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

[Andreas Tille]

Hi Sascha,

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.

Sorry for the nuisance

     Andreas.

----- 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,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-


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