Autopkgtest for prottest
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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