Your message dated Wed, 07 Apr 2021 21:48:59 +0000 with message-id <e1lug2l-0006er...@fasolo.debian.org> and subject line Bug#986256: fixed in simka 1.5.3-4 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: 1.5.3-4 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: Wed, 07 Apr 2021 23:12:25 +0200 Source: simka Architecture: source Version: 1.5.3-4 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 (1.5.3-4) unstable; urgency=medium . * Team upload. * debian/tests/run-unit-test: remove misleading argument from Python script. * Add high_cores_count.patch to fix deadlock with Python test script. (Closes: #986256) Checksums-Sha1: 44c0b305db0f78a5bb0a56dcccf7b9be9a8b961b 2207 simka_1.5.3-4.dsc 984ab9fc57981a62ef2807650babc6ee7acd37d1 21784 simka_1.5.3-4.debian.tar.xz c9a088c15f9bbebd02730c6c0fd86d99caf1140e 7837 simka_1.5.3-4_amd64.buildinfo Checksums-Sha256: 98f42490de732dd3e641e2320af0831b9ee897fe6a7641a138b126aaa978c154 2207 simka_1.5.3-4.dsc 63a13fef4fa13657f2090a546e7c46f3c74d8a87e99710d7d76a02ea16a9a14c 21784 simka_1.5.3-4.debian.tar.xz 49a303150a6844e4123c97e9af78aa1fe6035261c03c17357969b0ba362d3055 7837 simka_1.5.3-4_amd64.buildinfo Files: f7941189f9a72b5229dec157a5632e4d 2207 science optional simka_1.5.3-4.dsc 902ced246eaa8154299907f5406c8f6b 21784 science optional simka_1.5.3-4.debian.tar.xz dcd7ae5cc99a080088296f8f71b35099 7837 science optional simka_1.5.3-4_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJPBAEBCgA5FiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmBuJLUbHGV0aWVubmUu bW9sbGllckBtYWlsb28ub3JnAAoJEHk89n6PDRHa4uUQAMB9XA89d7RXRgyhgsON 06lnglMdZ4XlvQhBvAgkshkA5Xdo8b7v0/WQgET90ou1k0Sy+d6Wp+2htliyg3+u /D+umOoO5GkmAOYouXvSupndoQbF1Pg2QBshctx+1vShsNbYOgXo4IV6qLNh6K9I SzAjGd56NWMbj7Naoz+WFTVWPgonf3AcBFWw5f2Yma1llobD5MBa84pX7qc1pgwN P4yHQsAG6wjFWQAUUC8KWNlDYPylrrmZ2gfO727jGNyp+F4EdGpNybpeDYOjZdjv kMntiOhPKKuUyOrxKihCHGvC7xkavDj3sVTiD556V1K2QL8HwdMKwNOS1afz6+rr +AqGwLgq2GekRQlz/RS1e2q7x4hDkTBAO7fijkOYWVkrzjWtMO5r37ANIA4zstl5 wEvS3ajMvACuZPNhLTHD70I6rISRNqbDWXx1WZ+nbwDnkVDrsfD0RFwxtFTt5HVw d7ETksizdDfHpTp5ShIHjLJwCmRd+oWpmj0sSngjePcJtd55oM3qZ1gCkeSeDtGH YRRe96o4c9Ad8QI4eEnIxJtV4DjRva/fecWYqpSSMjwONtagCVuy/TzfpXvGxJ6o ib5bic/cFOvondtQJH/RNOlWIEK8jer2AVz8hmXnW4SrZ1Ur3HFdOCXxhe+3zsWL HGKOP4lXtgk1R0/GksCofOkO =MML7 -----END PGP SIGNATURE-----
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