[med-svn] r2256 - in trunk/packages/libsbml: . branches branches/libsbml2 branches/libsbml2/debian branches/libsbml2/debian/patches trunk/debian trunk/debian/patches
moriyoshi-guest at alioth.debian.org
moriyoshi-guest at alioth.debian.org
Fri Jul 18 00:53:00 UTC 2008
Author: moriyoshi-guest
Date: 2008-07-18 00:52:59 +0000 (Fri, 18 Jul 2008)
New Revision: 2256
Added:
trunk/packages/libsbml/branches/
trunk/packages/libsbml/branches/libsbml2/
trunk/packages/libsbml/branches/libsbml2/debian/
trunk/packages/libsbml/branches/libsbml2/debian/README.Debian-source
trunk/packages/libsbml/branches/libsbml2/debian/changelog
trunk/packages/libsbml/branches/libsbml2/debian/compat
trunk/packages/libsbml/branches/libsbml2/debian/control
trunk/packages/libsbml/branches/libsbml2/debian/copyright
trunk/packages/libsbml/branches/libsbml2/debian/dirs
trunk/packages/libsbml/branches/libsbml2/debian/docs
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-dev.dirs
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-dev.install
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-doc.docs
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-examples.examples
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.dirs
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.docs
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.install
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.links
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-perl.dirs
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-perl.install
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.dirs
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.install
trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.links
trunk/packages/libsbml/branches/libsbml2/debian/patches/
trunk/packages/libsbml/branches/libsbml2/debian/patches/00list
trunk/packages/libsbml/branches/libsbml2/debian/patches/01_extra_qualification.dpatch
trunk/packages/libsbml/branches/libsbml2/debian/patches/02_perl_man_install_dir.dpatch
trunk/packages/libsbml/branches/libsbml2/debian/patches/03_libtool_support.dpatch
trunk/packages/libsbml/branches/libsbml2/debian/patches/04_gcj_support.dpatch
trunk/packages/libsbml/branches/libsbml2/debian/patches/05_docs_destdir.dpatch
trunk/packages/libsbml/branches/libsbml2/debian/patches/06_matlab_support.dpatch
trunk/packages/libsbml/branches/libsbml2/debian/patches/07_swig_enum_oddity.dpatch
trunk/packages/libsbml/branches/libsbml2/debian/patches/08_swig_java_proto.dpatch
trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.dirs
trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.docs
trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.install
trunk/packages/libsbml/branches/libsbml2/debian/rules
trunk/packages/libsbml/trunk/debian/libsbml3-dev.dirs
trunk/packages/libsbml/trunk/debian/libsbml3-dev.install
trunk/packages/libsbml/trunk/debian/libsbml3-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml3-examples.docs
trunk/packages/libsbml/trunk/debian/libsbml3-examples.examples
trunk/packages/libsbml/trunk/debian/libsbml3-java-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml3-java.dirs
trunk/packages/libsbml/trunk/debian/libsbml3-java.docs
trunk/packages/libsbml/trunk/debian/libsbml3-java.install
trunk/packages/libsbml/trunk/debian/libsbml3-java.links
trunk/packages/libsbml/trunk/debian/libsbml3-octave.dirs
trunk/packages/libsbml/trunk/debian/libsbml3-octave.install
trunk/packages/libsbml/trunk/debian/libsbml3-perl-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml3-perl.dirs
trunk/packages/libsbml/trunk/debian/libsbml3-perl.install
trunk/packages/libsbml/trunk/debian/libsbml3-ruby1.8.dirs
trunk/packages/libsbml/trunk/debian/libsbml3-ruby1.8.install
trunk/packages/libsbml/trunk/debian/libsbml3.dirs
trunk/packages/libsbml/trunk/debian/libsbml3.install
trunk/packages/libsbml/trunk/debian/libsbml3.links
trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.dpatch
trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch
trunk/packages/libsbml/trunk/debian/patches/03_gcj_support.dpatch
trunk/packages/libsbml/trunk/debian/patches/04_docs_destdir.dpatch
trunk/packages/libsbml/trunk/debian/patches/05_lower_doxygen_ver_req.dpatch
trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch
trunk/packages/libsbml/trunk/debian/patches/07_perldoc_mod_name_fix.dpatch
trunk/packages/libsbml/trunk/debian/python-sbml3-doc.docs
trunk/packages/libsbml/trunk/debian/python-sbml3.dirs
trunk/packages/libsbml/trunk/debian/python-sbml3.docs
trunk/packages/libsbml/trunk/debian/python-sbml3.install
Removed:
trunk/packages/libsbml/trunk/debian/libsbml-dev.dirs
trunk/packages/libsbml/trunk/debian/libsbml-dev.install
trunk/packages/libsbml/trunk/debian/libsbml-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml-examples.examples
trunk/packages/libsbml/trunk/debian/libsbml-java.dirs
trunk/packages/libsbml/trunk/debian/libsbml-java.docs
trunk/packages/libsbml/trunk/debian/libsbml-java.install
trunk/packages/libsbml/trunk/debian/libsbml-java.links
trunk/packages/libsbml/trunk/debian/libsbml-perl.dirs
trunk/packages/libsbml/trunk/debian/libsbml-perl.install
trunk/packages/libsbml/trunk/debian/libsbml1.dirs
trunk/packages/libsbml/trunk/debian/libsbml1.install
trunk/packages/libsbml/trunk/debian/libsbml1.links
trunk/packages/libsbml/trunk/debian/patches/01_extra_qualification.dpatch
trunk/packages/libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch
trunk/packages/libsbml/trunk/debian/patches/03_libtool_support.dpatch
trunk/packages/libsbml/trunk/debian/patches/04_gcj_support.dpatch
trunk/packages/libsbml/trunk/debian/patches/05_docs_destdir.dpatch
trunk/packages/libsbml/trunk/debian/patches/06_matlab_support.dpatch
trunk/packages/libsbml/trunk/debian/patches/07_swig_enum_oddity.dpatch
trunk/packages/libsbml/trunk/debian/python-sbml.dirs
trunk/packages/libsbml/trunk/debian/python-sbml.docs
trunk/packages/libsbml/trunk/debian/python-sbml.install
Modified:
trunk/packages/libsbml/trunk/debian/changelog
trunk/packages/libsbml/trunk/debian/control
trunk/packages/libsbml/trunk/debian/patches/00list
trunk/packages/libsbml/trunk/debian/rules
Log:
* Import my local copies of libsbml build files.
Added: trunk/packages/libsbml/branches/libsbml2/debian/README.Debian-source
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/README.Debian-source (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/README.Debian-source 2008-07-18 00:52:59 UTC (rev 2256)
@@ -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: trunk/packages/libsbml/branches/libsbml2/debian/changelog
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/changelog (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/changelog 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,28 @@
+libsbml (2.3.5-2) UNRELEASED; urgency=low
+
+ * Changed package versioning scheme.
+
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Wed, 18 Jun 2008 18:20:25 +0900
+
+libsbml (2.3.5-1) unstable; 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 ]
+ * Merge Panchoat's changes and mine.
+
+ [ Charles Plessy ]
+ * Add Subversion repository URL to debian/control.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 4 Mar 2007 22:45:14 +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: trunk/packages/libsbml/branches/libsbml2/debian/compat
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/compat (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/compat 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+5
Added: trunk/packages/libsbml/branches/libsbml2/debian/control
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/control (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/control 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,163 @@
+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,
+ autoconf, automake, libtool (>= 1.5.0), build-essential,
+ libxerces27-dev, swig, python-dev, libperl-dev, java-gcj-compat-dev | java-sdk,
+ fastjar, python-support (>= 0.3), texlive (>=2007), texlive-pictures (>=2007), texlive-fonts-extra (>=2007), texlive-latex-extra (>=2007), texlive-font-utils (>=2007), texlive-pstricks (>=2007), texlive-math-extra (>=2007), texlive-publishers (>=2007), texlive-extra-utils (>=2007), latex2html, doxygen
+Standards-Version: 3.7.3
+Section: 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: libsbml2-dev
+Section: devel
+Provides: libsbml-dev
+Architecture: any
+Depends: libsbml2 (=${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: libsbml2
+Section: 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-sbml2
+Section: 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: libsbml2-java
+Section: libs
+Architecture: any
+Provides: libsbml-java
+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: libsbml2-perl
+Section: perl
+Architecture: any
+Provides: libsbml-perl
+Depends: ${shlibs:Depends}, ${perl:Depends}, ${misc:Depends}, perl
+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: libsbml2-doc
+Section: devel
+Architecture: all
+Depends:
+Description: HTML and PDF files for programming with libSBML
+ Documentation for the development with libsbml.
+
+Package: libsbml2-examples
+Section: doc
+Architecture: all
+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: trunk/packages/libsbml/branches/libsbml2/debian/copyright
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/copyright (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/copyright 2008-07-18 00:52:59 UTC (rev 2256)
@@ -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: trunk/packages/libsbml/branches/libsbml2/debian/dirs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/dirs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,3 @@
+usr/share/java
+usr/lib/jni
+usr/share/man
Added: trunk/packages/libsbml/branches/libsbml2/debian/docs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/docs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,7 @@
+AUTHORS.txt
+FUNDING.txt
+NEWS.txt
+README.txt
+README.txt
+VERSION.txt
+debian/README.Debian-source
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-dev.dirs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-dev.dirs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-dev.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+usr/lib
+usr/include
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-dev.install
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-dev.install (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-dev.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,4 @@
+usr/include/sbml/*
+usr/lib/libsbml.a
+usr/lib/libsbml.la
+usr/lib/libsbml.so
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-doc.docs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-doc.docs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-doc.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -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: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-examples.examples
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-examples.examples (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-examples.examples 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+examples/*
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.dirs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.dirs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+usr/lib/jni
+usr/share/java
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.docs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.docs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/java.txt
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.install
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.install (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,3 @@
+usr/lib/jni/libsbmlj.so
+usr/share/java/libsbmlj.jar
+
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.links
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.links (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-java.links 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/jni/libsbmlj.so usr/lib/jni/libsbmlj.so.1
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-perl.dirs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-perl.dirs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-perl.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+usr/lib/perl
+usr/share/man
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-perl.install
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-perl.install (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2-perl.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+usr/lib/perl/*
+usr/share/man/*
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.dirs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.dirs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.install
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.install (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/libsbml.so.*
Added: trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.links
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.links (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/libsbml2.links 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/libsbml.2.3.4.so usr/lib/libsbml.so.1
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/00list
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/00list (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/00list 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,8 @@
+01_extra_qualification.dpatch
+02_perl_man_install_dir.dpatch
+03_libtool_support.dpatch
+04_gcj_support.dpatch
+05_docs_destdir.dpatch
+06_matlab_support.dpatch
+07_swig_enum_oddity.dpatch
+08_swig_java_proto.dpatch
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/01_extra_qualification.dpatch
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/01_extra_qualification.dpatch (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/01_extra_qualification.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -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: trunk/packages/libsbml/branches/libsbml2/debian/patches/01_extra_qualification.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/02_perl_man_install_dir.dpatch
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/02_perl_man_install_dir.dpatch (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/02_perl_man_install_dir.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -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: trunk/packages/libsbml/branches/libsbml2/debian/patches/02_perl_man_install_dir.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/03_libtool_support.dpatch
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/03_libtool_support.dpatch (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/03_libtool_support.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,994 @@
+#! /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-2.3.5~/acinclude.m4 libsbml-2.3.5/acinclude.m4
+--- libsbml-2.3.5~/acinclude.m4 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.5/acinclude.m4 2008-06-25 16:05:36.000000000 +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-2.3.5~/config/makefile-common-actions.mk libsbml-2.3.5/config/makefile-common-actions.mk
+--- libsbml-2.3.5~/config/makefile-common-actions.mk 2008-06-25 16:05:27.767275542 +0900
++++ libsbml-2.3.5/config/makefile-common-actions.mk 2008-06-25 16:27:22.000000000 +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) $(extra_LDFLAGS) \
++ -module -avoid-version -export-dynamic -no-undefined \
++ -inst-prefix-dir "$(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-2.3.5~/config/makefile-common-vars.mk.in libsbml-2.3.5/config/makefile-common-vars.mk.in
+--- libsbml-2.3.5~/config/makefile-common-vars.mk.in 2008-06-25 16:05:27.767275542 +0900
++++ libsbml-2.3.5/config/makefile-common-vars.mk.in 2008-06-25 16:05:36.000000000 +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-2.3.5~/config/perl.m4.rej libsbml-2.3.5/config/perl.m4.rej
+--- libsbml-2.3.5~/config/perl.m4.rej 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.5/config/perl.m4.rej 2008-06-25 16:05:36.000000000 +0900
+@@ -0,0 +1,92 @@
++***************
++*** 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-2.3.5~/config/runldpath.m4.rej libsbml-2.3.5/config/runldpath.m4.rej
+--- libsbml-2.3.5~/config/runldpath.m4.rej 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.5/config/runldpath.m4.rej 2008-06-25 16:05:36.000000000 +0900
+@@ -0,0 +1,80 @@
++***************
++*** 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-2.3.5~/configure.ac libsbml-2.3.5/configure.ac
+--- libsbml-2.3.5~/configure.ac 2008-06-25 16:05:27.767275542 +0900
++++ libsbml-2.3.5/configure.ac 2008-06-25 16:05:36.000000000 +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-2.3.5~/install-sh libsbml-2.3.5/install-sh
+--- libsbml-2.3.5~/install-sh 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.5/install-sh 2008-06-25 16:05:36.000000000 +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-2.3.5~/mkinstalldirs libsbml-2.3.5/mkinstalldirs
+--- libsbml-2.3.5~/mkinstalldirs 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-2.3.5/mkinstalldirs 2008-06-25 16:05:36.000000000 +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-2.3.5~/src/bindings/java/Makefile.in libsbml-2.3.5/src/bindings/java/Makefile.in
+--- libsbml-2.3.5~/src/bindings/java/Makefile.in 2008-06-25 16:05:27.767275542 +0900
++++ libsbml-2.3.5/src/bindings/java/Makefile.in 2008-06-25 16:05:36.000000000 +0900
+@@ -99,7 +99,7 @@
+
+ extra_LDFLAGS = $(JAVA_LDFLAGS)
+
+-extra_LIBS = -L../.. -lsbml $(JAVA_LIBS)
++extra_LIBS = ../../libsbml.la $(JAVA_LIBS)
+
+ ifdef USE_EXPAT
+ extra_CPPFLAGS += $(EXPAT_CPPFLAGS)
+@@ -169,9 +169,9 @@
+ # 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.
+
+@@ -329,9 +329,19 @@
+ # -----------------------------------------------------------------------------
+
+ 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-2.3.5~/src/bindings/python/Makefile.in libsbml-2.3.5/src/bindings/python/Makefile.in
+--- libsbml-2.3.5~/src/bindings/python/Makefile.in 2008-06-25 16:05:27.767275542 +0900
++++ libsbml-2.3.5/src/bindings/python/Makefile.in 2008-06-25 16:05:36.000000000 +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)
+@@ -147,9 +147,9 @@
+ # -----------------------------------------------------------------------------
+
+ .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.
+@@ -276,14 +276,15 @@
+ # -----------------------------------------------------------------------------
+
+ 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-2.3.5~/src/sbml/Makefile.in libsbml-2.3.5/src/sbml/Makefile.in
+--- libsbml-2.3.5~/src/sbml/Makefile.in 2008-06-25 16:05:27.767275542 +0900
++++ libsbml-2.3.5/src/sbml/Makefile.in 2008-06-25 16:05:36.000000000 +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: trunk/packages/libsbml/branches/libsbml2/debian/patches/03_libtool_support.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/04_gcj_support.dpatch
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/04_gcj_support.dpatch (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/04_gcj_support.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,191 @@
+#! /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@
+diff -urNad libsbml-2.3.5~/config/java.m4 libsbml-2.3.5/config/java.m4
+--- libsbml-2.3.5~/config/java.m4 2008-06-24 17:10:32.566141826 +0900
++++ libsbml-2.3.5/config/java.m4 2008-06-24 17:15:10.000000000 +0900
+@@ -4,7 +4,7 @@
+ dnl Author(s) : SBML Team <sbml-team at caltech.edu>
+ dnl Organization: California Institute of Technology
+ dnl Created : 2004-07-07
+-dnl Revision : $Id: java.m4,v 1.5.2.1 2007/08/07 05:58:32 mhucka Exp $
++dnl Revision : $Id: java.m4,v 1.5 2005/08/31 22:11:51 mhucka Exp $
+ dnl Source : $Source: /cvsroot/sbml/libsbml/config/java.m4,v $
+ dnl
+ dnl Copyright 2004 California Institute of Technology and
+@@ -177,13 +177,15 @@
+ 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*)
++
++ JAVA_CPPFLAGS=
++ AC_MSG_CHECKING([for JAVA_HOME])
++ _AC_JAVA_FOLLOW_SYMLINKS("$JAVAC", [
++ _jtopdir=`echo "$JAVA_FOLLOWED" | sed -e 's://*:/:g' -e 's:/[[^/]]*$::'`
++
++ case "$host_os" in
++ *darwin*)
+ java_bail=no
+ java_mac_prefix="/System/Library/Frameworks/JavaVM.framework"
+ case $JAVA_VER_MINOR in
+@@ -199,29 +201,29 @@
+ fi
+ ;;
+ 4)
+- 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>
++ 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>
+
+- if test $JAVA_VER_SUBMINOR -eq 2; then
++ 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"
+- else
+- java_bail=yes
++ _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"
++ 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"
+- else
+- java_bail=yes
++ _jinc="$java_mac_prefix/Versions/1.4.1/Headers"
++ else
++ java_bail=yes
+ fi;
+- else
++ else
+ java_bail=yes
+ fi
+ ;;
+@@ -235,47 +237,55 @@
+ fi
+ ;;
+ *)
+- _jtopdir=`echo "$_jtopdir" | sed -e 's:/[[^/]]*$::'`
++ _jtopdir=`echo "$_jtopdir" | sed -e 's:/[[^/]]*$::'`
+ _jinc="$_jtopdir/Versions/Headers"
+ ;;
+ esac
+
+ 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.])
++ 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
+ ;;
+- *)
+- _jinc="$_jtopdir/include"
++ *)
++ _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"
++ 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"
++
++ if test -n "$JAVA_CPPFLAGS"; then
++ AC_MSG_RESULT([$_jtopdir])
++ break
+ fi
+- done
++ ])
++
++ if test -z "$JAVA_CPPFLAGS"; then
++ AC_MSG_ERROR([Cannot find Java include files.])
++ else
++ 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
++ fi
+ ])
+
+ dnl _AC_JAVA_FOLLOW_SYMLINKS <path>
+@@ -286,14 +296,13 @@
+ dnl find the include directory relative to the javac executable
+ _cur="$1"
+ while ls -ld "$_cur" 2>/dev/null | grep " -> " >/dev/null; do
+- AC_MSG_CHECKING(symlink for $_cur)
+ _slink=`ls -ld "$_cur" | sed 's/.* -> //'`
+ case "$_slink" in
+ /*) _cur="$_slink";;
+ dnl 'X' avoids triggering unwanted echo options.
+ *) _cur=`echo "X$_cur" | sed -e 's/^X//' -e 's:[[^/]]*$::'`"$_slink";;
+ esac
+- AC_MSG_RESULT($_cur)
++ JAVA_FOLLOWED="$_cur"
++ ifelse([$2], [], [:], [$2])
+ done
+- JAVA_FOLLOWED="$_cur"
+ ])# _AC_JAVA
Property changes on: trunk/packages/libsbml/branches/libsbml2/debian/patches/04_gcj_support.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/05_docs_destdir.dpatch
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/05_docs_destdir.dpatch (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/05_docs_destdir.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -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: trunk/packages/libsbml/branches/libsbml2/debian/patches/05_docs_destdir.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/06_matlab_support.dpatch
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/06_matlab_support.dpatch (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/06_matlab_support.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## matlab_support.dpatch by <panchoat at BioMaza>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad libsbml-2.3.4~/src/bindings/matlab/Makefile.in libsbml-2.3.4/src/bindings/matlab/Makefile.in
+--- libsbml-2.3.4~/src/bindings/matlab/Makefile.in 2005-10-03 23:36:53.000000000 +0800
++++ libsbml-2.3.4/src/bindings/matlab/Makefile.in 2007-02-06 01:18:03.000000000 +0800
+@@ -112,7 +112,7 @@
+ flags = $(MEX_FLAGS) $(MATLAB_CPPFLAGS) -I../.. -L../..
+
+ %.$(MEXEXT): %.c
+- $(MEX) -f mexopts-libsbml.sh $(flags) $^ -lsbml $(MATLAB_LIBS)
++ $(MEX) -f ./mexopts-libsbml.sh $(flags) $^ -lsbml $(MATLAB_LIBS)
+
+
+ # -----------------------------------------------------------------------------
Property changes on: trunk/packages/libsbml/branches/libsbml2/debian/patches/06_matlab_support.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/07_swig_enum_oddity.dpatch
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/07_swig_enum_oddity.dpatch (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/07_swig_enum_oddity.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,27 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 07_swig_enum_oddity.dpatch by <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~/src/math/ASTNodeType.h 2005-10-04 00:36:45.000000000 +0900
++++ libsbml-2.3.4/src/math/ASTNodeType.h 2007-02-07 01:59:08.000000000 +0900
+@@ -60,11 +60,11 @@
+ */
+ typedef enum
+ {
+- AST_PLUS = '+'
+- , AST_MINUS = '-'
+- , AST_TIMES = '*'
+- , AST_DIVIDE = '/'
+- , AST_POWER = '^'
++ AST_PLUS = 0x2b
++ , AST_MINUS = 0x2d
++ , AST_TIMES = 0x2a
++ , AST_DIVIDE = 0x2f
++ , AST_POWER = 0x5e
+
+ , AST_INTEGER = 256
+ , AST_REAL
Property changes on: trunk/packages/libsbml/branches/libsbml2/debian/patches/07_swig_enum_oddity.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libsbml/branches/libsbml2/debian/patches/08_swig_java_proto.dpatch
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/patches/08_swig_java_proto.dpatch (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/patches/08_swig_java_proto.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,76 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## swig_java_proto.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.orig/src/bindings/java/local.i 2005-10-04 00:36:52.000000000 +0900
++++ libsbml-2.3.4/src/bindings/java/local.i 2007-07-12 00:53:27.536648170 +0900
+@@ -106,11 +106,11 @@
+ */
+ %pragma(java) modulecode =
+ %{
+- public static SBase DowncastSBase(long cPtr, boolean owner)
++ public static SBase DowncastSBase(long cPtr, SBase ref, boolean owner)
+ {
+ if (cPtr == 0) return null;
+
+- switch( libsbmlJNI.SBase_getTypeCode(cPtr) )
++ switch( libsbmlJNI.SBase_getTypeCode(cPtr, ref) )
+ {
+ case libsbmlConstants.SBML_COMPARTMENT:
+ return new Compartment(cPtr, owner);
+@@ -189,11 +189,11 @@
+ */
+ %pragma(java) modulecode =
+ %{
+- public static SBase DowncastSBase(long cPtr, boolean owner)
++ public static SBase DowncastSBase(long cPtr, SBase ref, boolean owner)
+ {
+ if (cPtr == 0) return null;
+
+- switch( libsbmlJNI.SBase_getTypeCode(cPtr) )
++ switch( libsbmlJNI.SBase_getTypeCode(cPtr, ref) )
+ {
+ case libsbmlConstants.SBML_COMPARTMENT:
+ return new Compartment(cPtr, owner);
+@@ -309,7 +309,7 @@
+ */
+ %typemap("javaout") SBase*
+ {
+- return libsbml.DowncastSBase($jnicall, $owner);
++ return libsbml.DowncastSBase($jnicall, this, $owner);
+ }
+
+ /**
+@@ -317,7 +317,7 @@
+ */
+ %typemap("javaout") Rule*
+ {
+- return (Rule) libsbml.DowncastSBase($jnicall, $owner);
++ return (Rule) libsbml.DowncastSBase($jnicall, this, $owner);
+ }
+
+
+@@ -443,8 +443,11 @@
+ import java.io.File;
+ "
+
++/*
++
+ %javamethodmodifiers SBMLReader::readSBML "private";
+ %rename(readSBMLInternal) SBMLReader::readSBML;
++*/
+
+ %typemap("javacode") SBMLReader
+ %{
+@@ -452,7 +455,7 @@
+ {
+ File file = new java.io.File(filename);
+ String abspath = file.getAbsolutePath();
+- long cPtr = libsbmlJNI.SBMLReader_readSBMLInternal(swigCPtr, abspath);
++ long cPtr = libsbmlJNI.SBMLReader_readSBMLInternal(swigCPtr, this, abspath);
+ return (cPtr == 0) ? null : new SBMLDocument(cPtr, true);
+ }
+ %}
Added: trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.dirs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.dirs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+usr/lib
+usr/share/docs
Added: trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.docs
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.docs (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/python.txt
Added: trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.install
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.install (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/python-sbml2.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/python*/*
Added: trunk/packages/libsbml/branches/libsbml2/debian/rules
===================================================================
--- trunk/packages/libsbml/branches/libsbml2/debian/rules (rev 0)
+++ trunk/packages/libsbml/branches/libsbml2/debian/rules 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,156 @@
+#!/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=2.3.5
+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-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
+ -([ -r Makefile ] && $(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
+ # 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: trunk/packages/libsbml/branches/libsbml2/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/changelog 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,3 +1,10 @@
+libsbml (3.1.1-1) UNRELEASED; urgency=low
+
+ * New upstream release.
+ * Reenable language bindings.
+
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Fri, 18 Jul 2008 09:47:00 +0900
+
libsbml (3.1.0-1) UNRELEASED; urgency=low
* New upstream release
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/control 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,18 +1,21 @@
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 (>= 5.0.0), dpatch,
- autoconf, automake, libtool (>= 1.5.0), libxerces23-dev | libxerces24-dev |
- libxerces25-dev | libxerces26-dev | libxerces27-dev
+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
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libsbml/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libsbml/trunk/
+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: libsbml-dev
+Package: libsbml3-dev
Section: devel
+Provides: libsbml-dev
+Conflicts: libsbml2-dev
Architecture: any
-Depends: libsbml1 (=${Source-Version})
+Depends: libsbml3 (=${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
@@ -31,11 +34,12 @@
The LibSBML code is very portable and is supported on Linux, Windows
(native), and Mac OS X.
.
- This package contain the development files.
+ This package contains files necessary for development with libsbml.
Package: libsbml3
Section: libs
Architecture: any
+Conflicts: libsbml1, libsbml2
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: System Biology Markup Language Library
LibSBML is a library designed to help you read, write, manipulate,
@@ -55,10 +59,165 @@
The LibSBML code is very portable and is supported on Linux, Windows
(native), and Mac OS X.
-Package: libsbml-examples
-Section: contrib/doc
+Package: python-sbml3
+Section: python
+Provides: ${python:Provides}, python-sbml
+Conflicts: python-sbml2
+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: libsbml3-ruby1.8
+Section: libs
+Provides: libsbml3-ruby
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: System Biology Markup Language Library -- Ruby 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 Ruby binding of LibSBML.
+
+Package: libsbml3-java
+Section: libs
+Provides: libsbml-java
+Conflicts: libsbml2-java
+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 contains the Java binding of LibSBML.
+
+Package: libsbml3-perl
+Section: perl
+Provides: libsbml-perl
+Conflicts: libsbml2-perl
+Depends: ${shlibs:Depends}, ${perl:Depends}, ${misc:Depends}
+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 contains the Perl binding of LibSBML.
+
+Package: libsbml3-octave
+Section: math
+Depends: ${shlibs:Depends}, ${misc:Depends}, octave
+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 Octave binding of LibSBML.
+
+Package: libsbml3-doc
+Section: devel
Architecture: all
-Depends: libsbml-dev (>= ${Source-Version})
+Depends:
+Description: C / C++ API documentation of LibSBML
+ This package contains C / C++ API documentation of LibSBML.
+
+Package: libsbml3-java-doc
+Section: devel
+Architecture: all
+Depends:
+Description: Java API documentation of LibSBML
+ This package contains Java API documentation of LibSBML.
+
+Package: libsbml3-perl-doc
+Section: devel
+Architecture: all
+Depends:
+Description: Perl API documentation of LibSBML
+ This package contains Perl API documentation of LibSBML.
+
+Package: python-sbml3-doc
+Section: devel
+Architecture: all
+Depends:
+Description: python API documentation of LibSBML
+ This package contains Python API documentation of LibSBML.
+
+Package: libsbml3-examples
+Section: doc
+Architecture: all
+Depends: libsbml3-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
@@ -77,4 +236,4 @@
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.
+ This package contains C/C++, Java, Perl and layout examples.
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-dev.dirs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-dev.dirs 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-dev.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,2 +0,0 @@
-usr/lib
-usr/include
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-dev.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-dev.install 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-dev.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,2 +0,0 @@
-usr/include/sbml/*
-usr/lib/libsbml.a
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-doc.docs 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-doc.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,3 +0,0 @@
-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/*
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-examples.examples
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-examples.examples 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-examples.examples 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +0,0 @@
-examples/*
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-java.dirs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-java.dirs 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-java.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,2 +0,0 @@
-usr/lib/jni
-usr/share/java
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-java.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-java.docs 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-java.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/java.txt
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-java.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-java.install 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-java.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,3 +0,0 @@
-usr/lib/jni/libsbmlj.so
-usr/share/java/libsbmlj.jar
-
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-java.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-java.links 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-java.links 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +0,0 @@
-usr/lib/jni/libsbmlj.so usr/lib/jni/libsbmlj.so.1
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-perl.dirs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-perl.dirs 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-perl.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,2 +0,0 @@
-usr/lib/perl
-usr/share/man
Deleted: trunk/packages/libsbml/trunk/debian/libsbml-perl.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml-perl.install 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml-perl.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,2 +0,0 @@
-usr/lib/perl/*
-usr/share/man/*
Deleted: trunk/packages/libsbml/trunk/debian/libsbml1.dirs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml1.dirs 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml1.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +0,0 @@
-usr/lib
Deleted: trunk/packages/libsbml/trunk/debian/libsbml1.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml1.install 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml1.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +0,0 @@
-usr/lib/libsbml.so.*
Deleted: trunk/packages/libsbml/trunk/debian/libsbml1.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml1.links 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/libsbml1.links 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +0,0 @@
-usr/lib/libsbml.2.3.4.so usr/lib/libsbml.so.1
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-dev.dirs (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-dev.dirs)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-dev.dirs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-dev.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+usr/lib
+usr/include
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-dev.install (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-dev.install)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-dev.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-dev.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,5 @@
+usr/include/sbml/*
+usr/lib/libsbml.a
+usr/lib/libsbml.la
+usr/lib/libsbml.so
+usr/lib/pkgconfig/*
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-doc.docs (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-doc.docs)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-doc.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+debian/tmp/usr/share/doc/libsbml-*/c-api
+debian/tmp/usr/share/doc/libsbml-*/cpp-api
Added: trunk/packages/libsbml/trunk/debian/libsbml3-examples.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-examples.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-examples.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+examples/README.txt
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-examples.examples (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-examples.examples)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-examples.examples (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-examples.examples 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+examples/*
Added: trunk/packages/libsbml/trunk/debian/libsbml3-java-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-java-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-java-doc.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/java-api
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-java.dirs (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-java.dirs)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-java.dirs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-java.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+usr/lib/jni
+usr/share/java
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-java.docs (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-java.docs)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-java.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-java.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/java.txt
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-java.install (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-java.install)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-java.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-java.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,3 @@
+usr/lib/jni/libsbmlj.so
+usr/share/java/libsbmlj.jar
+
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-java.links (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-java.links)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-java.links (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-java.links 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/jni/libsbmlj.so usr/lib/jni/libsbmlj.so.1
Added: trunk/packages/libsbml/trunk/debian/libsbml3-octave.dirs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-octave.dirs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-octave.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/octave
Added: trunk/packages/libsbml/trunk/debian/libsbml3-octave.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-octave.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-octave.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/octave/*
Added: trunk/packages/libsbml/trunk/debian/libsbml3-perl-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-perl-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-perl-doc.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/perl-api
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-perl.dirs (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-perl.dirs)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-perl.dirs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-perl.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/perl
Copied: trunk/packages/libsbml/trunk/debian/libsbml3-perl.install (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml-perl.install)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-perl.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-perl.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/perl/*
Added: trunk/packages/libsbml/trunk/debian/libsbml3-ruby1.8.dirs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-ruby1.8.dirs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-ruby1.8.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/ruby/1.8
Added: trunk/packages/libsbml/trunk/debian/libsbml3-ruby1.8.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-ruby1.8.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-ruby1.8.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/ruby/1.8/*/*.so
Copied: trunk/packages/libsbml/trunk/debian/libsbml3.dirs (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml1.dirs)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3.dirs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib
Copied: trunk/packages/libsbml/trunk/debian/libsbml3.install (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml1.install)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/libsbml.so.*
Copied: trunk/packages/libsbml/trunk/debian/libsbml3.links (from rev 2255, trunk/packages/libsbml/trunk/debian/libsbml1.links)
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3.links (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml3.links 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/libsbml.2.3.4.so usr/lib/libsbml.so.1
Modified: trunk/packages/libsbml/trunk/debian/patches/00list
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/00list 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/patches/00list 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +1,7 @@
-01_add_soname_of_libsbml.dpatch
+01_java_cleanup_prevention
+02_libtool_support
+03_gcj_support
+04_docs_destdir
+05_lower_doxygen_ver_req
+06_javadoc_discovery
+07_perldoc_mod_name_fix
Deleted: trunk/packages/libsbml/trunk/debian/patches/01_extra_qualification.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/01_extra_qualification.dpatch 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/patches/01_extra_qualification.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,21 +0,0 @@
-#! /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:
Added: trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,23 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 01_java_cleanup_prevention.dpatch by <moriyoshi at dynein>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad libsbml-3.1.1~/src/bindings/java/Makefile.in libsbml-3.1.1/src/bindings/java/Makefile.in
+--- libsbml-3.1.1~/src/bindings/java/Makefile.in 2008-02-26 08:54:27.000000000 +0900
++++ libsbml-3.1.1/src/bindings/java/Makefile.in 2008-06-23 18:53:19.000000000 +0900
+@@ -128,10 +128,10 @@
+ # `extra_clean' and `extra_distclean' determine the files and directories
+ # removed during "make clean" and "make distclean".
+
+-extra_clean = $(class_files) $(check_sources:.java=.class) test_copy1.xml \
++extra_clean = $(check_sources:.java=.class) test_copy1.xml \
+ test_write.xml TestFilenameFilter.class
+
+-extra_distclean = java-files
++extra_distclean =
+
+
+ # -----------------------------------------------------------------------------
Property changes on: trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Copied: trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch (from rev 2255, trunk/packages/libsbml/trunk/debian/patches/03_libtool_support.dpatch)
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,699 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02_libtool_support.dpatch by <mozo at sfc.keio.ac.jp>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at 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 @@
+ config/libcheck.m4 \
+ config/libxml.m4 \
+ config/lisp.m4 \
++ config/lt_link_helper.sh.in \
+ config/makefile-common-actions.mk \
+ config/makefile-common-vars.mk.in \
+ config/matlab.m4 \
+ config/missing \
+ config/mkinstalldirs \
++ config/mkoctfile_wrapper.sh.in \
+ config/octave.m4 \
+ config/perl.m4 \
+ config/python.m4 \
+@@ -201,18 +203,14 @@
+ # makefile-common-actions.mk.
+
+ extra_distclean = config.status config.cache config.log autom4te.cache \
+- src/common/config.h src/common/stamp-h1
++ src/common/config.h src/common/stamp-h1 config/lt_link_helper.sh
+
+ # 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
+-
+-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
+@@ -0,0 +1,27 @@
++# generated automatically by aclocal 1.9.6 -*- Autoconf -*-
++
++# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
++# 2005 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/doxygen.m4])
++m4_include([config/expat.m4])
++m4_include([config/java.m4])
++m4_include([config/libcheck.m4])
++m4_include([config/libxml.m4])
++m4_include([config/lisp.m4])
++m4_include([config/matlab.m4])
++m4_include([config/octave.m4])
++m4_include([config/perl.m4])
++m4_include([config/python.m4])
++m4_include([config/ruby.m4])
++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
+@@ -0,0 +1,69 @@
++#!/bin/sh
++
++libdir=@prefix@/lib
++
++progname=`basename "$0"`
++
++dllibext=
++out_dir=
++out_file=
++out_filename=
++args=
++
++TAG=CXX
++
++if test -z "$1"; then
++ echo "${progname}: linker executable must be specified." >&2
++ exit
++fi
++
++linker_tmpdir=`mktemp -d`
++stage_dir="${linker_tmpdir}/stage"
++mkdir -p "${stage_dir}"
++
++LD="$1"
++shift
++
++while test -n "$1"; do
++ case "$1" in
++ --tag=*)
++ TAG=`echo "$1" | sed -e 's/^--tag=//'`
++ ;;
++ -o)
++ shift
++ out_file="$1"
++ dllibext=`echo "${out_file}" | sed -e 's/.*\(\.[^.]*\)$/\1/'`
++ out_dir=`dirname "${out_file}"`
++ out_filename=`basename "${out_file}" "${dllibext}"`
++ ;;
++ *.o)
++ lt_obj=`echo "$1" | sed -e 's/\.o$/.lo/'`
++ args="${args} \"${lt_obj}\""
++ ;;
++ --libdir)
++ shift
++ libdir="$1"
++ ;;
++ lib*.la | */lib*.la)
++ mkdir -p "${stage_dir}/${libdir}" && \
++ eval "@abs_top_srcdir@/libtool --mode=install cp \"$1\" \"${stage_dir}/${libdir}\""
++ libname=`basename "$1" | sed -e 's/lib\([^.]*\)\.la/\1/'`
++ args="${args} \"$1\""
++ ;;
++ *)
++ args="${args} \"$1\""
++ ;;
++ esac
++ shift
++done
++
++if test -z "$out_file"; then
++ echo "${progname}: -o option not specified." >&2
++ rm -rf "${linker_tmpdir}"
++ exit 1
++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}/${libdir}\"" && \
++ cp "${stage_dir}/${libdir}/${out_filename}${dllibext}" "${out_dir}"
++rm -rf "${linker_tmpdir}"
+diff -urNad libsbml-3.1.1~/config/makefile-common-actions.mk libsbml-3.1.1/config/makefile-common-actions.mk
+--- libsbml-3.1.1~/config/makefile-common-actions.mk 2008-07-18 05:50:16.907919523 +0900
++++ libsbml-3.1.1/config/makefile-common-actions.mk 2008-07-18 05:50:18.000000000 +0900
+@@ -40,7 +40,7 @@
+ # -----------------------------------------------------------------------------
+
+ .SUFFIXES:
+-.SUFFIXES: .a .so .dylib .jnilib .c .h .cpp .hpp .o .obj .Po .py .pyc .pyo .i .bundle
++.SUFFIXES: .a .so .dylib .jnilib .c .h .cpp .hpp .o .lo .la .obj .Po .py .pyc .pyo .i .bundle
+
+ # The following define default values of variables like `cxxcompile'. An
+ # enclosing makefile can define other values, in which case those
+@@ -50,28 +50,22 @@
+
+ default_includes ?= -I. -I$(top_include)
+
+-# Compiling under cygwin doesn't need -fPIC.
+-
+-ifneq "$(HOST_TYPE)" "cygwin"
+- FPIC = -fPIC
+-endif
+-
+ # Here follow the generic compilation commands. (Note: the use of 'sort'
+ # here is only to remove duplicates, which the 'sort' function does as a
+ # documented side-effect.)
+
+-compile ?= $(CC) $(FPIC) $(CPPFLAGS) $(extra_CPPFLAGS) \
+- $(CFLAGS) $(extra_CFLAGS) $(sort $(default_includes) $(INCLUDES))
++compile ?= $(LIBTOOL) --mode=compile $(CC) $(extra_CPPFLAGS) $(extra_CFLAGS) \
++ $(default_includes) $(CPPFLAGS) $(CFLAGS) $(INCLUDES)
+
+-cxxcompile ?= $(CXX) $(FPIC) $(CPPFLAGS) $(extra_CPPFLAGS) \
+- $(CXXFLAGS) $(extra_CXXFLAGS) $(sort $(default_includes) $(INCLUDES))
++cxxcompile ?= $(LIBTOOL) --mode=compile $(CXX) $(extra_CPPFLAGS) \
++ $(extra_CXXFLAGS) $(default_includes) $(CPPFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+ # 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)
++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.
+@@ -79,14 +73,9 @@
+ 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 $(library_version)
+-else
+-ifeq "$(HOST_TYPE)" "aix5.3.0.0"
+- platform_link_flags ?= -G
++ platform_link_flags ?= -dynamiclib -flat_namespace
+ else
+- platform_link_flags ?= -shared
+-endif
++ platform_link_flags ?=
+ endif
+
+ # The following defines the default function for linking objects into a
+@@ -97,8 +86,19 @@
+
+ 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
++ $(TOP_SRCDIR)/config/lt_link_helper.sh $(CXX) --libdir $(LIBDIR) \
++ $(LDFLAGS) $(extra_LDFLAGS) $(platform_link_flags) \
++ -o $(1) $(objfiles:.o=.lo) $(extra_LIBS) $(LIBS)
+ endef
+ endif
+
+@@ -121,16 +121,16 @@
+ # 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
+@@ -154,42 +154,18 @@
+
+ endif
+
+-%.so ../%.so: $(objfiles)
+- $(call link_shared_lib,$@)
+-
+-%.$(JNIEXT) ../%.$(JNIEXT): $(objfiles)
++%.la ../%.la: $(objfiles)
+ $(call link_shared_lib,$@)
+
+ %.$(SHAREDLIBEXT) ../%.$(SHAREDLIBEXT): $(objfiles)
+- $(call link_shared_lib,$@)
+-
+-# The following define generic rules for creating object files.
+-
+-ifeq "$(HOST_TYPE)" "aix"
+-
+-.c.$(OBJEXT):
+- $(compile) -c -o $@ $<
+-
+-.c.obj:
+- if $(compile) -c -o $@ \
+- `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(srcdir)/$<'; fi`; \
+- then mv "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.$(DEPEXT)"; \
+- else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; \
+- fi
+-
+-.cpp.$(OBJEXT) .cxx.$(OBJEXT):
+- $(cxxcompile) -c -o $@ $<
++ $(call link_dl_lib,$@)
+
+-.cpp.obj:
+- if $(cxxcompile) -c -o $@ \
+- `if test -f '$<'; then $(CYGPATH_W) '$<'; else $(CYGPATH_W) '$(srcdir)/$<'; fi`; \
+- then mv "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.$(DEPEXT)"; \
+- else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; \
+- fi
++%.$(JNIEXT) ../%.$(JNIEXT): $(objfiles)
++ $(call link_dl_lib,$@)
+
+-else
++# The following define generic rules for creating object files.
+
+-.c.$(OBJEXT):
++.c.lo:
+ $(compile) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.$(DEPEXT)" -c -o $@ $<
+
+ .c.obj:
+@@ -199,7 +175,7 @@
+ else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; \
+ fi
+
+-.cpp.$(OBJEXT) .cxx.$(OBJEXT):
++.cpp.lo .cxx.lo:
+ $(cxxcompile) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.$(DEPEXT)" -c -o $@ $<
+
+ .cpp.obj:
+@@ -209,8 +185,6 @@
+ else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; \
+ fi
+
+-endif
+-
+ ifeq "$(HOST_TYPE)" "darwin"
+
+ %.bundle ../%.bundle: $(objfiles)
+@@ -324,18 +298,7 @@
+
+ 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)
+ endef
+
+ to_install_libraries = $(addprefix install-,$(libraries))
+@@ -408,7 +371,7 @@
+
+ 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; \
+@@ -555,7 +518,7 @@
+ 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
+@@ -575,7 +538,7 @@
+ endif
+
+ mostlyclean-libtool:
+- -rm -f *.lo
++ -rm -f *.lo *.la *.loT
+
+ 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 @@
+ OCTAVE = @OCTAVE@
+ MKOCTFILE = @MKOCTFILE@
+ MKOCTFILE_FLAGS = @MKOCTFILE_FLAGS@
++MKOCTFILE_WRAPPER = $(SHELL) $(top_srcdir)/config/mkoctfile_wrapper.sh
++LOCALOCTFILEDIR = @LOCALOCTFILEDIR@
++OCTAVE_CONFIG = @OCTAVE_CONFIG@
+ OCTAVEEXT = @OCTAVEEXT@
+
+ USE_LISP = @USE_LISP@
+@@ -201,6 +204,7 @@
+ PACKAGE_VERSION = @PACKAGE_VERSION@
+ RANLIB = @RANLIB@
+ SHAREDLIBEXT = @SHAREDLIBEXT@
++LIBTOOL = @LIBTOOL@
+ SHELL = @SHELL@
+
+ 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
+@@ -0,0 +1,14 @@
++#!/bin/sh
++SHAREDLIBEXT=@SHAREDLIBEXT@
++
++args=
++while test ! -z "$1"; do
++ if test -f "$1" && expr "$1" : ".*lib.*\\.$SHAREDLIBEXT\$" > /dev/null; then
++ args="$args '-L`dirname \"$1\"`' '-l`basename \"$1\" \".$SHAREDLIBEXT\" | sed -e 's/^lib//'`'"
++ elif test "$1" != "-fPIC"; then
++ args="$args '$1'"
++ fi
++ shift
++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
+@@ -42,9 +42,13 @@
+ [no-octave-found], [$with_octave/bin])
+ AC_PATH_PROG([MKOCTFILE], [mkoctfile], [$with_octave/bin/mkoctfile],
+ [no-mkoctfile-found], [$with_octave/bin])
++ AC_PATH_PROG([OCTAVE_CONFIG], [octave-config],
++ [$with_octave/bin/octave-config],
++ [no-octave-config-found], [$with_octave/bin])
+ else
+ AC_PATH_PROG([OCTAVE], [octave])
+ AC_PATH_PROG([MKOCTFILE], [mkoctfile])
++ AC_PATH_PROG([OCTAVE_CONFIG], [octave-config])
+ fi
+
+ if test -z "$OCTAVE"; then
+@@ -131,13 +135,13 @@
+ fi
+ fi
+
+- dnl The following should probably be conditional on the platform, but I
+- dnl don't have enough experience right now to figure out what the
+- dnl variations need to be. So punt.
+-
+ MKOCTFILE_FLAGS="--mex"
+ OCTAVEEXT="mex"
+
++ dnl get rid of prefix part from the directory name of the local oct file
++ dnl repository in order to rebase it later.
++ LOCALOCTFILEDIR=`"$OCTAVE_CONFIG" -p LOCALOCTFILEDIR | sed -e "s#^\`\"$OCTAVE_CONFIG\" -p PREFIX\`##"`
++
+ AC_DEFINE([USE_OCTAVE], 1, [Define to 1 to use Octave])
+ AC_SUBST(USE_OCTAVE, 1)
+
+@@ -145,6 +149,7 @@
+ AC_SUBST(MKOCTFILE)
+ AC_SUBST(MKOCTFILE_FLAGS)
+ AC_SUBST(OCTAVEEXT)
++ AC_SUBST(LOCALOCTFILEDIR)
+
+ 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 @@
+ 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(1.3.33)
+ CONFIG_PROG_PYTHON
+@@ -225,7 +227,9 @@
+ dnl Output
+ dnl ---------------------------------------------------------------------------
+
++AC_CONFIG_FILES([config/lt_link_helper.sh], [chmod a+x config/lt_link_helper.sh])
+ AC_CONFIG_FILES([config/makefile-common-vars.mk])
++AC_CONFIG_FILES([config/mkoctfile_wrapper.sh], [chmod a+x config/mkoctfile_wrapper.sh])
+ 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
+@@ -60,9 +60,9 @@
+ extra_CPPFLAGS = $(JAVA_CPPFLAGS) -I../swig
+ SWIGFLAGS += $(JAVA_CPPFLAGS) -I../swig
+
+-extra_LDFLAGS = $(JAVA_LDFLAGS) -L../..
++extra_LDFLAGS = $(JAVA_LDFLAGS)
+
+-extra_LIBS = -lsbml $(JAVA_LIBS)
++extra_LIBS = ../../libsbml.la $(JAVA_LIBS)
+
+ ifdef USE_EXPAT
+ extra_CPPFLAGS += @EXPAT_CPPFLAGS@
+@@ -142,7 +142,7 @@
+ # 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 .la .o .obj .so .dylib
+
+ # The default action is to remake everything.
+
+@@ -285,9 +285,17 @@
+ # -----------------------------------------------------------------------------
+
+ 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)$$' >/dev/null; then \
++ $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR)/jni; \
++ $(INSTALL_SH) $$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-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
+@@ -76,7 +76,7 @@
+ # `extra_clean' and `extra_distclean' determine the files and directories
+ # removed during "make clean" and "make distclean".
+
+-extra_clean = TranslateSBML.$(OCTAVEEXT)
++extra_clean = TranslateSBML.$(OCTAVEEXT) libsbml.so* libsbml.a
+
+ extra_disclean = $(matlab_sources)
+
+@@ -95,10 +95,13 @@
+ fi; \
+ done
+
+-flags = $(MKOCTFILE_FLAGS) -DUSE_OCTAVE -I../.. -I../../../include -L../..
++flags = $(MKOCTFILE_FLAGS) -DUSE_OCTAVE -I../.. -I../../../include
+
+-%.$(OCTAVEEXT): %.c
+- $(MKOCTFILE) $(flags) $^ -lsbml $(MKOCTFILE_LIBS)
++TranslateSBML.lo: TranslateSBML.c
++ $(LIBTOOL) --tag=CC --mode=compile $(MKOCTFILE_WRAPPER) $(MKOCTFILE) -c -o $@ $(flags) $<
++
++%.$(OCTAVEEXT): %.lo
++ $(TOP_SRCDIR)/config/lt_link_helper.sh $(MKOCTFILE_WRAPPER) --libdir $(LIBDIR) $(MKOCTFILE) -o $@ $(flags) $^ ../../libsbml.la $(MKOCTFILE_LIBS)
+
+
+ # -----------------------------------------------------------------------------
+@@ -124,11 +127,17 @@
+ # Installation.
+ # -----------------------------------------------------------------------------
+
+-install: all install-libraries
++install: all
++ for i in $(libraries); do \
++ $(INSTALL_SH) $$i $(DESTDIR)$(prefix)$(LOCALOCTFILEDIR)/$$i; \
++ done
+
+ installdirs: all
+
+-uninstall: uninstall-libraries
++uninstall:
++ for i in $(libraries); do \
++ rm $(DESTDIR)$(prefix)$(LOCALOCTFILEDIR)/$$i; \
++ done
+
+
+ # -----------------------------------------------------------------------------
+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
+@@ -50,10 +50,9 @@
+ MAKEFILE => 'Makefile-perl',
+ INSTALLDIRS => "site",
+ LIBS => "@XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ -lm -lstdc++",
+- CC => "@CXX@",
+ CCFLAGS => "@PERL_CPPFLAGS@",
+ INC => "-I../swig -I../.. -I../../../include",
+- MYEXTLIB => "../../libsbml.a",
++ MYEXTLIB => "../../libsbml.la",
+ 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 @@
+ @ echo "Reconfigure --with-perl in order to build the perl-bindings"
+ exit 1
+ else
+- $(PERL) Makefile.PL $(if $(LIB),LIB=$(LIB),)
++ $(PERL) Makefile.PL $(if $(LIB),LIB=$(LIB),) \
++ CC="$(LIBTOOL) --mode=compile $(CXX)" \
++ LD="$(TOP_SRCDIR)/config/lt_link_helper.sh $(CXX) --libdir $(LIBDIR)"
+ # 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
+@@ -78,8 +78,8 @@
+ extra_CPPFLAGS += -Wno-long-double
+ endif
+
+-extra_LDFLAGS = $(PYTHON_LDFLAGS) -L../..
+-extra_LIBS = -lsbml $(PYTHON_LIBS)
++extra_LDFLAGS = $(PYTHON_LDFLAGS)
++extra_LIBS = ../../libsbml.la $(PYTHON_LIBS)
+
+ ifdef USE_EXPAT
+ extra_CPPFLAGS += @EXPAT_CPPFLAGS@
+@@ -146,9 +146,9 @@
+ # -----------------------------------------------------------------------------
+
+ .SUFFIXES:
+-.SUFFIXES: .i .cpp .py .pyc .pyo .o .obj
++.SUFFIXES: .i .cpp .py .pyc .pyo .lo .la .o .obj
+
+-objfiles = libsbml_wrap.$(OBJEXT)
++objfiles = libsbml_wrap.lo
+ 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
+@@ -79,7 +79,7 @@
+ endif
+
+ extra_LDFLAGS = $(RUBY_LDFLAGS)
+-extra_LIBS = -L../.. -lsbml $(RUBY_LIBS)
++extra_LIBS = ../../libsbml.la $(RUBY_LIBS)
+
+ ifdef USE_EXPAT
+ extra_CPPFLAGS += @EXPAT_CPPFLAGS@
+@@ -134,7 +134,7 @@
+ .SUFFIXES:
+ .SUFFIXES: .i .cpp .o .obj
+
+-objfiles = libsbml_wrap.$(OBJEXT)
++objfiles = libsbml_wrap.lo
+ test_objfiles = $(objfiles)
+
+ # The default action is to remake everything.
+@@ -237,13 +237,18 @@
+ # -----------------------------------------------------------------------------
+
+ install:
+- $(RUBY) -rfileutils -rrbconfig -e "include FileUtils::Verbose; mkpath(\"$(DESTDIR)$(LIBDIR)\")"
+- $(RUBY) -rfileutils -rrbconfig -e "include FileUtils::Verbose; install(\"$(libraries)\", \"$(DESTDIR)$(LIBDIR)\")"
++ archdir=`$(RUBY) -rrbconfig -e 'print Config::CONFIG["archdir"]'`; \
++ for i in $(libraries); do \
++ $(INSTALL_SH) $$i $(DESTDIR)$$archdir/$$i; \
++ done
+
+ installcheck:
+
+ uninstall:
+- $(RUBY) -rfileutils -rrbconfig -e "include FileUtils::Verbose; rm(\"$(DESTDIR)$(LIBDIR)\" + \"/\" + \"$(libraries)\")"
++ archdir=`$(RUBY) -rrbconfig -e 'print Config::CONFIG["archdir"]'`; \
++ for i in $(libraries); do \
++ rm $(DESTDIR)$$archdir/$$i; \
++ done
+
+ # -----------------------------------------------------------------------------
+ # 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 @@
+
+ # The libraries are actually placed in the parent directory.
+
+-ifeq "$(HOST_TYPE)" "aix"
+-# The nutty thing about AIX is that it uses the same extension (.a) for both
+-# shared and static libraries. You have to pick whether you want one or
+-# the other; you can't provide both at the same time. I'd like to know why
+-# they thought this was a good idea.
+-
+-libraries = ../$(PACKAGE).$(SHAREDLIBEXT)
+-
+-else
+-
+-libraries = ../$(PACKAGE).a ../$(PACKAGE).$(SHAREDLIBEXT)
+-
+-endif
++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
Deleted: trunk/packages/libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/patches/02_perl_man_install_dir.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,24 +0,0 @@
-#! /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:
Copied: trunk/packages/libsbml/trunk/debian/patches/03_gcj_support.dpatch (from rev 2255, trunk/packages/libsbml/trunk/debian/patches/04_gcj_support.dpatch)
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/03_gcj_support.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/03_gcj_support.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,241 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 03_gcj_support.dpatch by <moriyoshi at dynein>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad libsbml-3.1.1~/config/java.m4 libsbml-3.1.1/config/java.m4
+--- libsbml-3.1.1~/config/java.m4 2007-12-18 10:26:11.000000000 +0900
++++ libsbml-3.1.1/config/java.m4 2008-06-24 23:42:34.000000000 +0900
+@@ -158,116 +158,123 @@
+ 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*)
+- java_bail=no
+- java_mac_prefix="/System/Library/Frameworks/JavaVM.framework"
+- case $JAVA_VER_MINOR in
+- 6)
+- if test -e "$java_mac_prefix/Versions/CurrentJDK/Headers"; then
+- _jinc="$java_mac_prefix/Versions/CurrentJDK/Headers"
+- elif test -e "$java_mac_prefix/Versions/1.6.0/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.6.0/Headers"
+- elif test -e "$java_mac_prefix/Versions/1.6/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.6/Headers"
+- else
+- java_bail=yes
+- fi
+- ;;
+- 5)
+- if test -e "$java_mac_prefix/Versions/CurrentJDK/Headers"; then
+- _jinc="$java_mac_prefix/Versions/CurrentJDK/Headers"
+- elif test -e "$java_mac_prefix/Versions/1.5.0/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.5.0/Headers"
+- elif test -e "$java_mac_prefix/Versions/1.5/Headers"; then
+- _jinc="$java_mac_prefix/Versions/1.5/Headers"
+- else
+- java_bail=yes
+- fi
+- ;;
+- 4)
+- 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>
+- 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"
+- 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="$java_mac_prefix/Versions/1.4.1/Headers"
++
++ JAVA_CPPFLAGS=
++ AC_MSG_CHECKING([for JAVA_HOME])
++ _AC_JAVA_FOLLOW_SYMLINKS("$JAVAC", [
++ _jtopdir=`echo "$JAVA_FOLLOWED" | sed -e 's://*:/:g' -e 's:/[[^/]]*$::'`
++ case "$host_os" in
++ *darwin*)
++ java_bail=no
++ case $JAVA_VER_MINOR in
++ 6)
++ if test -e "$java_mac_prefix/Versions/CurrentJDK/Headers"; then
++ _jinc="$java_mac_prefix/Versions/CurrentJDK/Headers"
++ elif test -e "$java_mac_prefix/Versions/1.6.0/Headers"; then
++ _jinc="$java_mac_prefix/Versions/1.6.0/Headers"
++ elif test -e "$java_mac_prefix/Versions/1.6/Headers"; then
++ _jinc="$java_mac_prefix/Versions/1.6/Headers"
++ else
++ java_bail=yes
++ fi
++ ;;
++ 5)
++ if test -e "$java_mac_prefix/Versions/CurrentJDK/Headers"; then
++ _jinc="$java_mac_prefix/Versions/CurrentJDK/Headers"
++ elif test -e "$java_mac_prefix/Versions/1.5.0/Headers"; then
++ _jinc="$java_mac_prefix/Versions/1.5.0/Headers"
++ elif test -e "$java_mac_prefix/Versions/1.5/Headers"; then
++ _jinc="$java_mac_prefix/Versions/1.5/Headers"
++ else
++ java_bail=yes
++ fi
++ ;;
++ 4)
++ 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>
++ 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"
++ 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="$java_mac_prefix/Versions/1.4.1/Headers"
++ else
++ java_bail=yes
++ fi;
+ else
+- java_bail=yes
+- fi;
++ java_bail=yes
++ fi
++ ;;
++ 3)
++ if test -e "$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="$java_mac_prefix/Versions/1.3/Headers"
+ else
+- java_bail=yes
+- fi
+- ;;
+- 3)
+- if test -e "$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="$java_mac_prefix/Versions/1.3/Headers"
+- else
+- java_bail=yes
+- fi
+- ;;
+- *)
++ java_bail=yes
++ fi
++ ;;
++ *)
+ _jtopdir=`echo "$_jtopdir" | sed -e 's:/[[^/]]*$::'`
+- _jinc="$_jtopdir/Versions/Current/Headers"
+- ;;
+- esac
++ _jinc="$_jtopdir/Versions/Current/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\""
++ fi
+ fi
+- fi
+-
+- dnl Get the likely subdirectories for system specific Java includes.
+- case "$host_os" in
+- bsdi*) _java_inc_subdirs="bsdos";;
+- linux*) _java_inc_subdirs="linux genunix";;
+- osf*) _java_inc_subdirs="alpha";;
+- solaris*) _java_inc_subdirs="solaris";;
+- *cygwin*) _java_inc_subdirs="win32";;
+- *) _java_inc_subdirs="genunix";;
+- esac
++ if test -n "$JAVA_CPPFLAGS"; then
++ AC_MSG_RESULT([$_jtopdir])
++ break
++ fi
++ ])
++
++ if test -z "$JAVA_CPPFLAGS"; then
++ AC_MSG_ERROR([Cannot find Java include fiiles.] )
++ else
++ 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";;
++ *cygwin*) _java_inc_subdirs="win32";;
++ *) _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 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
++ fi
+ ])
+
+ dnl _AC_JAVA_FOLLOW_SYMLINKS <path>
+@@ -284,6 +291,7 @@
+ dnl 'X' avoids triggering unwanted echo options.
+ *) _cur=`echo "X$_cur" | sed -e 's/^X//' -e 's:[[^/]]*$::'`"$_slink";;
+ esac
++ JAVA_FOLLOWED="$_cur"
++ ifelse([$2],[],[:],[$2])
+ done
+- JAVA_FOLLOWED="$_cur"
+ ])# _AC_JAVA
Deleted: trunk/packages/libsbml/trunk/debian/patches/03_libtool_support.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/03_libtool_support.dpatch 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/patches/03_libtool_support.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,988 +0,0 @@
-#! /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
Copied: trunk/packages/libsbml/trunk/debian/patches/04_docs_destdir.dpatch (from rev 2255, trunk/packages/libsbml/trunk/debian/patches/05_docs_destdir.dpatch)
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/04_docs_destdir.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/04_docs_destdir.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,35 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 04_docs_destdir.dpatch.dpatch by <moriyoshi at dynein>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+
+--- libsbml-3.1.1.orig/docs/src/Makefile.in 2008-02-26 08:54:36.000000000 +0900
++++ libsbml-3.1.1/docs/src/Makefile.in 2008-06-19 02:11:56.375356412 +0900
+@@ -380,18 +380,18 @@
+ if test -d $$docdir; then d=.; else d=$(srcdir); fi; \
+ dirname=`basename "$$docdir"`; \
+ if test "$$dirname" != "$$docdir" && test "$$dirname" != "."; then \
+- $(MKINSTALLDIRS) "$(DOCDIR)/$$dirname"; \
++ $(MKINSTALLDIRS) "$(DESTDIR)$(DOCDIR)/$$dirname"; \
+ fi; \
+- echo Copying to $(DOCDIR)/$$dirname; \
++ echo Copying to $(DESTDIR)$(DOCDIR)/$$dirname; \
+ if test -d $$d/$$docdir; then \
+ if test -d $(srcdir)/$$docdir && test $$d != $(srcdir); then \
+- cp -pR $(srcdir)/$$docdir $(DOCDIR) || exit 1; \
++ cp -pR $(srcdir)/$$docdir $(DESTDIR)$(DOCDIR) || exit 1; \
+ else \
+- cp -pR $$d/$$docdir $(DOCDIR) || exit 1; \
++ cp -pR $$d/$$docdir $(DESTDIR)$(DOCDIR) || exit 1; \
+ fi; \
+ else \
+- test -f $(DOCDIR)/$$docdir \
+- || cp -p $$d/$$docdir $(DOCDIR)/$$dirname \
++ test -f $(DESTDIR)$(DOCDIR)/$$docdir \
++ || cp -p $$d/$$docdir $(DESTDIR)$(DOCDIR)/$$dirname \
+ || exit 1; \
+ fi; \
+ done; \
Deleted: trunk/packages/libsbml/trunk/debian/patches/04_gcj_support.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/04_gcj_support.dpatch 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/patches/04_gcj_support.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,178 +0,0 @@
-#! /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>
Deleted: trunk/packages/libsbml/trunk/debian/patches/05_docs_destdir.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/05_docs_destdir.dpatch 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/patches/05_docs_destdir.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,37 +0,0 @@
-#! /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; \
Added: trunk/packages/libsbml/trunk/debian/patches/05_lower_doxygen_ver_req.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/05_lower_doxygen_ver_req.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/05_lower_doxygen_ver_req.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 05_lower_doxyen_ver_req.dpatch by <moriyoshi at dynein>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+
+--- libsbml-3.1.1.orig/configure.ac 2008-01-23 07:32:22.000000000 +0900
++++ libsbml-3.1.1/configure.ac 2008-06-19 02:36:35.459644431 +0900
+@@ -150,7 +150,7 @@
+ CONFIG_PROG_LISP
+ CONFIG_PROG_RUBY
+
+-CONFIG_PROG_DOXYGEN(1.5.4)
++CONFIG_PROG_DOXYGEN(1.5.3)
+
+ dnl AC_LIBTOOL_WIN32_DLL
+ dnl AC_PROG_LIBTOOL
Property changes on: trunk/packages/libsbml/trunk/debian/patches/05_lower_doxygen_ver_req.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,151 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 06_javadoc_discovery.dpatch by <moriyoshi at dynein>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad libsbml-3.1.1~/config/java.m4 libsbml-3.1.1/config/java.m4
+--- libsbml-3.1.1~/config/java.m4 2008-06-21 17:43:27.907744015 +0900
++++ libsbml-3.1.1/config/java.m4 2008-06-21 17:43:37.000000000 +0900
+@@ -46,10 +46,13 @@
+ [no-javac-found], [$with_java/bin])
+ AC_PATH_PROG([JAR], [jar], [$with_java/bin/jar],
+ [no-jar-found], [$with_java/bin])
++ AC_PATH_PROG([JAVADOC], [javadoc], [$with_java/bin/javadoc],
++ [no-jar-found], [$with_java/bin])
+ else
+ AC_PATH_PROG([JAVA], [java])
+ AC_PATH_PROG([JAVAC], [javac])
+ AC_PATH_PROG([JAR], [jar])
++ AC_PATH_PROG([JAVADOC], [javadoc])
+ fi
+
+ dnl Sanity checks.
+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 2008-06-21 17:43:27.907744015 +0900
++++ libsbml-3.1.1/config/makefile-common-vars.mk.in 2008-06-21 17:43:37.000000000 +0900
+@@ -117,6 +117,7 @@
+ JAVA = @JAVA@
+ JAVAC = @JAVAC@
+ JAR = @JAR@
++JAVADOC = @JAVADOC@
+ JAVA_CPPFLAGS = @JAVA_CPPFLAGS@
+ JAVA_LDFLAGS = @JAVA_LDFLAGS@
+ JAVA_LIBS = @JAVA_LIBS@
+diff -urNad libsbml-3.1.1~/docs/src/ExcludeDoclet.java libsbml-3.1.1/docs/src/ExcludeDoclet.java
+--- libsbml-3.1.1~/docs/src/ExcludeDoclet.java 2008-06-21 17:43:26.907687077 +0900
++++ libsbml-3.1.1/docs/src/ExcludeDoclet.java 2008-06-21 17:50:42.000000000 +0900
+@@ -97,7 +97,6 @@
+
+ import java.io.*;
+ import java.util.*;
+-import com.sun.tools.javadoc.Main;
+ import com.sun.javadoc.*;
+
+ /**
+@@ -109,14 +108,14 @@
+ public class ExcludeDoclet extends Doclet {
+ private static List m_args = new ArrayList();
+ private static Set m_excludeSet = new HashSet();
+-
++
+ /**
+ * Iterate through the documented classes and remove the ones that should
+ * be excluded.
+ *
+ * @param root the initial RootDoc (before filtering).
+ */
+- public static boolean start(RootDoc root){
++ public static boolean start(RootDoc root) {
+ root.printNotice("ExcludeDoclet: removing excluded source files...");
+ ClassDoc[] classes = root.classes();
+ for (int i = 0; i < classes.length; i++) {
+@@ -126,10 +125,24 @@
+ continue;
+
+ }
++
+ m_args.add(classes[i].position().file().getPath());
+ }
+- return true;
+
++ Class[] callees = (new SecurityManager() {
++ public Class[] getClassContext() {
++ return super.getClassContext();
++ }
++ }).getClassContext();
++
++ try {
++ callees[callees.length - 1].getMethod("execute",
++ new Class[] { String[].class }).invoke(
++ null, new Object[] { m_args.toArray(new String[] {}) });
++ } catch (Exception e) {
++ e.printStackTrace();
++ }
++ return false;
+ }
+
+ /**
+@@ -151,8 +164,10 @@
+ }
+ continue;
+ }
+- if (options[i][0].equals("-subpackages")) {
+- continue;
++ if (options[i][0].equals("-subpackages") ||
++ options[i][0].equals("-doclet") ||
++ options[i][0].equals("-docletpath")) {
++ continue;
+ }
+ for (int j = 0; j < options[i].length; j++) {
+ m_args.add(options[i][j]);
+@@ -252,22 +267,12 @@
+ option.equals("-helpfile") ||
+ option.equals("-stylesheetfile") ||
+ option.equals("-charset") ||
+- option.equals("-overview")) {
++ option.equals("-overview") ||
++ option.equals("-doclet") ||
++ option.equals("-docletpath")) {
+ return 2;
+ } else {
+ return 0;
+ }
+ }
+-
+- /**
+- * Execute this doclet to filter out the unwanted classes and packages.
+- * Then execute the standard doclet.
+- *
+- * @param args the Javadoc arguments from the command line
+- */
+- public static void main(String[] args) {
+- String name = ExcludeDoclet.class.getName();
+- Main.execute(name, name, args);
+- Main.execute((String[]) m_args.toArray(new String[] {}));
+- }
+ }
+diff -urNad libsbml-3.1.1~/docs/src/Makefile.in libsbml-3.1.1/docs/src/Makefile.in
+--- libsbml-3.1.1~/docs/src/Makefile.in 2008-06-21 17:43:27.907744015 +0900
++++ libsbml-3.1.1/docs/src/Makefile.in 2008-06-21 17:43:37.000000000 +0900
+@@ -315,10 +315,6 @@
+ | sed -e 's/%%title%%/$(3)/g;s/%%version%%/@PACKAGE_VERSION@/g' > $(2)
+ endef
+
+-# FIXME this isn't portable, but I don't have time to solve it right now.
+-
+-javadoc-jar = /System/Library/Frameworks/JavaVM.framework/Classes/classes.jar
+-
+ # There are certain things I can't figure out how to make compatible
+ # between doxygen and javadoc. Let's ignore the warnings to avoid
+ # confusing users.
+@@ -326,7 +322,7 @@
+ ignorable-warnings = "warning - @param argument"
+
+ java-manual $(java-manual): $(core-sources)
+- $(JAVA) -cp $(javadoc-jar):. ExcludeDoclet -excludefile java-skip.txt \
++ $(JAVADOC) -docletpath . -doclet ExcludeDoclet -excludefile java-skip.txt \
+ -use -public -version -author -sourcetab 4 -keywords \
+ -header $(javadoc-header) \
+ -bottom $(javadoc-footer) \
Property changes on: trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/libsbml/trunk/debian/patches/06_matlab_support.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/06_matlab_support.dpatch 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/patches/06_matlab_support.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,19 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## matlab_support.dpatch by <panchoat at BioMaza>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
-
- at DPATCH@
-diff -urNad libsbml-2.3.4~/src/bindings/matlab/Makefile.in libsbml-2.3.4/src/bindings/matlab/Makefile.in
---- libsbml-2.3.4~/src/bindings/matlab/Makefile.in 2005-10-03 23:36:53.000000000 +0800
-+++ libsbml-2.3.4/src/bindings/matlab/Makefile.in 2007-02-06 01:18:03.000000000 +0800
-@@ -112,7 +112,7 @@
- flags = $(MEX_FLAGS) $(MATLAB_CPPFLAGS) -I../.. -L../..
-
- %.$(MEXEXT): %.c
-- $(MEX) -f mexopts-libsbml.sh $(flags) $^ -lsbml $(MATLAB_LIBS)
-+ $(MEX) -f ./mexopts-libsbml.sh $(flags) $^ -lsbml $(MATLAB_LIBS)
-
-
- # -----------------------------------------------------------------------------
Added: trunk/packages/libsbml/trunk/debian/patches/07_perldoc_mod_name_fix.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/07_perldoc_mod_name_fix.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/07_perldoc_mod_name_fix.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,20 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 07_perldoc_mod_name_fix.dpatch by <moriyoshi 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/docs/src/Makefile.in libsbml-3.1.1/docs/src/Makefile.in
+--- libsbml-3.1.1.orig/docs/src/Makefile.in 2008-02-26 08:54:36.000000000 +0900
++++ libsbml-3.1.1/docs/src/Makefile.in 2008-06-19 03:26:54.631697190 +0900
+@@ -268,7 +268,7 @@
+ endif
+
+ ifdef USE_PERL
+-perl-sources = ../../src/bindings/perl/libsbml.pm
++perl-sources = ../../src/bindings/perl/LibSBML.pm
+
+ perl-manual $(perl-manual): doxygen-config-perl.txt $(perl-sources)
+ $(call run_doxygen,doxygen-config-perl.txt,$(perl-manual))
Property changes on: trunk/packages/libsbml/trunk/debian/patches/07_perldoc_mod_name_fix.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Deleted: trunk/packages/libsbml/trunk/debian/patches/07_swig_enum_oddity.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/07_swig_enum_oddity.dpatch 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/patches/07_swig_enum_oddity.dpatch 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,27 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 07_swig_enum_oddity.dpatch by <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~/src/math/ASTNodeType.h 2005-10-04 00:36:45.000000000 +0900
-+++ libsbml-2.3.4/src/math/ASTNodeType.h 2007-02-07 01:59:08.000000000 +0900
-@@ -60,11 +60,11 @@
- */
- typedef enum
- {
-- AST_PLUS = '+'
-- , AST_MINUS = '-'
-- , AST_TIMES = '*'
-- , AST_DIVIDE = '/'
-- , AST_POWER = '^'
-+ AST_PLUS = 0x2b
-+ , AST_MINUS = 0x2d
-+ , AST_TIMES = 0x2a
-+ , AST_DIVIDE = 0x2f
-+ , AST_POWER = 0x5e
-
- , AST_INTEGER = 256
- , AST_REAL
Deleted: trunk/packages/libsbml/trunk/debian/python-sbml.dirs
===================================================================
--- trunk/packages/libsbml/trunk/debian/python-sbml.dirs 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/python-sbml.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1,2 +0,0 @@
-usr/lib
-usr/share/docs
Deleted: trunk/packages/libsbml/trunk/debian/python-sbml.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/python-sbml.docs 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/python-sbml.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +0,0 @@
-debian/tmp/usr/share/doc/libsbml-*/python.txt
Deleted: trunk/packages/libsbml/trunk/debian/python-sbml.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/python-sbml.install 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/python-sbml.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -1 +0,0 @@
-usr/lib/python*/*
Added: trunk/packages/libsbml/trunk/debian/python-sbml3-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/python-sbml3-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/python-sbml3-doc.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/python-api
Copied: trunk/packages/libsbml/trunk/debian/python-sbml3.dirs (from rev 2255, trunk/packages/libsbml/trunk/debian/python-sbml.dirs)
===================================================================
--- trunk/packages/libsbml/trunk/debian/python-sbml3.dirs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/python-sbml3.dirs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1,2 @@
+usr/lib
+usr/share/docs
Copied: trunk/packages/libsbml/trunk/debian/python-sbml3.docs (from rev 2255, trunk/packages/libsbml/trunk/debian/python-sbml.docs)
===================================================================
--- trunk/packages/libsbml/trunk/debian/python-sbml3.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/python-sbml3.docs 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+debian/tmp/usr/share/doc/libsbml-*/python.txt
Copied: trunk/packages/libsbml/trunk/debian/python-sbml3.install (from rev 2255, trunk/packages/libsbml/trunk/debian/python-sbml.install)
===================================================================
--- trunk/packages/libsbml/trunk/debian/python-sbml3.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/python-sbml3.install 2008-07-18 00:52:59 UTC (rev 2256)
@@ -0,0 +1 @@
+usr/lib/python*/*
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2008-07-17 23:34:27 UTC (rev 2255)
+++ trunk/packages/libsbml/trunk/debian/rules 2008-07-18 00:52:59 UTC (rev 2256)
@@ -25,8 +25,8 @@
endif
# shared library versions, option 1
-version=3.0.0
-major=3
+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)}'`
@@ -37,19 +37,34 @@
patch: patch-stamp
patch-stamp:
dpatch apply-all
+ libtoolize -c -f
+ aclocal -Iconfig
+ autoconf
+ eval `bash /usr/share/java-common/jvm-find.sh` && javac -cp $$JAVA_HOME/lib/tools.jar -sourcepath docs/src -d docs/src docs/src/ExcludeDoclet.java
touch patch-stamp
config.status: patch configure
dh_testdir
# Add here commands to configure the package.
CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs"
- chmod u+x configure
- chmod u+x config/install-sh
./configure --host=$(DEB_HOST_GNU_TYPE) \
--build=$(DEB_BUILD_GNU_TYPE) \
--prefix=/usr \
--mandir=\$${prefix}/share/man \
--infodir=\$${prefix}/share/info \
+ --with-perl=/usr \
+ --with-python=/usr \
+ --with-java=/usr \
+ --with-ruby=/usr \
+ --with-octave=/usr
+ touch \
+ src/bindings/java/java-files \
+ src/bindings/java/libsbml_wrap.cpp \
+ src/bindings/perl/LibSBML.pm \
+ src/bindings/perl/LibSBML_wrap.cxx \
+ src/bindings/python/libsbml.py \
+ src/bindings/python/libsbml_wrap.cpp \
+ src/bindings/ruby/libsbml_wrap.cpp
build: build-stamp build-stamp-indep
build-stamp: config.status
@@ -72,7 +87,6 @@
dh_testdir
dh_testroot
-([ -r Makefile ] && $(MAKE) distclean)
- -(cd examples && $(MAKE) clean)
clean: distclean unpatch
dh_testdir
@@ -82,8 +96,21 @@
rm -f config.status
rm -f config.log
# Clean not sufficient for dpkg-sources diff
- chmod u-x configure
- chmod u-x config/install-sh
+ rm -rf docs/formatted
+ dh_clean \
+ `find . -name "*.a" -o -name "*.la" -o -iname "*.Po" -o -iname "*.loT" -o -name "*pdf" -o -name "*.aux" -o -name "*.dvi" ` \
+ docs/src/ExcludeDoclet\\$$1.class \
+ src/bindings/octave/BuildTranslate_Win32.m \
+ src/bindings/octave/CheckAndConvert.m \
+ src/bindings/octave/Contents.m \
+ src/bindings/octave/README.txt \
+ src/bindings/octave/TranslateSBML.c \
+ src/bindings/octave/TranslateSBML.m \
+ src/bindings/octave/install_Win32.m \
+ src/bindings/octave/make.bat \
+ src/bindings/octave/matlab-tags-regexp.txt \
+ src/bindings/octave/test.xml
+
install: build
dh_testdir
dh_testroot
@@ -91,7 +118,7 @@
dh_installdirs
# Add here commands to install the package into debian/tmp
$(MAKE) install DESTDIR=$(CURDIR)/debian/tmp/
- mv $(CURDIR)/debian/tmp/usr/lib/libsbml.3.0.0.so $(CURDIR)/debian/tmp/usr/lib/libsbml.so.3.0.0
+ $(MAKE) install-docs DESTDIR=$(CURDIR)/debian/tmp/
# Build architecture-independent files here.
binary-indep: build-indep install
@@ -105,11 +132,13 @@
dh_installchangelogs
dh_installdocs
dh_installexamples
- dh_install --sourcedir=$(CURDIR)/debian/tmp
+ dh_install -Xlibsbml-java --sourcedir=$(CURDIR)/debian/tmp
dh_link
dh_strip
dh_compress
dh_fixperms
+ dh_perl
+ dh_pysupport
dh_makeshlibs
dh_installdeb
dh_shlibdeps
More information about the debian-med-commit
mailing list