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

Alexandros Stamatakis alexandros.stamatakis at gmail.com
Mon Jan 19 12:26:49 UTC 2015

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,


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


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