[med-svn] r187 - in libsbml/trunk: . debian debian/patches
Steffen Möller
smoe-guest at alioth.debian.org
Mon Feb 5 15:42:00 CET 2007
Author: smoe-guest
Date: 2007-02-05 15:42:00 +0100 (Mon, 05 Feb 2007)
New Revision: 187
Added:
libsbml/trunk/debian/
libsbml/trunk/debian/README.Debian-source
libsbml/trunk/debian/changelog
libsbml/trunk/debian/compat
libsbml/trunk/debian/control
libsbml/trunk/debian/copyright
libsbml/trunk/debian/dirs
libsbml/trunk/debian/docs
libsbml/trunk/debian/libsbml-dev.dirs
libsbml/trunk/debian/libsbml-dev.install
libsbml/trunk/debian/libsbml-doc.docs
libsbml/trunk/debian/libsbml-examples.examples
libsbml/trunk/debian/libsbml-examples.examplse
libsbml/trunk/debian/libsbml-java.dirs
libsbml/trunk/debian/libsbml-java.docs
libsbml/trunk/debian/libsbml-java.install
libsbml/trunk/debian/libsbml-java.links
libsbml/trunk/debian/libsbml-perl.dirs
libsbml/trunk/debian/libsbml-perl.install
libsbml/trunk/debian/libsbml1.dirs
libsbml/trunk/debian/libsbml1.install
libsbml/trunk/debian/libsbml1.links
libsbml/trunk/debian/patches/
libsbml/trunk/debian/patches/00list
libsbml/trunk/debian/patches/01_extra_qualification.dpatch
libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch
libsbml/trunk/debian/patches/03_libtool_support.dpatch
libsbml/trunk/debian/patches/04_gcj_support.dpatch
libsbml/trunk/debian/patches/05_docs_destdir.dpatch
libsbml/trunk/debian/python-sbml.dirs
libsbml/trunk/debian/python-sbml.docs
libsbml/trunk/debian/python-sbml.install
libsbml/trunk/debian/rules
libsbml/trunk/debian/rules.mine
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: libsbml/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: libsbml/trunk/debian/README.Debian-source
===================================================================
--- libsbml/trunk/debian/README.Debian-source 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/README.Debian-source 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,7 @@
+the source package have only .zip file format, and have some CVS directory
+which make lintian complain. So I repack it and delete all CVS directory.
+
+unzip libsbml.2.3.4.zip
+find libsbml.2.3.4 -name "CVS" -exec rm -rf {} \;
+tar cvzf libsbml.2.3.4 > libsbml.2.3.4.tar.gz
+
Added: libsbml/trunk/debian/changelog
===================================================================
--- libsbml/trunk/debian/changelog 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/changelog 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,12 @@
+libsbml (2.3.4-2) unstable; urgency=low
+
+ * Merge Panchoat's changes and mine.
+
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Mon, 5 Feb 2007 10:03:04 +0900
+
+libsbml (2.3.4-1) unstable; urgency=low
+
+ * Initial release (Closes: #241111)
+
+ -- Changyan Xie <panchoat at gmail.com> Mon, 22 Jan 2007 07:52:12 +0000
+
Added: libsbml/trunk/debian/compat
===================================================================
--- libsbml/trunk/debian/compat 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/compat 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+5
Added: libsbml/trunk/debian/control
===================================================================
--- libsbml/trunk/debian/control 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/control 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,159 @@
+Source: libsbml
+Priority: optional
+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, autotools-dev, libstdc++6-4.2-dev,
+ libxerces23-dev | libxerces24-dev | libxerces25-dev | libxerces26-dev |
+ libxerces27-dev, swig, python-dev, libperl-dev, libgcj-dev, fastjar,
+ tetex-bin, latex2html, libtool (>= 1.5.0), python-support (>= 0.3)
+Standards-Version: 3.7.2
+Section: contrib/science
+
+Package: libsbml-dev
+Section: contrib/devel
+Architecture: any
+Depends: libsbml1 (=${Source-Version})
+Description: Development files for System Biology Markup Language Library
+ 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 contain the development files.
+
+Package: libsbml1
+Section: contrib/libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: System Biology Markup Language Library
+ 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.
+
+Package: python-sbml
+Section: contrib/python
+Provides: ${python:Provides}
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Description: System Biology Markup Language Library -- Python 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 contain the python binding of libsbml.
+
+#Package: libsbml-java
+#Section: contrib/libs
+#Architecture: any
+#Depends: ${shlibs:Depends}, ${misc:Depends}
+#Description: System Biology Markup Language Library -- Java 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 contain the Java binding library.
+
+Package: libsbml-perl
+Section: contrib/perl
+Depends: ${shlibs:Depends}, ${perl:Depends}, ${misc:Depends}, perl
+Architecture: any
+Description: System Biology Markup Language Library --Perl 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 contain Perl binding.
+
+Package: libsbml-doc
+Section: devel
+Architecture: all
+Depends:
+Description: HTML and PDF files for programming with libSBML
+ Documentation for the development with libsbml.
+
+Package: libsbml-examples
+Section: contrib/doc
+Architecture: all
+Depends: libsbml-dev (= ${Source-Version})
+Description: System Biology Markup Language Library -- example files
+ 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 contain C/C++, Java, Perl and layout examples.
Added: libsbml/trunk/debian/copyright
===================================================================
--- libsbml/trunk/debian/copyright 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/copyright 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,33 @@
+This package was debianized by Changyan Xie <panchoat at gmail.com> on
+Mon, 22 Jan 2007 05:20:36 +0000.
+
+It was downloaded from http://www.sbml.org/software/libsbml/
+
+Upstream Author: Ben Bornstein with contributions from
+ Ben Kovitz, Stefan Hoops, Sarah Keating, Mike Hucka,
+ Martin Ginkel, Christoph Flamm, Rainer Machne,
+ and many others in the SBML community.
+
+ mailto:sbml-team at caltech.edu
+
+Copyright: SBML-TEAM (2005), the sponsors are listed below,such as :
+
+the National Institutes of Health (USA); the International
+Joint Research Program of NEDO (Japan); the JST ERATO-SORST Program
+(Japan); the Japanese Ministry of Agriculture; the Japanese Ministry of
+Education, Culture, Sports, Science and Technology; the BBSRC e-Science
+Initiative (UK); the DARPA IPTO Bio-Computation Program (USA); the Army
+Research Office's Institute for Collaborative Biotechnologies (USA); the
+Air Force Office of Scientific Research (USA); the California Institute of
+Technology (USA); the University of Hertfordshire (UK); the Molecular
+Sciences Institute (USA); and the Systems Biology Institute (Japan).
+
+License: LGPL
+
+The Debian packaging is (C) 2007, Changyan Xie <panchoat at gmail.com> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+
Added: libsbml/trunk/debian/dirs
===================================================================
--- libsbml/trunk/debian/dirs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/dirs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,3 @@
+usr/share/java
+usr/lib/jni
+usr/share/man
Added: libsbml/trunk/debian/docs
===================================================================
--- libsbml/trunk/debian/docs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/docs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,7 @@
+AUTHORS.txt
+FUNDING.txt
+NEWS.txt
+README.txt
+README.txt
+VERSION.txt
+debian/README.Debian-source
Added: libsbml/trunk/debian/libsbml-dev.dirs
===================================================================
--- libsbml/trunk/debian/libsbml-dev.dirs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-dev.dirs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,2 @@
+usr/lib
+usr/include
Added: libsbml/trunk/debian/libsbml-dev.install
===================================================================
--- libsbml/trunk/debian/libsbml-dev.install 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-dev.install 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,4 @@
+usr/include/sbml/*
+usr/lib/libsbml.a
+usr/lib/libsbml.la
+usr/lib/libsbml.so
Added: libsbml/trunk/debian/libsbml-doc.docs
===================================================================
--- libsbml/trunk/debian/libsbml-doc.docs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-doc.docs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,3 @@
+debian/tmp/usr/share/doc/libsbml-*/libsbml-manual.pdf
+debian/tmp/usr/share/doc/libsbml-*/libsbml-api-ref.pdf
+debian/tmp/usr/share/doc/libsbml-*/libsbml-manual/*
Added: libsbml/trunk/debian/libsbml-examples.examples
===================================================================
--- libsbml/trunk/debian/libsbml-examples.examples 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-examples.examples 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+examples/*
Added: libsbml/trunk/debian/libsbml-examples.examplse
===================================================================
--- libsbml/trunk/debian/libsbml-examples.examplse 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-examples.examplse 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+examples/*
Added: libsbml/trunk/debian/libsbml-java.dirs
===================================================================
--- libsbml/trunk/debian/libsbml-java.dirs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-java.dirs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,2 @@
+usr/lib/jni
+usr/share/java
Added: libsbml/trunk/debian/libsbml-java.docs
===================================================================
--- libsbml/trunk/debian/libsbml-java.docs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-java.docs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/java.txt
Added: libsbml/trunk/debian/libsbml-java.install
===================================================================
--- libsbml/trunk/debian/libsbml-java.install 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-java.install 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,3 @@
+usr/lib/jni/libsbmlj.so
+usr/share/java/libsbmlj.jar
+
Added: libsbml/trunk/debian/libsbml-java.links
===================================================================
--- libsbml/trunk/debian/libsbml-java.links 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-java.links 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+usr/lib/jni/libsbmlj.so usr/lib/jni/libsbmlj.so.1
Added: libsbml/trunk/debian/libsbml-perl.dirs
===================================================================
--- libsbml/trunk/debian/libsbml-perl.dirs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-perl.dirs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,2 @@
+usr/lib/perl
+usr/share/man
Added: libsbml/trunk/debian/libsbml-perl.install
===================================================================
--- libsbml/trunk/debian/libsbml-perl.install 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml-perl.install 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,2 @@
+usr/lib/perl/*
+usr/share/man/*
Added: libsbml/trunk/debian/libsbml1.dirs
===================================================================
--- libsbml/trunk/debian/libsbml1.dirs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml1.dirs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+usr/lib
Added: libsbml/trunk/debian/libsbml1.install
===================================================================
--- libsbml/trunk/debian/libsbml1.install 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml1.install 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+usr/lib/libsbml.so.*
Added: libsbml/trunk/debian/libsbml1.links
===================================================================
--- libsbml/trunk/debian/libsbml1.links 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/libsbml1.links 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+usr/lib/libsbml.2.3.4.so usr/lib/libsbml.so.1
Added: libsbml/trunk/debian/patches/00list
===================================================================
--- libsbml/trunk/debian/patches/00list 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/patches/00list 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,5 @@
+01_extra_qualification.dpatch
+02_perl_man_install_dir.dpatch
+03_libtool_support.dpatch
+04_gcj_support.dpatch
+05_docs_destdir.dpatch
Added: libsbml/trunk/debian/patches/01_extra_qualification.dpatch
===================================================================
--- libsbml/trunk/debian/patches/01_extra_qualification.dpatch 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/patches/01_extra_qualification.dpatch 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,21 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 01_extra_qualification.dpatch by <mozo at sfc.keio.ac.jp>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Avoid extra qualification in the class definition of
+## DP: SBMLSchemaInputSource.h
+
+ at DPATCH@
+
+diff -ur libsbml-2.3.4.orig/src/sbml/SBMLSchemaInputSource.h libsbml-2.3.4/src/sbml/SBMLSchemaInputSource.h
+--- libsbml-2.3.4.orig/src/sbml/SBMLSchemaInputSource.h 2007-01-19 19:05:12.000000000 +0900
++++ libsbml-2.3.4/src/sbml/SBMLSchemaInputSource.h 2007-01-19 19:05:48.000000000 +0900
+@@ -76,7 +76,7 @@
+
+ ~SBMLSchemaInputSource ();
+
+- BinInputStream* SBMLSchemaInputSource::makeStream () const;
++ BinInputStream* makeStream () const;
+
+
+ private:
Property changes on: libsbml/trunk/debian/patches/01_extra_qualification.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch
===================================================================
--- libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,24 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02_perl_man_install_dir.dpatch by <mozo at sfc.keio.ac.jp>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Fixes the installation directory of manpages generated from the pod
+
+ at DPATCH@
+
+diff -ur libsbml-2.3.4.orig/src/bindings/perl/Makefile.in libsbml-2.3.4/src/bindings/perl/Makefile.in
+--- libsbml-2.3.4.orig/src/bindings/perl/Makefile.in 2007-01-19 19:05:12.000000000 +0900
++++ libsbml-2.3.4/src/bindings/perl/Makefile.in 2007-01-19 19:06:09.000000000 +0900
+@@ -192,8 +192,10 @@
+ # -----------------------------------------------------------------------------
+
+ install: Makefile.PL Makefile-perl
+- $(MAKE) -f Makefile-perl install
+-
++ $(MAKE) -f Makefile-perl install \
++ PREFIX=$(prefix) \
++ INSTALLSITEMAN1DIR=$(prefix)/share/man/man1 \
++ INSTALLSITEMAN3DIR=$(prefix)/share/man/man3
+ installcheck:
+
+ uninstall:
Property changes on: libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: libsbml/trunk/debian/patches/03_libtool_support.dpatch
===================================================================
--- libsbml/trunk/debian/patches/03_libtool_support.dpatch 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/patches/03_libtool_support.dpatch 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,988 @@
+#! /bin/sh
+## 03_libtool_support.dpatch by <mozo at sfc.keio.ac.jp>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+/bin/sh -c '. /usr/share/dpatch/dpatch-run' $0 $@
+
+if [ "x$1" = "x-patch" ]; then
+ chmod ugo+rx install-sh mkinstalldirs
+fi
+
+exit 0
+
+ at DPATCH@
+diff -urNad libsbml-2.3.4~/acinclude.m4 libsbml-2.3.4/acinclude.m4
+--- libsbml-2.3.4~/acinclude.m4 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.4/acinclude.m4 2007-01-22 14:31:42.000000000 +0900
+@@ -0,0 +1,23 @@
++# generated automatically by aclocal 1.8.5 -*- Autoconf -*-
++
++# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004
++# Free Software Foundation, Inc.
++# This file is free software; the Free Software Foundation
++# gives unlimited permission to copy and/or distribute it,
++# with or without modifications, as long as this notice is preserved.
++
++# This program is distributed in the hope that it will be useful,
++# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
++# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
++# PARTICULAR PURPOSE.
++
++m4_include([config/expat.m4])
++m4_include([config/java.m4])
++m4_include([config/libcheck.m4])
++m4_include([config/lisp.m4])
++m4_include([config/matlab.m4])
++m4_include([config/perl.m4])
++m4_include([config/python.m4])
++m4_include([config/runldpath.m4])
++m4_include([config/swig.m4])
++m4_include([config/xercesc.m4])
+diff -urNad libsbml-2.3.4~/config/makefile-common-actions.mk libsbml-2.3.4/config/makefile-common-actions.mk
+--- libsbml-2.3.4~/config/makefile-common-actions.mk 2007-01-22 14:30:24.000000000 +0900
++++ libsbml-2.3.4/config/makefile-common-actions.mk 2007-01-22 14:31:42.000000000 +0900
+@@ -65,7 +65,7 @@
+ # -----------------------------------------------------------------------------
+
+ .SUFFIXES:
+-.SUFFIXES: .a .so .dylib .jnilib .c .h .cpp .hpp .o .obj .Po .py .pyc .pyo .i
++.SUFFIXES: .a .so .dylib .jnilib .c .h .cpp .hpp .o .lo .obj .Po .py .pyc .pyo .i
+
+ # The following define default values of variables like `cxxcompile'. An
+ # enclosing makefile can define other values, in which case those
+@@ -75,24 +75,22 @@
+
+ # Compiling under cygwin doesn't need -fPIC.
+
+-ifneq "$(HOST_TYPE)" "cygwin"
+- FPIC = -fPIC
+-endif
+-
+ # Here follow the generic compilation commands.
+
+-compile ?= $(CC) $(extra_CPPFLAGS) $(extra_CFLAGS) $(default_includes) \
+- $(CPPFLAGS) $(CFLAGS) $(INCLUDES) $(FPIC)
++compile ?= $(LIBTOOL) --mode=compile $(CC) $(extra_CPPFLAGS) $(extra_CFLAGS) \
++ $(default_includes) $(CPPFLAGS) $(CFLAGS) $(INCLUDES)
++
++cxxcompile ?= $(LIBTOOL) --mode=compile $(CXX) $(extra_CPPFLAGS) \
++ $(extra_CXXFLAGS) $(default_includes) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+-cxxcompile ?= $(CXX) $(extra_CPPFLAGS) $(extra_CXXFLAGS) $(default_includes) \
+- $(CPPFLAGS) $(CXXFLAGS) $(INCLUDES) $(FPIC)
+
+ # For linking libraries, we try to follow the result of the libtool
+ # numbering scheme, but at the final end, not in the input format. (The
+ # libtool input format is peculiar to us.) Curious, this makes the
+ # numbering very easy: it's a direct mapping of the libsbml version number.
+
+-library_version = $(PACKAGE_VERSION)
++empty =
++library_version = $(subst $(empty) $(empty),.,$(wordlist 1, 2, $(subst ., ,$(PACKAGE_VERSION)))).0
+
+ # `platform_link_flags' is used below in the definition of link_shared_lib.
+ # Generally, gcc and ld need -shared, but some systems think different.
+@@ -100,10 +98,9 @@
+ ifeq "$(HOST_TYPE)" "darwin"
+ # MacOS X's normal libraries have the extension .dylib, and "bundles"
+ # have .so. The default shared library definition here builds .dylib.
+- platform_link_flags ?= -dynamiclib -flat_namespace \
+- -current_version $(library_version)
++ platform_link_flags ?= -dynamiclib -flat_namespace
+ else
+- platform_link_flags ?= -shared
++ platform_link_flags ?=
+ endif
+
+ # The following defines the default function for linking objects into a
+@@ -114,8 +111,21 @@
+
+ ifndef link_shared_lib
+ define link_shared_lib
+- $(CXX) $(LDFLAGS) $(extra_LDFLAGS) $(platform_link_flags) \
+- -o $(1) $(objfiles) $(extra_LIBS) $(LIBS)
++ $(LIBTOOL) --mode=link $(CXX) $(LDFLAGS) $(extra_LDFLAGS) \
++ -version-info $(subst .,:,$(library_version)) \
++ -inst-prefix-dir "$(DESTDIR)" \
++ $(platform_link_flags) -rpath $(LIBDIR) -o $(1) $(objfiles:.o=.lo) \
++ $(extra_LIBS) $(LIBS)
++ endef
++endif
++
++ifndef link_dl_lib
++ define link_dl_lib
++ $(LIBTOOL) --mode=link $(CXX) $(LDFLAGS) $(extra_LDFLAGS) \
++ -module -avoid-version -export-dynamic \
++ -inst-prefix-dir "$(DESTDIR)" \
++ $(platform_link_flags) -rpath $(abspath $(dir $(1))) \
++ -o $(1:.$(SHAREDLIBEXT)=.la) $(objfiles:.o=.lo) $(extra_LIBS) $(LIBS)
+ endef
+ endif
+
+@@ -127,8 +137,9 @@
+
+ define link_static_lib
+ -rm -f $(1)
+- $(AR) -cru $(1) $(objfiles)
+- $(RANLIB) $(1)
++ $(LIBTOOL) --mode=link $(CXX) $(LDFLAGS) $(extra_LDFLAGS) \
++ -static -inst-prefix-dir $(DESTDIR) \
++ $(platform_link_flags) -o $(1) $(objfiles:.o=.lo)
+ endef
+
+ # Most of the sources are a mix of C and C++ files. They have separate
+@@ -138,16 +149,16 @@
+ # filter the results. This abstracts out this common operation.
+
+ make_objects_list = \
+- $(filter %.$(OBJEXT),\
+- $(patsubst %.cpp,%.$(OBJEXT),$(1)) $(patsubst %.c,%.$(OBJEXT),$(1)))
++ $(filter %.lo,\
++ $(patsubst %.cpp,%.lo,$(1)) $(patsubst %.c,%.lo,$(1)))
+
+ # The following generate the list of object file names and dependency file
+ # names from the list of source files. They're used for the generic
+ # compilation rules further below.
+
+-tmplist ?= $(sources:.cpp=.$(OBJEXT)) $(sources:.c=.$(OBJEXT))
+-objfiles ?= $(filter %.$(OBJEXT),$(tmplist))
+-depfiles ?= $(addprefix $(DEPDIR)/,$(objfiles:.$(OBJEXT)=.$(DEPEXT)))
++tmplist ?= $(sources:.cpp=.lo) $(sources:.c=.lo)
++objfiles ?= $(filter %.lo,$(tmplist))
++depfiles ?= $(addprefix $(DEPDIR)/,$(objfiles:.lo=.$(DEPEXT)))
+
+ # This next line includes the dependency files. This doesn't use
+ # $depfiles, but rather a wildcard on the actual files, so that if they
+@@ -164,21 +175,21 @@
+ %.a ../%.a: $(objfiles)
+ $(call link_static_lib,$@)
+
+-%.so ../%.so: $(objfiles)
++%.la ../%.la: $(objfiles)
+ $(call link_shared_lib,$@)
+
+-%.$(JNIEXT) ../%.$(JNIEXT): $(objfiles)
+- $(call link_shared_lib,$@)
++%.so ../%.la: $(objfiles)
++ $(call link_dl_lib,$@)
+
+-%.$(SHAREDLIBEXT) ../%.$(SHAREDLIBEXT): $(objfiles)
+- $(call link_shared_lib,$@)
++%.$(JNIEXT) ../%.$(JNIEXT): $(objfiles)
++ $(call link_dl_lib,$@)
+
+ # The following define generic rules for creating object files.
+
+-.c.$(OBJEXT):
++.c.lo:
+ $(compile) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.$(DEPEXT)" -c -o $@ $<
+
+-.cpp.$(OBJEXT):
++.cpp.lo:
+ $(cxxcompile) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.$(DEPEXT)" -c -o $@ $<
+
+ .c.obj:
+@@ -281,18 +292,19 @@
+
+ define install_library
+ $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR)
+- @if test "$(suffix $(1))" = ".so" -o "$(suffix $(1))" = ".dylib" -o "$(suffix $(1))" = ".jnilib"; then \
+- finalname="$(notdir $(basename $(1))).$(library_version)$(suffix $(1))"; \
+- echo $(INSTALL_SH) $(1) $(2)/$$finalname; \
+- $(INSTALL_SH) $(1) $(2)/$$finalname; \
+- echo $(install_strip) $(1) $(2)/$$finalname; \
+- $(install_strip) $(1) $(2)/$$finalname; \
+- echo ln -fs $$finalname $(2)/$(notdir $(1)); \
+- ln -fs $$finalname $(2)/$(notdir $(1)); \
+- else \
+- echo $(INSTALL_SH) $(1) $(2); \
+- $(INSTALL_SH) $(1) $(2); \
+- fi
++ $(LIBTOOL) --mode=install $(INSTALL_SH) $(1) $(DESTDIR)/$(LIBDIR)
++# @if test "$(suffix $(1))" = ".so" -o "$(suffix $(1))" = ".dylib" -o "$(suffix $(1))" = ".jnilib"; then \
++# finalname="$(notdir $(basename $(1)))$(suffix $(1)).$(library_version)"; \
++# echo $(INSTALL_SH) $(1) $(2)/$$finalname; \
++# $(INSTALL_SH) $(1) $(2)/$$finalname; \
++# echo $(install_strip) $(1) $(2)/$$finalname; \
++# $(install_strip) $(1) $(2)/$$finalname; \
++# echo ln -fs $$finalname $(2)/$(notdir $(1)); \
++# ln -fs $$finalname $(2)/$(notdir $(1)); \
++# else \
++# echo $(INSTALL_SH) $(1) $(2); \
++# $(INSTALL_SH) $(1) $(2); \
++# fi
+ endef
+
+ to_install_libraries = $(addprefix install-,$(libraries))
+@@ -367,7 +379,7 @@
+
+ define uninstall_library
+ @if test -f $(1); then \
+- finalname="$(notdir $(basename $(1))).$(library_version)$(suffix $(1))"; \
++ finalname="$(notdir $(basename $(1)))$(suffix $(1)).$(library_version)"; \
+ target="$(2)/$$finalname"; \
+ if test -f $$target ; then \
+ echo rm $$target; \
+@@ -514,7 +526,7 @@
+ clean-normal: mostlyclean clean-libraries clean-libtool clean-extras
+
+ clean-generic:
+- -rm -f *.$(OBJEXT) core *.core
++ -rm -f *.lo *.$(OBJEXT) core *.core
+
+ clean-libtool:
+ -rm -rf .libs _libs
+diff -urNad libsbml-2.3.4~/config/makefile-common-vars.mk.in libsbml-2.3.4/config/makefile-common-vars.mk.in
+--- libsbml-2.3.4~/config/makefile-common-vars.mk.in 2007-01-22 14:30:24.000000000 +0900
++++ libsbml-2.3.4/config/makefile-common-vars.mk.in 2007-01-22 14:31:42.000000000 +0900
+@@ -149,7 +149,7 @@
+ SWIGFLAGS = @SWIGFLAGS@
+
+ ACLOCAL = @ACLOCAL@
+-ACLOCAL_FLAGS = --acdir=$(top_srcdir)/config
++ACLOCAL_FLAGS = -I $(top_srcdir)/config
+ ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+ AUTOCONF = @AUTOCONF@
+
+@@ -178,10 +178,10 @@
+ HOST_TYPE = @HOST_TYPE@
+ HOST_CPU = @host_cpu@
+ INSTALL = @INSTALL@
+-INSTALL_SH = $(top_srcdir)/config/install-sh -c
++INSTALL_SH = $(top_srcdir)/install-sh -c
+ LDFLAGS = @LDFLAGS@
+ LIBS = @LIBS@
+-MKINSTALLDIRS = $(SHELL) $(top_srcdir)/config/mkinstalldirs
++MKINSTALLDIRS = $(SHELL) $(top_srcdir)/mkinstalldirs
+ OBJEXT = @OBJEXT@
+ PACKAGE = @PACKAGE_TARNAME@
+ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+@@ -189,8 +189,8 @@
+ PACKAGE_STRING = @PACKAGE_STRING@
+ PACKAGE_TARNAME = @PACKAGE_TARNAME@
+ PACKAGE_VERSION = @PACKAGE_VERSION@
+-RANLIB = @RANLIB@
+ SHAREDLIBEXT = @SHAREDLIBEXT@
++LIBTOOL = @LIBTOOL@
+ SHELL = @SHELL@
+
+
+diff -urNad libsbml-2.3.4~/config/perl.m4 libsbml-2.3.4/config/perl.m4
+--- libsbml-2.3.4~/config/perl.m4 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.4/config/perl.m4 2007-01-22 14:31:42.000000000 +0900
+@@ -0,0 +1,89 @@
++dnl
++dnl Filename : perl.m4
++dnl Description : Autoconf macro to check for existence of Perl
++dnl Author(s) : Mike Hucka
++dnl Organization: SBML Team
++dnl Created : 2005-05-01
++dnl Revision : $Id: perl.m4,v 1.1 2005/05/02 02:25:23 mhucka Exp $
++dnl Source : $Source: /cvsroot/sbml/libsbml/config/perl.m4,v $
++dnl
++dnl Copyright 2005 California Institute of Technology and
++dnl Japan Science and Technology Corporation.
++dnl
++dnl This library is free software; you can redistribute it and/or modify it
++dnl under the terms of the GNU Lesser General Public License as published
++dnl by the Free Software Foundation; either version 2.1 of the License, or
++dnl any later version.
++dnl
++dnl This library is distributed in the hope that it will be useful, but
++dnl WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
++dnl MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
++dnl documentation provided hereunder is on an "as is" basis, and the
++dnl California Institute of Technology and Japan Science and Technology
++dnl Corporation have no obligations to provide maintenance, support,
++dnl updates, enhancements or modifications. In no event shall the
++dnl California Institute of Technology or the Japan Science and Technology
++dnl Corporation be liable to any party for direct, indirect, special,
++dnl incidental or consequential damages, including lost profits, arising
++dnl out of the use of this software and its documentation, even if the
++dnl California Institute of Technology and/or Japan Science and Technology
++dnl Corporation have been advised of the possibility of such damage. See
++dnl the GNU Lesser General Public License for more details.
++dnl
++dnl You should have received a copy of the GNU Lesser General Public License
++dnl along with this library; if not, write to the Free Software Foundation,
++dnl Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
++dnl
++dnl The original code contained here was initially developed by:
++dnl
++dnl Michael Hucka
++dnl SBML Team
++dnl Control and Dynamical Systems, MC 107-81
++dnl California Institute of Technology
++dnl Pasadena, CA, 91125, USA
++dnl
++dnl http://www.sbml.org
++dnl mailto:sbml-team at caltech.edu
++dnl
++dnl Contributor(s):
++dnl
++
++dnl
++dnl Check --with-perl[=PREFIX]
++dnl
++
++AC_DEFUN([CONFIG_PROG_PERL],
++[
++ AC_ARG_VAR([PERL])
++
++ AC_ARG_WITH(perl,
++ AC_HELP_STRING([--with-perl=PREFIX],
++ [Generate Perl interface library [[default=no]]]),
++ [with_perl=$withval],
++ [with_perl=no])
++
++ if test $with_perl != no; then
++
++ dnl Find a perl executable.
++
++ if test $with_perl != yes; then
++ AC_PATH_PROG([PERL], [perl], [$with_perl/bin/perl],
++ [no-perl-found], [$with_perl/bin])
++ else
++ AC_PATH_PROG([PERL], [perl])
++ fi
++
++ AC_DEFINE([USE_PERL], 1, [Define to 1 to use Perl])
++ AC_SUBST(USE_PERL, 1)
++
++ AC_SUBST(PERL_CPPFLAGS)
++ AC_SUBST(PERL_LDFLAGS)
++ AC_SUBST(PERL_LIBS)
++
++ fi
++
++ dnl We record the USE_XXX flag, for later testing in Makefiles.
++
++ LIBSBML_OPTIONS="$LIBSBML_OPTIONS USE_PERL"
++
++])
+diff -urNad libsbml-2.3.4~/config/runldpath.m4 libsbml-2.3.4/config/runldpath.m4
+--- libsbml-2.3.4~/config/runldpath.m4 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.4/config/runldpath.m4 2007-01-22 14:31:42.000000000 +0900
+@@ -0,0 +1,77 @@
++dnl
++dnl Filename : runldpath.m4
++dnl Description : Autoconf macro to set special variable RUN_LDPATH
++dnl Author(s) : Mike Hucka
++dnl Created : 2005-04-30
++dnl Revision : $Id: runldpath.m4,v 1.2 2005/05/01 22:25:56 mhucka Exp $
++dnl Source : $Source: /cvsroot/sbml/libsbml/config/runldpath.m4,v $
++dnl
++dnl Copyright 2005 California Institute of Technology
++dnl
++dnl This library is free software; you can redistribute it and/or modify it
++dnl under the terms of the GNU Lesser General Public License as published
++dnl by the Free Software Foundation; either version 2.1 of the License, or
++dnl any later version.
++dnl
++dnl This library is distributed in the hope that it will be useful, but
++dnl WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
++dnl MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
++dnl documentation provided hereunder is on an "as is" basis, and the
++dnl California Institute of Technology and Japan Science and Technology
++dnl Corporation have no obligations to provide maintenance, support,
++dnl updates, enhancements or modifications. In no event shall the
++dnl California Institute of Technology or the Japan Science and Technology
++dnl Corporation be liable to any party for direct, indirect, special,
++dnl incidental or consequential damages, including lost profits, arising
++dnl out of the use of this software and its documentation, even if the
++dnl California Institute of Technology and/or Japan Science and Technology
++dnl Corporation have been advised of the possibility of such damage. See
++dnl the GNU Lesser General Public License for more details.
++dnl
++dnl You should have received a copy of the GNU Lesser General Public License
++dnl along with this library; if not, write to the Free Software Foundation,
++dnl Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
++dnl
++dnl The original code contained here was initially developed by:
++dnl
++dnl Mike Hucka
++dnl The SBML Team
++dnl Control and Dynamical Systems, MC 107-81
++dnl California Institute of Technology
++dnl Pasadena, CA, 91125, USA
++dnl
++dnl http://sbml.org
++dnl mailto:sbml-team at caltech.edu
++dnl
++dnl Contributor(s):
++
++dnl CONFIG_LDPATH needs to be called from configure.ac to initialize the
++dnl internal variable. It needs to be called fairly early.
++
++AC_DEFUN([CONFIG_LDPATH],
++[
++ AC_DEFINE([RUN_LDPATH])
++
++ dnl The initial value is the user's LD_LIBRARY_PATH or DYLD_LIBRARY_PATH
++
++ case $host in
++ *darwin*)
++ RUN_LDPATH="$DYLD_LIBRARY_PATH"
++ ;;
++ *)
++ RUN_LDPATH="$LD_LIBRARY_PATH"
++ ;;
++ esac
++
++ AC_SUBST(RUN_LDPATH)
++])
++
++
++dnl CONFIG_ADD_LDPATH(path) adds "path" to list of paths used to set
++dnl LD_LIBRARY_PATH.
++
++AC_DEFUN([CONFIG_ADD_LDPATH],
++[
++ RUN_LDPATH="$RUN_LDPATH:$1"
++])
++
+diff -urNad libsbml-2.3.4~/configure.ac libsbml-2.3.4/configure.ac
+--- libsbml-2.3.4~/configure.ac 2007-01-22 14:30:24.000000000 +0900
++++ libsbml-2.3.4/configure.ac 2007-01-22 14:31:42.000000000 +0900
+@@ -61,7 +61,6 @@
+ fi
+
+ AC_INIT([libSBML], LIBSBML_VERSION, [sbml-team at caltech.edu], [libsbml])
+-AC_CONFIG_AUX_DIR(config)
+
+ AC_REVISION($Revision: 1.56 $)
+
+@@ -72,7 +71,6 @@
+ AC_CONFIG_HEADERS(src/common/libsbml-config-unix.h)
+ AC_CONFIG_HEADERS(src/common/libsbml-package.h)
+
+-
+ dnl ---------------------------------------------------------------------------
+ dnl Command-line options
+ dnl ---------------------------------------------------------------------------
+@@ -154,13 +152,15 @@
+ AC_PROG_CXX
+ AC_PROG_CC
+ AC_PROG_CPP
+-AC_PROG_RANLIB
++AC_LIBTOOL_WIN32_DLL
++AC_PROG_LIBTOOL
+ AC_PROG_INSTALL
+ AC_PROG_MAKE_SET
+
++AC_SUBST(LIBTOOL)
++
+ AC_PATH_PROG([AUTOCONF],[autoconf],[autoconf])
+ AC_PATH_PROG([ACLOCAL],[aclocal],[aclocal])
+-AC_PATH_PROG([AR],[ar],[ar])
+
+ CONFIG_PROG_SWIG(1.3.24)
+ CONFIG_PROG_PYTHON
+@@ -169,9 +169,6 @@
+ CONFIG_PROG_MATLAB
+ CONFIG_PROG_LISP
+
+-dnl AC_LIBTOOL_WIN32_DLL
+-dnl AC_PROG_LIBTOOL
+-
+
+ dnl ---------------------------------------------------------------------------
+ dnl Checks for libraries.
+diff -urNad libsbml-2.3.4~/install-sh libsbml-2.3.4/install-sh
+--- libsbml-2.3.4~/install-sh 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.4/install-sh 2007-01-22 14:31:42.000000000 +0900
+@@ -0,0 +1,276 @@
++#!/bin/sh
++#
++# install - install a program, script, or datafile
++# This comes from X11R5 (mit/util/scripts/install.sh).
++#
++# Copyright 1991 by the Massachusetts Institute of Technology
++#
++# Permission to use, copy, modify, distribute, and sell this software and its
++# documentation for any purpose is hereby granted without fee, provided that
++# the above copyright notice appear in all copies and that both that
++# copyright notice and this permission notice appear in supporting
++# documentation, and that the name of M.I.T. not be used in advertising or
++# publicity pertaining to distribution of the software without specific,
++# written prior permission. M.I.T. makes no representations about the
++# suitability of this software for any purpose. It is provided "as is"
++# without express or implied warranty.
++#
++# Calling this script install-sh is preferred over install.sh, to prevent
++# `make' implicit rules from creating a file called install from it
++# when there is no Makefile.
++#
++# This script is compatible with the BSD install script, but was written
++# from scratch. It can only install one file at a time, a restriction
++# shared with many OS's install programs.
++
++
++# set DOITPROG to echo to test this script
++
++# Don't use :- since 4.3BSD and earlier shells don't like it.
++doit="${DOITPROG-}"
++
++
++# put in absolute paths if you don't have them in your path; or use env. vars.
++
++mvprog="${MVPROG-mv}"
++cpprog="${CPPROG-cp}"
++chmodprog="${CHMODPROG-chmod}"
++chownprog="${CHOWNPROG-chown}"
++chgrpprog="${CHGRPPROG-chgrp}"
++stripprog="${STRIPPROG-strip}"
++rmprog="${RMPROG-rm}"
++mkdirprog="${MKDIRPROG-mkdir}"
++
++transformbasename=""
++transform_arg=""
++instcmd="$mvprog"
++chmodcmd="$chmodprog 0755"
++chowncmd=""
++chgrpcmd=""
++stripcmd=""
++rmcmd="$rmprog -f"
++mvcmd="$mvprog"
++src=""
++dst=""
++dir_arg=""
++
++while [ x"$1" != x ]; do
++ case $1 in
++ -c) instcmd=$cpprog
++ shift
++ continue;;
++
++ -d) dir_arg=true
++ shift
++ continue;;
++
++ -m) chmodcmd="$chmodprog $2"
++ shift
++ shift
++ continue;;
++
++ -o) chowncmd="$chownprog $2"
++ shift
++ shift
++ continue;;
++
++ -g) chgrpcmd="$chgrpprog $2"
++ shift
++ shift
++ continue;;
++
++ -s) stripcmd=$stripprog
++ shift
++ continue;;
++
++ -t=*) transformarg=`echo $1 | sed 's/-t=//'`
++ shift
++ continue;;
++
++ -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
++ shift
++ continue;;
++
++ *) if [ x"$src" = x ]
++ then
++ src=$1
++ else
++ # this colon is to work around a 386BSD /bin/sh bug
++ :
++ dst=$1
++ fi
++ shift
++ continue;;
++ esac
++done
++
++if [ x"$src" = x ]
++then
++ echo "$0: no input file specified" >&2
++ exit 1
++else
++ :
++fi
++
++if [ x"$dir_arg" != x ]; then
++ dst=$src
++ src=""
++
++ if [ -d "$dst" ]; then
++ instcmd=:
++ chmodcmd=""
++ else
++ instcmd=$mkdirprog
++ fi
++else
++
++# Waiting for this to be detected by the "$instcmd $src $dsttmp" command
++# might cause directories to be created, which would be especially bad
++# if $src (and thus $dsttmp) contains '*'.
++
++ if [ -f "$src" ] || [ -d "$src" ]
++ then
++ :
++ else
++ echo "$0: $src does not exist" >&2
++ exit 1
++ fi
++
++ if [ x"$dst" = x ]
++ then
++ echo "$0: no destination specified" >&2
++ exit 1
++ else
++ :
++ fi
++
++# If destination is a directory, append the input filename; if your system
++# does not like double slashes in filenames, you may need to add some logic
++
++ if [ -d "$dst" ]
++ then
++ dst=$dst/`basename "$src"`
++ else
++ :
++ fi
++fi
++
++## this sed command emulates the dirname command
++dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
++
++# Make sure that the destination directory exists.
++# this part is taken from Noah Friedman's mkinstalldirs script
++
++# Skip lots of stat calls in the usual case.
++if [ ! -d "$dstdir" ]; then
++defaultIFS='
++ '
++IFS="${IFS-$defaultIFS}"
++
++oIFS=$IFS
++# Some sh's can't handle IFS=/ for some reason.
++IFS='%'
++set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
++IFS=$oIFS
++
++pathcomp=''
++
++while [ $# -ne 0 ] ; do
++ pathcomp=$pathcomp$1
++ shift
++
++ if [ ! -d "$pathcomp" ] ;
++ then
++ $mkdirprog "$pathcomp"
++ else
++ :
++ fi
++
++ pathcomp=$pathcomp/
++done
++fi
++
++if [ x"$dir_arg" != x ]
++then
++ $doit $instcmd "$dst" &&
++
++ if [ x"$chowncmd" != x ]; then $doit $chowncmd "$dst"; else : ; fi &&
++ if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd "$dst"; else : ; fi &&
++ if [ x"$stripcmd" != x ]; then $doit $stripcmd "$dst"; else : ; fi &&
++ if [ x"$chmodcmd" != x ]; then $doit $chmodcmd "$dst"; else : ; fi
++else
++
++# If we're going to rename the final executable, determine the name now.
++
++ if [ x"$transformarg" = x ]
++ then
++ dstfile=`basename "$dst"`
++ else
++ dstfile=`basename "$dst" $transformbasename |
++ sed $transformarg`$transformbasename
++ fi
++
++# don't allow the sed command to completely eliminate the filename
++
++ if [ x"$dstfile" = x ]
++ then
++ dstfile=`basename "$dst"`
++ else
++ :
++ fi
++
++# Make a couple of temp file names in the proper directory.
++
++ dsttmp=$dstdir/#inst.$$#
++ rmtmp=$dstdir/#rm.$$#
++
++# Trap to clean up temp files at exit.
++
++ trap 'status=$?; rm -f "$dsttmp" "$rmtmp" && exit $status' 0
++ trap '(exit $?); exit' 1 2 13 15
++
++# Move or copy the file name to the temp name
++
++ $doit $instcmd "$src" "$dsttmp" &&
++
++# and set any options; do chmod last to preserve setuid bits
++
++# If any of these fail, we abort the whole thing. If we want to
++# ignore errors from any of these, just make sure not to ignore
++# errors from the above "$doit $instcmd $src $dsttmp" command.
++
++ if [ x"$chowncmd" != x ]; then $doit $chowncmd "$dsttmp"; else :;fi &&
++ if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd "$dsttmp"; else :;fi &&
++ if [ x"$stripcmd" != x ]; then $doit $stripcmd "$dsttmp"; else :;fi &&
++ if [ x"$chmodcmd" != x ]; then $doit $chmodcmd "$dsttmp"; else :;fi &&
++
++# Now remove or move aside any old file at destination location. We try this
++# two ways since rm can't unlink itself on some systems and the destination
++# file might be busy for other reasons. In this case, the final cleanup
++# might fail but the new file should still install successfully.
++
++{
++ if [ -f "$dstdir/$dstfile" ]
++ then
++ $doit $rmcmd -f "$dstdir/$dstfile" 2>/dev/null ||
++ $doit $mvcmd -f "$dstdir/$dstfile" "$rmtmp" 2>/dev/null ||
++ {
++ echo "$0: cannot unlink or rename $dstdir/$dstfile" >&2
++ (exit 1); exit
++ }
++ else
++ :
++ fi
++} &&
++
++# Now rename the file to the real destination.
++
++ $doit $mvcmd "$dsttmp" "$dstdir/$dstfile"
++
++fi &&
++
++# The final little trick to "correctly" pass the exit status to the exit trap.
++
++{
++ (exit 0); exit
++}
+diff -urNad libsbml-2.3.4~/mkinstalldirs libsbml-2.3.4/mkinstalldirs
+--- libsbml-2.3.4~/mkinstalldirs 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.4/mkinstalldirs 2007-01-22 14:31:42.000000000 +0900
+@@ -0,0 +1,111 @@
++#! /bin/sh
++# mkinstalldirs --- make directory hierarchy
++# Author: Noah Friedman <friedman at prep.ai.mit.edu>
++# Created: 1993-05-16
++# Public domain
++
++errstatus=0
++dirmode=""
++
++usage="\
++Usage: mkinstalldirs [-h] [--help] [-m mode] dir ..."
++
++# process command line arguments
++while test $# -gt 0 ; do
++ case $1 in
++ -h | --help | --h*) # -h for help
++ echo "$usage" 1>&2
++ exit 0
++ ;;
++ -m) # -m PERM arg
++ shift
++ test $# -eq 0 && { echo "$usage" 1>&2; exit 1; }
++ dirmode=$1
++ shift
++ ;;
++ --) # stop option processing
++ shift
++ break
++ ;;
++ -*) # unknown option
++ echo "$usage" 1>&2
++ exit 1
++ ;;
++ *) # first non-opt arg
++ break
++ ;;
++ esac
++done
++
++for file
++do
++ if test -d "$file"; then
++ shift
++ else
++ break
++ fi
++done
++
++case $# in
++ 0) exit 0 ;;
++esac
++
++case $dirmode in
++ '')
++ if mkdir -p -- . 2>/dev/null; then
++ echo "mkdir -p -- $*"
++ exec mkdir -p -- "$@"
++ fi
++ ;;
++ *)
++ if mkdir -m "$dirmode" -p -- . 2>/dev/null; then
++ echo "mkdir -m $dirmode -p -- $*"
++ exec mkdir -m "$dirmode" -p -- "$@"
++ fi
++ ;;
++esac
++
++for file
++do
++ set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'`
++ shift
++
++ pathcomp=
++ for d
++ do
++ pathcomp="$pathcomp$d"
++ case $pathcomp in
++ -*) pathcomp=./$pathcomp ;;
++ esac
++
++ if test ! -d "$pathcomp"; then
++ echo "mkdir $pathcomp"
++
++ mkdir "$pathcomp" || lasterr=$?
++
++ if test ! -d "$pathcomp"; then
++ errstatus=$lasterr
++ else
++ if test ! -z "$dirmode"; then
++ echo "chmod $dirmode $pathcomp"
++ lasterr=""
++ chmod "$dirmode" "$pathcomp" || lasterr=$?
++
++ if test ! -z "$lasterr"; then
++ errstatus=$lasterr
++ fi
++ fi
++ fi
++ fi
++
++ pathcomp="$pathcomp/"
++ done
++done
++
++exit $errstatus
++
++# Local Variables:
++# mode: shell-script
++# sh-indentation: 2
++# End:
++# mkinstalldirs ends here
+diff -urNad libsbml-2.3.4~/src/bindings/java/Makefile.in libsbml-2.3.4/src/bindings/java/Makefile.in
+--- libsbml-2.3.4~/src/bindings/java/Makefile.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.4/src/bindings/java/Makefile.in 1970-01-01 09:00:00.000000000 +0900
+@@ -98,7 +98,7 @@
+
+ extra_LDFLAGS = $(JAVA_LDFLAGS)
+
+-extra_LIBS = -L../.. -lsbml $(JAVA_LIBS)
++extra_LIBS = ../../libsbml.la $(JAVA_LIBS)
+
+ ifdef USE_EXPAT
+ extra_CPPFLAGS += $(EXPAT_CPPFLAGS)
+@@ -153,9 +153,9 @@
+ # build directives of `makefile-common-actions.mk'.
+
+ .SUFFIXES:
+-.SUFFIXES: .i .cpp .h .java .class .jar .o .obj .so .dylib
++.SUFFIXES: .i .cpp .h .java .class .jar .lo .o .obj .so .dylib
+
+-objfiles = libsbml_wrap.$(OBJEXT)
++objfiles = libsbml_wrap.lo
+
+ # The default action is to remake everything.
+
+@@ -313,9 +313,19 @@
+ # -----------------------------------------------------------------------------
+
+ install: $(libraries)
+- @list='$(libraries)'; for lib in $$list; do \
+- echo "$(INSTALL) $$lib $(DESTDIR)$(LIBDIR)"; \
+- $(INSTALL) $$lib $(DESTDIR)$(LIBDIR); \
++ list='$(libraries)'; for lib in $$list; do \
++ if echo $$lib | grep '\.$(JNIEXT)$$' >/dev/null; then \
++ $(LIBTOOL) --mode=install $(INSTALL_SH) \
++ `echo $$lib | sed -e 's/\.$(JNIEXT)$$/\.la/'` $(abspath @top_srcdir@/$(thisdir))/$$lib && \
++ $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR)/jni; \
++ $(INSTALL_SH) $$lib $(DESTDIR)$(LIBDIR)/jni; \
++ elif echo $$lib | grep '\.jar$$' >/dev/null; then \
++ $(MKINSTALLDIRS) $(DESTDIR)$(DATADIR)/java; \
++ $(INSTALL_SH) $$lib $(DESTDIR)$(DATADIR)/java; \
++ else \
++ $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR); \
++ $(INSTALL_SH) $$lib $(DESTDIR)$(LIBDIR); \
++ fi; \
+ done;
+
+ uninstall:
+diff -urNad libsbml-2.3.4~/src/bindings/python/Makefile.in libsbml-2.3.4/src/bindings/python/Makefile.in
+--- libsbml-2.3.4~/src/bindings/python/Makefile.in 2007-01-22 14:30:24.000000000 +0900
++++ libsbml-2.3.4/src/bindings/python/Makefile.in 2007-01-22 14:31:42.000000000 +0900
+@@ -102,7 +102,7 @@
+ endif
+
+ extra_LDFLAGS = $(PYTHON_LDFLAGS)
+-extra_LIBS = -L../.. -lsbml $(PYTHON_LIBS)
++extra_LIBS = ../../libsbml.la $(PYTHON_LIBS)
+
+ ifeq "$(USE_EXPAT)" "1"
+ extra_CPPFLAGS += $(EXPAT_CPPFLAGS)
+@@ -146,9 +146,9 @@
+ # -----------------------------------------------------------------------------
+
+ .SUFFIXES:
+-.SUFFIXES: .i .cpp .py .pyc .pyo .o .obj
++.SUFFIXES: .i .cpp .py .pyc .pyo .lo .o .obj
+
+-objfiles = libsbml_wrap.$(OBJEXT)
++objfiles = libsbml_wrap.lo
+ test_objfiles = $(objfiles)
+
+ # The default action is to remake everything.
+@@ -275,14 +275,15 @@
+ # -----------------------------------------------------------------------------
+
+ install: setup.py create-build-dir
+- $(PYTHON) setup.py install --skip-build --prefix=$(prefix)
++ $(PYTHON) setup.py install --skip-build --prefix=$(DESTDIR)$(prefix)
+
+ installcheck:
+
+ create-build-dir: $(libraries)
+ mkdir -p build build/libsbml
+ echo "libsbml" > build/libsbml.pth
+- cp $(libraries) build
++ $(LIBTOOL) --mode=install cp $(libraries:.$(SHAREDLIBEXT)=.la) $(abspath .)
++ cp $(libraries) build
+ cp libsbml.py build/libsbml
+
+ uninstall: setup.py
+diff -urNad libsbml-2.3.4~/src/sbml/Makefile.in libsbml-2.3.4/src/sbml/Makefile.in
+--- libsbml-2.3.4~/src/sbml/Makefile.in 2007-01-22 14:30:24.000000000 +0900
++++ libsbml-2.3.4/src/sbml/Makefile.in 2007-01-22 14:31:42.000000000 +0900
+@@ -196,7 +196,7 @@
+
+ # The libraries are actually placed in the parent directory.
+
+-libraries = ../$(PACKAGE).a ../$(PACKAGE).$(SHAREDLIBEXT)
++libraries = ../$(PACKAGE).a ../$(PACKAGE).la
+
+ # `distfiles' determines the files and directories included in a distribution.
+ # `distfiles_exclude' is used to filter out specific items, so that even if
Property changes on: libsbml/trunk/debian/patches/03_libtool_support.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: libsbml/trunk/debian/patches/04_gcj_support.dpatch
===================================================================
--- libsbml/trunk/debian/patches/04_gcj_support.dpatch 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/patches/04_gcj_support.dpatch 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,178 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 04_gcj_support.dpatch by Moriyoshi Koizumi <mozo at sfc.keio.ac.jp>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+
+--- libsbml-2.3.4~/config/java.m4 2007-02-05 13:25:56.000000000 +0900
++++ libsbml-2.3.4/config/java.m4 2007-02-05 12:29:50.000000000 +0900
+@@ -177,94 +177,96 @@
+ dnl http://www.gnu.org/software/ac-archive/htmldoc/ac_jni_include_dirs.html
+
+ AC_DEFUN([AC_JAVA_INCLUDE_DIRS],[
+-
+ test "x$JAVAC" = x && AC_MSG_ERROR(['$JAVAC' undefined])
+
+ _AC_JAVA_FOLLOW_SYMLINKS("$JAVAC")
+ _jtopdir=`echo "$JAVA_FOLLOWED" | sed -e 's://*:/:g' -e 's:/[[^/]]*$::'`
+- case "$host_os" in
+- *darwin*)
+- dnl MacOS X's installation of Java 1.4.2 is broken: the header
+- dnl files are missing entirely, and there are dangling symlinks.
+- dnl The following are ugly kludges to try to do the best we can.
+- dnl One of the things this does deliberately is use the 1.4.1
+- dnl headers directory on the Mac even for Java 1.4.2 if the
+- dnl 1.4.2 headers directory can't be found. Yuck.
+- dnl 2004-07-07 <mhucka at caltech.edu>
+
+- java_bail=no
+- java_mac_prefix="/System/Library/Frameworks/JavaVM.framework"
+- case $JAVA_VER_MINOR in
+- 4)
+- if test $JAVA_VER_SUBMINOR -eq 2; then
+- if test -e "$java_mac_prefix/Versions/1.4.2/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.4.2/Headers"
++ AC_CHECK_HEADER([jni.h],, [
++ case "$host_os" in
++ *darwin*)
++ dnl MacOS X's installation of Java 1.4.2 is broken: the header
++ dnl files are missing entirely, and there are dangling symlinks.
++ dnl The following are ugly kludges to try to do the best we can.
++ dnl One of the things this does deliberately is use the 1.4.1
++ dnl headers directory on the Mac even for Java 1.4.2 if the
++ dnl 1.4.2 headers directory can't be found. Yuck.
++ dnl 2004-07-07 <mhucka at caltech.edu>
++
++ java_bail=no
++ java_mac_prefix="/System/Library/Frameworks/JavaVM.framework"
++ case $JAVA_VER_MINOR in
++ 4)
++ if test $JAVA_VER_SUBMINOR -eq 2; then
++ if test -e "$java_mac_prefix/Versions/1.4.2/Headers"; then
++ _jinc="$java_mac_prefix/Versions/1.4.2/Headers"
+ elif test -e "$java_mac_prefix/Versions/1.4.1/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.4.1/Headers"
++ _jinc="$java_mac_prefix/Versions/1.4.1/Headers"
+ else
+- java_bail=yes
+- fi;
+- elif test $JAVA_VER_SUBMINOR -eq 1; then
+- if test -e "$java_mac_prefix/Versions/1.4.1/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.4.1/Headers"
++ java_bail=yes
++ fi;
++ elif test $JAVA_VER_SUBMINOR -eq 1; then
++ if test -e "$java_mac_prefix/Versions/1.4.1/Headers"; then
++ _jinc="$java_mac_prefix/Versions/1.4.1/Headers"
+ else
+- java_bail=yes
+- fi;
++ java_bail=yes
++ fi;
+ else
+- java_bail=yes
+- fi
+- ;;
+- 3)
+- if test -e "$java_mac_prefix/Versions/1.3.1/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.3.1/Headers"
+- elif test -e "$java_mac_prefix/Versions/1.3/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.3/Headers"
+- else
+- java_bail=yes
+- fi
+- ;;
+- *)
++ java_bail=yes
++ fi
++ ;;
++ 3)
++ if test -e "$java_mac_prefix/Versions/1.3.1/Headers"; then
++ _jinc="$java_mac_prefix/Versions/1.3.1/Headers"
++ elif test -e "$java_mac_prefix/Versions/1.3/Headers"; then
++ _jinc="$java_mac_prefix/Versions/1.3/Headers"
++ else
++ java_bail=yes
++ fi
++ ;;
++ *)
+ _jtopdir=`echo "$_jtopdir" | sed -e 's:/[[^/]]*$::'`
+- _jinc="$_jtopdir/Versions/Headers"
+- ;;
+- esac
++ _jinc="$_jtopdir/Versions/Headers"
++ ;;
++ esac
+
+- if test $java_bail = yes; then
++ if test $java_bail = yes; then
+ AC_MSG_ERROR([Cannot find Java include files.])
+ AC_MSG_ERROR([MacOS X 10.3.x has known problems with its Java 1.4 installation.])
+ AC_MSG_ERROR([See http://developer.apple.com/java/faq.])
+- fi
+- ;;
+- *)
++ fi
++ ;;
++ *)
+ _jinc="$_jtopdir/include"
+- ;;
+- esac
+- if test -e "$_jinc/jni.h"; then
+- JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I$_jinc"
+- else
+- _jtopdir=`echo "$_jtopdir" | sed -e 's:/[[^/]]*$::'`
+- if test -e "$_jtopdir/include/jni.h"; then
+- JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I$_jtopdir/include"
++ ;;
++ esac
++ if test -e "$_jinc/jni.h"; then
++ JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I$_jinc"
+ else
+- AC_MSG_ERROR([Cannot find Java include files.])
++ _jtopdir=`echo "$_jtopdir" | sed -e 's:/[[^/]]*$::'`
++ if test -e "$_jtopdir/include/jni.h"; then
++ JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I$_jtopdir/include"
++ else
++ AC_MSG_ERROR([Cannot find Java include files.])
++ fi
+ fi
+- fi
+-
+- dnl Get the likely subdirectories for system specific Java includes.
+- case "$host_os" in
+- bsdi*) _java_inc_subdirs="bsdos";;
+- linux*) _java_inc_subdirs="linux genunix";;
+- osf*) _java_inc_subdirs="alpha";;
+- solaris*) _java_inc_subdirs="solaris";;
+- *) _java_inc_subdirs="genunix";;
+- esac
+-
+- dnl Add any subdirectories that are present.
+- for jsubdir in $_java_inc_subdirs; do
+- if test -d "$_jtopdir/include/$jsubdir"; then
+- JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I$_jtopdir/include/$jsubdir"
+- fi
+- done
++
++ dnl Get the likely subdirectories for system specific Java includes.
++ case "$host_os" in
++ bsdi*) _java_inc_subdirs="bsdos";;
++ linux*) _java_inc_subdirs="linux genunix";;
++ osf*) _java_inc_subdirs="alpha";;
++ solaris*) _java_inc_subdirs="solaris";;
++ *) _java_inc_subdirs="genunix";;
++ esac
++
++ dnl Add any subdirectories that are present.
++ for jsubdir in $_java_inc_subdirs; do
++ if test -d "$_jtopdir/include/$jsubdir"; then
++ JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I$_jtopdir/include/$jsubdir"
++ fi
++ done
++ ])
+ ])
+
+ dnl _AC_JAVA_FOLLOW_SYMLINKS <path>
Property changes on: libsbml/trunk/debian/patches/04_gcj_support.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: libsbml/trunk/debian/patches/05_docs_destdir.dpatch
===================================================================
--- libsbml/trunk/debian/patches/05_docs_destdir.dpatch 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/patches/05_docs_destdir.dpatch 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,37 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 05_docs_destdir.dpatch by Moriyoshi Koizumi <mozo at sfc.keio.ac.jp>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+
+--- libsbml-2.3.4~/docs/src/Makefile.in 2007-02-05 13:25:56.000000000 +0900
++++ libsbml-2.3.4/docs/src/Makefile.in 2007-02-05 13:31:19.000000000 +0900
+@@ -367,20 +367,20 @@
+ dir=`echo "$$dir" | sed -e 's,/[^/]*$$,,'`; \
+ if test "$$dir" != "$$file" && test "$$dir" != "."; then \
+ dir="$$dir"; \
+- $(MKINSTALLDIRS) "$(DOCDIR)/$$dir"; \
++ $(MKINSTALLDIRS) $(DESTDIR)"$(DOCDIR)/$$dir"; \
+ else \
+ dir=''; \
+ fi; \
+ if test -d $$d/$$file; then \
+ if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+ echo Copying $(srcdir)/$$file; \
+- cp -pR $(srcdir)/$$file $(DOCDIR)$$dir || exit 1; \
++ cp -pR $(srcdir)/$$file $(DESTDIR)$(DOCDIR)$$dir || exit 1; \
+ fi; \
+- cp -pR $$d/$$file $(DOCDIR)$$dir || exit 1; \
++ cp -pR $$d/$$file $(DESTDIR)$(DOCDIR)$$dir || exit 1; \
+ else \
+- echo Copying $(DOCDIR)/$$file; \
+- test -f $(DOCDIR)/$$file \
+- || cp -p $$d/$$file $(DOCDIR)/$$dir \
++ echo Copying $(DESTDIR)$(DOCDIR)/$$file; \
++ test -f $(DESTDIR)$(DOCDIR)/$$file \
++ || cp -p $$d/$$file $(DESTDIR)$(DOCDIR)/$$dir \
+ || exit 1; \
+ fi; \
+ done; \
Property changes on: libsbml/trunk/debian/patches/05_docs_destdir.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: libsbml/trunk/debian/python-sbml.dirs
===================================================================
--- libsbml/trunk/debian/python-sbml.dirs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/python-sbml.dirs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,2 @@
+usr/lib
+usr/share/docs
Added: libsbml/trunk/debian/python-sbml.docs
===================================================================
--- libsbml/trunk/debian/python-sbml.docs 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/python-sbml.docs 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/python.txt
Added: libsbml/trunk/debian/python-sbml.install
===================================================================
--- libsbml/trunk/debian/python-sbml.install 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/python-sbml.install 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1 @@
+usr/lib/python*/*
Added: libsbml/trunk/debian/rules
===================================================================
--- libsbml/trunk/debian/rules 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/rules 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,158 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# GNU copyright 1997 to 1999 by Joey Hess.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+
+# shared library versions, option 1
+version=2.3.4
+major=2
+# option 2, assuming the library is created as src/.libs/libfoo.so.2.0.5 or so
+#version=`ls src/.libs/lib*.so.* | \
+# awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'`
+#major=`ls src/.libs/lib*.so.* | \
+# awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'`
+
+
+patch: patch-stamp
+patch-stamp:
+ dpatch apply-all
+ libtoolize -c -f
+ aclocal -I config
+ autoconf
+ touch patch-stamp
+
+config.status: patch configure
+ dh_testdir
+ # Add here commands to configure the package.
+ CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs"
+ ./configure --host=$(DEB_HOST_GNU_TYPE) \
+ --build=$(DEB_BUILD_GNU_TYPE) \
+ --prefix=/usr \
+ --mandir=\$${prefix}/share/man \
+ --infodir=\$${prefix}/share/info \
+ --with-swig=/usr \
+ --with-perl=/usr \
+ --with-python=/usr
+
+# Please add back in later
+# --with-java=/usr
+
+build: build-stamp build-stamp-indep
+build-stamp: config.status
+ dh_testdir
+ $(MAKE) all DESTDIR=$(CURDIR)/debian/tmp/
+ touch build-stamp
+
+build-indep: build-stamp-indep
+build-stamp-indep: config.status
+ dh_testdir
+ -$(MAKE) docs
+ touch build-stamp-indep
+
+unpatch:
+ # Unpatch after distclean
+ dpatch deapply-all
+ rm -rf patch-stamp debian/patched
+
+distclean:
+ dh_testdir
+ dh_testroot
+ if [ -r Makefile ]; then -$(MAKE) distclean; fi
+ -(cd examples && $(MAKE) clean)
+
+clean: distclean unpatch
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+ rm -f build-stamp-indep
+ rm -f config.status
+ rm -f config.log
+ # Clean not sufficient for dpkg-sources diff
+ rm -rf docs/src/libsbml-manual/ docs/src/libsbml-manual.pdf docs/formatted/libsbml-manual.pdf debian/libsbml-java
+ dh_clean `find . -name "*.a" -o -name "*.la" -o -name "*pdf" -o -name "*.aux" -o -name "*.dvi" `
+# rm -f src/bindings/java/Makefile \
+# src/bindings/java/libsbml_wrap.cpp \
+# src/bindings/java/javadoc.i \
+# src/bindings/lisp/libsbml-config.lisp \
+# src/bindings/lisp/Makefile \
+# src/bindings/lisp/libsbml-config-run.lisp \
+# src/bindings/lisp/build.lisp
+# rm -f src/bindings/perl/Makefile.PL \
+# src/bindings/matlab/test/Makefile \
+# src/bindings/matlab/Makefile \
+# src/bindings/python/pydoc.i \
+# src/bindings/python/libsbml_wrap.cpp
+# rm -f src/bindings/python/libsbml.py \
+# src/sbml/layout/test/Makefile \
+# src/sbml/layout/Makefile \
+# docs/src/tex/libsbmlextras.sty \
+# src/common/libsbml-package.h \
+# aclocal.m4
+# rm -f win32/*/Makefile \
+# libsbml-2.3.4/ltmain.sh \
+# config.guess \
+# config.sub \
+# config/makefile-common-vars.mk
+# rm -f ltmain.sh \
+# src/common/libsbml-config-unix.h \
+# configure \
+# acinclude.m4
+
+install: build
+ dh_testdir
+ dh_testroot
+ 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/
+
+# Build architecture-independent files here.
+binary-indep: build-indep install
+ # Well, if I would need to separate the make install header files from the remainder
+ # and I do not like tampering too much with upstream source.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+ dh_install -Xlibsbml-java --sourcedir=$(CURDIR)/debian/tmp
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_perl
+ dh_pysupport
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install patch unpatch
Property changes on: libsbml/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: libsbml/trunk/debian/rules.mine
===================================================================
--- libsbml/trunk/debian/rules.mine 2007-02-05 14:41:45 UTC (rev 186)
+++ libsbml/trunk/debian/rules.mine 2007-02-05 14:42:00 UTC (rev 187)
@@ -0,0 +1,127 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# GNU copyright 1997 to 1999 by Joey Hess.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+
+# shared library versions, option 1
+version=2.3.4
+major=2
+# option 2, assuming the library is created as src/.libs/libfoo.so.2.0.5 or so
+#version=`ls src/.libs/lib*.so.* | \
+# awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'`
+#major=`ls src/.libs/lib*.so.* | \
+# awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'`
+
+
+patch: patch-stamp
+patch-stamp:
+ dpatch apply-all
+ libtoolize -c -f
+ aclocal -I config
+ autoconf
+ touch patch-stamp
+
+config.status: patch configure
+ dh_testdir
+ # Add here commands to configure the package.
+ CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs"
+ ./configure --host=$(DEB_HOST_GNU_TYPE) \
+ --build=$(DEB_BUILD_GNU_TYPE) \
+ --prefix=/usr \
+ --mandir=\$${prefix}/share/man \
+ --infodir=\$${prefix}/share/info \
+ --with-swig=/usr \
+ --with-perl=/usr \
+ --with-python=/usr \
+ --with-java=/usr
+
+build: build-stamp build-stamp-indep
+build-stamp: config.status
+ dh_testdir
+ $(MAKE) all DESTDIR=$(CURDIR)/debian/tmp/
+ touch $@
+
+build-indep: build-stamp-indep
+build-stamp-indep: config.status
+ dh_testdir
+ $(MAKE) docs
+ touch build-stamp-indep
+
+unpatch:
+ # Unpatch after distclean
+ dpatch deapply-all
+ rm -rf patch-stamp debian/patched
+
+distclean:
+ dh_testdir
+ dh_testroot
+ -$(MAKE) distclean
+ -(cd examples && $(MAKE) clean)
+
+clean: distclean unpatch
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+ rm -f build-stamp-indep
+ rm -f config.status
+ rm -f config.log
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ # Add here commands to install the package into debian/tmp
+ $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp/
+ mv $(CURDIR)/debian/tmp/usr/lib/libsbmlj.jar $(CURDIR)/debian/tmp/usr/share/java/libsbmlj-$(version).jar
+ mv $(CURDIR)/debian/tmp/usr/lib/libsbmlj.so $(CURDIR)/debian/tmp/usr/lib/jni/libsbmlj-$(version).so
+
+# Build architecture-independent files here.
+binary-indep: build-indep install
+ # Well, if I would need to separate the make install header files from the remainder
+ # and I do not like tampering too much with upstream source.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_install --sourcedir=$(CURDIR)/debian/tmp
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_perl
+ dh_pysupport
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install patch unpatch
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