Your message dated Wed, 23 Sep 2015 16:10:35 +0000
with message-id <e1zemct-0003tm...@franck.debian.org>
and subject line Bug#799820: fixed in python-biopython 1.65+dfsg-2
has caused the Debian Bug report #799820,
regarding python-biopython: FTBFS: No such file or directory:
'Phylip/interlaced2.phy_phyml_tree.txt'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
799820: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=799820
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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)
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.65+dfsg-2
We believe that the bug you reported is fixed in the latest version of
python-biopython, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 799...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated python-biopython package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 23 Sep 2015 15:18:58 +0200
Source: python-biopython
Binary: python-biopython python3-biopython python-biopython-doc
python-biopython-sql python3-biopython-sql
Architecture: source all amd64
Version: 1.65+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
python-biopython - Python library for bioinformatics (implemented in Python 2)
python-biopython-doc - Documentation for the Biopython library
python-biopython-sql - Biopython support for the BioSQL database schema
(Python 2)
python3-biopython - Python library for bioinformatics (implemented in Python 3)
python3-biopython-sql - Biopython support for the BioSQL database schema
(Python 3)
Closes: 799820
Changes:
python-biopython (1.65+dfsg-2) unstable; urgency=medium
.
* Build-Depends & Suggests: phylip + fixed test_phyml_tool
Closes: #799820
* debian/clean: Remove test results occuring now since phylip can be used
* Activate more tests formerly deactivated
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