Your message dated Sun, 07 Apr 2019 15:33:36 +0000
with message-id <e1hd9nc-000awn...@fasolo.debian.org>
and subject line Bug#925909: fixed in pbgenomicconsensus 2.3.2-5
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: 2.3.2-5
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.
Liubov Chuprikova <chuprikov...@gmail.com> (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: SHA256
Format: 1.8
Date: Sun, 07 Apr 2019 13:58:37 +0200
Source: pbgenomicconsensus
Binary: pbgenomicconsensus python-pbgenomicconsensus
Architecture: source
Version: 2.3.2-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Liubov Chuprikova <chuprikov...@gmail.com>
Description:
pbgenomicconsensus - Pacific Biosciences variant and consensus caller
python-pbgenomicconsensus - Pacific Biosciences variant and consensus caller
(Python 2)
Closes: 925909
Changes:
pbgenomicconsensus (2.3.2-5) unstable; urgency=medium
.
* Team upload.
* Fix autopkgtest dependencies
Closes: #925909
Checksums-Sha1:
3b66aefda41a10c6efc0bbb68eb4e9da02363c02 2525 pbgenomicconsensus_2.3.2-5.dsc
000ae613a5a54419564121511da922a75d1c04e6 20772
pbgenomicconsensus_2.3.2-5.debian.tar.xz
Checksums-Sha256:
72f282022832c82562cf590ccf7e0f9c92288db0c93eadb5a080b7e3d8cbc585 2525
pbgenomicconsensus_2.3.2-5.dsc
efd370ef90861470ea8c577c00e882a586722b7fe73eeba8fb6aaa08402e35ff 20772
pbgenomicconsensus_2.3.2-5.debian.tar.xz
Files:
9b769eb69fdc620a7af8d39aa771e948 2525 science optional
pbgenomicconsensus_2.3.2-5.dsc
5e418bfd3e208daf731fa54c3de52a81 20772 science optional
pbgenomicconsensus_2.3.2-5.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
iQJCBAEBCAAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlyqFGcOHHRpbGxlYUBy
a2kuZGUACgkQV4oElNHGRtH1tg/8CzJiuxvbVpvf31t/S8yf7tkBRSy4O+6dwfUf
pla44dBj6UfOc9j9zVEDdqKh1R9IpIHE3I44It7tcmCi/ijcZHvICziLKkxF/fYa
kCIhtoiBL/5e3vE+SEGjrdZrJx45OydttP2ac+fU5Yb5WVvV6feBK8SC7nR/6+F7
3/KOyEXlEsj+SO3Mwr0U6KPoBfI1TcYQD2mUQvWxL9Pq7YIF+FlDYctVHPG35zmS
mPEisixMh5agxmWIdGzkc293kFr5/+8Fps5VwX0lB6vq9HsKv3cBG4zl8Htwx0Xn
jnSGUT1qTjitb47WeEXSNEnUSj6BdwNTfMN4tk5V4P6BrWJEbyWOMZpNPqPwm/6v
cDsnk9PosqvBZVSshnoC+Xdpzjbt+4K4+VueZ62LlHpQM1XvW3isOidz0IwOt4jw
CWW5kEmzCz4qARdpfqvpBasNaOW+Zr3uSuUT7ZvjWzDuamnTSJCuYkmSAPmDYSJX
pqILdfcasaxWM1X1ZMr5zrYZDzCXhAWxPoe01ZzMSD1GA/NBhfWgWOjM70v4Lioc
85e/c8JgIetAIuj1Ndfz5ttoIb1gbxTF9NscD/7b6zcsL2lsXsENCTJF8Wx5tBIa
4cRt4jt84pP2uDmbfdQpfNV6irAuc0em32ZhMdp2Zs9hqZe3QOoV3PBod9jE35CU
ZvnT/0A=
=lbE1
-----END PGP SIGNATURE-----
--- End Message ---
