Source: pymol Version: 2.1.0+dfsg-1 Severity: normal User: debian...@lists.debian.org Usertags: regression timeout
With the upload of version 2.1.0+dfsg-1 of pymol, the autopkgtest¹ started to fail due to it timing out (> 11 hours) on 4 of the tests and additionally due to unexpected output to stderr (see the relevant part of the log copied below). Previous versions only required a couple of minutes. Therefore I assume a lot of tests got added (albeit no note in the changelog about that), otherwise it is really worth it to try and find out why it now takes so much longer. A note about time outs. Time outs can often be worked around by splitting a test into multiple autopkgtest because each gets its own timeout. On the other hand, is 11 hours or more really worth it? Couldn't a limited set of the test be run? Output to stderr normally causes a test to fail. One can overrule that by add allow-stderr to the test Restrictions if the output is expected and to be ignored. Don't hesitate to ask for help for the Debian CI team if you need help solving this issue. Paul PS: I don't want to threaten, but if the time out isn't going to be fixed soon, we'll probably add pymol to the ci.d.n blacklist. ¹ https://ci.debian.net/packages/p/pymol/unstable/amd64/ ² debian...@lists.debian.org autopkgtest [10:06:31]: test command1: 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)" autopkgtest [10:06:31]: test command1: [----------------------- Search pymol scripts in /tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/examples... Processing new directory /tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/examples Run 'pymol -c /tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/examples/chempy/generate_mmff.py'... [31;1mnot ok - line 'PyMOL: normal program termination.' was not found in pymol output[0m Run 'pymol -c /tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/examples/chempy/generate_amber.py'... [31;1mnot ok - line 'PyMOL: normal program termination.' was not found in pymol output[0m autopkgtest [12:53:11]: 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.abr4cnnf/downtmp/build.rFy/src"; mkdir -p -m 1777 -- "/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-artifacts"; export AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-artifacts"; export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 "/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive; export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=8; 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.abr4cnnf/downtmp/command1-stdout /tmp/autopkgtest-lxc.abr4cnnf/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)"' 2> >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-stderr >&2) > >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command1-stdout);" (kind: test) autopkgtest [12:53:12]: test command1: -----------------------] autopkgtest [12:53:12]: test command1: - - - - - - - - - - results - - - - - - - - - - command1 FAIL timed out autopkgtest [12:53:12]: test command1: - - - - - - - - - - stderr - - - - - - - - - - [31;1mnot ok - line 'PyMOL: normal program termination.' was not found in pymol output[0m [31;1mnot ok - line 'PyMOL: normal program termination.' was not found in pymol output[0m autopkgtest [12:53:45]: test command2: [----------------------- Search pymol scripts in /tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/data/demo... Processing new directory /tmp/autopkgtest-lxc.abr4cnnf/downtmp/build.rFy/src/data/demo autopkgtest [15:40:26]: 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.abr4cnnf/downtmp/build.rFy/src"; mkdir -p -m 1777 -- "/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-artifacts"; export AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-artifacts"; export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 "/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive; export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=8; 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.abr4cnnf/downtmp/command2-stdout /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-stderr; bash -ec 'sh debian/tests/call-pymol-scripts data/demo' 2> >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-stderr >&2) > >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command2-stdout);" (kind: test) autopkgtest [15:40:26]: test command2: -----------------------] autopkgtest [15:40:26]: test command2: - - - - - - - - - - results - - - - - - - - - - command2 FAIL timed out autopkgtest [15:41:40]: test command4: sh debian/tests/call-pymol-scripts /usr/share/pymol/examples \ "(cookbook/)|(xmlrpc01)|(sd_annotate)|(povray01)" autopkgtest [15:41:40]: test command4: [----------------------- Search pymol scripts in /usr/share/pymol/examples... Processing new directory /usr/share/pymol/examples Run 'pymol -c /usr/share/pymol/examples/chempy/generate_mmff.py'... [31;1mnot ok - line 'PyMOL: normal program termination.' was not found in pymol output[0m Run 'pymol -c /usr/share/pymol/examples/chempy/generate_amber.py'... [31;1mnot ok - line 'PyMOL: normal program termination.' was not found in pymol output[0m Skip /usr/share/pymol/examples/cookbook/scenes2movie.pml Skip /usr/share/pymol/examples/cookbook/packsurf.pml Skip /usr/share/pymol/examples/cookbook/packing.pml Skip /usr/share/pymol/examples/cookbook/multiclip_ray.pml Skip /usr/share/pymol/examples/cookbook/ss_xfer.pml Skip /usr/share/pymol/examples/cookbook/seq_match_sele.pml Skip /usr/share/pymol/examples/cookbook/contact.pml Skip /usr/share/pymol/examples/cookbook/area_diff.pml Skip /usr/share/pymol/examples/cookbook/ref_frame.pml autopkgtest [18:28:20]: 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.abr4cnnf/downtmp/build.rFy/src"; mkdir -p -m 1777 -- "/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-artifacts"; export AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-artifacts"; export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 "/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive; export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=8; 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.abr4cnnf/downtmp/command4-stdout /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-stderr; bash -ec 'sh debian/tests/call-pymol-scripts /usr/share/pymol/examples \ "(cookbook/)|(xmlrpc01)|(sd_annotate)|(povray01)"' 2> >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-stderr >&2) > >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command4-stdout);" (kind: test) autopkgtest [18:28:21]: test command4: -----------------------] autopkgtest [18:28:21]: test command4: - - - - - - - - - - results - - - - - - - - - - command4 FAIL timed out autopkgtest [18:28:21]: test command4: - - - - - - - - - - stderr - - - - - - - - - - [31;1mnot ok - line 'PyMOL: normal program termination.' was not found in pymol output[0m [31;1mnot ok - line 'PyMOL: normal program termination.' was not found in pymol output[0m autopkgtest [18:28:52]: test command5: sh debian/tests/call-pymol-scripts /usr/share/pymol/examples/cookbook multiclip_ray autopkgtest [18:28:52]: test command5: [----------------------- Search pymol scripts in /usr/share/pymol/examples/cookbook... Processing new directory /usr/share/pymol/examples/cookbook autopkgtest [21:15:32]: 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.abr4cnnf/downtmp/build.rFy/src"; mkdir -p -m 1777 -- "/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-artifacts"; export AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-artifacts"; export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755 "/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.abr4cnnf/downtmp/autopkgtest_tmp"; export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive; export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=8; 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.abr4cnnf/downtmp/command5-stdout /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-stderr; bash -ec 'sh debian/tests/call-pymol-scripts /usr/share/pymol/examples/cookbook multiclip_ray' 2> >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-stderr >&2) > >(tee -a /tmp/autopkgtest-lxc.abr4cnnf/downtmp/command5-stdout);" (kind: test) autopkgtest [21:15:32]: test command5: -----------------------] autopkgtest [21:15:32]: test command5: - - - - - - - - - - results - - - - - - - - - - command5 FAIL timed out
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