| Commit message (Collapse) | Author | Age | Files | Lines |
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* Warnings fixes (#1680)
* Clean stack size warnings in sio_engine (#1687)
* Fixes stack size warnings in tcoords.c (#1688)
* Address some warnings from casting away of const (#1684)
* Fixes stack size warnings in ntypes (#1695)
* Fixes stack size warnings in dtransform (#1696)
* Fixes stack size warnings in set_extent test (#1698)
* Be a bit safer with signed arithmetic, thus quieting some signed-overflow warnings from GCC (#1706)
* Avoid a signed overflow: check the range of `entry_ptr->age` before
increasing it instead of increasing it and then checking the range.
This quiets a GCC warning.
* Avoid the potential for signed overflow by rewriting expressions
`MAX(0, fwidth - n)` as `MAX(n, fwidth) - n` for various `n`.
This change quiets some GCC warnings.
* Change some local variables that cannot take sensible negative values
from signed to unsigned. This quiets GCC warnings about potential
signed overflow.
* In a handful of instances, check the range of a signed integer before
increasing/decreasing it, just in case the increase/decrease overflows.
This quiets a handful of GCC signed-overflow warnings.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Fix object size warnings in cache.c test (#1701)
* Fix some const cast and stack/static object size warnings (#1700)
* Fix various warnings
* Move HDfree_const to H5private.h for wider use
* Print output from all ranks in parallel tests on allocation failure
* Move const pointer freeing macro to h5test.h for now
* Stop lying about H5S_t const-ness (#1209)
Hyperslabs can be reworked inside several H5S callbacks, making H5S_t
non-const in some places where it is marked const. This change switches
these incorrectly const H5S_t pointer parameters and variables to
non-const where appropriate.
* Fix a few warnings after recent H5S const-related changes (#1225)
* Adjustments for HDF5 1.12
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* OESS-98 fix tools test for plugins
* sync fork
* Merge of changes from dev
* Move problem option to bottom of the list until fixed
* HDFFV-11106 - fix parsing optional args
* HDFFV-11106 add note
* grammer fix
* Whitespace after clang formatting
* Undo format version 11 changes
* Update check to working version
* Merge workflow and minor changes from develop
* Update supported platforms
* PR#3 merge from develop
* Merge gcc 10 diagnostics option from develop
* Merge #318 OSX changes from develop
* Merge serval small changes from dev
* fix typo
* Minor non-space formatting changes
* GH #386 copyright corrections for java folder
* revert because logic requires false return
* Merges from develop
#358 patches from vtk
#361 fix header guard spelling
* Remove case statement for H5I_EVENTSET
* Correct call with versioning
* Remove tabs
* Double underscore change
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file - src and test directories.
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* OESS-98 fix tools test for plugins
* sync fork
* Merge of changes from dev
* Move problem option to bottom of the list until fixed
* HDFFV-11106 - fix parsing optional args
* HDFFV-11106 add note
* grammer fix
* Whitespace after clang formatting
* Undo format version 11 changes
* Update check to working version
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* Basic alignment with async branch - trivial changes to reduce clutter in overall diff.
* Update minor error code to reflect change within library
* Update the error output to match library
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header file, FUNC_ENTER / LEAVE, etc). Removed remaining personal email
addresses from library source code (still needs cleaned from other directories).
Misc. warning, style, and whitespace cleanup.
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types. Modify H5VLwrap_register() to reject non-VOL-managed object
types. Also fix overisights in h5trace.c from previous changes.
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modified: test/dsets.c
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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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configure
option (also updated CMake).
Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial autotools
serial CMake (CMake 3.3.2)
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Mostly minor fixes like warnings, etc.
Tested on:
Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
serial only
(these changes have been in revise_chunks for a long time)
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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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Normalize trunk against the metadata_cache_merge branch, in preparation
for merging the branch into the trunk.
Tested on:
MacOSX/64 10.10.3 (amazon) w/serial & parallel
Linux/64 2.6.x (koala) w/serial
Linux/32 2.6.x (jam) w/serial & parallel
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protection measures:
1. If any opened object uses the filter, let it fail.
2. Flush all opened files to push any cached data to files.
Tested with h5committest.
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Add FUNC_ENTER macros for package-private routines and begin process of
switching package routines to use them. All H5G routines are currently
finished.
Tested on:
Mac OSX/64 10.7.3 (amazon) w/debug, production & parallel
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Refactor root group routines to centralize and simplify them some.
Also patch root group's file pointer when it doesn't match the querying
file, from H5G_rootof.
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
Mac OS X/32 10.6.6 (amazon) in debug mode
Mac OS X/32 10.6.6 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.6 (amazon) w/parallel, in debug mode
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Description:
Library versions 1.6.3 and earlier contain a bug which causes them to be unable
to perform certain operations on a group if that group's symbol table
information is not cached in the parent group's symbol table. Versions 1.8.0
to 1.8.5 did not cache this information. Modified library to cache this
information.
Tested: jam, amani, heiwa (h5committest)
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Correct traversal of user-defined links (including external links) to
retain path information of object, allowing H5Iget_name() queries to work
quickly (without searching entire destination file). This required some
refactoring and addition of a mechanism to detect if a "fast" query was
performed (for the tests).
Minor code cleanups, etc.
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
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
Mac OS X/32 10.6.4 (amazon) in debug mode
Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode
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Add prototype of new H5Oexists() API routine.
Tested on:
Mac OS X/32 10.6.2 (amazon)
(further tests pending shortly)
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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 "compress group's fractal heap" feature from branch back to
trunk.
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 10.6.1 (amazon) in debug mode
Mac OS X/32 10.6.1 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
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Final merge of changes from sblock_mdc branch back to trunk. The superblock is now managed by the metadata cache.
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 (kagiso) w/PGI compilers, 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 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
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Description:
Versions of the library between 1.3.0 and 1.6.3 have a bug which prevents them
from opening any file that does not have the root group's symbol table
information cached in the root group's entry in the superblock. Prior to 1.8
this was not an issue as this information was always cached. However, 1.8.0
stopped writing this information (which is not required by the file format
specification), and these older versions can therefore not read files created or
last written by versions 1.8.0 to 1.8.2. This fix modifies the library to once
again add this information to the superblock (when using the old file format).
Tested: jam, linew, smirom (h5committest)
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Description:
Some files apparently exist in the wild which have corrupt symbol table messages
on the root group. These files can be opened by 1.6 (which uses the cached
information in the superblock) but not by 1.8. This patch fixes 1.8 and 1.9 so
they can now open these files, and will correct them if necessary. Also fix
some potential (rare) problems with array datatype versions.
Tested: jam (parallel; h5committest not working on linew or smirom)
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Centralize all macros for declaring "magic numbers"/signatures for
objects in the file into src/H5Fprivate.h, so it's easier to know what values
have already been defined, etc.
Tested on:
Mac OS X/32 10.5.4 (amazon) in debug mode
Mac OS X/32 10.5.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
in production mode
FreeBSD/32 6.3 (duty) in debug mode
FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, 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 production mode
Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in production mode
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Add check to avoid mounting the a file on a group twice, then the mounts
are done on the same HDF5 file, but opened with separate H5Fopen calls.
Also add new 'mounted' flag to the H5G_info_t struct, queried with the
H5Gget_info() API call, to allow applications to detect and avoid this
situation.
This probably fixes Bz#1070 also, I'll check with Dan Anov (who reported
a different sort of behavior, but seems to have the same underlying problem).
Tested on:
Mac OS X/32 10.5.4 (amazon)
Linux/64 2.6 (chicago)
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Add H5Ovisit() and H5Ovisit_by_name() API routines.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Add H5Lvisit_by_name() API routine to library.
Eliminated all (five!) other group traversal routines and changed them
all to use the new API routine.
Cleaned up output of h5ls & h5stat:
- Issue error when requesting recursive traversal of a file
with the "group info" flag, but no group given
- Print info about root group in all(?) appropriate situations
- Don't print "verbose" information about root group until the
root group is in the list of objects to display
(mostly because h5ls & h5stat had a different twist on traversing the
groups in a file that the other utilities)
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
Linux/64-ia64 2.4 (tg-login3) w/parallel, w/FORTRAN, in production mode
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Change H5Literate -> H5Literate_by_name and add simpler form of
H5Literate, to bring this routine into alignment with the other new API
routines.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64-amd64 2.6 (smirom) w/default API=1.6.x, w/C++ & FORTRAN,
in production mode
Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
in production mode
Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
w/szip filter, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Finish deprecating last H5G symbol (H5G_obj_t) - yay!
Lots of misc. library fixes to remove confusion between links and
objects. The tools could still use another pass, to remove h5trav_type_t type
and make the correct distinction between links & objects.
Tested on:
FreeBSD/32 6.2 (duty) in debug mode
FreeBSD/64 6.2 (liberty) w/C++ & FORTRAN, in debug mode
Linux/32 2.6 (kagiso) w/PGI compilers, w/C++ & FORTRAN, w/threadsafe,
in debug mode
Linux/64 2.6 (smirom) 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
AIX/32 5.3 (copper) w/FORTRAN, w/parallel, in production mode
Mac OS X/32 10.4.10 (amazon) in debug mode
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Add H5O{set|get}_comment routines, which were overlooked before.
Move H5G{set|get}_comment routines to deprecated code section,
replacing internal calls with H5O{set|get}_comment.
Tested on:
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (kagiso)
Linux/64 2.6 (smirom)
Solaris/32 5.10 (linew)
AIX/32 5.3 (copper)
Mac OS X/32 10.4.10 (amazon)
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Add flag to bypass (expensive) B-tree & heap size retrieval for
internal calls to H5O_get_info().
Teted on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
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Various code cleanups and refactor recent changes for h5stat to fit
into the existing library data structures better.
Tested on:
Mac OS X/32 10.4.10 (amazon)
FreeBSD/32 6.2 (duty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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New feature.
Description:
Added routines to report on the amount of storage for:
1) 1.6 btree and heap storage info for groups
2) 1.8 btree, fractal heap storage info for groups, attributes and SOHM table
3) btree storage for chunked datasets
4) 1.8 superblock extension size.
Platform tested:
h5committested.
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Change H5[D|G|T]<foo>_expand() "temporary" API routines to
H5[D|G|T]<foo>2() "versioned" routines. Also added
H5[D|G|T](create|commit)_anon() routines to continue to allow "anonymous"
objects to be created in a file.
Tested on:
Mac OS X/32 10.4.9 (amazon)
FreeBSD/32 6.2 (duty)
FreeBSD/64 6.2 (liberty)
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Eliminate storing default values for "group info" fields.
Tested on:
FreeBSD/32 6.2 (duty)
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Move "creation order tracked" flag from "group info" to "link info"
object header message and make the "max. creation order value" optional in the
"link info", if the creation order for links is not tracked.
Also, get rid of unused "index names" flag - names are always indexed
currently.
Tested on:
FreeBSD/32 6.2 (duty)
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Remove unused "min. creation order" field from link info object
header message.
Tested on:
FreeBSD/32 6.2 (duty)
Mac OS X/32 10.4.8 (amazon)
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Checkpoint progress on H5Aiterate2().
Mark H5Aiterate() as deprecated.
Various code cleanups.
Tested on:
Linux/32 2.6 (chicago)
Linux/64 2.6 (chicago2)
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Fix new API routines to use same pattern of arguments for specifying an
object as the new H5G/L/O API routines.
Tested on:
Linux/32 2.6 (chicago)
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