| Commit message (Collapse) | Author | Age | Files | Lines |
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This reverts commit 8b9338ab57eec0cc8fa5a36c44d7b28e52e9a466.
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Description:
Applied the typo fixes from user's report.
The previous pull request couldn't be merged because it was too old,
and it was too complicated for me to resolve conflicts.
Platform tested:
Linux/64 (jelly) - very minor
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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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Clean up warnings (from 2774 -> 1560, with my standard debug build)
Tested on:
MacOSX/64 10.11.5 (amazon) w/serial, parallel & production
(h5committest forthcoming)
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Clean up many mismatches between malloc/free and H5MM_malloc/H5MM_xfree
in the library and tests (and use of H5free_memory and H5Dvlen_reclaim). Also
make H5Ocopy use a private version of H5Lexists, which doesn't internally
throw (and suppress) errors when an object (or the path to it) isn't found in
the destination.
Tested on:
MacOSX/64 10.11.2 (amazon) w/serial & parallel
(h5committest forthcoming)
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invalid
transform).
Tested: koala, ostrich (h5committest)
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Refactor property list code to "deep copy" properties in the correct way,
retraining the rest of the library to copy & release things correctly. This
cleans up another batch of memory leaks, etc. within the library.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/32 2.6.x (jam) w/serial & parallel
(h5committest forthcoming)
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Complete revamp of package initialization/shutdown mechanism in the library.
Each package now has a single init/term routine.
This new way should avoid packages being re-initialized during library
shutdown and is also be _much_ more proactive about giving feedback for
resource leaks internal to the library.
Introduces a new "module" header file for packages in the library
(e.g src/H5Fmodule.h) which sets up some necessary package configuration macros
for the FUNC_ENTER/LEAVE macros. (The VFL drivers have their own slightly
modified version of this header, src/H5FDdrvr_module.h)
Also cleaned up a bunch of resources leaks all across the library and tests,
along with addressing many warnings, as I encountered them.
Tested on:
MacOSX/64 10.10.5 (amazon) w/serial & parallel
Linux/64 3.10.x (kituo) w/serial & parallel
Linux/64 2.6.x (ostrich) w/serial
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gcc 4.9.2 was used to create the warning list
- implicit casts
- shadowed variables
- various enum issues
- other minor fixes (comments, unused macros, etc.)
Tested on: h5committest
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Bring r26500 from autotools_rework branch to trunk:
Remove the LLONG_TO_FP_CAST_WORKS macro/define, as it targets problems with
the Visual Studio 6 compilers.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
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Bring r26499 from autotools_rework branch to trunk:
Remove ULLONG_TO_FP_CAST_WORKS macro/define, as it only applies to older
platforms we aren't supporting any longer.
Tested on:
Linux/32 2.6.18 (jam) w/serial & parallel
(Daily tested on branch for 2+ days)
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project for
view objects. The addition of view objects in the fastforward project
is expected to be brough into the trunk sometimes in the future, which
is why we need to make this change.
Tested Manually on Jam and Ostrich.
Tested with h5commitest - Koala with intel compilers failed, but nothing had to do with those changes.
error on Koala: error while loading shared libraries: libirng.so
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Clean up warnings, switch library code to use Standard C/POSIX wrapper
macros, remove internal calls to API routines, update checkapi and checkposix
scripts.
Tested on:
Mac OSX/64 10.8.3 (amazon) w/C++ & FORTRAN
Big-Endian Linux/64 (ostrich)
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Bring generic improvements from encode/decode property list branch to
the trunk. This includes a better version of the property list comparison
routine, cleaned up compiler warnings, and some cleaned up property list
callbacks. Also, started on changes to clean up parallel test output, so that
it doesn't report successful tests from each process.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/debug, GCC 4.7.x, FORTRAN, C++, threadsafe and parallel
Linux 2.6/32 (jam) w/debug
Solaris 2.7/64 (linew) w/debug
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Switch propert list/class iteration from internal to external form of
iteration, cleaning up and simplifying the code a bit.
Bring other general improvements from plist_encode_decode branch back to
trunk.
Clean up many warnings.
Tested on:
Mac OSX/64 10.7.4 (amazon) w/gcc 4.7, debug and C++ & FORTRAN
(too minor to require h5committest)
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private functions and a macro according to Quincey's suggestion.
Tested on jam - simple change.
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(11.8-0) on jam and koala has trouble with the command "*p++ = *p OP tree_val" in the macro definition of H5Z_XFORM_DO_OP1 of H5Ztrans.c. It increments P first before doing the operation. So I break down the command into two lines: "*p = *p OP tree_val; p++;" I also reported the problem to PGI.
Tested on jam, koala, and ostrich.
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operations like x*-100.
The parser mistaked "-" as substraction. I fixed it and also fixed another problem
with some special cases like 100-x and 2/x.
Tested on jam, koala, and ostrich.
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Refactor function name macros and simplify the FUNC_ENTER macros, to clear
away the cruft and prepare for further cleanups.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
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Bring Coverity changes back to trunk:
r20340:
Address coverity issue 248. Set freed pointer to NULL if realloc fails, then check for NULL before attempting to close array of handles stored in memory addressed by pointer.
r20341:
Added initialization udata.path = NULL; udata.visited = NULL; to prevent unintialized use after done: label.
Do C-style initialization AFTER all variable definitions.
r20342:
Fix valgrind error in H5DUMP-XML-tall.h5
r20343:
Addressed Coverity issue 591 - check the return value of H5S_SELECT_ITER_RELEASE.
r20344:
Added initialization udata.path = NULL; to prevent uninitialized used after done: label
r20347:
Purpose: Fix memory leak in overhead.c
Description: Fixed leak in test() in overhead.c where array "had" was never
freed.
r20348:
Addressed Coverity issue 705 - added prototype for resize_configs_are_equal to cache_common.h.
r20392:
Purpose: Fix coverity issues 1677 and 1678
Description: Added return value checking for 4 funciton calls in
H5tools_get_symlink_info().
r20394:
Purpose: Fix coverity issues 1674 and 1675
Description: Modified H5Epush2() and H5E_printf_stack() to keep track of whether
va_start() has been called, and to call va_end() at the end if so.
r20395:
Should be H5MM_calloc(count * sizeof(void*)). Fixed --gh
r20396:
Should be H5MM_calloc(count * sizeof(void*)). Fixed. --gh
Tested on:
Mac OSX/32 10.6.7 (amazon) w/debug & production
(h5committested on branch)
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Bring revisions from Coverity branch back to trunk:
r19044:
Coverity #449 - Line 1560 called function H5O_chunk_protect for 2 pointers to allocate. But when there's failure on the second one, the first wasn't freed
(H5O_chunk_unprotect). We fixed it by freeing the pointers when an error happens.
r19045:
Fixed coverity issue # 319. Free sec_node in done if it is not NULL.
r19046:
Add intended but missing assignments to initialize pointers to NULL (coverity issue fixes).
r19049:
Hdf5_1_8_coverity branch was recreated from hdf5_1_8 branch in revision 18839 without fix for Coverity issue #84 having been propagated to the hdf5_1_8 branch. This revision adds the fix again.
r19060:
added parentheses to see if they will keep subversion from getting confused
r19061:
Fix coverity item 139. Fixed incorrect condition for freeing buffer on error.
Fix coverity items 20 and 21. Removed unused NTESTS facility from dtypes.c.
Cleanup in H5Shyper.c.
r19062:
Fix coverity item 450. Check to see if chk_proxy has been allocated before
attempting to free it.
Fix coverity item 454. Check to see if allocation of buf failed in
H5D_fill_refill_vl.
Fix coverity items 455-457. Initilize hid_t's to -1, check their value before
attempting to close them, and check if the close failed.
r19063:
New fix to address coverity issue #84. Check that pointers in H5Z_xform_find_type are not NULL before passing them to H5T_cmp.
Tested on:
Mac OS X/32 10.6.4 (amazon) w/debug & production
(Too minor to require h5committest)
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Bring r18169 from 'merge_metadata_journaling' branch back to trunk:
Converge changes on metadata_journaling branch and trunk:
- Remove H5F_t* parameter from H5HL_unprotect()
- Remove H5F_t* parameter from H5HL_dirty()
- Remove H5F_t* parameter from H5O_unprotect()
- Bring changes to metadata caching routines back:
- H5AC_pin_protected_entry()
- H5AC_resize_pinned_entry()
- H5AC_unpin_entry()
- H5AC_mark_pinned_entry_dirty()
- H5AC_mark_pinned_or_protected_entry_dirty()
- Revise internal H5C routines to drop H5F_t* and/or H5C_t* as
parameter where possible
- Revise tests to follow internal routine changes
Also, drop file/cache pointer parameter from create/destroy flush
dependency internal cache calls.
Also, other minor changes to speedup the 'cache' test.
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, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
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Bring r18030 from merge_metadata_journaling branch to trunk:
Bring "brush clearing" changes (whitespace & style issues, mostly) from
metadata_journaling branch to the "merging" branch, to converge the trunk and
the metadata_journaling branch.
Also, some other minor cleanups along the way.
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 (smirom) 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, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Bring Coverity changes into the trunk:
r17877:
Error 266: Uninitialized memspace set to -1. Changed malloc and free to HDmalloc and HDfree. Removed unused dtype var.
r17878:
Error 265: Uninitialized mem_space set to -1. Changed malloc and free to HDmalloc and HDfree.
Error 267: Uninitialized smspace set to -1. Changed malloc and free to HDmalloc and HDfree.
r17879:
Error 242: Uninitialized aid set to -1.
Error 243: Uninitialized sid set to -1.
Uninitialized tid set to -1 for consistency
r17880:
Error 242: reinitialized aid to -1 after close to be ready for reuse.
Error 243: reinitialized sid to -1 after close to be ready for reuse.
reinitialized tid to -1 for consistency after close to be ready for reuse.
r17881:
use valgrind to check there is a memory leak. The fix is to free ptrstr in line 5838 at xml_dump_group() of h5dump.c after it is used. run the valgrind after the fix, no memory leak for that part of the code.
r17882:
Fix Coverity items 256 and 269.
r17883:
Error 222-230: initialized hid_t vars to -1 after close to be ready for reuse.
Also added H5Tclose for tid in gent_bigdims
r17884:
Bug fix (Coverity run2, view 23, dead code)
(this is pair-program done by Albert, Elena and Larry).
Confirmed and fixed the deadcode in hyperslab read branch of function
diff_datasetid.
(Discovered other bad code that diff_datasetid() should be recoded.
Bug 1693 is entered for this.)
r17906:
Fix Coverity item 260.
r17907:
262: Initialized hid_t's dtype, dtype_tmp and file to -1. Initialized H5T_t * dt to NULL.
r17908:
Fix Coverity item 261.
r17909:
Fix Coverity item 248.
r17910:
Revise fix for Coverity item 248.
r17911:
Resolved coverity issues #s 263, 162, 163, 164. All issues in dsets.c. Initialized fid and did hid_t's. filter_corrupt function was returning in the middle of an if statement, bypassing free calls. Updated error handling to free buffers and hid_t's appropriately.
r17912:
(done by Larry and Albert)
Cleanup Coverity view warnings (#231-241) about
using uninitialized variables. Initialized all
of them.
r17913:
Resolved issue 251 and 264. Initialized tid2 to -1 and initialized buffers that were freed in case of an error.
r17914:
Resolved coverity issues 66, 220, and 221:
66: Negative Return assignment ignored
220,221: Initialized hid_t's.
r17915:
Fix Coverity item 247.
r17916:
Fix Coverity item 246.
r17917:
Fix Coverity item 245.
r17918:
Fix Coverity item 244.
r17919:
Coverity Issue #84: Moved asserts in H5T_cmp to the top of the function, and converted them to HDassert. Coverity complaining about using potentially NULL pointer without checking it. Want to see if Coverity will accept Assertions as acceptable checking before using the value.
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 (smirom) 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, in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in debug mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
Mac OS X/32 10.6.2 (amazon) in debug mode
Mac OS X/32 10.6.2 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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replacing all instances with long long.
Tested:
h5comittest
fedora 10 x64
Vista 32, VS2005, IVF101
XP32, Cygwin
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Remove trailing whitespace from C/C++ source files, with the following
script:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Tested on:
Mac OS X/32 10.5.5 (amazon)
No need for h5committest, just whitespace changes...
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Omnibus compiler warning cleanup & some reformatting also.
Tested on:
Mac OS X/32 10.5.4 (amazon)
Too minor to require h5committest
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copyright notice.
Tested platform:
Kagiso only since it is only a comment block change. If it works in one
machine, it should work in all, I hope. Still need to check the parallel
build on copper.
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Description: Fix a few memory-related bugs in the data transform code.
Tested:
kagiso (for real this time) w/ valgrind 3.2.1
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Finish new version of the I/O pipeline message, which is much smaller than
the previous version. This version is used with the "use the latest version
of the format" flag.
Closed several memory leaks/overruns (found with valgrind).
Also, lots of compiler & formatting cleanups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Fixed copyright notice.
Description:
A line is missing in the copyright notice. Fixed.
Platforms tested:
No test since it is only a fix in a comment block.
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Code cleanup
Description:
Trim trailing whitespace, which is making 'diff'ing the two branches
difficult.
Solution:
Ran this script in each directory:
foreach f (*.[ch] *.cpp)
sed 's/[[:blank:]]*$//' $f > sed.out && mv sed.out $f
end
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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New port
Description:
Elena asked me to check in her NEC SX-6 work, so here it is! :-)
Platforms tested:
FreeBSD 4.11 (sleipnir)
NEC SX-6 (by Elena)
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Code cleanup
Description:
Switch name & logic from H5_LLONG_TO_FP_CAST_BROKEN to
H5_LLONG_TO_FP_CAST_WORKS, to better match the rest of the library.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Bug fix
Description:
On visual studio 6.0, conversion from unsigned long long to double is not supported.
Even during compilation stage, it will fail.
Solution:
Albert changed the way the macro is handled so that for windowx MSVS 6.0,
the code that has conversion from unsigned long long to double will not compile.
Platforms tested:
windows, linux
Misc. update:
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bug fix (sorta)
Description:
Rename H5_LLONG_TO_FP_CAST_WORKS to H5_LLONG_TO_FP_CAST_BROKEN
Solution:
Since a test for H5_LLONG_TO_FP_CAST_WORKS is not present in the configure script,
the dtransform test would assume that this cast doesn't work and skip the test. Change the variable around
so that, by default, it is assumed a long long to double cast does work.
Platforms tested:
minor change: copper, sol
Misc. update:
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Bug fix
Description:
The intel compiler on windows doesn't support long long to double conversion.
Solution:
Added a flag H5_LLONG_TO_FP_CAST_WORKS. When it is not defined, the data transform will issue
an error when someone tries to perform a transform from long long to double and the long long to double
dtransform test will be skipped.
Platforms tested:
heping, sol, copper
Misc. update:
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Optimization
Description:
Speed up I/O on enumerated datatypes (including those nested in compound
datatypes, arrays, etc.) if the destination datatype is a proper superset of
the source datatype.
Solution:
Detect the situation and treat as no-op datatype conversion.
Platforms tested:
FreeBSD 4.11 (sleipnir)
Too minor to require h5committest
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Description: Removed PABLO from the source
Solution:
Platforms tested: arabica with 64-bit, copper with parallel,
heping with GNU C and C++ and PGI fortran (but
I disabled hl, there is some weird problem only
on heping: F9XMODFLAG is not
propagated to the Makefile files
Misc. update:
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Bug Fix/Code Cleanup/Doc Cleanup/Optimization/Branch Sync :-)
Description:
Generally speaking, this is the "signed->unsigned" change to selections.
However, in the process of merging code back, things got stickier and stickier
until I ended up doing a big "sync the two branches up" operation. So... I
brought back all the "infrastructure" fixes from the development branch to the
release branch (which I think were actually making some improvement in
performance) as well as fixed several bugs which had been fixed in one branch,
but not the other.
I've also tagged the repository before making this checkin with the label
"before_signed_unsigned_changes".
Platforms tested:
FreeBSD 4.10 (sleipnir) w/parallel & fphdf5
FreeBSD 4.10 (sleipnir) w/threadsafe
FreeBSD 4.10 (sleipnir) w/backward compatibility
Solaris 2.7 (arabica) w/"purify options"
Solaris 2.8 (sol) w/FORTRAN & C++
AIX 5.x (copper) w/parallel & FORTRAN
IRIX64 6.5 (modi4) w/FORTRAN
Linux 2.4 (heping) w/FORTRAN & C++
Misc. update:
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Bug Fix
Description:
Fixed off by one error in H5Pget_data_transform
Solution:
H5Pget_data_transform, when queried for the size of the property, should
return strlen() + 1 so that the user can allocate memory for the terminating
\0 in the string.
Also fixed a typo in a comment in H5Ztrans.c
Platforms tested:
eirene, too minor to require further testing.
Misc. update:
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Bug fix
Description:
Clean up potential buffer overflow in strncpy()
Platforms tested:
FreeBSD 4.10 (sleipnir)
Too minor to require h5committest
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Changed functionality of H5Pget_data_transform
Description:
H5Pget_data_transform no longer allocates memory for the transform string...it
is the user's responsbility to do so.
Solution:
Made H5Pget_data_transform be more in line with other functions that do
similiar things:
User now has to allocate memory for the string themselves and specify how much
of the string should be copied into the buffer. There is also support for
querying the length of the transform string.
Platforms tested:
sol + eirene + copper
Misc. update:
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Bug fix.
Description:
The previous H5_ULLONG_TO_FP_CAST_WORKS fix does not quite work
since the problem was an error during compiling while the fix
was trying to check for the error condition during runtime.
The MS-Compiler still complains about not supporting ULLONG
to Float.
Solution:
A temperary patch is to have two #define of H5Z_XFORM_TYPE_OP
according to if H5_ULLONG_TO_FP_CAST_WORKS is defined. This
works but a better solution is needed.
Platforms tested:
Windows (by Kent) and heping (Linux by me).
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Code refactor
Changed functionality of H5Pget_data_transform
Description:
Rewrote much of H5Ztrans.c to use macros, which cut down on the amount of code
significantly.
H5Pget_data_transform now allocates memory for the data transform string,
copies the string into this memory, and
returns this pointer to the user, instead of returning a pointer to the
internal transform string stored by hdf. It is the user's responsibility to free
this memory when they are done with it.
Platforms tested:
sol + eirene + copper
Misc. update:
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