[med-svn] r3504 - in trunk/packages/libsbml/trunk/debian: . patches
Moriyoshi Koizumi
moriyoshi-guest at alioth.debian.org
Fri Jun 19 08:27:46 UTC 2009
Author: moriyoshi-guest
Date: 2009-06-19 08:27:45 +0000 (Fri, 19 Jun 2009)
New Revision: 3504
Added:
trunk/packages/libsbml/trunk/debian/patches/09_docs_install_mkinstalldirs.dpatch
trunk/packages/libsbml/trunk/debian/patches/10_perl_binding_instdir.dpatch
Removed:
trunk/packages/libsbml/trunk/debian/libsbml3-java.links
trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.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/07_perldoc_mod_name_fix.dpatch
trunk/packages/libsbml/trunk/debian/patches/08_missing_includes.dpatch
Modified:
trunk/packages/libsbml/trunk/debian/changelog
trunk/packages/libsbml/trunk/debian/control
trunk/packages/libsbml/trunk/debian/libsbml3-cil.install
trunk/packages/libsbml/trunk/debian/libsbml3-perl.install
trunk/packages/libsbml/trunk/debian/patches/00list
trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch
trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch
trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch
trunk/packages/libsbml/trunk/debian/rules
Log:
* Synching with my local repository.
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/changelog 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,3 +1,15 @@
+libsbml (3.4.0-1) UNRELEASED; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Tue, 16 Jun 2009 19:42:00 +0900
+
+libsbml (3.3.2-1) UNRELEASED; urgency=low
+
+ * Upstream update.
+
+ -- Moriyoshi Koizumi <mozo at sfc.keio.ac.jp> Wed, 03 Jun 2009 02:30:07 +0900
+
libsbml (3.3.1-1) UNRELEASED; urgency=low
* Initial release (Closes: #241111)
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/control 2009-06-19 08:27:45 UTC (rev 3504)
@@ -9,20 +9,23 @@
Build-Depends: debhelper (>= 7),
autoconf,
automake,
+ dpatch,
ruby1.8,
libxml2-dev,
python2.5-dev,
ruby1.8-dev,
perl,
+ libperl-dev,
openjdk-6-jdk | java-gcj-compat-dev | java-sdk,
- octave2.9-headers,
+ octave3.0-headers,
python-support,
doxygen (>= 1.5.8),
graphviz,
zlib1g-dev,
libbz2-dev,
- cli-common (>= 0.5.7),
- mono-devel (>= 2.0)
+ c-sharp-compiler,
+ cli-common-dev (>= 0.5.7),
+ cli-runtime
Standards-Version: 3.8.0
Section: science
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/libsbml/trunk/
@@ -192,7 +195,7 @@
Section: math
Depends: ${shlibs:Depends},
${misc:Depends},
- octave
+ octave3.0
Architecture: any
Description: System Biology Markup Language library - Octave binding
LibSBML is a library designed to help you read, write, manipulate,
Modified: trunk/packages/libsbml/trunk/debian/libsbml3-cil.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-cil.install 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-cil.install 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,3 +1,2 @@
usr/lib/pkgconfig/libsbml-cil.pc
usr/lib/cli/*
-usr/lib/mono/*
Deleted: trunk/packages/libsbml/trunk/debian/libsbml3-java.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-java.links 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-java.links 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1 +0,0 @@
-usr/lib/jni/libsbmlj.so usr/lib/jni/libsbmlj.so.1
Modified: trunk/packages/libsbml/trunk/debian/libsbml3-perl.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml3-perl.install 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/libsbml3-perl.install 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1 +1 @@
-usr/lib/perl/*
+usr/lib/perl5/*
Modified: trunk/packages/libsbml/trunk/debian/patches/00list
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/00list 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/00list 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,8 +1,5 @@
-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
08_pkgconfig_file_gen
+09_docs_install_mkinstalldirs
+10_perl_binding_instdir
Deleted: trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/01_java_cleanup_prevention.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,23 +0,0 @@
-#! /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 =
-
-
- # -----------------------------------------------------------------------------
Modified: trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/02_libtool_support.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -5,13 +5,13 @@
## DP: No description.
@DPATCH@
-diff -urNad libsbml-3.2.0~/Makefile.in libsbml-3.2.0/Makefile.in
---- libsbml-3.2.0~/Makefile.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/Makefile.in 2008-09-02 04:51:41.000000000 +0900
+diff -urNad libsbml-3.3.2~/Makefile.in libsbml-3.3.2/Makefile.in
+--- libsbml-3.3.2~/Makefile.in 2009-06-06 15:12:13.215001166 +0900
++++ libsbml-3.3.2/Makefile.in 2009-06-06 15:12:16.195000642 +0900
@@ -185,11 +185,13 @@
+ config/java.m4 \
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 \
@@ -22,16 +22,16 @@
config/octave.m4 \
config/perl.m4 \
config/python.m4 \
-@@ -209,7 +211,7 @@
+@@ -210,7 +212,7 @@
# 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
++ src/common/config.h src/common/stamp-h1 config/lt_link_helper.sh config/mkoctfile_wrapper.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
-@@ -218,10 +220,6 @@
+@@ -219,10 +221,6 @@
extra_clean = include libsbml.pc
@@ -39,10 +39,10 @@
- extra_clean += libsbml.la
-endif
-
+ # Misc things used later below.
- # -----------------------------------------------------------------------------
- # Primary build actions.
-@@ -231,7 +229,7 @@
+ define nodoxygen
+@@ -242,7 +240,7 @@
# of the form `foo-recursive' to run 'make foo' in directories defined in
# variable `subdirs'.
@@ -50,8 +50,8 @@
+all: configure Makefile include all-recursive libsbml.pc
docs:;
- ifneq "$(MAKEFLAGS)" ""
-@@ -304,46 +302,10 @@
+ # Only in the case of Java can we make the docs without doxygen.
+@@ -321,42 +319,6 @@
# -----------------------------------------------------------------------------
@@ -94,12 +94,16 @@
# Installation.
# -----------------------------------------------------------------------------
+@@ -388,7 +350,7 @@
+
+ endef
+
-install: all install-recursive install-warnings install-pc install-la
+install: all install-recursive install-warnings install-pc
- install-docs: install-docs-recursive
-
-@@ -362,13 +324,7 @@
+ # Only in the case of Java can we make the docs without doxygen.
+ ifdef USE_JAVA
+@@ -415,13 +377,7 @@
install-pc: libsbml.pc
$(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
@@ -114,7 +118,7 @@
@if test -d "$(DESTDIR)$(LIBDIR)"; then \
if test -n "`find $(DESTDIR)$(LIBDIR) -maxdepth 0 -empty`"; then \
echo rmdir "$(DESTDIR)$(LIBDIR)"; \
-@@ -409,16 +365,6 @@
+@@ -463,16 +419,6 @@
fi; \
fi;
@@ -131,14 +135,12 @@
# -----------------------------------------------------------------------------
# Cleaning.
# -----------------------------------------------------------------------------
-diff -urNad libsbml-3.2.0~/acinclude.m4 libsbml-3.2.0/acinclude.m4
---- libsbml-3.2.0~/acinclude.m4 1970-01-01 09:00:00.000000000 +0900
-+++ libsbml-3.2.0/acinclude.m4 2008-09-02 04:51:33.000000000 +0900
-@@ -0,0 +1,27 @@
-+# generated automatically by aclocal 1.9.6 -*- Autoconf -*-
-+
+diff -urNad libsbml-3.3.2~/acinclude.m4 libsbml-3.3.2/acinclude.m4
+--- libsbml-3.3.2~/acinclude.m4 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.3.2/acinclude.m4 2009-06-06 15:12:16.195000642 +0900
+@@ -0,0 +1,28 @@
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
-+# 2005 Free Software Foundation, Inc.
++# 2005, 2006, 2007, 2008 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.
@@ -148,12 +150,13 @@
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
++m4_include([config/bzip2.m4])
++m4_include([config/csharp.m4])
+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])
@@ -161,10 +164,40 @@
+m4_include([config/ruby.m4])
+m4_include([config/runldpath.m4])
+m4_include([config/swig.m4])
++m4_include([config/univbinary.m4])
+m4_include([config/xercesc.m4])
-diff -urNad libsbml-3.2.0~/config/lt_link_helper.sh.in libsbml-3.2.0/config/lt_link_helper.sh.in
---- libsbml-3.2.0~/config/lt_link_helper.sh.in 1970-01-01 09:00:00.000000000 +0900
-+++ libsbml-3.2.0/config/lt_link_helper.sh.in 2008-09-02 04:51:33.000000000 +0900
++m4_include([config/zlib.m4])
+diff -urNad libsbml-3.3.2~/config/java.m4 libsbml-3.3.2/config/java.m4
+--- libsbml-3.3.2~/config/java.m4 2009-06-06 15:12:13.215001166 +0900
++++ libsbml-3.3.2/config/java.m4 2009-06-06 15:12:16.195000642 +0900
+@@ -105,7 +105,6 @@
+ dnl We need to get to the real directory first.
+ dnl (However, only do this if the user didn't request a specific path.)
+
+- if test "$with_java" = "yes"; then
+ while test -h "$JAVAC"; do
+ dnl
+ dnl This next case case statement does 2 things:
+@@ -129,7 +128,7 @@
+ break
+ ;;
+ *)
+- javaclink=`readlink "$JAVAC"`
++ javaclink=`readlink -f "$JAVAC"`
+ ;;
+ esac
+
+@@ -143,7 +142,6 @@
+ ;;
+ esac
+ done
+- fi
+
+ dnl Need to find the include files.
+
+diff -urNad libsbml-3.3.2~/config/lt_link_helper.sh.in libsbml-3.3.2/config/lt_link_helper.sh.in
+--- libsbml-3.3.2~/config/lt_link_helper.sh.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.3.2/config/lt_link_helper.sh.in 2009-06-06 15:12:16.195000642 +0900
@@ -0,0 +1,69 @@
+#!/bin/sh
+
@@ -185,7 +218,7 @@
+ exit
+fi
+
-+linker_tmpdir=`mktemp -d`
++linker_tmpdir=`mktemp -d $PWD/XXXXXXXX`
+stage_dir="${linker_tmpdir}/stage"
+mkdir -p "${stage_dir}/${libdir}"
+
@@ -231,13 +264,13 @@
+ 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\" $args" && \
++eval "@abs_top_srcdir@/libtool --tag=\"$TAG\" --mode=link \"$LD\" -rpath \"${libdir}\" -inst-prefix-dir \"${stage_dir}\" -module -avoid-version -export-dynamic -shrext "${dllibext}" -o \"${out_dir}/${out_filename}.la\" $args" && \
+ eval "@abs_top_srcdir@/libtool --mode=install cp \"${out_dir}/${out_filename}.la\" \"${stage_dir}/${libdir}/${out_filename}.la\"" && \
+ cp "${stage_dir}/${libdir}/${out_filename}${dllibext}" "${out_dir}"
+rm -rf "${linker_tmpdir}"
-diff -urNad libsbml-3.2.0~/config/makefile-common-actions.mk libsbml-3.2.0/config/makefile-common-actions.mk
---- libsbml-3.2.0~/config/makefile-common-actions.mk 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/config/makefile-common-actions.mk 2008-09-02 04:51:33.000000000 +0900
+diff -urNad libsbml-3.3.2~/config/makefile-common-actions.mk libsbml-3.3.2/config/makefile-common-actions.mk
+--- libsbml-3.3.2~/config/makefile-common-actions.mk 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/config/makefile-common-actions.mk 2009-06-06 15:12:16.195000642 +0900
@@ -40,7 +40,7 @@
# -----------------------------------------------------------------------------
@@ -247,64 +280,45 @@
# The following define default values of variables like `cxxcompile'. An
# enclosing makefile can define other values, in which case those
-@@ -50,28 +50,22 @@
+@@ -53,28 +53,20 @@
+ use_gcc = $(shell $(CXX) -dumpversion 2>&1 | grep '^[34]\.' )
+ use_suncc = $(shell $(CXX) -V 2>&1 | grep 'Sun C++' )
- default_includes ?= -I. -I$(top_include)
-
--# Compiling under cygwin doesn't need -fPIC.
+-# Compiling under cygwin and Sun cc doesn't need -fPIC.
-
-ifneq "$(HOST_TYPE)" "cygwin"
-- FPIC = -fPIC
+- ifeq "$(use_suncc)" ""
+- FPIC = -fPIC
+- endif
-endif
-
+ # Compiling under Sun cc must not use -Wall.
+
+ ifeq "$(use_suncc)" ""
+ WALL = -Wall
+ 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)
+-compile ?= $(CC) $(FPIC) $(WALL) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
+- $(extra_CPPFLAGS) $(CFLAGS) $(extra_CFLAGS)
++compile ?= $(LIBTOOL) --mode=compile $(CC) $(FPIC) $(WALL) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
++ $(extra_CPPFLAGS) $(CFLAGS) $(extra_CFLAGS)
--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)
+-cxxcompile ?= $(CXX) $(FPIC) $(WALL) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
++cxxcompile ?= $(LIBTOOL) --mode=compile $(CXX) $(FPIC) $(WALL) $(sort $(default_includes) $(INCLUDES)) $(CPPFLAGS) \
+ $(extra_CPPFLAGS) $(CXXFLAGS) $(extra_CXXFLAGS)
- # 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.
+ # The following two commands are used for dependency tracking only when
+@@ -118,8 +112,19 @@
--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) \
+- $(CXX) $(extra_LDFLAGS) $(LDFLAGS) $(platform_link_flags) \
- -o $(1) $(objfiles) $(extra_LIBS) $(LIBS)
-+ $(LIBTOOL) --mode=link $(CXX) $(LDFLAGS) $(extra_LDFLAGS) \
++ $(LIBTOOL) --mode=link $(CXX) $(extra_LDFLAGS) $(LDFLAGS) \
+ -version-info $(subst .,:,$(library_version)) \
+ -inst-prefix-dir "$(DESTDIR)" \
+ $(platform_link_flags) -rpath $(LIBDIR) -o $(1) $(objfiles:.o=.lo) \
@@ -315,12 +329,12 @@
+ifndef link_dl_lib
+ define link_dl_lib
+ $(TOP_SRCDIR)/config/lt_link_helper.sh $(CXX) --libdir $(LIBDIR) \
-+ $(LDFLAGS) $(extra_LDFLAGS) $(platform_link_flags) \
++ $(extra_LDFLAGS) $(LDFLAGS) $(platform_link_flags) \
+ -o $(1) $(objfiles:.o=.lo) $(extra_LIBS) $(LIBS)
endef
endif
-@@ -121,16 +121,16 @@
+@@ -142,16 +147,16 @@
# filter the results. This abstracts out this common operation.
make_objects_list = \
@@ -342,22 +356,30 @@
# 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 @@
+@@ -175,95 +180,27 @@
endif
-%.so ../%.so: $(objfiles)
-- $(call link_shared_lib,$@)
--
--%.$(JNIEXT) ../%.$(JNIEXT): $(objfiles)
+%.la ../%.la: $(objfiles)
$(call link_shared_lib,$@)
- %.$(SHAREDLIBEXT) ../%.$(SHAREDLIBEXT): $(objfiles)
+ %.$(JNIEXT) ../%.$(JNIEXT): $(objfiles)
- $(call link_shared_lib,$@)
-
--# The following define generic rules for creating object files.
--
+-#
+-# -install_name option should be used when building an universal binary on MacOSX.
+-#
+-%.$(SHAREDLIBEXT) ../%.$(SHAREDLIBEXT): $(objfiles)
+-ifeq "$(HOST_TYPE)" "darwin"
+- $(call link_shared_lib,$@ -install_name $@)
+-else
+- $(call link_shared_lib,$@)
+-endif
++ $(call link_dl_lib,$@)
+
+ # The following define generic rules for creating object files.
+
-ifeq "$(HOST_TYPE)" "aix"
-
-.c.$(OBJEXT):
@@ -372,47 +394,82 @@
-
-.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.$(OBJEXT):
+-ifndef USE_UNIVBINARY
+.c.lo:
+ ifneq "$(use_suncc)" ""
+ $(compile) -c -o $@ $<
+ else
$(compile) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.$(DEPEXT)" -c -o $@ $<
+ endif
+-else
+- $(compile_nocflags) -MT $@ -MM -MP -MF "$(DEPDIR)/$*.$(DEPEXT)" $<
+- $(compile) -c -o $@ $<
+-endif
+-
+-.c.obj:
+- if $(compile) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" \
+- -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
- .c.obj:
-@@ -199,7 +175,7 @@
- else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; \
- fi
-
-.cpp.$(OBJEXT) .cxx.$(OBJEXT):
+-ifndef USE_UNIVBINARY
+.cpp.lo .cxx.lo:
+ ifneq "$(use_suncc)" ""
+ $(cxxcompile) -c -o $@ $<
+ else
$(cxxcompile) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.$(DEPEXT)" -c -o $@ $<
-
- .cpp.obj:
-@@ -209,8 +185,6 @@
- else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; \
- fi
-
+ endif
+-else
+- $(cxxcompile_nocxxflags) -MT $@ -MM -MP -MF "$(DEPDIR)/$*.$(DEPEXT)" $<
+- $(cxxcompile) -c -o $@ $<
-endif
-
- ifeq "$(HOST_TYPE)" "darwin"
+-
+-.cpp.obj:
+- if $(cxxcompile) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" \
+- -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
+-
+-endif
+-
+-ifeq "$(HOST_TYPE)" "darwin"
+-
+-%.bundle ../%.bundle: $(objfiles)
+- $(call link_shared_lib,$@)
+-
+-endif
- %.bundle ../%.bundle: $(objfiles)
-@@ -324,18 +298,7 @@
+ # This next line ensures that the object output directory is created first.
+ # Got this from a posting by Paul D. Smith to gnu.utils.help, 2001-12-03.
+@@ -325,7 +263,7 @@
+ # in the including Makefile.
+ $(check_driver): $(test_objfiles)
+- $(CXX) $(extra_CPPFLAGS) $(extra_CXXFLAGS) $(default_includes) \
++ $(LIBTOOL) --mode=link $(CXX) $(extra_CPPFLAGS) $(extra_CXXFLAGS) $(default_includes) \
+ $(CPPFLAGS) $(CFLAGS) $(INCLUDES) \
+ $(test_objfiles) $(objfiles) $(extra_LDFLAGS) $(LDFLAGS) \
+ $(LIBS) $(extra_LIBS) -o $@
+@@ -361,19 +299,7 @@
+ # $(call install_library,$(libname),$(dest))
+
define install_library
- $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR)
+- $(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)/$$finalname; \
@@ -425,65 +482,33 @@
- echo $(INSTALL_SH) $(1) $(2); \
- $(INSTALL_SH) $(1) $(2); \
- fi
-+ $(LIBTOOL) --mode=install $(INSTALL_SH) $(1) $(DESTDIR)/$(LIBDIR)
++ $(MKINSTALLDIRS) $(2) && $(LIBTOOL) --mode=install $(INSTALL_SH) $(1) $(2)
endef
to_install_libraries = $(addprefix install-,$(libraries))
-@@ -408,7 +371,7 @@
-
- define uninstall_library
- @if test -f $(1); then \
-- finalname="$(notdir $(basename $(1))).$(library_version)$(suffix $(1))"; \
-+ finalname="$(notdir $(basename $(1)))$(suffix $(1)).$(library_version)"; \
- target="$(2)/$$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-3.2.0~/config/makefile-common-vars.mk.in libsbml-3.2.0/config/makefile-common-vars.mk.in
---- libsbml-3.2.0~/config/makefile-common-vars.mk.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/config/makefile-common-vars.mk.in 2008-09-02 04:51:33.000000000 +0900
-@@ -144,6 +144,9 @@
+diff -urNad libsbml-3.3.2~/config/makefile-common-vars.mk.in libsbml-3.3.2/config/makefile-common-vars.mk.in
+--- libsbml-3.3.2~/config/makefile-common-vars.mk.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/config/makefile-common-vars.mk.in 2009-06-06 15:12:16.195000642 +0900
+@@ -147,6 +147,7 @@
OCTAVE = @OCTAVE@
MKOCTFILE = @MKOCTFILE@
MKOCTFILE_FLAGS = @MKOCTFILE_FLAGS@
+MKOCTFILE_WRAPPER = $(SHELL) $(top_srcdir)/config/mkoctfile_wrapper.sh
-+LOCALOCTFILEDIR = @LOCALOCTFILEDIR@
-+OCTAVE_CONFIG = @OCTAVE_CONFIG@
+ LOCALOCTFILEDIR = @LOCALOCTFILEDIR@
+ OCTAVE_CONFIG = @OCTAVE_CONFIG@
OCTAVEEXT = @OCTAVEEXT@
-
- USE_LISP = @USE_LISP@
-@@ -219,7 +222,10 @@
+@@ -226,6 +227,7 @@
PACKAGE_VERSION = @PACKAGE_VERSION@
RANLIB = @RANLIB@
SHAREDLIBEXT = @SHAREDLIBEXT@
+LIBTOOL = @LIBTOOL@
SHELL = @SHELL@
-+SN = @SN@
-+GACUTIL = @GACUTIL@
LIBSBML_VERSION = @PACKAGE_VERSION@
- LIBSBML_VERSION_NUMERIC = @LIBSBML_VERSION_NUMERIC@
-diff -urNad libsbml-3.2.0~/config/mkoctfile_wrapper.sh.in libsbml-3.2.0/config/mkoctfile_wrapper.sh.in
---- libsbml-3.2.0~/config/mkoctfile_wrapper.sh.in 1970-01-01 09:00:00.000000000 +0900
-+++ libsbml-3.2.0/config/mkoctfile_wrapper.sh.in 2008-09-02 04:51:33.000000000 +0900
-@@ -0,0 +1,14 @@
+diff -urNad libsbml-3.3.2~/config/mkoctfile_wrapper.sh.in libsbml-3.3.2/config/mkoctfile_wrapper.sh.in
+--- libsbml-3.3.2~/config/mkoctfile_wrapper.sh.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.3.2/config/mkoctfile_wrapper.sh.in 2009-06-06 15:12:16.195000642 +0900
+@@ -0,0 +1,17 @@
+#!/bin/sh
+SHAREDLIBEXT=@SHAREDLIBEXT@
+
@@ -491,60 +516,20 @@
+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
++ elif expr "$1" : "-f" > /dev/null; then
++ CFLAGS="$CFLAGS $1"
++ else
+ args="$args '$1'"
+ fi
+ shift
+done
+
++export CFLAGS
+eval "exec $args"
-diff -urNad libsbml-3.2.0~/config/octave.m4 libsbml-3.2.0/config/octave.m4
---- libsbml-3.2.0~/config/octave.m4 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/config/octave.m4 2008-09-02 04:51:33.000000000 +0900
-@@ -42,9 +42,13 @@
- [no-octave-found], [$with_octave/bin])
- AC_PATH_PROG([MKOCTFILE], [mkoctfile], [$with_octave/bin/mkoctfile],
- [no-mkoctfile-found], [$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-3.2.0~/configure.ac libsbml-3.2.0/configure.ac
---- libsbml-3.2.0~/configure.ac 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/configure.ac 2008-09-02 04:51:33.000000000 +0900
-@@ -139,13 +139,17 @@
+diff -urNad libsbml-3.3.2~/configure.ac libsbml-3.3.2/configure.ac
+--- libsbml-3.3.2~/configure.ac 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/configure.ac 2009-06-06 15:12:16.205000623 +0900
+@@ -150,13 +150,17 @@
AC_PROG_CXX
AC_PROG_CC
AC_PROG_CPP
@@ -562,9 +547,9 @@
+AC_PATH_PROGS([SN], [sn])
+AC_PATH_PROGS([GACUTIL], [gacutil])
- CONFIG_PROG_SWIG(1.3.33)
- CONFIG_PROG_PYTHON
-@@ -234,7 +238,9 @@
+ # The Lisp language binding has been removed for the time being, because it
+ # no longer works in recent versions of libSBML.
+@@ -252,7 +256,9 @@
dnl Output
dnl ---------------------------------------------------------------------------
@@ -574,14 +559,37 @@
AC_CONFIG_FILES([./Makefile])
AC_CONFIG_FILES([src/Makefile])
-diff -urNad libsbml-3.2.0~/src/bindings/csharp/Makefile.in libsbml-3.2.0/src/bindings/csharp/Makefile.in
---- libsbml-3.2.0~/src/bindings/csharp/Makefile.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/src/bindings/csharp/Makefile.in 2008-09-02 04:51:33.000000000 +0900
-@@ -95,9 +95,9 @@
- SWIGFLAGS += $(CSHARP_SWIGFLAGS) -I../swig
- SWIGFLAGS_WIN = -DSWIGWIN -DSWIG_CSHARP_NO_WSTRING_HELPER
+diff -urNad libsbml-3.3.2~/src/annotation/test/Makefile.in libsbml-3.3.2/src/annotation/test/Makefile.in
+--- libsbml-3.3.2~/src/annotation/test/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/annotation/test/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -123,8 +123,8 @@
+ # dependencies on other subdirectoris of the source tree, we do some rummaging
+ # around in .. and ../../subdirs.
--extra_LDFLAGS = $(CSHARP_LDFLAGS) -L../..
+-tmp = $(test_sources:.cpp=.$(OBJEXT)) $(test_sources:.c=.$(OBJEXT))
+-localobjfiles = $(filter %.$(OBJEXT),$(tmp))
++tmp = $(test_sources:.cpp=.lo) $(test_sources:.c=.lo)
++localobjfiles = $(filter %.lo,$(tmp))
+ otherdirs = .. ../../util ../../xml ../../math ../../sbml ../../validator \
+ ../../validator/constraints ../../units ../../compress ../../common
+
+@@ -132,7 +132,7 @@
+ otherdirs += ../../sbml/layout
+ endif
+
+-otherobjfiles = $(wildcard $(addsuffix /*.$(OBJEXT),$(otherdirs)))
++otherobjfiles = $(wildcard $(addsuffix /*.lo,$(otherdirs)))
+ test_objfiles = $(localobjfiles) $(otherobjfiles)
+
+ ifdef USE_LIBCHECK
+diff -urNad libsbml-3.3.2~/src/bindings/csharp/Makefile.in libsbml-3.3.2/src/bindings/csharp/Makefile.in
+--- libsbml-3.3.2~/src/bindings/csharp/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/bindings/csharp/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -106,9 +106,9 @@
+ # -L../../ option appears first in command-line to always link
+ # with the libSBML's shared library file in the relative path.
+ #
+-extra_LDFLAGS = -L../../ $(CSHARP_LDFLAGS)
+extra_LDFLAGS = $(CSHARP_LDFLAGS)
-extra_LIBS = -lsbml
@@ -589,33 +597,27 @@
ifdef USE_EXPAT
extra_CPPFLAGS += @EXPAT_CPPFLAGS@
-@@ -181,7 +181,7 @@
- # `extra_clean' and `extra_distclean' determine the files and directories
- # removed during "make clean" and "make distclean".
+@@ -217,6 +217,12 @@
--extra_clean = $(csproxy_lib) $(dllimport_lib) $(check_runner_exe) $(tmpfiles)
-+extra_clean = $(csproxy_lib) $(dllimport_lib) $(check_runner_exe) $(tmpfiles) libsbmlcs.snk
+ ifeq "$(HOST_TYPE)" "darwin"
+ platform_link_flags = -bundle
++ # environment variable MACOSX_DEPLOYMENT_TARGET must be set to 10.3 or later
++ # to use -undefined dynamic_lookup.
++ macosx_version=$(shell sw_vers -productVersion | cut -d"." -f1,2)
++ export MACOSX_DEPLOYMENT_TARGET=${macosx_version}
++%.$(CSHARP_EXT): $(patsubst %.cpp, %.lo, $(patsubst %.c, %.lo, $(sources)))
++ $(call link_dl_lib,$@)
+ endif
- extra_distclean =
+ #
+@@ -448,16 +454,23 @@
+ install_prefix=$(DESTDIR)$(LIBDIR)/mono/$(assembly_name)
-@@ -290,7 +290,8 @@
-
-
- $(csproxy_lib): $(outpath)/libsbml.cs $(dllimport_lib)
-- "$(CSHARP_COMPILER)" $(CSC_OPT_SHARED) $(CSC_OPT_OUTPUT)$(csproxy_lib) $(outpath)/*.cs
-+ "$(SN)" -k libsbmlcs.snk
-+ "$(CSHARP_COMPILER)" $(CSC_OPT_SHARED) $(CSC_OPT_OUTPUT)$(csproxy_lib) $(outpath)/*.cs /keyfile:libsbmlcs.snk
-
-
- $(outpath)/libsbml.cs: libsbml_wrap.cpp
-@@ -424,18 +425,23 @@
- # -----------------------------------------------------------------------------
-
install: check_swigfile_consistency $(libraries)
-- @list='$(libraries)'; for lib in $$list; do \
-- echo "$(INSTALL) $$lib $(DESTDIR)$(LIBDIR)"; \
-- $(INSTALL) $$lib $(DESTDIR)$(LIBDIR); \
-- done;
+- -$(GACUTIL) -i $(csproxy_lib) -root $(DESTDIR)$(LIBDIR)
+- $(INSTALL_SH) $(csproxy_lib) $(install_prefix)/$(csproxy_lib)
+- $(INSTALL_SH) $(dllimport_lib) $(install_prefix)/$(dllimport_lib)
+- ln -sf ../../libsbml.$(SHAREDLIBEXT) $(install_prefix)/libsbml.$(SHAREDLIBEXT)
+ $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR)/cli/libsbml-3.0
+ for lib in $(csproxy_lib); do \
+ $(GACUTIL) /i $$lib /root $(DESTDIR)$(LIBDIR); \
@@ -626,12 +628,10 @@
+ done
uninstall:
-- @list='$(libraries)'; for lib in $$list; do \
-- if test -f "$(DESTDIR)$(LIBDIR)/$$lib"; then \
-- echo rm "$(DESTDIR)$(LIBDIR)/$$lib"; \
-- rm $(DESTDIR)$(LIBDIR)/$$lib; \
-- fi; \
-- done;
+- -$(GACUTIL) -u $(assembly_name) -root $(DESTDIR)$(LIBDIR)
+- rm -f $(install_prefix)/$(csproxy_lib)
+- rm -f $(install_prefix)/$(dllimport_lib)
+- rm -f $(install_prefix)/libsbml.$(SHAREDLIBEXT)
+ for lib in $(csproxy_lib); do \
+ rm -f $(DESTDIR)$(LIBDIR)/cli/libsbml-3.0/$$lib; \
+ $(GACUTIL) /u $$lib /root $(DESTDIR)$(LIBDIR); \
@@ -642,22 +642,22 @@
installcheck:
-diff -urNad libsbml-3.2.0~/src/bindings/java/Makefile.in libsbml-3.2.0/src/bindings/java/Makefile.in
---- libsbml-3.2.0~/src/bindings/java/Makefile.in 2008-09-02 04:51:33.000000000 +0900
-+++ libsbml-3.2.0/src/bindings/java/Makefile.in 2008-09-02 04:51:33.000000000 +0900
-@@ -60,9 +60,9 @@
- extra_CPPFLAGS = $(JAVA_CPPFLAGS) -I../swig
- SWIGFLAGS += $(JAVA_CPPFLAGS) -I../swig
-
--extra_LDFLAGS = $(JAVA_LDFLAGS) -L../..
+diff -urNad libsbml-3.3.2~/src/bindings/java/Makefile.in libsbml-3.3.2/src/bindings/java/Makefile.in
+--- libsbml-3.3.2~/src/bindings/java/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/bindings/java/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -64,9 +64,9 @@
+ # -L../../ option appears first in command-line to always link
+ # with the libSBML's shared library file in the relative path.
+ #
+-extra_LDFLAGS = -L../../ $(JAVA_LDFLAGS)
+extra_LDFLAGS = $(JAVA_LDFLAGS)
--extra_LIBS = -lsbml $(JAVA_LIBS)
+-extra_LIBS = -lsbml
+extra_LIBS = ../../libsbml.la $(JAVA_LIBS)
ifdef USE_EXPAT
extra_CPPFLAGS += @EXPAT_CPPFLAGS@
-@@ -142,7 +142,7 @@
+@@ -156,7 +156,7 @@
# build directives of `makefile-common-actions.mk'.
.SUFFIXES:
@@ -666,7 +666,7 @@
# The default action is to remake everything.
-@@ -315,9 +315,17 @@
+@@ -333,9 +333,17 @@
# -----------------------------------------------------------------------------
install: check_swigfile_consistency $(libraries)
@@ -687,9 +687,9 @@
done;
uninstall:
-diff -urNad libsbml-3.2.0~/src/bindings/octave/Makefile.in libsbml-3.2.0/src/bindings/octave/Makefile.in
---- libsbml-3.2.0~/src/bindings/octave/Makefile.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/src/bindings/octave/Makefile.in 2008-09-02 04:51:33.000000000 +0900
+diff -urNad libsbml-3.3.2~/src/bindings/octave/Makefile.in libsbml-3.3.2/src/bindings/octave/Makefile.in
+--- libsbml-3.3.2~/src/bindings/octave/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/bindings/octave/Makefile.in 2009-06-06 15:12:16.205000623 +0900
@@ -76,7 +76,7 @@
# `extra_clean' and `extra_distclean' determine the files and directories
# removed during "make clean" and "make distclean".
@@ -697,9 +697,9 @@
-extra_clean = TranslateSBML.$(OCTAVEEXT)
+extra_clean = TranslateSBML.$(OCTAVEEXT) libsbml.so* libsbml.a
- extra_disclean = $(matlab_sources)
+ extra_distclean = $(matlab_sources)
-@@ -95,10 +95,13 @@
+@@ -120,10 +120,13 @@
fi; \
done
@@ -716,45 +716,25 @@
# -----------------------------------------------------------------------------
-@@ -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-3.2.0~/src/bindings/perl/Makefile.PL.in libsbml-3.2.0/src/bindings/perl/Makefile.PL.in
---- libsbml-3.2.0~/src/bindings/perl/Makefile.PL.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/src/bindings/perl/Makefile.PL.in 2008-09-02 04:51:33.000000000 +0900
-@@ -50,10 +50,9 @@
- MAKEFILE => 'Makefile-perl',
+diff -urNad libsbml-3.3.2~/src/bindings/perl/Makefile.PL.in libsbml-3.3.2/src/bindings/perl/Makefile.PL.in
+--- libsbml-3.3.2~/src/bindings/perl/Makefile.PL.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/bindings/perl/Makefile.PL.in 2009-06-06 15:12:16.205000623 +0900
+@@ -53,10 +53,9 @@
INSTALLDIRS => "site",
LIBS => "@XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ @ZLIB_LIBS@ @BZ2_LIBS@ @LIBS@ -lm -lstdc++",
+ LDDLFLAGS => "@LDFLAGS@ $Config{lddlflags}",
- CC => "@CXX@",
- CCFLAGS => "@PERL_CPPFLAGS@",
+ CCFLAGS => "@PERL_CPPFLAGS@ @CXXFLAGS@",
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-3.2.0~/src/bindings/perl/Makefile.in libsbml-3.2.0/src/bindings/perl/Makefile.in
---- libsbml-3.2.0~/src/bindings/perl/Makefile.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/src/bindings/perl/Makefile.in 2008-09-02 04:51:33.000000000 +0900
-@@ -139,7 +139,9 @@
+diff -urNad libsbml-3.3.2~/src/bindings/perl/Makefile.in libsbml-3.3.2/src/bindings/perl/Makefile.in
+--- libsbml-3.3.2~/src/bindings/perl/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/bindings/perl/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -138,7 +138,9 @@
@ echo "Reconfigure --with-perl in order to build the perl-bindings"
exit 1
else
@@ -765,21 +745,32 @@
# 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-3.2.0~/src/bindings/python/Makefile.in libsbml-3.2.0/src/bindings/python/Makefile.in
---- libsbml-3.2.0~/src/bindings/python/Makefile.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/src/bindings/python/Makefile.in 2008-09-02 04:51:33.000000000 +0900
-@@ -78,8 +78,8 @@
- extra_CPPFLAGS += -Wno-long-double
+diff -urNad libsbml-3.3.2~/src/bindings/python/Makefile.in libsbml-3.3.2/src/bindings/python/Makefile.in
+--- libsbml-3.3.2~/src/bindings/python/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/bindings/python/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -56,6 +56,10 @@
+ ifeq "$(HOST_TYPE)" "darwin"
+ macosx_version=$(shell sw_vers -productVersion | cut -d"." -f1,2)
+ export MACOSX_DEPLOYMENT_TARGET=${macosx_version}
++%.$(PYTHON_EXT): $(patsubst %.cpp, %.lo, $(patsubst %.c, %.lo, $(sources)))
++ $(call link_dl_lib,$@)
++else
++ libraries = _libsbml.$(PYTHON_EXT)
endif
--extra_LDFLAGS = $(PYTHON_LDFLAGS) -L../..
+ # Variables `subdirs', `headers', `sources', `libraries', `extra_CPPFLAGS',
+@@ -80,8 +84,8 @@
+ # -L../../ option appears first in command-line to always link
+ # with the libSBML's shared library file in the relative path.
+ #
+-extra_LDFLAGS = -L../../ $(PYTHON_LDFLAGS)
-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 @@
+@@ -148,9 +152,9 @@
# -----------------------------------------------------------------------------
.SUFFIXES:
@@ -791,19 +782,21 @@
test_objfiles = $(objfiles)
# The default action is to remake everything.
-diff -urNad libsbml-3.2.0~/src/bindings/ruby/Makefile.in libsbml-3.2.0/src/bindings/ruby/Makefile.in
---- libsbml-3.2.0~/src/bindings/ruby/Makefile.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/src/bindings/ruby/Makefile.in 2008-09-02 04:51:33.000000000 +0900
-@@ -79,7 +79,7 @@
- endif
-
- extra_LDFLAGS = $(RUBY_LDFLAGS)
--extra_LIBS = -L../.. -lsbml $(RUBY_LIBS)
+diff -urNad libsbml-3.3.2~/src/bindings/ruby/Makefile.in libsbml-3.3.2/src/bindings/ruby/Makefile.in
+--- libsbml-3.3.2~/src/bindings/ruby/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/bindings/ruby/Makefile.in 2009-06-06 15:12:44.926875253 +0900
+@@ -82,8 +82,8 @@
+ # -L../../ option appears first in command-line to always link
+ # with the libSBML's shared library file in the relative path.
+ #
+-extra_LDFLAGS = -L../../ $(RUBY_LDFLAGS)
+-extra_LIBS = -lsbml $(RUBY_LIBS)
++extra_LDFLAGS = $(RUBY_LDFLAGS)
+extra_LIBS = ../../libsbml.la $(RUBY_LIBS)
ifdef USE_EXPAT
extra_CPPFLAGS += @EXPAT_CPPFLAGS@
-@@ -134,7 +134,7 @@
+@@ -138,7 +138,7 @@
.SUFFIXES:
.SUFFIXES: .i .cpp .o .obj
@@ -812,31 +805,50 @@
test_objfiles = $(objfiles)
# The default action is to remake everything.
-@@ -237,13 +237,18 @@
+@@ -245,7 +245,7 @@
# -----------------------------------------------------------------------------
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
-
+- archdir=`$(RUBY) -rrbconfig -e 's = File::SEPARATOR; a = Config::CONFIG["archdir"].squeeze(s); b = Config::CONFIG["libdir"].squeeze(s); print a.sub(/^#{b}#{s}ruby/, "$(LIBDIR)#{s}ruby#{s}site_ruby")'`; \
++ archdir=`$(RUBY) -rrbconfig -e 's = File::SEPARATOR; a = Config::CONFIG["archdir"].squeeze(s); b = Config::CONFIG["libdir"].squeeze(s); print a.sub(/^#{b}#{s}ruby/, "$(LIBDIR)#{s}ruby")'`; \
+ for i in $(libraries); do \
+ $(MKINSTALLDIRS) $(DESTDIR)$$archdir; \
+ $(INSTALL_SH) $$i $(DESTDIR)$$archdir/$$i; \
+@@ -254,7 +254,7 @@
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
+- -archdir=`$(RUBY) -rrbconfig -e 's = File::SEPARATOR; a = Config::CONFIG["archdir"].squeeze(s); b = Config::CONFIG["libdir"].squeeze(s); print a.sub(/^#{b}#{s}ruby/, "$(LIBDIR)#{s}ruby#{s}site_ruby")'`; \
++ -archdir=`$(RUBY) -rrbconfig -e 's = File::SEPARATOR; a = Config::CONFIG["archdir"].squeeze(s); b = Config::CONFIG["libdir"].squeeze(s); print a.sub(/^#{b}#{s}ruby/, "$(LIBDIR)#{s}ruby")'`; \
+ for i in $(libraries); do \
+ rm $(DESTDIR)$$archdir/$$i; \
+ done ; \
+diff -urNad libsbml-3.3.2~/src/math/test/Makefile.in libsbml-3.3.2/src/math/test/Makefile.in
+--- libsbml-3.3.2~/src/math/test/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/math/test/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -119,8 +119,8 @@
+ # dependencies on other subdirectoris of the source tree, we do some rummaging
+ # around in .. and ../../subdirs.
- # -----------------------------------------------------------------------------
- # Creating distribution (for libSBML maintainers only)
-diff -urNad libsbml-3.2.0~/src/sbml/Makefile.in libsbml-3.2.0/src/sbml/Makefile.in
---- libsbml-3.2.0~/src/sbml/Makefile.in 2008-09-02 04:51:32.000000000 +0900
-+++ libsbml-3.2.0/src/sbml/Makefile.in 2008-09-02 04:51:33.000000000 +0900
+-tmp = $(test_sources:.cpp=.$(OBJEXT)) $(test_sources:.c=.$(OBJEXT))
+-localobjfiles = $(filter %.$(OBJEXT),$(tmp))
++tmp = $(test_sources:.cpp=.lo) $(test_sources:.c=.lo)
++localobjfiles = $(filter %.lo,$(tmp))
+ otherdirs = .. ../../util ../../xml ../../sbml ../../annotation \
+ ../../validator ../../validator/constraints ../../units ../../compress \
+ ../../common
+@@ -128,7 +128,7 @@
+ ifdef USE_LAYOUT
+ otherdirs += ../../sbml/layout
+ endif
+-otherobjfiles = $(wildcard $(addsuffix /*.$(OBJEXT),$(otherdirs)))
++otherobjfiles = $(wildcard $(addsuffix /*.lo,$(otherdirs)))
+
+
+ test_objfiles = $(localobjfiles) $(otherobjfiles)
+diff -urNad libsbml-3.3.2~/src/sbml/Makefile.in libsbml-3.3.2/src/sbml/Makefile.in
+--- libsbml-3.3.2~/src/sbml/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/sbml/Makefile.in 2009-06-06 15:12:16.205000623 +0900
@@ -180,19 +180,7 @@
# The libraries are actually placed in the parent directory.
@@ -858,3 +870,121 @@
# `distfiles' determines the files and directories included in a distribution.
# `distfiles_exclude' is used to filter out specific items, so that even if
+diff -urNad libsbml-3.3.2~/src/sbml/layout/test/Makefile.in libsbml-3.3.2/src/sbml/layout/test/Makefile.in
+--- libsbml-3.3.2~/src/sbml/layout/test/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/sbml/layout/test/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -157,8 +157,8 @@
+ # dependencies on other subdirectoris of the source tree, we do some rummaging
+ # around in .. and ../../subdirs.
+
+-tmp = $(test_sources:.cpp=.$(OBJEXT)) $(test_sources:.c=.$(OBJEXT))
+-localobjfiles = $(filter %.$(OBJEXT),$(tmp))
++tmp = $(test_sources:.cpp=.lo) $(test_sources:.c=.lo)
++localobjfiles = $(filter %.lo,$(tmp))
+
+ otherdirs = .. ../.. ../../../util ../../../xml ../../../math ../../../validator \
+ ../../../validator/constraints ../../../annotation ../../../units \
+diff -urNad libsbml-3.3.2~/src/sbml/test/Makefile.in libsbml-3.3.2/src/sbml/test/Makefile.in
+--- libsbml-3.3.2~/src/sbml/test/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/sbml/test/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -164,8 +164,8 @@
+ # dependencies on other subdirectoris of the source tree, we do some rummaging
+ # around in .. and ../../subdirs.
+
+-tmp = $(test_sources:.cpp=.$(OBJEXT)) $(test_sources:.c=.$(OBJEXT))
+-localobjfiles = $(filter %.$(OBJEXT),$(tmp))
++tmp = $(test_sources:.cpp=.lo) $(test_sources:.c=.lo)
++localobjfiles = $(filter %.lo,$(tmp))
+
+ otherdirs = .. ../../util ../../xml ../../math ../../units \
+ ../../validator ../../validator/constraints ../../annotation \
+@@ -175,7 +175,7 @@
+ otherdirs += ../layout
+ endif
+
+-otherobjfiles = $(wildcard $(addsuffix /*.$(OBJEXT),$(otherdirs)))
++otherobjfiles = $(wildcard $(addsuffix /*.lo,$(otherdirs)))
+
+ test_objfiles = $(localobjfiles) $(otherobjfiles)
+
+diff -urNad libsbml-3.3.2~/src/units/test/Makefile.in libsbml-3.3.2/src/units/test/Makefile.in
+--- libsbml-3.3.2~/src/units/test/Makefile.in 2009-06-06 15:12:13.225002253 +0900
++++ libsbml-3.3.2/src/units/test/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -148,8 +148,8 @@
+ # dependencies on other subdirectoris of the source tree, we do some rummaging
+ # around in .. and ../../subdirs.
+
+-tmp = $(test_sources:.cpp=.$(OBJEXT)) $(test_sources:.c=.$(OBJEXT))
+-localobjfiles = $(filter %.$(OBJEXT),$(tmp))
++tmp = $(test_sources:.cpp=.lo) $(test_sources:.c=.lo)
++localobjfiles = $(filter %.lo,$(tmp))
+ otherdirs = .. ../../util ../../xml ../../math ../../sbml ../../validator \
+ ../../validator/constraints ../../annotation ../../compress ../../common
+
+@@ -158,7 +158,7 @@
+ endif
+
+
+-otherobjfiles = $(wildcard $(addsuffix /*.$(OBJEXT),$(otherdirs)))
++otherobjfiles = $(wildcard $(addsuffix /*.lo,$(otherdirs)))
+ test_objfiles = $(localobjfiles) $(otherobjfiles)
+
+ ifdef USE_LIBCHECK
+diff -urNad libsbml-3.3.2~/src/util/test/Makefile.in libsbml-3.3.2/src/util/test/Makefile.in
+--- libsbml-3.3.2~/src/util/test/Makefile.in 2009-06-06 15:12:13.235000759 +0900
++++ libsbml-3.3.2/src/util/test/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -121,10 +121,10 @@
+ # for running check are abstracted out into makefile-common-actions.mk,
+ # which is included at the bottom of this file.
+
+-tmp = $(test_sources:.cpp=.$(OBJEXT)) $(test_sources:.c=.$(OBJEXT))
+-objects = $(filter %.$(OBJEXT),$(tmp))
++tmp = $(test_sources:.cpp=.lo) $(test_sources:.c=.lo)
++objects = $(filter %.lo,$(tmp))
+
+-test_objfiles = $(objects) $(wildcard ../*.$(OBJEXT))
++test_objfiles = $(objects) $(wildcard ../*.lo)
+
+ ifdef USE_LIBCHECK
+ check: all run-checks
+diff -urNad libsbml-3.3.2~/src/validator/test/Makefile.in libsbml-3.3.2/src/validator/test/Makefile.in
+--- libsbml-3.3.2~/src/validator/test/Makefile.in 2009-06-06 15:12:13.235000759 +0900
++++ libsbml-3.3.2/src/validator/test/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -155,8 +155,8 @@
+ # dependencies on other subdirectoris of the source tree, we do some rummaging
+ # around in .. and ../../subdirs.
+
+-tmp = $(test_sources:.cpp=.$(OBJEXT)) $(test_sources:.c=.$(OBJEXT))
+-localobjfiles = $(filter %.$(OBJEXT),$(tmp))
++tmp = $(test_sources:.cpp=.lo) $(test_sources:.c=.lo)
++localobjfiles = $(filter %.lo,$(tmp))
+ otherdirs = .. ../constraints ../../util ../../xml ../../math ../../sbml \
+ ../../units ../../annotation ../../compress ../../common
+
+@@ -164,7 +164,7 @@
+ otherdirs += ../../sbml/layout
+ endif
+
+-otherobjfiles = $(wildcard $(addsuffix /*.$(OBJEXT),$(otherdirs)))
++otherobjfiles = $(wildcard $(addsuffix /*.lo,$(otherdirs)))
+ test_objfiles = $(localobjfiles) $(otherobjfiles)
+
+
+diff -urNad libsbml-3.3.2~/src/xml/test/Makefile.in libsbml-3.3.2/src/xml/test/Makefile.in
+--- libsbml-3.3.2~/src/xml/test/Makefile.in 2009-06-06 15:12:13.235000759 +0900
++++ libsbml-3.3.2/src/xml/test/Makefile.in 2009-06-06 15:12:16.205000623 +0900
+@@ -127,11 +127,11 @@
+ # dependencies on other subdirectoris of the source tree, we do some rummaging
+ # around in .. and ../../subdirs.
+
+-tmp = $(test_sources:.cpp=.$(OBJEXT)) $(test_sources:.c=.$(OBJEXT))
+-localobjfiles = $(filter %.$(OBJEXT),$(tmp))
++tmp = $(test_sources:.cpp=.lo) $(test_sources:.c=.lo)
++localobjfiles = $(filter %.lo,$(tmp))
+
+ otherdirs = .. ../../util ../../compress ../../common
+-otherobjfiles = $(wildcard $(addsuffix /*.$(OBJEXT),$(otherdirs)))
++otherobjfiles = $(wildcard $(addsuffix /*.lo,$(otherdirs)))
+
+ test_objfiles = $(localobjfiles) $(otherobjfiles)
+
Deleted: trunk/packages/libsbml/trunk/debian/patches/03_gcj_support.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/03_gcj_support.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/03_gcj_support.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,241 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 03_gcj_support.dpatch by <moriyoshi at dynein>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
-
- at DPATCH@
-diff -urNad libsbml-3.1.1~/config/java.m4 libsbml-3.1.1/config/java.m4
---- libsbml-3.1.1~/config/java.m4 2007-12-18 10:26:11.000000000 +0900
-+++ libsbml-3.1.1/config/java.m4 2008-06-24 23:42:34.000000000 +0900
-@@ -158,116 +158,123 @@
- dnl http://www.gnu.org/software/ac-archive/htmldoc/ac_jni_include_dirs.html
-
- AC_DEFUN([AC_JAVA_INCLUDE_DIRS],[
--
- test "x$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/04_docs_destdir.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/04_docs_destdir.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/04_docs_destdir.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,35 +0,0 @@
-#! /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/05_lower_doxygen_ver_req.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/05_lower_doxygen_ver_req.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/05_lower_doxygen_ver_req.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,19 +0,0 @@
-#! /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
Modified: trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/06_javadoc_discovery.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -8,13 +8,14 @@
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])
+@@ -47,12 +47,14 @@
+ AC_PATH_PROG([JAVA], [java], [no], [$with_java/bin])
+ AC_PATH_PROG([JAVAC], [javac], [no], [$with_java/bin])
+ AC_PATH_PROG([JAR], [jar], [no], [$with_java/bin])
++ AC_PATH_PROG([JAVADOC], [javadoc], [no], [$with_java/bin])
else
+ dnl No prefix directory path supplied for --with-java. Use defaults.
+
AC_PATH_PROG([JAVA], [java])
AC_PATH_PROG([JAVAC], [javac])
AC_PATH_PROG([JAR], [jar])
@@ -22,17 +23,42 @@
fi
dnl Sanity checks.
+@@ -194,7 +196,6 @@
+ if test -e "$headers/jni.h"; then
+ JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$headers\""
+ parent=`dirname "$headers"`
+- JAVADOC_JAR="$parent/Classes/classes.jar"
+ else
+ AC_MSG_ERROR([Cannot find Java include files.])
+ fi
+@@ -229,8 +230,6 @@
+ linux*) JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$parent/include/linux\"";;
+ solaris*) JAVA_CPPFLAGS="$JAVA_CPPFLAGS -I\"$parent/include/solaris\"";;
+ esac
+-
+- JAVADOC_JAR="$parent/lib/tools.jar"
+ ;;
+ esac
+
+@@ -273,7 +272,6 @@
+ AC_SUBST(JAVA_LDFLAGS)
+ AC_SUBST(JNIEXT)
+ AC_SUBST(JNIBASENAME)
+- AC_SUBST(JAVADOC_JAR)
+
+ fi
+
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 @@
+@@ -118,6 +118,6 @@
JAVA = @JAVA@
JAVAC = @JAVAC@
JAR = @JAR@
+-JAVADOC_JAR = @JAVADOC_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
@@ -129,23 +155,12 @@
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 @@
+@@ -372,7 +372,7 @@
ignorable-warnings = "warning - @param argument"
- java-manual $(java-manual): $(core-sources)
-- $(JAVA) -cp $(javadoc-jar):. ExcludeDoclet -excludefile java-skip.txt \
+ java-manual $(java-manual): $(core-sources) ExcludeDoclet.class
+- $(JAVA) -cp $(JAVADOC_JAR):. ExcludeDoclet -excludefile java-skip.txt \
+ $(JAVADOC) -docletpath . -doclet ExcludeDoclet -excludefile java-skip.txt \
- -use -public -version -author -sourcetab 4 -keywords \
+ -use -public -version -author -sourcetab 4 -keywords \
+ -nodeprecated \
-header $(javadoc-header) \
- -bottom $(javadoc-footer) \
Deleted: trunk/packages/libsbml/trunk/debian/patches/07_perldoc_mod_name_fix.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/07_perldoc_mod_name_fix.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/07_perldoc_mod_name_fix.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,20 +0,0 @@
-#! /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))
Deleted: trunk/packages/libsbml/trunk/debian/patches/08_missing_includes.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/08_missing_includes.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/08_missing_includes.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -1,276 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 08_missing_includes.dpatch by Moriyoshi Koizumi <root at dynein>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
-
- at DPATCH@
-
-diff -ur libsbml-3.1.1.orig/src/annotation/ModelHistory.cpp libsbml-3.1.1/src/annotation/ModelHistory.cpp
---- libsbml-3.1.1.orig/src/annotation/ModelHistory.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/annotation/ModelHistory.cpp 2008-07-20 02:18:47.000000000 +0000
-@@ -21,6 +21,7 @@
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-+#include <cstdlib>
-
- #include <sbml/annotation/ModelHistory.h>
-
-diff -ur libsbml-3.1.1.orig/src/common/libsbml-config-unix.h libsbml-3.1.1/src/common/libsbml-config-unix.h
---- libsbml-3.1.1.orig/src/common/libsbml-config-unix.h 2008-07-20 00:38:16.000000000 +0000
-+++ libsbml-3.1.1/src/common/libsbml-config-unix.h 2008-07-20 00:43:02.000000000 +0000
-@@ -44,7 +44,7 @@
-
-
- /* Define to 1 if you have the <check.h> header file. */
--#define HAVE_CHECK_H 1
-+/* #undef HAVE_CHECK_H */
-
- /* Define to 1 if you have the `check' library (-lcheck). */
- /* #undef HAVE_LIBCHECK */
-diff -ur libsbml-3.1.1.orig/src/sbml/Constraint.cpp libsbml-3.1.1/src/sbml/Constraint.cpp
---- libsbml-3.1.1.orig/src/sbml/Constraint.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/Constraint.cpp 2008-07-20 02:20:43.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/Delay.cpp libsbml-3.1.1/src/sbml/Delay.cpp
---- libsbml-3.1.1.orig/src/sbml/Delay.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/Delay.cpp 2008-07-20 02:20:58.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/EventAssignment.cpp libsbml-3.1.1/src/sbml/EventAssignment.cpp
---- libsbml-3.1.1.orig/src/sbml/EventAssignment.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/EventAssignment.cpp 2008-07-20 02:21:17.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/InitialAssignment.cpp libsbml-3.1.1/src/sbml/InitialAssignment.cpp
---- libsbml-3.1.1.orig/src/sbml/InitialAssignment.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/InitialAssignment.cpp 2008-07-20 02:21:35.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/KineticLaw.cpp libsbml-3.1.1/src/sbml/KineticLaw.cpp
---- libsbml-3.1.1.orig/src/sbml/KineticLaw.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/KineticLaw.cpp 2008-07-20 02:22:07.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/Model.cpp libsbml-3.1.1/src/sbml/Model.cpp
---- libsbml-3.1.1.orig/src/sbml/Model.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/Model.cpp 2008-07-20 02:24:07.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/Rule.cpp libsbml-3.1.1/src/sbml/Rule.cpp
---- libsbml-3.1.1.orig/src/sbml/Rule.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/Rule.cpp 2008-07-20 02:24:55.000000000 +0000
-@@ -22,6 +22,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/SBMLDocument.cpp libsbml-3.1.1/src/sbml/SBMLDocument.cpp
---- libsbml-3.1.1.orig/src/sbml/SBMLDocument.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/SBMLDocument.cpp 2008-07-20 02:25:13.000000000 +0000
-@@ -22,6 +22,7 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
- #include <iostream>
-
- #include <sbml/xml/XMLAttributes.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/SBase.cpp libsbml-3.1.1/src/sbml/SBase.cpp
---- libsbml-3.1.1.orig/src/sbml/SBase.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/SBase.cpp 2008-07-20 02:25:45.000000000 +0000
-@@ -21,6 +21,7 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
- #include <sstream>
-
- #include <sbml/xml/XMLError.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/StoichiometryMath.cpp libsbml-3.1.1/src/sbml/StoichiometryMath.cpp
---- libsbml-3.1.1.orig/src/sbml/StoichiometryMath.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/StoichiometryMath.cpp 2008-07-20 02:26:15.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/Trigger.cpp libsbml-3.1.1/src/sbml/Trigger.cpp
---- libsbml-3.1.1.orig/src/sbml/Trigger.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/Trigger.cpp 2008-07-20 02:26:30.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/Unit.cpp libsbml-3.1.1/src/sbml/Unit.cpp
---- libsbml-3.1.1.orig/src/sbml/Unit.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/Unit.cpp 2008-07-20 02:26:43.000000000 +0000
-@@ -21,6 +21,8 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-+
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
- #include <sbml/xml/XMLInputStream.h>
-diff -ur libsbml-3.1.1.orig/src/sbml/UnitDefinition.cpp libsbml-3.1.1/src/sbml/UnitDefinition.cpp
---- libsbml-3.1.1.orig/src/sbml/UnitDefinition.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/sbml/UnitDefinition.cpp 2008-07-20 02:26:58.000000000 +0000
-@@ -21,6 +21,7 @@
- * and also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
-
- #include <sbml/xml/XMLNode.h>
- #include <sbml/xml/XMLAttributes.h>
-diff -ur libsbml-3.1.1.orig/src/units/UnitFormulaFormatter.cpp libsbml-3.1.1/src/units/UnitFormulaFormatter.cpp
---- libsbml-3.1.1.orig/src/units/UnitFormulaFormatter.cpp 2008-07-20 00:38:15.000000000 +0000
-+++ libsbml-3.1.1/src/units/UnitFormulaFormatter.cpp 2008-07-20 02:17:52.000000000 +0000
-@@ -23,6 +23,7 @@
- * also available online as http://sbml.org/software/libsbml/license.html
- *----------------------------------------------------------------------- -->*/
-
-+#include <cstring>
- #include <sbml/units/UnitFormulaFormatter.h>
-
-
-diff -ur libsbml-3.1.1.orig/src/validator/constraints/AssignmentCycles.cpp libsbml-3.1.1/src/validator/constraints/AssignmentCycles.cpp
---- libsbml-3.1.1.orig/src/validator/constraints/AssignmentCycles.cpp 2008-07-20 00:38:15.000000000 +0000
-+++ libsbml-3.1.1/src/validator/constraints/AssignmentCycles.cpp 2008-07-20 00:59:21.000000000 +0000
-@@ -21,7 +21,7 @@
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
--
-+#include <cstring>
-
- #include <sbml/Model.h>
- #include <sbml/Rule.h>
-diff -ur libsbml-3.1.1.orig/src/validator/constraints/ConsistencyConstraints.cpp libsbml-3.1.1/src/validator/constraints/ConsistencyConstraints.cpp
---- libsbml-3.1.1.orig/src/validator/constraints/ConsistencyConstraints.cpp 2008-07-20 00:38:15.000000000 +0000
-+++ libsbml-3.1.1/src/validator/constraints/ConsistencyConstraints.cpp 2008-07-20 00:57:37.000000000 +0000
-@@ -24,7 +24,7 @@
-
- #ifndef AddingConstraintsToValidator
-
--//#include <string>
-+#include <cstring>
-
- #include <sbml/SBMLTypes.h>
- #include <sbml/SBMLTypeCodes.h>
-diff -ur libsbml-3.1.1.orig/src/validator/constraints/OverDeterminedCheck.cpp libsbml-3.1.1/src/validator/constraints/OverDeterminedCheck.cpp
---- libsbml-3.1.1.orig/src/validator/constraints/OverDeterminedCheck.cpp 2008-07-20 00:38:15.000000000 +0000
-+++ libsbml-3.1.1/src/validator/constraints/OverDeterminedCheck.cpp 2008-07-20 01:01:55.000000000 +0000
-@@ -21,6 +21,8 @@
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-+#include <cstring>
-+
- #include <sbml/Model.h>
- #include <sbml/Compartment.h>
- #include <sbml/util/List.h>
-diff -ur libsbml-3.1.1.orig/src/validator/constraints/SpeciesReactionOrRule.cpp libsbml-3.1.1/src/validator/constraints/SpeciesReactionOrRule.cpp
---- libsbml-3.1.1.orig/src/validator/constraints/SpeciesReactionOrRule.cpp 2008-07-20 00:38:15.000000000 +0000
-+++ libsbml-3.1.1/src/validator/constraints/SpeciesReactionOrRule.cpp 2008-07-20 01:02:49.000000000 +0000
-@@ -21,6 +21,8 @@
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-+#include <cstring>
-+
- #include <sbml/Model.h>
- #include <sbml/Rule.h>
- #include <sbml/Reaction.h>
-diff -ur libsbml-3.1.1.orig/src/validator/constraints/UniqueSpeciesTypesInCompartment.cpp libsbml-3.1.1/src/validator/constraints/UniqueSpeciesTypesInCompartment.cpp
---- libsbml-3.1.1.orig/src/validator/constraints/UniqueSpeciesTypesInCompartment.cpp 2008-07-20 00:38:15.000000000 +0000
-+++ libsbml-3.1.1/src/validator/constraints/UniqueSpeciesTypesInCompartment.cpp 2008-07-20 02:13:52.000000000 +0000
-@@ -21,6 +21,7 @@
- * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-+#include <cstring>
-
- #include <sbml/Model.h>
- #include <sbml/Rule.h>
-diff -ur libsbml-3.1.1.orig/src/xml/LibXMLParser.cpp libsbml-3.1.1/src/xml/LibXMLParser.cpp
---- libsbml-3.1.1.orig/src/xml/LibXMLParser.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/xml/LibXMLParser.cpp 2008-07-20 00:56:54.000000000 +0000
-@@ -22,6 +22,7 @@
- *----------------------------------------------------------------------- -->*/
-
- #include <iostream>
-+#include <cstring>
-
- #include <libxml/xmlerror.h>
-
-diff -ur libsbml-3.1.1.orig/src/xml/XMLNode.cpp libsbml-3.1.1/src/xml/XMLNode.cpp
---- libsbml-3.1.1.orig/src/xml/XMLNode.cpp 2008-07-20 00:38:14.000000000 +0000
-+++ libsbml-3.1.1/src/xml/XMLNode.cpp 2008-07-20 00:55:46.000000000 +0000
-@@ -22,6 +22,7 @@
- *----------------------------------------------------------------------- -->*/
-
- #include <sstream>
-+#include <cstdlib>
-
- #include <sbml/util/memory.h>
- #include <sbml/util/util.h>
Modified: trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/patches/08_pkgconfig_file_gen.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -5,52 +5,34 @@
## DP: No description.
@DPATCH@
-diff -urNad libsbml-3.2.0~/Makefile.in libsbml-3.2.0/Makefile.in
---- libsbml-3.2.0~/Makefile.in 2008-09-02 04:03:14.000000000 +0900
-+++ libsbml-3.2.0/Makefile.in 2008-09-02 04:03:29.000000000 +0900
-@@ -211,14 +211,15 @@
+diff -urNad libsbml-3.3.2~/Makefile.in libsbml-3.3.2/Makefile.in
+--- libsbml-3.3.2~/Makefile.in 2009-06-08 00:03:28.177956192 +0900
++++ libsbml-3.3.2/Makefile.in 2009-06-08 00:03:43.306875344 +0900
+@@ -212,7 +212,8 @@
# makefile-common-actions.mk.
extra_distclean = config.status config.cache config.log autom4te.cache \
-- src/common/config.h src/common/stamp-h1 config/lt_link_helper.sh
-+ src/common/config.h src/common/stamp-h1 config/lt_link_helper.sh \
+- src/common/config.h src/common/stamp-h1 config/lt_link_helper.sh config/mkoctfile_wrapper.sh
++ src/common/config.h src/common/stamp-h1 config/lt_link_helper.sh config/mkoctfile_wrapper.sh \
+ libsbml.pc libsbml-cil.pc
# It's safer to remove and recreate the copy of the include files (in the
# 'include' directory) after a make clean. Previously we did it in a make
- # distclean only, but I've run into situations where the copy didn't get
- # updated. This is a bit of a sledgehammer, but it's not too bad.
+@@ -279,45 +280,6 @@
--extra_clean = include libsbml.pc
-+extra_clean = include
-
-
- # -----------------------------------------------------------------------------
-@@ -229,7 +230,7 @@
- # of the form `foo-recursive' to run 'make foo' in directories defined in
- # variable `subdirs'.
-
--all: configure Makefile include all-recursive libsbml.pc
-+all: configure Makefile include all-recursive
-
- docs:;
- ifneq "$(MAKEFLAGS)" ""
-@@ -261,46 +262,6 @@
-
base-libs = -lsbml -lstdc++ -lm
--COMPRESS_CPFLAGS = ${ZLIB_CPPFLAGS} ${BZ2_CPPFLAGS}
--COMPRESS_LDFLAGS = ${ZLIB_LDFLAGS} ${BZ2_LDFLAGS}
--COMPRESS_LIBS = ${ZLIB_LIBS} ${BZ2_LIBS}
+-COMPRESS_CPFLAGS = ${ZLIB_CPPFLAGS} ${BZ2_CPPFLAGS}
+-COMPRESS_LDFLAGS = ${ZLIB_LDFLAGS} ${BZ2_LDFLAGS}
+-COMPRESS_LIBS = ${ZLIB_LIBS} ${BZ2_LIBS}
-
--XML_CPFLAGS = ${XERCES_CPPFLAGS} ${EXPAT_CPPFLAGS} ${LIBXML_CPPFLAGS}
--XML_LDFLAGS = ${XERCES_LDFLAGS} ${EXPAT_LDFLAGS} ${LIBXML_LDFLAGS}
--XML_LIBS = ${XERCES_LIBS} ${EXPAT_LIBS} ${LIBXML_LIBS}
+-XML_CPFLAGS = ${XERCES_CPPFLAGS} ${EXPAT_CPPFLAGS} ${LIBXML_CPPFLAGS}
+-XML_LDFLAGS = ${XERCES_LDFLAGS} ${EXPAT_LDFLAGS} ${LIBXML_LDFLAGS}
+-XML_LIBS = ${XERCES_LIBS} ${EXPAT_LIBS} ${LIBXML_LIBS}
-
-DEPENDENCY_CPPFLAGS = ${XML_CPPFLAGS} ${COMPRESS_CPPFLAGS}
-DEPENDENCY_LIBFLAGS = ${XML_LDFLAGS} ${COMPRESS_LDFLAGS} ${XML_LIBS} ${COMPRESS_LIBS}
-
--
-libsbml.pc: Makefile
- @rm -f libsbml.pc
- @echo "Name: @PACKAGE_NAME@" > libsbml.pc
@@ -82,20 +64,21 @@
# -----------------------------------------------------------------------------
# Installation.
# -----------------------------------------------------------------------------
-@@ -322,7 +283,9 @@
+@@ -375,7 +337,9 @@
endif
install-pc: libsbml.pc
+- $(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
+ $(MKINSTALLDIRS) $(DESTDIR)$(LIBDIR)/pkgconfig
- $(INSTALL_SH) libsbml.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
-+ $(INSTALL_SH) libsbml-cil.pc -m 0644 "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml-cil.pc"
++ $(INSTALL_SH) -m 0644 libsbml.pc "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml.pc"
++ $(INSTALL_SH) -m 0644 libsbml-cil.pc "$(DESTDIR)$(LIBDIR)/pkgconfig/libsbml-cil.pc"
uninstall: uninstall-recursive uninstall-libsbml-pc
@if test -d "$(DESTDIR)$(LIBDIR)"; then \
-diff -urNad libsbml-3.2.0~/configure.ac libsbml-3.2.0/configure.ac
---- libsbml-3.2.0~/configure.ac 2008-09-02 04:03:14.000000000 +0900
-+++ libsbml-3.2.0/configure.ac 2008-09-02 04:03:15.000000000 +0900
-@@ -243,6 +243,8 @@
+diff -urNad libsbml-3.3.2~/configure.ac libsbml-3.3.2/configure.ac
+--- libsbml-3.3.2~/configure.ac 2009-06-08 00:03:28.188125414 +0900
++++ libsbml-3.3.2/configure.ac 2009-06-08 00:03:28.625626680 +0900
+@@ -261,6 +261,8 @@
AC_CONFIG_FILES([config/mkoctfile_wrapper.sh], [chmod a+x config/mkoctfile_wrapper.sh])
AC_CONFIG_FILES([./Makefile])
@@ -104,9 +87,9 @@
AC_CONFIG_FILES([src/Makefile])
AC_CONFIG_FILES([src/common/Makefile])
-diff -urNad libsbml-3.2.0~/libsbml-cil.pc.in libsbml-3.2.0/libsbml-cil.pc.in
---- libsbml-3.2.0~/libsbml-cil.pc.in 1970-01-01 09:00:00.000000000 +0900
-+++ libsbml-3.2.0/libsbml-cil.pc.in 2008-09-02 04:03:15.000000000 +0900
+diff -urNad libsbml-3.3.2~/libsbml-cil.pc.in libsbml-3.3.2/libsbml-cil.pc.in
+--- libsbml-3.3.2~/libsbml-cil.pc.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.3.2/libsbml-cil.pc.in 2009-06-08 00:03:28.625626680 +0900
@@ -0,0 +1,9 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
@@ -117,9 +100,9 @@
+URL: http://sbml.org/software/libsbml
+Version: @PACKAGE_VERSION@
+Libs: -r:${libdir}/cli/libsbml-3.0/libsbmlcsP.dll
-diff -urNad libsbml-3.2.0~/libsbml.pc.in libsbml-3.2.0/libsbml.pc.in
---- libsbml-3.2.0~/libsbml.pc.in 1970-01-01 09:00:00.000000000 +0900
-+++ libsbml-3.2.0/libsbml.pc.in 2008-09-02 04:05:13.000000000 +0900
+diff -urNad libsbml-3.3.2~/libsbml.pc.in libsbml-3.3.2/libsbml.pc.in
+--- libsbml-3.3.2~/libsbml.pc.in 1970-01-01 09:00:00.000000000 +0900
++++ libsbml-3.3.2/libsbml.pc.in 2009-06-08 00:03:28.625626680 +0900
@@ -0,0 +1,11 @@
+prefix=@prefix@
+exec_prefix=@exec_prefix@
Added: trunk/packages/libsbml/trunk/debian/patches/09_docs_install_mkinstalldirs.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/09_docs_install_mkinstalldirs.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/09_docs_install_mkinstalldirs.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -0,0 +1,22 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 09_docs_install_mkinstalldirs.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-3.3.2~/docs/src/Makefile.in libsbml-3.3.2/docs/src/Makefile.in
+--- libsbml-3.3.2~/docs/src/Makefile.in 2009-03-04 08:26:10.000000000 +0900
++++ libsbml-3.3.2/docs/src/Makefile.in 2009-06-06 12:57:04.001386655 +0900
+@@ -434,8 +434,9 @@
+ list='$(docs)'; for docdir in $$list; do \
+ if test -d $$docdir; then d=.; else d=$(srcdir); fi; \
+ dirname=`basename "$$docdir"`; \
++ $(MKINSTALLDIRS) "$(DESTDIR)$(DOCDIR)"; \
+ if test "$$dirname" != "$$docdir" && test "$$dirname" != "."; then \
+- $(MKINSTALLDIRS) "$(DESTDIR)$(DOCDIR)/$$dirname"; \
++ mkdir "$(DESTDIR)$(DOCDIR)/$$dirname"; \
+ fi; \
+ echo Copying to $(DESTDIR)$(DOCDIR)/$$dirname; \
+ if test -d $$d/$$docdir; then \
+
Added: trunk/packages/libsbml/trunk/debian/patches/10_perl_binding_instdir.dpatch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/10_perl_binding_instdir.dpatch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/10_perl_binding_instdir.dpatch 2009-06-19 08:27:45 UTC (rev 3504)
@@ -0,0 +1,28 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 10_perl_binding_instdir.dpatch by <moriyoshi at dynein>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+ at DPATCH@
+diff -urNad libsbml-3.3.2~/src/bindings/perl/Makefile.PL.in libsbml-3.3.2/src/bindings/perl/Makefile.PL.in
+--- libsbml-3.3.2~/src/bindings/perl/Makefile.PL.in 2009-06-07 04:45:45.486875293 +0900
++++ libsbml-3.3.2/src/bindings/perl/Makefile.PL.in 2009-06-07 04:46:12.966907754 +0900
+@@ -50,7 +50,7 @@
+ NAME => "LibSBML",
+ PREFIX => "@prefix@",
+ MAKEFILE => 'Makefile-perl',
+- INSTALLDIRS => "site",
++ INSTALLDIRS => 'vendor',
+ LIBS => "@XERCES_LDFLAGS@ @EXPAT_LDFLAGS@ @LIBXML_LDFLAGS@ @XERCES_LIBS@ @EXPAT_LIBS@ @LIBXML_LIBS@ @ZLIB_LIBS@ @BZ2_LIBS@ @LIBS@ -lm -lstdc++",
+ LDDLFLAGS => "@LDFLAGS@ $Config{lddlflags}",
+ CCFLAGS => "@PERL_CPPFLAGS@ @CXXFLAGS@",
+@@ -95,7 +95,7 @@
+ LibSBML.pod: $(main_sources) ../swig/libsbml.i ../swig/swigdoc.py
+ ../swig/swigdoc.py perl -I../.. -D../../../docs/src ../swig/libsbml.i LibSBML.pod
+
+-MYPACKLIST = $(DESTINSTALLSITEARCH)/auto/$(FULLEXT)/.packlist
++MYPACKLIST = $(INST_ARCHLIB)/auto/$(FULLEXT)/.packlist
+ #MYPERLLOCAL = $(INSTALLARCHLIB)/perllocal.pod
+ myuninstall:
+ $(NOECHO) dirs=`cat $(MYPACKLIST) | xargs -n 1 dirname`; \
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2009-06-19 07:28:00 UTC (rev 3503)
+++ trunk/packages/libsbml/trunk/debian/rules 2009-06-19 08:27:45 UTC (rev 3504)
@@ -46,19 +46,19 @@
config.status: patch-stamp configure
dh_testdir
# Add here commands to configure the package.
- MONO_SHARED_DIR="$(CURDIR)" CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs" \
+ MONO_SHARED_DIR="$(CURDIR)" CFLAGS="$(CFLAGS)" \
./configure --host=$(DEB_HOST_GNU_TYPE) \
--build=$(DEB_BUILD_GNU_TYPE) \
--prefix=/usr \
--mandir=\$${prefix}/share/man \
--infodir=\$${prefix}/share/info \
+ --with-doxygen=/usr \
--with-perl=/usr \
--with-python=/usr \
--with-java=/usr \
--with-ruby=/usr \
--with-octave=/usr \
- --with-csharp=/usr \
- --with-csharp-compiler=/usr/bin/mcs
+ --with-csharp=/usr
touch \
src/bindings/java/java-files \
src/bindings/java/libsbml_wrap.cpp \
@@ -134,18 +134,19 @@
dh_installchangelogs
dh_installdocs
dh_installexamples
- dh_install -Xlibsbml-java --sourcedir=$(CURDIR)/debian/tmp
+ dh_install --sourcedir=$(CURDIR)/debian/tmp
dh_link
dh_strip
dh_compress
dh_fixperms
+ dh_makeshlibs
+ dh_makeclilibs -i -V
+ dh_installcligac -i
dh_perl
dh_pysupport
- dh_makeshlibs
- dh_makeclilibs
dh_installdeb
- dh_shlibdeps
- dh_clideps
+ dh_shlibdeps -Xlibsbml3-cil -Xlibsbml3-octave -Xlibsbml3-perl -Xlibsbml3-java -Xpython-sbml3 -Xlibsbml3-ruby1.8
+ dh_clideps -i -d -ldebian/libsbml3-cli/usr
dh_gencontrol
dh_md5sums
dh_builddeb
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