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* Squash my changes on branch `fprintf-experiment` into one commit forDavid Young2020-07-0783-996/+593
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | reapplication to my new warnings branch, `warnings-again`. These changes are included: commit 915551b7bf64e777dd2007386ec77b1d117770da Merge: 63858c2 a8892bb Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:39:49 2019 -0600 Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment commit a8892bb42d6f6e4fbc30fae0eb2b957f81c938b9 Merge: 5c911d8 f907b51 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:33:54 2019 -0600 Merge pull request #2055 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop * commit 'f907b511d06612dafc7814a7c30f2f3d2b76d52b': Oops, remove more C99 designated initializers for VS 2010 compatibility. commit 63858c22e168acaec0af8ced6641f26102cc6bb0 Merge: 20ae787 5c911d8 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 17:04:42 2019 -0600 Merge remote-tracking branch 'hdf5/develop' into fprintf-experiment commit 5c911d8baf3ee7fe654269088eebdf07f59a8192 Merge: b8a5671 62208b0 Author: David Young <dyoung@hdfgroup.org> Date: Mon Nov 25 16:58:27 2019 -0600 Merge pull request #2030 in HDFFV/hdf5 from ~DYOUNG/vchoi_fork:add-werror-and-squash-some to develop * commit '62208b056a09c01855fbac7f75146be58ad6bfe5': (44 commits) Add an #include to get a function declaration. Don't use C99 designated initializers, they're not compatible with Visual Studio 2010. Quiet some more maybe-uninitialized warnings---each is a false positive, *sigh*. This is more code that may not compile with VS2010, *sigh sigh*. Always warn on maybe-uninitialized. -Wincompatible-pointer-types was not available until GCC 5, so enable it only if that's the GCC version we're using. Only promote maybe-uninitialized warnings to errors on GCC 8. Even on GCC 8, there may be false positives at low optimization levels? I need to check. Only use -Werror=cast-function-type with GCC 8 and later. Put all of the -W options back into the order I found them in so that it's easier to compare old and new config/gnu-flags. Add new source files to CMakeLists.txt. Mention the -Werror= flags in libhdf5.settings.in. free -> HDfree Promote decleration-after-statement warnings to errors. Quiet decleration-after-statement warnings. Move a statement under some declarations since some vintages of Visual Studio don't like declarations after statements. Document H5D__chunk_mem_xfree_wrapper(). Undo accidental test deletion. Oops, delete a debug printf that snuck in here. Undo my changes to the HD macros, hadn't really intended those to be on this branch.... Make errors of some more warnings. Move disabled warnings to DEVELOPER_WARNING_CFLAGS. Put just one warning option on a line, and sort some of the options. Cast to the parameter type, H5VL_token_t *, instead of to unsigned char *. Change hdset_reg_ref_t and H5R_ref_t from arrays of unsigned char to structs containing those arrays. Encapsulating the arrays in this way makes it easier to write and think about pointers to these types, casts to/from these types, etc. ... commit 20ae7877e33931b95e8c3502b027d6c3fe94a11f Merge: 46f8c61 edd5297 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:34:09 2019 -0600 Merge remote-tracking branch 'origin/add-werror-and-squash-some' into fprintf-experiment commit 46f8c613d5117a8be5bc8385a072daa0b4262f06 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:29:00 2019 -0600 GCC really wants us to use `ll` to format `long long`, so try to make that work before any other format modifier. Seems like we're not compiling the autoconf test program with -Werror=format ? Probably should. commit eee35b8ef3759c391327cd48a9b3c56b6f8abc99 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:28:05 2019 -0600 It's hard to know just how wide an HDoff_t will be, and I don't think POSIX or C standards provide a PRI macro for it, so cast to intmax_t and format using PRIdMAX. commit 86eab12df7a89b546a38e99f8178dd2adbcb3433 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 15:26:25 2019 -0600 URemove some casts.se the right format string for the argument. Here and there stop casting a printf argument. commit f722f7cbecbaa99449941484b014426f62f1bed5 Merge: 58e3743 6d5ec83 Author: David Young <dyoung@hdfgroup.org> Date: Fri Nov 22 14:44:16 2019 -0600 Merge branch 'add-werror-and-squash-some' into fprintf-experiment commit 58e3743b7faa9836606ee91798fe80dfc0040da7 Author: David Young <dyoung@hdfgroup.org> Date: Wed Nov 20 21:07:21 2019 -0600 Remove custom HDfprintf implementation, using the standard library's, instead. Take a swipe at repairing fprintf format strings, mainly replacing "%Hu" with "%" PRIuHSIZE, "%a" with "%" PRIuHADDR, "%Zu" with "%zu". Here and there remove an awkward cast of a printf argument to `long long` and use PRI[doux]8, PRI[doux]32, or PRI[doux]64, instead. Change occurrences of "%t" to "%s" and perform a suitable change of argument, `cond` -> `cond ? "TRUE" : "FALSE"`. Some occurrences of %Hu, %a, and %t remain, they just weren't flagged by the compiler because of #ifdef'age. commit d4366909293fa970c23512ac80e5d865d76cddbf Author: David Young <dyoung@hdfgroup.org> Date: Wed Nov 20 20:54:32 2019 -0600 Promote format-string warnigns to errors.
* Merge pull request #2673 in HDFFV/hdf5 from monotonic_timer_fix_01 to developQuincey Koziol2020-07-032-2/+2
|\ | | | | | | | | * commit '13c9b3768e6193db89d06faf59194b77d7747f45': Address CMake and deprecated API build failures from monotonic timer patch.
| * Address CMake and deprecated API build failures from monotonic timer patch.Quincey Koziol2020-07-032-2/+2
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* Merge pull request #2672 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-021-1/+1
|\ | | | | | | | | * commit '870e3ba3f45e90a43ea824d67cc8562aa63a3f6f': Add missing '"'.
| * Add missing '"'.Larry Knox2020-07-021-1/+1
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* Merge pull request #2671 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to developAllen Byrne2020-07-026-224/+222
|\ | | | | | | | | * commit '88e8597cdef826c1087e4ec1383657a91dcb2a43': Small changes discovered with mingw and windows defines moved
| * Small changes discovered with mingw and windows defines movedAllen Byrne2020-07-026-224/+222
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* | Merge pull request #2670 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-023-1/+20
|\ \ | |/ |/| | | | | * commit 'fc69de0e8ae30e80c1c3c542b156226a75444525': Lib files needed are now copied to a subdirectory in the java/test directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. Fix for HDFFV-11063
| * Lib files needed are now copied to a subdirectory in the java/testLarry Knox2020-07-023-1/+20
|/ | | | | | directory, and on Macs the loader path for libhdf5.xxxs.so is changed in the temporary copy of libhdf5_java.dylib. Fix for HDFFV-11063
* Merge pull request #2668 in HDFFV/hdf5 from monotonic_timer to developQuincey Koziol2020-07-0223-909/+1817
|\ | | | | | | | | | | | | | | | | | | | | | | | | * commit '7371c83f9777b34b31909e99e052398b93c31bed': Remove non-existent example Add new source files to CMake build Clean up warnings va_arg -> HDva_arg Refactor code to remove remaining checks for H5_HAVE_GETTIMEOFDAY scattered around in various places. Also clean up iopipe.c. Correct mistake in H5_now_usec calculation for clock_gettime. Remove detection for mach/mach/time.h, since we're no longer using the time routines from that header. Update H5_now_usec to prefer using clock_gettime. Changes to make timers within the library monotonic.
| * Remove non-existent exampleQuincey Koziol2020-06-301-2/+2
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| * Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-303-7/+17
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| * | Add new source files to CMake buildQuincey Koziol2020-06-282-0/+2
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| * | Clean up warningsQuincey Koziol2020-06-287-54/+53
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| * | va_arg -> HDva_argQuincey Koziol2020-06-271-1/+1
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| * | Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-273-54/+134
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| * | | Refactor code to remove remaining checks for H5_HAVE_GETTIMEOFDAY scattered ↵Quincey Koziol2020-06-276-328/+190
| | | | | | | | | | | | | | | | around in various places. Also clean up iopipe.c.
| * | | Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2020-06-261843-181238/+348913
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| * | | | Correct mistake in H5_now_usec calculation for clock_gettime.Quincey Koziol2017-09-241-1/+1
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| * | | | Remove detection for mach/mach/time.h, since we're no longer using theQuincey Koziol2017-09-243-8/+0
| | | | | | | | | | | | | | | | | | | | time routines from that header.
| * | | | Update H5_now_usec to prefer using clock_gettime.Quincey Koziol2017-09-241-1/+8
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| * | | | Merge remote-tracking branch 'origin/develop' into monotonic_timerQuincey Koziol2017-09-0321-889/+846
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| * | | | | Changes to make timers within the library monotonic.Quincey Koziol2017-09-0315-520/+1563
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* | | | | | Merge pull request #2669 in HDFFV/hdf5 from ↵Jake Smith2020-06-301-1/+1
|\ \ \ \ \ \ | |_|_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~JAKE.SMITH/hdf5:bugfix/HDftell_macro_typo to develop * commit 'ef05e68c38d2086c6f262744b4087f65a6e58957': Fix typo in HDftell macro definition: 'ftello -> ftell'
| * | | | | Fix typo in HDftell macro definition: 'ftello -> ftell'Jacob Smith2020-06-291-1/+1
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* | | | | Merge pull request #2609 in HDFFV/hdf5 from ~BMRIBLER/hdf5-bmr:develop to ↵Binh-Minh Ribler2020-06-302-1/+15
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | develop Fix HDFFV-11053 (CVE-2020-10810) * commit 'b155a777629e991374fa2f8609719cb861de4cc2': Changed wording in comment. - added comment to explain a kluge - added the associated entry to release notes Fix HDFFV-11053
| * | | | | Changed wording in comment.Binh-Minh Ribler2020-06-301-2/+2
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| * | | | | - added comment to explain a klugeBinh-Minh Ribler2020-06-292-1/+11
| | | | | | | | | | | | | | | | | | | | | | | | - added the associated entry to release notes
| * | | | | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Binh-Minh Ribler2020-06-29123-4381/+5132
| |\ \ \ \ \ | | |/ / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '30776671fb0a27a98b0640aa968f850241a862ce': (31 commits) * Fix intermittent error with Splitter VFD. Mismatch in time of test file creation was creating false negatives. Added note for HDFFV-10591. Fix HDFFV-10591 Reduce overhead for H5open, which is involved in the public symbols like H5T_NATIVE_INT, etc. Remove unnecessary version conditions for Clang compilers. Fix for HDFFV-10961: Couple changes to the tests' usage output files for h5clear. Fix for HDFFV-10961: add description to usage for --increment option. Add c++ to --enable-sanitize-checks option. Remove duplicate entries in MANIFEST. Make changes to CMake CompilerFlags.cmake files so extra flags are loaded for non-GNU compilers. Fix MANIFEST Add tests for all version to H5_NO_DEPRECATED_SYMBOLS section and to section for current version, with and without default API version flags. HDFFV-11000: update-testh5cc.sh.in to test sample versioned functions in HDF5 1.10, 1.12 and develop. Remember the info for the last ID looked up for a given ID type. Eliminate allocating file & memory offset & length arrays when performing I/O on a single element. Update new clang files to not pick up clang as vendor for pgCC. Add new files to MANIFEST Temporary demotion of 2 -Werror warning flags that fail on macos 10.12 Remove Production flag unknown to Apple clang. Remove redundant metadata cache tagging from some low-level internal chunk functions. The metadata cache tagging has already been done by routines further up the call stack. Clean up code to get clang version in config/linux-gnulibc1 Minor normalizations with HDF5 1.10. Add flags from config/clang-warnings/*general files to H5 C and CXX flags for all versions of Clang and Clang++ compilers. Switched from cut to awk in testcheck_version.sh.in to avoid dependence on tab vs. " " in version definitions in H5public.h. ...
| * | | | | Fix HDFFV-11053Binh-Minh Ribler2020-05-261-0/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: A superblock pointer was set to a temporary structure, as a kluge, and meant to be reset back to NULL after the processing was completed. However, in the case of failure before the completion, this setting caused the superblock pointer to be unpinned twice in the error recovery process. As a result, that generated a segfault in h5clear. The fix resets the superblock pointer to NULL after H5F__super_ext_remove_msg fails so that h5clear can fail properly. Note: After the fix, when built in debug mode, there will be an assertion failure with the user's file, which appeared to be corrupted: H5MM_final_sanity_check: Assertion `0 == H5MM_curr_alloc_bytes_s' failed. This did not happen on a good file or on the corrupted file with the library built in production mode. The un-freed memory were allocated during error recovery. Platforms tested: Linux/64 (jelly)
* | | | | | Merge pull request #2667 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-06-301-6/+2
|\ \ \ \ \ \ | |_|/ / / / |/| | | | | | | | | | | | | | | | | * commit '32c483cb86031962a09ecdb49dcb331d28dddee9': Copy lib files for junit.sh to temporary subdirectory of <build directory>/java/test instead of to the prefix/lib directory. Fix for HDFFV-11063.
| * | | | | Copy lib files for junit.sh to temporary subdirectory of <buildLarry Knox2020-06-271-6/+2
|/ / / / / | | | | | | | | | | | | | | | | | | | | directory>/java/test instead of to the prefix/lib directory. Fix for HDFFV-11063.
* | | | | Merge pull request #2665 in HDFFV/hdf5 from ↵Jake Smith2020-06-263-54/+134
|\ \ \ \ \ | |_|_|_|/ |/| | | | | | | | | | | | | | | | | | | | | | | | ~JAKE.SMITH/hdf5:bugfix/splitter_file_bytes_check to develop * commit 'e1215177b6b87887233a90992a0264f11d78b88c': * Fix intermittent error with Splitter VFD. Mismatch in time of test file creation was creating false negatives.
| * | | | * Fix intermittent error with Splitter VFD.Jacob Smith2020-06-253-54/+134
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Mismatch in time of test file creation was creating false negatives. Add file-duplication routine: `h5_duplicate_file_by_bytes()`. * Change library calls in `h5test.c:h5_compare_file_bytes()` to their HD-prefixed equivalents.
* | | | | Merge pull request #2654 in HDFFV/hdf5 from bmr_HDFFV-10591 to developBinh-Minh Ribler2020-06-224-12/+41
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Fixed HDFFV-10591 * commit '7d58d115079d286a566207c529e59bbccc952b03': Added note for HDFFV-10591. Fix HDFFV-10591
| * | | | | Added note for HDFFV-10591.Binh-Minh Ribler2020-06-191-0/+12
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| * | | | | Fix HDFFV-10591Binh-Minh Ribler2020-06-193-12/+29
| |/ / / / | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Description: h52gif produced a segfault when a buffer overflow occurred because the data size was corrupted and became very large. This commit added a check on the data size against the buffer size to prevent the segfault. It also added error reporting to h52gif to display an error message instead of silently exiting when the failure occurred. Platforms tested: Linux/64 (jelly) SunOS 5.11 (emu)
* | | | | Merge pull request #2648 in HDFFV/hdf5 from opt_h5open_overhead to developQuincey Koziol2020-06-182-5/+32
|\ \ \ \ \ | |/ / / / |/| | | | | | | | | | | | | | * commit '49fad72f3e003e1e2d7d72edd9b7ec47c802d9f1': Reduce overhead for H5open, which is involved in the public symbols like H5T_NATIVE_INT, etc.
| * | | | Reduce overhead for H5open, which is involved in the public symbols like ↵Quincey Koziol2020-06-162-5/+32
|/ / / / | | | | | | | | | | | | H5T_NATIVE_INT, etc.
* | | | Merge pull request #2610 in HDFFV/hdf5 from ↵David Young2020-06-166-12/+12
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DYOUNG/werror:hdffv-11060-examples-destdir to develop * commit '4cebd8aa6c965fe2e5dde6dbff36b2be3ca58bf1': Make examples installation respect DESTDIR. Fixes HDFFV-11060.
| * | | | Make examples installation respect DESTDIR. FixesDavid Young2020-05-266-12/+12
| |/ / / | | | | | | | | | | | | HDFFV-11060.
* | | | Merge pull request #2615 in HDFFV/hdf5 from ↵Jake Smith2020-06-152-1/+5
|\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~JAKE.SMITH/hdf5:bugfix/splitter_valgrind_patch to develop * commit '6462c67b6578e48c1ef6d847be59c0b5e3598a50': Patch a few holes in the Splitter VFD implementation.
| * | | | Patch a few holes in the Splitter VFD implementation.Jacob Smith2020-05-292-1/+5
| | | | | | | | | | | | | | | | | | | | | | | | | * Missing logfile close on driver-open failure. * Initialize empty string in test/vfd (logfile path in W/O compat check).
* | | | | Merge pull request #2646 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-06-122-28/+6
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '998c6470d78e14228695419c3b514c35ecf3d69e': Remove unnecessary version conditions for Clang compilers.
| * | | | | Remove unnecessary version conditions for Clang compilers.Larry Knox2020-06-122-28/+6
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* | | | | Merge pull request #2643 in HDFFV/hdf5 from ↵Vailin Choi2020-06-113-6/+23
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-10961-h5clear-usage-statement-give to develop * commit '01b632c69ca1c97c2b0e1aaeeab1dd2362b580a6': Fix for HDFFV-10961: Couple changes to the tests' usage output files for h5clear. Fix for HDFFV-10961: add description to usage for --increment option.
| * | | | | Fix for HDFFV-10961:vchoi2020-06-112-4/+16
| | | | | | | | | | | | | | | | | | | | | | | | Couple changes to the tests' usage output files for h5clear.
| * | | | | Fix for HDFFV-10961: add description to usage for --increment option.vchoi2020-06-111-2/+7
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* | | | | Merge pull request #2636 in HDFFV/hdf5 from ↵Larry Knox2020-06-111-4/+126
|\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~LRKNOX/hdf5_lrk:HDFFV-11000-update-testh5cc.sh.in-for-version to develop * commit '5c0bd670d6e9919c463fbc05de99e2ba55b0761e': Add tests for all version to H5_NO_DEPRECATED_SYMBOLS section and to section for current version, with and without default API version flags. HDFFV-11000: update-testh5cc.sh.in to test sample versioned functions in HDF5 1.10, 1.12 and develop.
| * | | | | Add tests for all version to H5_NO_DEPRECATED_SYMBOLS sectionLarry Knox2020-06-101-2/+13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | and to section for current version, with and without default API version flags.
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