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Re: PhyML error - does that ring any bell? Re: RFS: python-biopython



Hi Andreas,

Andreas Tille, on 2020-06-17 08:05:57 +0200:
> On Tue, Jun 16, 2020 at 10:41:28PM +0200, Étienne Mollier wrote:
> > I pushed a little change in the d/control file of the package
> > python-biopython in version 1.77+dfsg-2.  This was the suggested
> > way to address the bug #962944:
> > 
> > 	https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962944
> > 
> > I couldn't reproduce any particular problem with the few last
> > rounds of `gbp buildpackage` and `autopkgtest`, and `lintian`
> > has nothing outstanding to complain about, so it is ready for
> > review.
> 
> I've just uploaded (today the build went smoothly).

Thank you for the review and upload.  :)

> > Unfortunately, the PhyML issue below is left aside for the
> > moment.
> 
> As far as I can see this was the urgent issue that was
> reflected in a RC bug that should be fixed quickly.

Indeed, I thought as well.

> > Steffen Möller, on 2020-06-12 19:40:37 +0200:
> > > FAIL: test_phyml (test_phyml_tool.AppTests)
> > > Run PhyML using the wrapper.
> > > ----------------------------------------------------------------------
> > > Traceback (most recent call last):
> > >  File "/home/moeller/git/med-team/python-biopython/.pybuild/cpython3_3.8/build/Tests/test_phyml_tool.py",
> > > line 51, in test_phyml
> > >    self.assertEqual(len(err), 0)
> > > AssertionError: 192 != 0
> > 
> > It is sad to only have the length of the error message, so  I
> > tried to get the full error message with a litte patch for
> > debug, but have been at loss to reproduce the PhyML issue after
> > having reduced my pid_max to not be affected by #962974 anymore;
> > I am wondering if the two problems are related somehow, or if I
> > just didn't trigger the test in the proper environment.
> > 
> > 	https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962974
> 
> Thanks a lot for your investigation

You're welcome.  Next in my to do list is to have a deeper look
at the whole test suite.  I wouldn't be surprised to find a few
more warnings in need to be sorted.  Will have a look at it this
evening UTC+0200.

Have a nice day,  :)
-- 
Étienne Mollier <etienne.mollier@mailoo.org>
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