[med-svn] r2448 - in trunk/packages/libsbml/trunk/debian: . patches
moriyoshi-guest at alioth.debian.org
moriyoshi-guest at alioth.debian.org
Mon Sep 1 23:55:51 UTC 2008
Author: moriyoshi-guest
Date: 2008-09-01 23:55:50 +0000 (Mon, 01 Sep 2008)
New Revision: 2448
Added:
trunk/packages/libsbml/trunk/debian/jvm-find.sh
trunk/packages/libsbml/trunk/debian/libsbml3-cil.dirs
trunk/packages/libsbml/trunk/debian/libsbml3-cil.install
trunk/packages/libsbml/trunk/debian/patches/08_missing_includes.dpatch
trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch
Modified:
trunk/packages/libsbml/trunk/debian/changelog
trunk/packages/libsbml/trunk/debian/control
trunk/packages/libsbml/trunk/debian/libsbml3-dev.install
trunk/packages/libsbml/trunk/debian/patches/00list
trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch
trunk/packages/libsbml/trunk/debian/rules
Log:
* Upstream update.
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2008-09-01 22:29:36 UTC (rev 2447)
+++ trunk/packages/libsbml/trunk/debian/changelog 2008-09-01 23:55:50 UTC (rev 2448)
@@ -1,37 +1,27 @@
-libsbml (3.1.1-1) UNRELEASED; urgency=low
+libsbml (3.2.0-1) lenny; urgency=low
- * New upstream release.
- * Reenable language bindings.
+ * Upstream update.
- -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Fri, 18 Jul 2008 09:47:00 +0900
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Sun, 24 Aug 2008 19:27:26 +0900
-libsbml (3.1.0-1) UNRELEASED; urgency=low
+libsbml (3.1.1-1) lenny; urgency=low
- * New upstream release
- * Updated to Standards-Version 3.7.3 (no changes needed)
+ * Upstream update.
- -- David Paleino <d.paleino at gmail.com> Wed, 06 Feb 2008 13:39:28 +0100
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Wed, 18 Jun 2008 18:35:01 +0900
-libsbml (3.0.0beta2-1) unstable; urgency=low
+libsbml (2.3.5-2) lenny; urgency=low
- [ Changyan Xie ]
- * Upstream upgrade.
- * Remove all patches, since not neccessary now.
- * Upstream seperate docs into another package, so this package can now be in
- main section other than contrib. And also delete the libsbml-doc entry.
- * New version contain no bindings except C/C++. so remove libsbml-java,
- libsbml-perl, python-sbml entries.
- * Add chmod u+x to configure and config/install-sh in debian/rules since dpatch
- cannot handle these.
- * Add one dpatch to handle the soname absence.
- * Change Build-Dep, remove bindings' requirements and correct the debhelper
- compat version problem.
+ * Changed package versioning scheme
- [ Nelson A. de Oliveira ]
- * Added watch file.
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Wed, 18 Jun 2008 18:20:25 +0900
- -- Nelson A. de Oliveira <naoliv at debian.org> Thu, 23 Aug 2007 16:00:45 -0300
+libsbml (2.3.5-1) lenny; urgency=low
+ * Upstream release.
+
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Sat, 15 Dec 2007 09:24:43 +0900
+
libsbml (2.3.4-2) unstable; urgency=low
[ Moriyoshi Koizumi ]
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2008-09-01 22:29:36 UTC (rev 2447)
+++ trunk/packages/libsbml/trunk/debian/control 2008-09-01 23:55:50 UTC (rev 2448)
@@ -3,15 +3,16 @@
Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>, Changyan Xie <panchoat at gmail.com>, Moriyoshi Koizumi <mozo at sfc.keio.ac.jp>
Build-Depends: debhelper (>= 4.0.0), dpatch, bash, autoconf, automake, ruby,
libtool (>= 1.5.0), build-essential, libxml2-dev, python-dev, ruby1.8-dev,
- libperl-dev, java-gcj-compat-dev | java-sdk, octave2.9-headers, fastjar,
- python-support (>= 0.3), doxygen, graphviz
-Standards-Version: 3.7.3
-Section: science
+ libperl-dev, openjdk-6-jdk | java-gcj-compat-dev | java-sdk, octave2.9-headers, fastjar,
+ python-support (>= 0.3), doxygen, graphviz, libz-dev, libbz2-dev,
+ cli-common-dev, cli-runtime, mono-mcs
+Standards-Version: 3.7.2
+Section: contrib/science
XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libsbml/trunk/
XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libsbml
Package: libsbml3-dev
-Section: devel
+Section: contrib/devel
Provides: libsbml-dev
Conflicts: libsbml2-dev
Architecture: any
@@ -37,7 +38,7 @@
This package contains files necessary for development with libsbml.
Package: libsbml3
-Section: libs
+Section: contrib/libs
Architecture: any
Conflicts: libsbml1, libsbml2
Depends: ${shlibs:Depends}, ${misc:Depends}
@@ -60,7 +61,7 @@
(native), and Mac OS X.
Package: python-sbml3
-Section: python
+Section: contrib/python
Provides: ${python:Provides}, python-sbml
Conflicts: python-sbml2
Architecture: any
@@ -86,7 +87,7 @@
This package contain the Python binding of LibSBML.
Package: libsbml3-ruby1.8
-Section: libs
+Section: contrib/libs
Provides: libsbml3-ruby
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
@@ -111,7 +112,7 @@
This package contain the Ruby binding of LibSBML.
Package: libsbml3-java
-Section: libs
+Section: contrib/libs
Provides: libsbml-java
Conflicts: libsbml2-java
Architecture: any
@@ -137,7 +138,7 @@
This Package contains the Java binding of LibSBML.
Package: libsbml3-perl
-Section: perl
+Section: contrib/perl
Provides: libsbml-perl
Conflicts: libsbml2-perl
Depends: ${shlibs:Depends}, ${perl:Depends}, ${misc:Depends}
@@ -163,7 +164,7 @@
This package contains the Perl binding of LibSBML.
Package: libsbml3-octave
-Section: math
+Section: contrib/math
Depends: ${shlibs:Depends}, ${misc:Depends}, octave
Architecture: any
Description: System Biology Markup Language Library -- Octave binding
@@ -186,6 +187,30 @@
.
This package contains the Octave binding of LibSBML.
+Package: libsbml3-cil
+Section: contrib/libs
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${cli:Depends}
+Architecture: any
+Description: System Biology Markup Language Library -- Octave binding
+ LibSBML is a library designed to help you read, write, manipulate,
+ translate, and validate SBML files and data streams. It is not an
+ application itself (though it does come with many example programs),
+ but rather a library you can embed in your own applications.
+ .
+ LibSBML is written in ISO C and C++ but as a library it may be
+ used from all the programming languages listed to the left. In fact,
+ we strive to adhere to the natural idioms of each particular language
+ to make the libSBML programming experience seamless. For example, SBML
+ <listOf> elements behave like lists and sequences in Python, but
+ vectors in Matlab. Also, the C and C++ interfaces are completely
+ distinct (it's possible to program in pure C), but in C++ the C APIs
+ may be called without sacrifcing type safety.
+ .
+ The LibSBML code is very portable and is supported on Linux, Windows
+ (native), and Mac OS X.
+ .
+ This package contains the CIL binding of LibSBML.
+
Package: libsbml3-doc
Section: devel
Architecture: all
@@ -215,7 +240,7 @@
This package contains Python API documentation of LibSBML.
Package: libsbml3-examples
-Section: doc
+Section: contrib/doc
Architecture: all
Depends: libsbml3-dev (= ${Source-Version})
Description: System Biology Markup Language Library -- example files
Added: trunk/packages/libsbml/trunk/debian/jvm-find.sh
===================================================================
--- trunk/packages/libsbml/trunk/debian/jvm-find.sh (rev 0)
+++ trunk/packages/libsbml/trunk/debian/jvm-find.sh 2008-09-01 23:55:50 UTC (rev 2448)
@@ -0,0 +1,3 @@
+#!/bin/sh
+TARGET_JAVAC=`env LANG=C update-alternatives --display javac | sed -e "s/Current \\\`best' version is \\(.*\\)\.\$/\\1/; t e; d; :e"`
+echo JAVA_HOME=/usr/lib/jvm/`find /usr/lib/jvm -maxdepth 1 -iname "*.jinfo" | head -n 1 | while read file; do test \`sed -e 's/^jdk *javac *//; t e; d; :e' $file\` = "$TARGET_JAVAC" && sed -e 's/name= *//; t e; d; :e' $file; done`
Property changes on: trunk/packages/libsbml/trunk/debian/jvm-find.sh
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mime-type
+ text/x-sh
Name: svn:eol-style
+ native
Added: trunk/packages/libsbml/trunk/debian/libsbml3-cil.dirs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-cil.dirs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-cil.dirs 2008-09-01 23:55:50 UTC (rev 2448)
@@ -0,0 +1 @@
+usr/lib
Added: trunk/packages/libsbml/trunk/debian/libsbml3-cil.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-cil.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-cil.install 2008-09-01 23:55:50 UTC (rev 2448)
@@ -0,0 +1,3 @@
+usr/lib/pkgconfig/libsbml-cil.pc
+usr/lib/cli/*
+usr/lib/mono/*
Modified: trunk/packages/libsbml/trunk/debian/libsbml3-dev.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-dev.install 2008-09-01 22:29:36 UTC (rev 2447)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-dev.install 2008-09-01 23:55:50 UTC (rev 2448)
@@ -2,4 +2,4 @@
usr/lib/libsbml.a
usr/lib/libsbml.la
usr/lib/libsbml.so
-usr/lib/pkgconfig/*
+usr/lib/pkgconfig/libsbml.pc
Modified: trunk/packages/libsbml/trunk/debian/patches/00list
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/00list 2008-09-01 22:29:36 UTC (rev 2447)
+++ trunk/packages/libsbml/trunk/debian/patches/00list 2008-09-01 23:55:50 UTC (rev 2448)
@@ -5,3 +5,4 @@
05_lower_doxygen_ver_req
06_javadoc_discovery
07_perldoc_mod_name_fix
+08_pkgconfig_file_gen
Modified: trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch 2008-09-01 22:29:36 UTC (rev 2447)
+++ trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch 2008-09-01 23:55:50 UTC (rev 2448)
@@ -5,10 +5,10 @@
## DP: No description.
@DPATCH@
-diff -urNad libsbml-3.1.1~/Makefile.in libsbml-3.1.1/Makefile.in
---- libsbml-3.1.1~/Makefile.in 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/Makefile.in 2008-07-18 05:50:18.000000000 +0900
-@@ -180,11 +180,13 @@
+diff -urNad libsbml-3.2.0~/Makefile.in libsbml-3.2.0/Makefile.in
+--- libsbml-3.2.0~/Makefile.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/Makefile.in 2008-09-02 04:51:41.000000000 +0900
+@@ -185,11 +185,13 @@
config/libcheck.m4 \
config/libxml.m4 \
config/lisp.m4 \
@@ -22,7 +22,7 @@
config/octave.m4 \
config/perl.m4 \
config/python.m4 \
-@@ -201,18 +203,14 @@
+@@ -209,7 +211,7 @@
# makefile-common-actions.mk.
extra_distclean = config.status config.cache config.log autom4te.cache \
@@ -31,21 +31,109 @@
# It's safer to remove and recreate the copy of the include files (in the
# 'include' directory) after a make clean. Previously we did it in a make
- # distclean only, but I've run into situations where the copy didn't get
- # updated. This is a bit of a sledgehammer, but it's not too bad.
+@@ -218,10 +220,6 @@
--extra_clean = include libsbml.pc
--
+ extra_clean = include libsbml.pc
+
-ifeq "$(HOST_TYPE)" "cygwin"
- extra_clean += libsbml.la
-endif
-+extra_clean = include libsbml.pc libsbml.la
+-
-
# -----------------------------------------------------------------------------
-diff -urNad libsbml-3.1.1~/acinclude.m4 libsbml-3.1.1/acinclude.m4
---- libsbml-3.1.1~/acinclude.m4 1970-01-01 09:00:00.000000000 +0900
-+++ libsbml-3.1.1/acinclude.m4 2008-07-18 05:50:18.000000000 +0900
+ # Primary build actions.
+@@ -231,7 +229,7 @@
+ # of the form `foo-recursive' to run 'make foo' in directories defined in
+ # variable `subdirs'.
+
+-all: configure Makefile include all-recursive libsbml.pc libsbml.la
++all: configure Makefile include all-recursive libsbml.pc
+
+ docs:;
+ ifneq "$(MAKEFLAGS)" ""
+@@ -304,46 +302,10 @@
+
+
+ # -----------------------------------------------------------------------------
+-# libsbml.la.
+-# -----------------------------------------------------------------------------
+-
+-# Currently we only need to provide this under cygwin. Maybe we should also
+-# provide it for libtool users on other platforms?
+-
+-libsbml.la: Makefile
+-ifeq "$(HOST_TYPE)" "cygwin"
+- @rm -f libsbml.pc
+- @echo "# libsbml.la" > libsbml.la
+- @echo "# Generated by libSBML's Makefile." >> libsbml.la
+- @echo "" >> libsbml.la
+- @echo "library_names='libsbml.$(SHAREDLIBEXT)'" >> libsbml.la
+- @echo "libdir='$(LIBDIR)'" >> libsbml.la
+- @echo "dlname=''" >> libsbml.la
+- @echo "dlopen=''" >> libsbml.la
+- @echo "dlpreopen=''" >> libsbml.la
+- @echo "old_library=''" >> libsbml.la
+- @echo "current=0" >> libsbml.la
+- @echo "age=0" >> libsbml.la
+- @echo "revision=0" >> libsbml.la
+- @echo "installed=yes" >> libsbml.la
+- @echo "shouldnotlink=no" >> libsbml.la
+- ifdef USE_XERCES
+- @echo "dependency_libs='${DEPENDENCY_LIBFLAGS}'" >> libsbml.la
+- endif
+- ifdef USE_EXPAT
+- @echo "dependency_libs='${DEPENDENCY_LIBFLAGS}'" >> libsbml.la
+- endif
+- ifdef USE_LIBXML
+- @echo "dependency_libs='${DEPENDENCY_LIBFLAGS}'" >> libsbml.la
+- endif
+-endif
+-
+-
+-# -----------------------------------------------------------------------------
+ # Installation.
+ # -----------------------------------------------------------------------------
+
+-install: all install-recursive install-warnings install-pc install-la
++install: all install-recursive install-warnings install-pc
+
+ install-docs: install-docs-recursive
+
+@@ -362,13 +324,7 @@
+ install-pc: libsbml.pc
+ $(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
+
+-install-la: libsbml.la
+-ifeq "$(HOST_TYPE)" "cygwin"
+- $(INSTALL_SH) libsbml.la -m 0644 "$(DESTDIR)$(LIBDIR)/libsbml.la"
+-endif
+-
+-
+-uninstall: uninstall-recursive uninstall-libsbml-pc uninstall-libsbml-la
++uninstall: uninstall-recursive uninstall-libsbml-pc
+ @if test -d "$(DESTDIR)$(LIBDIR)"; then \
+ if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \
+ echo rmdir "$(DESTDIR)$(LIBDIR)"; \
+@@ -409,16 +365,6 @@
+ fi; \
+ fi;
+
+-uninstall-libsbml-la:
+-ifeq "$(HOST_TYPE)" "cygwin"
+- @target="$(DESTDIR)$(LIBDIR)/libsbml.la"; \
+- if test -f $$target ; then \
+- echo rm $$target; \
+- rm $$target; \
+- fi;
+-endif
+-
+-
+ # -----------------------------------------------------------------------------
+ # Cleaning.
+ # -----------------------------------------------------------------------------
+diff -urNad libsbml-3.2.0~/acinclude.m4 libsbml-3.2.0/acinclude.m4
+--- libsbml-3.2.0~/acinclude.m4 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.2.0/acinclude.m4 2008-09-02 04:51:33.000000000 +0900
@@ -0,0 +1,27 @@
+# generated automatically by aclocal 1.9.6 -*- Autoconf -*-
+
@@ -74,9 +162,9 @@
+m4_include([config/runldpath.m4])
+m4_include([config/swig.m4])
+m4_include([config/xercesc.m4])
-diff -urNad libsbml-3.1.1~/config/lt_link_helper.sh.in libsbml-3.1.1/config/lt_link_helper.sh.in
---- libsbml-3.1.1~/config/lt_link_helper.sh.in 1970-01-01 09:00:00.000000000 +0900
-+++ libsbml-3.1.1/config/lt_link_helper.sh.in 2008-07-18 05:50:18.000000000 +0900
+diff -urNad libsbml-3.2.0~/config/lt_link_helper.sh.in libsbml-3.2.0/config/lt_link_helper.sh.in
+--- libsbml-3.2.0~/config/lt_link_helper.sh.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.2.0/config/lt_link_helper.sh.in 2008-09-02 04:51:33.000000000 +0900
@@ -0,0 +1,69 @@
+#!/bin/sh
+
@@ -99,7 +187,7 @@
+
+linker_tmpdir=`mktemp -d`
+stage_dir="${linker_tmpdir}/stage"
-+mkdir -p "${stage_dir}"
++mkdir -p "${stage_dir}/${libdir}"
+
+LD="$1"
+shift
@@ -144,12 +232,12 @@
+fi
+
+eval "@abs_top_srcdir@/libtool --tag=\"$TAG\" --mode=link \"$LD\" -rpath \"${libdir}\" -inst-prefix-dir \"${stage_dir}\" -module -avoid-version -export-dynamic -no-undefined -shrext "${dllibext}" -o \"${out_dir}/${out_filename}.la\" $args" && \
-+ eval "@abs_top_srcdir@/libtool --mode=install cp \"${out_dir}/${out_filename}.la\" \"${stage_dir}/${libdir}\"" && \
++ eval "@abs_top_srcdir@/libtool --mode=install cp \"${out_dir}/${out_filename}.la\" \"${stage_dir}/${libdir}/${out_filename}.la\"" && \
+ cp "${stage_dir}/${libdir}/${out_filename}${dllibext}" "${out_dir}"
+rm -rf "${linker_tmpdir}"
-diff -urNad libsbml-3.1.1~/config/makefile-common-actions.mk libsbml-3.1.1/config/makefile-common-actions.mk
---- libsbml-3.1.1~/config/makefile-common-actions.mk 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/config/makefile-common-actions.mk 2008-07-18 05:50:18.000000000 +0900
+diff -urNad libsbml-3.2.0~/config/makefile-common-actions.mk libsbml-3.2.0/config/makefile-common-actions.mk
+--- libsbml-3.2.0~/config/makefile-common-actions.mk 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/config/makefile-common-actions.mk 2008-09-02 04:51:33.000000000 +0900
@@ -40,7 +40,7 @@
# -----------------------------------------------------------------------------
@@ -368,10 +456,10 @@
distclean: clean distclean-compile distclean-depend distclean-generic \
distclean-tags distclean-libtool
-diff -urNad libsbml-3.1.1~/config/makefile-common-vars.mk.in libsbml-3.1.1/config/makefile-common-vars.mk.in
---- libsbml-3.1.1~/config/makefile-common-vars.mk.in 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/config/makefile-common-vars.mk.in 2008-07-18 05:50:18.000000000 +0900
-@@ -136,6 +136,9 @@
+diff -urNad libsbml-3.2.0~/config/makefile-common-vars.mk.in libsbml-3.2.0/config/makefile-common-vars.mk.in
+--- libsbml-3.2.0~/config/makefile-common-vars.mk.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/config/makefile-common-vars.mk.in 2008-09-02 04:51:33.000000000 +0900
+@@ -144,6 +144,9 @@
OCTAVE = @OCTAVE@
MKOCTFILE = @MKOCTFILE@
MKOCTFILE_FLAGS = @MKOCTFILE_FLAGS@
@@ -381,17 +469,20 @@
OCTAVEEXT = @OCTAVEEXT@
USE_LISP = @USE_LISP@
-@@ -201,6 +204,7 @@
+@@ -219,7 +222,10 @@
PACKAGE_VERSION = @PACKAGE_VERSION@
RANLIB = @RANLIB@
SHAREDLIBEXT = @SHAREDLIBEXT@
+LIBTOOL = @LIBTOOL@
SHELL = @SHELL@
++SN = @SN@
++GACUTIL = @GACUTIL@
LIBSBML_VERSION = @PACKAGE_VERSION@
-diff -urNad libsbml-3.1.1~/config/mkoctfile_wrapper.sh.in libsbml-3.1.1/config/mkoctfile_wrapper.sh.in
---- libsbml-3.1.1~/config/mkoctfile_wrapper.sh.in 1970-01-01 09:00:00.000000000 +0900
-+++ libsbml-3.1.1/config/mkoctfile_wrapper.sh.in 2008-07-18 05:50:39.000000000 +0900
+ LIBSBML_VERSION_NUMERIC = @LIBSBML_VERSION_NUMERIC@
+diff -urNad libsbml-3.2.0~/config/mkoctfile_wrapper.sh.in libsbml-3.2.0/config/mkoctfile_wrapper.sh.in
+--- libsbml-3.2.0~/config/mkoctfile_wrapper.sh.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.2.0/config/mkoctfile_wrapper.sh.in 2008-09-02 04:51:33.000000000 +0900
@@ -0,0 +1,14 @@
+#!/bin/sh
+SHAREDLIBEXT=@SHAREDLIBEXT@
@@ -407,9 +498,9 @@
+done
+
+eval "exec $args"
-diff -urNad libsbml-3.1.1~/config/octave.m4 libsbml-3.1.1/config/octave.m4
---- libsbml-3.1.1~/config/octave.m4 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/config/octave.m4 2008-07-18 05:50:18.000000000 +0900
+diff -urNad libsbml-3.2.0~/config/octave.m4 libsbml-3.2.0/config/octave.m4
+--- libsbml-3.2.0~/config/octave.m4 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/config/octave.m4 2008-09-02 04:51:33.000000000 +0900
@@ -42,9 +42,13 @@
[no-octave-found], [$with_octave/bin])
AC_PATH_PROG([MKOCTFILE], [mkoctfile], [$with_octave/bin/mkoctfile],
@@ -450,10 +541,10 @@
fi
-diff -urNad libsbml-3.1.1~/configure.ac libsbml-3.1.1/configure.ac
---- libsbml-3.1.1~/configure.ac 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/configure.ac 2008-07-18 05:50:18.000000000 +0900
-@@ -133,13 +133,15 @@
+diff -urNad libsbml-3.2.0~/configure.ac libsbml-3.2.0/configure.ac
+--- libsbml-3.2.0~/configure.ac 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/configure.ac 2008-09-02 04:51:33.000000000 +0900
+@@ -139,13 +139,17 @@
AC_PROG_CXX
AC_PROG_CC
AC_PROG_CPP
@@ -468,10 +559,12 @@
AC_PATH_PROG([AUTOCONF],[autoconf],[autoconf])
AC_PATH_PROG([ACLOCAL],[aclocal],[aclocal])
-AC_PATH_PROG([AR],[ar],[ar])
++AC_PATH_PROGS([SN], [sn])
++AC_PATH_PROGS([GACUTIL], [gacutil])
CONFIG_PROG_SWIG(1.3.33)
CONFIG_PROG_PYTHON
-@@ -225,7 +227,9 @@
+@@ -234,7 +238,9 @@
dnl Output
dnl ---------------------------------------------------------------------------
@@ -481,9 +574,77 @@
AC_CONFIG_FILES([./Makefile])
AC_CONFIG_FILES([src/Makefile])
-diff -urNad libsbml-3.1.1~/src/bindings/java/Makefile.in libsbml-3.1.1/src/bindings/java/Makefile.in
---- libsbml-3.1.1~/src/bindings/java/Makefile.in 2008-07-18 05:50:17.907976893 +0900
-+++ libsbml-3.1.1/src/bindings/java/Makefile.in 2008-07-18 05:50:18.000000000 +0900
+diff -urNad libsbml-3.2.0~/src/bindings/csharp/Makefile.in libsbml-3.2.0/src/bindings/csharp/Makefile.in
+--- libsbml-3.2.0~/src/bindings/csharp/Makefile.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/src/bindings/csharp/Makefile.in 2008-09-02 04:51:33.000000000 +0900
+@@ -95,9 +95,9 @@
+ SWIGFLAGS += $(CSHARP_SWIGFLAGS) -I../swig
+ SWIGFLAGS_WIN = -DSWIGWIN -DSWIG_CSHARP_NO_WSTRING_HELPER
+
+-extra_LDFLAGS = $(CSHARP_LDFLAGS) -L../..
++extra_LDFLAGS = $(CSHARP_LDFLAGS)
+
+-extra_LIBS = -lsbml
++extra_LIBS = ../../libsbml.la
+
+ ifdef USE_EXPAT
+ extra_CPPFLAGS += @EXPAT_CPPFLAGS@
+@@ -181,7 +181,7 @@
+ # `extra_clean' and `extra_distclean' determine the files and directories
+ # removed during "make clean" and "make distclean".
+
+-extra_clean = $(csproxy_lib) $(dllimport_lib) $(check_runner_exe) $(tmpfiles)
++extra_clean = $(csproxy_lib) $(dllimport_lib) $(check_runner_exe) $(tmpfiles) libsbmlcs.snk
+
+ extra_distclean =
+
+@@ -290,7 +290,8 @@
+
+
+ $(csproxy_lib): $(outpath)/libsbml.cs $(dllimport_lib)
+- "$(CSHARP_COMPILER)" $(CSC_OPT_SHARED) $(CSC_OPT_OUTPUT)$(csproxy_lib) $(outpath)/*.cs
++ "$(SN)" -k libsbmlcs.snk
++ "$(CSHARP_COMPILER)" $(CSC_OPT_SHARED) $(CSC_OPT_OUTPUT)$(csproxy_lib) $(outpath)/*.cs /keyfile:libsbmlcs.snk
+
+
+ $(outpath)/libsbml.cs: libsbml_wrap.cpp
+@@ -424,18 +425,23 @@
+ # -----------------------------------------------------------------------------
+
+ install: check_swigfile_consistency $(libraries)
+- @list='$(libraries)'; for lib in $$list; do \
+- echo "$(INSTALL) $$lib $(DESTDIR)$(LIBDIR)"; \
+- $(INSTALL) $$lib $(DESTDIR)$(LIBDIR); \
+- done;
++ $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR)/cli/libsbml-3.0
++ for lib in $(csproxy_lib); do \
++ $(GACUTIL) /i $$lib /root $(DESTDIR)$(LIBDIR); \
++ $(INSTALL_SH) $$lib $(DESTDIR)$(LIBDIR)/cli/libsbml-3.0/$$lib; \
++ done
++ for lib in $(dllimport_lib); do \
++ $(INSTALL_SH) $$lib $(DESTDIR)$(LIBDIR)/cli/libsbml-3.0/$$lib; \
++ done
+
+ uninstall:
+- @list='$(libraries)'; for lib in $$list; do \
+- if test -f "$(DESTDIR)$(LIBDIR)/$$lib"; then \
+- echo rm "$(DESTDIR)$(LIBDIR)/$$lib"; \
+- rm $(DESTDIR)$(LIBDIR)/$$lib; \
+- fi; \
+- done;
++ for lib in $(csproxy_lib); do \
++ rm -f $(DESTDIR)$(LIBDIR)/cli/libsbml-3.0/$$lib; \
++ $(GACUTIL) /u $$lib /root $(DESTDIR)$(LIBDIR); \
++ done
++ for lib in $(dllimport_lib); do \
++ rm -f $(DESTDIR)$(LIBDIR)/cli/libsbml-3.0/$$lib; \
++ done
+
+ installcheck:
+
+diff -urNad libsbml-3.2.0~/src/bindings/java/Makefile.in libsbml-3.2.0/src/bindings/java/Makefile.in
+--- libsbml-3.2.0~/src/bindings/java/Makefile.in 2008-09-02 04:51:33.000000000 +0900
++++ libsbml-3.2.0/src/bindings/java/Makefile.in 2008-09-02 04:51:33.000000000 +0900
@@ -60,9 +60,9 @@
extra_CPPFLAGS = $(JAVA_CPPFLAGS) -I../swig
SWIGFLAGS += $(JAVA_CPPFLAGS) -I../swig
@@ -505,10 +666,10 @@
# The default action is to remake everything.
-@@ -285,9 +285,17 @@
+@@ -315,9 +315,17 @@
# -----------------------------------------------------------------------------
- install: $(libraries)
+ install: check_swigfile_consistency $(libraries)
- @list='$(libraries)'; for lib in $$list; do \
- echo "$(INSTALL) $$lib $(DESTDIR)$(LIBDIR)"; \
- $(INSTALL) $$lib $(DESTDIR)$(LIBDIR); \
@@ -526,9 +687,9 @@
done;
uninstall:
-diff -urNad libsbml-3.1.1~/src/bindings/octave/Makefile.in libsbml-3.1.1/src/bindings/octave/Makefile.in
---- libsbml-3.1.1~/src/bindings/octave/Makefile.in 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/src/bindings/octave/Makefile.in 2008-07-18 05:50:18.000000000 +0900
+diff -urNad libsbml-3.2.0~/src/bindings/octave/Makefile.in libsbml-3.2.0/src/bindings/octave/Makefile.in
+--- libsbml-3.2.0~/src/bindings/octave/Makefile.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/src/bindings/octave/Makefile.in 2008-09-02 04:51:33.000000000 +0900
@@ -76,7 +76,7 @@
# `extra_clean' and `extra_distclean' determine the files and directories
# removed during "make clean" and "make distclean".
@@ -575,13 +736,13 @@
# -----------------------------------------------------------------------------
-diff -urNad libsbml-3.1.1~/src/bindings/perl/Makefile.PL.in libsbml-3.1.1/src/bindings/perl/Makefile.PL.in
---- libsbml-3.1.1~/src/bindings/perl/Makefile.PL.in 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/src/bindings/perl/Makefile.PL.in 2008-07-18 05:50:18.000000000 +0900
+diff -urNad libsbml-3.2.0~/src/bindings/perl/Makefile.PL.in libsbml-3.2.0/src/bindings/perl/Makefile.PL.in
+--- libsbml-3.2.0~/src/bindings/perl/Makefile.PL.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/src/bindings/perl/Makefile.PL.in 2008-09-02 04:51:33.000000000 +0900
@@ -50,10 +50,9 @@
MAKEFILE => 'Makefile-perl',
INSTALLDIRS => "site",
- LIBS => "@XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ -lm -lstdc++",
+ LIBS => "@XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ @ZLIB_LIBS@ @BZ2_LIBS@ @LIBS@ -lm -lstdc++",
- CC => "@CXX@",
CCFLAGS => "@PERL_CPPFLAGS@",
INC => "-I../swig -I../.. -I../../../include",
@@ -590,10 +751,10 @@
macro => {USE_SWIG => q[@USE_SWIG@]},
OBJECT => "LibSBML_wrap.o",
MAN1PODS => {},
-diff -urNad libsbml-3.1.1~/src/bindings/perl/Makefile.in libsbml-3.1.1/src/bindings/perl/Makefile.in
---- libsbml-3.1.1~/src/bindings/perl/Makefile.in 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/src/bindings/perl/Makefile.in 2008-07-18 05:50:18.000000000 +0900
-@@ -138,7 +138,9 @@
+diff -urNad libsbml-3.2.0~/src/bindings/perl/Makefile.in libsbml-3.2.0/src/bindings/perl/Makefile.in
+--- libsbml-3.2.0~/src/bindings/perl/Makefile.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/src/bindings/perl/Makefile.in 2008-09-02 04:51:33.000000000 +0900
+@@ -139,7 +139,9 @@
@ echo "Reconfigure --with-perl in order to build the perl-bindings"
exit 1
else
@@ -604,9 +765,9 @@
# The following perl commands add missing -lstdc++ option to EXTRALIBS and
# LDLOADLIBS in Makefile-perl.
# ExtUtil::Makemaker may ignore -lstdc++ option in some environments (e.g. MacOSX, cygwin)
-diff -urNad libsbml-3.1.1~/src/bindings/python/Makefile.in libsbml-3.1.1/src/bindings/python/Makefile.in
---- libsbml-3.1.1~/src/bindings/python/Makefile.in 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/src/bindings/python/Makefile.in 2008-07-18 05:50:18.000000000 +0900
+diff -urNad libsbml-3.2.0~/src/bindings/python/Makefile.in libsbml-3.2.0/src/bindings/python/Makefile.in
+--- libsbml-3.2.0~/src/bindings/python/Makefile.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/src/bindings/python/Makefile.in 2008-09-02 04:51:33.000000000 +0900
@@ -78,8 +78,8 @@
extra_CPPFLAGS += -Wno-long-double
endif
@@ -630,9 +791,9 @@
test_objfiles = $(objfiles)
# The default action is to remake everything.
-diff -urNad libsbml-3.1.1~/src/bindings/ruby/Makefile.in libsbml-3.1.1/src/bindings/ruby/Makefile.in
---- libsbml-3.1.1~/src/bindings/ruby/Makefile.in 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/src/bindings/ruby/Makefile.in 2008-07-18 05:50:18.000000000 +0900
+diff -urNad libsbml-3.2.0~/src/bindings/ruby/Makefile.in libsbml-3.2.0/src/bindings/ruby/Makefile.in
+--- libsbml-3.2.0~/src/bindings/ruby/Makefile.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/src/bindings/ruby/Makefile.in 2008-09-02 04:51:33.000000000 +0900
@@ -79,7 +79,7 @@
endif
@@ -673,10 +834,10 @@
# -----------------------------------------------------------------------------
# Creating distribution (for libSBML maintainers only)
-diff -urNad libsbml-3.1.1~/src/sbml/Makefile.in libsbml-3.1.1/src/sbml/Makefile.in
---- libsbml-3.1.1~/src/sbml/Makefile.in 2008-07-18 05:50:16.907919523 +0900
-+++ libsbml-3.1.1/src/sbml/Makefile.in 2008-07-18 05:50:18.000000000 +0900
-@@ -170,19 +170,7 @@
+diff -urNad libsbml-3.2.0~/src/sbml/Makefile.in libsbml-3.2.0/src/sbml/Makefile.in
+--- libsbml-3.2.0~/src/sbml/Makefile.in 2008-09-02 04:51:32.000000000 +0900
++++ libsbml-3.2.0/src/sbml/Makefile.in 2008-09-02 04:51:33.000000000 +0900
+@@ -180,19 +180,7 @@
# The libraries are actually placed in the parent directory.
Added: trunk/packages/libsbml/trunk/debian/patches/08_missing_includes.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/08_missing_includes.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/08_missing_includes.dpatch 2008-09-01 23:55:50 UTC (rev 2448)
@@ -0,0 +1,276 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 08_missing_includes.dpatch by Moriyoshi Koizumi <root at dynein>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+
+diff -ur libsbml-3.1.1.orig/src/annotation/ModelHistory.cpp libsbml-3.1.1/src/annotation/ModelHistory.cpp
+--- libsbml-3.1.1.orig/src/annotation/ModelHistory.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/annotation/ModelHistory.cpp 2008-07-20 02:18:47.000000000 +0000
+@@ -21,6 +21,7 @@
+ * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
++#include <cstdlib>
+
+ #include <sbml/annotation/ModelHistory.h>
+
+diff -ur libsbml-3.1.1.orig/src/common/libsbml-config-unix.h libsbml-3.1.1/src/common/libsbml-config-unix.h
+--- libsbml-3.1.1.orig/src/common/libsbml-config-unix.h 2008-07-20 00:38:16.000000000 +0000
++++ libsbml-3.1.1/src/common/libsbml-config-unix.h 2008-07-20 00:43:02.000000000 +0000
+@@ -44,7 +44,7 @@
+
+
+ /* Define to 1 if you have the <check.h> header file. */
+-#define HAVE_CHECK_H 1
++/* #undef HAVE_CHECK_H */
+
+ /* Define to 1 if you have the `check' library (-lcheck). */
+ /* #undef HAVE_LIBCHECK */
+diff -ur libsbml-3.1.1.orig/src/sbml/Constraint.cpp libsbml-3.1.1/src/sbml/Constraint.cpp
+--- libsbml-3.1.1.orig/src/sbml/Constraint.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/Constraint.cpp 2008-07-20 02:20:43.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/Delay.cpp libsbml-3.1.1/src/sbml/Delay.cpp
+--- libsbml-3.1.1.orig/src/sbml/Delay.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/Delay.cpp 2008-07-20 02:20:58.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/EventAssignment.cpp libsbml-3.1.1/src/sbml/EventAssignment.cpp
+--- libsbml-3.1.1.orig/src/sbml/EventAssignment.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/EventAssignment.cpp 2008-07-20 02:21:17.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/InitialAssignment.cpp libsbml-3.1.1/src/sbml/InitialAssignment.cpp
+--- libsbml-3.1.1.orig/src/sbml/InitialAssignment.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/InitialAssignment.cpp 2008-07-20 02:21:35.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/KineticLaw.cpp libsbml-3.1.1/src/sbml/KineticLaw.cpp
+--- libsbml-3.1.1.orig/src/sbml/KineticLaw.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/KineticLaw.cpp 2008-07-20 02:22:07.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/Model.cpp libsbml-3.1.1/src/sbml/Model.cpp
+--- libsbml-3.1.1.orig/src/sbml/Model.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/Model.cpp 2008-07-20 02:24:07.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/Rule.cpp libsbml-3.1.1/src/sbml/Rule.cpp
+--- libsbml-3.1.1.orig/src/sbml/Rule.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/Rule.cpp 2008-07-20 02:24:55.000000000 +0000
+@@ -22,6 +22,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/SBMLDocument.cpp libsbml-3.1.1/src/sbml/SBMLDocument.cpp
+--- libsbml-3.1.1.orig/src/sbml/SBMLDocument.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/SBMLDocument.cpp 2008-07-20 02:25:13.000000000 +0000
+@@ -22,6 +22,7 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
+ #include <iostream>
+
+ #include <sbml/xml/XMLAttributes.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/SBase.cpp libsbml-3.1.1/src/sbml/SBase.cpp
+--- libsbml-3.1.1.orig/src/sbml/SBase.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/SBase.cpp 2008-07-20 02:25:45.000000000 +0000
+@@ -21,6 +21,7 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
+ #include <sstream>
+
+ #include <sbml/xml/XMLError.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/StoichiometryMath.cpp libsbml-3.1.1/src/sbml/StoichiometryMath.cpp
+--- libsbml-3.1.1.orig/src/sbml/StoichiometryMath.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/StoichiometryMath.cpp 2008-07-20 02:26:15.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/Trigger.cpp libsbml-3.1.1/src/sbml/Trigger.cpp
+--- libsbml-3.1.1.orig/src/sbml/Trigger.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/Trigger.cpp 2008-07-20 02:26:30.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/Unit.cpp libsbml-3.1.1/src/sbml/Unit.cpp
+--- libsbml-3.1.1.orig/src/sbml/Unit.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/Unit.cpp 2008-07-20 02:26:43.000000000 +0000
+@@ -21,6 +21,8 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
++
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+ #include <sbml/xml/XMLInputStream.h>
+diff -ur libsbml-3.1.1.orig/src/sbml/UnitDefinition.cpp libsbml-3.1.1/src/sbml/UnitDefinition.cpp
+--- libsbml-3.1.1.orig/src/sbml/UnitDefinition.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/sbml/UnitDefinition.cpp 2008-07-20 02:26:58.000000000 +0000
+@@ -21,6 +21,7 @@
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
+
+ #include <sbml/xml/XMLNode.h>
+ #include <sbml/xml/XMLAttributes.h>
+diff -ur libsbml-3.1.1.orig/src/units/UnitFormulaFormatter.cpp libsbml-3.1.1/src/units/UnitFormulaFormatter.cpp
+--- libsbml-3.1.1.orig/src/units/UnitFormulaFormatter.cpp 2008-07-20 00:38:15.000000000 +0000
++++ libsbml-3.1.1/src/units/UnitFormulaFormatter.cpp 2008-07-20 02:17:52.000000000 +0000
+@@ -23,6 +23,7 @@
+ * also available online as http://sbml.org/software/libsbml/license.html
+ *----------------------------------------------------------------------- -->*/
+
++#include <cstring>
+ #include <sbml/units/UnitFormulaFormatter.h>
+
+
+diff -ur libsbml-3.1.1.orig/src/validator/constraints/AssignmentCycles.cpp libsbml-3.1.1/src/validator/constraints/AssignmentCycles.cpp
+--- libsbml-3.1.1.orig/src/validator/constraints/AssignmentCycles.cpp 2008-07-20 00:38:15.000000000 +0000
++++ libsbml-3.1.1/src/validator/constraints/AssignmentCycles.cpp 2008-07-20 00:59:21.000000000 +0000
+@@ -21,7 +21,7 @@
+ * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+-
++#include <cstring>
+
+ #include <sbml/Model.h>
+ #include <sbml/Rule.h>
+diff -ur libsbml-3.1.1.orig/src/validator/constraints/ConsistencyConstraints.cpp libsbml-3.1.1/src/validator/constraints/ConsistencyConstraints.cpp
+--- libsbml-3.1.1.orig/src/validator/constraints/ConsistencyConstraints.cpp 2008-07-20 00:38:15.000000000 +0000
++++ libsbml-3.1.1/src/validator/constraints/ConsistencyConstraints.cpp 2008-07-20 00:57:37.000000000 +0000
+@@ -24,7 +24,7 @@
+
+ #ifndef AddingConstraintsToValidator
+
+-//#include <string>
++#include <cstring>
+
+ #include <sbml/SBMLTypes.h>
+ #include <sbml/SBMLTypeCodes.h>
+diff -ur libsbml-3.1.1.orig/src/validator/constraints/OverDeterminedCheck.cpp libsbml-3.1.1/src/validator/constraints/OverDeterminedCheck.cpp
+--- libsbml-3.1.1.orig/src/validator/constraints/OverDeterminedCheck.cpp 2008-07-20 00:38:15.000000000 +0000
++++ libsbml-3.1.1/src/validator/constraints/OverDeterminedCheck.cpp 2008-07-20 01:01:55.000000000 +0000
+@@ -21,6 +21,8 @@
+ * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
++#include <cstring>
++
+ #include <sbml/Model.h>
+ #include <sbml/Compartment.h>
+ #include <sbml/util/List.h>
+diff -ur libsbml-3.1.1.orig/src/validator/constraints/SpeciesReactionOrRule.cpp libsbml-3.1.1/src/validator/constraints/SpeciesReactionOrRule.cpp
+--- libsbml-3.1.1.orig/src/validator/constraints/SpeciesReactionOrRule.cpp 2008-07-20 00:38:15.000000000 +0000
++++ libsbml-3.1.1/src/validator/constraints/SpeciesReactionOrRule.cpp 2008-07-20 01:02:49.000000000 +0000
+@@ -21,6 +21,8 @@
+ * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
++#include <cstring>
++
+ #include <sbml/Model.h>
+ #include <sbml/Rule.h>
+ #include <sbml/Reaction.h>
+diff -ur libsbml-3.1.1.orig/src/validator/constraints/UniqueSpeciesTypesInCompartment.cpp libsbml-3.1.1/src/validator/constraints/UniqueSpeciesTypesInCompartment.cpp
+--- libsbml-3.1.1.orig/src/validator/constraints/UniqueSpeciesTypesInCompartment.cpp 2008-07-20 00:38:15.000000000 +0000
++++ libsbml-3.1.1/src/validator/constraints/UniqueSpeciesTypesInCompartment.cpp 2008-07-20 02:13:52.000000000 +0000
+@@ -21,6 +21,7 @@
+ * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
++#include <cstring>
+
+ #include <sbml/Model.h>
+ #include <sbml/Rule.h>
+diff -ur libsbml-3.1.1.orig/src/xml/LibXMLParser.cpp libsbml-3.1.1/src/xml/LibXMLParser.cpp
+--- libsbml-3.1.1.orig/src/xml/LibXMLParser.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/xml/LibXMLParser.cpp 2008-07-20 00:56:54.000000000 +0000
+@@ -22,6 +22,7 @@
+ *----------------------------------------------------------------------- -->*/
+
+ #include <iostream>
++#include <cstring>
+
+ #include <libxml/xmlerror.h>
+
+diff -ur libsbml-3.1.1.orig/src/xml/XMLNode.cpp libsbml-3.1.1/src/xml/XMLNode.cpp
+--- libsbml-3.1.1.orig/src/xml/XMLNode.cpp 2008-07-20 00:38:14.000000000 +0000
++++ libsbml-3.1.1/src/xml/XMLNode.cpp 2008-07-20 00:55:46.000000000 +0000
+@@ -22,6 +22,7 @@
+ *----------------------------------------------------------------------- -->*/
+
+ #include <sstream>
++#include <cstdlib>
+
+ #include <sbml/util/memory.h>
+ #include <sbml/util/util.h>
Added: trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch 2008-09-01 23:55:50 UTC (rev 2448)
@@ -0,0 +1,134 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 08_pkgconfig_file_gen.dpatch by <moriyoshi at dynein>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad libsbml-3.2.0~/Makefile.in libsbml-3.2.0/Makefile.in
+--- libsbml-3.2.0~/Makefile.in 2008-09-02 04:03:14.000000000 +0900
++++ libsbml-3.2.0/Makefile.in 2008-09-02 04:03:29.000000000 +0900
+@@ -211,14 +211,15 @@
+ # makefile-common-actions.mk.
+
+ extra_distclean = config.status config.cache config.log autom4te.cache \
+- src/common/config.h src/common/stamp-h1 config/lt_link_helper.sh
++ src/common/config.h src/common/stamp-h1 config/lt_link_helper.sh \
++ libsbml.pc libsbml-cil.pc
+
+ # It's safer to remove and recreate the copy of the include files (in the
+ # 'include' directory) after a make clean. Previously we did it in a make
+ # distclean only, but I've run into situations where the copy didn't get
+ # updated. This is a bit of a sledgehammer, but it's not too bad.
+
+-extra_clean = include libsbml.pc
++extra_clean = include
+
+
+ # -----------------------------------------------------------------------------
+@@ -229,7 +230,7 @@
+ # of the form `foo-recursive' to run 'make foo' in directories defined in
+ # variable `subdirs'.
+
+-all: configure Makefile include all-recursive libsbml.pc
++all: configure Makefile include all-recursive
+
+ docs:;
+ ifneq "$(MAKEFLAGS)" ""
+@@ -261,46 +262,6 @@
+
+ base-libs = -lsbml -lstdc++ -lm
+
+-COMPRESS_CPFLAGS = ${ZLIB_CPPFLAGS} ${BZ2_CPPFLAGS}
+-COMPRESS_LDFLAGS = ${ZLIB_LDFLAGS} ${BZ2_LDFLAGS}
+-COMPRESS_LIBS = ${ZLIB_LIBS} ${BZ2_LIBS}
+-
+-XML_CPFLAGS = ${XERCES_CPPFLAGS} ${EXPAT_CPPFLAGS} ${LIBXML_CPPFLAGS}
+-XML_LDFLAGS = ${XERCES_LDFLAGS} ${EXPAT_LDFLAGS} ${LIBXML_LDFLAGS}
+-XML_LIBS = ${XERCES_LIBS} ${EXPAT_LIBS} ${LIBXML_LIBS}
+-
+-DEPENDENCY_CPPFLAGS = ${XML_CPPFLAGS} ${COMPRESS_CPPFLAGS}
+-DEPENDENCY_LIBFLAGS = ${XML_LDFLAGS} ${COMPRESS_LDFLAGS} ${XML_LIBS} ${COMPRESS_LIBS}
+-
+-
+-libsbml.pc: Makefile
+- @rm -f libsbml.pc
+- @echo "Name: @PACKAGE_NAME@" > libsbml.pc
+- @echo "Description: An API library for reading/writing/manipulating SBML" >> libsbml.pc
+- @echo "URL: http://sbml.org/software/libsbml" >> libsbml.pc
+- @echo "Version: @PACKAGE_VERSION@" >> libsbml.pc
+- @echo "" >> libsbml.pc
+- @echo "prefix=@prefix@" >> libsbml.pc
+- @echo "exec_prefix=@exec_prefix@" >> libsbml.pc
+- @echo "libdir=@libdir@" >> libsbml.pc
+- @echo "includedir=@includedir@" >> libsbml.pc
+- @echo "" >> libsbml.pc
+-ifdef USE_XERCES
+- @echo "Libs: -L\$${libdir} ${DEPENDENCY_LIBFLAGS} ${base-libs}" >> libsbml.pc
+- @echo "Cflags: -I\$${includedir} ${DEPENDENCY_CPPFLAGS}" >> libsbml.pc
+- @echo "Conflicts: xerces-c = 2.6.0" >> libsbml.pc
+-endif
+-ifdef USE_EXPAT
+- @echo "Libs: -L\$${libdir} ${DEPENDENCY_LIBFLAGS} ${base-libs}" >> libsbml.pc
+- @echo "Cflags: -I\$${includedir} ${DEPENDENCY_CPPFLAGS}" >> libsbml.pc
+-endif
+-ifdef USE_LIBXML
+- @echo "Libs: -L\$${libdir} ${DEPENDENCY_LIBFLAGS} ${base-libs}" >> libsbml.pc
+- @echo "Cflags: -I\$${includedir} ${DEPENDENCY_CPPFLAGS}" >> libsbml.pc
+- @echo "Requires: libxml-2.0 >= 2.6.22" >> libsbml.pc
+-endif
+-
+-
+ # -----------------------------------------------------------------------------
+ # Installation.
+ # -----------------------------------------------------------------------------
+@@ -322,7 +283,9 @@
+ endif
+
+ install-pc: libsbml.pc
++ $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR)/pkgconfig
+ $(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
++ $(INSTALL_SH) libsbml-cil.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml-cil.pc"
+
+ uninstall: uninstall-recursive uninstall-libsbml-pc
+ @if test -d "$(DESTDIR)$(LIBDIR)"; then \
+diff -urNad libsbml-3.2.0~/configure.ac libsbml-3.2.0/configure.ac
+--- libsbml-3.2.0~/configure.ac 2008-09-02 04:03:14.000000000 +0900
++++ libsbml-3.2.0/configure.ac 2008-09-02 04:03:15.000000000 +0900
+@@ -243,6 +243,8 @@
+ AC_CONFIG_FILES([config/mkoctfile_wrapper.sh], [chmod a+x config/mkoctfile_wrapper.sh])
+ AC_CONFIG_FILES([./Makefile])
+
++AC_CONFIG_FILES([./libsbml.pc ./libsbml-cil.pc])
++
+ AC_CONFIG_FILES([src/Makefile])
+
+ AC_CONFIG_FILES([src/common/Makefile])
+diff -urNad libsbml-3.2.0~/libsbml-cil.pc.in libsbml-3.2.0/libsbml-cil.pc.in
+--- libsbml-3.2.0~/libsbml-cil.pc.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.2.0/libsbml-cil.pc.in 2008-09-02 04:03:15.000000000 +0900
+@@ -0,0 +1,9 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++
++Name: @PACKAGE_NAME at -cil
++Description: CLR binding for libSBML
++URL: http://sbml.org/software/libsbml
++Version: @PACKAGE_VERSION@
++Libs: -r:${libdir}/cli/libsbml-3.0/libsbmlcsP.dll
+diff -urNad libsbml-3.2.0~/libsbml.pc.in libsbml-3.2.0/libsbml.pc.in
+--- libsbml-3.2.0~/libsbml.pc.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.2.0/libsbml.pc.in 2008-09-02 04:05:13.000000000 +0900
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: @PACKAGE_NAME@
++Description: An API library for reading/writing/manipulating SBML
++URL: http://sbml.org/software/libsbml
++Version: @PACKAGE_VERSION@
++Libs: @XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @ZLIB_LDFLAGS@ @BZ2_LDFLAGS@ @ZLIB_LIBS@ @BZ2_LIBS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ -lsbml
++Cflags: -I${includedir} @ZLIB_CPPFLAGS@ @BZ2_CPPFLAGS@ @XERCES_CPPFLAGS@ @EXPAT_CPPFLAGS@ @LIBXML_CPPFLAGS@
Property changes on: trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2008-09-01 22:29:36 UTC (rev 2447)
+++ trunk/packages/libsbml/trunk/debian/rules 2008-09-01 23:55:50 UTC (rev 2448)
@@ -40,13 +40,13 @@
libtoolize -c -f
aclocal -Iconfig
autoconf
- eval `bash /usr/share/java-common/jvm-find.sh` && javac -cp $$JAVA_HOME/lib/tools.jar -sourcepath docs/src -d docs/src docs/src/ExcludeDoclet.java
+ eval `bash ./debian/jvm-find.sh` && javac -cp $$JAVA_HOME/lib/tools.jar -sourcepath docs/src -d docs/src docs/src/ExcludeDoclet.java
touch patch-stamp
-config.status: patch configure
+config.status: patch-stamp configure
dh_testdir
# Add here commands to configure the package.
- CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs"
+ MONO_SHARED_DIR="$(CURDIR)" CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs" \
./configure --host=$(DEB_HOST_GNU_TYPE) \
--build=$(DEB_BUILD_GNU_TYPE) \
--prefix=/usr \
@@ -56,7 +56,9 @@
--with-python=/usr \
--with-java=/usr \
--with-ruby=/usr \
- --with-octave=/usr
+ --with-octave=/usr \
+ --with-csharp=/usr \
+ --with-csharp-compiler=/usr/bin/mcs
touch \
src/bindings/java/java-files \
src/bindings/java/libsbml_wrap.cpp \
@@ -69,13 +71,13 @@
build: build-stamp build-stamp-indep
build-stamp: config.status
dh_testdir
- $(MAKE) all DESTDIR=$(CURDIR)/debian/tmp/
+ MONO_SHARED_DIR="$(CURDIR)" $(MAKE) all DESTDIR=$(CURDIR)/debian/tmp/
touch build-stamp
build-indep: build-stamp-indep
build-stamp-indep: config.status
dh_testdir
- -$(MAKE) docs
+ MONO_SHARED_DIR="$(CURDIR)" $(MAKE) docs
touch build-stamp-indep
unpatch:
@@ -117,8 +119,8 @@
dh_clean -k
dh_installdirs
# Add here commands to install the package into debian/tmp
- $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp/
- $(MAKE) install-docs DESTDIR=$(CURDIR)/debian/tmp/
+ MONO_SHARED_DIR="$(CURDIR)" $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp/
+ MONO_SHARED_DIR="$(CURDIR)" $(MAKE) install-docs DESTDIR=$(CURDIR)/debian/tmp/
# Build architecture-independent files here.
binary-indep: build-indep install
@@ -140,8 +142,10 @@
dh_perl
dh_pysupport
dh_makeshlibs
+ dh_makeclilibs
dh_installdeb
dh_shlibdeps
+ dh_clideps
dh_gencontrol
dh_md5sums
dh_builddeb
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