[Debian-med-packaging] Bug#682198: qiime: Should depend on python >= 2.7.

[Andreas Tille]

Hi,

would you mind reporting this upstream?

Kind regards

       Andreas.

On Fri, Jul 20, 2012 at 05:52:49PM +0900, Charles Plessy wrote:
> Package: qiime
> Version: 1.5.0-1
> Severity: important
> 
> Hi all,
> 
> it looks like /usr/lib/qiime/bin/subsample_fasta.py needs a python
> library that is not in python 2.6.
> 
> $ /usr/lib/qiime/bin/subsample_fasta.py
> Traceback (most recent call last):
>   File "/usr/lib/qiime/bin/subsample_fasta.py", line 15, in <module>
>     from qiime.util import parse_command_line_parameters, get_options_lookup,\
>   File "/usr/lib/python2.6/dist-packages/qiime/util.py", line 25, in <module>
>     from collections import defaultdict, Counter
> ImportError: cannot import name Counter
> 
> After changing its first line to '#!/usr/bin/python2.7', the error dissapeared.
> 
> Cheers,
> 
> -- Charles Plessy, Tsurumi, Kanagawa, Japan.
> 
> 
> 
> -- System Information:
> Debian Release: wheezy/sid
>   APT prefers stable
>   APT policy: (910, 'stable'), (900, 'testing'), (800, 'unstable'), (500, 'stable-updates'), (1, 'experimental')
> Architecture: amd64 (x86_64)
> 
> Kernel: Linux 3.2.0-2-amd64 (SMP w/8 CPU cores)
> Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> 
> Versions of packages qiime depends on:
> ii  king                      2.21.120420-2  interactive system for three-dimen
> ii  libc6                     2.13-21        Embedded GNU C Library: Shared lib
> ii  libffi5                   3.0.9-3        Foreign Function Interface library
> ii  libgmp10                  2:5.0.2+dfsg-1 Multiprecision arithmetic library
> ii  pynast [python-pynast]    1.1-3          alignment of short DNA sequences
> ii  python                    2.6.6-14       interactive high-level object-orie
> ii  python-cogent             1.5.1-2        framework for genomic biology
> ii  python2.6                 2.6.6-8+b1     An interactive high-level object-o
> ii  python2.7                 2.7.3-2        Interactive high-level object-orie
> 
> Versions of packages qiime recommends:
> ii  ampliconnoise        1.25-1              Programs for the removal of noise 
> ii  blast2               1:2.2.21.20090809-2 Basic Local Alignment Search Tool
> ii  cd-hit               4.5.7-1             suite of programs designed to quic
> pn  chimeraslayer        <none>              (no description available)
> pn  fasttree             <none>              (no description available)
> ii  infernal             1.0.2-1             inference of RNA secondary structu
> ii  muscle               1:3.8.31-1          Multiple alignment program of prot
> ii  python-matplotlib    1.1.0-1             Python based plotting system in a 
> ii  python-numpy         1:1.5.1-3           Numerical Python adds a fast array
> pn  rdp-classifier       <none>              (no description available)
> 
> Versions of packages qiime suggests:
> pn  cytoscape                   <none>       (no description available)
> ii  t-coffee                    9.02.r1228-2 Multiple Sequence Alignment
> 
> -- no debconf information
> 
> -- debsums errors found:
> debsums: changed file /usr/lib/qiime/bin/subsample_fasta.py (from qiime package)
> 
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