Bug#1039917: gemmi breaks finalcif autopkgtest: causes autopkgtest timeout

[Paul Gevers]

Source: gemmi, finalcif
Control: found -1 gemmi/0.6.2+ds-2
Control: found -1 finalcif/113+dfsg-2
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),



                       pass            fail
gemmi                  from testing    0.6.2+ds-2
finalcif               from testing    113+dfsg-2
all others             from testing    from testing





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=gemmi

https://ci.debian.net/data/autopkgtest/testing/amd64/f/finalcif/34924025/log.gz


 73s platform linux -- Python 3.11.4, pytest-7.2.1, pluggy-1.0.0+repack
 73s rootdir: /tmp/autopkgtest-lxc.pb_ivzjf/downtmp/build.E5g/src
 73s collected 312 items

10071s autopkgtest [10:02:06]: test command1

With a recent upload of gemmi the autopkgtest of finalcif fails in testing when that autopkgtest is run with the binary packages of gemmi from unstable. It passes when run with only packages from testing. In tabular form: I copied some of the output at the bottom of this report. After the fifth test, there's no output until autopkgtest aborts after 2:47 hours. Normally the test takes 2 to 3 minutes. Currently this regression is blocking the migration of gemmi to testing [1]. Due to the nature of this issue, I filed this bug report against both packages. Can you please investigate the situation and reassign the bug to the right package? 73s ============================= test session starts ============================== 73s 73s tests/test_SADABS.py ............ [ 3%] 73s tests/test_atoms.py ...... [ 5%] 81s tests/test_author_templates.py ............. [ 9%] 81s tests/test_bruker_frame.py .......... [ 13%] 81s tests/test_ccdc.py ... [ 14%] 10071s tests/test_changes_cif.py .autopkgtest [10:02:06]: 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.pb_ivzjf/downtmp/build.E5g/src"; mkdir -p -m 1777 -- "/tmp/autopkgtest-lxc.pb_ivzjf/downtmp/command1-artifacts"; export AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.pb_ivzjf/downtmp/command1-artifacts"; export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 "/tmp/autopkgtest-lxc.pb_ivzjf/downtmp/autopkgtest_tmp"; export AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.pb_ivzjf/downtmp/autopkgtest_tmp"; export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive; export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=64; 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;cd "$buildtree"; exec /tmp/autopkgtest-lxc.pb_ivzjf/downtmp/wrapper.sh --script-pid-file=/tmp/autopkgtest_script_pid --stderr=/tmp/autopkgtest-lxc.pb_ivzjf/downtmp/command1-stderr --stdout=/tmp/autopkgtest-lxc.pb_ivzjf/downtmp/command1-stdout -- bash -ec 'xvfb-run pytest-3' ;" (kind: test)

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