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

[Andreas Tille]

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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