Your message dated Tue, 02 Apr 2019 09:35:23 +0000
with message-id <[email protected]>
and subject line Bug#925909: fixed in pbgenomicconsensus 2.3.2-2
has caused the Debian Bug report #925909,
regarding pbgenomicconsensus: autopkgtest regression
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
925909: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925909
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: pbgenomicconsensus
Version: 2.3.2-1
Severity: serious
X-Debbugs-CC: [email protected]
User: [email protected]
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/
--- End Message ---
--- Begin Message ---
Source: pbgenomicconsensus
Source-Version: 2.3.2-2
We believe that the bug you reported is fixed in the latest version of
pbgenomicconsensus, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated pbgenomicconsensus
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 02 Apr 2019 11:02:18 +0200
Source: pbgenomicconsensus
Binary: pbgenomicconsensus python-pbgenomicconsensus
Architecture: source
Version: 2.3.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
pbgenomicconsensus - Pacific Biosciences variant and consensus caller
python-pbgenomicconsensus - Pacific Biosciences variant and consensus caller
(Python 2)
Closes: 925909
Changes:
pbgenomicconsensus (2.3.2-2) unstable; urgency=medium
.
[ Afif Elghraoui ]
* Remove myself from Uploaders
.
[ Andreas Tille ]
* Add myself to Uploaders
* python-pbgenomicconsensus Depends: python-pbconsensuscore
* Test Depends: poa
* Ignore some warnings which are breaking test results, remove
tests that are based on non-existing input data
* Move exclusion of tests to upstream Makefile via patch rather than
in d/rules. This is needed to run autopkgtest successfully
Closes: #925909
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