[Debian-med-packaging] Bug#925909: pbgenomicconsensus: autopkgtest regression

[Graham Inggs]

Source: pbgenomicconsensus
Version: 2.3.2-1
Severity: serious
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: regression

Hi Maintainer

Since the upload of 2.3.2-1, pbgenomicconsensus has been failing its own 
autopkgtests [1] with the following error:

autopkgtest [12:23:51]: test command2: [-----------------------
# Tests that need to be run by Jenkins but are slowing
# down the development cycle, so aren't run by "tests"
# target.
PATH=`pwd`:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games cram 
--verbose --xunit-file=gc-extra-cram.xml `ls tests/cram/extra/*.t | grep 
-v arrow`
tests/cram/extra/plurality-fluidigm.t: failed
--- tests/cram/extra/plurality-fluidigm.t
+++ tests/cram/extra/plurality-fluidigm.t.err
@@ -8,12 +8,26 @@
  Set the QV threshold to 10.

    $ variantCaller --algorithm=plurality -r $REFERENCE -q 10 -o 
variants.gff -o consensus.csv -o consensus.fastq $INPUT
+  Traceback (most recent call last):
+    File "/usr/bin/variantCaller", line 3, in <module>
+      from GenomicConsensus.main import main
+    File "/usr/lib/python2.7/dist-packages/GenomicConsensus/main.py", 
line 16, in <module>
+      from GenomicConsensus import reference
+    File 
"/usr/lib/python2.7/dist-packages/GenomicConsensus/reference.py", line 
8, in <module>
+      from .windows import holes, kCoveredIntervals, enumerateIntervals
+    File 
"/usr/lib/python2.7/dist-packages/GenomicConsensus/windows.py", line 14, 
in <module>
+      from ConsensusCore import CoveredIntervals
+  ImportError: No module named ConsensusCore
+  [1]

  There are two true SNVs (and one diploid SNV that we miss right now).

    $ grep insertion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep deletion variants.gff | wc | awk '{print $1}'
+  grep: variants.gff: No such file or directory
    0
    $ grep substitution variants.gff
- 
EGFR_Exon_23\t.\tsubstitution\t48\t48\t.\t.\t.\treference=T;variantSeq=C;frequency=97;coverage=100;confidence=40 
(esc)
+  grep: variants.gff: No such file or directory
+  [2]
# Ran 1 tests, 0 skipped, 1 failed.
make: *** [Makefile:25: extra-tests] Error 1
autopkgtest [12:23:52]: test command2: -----------------------]
autopkgtest [12:23:52]: test command2:  - - - - - - - - - - results - - 
- - - - - - - -
command2             FAIL non-zero exit status 2

Regards
Graham


[1] https://ci.debian.net/packages/p/pbgenomicconsensus/unstable/amd64/