Changelog for netcdf_4_9_2-gnu-openmpi4-hpc-devel-4.9.2-2.4.x86_64.rpm :

* Mon Oct 23 2023 Egbert Eich - Disable HPC flavors on i586
* Mon Oct 23 2023 Nicolas Morey - Drop support for obsolete openmpi[123]- Prepare support for openmpi5
* Wed Apr 05 2023 Dirk Stoecker - add build require pkgconfig(zstd) to fix build for Leap 15.4
* Sun Mar 19 2023 Dirk Müller - update to 4.9.2:
* Update `nc-config` to remove inclusion from automatically-detected `nf-config` and `ncxx-config` files, as the wrong files could be included in the output.
* Update H5FDhttp.[ch] to work with HDF5 version 1.13.2 and later.
* [Bug Fix] Update DAP code to enable CURLOPT_ACCEPT_ENCODING by default.
* [Bug Fix] Fix byterange failures for certain URLs.
* [Bug Fix] Fix \'make distcheck\' error in run_interop.sh.
* [Enhancement] Update `nc-config` to remove inclusion from automatically-detected `nf-config` and `ncxx-config` files, as the wrong files could be included in the output.
* [Enhancement] Update H5FDhttp.[ch] to work with HDF5 version 1.14.0.
* Fix nc_def_var_fletcher32 operation
* Merge relevant info updates back into `main`
* Add manual GitHub actions triggers for the tests.
* Make public a limited API for programmatic access to internal .rc tables
* Fix typo in CMakeLists.txt
* Fix choice of HOME dir
* Check for libxml2 development files
* Updating Doxyfile.in with doxygen-1.8.17, turned on WARN_AS_ERROR, added doxygen build to CI run
* updated release notes
* increase read block size from 1 KB to 4 MB
* fixed RELEASE_NOTES.md
* Fix pnetcdf tests in cmake
* Updated CMakeLists to avoid corner case cmake error
* Add `--disable-quantize` to configure
* Fix the way CMake handles -DPLUGIN_INSTALL_DIR
* fix and test quantize mode for NC_CLASSIC_MODEL
* Guard _declspec(dllexport) in support of #2446
* Ensure that netcdf_json.h does not interfere with ncjson.
* Prevent cmake writing to source dir
* more quantize testing and adding pre-processor constant NC_MAX_FILENAME to nc_tests.h
* Provide a default enum const when fill value does not match any enum constant
* Fix support for reading arrays of HDF5 fixed size strings
* Fix AWS SDK linking errors
* Address jump-misses-init issue.
* Remove stray merge conflict markers
* Add support for Zarr string type to NCZarr
* Fix some problems with PR 2492
* Fix some bugs in the blosc filter wrapper
* Add option to control accessing external servers
* Changed attribute case in documentation
* Adding all-error-codes.md back in to distribution documentation.
* Update hdf5 version in github actions.
* Minor update to doxygen function documentation
* Fix some addtional errors in NCZarr
* Cleanup szip handling some more
* Check for zstd development headers in autotools
* Add new options to nc-config
* Cleanup built test sources in nczarr_test
* Fix inconsistency in netcdf_meta.h
* Small fix in nc-config.in
* For loop initial declarations are only allowed in C99 mode
* Fix some dependencies in tst_nccopy3
* Update plugins/Makefile.am
* Fix prereqs in ncdump/tst_nccopy4 in order to avoid race conditions.
* Move construction of VERSION file to end of the build
* Add draft filter quickstart guide
* Turn off extraneous debug output
* Fri Dec 30 2022 Stefan Brüns - Update to version 4.9.0:
* [Enhancement] Improve filter installation process to avoid use of an extra shell script. See gh#Unidata/netcdf-c#2348.
* [Bug Fix] Get \"make distcheck\" to work See gh#Unidata/netcdf-c#/2343.
* [Enhancement] Allow the read/write of JSON-valued Zarr attributes to allow for domain specific info such as used by GDAL/Zarr. See gh#Unidata/netcdf-c#2278.
* [Enhancement] Turn on the XArray convention for NCZarr files by default. WARNING, this means that the mode should explicitly specify nczarr\" or \"zarr\" even if \"xarray\" or \"noxarray\" is specified. See gh#Unidata/netcdf-c#2257.
* [Enhancement] Update the documentation to match the current filter capabilities See gh#Unidata/netcdf-c#2249.
* [Enhancement] Support installation of pre-built standard filters into user-specified location. See gh#Unidata/netcdf-c#2318.
* [Enhancement] Improve filter support. More specifically (1) add nc_inq_filter_avail to check if a filter is available, (2) add the notion of standard filters, (3) cleanup szip support to fix interaction with NCZarr. See gh#Unidata/netcdf-c#2245.
* [Enhancement] Switch to tinyxml2 as the default xml parser implementation. See gh#Unidata/netcdf-c#2170.
* [Bug Fix] Require that the type of the variable in nc_def_var_filter is not variable length. See gh#Unidata/netcdf-c#/2231.
* [File Change] Apply HDF5 v1.8 format compatibility when writing to previous files, as well as when creating new files. The superblock version remains at 2 for newly created files. Full backward read/write compatibility for netCDF-4 is maintained in all cases. See gh#Unidata/netcdf-c#2176.
* [Enhancement] Add ability to set dataset alignment for netcdf-4/HDF5 files. See gh#Unidata/netcdf-c#2206.
* [Bug Fix] Improve UTF8 support on windows so that it can use utf8 natively. See gh#Unidata/netcdf-c#2222.
* [Enhancement] Add complete bitgroom support to NCZarr. See gh#Unidata/netcdf-c#2197.
* [Bug Fix] Clean up the handling of deeply nested VLEN types. Marks nc_free_vlen() and nc_free_string as deprecated in favor of ncaux_reclaim_data(). See gh#Unidata/netcdf-c#2179.
* [Bug Fix] Make sure that netcdf.h accurately defines the flags in the open/create mode flags. See gh#Unidata/netcdf-c#2183.
* [Enhancement] Improve support for msys2+mingw platform. See gh#Unidata/netcdf-c#2171.
* [Bug Fix] Clean up the various inter-test dependencies in ncdump for CMake. See gh#Unidata/netcdf-c#2168.
* [Bug Fix] Fix use of non-aws appliances. See gh#Unidata/netcdf-c#2152.
* [Enhancement] Added options to suppress the new behavior from gh#Unidata/netcdf-c#2135.
* [Enhancement] Support optional use of libxml2, otherwise default to ezxml. See gh#Unidata/netcdf-c#2135
* [Bug Fix] Fix several os related errors. See gh#Unidata/netcdf-c#2138.
* [Enhancement] Support byte-range reading of netcdf-3 files stored in private buckets in S3. See gh#Unidata/netcdf-c#2134
* [Enhancement] Support Amazon S3 access for NCZarr. Also support use of the existing Amazon SDK credentials system. See gh#Unidata/netcdf-c#2114
* [Bug Fix] Fix string allocation error in H5FDhttp.c. See gh#Unidata/netcdf-c#2127.
* [Bug Fix] Apply patches for ezxml and for selected oss-fuzz detected errors. See gh#Unidata/netcdf-c#2125.
* [Bug Fix] Ensure that internal Fortran APIs are always defined. See gh#Unidata/netcdf-c#2098.
* [Enhancement] Support filters for NCZarr. See gh#Unidata/netcdf-c#2101
* [Bug Fix] Make PR 2075 long file name be idempotent. See gh#Unidata/netcdf-c#2094.- Remove unused doxygen build dependency.- Remove some obsolete Provides/Obsoletes from library package.- Drop upstream patches:
* swap-4-8-b-Satisfy-strict-aliasing-rules.patch
* Fix-type-punning-in-val_NC_check_voff-by-using-memcpy-instead-of-assignment.patch
* Fix-type-punning-in-xxdrntohdouble-by-using-memcpy-instead-of-assignment.patch
* NCD4_dumpbytes-use-correct-swapline-for-object-size.patch
* d4util.h-make-swapinlineXX-more-robust-against-type-punning.patch
* bin_reclaim_compound-Fixed-uninitialized-variable.patch- Drop ezxml patches (replaced by tinyxml2/libxml2):
* Fix-for-CVE-2019-20200-ezxml-bug-19.patch
* Fix-for-CVE-2019-20006-CVE-2019-20202-CVE-2021-31598-ezxml-bug-15-17-28.patch
* Fix-for-CVE-2019-20199-ezxml-bug-18.patch
* Fix-for-CVE-2019-20007-ezxml-bug-13.patch
* Fix-for-CVE-2021-26221-ezxml-bug-21.patch
* Fix-for-CVE-2021-26222-ezxml-bug-22.patch
* Fix-CVE-2021-30485-bug-25.patch
* Fix-CVE-2021-31229-bug-26-CVE-2019-20201-bug-16-CVE-2019-20198-bug-20.patch
* Fix-CVE-2021-31347-bug-27.patch
* Mon Dec 12 2022 Egbert Eich - Add BuildRequires for libhdf5[_hl]-[--hpc explicitly so that %%{requires_eq ..} is able to find the package and obtain the version number (boo#1206334).
* Sat Apr 02 2022 Egbert Eich - Add a \'\\--whatprovides\' to the \'%%requires_eq libhdf5%{p_suffix}\' to catch the the library package even without an so-name.
* Sat Feb 26 2022 Stefan Brüns - Correct Source: URL
* Wed Feb 16 2022 Atri Bhattacharya - Update to version 4.8.1:
* [Bug Fix] Fix multiple bugs in libnczarr. See gh#Unidata/netcdf-c#2066.
* [Enhancement] Support windows network paths (e.g. \\svc...). See gh#Unidata/netcdf-c#2065.
* [Enhancement] Convert to a new representation of the NCZarr meta-data extensions: version 2. Read-only backward compatibility is provided. See gh#Unidata/netcdf-c#2032.
* [Bug Fix] Fix dimension_separator bug in libnczarr. See gh#Unidata/netcdf-c#2035.
* [Bug Fix] Fix bugs in libdap4. See gh#Unidata/netcdf-c#2005.
* [Bug Fix] Store NCZarr fillvalue as a singleton instead of a 1-element array. See gh#Unidata/netcdf-c#2017.
* [Bug Fixes] The netcdf-c library was incorrectly determining the scope of dimension; similar to the type scope problem. See gh#Unidata/netcdf-c#2012 for more information.
* [Bug Fix] Re-enable DAP2 authorization testing. See gh#Unidata/netcdf-c#2011.
* [Bug Fix] Fix bug with windows version of mkstemp that causes failure to create more than 26 temp files. See gh#Unidata/netcdf-c#1998.
* [Bug Fix] Fix ncdump bug when printing VLENs with basetype char. See gh#Unidata/netcdf-c#1986.
* [Bug Fixes] The netcdf-c library was incorrectly determining the scope of types referred to by nc_inq_type_equal. See gh#Unidata/netcdf-c#1959 for more information.
* [Bug Fix] Fix bug in use of XGetopt when building under Mingw. See gh#Unidata/netcdf-c#2009.
* [Enhancement] Improve the error reporting when attempting to use a filter for which no implementation can be found in HDF5_PLUGIN_PATH. See gh#Unidata/netcdf-c#2000 for more information.
* [Bug Fix] Fix make distcheck issue in nczarr_test/ directory. See gh#Unidata/netcdf-c#2007.
* [Bug Fix] Fix bug in NCclosedir in dpathmgr.c. See gh#Unidata/netcdf-c#2003.
* [Bug Fix] Fix bug in ncdump that assumes that there is a relationship between the total number of dimensions and the max dimension id. See gh#Unidata/netcdf-c#2004.
* [Bug Fix] Fix bug in JSON processing of strings with embedded quotes. See gh#Unidata/netcdf-c#1993.
* [Enhancement] Add support for the new \"dimension_separator\" enhancement to Zarr v2. See gh#Unidata/netcdf-c#1990 for more information.
* [Bug Fix] Fix hack for handling failure of shell programs to properly handle escape characters. See gh#Unidata/netcdf-c#1989.
* [Bug Fix] Allow some primitive type names to be used as identifiers depending on the file format. See gh#Unidata/netcdf-c#1984.
* [Enhancement] Add support for reading/writing pure Zarr storage format that supports the XArray _ARRAY_DIMENSIONS attribute. See gh#Unidata/netcdf-c#1952 for more information.
* [Update] Updated version of bzip2 used in filter testing/functionality, in support of gh#Unidata/netcdf-c#1969.
* [Bug Fix] Corrected HDF5 version detection logic as described in gh#Unidata/netcdf-c#1962.- New BuildRequires: unzip needed for one of the tests.
* Tue Feb 15 2022 Dominique Leuenberger - Move rpm macros from /etc/rpm to /usr/lib/rpm/macros.d (boo#1191393).
* Mon Oct 25 2021 Egbert Eich - Fix:
* CVE-2019-20007 https://sourceforge.net/p/ezxml/bugs/13
* CVE-2019-20006 https://sourceforge.net/p/ezxml/bugs/15
* CVE-2019-20201 https://sourceforge.net/p/ezxml/bugs/16
* CVE-2019-20202 https://sourceforge.net/p/ezxml/bugs/17
* CVE-2019-20199 https://sourceforge.net/p/ezxml/bugs/18
* CVE-2019-20200 https://sourceforge.net/p/ezxml/bugs/19
* CVE-2019-20198 https://sourceforge.net/p/ezxml/bugs/20
* CVE-2021-26221 https://sourceforge.net/p/ezxml/bugs/21
* CVE-2021-26222 https://sourceforge.net/p/ezxml/bugs/22
* CVE-2021-30485 https://sourceforge.net/p/ezxml/bugs/25
* CVE-2021-31229 https://sourceforge.net/p/ezxml/bugs/26
* CVE-2021-31347 &
* CVE-2021-31348 https://sourceforge.net/p/ezxml/bugs/27
* CVE-2021-31598 https://sourceforge.net/p/ezxml/bugs/28 (bsc#1191856) Note:
* CVE-2021-26220 https://sourceforge.net/p/ezxml/bugs/23 not relevant for netcdf: code isn\'t used.
* CVE-2019-20005 https://sourceforge.net/p/ezxml/bugs/14 Issue cannot be reproduced and no patch is available upstream. Added:
* Fix-CVE-2021-30485-bug-25.patch
* Fix-CVE-2021-31229-bug-26-CVE-2019-20201-bug-16-CVE-2019-20198-bug-20.patch
* Fix-CVE-2021-31347-bug-27.patch
* Fix-for-CVE-2019-20006-CVE-2019-20202-CVE-2021-31598-ezxml-bug-15-17-28.patch
* Fix-for-CVE-2019-20007-ezxml-bug-13.patch
* Fix-for-CVE-2019-20199-ezxml-bug-18.patch
* Fix-for-CVE-2019-20200-ezxml-bug-19.patch
* Fix-for-CVE-2021-26221-ezxml-bug-21.patch
* Fix-for-CVE-2021-26222-ezxml-bug-22.patch
* Thu Oct 21 2021 Egbert Eich - Add Patches: These should allow us to reenable strict aliasing.
* swap-4-8-b-Satisfy-strict-aliasing-rules.patch
* Fix-type-punning-in-val_NC_check_voff-by-using-memcpy-instead-of-assignment.patch
* Fix-type-punning-in-xxdrntohdouble-by-using-memcpy-instead-of-assignment.patch
* NCD4_dumpbytes-use-correct-swapline-for-object-size.patch
* d4util.h-make-swapinlineXX-more-robust-against-type-punning.patch
* parseServers-Fix-uninitialized-variable-simplify-error-path.patch
* bin_reclaim_compound-Fixed-uninitialized-variable.patch
* val_NC_check_voff-Fix-uninitialized-variable-warning.patch
* pr_att-Fix-uninitialized-variable.patch
* NCD4_dumpbytes-Add-missing-initialization-of-float-types.patch
* NCZ_def_var_chunking-make-sure-cs-is-set-before-used.patch
* Fix-spurious-uninitialized-variable-warning.patch
* Sun Aug 08 2021 Egbert Eich - Removed generation of libsrc/ncx.c: This was an issue with an older version and has been fixed since. With this, no longer requiring m4 explicitly.- Valgrind is used for validation tests only, these have not been performed. When they were added some of them failed. This requires further investigations. For now, valgrind testing has been made optional.
* Tue Jul 06 2021 Egbert Eich - Gcc11 has raised the bar on strict aliasing requirements even further. This has given rise to seemingly senseless warnings like: ncx.c: In function \'ncx_putn_float_double\': ncx.c:272:20: warning: \'xx\' may be used uninitialized [-Wmaybe-uninitialized] 272 | uint32_t tmp =
*(uint32_t
*)src; | ^~~~~~~~~~~~~~~ ncx.c:3562:14: note: \'xx\' was declared here 3562 | ix_float xx = NC_FILL_FLOAT; | ^~ but what is worse, data in netcdf files is missing. Luckily, this was caught by the test suite. These warnings and further type punning warnings should be fixed eventually. However, for now, lets cry defeat, disable strict aliasing and get netcdf back working again.
* Sun Jul 04 2021 Egbert Eich - Add build support for gcc11 to HPC build.- Update to version 4.7.4.
* Enhancements: - Bump the NC_DISPATCH_VERSION from 2 to 3 - Better cross platform path name management. This converts paths for various platforms (e.g. Windows, MSYS, etc.) so that they are in the proper format for the executing platform. See Github #1958. - Add support for storing NCZarr data in zip files. See Github #1908. - Optimizations to NCZarr, cleanup of code cruft, NCZarr test cases, performance test to NCZarr. See Github #1942. - Provide .rc fields for S3 authentication: HTTP.S3.ACCESSID and HTTP.S3.SECRETKEY. - Give the client control over what parts of a DAP2 URL are URL encoded (i.e. xx). This is to support the different decoding rules that servers apply to incoming URLS. See Github #1884 for more information. - Added new parallel I/O benchmark program to mimic NOAA UFS data writes. See [https://github.com/Unidata/netcdf-c/pull/1777]. - Add support for cloud storage using a variant of the Zarr storage format. Warning: this feature is highly experimental and is subject to rapid evolution [https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in]. - When a filter is applied twice with different parameters, the second set is used for writing the dataset [https://github.com/Unidata/netcdf-c/issues/1713].
* Bug Fixes: - The nccopy program was treating -d0 as turning deflation on rather than interpreting it as \"turn off deflation\". See Github #1944. - Make fillmismatch the default for DAP2 and DAP4; too many servers ignore this requirement. - Fix some memory leaks in NCZarr, fix a bug with long strides in NCZarr. See Github #1913. - Implement a better chunk cache system for NCZarr. The cache now uses extendible hashing plus a linked list for provide a combination of expandibility, fast access, and LRU behavior. See Github #1887. - Fix incorrect time offsets from ncdump -t, in some cases when the time units attribute contains both a non-zero time-of-day, and a time zone suffix containing the letter \"T\", such as \"UTC\". See Github #1866. - Cleanup the NCZarr S3 build options. See Github #1869. - Support aligned access for selected ARM processors. See Github #1871. - Revert the internal filter code to simplify it. From the user\'s point of view, the only visible change should be that (1) the functions that convert text to filter specs have had their signature reverted and renamed and have been moved to netcdf_aux.h, and (2) Some filter API functions now return NC_ENOFILTER when inquiry is made about some filter. Internally, the dispatch table has been modified to get rid of the complex structures. - If the HDF5 byte-range Virtual File Driver is available) HDf5 1.10.6 or later) then use it because it has better performance than the one currently built into the netcdf library. - Fixed byte-range support with cURL > 7.69. See https://github.com/Unidata/netcdf-c/pull/1798. - Added new test for using compression with parallel I/O: nc_test4/tst_h_par_compress.c. See [https://github.com/Unidata/netcdf-c/pull/1784]. - Don\'t return error for extra calls to nc_redef() for netCDF/HDF5 files, unless classic model is in use. See [https://github.com/Unidata/netcdf-c/issues/1779]. - Now allow szip to be used on variables with unlimited dimension [https://github.com/Unidata/netcdf-c/issues/1774]. - Fix nccopy to properly set default chunking parameters when not otherwise specified. This can significantly improve performance in selected cases. Note that if seeing slow performance with nccopy, then, as a work-around, specifically set the chunking parameters. [https://github.com/Unidata/netcdf-c/issues/1763]. - Fix some protocol bugs/differences between the netcdf-c library and the OPeNDAP Hyrax server. Also cleanup checksum handling [https://github.com/Unidata/netcdf-c/issues/1712].
* - IMPORTANT: Ncgen was not properly handling large data sections. The problem manifests as incorrect ordering of data in the created file. Aside from examining the file with ncdump, the error can be detected by running ncgen with the -lc flag (to produce a C file). Examine the file to see if any variable is written in pieces as opposed to a single call to nc_put_vara. If multiple calls to nc_put_vara are used to write a variable, then it is probable that the data order is incorrect. Such multiple writes can occur for large variables and especially when one of the dimensions is unlimited. - Add necessary __declspec declarations to allow compilation of netcdf library without causing errors or (_declspec related) warnings [https://github.com/Unidata/netcdf-c/issues/1725]. - Now larger cache settings are used for sequential HDF5 file creates/opens on parallel I/O capable builds; see Github #1716. - Add functions to libdispatch/dnotnc4.c to support dispatch table operations that should work for any dispatch table, even if they do not do anything; functions such as nc_inq_var_filter [https://github.com/Unidata/netcdf-c/issues/1693]. - Fixed a scalar annotation error when scalar == 0; see Github #1707. - Use proper CURLOPT values for VERIFYHOST and VERIFYPEER; the semantics for VERIFYHOST in particular changed. Documented in NUG/DAP2.md. See [https://github.com/Unidata/netcdf-c/issues/1684]. - [cmake] Correct an issue with parallel filter test logic in CMake-based builds. - Now allow nc_inq_var_deflate()/nc_inq_var_szip() to be called for all formats, not just HDF5. Non-HDF5 files return NC_NOERR and report no compression in use. This reverts behavior that was changed in the 4.7.4 release. See [https://github.com/Unidata/netcdf-c/issues/1691]. - Compiling on a big-endian machine exposes some missing forward delcarations in dfilter.c.
* Documentation: - Migrated the documents in the NUG/ directory to the dedicated NUG repository found at https://github.com/Unidata/netcdf
* Remove obsolete: Define-byteswap-functions-before-use.patch Fix-logging-argument.patch get_filter_info-get-correct-number-of-filter-elements.patch
* Fri Jan 29 2021 Egbert Eich - Define-byteswap-functions-before-use.patch: Define byteswap() functions before use (bsc#1181523).