[Debian-med-packaging] Bug#851830: khmer FTBFS on arm64: test failures

[Adrian Bunk]

Source: khmer
Version: 2.0+dfsg-8
Severity: serious

https://buildd.debian.org/status/fetch.php?pkg=khmer&arch=arm64&ver=2.0%2Bdfsg-8&stamp=1484489855&raw=0

...
changing mode of /«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 775
changing mode of /«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 775
changing mode of /«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 775
changing mode of /«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 775
changing mode of /«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 775
changing mode of /«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 775
PYBUILD_SYSTEM=custom \
    PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$PATH ; \
    cd {build_dir}; {interpreter} -m nose --attr \
    '!known_failing,!jenkins,!huge'" dh_auto_test
	pybuild --test --test-nose -i python{version} -p 3.5
I: pybuild base:184: cd /«BUILDDIR»/khmer-2.0+dfsg; export PATH=/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ;     cd /«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose --attr     '!known_failing,!jenkins,!huge'
......................................................................................................................................................................................................................................................................................................................................................Exception in thread Thread-12:
Traceback (most recent call last):
  File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
    self.run()
  File "/usr/lib/python3.5/threading.py", line 862, in run
    self._target(*self._args, **self._kwargs)
  File "/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py", line 218, in count_reads
    counters[tnum] = reduce(operator.add, (1 for read in rparser))
  File "/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py", line 218, in <genexpr>
    counters[tnum] = reduce(operator.add, (1 for read in rparser))
OSError: p	

FException in thread Thread-17:
Traceback (most recent call last):
  File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
    self.run()
  File "/usr/lib/python3.5/threading.py", line 862, in run
    self._target(*self._args, **self._kwargs)
  File "/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py", line 218, in count_reads
    counters[tnum] = reduce(operator.add, (1 for read in rparser))
  File "/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py", line 218, in <genexpr>
    counters[tnum] = reduce(operator.add, (1 for read in rparser))
OSError: x

F........SSSSSSSSSS.....................................................................................................................................................................................................................................................
======================================================================
FAIL: khmer.tests.test_read_parsers.test_with_multiple_threads
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py", line 236, in test_with_multiple_threads
    reads_counts_per_thread
AssertionError: [1120, 0, 724, 588]

======================================================================
FAIL: khmer.tests.test_read_parsers.test_with_multiple_threads_big
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
    self.test(*self.arg)
  File "/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py", line 241, in test_with_multiple_threads_big
    test_with_multiple_threads(testfile="test-large.fa")
  File "/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py", line 236, in test_with_multiple_threads
    reads_counts_per_thread
AssertionError: [2866, 6192, 0, 3721]

----------------------------------------------------------------------
Ran 607 tests in 163.458s

FAILED (SKIP=10, failures=2)
E: pybuild pybuild:276: test: plugin custom failed with: exit code=1: cd /«BUILDDIR»/khmer-2.0+dfsg; export PATH=/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ;     cd /«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose --attr     '!known_failing,!jenkins,!huge'
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned exit code 13
debian/rules:26: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25