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hdf5_110: HDF5 is a data model, library, and file format for storing and managing data.
Module Name: pkgsrc-wip
Committed By: Paul Ripke <stix%stix.id.au@localhost>
Pushed By: stix
Date: Wed Apr 2 21:16:11 2025 +1100
Changeset: b463938e8be9252a9a9eff5cc93996b061951e70
Added Files:
hdf5_110/COMMIT_MSG
hdf5_110/DESCR
hdf5_110/Makefile
hdf5_110/PLIST
hdf5_110/TODO
hdf5_110/buildlink3.mk
hdf5_110/distinfo
hdf5_110/options.mk
hdf5_110/patches/patch-configure
hdf5_110/patches/patch-tools_test_h5dump_testh5dump.sh.in
hdf5_110/patches/patch-tools_test_h5repack_h5repack.sh.in
Log Message:
hdf5_110: HDF5 is a data model, library, and file format for storing and managing data.
This is version 1.10.x for use with aster modules (science/med).
Based on devel/hdf5 1.12.2.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=b463938e8be9252a9a9eff5cc93996b061951e70
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
hdf5_110/COMMIT_MSG | 9 ++
hdf5_110/DESCR | 9 ++
hdf5_110/Makefile | 59 +++++++++
hdf5_110/PLIST | 141 +++++++++++++++++++++
hdf5_110/TODO | 7 +
hdf5_110/buildlink3.mk | 22 ++++
hdf5_110/distinfo | 8 ++
hdf5_110/options.mk | 28 ++++
hdf5_110/patches/patch-configure | 14 ++
.../patch-tools_test_h5dump_testh5dump.sh.in | 20 +++
.../patch-tools_test_h5repack_h5repack.sh.in | 24 ++++
11 files changed, 341 insertions(+)
diffs:
diff --git a/hdf5_110/COMMIT_MSG b/hdf5_110/COMMIT_MSG
new file mode 100644
index 0000000000..6c548debf1
--- /dev/null
+++ b/hdf5_110/COMMIT_MSG
@@ -0,0 +1,9 @@
+HDF5 is a data model, library, and file format for storing and
+managing data. It supports an unlimited variety of datatypes, and
+is designed for flexible and efficient I/O and for high volume and
+complex data. HDF5 is portable and is extensible, allowing applications
+to evolve in their use of HDF5. The HDF5 Technology suite includes
+tools and applications for managing, manipulating, viewing, and
+analyzing data in the HDF5 format.
+
+This is version 1.10.x for use with aster modules (science/med).
diff --git a/hdf5_110/DESCR b/hdf5_110/DESCR
new file mode 100644
index 0000000000..6c548debf1
--- /dev/null
+++ b/hdf5_110/DESCR
@@ -0,0 +1,9 @@
+HDF5 is a data model, library, and file format for storing and
+managing data. It supports an unlimited variety of datatypes, and
+is designed for flexible and efficient I/O and for high volume and
+complex data. HDF5 is portable and is extensible, allowing applications
+to evolve in their use of HDF5. The HDF5 Technology suite includes
+tools and applications for managing, manipulating, viewing, and
+analyzing data in the HDF5 format.
+
+This is version 1.10.x for use with aster modules (science/med).
diff --git a/hdf5_110/Makefile b/hdf5_110/Makefile
new file mode 100644
index 0000000000..fac105ebcb
--- /dev/null
+++ b/hdf5_110/Makefile
@@ -0,0 +1,59 @@
+# $NetBSD$
+
+PKGVERSION= 1.10.11
+PKGNAME= hdf5_${PKGNAMESUFFIX}-${PKGVERSION}
+DISTNAME= hdf5-${PKGVERSION}
+PKGNAMESUFFIX= 110
+CATEGORIES= devel
+MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${PKGVERSION_NOREV:R}/hdf5-${PKGVERSION_NOREV}/src/
+EXTRACT_SUFX= .tar.bz2
+COMMENT= Hierarchical Data Format (new generation) 1.10.x
+
+MAINTAINER= pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE= https://www.hdfgroup.org/HDF5/
+LICENSE= original-bsd
+
+USE_LIBTOOL= yes
+USE_TOOLS+= pax tr
+USE_LANGUAGES= c c++ fortran
+GNU_CONFIGURE= yes
+CONFIGURE_ARGS+= --with-examplesdir=${PREFIX}/share/examples/hdf5-${PKGNAMESUFFIX}
+CONFIGURE_ARGS+= --includedir=${PREFIX}/include/hdf5-${PKGNAMESUFFIX}
+CONFIGURE_ARGS+= --program-suffix=-${PKGNAMESUFFIX}
+CONFIGURE_ARGS+= --with-default-api-version=v110
+TEST_TARGET= check
+
+CFLAGS.SunOS+= -std=c99 -D_XOPEN_SOURCE=600 -D__EXTENSIONS__
+CONFIGURE_ENV.SunOS+= ac_cv_func_gettimeofday=yes
+
+#DISTINFO_FILE= ${.CURDIR}/../../devel/hdf5/distinfo
+#PATCHDIR= ${.CURDIR}/../../devel/hdf5/patches
+
+# These 2 files are not used in the build. They use [[ ... ]].
+# CHECK_PORTABILITY_SKIP= bin/snapshot hl/tools/h5watch/testh5watch.sh.in
+
+# it appears that this file is informative only and is not actually
+# used by any installed tools
+# CHECK_WRKREF_SKIP= ${PREFIX}/lib/libhdf5.settings
+
+INSTALL_ENV+= INSTALL_SCRIPT=${INSTALL_SCRIPT:Q}
+
+post-extract:
+ ${CP} ${WRKSRC}/config/freebsd ${WRKSRC}/config/netbsd
+ ${CP} ${WRKSRC}/config/freebsd ${WRKSRC}/config/netbsdelf
+
+post-install:
+ ${MV} ${DESTDIR}${PREFIX}/bin/h5cc ${DESTDIR}${PREFIX}/bin/h5cc-${PKGNAMESUFFIX}
+ ${MV} ${DESTDIR}${PREFIX}/lib/libhdf5.settings ${DESTDIR}${PREFIX}/lib/libhdf5-${PKGNAMESUFFIX}.settings
+
+SUBST_CLASSES+= libname
+SUBST_STAGE.libname= pre-configure
+SUBST_FILES.libname= Makefile.in */Makefile.in */*/Makefile.in */*/*/Makefile.in \
+ */*/*/*/Makefile.in test/test_libinfo.sh.in
+SUBST_SED.libname+= -e "s|libhdf5|libhdf5-${PKGNAMESUFFIX}|g"
+SUBST_SED.libname+= -e "s|libhdf5-${PKGNAMESUFFIX}.settings|libhdf5.settings|g"
+
+.include "options.mk"
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/hdf5_110/PLIST b/hdf5_110/PLIST
new file mode 100644
index 0000000000..704764af48
--- /dev/null
+++ b/hdf5_110/PLIST
@@ -0,0 +1,141 @@
+@comment $NetBSD: PLIST,v 1.32 2023/08/31 11:57:27 adam Exp $
+bin/h5cc-110
+bin/h5clear-110
+bin/h5copy-110
+bin/h5debug-110
+bin/h5diff-110
+bin/h5dump-110
+bin/h5format_convert-110
+bin/h5import-110
+bin/h5jam-110
+bin/h5ls-110
+bin/h5mkgrp-110
+bin/h5perf_serial-110
+bin/h5redeploy-110
+bin/h5repack-110
+bin/h5repart-110
+bin/h5stat-110
+bin/h5unjam-110
+${PLIST.hl}bin/h5watch-110
+include/hdf5-110/H5ACpublic.h
+include/hdf5-110/H5Apublic.h
+include/hdf5-110/H5Cpublic.h
+${PLIST.hl}include/hdf5-110/H5DOpublic.h
+${PLIST.hl}include/hdf5-110/H5DSpublic.h
+include/hdf5-110/H5Dpublic.h
+include/hdf5-110/H5Epubgen.h
+include/hdf5-110/H5Epublic.h
+include/hdf5-110/H5FDcore.h
+include/hdf5-110/H5FDdirect.h
+include/hdf5-110/H5FDfamily.h
+include/hdf5-110/H5FDhdfs.h
+include/hdf5-110/H5FDlog.h
+include/hdf5-110/H5FDmirror.h
+include/hdf5-110/H5FDmpi.h
+include/hdf5-110/H5FDmpio.h
+include/hdf5-110/H5FDmulti.h
+include/hdf5-110/H5FDpublic.h
+include/hdf5-110/H5FDros3.h
+include/hdf5-110/H5FDsec2.h
+include/hdf5-110/H5FDsplitter.h
+include/hdf5-110/H5FDstdio.h
+include/hdf5-110/H5FDwindows.h
+include/hdf5-110/H5Fpublic.h
+include/hdf5-110/H5Gpublic.h
+${PLIST.hl}include/hdf5-110/H5IMpublic.h
+include/hdf5-110/H5Ipublic.h
+${PLIST.hl}include/hdf5-110/H5LDpublic.h
+${PLIST.hl}include/hdf5-110/H5LTpublic.h
+include/hdf5-110/H5Lpublic.h
+include/hdf5-110/H5MMpublic.h
+include/hdf5-110/H5Opublic.h
+include/hdf5-110/H5PLextern.h
+include/hdf5-110/H5PLpublic.h
+${PLIST.hl}include/hdf5-110/H5PTpublic.h
+include/hdf5-110/H5Ppublic.h
+include/hdf5-110/H5Rpublic.h
+include/hdf5-110/H5Spublic.h
+${PLIST.hl}include/hdf5-110/H5TBpublic.h
+include/hdf5-110/H5Tpublic.h
+include/hdf5-110/H5Zpublic.h
+include/hdf5-110/H5api_adpt.h
+include/hdf5-110/H5overflow.h
+include/hdf5-110/H5pubconf.h
+include/hdf5-110/H5public.h
+include/hdf5-110/H5version.h
+include/hdf5-110/hdf5.h
+${PLIST.hl}include/hdf5-110/hdf5_hl.h
+lib/libhdf5-110.a
+lib/libhdf5-110.la
+lib/libhdf5-110.settings
+lib/libhdf5-110.so
+lib/libhdf5-110.so.103
+lib/libhdf5-110.so.103.4.1
+${PLIST.hl}lib/libhdf5-110_hl.a
+${PLIST.hl}lib/libhdf5-110_hl.la
+${PLIST.hl}lib/libhdf5-110_hl.so
+${PLIST.hl}lib/libhdf5-110_hl.so.100
+${PLIST.hl}lib/libhdf5-110_hl.so.100.1.8
+share/examples/hdf5-110/README
+share/examples/hdf5-110/c/h5_attribute.c
+share/examples/hdf5-110/c/h5_chunk_read.c
+share/examples/hdf5-110/c/h5_cmprss.c
+share/examples/hdf5-110/c/h5_compound.c
+share/examples/hdf5-110/c/h5_crtatt.c
+share/examples/hdf5-110/c/h5_crtdat.c
+share/examples/hdf5-110/c/h5_crtgrp.c
+share/examples/hdf5-110/c/h5_crtgrpar.c
+share/examples/hdf5-110/c/h5_crtgrpd.c
+share/examples/hdf5-110/c/h5_debug_trace.c
+share/examples/hdf5-110/c/h5_drivers.c
+share/examples/hdf5-110/c/h5_elink_unix2win.c
+share/examples/hdf5-110/c/h5_extend.c
+share/examples/hdf5-110/c/h5_extend_write.c
+share/examples/hdf5-110/c/h5_extlink.c
+share/examples/hdf5-110/c/h5_group.c
+share/examples/hdf5-110/c/h5_mount.c
+share/examples/hdf5-110/c/h5_rdwt.c
+share/examples/hdf5-110/c/h5_read.c
+share/examples/hdf5-110/c/h5_ref2reg.c
+share/examples/hdf5-110/c/h5_reference.c
+share/examples/hdf5-110/c/h5_select.c
+share/examples/hdf5-110/c/h5_shared_mesg.c
+share/examples/hdf5-110/c/h5_subset.c
+share/examples/hdf5-110/c/h5_vds-eiger.c
+share/examples/hdf5-110/c/h5_vds-exc.c
+share/examples/hdf5-110/c/h5_vds-exclim.c
+share/examples/hdf5-110/c/h5_vds-percival-unlim-maxmin.c
+share/examples/hdf5-110/c/h5_vds-percival-unlim.c
+share/examples/hdf5-110/c/h5_vds-percival.c
+share/examples/hdf5-110/c/h5_vds-simpleIO.c
+share/examples/hdf5-110/c/h5_vds.c
+share/examples/hdf5-110/c/h5_write.c
+share/examples/hdf5-110/c/ph5_filtered_writes.c
+share/examples/hdf5-110/c/ph5_filtered_writes_no_sel.c
+share/examples/hdf5-110/c/ph5example.c
+share/examples/hdf5-110/c/run-c-ex.sh
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_ds1.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_image1.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_image2.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_lite1.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_lite2.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_lite3.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_01.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_02.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_03.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_04.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_05.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_06.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_07.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_08.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_09.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_10.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_11.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/ex_table_12.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/image24pixel.txt
+${PLIST.hl}share/examples/hdf5-110/hl/c/image8.txt
+${PLIST.hl}share/examples/hdf5-110/hl/c/pal_rgb.h
+${PLIST.hl}share/examples/hdf5-110/hl/c/ptExampleFL.c
+${PLIST.hl}share/examples/hdf5-110/hl/c/run-hlc-ex.sh
+${PLIST.hl}share/examples/hdf5-110/hl/run-hl-ex.sh
+share/examples/hdf5-110/run-all-ex.sh
diff --git a/hdf5_110/TODO b/hdf5_110/TODO
new file mode 100644
index 0000000000..943ab88a63
--- /dev/null
+++ b/hdf5_110/TODO
@@ -0,0 +1,7 @@
+pkglint warnings like:
+
+WARN: PLIST:68: Redundant library found. The libtool library is in line 69.
+WARN: PLIST:71: Redundant library found. The libtool library is in line 69.
+WARN: PLIST:72: Redundant library found. The libtool library is in line 69.
+WARN: PLIST:73: Redundant library found. The libtool library is in line 69.
+
diff --git a/hdf5_110/buildlink3.mk b/hdf5_110/buildlink3.mk
new file mode 100644
index 0000000000..684c9e5b0a
--- /dev/null
+++ b/hdf5_110/buildlink3.mk
@@ -0,0 +1,22 @@
+# $NetBSD: buildlink3.mk,v 1.16 2021/06/07 11:52:48 adam Exp $
+
+BUILDLINK_TREE+= hdf5_110
+
+.if !defined(HDF5_110_BUILDLINK3_MK)
+HDF5_110_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.hdf5_110+= hdf5_110>=1.10.7
+BUILDLINK_ABI_DEPENDS.hdf5_110+= hdf5_110>=1.10.11
+BUILDLINK_PKGSRCDIR.hdf5_110?= ../../wip/hdf5_110
+
+pkgbase := hdf5_110
+.include "../../mk/pkg-build-options.mk"
+
+.if ${PKG_BUILD_OPTIONS.hdf5_110:Mszip}
+.include "../../archivers/libaec/buildlink3.mk"
+.endif
+
+.include "../../devel/zlib/buildlink3.mk"
+.endif # HDF5_110_BUILDLINK3_MK
+
+BUILDLINK_TREE+= -hdf5_110
diff --git a/hdf5_110/distinfo b/hdf5_110/distinfo
new file mode 100644
index 0000000000..0f51308009
--- /dev/null
+++ b/hdf5_110/distinfo
@@ -0,0 +1,8 @@
+$NetBSD: distinfo,v 1.49 2023/08/31 11:57:27 adam Exp $
+
+BLAKE2s (hdf5-1.10.11.tar.bz2) = 28bd067d2ddce9ce980556ccec39f28b5f26ba5882ee030aa9034d3b955a6d35
+SHA512 (hdf5-1.10.11.tar.bz2) = 883a46eb82e248fa47f114d92519c45964ee72298cb32aa63a82cebea0c4827c864a87f13475c9cd725bab44309a9c480bc9672ba8a344b8fc978e4579cd71b7
+Size (hdf5-1.10.11.tar.bz2) = 15286914 bytes
+SHA1 (patch-configure) = e7f141d54c39cbee2f7d703ab7d6ff582158904e
+SHA1 (patch-tools_test_h5dump_testh5dump.sh.in) = 97c70174d10e6e3671975cf3b09c74add27ce9c5
+SHA1 (patch-tools_test_h5repack_h5repack.sh.in) = 7e6f3ce52d4d282f341a93ff4c8231ec8c04a37c
diff --git a/hdf5_110/options.mk b/hdf5_110/options.mk
new file mode 100644
index 0000000000..1f2b30f2d1
--- /dev/null
+++ b/hdf5_110/options.mk
@@ -0,0 +1,28 @@
+# $NetBSD: options.mk,v 1.12 2023/12/18 15:53:27 thor Exp $
+
+PKG_OPTIONS_VAR= PKG_OPTIONS.hdf5_110
+PKG_SUPPORTED_OPTIONS= szip threads hdf5-unsafe-threads
+PKG_SUGGESTED_OPTIONS= szip
+
+.include "../../mk/bsd.options.mk"
+
+.if !empty(PKG_OPTIONS:Mszip)
+CONFIGURE_ARGS+= --with-szlib
+.include "../../archivers/libaec/buildlink3.mk"
+.endif
+
+# Threadsafe API is incompatible with high-level and C++ APIs.
+PLIST_VARS+= hl
+.if !empty(PKG_OPTIONS:Mthreads)
+CONFIGURE_ARGS+= --enable-threadsafe --disable-hl
+.include "../../mk/pthread.buildlink3.mk"
+.else
+PLIST.hl= yes
+.endif
+
+# You can still enable threads if you are adventurous. There
+# are scientists like that. Not supported, but possible.
+.if !empty(PKG_OPTIONS:Mhdf5-unsafe-threads)
+CONFIGURE_ARGS+= --enable-threadsafe --enable-unsupported
+.include "../../mk/pthread.buildlink3.mk"
+.endif
diff --git a/hdf5_110/patches/patch-configure b/hdf5_110/patches/patch-configure
new file mode 100644
index 0000000000..6cf9cbb303
--- /dev/null
+++ b/hdf5_110/patches/patch-configure
@@ -0,0 +1,14 @@
+$NetBSD: patch-configure,v 1.3 2015/11/26 11:25:10 adam Exp $
+
+Avoid reference to WRAPPER_BINDIR in final binaries.
+
+--- configure.orig 2015-11-10 14:01:10.000000000 +0000
++++ configure
+@@ -27779,7 +27779,6 @@ else
+ CC_VERSION="$CC";
+ for x in `echo $PATH | sed -e 's/:/ /g'`; do
+ if test -x $x/$CC_NOFLAGS; then
+- CC_VERSION="$x/$CC"
+ break
+ fi
+ done
diff --git a/hdf5_110/patches/patch-tools_test_h5dump_testh5dump.sh.in b/hdf5_110/patches/patch-tools_test_h5dump_testh5dump.sh.in
new file mode 100644
index 0000000000..f56e8fade0
--- /dev/null
+++ b/hdf5_110/patches/patch-tools_test_h5dump_testh5dump.sh.in
@@ -0,0 +1,20 @@
+$NetBSD: patch-tools_test_h5dump_testh5dump.sh.in,v 1.1 2022/11/06 17:00:56 adam Exp $
+
+Portability fix.
+
+--- tools/test/h5dump/testh5dump.sh.in.orig 2022-11-05 18:51:12.000000000 +0000
++++ tools/test/h5dump/testh5dump.sh.in
+@@ -883,11 +883,11 @@ TOOLTEST_FAIL() {
+ ) >&$actual
+ RET=$?
+ # Segfault occurred
+- if [ $RET == 139 ] ; then
++ if [ $RET = 139 ] ; then
+ nerrors="`expr $nerrors + 1`"
+ echo "*FAILED - test on $infile failed with segmentation fault"
+ # Should fail but didn't
+- elif [ $RET == 0 ] ; then
++ elif [ $RET = 0 ] ; then
+ nerrors="`expr $nerrors + 1`"
+ echo "*FAILED - test on $infile did not fail as expected"
+ else
diff --git a/hdf5_110/patches/patch-tools_test_h5repack_h5repack.sh.in b/hdf5_110/patches/patch-tools_test_h5repack_h5repack.sh.in
new file mode 100644
index 0000000000..906ca8e013
--- /dev/null
+++ b/hdf5_110/patches/patch-tools_test_h5repack_h5repack.sh.in
@@ -0,0 +1,24 @@
+$NetBSD: patch-tools_test_h5repack_h5repack.sh.in,v 1.3 2022/11/06 17:00:56 adam Exp $
+
+Portability fix.
+
+--- tools/test/h5repack/h5repack.sh.in.orig 2022-05-25 21:09:13.000000000 +0000
++++ tools/test/h5repack/h5repack.sh.in
+@@ -891,7 +891,7 @@ TOOLTEST_FAIL()
+ echo " FAILED"
+ echo " $failure"
+ else
+- if [ $RET == 0 ] ; then
++ if [ $RET = 0 ] ; then
+ nerrors="`expr $nerrors + 1`"
+ echo " FAILED"
+ else
+@@ -990,7 +990,7 @@ TOOLFAILSV()
+ $RUNSERIAL $H5DIFF_BIN -v $infile $outfile
+ ) >$actual 2>$actual_err
+ RET=$?
+- if [ $RET == 0 ] ; then
++ if [ $RET = 0 ] ; then
+ echo "*FAILED*"
+ nerrors="`expr $nerrors + 1`"
+ else
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