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* [svn-r24906] Merge latest CMake changes from trunk.Allen Byrne2014-03-2625-1408/+1504
| | | | Tested: local linux
* [svn-r24894] Description:Quincey Koziol2014-03-251-104/+95
| | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24869 & r24875 from trunk to 1.8 branch: Clean up more compiler warnings, plus merge a few Coverity bug fixes from the hdf5_1_8_coverity branch back to the trunk: r20877: Purpose: Fix coverity issue 1723 Description: Modified test_generate in hl/test_image to close file "f" before exit, even if an error occurs. r20879: Issue 63: change check of return of H5Tget_nmembers to <=0. No need to go futher if call fails as well as empty. r20881: Coverity #659 in Run 46: I changed the Line 442 where it tries to check whether FLAG_PRINTED is TRUE. But it had just been set to FALSE. I took out the condition check in the print statement. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & Parallel (daily tested on trunk)
* [svn-r24878] Description:Quincey Koziol2014-03-2413-75/+20
| | | | | | | | | | | | | | | | | | | | | Bring r24864 from trunk to 1.8 branch: Remove all traces of MPI-POSIX VFD and GPFS detection/code. Remove remaining traces of stream VFD. Remove testpar/t_posix_compliant test (it's not actually verifying anything). Clean up H5D__mpio_opt_possible() further. Moved environment variable that disables MPI collective operations into MPI-IO VFD (instead of it being in src/H5S.c). A few other small code cleanups. Tested on: Mac OSX/64 10.9.2 (amazon) w/parallel & serial (daily tested on trunk)
* [svn-r24810] Description:Quincey Koziol2014-03-178-134/+77
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24803 & r24804 from trunk to 1.8 branch: r24804: Brought changes from Coverity branch back to trunk, and cleaned up misc. other warnings & formatting issues: r20833: Fixed Coverity 667 and 668 with real integer overflow tests this time. r20834: Use HDstrncpy and HDstrncat. --gh r20835: Change to use strncpy - use base_len + 1 for line 156, use HDstrlen(path) + 1 for line 159 r20836: Fixed coverity 585 by casting output of fgetc() to a char. r20837: Changed sprintf calls to snprintf with size 1 less than the allocated buffer to address coverity issue #967. r24803: Rename GCC_DIAG_OFF/ON macros to H5_GCC_DIAG_OFF/ON and move from src/H5private.h to src/H5public.h. Wrap typedef of hsize_t and hssize_t in DIAG_OFF(long-long) macros. Clean up a bunch of "macro '-' is unused" warnings. Tested on: Mac OSX/64 10.9.2 (amazon) w/C++, FORTRAN & parallel (too minor to require h5committest)
* [svn-r24746] Merge trunk revision 24744 from cmake branch includes;Allen Byrne2014-02-276-142/+299
| | | | | | HDFFV-8505: UD filter changes to remove filters in h5repack. Tested: local linux
* [svn-r24732] Fix for reconfigure, which fails because ↵Larry Knox2014-02-2211-0/+11
| | | | | | LT_ADD_LIBHDF5_DEPENDENCY is used in Makefiles but the declaration in configure.ac is missing. Copied declaration from trunk. Tested with h5committest on jam ostrich koala and platypus(cmake).
* [svn-r24728] Description:Quincey Koziol2014-02-213-68/+83
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24726 & r24727 from trunk to 1.8 branch: Description: Revert some earlier usage of strncpy, which was incorrect. Bring Coverity changes from branch back to trunk: r20821: Use HDstrncpy. --gh (Fixed already, with strdup) r20822: (Not merged, incorrect use of HDstrncpy()) r20823: (Not merged, incorrect use of HDstrncpy()) r20824: Maintenance: Bug fix: addressed CID 666. Value stored at *expression_len should be used in the call to HD5packFstring to avoid overflow (and unnecessary arithmetic calculation and casting) r20825: Issue 642: Added check for error and handler with print to stderr and exit. r20826: Undo revision 20818, as that issue has already been fixed in the 1.8 branch and trunk (but not coverity branch) r20827: (Not merged, incorrect use of HDstrncpy()) r20828: Use HDstrncpy. --gh (Corrected use of strncpy()) r20829: Check return of H5Lget_val(print_udata->fid, path, targbuf, linfo->u.val_size + 1, H5P_DEFAULT) and if error set trgbuf[0] to 0. Check if H5Lunpack_elink_val(targbuf, linfo->u.val_size, NULL, &filename, &objname) was successful and allow print. Otherwise filename and objname are not created. (init those to NULL) r20830: resolved coverity issues 939, 940, 941, 944, and 947. all were complaints about use of sprintf, and in all cases, the buffers used were large enough for all eventualities. Resolved issue by replacing calls to sprintf with calls to snprintf. r20831: Maintenance: Addressed CID 852 Replaced sprintf with snprintf r20832: Purpose: Fix valgrind issues with hl/examples/ex_image2 Description: Modified hl/examples/ex_image2 to free global "gbuf" before exit. Tested on: Mac OSX/64 10.9.1 (amaon) w/C++, FORTRAN & Threadsafety (too minor to require h5committest)
* [svn-r24684] Add IF SHARED block around Windows PDB file generation command.Allen Byrne2014-02-041-2/+3
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* [svn-r24680] Remove acknowledgment file from install.Allen Byrne2014-02-036-74/+89
| | | | | | | Remove obsolete CPack.cmake file. Merge h5repack and h5mkgrp test folder changes from trunk. Tested: local linux
* [svn-r24654] HDFFV-8640: Remove XLATE_UTILITYAllen Byrne2014-01-2845-118/+3180
| | | | Update tools testfiles
* [svn-r24479] Description:Quincey Koziol2013-11-303-148/+153
| | | | | | | | Fix ph5diff worker command handling so it can correctly respond to situations where there's no work to perform. Also, a few minor code cleanups. Tested on: Mac OSX/64 10.9.0 (amazon) w/parallel
* [svn-r24468] tfilters.h5 was created and checked in on 21 Feb 05, rev 10060, ↵Allen Byrne2013-11-263-3/+3
| | | | | | | | and never regenerated. The code for scaleoffset continued to change and the number of params for scaleoffset changed from 7 to 20 on the checkin of 23 Mar 05, rev 10384. The h5dump tests only looked at headers and never the data. Data reads would fail with invalid number of params (7 expected 20). Regenerated file and replacement ddls updated. New h5dump test will be added to read the data.
* [svn-r24395] Missed script file for cleanupAllen Byrne2013-11-011-0/+17
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* [svn-r24393] Cleanup testfiles from scripts. Update lists of files to be ↵Allen Byrne2013-11-0114-8/+208
| | | | | | cleaned. CMake update to clean testfiles. Tested: local cmake, autotools
* [svn-r24228] HDFFV-8529: Space separate define stringsAllen Byrne2013-09-303-8/+8
| | | | Tested: local linux
* [svn-r24205] Merge HDFFV-8513/8522 from trunk (via cmake branch), h5repack ↵Allen Byrne2013-09-2631-4442/+5444
| | | | | | | | UD plugins. Also warning session fixes. Tested: CMake local linux
* [svn-r24201] Merged changes from trunk revisions 23431, 23527 and 24077.Larry Knox2013-09-251-14/+29
| | | | | | | | | | Switched default to link to shared lib files when HDF5 is configure with --disable-static. This addressed HDFFV-8141, h5cc failed because it defaulted to link to lib*.a files which aren't built with --disable-static. -help message also updated. Tested in trunk. Merged code tested with h5committest.
* [svn-r24112] Description:Quincey Koziol2013-09-065-33/+43
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r24101 & 24111 from trunk to 1.8 branch: r24101: ======= Description: Clean up warnings, enable new compiler warning flag(s) and bring back changes from Coverity branch: r20813: Remove the dead code as listed for coverity bug #1722. h5committested. r20814: Issue 69: Check return value and throw error if negative return. Also free datatype id on error r20815: Use HDstrncpy. --gh r20816: Replaced one last HDstrcat call with HDstrncat to resolve coverity issue 832. r20817: Use HDstrncpy and HDstrncat. --gh r20818: Purpose: Fix valgrind issues with h5jam Description: Modified h5jam to free strings strdup'd in parse_command_line before exit. Note that they may still not be freed in case of error, due to the widespread use of exit(). r20819: Issue 80: change loop to use int as loop index. r20820: Maintenance: Fixed the bug found by coverity CID 788 There were two problems with this function: 1) it tried to unnecessary free NULL pointer 2) it tried to allocate c_name buffer that is done by H5Pget_class_name r24111: ======= Description: Restrict GCC diagnostic pragmas to only gcc 4.6+ Tested on: Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN (too minor to require h5committest)
* [svn-r24108] Remove file from the future.Allen Byrne2013-09-061-158/+0
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* [svn-r24106] Add help text tests for h5dump and h5repack to the linux ↵Allen Byrne2013-09-0610-108/+1079
| | | | | | scripts. HDFFV-8498 merge from trunk. Tested: local linux - cmake and autotools
* [svn-r24072] Merge trunk cmake changes to 1.8 branch. Allen Byrne2013-08-2639-6681/+7118
| | | | | | | Also add default switch blocks to h5import. Merge h5dump any_path option from trunk. Tested: local linux
* [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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