[Debian-med-packaging] Bug#870362: ariba FTBFS with bowtie2 2.3.2-2

[Adrian Bunk]

Source: ariba
Version: 2.10.0+ds-1
Severity: serious

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/ariba.html

...
======================================================================
FAIL: Test run_bowtie2 unsorted
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/1st/ariba-2.10.0+ds/ariba/tests/mapping_test.py", line 62, 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[795 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', 101, 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 "/build/1st/ariba-2.10.0+ds/ariba/tests/mapping_test.py", line 105, 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', 101, None, 30, [], 'AGCCCTCCACAGGATGGTGGT[795 chars]TG')]

First differing element 0:
('1', 99, 'ref', 0, [(4, 5), (0, 20)], 'AGCCCTCCACAGGATGGTGGTATAC')
('1', 101, None, 30, [], 'AGCCCTCCACAGGATGGTGGTATAC')

Diff is 1434 characters long. Set self.maxDiff to None to see it.

----------------------------------------------------------------------
Ran 335 tests in 173.301s

FAILED (failures=2)
debian/rules:23: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1