[Debian-med-packaging] Bug#747494: python3-biopython: Does not use C implementations of cpairwise2 functions

[Andreas Tille]

Hi Jamie,

thanks for your bug report.  I think this should work out of the box but
I personally not comfortable with cpython to know how this could be
fixed.  I keep the Debian Python list in CC - perhaps they might have
some helpful advise.

It seems this module is not affected by the test suite since this runs
fine.  If you would like to help making sure that this will be detected
soon before we upload in the future it might make sense if you could
provide a test case to the upstream developers who could include this
test in their unit tests.

Kind regards

       Andreas.

On Fri, May 09, 2014 at 10:08:15PM +1200, Jamie Norrish wrote:
> Package: python3-biopython
> Version: 1.63+dfsg-4
> Severity: normal
> 
> Dear Maintainer,
> 
> After installing this package, the cpairwise2 C implementations of
> functions are not available (see the end of Bio/pairwise2.py for the
> attempted loading of these):
> 
> Python 3.3.5 (default, Mar 22 2014, 13:24:53)
> [GCC 4.8.2] on linux
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from cpairwise2 import rint
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> ImportError: No module named 'cpairwise2'
> 
> But some (presumably relevant; I know nothing about how Python
> interfaces with C code) files are installed:
> 
> $ locate pairwise2
> /usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-33m-x86_64-linux-gnu.so
> /usr/lib/python3/dist-packages/Bio/cpairwise2.cpython-34m-x86_64-linux-gnu.so
> 
> Is this meant to work out of the box, or is there some action I can and
> should take to be able to take advantage of the C implementation?
> 
> Thanks,
> 
> Jamie
> 
> -- System Information:
> Debian Release: jessie/sid
>   APT prefers unstable
>   APT policy: (500, 'unstable')
> Architecture: amd64 (x86_64)
> Foreign Architectures: i386
> 
> Kernel: Linux 3.14-1-amd64 (SMP w/4 CPU cores)
> Locale: LANG=en_NZ.utf8, LC_CTYPE=en_NZ.utf8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> 
> Versions of packages python3-biopython depends on:
> ii  libc6                               2.18-5
> ii  python3                             3.3.4-1
> ii  python3-numpy [python3-numpy-abi9]  1:1.8.1-1
> ii  python3-reportlab                   3.0-1
> pn  python3:any                         <none>
> 
> Versions of packages python3-biopython recommends:
> pn  ncbi-blast+           <none>
> ii  python-biopython-doc  1.63+dfsg-4
> 
> Versions of packages python3-biopython suggests:
> pn  bwa                 <none>
> pn  clustalo            <none>
> pn  clustalw            <none>
> pn  dialign             <none>
> pn  dssp                <none>
> pn  emboss              <none>
> pn  fasttree            <none>
> pn  mafft               <none>
> pn  muscle              <none>
> pn  phyml               <none>
> pn  prank               <none>
> pn  probcons            <none>
> ii  python-matplotlib   1.3.1-1+b1
> ii  python-mysqldb      1.2.3-2
> ii  python-numpy        1:1.8.1-1
> ii  python-pil          2.3.0-2
> ii  python-psycopg2     2.5.2-1
> pn  python-rdflib       <none>
> ii  python-renderpm     3.0-1
> ii  python-reportlab    3.0-1
> ii  python3-matplotlib  1.3.1-1+b1
> ii  python3-pil         2.3.0-2
> ii  python3-psycopg2    2.5.2-1
> pn  python3-renderpm    <none>
> ii  python3-tk          3.3.4-1
> pn  raxml               <none>
> pn  t-coffee            <none>
> pn  wise                <none>
> 
> -- no debconf information
> 
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