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-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),

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:

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

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?

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 ============================= test session starts 
==============================
  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
  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)
10071s autopkgtest [10:02:06]: test command1

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