[Debian-med-packaging] Bug#921566: deepnano: autopkgtest times out since 2019-01-11

[Paul Gevers]

Source: deepnano
Version: 0.0+git20170813.e8a621e-2
Severity: important
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: timeout fails-always

Dear maintainers,

Since 2019-01-11 your package has failed its autopkgtest on the
ci.debian.net infrastructure (both testing and unstable) due to timeouts
of autopkgtest (after 10000 seconds). In the past, your test failed in
about 1 minute. Could you please investigate and make your autopkgtest
more robust against this time out? Please contact me if you need help
and you think I can provide that (I am not subscribed to this bug).

For now, I have blacklisted deepnano on our infrastructure, I'll remove
it when this bug is closed.

Paul

https://ci.debian.net/data/autopkgtest/testing/amd64/d/deepnano/1834069/log.gz

autopkgtest [15:24:56]: test run-test.sh: [-----------------------

#1 - deepnano_basecall
/usr/lib/python2.7/dist-packages/theano/configdefaults.py:560:
UserWarning: DeprecationWarning: there is no c++ compiler.This is
deprecated and with Theano 0.11 a c++ compiler will be mandatory
  warnings.warn("DeprecationWarning: there is no c++ compiler."
WARNING (theano.configdefaults): g++ not detected ! Theano will be
unable to execute optimized C-implementations (for both CPU and GPU) and
will default to Python implementations. Performance will be severely
degraded. To remove this warning, set Theano flags cxx to an empty string.
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for
BLAS functions.
loading template net
done
loading complement net
done
loading 2D net
done

calling read 0/69 test_data/2016_3_4_3507_1_ch120_read240_strand.fast5
calling read 1/69 test_data/2016_3_4_3507_1_ch120_read353_strand.fast5
calling read 2/69 test_data/2016_3_4_3507_1_ch120_read415_strand.fast5
calling read 3/69 test_data/2016_3_4_3507_1_ch120_read418_strand.fast5
calling read 4/69 test_data/2016_3_4_3507_1_ch120_read433_strand.fast5
calling read 5/69 test_data/2016_3_4_3507_1_ch120_read443_strand.fast5
calling read 6/69 test_data/2016_3_4_3507_1_ch120_read505_strand.fast5
calling read 7/69 test_data/2016_3_4_3507_1_ch120_read521_strand.fast5
calling read 8/69 test_data/2016_3_4_3507_1_ch120_read542_strand.fast5
calling read 9/69 test_data/2016_3_4_3507_1_ch120_read586_strand.fast5
calling read 10/69 test_data/2016_3_4_3507_1_ch120_read635_strand.fast5
calling read 11/69 test_data/2016_3_4_3507_1_ch120_read706_strand.fast5
calling read 12/69 test_data/2016_3_4_3507_1_ch120_read83_strand.fast5
calling read 13/69 test_data/2016_3_4_3507_1_ch120_read89_strand.fast5
calling read 14/69
test_data/2016_3_4_3507_1_ch126_read1066_strand.fast5autopkgtest
[18:11:36]: 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.fc9prhyw/downtmp/build.lqo/src"; mkdir
-p -m 1777 --
"/tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-artifacts"; export
AUTOPKGTEST_ARTIFACTS="/tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-artifacts";
export ADT_ARTIFACTS="$AUTOPKGTEST_ARTIFACTS"; mkdir -p -m 755
"/tmp/autopkgtest-lxc.fc9prhyw/downtmp/autopkgtest_tmp"; export
AUTOPKGTEST_TMP="/tmp/autopkgtest-lxc.fc9prhyw/downtmp/autopkgtest_tmp";
export ADTTMP="$AUTOPKGTEST_TMP"; export DEBIAN_FRONTEND=noninteractive;
export LANG=C.UTF-8; export DEB_BUILD_OPTIONS=parallel=2; 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.fc9prhyw/downtmp/build.lqo/src/debian/tests/run-test.sh;
touch /tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-stdout
/tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-stderr;
/tmp/autopkgtest-lxc.fc9prhyw/downtmp/build.lqo/src/debian/tests/run-test.sh
2> >(tee -a /tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-stderr
>&2) > >(tee -a
/tmp/autopkgtest-lxc.fc9prhyw/downtmp/run-test.sh-stdout);" (kind: test)
autopkgtest [18:11:37]: test run-test.sh: -----------------------]
run-test.sh          FAIL timed out

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