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* Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5 into ↵Binh-Minh Ribler2020-07-2223-236/+162
|\ | | | | | | bmr-HDFFV-11120
| * Merge pull request #2703 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-07-2023-236/+162
| |\ | | | | | | | | | | | | | | | | | | to develop * commit '242459231b40a88741cbc85df4272914b5d8bed3': Minor normalization with 1.10.
| | * Minor normalization with 1.10.Dana Robinson2020-07-2023-236/+162
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* | | Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)Binh-Minh Ribler2020-07-222-1/+29
|/ / | | | | | | | | | | | | | | | | | | | | | | Description: When a buffer overflow occurred because a name length was corrupted and became very large, h5dump produced a segfault on one file and a memcpy parameter overlap on another file. This commit added checks that detect a read pass the end of the buffer to prevent these error conditions. Platforms tested: Linux/64 (jelly) SunOS 5.11 (emu)
* | Merge pull request #2693 in HDFFV/hdf5 from ↵Vailin Choi2020-07-178-1/+200
|\ \ | | | | | | | | | | | | | | | | | | | | | ~VCHOI/my_third_fork:bugfix/HDFFV-11080-heap-use-after-free-by-the-call to develop * commit '3023b34272cc6ada84aebfa7441a6a55afa3621c': Update MANIFEST. Add new test to Cmake. Fix for jira issue HDFFV-11080: (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
| * | Update MANIFEST.vchoi2020-07-162-0/+2
| | | | | | | | | | | | Add new test to Cmake.
| * | Fix for jira issue HDFFV-11080:vchoi2020-07-146-1/+198
| | | | | | | | | | | | | | | (1) Patch up the file pointer when reading attribute of variable length datatype (2) Test to verify the fix when doing multiple threads
* | | Merge pull request #2700 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-07-174-31/+30
|\ \ \ | | |/ | |/| | | | | | | | | | | | | to develop * commit '6388a6750ff1dc476b8631d26cd1742730df9fe8': Minor normalization with 1.10
| * | Minor normalization with 1.10Dana Robinson2020-07-174-31/+30
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* | Merge pull request #2694 in HDFFV/hdf5 from ~JSOUMAGNE/hdf5:fix_vlen_ref to ↵Jerome Soumagne2020-07-164-25/+336
|\ \ | | | | | | | | | | | | | | | | | | develop * commit 'aa9d2bd9bcce7a1a53c9d9cf519df5401041bb74': H5R: fix type conversion of references within vlen type
| * | H5R: fix type conversion of references within vlen typeJerome Soumagne2020-07-164-25/+336
|/ / | | | | | | Update trefer.c with vlen test case
* | Merge pull request #2692 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-07-142-29/+8
|\ \ | |/ |/| | | | | | | | | | | to develop * commit 'b8013380792a3503003f0a2bd60d7541656b03c7': Removed POSIX #defines from configure on Solaris. Fallback to older time functions in new timer code.
| * Removed POSIX #defines from configure on Solaris.Dana Robinson2020-07-141-6/+0
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| * Fallback to older time functions in new timer code.Dana Robinson2020-07-141-23/+8
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* Merge pull request #2686 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-111-1/+4
|\ | | | | | | | | * commit '800f93f7c994f88dfa716746153ded4b1e690e3a': Remove path to szip header file from AM_CPPFLAGS when configure check of libsz fails. Fix for HDFFV-10830.
| * Merge branch 'develop' of ↵Larry Knox2020-07-1023-1079/+1078
| |\ | | | | | | | | | https://bitbucket.hdfgroup.org/scm/~lrknox/hdf5_lrk into develop
| * | Remove path to szip header file from AM_CPPFLAGS when configure check of ↵Larry Knox2020-07-101-1/+4
| | | | | | | | | | | | | | | | | | libsz fails. Fix for HDFFV-10830.
* | | Merge pull request #2684 in HDFFV/hdf5 from ↵Allen Byrne2020-07-116-4/+90
|\ \ \ | |_|/ |/| | | | | | | | | | | | | | ~BYRN/hdf5_adb:feature/HDFFV-11116-trilabs-mod-location to develop * commit '07a52ecb2ffa1d8d32f06db23470833899db3deb': HDFFV-11116 Add option for install location of Fortran MOD files
| * | HDFFV-11116 Add option for install location of Fortran MOD filesAllen Byrne2020-07-096-4/+90
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| * | Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-083-6/+24
| |\ \ | | | | | | | | | | | | | | | | | | | | * commit '188c43b8ee78d830c22f30fb9adb802e46722fcd': Change load path in libhdf5_java.dylib to unversioned libhdf5.dylib for junit tests on Macs. Fixes Autotools builds on Solaris after monotonic timer changes
| * \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-032-2/+2
| |\ \ \ | | | | | | | | | | | | | | | | | | | | * commit 'd52b27ad1d8142945a92310b79ab79171e76a3c3': Address CMake and deprecated API build failures from monotonic timer patch.
| * \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-031-1/+1
| |\ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | * commit '7443e5d53d1c6f15e095de7c44bcc3a5a46d9cf7': Add missing '"'.
| * \ \ \ \ Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)Allen Byrne2020-07-023-1/+20
| |\ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | * commit '4c2071bfd3270dc3a688914b4a058147b94b7023': 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
* | \ \ \ \ \ Merge pull request #2683 in HDFFV/hdf5 from ↵Dana Robinson2020-07-0921-1074/+1055
|\ \ \ \ \ \ \ | |_|_|_|_|/ / |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ~DEROBINS/hdf5_der:develop_normalization to develop * commit '127d1cfdf06e9c1cd264595c496a063848358a0a': Minor changes from normalization with 1.10
| * | | | | | Minor changes from normalization with 1.10Dana Robinson2020-07-0921-1074/+1055
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* | | | | | | Merge pull request #2680 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:develop_minor ↵Dana Robinson2020-07-072-5/+23
|\ \ \ \ \ \ \ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to develop * commit 'd9105b2fcf04f36ea348bf9726a49c05cacc0b78': Fixes Autotools builds on Solaris after monotonic timer changes
| * | | | | | | Fixes Autotools builds on Solaris after monotonic timer changesDana Robinson2020-07-072-5/+23
| | |_|_|_|/ / | |/| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | clock_gettime() wasn't being found, so some configure changes were needed to set an appropriate POSIX level and use a C99 compiler. This required several compiler flag changes. Autotools only
* | | | | | | Merge pull request #2677 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:develop to developLarry Knox2020-07-071-1/+1
|\ \ \ \ \ \ \ | |/ / / / / / |/| | | | | / | | |_|_|_|/ | |/| | | | * commit 'da607fe4638c9cc08f717fbe65e799c1676c17ff': Change load path in libhdf5_java.dylib to unversioned libhdf5.dylib for junit tests on Macs.
| * | | | | Change load path in libhdf5_java.dylib to unversioned libhdf5.dylib forLarry Knox2020-07-071-1/+1
|/ / / / / | | | | | | | | | | | | | | | junit tests on Macs.
* | | | | 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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