rpms/openbabel/devel .cvsignore, 1.12, 1.13 openbabel-gcc43.patch, 1.16, 1.17 openbabel-rpm.patch, 1.3, 1.4 openbabel.spec, 1.45, 1.46 sources, 1.12, 1.13

Sun Mar 1 12:19:03 UTC 2009

Author: rathann

Update of /cvs/pkgs/rpms/openbabel/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv13774

Modified Files:
	.cvsignore openbabel-gcc43.patch openbabel-rpm.patch 
	openbabel.spec sources 
Log Message:
* Sun Mar 01 2009 Dominik Mierzejewski <rpm at greysector.net> 2.2.1-0.1.b3
- update to 2.2.1 beta3
- drop some obsolete workarounds



Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/openbabel/devel/.cvsignore,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13

--- .cvsignore	6 Jul 2008 14:57:34 -0000	1.12
+++ .cvsignore	1 Mar 2009 12:18:32 -0000	1.13
@@ -1 +1 @@
-openbabel-2.2.0.tar.gz
+openbabel-2.2.1b3-20090215-r2890.tar.gz

openbabel-gcc43.patch:

Index: openbabel-gcc43.patch
===================================================================
RCS file: /cvs/pkgs/rpms/openbabel/devel/openbabel-gcc43.patch,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- openbabel-gcc43.patch	2 Jul 2008 18:49:45 -0000	1.16
+++ openbabel-gcc43.patch	1 Mar 2009 12:18:32 -0000	1.17
@@ -1,63 +1,64 @@
-diff -up openbabel-2.2.0b7/src/zipstreamimpl.h.gcc43 openbabel-2.2.0b7/src/zipstreamimpl.h
---- openbabel-2.2.0b7/src/zipstreamimpl.h.gcc43	2008-06-21 15:58:02.000000000 +0200
-+++ openbabel-2.2.0b7/src/zipstreamimpl.h	2008-07-02 20:16:21.000000000 +0200
-@@ -31,6 +31,8 @@ Altered by: Geoffrey Hutchison 2005 for 
-             minor namespace modifications, VC++ compatibility
- */
- 
-+#include <string.h>
-+
- //*****************************************************************************
- //  template class basic_zip_streambuf
- //*****************************************************************************
-diff -up openbabel-2.2.0b7/src/residue.cpp.gcc43 openbabel-2.2.0b7/src/residue.cpp
---- openbabel-2.2.0b7/src/residue.cpp.gcc43	2008-06-21 15:58:02.000000000 +0200
-+++ openbabel-2.2.0b7/src/residue.cpp	2008-07-02 20:16:21.000000000 +0200
-@@ -26,6 +26,8 @@ obtained in part or whole from RasMol2 b
- // File Includes
- ///////////////////////////////////////////////////////////////////////////////
- 
-+#include <cstring>
-+
+diff -up openbabel-2.2.1b3-20090215-r2890/include/openbabel/data.h.gcc43 openbabel-2.2.1b3-20090215-r2890/include/openbabel/data.h
+--- openbabel-2.2.1b3-20090215-r2890/include/openbabel/data.h.gcc43	2008-12-01 18:42:20.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/include/openbabel/data.h	2009-03-01 10:54:43.000000000 +0100
+@@ -23,7 +23,7 @@ GNU General Public License for more deta
  #include <openbabel/babelconfig.h>
  
- #include <openbabel/residue.h>
-diff -up openbabel-2.2.0b7/src/obconversion.cpp.gcc43 openbabel-2.2.0b7/src/obconversion.cpp
---- openbabel-2.2.0b7/src/obconversion.cpp.gcc43	2008-06-21 15:58:02.000000000 +0200
-+++ openbabel-2.2.0b7/src/obconversion.cpp	2008-07-02 20:17:00.000000000 +0200
-@@ -37,6 +37,7 @@ GNU General Public License for more deta
+ #include <stdio.h>
+-
++#include <cstring>
+ #include <fstream>
+ #include <vector>
  #include <string>
+diff -up openbabel-2.2.1b3-20090215-r2890/include/openbabel/obconversion.h.gcc43 openbabel-2.2.1b3-20090215-r2890/include/openbabel/obconversion.h
+--- openbabel-2.2.1b3-20090215-r2890/include/openbabel/obconversion.h.gcc43	2008-12-01 18:42:19.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/include/openbabel/obconversion.h	2009-03-01 10:54:43.000000000 +0100
+@@ -28,6 +28,7 @@ GNU General Public License for more deta
+ #include <string>
+ #include <vector>
  #include <map>
- #include <locale>
-+#include <typeinfo>
++#include <strings.h>
  
- #include <stdlib.h>
+ #include <openbabel/dlhandler.h>
+ #include <openbabel/oberror.h>
+diff -up openbabel-2.2.1b3-20090215-r2890/include/openbabel/obmolecformat.h.gcc43 openbabel-2.2.1b3-20090215-r2890/include/openbabel/obmolecformat.h
+--- openbabel-2.2.1b3-20090215-r2890/include/openbabel/obmolecformat.h.gcc43	2008-12-01 18:42:20.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/include/openbabel/obmolecformat.h	2009-03-01 10:54:43.000000000 +0100
+@@ -23,6 +23,8 @@ GNU General Public License for more deta
+   #include <hash_map>
+ #endif
  
-diff -up openbabel-2.2.0b7/src/formats/rxnformat.cpp.gcc43 openbabel-2.2.0b7/src/formats/rxnformat.cpp
---- openbabel-2.2.0b7/src/formats/rxnformat.cpp.gcc43	2008-06-21 15:58:01.000000000 +0200
-+++ openbabel-2.2.0b7/src/formats/rxnformat.cpp	2008-07-02 20:16:21.000000000 +0200
-@@ -16,6 +16,7 @@ GNU General Public License for more deta
- #include "openbabel/babelconfig.h"
- #include <string>
- #include <iomanip>
 +#include <typeinfo>
- #include "openbabel/mol.h"
- #include "openbabel/obconversion.h"
- #include "openbabel/reaction.h"
-diff -up openbabel-2.2.0b7/src/formats/fchkformat.cpp.gcc43 openbabel-2.2.0b7/src/formats/fchkformat.cpp
---- openbabel-2.2.0b7/src/formats/fchkformat.cpp.gcc43	2008-06-13 22:48:02.000000000 +0200
-+++ openbabel-2.2.0b7/src/formats/fchkformat.cpp	2008-07-02 20:16:21.000000000 +0200
-@@ -12,6 +12,7 @@ GNU General Public License for more deta
++
+ #include <openbabel/mol.h>
+ #include <openbabel/babelconfig.h>
+ #include <openbabel/obconversion.h>
+diff -up openbabel-2.2.1b3-20090215-r2890/include/openbabel/xml.h.gcc43 openbabel-2.2.1b3-20090215-r2890/include/openbabel/xml.h
+--- openbabel-2.2.1b3-20090215-r2890/include/openbabel/xml.h.gcc43	2008-12-01 18:42:19.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/include/openbabel/xml.h	2009-03-01 10:54:43.000000000 +0100
+@@ -13,6 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICU
+ GNU General Public License for more details.
  ***********************************************************************/
  
- #include <numeric>
 +#include <typeinfo>
++
+ #include <openbabel/mol.h>
+ #include <openbabel/obconversion.h>
+ #include <openbabel/obmolecformat.h>
+diff -up openbabel-2.2.1b3-20090215-r2890/src/dlhandler_unix.cpp.gcc43 openbabel-2.2.1b3-20090215-r2890/src/dlhandler_unix.cpp
+--- openbabel-2.2.1b3-20090215-r2890/src/dlhandler_unix.cpp.gcc43	2009-01-16 16:43:58.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/src/dlhandler_unix.cpp	2009-03-01 10:59:50.000000000 +0100
+@@ -27,6 +27,7 @@ GNU General Public License for more deta
+ #include <dlfcn.h>
+ #include <cstring>
+ #include <cstdlib>
++#include <cstdio>
  
- // No diagnoalization yet. Perhaps for 2.2 -GRH
- // #include <eigen/matrix.h>
-diff -up openbabel-2.2.0b7/src/fingerprint.cpp.gcc43 openbabel-2.2.0b7/src/fingerprint.cpp
---- openbabel-2.2.0b7/src/fingerprint.cpp.gcc43	2008-06-26 20:55:14.000000000 +0200
-+++ openbabel-2.2.0b7/src/fingerprint.cpp	2008-07-02 20:16:21.000000000 +0200
+ using namespace std;
+ 
+diff -up openbabel-2.2.1b3-20090215-r2890/src/fingerprint.cpp.gcc43 openbabel-2.2.1b3-20090215-r2890/src/fingerprint.cpp
+--- openbabel-2.2.1b3-20090215-r2890/src/fingerprint.cpp.gcc43	2008-12-01 18:42:02.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/src/fingerprint.cpp	2009-03-01 10:54:43.000000000 +0100
 @@ -21,7 +21,7 @@ GNU General Public License for more deta
  #include <vector>
  #include <algorithm>
@@ -67,56 +68,66 @@
  #include <fstream>
  
  #include <openbabel/fingerprint.h>
-diff -up openbabel-2.2.0b7/include/openbabel/xml.h.gcc43 openbabel-2.2.0b7/include/openbabel/xml.h
---- openbabel-2.2.0b7/include/openbabel/xml.h.gcc43	2008-06-21 15:58:05.000000000 +0200
-+++ openbabel-2.2.0b7/include/openbabel/xml.h	2008-07-02 20:16:21.000000000 +0200
-@@ -13,6 +13,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICU
- GNU General Public License for more details.
+diff -up openbabel-2.2.1b3-20090215-r2890/src/formats/fchkformat.cpp.gcc43 openbabel-2.2.1b3-20090215-r2890/src/formats/fchkformat.cpp
+--- openbabel-2.2.1b3-20090215-r2890/src/formats/fchkformat.cpp.gcc43	2009-02-10 23:40:18.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/src/formats/fchkformat.cpp	2009-03-01 10:54:43.000000000 +0100
+@@ -12,6 +12,7 @@ GNU General Public License for more deta
  ***********************************************************************/
  
+ #include <numeric>
 +#include <typeinfo>
-+
- #include <openbabel/mol.h>
- #include <openbabel/obconversion.h>
- #include <openbabel/obmolecformat.h>
-diff -up openbabel-2.2.0b7/include/openbabel/obconversion.h.gcc43 openbabel-2.2.0b7/include/openbabel/obconversion.h
---- openbabel-2.2.0b7/include/openbabel/obconversion.h.gcc43	2008-06-21 15:58:05.000000000 +0200
-+++ openbabel-2.2.0b7/include/openbabel/obconversion.h	2008-07-02 20:16:21.000000000 +0200
-@@ -28,6 +28,7 @@ GNU General Public License for more deta
+ 
+ // No diagnoalization yet. Perhaps for 2.2 -GRH
+ // #include <eigen/matrix.h>
+diff -up openbabel-2.2.1b3-20090215-r2890/src/formats/rxnformat.cpp.gcc43 openbabel-2.2.1b3-20090215-r2890/src/formats/rxnformat.cpp
+--- openbabel-2.2.1b3-20090215-r2890/src/formats/rxnformat.cpp.gcc43	2009-01-14 23:52:20.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/src/formats/rxnformat.cpp	2009-03-01 10:54:43.000000000 +0100
+@@ -16,6 +16,7 @@ GNU General Public License for more deta
+ #include "openbabel/babelconfig.h"
  #include <string>
- #include <vector>
+ #include <iomanip>
++#include <typeinfo>
+ #include "openbabel/mol.h"
+ #include "openbabel/obconversion.h"
+ #include "openbabel/reaction.h"
+diff -up openbabel-2.2.1b3-20090215-r2890/src/obconversion.cpp.gcc43 openbabel-2.2.1b3-20090215-r2890/src/obconversion.cpp
+--- openbabel-2.2.1b3-20090215-r2890/src/obconversion.cpp.gcc43	2009-01-28 21:38:24.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/src/obconversion.cpp	2009-03-01 10:54:43.000000000 +0100
+@@ -38,6 +38,7 @@ GNU General Public License for more deta
  #include <map>
-+#include <strings.h>
+ #include <locale>
+ #include <limits>
++#include <typeinfo>
  
- #include <openbabel/dlhandler.h>
- #include <openbabel/oberror.h>
-diff -up openbabel-2.2.0b7/include/openbabel/data.h.gcc43 openbabel-2.2.0b7/include/openbabel/data.h
---- openbabel-2.2.0b7/include/openbabel/data.h.gcc43	2008-06-21 15:58:05.000000000 +0200
-+++ openbabel-2.2.0b7/include/openbabel/data.h	2008-07-02 20:16:21.000000000 +0200
-@@ -23,7 +23,7 @@ GNU General Public License for more deta
- #include <openbabel/babelconfig.h>
+ #include <stdlib.h>
  
- #include <stdio.h>
--
-+#include <cstring>
- #include <fstream>
- #include <vector>
- #include <string>
-diff -up openbabel-2.2.0b7/include/openbabel/obmolecformat.h.gcc43 openbabel-2.2.0b7/include/openbabel/obmolecformat.h
---- openbabel-2.2.0b7/include/openbabel/obmolecformat.h.gcc43	2008-06-21 15:58:05.000000000 +0200
-+++ openbabel-2.2.0b7/include/openbabel/obmolecformat.h	2008-07-02 20:16:21.000000000 +0200
-@@ -23,6 +23,8 @@ GNU General Public License for more deta
-   #include <hash_map>
- #endif
+diff -up openbabel-2.2.1b3-20090215-r2890/src/residue.cpp.gcc43 openbabel-2.2.1b3-20090215-r2890/src/residue.cpp
+--- openbabel-2.2.1b3-20090215-r2890/src/residue.cpp.gcc43	2008-12-01 18:42:02.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/src/residue.cpp	2009-03-01 10:54:43.000000000 +0100
+@@ -26,6 +26,8 @@ obtained in part or whole from RasMol2 b
+ // File Includes
+ ///////////////////////////////////////////////////////////////////////////////
  
-+#include <typeinfo>
++#include <cstring>
 +
- #include <openbabel/mol.h>
  #include <openbabel/babelconfig.h>
- #include <openbabel/obconversion.h>
-diff -up openbabel-2.2.0b7/tools/babel.cpp.gcc43 openbabel-2.2.0b7/tools/babel.cpp
---- openbabel-2.2.0b7/tools/babel.cpp.gcc43	2008-06-21 15:58:03.000000000 +0200
-+++ openbabel-2.2.0b7/tools/babel.cpp	2008-07-02 20:16:21.000000000 +0200
+ 
+ #include <openbabel/residue.h>
+diff -up openbabel-2.2.1b3-20090215-r2890/src/zipstreamimpl.h.gcc43 openbabel-2.2.1b3-20090215-r2890/src/zipstreamimpl.h
+--- openbabel-2.2.1b3-20090215-r2890/src/zipstreamimpl.h.gcc43	2008-12-01 18:42:02.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/src/zipstreamimpl.h	2009-03-01 10:54:43.000000000 +0100
+@@ -31,6 +31,8 @@ Altered by: Geoffrey Hutchison 2005 for 
+             minor namespace modifications, VC++ compatibility
+ */
+ 
++#include <cstring>
++
+ //*****************************************************************************
+ //  template class basic_zip_streambuf
+ //*****************************************************************************
+diff -up openbabel-2.2.1b3-20090215-r2890/tools/babel.cpp.gcc43 openbabel-2.2.1b3-20090215-r2890/tools/babel.cpp
+--- openbabel-2.2.1b3-20090215-r2890/tools/babel.cpp.gcc43	2008-12-01 18:42:04.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/tools/babel.cpp	2009-03-01 10:54:43.000000000 +0100
 @@ -42,6 +42,7 @@ extern "C" int strncasecmp(const char *s
  #include <openbabel/obconversion.h>
  #include <openbabel/plugin.h>

openbabel-rpm.patch:

Index: openbabel-rpm.patch
===================================================================
RCS file: /cvs/pkgs/rpms/openbabel/devel/openbabel-rpm.patch,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- openbabel-rpm.patch	6 Jul 2008 14:57:34 -0000	1.3
+++ openbabel-rpm.patch	1 Mar 2009 12:18:33 -0000	1.4
@@ -1,20 +1,7 @@
-diff -up openbabel-2.2.0/scripts/Makefile.am.r openbabel-2.2.0/scripts/Makefile.am
---- openbabel-2.2.0/scripts/Makefile.am.r	2008-07-03 20:25:54.000000000 +0200
-+++ openbabel-2.2.0/scripts/Makefile.am	2008-07-06 15:59:23.000000000 +0200
-@@ -63,8 +63,8 @@ ruby/openbabel_ruby.cpp: openbabel-ruby.
- 	$(SWIG) -small -O -ruby -naturalvar -autorename -c++ -o $@ \
- 	-templatereduce -I$(top_srcdir)/include -I$(top_builddir)/include $<;
- 	(cd ruby; ruby extconf.rb \
--  --with-openbabel-include=$(includedir)/openbabel-2.0 \
--  --with-openbabel-lib=$(libdir) )
-+  --with-openbabel-include=../../include/openbabel \
-+  --with-openbabel-lib=../../src/.libs )
- 	sed -e 's/rb_define_module(\"Openbabel\")/rb_define_module(\"OpenBabel\")/' -e 's/void Init_OpenBabel/void Init_openbabel/' <ruby/openbabel_ruby.cpp >ruby/openbabel_ruby.new 
- 	mv ruby/openbabel_ruby.new ruby/openbabel_ruby.cpp
- endif # BUILD_RUBY
-diff -up openbabel-2.2.0/scripts/perl/Makefile.PL.r openbabel-2.2.0/scripts/perl/Makefile.PL
---- openbabel-2.2.0/scripts/perl/Makefile.PL.r	2008-07-06 16:16:45.000000000 +0200
-+++ openbabel-2.2.0/scripts/perl/Makefile.PL	2008-07-06 16:48:59.000000000 +0200
+diff -up openbabel-2.2.1b3-20090215-r2890/scripts/Makefile.am.r openbabel-2.2.1b3-20090215-r2890/scripts/Makefile.am
+diff -up openbabel-2.2.1b3-20090215-r2890/scripts/perl/Makefile.PL.r openbabel-2.2.1b3-20090215-r2890/scripts/perl/Makefile.PL
+--- openbabel-2.2.1b3-20090215-r2890/scripts/perl/Makefile.PL.r	2008-12-01 18:41:42.000000000 +0100
++++ openbabel-2.2.1b3-20090215-r2890/scripts/perl/Makefile.PL	2009-03-01 10:43:01.000000000 +0100
 @@ -3,8 +3,8 @@ use ExtUtils::MakeMaker;
  use lib 'inc';
  use Devel::CheckLib;


Index: openbabel.spec
===================================================================
RCS file: /cvs/pkgs/rpms/openbabel/devel/openbabel.spec,v
retrieving revision 1.45
retrieving revision 1.46
diff -u -r1.45 -r1.46
--- openbabel.spec	26 Feb 2009 08:21:12 -0000	1.45
+++ openbabel.spec	1 Mar 2009 12:18:33 -0000	1.46
@@ -4,12 +4,12 @@
 %{!?python_sitearch: %define python_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
 %define ruby_sitearch %(ruby -rrbconfig -e 'puts Config::CONFIG["sitearchdir"]')
 
-%define beta_ver %{nil}
-%define beta_str %{nil}
+%define beta_ver b3
+%define beta_str b3-20090215-r2890
 
 Name: openbabel
-Version: 2.2.0
-Release: 3%{?dist}
+Version: 2.2.1
+Release: 0.1.%{beta_ver}%{?dist}
 Summary: Chemistry software file format converter
 License: GPLv2
 Group: Applications/File
@@ -89,16 +89,13 @@
 Ruby wrapper for the Open Babel library.
 
 %prep
-%setup -q -n %{name}-%{version}%{beta_ver}
+%setup -q -n %{name}-%{version}%{beta_str}
 %patch -p1 -b .gcc43
 %patch1 -p1 -b .r
 %patch2 -p1 -b .chk
 chmod 644 src/formats/{mmcif,fchk}format.cpp
 
 %build
-# don't reference m4 include directory which isn't shipped in the tarball
-# there's also a typo ("autconf" instead of "autoconf")
-sed -i -e 's/ACLOCAL_AMFLAGS=/#ACLOCAL_AMFLAGS=/g' Makefile.am
 autoreconf --force --install
 %configure --enable-shared=yes --enable-static=no --disable-inchi --enable-maintainer-mode
 %{__make} %{?_smp_mflags}
@@ -113,6 +110,7 @@
 popd
 
 pushd scripts/ruby
+ruby extconf.rb --with-openbabel-include=../../include --with-openbabel-lib=../../src/.libs
 %{__make} %{?_smp_mflags}
 popd
 
@@ -140,9 +138,6 @@
 %{__make} install DESTDIR=$RPM_BUILD_ROOT
 popd
 
-# work around testsuite crash
-%{__rm} src/formats/.libs/*.soT
-
 %clean
 %{__rm} -rf $RPM_BUILD_ROOT
 
@@ -188,6 +183,10 @@
 %{ruby_sitearch}/openbabel.so
 
 %changelog
+* Sun Mar 01 2009 Dominik Mierzejewski <rpm at greysector.net> 2.2.1-0.1.b3
+- update to 2.2.1 beta3
+- drop some obsolete workarounds
+
 * Thu Feb 26 2009 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 2.2.0-3
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
 


Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/openbabel/devel/sources,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- sources	6 Jul 2008 14:57:34 -0000	1.12
+++ sources	1 Mar 2009 12:18:33 -0000	1.13
@@ -1 +1 @@
-643a18c7ba09254d36e93afd6277346f  openbabel-2.2.0.tar.gz
+b71b29d0e42dbcd779bded9f583a172f  openbabel-2.2.1b3-20090215-r2890.tar.gz


