debian/changelog

@@ -18,7 +18,11 @@ libsbml (5.17.0+dfsg-1) UNRELEASED; urgency=medium
   * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
   * Remove trailing whitespace in debian/changelog
   * Do not parse d/changelog
-  * Build-Depends: libnewlib-dev
+  * Build-Depends: libnewlib-dev, check
+  * Remove Matlab related options from debian/cmake_opts (thanks for the
+    hint to Nicolas Mora)
+  TODO: Issue when building with Python 3.7 reported here:
+     https://groups.google.com/forum/#!topic/libsbml-development/hiqhyd6-7s0
 
  -- Andreas Tille <tille@debian.org>  Mon, 03 Dec 2018 16:11:35 +0100
 

debian/cmake_opts

@@ -7,7 +7,6 @@
 -DENABLE_LAYOUT:BOOL=ON
 -DENABLE_QUAL:BOOL=ON
 -DENABLE_RENDER:BOOL=ON
--DMATLAB_ROOT_PATH:PATH=/usr/share/matlab
 -DWITH_BZIP2:BOOL=ON
 -DWITH_CHECK:BOOL=OFF
 -DWITH_CPP_NAMESPACE:BOOL=OFF
@@ -17,8 +16,6 @@
 -DWITH_EXPAT:BOOL=OFF
 -DWITH_JAVA:BOOL=ON
 -DWITH_LIBXML:BOOL=ON
--DWITH_MATLAB:BOOL=ON
--DWITH_MATLAB_MEX:BOOL=ON
 -DWITH_OCTAVE:BOOL=ON
 -DWITH_PERL:BOOL=ON
 -DWITH_PYTHON:BOOL=ON

debian/cmake_opts.matlab

+-DCMAKE_BINARY_DIR=build
+-DCMAKE_COLOR_MAKEFILE:BOOL=ON
+-DCMAKE_INSTALL_PREFIX:PATH=/usr
+-DENABLE_COMP:BOOL=ON
+-DENABLE_FBC:BOOL=ON
+-DENABLE_GROUPS:BOOL=ON
+-DENABLE_LAYOUT:BOOL=ON
+-DENABLE_QUAL:BOOL=ON
+-DENABLE_RENDER:BOOL=ON
+-DMATLAB_ROOT_PATH:PATH=/usr/share/matlab
+-DWITH_BZIP2:BOOL=ON
+-DWITH_CHECK:BOOL=OFF
+-DWITH_CPP_NAMESPACE:BOOL=OFF
+-DWITH_CSHARP:BOOL=ON
+-DWITH_DOXYGEN:BOOL=ON
+-DWITH_EXAMPLES:BOOL=OFF
+-DWITH_EXPAT:BOOL=OFF
+-DWITH_JAVA:BOOL=ON
+-DWITH_LIBXML:BOOL=ON
+-DWITH_MATLAB:BOOL=ON
+-DWITH_MATLAB_MEX:BOOL=ON
+-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=OFF
+-DWITH_SWIG:BOOL=ON
+-DWITH_WALL:BOOL=ON
+-DWITH_XERCES:BOOL=OFF
+-DWITH_ZLIB:BOOL=ON
+-DJDK_PATH:STRING=/usr/lib/jvm/default-java
+-DJAVA_INCLUDE_PATH:STRING=/usr/lib/jvm/default-java/include

debian/control

@@ -21,6 +21,7 @@ Build-Depends: debhelper (>= 11~),
                zlib1g-dev,
                libbz2-dev,
                libnewlib-dev,
+               check,
                mono-devel,
                mono-mcs,
                cli-common-dev,

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: libsbml
+Upstream-Contact: https://groups.google.com/forum/#!forum/libsbml-development
 Source: http://www.sbml.org/software/libsbml/
 Files-Excluded:
  */docs/src/utilities/prettify
@@ -10,7 +11,8 @@ Copyright: 2005-2012 SBML-TEAM mailto:sbml-team@caltech.edu
 License: LGPL-2.1
 
 Files: debian/*
-Copyright: 2012 Ivo Maintz <ivo@maintz.de>
+Copyright: 2012-2015 Ivo Maintz <ivo@maintz.de>
+           2014-2018 Andreas Tille <tille@debian.org>
 License: GPL-2.0+
 
 License: GPL-2.0+
@@ -24,9 +26,6 @@ License: GPL-2.0+
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
  .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
  On Debian systems, the complete text of the GNU General
  Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
 

debian/patches/fix_cmake_configuration.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 03 Dec 2018 16:11:35 +0100
+Description: Desperately trying to fix CMake config by simply
+ commenting the line which causes an error
+
+--- a/src/bindings/r/CMakeLists.txt
++++ b/src/bindings/r/CMakeLists.txt
+@@ -336,7 +336,12 @@ configure_file (
+   "${CMAKE_CURRENT_BINARY_DIR}/libSBML/NAMESPACE"
+ )
+ 
+-get_target_property(LIBSBML_R_NATIVELIB binding_r_lib LOCATION)
++# get_target_property(LIBSBML_R_NATIVELIB binding_r_lib LOCATION)
++# Commented since it leads to
++#CMake Error at src/bindings/r/CMakeLists.txt:339 (get_target_property):
++#  The LOCATION property may not be read from target "binding_r_lib".  Use the
++#  target name directly with add_custom_command, or use the generator
++#  expression $<TARGET_FILE>, as appropriate.
+ 
+ if (APPLE AND ENABLE_UNIVERSAL)
+ 

debian/patches/series

@@ -8,3 +8,4 @@ mips-compile-with-O1.patch
 javadoc_java9.patch
 javadoc.patch
 remove_SBMLDoclet.patch
+fix_cmake_configuration.patch