- updated to 2.2.3

- dropped obsolete patch - fix configure to detect external inchi-1.0.2
2009-09-13 17:27:34 +00:00 · 2009-09-13 17:27:34 +00:00 · c0d8acee97
parent 74b3a72dc5
commit c0d8acee97
4 changed files with 30 additions and 169 deletions
--- a/openbabel-check.patch
+++ b/openbabel-check.patch
@ -1,10 +1,10 @@
-diff -up openbabel-2.2.1b3-20090215-r2890/test/wrapper.sh.chk openbabel-2.2.1b3-20090215-r2890/test/wrapper.sh
--- openbabel-2.2.1b3-20090215-r2890/test/wrapper.sh.chk	2009-01-12 20:10:33.000000000 +0100
-+++ openbabel-2.2.1b3-20090215-r2890/test/wrapper.sh	2009-03-01 16:19:28.000000000 +0100
+diff -up openbabel-2.2.3/test/wrapper.sh.chk openbabel-2.2.3/test/wrapper.sh
+--- openbabel-2.2.3/test/wrapper.sh.chk	2009-07-29 01:05:03.000000000 +0200
+++ openbabel-2.2.3/test/wrapper.sh	2009-08-26 15:55:28.000000000 +0200
@@ -16,11 +16,11 @@ TESTS="${TESTS} logp_psa math"
 TESTS="${TESTS} mol phmodel residue rings"
- TESTS="${TESTS} smarts smilesmatch unitcell"
- TESTS="${TESTS} cml.sh test-set.sh"
+ TESTS="${TESTS} smarts smilesmatch strip unitcell"
+ TESTS="${TESTS} zipstream cml.sh test-set.sh"
 -if [ "x${srcdir}" != "x" ]; then
 -  TESTS="${TESTS} ${srcdir}/inchi.pl ${srcdir}/inchi2.pl"
 -else
@ -18,21 +18,3 @@ diff -up openbabel-2.2.1b3-20090215-r2890/test/wrapper.sh.chk openbabel-2.2.1b3-
 PROVE=prove
 
 echo "top srcdir: .${topsrcdir}."
-@@ -45,4 +45,4 @@ if [ -d ../src/formats/.libs ]; then
-     fi
- fi
- 
-${PROVE} "$@" ${TESTS}
-+${PROVE} --verbose "$@" ${TESTS}
-diff -up openbabel-2.2.0/test/bond.cpp.chk openbabel-2.2.0/test/bond.cpp
--- openbabel-2.2.0/test/bond.cpp.chk	2008-06-13 22:48:05.000000000 +0200
-+++ openbabel-2.2.0/test/bond.cpp	2008-07-06 21:45:44.000000000 +0200
-@@ -58,7 +58,7 @@ int main(int argc,char *argv[])
- 
-   bond1.SetBegin(&begin1);
-   bond1.SetEnd(&end1);
-  cout << "ok 4\n";
-+  cout << "ok 3\n";
- 
-   return(0);
- }
--- a/openbabel-gcc43.patch
+++ b/openbabel-gcc43.patch
@ -1,138 +0,0 @@
-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 <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 <strings.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
- 
-+#include <typeinfo>
-+
- #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 <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>
- 
- 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>
- #include <iosfwd>
-#include <vector>
-+#include <cstring>
- #include <fstream>
- 
- #include <openbabel/fingerprint.h>
-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>
- 
- // 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 <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 <locale>
- #include <limits>
-+#include <typeinfo>
- 
- #include <stdlib.h>
- 
-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 <cstring>
-+
- #include <openbabel/babelconfig.h>
- 
- #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>
- #include <cstdlib>
-+#include <cstring>
- 
- using namespace std;
- using namespace OpenBabel;
--- a/openbabel-inchi.patch
+++ b/openbabel-inchi.patch
@ -0,0 +1,12 @@
+diff -up openbabel-2.2.3/configure.in.inchi openbabel-2.2.3/configure.in
+--- openbabel-2.2.3/configure.in.inchi	2009-07-29 03:05:04.000000000 +0200
+++ openbabel-2.2.3/configure.in	2009-08-26 16:26:08.000000000 +0200
+@@ -239,7 +239,7 @@ AC_SUBST(LIBDL)
+ AM_PATH_XML2(2.6.5)
+ AM_CONDITIONAL(BUILD_XML, test x"$XML_LIBS" != "x")
+ 
+-AC_CHECK_LIB(inchi, GetINCHI, LIBINCHI="-linchi", LIBINCHI="")
+AC_CHECK_LIB(stdinchi, GetStdINCHI, LIBINCHI="-lstdinchi", LIBINCHI="")
+ AM_CONDITIONAL(BUILD_INCHI, test x"$LIBINCHI" = "x" -o "$inchi" = "yes")
+ 
+ AC_CHECK_LIB(z, inflateEnd, [zlib_cv_libz=yes], [zlib_cv_libz=no])
--- a/openbabel.spec
+++ b/openbabel.spec
@ -4,20 +4,20 @@
 %{!?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 b3
-%define beta_str b3-20090215-r2890
+%define beta_ver %{nil}
+%define beta_str %{nil}

 Name: openbabel
-Version: 2.2.1
-Release: 0.2.%{beta_ver}%{?dist}
+Version: 2.2.3
+Release: 1%{beta_ver}%{?dist}
 Summary: Chemistry software file format converter
 License: GPLv2
 Group: Applications/File
 URL: http://openbabel.org/
-Source: http://dl.sourceforge.net/sourceforge/openbabel/%{name}-%{version}%{beta_str}.tar.gz
-Patch: %{name}-gcc43.patch
+Source: http://downloads.sourceforge.net/sourceforge/openbabel/%{name}-%{version}%{beta_str}.tar.gz
 Patch1: %{name}-rpm.patch
 Patch2: %{name}-check.patch
+Patch3: %{name}-inchi.patch
 BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 BuildRequires: inchi-devel
 BuildRequires: libtool
@ -90,10 +90,10 @@ Ruby wrapper for the Open Babel library.

 %prep
 %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
+%patch3 -p1 -b .inchi
+chmod 644 src/formats/mmcifformat.cpp

 %build
 autoreconf --force --install
@ -183,6 +183,11 @@ popd
 %{ruby_sitearch}/openbabel.so

 %changelog
+* Wed Aug 26 2009 Dominik Mierzejewski <rpm@greysector.net> 2.2.3-1
+- updated to 2.2.3
+- dropped obsolete patch
+- fix configure to detect external inchi-1.0.2
+
 * Sat Jul 25 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 2.2.1-0.2.b3
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild