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

[Nilesh]

Control: tags -1 moreinfo
Control: tags -1 unreproducible

Hi,

On Tue, 28 Apr 2020 21:54:05 +0200 Paul Gevers <elbrus at debian.org> wrote:

> 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


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


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