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

[Peter Cock]

Thanks Andreas,

I've logged this as:
https://github.com/biopython/biopython/issues/623

Which version of phyml is being used here?

Eric - can you look at this please?

Peter

On Wed, Sep 23, 2015 at 12:48 PM, Andreas Tille <andreas at an3as.eu> wrote:
> 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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>> Debian-med-packaging at lists.alioth.debian.org
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>>
>
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