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

[Jamie Norrish]

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