[Debian-med-packaging] Bug#668999: ImportError: No module named qiime.util

[Andreas Tille]

Hi Charles,

could you please build and try the current packaging in SVN and do
some tests.  With the current packaging it reads:

$ /usr/lib/qiime/bin/print_qiime_config.py

System information
==================
         Platform:      linux2
   Python version:      2.7.2+ (default, Nov 30 2011, 19:22:03)  [GCC 4.6.2]
Python executable:      /usr/bin/python

Dependency versions
===================
                     PyCogent version:  1.5.1
                        NumPy version:  1.5.1
                   matplotlib version:  1.1.1rc
                QIIME library version:  1.4.0
                 QIIME script version:  1.4.0
        PyNAST version (if installed):  1.1
RDP Classifier version (if installed):  Not installed.

QIIME config values
===================
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 642, in <module>
    main()
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 631, in main
    max_len =  max([len(key) for key in qiime_config])
ValueError: max() arg is an empty sequence



which is a bit better but has obvious issues as well.  I have no idea
how critical this might be but perhaps other things might work
sufficiently.

Kind regards

        Andreas.


On Mon, Apr 16, 2012 at 08:55:27PM +0900, Charles Plessy wrote:
> Package: qiime
> Version: 1.4.0-1
> Severity: normal
> 
> Hello everybody,
> 
> did I miss something, or is qiime not working out of the box ?
> Whatever the tool I try to run, I have an error such as in the
> following.
> 
>   $ /usr/lib/qiime/bin/print_qiime_config.py 
>   Traceback (most recent call last):
>     File "/usr/lib/qiime/bin/print_qiime_config.py", line 15, in <module>
>       from qiime.util import make_option
>   ImportError: No module named qiime.util
> 
> Cheers,
> 
> -- Charles
> 
> -- 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 2.6.39-bpo.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  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
> 
> 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
> 
> 
> 
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