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

[Andreas Tille]

On Mon, Jun 22, 2020 at 04:41:10PM +0200, Sascha Steinbiss wrote:
> 
> That's because it is not an error: ariba supports multiple assemblers,

Sure its not an error - but I've thought that testing what *can*
be tested might not harm.

> and by default it looks like the much more lightweight fermi-lite
> (libfml) is used. Hence I wouldn't depend on it; it might be a good
> Suggestion though?

You are the expert.  A grep uncovered some instances of the string
spades.  I have no idea whether Recommends or Suggests is correct
and totally leave it to your insight.

Kind regards

 Andreas.

-- 
http://fam-tille.de

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

[Sascha Steinbiss]

Hi Andreas,

thanks for your email!

[Test failures]
[...]
>>> --
>>> Ran 356 tests in 57.387s
>>>
>>> FAILED (SKIP=2, errors=6)
>>> E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd 
>>> /<>/.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.

Okay, I can take a look.

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

That's because it is not an error: ariba supports multiple assemblers,
and by default it looks like the much more lightweight fermi-lite
(libfml) is used. Hence I wouldn't depend on it; it might be a good
Suggestion though?

Best regards
Sascha



signature.asc
Description: OpenPGP digital signature

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 
> > "/<>/.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   
> > genecontig
> > 
> > ==
> > 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 
> > "/<>/.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   
> > genecontig
> > 
> > ==
> > 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 
> > "/<>/.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_absencecontig1
> > 
> > ==
> > 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 
> > "/<>/.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
> >