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