[Debian-med-packaging] [lamby at debian.org: Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted]

[Sascha Steinbiss]

Hi Andreas,

> can you have a look?  Please note that I naively used master branch for an
> upload to experimental.  Either move this to experimental branch or use
> a separate debian/stretch branch for commits regarding this issue - no
> idea what might be the better choice.

OK. I'd rather keep master free for fixes to stretch, so I'll move the
branch with the experimental stuff to a separate branch and revert the
changes in master.

I figure it may have to do with a change in what bowtie returns as
results and ariba expecting a certain outcome, regardless of whether
it's 'right' or 'wrong'. I'll contact upstream and see what they say,
maybe it's even OK to adjust test expectations.
It might take a couple of days until I can find the time to look at it
as I'll be traveling without laptop until Monday.

Cheers
Sascha

> ----- Forwarded message from Chris Lamb <lamby at debian.org> -----
> 
> Date: Thu, 30 Mar 2017 13:46:26 +0100
> From: Chris Lamb <lamby at debian.org>
> To: submit at bugs.debian.org
> Subject: Bug#859111: ariba: FTBFS: FAIL: Test run_bowtie2 unsorted
> X-Debian-PR-Message: report 859111
> X-Debian-PR-Package: src:ariba
> X-Debian-PR-Keywords: 
> X-Debian-PR-Source: ariba
> 
> Source: ariba
> Version: 2.7.1+ds-1
> Severity: serious
> Justification: fails to build from source
> User: reproducible-builds at lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-bugs at lists.alioth.debian.org
> 
> Dear Maintainer,
> 
> ariba fails to build from source in unstable/amd64:
> 
>   […]
> 
>   ======================================================================
>   FAIL: Test run_bowtie2 unsorted
>   ----------------------------------------------------------------------
>   Traceback (most recent call last):
>     File "«BUILDDIR»/ariba/tests/mapping_test.py", line 61, in test_run_bowtie2
>       self.assertListEqual(expected, got)
>   AssertionError: Lists differ: [('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTC[857 chars]AT')] != [('1', 153, 'ref', 30, [(0, 25)], 'AGGATACAGATCT[794 chars]AT')]
>   
>   First differing element 0:
>   ('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTCCACAGGATGGTGGTATAC')
>   ('1', 153, 'ref', 30, [(0, 25)], 'AGGATACAGATCTTGTGGGAAAGGT')
>   
>   - [('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTCCACAGGATGGTGGTATAC'),
>   -  ('1', 147, 'ref', 30, [(0, 25)], 'AGGATACAGATCTTGTGGGAAAGGT'),
>   ? ^       ^^
>   
>   + [('1', 153, 'ref', 30, [(0, 25)], 'AGGATACAGATCTTGTGGGAAAGGT'),
>   ? ^       ^^
>   
>   +  ('1', 69, None, 30, [], 'AGCCCTCCACAGGATGGTGGTATAC'),
>   -  ('2', 99, 'ref', 124, [(0, 25)], 'TAATGTTCTTAGGGCTTACCATAGA'),
>   ?        ^^
>   
>   +  ('2', 73, 'ref', 124, [(0, 25)], 'TAATGTTCTTAGGGCTTACCATAGA'),
>   ?        ^^
>   
>   -  ('2', 147, 'ref', 170, [(0, 20), (4, 5)], 'TCCACCTTAGCTAAGCGCAGACTCG'),
>   +  ('2', 133, None, 124, [], 'CGAGTCTGCGCTTAGCTAAGGTGGA'),
>      ('3', 73, 'ref', 86, [(0, 25)], 'TCGGGTCTGTACAAGGACGGATGGT'),
>      ('3', 133, None, 86, [], 'CGTACTGACTGACTGACGTACTGCA'),
>      ('4', 99, 'ref', 55, [(0, 25)], 'CCGCCGGGAAGTCCTTCTGTCGTGC'),
>      ('4', 147, 'ref', 136, [(0, 25)], 'GGCTTACCATAGAGGTACACTAAAA'),
>   -  ('5', 99, 'ref', 0, [(4, 2), (0, 23)], 'CCTCCACAGGATGGTGGTATACCTG'),
>   ?        ^^  ^^ --  ^   ---------------
>   
>   +  ('5', 77, None, -1, [], 'CCTCCACAGGATGGTGGTATACCTG'),
>   ?        ^^  ^^^   ^^
>   
>   -  ('5', 147, 'ref', 166, [(0, 24), (4, 1)], 'TTCATCCACCTTAGCTAAGCGCAGA'),
>   +  ('5', 141, None, -1, [], 'TCTGCGCTTAGCTAAGGTGGATGAA'),
>      ('6', 77, None, -1, [], 'CAGTTGCATGACGTCATGCAGTCAT'),
>      ('6', 141, None, -1, [], 'AATGAGTATGATGAGTAATGGTATG'),
>      ('7', 99, 'ref', 56, [(4, 1), (0, 23), (4, 1)], 'ACGCCGGGAAGTCCTTCTGTCGTGT'),
>      ('7', 147, 'ref', 136, [(0, 24), (4, 1)], 'GGCTTACCATAGAGGTACACTAAAT')]
>   
>   ======================================================================
>   FAIL: Test run_bowtie2 sorted
>   ----------------------------------------------------------------------
>   Traceback (most recent call last):
>     File "«BUILDDIR»/ariba/tests/mapping_test.py", line 102, in test_run_bowtie2_and_sort
>       self.assertListEqual(expected, got)
>   AssertionError: Lists differ: [('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTC[857 chars]TG')] != [('1', 69, None, 30, [], 'AGCCCTCCACAGGATGGTGGTA[794 chars]TG')]
>   
>   First differing element 0:
>   ('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTCCACAGGATGGTGGTATAC')
>   ('1', 69, None, 30, [], 'AGCCCTCCACAGGATGGTGGTATAC')
>   
>   Diff is 1432 characters long. Set self.maxDiff to None to see it.
>   
>   ----------------------------------------------------------------------
>   Ran 317 tests in 59.987s
>   
>   FAILED (failures=2)
>   debian/rules:23: recipe for target 'override_dh_auto_test' failed
>   make[1]: *** [override_dh_auto_test] Error 1
>   make[1]: Leaving directory '«BUILDDIR»'
>   debian/rules:10: recipe for target 'build' failed
>   make: *** [build] Error 2
>   dpkg-buildpackage: error: debian/rules build gave error exit status 2
> 
>   […]
> 
> The full build log is attached.
> 
> 
> Regards,
>