Public bug reported: Whenever running autopkgtests there are times where armhf seems to fail:
https://autopkgtest.ubuntu.com/packages/s/seqtools/groovy/armhf Full failing test output: https://objectstorage.prodstack4-5.canonical.com/v1/AUTH_77e2ada1e7a84929a74ba3b87153c0ac/autopkgtest-groovy/groovy/armhf/s/seqtools/20200621_014234_23cb5@/log.gz And that happens because of Test 4: debian/tests/control run all tests using a virtual desktop environment: xvfb-run -s "-screen 0 1024x768x24 -ac +extension GLX +render -noreset" sh debian/tests/run-unit-test and Test 4 is: dotter chr4_ref_seq_short.fasta Q9H8G1.fasta -e test4 -r (file comes from libgbtools-dev as input example for dotter, blixem, belvu. ---- When test does NOT work: ... ... => Expected MSP length = 24 4700 vs. 866 residues => 4.07 million dots. Exporting graphical image to 'test3'. Exporting graphical image to 'test3'. Exiting Dotter PASS ============================================================== Test 4 Detected sequence types: DNA vs. Protein Karlin/Altschul statistics for these sequences and score matrix: K = 0.128 Lambda = 0.299 => Expected MSP score in a 100x100 matrix = 23.934 Expected residue score in MSP = 1.362 => Expected MSP length = 18 Karlin/Altschul statistics for these sequences and score matrix: K = 0.131 Lambda = 0.306 => Expected MSP score in a 100x100 matrix = 23.493 Expected residue score in MSP = 1.363 => Expected MSP length = 17 Karlin/Altschul statistics for these sequences and score matrix: K = 0.129 Lambda = 0.300 => Expected MSP score in a 100x100 matrix = 23.861 Expected residue score in MSP = 1.388 => Expected MSP length = 17 4700 vs. 570 residues => 8.04 million dots. Exporting graphical image to 'test4'. Bus error When test works: ============================================================== Test 4 Detected sequence types: DNA vs. Protein Karlin/Altschul statistics for these sequences and score matrix: K = 0.128 Lambda = 0.299 => Expected MSP score in a 100x100 matrix = 23.934 Expected residue score in MSP = 1.362 => Expected MSP length = 18 Karlin/Altschul statistics for these sequences and score matrix: K = 0.131 Lambda = 0.306 => Expected MSP score in a 100x100 matrix = 23.493 Expected residue score in MSP = 1.363 => Expected MSP length = 17 Karlin/Altschul statistics for these sequences and score matrix: K = 0.129 Lambda = 0.300 => Expected MSP score in a 100x100 matrix = 23.861 Expected residue score in MSP = 1.388 => Expected MSP length = 17 4700 vs. 570 residues => 8.04 million dots. Exporting graphical image to 'test4'. Exporting graphical image to 'test4'. Exiting Dotter PASS ============================================================== Test 5 PileUp PF02171_seed.stock MSF: 412 Type: X Check: 4875 .. Name: YQ53_CAEEL/650-977 Len: 412 Check: 5009 Weight: 1.0000 Name: Q21691_CAEEL/673-1001 Len: 412 Check: 9881 Weight: 1.0000 Name: O48771_ARATH/542-860 Len: ... ... ** Affects: seqtools (Ubuntu) Importance: Undecided Assignee: Rafael David Tinoco (rafaeldtinoco) Status: In Progress ** Changed in: seqtools (Ubuntu) Status: New => Fix Committed ** Changed in: seqtools (Ubuntu) Status: Fix Committed => In Progress ** Changed in: seqtools (Ubuntu) Assignee: (unassigned) => Rafael David Tinoco (rafaeldtinoco) ** Description changed: Whenever running autopkgtests there are times where armhf seems to fail: https://autopkgtest.ubuntu.com/packages/s/seqtools/groovy/armhf + + Full failing test output: + https://objectstorage.prodstack4-5.canonical.com/v1/AUTH_77e2ada1e7a84929a74ba3b87153c0ac/autopkgtest-groovy/groovy/armhf/s/seqtools/20200621_014234_23cb5@/log.gz And that happens because of Test 4: debian/tests/control run all tests using a virtual desktop environment: xvfb-run -s "-screen 0 1024x768x24 -ac +extension GLX +render -noreset" sh debian/tests/run-unit-test and Test 4 is: dotter chr4_ref_seq_short.fasta Q9H8G1.fasta -e test4 -r (file comes from libgbtools-dev as input example for dotter, blixem, belvu. ---- When test does NOT work: ... ... - => Expected MSP length = 24 - 4700 vs. 866 residues => 4.07 million dots. + => Expected MSP length = 24 + 4700 vs. 866 residues => 4.07 million dots. Exporting graphical image to 'test3'. Exporting graphical image to 'test3'. Exiting Dotter PASS ============================================================== Test 4 Detected sequence types: DNA vs. Protein Karlin/Altschul statistics for these sequences and score matrix: - K = 0.128 - Lambda = 0.299 - => Expected MSP score in a 100x100 matrix = 23.934 - Expected residue score in MSP = 1.362 - => Expected MSP length = 18 + K = 0.128 + Lambda = 0.299 + => Expected MSP score in a 100x100 matrix = 23.934 + Expected residue score in MSP = 1.362 + => Expected MSP length = 18 Karlin/Altschul statistics for these sequences and score matrix: - K = 0.131 - Lambda = 0.306 - => Expected MSP score in a 100x100 matrix = 23.493 - Expected residue score in MSP = 1.363 - => Expected MSP length = 17 + K = 0.131 + Lambda = 0.306 + => Expected MSP score in a 100x100 matrix = 23.493 + Expected residue score in MSP = 1.363 + => Expected MSP length = 17 Karlin/Altschul statistics for these sequences and score matrix: - K = 0.129 - Lambda = 0.300 - => Expected MSP score in a 100x100 matrix = 23.861 - Expected residue score in MSP = 1.388 - => Expected MSP length = 17 - 4700 vs. 570 residues => 8.04 million dots. + K = 0.129 + Lambda = 0.300 + => Expected MSP score in a 100x100 matrix = 23.861 + Expected residue score in MSP = 1.388 + => Expected MSP length = 17 + 4700 vs. 570 residues => 8.04 million dots. Exporting graphical image to 'test4'. Bus error When test works: ============================================================== Test 4 Detected sequence types: DNA vs. Protein Karlin/Altschul statistics for these sequences and score matrix: - K = 0.128 - Lambda = 0.299 - => Expected MSP score in a 100x100 matrix = 23.934 - Expected residue score in MSP = 1.362 - => Expected MSP length = 18 + K = 0.128 + Lambda = 0.299 + => Expected MSP score in a 100x100 matrix = 23.934 + Expected residue score in MSP = 1.362 + => Expected MSP length = 18 Karlin/Altschul statistics for these sequences and score matrix: - K = 0.131 - Lambda = 0.306 - => Expected MSP score in a 100x100 matrix = 23.493 - Expected residue score in MSP = 1.363 - => Expected MSP length = 17 + K = 0.131 + Lambda = 0.306 + => Expected MSP score in a 100x100 matrix = 23.493 + Expected residue score in MSP = 1.363 + => Expected MSP length = 17 Karlin/Altschul statistics for these sequences and score matrix: - K = 0.129 - Lambda = 0.300 - => Expected MSP score in a 100x100 matrix = 23.861 - Expected residue score in MSP = 1.388 - => Expected MSP length = 17 - 4700 vs. 570 residues => 8.04 million dots. + K = 0.129 + Lambda = 0.300 + => Expected MSP score in a 100x100 matrix = 23.861 + Expected residue score in MSP = 1.388 + => Expected MSP length = 17 + 4700 vs. 570 residues => 8.04 million dots. Exporting graphical image to 'test4'. Exporting graphical image to 'test4'. Exiting Dotter PASS ============================================================== Test 5 PileUp - PF02171_seed.stock MSF: 412 Type: X Check: 4875 .. + PF02171_seed.stock MSF: 412 Type: X Check: 4875 .. - Name: YQ53_CAEEL/650-977 Len: 412 Check: 5009 Weight: 1.0000 - Name: Q21691_CAEEL/673-1001 Len: 412 Check: 9881 Weight: 1.0000 - Name: O48771_ARATH/542-860 Len: + Name: YQ53_CAEEL/650-977 Len: 412 Check: 5009 Weight: 1.0000 + Name: Q21691_CAEEL/673-1001 Len: 412 Check: 9881 Weight: 1.0000 + Name: O48771_ARATH/542-860 Len: ... ... -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1887858 Title: armhf crashes when running autopkgtest To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/seqtools/+bug/1887858/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
