[Debichem-devel] Bug#987963: pymol: flaky autopkgtest on arm64: hits autopkgtest timeout

[Paul Gevers]

Source: pymol
Version: 2.4.0+dfsg-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: flaky

Dear maintainer(s),

Your package has an autopkgtest, great. However, because of the failure
"caused" by glbic, I looked into the history of your autopkgtest [1] and
I noticed it fails regularly on arm64 because it hits the autopkgtest
timeout after 2:47 hours.

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/p/pymol/testing/arm64/

https://ci.debian.net/data/autopkgtest/testing/arm64/p/pymol/11477449/log.gz

Run 'pymol -c
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/build_peptide.py'...
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/contact.pml
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/dali.py
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/density.pml
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/groel_es.pml
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/multiclip_ray.pml
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/packing.pml
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/packsurf.pml
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/ref_frame.pml
Skip
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/ribosome.pml
<string>:1: DeprecationWarning: the imp module is deprecated in favour
of importlib; see the module's documentation for alternative uses
Run 'pymol -c
/tmp/autopkgtest-lxc.q81vxtos/downtmp/build.HQz/src/examples/cookbook/scenes2movie.pml'...
<string>:1: DeprecationWarning: the imp module is deprecated in favour
of importlib; see the module's documentation for alternative uses
autopkgtest [04:22:04]: 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.q81vxtos/downtmp/build.HQz/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.q81vxtos/downtmp/command1-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.q81vxtos/downtmp/command1-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.q81vxtos/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.q81vxtos/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=4; 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"; touch
/tmp/autopkgtest-lxc.q81vxtos/downtmp/command1-stdout
/tmp/autopkgtest-lxc.q81vxtos/downtmp/command1-stderr; bash -ec 'sh
debian/tests/call-pymol-scripts examples/ \
"(start_pymol)|(xmlrpc01)|(sd_annotate)|(povray01)|(contact)|(dali)|(density)|(groel_es)|(packing)|(packsurf)|(ref_frame)|(ribosome)|(ss_xfer)|(multiclip_ray)|(tkwindow)"'
2> >(tee -a /tmp/autopkgtest-lxc.q81vxtos/downtmp/command1-stderr >&2) >
>(tee -a /tmp/autopkgtest-lxc.q81vxtos/downtmp/command1-stdout);" (kind:
test)
autopkgtest [04:22:04]: test command1: -----------------------]


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