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

[Sascha Steinbiss]

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.
>>
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>>
> 


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