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

[Andreas Tille]

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.

Kind regards

       Andreas.

[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

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