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<pre class="message">Control: tags -1 moreinfo
Control: tags -1 unreproducible</pre>
<p>Hi,<br>
</p>
<p>On Tue, 28 Apr 2020 21:54:05 +0200 Paul Gevers
<a class="moz-txt-link-rfc2396E" href="mailto:elbrus@debian.org"><elbrus@debian.org></a> wrote:</p>
> Source: sibelia<br>
> Version: 3.0.7+dfsg-3<br>
> X-Debbugs-CC: <a class="moz-txt-link-abbreviated" href="mailto:debian-ci@lists.debian.org">debian-ci@lists.debian.org</a><br>
> Severity: serious<br>
> User: <a class="moz-txt-link-abbreviated" href="mailto:debian-ci@lists.debian.org">debian-ci@lists.debian.org</a><br>
> Usertags: fails-always timesout<br>
> <br>
> Dear maintainer(s),<br>
> <br>
> Your new package sibelia has an autopkgtest, great. However, it
fails on<br>
> arm64 because it times out. I copied some of the output at the
bottom of<br>
> this report.<br>
> <br>
> Currently this regression is blocking the migration to testing
[1]. Can<br>
> you please investigate the situation and fix it?<br>
> <br>
> More information about this bug and the reason for filing it
can be found on<br>
>
<a class="moz-txt-link-freetext" href="https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation">https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation</a><br>
> <br>
> Paul<br>
> <br>
> [1] <a class="moz-txt-link-freetext" href="https://qa.debian.org/excuses.php?package=sibelia">https://qa.debian.org/excuses.php?package=sibelia</a><br>
> <br>
>
<a class="moz-txt-link-freetext" href="https://ci.debian.net/data/autopkgtest/testing/arm64/s/sibelia/5172443/log.gz">https://ci.debian.net/data/autopkgtest/testing/arm64/s/sibelia/5172443/log.gz</a><br>
> <br>
> autopkgtest [19:32:15]: test run-unit-test:
[-----------------------<br>
> + cd C-Sibelia/Staphylococcus_aureus<br>
> + C-Sibelia.py NCTC8325.fasta RN4220.fasta<br>
> Simplification stage 1 of 3<br>
> Enumerating vertices of the graph, then performing bulge
removal...<br>
> [..................................................]<br>
> Simplification stage 2 of 3<br>
> Enumerating vertices of the graph, then performing bulge
removal...<br>
> [..................................................]<br>
> Simplification stage 3 of 3<br>
> Enumerating vertices of the graph, then performing bulge
removal...<br>
> [..................................................]<br>
> Finding synteny blocks and generating the output...<br>
> Calculating synteny blocks...<br>
> Calling variants...<br>
> An error occured: b"mlagan: multial.c:459: readSubstMatrix:
Assertion<br>
> `file' failed.\n"<br>
> autopkgtest [22:18:56]: ERROR: timed out on command "su -s
/bin/bash<br>
> debci -c set -e; export USER=`id -nu`; . /etc/profile
>/dev/null 2>&1 ||<br>
> true; . ~/.profile >/dev/null 2>&1 || true;<br>
>
buildtree="/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/build.oIa/src";
mkdir<br>
> -p -m 1777 --<br>
>
"/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/run-unit-test-artifacts";
export<br>
>
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/run-unit-test-artifacts";<br>
> export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755<br>
> "/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/autopkgtest_tmp"; export<br>
>
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.cdi3m4hf/downtmp/autopkgtest_tmp";<br>
> export ADTTMP="$AUTOPKGTEST_TMP"; export
DEBIAN_FRONTEND=noninteractive;<br>
> export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=32;
unset<br>
> LANGUAGE LC_CTYPE LC_NUMERIC LC_TIME LC_COLLATE LC_MONETARY<br>
> LC_MESSAGES LC_PAPER LC_NAME LC_ADDRESS LC_TELEPHONE
LC_MEASUREMENT<br>
> LC_IDENTIFICATION LC_ALL;rm -f /tmp/autopkgtest_script_pid; set
-C; echo<br>
> $$ > /tmp/autopkgtest_script_pid; set +C; trap "rm -f<br>
> /tmp/autopkgtest_script_pid" EXIT INT QUIT PIPE; cd
"$buildtree"; chmod<br>
<p>> +x</p>
<p><br>
</p>
<p>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<br>
Is this an occasional failure, or am I missing something here? -
Please let me know.<br>
</p>
<p>[1]:
<a class="moz-txt-link-freetext" href="https://ci.debian.net/data/autopkgtest/testing/armhf/s/sibelia/7169740/log.gz">https://ci.debian.net/data/autopkgtest/testing/armhf/s/sibelia/7169740/log.gz</a></p>
<p>Kind Regards,<br>
Nilesh<br>
</p>
<br>
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