diff --git a/.cvsignore b/.cvsignore index 6bf83c9..c4c193b 100644 --- a/.cvsignore +++ b/.cvsignore @@ -1 +1 @@ -openbabel-2.2.0.tar.gz +openbabel-2.2.1b3-20090215-r2890.tar.gz diff --git a/openbabel-gcc43.patch b/openbabel-gcc43.patch index e2a8ba8..9ed3ef6 100644 --- a/openbabel-gcc43.patch +++ b/openbabel-gcc43.patch @@ -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 -+ - //***************************************************************************** - // 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 -+ +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 - #include -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 +- ++#include + #include + #include #include +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 + #include #include - #include -+#include ++#include - #include + #include + #include +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 + #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 - #include +#include - #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 + #include + #include +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 +#include ++ + #include + #include + #include +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 + #include + #include ++#include - // No diagnoalization yet. Perhaps for 2.2 -GRH - // #include -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 #include @@ -67,56 +68,66 @@ diff -up openbabel-2.2.0b7/src/fingerprint.cpp.gcc43 openbabel-2.2.0b7/src/finge #include #include -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 +#include -+ - #include - #include - #include -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 +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 - #include + #include ++#include + #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 -+#include + #include + #include ++#include - #include - #include -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 + #include - #include -- -+#include - #include - #include - #include -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 - #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 ++#include + - #include #include - #include -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 +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 ++ + //***************************************************************************** + // 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 #include diff --git a/openbabel-rpm.patch b/openbabel-rpm.patch index ef26b76..b386b89 100644 --- a/openbabel-rpm.patch +++ b/openbabel-rpm.patch @@ -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.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; diff --git a/openbabel.spec b/openbabel.spec index f93944f..55a1878 100644 --- a/openbabel.spec +++ b/openbabel.spec @@ -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 @@ Requires: %{name} = %{version}-%{release} 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 @@ python setup.py build popd pushd scripts/ruby +ruby extconf.rb --with-openbabel-include=../../include --with-openbabel-lib=../../src/.libs %{__make} %{?_smp_mflags} popd @@ -140,9 +138,6 @@ pushd scripts/ruby %{__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 @@ popd %{ruby_sitearch}/openbabel.so %changelog +* Sun Mar 01 2009 Dominik Mierzejewski 2.2.1-0.1.b3 +- update to 2.2.1 beta3 +- drop some obsolete workarounds + * Thu Feb 26 2009 Fedora Release Engineering - 2.2.0-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild diff --git a/sources b/sources index 53ce2b4..c3d3432 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -643a18c7ba09254d36e93afd6277346f openbabel-2.2.0.tar.gz +b71b29d0e42dbcd779bded9f583a172f openbabel-2.2.1b3-20090215-r2890.tar.gz