From 43057e6f650ba2e0a023f66a0d02d48a121a273a Mon Sep 17 00:00:00 2001 From: asau Date: Sat, 27 Oct 2012 08:54:48 +0000 Subject: Update to HDF5 1.8.9 This doesn't pass self-tests, but it isn't regression, previous package didn't pass them as well. (While here, make both packages share the same distinfo.) Changes in HDF5 1.8.9 HDF5 1.8.9 is a minor release, but contains several important new features and bug fixes. Changes in this release include the following: * Committed datatypes can now be merged when copying objects, using the new flag H5O_COPY_MERGE_COMMITTED_DTYPE_FLAG. Several new API routines have been included in support of this feature. * A file in memory can now be accessed in the same way as a file on disk. New APIs were added to support this feature. * Many changes to the tools have been made, including the following: + The h5repack performance has been improved dramatically for large chunked datasets. + The -S (or --summary) option was added to h5stat to display a summary of the file space usage for a file. + A wildcard can now be used with h5dump to specify multiple files. * H5LTpath_valid was added to determine if a path is correct and a link resolves to a valid object. * The Fortran counterpart to H5Ocopy, h5ocopy_f, was added. This release contains many other changes and bug fixes not listed here. Please be sure to read the Release Notes for a comprehensive list of new features and bug fixes. Changes in HDF5 1.8.8 HDF5 1.8.8 is a minor release, but contains a few important new features and bug fixes. Changes in this release include the following: * Changes to the Fortran interface: + Fortran wrappers for the Dimension Scales APIs were added. For the new subroutine signatures, see: http://www.hdfgroup.org/HDF5/doc/HL/RM_H5DS.html + The Fortran interface now uses the Fortran 2003 standard, enabling a wider set of Fortran and HDF5 datatypes to be supported, including: o Any kind of INTEGER or REAL o Fortran derived types o Fortran and HDF5 enumeration o HDF5 variable-length datatypes o HDF5 compound datatypes of any complexity It also contains new subroutines corresponding to those C APIs which have callback functions as parameters. For a general overview and information on how to enable these new Fortran features, please see the following paper: http://www.hdfgroup.org/HDF5/doc/fortran/NewFeatures_F2003.pdf HDF5 examples that use Fortran 2003 (with the suffix "F03") can be found here: http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/api18-fortran.html The --enable-fortran2003 configure flag was added to enable Fortran 2003 support in the HDF5 Fortran library. This flag should be used along with the --enable-fortran flag and takes affect only when a Fortran compiler is Fortran 2003 compliant. * H5Tcreate now supports a string type (fixed-length and variable-length). * New APIs, H5Pget_mpio_actual_chunk_opt_mode and H5Pget_mpio_actual_io_mode, were added for querying whether/how a collective I/O operation completed. * Numerous changes were made to the tools (h5diff, h5repack, h5jam, h5dump). --- devel/hdf5-c++/distinfo | 14 ----------- devel/hdf5/Makefile.common | 5 ++-- devel/hdf5/PLIST | 3 ++- devel/hdf5/distinfo | 16 +++++++++---- .../hdf5/patches/patch-tools_h5copy_testh5copy.sh | 15 ++++++++++++ .../hdf5/patches/patch-tools_h5diff_testh5diff.sh | 15 ++++++++++++ .../patches/patch-tools_h5dump_testh5dump.sh.in | 15 ++++++++++++ .../patch-tools_h5import_h5importtestutil.sh | 15 ++++++++++++ .../hdf5/patches/patch-tools_h5jam_testh5jam.sh.in | 28 ++++++++++++++++++++++ devel/hdf5/patches/patch-tools_h5ls_testh5ls.sh.in | 15 ++++++++++++ .../patches/patch-tools_h5repack_h5repack.sh.in | 15 ++++++++++++ .../patches/patch-tools_h5stat_testh5stat.sh.in | 15 ++++++++++++ 12 files changed, 150 insertions(+), 21 deletions(-) delete mode 100644 devel/hdf5-c++/distinfo create mode 100644 devel/hdf5/patches/patch-tools_h5copy_testh5copy.sh create mode 100644 devel/hdf5/patches/patch-tools_h5diff_testh5diff.sh create mode 100644 devel/hdf5/patches/patch-tools_h5dump_testh5dump.sh.in create mode 100644 devel/hdf5/patches/patch-tools_h5import_h5importtestutil.sh create mode 100644 devel/hdf5/patches/patch-tools_h5jam_testh5jam.sh.in create mode 100644 devel/hdf5/patches/patch-tools_h5ls_testh5ls.sh.in create mode 100644 devel/hdf5/patches/patch-tools_h5repack_h5repack.sh.in create mode 100644 devel/hdf5/patches/patch-tools_h5stat_testh5stat.sh.in (limited to 'devel') diff --git a/devel/hdf5-c++/distinfo b/devel/hdf5-c++/distinfo deleted file mode 100644 index 4c1ff1c9102..00000000000 --- a/devel/hdf5-c++/distinfo +++ /dev/null @@ -1,14 +0,0 @@ -$NetBSD: distinfo,v 1.1.1.1 2011/10/07 10:42:18 alnsn Exp $ - -SHA1 (hdf5-1.8.7.tar.gz) = cb8a2a353a7aabbae923029ebfb66426ddc28ff0 -RMD160 (hdf5-1.8.7.tar.gz) = 6629b3300e4bc86ced62085f4036550ce5cb9cd9 -Size (hdf5-1.8.7.tar.gz) = 7827944 bytes -SHA1 (patch-c++_examples_Makefile.in) = 4c063e3138507a5dbf99f4c7785611a45ffcf753 -SHA1 (patch-c++_examples_run-c++-ex.sh.in) = 58c38b2ba5557cdae2c4fe1e72c6fa55e5606f1e -SHA1 (patch-configure.in) = c08f39c3aba0ff34022d4afc26cdfd8785f504b7 -SHA1 (patch-examples_Makefile.in) = 3049b17a6656e7b9818ec69607b278b6e7dc937d -SHA1 (patch-examples_run-c-ex.sh.in) = 744d3e6bbae1a9b496e3657db6a62fac78fcd7ed -SHA1 (patch-hl_c++_examples_Makefile.in) = 6e651fae42365e67c281d8bc80e2c60faeddec01 -SHA1 (patch-hl_c++_examples_run-hlc++-ex.sh.in) = fba3d976adb02d80682ddc42a8ef64f6dddffa41 -SHA1 (patch-hl_examples_Makefile.in) = 2fe09e8a88eeca49db58908a6b4a3a70f01cb0b4 -SHA1 (patch-hl_examples_run-hlc-ex.sh.in) = 38c2c112439d6febb023d638d965f04bbaa45d5f diff --git a/devel/hdf5/Makefile.common b/devel/hdf5/Makefile.common index a68de6abc90..0a9177d8e37 100644 --- a/devel/hdf5/Makefile.common +++ b/devel/hdf5/Makefile.common @@ -1,7 +1,7 @@ -# $NetBSD: Makefile.common,v 1.2 2012/02/16 18:45:59 hans Exp $ +# $NetBSD: Makefile.common,v 1.3 2012/10/27 08:54:48 asau Exp $ # used by devel/hdf5-c++/Makefile -HDF5_VER= 1.8.7 +HDF5_VER= 1.8.9 DISTNAME= hdf5-${HDF5_VER} CATEGORIES= devel MASTER_SITES= ftp://ftp.hdfgroup.org/HDF5/current/src/ @@ -19,6 +19,7 @@ PKG_DESTDIR_SUPPORT= user-destdir CFLAGS.SunOS+= -std=c99 -D_XOPEN_SOURCE=600 -D__EXTENSIONS__ +DISTINFO_FILE= ${.CURDIR}/../../devel/hdf5/distinfo PATCHDIR= ${.CURDIR}/../../devel/hdf5/patches # it appears that this file is informative only and is not actually diff --git a/devel/hdf5/PLIST b/devel/hdf5/PLIST index e5bf2cf1c46..9ae6a825720 100644 --- a/devel/hdf5/PLIST +++ b/devel/hdf5/PLIST @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.20 2011/10/07 10:38:50 alnsn Exp $ +@comment $NetBSD: PLIST,v 1.21 2012/10/27 08:54:48 asau Exp $ bin/gif2h5 bin/h52gif bin/h5cc @@ -63,6 +63,7 @@ share/doc/hdf5/COPYING share/doc/hdf5/HISTORY-1_0-1_8_0_rc3.txt share/doc/hdf5/HISTORY-1_8.txt share/doc/hdf5/RELEASE.txt +share/examples/hdf5/README share/examples/hdf5/c/h5_attribute.c share/examples/hdf5/c/h5_chunk_read.c share/examples/hdf5/c/h5_compound.c diff --git a/devel/hdf5/distinfo b/devel/hdf5/distinfo index 7de92da9cf3..a60786d1529 100644 --- a/devel/hdf5/distinfo +++ b/devel/hdf5/distinfo @@ -1,8 +1,8 @@ -$NetBSD: distinfo,v 1.27 2011/10/07 10:38:50 alnsn Exp $ +$NetBSD: distinfo,v 1.28 2012/10/27 08:54:48 asau Exp $ -SHA1 (hdf5-1.8.7.tar.gz) = cb8a2a353a7aabbae923029ebfb66426ddc28ff0 -RMD160 (hdf5-1.8.7.tar.gz) = 6629b3300e4bc86ced62085f4036550ce5cb9cd9 -Size (hdf5-1.8.7.tar.gz) = 7827944 bytes +SHA1 (hdf5-1.8.9.tar.gz) = 4ba3ede947b1571e9586fdeb8351d6585a56133c +RMD160 (hdf5-1.8.9.tar.gz) = a971f0f666786d93f33f8cc59d67e29fab77a351 +Size (hdf5-1.8.9.tar.gz) = 8258774 bytes SHA1 (patch-c++_examples_Makefile.in) = 4c063e3138507a5dbf99f4c7785611a45ffcf753 SHA1 (patch-c++_examples_run-c++-ex.sh.in) = 58c38b2ba5557cdae2c4fe1e72c6fa55e5606f1e SHA1 (patch-configure.in) = c08f39c3aba0ff34022d4afc26cdfd8785f504b7 @@ -12,3 +12,11 @@ SHA1 (patch-hl_c++_examples_Makefile.in) = 6e651fae42365e67c281d8bc80e2c60faedde SHA1 (patch-hl_c++_examples_run-hlc++-ex.sh.in) = fba3d976adb02d80682ddc42a8ef64f6dddffa41 SHA1 (patch-hl_examples_Makefile.in) = 2fe09e8a88eeca49db58908a6b4a3a70f01cb0b4 SHA1 (patch-hl_examples_run-hlc-ex.sh.in) = 38c2c112439d6febb023d638d965f04bbaa45d5f +SHA1 (patch-tools_h5copy_testh5copy.sh) = 745f951117bbc1a05fbfb6df8cdff3d58771c635 +SHA1 (patch-tools_h5diff_testh5diff.sh) = 62e02ee65a4b9284f548f872aad9bcf7884fb477 +SHA1 (patch-tools_h5dump_testh5dump.sh.in) = d373f9a0618499bbb71827df6ffe6bed2b5dab17 +SHA1 (patch-tools_h5import_h5importtestutil.sh) = 7bd31ce6ca50c0a8d4040b7d2518dc4658b51c5c +SHA1 (patch-tools_h5jam_testh5jam.sh.in) = 1d8d618ee90adfe6735a22eecd1a6c60c1437da6 +SHA1 (patch-tools_h5ls_testh5ls.sh.in) = 71bfe26ce98d3579bf8decaf7ef10a5f5f27e255 +SHA1 (patch-tools_h5repack_h5repack.sh.in) = c235aef4f6c781ef0028685b505fd77aa7b5722d +SHA1 (patch-tools_h5stat_testh5stat.sh.in) = 962ff9cdf8c7c459e47147cf85826e190aee4179 diff --git a/devel/hdf5/patches/patch-tools_h5copy_testh5copy.sh b/devel/hdf5/patches/patch-tools_h5copy_testh5copy.sh new file mode 100644 index 00000000000..ddda89c8b4e --- /dev/null +++ b/devel/hdf5/patches/patch-tools_h5copy_testh5copy.sh @@ -0,0 +1,15 @@ +$NetBSD: patch-tools_h5copy_testh5copy.sh,v 1.1 2012/10/27 08:54:48 asau Exp $ + +Use portable construct to check file existence. + +--- tools/h5copy/testh5copy.sh.orig 2012-05-09 15:06:14.000000000 +0000 ++++ tools/h5copy/testh5copy.sh +@@ -105,7 +105,7 @@ COPY_TESTFILES_TO_TESTDIR() + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then +- if [ -a $tstfile ]; then ++ if [ -e $tstfile ]; then + $CP -f $tstfile $TESTDIR + else + echo "Error: FAILED to copy $tstfile." diff --git a/devel/hdf5/patches/patch-tools_h5diff_testh5diff.sh b/devel/hdf5/patches/patch-tools_h5diff_testh5diff.sh new file mode 100644 index 00000000000..8f66b554c01 --- /dev/null +++ b/devel/hdf5/patches/patch-tools_h5diff_testh5diff.sh @@ -0,0 +1,15 @@ +$NetBSD: patch-tools_h5diff_testh5diff.sh,v 1.1 2012/10/27 08:54:48 asau Exp $ + +Use portable construct to check file existence. + +--- tools/h5diff/testh5diff.sh.orig 2012-05-09 15:06:12.000000000 +0000 ++++ tools/h5diff/testh5diff.sh +@@ -313,7 +313,7 @@ COPY_TESTFILES_TO_TESTDIR() + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then +- if [ -a $tstfile ]; then ++ if [ -e $tstfile ]; then + $CP -f $tstfile $TESTDIR + else + echo "Error: FAILED to copy $tstfile ." diff --git a/devel/hdf5/patches/patch-tools_h5dump_testh5dump.sh.in b/devel/hdf5/patches/patch-tools_h5dump_testh5dump.sh.in new file mode 100644 index 00000000000..8096d2f250e --- /dev/null +++ b/devel/hdf5/patches/patch-tools_h5dump_testh5dump.sh.in @@ -0,0 +1,15 @@ +$NetBSD: patch-tools_h5dump_testh5dump.sh.in,v 1.1 2012/10/27 08:54:48 asau Exp $ + +Use portable construct to check file existence. + +--- tools/h5dump/testh5dump.sh.in.orig 2012-05-09 15:06:02.000000000 +0000 ++++ tools/h5dump/testh5dump.sh.in +@@ -448,7 +448,7 @@ COPY_TESTFILES_TO_TESTDIR() + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then +- if [ -a $tstfile ]; then ++ if [ -e $tstfile ]; then + $CP -f $tstfile $TESTDIR + else + echo "Error: FAILED to copy $tstfile" diff --git a/devel/hdf5/patches/patch-tools_h5import_h5importtestutil.sh b/devel/hdf5/patches/patch-tools_h5import_h5importtestutil.sh new file mode 100644 index 00000000000..7fdde4083aa --- /dev/null +++ b/devel/hdf5/patches/patch-tools_h5import_h5importtestutil.sh @@ -0,0 +1,15 @@ +$NetBSD: patch-tools_h5import_h5importtestutil.sh,v 1.1 2012/10/27 08:54:48 asau Exp $ + +Use portable construct to check file existence. + +--- tools/h5import/h5importtestutil.sh.orig 2012-05-09 15:06:14.000000000 +0000 ++++ tools/h5import/h5importtestutil.sh +@@ -115,7 +115,7 @@ COPY_TESTFILES_TO_TESTDIR() + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then +- if [ -a $tstfile ]; then ++ if [ -e $tstfile ]; then + $CP -f $tstfile $TESTDIR + else + echo "Error: FAILED to copy $tstfile" diff --git a/devel/hdf5/patches/patch-tools_h5jam_testh5jam.sh.in b/devel/hdf5/patches/patch-tools_h5jam_testh5jam.sh.in new file mode 100644 index 00000000000..160e37d0d4c --- /dev/null +++ b/devel/hdf5/patches/patch-tools_h5jam_testh5jam.sh.in @@ -0,0 +1,28 @@ +$NetBSD: patch-tools_h5jam_testh5jam.sh.in,v 1.1 2012/10/27 08:54:48 asau Exp $ + +Use portable construct to check file existence. +Use portable "=" to test string equality. + +--- tools/h5jam/testh5jam.sh.in.orig 2012-05-09 15:06:08.000000000 +0000 ++++ tools/h5jam/testh5jam.sh.in +@@ -103,7 +103,7 @@ COPY_TESTFILES_TO_TESTDIR() + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then +- if [ -a $tstfile ]; then ++ if [ -e $tstfile ]; then + $CP -f $tstfile $TESTDIR + else + echo "Error: FAILED to copy $tstfile" +@@ -456,9 +456,9 @@ UNJAMTEST () { + # + + TOOLTEST_OUTPUT() { +- if [ "$1" == "JAM" ]; then ++ if [ "$1" = "JAM" ]; then + TOOLCMD=$JAM_BIN/$JAM +- elif [ "$1" == "UNJAM" ]; then ++ elif [ "$1" = "UNJAM" ]; then + TOOLCMD=$JAM_BIN/$UNJAM + fi + shift diff --git a/devel/hdf5/patches/patch-tools_h5ls_testh5ls.sh.in b/devel/hdf5/patches/patch-tools_h5ls_testh5ls.sh.in new file mode 100644 index 00000000000..38ffd45dd8a --- /dev/null +++ b/devel/hdf5/patches/patch-tools_h5ls_testh5ls.sh.in @@ -0,0 +1,15 @@ +$NetBSD: patch-tools_h5ls_testh5ls.sh.in,v 1.1 2012/10/27 08:54:48 asau Exp $ + +Use portable construct to check file existence. + +--- tools/h5ls/testh5ls.sh.in.orig 2012-05-09 15:06:15.000000000 +0000 ++++ tools/h5ls/testh5ls.sh.in +@@ -167,7 +167,7 @@ COPY_TESTFILES_TO_TESTDIR() + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then +- if [ -a $tstfile ]; then ++ if [ -e $tstfile ]; then + $CP -f $tstfile $TESTDIR + else + echo "Error: FAILED to copy $tstfile" diff --git a/devel/hdf5/patches/patch-tools_h5repack_h5repack.sh.in b/devel/hdf5/patches/patch-tools_h5repack_h5repack.sh.in new file mode 100644 index 00000000000..eb70dac9b97 --- /dev/null +++ b/devel/hdf5/patches/patch-tools_h5repack_h5repack.sh.in @@ -0,0 +1,15 @@ +$NetBSD: patch-tools_h5repack_h5repack.sh.in,v 1.1 2012/10/27 08:54:48 asau Exp $ + +Use portable construct to check file existence. + +--- tools/h5repack/h5repack.sh.in.orig 2012-05-09 15:06:03.000000000 +0000 ++++ tools/h5repack/h5repack.sh.in +@@ -137,7 +137,7 @@ COPY_TESTFILES_TO_TESTDIR() + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then +- if [ -a $tstfile ]; then ++ if [ -e $tstfile ]; then + $CP -f $tstfile $TESTDIR + else + echo "Error: FAILED to copy $tstfile" diff --git a/devel/hdf5/patches/patch-tools_h5stat_testh5stat.sh.in b/devel/hdf5/patches/patch-tools_h5stat_testh5stat.sh.in new file mode 100644 index 00000000000..f5d3d05cc9e --- /dev/null +++ b/devel/hdf5/patches/patch-tools_h5stat_testh5stat.sh.in @@ -0,0 +1,15 @@ +$NetBSD: patch-tools_h5stat_testh5stat.sh.in,v 1.1 2012/10/27 08:54:48 asau Exp $ + +Use portable construct to check file existence. + +--- tools/h5stat/testh5stat.sh.in.orig 2012-05-09 15:06:15.000000000 +0000 ++++ tools/h5stat/testh5stat.sh.in +@@ -105,7 +105,7 @@ COPY_TESTFILES_TO_TESTDIR() + echo $tstfile | tr -d ' ' | grep '^#' > /dev/null + RET=$? + if [ $RET -eq 1 ]; then +- if [ -a $tstfile ]; then ++ if [ -e $tstfile ]; then + $CP -f $tstfile $TESTDIR + else + echo "Error: FAILED to copy $tstfile" -- cgit v1.2.3