Your message dated Mon, 18 May 2020 08:19:39 +0000
with message-id <e1jaazr-000agc...@fasolo.debian.org>
and subject line Bug#958840: fixed in kmer 0~20150903+r2013-8
has caused the Debian Bug report #958840,
regarding kmer: autopkgtest regression: No module named 'localAlignerInterface'
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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--
958840: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=958840
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: kmer
Version: 0~20150903+r2013-7
X-Debbugs-CC: debian...@lists.debian.org
Severity: serious
User: debian...@lists.debian.org
Usertags: regression
Dear maintainer(s),
With a recent upload of kmer the autopkgtest of kmer fails in testing
when that autopkgtest is run with the binary packages of kmer from
unstable. It passes when run with only packages from testing. In tabular
form:
pass fail
kmer from testing 0~20150903+r2013-7
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration to testing [1]. Can
you please investigate the situation and fix it?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=kmer
https://ci.debian.net/data/autopkgtest/testing/amd64/k/kmer/5152781/log.gz
autopkgtest [14:11:18]: test atac-unit-test: [-----------------------
Rewriting
'/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/GCF_000195855.1_ASM19585v1_genomic.fna'
to
'/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Lepr.fasta',
removing newlines.
Rewriting
'/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/GCF_000195955.2_ASM19595v2_genomic.fna'
to
'/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Tuber.fasta',
removing newlines.
/usr/bin/meryl -B -C -threads 2 -m 20 -s
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Lepr.fasta
-o /tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Lepr.ms20
/usr/bin/meryl -v -M lessthanorequal 1 -s
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Lepr.ms20
-o
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Lepr.ms20.le1
/usr/bin/meryl -B -C -threads 2 -m 20 -s
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Tuber.fasta
-o
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Tuber.ms20
/usr/bin/meryl -v -M lessthanorequal 1 -s
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Tuber.ms20
-o
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Tuber.ms20.le1
Finding the min count between Lepr.ms20.le1 and Tuber.ms20.le1.
/usr/bin/meryl -M min -s
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Lepr.ms20.le1
-s
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Tuber.ms20.le1
-o
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/min.Lepr.ms20.le1.Tuber.ms20.le1
includeSize is proportional to 1048608.
excludeSize is proportional to 15724920.
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/min.Lepr.ms20.le1.Tuber.ms20.le1
has 33265 mers.
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Lepr.ms20
has 3268184 mers.
includeSize is exactly 33265 mers.
excludeSize is exactly 3234919 mers.
/usr/bin/../lib/atac/bin/seatac -verbose -mersize 20 -minlength 20
-maxgap 0 -numthreads 4 -table
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Lepr.fasta
-stream
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/meryldir/Tuber.fasta
-only
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/LeprvsTuber.include
-output
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/LeprvsTuber-segment-000.matches
-filtername /usr/bin/../lib/atac/lib/filter-heavychains.so -filteropts
"-1 Lepr -2 Tuber -S 100 -J 100000" >
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/LeprvsTuber-000.out
2>&1
/usr/bin/../lib/atac/bin/matchExtender
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/LeprvsTuber.header
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/LeprvsTuber-segment-000.matches
>
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended
WARNING: TMPDIR not set, defaulting to
'/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results'.
python3 /usr/bin/../lib/atac/bin/AtacDriver.py
/tmp/autopkgtest-lxc.pom4prd4/downtmp/autopkgtest_tmp/results/work/LeprvsTuber.matches.extended
Traceback (most recent call last):
File "/usr/bin/../lib/atac/bin/AtacDriver.py", line 26, in <module>
import localAlignerInterface
ModuleNotFoundError: No module named 'localAlignerInterface'
PYTHONPATH=/usr/bin/../lib/atac/lib
Chainer failed.
autopkgtest [14:11:24]: test atac-unit-test: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: kmer
Source-Version: 0~20150903+r2013-8
Done: Antoni Villalonga <ant...@friki.cat>
We believe that the bug you reported is fixed in the latest version of
kmer, 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 958...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Antoni Villalonga <ant...@friki.cat> (supplier of updated kmer 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, 19 Apr 2020 17:59:48 +0200
Source: kmer
Architecture: source
Version: 0~20150903+r2013-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Antoni Villalonga <ant...@friki.cat>
Closes: 958840
Changes:
kmer (0~20150903+r2013-8) unstable; urgency=medium
.
* Team upload.
.
[ Antoni Villalonga ]
* d/upstream/metadata: Repository and Bug
* Updated spelling.patch
* Final Python2 to Python3 adjustements
Closes: #958840
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