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.supp...@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.
