[Debian-med-packaging] Problems with libmtj-java and new version of beast-mcmc

[Andreas Tille]

Hi,

any news about this?

Kind regards

     Andreas.

On Wed, Sep 02, 2015 at 10:46:00AM +0200, Olivier Sallou wrote:
> 
> 
> ----- Mail original -----
> > De: "Andreas Tille" <andreas at an3as.eu>
> > À: "Olivier Sallou" <olivier.sallou at irisa.fr>, "Debian Med Packaging Team"
> > <debian-med-packaging at lists.alioth.debian.org>
> > Envoyé: Mardi 1 Septembre 2015 13:51:17
> > Objet: Problems with libmtj-java and new version of beast-mcmc
> > 
> > Hi Olivier,
> > 
> > I have updated beast-mcmc to latest upstream version (in
> > testing/unstable as well as jessie-backports).  A local user stumbled upon
> > a problem that is connected to the Debian packaged version of libmtj-java
> > that does not contain all classes as the lib/mtj.jar[1] from upstream.
> > The latter provides classes in
> > 
> >    org/netlib/util
> > 
> > which are part of the Debian package libnetlib-java in
> > /usr/share/java/netlib-java.jar.  Unfortunately it seems that the Beast
> > upstream found a newer version of netlib-java to include into mtj.jar
> > than we have packaged for Debian.
> > 
> >    Exception in thread "Thread-1" java.lang.NoClassDefFoundError:
> >    org/netlib/util/intW
> > 
> > Unfortunately I was not able to reproduce this problem with the example
> > data sets inside Beast - feel free to ping me in private to reproduce
> > this issue.
> > 
> > The class org/netlib/util/intW is not part of the netlib version we have
> > packaged for Debian.  However, if I try to upgrade libnetlib-java for
> > Debian (we are lagging several versions behind upstream since it was
> > moved to Github[2]) I'm running into two types of trouble:
> > 
> >    1. The latest version also does not have org/netlib/util/intW
> 
> Seems to be part of f2j software
> 
> http://icl.cs.utk.edu/projectsfiles/f2j/javadoc/org/netlib/util/intW.html
> 
> Olivier
> 
> >    2. I would need to change the packaging of libnetlib-java
> >       from ant to maven (and I was not very lucky with this in
> >       the past.
> > 
> > Any idea how we could provide org/netlib/util/intW?
> > 
> > Kind regards
> > 
> >       Andreas.
> > 
> > [1] https://github.com/beast-dev/beast-mcmc/blob/master/lib/mtj.jar
> > [2] https://github.com/fommil/netlib-java
> > 
> > --
> > http://fam-tille.de
> >
> 
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