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

[Olivier Sallou]

----- 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
>    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?
> 
I will have a look

Regarding maven, it is not easy in Debian, but we should be able to keep ant build with a build.xml file.

Olivier

> 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
>