[Debian-med-packaging] Bug#799820: python-biopython: FTBFS: No such file or directory: 'Phylip/interlaced2.phy_phyml_tree.txt'

[Andreas Tille]

Hi BioPython developers,

the problem is fixed by the patch you can find here:

   https://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biopython/trunk/debian/patches/fix_test_phyml_tool.patch?view=markup

Please review and include it in your next release.

Kind regards and thanks for providing BioPython as free software

      Andreas.

On Tue, Sep 22, 2015 at 11:30:39PM +0100, Chris West (Faux) wrote:
> Source: python-biopython
> Version: 1.65+dfsg-1
> Severity: serious
> Justification: fails to build from source
> Tags: sid stretch
> User: reproducible-builds at lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-CC: reproducible-builds at lists.alioth.debian.org
> 
> Dear Maintainer,
> 
> The package fails to build:
> 
> Bio.PDB.Selection docstring test ... ok
> ======================================================================
> ERROR: test_phyml (test_phyml_tool.AppTests)
> Run PhyML using the wrapper.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_phyml_tool.py", line 50, in test_phyml
>     tree = Phylo.read(EX_PHYLIP + '_phyml_tree.txt', 'newick')
>   File "/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/_io.py", line 65, in read
>     tree = next(tree_gen)
>   File "/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Phylo/_io.py", line 52, in parse
>     with File.as_handle(file, 'r') as fp:
>   File "/usr/lib/python2.7/contextlib.py", line 17, in __enter__
>     return self.gen.next()
>   File "/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/File.py", line 90, in as_handle
>     with open(handleish, mode, **kwargs) as fp:
> IOError: [Errno 2] No such file or directory: 'Phylip/interlaced2.phy_phyml_tree.txt'
> 
> ----------------------------------------------------------------------
> Ran 219 tests in 81.776 seconds
> 
> FAILED (failures = 1)
> 
> Full build log:
> https://reproducible.debian.net/rb-pkg/unstable/amd64/python-biopython.html
> 
> -- System Information:
> Debian Release: stretch/sid
> APT prefers unstable
> APT policy: (500, 'unstable')
> Architecture: amd64 (x86_64)
> 
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