[med-svn] r16422 - in trunk/packages/libsbml/branches: . libsbml5 libsbml5/debian libsbml5/debian/bin libsbml5/debian/patches
Ivo Maintz
ivomaintz-guest at moszumanska.debian.org
Tue Mar 11 15:40:06 UTC 2014
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 <tille at debian.org> 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 <ivo at maintz.de> 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 <ivo at maintz.de>
+
+---
+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 $(CXX
+Index: libsbml-5.9.0/src/bindings/perl/Makefile.in
+===================================================================
+--- libsbml-5.9.0.orig/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.9.0/src/bindings/perl/Makefile.in 2013-11-28 14:51:16.183345349 +0100
+@@ -177,6 +177,8 @@
endif
@@ -61,9 +67,11 @@
# If the last run was made with --enable-layout and this one isn't, or
# vice-versa, the swig wrap files will be wrong for this run. However, you
# can't tell just by looking at file mod times, so you can't use normal
---- a/config/makefile-common-actions.mk
-+++ b/config/makefile-common-actions.mk
-@@ -72,6 +72,15 @@ endif
+Index: libsbml-5.9.0/config/makefile-common-actions.mk
+===================================================================
+--- libsbml-5.9.0.orig/config/makefile-common-actions.mk 2013-11-28 14:51:16.191345434 +0100
++++ libsbml-5.9.0/config/makefile-common-actions.mk 2013-11-28 14:51:16.183345349 +0100
+@@ -72,6 +72,15 @@
# here is only to remove duplicates, which the 'sort' function does as a
# documented side-effect.)
Modified: trunk/packages/libsbml/branches/libsbml5/debian/patches/mexext.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2014-03-04 18:49:47 UTC (rev 16381)
+++ trunk/packages/libsbml/branches/libsbml5/debian/patches/mexext.patch 2014-03-11 15:40:06 UTC (rev 16422)
@@ -4,11 +4,11 @@
Author: Ivo Maintz <ivo at maintz.de>
---
-Last-Update: <2013-03-14>
+Last-Update: <2014-03-01>
---- a/src/bindings/matlab/FindMatlab.cmake
-+++ b/src/bindings/matlab/FindMatlab.cmake
-@@ -194,7 +194,7 @@ IF(WIN32)
+--- libsbml-5.9.2.orig/src/bindings/matlab/FindMatlab.cmake
++++ libsbml-5.9.2/src/bindings/matlab/FindMatlab.cmake
+@@ -162,7 +162,7 @@ IF(WIN32)
SET(MATLAB_MATLAB_COMMAND "${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
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