Your message dated Sat, 10 May 2014 06:34:14 +0000
with message-id <[email protected]>
and subject line Bug#747494: fixed in python-biopython 1.63+dfsg-5
has caused the Debian Bug report #747494,
regarding python3-biopython: Does not use C implementations of cpairwise2
functions
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
747494: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=747494
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.63+dfsg-5
We believe that the bug you reported is fixed in the latest version of
python-biopython, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated python-biopython package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sat, 10 May 2014 07:52:48 +0200
Source: python-biopython
Binary: python-biopython python3-biopython python-biopython-doc
python-biopython-sql python3-biopython-sql
Architecture: source amd64 all
Version: 1.63+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
python-biopython - Python library for bioinformatics (implemented in Python 2)
python-biopython-doc - Documentation for the Biopython library
python-biopython-sql - Biopython support for the BioSQL database schema
(Python 2)
python3-biopython - Python library for bioinformatics (implemented in Python 3)
python3-biopython-sql - Biopython support for the BioSQL database schema
(Python 3)
Closes: 747494
Changes:
python-biopython (1.63+dfsg-5) unstable; urgency=medium
.
* Apply upstream fix to fix cpairwise2 import issue under python3
Closes: #747494
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