[Debian-med-packaging] Bug#813262: python-biopython: FTBFS: ApplicationError: Non-zero return code 255 from 'phyml -i Phylip/interlaced2.phy -d aa'

[Peter Cock]

Hi all,

I spotted this via an automated @DebianBug Twitter posting:
https://twitter.com/DebianBug/status/693569490655776768
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=813262

Andreas has dealt with other issues like this in the past, but
I wanted to make this explicit on the issue tracker:

This isn't a problem in Biopython itself, but a Biopython test
case calling phyml indicates there is a problem with the Debian
phyml package.

Should the phyml GPU problem be filed under the phyml Debian
package, perhaps adding a simple basic check to its tests?:

phyml -i Phylip/interlaced2.phy -d aa

This sample input test file is available here, also used as an example
in the EMBOSS suite:

https://github.com/biopython/biopython/blob/master/Tests/Phylip/interlaced2.phy

I suspect any PHYLIP input file would work for checking the
binary works and might help catch this apparent compilation
issue earlier. Looking over the upstream Makefile it was not
obvious that there is any testing like this being done at the
moment, but there are example files likely to be useful for
adding such a test:

https://github.com/stephaneguindon/phyml

Thanks,

Peter
(Biopython developer)