[Biopython-dev] PAML yn00 under Windows

[Peter Cock]

Hi again,

You may have noticed from the buildbot emails that there is a
separate issue with the PAML tests on Python (2.4 and) 2.5,
applying to executing all three binaries tried: yn00, baseml
and codeml, e.g.

http://testing.open-bio.org:8010/builders/Windows%20XP%20-%20Python%202.4/builds/259/steps/shell/logs/stdio

======================================================================
ERROR: Test that the yn00 binary runs and generates correct output.
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Traceback (most recent call last):
  File "c:\repositories\BuildBot\win24\build\Tests\test_PAML_tools.py",
line 139, in testYn00Binary
    results = self.yn.run()
  File "c:\repositories\BuildBot\win24\build\build\lib.win32-2.4\Bio\Phylo\PAML\yn00.py",
line 104, in run
    Paml.run(self, ctl_file, verbose, command)
  File "c:\repositories\BuildBot\win24\build\build\lib.win32-2.4\Bio\Phylo\PAML\_paml.py",
line 148, in run
    raise EnvironmentError, "The %s process was killed." % command
EnvironmentError: The yn00 process was killed.

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I can reproduce this at the terminal window, and it is specific
to Python (2.4 and) 2.5, using Python 2.6 and 2.7 is fine, as
are Python 3.1 and 3.2.

Peter