Hi Tássia,

thanks for having a look into prottest autopkgtest.  Your research into
the docs helped to write some sensible test.  I took the freedom to
enhance it a bit.

  1. The Debian Med team provides a wrapper script /usr/bin/prottest
     which saves the user the typing of `java -jar ...`.  This is
     what I used in the test.

  2. In my pbuilder invironment the test is started as root which
     conflicts with MPI (which is used in phyml).  Adding some
     variables[1] enabled this.

Now the test is passing.  However, I'm stumbling upon the lines

   Model optimization exception: there was an error while executing there was 
an error parsing PhyML stats file: Stats file does not exist. Please check if 
PhyML is working.

which are printed here[2] and which make me wonder whether prottest is
working fully correctly or whether there is some issue to fix.  May be
some Java programmer might have a look and could debug the output of
phyml which might be not as expected?

Moreover I realised that there seems to be another issue:

$ runXProtTestHPC 
Error: Could not find or load main class es.uvigo.darwin.xprottest.XProtTestApp
Caused by: java.lang.NoClassDefFoundError: 
org/jdesktop/application/SingleFrameApplication


Pierre, could you lend a helping hand here?

Kind regards

     Andreas.

PS: Tássia, I also uploaded the changelog to make the entry featuring
    the autopkgtest yours.  Please verify that this is the e-mail
    address that should show up for you.

[1] 
https://salsa.debian.org/med-team/prottest/-/blob/master/debian/tests/run-unit-test#L14
[2] 
https://salsa.debian.org/med-team/prottest/-/blob/master/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java#L383

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