@suse.com

29
hdf5.spec
View File

@ -34,8 +34,8 @@
%define use_sz2 0
%define vers 1.10.5
%define _vers 1_10_5
%define vers 1.10.7
%define _vers 1_10_7
%define short_ver 1.10
%define src_ver %{version}
%define pname hdf5
@ -785,13 +785,13 @@ make install DESTDIR=%{buildroot}
find %{buildroot} -type f -name "*.la" -delete -print
%if %{without mpi}
find %{buildroot}%{_prefix}/share/hdf5_examples -type f \
| grep -v ".sh$" | xargs chmod 644
%if %{with hpc}
# copy to versioned subdir
install -m 755 -d %{buildroot}%{_prefix}/share/%{version}
mv %{buildroot}%{_prefix}/share/hdf5_examples/* \
%{buildroot}%{_prefix}/share/%{version}
install -m 755 -d %{buildroot}%{_prefix}/share/hdf5_examples
mv %{buildroot}%{_prefix}/lib/hpc/*/hdf5/*/share/hdf5_examples/* \
%{buildroot}%{_prefix}/share/%{version}/
mv %{buildroot}%{_prefix}/share/%{version} \
%{buildroot}%{_prefix}/share/hdf5_examples
%else
@ -805,9 +805,10 @@ cat > %{buildroot}%{_rpmconfigdir}/macros.d/macros.hdf5 <<EOF
%_hdf5_version %{version}
EOF
%endif
%else
# delete examples from parallel builds
rm -rf %{buildroot}%{_prefix}/share/hdf5_examples
find %{buildroot} -type d -name "hdf5_examples" -exec rm -rf {} +;
%endif
%fdupes -s %{buildroot}/%{_datadir}
@ -906,19 +907,16 @@ export HDF5_Make_Ignore=yes
%if %{without mpi}
%files -n %{vname}-examples
%defattr(-,root,root)
%{?with_hpc:%dir %{_prefix}/share/hdf5_examples}
%{_prefix}/share/hdf5_examples%{?with_hpc:/%{version}}
%if %{without hpc}
%files -n %{pname}-devel-data
%defattr(-,root,root,-)
%{_rpmconfigdir}/macros.d/macros.hdf5
%endif
%endif # ?mpi
%files -n %{name}
%defattr(-,root,root)
%{?with_hpc:%dir %my_bindir}
%{my_bindir}/gif2h5
%{my_bindir}/h52gif
@ -943,9 +941,10 @@ export HDF5_Make_Ignore=yes
%{my_bindir}/h5stat
%{my_bindir}/h5unjam
%{my_bindir}/h5watch
%{my_bindir}/mirror_server
%{my_bindir}/mirror_server_stop
%files -n %{libname -s %{sonum}}
%defattr(-,root,root)
%doc ACKNOWLEDGMENTS README.txt
%mylicense COPYING
##
@ -959,7 +958,6 @@ export HDF5_Make_Ignore=yes
%{my_libdir}/libhdf5.so.%{sonum}.*
%files -n %{libname -l _hl -s %{sonum_HL}}
%defattr(-,root,root)
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
@ -967,7 +965,6 @@ export HDF5_Make_Ignore=yes
%{my_libdir}/libhdf5_hl.so.%{sonum_HL}.*
%files -n %{libname -l _cpp -s %{sonum_CXX}}
%defattr(-,root,root)
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
@ -975,7 +972,6 @@ export HDF5_Make_Ignore=yes
%{my_libdir}/libhdf5_cpp.so.%{sonum_CXX}.*
%files -n %{libname -l _hl_cpp -s %{sonum_HL_CXX}}
%defattr(-,root,root)
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
@ -983,7 +979,6 @@ export HDF5_Make_Ignore=yes
%{my_libdir}/libhdf5_hl_cpp.so.%{sonum_HL_CXX}.*
%files -n %{libname -l _fortran -s %{sonum_F}}
%defattr(-,root,root)
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
@ -991,7 +986,6 @@ export HDF5_Make_Ignore=yes
%{my_libdir}/libhdf5_fortran.so.%{sonum_F}.*
%files -n %{libname -l hl_fortran -s %{sonum_HL_F}}
%defattr(-,root,root)
%mylicense COPYING
%defattr(0755,root,root)
%{?with_hpc:%hpc_dirs}
@ -1000,12 +994,10 @@ export HDF5_Make_Ignore=yes
%if %{with hpc}
%files module
%defattr(-,root,root)
%hpc_modules_files
%endif
%files devel
%defattr(-,root,root)
##
%{?with_hpc:%dir %{my_incdir}}
%doc release_docs/HISTORY-1_0-1_8_0_rc3.txt
@ -1031,7 +1023,6 @@ export HDF5_Make_Ignore=yes
%{my_incdir}/*.mod
%files devel-static
%defattr(-,root,root)
%{my_libdir}/*.a
%changelog