Author: ivomaintz-guest Date: 2014-03-11 15:40:06 +0000 (Tue, 11 Mar 2014) New Revision: 16422
Added: trunk/packages/libsbml/branches/libsbml5/ trunk/packages/libsbml/branches/libsbml5/debian/ trunk/packages/libsbml/branches/libsbml5/debian/bin/python_fix.sh trunk/packages/libsbml/branches/libsbml5/debian/patches/doxygen.patch Removed: trunk/packages/libsbml/branches/libsbml5/debian/libsbml5-ruby1.8.docs trunk/packages/libsbml/branches/libsbml5/debian/libsbml5-ruby1.8.install Modified: trunk/packages/libsbml/branches/libsbml5/debian/README.source trunk/packages/libsbml/branches/libsbml5/debian/changelog trunk/packages/libsbml/branches/libsbml5/debian/cmake_opts trunk/packages/libsbml/branches/libsbml5/debian/control trunk/packages/libsbml/branches/libsbml5/debian/control.in trunk/packages/libsbml/branches/libsbml5/debian/patches/hardening.patch trunk/packages/libsbml/branches/libsbml5/debian/patches/mexext.patch trunk/packages/libsbml/branches/libsbml5/debian/patches/series trunk/packages/libsbml/branches/libsbml5/debian/rules Log: added a branch for libsbml5 removed libsbml5-ruby* fixed some build issues regarding doxygen and python tested with debuild Modified: trunk/packages/libsbml/branches/libsbml5/debian/README.source =================================================================== --- trunk/packages/libsbml/trunk/debian/README.source 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/README.source 2014-03-11 15:40:06 UTC (rev 16422) @@ -1,3 +1,14 @@ +libsbml (5.9.2) + * render extension is now included in the source distribution, no extra work to do + +libsbml (5.9.0) + * again, include the render extension + +libsbml (5.8.0) + * We want to integrate the render extension: + download the render extension --> http://sourceforge.net/projects/sbml/files/libsbml/5.8.0/experimental/src/ + unpack it to the libsbml source directory and repack the stuff + libsbml (5.7.0) * upstream ships two versions: libSBML-core-src.tar.gz and libSBML-5.7.0-core-plus-packages-src.tar.gz (with the COMP extension) Added: trunk/packages/libsbml/branches/libsbml5/debian/bin/python_fix.sh =================================================================== --- trunk/packages/libsbml/branches/libsbml5/debian/bin/python_fix.sh (rev 0) +++ trunk/packages/libsbml/branches/libsbml5/debian/bin/python_fix.sh 2014-03-11 15:40:06 UTC (rev 16422) @@ -0,0 +1,5 @@ +#!/bin/sh +PYTH=$(basename $(python-config --includes | awk '{print $1}' | cut -dI -f2)) +LINE=$(grep -n src/bindings/python/CMakeFiles/binding_python_lib.dir/depend build/CMakeFiles/Makefile2 | cut -d: -f1) + +sed -i ""$LINE"i\\\tsed -i \"s#<Python.h>#<"$PYTH"/Python.h>#g\" src/bindings/python/libsbml_wrap.cpp" build/CMakeFiles/Makefile2 Modified: trunk/packages/libsbml/branches/libsbml5/debian/changelog =================================================================== --- trunk/packages/libsbml/trunk/debian/changelog 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/changelog 2014-03-11 15:40:06 UTC (rev 16422) @@ -1,11 +1,16 @@ libsbml (5.9.2-1) UNRELEASED; urgency=medium + [ Andreas Tille ] * New upstream version * debian/upstream -> debian/upstream/metadata * debian/control: Drop explicite ruby version in Build-Dependencies - -- Andreas Tille <[email protected]> Thu, 27 Feb 2014 08:17:40 +0000 + [ Ivo Maintz ] + * added debian/bin/python_fix.sh to bypass a wrong path to the file Python.h + * drop ruby bindings, can't get it compiled + -- Ivo Maintz <[email protected]> Wed, 05 Mar 2014 10:16:44 +0100 + libsbml (5.8.0-2) unstable; urgency=medium * Put *.m files in the Octave path (thanks for the patch to @@ -20,10 +25,6 @@ * update from upstream * switched to cmake for configure (following upstream) * added a patch to use correct matlab extensions in chrooted environments - * (re)added doc packages for libsbml5, libsbml5-cil, libsbml5-java, - libsbml5-python and libsbml5-perl - * debian/*postinst and debian/*postrm: - fixed to work on upgrade/downgrade too [ Andreas Tille ] * debian/control: Modified: trunk/packages/libsbml/branches/libsbml5/debian/cmake_opts =================================================================== --- trunk/packages/libsbml/trunk/debian/cmake_opts 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/cmake_opts 2014-03-11 15:40:06 UTC (rev 16422) @@ -4,6 +4,8 @@ -DENABLE_COMP:BOOL=ON -DENABLE_FBC:BOOL=ON -DENABLE_LAYOUT:BOOL=ON +-DENABLE_GROUPS=ON +-DENABLE_RENDER=ON -DWITH_BZIP2:BOOL=ON -DWITH_CHECK:BOOL=OFF -DWITH_CPP_NAMESPACE:BOOL=ON @@ -19,6 +21,7 @@ -DWITH_OCTAVE:BOOL=ON -DWITH_PERL:BOOL=ON -DWITH_PYTHON:BOOL=ON +-DWITH_PYTHON_INCLUDE:PATH=/usr/include/python2.7 -DWITH_R:BOOL=ON -DWITH_RUBY:BOOL=ON -DWITH_SWIG:BOOL=ON Modified: trunk/packages/libsbml/branches/libsbml5/debian/control =================================================================== --- trunk/packages/libsbml/trunk/debian/control 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/control 2014-03-11 15:40:06 UTC (rev 16422) @@ -5,30 +5,29 @@ Section: science Priority: optional Build-Depends: autoconf, - automake, - debhelper (>= 9.0.0), - cmake, - doxygen (>= 1.8.0), - swig (>= 2), - ruby, - libxml2-dev, - python-dev, - ruby-dev, - perl, - libperl-dev, - default-jdk | openjdk-7-jdk, - octave-pkg-dev, - r-base-dev, - r-base-core, - python-support, - graphviz, - zlib1g-dev, - libbz2-dev, - mono-devel, - mono-gmcs, - cli-common-dev, - mono-runtime | cli-runtime, - dpkg-dev (>= 1.16.1~) + automake, + debhelper (>= 9.0.0), + cmake, + doxygen (>= 1.8.0), + swig (>= 2), + libxml2-dev, + python-dev, + perl, + libperl-dev, + default-jdk | openjdk-7-jdk | java-gcj-compat-dev | java-sdk, + octave-pkg-dev, + r-base-dev, + r-base-core, + python-support, + graphviz, + zlib1g-dev, + libbz2-dev, + mono-devel, + mono-gmcs, + cli-common-dev, + cli-runtime, + dpkg-dev (>= 1.16.1~), + texlive-latex-base Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsbml/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libsbml/trunk/ @@ -97,19 +96,18 @@ but rather a library you can embed in your own applications. This package contains the Python bindings of LibSBML. - -Package: libsbml5-ruby +Package: libsbml5-matlab +Section: contrib/math +Provides: libsbml-matlab +Conflicts: libsbml4-matlab Architecture: any -Section: ruby -Depends: ${shlibs:Depends}, - ${misc:Depends} -Provides: libsbml-ruby -Description: System Biology Markup Language library - Ruby binding +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: System Biology Markup Language library - Matlab bindings 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. - This package contains the Ruby binding of LibSBML. + This package contains the Matlab bindings of LibSBML. Package: libsbml5-java Architecture: any Modified: trunk/packages/libsbml/branches/libsbml5/debian/control.in =================================================================== --- trunk/packages/libsbml/trunk/debian/control.in 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/control.in 2014-03-11 15:40:06 UTC (rev 16422) @@ -5,30 +5,29 @@ Section: science Priority: optional Build-Depends: autoconf, - automake, - debhelper (>= 9.0.0), - cmake, - doxygen (>= 1.8.0), - swig (>= 2), - ruby, - libxml2-dev, - python-dev, - ruby-dev, - perl, - libperl-dev, - default-jdk | openjdk-7-jdk, - octave-pkg-dev, - r-base-dev, - r-base-core, - python-support, - graphviz, - zlib1g-dev, - libbz2-dev, - mono-devel, - mono-gmcs, - cli-common-dev, - mono-runtime | cli-runtime, - dpkg-dev (>= 1.16.1~) + automake, + debhelper (>= 9.0.0), + cmake, + doxygen (>= 1.8.0), + swig (>= 2), + libxml2-dev, + python-dev, + perl, + libperl-dev, + default-jdk | openjdk-7-jdk | java-gcj-compat-dev | java-sdk, + octave-pkg-dev, + r-base-dev, + r-base-core, + python-support, + graphviz, + zlib1g-dev, + libbz2-dev, + mono-devel, + mono-gmcs, + cli-common-dev, + cli-runtime, + dpkg-dev (>= 1.16.1~), + texlive-latex-base Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libsbml/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libsbml/trunk/ @@ -110,19 +109,6 @@ # but rather a library you can embed in your own applications. # This package contains the Matlab bindings of LibSBML. -Package: libsbml5-ruby -Architecture: any -Section: ruby -Depends: ${shlibs:Depends}, - ${misc:Depends} -Provides: libsbml-ruby -Description: System Biology Markup Language library - Ruby binding - LibSBML is a library designed to help you read, write, manipulate, - translate, and validate SBML files and data streams. It is not an - application itself (though it does come with many example programs), - but rather a library you can embed in your own applications. - This package contains the Ruby binding of LibSBML. - Package: libsbml5-java Architecture: any Section: java Deleted: trunk/packages/libsbml/branches/libsbml5/debian/libsbml5-ruby1.8.docs =================================================================== --- trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.docs 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/libsbml5-ruby1.8.docs 2014-03-11 15:40:06 UTC (rev 16422) @@ -1 +0,0 @@ -changelog Deleted: trunk/packages/libsbml/branches/libsbml5/debian/libsbml5-ruby1.8.install =================================================================== --- trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/libsbml5-ruby1.8.install 2014-03-11 15:40:06 UTC (rev 16422) @@ -1 +0,0 @@ -usr/lib/ruby Added: trunk/packages/libsbml/branches/libsbml5/debian/patches/doxygen.patch =================================================================== --- trunk/packages/libsbml/branches/libsbml5/debian/patches/doxygen.patch (rev 0) +++ trunk/packages/libsbml/branches/libsbml5/debian/patches/doxygen.patch 2014-03-11 15:40:06 UTC (rev 16422) @@ -0,0 +1,30 @@ +Description: fix a wrong file name + docs/CMakeLists.txt contains a wrong file name: doxygen-tabs.css instead of libsbml-doxygen-tabs.css + . + libsbml (5.9.2-1) UNRELEASED; urgency=medium + . + * New upstream version + * debian/upstream -> debian/upstream/metadata + * debian/control: Drop explicite ruby version in Build-Dependencies +Author: Ivo Miantz <[email protected]> + +--- +Last-Update: 2014-02-27 + +Index: libsbml-5.9.2/docs/CMakeLists.txt +=================================================================== +--- libsbml-5.9.2.orig/docs/CMakeLists.txt 2014-02-27 17:13:31.272841048 +0100 ++++ libsbml-5.9.2/docs/CMakeLists.txt 2014-02-27 17:15:58.322470772 +0100 +@@ -99,9 +99,9 @@ + file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/common-graphics/official-sbml-supported-40.jpg logo_file) + file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/common-graphics/right-arrow.gif right_arrow) + file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/sbml.js sbml_js) +- file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/doxygen-tabs.css tabs_css) +- file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/search.png search_png) +- file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/search.css search_css) ++ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/css/libsbml-doxygen-tabs.css tabs_css) ++ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/css/search.png search_png) ++ file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/css/search.css search_css) + + file(TO_NATIVE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/doxygen-config-${lang}.txt api_doc) + Modified: trunk/packages/libsbml/branches/libsbml5/debian/patches/hardening.patch =================================================================== --- trunk/packages/libsbml/trunk/debian/patches/hardening.patch 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/patches/hardening.patch 2014-03-11 15:40:06 UTC (rev 16422) @@ -8,9 +8,11 @@ --- Last-Update: <2013-01-22> ---- a/src/bindings/matlab/Makefile.in -+++ b/src/bindings/matlab/Makefile.in -@@ -70,12 +70,7 @@ distfiles = \ +Index: libsbml-5.9.0/src/bindings/matlab/Makefile.in +=================================================================== +--- libsbml-5.9.0.orig/src/bindings/matlab/Makefile.in 2013-11-28 14:51:16.191345434 +0100 ++++ libsbml-5.9.0/src/bindings/matlab/Makefile.in 2013-11-28 14:51:16.183345349 +0100 +@@ -70,12 +70,7 @@ installSBML.m \ isoctave.m \ matlab-tags-regexp.txt \ @@ -24,7 +26,7 @@ test.xml \ test/CMakeLists.txt -@@ -142,7 +137,7 @@ endif +@@ -142,7 +137,7 @@ # is really necessary, but it seems prudent. define matlabrun @@ -33,9 +35,11 @@ $(LIBTOOL) -dlopen $(TOP_BUILDDIR)/src/libsbml.la --mode=execute $(1) endef ---- a/src/bindings/matlab/mexopts-R2009-R2010.sh -+++ b/src/bindings/matlab/mexopts-R2009-R2010.sh -@@ -324,7 +324,13 @@ echo "Error: Did not imbed 'options.sh' +Index: libsbml-5.9.0/src/bindings/matlab/mexopts-R2009-R2010.sh +=================================================================== +--- libsbml-5.9.0.orig/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.191345434 +0100 ++++ libsbml-5.9.0/src/bindings/matlab/mexopts-R2009-R2010.sh 2013-11-28 14:51:16.183345349 +0100 +@@ -324,7 +324,13 @@ # #---------------------------------------------------------------------------- # CC="$CC" @@ -50,9 +54,11 @@ # COPTIMFLAGS="$COPTIMFLAGS" # CDEBUGFLAGS="$CDEBUGFLAGS" # CLIBS="$CLIBS" ---- a/src/bindings/perl/Makefile.in -+++ b/src/bindings/perl/Makefile.in -@@ -177,6 +177,8 @@ ifeq (GCC,$(findstring GCC,$(shell $(CXX +Index: libsbml-5.9.0/src/bindings/perl/Makefile.in +=================================================================== +--- libsbml-5.9.0.orig/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.191345434 +0100 ++++ libsbml-5.9.0/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.183345349 +0100 +@@ -177,6 +177,8 @@ endif @@ -61,9 +67,11 @@ # If the last run was made with --enable-layout and this one isn't, or # vice-versa, the swig wrap files will be wrong for this run. However, you # can't tell just by looking at file mod times, so you can't use normal ---- a/config/makefile-common-actions.mk -+++ b/config/makefile-common-actions.mk -@@ -72,6 +72,15 @@ endif +Index: libsbml-5.9.0/config/makefile-common-actions.mk +=================================================================== +--- libsbml-5.9.0.orig/config/makefile-common-actions.mk 2013-11-28 14:51:16.191345434 +0100 ++++ libsbml-5.9.0/config/makefile-common-actions.mk 2013-11-28 14:51:16.183345349 +0100 +@@ -72,6 +72,15 @@ # here is only to remove duplicates, which the 'sort' function does as a # documented side-effect.) Modified: trunk/packages/libsbml/branches/libsbml5/debian/patches/mexext.patch =================================================================== --- trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/patches/mexext.patch 2014-03-11 15:40:06 UTC (rev 16422) @@ -4,11 +4,11 @@ Author: Ivo Maintz <[email protected]> --- -Last-Update: <2013-03-14> +Last-Update: <2014-03-01> ---- a/src/bindings/matlab/FindMatlab.cmake -+++ b/src/bindings/matlab/FindMatlab.cmake -@@ -194,7 +194,7 @@ IF(WIN32) +--- libsbml-5.9.2.orig/src/bindings/matlab/FindMatlab.cmake ++++ libsbml-5.9.2/src/bindings/matlab/FindMatlab.cmake +@@ -162,7 +162,7 @@ IF(WIN32) SET(MATLAB_MATLAB_COMMAND "${MATLAB_ROOT_PATH}/bin/matlab.bat") ELSE (WIN32) SET(MATLAB_MEX_COMMAND "${MATLAB_ROOT_PATH}/bin/mex") Modified: trunk/packages/libsbml/branches/libsbml5/debian/patches/series =================================================================== --- trunk/packages/libsbml/trunk/debian/patches/series 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/patches/series 2014-03-11 15:40:06 UTC (rev 16422) @@ -1,3 +1,4 @@ hardening.patch mexext.patch format-security.patch +doxygen.patch Modified: trunk/packages/libsbml/branches/libsbml5/debian/rules =================================================================== --- trunk/packages/libsbml/trunk/debian/rules 2014-03-04 18:49:47 UTC (rev 16381) +++ trunk/packages/libsbml/branches/libsbml5/debian/rules 2014-03-11 15:40:06 UTC (rev 16422) @@ -47,6 +47,7 @@ sed -i 's/overriden/overridden/g' $(shell grep -Rl overriden src/) || true mkdir -p build cd build ; cmake $(CMAKE_OPTS) ../ + /bin/sh debian/bin/python_fix.sh override_dh_auto_build: cd build ; make _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
