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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