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update to 2.3.1 

update to 2.3.1
drop obsolete patches (merged upstream)
This commit is contained in:
Dominik Mierzejewski 2011-10-21 12:45:13 +02:00
parent 40acebaf95
commit 257aff8dfa
6 changed files with 19 additions and 152 deletions
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1
.gitignore vendored
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@ -1,3 +1,4 @@
openbabel-2.0.2.tar.gz
/openbabel-2.3.0b2-20100803-r3942.tar.gz
/openbabel-2.3.0.tar.gz
/openbabel-2.3.1.tar.gz

18
openbabel-2.3.0-obenergy-fflist.patch
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@ -1,18 +0,0 @@
--- openbabel-2.3.0_orig/tools/obenergy.cpp 2010-10-10 06:05:20.000000000 +0400
+++ openbabel-2.3.0/tools/obenergy.cpp 2011-03-19 18:58:18.000000000 +0300
@@ -40,6 +40,7 @@
int verbose = 0;
bool hydrogens = false;
string basename, filename = "", option, option2, ff = "";
+ OBConversion conv;
if (argc < 2) {
cout << "Usage: obenergy [options] <filename>" << endl;
@@ -89,7 +90,6 @@
}
// Find Input filetype
- OBConversion conv;
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
if (!format_in || !conv.SetInFormat(format_in)) {

37
openbabel-inchi.patch
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@ -1,37 +0,0 @@
diff -up openbabel-2.3.0/cmake/modules/FindInchi.cmake.r openbabel-2.3.0/cmake/modules/FindInchi.cmake
--- openbabel-2.3.0/cmake/modules/FindInchi.cmake.r 2010-10-13 02:37:01.000000000 +0200
+++ openbabel-2.3.0/cmake/modules/FindInchi.cmake 2010-11-23 01:56:55.081622107 +0100
@@ -13,7 +13,7 @@ if(INCHI_INCLUDE_DIR AND INCHI_LIBRARY)
# in cache already
set(INCHI_FOUND TRUE)
else()
- find_path(INCHI_INCLUDE_DIR NAMES inchi_api.h)
+ find_path(INCHI_INCLUDE_DIR NAMES inchi_api.h PATHS /usr/include/inchi )
find_library(INCHI_LIBRARY NAMES inchi Inchi)
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(INCHI DEFAULT_MSG INCHI_LIBRARY
diff -up openbabel-2.3.0/include/CMakeLists.txt.r openbabel-2.3.0/include/CMakeLists.txt
--- openbabel-2.3.0/include/CMakeLists.txt.r 2010-09-25 17:05:05.000000000 +0200
+++ openbabel-2.3.0/include/CMakeLists.txt 2010-11-23 01:56:55.082628237 +0100
@@ -4,7 +4,9 @@ file(GLOB math_headers openbabel/ma
file(GLOB stereo_headers openbabel/stereo/*.h)
file(GLOB depict_headers openbabel/stereo/*.h)
+if(NOT OPENBABEL_USE_SYSTEM_INCHI)
install(FILES inchi_api.h DESTINATION include/inchi)
+endif(NOT OPENBABEL_USE_SYSTEM_INCHI)
install(FILES chemdrawcdx.h DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
install(FILES ${openbabel_headers} DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
install(FILES ${math_headers} DESTINATION ${OB_INCLUDE_DIRS}/openbabel/math)
diff -up openbabel-2.3.0/scripts/ruby/extconf.rb.r openbabel-2.3.0/scripts/ruby/extconf.rb
--- openbabel-2.3.0/scripts/ruby/extconf.rb.r 2010-10-23 03:54:40.000000000 +0200
+++ openbabel-2.3.0/scripts/ruby/extconf.rb 2010-11-23 01:56:55.083627521 +0100
@@ -17,7 +17,7 @@ dir_config('openbabel')
# Find a trivial header in order to add the proper include path
# to the build flags.
here = File.dirname(__FILE__)
-find_header('inchi_api.h', here + '/../../include')
+find_header('inchi_api.h', '/usr/include/inchi', '/usr/include', here + '/../../include')
# Prevent Ruby 1.8.x from trying to compile and link the extension
# using gcc.

95
openbabel-rpm.patch
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@ -1,91 +1,12 @@
diff -up openbabel-2.3.0/scripts/CMakeLists.txt.r openbabel-2.3.0/scripts/CMakeLists.txt
--- openbabel-2.3.0/scripts/CMakeLists.txt.r 2010-10-25 19:37:42.000000000 +0200
+++ openbabel-2.3.0/scripts/CMakeLists.txt 2010-11-24 22:53:29.250004683 +0100
@@ -82,6 +82,7 @@ if (DO_PYTHON_BINDINGS)
COMMAND ${CMAKE_COMMAND} -E copy ob.py ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py
COMMAND ${CMAKE_COMMAND} -E remove ob.py
VERBATIM)
+ add_dependencies(_openbabel openbabel)
if (PYTHON_PREFIX)
install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/python/setup.py install --prefix=${PYTHON_PREFIX} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts)")
@@ -89,7 +90,7 @@ if (DO_PYTHON_BINDINGS)
if (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local")
install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/python/setup.py install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts)")
else (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local")
- install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/python/setup.py install --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts)")
+ install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/python/setup.py install --prefix=$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts)")
endif (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local")
endif (PYTHON_PREFIX)
@@ -228,8 +229,8 @@ if (DO_PERL_BINDINGS)
DEPENDS ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp
diff -up openbabel-2.3.1/scripts/CMakeLists.txt.r openbabel-2.3.1/scripts/CMakeLists.txt
--- openbabel-2.3.1/scripts/CMakeLists.txt.r 2011-10-08 22:09:17.000000000 +0200
+++ openbabel-2.3.1/scripts/CMakeLists.txt 2011-10-12 18:57:31.000000000 +0200
@@ -251,7 +251,7 @@ if (DO_PERL_BINDINGS)
WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl
)
- add_dependencies(bindings_perl pre_bindings_perl)
- install(CODE "execute_process(COMMAND make install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)")
+ add_dependencies(bindings_perl pre_bindings_perl openbabel)
+ install(CODE "execute_process(COMMAND make install_vendor WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)")
add_dependencies(bindings_perl pre_bindings_perl openbabel)
- install(CODE "execute_process(COMMAND make install DESTDIR=\$ENV{DESTDIR} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)")
+ install(CODE "execute_process(COMMAND make install_vendor DESTDIR=\$ENV{DESTDIR} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)")
else (NOT MSVC)
add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp)
@@ -282,20 +283,20 @@ if (DO_RUBY_BINDINGS)
COMMAND ${CMAKE_COMMAND} -E make_directory ${openbabel_BINARY_DIR}/scripts/ruby
)
add_custom_target(bindings_ruby ALL
- COMMAND ${RUBY_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/ruby/extconf.rb --with-openbabel-lib=${BABEL_LIBRARY} --with-openbabel-include=${openbabel_BINARY_DIR}/include
+ COMMAND ${RUBY_EXECUTABLE} ${openbabel_SOURCE_DIR}/scripts/ruby/extconf.rb --with-openbabel-lib=${openbabel_BINARY_DIR}/lib${LIB_SUFFIX} --with-openbabel-include=${openbabel_BINARY_DIR}/include
COMMAND ${CMAKE_COMMAND} -E echo "Compiling Ruby bindings"
COMMAND make
DEPENDS ${openbabel_SOURCE_DIR}/scripts/ruby/openbabel-ruby.cpp
WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby
)
- add_dependencies(bindings_ruby pre_bindings_ruby)
+ add_dependencies(bindings_ruby pre_bindings_ruby openbabel)
if (RUBY_PREFIX)
install(CODE "execute_process(COMMAND DESTDIR=${RUBY_PREFIX} make install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby)")
else (RUBY_PREFIX)
if (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local")
install(CODE "execute_process(COMMAND make install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby)")
else (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local")
- install(CODE "execute_process(COMMAND DESTDIR=${CMAKE_INSTALL_PREFIX} make install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby)")
+ install(CODE "execute_process(COMMAND make DESTDIR=$ENV{DESTDIR} install WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/ruby)")
endif (${CMAKE_INSTALL_PREFIX} STREQUAL "/usr/local")
endif (RUBY_PREFIX)
else(NOT MSVC)
diff -up openbabel-2.3.0/scripts/perl/Makefile.PL.r openbabel-2.3.0/scripts/perl/Makefile.PL
--- openbabel-2.3.0/scripts/perl/Makefile.PL.r 2010-10-23 03:44:58.000000000 +0200
+++ openbabel-2.3.0/scripts/perl/Makefile.PL 2010-11-24 22:53:46.417249628 +0100
@@ -12,6 +12,9 @@ $cmakebindir = @ENV{"OBJ_DIR"};
if (-e "$cmakebindir/lib/libopenbabel.so" || -e "$cmakebindir/lib/libopenbabel.dylib") {
check_lib_or_exit( lib => 'openbabel' , libpath => "$cmakebindir/lib");
}
+elsif (-e "$cmakebindir/lib64/libopenbabel.so") {
+ check_lib_or_exit( lib => 'openbabel' , libpath => "$cmakebindir/lib64");
+}
else {
check_lib_or_exit( lib => 'openbabel' , libpath => @ENV{"LD_LIBRARY_PATH"});
}
@@ -21,6 +24,8 @@ $ldfrom = "\$(OBJECT) -L$cmakebindir/lib
if (-r "$cmakebindir/lib/libopenbabel.dylib") and (-s _) and (-B _);
$ldfrom = "\$(OBJECT) -L$cmakebindir/lib -lopenbabel"
if (-r "$cmakebindir/lib/libopenbabel.so") and (-s _) and (-B _);
+$ldfrom = "\$(OBJECT) -L$cmakebindir/lib64 -lopenbabel"
+ if (-r "$cmakebindir/lib64/libopenbabel.so") and (-s _) and (-B _);
# See lib/ExtUtils/MakeMaker.pm for details of how to influence
# the contents of the Makefile that is written.
diff -up openbabel-2.3.0/scripts/python/setup.py.r openbabel-2.3.0/scripts/python/setup.py
--- openbabel-2.3.0/scripts/python/setup.py.r 2010-10-26 16:39:01.000000000 +0200
+++ openbabel-2.3.0/scripts/python/setup.py 2010-11-23 01:56:55.083627521 +0100
@@ -17,7 +17,9 @@ obExtension = Extension('_openbabel',
[os.path.join(srcdir, "openbabel-python.cpp")],
include_dirs=[os.path.join(srcdir, "..", "..", "include"),
os.path.join("..", "include")],
- library_dirs=[os.path.join("..", "lib")],
+ library_dirs=[os.path.join(srcdir, "..", "..", "lib"),
+ os.path.join(srcdir, "..", "..", "lib64"),
+ os.path.join("..", "lib")],
libraries=['openbabel']
)

18
openbabel.spec
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@ -9,19 +9,16 @@
%define beta_dir %{nil}
Name: openbabel
Version: 2.3.0
Release: 5%{beta_ver}%{?dist}
Version: 2.3.1
Release: 1%{beta_ver}%{?dist}
Summary: Chemistry software file format converter
License: GPLv2
Group: Applications/File
URL: http://openbabel.org/
Source: http://downloads.sourceforge.net/sourceforge/openbabel/%{name}-%{version}%{beta_str}.tar.gz
Patch1: %{name}-rpm.patch
Patch3: %{name}-inchi.patch
# fix plugin directory location (#680292, patch by lg)
Patch4: openbabel-2.3.0-plugindir.patch
# show forcefields list in obenergy output (#680292, patch by lg)
Patch5: openbabel-2.3.0-obenergy-fflist.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: cmake
BuildRequires: eigen2-devel
@ -122,9 +119,7 @@ Ruby wrapper for the Open Babel library.
%prep
%setup -q -n %{name}-%{version}%{beta_dir}
%patch1 -p1 -b .r
%patch3 -p1 -b .inchi
%patch4 -p1 -b .plugindir
%patch5 -p1 -b .obenergy-fflist
chmod 644 src/formats/{fchk,genbank,mmcif}format.cpp
chmod 644 src/math/align.cpp
chmod 644 include/openbabel/{graphsym.h,math/align.h}
@ -145,7 +140,8 @@ make VERBOSE=1 %{?_smp_mflags}
touch scripts/CMakeLists.txt
make VERBOSE=1 DESTDIR=$RPM_BUILD_ROOT install
rm $RPM_BUILD_ROOT%{perl_archlib}/perllocal.pod
rm $RPM_BUILD_ROOT%{_libdir}/cmake/openbabel2/*.cmake
rm $RPM_BUILD_ROOT%{_libdir}/perl5/perllocal.pod
rm -f $RPM_BUILD_ROOT%{perl_vendorarch}/auto/Chemistry/OpenBabel/{.packlist,OpenBabel.bs}
chmod 755 $RPM_BUILD_ROOT%{perl_vendorarch}/auto/Chemistry/OpenBabel/OpenBabel.so
@ -170,7 +166,7 @@ chmod 755 $RPM_BUILD_ROOT%{perl_vendorarch}/auto/Chemistry/OpenBabel/OpenBabel.s
%files gui
%defattr(-,root,root,-)
%{_bindir}/OBGUI
%{_bindir}/obgui
%files libs
%defattr(-,root,root,-)
@ -205,6 +201,10 @@ chmod 755 $RPM_BUILD_ROOT%{perl_vendorarch}/auto/Chemistry/OpenBabel/OpenBabel.s
%{ruby_sitearch}/openbabel.so
%changelog
* Fri Oct 21 2011 Dominik Mierzejewski <rpm@greysector.net> 2.3.0-1
- update to 2.3.1
- drop obsolete patches (merged upstream)
* Mon Jun 20 2011 Marcela Mašláňová <mmaslano@redhat.com> - 2.3.0-5
- Perl mass rebuild

2
sources
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@ -1 +1 @@
effda01ed4a31d18d8e3d08191799608 openbabel-2.3.0.tar.gz
1f029b0add12a3b55582dc2c832b04f8 openbabel-2.3.1.tar.gz