[Debian-med-packaging] [tille at debian.org: Re: Bug#820308: qiime: many unsatisfiable dependencies]

[Andreas Tille]

Hi Tim,

On Mon, Apr 11, 2016 at 05:14:34PM +0100, Tim Booth wrote:
> My e-mail address expired when I left my old job, and I've not done
> anything substantial regarding Bio-Linux or Debian packaging since that
> date.  My plan when I moved jobs was to take a 6 month break from
> anything packaging related in order to give my full attention to my new
> job, which is requiring me to learn a lot of new things.  I'm still
> sticking to that plan, so you should start to hear more from me after
> June.

Fully understood.
 
> Having said that, I don't want to leave you floundering with QIIME so
> I'll try to help.

Thanks a lot.

> The bad news is that the upstream developers seem to
> have abandoned fixing the mess that we discussed back in October, and
> they are proceeding to a ground-up rewrite as QIIME 2.  This leaves us
> with QIIME 1.9.1 which is a mess but nevertheless a lot of people want
> to use it and it is not going to go away soon.  Plus I did have it
> working under Ubuntu 14.04, even if Lintian was not entirely happy with
> my packages.
> 
> The key package here is python-burrito-fillings.  It comes with a test
> suite which is not comprehensive but nevertheless is useful.  I see you
> modified the package so presumably you did a local test build.  What was
> the result of doing that?  Did it build and self-test OK?

No.  When Itry to build the current state in SVN I get errors like

...
raxml should raise exception if missing required params ... ok

======================================================================
ERROR: bfillings.tests.test_vsearch (unittest.loader.ModuleImportFailure)
----------------------------------------------------------------------
ImportError: Failed to import test module: bfillings.tests.test_vsearch
Traceback (most recent call last):
  File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests
    module = self._get_module_from_name(name)
  File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name
    __import__(name)
  File "bfillings/tests/test_vsearch.py", line 23, in <module>
    from skbio.parse.sequences import parse_fasta
ImportError: No module named parse.sequences


======================================================================
ERROR: bfillings.tests.test_blast (unittest.loader.ModuleImportFailure)
----------------------------------------------------------------------
ImportError: Failed to import test module: bfillings.tests.test_blast
Traceback (most recent call last):
  File "/usr/lib/python2.7/unittest/loader.py", line 254, in _find_tests
    module = self._get_module_from_name(name)
  File "/usr/lib/python2.7/unittest/loader.py", line 232, in _get_module_from_name
    __import__(name)
  File "bfillings/tests/test_blast.py", line 18, in <module>
    from bfillings.blast import (seqs_to_stream, make_subject_match_scorer,
  File "bfillings/blast.py", line 21, in <module>
    from skbio.parse.sequences.fasta import FastaFinder, is_fasta_label
ImportError: No module named parse.sequences.fasta


...


This somehow locked like missing python-biopython (which I added but
failed with the same error).

Any hint?

Kind regards

       Andreas.
 

-- 
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