[Debian-med-packaging] Bug#892644: python-pybedtools FTBFS: test failures

[Adrian Bunk]

Source: python-pybedtools
Version: 0.7.10-2
Severity: serious

Some recent change in usntable makes python-pybedtools FTBFS:

https://tests.reproducible-builds.org/debian/history/python-pybedtools.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/python-pybedtools.html

...
   dh_auto_test -O--buildsystem=pybuild
I: pybuild pybuild:219: cp /build/1st/python-pybedtools-0.7.10/debian/mpl-expected.png /build/1st/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/
I: pybuild base:184: cd /build/1st/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url' 
...................................F......................................F.......................
*****
*****WARNING: Genome (-g) files are ignored when BAM input is provided. 
*****
..............................................................................................................................................................................................................................................................................................................................FFFFFFFF.........FFFF..........
*****
*****WARNING: Genome (-g) files are ignored when BAM input is provided. 
*****
.
*****
*****WARNING: Genome (-g) files are ignored when BAM input is provided. 
*****
........................................S..
======================================================================
FAIL: pybedtools.test.test1.test_randomstats
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/build/1st/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/test1.py", line 796, in test_randomstats
    assert results['percentile'] == 89.5
AssertionError

======================================================================
FAIL: pybedtools.test.test1.test_reldist
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/build/1st/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/test1.py", line 1461, in test_reldist
    assert results == {'reldist': [0.15, 0.21, 0.28], 'count': [1, 1, 1], 'total': [3, 3, 3], 'fraction': [0.333, 0.333, 0.333]}, results
AssertionError: {'reldist': [0.21], 'count': [1], 'total': [1], 'fraction': [1.0]}

======================================================================
FAIL: merge, i=filename ibam=False, {'s': True}
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/build/1st/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/test_iter.py", line 68, in run
    assert res == expected
AssertionError: 
-------------------- >> begin captured stdout << ---------------------
/build/1st/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/tmp/pybedtools.0oti4rl_.tmp
Method call:
BedTool.merge(s=True)
Got:
chr1	1	200
chr1	150	500
chr1	900	950

Expected:
chr1	1	200	+
chr1	150	500	-
chr1	900	950	+

Diff:
--- 
 +++ 
 @@ -1,3 +1,3 @@
 -chr1	1	200
 -chr1	150	500
 -chr1	900	950
 +chr1	1	200	+
 +chr1	150	500	-
 +chr1	900	950	+
 Showing special characters:
Got:
chr1\t1\t200\n
chr1\t150\t500\n
chr1\t900\t950\n

Expected:
chr1\t1\t200\t+\n
chr1\t150\t500\t-\n
chr1\t900\t950\t+\n

Diff:
--- 
 +++ 
 @@ -1,3 +1,3 @@
 -chr1\t1\t200\n
 -chr1\t150\t500\n
 -chr1\t900\t950\n
 +chr1\t1\t200\t+\n
 +chr1\t150\t500\t-\n
 +chr1\t900\t950\t+\n
 
--------------------- >> end captured stdout << ----------------------
...
FAILED (SKIP=1, failures=14)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/1st/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url' 
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned exit code 13
make: *** [debian/rules:14: build] Error 25