[Debian-med-packaging] Bug#963332: ariba: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 returned exit code 13

[Andreas Tille]

Hi Sascha,

On Sun, Jun 21, 2020 at 10:03:49PM +0200, Lucas Nussbaum wrote:
> > ======================================================================
> > ERROR: test filter_mummer_variants
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in __init__
> >     self.reverse = {'1': False, '-1': True}[l[-3]]
> > KeyError: 'x'
> > 
> > During handling of the above exception, another exception occurred:
> > 
> > Traceback (most recent call last):
> >   File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", line 96, in test_filter_mummer_variants
> >     v1 = pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in __init__
> >     raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line)
> > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer show-snps output at this line:
> > 4	C	T	4	x	x	39	39	x	x	gene	contig
> > 
> > ======================================================================
> > ERROR: test _get_variant_effect
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in __init__
> >     self.reverse = {'1': False, '-1': True}[l[-3]]
> > KeyError: 'x'
> > 
> > During handling of the above exception, another exception occurred:
> > 
> > Traceback (most recent call last):
> >   File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", line 55, in test_get_variant_effect
> >     v1 = pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig'))
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in __init__
> >     raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line)
> > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer show-snps output at this line:
> > 6	C	T	6	x	x	39	39	x	x	gene	contig
> > 
> > ======================================================================
> > ERROR: test get_variants presence absence genes
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in __init__
> >     self.reverse = {'1': False, '-1': True}[l[-3]]
> > KeyError: 'x'
> > 
> > During handling of the above exception, another exception occurred:
> > 
> > Traceback (most recent call last):
> >   File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", line 309, in test_get_variants_presence_absence
> >     v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig1'))
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in __init__
> >     raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line)
> > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer show-snps output at this line:
> > 14	C	A	14	x	x	42	42	x	x	presence_absence	contig1
> > 
> > ======================================================================
> > ERROR: test get_variants variants only
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in __init__
> >     self.reverse = {'1': False, '-1': True}[l[-3]]
> > KeyError: 'x'
> > 
> > During handling of the above exception, another exception occurred:
> > 
> > Traceback (most recent call last):
> >   File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", line 357, in test_get_variants_variants_only
> >     v2 = pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tvariants_only\tcontig1'))
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in __init__
> >     raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line)
> > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer show-snps output at this line:
> > 14	C	A	14	x	x	42	42	x	x	variants_only	contig1
> > 
> > ======================================================================
> > ERROR: test _get_one_variant_for_one_contig_coding
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in __init__
> >     self.reverse = {'1': False, '-1': True}[l[-3]]
> > KeyError: 'x'
> > 
> > During handling of the above exception, another exception occurred:
> > 
> > Traceback (most recent call last):
> >   File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", line 156, in test_one_var_one_ctg_cdg
> >     v0 = pymummer.variant.Variant(pymummer.snp.Snp('6\tT\tA\t6\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig'))
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in __init__
> >     raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line)
> > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer show-snps output at this line:
> > 6	T	A	6	x	x	42	42	x	x	presence_absence	contig
> > 
> > ======================================================================
> > ERROR: test _get_one_variant_for_one_contig_non_coding
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in __init__
> >     self.reverse = {'1': False, '-1': True}[l[-3]]
> > KeyError: 'x'
> > 
> > During handling of the above exception, another exception occurred:
> > 
> > Traceback (most recent call last):
> >   File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", line 113, in test_one_var_one_ctg_noncdg
> >     v0 = pymummer.variant.Variant(pymummer.snp.Snp('2\tT\tA\t2\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig'))
> >   File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in __init__
> >     raise Error('Error constructing pymummer.snp.Snp from mummer show-snps output at this line:\n' + line)
> > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer show-snps output at this line:
> > 2	T	A	2	x	x	42	42	x	x	non_coding	contig
> > 
> > ----------------------------------------------------------------------
> > Ran 356 tests in 57.387s
> > 
> > FAILED (SKIP=2, errors=6)
> > E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build; python3.8 -m nose -v 
> > dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 returned exit code 13

It seems the test failures are all connected to pymummer which was
upgraded recently.

BTW, I've added a (Build-)Depends on spades which also shows up in the
test log as missing without causing an actual error.

Kind regards

         Andreas.

-- 
http://fam-tille.de