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

[Andreas Tille]

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?

Kind regards

      Andreas.

[1] https://github.com/beast-dev/beast-mcmc/blob/master/lib/mtj.jar
[2] https://github.com/fommil/netlib-java

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