pool/hdf5
SHA256
3
0
Fork 1
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Accepting request 107061 from devel:libraries:c_c++

Browse Source 
Fixed the rpmlint warning for the license. Changed from BSD to BSD-3-Clause.

OBS-URL: https://build.opensuse.org/request/show/107061
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/hdf5?expand=0&rev=1
This commit is contained in:
Stephan Kulow 2012-03-09 20:23:35 +00:00 committed by Git OBS Bridge
commit 70208ce99f
8 changed files with 587 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

23
.gitattributes vendored Normal file
View File

@ -0,0 +1,23 @@
## Default LFS
*.7z filter=lfs diff=lfs merge=lfs -text
*.bsp filter=lfs diff=lfs merge=lfs -text
*.bz2 filter=lfs diff=lfs merge=lfs -text
*.gem filter=lfs diff=lfs merge=lfs -text
*.gz filter=lfs diff=lfs merge=lfs -text
*.jar filter=lfs diff=lfs merge=lfs -text
*.lz filter=lfs diff=lfs merge=lfs -text
*.lzma filter=lfs diff=lfs merge=lfs -text
*.obscpio filter=lfs diff=lfs merge=lfs -text
*.oxt filter=lfs diff=lfs merge=lfs -text
*.pdf filter=lfs diff=lfs merge=lfs -text
*.png filter=lfs diff=lfs merge=lfs -text
*.rpm filter=lfs diff=lfs merge=lfs -text
*.tbz filter=lfs diff=lfs merge=lfs -text
*.tbz2 filter=lfs diff=lfs merge=lfs -text
*.tgz filter=lfs diff=lfs merge=lfs -text
*.ttf filter=lfs diff=lfs merge=lfs -text
*.txz filter=lfs diff=lfs merge=lfs -text
*.whl filter=lfs diff=lfs merge=lfs -text
*.xz filter=lfs diff=lfs merge=lfs -text
*.zip filter=lfs diff=lfs merge=lfs -text
*.zst filter=lfs diff=lfs merge=lfs -text

1
.gitignore vendored Normal file
View File

@ -0,0 +1 @@
.osc

10
h5comp Normal file
View File

@ -0,0 +1,10 @@
#!/bin/bash
ARCH=$(uname -m)
case $ARCH in
x86_64 | ppc64 | ia64 | s390 ) BITS=64;;
* ) BITS=32;;
esac
exec $0-${BITS} "$@"

3
hdf5-1.8.8.tar.bz2 Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:b0ebb0b5478c6c0427631d4ad08f96e39f1b09fde615aa98d2a1b8fb7f6dced3
size 5827394

33
hdf5-LD_LIBRARY_PATH.patch Normal file
View File

@ -0,0 +1,33 @@
diff -up hdf5-1.8.8/configure.LD_LIBRARY_PATH hdf5-1.8.8/configure
--- hdf5-1.8.8/configure.LD_LIBRARY_PATH 2011-11-16 11:21:54.511269486 -0700
+++ hdf5-1.8.8/configure 2011-11-16 11:28:18.673392600 -0700
@@ -26746,8 +26746,6 @@ $as_echo_n "checking how to print long l
if ${hdf5_cv_printf_ll+:} false; then :
$as_echo_n "(cached) " >&6
else
- LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
-export LD_LIBRARY_PATH
for hdf5_cv_printf_ll in l ll L q unknown; do
if test "$cross_compiling" = yes; then :
diff -up hdf5-1.8.8/src/Makefile.in.LD_LIBRARY_PATH hdf5-1.8.8/src/Makefile.in
--- hdf5-1.8.8/src/Makefile.in.LD_LIBRARY_PATH 2011-11-15 08:13:54.000000000 -0700
+++ hdf5-1.8.8/src/Makefile.in 2011-11-16 11:43:42.938914069 -0700
@@ -1267,8 +1267,6 @@ help:
# 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) $@ ; exit 1)
@@ -1279,8 +1277,6 @@ H5Tinit.c: H5detect$(EXEEXT)
# 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)

50
hdf5-non_void_return.patch Normal file
View File

@ -0,0 +1,50 @@
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
===================================================================
--- test/dt_arith.c.orig 2011-11-27 14:22:13.000000000 +0100
+++ test/dt_arith.c 2011-11-27 14:22:21.908435252 +0100
@@ -3470,6 +3470,7 @@ error:
else if(run_test==TEST_DENORM || run_test==TEST_SPECIAL)
return 1;
#endif
+ return 1; // return from non void fix
}
Index: tools/h5diff/h5diff_common.c
===================================================================
--- tools/h5diff/h5diff_common.c.orig 2011-11-07 23:11:35.000000000 +0100
+++ tools/h5diff/h5diff_common.c 2011-11-27 14:23:49.105943847 +0100
@@ -69,6 +69,7 @@ static check_options(diff_opt_t* options
printf("Try '-h' or '--help' option for more information or see the %s entry in the 'HDF5 Reference Manual'.\n", PROGRAMNAME);
h5diff_exit(EXIT_FAILURE);
}
+ return (0); // no return in non void function fix
}
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()

250
hdf5.changes Normal file
View File

@ -0,0 +1,250 @@
-------------------------------------------------------------------
Sun Feb 19 04:46:42 UTC 2012 - ocefpaf@gmail.com
- Removed "Fixup headers and scripts for multiarch".
-------------------------------------------------------------------
Wed Nov 30 09:02:37 UTC 2011 - jengelh@medozas.de
- Remove redundant/unwanted tags/section (cf. specfile guidelines)
- Use %_smp_mflags for parallel building
- Accurate rpmgroup selection for shared library packages
-------------------------------------------------------------------
Tue Nov 29 20:05:19 UTC 2011 - ocefpaf@gmail.com
- un-commented --with-pthread and --with-ssl.
-------------------------------------------------------------------
Mon Nov 28 14:34:24 UTC 2011 - ocefpaf@gmail.com
- Update to 1.8.8
* Add patch to avoid setting LD_LIBRARY_PATH
* Add patch hdf5-non_void_return.patch
* Fixed non_void_return (thanks to Boris Manojlovic).
* Drop tstlite patch
* drop ppc64 longdouble patch, not required anymore
* Catch up with some Fedora modifications
- Add rpm macro %%{_hdf5_version} for convenience
* No Fortran modules for opensuse < 11.4 (Do not pass make check)
New Features
============
Configuration
-------------
- Added the --enable-fortran2003 flag to enable Fortran2003 support
in the HDF5 Fortran library. The flag should be used along with the
--enable-fortran flag and takes affect only when the Fortran compiler
is Fortran2003 compliant. (EIP - 2011/11/14)
- Added checks for clock_gettime and mach/mach_time.h to both configure and
CMake. This will support the move from gettimeofday to clock_gettime's
monotonic timer in the profiling code in a future release.
(DER - 2011/10/12)
Library
-------
- The Windows VFD code has been removed with the exception of the functions
which set it (H5Pset_fapl_windows, for example). Setting the Windows
VFD now really sets the SEC2 VFD. The WINDOWS_MAX_BUF and
WINDOWS_USE_STDIO configuration options and #defines have also been
removed. NOTE: Since the Windows VFD was a clone of the SEC2 VFD, this
change should be transparent to users.
(DER - 2011/10/12 - HDFFV-7740, HDFFV-7744)
- H5Tcreate now supports the string type (fixed-length and variable-
length). (SLU - 2011/05/20)
Parallel Library
----------------
- Added new H5Pget_mpio_actual_chunk_opt_mode and
H5Pget_mpio_actual_io_mode API routines for querying whether/how
a collective I/O operation completed. (QAK - 2011/10/12)
Tools
-----
- None
High-Level APIs
---------------
- Added the following Fortran wrappers for the Dimension Scale APIs:
h5dsset_scale_f
h5dsattach_scale_f
h5dsdetach_scale_f
h5dsis_attached_f
h5dsis_scale_f
h5dsset_label_f
h5dsget_label_f
h5dsget_scale_name_f
h5dsget_num_scales_f
(EIP for SB - 2011/10/13 - HDFFV-3797)
Fortran API
-----------
- The HDF5 Fortran library was enhanced to support the Fortran 2003 standard.
The following features are available when the HDF5 library is configured
using the --enable-fortran and --enable-fortran2003 configure flags AND
if the Fortran compiler is Fortran 2003 compliant:
- Subroutines overloaded with the C_PTR derived type:
h5pget_f
h5pget_fill_value_f
h5pinsert_f
h5pregister_f
h5pset_f
h5pset_fill_value_f
h5rcreate_f
h5rderefrence_f
h5rget_name_f
h5rget_obj_type_f
- Subroutines overloaded with the C_PTR derived type
and simplified signatures:
h5aread_f
h5awrite_f
h5dread_f
h5dwrite_f
- New subroutines
h5dvlen_reclaim_f
h5literate_by_name_f
h5literate_f
h5ovisit_f
h5tconvert_f
h5pset_nbit_f
h5pset_scaleoffset_f
- Subroutines with additional optional parameters:
h5pcreate_class_f
(EIP - 2011/10/14)
C++ API
-------
- None
-------------------------------------------------------------------
Thu Jun 2 20:39:35 UTC 2011 - ocefpaf@yahoo.com.br
- uncomment make check
-------------------------------------------------------------------
Tue May 24 14:37:23 UTC 2011 - pgajdos@novell.com
- updated to 1.8.7
-------------------------------------------------------------------
Fri Apr 29 16:11:29 CEST 2011 - pth@suse.de
- undrop package.
- Do type-punning using unions to be able to compile without
-fno-strict-aliasing.
- Don't use macros in patch names.
- Use _cv_ in variables to be cached by configure.
-------------------------------------------------------------------
Thu May 7 19:40:59 CEST 2009 - pgajdos@suse.cz
- fixed build with new gcc, see [bnc#501751]
-------------------------------------------------------------------
Mon Mar 2 17:00:47 CET 2009 - crrodriguez@suse.de
- save 9MB removing static libraries
-------------------------------------------------------------------
Tue Jan 13 11:41:28 CET 2009 - pgajdos@suse.cz
- updated to 1.8.2:
- Upgraded libtool to version 2.2.6a. (MAM - 2008/10/15).
- Added two new public routines: H5Pget_elink_fapl() and
H5Pset_elink_fapl(). (see bug #1247) (VC - 2008/10/13)
- Improved free space tracking in file to be faster. (QAK - 2008/10/06)
- Added 'mounted' field to H5G_info_t struct. (QAK - 2008/07/15)
- h5repack: added new options -u and -b to add a userblock to an HDF5
file during the repack. (PVN - 2008/08/26)
- h5repack: added options -t and -a to call H5Pset_alignment while
creating a repacked file. (PVN - 2008/08/29)
- h5ls: added capability to traverse through external links when the -r
(recursive) flag is given. (NAF - 2008/09/16)
- h5ls: added -E option to enable traversal of external links.
h5ls will not traverse external links without this flag being set.
(NAF - 2008/10/06)
- h5dump: when -b flag is used without a keyword after it, binary
output defaults to NATIVE. MEMORY keyword was deprecated
and replaced by NATIVE keyword. (PVN - 2008/10/30)
- h5diff: returns 1 when file graphs differ by any object.
Error return code was changed to 2 from -1. (PVN - 2008/10/30)
- h5import: TEXTFPE (scientific format) was deprecated. Use TEXTFP
instead (PVN - 2008/10/30)
- Added optional parameter 'mounted' to H5Gget_info_f,
H5Gget_info_by_idx_f, H5Gget_info_by_name_f (MSB - 2008/09/24)
- Added H5Tget_native_type_f (MSB - 2008/09/30)
- These member functions were added as wrapper for H5Rdereference to
replace the incorrect IdComponent::dereference().
void H5Object::dereference(H5Object& obj, void* ref,
H5R_type_t ref_type=H5R_OBJECT)
void H5Object::dereference(H5File& h5file, void* ref,
H5R_type_t ref_type=H5R_OBJECT)
void H5Object::dereference(Attribute& obj, void* ref,
H5R_type_t ref_type=H5R_OBJECT)
In addition, these constructors were added to create the associated
objects by way of dereference:
DataSet(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataSet(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataSet(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
Group(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
Group(H5File& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
Group(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataType(H5Object& obj, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataType(H5File& file, void* ref, H5R_type_t ref_type=H5R_OBJECT)
DataType(Attribute& attr, void* ref, H5R_type_t ref_type=H5R_OBJECT)
(BMR - 2008/10/29)
- removed destdir.patch
-------------------------------------------------------------------
Mon Jan 12 11:13:33 CET 2009 - pgajdos@suse.cz
- fortran modules builds from now [bnc#457593]
-------------------------------------------------------------------
Tue Nov 11 11:49:54 CET 2008 - pgajdos@suse.cz
- fixing build of fortran interface moved to the future
-------------------------------------------------------------------
Wed Jul 2 10:45:51 CEST 2008 - pgajdos@suse.cz
- updated to 1.8.1 [bnc#401626]
* Enhanced group object management
* Enhanced attribute management and more efficient meta data handling
* Expanded datatype features
* Creation order tracking and indexing
* Improved meta data caching and cache control
* UTF-8 encoding
* New I/O filters: n-bit and scale+offset compression
* New link (H5L) and object (H5O) interfaces and features
* External and user-defined links
* New high-level APIs:
HDF5 Packet Table (H5PT) and HDF5 Dimension Scale (H5DS)
* C++ and Fortran interfaces for older high-level APIs:
H5Lite (H5LT), H5Image (H5IM), and H5Table (H5TB)
* New and improved tools
- removed doc package (doc/html no longer provided with package)
- octave builds againist 1.6 compatibility stuff
-------------------------------------------------------------------
Wed May 7 13:12:11 CEST 2008 - pgajdos@suse.cz
- repaired no-return-in-nonvoid-function
(noreturn.patch)
-------------------------------------------------------------------
Mon Apr 28 11:43:08 CEST 2008 - pgajdos@suse.cz
- repaired build for
* ia64 (%ifarch in hdf5.spec)
* s390, s390x (s390.patch)
-------------------------------------------------------------------
Tue Mar 25 11:11:13 CET 2008 - pgajdos@suse.cz
- package moved from BS, project science
- needed by octave 3.0

217
hdf5.spec Normal file
View File

@ -0,0 +1,217 @@
#
# spec file for package hdf5 (Version 1.8.8)
#
# Copyright (c) 2009-2011 SUSE LINUX Products GmbH, Nuernberg, Germany.
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
%define hdf5_libver 0
%define libname libhdf5
Name: hdf5
Version: 1.8.8
Release: 0
Summary: A general purpose library and file format for storing scientific data
License: BSD-3-Clause
Group: Development/Libraries/Other
URL: http://www.hdfgroup.org/HDF5/
Source0: http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-%{version}%{?snaprel}.tar.bz2
Source1: h5comp
Patch0: hdf5-LD_LIBRARY_PATH.patch
Patch1: hdf5-non_void_return.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-build
BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-fortran, gcc-c++
BuildRequires: fdupes
%description
HDF5 is a general purpose library and file format for storing scientific data.
HDF5 can store two primary objects: datasets and groups. A dataset is
essentially a multidimensional array of data elements, and a group is a
structure for organizing objects in an HDF5 file. Using these two basic
objects, one can create and store almost any kind of scientific data
structure, such as images, arrays of vectors, and structured and unstructured
grids. You can also mix and match them in HDF5 files according to your needs.
%package -n %{libname}-%{hdf5_libver}
Summary: HDF 5 runtime libraries
Group: System/Libraries
%description -n %{libname}-%{hdf5_libver}
The HDF project involves the development and support of software and
file formats for scientific data management. The HDF software includes
I/O libraries and tools for analyzing, visualizing, and converting
scientific data.
This package contains the HDF 5 runtime libraries.
%package -n %{libname}_hl%{hdf5_libver}
Summary: HDF 5 runtimelibraries
Group: System/Libraries
%description -n %{libname}_hl%{hdf5_libver}
The HDF project involves the development and support of software and
file formats for scientific data management. The HDF software includes
I/O libraries and tools for analyzing, visualizing, and converting
scientific data.
This package contains the HDF 5 runtime libraries.
%package devel
Summary: Hierarchical Data File Format Version 5
Group: Development/Libraries/Parallel
Requires: %{name} = %{version}
# Required by Fortran programs?
Requires: %{libname}-%{hdf5_libver} = %{version}
Requires: %{libname}_hl%{hdf5_libver} = %{version}
%description devel
The HDF project involves the development and support of software and
file formats for scientific data management. The HDF software includes
I/O libraries and tools for analyzing, visualizing, and converting
scientific data.
This package contains all files needed to create projects that use
hdf5.
%package devel-static
Summary: Hierarchical Data File Format Version 5 - static libraries
Group: Development/Libraries/C and C++
Requires: hdf5-devel
%description devel-static
The HDF project involves the development and support of software and
file formats for scientific data management. The HDF software includes
I/O libraries and tools for analyzing, visualizing, and converting
scientific data.
This package provides the static libraries.
%package examples
Summary: Examples for HDF5
Group: Development/Libraries/Parallel
Requires: %{libname}-%{hdf5_libver} = %{version}
Requires: %{libname}_hl%{hdf5_libver} = %{version}
%description examples
Examples of HDF5 library use.
%prep
%setup -q
%patch0 -p1 -b .LD_LIBRARY_PATH
%patch1 -b .non_void_return
#This should be fixed in 1.8.7
find \( -name '*.[ch]*' -o -name '*.f90' -o -name '*.txt' \) -exec chmod -x {} +
%build
export CC=gcc
export CXX=g++
export F9X=gfortran
export CFLAGS="${RPM_OPT_FLAGS/O2/O0}"
# export CFLAGS="%%{optflags} -fno-strict-aliasing"
%configure \
--disable-dependency-tracking \
%if 0%{?suse_version} > 1140
--enable-fortran \
%endif
--enable-hl \
--enable-shared \
--enable-cxx \
--with-pthread \
--with-ssl \
# --with-pic
make %{?_smp_mflags}
%install
%makeinstall docdir=%{buildroot}%{_docdir}
rm -rf %{buildroot}/%{_libdir}/*.la %{buildroot}/%{_libdir}/*.settings
find %{buildroot}%{_datadir}/hdf5_examples -type f \
| grep -v ".sh$" | xargs chmod 644
%fdupes -s %{buildroot}/%{_datadir}
%if 0%{?suse_version} > 1140
binaries="h5c++ h5cc h5fc"
%else
binaries="h5c++ h5cc"
%endif
# rpm macro for version checking
mkdir -p %{buildroot}%{_sysconfdir}/rpm
cat > %{buildroot}%{_sysconfdir}/rpm/macros.hdf5 <<EOF
#
# RPM macros for R packaging
#
#
# Make R search index.txt
#
%_hdf5_version %{version}
EOF
%check
make check
%post -n %{libname}-%{hdf5_libver} -p /sbin/ldconfig
%postun -n %{libname}-%{hdf5_libver} -p /sbin/ldconfig
%post -n %{libname}_hl%{hdf5_libver} -p /sbin/ldconfig
%postun -n %{libname}_hl%{hdf5_libver} -p /sbin/ldconfig
%files
%defattr(-,root,root)
%doc COPYING MANIFEST README.txt release_docs/RELEASE.txt
%doc release_docs/HISTORY-1_0-1_8_0_rc3.txt release_docs/HISTORY-1_8.txt
%doc release_docs/RELEASE.txt
%{_bindir}/*
%files -n %{libname}-%{hdf5_libver}
%defattr(0755,root,root)
%{_libdir}/libhdf5.so.*
%{_libdir}/libhdf5_cpp.so.*
%if 0%{?suse_version} > 1140
%{_libdir}/libhdf5_fortran.so.*
%endif
%files -n libhdf5_hl%{hdf5_libver}
%defattr(0755,root,root)
%{_libdir}/libhdf5_hl.so.*
%{_libdir}/libhdf5_hl_cpp.so.*
%if 0%{?suse_version} > 1140
%{_libdir}/libhdf5hl_fortran.so.*
%endif
%files devel
%defattr(-,root,root)
%config(noreplace) %{_sysconfdir}/rpm/macros.hdf5
%{_includedir}/*.h
%{_libdir}/*.so
%if 0%{?suse_version} > 1140
%{_includedir}/*.mod
%endif
%files devel-static
%defattr(-,root,root)
%{_libdir}/*.a
%files examples
%defattr(-,root,root)
%{_datadir}/hdf5_examples
%changelog