[Debian-med-packaging] Bug#917143: t-coffee breaks libbio-tools-run-alignment-tcoffee-perl autopkgtest: COREDUMP

[Carnë Draug]

On Fri, 1 Feb 2019 at 14:20, Andreas Tille <andreas at an3as.eu> wrote:
>
> Hi,
>
> I tried to have a look at the issue caused by t-coffee 12 which became
> visible in the smoke test of libbio-tools-run-alignment-tcoffee-perl.
> Liubov had checked it before and filed an issue upstream[1] but at my
> side the test to reproduce the bug does not fail.

The t-coffee tests fail on their own.  I don't know why you can't
reproduce it.  See the results for the latest failure:

    https://ci.debian.net/data/autopkgtest/unstable/amd64/t/t-coffee/1817091/log.gz

of for the previous runs:

    https://ci.debian.net/packages/t/t-coffee/unstable/amd64/

> I wonder if someone
> from the Perl team would be able to iron out the actual t-coffee call
> that causes the coredump.  If we would have some
>
>    t-coffee options / args
>      --> COREDUMP
>
> we could start to run this through gdb.  If I do not get any help of
> this kind I have no idea to hunt this down.
>

The results from the last autopkgtests show that it's this command
that fails:

    t_coffee -aln sproteases_small.cw_aln sproteases_small.muscle \
        sproteases_small.tc_aln -outfile combined_aln.aln

The test script is part of t-coffee:

    https://salsa.debian.org/med-team/t-coffee/blob/master/debian/tests/run-unit-test

If the command on its own does not fail, maybe it needs to
be ran in series after the others?

Maybe not related, but something odd that I noticed is that the '='
does not appear in the log of the test suite.  While the test script
has:

    -outfile=combined_aln.aln

The logs only show:

    -outfile combined_aln.aln