Your message dated Fri, 9 May 2014 13:28:40 +0200 with message-id <[email protected]> and subject line Re: Bug#747494: python3-biopython: Does not use C implementations of cpairwise2 functions 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 message is talking about, this may indicate a serious mail system 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
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--- Begin Message ---Thanks to the hint of Piotr I'm closing this bug report since from Bio.cpairwise2 import rint works nicely. Thanks for your report anyway Andreas. On Fri, May 09, 2014 at 01:21:05PM +0200, Piotr Ożarowski wrote: > [Andreas Tille, 2014-05-09] > > > >>> 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 > > Bio.cpairwise2 != cpairwise2 > -- > Piotr Ożarowski Debian GNU/Linux Developer > www.ozarowski.pl www.griffith.cc www.debian.org > GPG Fingerprint: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645 > > _______________________________________________ > Debian-med-packaging mailing list > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
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