[med-svn] r13350 - in trunk/packages/libsbml/trunk/debian: . bin etc/csh/login.d etc/profile.d lintian patches
Ivo Maintz
ivomaintz-guest at alioth.debian.org
Fri Apr 19 13:14:24 UTC 2013
Author: ivomaintz-guest
Date: 2013-04-19 13:14:23 +0000 (Fri, 19 Apr 2013)
New Revision: 13350
Added:
trunk/packages/libsbml/trunk/debian/bin/
trunk/packages/libsbml/trunk/debian/bin/mexext
trunk/packages/libsbml/trunk/debian/cmake_opts
trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-dev.links
trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-matlab.links.amd64
trunk/packages/libsbml/trunk/debian/libsbml5-matlab.links.i386
trunk/packages/libsbml/trunk/debian/libsbml5-matlab.postinst
trunk/packages/libsbml/trunk/debian/libsbml5-matlab.postrm
trunk/packages/libsbml/trunk/debian/libsbml5-octave.install
trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.amd64
trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.i386
trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.links
trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs
trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.links
trunk/packages/libsbml/trunk/debian/lintian/libsbml5-python
trunk/packages/libsbml/trunk/debian/patches/mexext.patch
Removed:
trunk/packages/libsbml/trunk/debian/lintian/libsbml5-perl
trunk/packages/libsbml/trunk/debian/patches/comp.patch
trunk/packages/libsbml/trunk/debian/patches/spelling.patch
Modified:
trunk/packages/libsbml/trunk/debian/README.source
trunk/packages/libsbml/trunk/debian/changelog
trunk/packages/libsbml/trunk/debian/control
trunk/packages/libsbml/trunk/debian/control.in
trunk/packages/libsbml/trunk/debian/etc/csh/login.d/libsbml-matlab.csh
trunk/packages/libsbml/trunk/debian/etc/profile.d/libsbml-matlab.sh
trunk/packages/libsbml/trunk/debian/libsbml5-dev.install
trunk/packages/libsbml/trunk/debian/libsbml5-matlab.docs
trunk/packages/libsbml/trunk/debian/libsbml5-matlab.install
trunk/packages/libsbml/trunk/debian/libsbml5-python.install
trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install
trunk/packages/libsbml/trunk/debian/lintian/libsbml5-java
trunk/packages/libsbml/trunk/debian/patches/series
trunk/packages/libsbml/trunk/debian/rules
Log:
libsbml_5.8.0 seems to be ready for upload
some major changes: switch to cmake, (re)added doc packages
Modified: trunk/packages/libsbml/trunk/debian/README.source
===================================================================
--- trunk/packages/libsbml/trunk/debian/README.source 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/README.source 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,15 +1,13 @@
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)
- we use libSBML-5.7.0-core-plus-packages-src.tar.gz, uscan with the option "rename"
- instead of "symlink" can handle this.
+ we use libSBML-5.7.0-core-plus-packages-src.tar.gz, simply linking it to
+ libsbml_5.7.0.orig.tar.gz
- -- Ivo Maintz <ivo at maintz.de> 04 Feb 2013 16:30:19 +0100
-
libsbml (5.5.0)
* a lot of spelling errors, remove with
- find docs -type f -exec sed -i -e 's/overriden/overridden/' -e 's/pacakge/package/' {} +
- find src -type f -exec sed -i -e 's/overriden/overridden/' -e 's/pacakge/package/' {} +
+ find docs -type f -exec sed -i -e 's/overridden/overridden/' -e 's/pacakge/package/' {} +
+ find src -type f -exec sed -i -e 's/overridden/overridden/' -e 's/pacakge/package/' {} +
libsbml (5.4.1-1)
* We don't build the documentation yet; it is impossible to get _working_
Added: trunk/packages/libsbml/trunk/debian/bin/mexext
===================================================================
--- trunk/packages/libsbml/trunk/debian/bin/mexext (rev 0)
+++ trunk/packages/libsbml/trunk/debian/bin/mexext 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+### simply uses matlab to get the correct mex extension ###
+matlab -nosplash -nodesktop -nojvm -r "fprintf(2 , '%s\n', mexext); quit" 2>&1 | grep mex
Property changes on: trunk/packages/libsbml/trunk/debian/bin/mexext
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/packages/libsbml/trunk/debian/changelog
===================================================================
--- trunk/packages/libsbml/trunk/debian/changelog 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/changelog 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,8 +1,14 @@
-libsbml (5.7.0-1) UNRELEASED; urgency=low
+libsbml (5.8.0-1) UNRELEASED; urgency=low
* 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
- -- Ivo Maintz <ivo at maintz.de> Wed, 23 Jan 2013 12:39:29 +0100
+ -- Ivo Maintz <ivo at maintz.de> Thu, 18 Apr 2013 14:02:27 +0200
libsbml (5.6.0-1) unstable; urgency=low
Added: trunk/packages/libsbml/trunk/debian/cmake_opts
===================================================================
--- trunk/packages/libsbml/trunk/debian/cmake_opts (rev 0)
+++ trunk/packages/libsbml/trunk/debian/cmake_opts 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,27 @@
+-DCMAKE_BINARY_DIR=build
+-DCMAKE_INSTALL_PREFIX:PATH=/usr
+-DCMAKE_COLOR_MAKEFILE:BOOL=ON
+-DENABLE_COMP:BOOL=ON
+-DENABLE_FBC:BOOL=ON
+-DENABLE_LAYOUT:BOOL=ON
+-DWITH_BZIP2:BOOL=ON
+-DWITH_CHECK:BOOL=OFF
+-DWITH_CPP_NAMESPACE:BOOL=ON
+-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
+-DMATLAB_ROOT_PATH:PATH=/usr/share/matlab
+-DWITH_OCTAVE:BOOL=ON
+-DWITH_PERL:BOOL=ON
+-DWITH_PYTHON:BOOL=ON
+-DWITH_R:BOOL=ON
+-DWITH_RUBY:BOOL=ON
+-DWITH_SWIG:BOOL=ON
+-DWITH_WALL:BOOL=ON
+-DWITH_XERCES:BOOL=OFF
+-DWITH_ZLIB:BOOL=ON
Modified: trunk/packages/libsbml/trunk/debian/control
===================================================================
--- trunk/packages/libsbml/trunk/debian/control 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/control 2013-04-19 13:14:23 UTC (rev 13350)
@@ -5,8 +5,9 @@
DM-Upload-Allowed: yes
Build-Depends: autoconf,
automake,
- debhelper (>= 9.20120101),
- doxygen,
+ debhelper (>= 9.0.0),
+ cmake,
+ doxygen (>= 1.8.0),
swig (>= 2),
ruby1.8,
libxml2-dev,
@@ -16,6 +17,8 @@
libperl-dev,
default-jdk | openjdk-6-jdk | java-gcj-compat-dev | java-sdk,
octave-pkg-dev,
+ r-base-dev,
+ r-base-core,
python-support,
graphviz,
zlib1g-dev,
@@ -66,6 +69,7 @@
Architecture: any
Provides: libsbml
Conflicts: libsbml1, libsbml2, libsbml3
+Pre-Depends: multiarch-support
Depends: ${shlibs:Depends},
${misc:Depends}
Description: System Biology Markup Language library
@@ -124,8 +128,9 @@
Conflicts: libsbml3-java,
libsbml4-java
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
+Pre-Depends: multiarch-support
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ jarwrapper
Description: System Biology Markup Language library - Java binding
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -152,7 +157,8 @@
Section: math
Provides: libsbml-octave
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ octave
Architecture: any
Description: System Biology Markup Language library - Octave binding
LibSBML is a library designed to help you read, write, manipulate,
@@ -185,3 +191,63 @@
application itself (though it does come with many example programs),
but rather a library you can embed in your own applications.
This package contains C/C++, Java, Perl and layout examples.
+
+Package: libsbml5-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- Documentation
+ 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 C/C++ documentation
+
+Package: libsbml5-cil-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- CIL Documentation
+ 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 documentation for mono/cil bindings
+
+Package: libsbml5-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- Java Documentation
+ 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 documentation for java bindings
+
+Package: libsbml5-perl-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- Perl Documentation
+ 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 documentation for perl bindings
+
+Package: libsbml5-python-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- Python Documentation
+ 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 documentation for python bindings
Modified: trunk/packages/libsbml/trunk/debian/control.in
===================================================================
--- trunk/packages/libsbml/trunk/debian/control.in 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/control.in 2013-04-19 13:14:23 UTC (rev 13350)
@@ -5,8 +5,9 @@
DM-Upload-Allowed: yes
Build-Depends: autoconf,
automake,
- debhelper (>= 9.20120101),
- doxygen,
+ debhelper (>= 9.0.0),
+ cmake,
+ doxygen (>= 1.8.0),
swig (>= 2),
ruby1.8,
libxml2-dev,
@@ -16,6 +17,8 @@
libperl-dev,
default-jdk | openjdk-6-jdk | java-gcj-compat-dev | java-sdk,
octave-pkg-dev,
+ r-base-dev,
+ r-base-core,
python-support,
graphviz,
zlib1g-dev,
@@ -66,6 +69,7 @@
Architecture: any
Provides: libsbml
Conflicts: libsbml1, libsbml2, libsbml3
+Pre-Depends: multiarch-support
Depends: ${shlibs:Depends},
${misc:Depends}
Description: System Biology Markup Language library
@@ -124,8 +128,9 @@
Conflicts: libsbml3-java,
libsbml4-java
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
+Pre-Depends: multiarch-support
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ jarwrapper
Description: System Biology Markup Language library - Java binding
LibSBML is a library designed to help you read, write, manipulate,
translate, and validate SBML files and data streams. It is not an
@@ -152,7 +157,8 @@
Section: math
Provides: libsbml-octave
Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ octave
Architecture: any
Description: System Biology Markup Language library - Octave binding
LibSBML is a library designed to help you read, write, manipulate,
@@ -185,3 +191,63 @@
application itself (though it does come with many example programs),
but rather a library you can embed in your own applications.
This package contains C/C++, Java, Perl and layout examples.
+
+Package: libsbml5-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- Documentation
+ 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 C/C++ documentation
+
+Package: libsbml5-cil-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- CIL Documentation
+ 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 documentation for mono/cil bindings
+
+Package: libsbml5-java-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- Java Documentation
+ 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 documentation for java bindings
+
+Package: libsbml5-perl-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- Perl Documentation
+ 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 documentation for perl bindings
+
+Package: libsbml5-python-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: libsbml5-dev (= ${binary:Version})
+Description: System Biology Markup Language library -- Python Documentation
+ LibSBML is a library designed to help you read, write, manipulate,
+ translate, and validate SBML files and data streams. It is not an
+ application itself (though it does come with many example programs),
+ but rather a library you can embed in your own applications.
+ This package contains documentation for python bindings
Modified: trunk/packages/libsbml/trunk/debian/etc/csh/login.d/libsbml-matlab.csh
===================================================================
--- trunk/packages/libsbml/trunk/debian/etc/csh/login.d/libsbml-matlab.csh 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/etc/csh/login.d/libsbml-matlab.csh 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,3 +1,3 @@
-setenv | grep MATLABPATH | grep /usr/lib: >& /dev/null && exit
-setenv | grep MATLABPATH >& /dev/null && setenv MATLABPATH /usr/lib:$MATLABPATH && exit
-setenv MATLABPATH /usr/lib
+setenv | grep MATLABPATH | grep /usr/share/libsbml-matlab: >& /dev/null && exit
+setenv | grep MATLABPATH >& /dev/null && setenv MATLABPATH /usr/share/libsbml-matlab:$MATLABPATH && exit
+setenv MATLABPATH /usr/share/libsbml-matlab
Modified: trunk/packages/libsbml/trunk/debian/etc/profile.d/libsbml-matlab.sh
===================================================================
--- trunk/packages/libsbml/trunk/debian/etc/profile.d/libsbml-matlab.sh 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/etc/profile.d/libsbml-matlab.sh 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1 +1,2 @@
-echo $MATLABPATH | grep /usr/lib: || export MATLABPATH=/usr/lib:$MATLABPATH
+TB="/usr/share/libsbml-matlab"
+echo $MATLABPATH | grep "$TB" || export MATLABPATH=$TB:$MATLABPATH
Added: trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.docs 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+debian/tmp/usr/share/libsbml/docs/csharp-api/
Added: trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.links (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-cil-doc.links 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+usr/share/doc/libsbml5-cil-doc/csharp-api usr/share/doc/libsbml5/csharp-api
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-dev.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-dev.install 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-dev.install 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,5 +1,2 @@
-usr/include/sbml/*
-usr/lib/libsbml.a
-usr/lib/libsbml.la
-usr/lib/libsbml.so
-usr/lib/pkgconfig/libsbml.pc
+usr/include/*
+usr/lib/libsbml-static.a
Added: trunk/packages/libsbml/trunk/debian/libsbml5-dev.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-dev.links (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-dev.links 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+usr/lib/libsbml.so.5.8.0 usr/lib/libsbml.so
Added: trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-doc.docs 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,2 @@
+debian/tmp/usr/share/libsbml/docs/c-api
+debian/tmp/usr/share/libsbml/docs/cpp-api
Added: trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.docs 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+debian/tmp/usr/share/libsbml/docs/java-api/
Added: trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.links (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-java-doc.links 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+usr/share/doc/libsbml5-java-doc/java-api usr/share/doc/libsbml5/java-api
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-matlab.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab.docs 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab.docs 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1 +1,2 @@
changelog
+debian/etc/profile.d/libsbml-matlab.sh
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-matlab.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab.install 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab.install 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,6 +1,5 @@
-usr/lib/TranslateSBML*
-usr/lib/OutputSBML*
-usr/lib/*.m
-etc/profile.d/libsbml-matlab.sh
-etc/csh/login.d/libsbml-matlab.csh
+usr/lib/*mex* usr/lib/
+usr/lib/*.m usr/share/libsbml-matlab/
+debian/etc/profile.d/libsbml-matlab.sh etc/profile.d/
+debian/etc/csh/login.d/libsbml-matlab.csh etc/csh/login.d/
../lintian/libsbml5-matlab usr/share/lintian/overrides
Added: trunk/packages/libsbml/trunk/debian/libsbml5-matlab.links.amd64
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab.links.amd64 (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab.links.amd64 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,2 @@
+usr/lib/TranslateSBML.mexa64 usr/share/libsbml-matlab/TranslateSBML.mexa64
+usr/lib/OutputSBML.mexa64 usr/share/libsbml-matlab/OutputSBML.mexa64
Added: trunk/packages/libsbml/trunk/debian/libsbml5-matlab.links.i386
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab.links.i386 (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab.links.i386 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,2 @@
+usr/lib/TranslateSBML.mexglx usr/share/libsbml-matlab/TranslateSBML.mexglx
+usr/lib/OutputSBML.mexglx usr/share/libsbml-matlab/OutputSBML.mexglx
Added: trunk/packages/libsbml/trunk/debian/libsbml5-matlab.postinst
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab.postinst (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab.postinst 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+# postinst script for libsbml-matlab
+
+set -e
+
+mkdir -p /etc/profile.d/
+cp -a /usr/share/doc/libsbml5-matlab/libsbml-matlab.sh /etc/profile.d/
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/libsbml/trunk/debian/libsbml5-matlab.postrm
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-matlab.postrm (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-matlab.postrm 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,10 @@
+#!/bin/sh
+# postrm script for libsbml-matlab
+
+set -e
+
+rm -f /etc/profile.d/libsbml-matlab.sh
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/libsbml/trunk/debian/libsbml5-octave.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.install (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.install 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,2 @@
+usr/lib/octave/site/oct/*/*.mex
+usr/lib/octave/site/oct/*/*.m usr/share/octave/site/libsbml-5.8.0
Added: trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.amd64
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.amd64 (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.amd64 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,2 @@
+usr/lib/octave/site/oct/x86_64-pc-linux-gnu/OutputSBML.mex usr/share/octave/site/libsbml-5.8.0/OutputSBML.mex
+usr/lib/octave/site/oct/x86_64-pc-linux-gnu/TranslateSBML.mex usr/share/octave/site/libsbml-5.8.0/TranslateSBML.mex
Added: trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.i386
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.i386 (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-octave.links.i386 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,2 @@
+usr/lib/octave/site/oct/i386-linux-gnu/OutputSBML.mex usr/share/octave/site/libsbml-5.8.0/OutputSBML.mex
+usr/lib/octave/site/oct/i386-linux-gnu/TranslateSBML.mex usr/share/octave/site/libsbml-5.8.0/TranslateSBML.mex
Added: trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.docs 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+debian/tmp/usr/share/libsbml/docs/perl-api/
Added: trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.links (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-perl-doc.links 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+usr/share/doc/libsbml5-perl-doc/perl-api usr/share/doc/libsbml5/perl-api
Added: trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.docs 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+debian/tmp/usr/share/libsbml/docs/python-api/
Added: trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.links
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.links (rev 0)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python-doc.links 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+usr/share/doc/libsbml5-python-doc/python-api usr/share/doc/libsbml5/python-api
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-python.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-python.install 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-python.install 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1 +1,2 @@
usr/lib/python*
+../lintian/libsbml5-python usr/share/lintian/overrides
Modified: trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install
===================================================================
--- trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/libsbml5-ruby1.8.install 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1 +1 @@
-usr/lib/ruby/*/*/*/*.so /usr/lib/ruby/1.8/x86_64-linux/
+usr/lib/ruby
Modified: trunk/packages/libsbml/trunk/debian/lintian/libsbml5-java
===================================================================
--- trunk/packages/libsbml/trunk/debian/lintian/libsbml5-java 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/lintian/libsbml5-java 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,2 +1,3 @@
libsbml5-java: package-name-doesnt-match-sonames
libsbml5-java: shlib-without-versioned-soname
+libsbml5-java: hardening-no-fortify-functions
Deleted: trunk/packages/libsbml/trunk/debian/lintian/libsbml5-perl
===================================================================
--- trunk/packages/libsbml/trunk/debian/lintian/libsbml5-perl 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/lintian/libsbml5-perl 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,3 +0,0 @@
-libsbml5-perl: incorrect-libdir-in-la-file
-libsbml5-perl: hardening-no-relro
-libsbml5-perl: hardening-no-fortify-functions
\ No newline at end of file
Added: trunk/packages/libsbml/trunk/debian/lintian/libsbml5-python
===================================================================
--- trunk/packages/libsbml/trunk/debian/lintian/libsbml5-python (rev 0)
+++ trunk/packages/libsbml/trunk/debian/lintian/libsbml5-python 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1 @@
+libsbml5-python: hardening-no-fortify-functions
\ No newline at end of file
Deleted: trunk/packages/libsbml/trunk/debian/patches/comp.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/comp.patch 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/patches/comp.patch 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,26 +0,0 @@
-Description: enable comp
- enable hierarchical model composition package
- .
- libsbml (5.7.0-1) UNRELEASED; urgency=low
- .
- * update from upstream
-Author: Ivo Maintz <ivo at maintz.de>
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Last-Update: <2012-01-25>
-
---- libsbml-5.7.0.orig/comp-package.cmake
-+++ libsbml-5.7.0/comp-package.cmake
-@@ -7,7 +7,7 @@
- # $HeadURL$
- #
-
--option(ENABLE_COMP "Enable hierarchical model composition package" OFF )
-+option(ENABLE_COMP "Enable hierarchical model composition package" ON )
-
- if(ENABLE_COMP)
- add_definitions(-DUSE_COMP)
Added: trunk/packages/libsbml/trunk/debian/patches/mexext.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/mexext.patch (rev 0)
+++ trunk/packages/libsbml/trunk/debian/patches/mexext.patch 2013-04-19 13:14:23 UTC (rev 13350)
@@ -0,0 +1,19 @@
+Description: get the matching mex extension
+ Matlabs script $MATLABROOT/bin/mexext fails in an chrooted environment.
+ .
+Author: Ivo Maintz <ivo at maintz.de>
+
+---
+Last-Update: <2013-03-14>
+
+--- libsbml-5.8.0.orig/src/bindings/matlab/FindMatlab.cmake
++++ libsbml-5.8.0/src/bindings/matlab/FindMatlab.cmake
+@@ -162,7 +162,7 @@ IF(WIN32)
+ SET(MATLAB_MATLAB_COMMAND "${MATLAB_ROOT_PATH}/bin/matlab.bat")
+ ELSE (WIN32)
+ SET(MATLAB_MEX_COMMAND "${MATLAB_ROOT_PATH}/bin/mex")
+- SET(MATLAB_MEXEXT ${MATLAB_ROOT_PATH}/bin/mexext)
++ SET(MATLAB_MEXEXT "${CMAKE_SOURCE_DIR}/debian/bin/mexext")
+ SET(MATLAB_MATLAB_COMMAND "${MATLAB_ROOT_PATH}/bin/matlab")
+ MESSAGE(STATUS ${MATLAB_ROOT_PATH}/bin/maci64/)
+ if(APPLE)
Modified: trunk/packages/libsbml/trunk/debian/patches/series
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/series 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/patches/series 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,3 +1,2 @@
-spelling.patch
hardening.patch
-comp.patch
+mexext.patch
Deleted: trunk/packages/libsbml/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/patches/spelling.patch 2013-04-19 13:14:23 UTC (rev 13350)
@@ -1,595 +0,0 @@
-Description: Spelling errors
- There are still a lot of similar spellling errors, so I did simply
- "grep -Rl overriden * | xargs sed -i 's/overriden/overridden/'"
- .
- libsbml (5.7.0-1) UNRELEASED; urgency=low
- .
- * update from upstream
-Author: Ivo Maintz <ivo at maintz.de>
-
----
-The information above should follow the Patch Tagging Guidelines, please
-checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
-are templates for supplementary fields that you might want to add:
-
-Last-Update: <2013-01-22>
-
---- libsbml-5.7.0.orig/src/bindings/csharp/csdoc.i
-+++ libsbml-5.7.0/src/bindings/csharp/csdoc.i
-@@ -49197,7 +49197,7 @@ GroupsExtension::init()
- %csmethodmodifiers SBMLExtensionRegistry::removeL2Namespaces(XMLNamespaces *xmlns) const "
- /**
- * Remove all L2 Extension namespaces from the namespace list. This will call all
-- * overriden SBMLExtension::removeL2Namespaces methods.
-+ * overridden SBMLExtension::removeL2Namespaces methods.
- */ public
- ";
-
-@@ -49205,7 +49205,7 @@ GroupsExtension::init()
- %csmethodmodifiers SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const "
- /**
- * adds all L2 Extension namespaces to the namespace list. This will call all
-- * overriden SBMLExtension::addL2Namespaces methods.
-+ * overridden SBMLExtension::addL2Namespaces methods.
- */ public
- ";
-
---- libsbml-5.7.0.orig/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs
-+++ libsbml-5.7.0/src/bindings/csharp/csharp-files/SBMLExtensionRegistry.cs
-@@ -105,7 +105,7 @@ public class SBMLExtensionRegistry : IDi
-
- /**
- * Remove all L2 Extension namespaces from the namespace list. This will call all
-- * overriden SBMLExtension::removeL2Namespaces methods.
-+ * overridden SBMLExtension::removeL2Namespaces methods.
- */ public
- void removeL2Namespaces(XMLNamespaces xmlns) {
- libsbmlPINVOKE.SBMLExtensionRegistry_removeL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
-@@ -114,7 +114,7 @@ public class SBMLExtensionRegistry : IDi
-
- /**
- * adds all L2 Extension namespaces to the namespace list. This will call all
-- * overriden SBMLExtension::addL2Namespaces methods.
-+ * overridden SBMLExtension::addL2Namespaces methods.
- */ public
- void addL2Namespaces(XMLNamespaces xmlns) {
- libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
---- libsbml-5.7.0.orig/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs
-+++ libsbml-5.7.0/src/bindings/csharp/csharp-files-win/SBMLExtensionRegistry.cs
-@@ -104,7 +104,7 @@ public class SBMLExtensionRegistry : IDi
-
- /**
- * Remove all L2 Extension namespaces from the namespace list. This will call all
-- * overriden SBMLExtension::removeL2Namespaces methods.
-+ * overridden SBMLExtension::removeL2Namespaces methods.
- */ public
- void removeL2Namespaces(XMLNamespaces xmlns) {
- libsbmlPINVOKE.SBMLExtensionRegistry_removeL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
-@@ -113,7 +113,7 @@ public class SBMLExtensionRegistry : IDi
-
- /**
- * adds all L2 Extension namespaces to the namespace list. This will call all
-- * overriden SBMLExtension::addL2Namespaces methods.
-+ * overridden SBMLExtension::addL2Namespaces methods.
- */ public
- void addL2Namespaces(XMLNamespaces xmlns) {
- libsbmlPINVOKE.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, XMLNamespaces.getCPtr(xmlns));
---- libsbml-5.7.0.orig/src/bindings/java/javadoc.i
-+++ libsbml-5.7.0/src/bindings/java/javadoc.i
-@@ -51801,7 +51801,7 @@ void
- %javamethodmodifiers SBMLExtensionRegistry::removeL2Namespaces(XMLNamespaces *xmlns) const "
- /**
- * Remove all L2 Extension namespaces from the namespace list. This will call all
-- * overriden SBMLExtension.removeL2Namespaces methods.
-+ * overridden SBMLExtension.removeL2Namespaces methods.
- */ public
- ";
-
-@@ -51809,7 +51809,7 @@ void
- %javamethodmodifiers SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const "
- /**
- * adds all L2 Extension namespaces to the namespace list. This will call all
-- * overriden SBMLExtension.addL2Namespaces methods.
-+ * overridden SBMLExtension.addL2Namespaces methods.
- */ public
- ";
-
---- libsbml-5.7.0.orig/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java
-+++ libsbml-5.7.0/src/bindings/java/java-files/org/sbml/libsbml/SBMLExtensionRegistry.java
-@@ -96,7 +96,7 @@ public class SBMLExtensionRegistry {
-
- /**
- * Remove all L2 Extension namespaces from the namespace list. This will call all
-- * overriden SBMLExtension.removeL2Namespaces methods.
-+ * overridden SBMLExtension.removeL2Namespaces methods.
- */ public
- void removeL2Namespaces(XMLNamespaces xmlns) {
- libsbmlJNI.SBMLExtensionRegistry_removeL2Namespaces(swigCPtr, this, XMLNamespaces.getCPtr(xmlns), xmlns);
-@@ -105,7 +105,7 @@ public class SBMLExtensionRegistry {
-
- /**
- * adds all L2 Extension namespaces to the namespace list. This will call all
-- * overriden SBMLExtension.addL2Namespaces methods.
-+ * overridden SBMLExtension.addL2Namespaces methods.
- */ public
- void addL2Namespaces(XMLNamespaces xmlns) {
- libsbmlJNI.SBMLExtensionRegistry_addL2Namespaces(swigCPtr, this, XMLNamespaces.getCPtr(xmlns), xmlns);
---- libsbml-5.7.0.orig/src/bindings/perl/LibSBML.pm
-+++ libsbml-5.7.0/src/bindings/perl/LibSBML.pm
-@@ -40598,13 +40598,13 @@ extension is to be freed (i.e.: deleted)
- =item SBMLExtensionRegistry::removeL2Namespaces
-
- Remove all L2 Extension namespaces from the namespace list. This will call all
--overriden SBMLExtension::removeL2Namespaces methods.
-+overridden SBMLExtension::removeL2Namespaces methods.
-
-
- =item SBMLExtensionRegistry::addL2Namespaces
-
- adds all L2 Extension namespaces to the namespace list. This will call all
--overriden SBMLExtension::addL2Namespaces methods.
-+overridden SBMLExtension::addL2Namespaces methods.
-
-
- =item SBMLExtensionRegistry::enableL2NamespaceForDocument
---- libsbml-5.7.0.orig/src/bindings/perl/LibSBML.pod
-+++ libsbml-5.7.0/src/bindings/perl/LibSBML.pod
-@@ -40585,13 +40585,13 @@ extension is to be freed (i.e.: deleted)
- =item SBMLExtensionRegistry::removeL2Namespaces
-
- Remove all L2 Extension namespaces from the namespace list. This will call all
--overriden SBMLExtension::removeL2Namespaces methods.
-+overridden SBMLExtension::removeL2Namespaces methods.
-
-
- =item SBMLExtensionRegistry::addL2Namespaces
-
- adds all L2 Extension namespaces to the namespace list. This will call all
--overriden SBMLExtension::addL2Namespaces methods.
-+overridden SBMLExtension::addL2Namespaces methods.
-
-
- =item SBMLExtensionRegistry::enableL2NamespaceForDocument
---- libsbml-5.7.0.orig/src/bindings/python/libsbml-doxygen.py
-+++ libsbml-5.7.0/src/bindings/python/libsbml-doxygen.py
-@@ -51084,7 +51084,7 @@ class SBMLExtensionRegistry(_object):
- removeL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)
-
- Remove all L2 Extension namespaces from the namespace list. This will call all
-- overriden SBMLExtension::removeL2Namespaces methods.
-+ overridden SBMLExtension::removeL2Namespaces methods.
-
- """
- return _libsbml.SBMLExtensionRegistry_removeL2Namespaces(self, *args)
-@@ -51094,7 +51094,7 @@ class SBMLExtensionRegistry(_object):
- addL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)
-
- adds all L2 Extension namespaces to the namespace list. This will call all
-- overriden SBMLExtension::addL2Namespaces methods.
-+ overridden SBMLExtension::addL2Namespaces methods.
-
- """
- return _libsbml.SBMLExtensionRegistry_addL2Namespaces(self, *args)
---- libsbml-5.7.0.orig/src/bindings/python/libsbml.py
-+++ libsbml-5.7.0/src/bindings/python/libsbml.py
-@@ -51204,7 +51204,7 @@ class SBMLExtensionRegistry(_object):
- removeL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)
-
- Remove all L2 Extension namespaces from the namespace list. This will
-- call all overriden SBMLExtension::removeL2Namespaces methods.
-+ call all overridden SBMLExtension::removeL2Namespaces methods.
-
- """
- return _libsbml.SBMLExtensionRegistry_removeL2Namespaces(self, *args)
-@@ -51214,7 +51214,7 @@ class SBMLExtensionRegistry(_object):
- addL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)
-
- adds all L2 Extension namespaces to the namespace list. This will
-- call all overriden SBMLExtension::addL2Namespaces methods.
-+ call all overridden SBMLExtension::addL2Namespaces methods.
-
- """
- return _libsbml.SBMLExtensionRegistry_addL2Namespaces(self, *args)
---- libsbml-5.7.0.orig/src/bindings/python/libsbml_wrap.cpp
-+++ libsbml-5.7.0/src/bindings/python/libsbml_wrap.cpp
-@@ -134460,14 +134460,14 @@ static PyMethodDef SwigMethods[] = {
- "SBMLExtensionRegistry_removeL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)\n"
- "\n"
- "Remove all L2 Extension namespaces from the namespace list. This will\n"
-- "call all overriden SBMLExtension::removeL2Namespaces methods.\n"
-+ "call all overridden SBMLExtension::removeL2Namespaces methods.\n"
- "\n"
- ""},
- { (char *)"SBMLExtensionRegistry_addL2Namespaces", _wrap_SBMLExtensionRegistry_addL2Namespaces, METH_VARARGS, (char *)"\n"
- "SBMLExtensionRegistry_addL2Namespaces(SBMLExtensionRegistry self, XMLNamespaces xmlns)\n"
- "\n"
- "adds all L2 Extension namespaces to the namespace list. This will\n"
-- "call all overriden SBMLExtension::addL2Namespaces methods.\n"
-+ "call all overridden SBMLExtension::addL2Namespaces methods.\n"
- "\n"
- ""},
- { (char *)"SBMLExtensionRegistry_enableL2NamespaceForDocument", _wrap_SBMLExtensionRegistry_enableL2NamespaceForDocument, METH_VARARGS, (char *)"\n"
---- libsbml-5.7.0.orig/src/bindings/python/pydoc-doxygen.i
-+++ libsbml-5.7.0/src/bindings/python/pydoc-doxygen.i
-@@ -43304,13 +43304,13 @@ in their packages, otherwise package dev
-
- %feature("docstring") SBMLExtensionRegistry::removeL2Namespaces "
- Remove all L2 Extension namespaces from the namespace list. This will call all
-- overriden SBMLExtension::removeL2Namespaces methods.
-+ overridden SBMLExtension::removeL2Namespaces methods.
- ";
-
-
- %feature("docstring") SBMLExtensionRegistry::addL2Namespaces "
- adds all L2 Extension namespaces to the namespace list. This will call all
-- overriden SBMLExtension::addL2Namespaces methods.
-+ overridden SBMLExtension::addL2Namespaces methods.
- ";
-
-
---- libsbml-5.7.0.orig/src/bindings/python/pydoc-normal.i
-+++ libsbml-5.7.0/src/bindings/python/pydoc-normal.i
-@@ -41526,13 +41526,13 @@
-
- %feature("docstring") SBMLExtensionRegistry::removeL2Namespaces "
- Remove all L2 Extension namespaces from the namespace list. This will
-- call all overriden SBMLExtension::removeL2Namespaces methods.
-+ call all overridden SBMLExtension::removeL2Namespaces methods.
- ";
-
-
- %feature("docstring") SBMLExtensionRegistry::addL2Namespaces "
- adds all L2 Extension namespaces to the namespace list. This will
-- call all overriden SBMLExtension::addL2Namespaces methods.
-+ call all overridden SBMLExtension::addL2Namespaces methods.
- ";
-
-
---- libsbml-5.7.0.orig/src/sbml/extension/SBMLExtensionRegistry.cpp
-+++ libsbml-5.7.0/src/sbml/extension/SBMLExtensionRegistry.cpp
-@@ -304,7 +304,7 @@ SBMLExtensionRegistry::removeL2Namespace
-
- /**
- * adds all L2 Extension namespaces to the namespace list. This will call all
-- * overriden SBMLExtension::addL2Namespaces methods.
-+ * overridden SBMLExtension::addL2Namespaces methods.
- */
- void
- SBMLExtensionRegistry::addL2Namespaces(XMLNamespaces *xmlns) const
---- libsbml-5.7.0.orig/src/sbml/extension/SBMLExtensionRegistry.h
-+++ libsbml-5.7.0/src/sbml/extension/SBMLExtensionRegistry.h
-@@ -98,13 +98,13 @@ public:
-
- /**
- * Remove all L2 Extension namespaces from the namespace list. This will call all
-- * overriden SBMLExtension::removeL2Namespaces methods.
-+ * overridden SBMLExtension::removeL2Namespaces methods.
- */
- void removeL2Namespaces(XMLNamespaces *xmlns) const;
-
- /**
- * adds all L2 Extension namespaces to the namespace list. This will call all
-- * overriden SBMLExtension::addL2Namespaces methods.
-+ * overridden SBMLExtension::addL2Namespaces methods.
- */
- void addL2Namespaces(XMLNamespaces *xmlns) const;
-
---- libsbml-5.7.0.orig/src/sbml/packages/comp/validator/constraints/CompIdBase.cpp
-+++ libsbml-5.7.0/src/sbml/packages/comp/validator/constraints/CompIdBase.cpp
-@@ -68,7 +68,7 @@ CompIdBase::getFieldname ()
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- const char*
---- libsbml-5.7.0.orig/src/sbml/packages/comp/validator/constraints/CompIdBase.h
-+++ libsbml-5.7.0/src/sbml/packages/comp/validator/constraints/CompIdBase.h
-@@ -113,7 +113,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/ArgumentsUnitsCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/ArgumentsUnitsCheck.h
-@@ -75,7 +75,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/ArgumentsUnitsCheckWarnings.h
-@@ -75,7 +75,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/CiElementMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/CiElementMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/EqualityArgsMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/EqualityArgsMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/ExponentUnitsCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/ExponentUnitsCheck.h
-@@ -75,7 +75,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/FunctionApplyMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/FunctionApplyMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/FunctionNoArgsMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/IdBase.cpp
-+++ libsbml-5.7.0/src/sbml/validator/constraints/IdBase.cpp
-@@ -71,7 +71,7 @@ IdBase::getFieldname ()
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- const char*
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/IdBase.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/IdBase.h
-@@ -112,7 +112,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp
-+++ libsbml-5.7.0/src/sbml/validator/constraints/KineticLawUnitsCheck.cpp
-@@ -80,7 +80,7 @@ KineticLawUnitsCheck::getFieldname ()
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- const char*
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/KineticLawUnitsCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/KineticLawUnitsCheck.h
-@@ -79,7 +79,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/LambdaMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/LambdaMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/LocalParameterMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/LocalParameterMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/LogicalArgsMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/LogicalArgsMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/MathMLBase.cpp
-+++ libsbml-5.7.0/src/sbml/validator/constraints/MathMLBase.cpp
-@@ -69,7 +69,7 @@ MathMLBase::getFieldname ()
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- const char*
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/MathMLBase.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/MathMLBase.h
-@@ -101,7 +101,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/NumberArgsMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/NumberArgsMathCheck.h
-@@ -99,7 +99,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/NumericArgsMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/NumericArgsMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/NumericReturnMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/NumericReturnMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/PieceBooleanMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/PieceBooleanMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/PiecewiseValueMathCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/PiecewiseValueMathCheck.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/PowerUnitsCheck.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/PowerUnitsCheck.h
-@@ -75,7 +75,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/UniqueMetaId.cpp
-+++ libsbml-5.7.0/src/sbml/validator/constraints/UniqueMetaId.cpp
-@@ -74,7 +74,7 @@ UniqueMetaId::getFieldname ()
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- const char*
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/UniqueMetaId.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/UniqueMetaId.h
-@@ -119,7 +119,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/UnitsBase.cpp
-+++ libsbml-5.7.0/src/sbml/validator/constraints/UnitsBase.cpp
-@@ -80,7 +80,7 @@ UnitsBase::getFieldname ()
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- const char*
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/UnitsBase.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/UnitsBase.h
-@@ -104,7 +104,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
---- libsbml-5.7.0.orig/src/sbml/validator/constraints/ValidCnUnitsValue.h
-+++ libsbml-5.7.0/src/sbml/validator/constraints/ValidCnUnitsValue.h
-@@ -74,7 +74,7 @@ protected:
-
- /**
- * @return the preamble to use when logging constraint violations. The
-- * preamble will be prepended to each log message. If not overriden,
-+ * preamble will be prepended to each log message. If not overridden,
- * returns an empty string.
- */
- virtual const char* getPreamble ();
Modified: trunk/packages/libsbml/trunk/debian/rules
===================================================================
--- trunk/packages/libsbml/trunk/debian/rules 2013-04-18 17:36:11 UTC (rev 13349)
+++ trunk/packages/libsbml/trunk/debian/rules 2013-04-19 13:14:23 UTC (rev 13350)
@@ -2,181 +2,69 @@
# -*- makefile -*-
# debian/rules for libsbml
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-# hardening
-
-CFLAGS = `dpkg-buildflags --get CFLAGS`
-CFLAGS += -Wall
-CXXFLAGS = `dpkg-buildflags --get CXXFLAGS`
-CXXFLAGS += -Wall
-LDFLAGS = `dpkg-buildflags --get LDFLAGS`
-CPPFLAGS = `dpkg-buildflags --get CPPFLAGS`
-
-# These are used for cross-compiling and for saving the configure script
-# from having to guess our platform (since we know it already)
-DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
-DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
-ifneq ($(DEB_HOST_GNU_TYPE),$(DEB_BUILD_GNU_TYPE))
-CROSS= --build $(DEB_BUILD_GNU_TYPE) --host $(DEB_HOST_GNU_TYPE)
-else
-CROSS= --build $(DEB_BUILD_GNU_TYPE)
-endif
-
-### part1 of a dirty hack for octave bindings, see install: section ###
+### define the VARS ###
+### part 1 of a dirty hack for octave bindings ###
OCTAVE_PATH ?= usr$(shell grep LOCALOCTFILEDIR config/makefile-common-vars.mk | tr -s ' ' ' ' | cut -d\ -f3)
-
-# prevent the examples from beeing compressed...
-DEB_COMPRESS_EXCLUDE := .xml .pdf .py .c .h .cpp .in .cs .java .pl .rb .xsl
-
-version= $(shell dpkg-parsechangelog | grep Version | cut -d\ -f2 | cut -d- -f1)
-major= $(shell dpkg-parsechangelog | grep Version | cut -d\ -f2 | cut -d. -f1)
-
+version := $(shell dpkg-parsechangelog | grep Version | cut -d\ -f2 | cut -d- -f1)
+major := $(shell dpkg-parsechangelog | grep Version | cut -d\ -f2 | cut -d. -f1)
libpack := libsbml
-devpack := $(libpack)-dev
-mathpack := $(libpack)-matlab
-perlpack := $(libpack)-dev
-pythonpack := $(libpack)-dev
-javapack := $(libpack)-dev
debtmp := $(CURDIR)/debian/tmp
dbgpack := $(libpack)$(major)-dbg
SRC_TMP := $(CURDIR)/SRC_TMP
# Test for matlab
-BIND_MATLAB := $(shell which matlab | grep -q matlab && echo '--with-matlab')
-
-get-orig-source:
- uscan --verbose --force-download --repack --rename
-
-config.status: configure
- dh_testdir
- # Add here commands to configure the package.
-ifneq "$(wildcard /usr/share/misc/config.sub)" ""
- cp -f /usr/share/misc/config.sub config.sub
+CMAKE_OPTS := $(shell sed '/MATLAB/d' debian/cmake_opts)
+BIND_MATLAB := $(shell which matlab | grep -q matlab && echo 'yes')
+ifdef BIND_MATLAB
+CMAKE_OPTS := $(shell cat debian/cmake_opts)
endif
-ifneq "$(wildcard /usr/share/misc/config.guess)" ""
- cp -f /usr/share/misc/config.guess config.guess
-endif
-# prepare the debian/control file
- if [ "$(BIND_MATLAB)" = "--with-matlab" ] ; then \
- sed -e 's/^#//' debian/control.in > debian/control ; else \
- grep -v ^# debian/control.in > debian/control ; fi
-###-deactivated, because the docu only builds with doxygen-1.6.3-###
+### let's do it ###
- ./configure $(CROSS) --prefix=/usr \
- --with-perl \
- --with-python \
- --with-java \
- --with-swig \
- --with-ruby \
- --with-doxygen \
- --with-octave \
- $(BIND_MATLAB) \
- --enable-layout \
- --enable-cpp-namespace \
- --with-csharp \
- --mandir=\$${prefix}/share/man \
- --infodir=\$${prefix}/share/info \
- CFLAGS="$(CFLAGS)" \
- LDFLAGS="-Wl,-z,defs"
+DEB_COMPRESS_EXCLUDE = .pdf
-build: build-arch build-indep
-build-arch: build-stamp
-build-indep: build-stamp
-build-stamp: config.status
- dh_testdir
+%:
+ dh $@ --with-python2 --dbg-package=${dbgpack}
- # Add here commands to compile the package.
- $(MAKE)
+get-orig-source:
+ uscan --verbose --force-download --repack
- touch $@
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp
- # Add here commands to clean up after the build process.
- [ ! -f Makefile ] || $(MAKE) distclean
- ### remove the by debian/rules created files ###
- rm -f debian/libsbml5-octave.install
- rm -f changelog
+override_dh_auto_clean:
### the clean target of the libsbml makefile is highly b0rken ###
- ### verx ugly ###
- rm -rf .pc .debs config docs examples macosx src config.guess config.sub
+ ### the switch to cmake didn't result in great approvements ###
+ ### still inline changes of files ###
+ ### very ugly ###
+ rm -rf .pc .debs config docs examples macosx src config.guess config.sub build
+ find -maxdepth 1 -type f -delete
dh_clean
tar --no-same-owner -xzf ../libsbml_$(version).orig.tar.gz --strip-components=1
-install: build
- dh_testdir
- dh_testroot
- dh_prep
- dh_installdirs
+override_dh_auto_configure:
+ifdef BIND_MATLAB
+ sed -e 's/^#//' debian/control.in > debian/control || true
+else
+ grep -v ^# debian/control.in > debian/control
+endif
+ sed -i 's/overriden/overridden/g' $(shell grep -Rl overriden src/) || true
+ mkdir -p build
+ cd build ; cmake $(CMAKE_OPTS) ../
- # Add here commands to install the package into debian/libsbml.
- mkdir -p $(debtmp)/etc
- cp -a debian/etc $(debtmp)
-###-deactivated, because the docu only builds with doxygen-1.6.3-###
-# $(MAKE) install-docs DESTDIR=$(debtmp)
- $(MAKE) install DESTDIR=$(debtmp)
-# ### not required for python2.7 ###
- [ ! -d $(debtmp)/usr/lib/python2.6/ ] || find $(debtmp)/usr/lib/python2.6/ -type d -name site-packages -exec mv {} $(debtmp)/usr/lib/python2.6/dist-packages \; || true
-# ### _very_ dirty hack for working octave bindings ###
- mkdir -p $(debtmp)/$(OCTAVE_PATH)
- cp src/bindings/matlab/buildSBML.m $(debtmp)/$(OCTAVE_PATH)/
- cp src/bindings/matlab/CheckAndConvert.m $(debtmp)/$(OCTAVE_PATH)/
- cp src/bindings/matlab/ConvertFormulaToMathML.m $(debtmp)/$(OCTAVE_PATH)/
- cp src/bindings/matlab/Contents.m $(debtmp)/$(OCTAVE_PATH)/
- cp src/bindings/matlab/isoctave.m $(debtmp)/$(OCTAVE_PATH)/
- cp src/bindings/matlab/isSBML_Model.m $(debtmp)/$(OCTAVE_PATH)/
- rm $(debtmp)/usr/lib/*/dist-packages/libsbml/*.pyc || true
- mkdir $(debtmp)/usr/lib/perl5
- mv $(debtmp)/usr/lib/perl/*/* $(debtmp)/usr/lib/perl5/
- chmod 644 $(debtmp)/usr/share/java/libsbmlj.jar
- find $(debtmp)/usr/lib/ -type f -exec chmod 644 {} +
- find $(debtmp)/usr/lib/ -type f -name .packlist -exec rm -f {} +
- find $(debtmp)/usr/lib/ -type d -iname "*.libs" -exec rm -rf {} +
- find examples -type f -name "*.R" -exec chmod -x {} + || true
- sed -i "/dependency_libs/ s/'.*'/''/" `find $(debtmp)/usr/lib/ -name '*.la'`
- strip --strip-unneeded $(debtmp)/usr/lib/*.mex* || true
- strip --strip-unneeded $(debtmp)/$(OCTAVE_PATH)/*.mex || true
- strip --strip-unneeded $(debtmp)/$(OCTAVE_PATH)/*.mex || true
- echo $(OCTAVE_PATH) >debian/libsbml5-octave.install
+override_dh_auto_build:
+ cd build ; make
cp NEWS.txt changelog
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
+override_dh_auto_test:
+ echo "no tests"
-# Build architecture-dependent files here.
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs
- dh_installexamples
- dh_install
- dh_installman
- dh_link
- dh_strip --dbg-package=${dbgpack}
- if [ "$(BIND_MATLAB)" = "--with-matlab" ] ; then \
- strip --remove-section=.comment debian/libsbml5-matlab/usr/lib/*.mexa64 || true ; fi
- strip --remove-section=.comment debian/libsbml5-octave/$(OCTAVE_PATH)/*.mex || true
- dh_compress
- dh_fixperms
- dh_makeshlibs
- dpkg-shlibdeps debian/libsbml5-octave/$(OCTAVE_PATH)/* -Tdebian/libsbml5-octave.substvars
- if [ "$(BIND_MATLAB)" = "--with-matlab" ] ; then \
- dpkg-shlibdeps debian/libsbml5-matlab/usr/lib/* -Tdebian/libsbml5-matlab.substvars ; fi
- dh_makeclilibs -i -V
- dh_installcligac -i
- dh_perl
- dh_python2 --no-guessing-versions
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
+override_dh_auto_install:
+ cd build ; DESTDIR=../debian/tmp make install
+ dh_auto_install
+ pyclean $(debtmp)/usr/lib/python*
+ find $(debtmp)/usr -type f -name "*.js" -delete
+ find $(debtmp)/usr -type f -exec chmod 644 {} +
+ test -e $(debtmp)/usr/lib/python2.7/site-packages && mv $(debtmp)/usr/lib/python2.7/site-packages $(debtmp)/usr/lib/python2.7/dist-packages || true
+ find $(debtmp)/usr/lib -name "*.mex*" -exec strip --strip-unneeded {} + || true
+ find $(debtmp)/usr/lib -name "*.mex*" -exec strip --remove-section=.comment {} + || true
+ dpkg-shlibdeps $(debtmp)/usr/lib/*/*/*/*/*.mex -Tdebian/libsbml5-octave.substvars
+ifdef BIND_MATLAB
+ dpkg-shlibdeps $(debtmp)/usr/lib/*.mex* -Tdebian/libsbml5-matlab.substvars
+endif
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