Your message dated Tue, 1 Dec 2020 18:43:23 +0530
with message-id <7c34ed17-851e-4657-ba95-014075d51...@gmail.com>
and subject line Re: sibelia: autopkgtest arm64 failure: times out after
multial.c:459: readSubstMatrix: Assertion `file` failed.
has caused the Debian Bug report #959059,
regarding sibelia: autopkgtest arm64 failure: times out after multial.c:459:
readSubstMatrix: Assertion `file` failed.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
959059: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959059
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
I re-triggered the test, it passes hence closing.
Logs can be found here[1][2]
[1]:
https://ci.debian.net/data/autopkgtest/testing/arm64/s/sibelia/8544562/log.gz
[2]:
https://ci.debian.net/data/autopkgtest/testing/arm64/s/sibelia/8544341/log.gz
--- End Message ---
