[Debian-med-packaging] Bug#947463: bio-tradis: autopkgtest regression: Use of uninitialized value $total_uis (and lots of mv: cannot stat '/tmp/aut.....)

[Michael Crusoe]

Control: forwarded -1
https://github.com/sanger-pathogens/Bio-Tradis/issues/116


On Fri, 27 Dec 2019 11:42:05 +0100 Paul Gevers <elbrus at debian.org> wrote:
> Dear maintainers,
>
> With a recent upload of bio-tradis the autopkgtest of bio-tradis fails
> in testing when that autopkgtest is run with the binary packages of
> bio-tradis from unstable. It passes when run with only packages from
> testing.

Why are we mixing testing scripts and binaries?

> Additionally, looking at the failure mode in unstable, it seems some
> package (samtools?) made your (test?) dependencies non-installable in
> unstable. You probably need to fix that as well, or raise the issue with
> the samtools maintainer.

Yes, we did this. bio-tradis has a version parsing bug and it thinks that
samtools 1.10 is older than samtools 1.0, thus passing arguments to
samtools in the wrong form

This has been fixed in https://salsa.debian.org/med-team/bio-tradis but
there are other test issues, so I've asked upstream to investigate their
seriousness at https://github.com/sanger-pathogens/Bio-Tradis/issues/116
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