[Biopython-dev] MSAprobs test fails

[Zheng Ruan]

Hi,

The MASprobs wrapper fails when I run the test using the latest code. The
problem seems to be the err.returncode is -11 rather than 139, at least in
my machine (Linux 3.12 x86_64) python2.7 and 3.3 will both generate the
error.

Here is scratch of the err message:

FAIL: test_single_sequence (test_MSAProbs_tool.MSAProbsTestErrorConditions)
Test an input file containing a single sequence.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./test_MSAProbs_tool.py", line 86, in test_single_sequence
    stdout, stderr = cline()
Bio.Application.ApplicationError: Command 'msaprobs Fasta/f001' returned
non-zero exit status -11, '-------------------------------------'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "./test_MSAProbs_tool.py", line 88, in test_single_sequence
    self.assertEqual(err.returncode, 139)
AssertionError: -11 != 139


Best,
Zheng Ruan