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Accepting request 142035 from devel:libraries:c_c++

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- Update to 1.8.10, changes documented here:
  http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
- remove hdf5-ph5diff.patch (fixed by upstream)
- add hdf5-fix_printf.patch (forwarded request 142034 from rudi_m)

OBS-URL: https://build.opensuse.org/request/show/142035
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/hdf5?expand=0&rev=10
This commit is contained in:
Stephan Kulow 2012-11-21 16:00:51 +00:00 committed by Git OBS Bridge
parent 151f2f8746
commit c08d405a85
10 changed files with 75 additions and 114 deletions
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10
hdf5-1.8.10-tests-arm.patch Normal file
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@ -0,0 +1,10 @@
--- ./test/testhdf5.c.orig 2012-05-09 17:05:49.000000000 +0200
+++ ./test/testhdf5.c 2012-06-20 19:22:33.332532223 +0200
@@ -57,7 +57,6 @@ main(int argc, char *argv[])
AddTest("coords", test_coords, cleanup_coords, "Dataspace coordinates", NULL);
AddTest("sohm", test_sohm, cleanup_sohm, "Shared Object Header Messages", NULL);
AddTest("attr", test_attr, cleanup_attr, "Attributes", NULL);
- AddTest("select", test_select, cleanup_select, "Selections", NULL);
AddTest("time", test_time, cleanup_time, "Time Datatypes", NULL);
AddTest("reference", test_reference, cleanup_reference, "References", NULL);
AddTest("vltypes", test_vltypes, cleanup_vltypes, "Variable-Length Datatypes", NULL);

3
hdf5-1.8.10.tar.bz2 Normal file
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@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:fa6e6b37b7976edac860732b87c50370e3beba3ae784d05f16f298c033a45a44
size 6024645

47
hdf5-1.8.9-tests-arm.patch
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@ -1,47 +0,0 @@
--- ./test/testhdf5.c.orig 2012-05-09 17:05:49.000000000 +0200
+++ ./test/testhdf5.c 2012-06-20 19:22:33.332532223 +0200
@@ -57,7 +57,6 @@ main(int argc, char *argv[])
AddTest("coords", test_coords, cleanup_coords, "Dataspace coordinates", NULL);
AddTest("sohm", test_sohm, cleanup_sohm, "Shared Object Header Messages", NULL);
AddTest("attr", test_attr, cleanup_attr, "Attributes", NULL);
- AddTest("select", test_select, cleanup_select, "Selections", NULL);
AddTest("time", test_time, cleanup_time, "Time Datatypes", NULL);
AddTest("reference", test_reference, cleanup_reference, "References", NULL);
AddTest("vltypes", test_vltypes, cleanup_vltypes, "Variable-Length Datatypes", NULL);
--- ./test/big.c.orig 2012-05-09 17:05:49.000000000 +0200
+++ ./test/big.c 2012-06-22 11:26:13.954168044 +0200
@@ -793,7 +793,7 @@ main (int ac, char **av)
if (testvfd(SEC2_VFD) != 0)
goto error;
if (testvfd(STDIO_VFD) != 0)
- goto error;
+ HDfprintf(stderr, "Test for stdio fails on arm as expected.\n");
/* End with normal exit code */
return 0;
--- test/Makefile.am.orig 2012-05-09 17:05:49.000000000 +0200
+++ test/Makefile.am 2012-06-22 11:27:02.944607103 +0200
@@ -41,8 +41,8 @@ TEST_PROG=testhdf5 lheap ohdr stab gheap
dtypes dsets cmpd_dset filter_fail extend external efc objcopy links unlink \
big mtime fillval mount flush1 flush2 app_ref enum \
set_extent ttsafe \
- getname vfd ntypes dangle dtransform reserved cross_read \
- freespace mf btree2 fheap file_image
+ getname ntypes dangle dtransform reserved cross_read \
+ freespace mf btree2 fheap
# List programs to be built when testing here. error_test and err_compat are
# built at the same time as the other tests, but executed by testerror.sh.
--- test/Makefile.in.orig 2012-05-09 17:07:36.000000000 +0200
+++ test/Makefile.in 2012-06-22 11:26:54.270883504 +0200
@@ -769,8 +769,8 @@ TEST_PROG = testhdf5 lheap ohdr stab ghe
dtypes dsets cmpd_dset filter_fail extend external efc objcopy links unlink \
big mtime fillval mount flush1 flush2 app_ref enum \
set_extent ttsafe \
- getname vfd ntypes dangle dtransform reserved cross_read \
- freespace mf btree2 fheap file_image
+ getname ntypes dangle dtransform reserved cross_read \
+ freespace mf btree2 fheap
# These programs generate test files for the tests. They don't need to be

3
hdf5-1.8.9.tar.bz2
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:fafe54856b00f0d6531629f66e2c476ab6ee03458803088f270bbfc4a60966c7
size 6006715

23
hdf5-LD_LIBRARY_PATH.patch
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@ -1,19 +1,18 @@
diff -up hdf5-1.8.8/configure.LD_LIBRARY_PATH hdf5-1.8.8/configure --- hdf5-1.8.10/configure.orig 2012-10-27 02:14:59.000000000 +0200
--- hdf5-1.8.8/configure.LD_LIBRARY_PATH 2011-11-16 11:21:54.511269486 -0700 +++ hdf5-1.8.10/configure 2012-11-18 14:17:44.572966644 +0100
+++ hdf5-1.8.8/configure 2011-11-16 11:28:18.673392600 -0700 @@ -27496,9 +27496,6 @@ if ${hdf5_cv_printf_ll+:} false; then :
@@ -26746,8 +26746,6 @@ $as_echo_n "checking how to print long l
if ${hdf5_cv_printf_ll+:} false; then :
$as_echo_n "(cached) " >&6 $as_echo_n "(cached) " >&6
else else
- LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
-export LD_LIBRARY_PATH
-LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
-export LD_LIBRARY_PATH
-
for hdf5_cv_printf_ll in l ll L q unknown; do for hdf5_cv_printf_ll in l ll L q unknown; do
if test "$cross_compiling" = yes; then : if test "$cross_compiling" = yes; then :
diff -up hdf5-1.8.8/src/Makefile.in.LD_LIBRARY_PATH hdf5-1.8.8/src/Makefile.in continue
--- hdf5-1.8.8/src/Makefile.in.LD_LIBRARY_PATH 2011-11-15 08:13:54.000000000 -0700 --- hdf5-1.8.10/src/Makefile.in.orig 2012-10-27 02:14:55.000000000 +0200
+++ hdf5-1.8.8/src/Makefile.in 2011-11-16 11:43:42.938914069 -0700 +++ hdf5-1.8.10/src/Makefile.in 2012-11-17 11:11:17.755746326 +0100
@@ -1267,8 +1267,6 @@ help: @@ -1327,8 +1327,6 @@ help:
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error. # is set to ignore the error.
H5Tinit.c: H5detect$(EXEEXT) H5Tinit.c: H5detect$(EXEEXT)
@ -22,7 +21,7 @@ diff -up hdf5-1.8.8/src/Makefile.in.LD_LIBRARY_PATH hdf5-1.8.8/src/Makefile.in
$(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \ $(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \ (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1) ($(RM) $@ ; exit 1)
@@ -1279,8 +1277,6 @@ H5Tinit.c: H5detect$(EXEEXT) @@ -1339,8 +1337,6 @@ H5Tinit.c: H5detect$(EXEEXT)
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error. # is set to ignore the error.
H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings

11
hdf5-fix_printf.patch Normal file
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@ -0,0 +1,11 @@
--- test/testhdf5.h.orig 2012-10-11 19:30:43.000000000 +0200
+++ test/testhdf5.h 2012-11-19 12:34:25.021980147 +0100
@@ -142,7 +142,7 @@
if(VERBOSE_HI) \
print_func(" Call to routine: %15s at line %4d in %s returned " \
"invalid result\n", where, (int)__LINE__, __FILE__); \
- TestErrPrintf("*** UNEXPECTED RESULT from %s at line %4d in %s\n" \
+ TestErrPrintf("*** UNEXPECTED RESULT from %s at line %4d in %s\n", \
where, (int)__LINE__, __FILE__); \
} while(0)

26
hdf5-non_void_return.patch
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@ -1,15 +1,3 @@
Index: hl/src/H5LTanalyze.l
===================================================================
--- hl/src/H5LTanalyze.l.orig 2011-11-27 14:19:17.000000000 +0100
+++ hl/src/H5LTanalyze.l 2011-11-27 14:20:12.619164660 +0100
@@ -184,6 +184,7 @@ int my_yyinput(char *buf, int max_size)
int H5LTyyerror(char *msg)
{
printf("ERROR: %s before \"%s\".\n", msg, yytext);
+ return (0); // return from non void fix
}
int yywrap()
Index: test/dt_arith.c Index: test/dt_arith.c
=================================================================== ===================================================================
--- test/dt_arith.c.orig 2011-11-27 14:22:13.000000000 +0100 --- test/dt_arith.c.orig 2011-11-27 14:22:13.000000000 +0100
@ -34,20 +22,6 @@ Index: tools/h5diff/h5diff_common.c
} }
Index: hl/src/H5LTanalyze.c
===================================================================
--- hl/src/H5LTanalyze.c.orig 2011-11-07 23:11:38.000000000 +0100
+++ hl/src/H5LTanalyze.c 2011-11-27 21:59:27.188216404 +0100
@@ -2332,6 +2332,9 @@ int my_yyinput(char *buf, int max_size)
int H5LTyyerror(char *msg)
{
printf("ERROR: %s before \"%s\".\n", msg, yytext);
+ return (0); // return from non void fix. Fix is already applied at lexer
+ // file but i will not re-generate this file as it looks it is changed
+ // by hand ...
}
int yywrap()
--- test/filter_fail.c.orig 2012-05-09 17:05:49.000000000 +0200 --- test/filter_fail.c.orig 2012-05-09 17:05:49.000000000 +0200
+++ test/filter_fail.c 2012-06-22 09:03:42.885161176 +0200 +++ test/filter_fail.c 2012-06-22 09:03:42.885161176 +0200
@@ -408,4 +408,5 @@ error: @@ -408,4 +408,5 @@ error:

12
hdf5-ph5diff.patch
View File

@ -1,12 +0,0 @@
diff -up hdf5-1.8.8/tools/lib/h5diff.c.ph5diff hdf5-1.8.8/tools/lib/h5diff.c
--- hdf5-1.8.8/tools/lib/h5diff.c.ph5diff 2011-11-07 15:11:35.000000000 -0700
+++ hdf5-1.8.8/tools/lib/h5diff.c 2012-02-09 12:14:59.788422152 -0700
@@ -1391,7 +1391,7 @@ hsize_t diff_match(hid_t file1_id, const
options->not_cmp = options->not_cmp | nFoundbyWorker.not_cmp;
busyTasks--;
} /* end if */
- else if(Status.MPI_TAG == MPI_TAG_TOK_RETURN)
+ else if(Status.MPI_TAG == MPI_TAG_DONE)
{
MPI_Recv(&nFoundbyWorker, sizeof(nFoundbyWorker), MPI_BYTE, Status.MPI_SOURCE, MPI_TAG_DONE, MPI_COMM_WORLD, &Status);
nfound += nFoundbyWorker.nfound;

14
hdf5.changes
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@ -1,3 +1,17 @@
-------------------------------------------------------------------
Sun Nov 18 12:31:34 UTC 2012 - sweet_f_a@gmx.de
- Update to 1.8.10, changes documented here:
http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
- remove hdf5-ph5diff.patch (fixed by upstream)
- add hdf5-fix_printf.patch
-------------------------------------------------------------------
Fri Nov 16 16:23:18 UTC 2012 - sweet_f_a@gmx.de
- cosmetics, enable parallel build for suse only
- fix build for old findutils
------------------------------------------------------------------- -------------------------------------------------------------------
Mon Nov 5 12:31:22 UTC 2012 - coolo@suse.com Mon Nov 5 12:31:22 UTC 2012 - coolo@suse.com

40
hdf5.spec
View File

@ -20,13 +20,17 @@
%define libname libhdf5 %define libname libhdf5
%if 0%{?sles_version} %if 0%{?sles_version}
%define _mpi openmpi mvapich2 %define _mvapich2 1
%else %endif
%define _mpi openmpi %if 0%{?suse_version}
%define _openmpi 1
%endif %endif
%define _mpi %{?_openmpi:openmpi} %{?_mvapich2:mvapich2}
Name: hdf5 Name: hdf5
Version: 1.8.9 Version: 1.8.10
Release: 0 Release: 0
Summary: A general purpose library and file format for storing scientific data Summary: A general purpose library and file format for storing scientific data
License: BSD-3-Clause License: BSD-3-Clause
@ -35,10 +39,10 @@ Url: http://www.hdfgroup.org/HDF5/
Source0: http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-%{version}%{?snaprel}.tar.bz2 Source0: http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-%{version}%{?snaprel}.tar.bz2
Patch0: hdf5-LD_LIBRARY_PATH.patch Patch0: hdf5-LD_LIBRARY_PATH.patch
Patch1: hdf5-non_void_return.patch Patch1: hdf5-non_void_return.patch
# Fix typo bug in parallel h5diff (fixed in 1.9.x) # fix broken printf call, sent upstream
Patch3: hdf5-ph5diff.patch Patch2: hdf5-fix_printf.patch
%ifarch %arm %ifarch %arm
Patch4: hdf5-1.8.9-tests-arm.patch Patch4: hdf5-1.8.10-tests-arm.patch
%endif %endif
BuildRoot: %{_tmppath}/%{name}-%{version}-build BuildRoot: %{_tmppath}/%{name}-%{version}-build
BuildRequires: gcc-c++ BuildRequires: gcc-c++
@ -51,8 +55,10 @@ BuildRequires: zlib-devel
%if 0%{?suse_version} >= 1110 %if 0%{?suse_version} >= 1110
BuildRequires: fdupes BuildRequires: fdupes
%endif %endif
%if 0%{?_openmpi}
BuildRequires: openmpi-devel BuildRequires: openmpi-devel
%if 0%{?sles_version} %endif
%if 0%{?_mvapich2}
BuildRequires: mvapich2-devel BuildRequires: mvapich2-devel
%endif %endif
@ -129,6 +135,7 @@ Requires: %{libname}_hl%{hdf5_libver} = %{version}
Examples of HDF5 library use. Examples of HDF5 library use.
%if 0%{?_openmpi}
%package -n %{name}-openmpi %package -n %{name}-openmpi
Summary: A general purpose library and file format for storing scientific data Summary: A general purpose library and file format for storing scientific data
Group: Development/Libraries/Other Group: Development/Libraries/Other
@ -195,9 +202,9 @@ I/O libraries and tools for analyzing, visualizing, and converting
scientific data. scientific data.
This package provides the static libraries. This package provides the static libraries.
%endif
%if 0%{?_mvapich2}
%if 0%{?sles_version}
%package -n %{name}-mvapich2 %package -n %{name}-mvapich2
Summary: A general purpose library and file format for storing scientific data Summary: A general purpose library and file format for storing scientific data
Group: Development/Libraries/Other Group: Development/Libraries/Other
@ -270,11 +277,12 @@ This package provides the static libraries.
%setup -q %setup -q
%patch0 -p1 -b .LD_LIBRARY_PATH %patch0 -p1 -b .LD_LIBRARY_PATH
%patch1 -p0 -b .non_void_return %patch1 -p0 -b .non_void_return
%patch3 -p1 -b .ph5diff %patch2 -p0 -b .fix_printf
%ifarch %arm %ifarch %arm
%patch4 -p0 -b .tests-arm %patch4 -p0 -b .tests-arm
%endif %endif
echo "prepare parallel builds: %_mpi"
for build_dir in build %_mpi; do for build_dir in build %_mpi; do
mkdir $build_dir mkdir $build_dir
ln -s ../configure $build_dir ln -s ../configure $build_dir
@ -337,7 +345,7 @@ for build_dir in %_mpi build; do
make install DESTDIR="%buildroot" -C "$build_dir" make install DESTDIR="%buildroot" -C "$build_dir"
done done
find "%buildroot/%_libdir" -type f -name "*.la" -delete find "%buildroot/%_libdir" -type f -name "*.la" | xargs rm -f
find %{buildroot}%{_datadir}/hdf5_examples -type f \ find %{buildroot}%{_datadir}/hdf5_examples -type f \
| grep -v ".sh$" | xargs chmod 644 | grep -v ".sh$" | xargs chmod 644
# delete examples from parallel builds # delete examples from parallel builds
@ -375,6 +383,7 @@ done
%postun -n %{libname}_hl%{hdf5_libver} -p /sbin/ldconfig %postun -n %{libname}_hl%{hdf5_libver} -p /sbin/ldconfig
%if 0%{?_openmpi}
%post -n %{libname}-%{hdf5_libver}-openmpi -p /sbin/ldconfig %post -n %{libname}-%{hdf5_libver}-openmpi -p /sbin/ldconfig
%postun -n %{libname}-%{hdf5_libver}-openmpi -p /sbin/ldconfig %postun -n %{libname}-%{hdf5_libver}-openmpi -p /sbin/ldconfig
@ -382,8 +391,9 @@ done
%post -n %{libname}_hl%{hdf5_libver}-openmpi -p /sbin/ldconfig %post -n %{libname}_hl%{hdf5_libver}-openmpi -p /sbin/ldconfig
%postun -n %{libname}_hl%{hdf5_libver}-openmpi -p /sbin/ldconfig %postun -n %{libname}_hl%{hdf5_libver}-openmpi -p /sbin/ldconfig
%endif
%if 0%{?sles_version} %if 0%{?_mvapich2}
%post -n %{libname}-%{hdf5_libver}-mvapich2 -p /sbin/ldconfig %post -n %{libname}-%{hdf5_libver}-mvapich2 -p /sbin/ldconfig
%postun -n %{libname}-%{hdf5_libver}-mvapich2 -p /sbin/ldconfig %postun -n %{libname}-%{hdf5_libver}-mvapich2 -p /sbin/ldconfig
@ -454,6 +464,7 @@ done
%defattr(-,root,root) %defattr(-,root,root)
%{_datadir}/hdf5_examples %{_datadir}/hdf5_examples
%if 0%{?_openmpi}
%files -n %{name}-openmpi %files -n %{name}-openmpi
%defattr(-,root,root) %defattr(-,root,root)
%doc COPYING MANIFEST README.txt release_docs/RELEASE.txt %doc COPYING MANIFEST README.txt release_docs/RELEASE.txt
@ -508,8 +519,9 @@ done
%files openmpi-devel-static %files openmpi-devel-static
%defattr(-,root,root) %defattr(-,root,root)
%{_libdir}/mpi/gcc/openmpi/%_lib/*.a %{_libdir}/mpi/gcc/openmpi/%_lib/*.a
%endif
%if 0%{?sles_version} %if 0%{?_mvapich2}
%files -n %{name}-mvapich2 %files -n %{name}-mvapich2
%defattr(-,root,root) %defattr(-,root,root)
%doc COPYING MANIFEST README.txt release_docs/RELEASE.txt %doc COPYING MANIFEST README.txt release_docs/RELEASE.txt