[Debian-med-packaging] Bug#900485: Bug#900485: python-pbcore: FTBFS and Debci failure with NumPy 1.14

Afif Elghraoui afif at debian.org
Mon Jun 25 08:41:11 BST 2018


Hi, Andreas

On June 25, 2018 3:32:00 AM EDT, Andreas Tille <tille at debian.org> wrote:
>Hi Graham,
>
>On Sun, Jun 24, 2018 at 08:48:32PM +0200, Graham Inggs wrote:
>> Control: tags -1 + patch
>
>thanks for the patch.  Since we are targeting in Git at version 1.4.2 I
>adapted the patch to this version and it works for this.  I also fixed
>another issue in the test suite[1].  Unfortunately there are remaining
>errors in the test suite which are all connected to a possible issue
>with
>XML files:
>
>$ grep "ERROR: Invalid file produced"
>python-pbcore_1.4.2+dfsg-1_amd64.build 
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpiOHCZI.alignmentset.xml.disabled
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmplAqR2T.alignmentset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpMyWNXh.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmps4GD0E.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmp71IS22dataset-unittest/test.alignmentset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpUn37tBdataset unittest/spaced.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpMouabqdataset-unittest/tempfile.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpN0pUz2alignmentset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpeQ4v3jalignmentset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmp0Kb6RWdataset-doctest/tempfile.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpj20209.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmp2XGDAY.barcodeset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpXtaXG3.consensusreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpJlLjAA.contigset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpDKGXFh.contigset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmptZ4Kro.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmp6ySKmX.contigset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpvYTcX1.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpiXc1ez.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpdiSRmI.subreadset.xml
>pbcore.io.dataset.DataSetIO: ERROR: Invalid file produced:
>/tmp/tmpveTAsa.subreadset.xml
>
>
>Before I start diving into this:  Afif, upstream seems to have released
>1.5.0 which might be worth a try.  While I asked for creating according
>release tags[2] I remember you said that upstream does not care much
>about this metadata.  I wonder whether we should possibly use mode=git
>inside the watch file, inject version 1.5.0 into packaging Git, cross
>fingers that the issue might be fixed and if not report the issue
>upstream.
>

I believe that error had to do with the package requiring an older version of some dependency. At least, the error I was seeing at the time was for that reason, which prevented me from uploading.

regards
Afif
.
>
>[1]
>https://salsa.debian.org/med-team/python-pbcore/blob/master/debian/patches/relax_test_constraint.patch
>[2] https://github.com/PacificBiosciences/pbcore/issues/116
>
>-- 
>http://fam-tille.de
>
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