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File hdf5.changes of Package hdf5.24260
------------------------------------------------------------------- Wed May 4 06:39:53 UTC 2022 - Egbert Eich <eich@suse.com> - Security Fix: Add configure option --disable-hltools to disable GIF tools as recommended in the 1.10.8 release: CVE-2018-17433 (bsc#1109565), CVE-2018-17436 (bsc#1109568), CVE-2020-10809 (bsc#1167404). ------------------------------------------------------------------- Thu Apr 7 23:51:05 UTC 2022 - Christoph Junghans <junghans@votca.org> - add hdf5-wrappers.patch from Fedora, so strip flags from wrappers and prefer shared linking - add missing zlib-devel devel dep ------------------------------------------------------------------- Thu Mar 31 08:25:44 UTC 2022 - Ben Greiner <code@bnavigator.de> - Add hdf5-1.10.8-pr1494-fix-release-check-version.patch * boo#1179521, boo#1196682, gh#HDFGroup/hdf5#1494 * Avoids package crashes due to an overeager version check. Packages depending on the shared libraries are not being rebuilt in Factory after a patchlevel version bump of hdf5 without SONAME changes. ------------------------------------------------------------------- Wed Feb 16 11:18:17 UTC 2022 - Atri Bhattacharya <badshah400@gmail.com> - Update to version 1.10.8: * Added new option to control the build of High-Level tools * Adds C++ Autotools configuration file for Intel * Adds C++ Autotools configuration file for PGI * Updates PGI C options * CMake will now run the shell script tests in test/ by default * Removed unused HDF5_ENABLE_HSIZET option from CMake * CMake no longer builds the C++ library by default * Removal of pre-VS2015 work-arounds * Add CMake variable HDF5_LIB_INFIX * Added a configure-time option to control certain compiler warnings * CMake option to build the HDF filter plugins project as an external project * Added a configure-time option to consider certain compiler warnings * Autotools and CMake target added to produce doxygen generated documentation * CMake option to build the HDF filter plugins project as an external project * Added CMake option to format source files * Change how the release part of version, in major.minor.release is checked * H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX * H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID * Fixes a segfault when H5Pset_mdc_log_options() is called multiple times * File locking now works on Windows * H5Epush_ret() now requires a trailing semicolon * Improved performance of H5Sget_select_elem_pointlist * H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers. * Added new H5S functions. * Refactored the perform tools and removed dependencies on test library. * h5repack added help text for user-defined filters. * Doxygen documentation is available when configured and generated. * Fixed CVE-2018-17432 (bsc#1109564) * Fixed a segmentation fault * Detection of simple data transform function "x" * Fixed CVE-2020-10810 - an invalid read and memory leak when parsing (bsc#1167401) * Fixed CVE-2018-14460 (bsc#1102175) * Fixed CVE-2018-11206 (bsc#1093657) (same issue as CVE-2018-14032 (bsc#1101474)) * Fixed CVE-2018-14033 (bsc#1101471) (same issue as CVE-2020-10811 (bsc#1167405)) * Remove underscores on header file guards * H5FArray.java class: - Convert the entire byte array into a 1-d array of the desired type, rather than performing 1 conversion per row; - Use the Java Arrays method copyOfRange to grab the section of the array from (1) that is desired to be inserted into the destination array. * Corrected path searched by CMake find_package command * Corrected pkg-config compile script * Fixed CMake C++ compiler flags * Autotools clang debug optimization level change * Better support for libaec (open-source Szip library) in CMake * Refactor CMake configure for Fortran * Remove arbitrary warning flag groups from CMake builds * Reclassify CMake messages, to allow new modes and --log-level option * Fixes Autotools determination of the stat struct having an st_blocks field * Changed how h5dump and h5ls identify long double. * Fixed tools argument parsing. * Updated doxygen comments with changes for release - Minor rebase of patches to apply cleanly. ------------------------------------------------------------------- Fri Jan 29 22:05:44 UTC 2021 - Egbert Eich <eich@suse.com> - Fix update_so_version.sh, write so versions to file being included. ------------------------------------------------------------------- Fri Nov 6 10:41:02 UTC 2020 - Ana Guerrero Lopez <aguerrero@suse.com> - Update to version 1.10.7 * Add metadata cache optimization to reduce skip list usage. * Add BEST_EFFORT value to HDF5_USE_FILE_LOCKING environment variable. * Add H5Pset/get_file_locking() API calls. * Add Mirror VFD. Use TCP/IP sockets to perform write-only (W/O) file I/O on a remote machine. Must be used in conjunction with the Splitter VFD. * Add Splitter VFD. Maintain separate R/W and W/O channels for "concurrent" file writes to two files using a single HDF5 file handle. * Fixed an assertion failure in the parallel library when collectively filling chunks. * Fortran/C++ libs: Add wrappers for H5Pset/get_file_locking() API calls. h5pget_file_locking_f() h5pset_file_locking_f() * Added new Fortran parameters: H5F_LIBVER_ERROR_F H5F_LIBVER_NBOUNDS_F H5F_LIBVER_V18_F H5F_LIBVER_V110_F * Add new Fortran API: h5pget_libver_bounds_f. * h5repack added options to control how external links are handled. * The tools library was updated by standardizing the error stack process. * The H5DSis_scale function was updated to return "not a dimension scale" (0) instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are not written according to Dimension Scales Specification. * Bug Fixes: + Fix bug and simplify collective metadata write operation when some ranks have no entries to contribute. This fixes parallel regression test failures with IBM SpectrumScale MPI on the Summit system at ORNL. + Fixed use-of-uninitialized-value error. Appropriate initialization of local structs was added to remove the use-of-uninitialized-value errors reported by MemorySanitizer. + Creation of dataset with optional filter. A fix is applied to allow the creation of a dataset in such situation, as specified in the user documentation. + Explicitly declared dlopen to use RTLD_LOCAL. + H5Sset_extent_none() sets the dataspace class to H5S_NO_CLASS which causes asserts/errors when passed to other dataspace API calls. + Fixed the segmentation fault when reading attributes with multiple threads The problem was fixed by setting the file pointer to the current opened file pointer when the attribute was accessed. Similar patch up was done before when reading dataset with variable length string datatype. + Don't allocate an empty (0-dimensioned) chunked dataset's chunk index, until the dataset's dimensions are increased. + Fortan: Corrected INTERFACE INTENT(IN) to INTENT(OUT) for buf_size in h5fget_file_image_f. + h5diff fixed a command line parsing error. + h5diff added a command line option to ignore attributes. + h5diff added another level to the verbose argument to print filenames. + h5repack was fixed to repack the reference attributes properly. * For details check: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7-RELEASE.txt - version 1.10.6 * Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5. Instructions to enable them when configuring HDF5 on Linux and Mac may be found at. https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS. * Added new wrappers for H5Pset/get_create_intermediate_group() LinkCreatPropList::setCreateIntermediateGroup() LinkCreatPropList::getCreateIntermediateGroup() * h5repack was fixed to repack datasets with external storage to other types of storage. * Bug Fixes: + Improved performance when creating a large number of small datasets by retrieving default property values from the API context instead of doing skip list searches. More work is required to achieve parity with HDF5 1.8. + Fixed user-created data access properties not existing in the property list returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a reproducer and a patch. + Inappropriate linking with deprecated MPI C++ libraries. HDF5 does not define *_SKIP_MPICXX in the public headers, so applications can inadvertently wind up linking to the deprecated MPI C++ wrappers. MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h so this should no longer be an issue. HDF5 makes no use of the deprecated MPI C++ wrappers. + fcntl(2)-based file locking incorrectly passed the lock argument struct instead of a pointer to the struct, causing errors on systems where flock(2) is not available. This bug affects HDF5 1.10.0 through 1.10.5. fcntl(2)-based file locking now correctly passes the struct pointer. + Fixed a bug caused by a bad tag value when condensing object header messages. + Fixed an issue when creating a file with non-default file space info together with library high bound setting to H5F_LIBVER_V18. This was fixed by setting and checking the proper version in the file space info message based on the library low and high bounds when creating and opening the HDF5 file. + Fixed an issue where copying a version 1.8 dataset between files using H5Ocopy fails due to an incompatible fill version. + Fixed a bug that would cause an error or cause fill values to be incorrectly read from a chunked dataset using the "single chunk" index if + Fixed a bug that could cause an error or cause fill values to be incorrectly read from a dataset that was written to using H5Dwrite_chunk if the dataset was not closed after writing. + Fixed memory leak in scale offset filter. * For details check: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6-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 (bsc#1109570) 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> - Add build support for gcc10 to HPC build (bsc#1174439). ------------------------------------------------------------------- Mon Jul 20 14:48:42 UTC 2020 - Egbert Eich <eich@suse.com> - Add missing openmpi4 flavors. - Enable build of non-HPC flavors for all non-HPC builds. ------------------------------------------------------------------- Wed Jun 24 07:32:58 UTC 2020 - Alin M Elena <alinm.elena@gmail.com> - add openmpi4 packages to build and disable build for leap ------------------------------------------------------------------- Fri Apr 17 14:54:44 UTC 2020 - Egbert Eich <eich@suse.com> - Fix .so number in baselibs.conf for libhdf5_fortran libs (boo#1169793). ------------------------------------------------------------------- Thu Apr 2 07:49:26 UTC 2020 - Egbert Eich <eich@suse.com> - Fix library link flags on pkg-config file for HPC builds (boo#1134298). ------------------------------------------------------------------- Mon Jan 20 00:47:04 UTC 2020 - Stefan Brüns <stefan.bruens@rwth-aachen.de> - Remove bogus undefines of suffix and mpi_flavor. suffix is the name of an RPM built-in (like expand or echo), and since RPM 4.15 trying to alter a built-in is an error. Fixes built of serial flavor on Tumbleweed. See https://rpm.org/user_doc/macros.html ------------------------------------------------------------------- Tue Dec 10 16:30:03 UTC 2019 - Stefan Brüns <stefan.bruens@rwth-aachen.de> - Add compat provides for renamed hdf5-openmpi{,-devel} package, see https://en.opensuse.org/openSUSE:Package_dependencies - Fix openmpi1 package naming for SLE/Leap <= 15.1 ------------------------------------------------------------------- Thu Nov 28 18:13:10 UTC 2019 - Egbert Eich <eich@suse.com> - Add HPC support for gcc8 and gcc9 (jsc#SLE-7766 & jsc#SLE-8604). ------------------------------------------------------------------- Thu Nov 28 15:54:19 UTC 2019 - Egbert Eich <eich@suse.com> - Disable openmpi1 builds for SLE/Leap > 15.1. - Enable openmpi3 builds for Leap and SLE > 15.1 (jsc#SLE-7773). ------------------------------------------------------------------- Thu Oct 24 06:37:26 UTC 2019 - Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com> - openmpi has been renamed into openmpi1 ------------------------------------------------------------------- Tue Sep 10 07:54:05 UTC 2019 - Ana Guerrero Lopez <aguerrero@suse.com> - Use -ffat-lto-objects to provide a proper static library. ------------------------------------------------------------------- Tue Sep 3 10:17:31 UTC 2019 - Ana Guerrero Lopez <aguerrero@suse.com> - Re-list hdf5-mpi.patch in the spec file for the sake of a avoiding a script rejecting the package automatically. ------------------------------------------------------------------- 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-2018-17234: Memory leak in the H5O__chunk_deserialize() function in H5Ocache.c (bsc#1109167) * CVE-2018-17434: A SIGFPE signal is raised in function apply_filters() of h5repack_filters.c (bsc#1109566) * CVE-2018-17437: Memory leak in the H5O_dtype_decode_helper() function in H5Odtype.c. (bsc#1109569) * CVE-2018-17237: A SIGFPE signal is raised in the function H5D__chunk_set_info_real (bsc#1109168) (commit 4e31361d). - 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 - Patches refreshed: * hdf5-LD_LIBRARY_PATH.patch * hdf5-1.8.11-abort_unknown_host_config.patch * PPC64LE-Fix-long-double-handling.patch * hdf5-Remove-timestamps-from-binaries.patch * Disable-phdf5-tests.patch - Patch disabled, upstream have changed the file that was being patched, while it could be ported, it's unknown if this patch is still needed. * hdf5-mpi.patch - 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> - Since build machine size issues do not seem to go way, make the %check stage optional: enable with '--with check'. ------------------------------------------------------------------- Thu Apr 25 08:51:47 UTC 2019 - Christian Goll <cgoll@suse.com> - set higher constraints for succesfull mpich tests (boo#1133222) ------------------------------------------------------------------- Mon Apr 1 12:41:23 UTC 2019 - normand@linux.vnet.ibm.com - Add _constraints to avoid transient build error ppc64le ------------------------------------------------------------------- Sat Mar 9 15:04:06 UTC 2019 - Stefan Brüns <stefan.bruens@rwth-aachen.de> - Update URL: and Source: to use https://. ------------------------------------------------------------------- Fri Mar 1 12:19:33 UTC 2019 - Egbert Eich <eich@suse.com> - Like on PPC ignore transient 'make check' failures on aarch64. ------------------------------------------------------------------- Fri Mar 1 09:37:54 UTC 2019 - Egbert Eich <eich@suse.com> - Remove ringdisabled magic as hdf5 is no longer a ring package. This should resolve a number of problems in the review channels for Factory with packages requiring hdf5 libs. ------------------------------------------------------------------- Wed Feb 13 10:37:28 UTC 2019 - Egbert Eich <eich@suse.com> - Consolidate use of openmpi1, openmpi2, openmpi3 for non-HPC builds. ------------------------------------------------------------------- Fri Jan 25 19:14:31 UTC 2019 - eich@suse.com - Remove dependency to the hdf5-devel-data file for HPC: Currently, there are no macro files for HPC - these files will have to be handled differently. - Re-disable all non-HPC builds for SLE. ------------------------------------------------------------------- Mon Jan 14 08:56:39 UTC 2019 - eich@suse.com - Reenable 'serial' build for SLE: this build creates hdf5-devel-data. ------------------------------------------------------------------- Thu Jan 3 11:39:58 UTC 2019 - eich@suse.com - Do not build non-HPC on SLE: This helps to save some build cycles. ------------------------------------------------------------------- Wed Dec 19 19:54:05 UTC 2018 - Todd R <toddrme2178@gmail.com> - Use upstream-recommended %{_rpmconfigdir}/macros.d directory for the rpm macros. ------------------------------------------------------------------- Wed Dec 12 15:28:48 UTC 2018 - Todd R <toddrme2178@gmail.com> - Also build for regular openmpi2 and openmpi3 ------------------------------------------------------------------- Thu Nov 22 18:15:55 UTC 2018 - Stefan Brüns <stefan.bruens@rwth-aachen.de> - Build HDF5 C++ bindings also for the MPI variants, there is no reason not to do it. - Enable sz2 support also for MPI variants. ------------------------------------------------------------------- Mon Nov 19 08:52:43 UTC 2018 - eich@suse.com - Replace git-archive generated by downloaded tar-ball. ------------------------------------------------------------------- Sat Nov 17 17:21:00 UTC 2018 - eich@suse.com - Update to 1.10.4: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.4/src/hdf5-1.10.4-RELEASE.txt * Update Disable-phdf5-tests.patch * Replace and update hdf5-buildcompare.patch by hdf5-Remove-timestamps-from-binaries.patch ------------------------------------------------------------------- Fri Nov 16 23:09:01 UTC 2018 - eich@suse.com - Remove lib*_cpp and lib*_hl_cpp dependencies for MPI for the time being. ------------------------------------------------------------------- Sun Nov 11 12:15:14 UTC 2018 - eich@suse.com - Create main master package, fix dependencies. ------------------------------------------------------------------- Fri Sep 21 14:50:12 UTC 2018 - Stefan Brüns <stefan.bruens@rwth-aachen.de> - Update to 1.10.3: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.3/src/hdf5-1.10.3-RELEASE.txt - Update to 1.10.2: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt - Bump soversions (101 -> 103) for libhdf5 and libhdf5_cpp - Drop Fix-warnings-for-missing-returns.patch, fixed upstream - Add 0001-Fix-return-value-in-test_libver_bounds_open.patch - Rebase patches (tab / space conversion): * PPC64LE-Fix-long-double-handling.patch * 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 - Handle license file using %license where applicable. - Package example package also for HPC build and create a master file for it. ------------------------------------------------------------------- Fri Apr 27 14:20:25 UTC 2018 - eich@suse.com - Fix HPC library master packages dependency: make it require the correct flavor (bsc#1091237). ------------------------------------------------------------------- Sat Apr 7 22:31:05 UTC 2018 - eich@suse.com - Only build one examples package for all flavors, do not include dependencies as these would be flavor specific (bsc#1088547). ------------------------------------------------------------------- Sat Mar 31 23:53:50 UTC 2018 - stefan.bruens@rwth-aachen.de - Fix some typos, one trivial, two mispelled macros ------------------------------------------------------------------- Sat Feb 10 23:04:47 UTC 2018 - jengelh@inai.de - Trim description for size and drop most of the marketing blurb. Fix RPM groups. ------------------------------------------------------------------- Sat Feb 10 17:40:10 UTC 2018 - eich@suse.com - Make module files package arch dependent: it contains arch-dependent paths (boo#1080442). ------------------------------------------------------------------- Sat Feb 10 07:31:46 UTC 2018 - eich@suse.com - Prepend PKG_CONFIG_PATH in modules file (boo#1080426). ------------------------------------------------------------------- Fri Feb 9 20:10:17 UTC 2018 - eich@suse.com - Add support for openmpi2 for HPC (FATE#325089). ------------------------------------------------------------------- Fri Feb 9 13:48:43 UTC 2018 - cgoll@suse.com - Fix summary in module files (bnc#1080259) ------------------------------------------------------------------- Thu Feb 8 11:37:06 UTC 2018 - eich@suse.com - Disable %check stage for mpich builds on s390(x) (bsc#1080022). ------------------------------------------------------------------- Fri Jan 12 15:38:59 UTC 2018 - eich@suse.com - Disable the openmpi3 flavor in some products. ------------------------------------------------------------------- Fri Jan 5 18:34:20 UTC 2018 - eich@suse.com - Switch from gcc6 to gcc7 as additional compiler flavor for HPC on SLES. - Add support for mpich and openmpi3 for HPC. ------------------------------------------------------------------- Thu Nov 9 15:02:35 UTC 2017 - normand@linux.vnet.ibm.com - temporarily disable make check for PowerPC boo#1058563 ------------------------------------------------------------------- Tue Nov 7 13:23:40 UTC 2017 - eich@suse.com - Update to 1.10.1: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1-RELEASE.txt - Fix-warnings-for-missing-returns.patch: replace: hdf5-non_void_return.patch - PPC64LE-Fix-long-double-handling.patch: replace: hdf5-ldouble-ppc64le.patch - Disable-phdf5-tests.patch: replace: hdf5_disable_testphdf5.patch - Disabling validation tests for the MPI variant for now as they seem to cause issues in OBS. ------------------------------------------------------------------- Thu Oct 26 15:51:18 UTC 2017 - eich@suse.com - Fix name: baselib.conf -> baselibs.conf ------------------------------------------------------------------- Sun Oct 22 08:46:29 UTC 2017 - eich@suse.com - Remove openssl-devel and krb5-devel from the BuildRequires. ------------------------------------------------------------------- Tue Oct 17 14:07:15 UTC 2017 - eich@suse.com - Add magic to limit the number of flavors built in the OBS ring to non-HPC and mvapich2 builds. - Fix %libname() for non-HPC builds. - Fix some summaries and a Requires: of devel-static. ------------------------------------------------------------------- Fri Sep 8 14:35:32 UTC 2017 - eich@suse.com - Convert package to multibuild. - Add HPC build using environment modules (FATE#321717, FATE#321710). ------------------------------------------------------------------- Tue Aug 29 12:03:27 UTC 2017 - hpj@urpla.net - fix compiler flag substitution ------------------------------------------------------------------- Mon Jul 3 12:53:05 UTC 2017 - badshah400@gmail.com - Add libsz2-devel to list of Requires for -devel packages, this is required for compilation against hdf5 when szlib support is enabled. - Minor specfile cleanups using spec-cleaner. ------------------------------------------------------------------- Fri Jun 16 21:13:30 UTC 2017 - junghans@votca.org - Enabled szlib support through libaec's szlib API ------------------------------------------------------------------- Wed Oct 5 19:03:35 UTC 2016 - toddrme2178@gmail.com - Fix baselibs.conf so numbers. Fixes bnc#1002569 ------------------------------------------------------------------- Tue Sep 6 08:51:09 UTC 2016 - normand@linux.vnet.ibm.com - new hdf5_disable_testphdf5.patch to disable only testphdf5 for all arches and not all mpi tests for ppc64le tempo patch as long as boo#997252 not solved ------------------------------------------------------------------- Mon Sep 5 11:00:59 UTC 2016 - normand@linux.vnet.ibm.com - temporarily disable mpi test for ppc64le ------------------------------------------------------------------- Tue Jul 26 15:50:22 UTC 2016 - adrian@suse.de - update to 1.10.0-patch1 https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.0-patch1/src/hdf5-1.10.0-patch1-RELEASE.txt ------------------------------------------------------------------- Mon May 23 21:29:44 UTC 2016 - toddrme2178@gmail.com - update to 1.8.17, changes documented here: https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.17/src/hdf5-1.8.17-RELEASE.txt ------------------------------------------------------------------- Fri Apr 15 11:26:40 UTC 2016 - normand@linux.vnet.ibm.com - add hdf5-mpi.patch same as fedora commit id 78ddcff82b10fd80eafb7b2dc5e4ce2bb9ecbe3c should avoid transient hung of t_pflush1 test ------------------------------------------------------------------- Fri Mar 18 14:26:42 UTC 2016 - toddrme2178@gmail.com - Split libraries into C, C++, and Fortran versions to comply with openSUSE library packaging policies. Fixes BNC#971602 - Make Fortran builds required. - Manually set so numbers. The autodetected ones weren't matching the real ones. ------------------------------------------------------------------- Mon Mar 7 14:35:44 UTC 2016 - olaf@aepfle.de - Remove timestamps from binaries hdf5-buildcompare.patch ------------------------------------------------------------------- Thu Jan 28 00:08:01 UTC 2016 - sweet_f_a@gmx.de - update to 1.8.16, changes documented here: https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.16/src/hdf5-1.8.16-RELEASE.txt - rebase hdf5-ldouble-ppc64le.patch - remove hdf5-cpp-compilation-errors.patch - prepare independent so versions and add TODO ------------------------------------------------------------------- Fri Aug 21 09:45:05 UTC 2015 - toddrme2178@gmail.com - Currently the regular, openmpi, and mpivachi2 versions of the library packages all provide the exact same libraries. So any package built against the -devel package will end up with an "unresolvable" build error because there are multiple versions of the library it can use. To avoid this, I have added generic provides for the library package so packages can depend on the version they really need, avoiding these build issues. ------------------------------------------------------------------- Thu Aug 13 07:42:07 UTC 2015 - badshah400@gmail.com - Add hdf5-cpp-compilation-errors.patch: Reverts a change from v1.8.15 to H5api_adpt.h that caused compilation errors for C++ HDF5 applications; patch taken from upstream svn. ------------------------------------------------------------------- Mon Jul 27 11:11:12 UTC 2015 - toddrme2178@gmail.com - Update subpackage groups - Make subpackage summaries and descriptions more consistent - Provide rpm macros for version identification - Spec file cleanups ------------------------------------------------------------------- Mon Jul 27 10:06:49 UTC 2015 - toddrme2178@gmail.com - Use explicit library requirements to avoid ambiguities. Without this, packages that depend on hdf5 won't know which library to use. ------------------------------------------------------------------- Thu Jul 23 11:30:56 UTC 2015 - toddrme2178@gmail.com - Fix baselibs.conf ------------------------------------------------------------------- Wed Jul 22 11:23:14 UTC 2015 - toddrme2178@gmail.com - update to 1.8.15 * New Features + Library - Added Memory Allocation Functions that Use the Library's Allocator - H5Pset_istore_k and H5Pset_sym_k added validation of "ik" to not exceed the max v1 btree entries (2 bytes) to these two routines. - Added Functions to Control the Value of H5PL_no_plugin_g without Using an Environment Variable + Parallel Library - Attached an attribute destroy callback to MPI_COMM_SELF that shuts down the HDF5 library when MPI_COMM_SELF is destroyed, in other words, on MPI_Finalize. This should fix several issues that users see when they forget to close HDF5 objects before + Fortran API - Added Global Variables. These new global variables are equivalent to the C definitions without the '_F': o H5G_UDLINK_F o H5G_SAME_LOC_F o H5O_TYPE_UNKNOWN_F o H5O_TYPE_GROUP_F o H5O_TYPE_DATASET_F o H5O_NAMED_DATATYPE_F o H5O_TYPE_NTYPES_F + C++ API - New Wrappers for C Functions H5P[s/g]et_libver_bounds - New Wrappers to Get the Object Header's Version - New DataType Constructor + Support for New Platforms, Languages, and Compilers - Support for Linux 3.10.0-123.20.1.el7 added (LK - 2015/04/01) * Bug Fixes since HDF5-1.8.14 + Library - Addition of Error Tracing Functionality to Several C API Calls - H5Rdereference Now Checks for HADDR_UNDEF or Uninitialized References - Fixed Bugs in H5Sextent_copy + Parallel Library - Fixed a Potential Memory Error - Parallel Test Problem Fixed - MPE Support + Tools - h5repack crashed on enumerated 8-bit type. - h52gif crashed non-8bit images. - perform/benchpar.c retired. - Source perform/ directory moved to tools/perform. + Fortran API - Fortran Fails with --enable-fortran2003 and Intel 15.x Compilers - h5tenum_insert_f Does Not Work with Default 8 Byte Integers (xlf compiler) - Some Fortran APIs Never Returned the Error State - Fixed h5pget_class_f + C++ API - Combined Two H5File::getObjCount Overloaded Methods The following two methods o ssize_t getObjCount(unsigned types) const; o ssize_t getObjCount() const; were combined into one: o ssize_t getObjCount(unsigned types = H5F_OBJ_ALL) const; - Many Warnings Were Removed - Functionality Deprecation The following two constructors of classes AbstractDs, IdComponent, H5Location, and H5Object are no longer appropriate after the data member "id" had been moved from IdComponent to the sub-classes in previous releases. o <Classname>(const hid_t h5_id); o <Classname>(const <Classname>& original); The copy constructors were no-op and removed in 1.8.15. The other constructors will be removed from 1.10 release, and then from 1.8.17 if their removal does not cause any problems. + High-Level APIs: - Suppress Warnings from Flex/Bison-generated Code - Changed hdf5_hl.h to Include the HDF5 Main Library "hdf5.h" - H5PTcreate_fl Does Not Convert to Memory Datatype - Fix for H5LT Attribute Functions + Fortran High-Level APIs: - Internal Library Fix for Missing Argument Declaration - Build in thread-safe mode to allow parallel reads * These are only unsupported to avoid confusing casual users. The fotran and C++ libraries don't support thread-safe mode, while the C library does. So you have to explicitly allow building the thread-safe C library and the non-thread-safe C++ and fortran libraries in order to make sure only people who have done their research do so. Since users are going to be accessing this through other programs, this doesn't matter. - Build fortran 2003 libraries - Rebase hdf5-non_void_return.patch - Remove irrelevant hdf5-configure-long-double.patch ------------------------------------------------------------------- Mon May 11 13:37:50 UTC 2015 - dmueller@suse.com - update hdf5-non_void_return.patch for GCC 5.x ------------------------------------------------------------------- Tue Jan 13 11:07:12 CET 2015 - pth@suse.de - Tag baselibs.conf as source. ------------------------------------------------------------------- Fri Jan 9 12:45:39 UTC 2015 - sweet_f_a@gmx.de - fix typos in ChangeLog ------------------------------------------------------------------- Wed Nov 19 10:52:32 UTC 2014 - pgajdos@suse.com - updated to 1.8.14: * bugfix release, see RELEASE.txt ------------------------------------------------------------------- Mon Jun 23 11:57:36 UTC 2014 - pgajdos@suse.com - updated to 1.8.13: - Added an H5free_memory API call. This should be used to free memory that has been allocated by HDF5 API calls. H5Tget_member_name and H5Pget_class_name are two examples. The main motivation for this call is Windows, where it is common for application code and the HDF5 Library to be using different C run-time libraries (CRT). Using the new call ensures that the same CRT handles both the allocation and free. This new function can also be useful in any case where the library uses a different memory manager than the application, such as when a debug memory manager is in use or when the HDF5 Library is wrapped for use in a managed language like Python or Java. Fixes HDFFV-7710, 8519, and 8851. (DER - 2014/04/11) - The Core VFD (aka Memory VFD) can now be configured to track dirty regions in the file and only write out the changed regions on flush/close. Additionally, a "page aggregation" size can be set that will aggregate small writes into larger writes. For example, setting a 1 MiB page aggregation size will logically partition the the in-memory file into 1 MiB pages that will be written out in their entirety if even a single byte is dirtied. The feature is controlled via the new H5Pset/get_core_write_tracking() API call. A new "core_paged" target has been added to the check-vfd target in test/Makefile.am that exercises the feature over all HDF5 VFD-aware tests. (DER - 2014/04/12) - see http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.13-RELEASE.txt for more - modified patches: * hdf5-LD_LIBRARY_PATH.patch ------------------------------------------------------------------- Sun Jan 5 03:59:20 UTC 2014 - matz@suse.de - Detect IBM long double specialness on ppc64le and don't segfault int the testsuite when checking that type. Added patches: * hdf5-ldouble-ppc64le.patch ------------------------------------------------------------------- Tue Nov 26 14:27:16 UTC 2013 - pgajdos@suse.com - update to 1.8.12: - Added a configuration option to change the default plugin path. The configure option is --with-default-plugindir=location. The cmake option is -DH5_DEFAULT_PLUGINDIR:PATH=location. HDFFV-8513. (ADB 2013/09/04) - Renamed FFLAGS to FCFLAGS in configure. (ADB 2013/08/13) - CMake can now package a compressed examples file, the default for Windows binaries from HDF Group. (ADB - 2013/07/22) - h5repack: Added the ability to use plugin filters to read and write files. The option uses the filter number. HDFFV-8345 (ADB - 2013/09/04). - h5dump: Added the option -N --any_path, which searches the file for paths that match the search path. HDFFV-7989 (ADB - 2013/08/12). - h5dump: Added the optional arg 0 to -A, which excludes attributes from display. HDFFV-8134 (ADB - 2013/08/01). - Added tutorial examples to C++/examples. They can be installed by "make install-examples" and, in the installed directory, they can be executed by running the script file run-c++-ex.sh. (BMR - 2013/09/28) - A new class, H5::H5Location, is added to represent the location concept in the C library. It is a base class to H5::H5File and H5::H5Ojbect, whose member functions are moved into H5::H5Location. H5::H5File can now inherent those functions. As a result, an H5::H5File object can have an attribute. (BMR - 2013/09/27) - Added wrappers for H5Rget_obj_type2 to retrieve the type of the object that an object reference points to. (BMR - 2013/09/27) H5O_type_t H5Location::getRefObjType(void *ref, H5R_type_t ref_type) - Added wrappers for H5Aexist to check whether an attribute exists given a name. (BMR - 2013/09/27) bool H5::H5Location::attrExists(const char* name) bool H5::H5Location::attrExists(const H5std_string& name) - Added a number of overloaded functions for convenience. (BMR - 2013/09/27) - bugfixes - see http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.12-RELEASE.txt for more ------------------------------------------------------------------- Tue Sep 24 07:04:42 UTC 2013 - schwab@suse.de - hdf5-configure-long-double.patch: fix configure check for unsigned long long to long double conversion to not fail spuriously for 128bit long double - Increase testsuite timeout for qemu user space build ------------------------------------------------------------------- Fri Sep 13 12:18:27 UTC 2013 - pgajdos@suse.com - build with -O0 also for gcc 4.8 ------------------------------------------------------------------- Fri Jun 14 00:09:30 UTC 2013 - sweet_f_a@gmx.de - increase hdf5_libver to 8 ------------------------------------------------------------------- Wed Jun 12 11:22:35 UTC 2013 - sweet_f_a@gmx.de - use host config "linux-gnu" for arm (linux-gnueabi) to get useful H5_CFLAGS too - add hdf5-1.8.11-abort_unknown_host_config.patch, to get noticed if hdf5 doesn' t know our host - minimize hdf5-non_void_return.patch, false positives doesn't make problems anymore since now we have always -Wmissing-noreturn - make verbose - gcc 4.6.x needs -O0 on some systems ------------------------------------------------------------------- Tue Jun 11 13:45:26 UTC 2013 - sweet_f_a@gmx.de - Update to 1.8.11, changes documented here: http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - remove hdf5-fix_printf.patch, fixed by upstream - use default CFLAGS (-O2) again if possible ------------------------------------------------------------------- Fri Apr 12 19:25:06 UTC 2013 - sweet_f_a@gmx.de - Update to 1.8.10-patch1: * official important bug fixes for 1.8.10 * see RELEASE.txt "Bug Fixes since HDF5-1.8.10" ------------------------------------------------------------------- Sun Nov 18 12:31:34 UTC 2012 - sweet_f_a@gmx.de - Update to 1.8.10, changes documented here: http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html - remove hdf5-ph5diff.patch (fixed by upstream) - add hdf5-fix_printf.patch ------------------------------------------------------------------- Fri Nov 16 16:23:18 UTC 2012 - sweet_f_a@gmx.de - cosmetics, enable parallel build for suse only - fix build for old findutils ------------------------------------------------------------------- Mon Nov 5 12:31:22 UTC 2012 - coolo@suse.com - fixing baselibs.conf ------------------------------------------------------------------- Wed Sep 26 13:17:45 UTC 2012 - sweet_f_a@gmx.de - make sure to install the examples from non-parallel build ------------------------------------------------------------------- Mon Sep 24 12:29:04 UTC 2012 - sweet_f_a@gmx.de - don't use deprecated macro makeinstall - enable test suite for parallel builds - always build out of tree instead of copying sources ------------------------------------------------------------------- Fri Sep 7 17:24:21 UTC 2012 - scorot@free.fr - parallel versions for openmpi and mvapich2 - add baselibs.conf ------------------------------------------------------------------- Wed Jun 20 09:39:44 UTC 2012 - sweet_f_a@gmx.de - minor rpm portability build fixes - remove unused source file h5comp - enable all tests on ppc again (remove hdf5-1.8.8-tstlite.patch) - build fixes for arm * avoid some false positives "no-return-in-nonvoid-function" * disable some tests on arm only (hdf5-1.8.9-tests-arm.patch) ------------------------------------------------------------------- Mon May 28 15:05:43 UTC 2012 - ocefpaf@gmail.com - Update to 1.8.9 * Changes documented here: http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html ------------------------------------------------------------------- Mon Mar 12 11:57:39 UTC 2012 - sweet_f_a@gmx.de - install libhdf5.settings (bnc#751747) - move executables h5cc and h5c++ to the devel package ------------------------------------------------------------------- Sun Feb 19 04:46:42 UTC 2012 - ocefpaf@gmail.com - Removed "Fixup headers and scripts for multiarch". ------------------------------------------------------------------- Wed Nov 30 09:02:37 UTC 2011 - jengelh@medozas.de - Remove redundant/unwanted tags/section (cf. specfile guidelines) - Use %_smp_mflags for parallel building - Accurate rpmgroup selection for shared library packages ------------------------------------------------------------------- Tue Nov 29 20:05:19 UTC 2011 - ocefpaf@gmail.com - un-commented --with-pthread and --with-ssl. ------------------------------------------------------------------- Mon Nov 28 14:34:24 UTC 2011 - ocefpaf@gmail.com - Update to 1.8.8 * Add patch to avoid setting LD_LIBRARY_PATH * Add patch hdf5-non_void_return.patch * Fixed non_void_return (thanks to Boris Manojlovic). * Drop tstlite patch * drop ppc64 longdouble patch, not required anymore * Catch up with some Fedora modifications - Add rpm macro %%{_hdf5_version} for convenience * No Fortran modules for opensuse < 11.4 (Do not pass make check) New Features ============ Configuration ------------- - Added the --enable-fortran2003 flag to enable Fortran2003 support in the HDF5 Fortran library. The flag should be used along with the --enable-fortran flag and takes affect only when the Fortran compiler is Fortran2003 compliant. (EIP - 2011/11/14) - Added checks for clock_gettime and mach/mach_time.h to both configure and CMake. This will support the move from gettimeofday to clock_gettime's monotonic timer in the profiling code in a future release. (DER - 2011/10/12) Library ------- - The Windows VFD code has been removed with the exception of the functions which set it (H5Pset_fapl_windows, for example). Setting the Windows VFD now really sets the SEC2 VFD. The WINDOWS_MAX_BUF and WINDOWS_USE_STDIO configuration options and #defines have also been removed. NOTE: Since the Windows VFD was a clone of the SEC2 VFD, this change should be transparent to users. (DER - 2011/10/12 - HDFFV-7740, HDFFV-7744) - H5Tcreate now supports the string type (fixed-length and variable- length). (SLU - 2011/05/20) Parallel Library ---------------- - Added new H5Pget_mpio_actual_chunk_opt_mode and H5Pget_mpio_actual_io_mode API routines for querying whether/how a collective I/O operation completed. (QAK - 2011/10/12) Tools ----- - None High-Level APIs --------------- - Added the following Fortran wrappers for the Dimension Scale APIs: h5dsset_scale_f h5dsattach_scale_f h5dsdetach_scale_f h5dsis_attached_f h5dsis_scale_f h5dsset_label_f h5dsget_label_f h5dsget_scale_name_f h5dsget_num_scales_f (EIP for SB - 2011/10/13 - HDFFV-3797) Fortran API ----------- - The HDF5 Fortran library was enhanced to support the Fortran 2003 standard. The following features are available when the HDF5 library is configured using the --enable-fortran and --enable-fortran2003 configure flags AND if the Fortran compiler is Fortran 2003 compliant: - Subroutines overloaded with the C_PTR derived type: h5pget_f h5pget_fill_value_f h5pinsert_f h5pregister_f h5pset_f h5pset_fill_value_f h5rcreate_f h5rderefrence_f h5rget_name_f h5rget_obj_type_f - Subroutines overloaded with the C_PTR derived type and simplified signatures: h5aread_f h5awrite_f h5dread_f h5dwrite_f - New subroutines h5dvlen_reclaim_f h5literate_by_name_f h5literate_f h5ovisit_f h5tconvert_f h5pset_nbit_f h5pset_scaleoffset_f - Subroutines with additional optional parameters: h5pcreate_class_f (EIP - 2011/10/14) C++ API ------- - None ------------------------------------------------------------------- Thu Jun 2 20:39:35 UTC 2011 - ocefpaf@yahoo.com.br - uncomment make check ------------------------------------------------------------------- Tue May 24 14:37:23 UTC 2011 - pgajdos@novell.com - updated to 1.8.7 ------------------------------------------------------------------- Fri Apr 29 16:11:29 CEST 2011 - pth@suse.de - undrop package. - Do type-punning using unions to be able to compile without -fno-strict-aliasing. - Don't use macros in patch names. - Use _cv_ in variables to be cached by configure. ------------------------------------------------------------------- Thu May 7 19:40:59 CEST 2009 - pgajdos@suse.cz - fixed build with new gcc, see [bnc#501751] ------------------------------------------------------------------- Mon Mar 2 17:00:47 CET 2009 - crrodriguez@suse.de - save 9MB removing static libraries ------------------------------------------------------------------- Tue Jan 13 11:41:28 CET 2009 - pgajdos@suse.cz - updated to 1.8.2: - Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15). - Added two new public routines: H5Pget_elink_fapl() and H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13) - Improved free space tracking in file to be faster. (QAK - 2008/10/06) - Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15) - h5repack: added new options -u and -b to add a userblock to an HDF5 file during the repack. (PVN - 2008/08/26) - h5repack: added options -t and -a to call H5Pset_alignment while creating a repacked file. (PVN - 2008/08/29) - h5ls: added capability to traverse through external links when the -r (recursive) flag is given. (NAF - 2008/09/16) - h5ls: added -E option to enable traversal of external links. h5ls will not traverse external links without this flag being set. (NAF - 2008/10/06) - h5dump: when -b flag is used without a keyword after it, binary output defaults to NATIVE. MEMORY keyword was deprecated and replaced by NATIVE keyword. (PVN - 2008/10/30) - h5diff: returns 1 when file graphs differ by any object. Error return code was changed to 2 from -1. (PVN - 2008/10/30) - h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP instead (PVN - 2008/10/30) - Added optional parameter 'mounted' to H5Gget_info_f, H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24) - Added H5Tget_native_type_f (MSB - 2008/09/30) - These member functions were added as wrapper for H5Rdereference to replace the incorrect IdComponent::dereference(). void H5Object::dereference(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) void H5Object::dereference(H5File& h5file, void* ref, H5R_type_t ref_type=H5R_OBJECT) void H5Object::dereference(Attribute& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) In addition, these constructors were added to create the associated objects by way of dereference: DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT) DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT) (BMR - 2008/10/29) - removed destdir.patch ------------------------------------------------------------------- Mon Jan 12 11:13:33 CET 2009 - pgajdos@suse.cz - fortran modules builds from now [bnc#457593] ------------------------------------------------------------------- Tue Nov 11 11:49:54 CET 2008 - pgajdos@suse.cz - fixing build of fortran interface moved to the future ------------------------------------------------------------------- Wed Jul 2 10:45:51 CEST 2008 - pgajdos@suse.cz - updated to 1.8.1 [bnc#401626] * Enhanced group object management * Enhanced attribute management and more efficient meta data handling * Expanded datatype features * Creation order tracking and indexing * Improved meta data caching and cache control * UTF-8 encoding * New I/O filters: n-bit and scale+offset compression * New link (H5L) and object (H5O) interfaces and features * External and user-defined links * New high-level APIs: HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS) * C++ and Fortran interfaces for older high-level APIs: H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB) * New and improved tools - removed doc package (doc/html no longer provided with package) - octave builds againist 1.6 compatibility stuff ------------------------------------------------------------------- Wed May 7 13:12:11 CEST 2008 - pgajdos@suse.cz - repaired no-return-in-nonvoid-function (noreturn.patch) ------------------------------------------------------------------- Mon Apr 28 11:43:08 CEST 2008 - pgajdos@suse.cz - repaired build for * ia64 (%ifarch in hdf5.spec) * s390, s390x (s390.patch) ------------------------------------------------------------------- Tue Mar 25 11:11:13 CET 2008 - pgajdos@suse.cz - package moved from BS, project science - needed by octave 3.0
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