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: -----------------------]
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