[Debian-med-packaging] Bug#986256: simka: flaky amd64 autopkgtest: regularly times out after 2:47 h

[Paul Gevers]

Source: simka
Version: 1.5.3-2
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: flaky timeout

Dear maintainer(s),

Your package has an autopkgtest, great. However, I looked into
the history of your autopkgtest [1] and I noticed version 1.5.3-2 fails
regularly on amd64, while sporadically a rerun passes. I copied some of
the output at the bottom of this report. It hits the autopkgtest time
out after 2hours and 47 minutes. Successful runs pass in less than a minute.

Because the unstable-to-testing migration software now blocks on
regressions in testing, flaky tests, i.e. tests that flip between
passing and failing without changes to the list of installed packages,
are causing people unrelated to your package to spend time on these
tests.

Paul

[1] https://ci.debian.net/packages/s/simka/testing/amd64/

https://ci.debian.net/data/autopkgtest/testing/amd64/s/simka/11355132/log.gz

Computing stats...

Stats
	Reads
		Total:    847    0M    0G
		Min:    98    0M    0G
		Max:    402    0M    0G
		Average:    169    0M    0G
	Kmers
		Distinct Kmers (before merging):    14670    0M    0G
		Distinct Kmers (after merging):    8123    0M    0G
		Shared distinct Kmers:    4322    0M    0G
		Kmers:    50130    0M    0G
		Mean k-mer coverage: 2.66341


Output dir: ./simka_results/




*** Test: PASSED

Command used:
	/usr/bin/simka -in ../example/simka_input.txt -out ./simka_results/
-out-tmp ./simka_temp_output

Command for visualizing results:
	python ../scripts/visualization/run-visualization.py -in
./simka_results/ -out ./simka_results/ -pca -heatmap -tree

Command for visualizing results with metadata annotations:
	python ../scripts/visualization/run-visualization.py -in
./simka_results/ -out ./simka_results/ -pca -heatmap -tree -metadata-in
../example/dataset_metadata.csv -metadata-variable VARIABLE_1
autopkgtest [07:42:20]: 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.zk5p_5wg/downtmp/build.NZn/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.zk5p_5wg/downtmp/run-unit-test-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.zk5p_5wg/downtmp/run-unit-test-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.zk5p_5wg/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.zk5p_5wg/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=48; 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.zk5p_5wg/downtmp/build.NZn/src/debian/tests/run-unit-test;
touch /tmp/autopkgtest-lxc.zk5p_5wg/downtmp/run-unit-test-stdout
/tmp/autopkgtest-lxc.zk5p_5wg/downtmp/run-unit-test-stderr;
/tmp/autopkgtest-lxc.zk5p_5wg/downtmp/build.NZn/src/debian/tests/run-unit-test
2> >(tee -a /tmp/autopkgtest-lxc.zk5p_5wg/downtmp/run-unit-test-stderr
>&2) > >(tee -a
/tmp/autopkgtest-lxc.zk5p_5wg/downtmp/run-unit-test-stdout);" (kind: test)
autopkgtest [07:42:20]: test run-unit-test: -----------------------]

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