[Biopython-dev] PAML yn00 under Windows

[Peter Cock]

On Wed, Aug 17, 2011 at 6:02 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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.
> ...
> 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.

I'm getting -1 back from the subprocess.call(...)
https://github.com/biopython/biopython/commit/2d94a24ca223851d9fd895a82780dd0f23dc2dca

Some debugging later I realised the paths in the control file
were using Unix slashes rather than Windows slashes:
https://github.com/biopython/biopython/commit/4125e55b291922053380b5fe688bd687c70035fa

That should now just leave the yn00 stats parsing for you
to check (which offset should the fix use, assuming that
is the right fix).

It was worth insisting on more tests and running them on Windows :)

Regards,

Peter