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 >>> [email protected] >>> 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 >>> [email protected] >>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging >>> >> -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
