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

Fri Jun 27 14:03:47 UTC 2014

Hi Ivo,

ping?  Any idea how we could proceed here?

Kind regards

        Andreas.

On Mon, May 05, 2014 at 03:14:10PM +0200, Andreas Tille wrote:
> 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

> 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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-- 
http://fam-tille.de