[Debian-med-packaging] Bug#735453: Changes to libsbml

Mon May 5 13:14:10 UTC 2014

Hi Ivo,

please always either keep the bug report we are working on or at least
the maintainers list in CC to keep others informed that we are working
on the issue.

On Mon, May 05, 2014 at 01:07:26PM +0200, Ivo Maintz wrote:
> Hi Andreas,
> 
> Andreas Tille <tille at debian.org> schrieb :
> 
> > > > However, I just realised that version 5.10.0 is out and this does
> > > > not contain prettify.js any more.  Would you be able to adapt the
> > > > patches and we try again with this version? 
> > > 
> > > Is done; one issue: get-orig-source don't exclude docs/src/prettify
> > > (it is still included in the main source), but it is still listed in
> > > debian/copyright.
> > 
> > This is what I thought in the first place.  However, lintian seems to
> > try to tell us something else.   The file is not even in upstream
> > tarball any more but I have no idea what lintian tries to express.
> > If I were you I would ask for help on debian-mentors at l.d.o for help
> > since I have no good idea what to do.
> 
> 
> It works now. Simple solution: the path to prettify had changed...
> Would you double-check it?

Sorry, I can't help myself but I do not manage to build.  I have commited
some slight change that should deal with xz compressed tarballs which
would be pretty useful in this case.  However, even if I work with a
*.gz tarball the package does not build and stumbles after the clean
target.  I have attached a build log and the diff that dpkg-source has
found.  I keep on beeing sceptical about this strange way to build the
package - at least for me it only works not reliable. :-(

Kind regards

          Andreas. 

-- 
http://fam-tille.de
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dpkg-checkbuilddeps: Unmet build dependencies: swig (>= 2) libperl-dev octave-pkg-dev mono-devel mono-gmcs cli-common-dev cli-runtime
W: Unmet build-dependency in source
dpkg-buildpackage: source package libsbml
dpkg-buildpackage: source version 5.10.0+dfsg-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Andreas Tille <tille at debian.org>
 dpkg-source -i.git -I.git --before-build libSBML-5.10.0-Source
dpkg-checkbuilddeps: Unmet build dependencies: swig (>= 2) libperl-dev octave-pkg-dev mono-devel mono-gmcs cli-common-dev cli-runtime
dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting
dpkg-buildpackage: warning: (Use -d flag to override.)
dpkg-buildpackage: warning: this is currently a non-fatal warning with -S, but will probably become fatal in the future
 fakeroot debian/rules clean
dh  clean --with-python2 --dbg-package=libsbml5-dbg
   dh_testdir -O--with-python2 -O--dbg-package=libsbml5-dbg
   debian/rules override_dh_auto_clean
make[1]: Entering directory `/home/andreas/debian-maintain/repack/libsmbl5/libSBML-5.10.0-Source'
### the clean target of the libsbml makefile is highly b0rken ###
### the switch to cmake didn't result in great approvements ###
### still inline changes of files ###
### very ugly ###
rm -rf .debs config docs examples macosx src config.guess config.sub build
find -maxdepth 1 -type f -delete
dh_clean
if [ -e ../libsbml_5.10.0+dfsg.orig.tar.xz ] ; then COMP=xz ; else COMP=gz ; fi ; \
	tar --no-same-owner -xaf ../libsbml_5.10.0+dfsg.orig.tar.${COMP} --strip-components=1
make[1]: Leaving directory `/home/andreas/debian-maintain/repack/libsmbl5/libSBML-5.10.0-Source'
   dh_clean -O--with-python2 -O--dbg-package=libsbml5-dbg
 dpkg-source -i.git -I.git -b libSBML-5.10.0-Source
dpkg-source: info: using source format `3.0 (quilt)'
dpkg-source: info: building libsbml using existing ./libsbml_5.10.0+dfsg.orig.tar.gz
dpkg-source: info: local changes detected, the modified files are:
 libSBML-5.10.0-Source/OLD_NEWS.txt
 libSBML-5.10.0-Source/config/makefile-common-actions.mk
 libSBML-5.10.0-Source/docs/CMakeLists.txt
 libSBML-5.10.0-Source/docs/src/libsbml-accessing.html
 libSBML-5.10.0-Source/src/bindings/csharp/csdoc.i
 libSBML-5.10.0-Source/src/bindings/csharp/csharp-files-win/Reaction.cs
 libSBML-5.10.0-Source/src/bindings/csharp/csharp-files-win/SBMLError.cs
 libSBML-5.10.0-Source/src/bindings/csharp/csharp-files-win/SBMLReader.cs
 libSBML-5.10.0-Source/src/bindings/csharp/csharp-files-win/SBase.cs
 libSBML-5.10.0-Source/src/bindings/csharp/csharp-files/Reaction.cs
 libSBML-5.10.0-Source/src/bindings/csharp/csharp-files/SBMLError.cs
 libSBML-5.10.0-Source/src/bindings/csharp/csharp-files/SBMLReader.cs
 libSBML-5.10.0-Source/src/bindings/csharp/csharp-files/SBase.cs
 libSBML-5.10.0-Source/src/bindings/java/java-files/org/sbml/libsbml/Reaction.java
 libSBML-5.10.0-Source/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
 libSBML-5.10.0-Source/src/bindings/java/java-files/org/sbml/libsbml/SBMLReader.java
 libSBML-5.10.0-Source/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
 libSBML-5.10.0-Source/src/bindings/java/javadoc.i
 libSBML-5.10.0-Source/src/bindings/matlab/FindMatlab.cmake
 libSBML-5.10.0-Source/src/bindings/matlab/Makefile.in
 libSBML-5.10.0-Source/src/bindings/matlab/mexopts-R2009-R2010.sh
 libSBML-5.10.0-Source/src/bindings/perl/LibSBML.pm
 libSBML-5.10.0-Source/src/bindings/perl/LibSBML.pod
 libSBML-5.10.0-Source/src/bindings/perl/Makefile.in
 libSBML-5.10.0-Source/src/bindings/python/libsbml-doxygen.py
 libSBML-5.10.0-Source/src/bindings/python/libsbml.py
 libSBML-5.10.0-Source/src/bindings/python/libsbml_wrap.cpp
 libSBML-5.10.0-Source/src/bindings/python/local.i
 libSBML-5.10.0-Source/src/bindings/python/pydoc-doxygen.i
 libSBML-5.10.0-Source/src/bindings/python/pydoc-normal.i
 libSBML-5.10.0-Source/src/sbml/Reaction.h
 libSBML-5.10.0-Source/src/sbml/SBMLReader.cpp
 libSBML-5.10.0-Source/src/sbml/SBMLReader.h
 libSBML-5.10.0-Source/src/sbml/SBase.h
 libSBML-5.10.0-Source/src/sbml/common/common-documentation.h
 libSBML-5.10.0-Source/src/sbml/packages/comp/validator/CompSBMLError.h
 libSBML-5.10.0-Source/src/sbml/packages/comp/validator/CompSBMLErrorTable.h
dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/libsbml_5.10.0+dfsg-1.diff.KtELfa
dpkg-source: info: you can integrate the local changes with dpkg-source --commit
dpkg-buildpackage: error: dpkg-source -i.git -I.git -b libSBML-5.10.0-Source gave error exit status 2
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