Hi Peter, On Mon, Feb 01, 2016 at 11:25:13AM +0000, Peter Cock wrote: > 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
Thanks a lot for watching! > 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, Yes. BioPython is OK - I need to reassign the bug - probably to libhmsbeagle-dev which is possibly not featuring the correct dependencies. I just wanted to investigate the issue before I do the reassigning since for the moment it is just the BioPython *package* *in* *debian* that fails. > 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 I agree that we could add this check even to the phyml package. > 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 My plan for this years GSoC is to find a student who could add as much testing to Debian Med packages as possible. In this sense BioPython is a great test suite since it somehow adds tests to those packages that come without one. :-) Thanks again for getting involved into this bug report. I think I will use the upcoming Debian Med sprint[1] to sort these things out. Kind regards Andreas. [1] https://wiki.debian.org/Sprints/2016/DebianMed2016 -- http://fam-tille.de
