[Help] Re: pbgenomicconsensus: autopkgtest regression

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[Help] Re: pbgenomicconsensus: autopkgtest regression

Andreas Tille-5
Control: reopen -1

Hi,

it seems my third attempt to fix the autopkgtest failed again. :-(

The nasty thing is that since the last two uploads the test worked in
the pbuilder environment which I'm usually use to build.  Before I
uploaded yesterday the debci log provided some information (missing
dependency from python-h5py) but when I look at

  https://ci.debian.net/data/autopkgtest/unstable/amd64/p/pbgenomicconsensus/2208809/log.gz

now it just has:

autopkgtest [15:40:15]: test command2:  cp -r Makefile tests $AUTOPKGTEST_TMP && cd $AUTOPKGTEST_TMP && make extra-tests
autopkgtest [15:40:15]: test command2: [-----------------------
# Tests that need to be run by Jenkins but are slowing
# down the development cycle, so aren't run by "tests"
# target.
PATH=`pwd`:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games cram --verbose --xunit-file=gc-extra-cram.xml `ls tests/cram/extra/*.t | grep -v arrow`
tests/cram/extra/plurality-fluidigm.t: passed
# Ran 1 tests, 0 skipped, 0 failed.
autopkgtest [15:40:22]: test command2: -----------------------]
autopkgtest [15:40:22]: test command2:  - - - - - - - - - - results - - - - - - - - - -
command2             PASS
autopkgtest [15:40:22]: @@@@@@@@@@@@@@@@@@@@ summary
command1             FAIL non-zero exit status 2
command2             PASS


I have no idea why command1 is failing.  Anybody who can reproduce
this test result and can fix this test?

Kind regards

         Andreas.

--
http://fam-tille.de

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Re: [Help] Re: pbgenomicconsensus: autopkgtest regression

Graham Inggs-3
Hi Andeas

On Sun, 7 Apr 2019 at 07:50, Andreas Tille <[hidden email]> wrote:
> I have no idea why command1 is failing.  Anybody who can reproduce
> this test result and can fix this test?

The output of command1 is the following:

autopkgtest [15:39:43]: test command1: unset GZIP && cp -r Makefile
tests $AUTOPKGTEST_TMP && cd $AUTOPKGTEST_TMP && make tests
autopkgtest [15:39:43]: test command1: [-----------------------
# Unit tests
# ignore tests requiring
https://github.com/PacificBiosciences/PacBioTestData which is not
packaged
set -e ; \
TMPDIR=$(mktemp -d /tmp/test_ignore_XXXXXX) ; \
mv tests/unit/test_tool_contract.py ${TMPDIR} ; \
py.test --junit-xml=nosetests.xml tests/unit ; \
rm -rf tests/unit/__pycache__ ; \
mv ${TMPDIR}/* tests/unit ; \
rmdir ${TMPDIR}
/bin/bash: line 3: py.test: command not found
make: *** [Makefile:12: unit-tests] Error 127
autopkgtest [15:39:44]: test command1: -----------------------]
autopkgtest [15:39:44]: test command1:  - - - - - - - - - - results -
- - - - - - - - -
command1             FAIL non-zero exit status 2

I think all that is needed here is adding a test dependency on
python-pytest.  See the 'available diffs' section on Steve Langasek's
upload [1].

Regards
Graham


[1] https://launchpad.net/ubuntu/+source/pbgenomicconsensus/2.3.2-1ubuntu1

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Re: [Help] Re: pbgenomicconsensus: autopkgtest regression

Liubov Chuprikova
Hi,

On Sun, 7 Apr 2019 at 11:30, Graham Inggs <[hidden email]> wrote:
Hi Andeas

On Sun, 7 Apr 2019 at 07:50, Andreas Tille <[hidden email]> wrote:
> I have no idea why command1 is failing.  Anybody who can reproduce
> this test result and can fix this test?

The output of command1 is the following:

autopkgtest [15:39:43]: test command1: unset GZIP && cp -r Makefile
tests $AUTOPKGTEST_TMP && cd $AUTOPKGTEST_TMP && make tests
autopkgtest [15:39:43]: test command1: [-----------------------
# Unit tests
# ignore tests requiring
https://github.com/PacificBiosciences/PacBioTestData which is not
packaged
set -e ; \
TMPDIR=$(mktemp -d /tmp/test_ignore_XXXXXX) ; \
mv tests/unit/test_tool_contract.py ${TMPDIR} ; \
py.test --junit-xml=nosetests.xml tests/unit ; \
rm -rf tests/unit/__pycache__ ; \
mv ${TMPDIR}/* tests/unit ; \
rmdir ${TMPDIR}
/bin/bash: line 3: py.test: command not found
make: *** [Makefile:12: unit-tests] Error 127
autopkgtest [15:39:44]: test command1: -----------------------]
autopkgtest [15:39:44]: test command1:  - - - - - - - - - - results -
- - - - - - - - -
command1             FAIL non-zero exit status 2

I think all that is needed here is adding a test dependency on
python-pytest.  See the 'available diffs' section on Steve Langasek's
upload [1].

I have just added python-pytest and one more missing library. Now the tests should pass.

With regards,
Liubov


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Re: [Help] Re: pbgenomicconsensus: autopkgtest regression

Andreas Tille-5
On Sun, Apr 07, 2019 at 02:08:54PM +0200, Liubov Chuprikova wrote:
> I have just added python-pytest and one more missing library. Now the tests
> should pass.

Finally it passes now.

Thanks a lot, Andreas.

--
http://fam-tille.de