[Debian-med-packaging] Help getting missing classes found by prottest

[Andreas Tille]

Hi

On Fri, Oct 16, 2015 at 11:32:18PM +0200, Emmanuel Bourg wrote:
> Le 16/10/2015 23:26, Markus Koschany a écrit :
> 
> > P.S.: Please note that the swing-worker.jar is still imported from the
> > libs directory. I don't know if this one is already packaged for Debian.
> 
> I don't think we have it, but SwingWorker is a standard class of the JDK
> since Java 6, it should be easy to adapt the code to use it.

Thanks to Markus's patch I was able to build the package.  However,
after now removing all *.jar files I have a new problem:

...
-do-jar-with-libraries:
    
BUILD FAILED
/build/prottest-3.4+dfsg/buildconf/build-impl.xml:595: The following error occurred while executing this line:
/build/prottest-3.4+dfsg/buildconf/build-impl.xml:429: taskdef class org.netbeans.modules.java.j2seproject.copylibstask.CopyLibs cannot be found
 using the classloader AntClassLoader[]

Total time: 4 seconds
dh_auto_build: ant returned exit code 1
...


How can I resolve this netbeans dependency?

Moreover I have no idea how to tweak

    src/main/resources/runProtTestHPC.sh

which I copied to debian/bin to properly use mpj.  It is referencing a
mpjrun.sh script that was part of the (now also removed code copy of mpj)
which in turn uses a starter.jar that is not part of the libmpj-java
package:

    java -jar $MPJ_HOME/lib/starter.jar "$@"

I wonder how to easily use prottest mpi features (once the build problem
might be solved).

Thanks for any help

    Andreas.

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