[Debian-med-packaging] Bug#775621: python-biopython: FTBFS in jessie: Tests failures

Andreas Tille tille at debian.org
Mon Jan 19 12:34:00 UTC 2015

Hi Alexandros,


Thanks a lot for your very prompt response.  Its fun to work together
with upstream developers like you.  Please note that since we are
currently in Freeze for the next stable release this new version will
not be part of the next stable release but will be available in
Debian experimental soon.

Thanks again


On Mon, Jan 19, 2015 at 01:26:49PM +0100, Alexandros Stamatakis wrote:
> okay, RAxML will now set the number of threads to 2 if -T is not
> specified, it's available in RAxML v 8.1.16 that I just pushed to
> github,
> alexis
> On 19.01.2015 12:43, Andreas Tille wrote:
> >On Mon, Jan 19, 2015 at 11:40:39AM +0100, Alexandros Stamatakis wrote:
> >>Dear All,
> >>
> >>I am not exactly sure what you need, do you want the
> >>Pthreads-version to automatically set the number of threads to 2 if
> >>the -T option is not specified?
> >>
> >>If that's the case I can easily fix this.
> >
> >It would be great if all flavours of raxmlHPC would be able to run
> >without the -T option (by setting a decent default) since wrappers like
> >BioPython (and probably others) do not use -T.  This would be a solution
> >that is helpful for all distributions.  For our specific case in Debian
> >there would be an alternative solution that the -T option would be
> >simply ignored on machines with no Pthreads support (instead of throwing
> >an error).  Please find any solution which makes all binaries compatible
> >regarding the options you are allowed to add to the command line.
> >
> >Thanks for your quick response
> >
> >          Andreas.
> >
> -- 
> Alexandros (Alexis) Stamatakis
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
> www.exelixis-lab.org


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