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-bui...@lists.alioth.debian.org > Usertags: ftbfs > X-Debbugs-CC: reproducible-bui...@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) > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de