[Debian-med-packaging] Bug#959059: sibelia: autopkgtest arm64 failure: times out after multial.c:459: readSubstMatrix: Assertion `file` failed.

[Paul Gevers]

Source: sibelia
Version: 3.0.7+dfsg-3
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at 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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