[Debian-med-packaging] Bug#818584: Bug#818584: ImportError: No module named pyyaml2

[Sascha Steinbiss]

I have just pushed come changes to git. Feel free to try (and upload) if
that solves your problem, Afif.

Cheers
Sascha


On 18/03/2016 14:20, Sascha Steinbiss wrote:
> Hi Afif and Andreas,
> 
> I think that this is it. If you look at the spades patch
> 0001_use_debian_packaged_python-yaml.patch this seems to have been done
> in several places already. The ones causing this bug seem to have been
> missed because they probably were not covered by the spades tests.
> 
> Cheers
> Sascha
> 
> On 18/03/2016 12:24, Andreas Tille wrote:
>> I've currently no sensible internet access and can't sensibly check.  I
>> have solved this issue on my previous attempts by a patch which was
>> quite simple: Spades is shipping its own copies of the python module.
>> You simply need to drop the 2 / 3 in the module name.  Just grep for
>> the string and replace it my the canonical Debian name of the module
>> where no Python version distinction is needed.
>> Hope this helps
>>     Andreas.
>>
>> On Fri, Mar 18, 2016 at 02:18:23AM -0700, Afif Elghraoui wrote:
>>> Package: spades
>>> Version: 3.7.1+dfsg-1
>>> Severity: important
>>> Control: block 818575 by -1
>>>
>>> Tests for the circlator package in progress failed while runnining spades:
>>>
>>> ~~~
>>>   0:00:47.008    92M / 484M  INFO    General                 (path_extend_launch.hpp    : 247)   Traversing tandem repeats
>>>   0:00:47.008    92M / 484M  INFO   PathExtendIO             (pe_io.hpp                 : 190)   Writing contigs to /tmp/adt-run.gG5zgN/build.2PK/circlator-1.2.0/test/test-dir/OUT/03.assemble.tmp.spades.107.c0mblm8f//K107/scaffolds
>>>   0:00:47.061    92M / 484M  INFO    General                 (launch.hpp                : 114)   SPAdes finished
>>>   0:00:47.068    84M / 484M  INFO    General                 (main.cpp                  : 169)   Assembling time: 0 hours 0 minutes 47 seconds
>>>
>>> ===== Assembling finished. 
>>>
>>>
>>> ===== Mismatch correction started.
>>>
>>> == Processing of contigs
>>>
>>> No module named pyyaml2
>>> Traceback (most recent call last):
>>>   File "/usr/lib/spades/bin/spades.py", line 844, in main
>>>     ext_python_modules_home, log, assembled, result_corrected_filename)
>>>   File "/usr/share/spades/spades_pipeline/corrector_logic.py", line 43, in run_corrector
>>>     import pyyaml2 as pyyaml
>>> ImportError: No module named pyyaml2
>>>
>>>
>>> == Error ==  exception caught: <type 'exceptions.ImportError'>
>>>
>>> In case you have troubles running SPAdes, you can write to spades.support at bioinf.spbau.ru
>>> Please provide us with params.txt and spades.log files from the output directory.
>>> ~~~
>>>
>>> Although spades declares a dependency on python-yaml, either the import statement needs to be patched to say "import yaml" (if the interface is the same), or this other python yaml library may need to be packaged.
>>>
>>> _______________________________________________
>>> Debian-med-packaging mailing list
>>> Debian-med-packaging at lists.alioth.debian.org
>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>>>
>>


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