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* [svn-r21343] Issue 7674 - clang compiler with -fcatch-undefined-behavior ↵Raymond Lu2011-08-311-6/+12
| | | | | | | | | -ftrapv discovered several problems in the test suite. One of them is in the INIT_INTEGER macro definition in dt_arith.c. It complained about line 150 where it tried to subtract 1 from the negative minimal value of "int", causing it to overflow (or underflow). So I revised the code to avoid it. Tested on jam and Mac OS Lion with CLANG compiler. But I tested the same change for the trunk with h5committest.
* [svn-r21311] add variables and commands to create libhdf5.settings. Add ↵Allen Byrne2011-08-251-0/+14
| | | | | | option to enable embedded strings. Add test to grep for string. Trunk cycle passed and verified on windows.
* [svn-r21255] Issue 7674 - clang compiler reported an error with line 334:Raymond Lu2011-08-181-1/+1
| | | | | | | | | temp_point->l = (unsigned long long)((i * 100 + j * 1000) * n); The value can overflow the signed int before being converted to unsigned long long. So I changed it to temp_point->l = (unsigned long long)((i * 40 + j * 400) * n); to keep it under the maximal value. Tested on jam. Simple change.
* [svn-r21250] I skipped two test cases (in two functions ↵Raymond Lu2011-08-181-0/+2
| | | | | | test_delete_obj_named and test_delete_obj_named_fileid) for VMS using the macro H5_CANNOT_OPEN_TWICE because they open the same file twice. Tested on jam.
* [svn-r21221] The original code Raymond Lu2011-08-121-1/+12
| | | | | | | | | i_mask = ~((unsigned)~0 << (precision[0] + offset[0])) & ((unsigned)~0 << offset[0]); in line 3680 left shifted a 32-bit integer for 32-bit. The result is undefined by C language. A user discovered it using clang compiler with -fcatch-undefined-behavior option (see Issue 7674 in Jira). So I changed it in a funny way to avoid it. Tested on jam. But I tested the same change for the trunk with h5committest.
* [svn-r21164] Remove test library from export listAllen Byrne2011-08-011-1/+0
| | | | Tested: local linux
* [svn-r21153] Description:Quincey Koziol2011-07-282-0/+160
| | | | | | | | | | | | | | Bring r21152 from trunk to 1.8 branch: Further patches for Jira 7638, to ensure that H5D/Aget_type will be attached to the correct top file. (This change to the library should reverted when Jira 7638 is finally finished) Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode (h5committested on trunk)
* [svn-r21132] Description:Quincey Koziol2011-07-201-3/+16
| | | | | | | | | | | | | Bring r21131 from trunk to 1.8 branch: Disable some test code that isn't going to work correctly again until we've completely resolved Jira issue #7638. Tested on: FreeBSD/32 8.2 (loyalty) w/gcc4.6, w/C++ & FORTRAN, in debug mode Linux/64-amd64 2.6 (koala) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode (h5committested on trunk)
* [svn-r21128] Description:Quincey Koziol2011-07-201-4/+4
| | | | | | | | | | | Bring r21127 from trunk to 1.8 branch: Correct to use correct FAPL, to fix error when running 'make check-vfd' Tested on: Linux/64 2.6 (koala) w/make check-vfd FreeBSD/32 8.2 (loyalty) w/debug (h5committested on trunk)
* [svn-r21122] Description:Quincey Koziol2011-07-183-2/+201
| | | | | | | | | | | | | Bring r21120 from trunk to 1.8 branch: Check in ugly version of fix for Jira #7638. I'm going to leave the issue open in Jira and when the library has been refactored to use shared file pointers (instead of top file pointers) for file operations, I'll uncomment the check in src/H5Oshared.c Tested on: Mac OS X/32 10.6.8 (amazon) w/debug (too small for h5committest)
* [svn-r21079] Update test script to remove generated test files per test ↵Allen Byrne2011-07-081-21/+77
| | | | rather then in one group. Discovered from public 1.8 CDash reports.
* [svn-r21044] Purpose:Mike McGreevy2011-06-281-1/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fix HDFFV-7592 "Remove PACKEDBITS option from autotools files" Description: The code for h5dump's packed bits feature was conditionally compiled in via this option during its 'beta' release in 1.8.5. Now that the feature is fully supported, h5dump has since been changed to always compile the packed bits code (having removed the #ifdef H5_HAVE_H5DUMP_PACKED_BITS checks), so this option in configure is no longer needed. This commit removes the --enable-h5dump-packed-bits configure option, including the help summary from './configure --help' and the libhdf5.settings output summary, the PACKED_BITS Makefile variable, and the definition of H5_HAVE_H5DUMP_PACKED_BITS define in appropriate pubconf header files (which has already been removed from use in source code as of r20722). Note that this option was never added to the trunk, thus this commit only need occur on the 1.8 branch. Tested: - Configure output, help, & summary verified on jam - h5committested
* [svn-r21024] Bug fix for Issue 2598 - In v1.6 library, there was EOA for the ↵Raymond Lu2011-06-236-3/+181
| | | | | | | | | | | | | whole MULTI file saved in the super block. We took it out in v1.8 library because it's meaningless for the MULTI file. v1.8 library saves the EOA for the metadata file, instead. But this caused some backward compatibility problem. v1.8 library couldn't open the file created with v1.6 library. I fixed the problem by checking the EOA value to detect the file created with v1.6 library. Tested on jam, koala, and linew.
* [svn-r20970] Issue 4278 - When reading data fails, the error message should ↵Raymond Lu2011-06-131-2/+3
| | | | | | say which filter isn't registered. This is the follow-up commit. The previous way to construct the name of the existent data file wasn't very safe. It could be cleaned up if any user builds the library in the source directory. Tested on jam - simple change.
* [svn-r20945] Issue 4278 - When reading data fails, the error message should ↵Raymond Lu2011-06-071-14/+15
| | | | | | say which filter isn't registered. This is the follow-up commit. In my previous commit, I changed HDsnprintf to snprintf, which caused trouble for Windows because the name is _snprintf instead. So I changed it back to HDsnprintf for properly defined macro. I also changed all fprintf to HDprintf to be consistent. Tested on jam - simple change.
* [svn-r20943] Add filter_error.h5 test file to list - used by error_test test.Allen Byrne2011-06-071-0/+1
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* [svn-r20936] Issue 4278 - When reading data fails, the error message should ↵Raymond Lu2011-06-064-22/+236
| | | | | | say which filter isn't registered. The fix is simple. Most of the effort is on the test. The file with filter enabled is created in gen_filter.c. The verification of the error message is in test_error.c. The output is compared against the standard output. Tested on jam, koala, and heiwa.
* [svn-r20920] Issue 7579 - The overflowing ENUM values are inconsistent. ↵Raymond Lu2011-05-272-8/+121
| | | | | | | | | | When no conversion is involved in reading or writing the data, overflowing values are retained. When conversion happens, the values become -1. The conversion function puts -1 when overflow happens. I added two new dataset transfer property to control whether to fill 0xff in the destination data or convert to the destination data when overflow happens. The two new functions are H5Pset(get)_enum_conv_overflow. I also added test cases in enum.c and dtypes.c. Tested on jam, koala, and heiwa.
* [svn-r20873] Issue 7564 - Allow H5Tcreat to create string type (fixed-length ↵Raymond Lu2011-05-201-1/+62
| | | | | | and variable-length). I also added a test case in dtypes.c. The commit is only for test/dtypes.c, src/H5T.c, and release_docs/RELEASE.txt. All others are property changes due to the merge from the trunk. Tested on jam but I tested the same change for the trunk on jam and linew - relatively simple.
* [svn-r20863] Adjust CPack configuration location by removing version ↵Allen Byrne2011-05-181-1/+0
| | | | extension in folder name. Add install configuration commands if ext libs are packaged with project.
* [svn-r20859] Issue 2599 - Cross-test BE and LE data. I added the test for ↵Raymond Lu2011-05-185-750/+799
| | | | | | deflate, szip, fletcher32, shuffle and nbit filter in cross_read.c and gen_cross.c. I also took out the data file for OpenVMS because the data isn't native but IEEE for floating-numbers. Tested on jam and linew. But I tested the same change to the trunk with h5committest.
* [svn-r20758] I commented out 2 test cases using H5_CANNOT_OPEN_TWICE because ↵Raymond Lu2011-05-051-2/+4
| | | | | | | | they open the same file twice. OpenVMS can't do it. Tested on jam.
* [svn-r20695] Add description for new "external_open_twice" test.Neil Fortner2011-05-021-1/+2
| | | | Tested: jam
* [svn-r20692] Purpose: Fix problem exposed by external link cacheNeil Fortner2011-05-021-2/+245
| | | | | | | | | | | | | Description: When closing an object that had two open id's, the library would previously fail to account for the status of the "holding_file" field, potentially causing the file's "nopen_objs" field to become inconsistent. This caused problems when opening the same object twice through an external link using th external file cache. Modified the library to properly account for the status of the "holding_file" field when closing an object id, even when the underlying "shared" object isn't closed. Tested: jam, koala, heiwa (h5committest)
* [svn-r20661] Bug fix: VMS has trouble to deal with absolute path. I changed ↵Raymond Lu2011-04-281-0/+4
| | | | | | | | dtypes.c to use the file name only. I also updated the current directory path in vms/test/H5srcdir_str.h. Tested on jam and OpenVMS.
* [svn-r20608] OpenVMS complainted about a test case in th5o.c which opened ↵Raymond Lu2011-04-222-0/+6
| | | | | | | the same file twice. VMS doesn't allow it. I used the macro H5_CANNOT_OPEN_TWICE to skip the test case. In th5s.c, I created an attribute but fogot to close it in the test case for zero dimension size. Tested on amani, jam. But I haven't tested on OpenVMS yet.
* [svn-r20552] Description:Quincey Koziol2011-04-191-2/+2
| | | | | | | | | Bring r20551 from trunk to 1.8 branch: Correct 'FILE **' back to 'FILE *' for H5Fget_vfd_handle call. Tested on: FreeBSD/32 6.3 (duty) w/debug (h5committest performed on trunk)
* [svn-r20549] Fixed bug in test/vfd.c (HDFFV-5936) that caused STDIO VFD test ↵Dana Robinson2011-04-181-11/+2
| | | | | | to fail on some platforms. The problem was that the test was a clone of the SEC2 test. The SEC2 test accepts a file descriptor (int) via a void pointer from H5Fget_vfd_handle() whereas the STDIO test needs to accept a FILE pointer. Storing the FILE pointer in an integer failed on some systems. The STDIO test now stores the file handle in FILE pointer and checks it for NULL instead of < 0.
* [svn-r20537] Description:Quincey Koziol2011-04-174-19/+142
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r20535 & r20536 from trunk to 1.8 branch: Add explicit test that checks that the 'fileno' field in H5O_info_t is the same for objects in the same file, whether the file was opened twice or not. Clean up various warnings & code formatting issues. Bring changes from Coverity branch to trunk: r20085: Purpose: Fix coverity issue 793 Description: Modified H5S_hyper_project_simple_higher() to free the entire span list in new_space on failure. r20091: This is a fix for coverity bug #1683. Changed the two printfs to use %lu (unsigned long) for printing "dset_size". r20162: Purpose: Fix coverity issue 785 Description: Modified H5T_enum_nameof() to free "name" on failure if it was allocated. Also clarified some code in H5S_hyper_rebuild_helper(). r20189: Addressed coverity defect 783. H5SL_new_node() in H5SL.c was failing to free space allocated in its first alloc if the second alloc failed. Added a call to H5FL_FREE to address this issue. This is purely to keep coverity happy -- if this code is ever triggered, we have much larger problems. Note that this fix will trigger an unused return value complaint from coverity next week. r20190: Fixed Coverity issues 1561 1565 and 1678 (UNUSED_VALUES) by moving checks of return values to after the function call. r20191: Fixed coverity issues 643 644 and 1678 (CHECKED_RETURN). r20232: Addressed coverity issues 923-925. Replaced calls to sprintf with calls to HDsnprintf. r20233: Fix coverity issue 662. Don't try to sort 0 attributes in H5Aint.c. r20234: Fix coverity issue 664. Check for NULL before dereferencing in H5Gdeprec.c. r20271: Purpose: Fix coverity issue 784 Description: Modified H5_debug_mask() to keep a list of files opened for use as a debugging output stream, and modified H5_term_library to close these files on exit. r20272: addressed coverity issues 838 & 955. Issue was use of strcpy() -- existing code was safe, but modified to use strncpy() to keep coverity happy. r20273: Addresed coverity issues 1388 and 1389. Initialized sel_iter->type to NULL in H5S_select_iter_init. r20275: Purpose: Fix valgrind issue in mf.c Description: Fixed bug (incomplete if statement) in test_mf_fs_alloc_free() so the retrieved node gets freed. Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
* [svn-r20531] Purpose: Add testing for bug 1864Neil Fortner2011-04-1527-0/+173
| | | | | | | | | Description: Added internal tesitng routines to traverse a file and verify that symbol table information is *always* cached, whenever possible. Added this check to the end of many tests to check all the test files, right before the call to h5_cleanup. Tested: jam, amani, heiwa (h5committest)
* [svn-r20525] Description:Mike McGreevy2011-04-152-98/+107
| | | | | | | | Merge revisions 20475, 20502, and 20504 from trunk to 1.8 branch. Tested: Tested on jam, fred, bangan (CYGWIN), and h5committested.
* [svn-r20517] Description:Quincey Koziol2011-04-153-0/+216
| | | | | | | | | | | | | | | | | | | | | | | | Bring r20513 from trunk to 1.8 branch: Correct several problems with compound datatypes that don't have any fields added: - Change assertion to error report when a file is encountered which has this situation. - Added check to attribute creation to avoid creating attributes with a datatype like this (datasets and named datatypes already have the check) Tested on: FreeBSD/32 6.3 (duty) in debug mode FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x, w/C++ & FORTRAN, w/threadsafe, in debug mode Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x, w/C++ & FORTRAN, in production mode Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN, w/szip filter, w/threadsafe, in production mode Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
* [svn-r20498] Bug 1386 - allow dimension size to be zero even though it isn't ↵Raymond Lu2011-04-141-0/+8
| | | | | | | | | unlimited. I made a change in H5Sset_extent_simple to forbid setting the dimension size bigger than existing maximal size. In this checkin, I restored it to the previous behavior that any change will wipe out previous record of dimensionality. I brought the changes from the trunk. Tested on jam - a simple change.
* [svn-r20492] Rename H5Frelease_file_cache to H5Fclear_elink_file_cache.Neil Fortner2011-04-131-3/+3
| | | | Tested: Fedora (too minor for full committest)
* [svn-r20489] Bug 1386 - allow dimension size to be zero even though it isn't ↵Raymond Lu2011-04-133-23/+618
| | | | | | | | | | | | | | | | unlimited. I brought the changes from the trunk as below: 1. I added test cases for contiguous, compact, and chunked, and external storage datasets, and also attribute. The test includes dataspace selections. 2. I added a test case of extending dataset of zero dimension size and shrinking back to zero dimension size. 3. I updated the Makefile to include the new data file to be cleaned up. 4. The dataspace code has another bug - when the maximal dimension isn't passed in for H5Sset_extent_simple, it is supposed to be same as the dimension. The current library sets NULL to it. I corrected it and added a test case to it. 5. I corrected the tests of Fortran and C++ for the problem in point 3. Tested on jam, heiwa, and amani.
* [svn-r20481] Description:Quincey Koziol2011-04-121-4/+4
| | | | | | | | | | | Bring r20480 from trunk to 1.8 branch: Remove global variable for the path name in the group traversal code. Also clean up a bunch of compiler warnings. Tested on: Mac OS X/32 10.6.7 (amazon) w/debug & production (h5committested on trunk)
* [svn-r20471] Merged 20453 from trunk (minor fix to quiet compiler warning ↵Dana Robinson2011-04-111-2/+2
| | | | about integer overflow).
* [svn-r20470] Merged 20459 and 20462 (new and updated VFD tests) from trunk.Dana Robinson2011-04-112-69/+333
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* [svn-r20464] Merge cmake changes from trunk r20463, after weekend of tests ↵Allen Byrne2011-04-111-0/+3
| | | | | | on trunk. Tested: local linux
* [svn-r20317] Removed includes which are included with proper config checks ↵Allen Byrne2011-03-241-15/+1
| | | | | | in h5private.h. Tested: local linux, windows
* [svn-r20301] brought revisions 19868:20300 from the 1.8.6_vms branch to the ↵Raymond Lu2011-03-236-4/+29
| | | | 1.8 branch
* [svn-r20261] In my previous checkin (20256), I used H5Gcreate instead of ↵Raymond Lu2011-03-161-1/+1
| | | | | | H5Gcreate2 in my test. I just corrected it. Tested on jam with v16 API as the default.
* [svn-r20256] Bug 2115 - add H5_VERSION_GE and H5_VERSION_LE macros. I added ↵Raymond Lu2011-03-151-0/+69
| | | | | | a new test case to show how to use them. Tested on jam - simple change.
* [svn-r20181] Bug 2115/605 - I added 2 public macros to the H5public.h - ↵Raymond Lu2011-03-031-0/+49
| | | | | | H5_VERSION_GE and H5_VERSION_LE - and put some test cases in tfile.c. Tested on jam - simple change. I did h5committest on the same change for the trunk.
* [svn-r20157] Bring CMake changes to branch up to r20156 from trunkAllen Byrne2011-02-251-10/+11
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* [svn-r20128] Add fortran mod folder to INCLUDE_DIRS for gfortran 4.2.x.Allen Byrne2011-02-211-1/+3
| | | | | | Add test dependicies to correct the order of tests - cmake 2.8.4 bug - but also will improve cmake parallel testing. Tested: local linux, jam
* [svn-r20125] Bug 1586 - the datatype handler created with H5Tencode/decode ↵Raymond Lu2011-02-181-11/+71
| | | | | | had the reference count 0. I fixed it by changing the APP_REF parameter of H5I_register from FALSE to TRUE and added a test case in dtypes.c. The changes to configture.in, tools/misc, tools/lib, config, c++/test, Makefile.am, and fortran are only property changes when I merged from the trunk. Tested on jam. But I tested the same fix in the trunk with h5committest.
* [svn-r20114] Merge r20112 (open_file_pool) into 1_8 branch.Neil Fortner2011-02-175-63/+3736
| | | | Tested: jam (open_file_pool branch tested with h5committest)
* [svn-r20062] Description:Quincey Koziol2011-02-081-22/+17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r20061 from trunk to 1.8 branch: Bring changes from Coverity branch to trunk: r19930: Fix memory leaks involving VL attributes in h5repack and h5diff. The buffers in copy_attr and diff_attr were not checked for the presence of a vlen before being freed, and vlen storage was never reclaimed. Added checks and calls to H5D_vlen_reclaim(). r19933: Purpose: Fix memory leak in H5L_move_cb() Description: H5L_move_cb copied the source link using H5O_msg_copy() but freed it manually using H5MM_xfree(). Since H5O_link_copy allocates the link using H5FL_MALLOC, this causes the link to be allocated from the free list but is never put back on the free list when it is freed. This prevents the link free list from shutting down properly. Modified H5L_move_cb() and H5L_move_dest_cb() to free the link properly using H5O_msg_free(). r19973: Fix resource leaks by freeing string created by HD5f2string r19974: Issue #345: Inialize buf variable to null Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on Coverity branch)
* [svn-r20053] Description:Quincey Koziol2011-02-061-31/+61
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bring r20052 from trunk to 1.8 branch: Clean up Coverity warnings, and fix some style issues: r19735: Fix for memory leak in test/mf found by valgrind. r19736: Fix memory leak in h5repack. The buffer in copy_objects, when copying the entire dataset at once, was not checked for the presence of a vlen, and vlen storage was never reclaimed. Added check and call to H5D_vlen_reclaim(). r19772: Change H5assert() to if (H5T_VLEN != src->shared->type || H5T_VLEN != dst->shared->type) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a H5T_VLEN datatype") r19774: removed unused priv. r19775: removed unused variables r19778: Fix memory leak comparing for variable length data types. r19834: Fixed memory leaks found by valgrind. Memory errors remain for another day. Tested on: Mac OS X/32 10.6.6 (amazon) w/debug & production (h5committested on branch)
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