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 /tmp/autopkgtest-lxc.cdi3m4hf/downtmp/build.oIa/src/debian/tests/run-unit-test; touch /tmp/autopkgtest-lxc.cdi3m4hf/downtmp/run-unit-test-stdout /tmp/autopkgtest-lxc.cdi3m4hf/downtmp/run-unit-test-stderr; /tmp/autopkgtest-lxc.cdi3m4hf/downtmp/build.oIa/src/debian/tests/run-unit-test 2> >(tee -a /tmp/autopkgtest-lxc.cdi3m4hf/downtmp/run-unit-test-stderr >&2) > >(tee -a /tmp/autopkgtest-lxc.cdi3m4hf/downtmp/run-unit-test-stdout);" (kind: test) autopkgtest [22:18:56]: test run-unit-test: -----------------------] a
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