Your message dated Mon, 05 Apr 2021 20:20:33 +0000 with message-id <e1ltvi5-000gxf...@fasolo.debian.org> and subject line Bug#986256: fixed in simka 1.5.3-3 has caused the Debian Bug report #986256, regarding simka: flaky amd64 autopkgtest: regularly times out after 2:47 h 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. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 986256: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=986256 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: simka Version: 1.5.3-2 Severity: serious Tags: sid bullseye X-Debbugs-CC: debian...@lists.debian.org User: debian...@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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--- Begin Message ---Source: simka Source-Version: 1.5.3-3 Done: Étienne Mollier <etienne.moll...@mailoo.org> We believe that the bug you reported is fixed in the latest version of simka, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 986...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Étienne Mollier <etienne.moll...@mailoo.org> (supplier of updated simka package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 05 Apr 2021 20:02:58 +0200 Source: simka Architecture: source Version: 1.5.3-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Étienne Mollier <etienne.moll...@mailoo.org> Closes: 986256 Changes: simka (1.5.3-3) unstable; urgency=medium . * Team upload. * d/tests/run-unit-test: cap nb-cores to 8 cpus when running tests, to avoid the test suite to hang on high cores count machines. (Closes: #986256) Checksums-Sha1: 6eb6f2d16240544f6c842d5de7b2d7b4d811360c 2207 simka_1.5.3-3.dsc 5c4cac88d574e52815e0a5a417d509a71442c558 21328 simka_1.5.3-3.debian.tar.xz 3ffa760ea815deab2d327ec70739bc7dbc4bc30c 7837 simka_1.5.3-3_amd64.buildinfo Checksums-Sha256: b2d25d5796c93864183ab975a1b6edae432ffa067e0f185bc406724d0c7f351c 2207 simka_1.5.3-3.dsc 346578591de33df73515b88bf7f1e9e924c482b225884c3ee386dd1f7d0ec440 21328 simka_1.5.3-3.debian.tar.xz 54785e5ffdf8b0f4750634be901c7fcd8aa0f0acbcb09e337fc3040ebc17a072 7837 simka_1.5.3-3_amd64.buildinfo Files: 054dc4ace06344260f17bddeebec3eb4 2207 science optional simka_1.5.3-3.dsc f7e8a4e2afcf9e8ba43088869b6843dd 21328 science optional simka_1.5.3-3.debian.tar.xz 45b093e18dd6741bba0e30d74f5ed31d 7837 science optional simka_1.5.3-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJPBAEBCgA5FiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmBram8bHGV0aWVubmUu bW9sbGllckBtYWlsb28ub3JnAAoJEHk89n6PDRHao94QAI0wjh8KJtbcfM2BCm4N mrjJwssZzICVUtAHDf6AyIGJlnBLtN9hB13sB0Gdx7O1vWMc2CYwZ2GiyPviXXBg vC6hnE1XDhQO71Rv6bWwV6OwnouWNiyuHRaWu9wdoSI/AQw6N5hkcjiZ7yoIqoqW RaxOJ93vZqhU2hcxpETIvvuQzn1eZdn/d9dNQXLOkictbHk0RjhJmYTPpUj/9ioR 3m+1nHIz9nsRQtUcmmLMER/a0Cqq+QpZUK0nxsbUVjTUG0u87PKBLYDO7wCrSOzl DJaYSVFZqjSgLM13GFSjnv8y/IS6EYBKclkBlyC6bO1pRG479wFHf/zADTTkgAJE sx60SlT1DQ6IklwsYUVaqisYTvdQyD4bGEfxVRREWvJZBkNHu4DjK/j+leDAo6nr TB1Mx2YSR6jRkCAP2ohQ4odM0IDmcPJAQtlVMrnDZhtvb6fmFaaRvzeMlNs1jDdy tuGJz1UjDQKd2z+PbqMvzcMNTVjszYupzflKHHnWhVnm722kMg3gIcDevZMBKGMK Qp1FXOtJm6c+jiKEbfqxRXvfLh5U3PqjnbbVsodYmBjbvVfVFAwtkGvspf2vSk8W rWjx8RHv6wdTMz/ZmQ2tAnq+z7cXilE2rcOW4EGmwtDF0s9WM431jNrtO3TO/V7y 24x/m1RU6nxKIW2dvx4hIs35 =6rL9 -----END PGP SIGNATURE-----
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