Control: tags -1 moreinfo Control: tags -1 unreproducible Hi,
On Tue, 28 Apr 2020 21:54:05 +0200 Paul Gevers <elb...@debian.org> wrote: > Source: sibelia > Version: 3.0.7+dfsg-3 > X-Debbugs-CC: debian...@lists.debian.org > Severity: serious > User: debian...@lists.debian.org > Usertags: fails-always timesout > > Dear maintainer(s), > > Your new package sibelia has an autopkgtest, great. However, it fails on > arm64 because it times out. 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=sibelia > > https://ci.debian.net/data/autopkgtest/testing/arm64/s/sibelia/5172443/log.gz > > autopkgtest [19:32:15]: test run-unit-test: [----------------------- > + cd C-Sibelia/Staphylococcus_aureus > + C-Sibelia.py NCTC8325.fasta RN4220.fasta > Simplification stage 1 of 3 > Enumerating vertices of the graph, then performing bulge removal... > [..................................................] > Simplification stage 2 of 3 > Enumerating vertices of the graph, then performing bulge removal... > [..................................................] > Simplification stage 3 of 3 > Enumerating vertices of the graph, then performing bulge removal... > [..................................................] > Finding synteny blocks and generating the output... > Calculating synteny blocks... > Calling variants... > An error occured: b"mlagan: multial.c:459: readSubstMatrix: Assertion > `file' failed.\n" > autopkgtest [22:18:56]: ERROR: timed out on command "su -s /bin/bash > debci -c set -e; export USER=`id -nu`; . /etc/profile >/dev/null 2>&1 || > true; . ~/.profile >/dev/null 2>&1 || true; > buildtree="/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/build.oIa/src"; mkdir > -p -m 1777 -- > "/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/run-unit-test-artifacts"; export > AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/run-unit-test-artifacts"; > export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 > "/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/autopkgtest_tmp"; export > AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/autopkgtest_tmp"; > export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive; > export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=32; unset > LANGUAGE LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY > LC_MESSAGES LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE LC_MEASUREMENT > LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set -C; echo > $$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f > /tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd "$buildtree"; chmod > +x It passes for me in an arm64 schroot. Futher more, it passes even armhf as per CI logs[1]. This creates further suspicion for not passing on arm64 Is this an occasional failure, or am I missing something here? - Please let me know. [1]: https://ci.debian.net/data/autopkgtest/testing/armhf/s/sibelia/7169740/log.gz Kind Regards, Nilesh