Your message dated Sat, 06 Apr 2019 10:18:35 +0000
with message-id <e1hcipd-000agd...@fasolo.debian.org>
and subject line Bug#925909: fixed in pbgenomicconsensus 2.3.2-4
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
925909: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=925909
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: pbgenomicconsensus
Version: 2.3.2-1
Severity: serious
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@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/
--- End Message ---
--- Begin Message ---
Source: pbgenomicconsensus
Source-Version: 2.3.2-4
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 925...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 06 Apr 2019 11:16:49 +0200
Source: pbgenomicconsensus
Architecture: source
Version: 2.3.2-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 925909
Changes:
pbgenomicconsensus (2.3.2-4) unstable; urgency=medium
.
* Fix dependencies
Closes: #925909
* unset GZIP in autopkgtest
Checksums-Sha1:
06f6ec6a5ac0aad5177fadc186b420ffc328dabe 2491 pbgenomicconsensus_2.3.2-4.dsc
50786c80d8b3610372d3e7c4bf90c28da55f99c1 20716
pbgenomicconsensus_2.3.2-4.debian.tar.xz
eefe2c79d5720e041db99ed1dc01b9be22e851df 8515
pbgenomicconsensus_2.3.2-4_amd64.buildinfo
Checksums-Sha256:
88397563f058189468182f93c6fbd2f0b09d2da50736b74d99c0506733c82b77 2491
pbgenomicconsensus_2.3.2-4.dsc
f43bc2527928c224bf07f891030190b95aafcd0402df09d3cfed9a40d20c6bc3 20716
pbgenomicconsensus_2.3.2-4.debian.tar.xz
89574343d7365ed5ad4fb295d2d65a9daf572064195d2f142fc5c59810d53897 8515
pbgenomicconsensus_2.3.2-4_amd64.buildinfo
Files:
1ed52cce75cadb23439c76e9625ef80e 2491 science optional
pbgenomicconsensus_2.3.2-4.dsc
4cea3a8d9c32862eb466b249ae620c9b 20716 science optional
pbgenomicconsensus_2.3.2-4.debian.tar.xz
5226f2133c90ec1b172243ab9059fb0b 8515 science optional
pbgenomicconsensus_2.3.2-4_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=VFh2
-----END PGP SIGNATURE-----
--- End Message ---
