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Pullup ticket #5171 - requested by bsiegert
devel/hdf5: security update Revisions pulled up: - devel/hdf5/Makefile.common 1.13-1.14 - devel/hdf5/distinfo 1.37-1.38 - devel/hdf5/patches/patch-c++_examples_Makefile.in 1.4 - devel/hdf5/patches/patch-c++_examples_run-c++-ex.sh.in 1.3 - devel/hdf5/patches/patch-examples_Makefile.in 1.4 - devel/hdf5/patches/patch-examples_run-c-ex.sh.in 1.3 - devel/hdf5/patches/patch-hl_c++_examples_Makefile.in 1.4 - devel/hdf5/patches/patch-hl_c++_examples_run-hlc++-ex.sh.in 1.3 - devel/hdf5/patches/patch-hl_examples_Makefile.in 1.4 - devel/hdf5/patches/patch-hl_examples_run-hlc-ex.sh.in 1.3 ------------------------------------------------------------------- Module Name: pkgsrc Committed By: alnsn Date: Sun Oct 9 18:44:35 UTC 2016 Modified Files: pkgsrc/devel/hdf5: Makefile.common distinfo pkgsrc/devel/hdf5/patches: patch-c++_examples_Makefile.in patch-c++_examples_run-c++-ex.sh.in patch-examples_Makefile.in patch-examples_run-c-ex.sh.in patch-hl_c++_examples_Makefile.in patch-hl_c++_examples_run-hlc++-ex.sh.in patch-hl_examples_Makefile.in patch-hl_examples_run-hlc-ex.sh.in Log Message: Update hdf5 to 1.8.17. New Features ============ Configuration ------------- - Cmakehdf5: Added Ability to Run Multiple Make Commands Added option --njobs to specify up to how many jobs to launch during build (cmake) and testing (ctest). (AKC - 2015/12/13, HDFFV-9612) - Cmakehdf5: Added Szip Support and Verbose Option Added --with-szlib to support the Szip library; and --enable/disable-verbose to display all CMake process output. (AKC - 2015/11/16, HDFFV-8932 and DAILYTEST-195) - CMake minimum is now 3.1.0. (ADB - 2015/11/14) - Large File System (LFS) Support has Changed in the Autotools We assume that fseeko and ftello exist. The *64 I/O functions and types are no longer explicitly used. We now rely on a mapping provided by _FILE_OFFSET_BITS (or its equivalent). _LARGEFILE(64)_SOURCE is no longer exposed via AM_CPPFLAGS. (DER - 2016/03/29, HDFFV-9626 and HDFFV-9541) Library ------- - New API Calls for Searching for External Dataset Storage API calls that determine the search path for dataset external storage were added. H5Pset/get_efile_prefix() API calls were added to the library. These functions give control over the search path for dataset external storage that has been configured with H5Pset_external(). Additionally, the HDF5_EXTFILE_PREFIX environment variable can be used to control the search path. (DER - 2016/04/20, HDFFV-8740) High-Level APIs --------------- C Packet Table API ------------------ - Replacement of a Public Function with H5PTcreate The existing function H5PTcreate_fl limits applications so they can use the deflate compression only. The public function H5PTcreate has been added to replace H5PTcreate_fl. H5PTcreate takes a property list identifier to provide flexibility on creation properties. This also removes the following warning: "deprecated conversion from string constant to "char*" [-Wwrite-strings]". (BMR - 2016/04/25, HDFFV-9708, HDFFV-8615) - New Public Functions: H5PTget_dataset and H5PTget_type Two accessor functions have been added. H5PTget_dataset returns the identifier of the dataset associated with the packet table, and H5PTget_type returns the identifier of the datatype used by the packet table. (BMR - 2016/04/25, HDFFV-8623 patch 3) - Regarding #ifdef VLPT_REMOVED The #ifdef VLPT_REMOVED blocks have been removed from the packet table (PT) library source except for the following functions: + H5PTis_varlen() has been made available again + H5PTfree_vlen_readbuff() is now H5PTfree_vlen_buff() (BMR - 2016/04/25, HDFFV-442) C++ Packet Table API -------------------- - New Constructor in FL_PacketTable An overloaded constructor has been added to FL_PacketTable and takes a property list identifier to provide flexibility on creation properties such as compression. FL_PacketTable(hid_t fileID, const char* name, hid_t dtypeID, hsize_t chunkSize = 0, hid_t plistID = H5P_DEFAULT) (BMR - 2016/04/25, HDFFV-8623 patch 5) - New Member Functions in PacketTable Two accessor wrappers were added to class PacketTable. PacketTable::GetDataset() returns the identifier of the dataset associated with the packet table, and PacketTable::GetDatatype() returns the identifier of the datatype that the packet table uses. (BMR - 2016/04/25, HDFFV-8623 patch 4) - New Member Functions with "char*" as an Argument Overloaded functions were added to provide the "const char*" argument; the existing version will be deprecated in future releases. This also removes the following warning: "deprecated conversion from string constant to "char*" [-Wwrite-strings]". (BMR - 2016/04/25, HDFFV-8623 patch 1, HDFFV-8615) - Regarding #ifdef VLPT_REMOVED The #ifdef VLPT_REMOVED blocks have been removed from the packet table library source code except for the following functions: + VL_PacketTable::IsVariableLength() was moved to PacketTable + VL_PacketTable::FreeReadBuff() is now PacketTable::FreeBuff() (BMR - 2016/04/25, HDFFV-442) C++ API ------- - New Member Function in DSetCreatPropList DSetCreatPropList::setNbit() was added to setup N-bit compression for a dataset. (BMR - 2016/04/25, HDFFV-8623 patch 7) - New Overloaded "const" Member Functions in ArrayType The two following functions were added: ArrayType::getArrayNDims() const ArrayType::getArrayDims() const to provide const version, and the non-const version was marked deprecated. In-memory array information, ArrayType::rank and ArrayType::dimensions, were removed. This is an implementation detail and should not affect applications. (BMR, 2016/04/25, HDFFV-9725) - New member function added The assignment operator ArrayType::operator= is added because ArrayType has pointer data members. (BMR, 2016/03/07, HDFFV-9562) Support for New Platforms, Languages, and Compilers =================================================== - Mac OS X El Capitan 10.11.4 with compilers Apple clang/clang++ version 7.3.0 from Xcode 7.3, gfortran GNU Fortran (GCC) 5.2.0 and Intel icc/icpc/ifort version 16.0.2 Bug Fixes since HDF5-1.8.16 =========================== Configuration ------------- - Updated Linux Language Level Flags to Match the Autotools. Removed Linux-specific Flags from OS X. An addition to the flags simply being out of sync with the Autotools, the Linux flags were used on OS X builds which led to symbols not being found. Although this was non-fatal and compilation continued (implicit definitions were used by the compiler and the symbols resolved at link time), a large number of warnings were raised. Linux changes: * CHANGED: _POSIX_C_SOURCE (from 199605 to 200112L) * ADDED: _GNU_SOURCE * REMOVED: _BSD_SOURCE * REMOVED: _DEFAULT_SOURCE (DER - 2015/12/08, HDFFV-9627) - The --enable-clear-file-buffers configure Option was Non-functional so the Feature was Always Enabled (its default value). Regardless of the configure flag, the setting was always enabled when the Autotools were used to configure HDF5. This was due to the "no" option being processed after the "*" option in configure.ac so "*" matched first. CMake was unaffected. The option now works correctly. NOTE that builders are always advised to leave this option enabled. When disabled, buffers that are written to disk may contain the memory's previous contents, which may include secure information. The performance overhead of the feature (a single memset call per allocation) is minimal. (DER - 2016/02/03, HDFFV-9676) - Added a patch to remove '"'s from arguments for MPI compilers that were causing errors compiling H5lib_settings.c with SGI MPT. (LRK - 2016/04/20, HDFFV-9439) Library ------- - Fixed shared file pointer problem which caused a crash when running a program provided by a user. (VC - 2016/04/01, HDFFV-9469) - Fixed some format string warnings that prevent compiling with -Werror=format-security on gcc. These only appeared in error messages and would not cause problems under normal operation. (DER - 2016/01/13, HDFFV-9640) - Fixed a library segmentation fault when accessing a corrupted file provided by a user. (MSC - 2016/02/19, HDFFV-9670) Tools ----- - h5dump: Sub-setting Fixed for Dimensions Greater than Two When a dataset has more than two dimensions, sub-setting would incorrectly calculate the data that needed to be displayed. Added in block and stride calculations that account for dimensions greater than two. NOTE: lines that have line breaks inserted because of display length calculations may have index info that is incorrect until the next dimension break. (ADB - 2016/03/07, HDFFV-9698) - h5dump: Issue with Argument Segmentation Fault When an argument with an optional value was at the end of the command line with a value, h5dump would crash. Reworked check for remaining arguments. (ADB - 2016/03/07, HDFFV-9570, HDFFV-9684) - h5dump: Issue with Default Fill Value Added all default cases of fill value to the display of fill value. (ADB -, 2016/03/07, HDFFV-9241) - h5dump: Clarified Help Clarified usage of -O F option in h5dump utility help. (ADB - 2016/03/07, HDFFV-9066) - h5dump: Issue with Double Free Fault Added a check for filename not null before calling free(). (ADB - 2016/01/27, HDFFV-9639) - VS2015 Release Changed how Timezone was Handled Created a function, HDget_timezone, in H5system.c. Replaced timezone variable usage with function call. (ADB - 2015/11/02, HDFFV-9550) C++ API ------- - Removal of Obsolete Methods The overloaded methods which had parameters that should be const but were not have been removed. (BMR - 2016/01/13, HDFFV-9789) High-Level APIs: --------------- - Fixed Memory Leak in Packet Table API Applied user's patch to fix memory leak in the creation of a packet table. (BMR - 2016/04/25, HDFFV-9700) Known Problems ============== * On windows platforms in debug configurations, the VFD flush1 tests will fail with the split and multi VFD drivers. These tests will display a modal debug dialog which must be answered or wait for the test timeout to expire. (ADB - 2014/06/23 - HDFFV-8851) * CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv catches some undefined behavior in the alignment algorithm of the macro DETECT_I in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for H5detect.c. In the future, we can separate flags for H5detect.c from the rest of the library. (SLU - 2013/10/16) * Make provided by Solaris fails in "make check". Solaris users should use gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) * The C++ and FORTRAN bindings are not currently working on FreeBSD with the native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the ports (and probably gcc releases after that). (QAK - 2012/10/19) * The following h5dump test case fails in BG/P machines (and potentially other machines that use a command script to launch executables): h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" tno-subset.h5 This is due to the embedded spaces in the dataset name being interpreted by the command script launcher as meta-characters, thus passing three arguments to h5dump's -d flag. The command passes if run by hand, just not via the test script. (AKC - 2012/05/03) * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release. (DER - 2011/10/14 - HDFFV-8235) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in a future release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ (NAF - 2011/01/19) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. (MAM - 2009/11/04) * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. (SLU - 2005/06/30) To generate a diff of this commit: cvs rdiff -u -r1.12 -r1.13 pkgsrc/devel/hdf5/Makefile.common cvs rdiff -u -r1.36 -r1.37 pkgsrc/devel/hdf5/distinfo cvs rdiff -u -r1.3 -r1.4 \ pkgsrc/devel/hdf5/patches/patch-c++_examples_Makefile.in \ pkgsrc/devel/hdf5/patches/patch-examples_Makefile.in \ pkgsrc/devel/hdf5/patches/patch-hl_c++_examples_Makefile.in \ pkgsrc/devel/hdf5/patches/patch-hl_examples_Makefile.in cvs rdiff -u -r1.2 -r1.3 \ pkgsrc/devel/hdf5/patches/patch-c++_examples_run-c++-ex.sh.in \ pkgsrc/devel/hdf5/patches/patch-examples_run-c-ex.sh.in \ pkgsrc/devel/hdf5/patches/patch-hl_c++_examples_run-hlc++-ex.sh.in \ pkgsrc/devel/hdf5/patches/patch-hl_examples_run-hlc-ex.sh.in ------------------------------------------------------------------- Module Name: pkgsrc Committed By: alnsn Date: Sat Dec 3 18:56:36 UTC 2016 Modified Files: pkgsrc/devel/hdf5: Makefile.common distinfo Log Message: Update devel/hdf5 and devel/hdf5-c++ to version 1.8.18. New Features ============ Configuration ------------- - CMake: Added NAMESPACE hdf5:: to package configuration files to allow projects using installed HDF5 binaries built with CMake to link with them without specifying the HDF5 library location via IMPORTED_LOCATION. (ADB, 2016/10/17, HDFFV-10003) - CMake: Changed the CTEST_BUILD_CONFIGURATION option to CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation. (ADB, 2016/10/17, HDFFV-9971) - CMake: Added support for GIT (ADB, 2016/07/12) Bug Fixes since HDF5-1.8.17 =========================== Configuration ------------- - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by condensing cygwin configuration files into a single file and removing outdated compiler settings. (ABD, 2016/07/12, HDFFV-9946) - CMake: Fixed a command length overflow error by converting custom commands inside CMakeTest.cmake files into regular dependencies and targets. (ABD, 2016/07/12, HDFFV-9939) - CMake: Fixed a timeout error that would occasionally occur when running the virtual file driver tests simultaneously due to test directory and file name collisions. (ABD, 2016/09/19, HDFFV-9431) Library ------- - Fixed a memory leak that would occur when the library allocated memory for an external file prefix (H5Pset_efile_prefix) and failed to free it. (DER, 2016/04/29) - Fixed an error that would occur when calling H5Adelete on an attribute which is attached to an externally linked object in the target file and whose datatype is a committed datatype in the main file. (VC, 2016-07-04, HDFFV-9940) - Fixed a problem where a plugin compiled into a DLL in the default plugin directory could not be found by the HDF5 library at runtime on Windows when the HDF5_PLUGIN_PATH environment variable was not set. (ABD, 2016/08/01, HDFFV-9706) - Fixed an issue where H5Pset_alignment could result in misaligned blocks with some input combinations, causing an assertion failure in debug mode. (NAF, 2016/08/11, HDFFV-9948) - A number of issues were fixed when reading/writing from/to corrupted files to ensure that the library fails gracefully in these cases: * Writing to a corrupted file that has an object message which is incorrectly marked as sharable on disk results in a buffer overflow / invalid write instead of a clean error message. * Decoding data from a corrupted file with a dataset encoded with the H5Z_NBIT decoding can result in a code execution vulnerability under the context of the application using the HDF5 library. * When decoding an array datatype from a corrupted file, the HDF5 library fails to return an error in production if the number of dimensions decoded is greater than the maximum rank. * When decoding an "old style" array datatype from a corrupted file, the HDF5 library fails to return an error in production if the number of dimensions decoded is greater than the maximum rank. (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993) - Fixed an error that would occur when copying an object with an attribute which is a compound datatype consisting of a variable length string. (VC, 2016-10-17, HDFFV-7991) Parallel Library ---------------- - Fixed a bug that could occur when allocating a chunked dataset in parallel with an alignment set and an alignment threshold greater than the chunk size but less than or equal to the raw data aggregator size. (NAF, 2016/08/11, HDFFV-9969) Performance ------------- - None Tools ----- - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.) in which they would erroneously drop the file argument specified via the -o flag when the -o flag was specified before the -c flag on the command line, resulting in a failure to compile. (LRK, 2016/06/08, HDFFV-9938, HDFFV-9530) - h5repack User Defined (UD) filter parameters were not parsed correctly. The UD filter parameters were not being parsed correctly. Reworked coding section to parse the correct values and verify number of parameters. (ADB, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039) Fortran API ----------- - Fortran library fails to compile and fails tests with NAG compiler. * Removed the non-standard assumption that KIND=SIZEOF, in the HDF5 configure programs. * Removed Fortran 66 character/integer conversions from tests. * Removed the use of C_SIZEOF in the test programs * Changed to using STORAGE_SIZE in the test programs if available. Otherwise, uses C_SIZEOF or SIZEOF. (MSB, 2016/9/22, HDFFV-9973) - Fortran segfaults for F03 tests with NAG compiler * Removed INTENT(OUT) from 'fillvalue' in F2003 interface for H5Pget_fill_value_f. (MSB, 2016/9/22, HDFFV-9980) C++ API ------- - The macro H5_NO_NAMESPACE is deprecated from the HDF5 C++ API library. In future releases, the macros H5_NO_STD and OLD_HEADER_FILENAME may also be removed. (BMR, 2016/10/27, HDFFV-9532) High-Level APIs: --------------- - The high-level API Packet Table (PT) did not write data correctly when the datatype is a compound type that has string type as one of the members. This problem started in 1.8.15, after the fix of HDFFV-9042 was applied, which caused the Packet Table to use native type to access the data. It should be up to the application to specify whether the buffer to be read into memory in the machine’s native architecture. Thus, the PT is fixed to not use native type but to make a copy of the user's provided datatype during creation or the packet table's datatype during opening. If an application wishes to use native type to read the data, then the application will request that. However, the Packet Table doesn't provide a way to specify memory datatype in this release. This feature will be available in future releases, HDFFV-10023. (BMR, 2016/10/27, HDFFV-9758) Fortran High-Level APIs: ------------------------ - None Testing ------- - None Supported Platforms =================== The following platforms are supported and have been tested for this release. They are built with the configure process unless specified otherwise. Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: (platypus/mayll) Version 4.4.7 20120313 Versions 4.8.4, 4.9.3, 5.2.0 PGI C, Fortran, C++ for 64-bit target on x86-64; Version 15.7-0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 15.0.3.187 Build 20150407 MPICH 3.1.4 compiled with GCC 4.9.3 Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16) IBM XL C/C++ V13.1 IBM XL Fortran V15.1 Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: (kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4) Versions 4.9.3, 5.2.0 Intel(R) C (icc), C++ (icpc), Fortran (icc) compilers: Version 15.0.3.187 Build 20150407 MPICH 3.1.4 compiled with GCC 4.9.3 SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc (emu) Sun Fortran 95 8.6 SunOS_sparc Sun C++ 5.12 SunOS_sparc Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake) Visual Studio 2013 w/ Intel Fortran 15 (cmake) Visual Studio 2015 w/ Intel Fortran 16 (cmake) Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran) (cmake and autotools) Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) Visual Studio 2013 w/ Intel Fortran 15 (cmake) Visual Studio 2015 w/ Intel Fortran 16 (cmake) Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake) Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake) Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40) 64-bit gfortran GNU Fortran (GCC) 4.8.2 (swallow/kite) Intel icc/icpc/ifort version 15.0.3 Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57) 64-bit gfortran GNU Fortran (GCC) 4.9.2 (wren/quail) Intel icc/icpc/ifort version 15.0.3 Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53) 64-bit gfortran GNU Fortran (GCC) 4.9.2 (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29) 64-bit gfortran GNU Fortran (GCC) 5.2.0 (VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 Tested Configuration Features Summary ===================================== In the tables below y = tested n = not tested in this release C = Cluster W = Workstation x = not working in this release dna = does not apply ( ) = footnote appears below second table <blank> = testing incomplete on this feature or platform Platform C F90/ F90 C++ zlib SZIP parallel F2003 parallel SunOS 5.11 32-bit n y/y n y y y SunOS 5.11 64-bit n y/y n y y y Windows 7 y y/y n y y y Windows 7 x64 y y/y n y y y Windows 7 Cygwin n y/y n y y n Windows 10 n y/y n y y y Windows 10 x64 n y/y n y y y Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y AIX 6.1 32- and 64-bit n y/n n y y y CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe SunOS 5.11 32-bit y y y y SunOS 5.11 64-bit y y y y Windows 7 y y y y Windows 7 x64 y y y y Windows 7 Cygwin n n n y Windows 10 y y y y Windows 10 x64 y y y y Mac OS X Mountain Lion 10.8.5 64-bit y n y y Mac OS X Mavericks 10.9.5 64-bit y n y y Mac OS X Yosemite 10.10.5 64-bit y n y y AIX 6.1 32- and 64-bit y n n y CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y Linux 2.6.32-431.11.2.el6.ppc64 y y y y Compiler versions for each platform are listed in the preceding "Supported Platforms" table. More Tested Platforms ===================== The following platforms are not supported but have been tested for this release. Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!) #1 SMP x86_64 GNU/Linux (platypus) Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux gcc (Debian 4.9.2-10) 4.9.2 GNU Fortran (Debian 4.9.2-10) 4.9.2 (cmake and autotools) Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3) (cmake and autotools) CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) (cmake and autotools) Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 (cmake and autotools) Known Problems ============== * On windows platforms in debug configurations, the VFD flush1 tests will fail with the split and multi VFD drivers. These tests will display a modal debug dialog which must be answered or wait for the test timeout to expire. (ADB - 2014/06/23 - HDFFV-8851) * CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv catches some undefined behavior in the alignment algorithm of the macro DETECT_I in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for H5detect.c. In the future, we can separate flags for H5detect.c from the rest of the library. (SLU - 2013/10/16) * Make provided by Solaris fails in "make check". Solaris users should use gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534) * The C++ and FORTRAN bindings are not currently working on FreeBSD with the native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the ports (and probably gcc releases after that). (QAK - 2012/10/19) * The following h5dump test case fails in BG/P machines (and potentially other machines that use a command script to launch executables): h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0" tno-subset.h5 This is due to the embedded spaces in the dataset name being interpreted by the command script launcher as meta-characters, thus passing three arguments to h5dump's -d flag. The command passes if run by hand, just not via the test script. (AKC - 2012/05/03) * The STDIO VFD does not work on some architectures, possibly due to 32/64 bit or large file issues. The basic STDIO VFD test is known to fail on 64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin 10.7.0. The STDIO VFD test has been disabled while we investigate and a fix should appear in a future release. (DER - 2011/10/14 - HDFFV-8235) * h5diff can report inconsistent results when comparing datasets of enum type that contain invalid values. This is due to how enum types are handled in the library and will be addressed in a future release. (DER - 2011/10/14 - HDFFV-7527) * The links test can fail under the stdio VFD due to some issues with external links. This will be investigated and fixed in a future release. (DER - 2011/10/14 - HDFFV-7768) * After the shared library support was fixed for some bugs, it was discovered that "make prefix=XXX install" no longer works for shared libraries. It still works correctly for static libraries. Therefore, if you want to install the HDF5 shared libraries in a location such as /usr/local/hdf5, you need to specify the location via the --prefix option during configure time. E.g, ./configure --prefix=/usr/local/hdf5 ... (AKC - 2011/05/07 - HDFFV-7583) * The parallel test, t_shapesame, in testpar/, may run for a long time and may be terminated by the alarm signal. If that happens, one can increase the alarm seconds (default is 1200 seconds = 20 minutes) by setting the environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600 (60 minutes). Note that the t_shapesame test may fail in some systems (see the "While working on the 1.8.6 release..." problem below). If it does, it will waste more time if $HDF5_ALARM_SECONDS is set to a larger value. (AKC - 2011/05/07) * Shared Fortran libraries are not quite working on AIX. While they are generated when --enable-shared is specified, the fortran and hl/fortran tests fail. the issue. HL and C++ shared libraries should now be working as intended, however. (MAM - 2011/04/20) * While working on the 1.8.6 release of HDF5, a bug was discovered that can occur when reading from a dataset in parallel shortly after it has been written to collectively. The issue was exposed by a new test in the parallel HDF5 test suite, but had existed before that. We believe the problem lies with certain MPI implementations and/or file systems. We have provided a pure MPI test program, as well as a standalone HDF5 program, that can be used to determine if this is an issue on your system. They should be run across multiple nodes with a varying number of processes. These programs can be found at: http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/ (NAF - 2011/01/19) * All the VFL drivers aren't backward compatible. In H5FDpublic.h, the structure H5FD_class_t changed in 1.8. There is new parameter added to get_eoa and set_eoa callback functions. A new callback function get_type_map was added in. The public function H5FDrealloc was taken out in 1.8. The problem only happens when users define their own driver for 1.6 and try to plug in 1.8 library. Because there's only one user complaining about it, we (Elena, Quincey, and I) decided to leave it as it is (see bug report #1279). Quincey will make a plan for 1.10. (SLU - 2010/02/02) * The --enable-static-exec configure flag will only statically link libraries if the static version of that library is present. If only the shared version of a library exists (i.e., most system libraries on Solaris, AIX, and Mac, for example, only have shared versions), the flag should still result in a successful compilation, but note that the installed executables will not be fully static. Thus, the only guarantee on these systems is that the executable is statically linked with just the HDF5 library. (MAM - 2009/11/04) * A dataset created or rewritten with a v1.6.3 library or after cannot be read with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled. There was a bug in the calculation of the Fletcher32 checksum in the library before v1.6.3; the checksum value was not consistent between big- endian and little-endian systems. This bug was fixed in Release 1.6.3. However, after fixing the bug, the checksum value was no longer the same as before on little-endian system. Library releases after 1.6.4 can still read datasets created or rewritten with an HDF5 library of v1.6.2 or before. (SLU - 2005/06/30) To generate a diff of this commit: cvs rdiff -u -r1.13 -r1.14 pkgsrc/devel/hdf5/Makefile.common cvs rdiff -u -r1.37 -r1.38 pkgsrc/devel/hdf5/distinfo
1 parent 08c87e2 commit cd3defa

10 files changed

+44
-45
lines changed

‎devel/hdf5/Makefile.common

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@@ -1,11 +1,10 @@
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# $NetBSD: Makefile.common,v 1.12 2016/09/14 21:34:34 alnsn Exp $
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# $NetBSD: Makefile.common,v 1.12.2.1 2016/12/11 17:18:01 spz Exp $
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# used by devel/hdf5/Makefile
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# used by devel/hdf5-c++/Makefile
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5-
DISTNAME= hdf5-1.8.16
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PKGREVISION= 1
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DISTNAME= hdf5-1.8.18
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CATEGORIES= devel
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MASTER_SITES= ftp://ftp.hdfgroup.org/HDF5/current/src/
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MASTER_SITES= ftp://ftp.hdfgroup.org/HDF5/current18/src/
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EXTRACT_SUFX= .tar.bz2
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MAINTAINER= [email protected]

‎devel/hdf5/distinfo

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$NetBSD: distinfo,v 1.36 2015/11/26 11:25:10 adam Exp $
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$NetBSD: distinfo,v 1.36.8.1 2016/12/11 17:18:01 spz Exp $
22

3-
SHA1 (hdf5-1.8.16.tar.bz2) = a7b631778cb289edec670f665d2c3265983a0d53
4-
RMD160 (hdf5-1.8.16.tar.bz2) = f72c7029b08dfae4562b9aa23f03aa43bd02617e
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SHA512 (hdf5-1.8.16.tar.bz2) = f3ca50ca50bb51057818165fcc36f199a7bd7a9b7c42e299314381a269c4d882f60a780b0005fc2443596e06535ff40019b3483763d926e462a90bea4fe84033
6-
Size (hdf5-1.8.16.tar.bz2) = 10047405 bytes
3+
SHA1 (hdf5-1.8.18.tar.bz2) = d7e008cbfcf5cb6913b5327a81bbcaf34cc9436d
4+
RMD160 (hdf5-1.8.18.tar.bz2) = a3910b7129f80080c0574bb798f6d40849724005
5+
SHA512 (hdf5-1.8.18.tar.bz2) = 01f6d14bdd3be2ced9c63cc9e1820cd7ea11db649ff9f3a3055c18c4b0fffe777fd23baad536e3bce31c4d76fe17db64a3972762e1bb4d232927c1ca140e72b2
6+
Size (hdf5-1.8.18.tar.bz2) = 10081294 bytes
77
SHA1 (patch-bin_cmakehdf5) = c31107e3f67dd2b58318ebc94e6044c8c76df049
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SHA1 (patch-c++_examples_Makefile.in) = 2df6015f121e9e86080cf937b64990a39acf9f65
9-
SHA1 (patch-c++_examples_run-c++-ex.sh.in) = b5b68a72a7b93ac0c87bbce229171136dbe3fcd2
8+
SHA1 (patch-c++_examples_Makefile.in) = 2b62c0b30258fcce5e22b5932bd400ca5897e0c3
9+
SHA1 (patch-c++_examples_run-c++-ex.sh.in) = f0605ce2cf35e72f47a1c848aa637342eab65070
1010
SHA1 (patch-configure) = e7f141d54c39cbee2f7d703ab7d6ff582158904e
11-
SHA1 (patch-examples_Makefile.in) = 42b325b87e640f2731ec9b7f48d6a63c3226ffd4
12-
SHA1 (patch-examples_run-c-ex.sh.in) = fa1c4fd2ec50450fc738b6e0af6ce7ccad610756
13-
SHA1 (patch-hl_c++_examples_Makefile.in) = 4bc7501f3f221d2d2c02d01af78c5ba69e8d9fea
14-
SHA1 (patch-hl_c++_examples_run-hlc++-ex.sh.in) = 422a7386f1480ad7493bfb2e1e630245b0b66d90
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SHA1 (patch-hl_examples_Makefile.in) = ae28809d58465c380ff27d5cbe6b1ac9a5eef569
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SHA1 (patch-hl_examples_run-hlc-ex.sh.in) = e317704c96f41d569ce3d2550f637f903bde659e
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SHA1 (patch-examples_Makefile.in) = af9cf68a50544312a759b7732aea9297a6881582
12+
SHA1 (patch-examples_run-c-ex.sh.in) = 3614da26657a1428d134d915593d03cd408292d3
13+
SHA1 (patch-hl_c++_examples_Makefile.in) = a65d0461a6e1ac464e089703f9f5ab6c1dcf1666
14+
SHA1 (patch-hl_c++_examples_run-hlc++-ex.sh.in) = 48050e21799cca24b19a60b6242fd7d156a7cb59
15+
SHA1 (patch-hl_examples_Makefile.in) = df3650c121152471a045e1fec169eedeea757377
16+
SHA1 (patch-hl_examples_run-hlc-ex.sh.in) = a7cd97c716c598cd3aac05f0b1dcee46d77bd968
1717
SHA1 (patch-tools_h5jam_testh5jam.sh.in) = 89068ae1694c586f85b25240fda30549eddf2d0f

‎devel/hdf5/patches/patch-c++_examples_Makefile.in

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$NetBSD: patch-c++_examples_Makefile.in,v 1.3 2015/11/26 11:25:10 adam Exp $
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$NetBSD: patch-c++_examples_Makefile.in,v 1.3.8.1 2016/12/11 17:18:02 spz Exp $
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Fix paths to examples.
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--- c++/examples/Makefile.in.orig 2015-11-10 14:01:02.000000000 +0000
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--- c++/examples/Makefile.in.orig 2016-05-10 21:24:51.000000000 +0000
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+++ c++/examples/Makefile.in
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@@ -626,8 +626,8 @@ CXX_API = yes
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# Where to install examples
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# Note: no '/' after DESTDIR. Explanation in commence.am
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-EXAMPLEDIR = ${DESTDIR}$(datarootdir)/hdf5_examples/c++
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-EXAMPLETOPDIR = ${DESTDIR}$(datarootdir)/hdf5_examples
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-EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/c++
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-EXAMPLETOPDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples
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+EXAMPLEDIR = ${DESTDIR}$(datarootdir)/examples/hdf5/c++
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+EXAMPLETOPDIR = ${DESTDIR}$(datarootdir)/examples/hdf5
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‎devel/hdf5/patches/patch-c++_examples_run-c++-ex.sh.in

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$NetBSD: patch-c++_examples_run-c++-ex.sh.in,v 1.2 2015/11/26 11:25:10 adam Exp $
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$NetBSD: patch-c++_examples_run-c++-ex.sh.in,v 1.2.8.1 2016/12/11 17:18:02 spz Exp $
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Fix paths to examples.
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--- c++/examples/run-c++-ex.sh.in.orig 2015-10-24 05:14:06.000000000 +0000
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--- c++/examples/run-c++-ex.sh.in.orig 2016-04-26 12:44:06.000000000 +0000
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+++ c++/examples/run-c++-ex.sh.in
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# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
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# Where the tool is installed.
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# default is relative path to installed location of the tools
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-prefix="${prefix:-../../..}"
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-prefix="${prefix:-../../../}"
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+prefix="${prefix:-../../../..}"
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AR="@AR@"
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RANLIB="@RANLIB@"

‎devel/hdf5/patches/patch-examples_Makefile.in

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$NetBSD: patch-examples_Makefile.in,v 1.3 2015/11/26 11:25:10 adam Exp $
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$NetBSD: patch-examples_Makefile.in,v 1.3.8.1 2016/12/11 17:18:02 spz Exp $
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--- examples/Makefile.in.orig 2015-11-10 14:01:03.000000000 +0000
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--- examples/Makefile.in.orig 2016-05-10 21:24:51.000000000 +0000
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@@ -636,8 +636,8 @@ EXTLINK_DIRS = red blue u2w
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# Example directory
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# Note: no '/' after DESTDIR. Explanation in commence.am
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-EXAMPLEDIR = ${DESTDIR}$(datarootdir)/hdf5_examples/c
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-EXAMPLETOPDIR = ${DESTDIR}$(datarootdir)/hdf5_examples
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-EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/c
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-EXAMPLETOPDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples
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+EXAMPLEDIR = ${DESTDIR}$(datarootdir)/examples/hdf5/c
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+EXAMPLETOPDIR = ${DESTDIR}$(datarootdir)/examples/hdf5
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@BUILD_SHARED_SZIP_CONDITIONAL_TRUE@LD_LIBRARY_PATH = $(LL_PATH)

‎devel/hdf5/patches/patch-examples_run-c-ex.sh.in

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$NetBSD: patch-examples_run-c-ex.sh.in,v 1.2 2015/11/26 11:25:10 adam Exp $
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$NetBSD: patch-examples_run-c-ex.sh.in,v 1.2.8.1 2016/12/11 17:18:02 spz Exp $
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Fix path to examples.
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--- examples/run-c-ex.sh.in.orig 2015-10-24 05:14:08.000000000 +0000
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--- examples/run-c-ex.sh.in.orig 2016-04-26 12:44:10.000000000 +0000
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+++ examples/run-c-ex.sh.in
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@@ -20,7 +20,7 @@
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# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
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# Where the tool is installed.
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# default is relative path to installed location of the tools
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-prefix="${prefix:-../../..}"
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-prefix="${prefix:-../../../}"
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+prefix="${prefix:-../../../..}"
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PARALLEL=@PARALLEL@ # Am I in parallel mode?
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AR="@AR@"

‎devel/hdf5/patches/patch-hl_c++_examples_Makefile.in

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$NetBSD: patch-hl_c++_examples_Makefile.in,v 1.3 2015/11/26 11:25:10 adam Exp $
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$NetBSD: patch-hl_c++_examples_Makefile.in,v 1.3.8.1 2016/12/11 17:18:02 spz Exp $
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Fix paths to examples.
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--- hl/c++/examples/Makefile.in.orig 2015-11-10 14:01:04.000000000 +0000
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--- hl/c++/examples/Makefile.in.orig 2016-05-10 21:24:52.000000000 +0000
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+++ hl/c++/examples/Makefile.in
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# Where to install examples
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# Note: no '/' after DESTDIR. Explanation in commence.am
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-EXAMPLEDIR = ${DESTDIR}$(datarootdir)/hdf5_examples/hl/c++
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-EXAMPLETOPDIR = ${DESTDIR}$(datarootdir)/hdf5_examples/hl
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-EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/hl/c++
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-EXAMPLETOPDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/hl
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+EXAMPLEDIR = ${DESTDIR}$(datarootdir)/examples/hdf5/hl/c++
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+EXAMPLETOPDIR = ${DESTDIR}$(datarootdir)/examples/hdf5/hl
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‎devel/hdf5/patches/patch-hl_c++_examples_run-hlc++-ex.sh.in

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$NetBSD: patch-hl_c++_examples_run-hlc++-ex.sh.in,v 1.2 2015/11/26 11:25:10 adam Exp $
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$NetBSD: patch-hl_c++_examples_run-hlc++-ex.sh.in,v 1.2.8.1 2016/12/11 17:18:02 spz Exp $
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Fix paths to examples.
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--- hl/c++/examples/run-hlc++-ex.sh.in.orig 2015-10-24 05:14:02.000000000 +0000
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--- hl/c++/examples/run-hlc++-ex.sh.in.orig 2016-04-26 12:43:57.000000000 +0000
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+++ hl/c++/examples/run-hlc++-ex.sh.in
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# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
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EXIT_FAILURE=1
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# Where the tool is installed.
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# default is relative path to installed location of the tools
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-prefix="${prefix:-../../../..}"
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-prefix="${prefix:-../../../../}"
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+prefix="${prefix:-../../../../..}"
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AR="@AR@"
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RANLIB="@RANLIB@"

‎devel/hdf5/patches/patch-hl_examples_Makefile.in

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$NetBSD: patch-hl_examples_Makefile.in,v 1.3 2015/11/26 11:25:10 adam Exp $
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$NetBSD: patch-hl_examples_Makefile.in,v 1.3.8.1 2016/12/11 17:18:02 spz Exp $
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Fix paths to examples.
44

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--- hl/examples/Makefile.in.orig 2015-11-10 14:01:04.000000000 +0000
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--- hl/examples/Makefile.in.orig 2016-05-10 21:24:53.000000000 +0000
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@@ -604,8 +604,8 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.c
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# Example directory
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# Note: no '/' after DESTDIR. Explanation in commence.am
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-EXAMPLEDIR = ${DESTDIR}$(datarootdir)/hdf5_examples/hl/c
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-EXAMPLETOPDIR = ${DESTDIR}$(datarootdir)/hdf5_examples/hl
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-EXAMPLEDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/hl/c
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-EXAMPLETOPDIR = ${DESTDIR}$(exec_prefix)/share/hdf5_examples/hl
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+EXAMPLEDIR = ${DESTDIR}$(datarootdir)/examples/hdf5/hl/c
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+EXAMPLETOPDIR = ${DESTDIR}$(datarootdir)/examples/hdf5/hl
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INSTALL_SCRIPT_FILES = run-hlc-ex.sh

‎devel/hdf5/patches/patch-hl_examples_run-hlc-ex.sh.in

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
1-
$NetBSD: patch-hl_examples_run-hlc-ex.sh.in,v 1.2 2015/11/26 11:25:10 adam Exp $
1+
$NetBSD: patch-hl_examples_run-hlc-ex.sh.in,v 1.2.8.1 2016/12/11 17:18:02 spz Exp $
22

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Fix paths to examples.
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5-
--- hl/examples/run-hlc-ex.sh.in.orig 2015-10-24 05:14:03.000000000 +0000
5+
--- hl/examples/run-hlc-ex.sh.in.orig 2016-04-26 12:43:59.000000000 +0000
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+++ hl/examples/run-hlc-ex.sh.in
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@@ -20,7 +20,7 @@
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# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
@@ -17,7 +17,7 @@ Fix paths to examples.
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# Where the tool is installed.
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# default is relative path to installed location of the tools
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-prefix="${prefix:-../../../..}"
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-prefix="${prefix:-../../../../}"
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+prefix="${prefix:-../../../../..}"
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PARALLEL=@PARALLEL@ # Am I in parallel mode?
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AR="@AR@"

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