[Biopython-dev] MSAprobs test fails

[Peter Cock]

Hi Zheng,

Negative error codes (from Python subprocess) are really Unix signals,
https://docs.python.org/2/library/subprocess.html

i.e. Linux killed the job with signal 11, probably SIGSEGV - Invalid
memory reference.


Can you run the tool by hand? Does it seg fault or something like that?

Peter

On Tue, Apr 22, 2014 at 10:18 PM, Zheng Ruan <zruan1991 at gmail.com> wrote:
> 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
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