Source: kmer
Version: 0~20150903+r2013-7
X-Debbugs-CC: debian-ci@lists.debian.org
Severity: serious
User: debian-ci@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: -----------------------]
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