[Debian-med-packaging] Bug#958840: kmer: autopkgtest regression: No module named 'localAlignerInterface'

[Paul Gevers]

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 488 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200425/0d6e86a1/attachment.sig>