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* [svn-r24032] Description:Quincey Koziol2013-08-207-135/+144
| | | | | | | | | | Bring r24030 from trunk to 1.8 branch: Clean up more compiler warnings. Tested on: Mac OSX/64 10.8.4 (amazon) w/gcc, C++ & FORTRAN (too minor to require h5committest)
* [svn-r24024] JAVA-1714: CMake packaging for macs improvedAllen Byrne2013-08-1916-2/+411
| | | | | | | HDFFV-7989: h5dump any_path and help text grouping Added cygwin-64 support Merged from trunk, tested local linux
* [svn-r24021] Description:Quincey Koziol2013-08-188-43/+44
| | | | | | | | | | Bring r24020 from trunk to 1.8 branch: Clean up compiler warnings Tested on: Mac OSX/64 10.8.4 (amazon) w/C++ & FORTRAN (too minor to require h5committest)
* [svn-r24014] This checkin is a merge of the checkin for h5stat to the trunk ↵Vailin Choi2013-08-1631-113/+949
| | | | | | | | | | | | (rev #23975-23977) + an additional bug fix-- A) Fix for HDFFV-1238: --Add 3 new options to allow users in setting threshold for small groups/datasets/attributes (tools/h5stat/h5stat.c) --Generate new test file for testing the new options (tools/h5stat/h5stat_gentest.c) --Add tests for the new options (tools/h5stat/testh5stat.sh.in) --Update expected output files (tools/h5stat/testfiles/*.ddl) B) Fix a bug in determining maximum dimension size for 1-D dataset in dataset_stats() (tools/h5stat/h5stat.c) C) Fix a bug when using opt_arg that is NULL for the new options.
* [svn-r24012] Description:Quincey Koziol2013-08-154-3/+27
| | | | | | | | | | Bring r24011 from trunk to 1.8 branch: Clean up a few warnings Tested on: Mac OSX 10.8.4 (amazon) w/C++ & FORTRAN (too minor to require h5committest)
* [svn-r23995] Correct printf % handlingAllen Byrne2013-08-129-9/+9
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* [svn-r23992] HDFFV-8490 and H5UNJAM file handling. Merge from trunk.Allen Byrne2013-08-1212-572/+695
| | | | Tested: local linux
* [svn-r23965] Corrected "continuous" layout to "contiguous" in h5repack -h ↵Larry Knox2013-08-022-2/+2
| | | | | | | | output and comment. Jira issue HDFFV-8493. No test - text only change.
* [svn-r23921] Bug fix: HDFFV-8392Albert Cheng2013-07-192-2/+2
| | | | | | | | | | | | | | | | | | | | [folded fix to v18 branch.] tools/h5diff/testh5diff.sh is run in every "make check", even after it has passed in the previous run. The error was in the previous change made to Makefile.am when testh5diff.sh.in was created. The mistake was in the SCRIPT_DEPEND=h5diff$(EXEEXT) $(H5PDIFF) $(srcdir)/testh5diff.sh $(srcdir)/testh5diff.sh no longer existed. It is now generated in the current built directory from $(srcdir)/testh5diff.sh.in (which configure takes care of). I updated the dependance to SCRIPT_DEPEND=h5diff$(EXEEXT) $(H5PDIFF) testh5diff.sh and that fixes the error. Reviewed: HDF5-149 Tested: h5committested.
* [svn-r23898] HDFFV-8476: Add optional arg to -A for excluding attributes.Allen Byrne2013-07-1517-31/+144
| | | | | | Merged from trunk. Tested: local linux
* [svn-r23885] Issue VMS-3: OpenVMS needs special printing format "%hd" for ↵Raymond Lu2013-07-101-0/+4
| | | | | | | | 1-byte integer. I used the macro H5_VMS to choose the correct format in the initialization of ls_dataformat. Tested with h5committest.
* [svn-r23868] bring r 23862 from trunk:Mohamad Chaarawi2013-07-081-2/+2
| | | | | Change printfs in perform output and h5dump to prevent overflow. This fixes: https://jira.hdfgroup.uiuc.edu/browse/HDFFV-8450
* [svn-r23855] I added macro condition for OpenVMS in the hard-coded ↵Raymond Lu2013-07-011-0/+4
| | | | | | initialization of h5tools_dataformat. Tested on jam and OpenVMS - simple change.
* [svn-r23826] Bug HDFFV-8469: C++ comments in C code.Albert Cheng2013-06-262-3/+0
| | | | | | | | Found and removed two more "//" comments. Tested: in Koala by $ env CFLAGS="-ansi" ../hdf5/bin/buildhdf5 -fortran -cxx -config # enable fortran and cxx, configure only $ make AM_CFLAGS=-ansi # compile all source file by setting HDF5 build CFLAGS as "-ansi" only
* [svn-r23820] Change name of generated file in test to use the macro based ↵Allen Byrne2013-06-251-8/+2
| | | | | | removal line. Tested: local linux
* [svn-r23818] The forgotten testfile changesAllen Byrne2013-06-2559-59/+59
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* [svn-r23816] HDFFV-8455: moved h5dump before h5importAllen Byrne2013-06-244-5/+4
| | | | | | | HDFFV-8465: corrected DTD reference path Merged from trunk Tested: local linux with cmake
* [svn-r23797] remove commented line with c++ styleAllen Byrne2013-06-201-2/+0
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* [svn-r23771] HDFFV-8434,-8437,-8445,-8447,-8461: Merge changes from Trunk.Allen Byrne2013-06-1416-9/+66
| | | | Tested: local linux
* [svn-r23696] Description:Quincey Koziol2013-05-115-180/+211
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r23695 from trunk to 1.8 branch: Clean up warnings in H5Tconv.c (down to _only_ 9000 lines of output now!) Merge changes from Coverity branch back to trunk: r20684: Fix for coverity bug #1721 which was due to the fix for coverity bug #943. r20685: Use HDstrncpy. --gh r20761: Purpose: Fix valgrind issues Description: Free image_data and data as appropriate in test_image. r20762: Purpose: Fix coverity issue 600 Description: Add check for return value of H5O_close in H5Ocopy. Also cleaned up various warnings. r20763: Purpose: Fix valgrind issues with h5stat Description: Modified h5stat to free "iter" before exit, and free "hand" before exit if parse_command_line exits directly. r20764: fixed coverity issues: 69, 327, 614, 684, 685, 696, 697, 1681, 967, 826, 660, 80 r20765: Fixed coverity bug 668 Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning. No actual integer overflow tests are performed since it's just a test program but I did add a check that n_elements is >= 1. I also changed an error condition from doing its own close and returning -1 to "goto out;" like the rest of the program. r20766: Fixed coverity bug 667 Pulled x * y * z multiply out of malloc operand into a separate n_elements variable to quiet integer overflow warning. No actual integer overflow tests are performed since it's just a test program. Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN (h5committest upcoming)
* [svn-r23573] Removed inappropriate executable properties from a few files. ↵Dana Robinson2013-04-102-0/+0
| | | | | | | | These are often added by Windows text editors. Tested on: jam (just tested to make sure it builds - no code changes)
* [svn-r23559] Fix valgrind configure errorAllen Byrne2013-04-081-2/+28
| | | | Tested: local linux - with and without valgrind
* [svn-r23556] Bug fix: HDFFV-8358Albert Cheng2013-04-051-54/+35
| | | | | | | | | | | | | | | | | | | | | | The previous change set exec_prefix, libdir and includedir to actual values. That removed the option for user to hand edit just the first prefix=... to make "everything" to work. Changed h5redeploy to do this by default: ## Installation directories: ## ## prefix architecture-independent files. ## ## exec_prefix architecture-dependent files, default is <prefix>. ## ## libdir libraries, default is <exec_prefix>/lib. ## ## includedir header files, default is <prefix/include>. ## ############################################################################ This allows users to just change the first line of prefix=<...> and the effect will change libdir and includedir too. This was also try to accommodate the -prefix option of h5XX. Unfortunately, after changing h5redeploy, I found out the h5XX code to support -prefix actually does not provide the stated efffect. This will be fixed in the release. Tested: h5committested plus hand test.
* [svn-r23510] I merged the changes for DESY project from the trunk (r23496) ↵Raymond Lu2013-04-012-1/+69
| | | | | | into this 1.8 DESY branch. Tested with h5committest (duck failed with CMake because I don't know how to change test/CMakeLists.txt. I'll wait for Allen to do it).
* [svn-r23498] Bug fix: HDFFV-8358Albert Cheng2013-03-301-7/+64
| | | | | | | | Change h5redeploy to change all 4 lines, prefix=..., exec_prefix=..., libdir=..., and includedir=... This way, it reset all 4 lines. Should work for both version of h5cc created by configure or by rpm. Tested: hand tested in jam.
* [svn-r23477] HDFFV-8359: correct script function calls.Allen Byrne2013-03-281-5/+5
| | | | Tested: local linux
* [svn-r23464] Purpose: Jonathan Kim2013-03-273-10/+24
| | | | | | | | | | | | | HDFFV-8214 - h5repack failed converting small chunked dataset (size < 1K) to contiguous layout. Description: h5repack failed converting small chunked dataset (size < 1K) to contiguous layout. The first case was when chunk dim is bigger than the dataset dim (at leat one), h5repack failed with displaying error stacks. The other case is when chunk dim is smaller than the dataset dim, h5repack failed to change layout. Merged from HDF5 trunk 23407 Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), emu (solaris-BE), fred (mac64-LE), Windows (32-LE cmake), cmake (jam)
* [svn-r23460] Add missing infile assignment and error countsAllen Byrne2013-03-261-0/+2
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* [svn-r23459] HDFFV-8355 h5repack.sh was wrong for the two test cases.Peter Cao2013-03-261-3/+17
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* [svn-r23448] HDFFV-8322: valgrind leaksAllen Byrne2013-03-252-38/+29
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* [svn-r23416] Description:Quincey Koziol2013-03-211-2/+2
| | | | | | | | | Bring r23415 from trunk to 1.8 branch: Avoid using fpclassify() for detecting zero/non-zero values. Tested on: Mac OSX/64 10.8.3 (amazon) w/debug
* [svn-r23396] Description:Quincey Koziol2013-03-207-611/+619
| | | | | | | | | | | | | | Bring r23395 from trunk to 1.8 branch: Bring Coverity changes from branch to trunk: r20682: fixed coverity: 76, 77, 635, 636, 1164, 1165, 1166, 1121, 1122, 1117, 1343 Tested on: Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN (too minor to require h5committest)
* [svn-r23383] fixed HDFFV-8344 and HDFFV-8346: add info for user registered ↵Peter Cao2013-03-194-7/+17
| | | | filter in h5dump
* [svn-r23355] Correct target nameAllen Byrne2013-03-151-1/+1
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* [svn-r23324] Snapshot version 1.8 release 11 (snap11)HDF Tester2013-03-0411-11/+11
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* [svn-r23318] HDFFV-8311: Improve tools testing and eliminate dependency problemsAllen Byrne2013-02-255-675/+663
| | | | Tested: local linux
* [svn-r23315] Correct typo in DEPENDSAllen Byrne2013-02-251-1/+1
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* [svn-r23309] Purpose:Jonathan Kim2013-02-214-4/+11
| | | | | | | | | | | | | HDFFV-7643 - h5diff - incorrect exit-code returns for extra attribute exist Description: h5diff: Fixed to return correct exit code 1 when detect unique attribute. Prior to this fix, h5diff returned exit code 0 indicating two files are identical. Merged from HDF5 trunk r23304. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), emu (solaris-BE), Windows (32-LE cmake), cmake (jam)
* [svn-r23302] Remove old file namesAllen Byrne2013-02-187-104/+0
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* [svn-r23301] Allen Byrne2013-02-1868-1290/+4705
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* [svn-r23229] Jonathan Kim2013-02-051-1/+1
| | | | | | | | | | | | Purpose: Revert back one of the coverity updates from previous (r23220) checkin. "r20457: Coverity issue 691" in previous svn log. Only revert the change about using "STDOUT_FILENO". Description: Using "STDOUT_FILENO" caused error on Windows. On unix it's defined in <unistd.h>, but not in Windows. After a little discussion with Allen, he remembered how the similar case were handled for h5dump redirecting those streams. (in h5dump.c) However it would requires more attention to apply, so this issue is entered as a separate task in jira HDDFV-8306. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE)
* [svn-r23220] Description:Quincey Koziol2013-02-022-118/+99
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r23219 from trunk to 1.8 branch: Bring reviewed changes from Coverity branch back to trunk (QK & JK): r20457: Coverity issue 691: return of H5duo could be negative. Fixed by using STDOUT_FILENO and redesign parse_command_line and main to cleanup file allocations. The output_file var is null when using stdout. In cleanup do not close output_file if NULL. r20510: Initialize ufid = -1 and predicate HDclose call on ufid != -1 r20511: Purpose: Fix coverity issue 1715 Description: Free "file" and nested data on failure in H5FD_core_open. r20512: Initialize ifid = -1 and predicate HDclose call on ifid != -1 r20514: Initialize h5fid = -1 and predicate HDclose call on h5fid != -1 r20516: Added else branch to the if (ret_value < 0) check. r20522: Addressed coverity issues 930-933, 850, 836, 835, 1307. All minor potential buffer overwrite bugs, or coverity errors. Fixed by replacing strcpy and sprintf with strncpy and snprintf. r20523: fixed coverity issues 68, 1120, 1116i r20524: Check H5Z_SZIP->encoder_present < 1 assuming 0 represents absence. r20601: Purpose: Fix coverity issues 1703-1705 Description: Modified the cleanup code in test_free in accum.c to reset allocated buffers to NULL after they are freed, and modified the error cleanup code to check if these buffers are NULL before freeing them. Also fixed some unrelated warnings in accum.c. r20602: Use HDsnprintf and HDstrncat r20603: Purpose: Fix coverity issues 808-809 Description: Modified test_core in vfd.c to check the returns from malloc, and keep track of whether points and check are allocated by setting them to NULL when they are not. Added code to free points and check on error if they are not NULL. Also fixed unrelated warnings in vfd.c. r20604: Use HDstrncpy. r20605: Use HDstrncpy and HDstrncat. r20606: Purpose: Fix coverity issue 807 Description: Modified long_compact in stab.c to keep track of whether objname is allocated by setting it to NULL when it is not. Added code to free objname on error if it is not NULL. r20607: Changed string function calls to use versions that specify the string length to fix coverity issues 832 and 839. Tested on: Mac OSX/64 10.8.2 (amazon) (Too minor to require h5committest)
* [svn-r23211] Merge trunk CMake changes for minimum cmake version of 2.8.10. ↵Allen Byrne2013-01-3111-11/+11
| | | | | | This was prompted by HDFFV-8227, OS X requires latest version of cmake for proper support. Tested: local linux
* [svn-r23187] HDFFV-8169: Binary output of String types are wrongAllen Byrne2013-01-224-13/+156
| | | | | | Merge from trunk Add testfiles. Tested: local linux
* [svn-r23186] HDFFV-8169: Binary output of String types are wrongAllen Byrne2013-01-221-1/+1
| | | | Merge from trunk
* [svn-r23069] Bug fix: HDFFV-8233Albert Cheng2012-11-301-2/+12
| | | | | | | | | | | | | testh5stat.sh fails in LLNL uDawn. The test actually ran as expected but it did not prepare for the extra error messages from the MPI process. Solution: This sort of problem has been fixed by using the output filters in output_filter.sh. testh5stat.sh is updated to use the output filters. Tested: uDawn.
* [svn-r23000] Description:Quincey Koziol2012-11-012-23/+30
| | | | | | | | | | | | | | | | | | | | | | | | | Bring r22998 from trunk to 1.8 branch: Clean up warnings and bring changes from Coverity branch back to trunk: r20451: Fixed coverity 810 r20454: Purpose: Fix coverity issue 816 Description: Modified various file drivers to always check the return value from H5P_get_driver_info. r20455: Purpose: Cleanup fix for coverity issue 816 Description: Removed redundant check for "fa" in H5FD_core_open. Tested on: Mac OSX/64 10.8.2 (amazon) w/debug (Too minor to require h5committest)
* [svn-r22934] Purpose:Jonathan Kim2012-10-191-0/+18
| | | | | | | | | | | HDFFV-8145 h5diff slowness with version >= 1.8.7 Description: Improved speed when comparing HDF5 files with lots of attributes. Much slower performance was identified with release version from 1.8.7 to 1.8.10 compared to 1.8.6. Merged from HDF5 trunk r22933. Tested: jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), cmake (jam)
* [svn-r22929] Description:Quincey Koziol2012-10-198-263/+192
| | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r22921 from trunk to 1.8 branch: Review Coverity changes and bring them back to trunk. (QK & JK) r20402: Added #includes for h5tools.y or h5tools_utils.h as required to remedy implicit function declarations which caused compiler warnings and coverity issues 703-4 and 708-11. r20414: This is related to the previous checkin r20399. There were incorrect updates which caused incorrect behavior when no file was given. Also possible segfault when handling hyperslab options. Simplify the code changes. r20449: Description: Modified H5E_walk2_cb to check return value of H5I_object_verify. r20450: fixed coverity 813 Tested on: Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, debug & threadsafe (too minor to require h5committest)
* [svn-r22916] Description:Quincey Koziol2012-10-171-7/+8
| | | | | | | | | | | | | | | | | | | | | | | | | Bring r22915 from trunk to 1.8 branch: Bring Coverity changes back to trunk: r20399: Change parse_command_line to free hand structure on error and only "leave()" at end of main. r20400: Purpose: Fix coverity issue 592 Description: Added void cast to call to H5F_sfile_assert_num() in H5F_term)interface(). There is no need to check the return value of this function in general, and there would be nothing to do even if it did fail. r20401: Added free(src_sizes) and free(src_offset). --gh Tested on: Mac OSX/64 10.8.2 (amazon) w/C++, FORTRAN, threadsafe (too minor for h5committest)
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