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 <andr...@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-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