Merge 64-bit ID changes from branch to trunk. (Plus a few minor cleanups
that aren't on the branch)
Tested on:
Mac OSX/64 10.9.4 (amazon) w/C++ & FORTRAN
(h5committested on branch already for a week)
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
(too minor to require h5committest)
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
Tested on:
Mac OSX 10.8.4 (amazon) w/gcc 4.8.1, C++ & FORTRAN
(too minor to require h5committest)
HDFFV-7523 JPSS: h5dump fails to open an attribute when using the -a option to specify an attribute with a slash in the name
Description:
Update command line help page and test generating file.
Previous commits: r22052, r22063
Tested:
jam (linux32-LE), koala (linux64-LE), cmake (jam)
HDFFV-5948 - CHICAGO: Tools - implement missing external link test cases
Description:
Add three test cases for h5dump and h5ls.
- h5ls: external link to soft link with follow symlink.
- h5dump: external link to soft link with follow symlink.
- h5ls: external link to soft link without follow symlink.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
Remove old, uneeded configuration customizations for FreeBSD systems.
(config/freebsd)
Also, convert a large stack variable into a dynamic memory allocation
and clean up a few compiler warnings (tools/h5dump/h5dumpgentest.c)
Tested on:
FreeBSD/32 8.2 (loyalty) w/debug & production
FreeBSD/64 8.2 (freedom) w/debug & production
Fixing Bug 2092 - h5dump does not display index for a dataset
Description:
improve the test case from previous checkin r20108, which also display
dataset via region reference.
Previous Log:
h5dump skip displaying array indices every certain number when the
array type dataset is relatively big. The certain number varies
according to the size of each array.
This checkin fix the skipping array indices problem. This fix also
correct indentation of the dataset data output.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake - jam
Fixing Bug 2092 - h5dump does not display index for a dataset
Description:
h5dump skip displaying array indices every certain number when the
array type dataset is relatively big. The certain number varies
according to the size of each array.
This checkin fix the skipping array indices problem. This fix also
correct indentation of the dataset data output.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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)
Fixed Windows compile error. Renamed to use 'gid1' and 'gid2' instead of 'grp1' and 'grp2'.
Description:
There is variable name confliction with 'grp1' ~ 'grp9' in Windows system. It occurs if H5private.h is included in the code.
Support follow symbolic links.
Description:
Add '--follow-symlinks' option to follow symbolic links (soft and external).
Update help page according to RM.
Remove some warning messages from compiler.
Tested:
jam, amani and linew
Enable tools lib to be built as a dll on windows. Added two get/set functions for progname and d_status.
Also add windows import/export declarations to functions.
Updated error_mesg() and warn_mesg() to remove progname argument and use get functions
Tested:
Windows, linux
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
Bring changes from file free space branch back to the trunk. *yay!*
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 10.5.8 (amazon) in debug mode
Mac OS X/32 10.5.8 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Generic function name is used but that would fail when v16API is used.
Changed the H5Dcreate() and H5Acreate() to v18 names as H5Dcreate2() and H5Acreate2().
tested: jam (regular and --with-default-api-version=v16).
Bring r17266 from 1.8 branch to trunk:
Clean up various compiler warnings from IRIX64 build
Tested on:
Mac OS X/32 (amazon) debug & production
(yes, I know it's not an IRIX64 system :-)
Too minor to require h5committest
Description:
Previously, there was no versioning for H5Z_class_t. This prevented applications
written for 1.6 using custom filters from being able to use the 1.8 library.
There is now an H5Z_class1_t and H5Z_class2_t to enable compatibility. H5Zregister is
*not* versioned, it determines which version of the struct has been passed in by the
value of the first field (id or version, both are ints).
Tested: jam, linew, smirom (h5committest), jam (--with-default-api-version=v16)
