import hdf5-1.12.1-7.el9.1

.gitignore

@@ -0,0 +1,2 @@
+SOURCES/hdf5_1.12.0+repack-1~exp2.debian.tar.xz
+SOURCES/hdf5-1.12.1.tar.bz2

.hdf5.metadata

@@ -0,0 +1,2 @@
+0e304458d9a9b7524534f84a979cec9da2840722  SOURCES/hdf5_1.12.0+repack-1~exp2.debian.tar.xz
+665eed49a004f96f852887bb2b232dd7d3d8d8a0  SOURCES/hdf5-1.12.1.tar.bz2

SOURCES/h5comp

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+ARCH=$(uname -m)
+
+case $ARCH in
+    x86_64 | ppc64 | ia64 | s390x ) BITS=64;;
+                                * ) BITS=32;;
+esac
+
+exec $0-${BITS} "$@"

SOURCES/hdf5-LD_LIBRARY_PATH.patch

@@ -0,0 +1,20 @@
+--- hdf5-1.12.0/src/Makefile.am~	2020-02-29 00:29:58.000000000 +0100
++++ hdf5-1.12.0/src/Makefile.am	2021-02-26 16:10:03.612252484 +0100
+@@ -156,8 +156,6 @@
+ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
+ # is set to ignore the error.
+ H5Tinit.c: H5detect$(EXEEXT)
+-	LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) |                  \
+-		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
+ 	$(RUNSERIAL) ./H5detect$(EXEEXT)  $@  ||                               \
+ 	    (test $$HDF5_Make_Ignore && echo "*** Error ignored") ||          \
+ 	    ($(RM) $@ ; exit 1)
+@@ -168,8 +166,6 @@
+ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
+ # is set to ignore the error.
+ H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
+-	LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) |                  \
+-		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
+ 	$(RUNSERIAL) ./H5make_libsettings$(EXEEXT)  $@  ||                               \
+ 	    (test $$HDF5_Make_Ignore && echo "*** Error ignored") ||          \
+ 	    ($(RM) $@ ; exit 1)

SOURCES/hdf5-build.patch

@@ -0,0 +1,145 @@
+diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in
+index f29739a..fc9cddb 100644
+--- a/java/examples/datasets/JavaDatasetExample.sh.in
++++ b/java/examples/datasets/JavaDatasetExample.sh.in
+@@ -39,7 +39,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
+ BLDDIR="."
+ BLDLIBDIR="$BLDDIR/testlibs"
+ HDFTEST_HOME="$top_srcdir/java/examples/datasets"
+-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
++JARFILE=@PACKAGE_TARNAME@.jar
+ TESTJARFILE=jar@PACKAGE_TARNAME@datasets.jar
+ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
+ 
+diff --git a/java/examples/datasets/Makefile.am b/java/examples/datasets/Makefile.am
+index 41a914b..195201a 100644
+--- a/java/examples/datasets/Makefile.am
++++ b/java/examples/datasets/Makefile.am
+@@ -26,7 +26,7 @@ classes:
+ 	test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
+ 
+ pkgpath = examples/datasets
+-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
++hdfjarfile = $(PACKAGE_TARNAME).jar
+ CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
+ 
+ jarfile = jar$(PACKAGE_TARNAME)datasets.jar
+diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in
+index e26d8c0..f6a9d87 100644
+--- a/java/examples/datatypes/JavaDatatypeExample.sh.in
++++ b/java/examples/datatypes/JavaDatatypeExample.sh.in
+@@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
+ BLDDIR="."
+ BLDLIBDIR="$BLDDIR/testlibs"
+ HDFTEST_HOME="$top_srcdir/java/examples/datatypes"
+-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
++JARFILE=@PACKAGE_TARNAME@.jar
+ TESTJARFILE=jar@PACKAGE_TARNAME@datatypes.jar
+ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
+ 
+diff --git a/java/examples/datatypes/Makefile.am b/java/examples/datatypes/Makefile.am
+index 90790f7..450edef 100644
+--- a/java/examples/datatypes/Makefile.am
++++ b/java/examples/datatypes/Makefile.am
+@@ -26,7 +26,7 @@ classes:
+ 	test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
+ 
+ pkgpath = examples/datatypes
+-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
++hdfjarfile = $(PACKAGE_TARNAME).jar
+ CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
+ 
+ jarfile = jar$(PACKAGE_TARNAME)datatypes.jar
+diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in
+index 3b0e9d1..416c69f 100644
+--- a/java/examples/groups/JavaGroupExample.sh.in
++++ b/java/examples/groups/JavaGroupExample.sh.in
+@@ -37,7 +37,7 @@ BLDDIR="."
+ BLDLIBDIR="$BLDDIR/testlibs"
+ BLDITERDIR="./groups"
+ HDFTEST_HOME="$top_srcdir/java/examples/groups"
+-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
++JARFILE=@PACKAGE_TARNAME@.jar
+ TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar
+ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
+ test -d $BLDITERDIR || mkdir -p $BLDITERDIR
+diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am
+index bfde9ae..f48a5b9 100644
+--- a/java/examples/groups/Makefile.am
++++ b/java/examples/groups/Makefile.am
+@@ -26,7 +26,7 @@ classes:
+ 	test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
+ 
+ pkgpath = examples/groups
+-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
++hdfjarfile = $(PACKAGE_TARNAME).jar
+ CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
+ 
+ jarfile = jar$(PACKAGE_TARNAME)groups.jar
+diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in
+index db741e5..d0ba65d 100644
+--- a/java/examples/intro/JavaIntroExample.sh.in
++++ b/java/examples/intro/JavaIntroExample.sh.in
+@@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib"
+ BLDDIR="."
+ BLDLIBDIR="$BLDDIR/testlibs"
+ HDFTEST_HOME="$top_srcdir/java/examples/intro"
+-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
++JARFILE=@PACKAGE_TARNAME@.jar
+ TESTJARFILE=jar@PACKAGE_TARNAME@intro.jar
+ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
+ 
+diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am
+index 7d1aeab..01a10c9 100644
+--- a/java/examples/intro/Makefile.am
++++ b/java/examples/intro/Makefile.am
+@@ -26,7 +26,7 @@ classes:
+ 	test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
+ 
+ pkgpath = examples/intro
+-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
++hdfjarfile = $(PACKAGE_TARNAME).jar
+ CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
+ 
+ jarfile = jar$(PACKAGE_TARNAME)intro.jar
+diff --git a/java/src/Makefile.am b/java/src/Makefile.am
+index 98630e6..fd8d057 100644
+--- a/java/src/Makefile.am
++++ b/java/src/Makefile.am
+@@ -32,8 +32,8 @@ JAVAROOT = .classes
+ classes:
+ 	test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
+ 
+-jarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
+-hdf5_javadir = $(libdir)
++jarfile = $(PACKAGE_TARNAME).jar
++hdf5_javadir = $(prefix)/lib/java
+ 
+ pkgpath = hdf/hdf5lib
+ CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$CLASSPATH
+diff --git a/java/test/Makefile.am b/java/test/Makefile.am
+index 08e79e3..b336c2f 100644
+--- a/java/test/Makefile.am
++++ b/java/test/Makefile.am
+@@ -26,7 +26,7 @@ classes:
+ 	test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT)
+ 
+ pkgpath = test
+-hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
++hdfjarfile = $(PACKAGE_TARNAME).jar
+ CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
+ 
+ jarfile = jar$(PACKAGE_TARNAME)test.jar
+diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
+index 39db296..83d6c7c 100644
+--- a/java/test/junit.sh.in
++++ b/java/test/junit.sh.in
+@@ -47,7 +47,7 @@ BLDLIBDIR="$BLDDIR/testlibs"
+ HDFTEST_HOME="$top_srcdir/java/test"
+ TOOLS_TESTFILES="$top_srcdir/tools/testfiles"
+ 
+-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
++JARFILE=@PACKAGE_TARNAME@.jar
+ TESTJARFILE=jar@PACKAGE_TARNAME@test.jar
+ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
+ 

SOURCES/hdf5-gfortran12.patch

@@ -0,0 +1,37 @@
+commit 3ea6f8c17228d2629e419563138a6180bc4a5a6a
+Author: Orion Poplawski <orion@nwra.com>
+Date:   Sun Jan 30 15:21:08 2022 -0700
+
+    Mark minusone as a PARAMETER in tH5A_1_8.F90.
+
+diff --git a/fortran/test/tH5A_1_8.F90 b/fortran/test/tH5A_1_8.F90
+index 4e02c58a39..c2f8e9984a 100644
+--- a/fortran/test/tH5A_1_8.F90
++++ b/fortran/test/tH5A_1_8.F90
+@@ -776,7 +776,7 @@ SUBROUTINE test_attr_info_by_idx(new_format, fcpl, fapl, total_error)
+ 
+   INTEGER :: Input1
+   INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T
+-  INTEGER :: minusone = -1
++  INTEGER, PARAMETER :: minusone = -1
+   INTEGER(HSIZE_T) :: htmp
+ 
+   data_dims = 0
+@@ -1427,7 +1427,7 @@ SUBROUTINE test_attr_delete_by_idx(new_format, fcpl, fapl, total_error)
+   INTEGER :: u     !  Local index variable
+   INTEGER :: Input1
+   INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T
+-  INTEGER :: minusone = -1
++  INTEGER, PARAMETER :: minusone = -1
+ 
+   data_dims = 0
+ 
+@@ -2268,7 +2268,7 @@ SUBROUTINE test_attr_corder_create_basic( fcpl, fapl, total_error )
+   INTEGER :: error
+ 
+   INTEGER :: crt_order_flags
+-  INTEGER :: minusone = -1
++  INTEGER, PARAMETER :: minusone = -1
+ 
+   !  Output message about test being performed
+ !  WRITE(*,*) "     - Testing Basic Code for Attributes with Creation Order Info"

SOURCES/hdf5-wrappers.patch

@@ -0,0 +1,109 @@
+diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in
+--- hdf5-1.10.7/bin/h5cc.in.wrappers	2020-10-07 20:24:29.127283333 -0600
++++ hdf5-1.10.7/bin/h5cc.in	2020-10-07 20:27:05.289536904 -0600
+@@ -89,10 +89,10 @@ CLINKERBASE="@CC@"
+ # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
+ # from the hdf5 build. The order of the flags is intended to give precedence
+ # to the user's flags.
+-H5BLD_CFLAGS="@AM_CFLAGS@ @CFLAGS@"
++H5BLD_CFLAGS=
+ H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
+-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
+-H5BLD_LIBS="@LIBS@"
++H5BLD_LDFLAGS=
++H5BLD_LIBS=
+ 
+ CC="${HDF5_CC:-$CCBASE}"
+ CLINKER="${HDF5_CLINKER:-$CLINKERBASE}"
+@@ -105,7 +105,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
+ # available library is shared, it will be used by default.  The user can
+ # override either default, although choosing an unavailable library will result
+ # in link errors.
+-STATIC_AVAILABLE="@enable_static@"
++# Fedora prefers shared libraries
++STATIC_AVAILABLE=no
+ if test "${STATIC_AVAILABLE}" = "yes"; then
+   USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
+ else
+@@ -385,7 +386,7 @@ if test "x$do_link" = "xyes"; then
+   # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
+   # from the hdf5 build. The order of the flags is intended to give precedence
+   # to the user's flags.
+-  $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
++  $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args
+   status=$?
+ fi
+ 
+diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in
+--- hdf5-1.10.7/c++/src/h5c++.in.wrappers	2020-08-27 21:38:23.000000000 -0600
++++ hdf5-1.10.7/c++/src/h5c++.in	2020-10-07 20:24:29.126283325 -0600
+@@ -87,10 +87,10 @@ CXXLINKERBASE="@CXX@"
+ # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
+ # from the hdf5 build. The order of the flags is intended to give precedence
+ # to the user's flags.
+-H5BLD_CXXFLAGS="@AM_CXXFLAGS@ @CXXFLAGS@"
++H5BLD_CXXFLAGS=
+ H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
+-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
+-H5BLD_LIBS="@LIBS@"
++H5BLD_LDFLAGS=
++H5BLD_LIBS=
+ 
+ CXX="${HDF5_CXX:-$CXXBASE}"
+ CXXLINKER="${HDF5_CLINKER:-$CXXLINKERBASE}"
+@@ -103,7 +103,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
+ # available library is shared, it will be used by default.  The user can
+ # override either default, although choosing an unavailable library will result
+ # in link errors.
+-STATIC_AVAILABLE="@enable_static@"
++# Fedora prefers shared libraries
++STATIC_AVAILABLE=no
+ if test "${STATIC_AVAILABLE}" = "yes"; then
+   USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
+ else
+@@ -385,7 +386,7 @@ if test "x$do_link" = "xyes"; then
+   # from the hdf5 build. The order of the flags is intended to give precedence
+   # to the user's flags.
+ 
+-  $SHOW $CXXLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CXXFLAGS $CXXFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
++  $SHOW $CXXLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CXXFLAGS $CXXFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args
+ 
+   status=$?
+ fi
+diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.in
+--- hdf5-1.10.7/fortran/src/h5fc.in.wrappers	2020-08-27 21:38:23.000000000 -0600
++++ hdf5-1.10.7/fortran/src/h5fc.in	2020-10-07 20:25:53.793962985 -0600
+@@ -83,11 +83,11 @@ FLINKERBASE="@FC@"
+ # libraries in $link_args, followed by any external library paths and libraries
+ # from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build.
+ # The order of the flags is intended to give precedence to the user's flags.
+-H5BLD_FCFLAGS="@AM_FCFLAGS@ @FCFLAGS@"
++H5BLD_FCFLAGS=
+ F9XMODFLAG="@F9XMODFLAG@"
+ F9XSUFFIXFLAG="@F9XSUFFIXFLAG@"
+-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
+-H5BLD_LIBS="@LIBS@"
++H5BLD_LDFLAGS=
++H5BLD_LIBS=
+ 
+ FC="${HDF5_FC:-$FCBASE}"
+ FLINKER="${HDF5_FLINKER:-$FLINKERBASE}"
+@@ -99,7 +99,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}"
+ # available library is shared, it will be used by default.  The user can
+ # override either default, although choosing an unavailable library will result
+ # in link errors.
+-STATIC_AVAILABLE="@enable_static@"
++# Fedora prefers shared libraries
++STATIC_AVAILABLE=no
+ if test "${STATIC_AVAILABLE}" = "yes"; then
+   USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}"
+ else
+@@ -363,7 +364,7 @@ if test "x$do_link" = "xyes"; then
+   # libraries in $link_args, followed by any external library paths and libraries
+   # from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build.
+   # The order of the flags is intended to give precedence to the user's flags.
+-  $SHOW $FLINKER $FCFLAGS $H5BLD_FCFLAGS $F9XSUFFIXFLAG $LDFLAGS $fmodules $link_objs $LIBS $link_args $shared_link
++  $SHOW $FLINKER $FCFLAGS $H5BLD_FCFLAGS $F9XSUFFIXFLAG $LDFLAGS $fmodules $link_objs $LIBS $link_args
+   status=$?
+ fi
+