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).

12 files changed, 150 insertions, 21 deletions

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"