Your message dated Wed, 09 Mar 2016 16:26:16 +0000
with message-id <[email protected]>
and subject line Bug#813262: fixed in python-biopython 1.66+dfsg-2
has caused the Debian Bug report #813262,
regarding python-biopython: FTBFS: ApplicationError: Non-zero return code 255
from 'phyml -i Phylip/interlaced2.phy -d aa'
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.
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--
813262: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=813262
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-biopython
Version: 1.66+dfsg-1
Severity: serious
Justification: fails to build from source
User: [email protected]
Usertags: ftbfs
X-Debbugs-Cc: [email protected]
Dear Maintainer,
python-biopython fails to build from source in unstable/amd64:
[..]
======================================================================
ERROR: test_phyml (test_phyml_tool.AppTests)
Run PhyML using the wrapper.
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_phyml_tool.py",
line 46, in test_phyml
out, err = cmd()
File
"/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py",
line 517, in __call__
stdout_str, stderr_str)
ApplicationError: Non-zero return code 255 from 'phyml -i
Phylip/interlaced2.phy -d aa', message 'beignet-opencl-icd: no supported GPU
found, this is probably the wrong opencl-icd package for this hardware'
----------------------------------------------------------------------
Ran 229 tests in 103.372 seconds
FAILED (failures = 1)
Skipping any tests requiring internet access
Python version: 2.7.11 (default, Jan 11 2016, 21:04:40)
[GCC 5.3.1 20160101]
Operating system: posix linux2
E: pybuild pybuild:274: test: plugin custom failed with: exit code=1: set -e;
\
mkdir -p
/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home;
\
mkdir -p
/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc/examples;
\
cp -a Doc/Tutorial.tex
/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc;
\
cp -a Doc/Tutorial
/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc;
\
cp -a Doc/examples
/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc;
\
cp -a Tests
/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build;
\
cd
/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests;
\
env DIALIGN2_DIR=/usr/share/dialign
EMBOSS_ROOT=/usr/lib/emboss
HOME=/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home
python2.7 run_tests.py --offline
dh_auto_test: pybuild --test -i python{version} -p 2.7 --test --system=custom
--test-args=set -e; \
mkdir -p {build_dir}/home; \
mkdir -p {build_dir}/Doc/examples; \
cp -a Doc/Tutorial.tex {build_dir}/Doc; \
cp -a Doc/Tutorial {build_dir}/Doc; \
cp -a Doc/examples {build_dir}/Doc; \
cp -a Tests {build_dir}; \
cd {build_dir}/Tests; \
env DIALIGN2_DIR=/usr/share/dialign
EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py
--offline --dir . returned exit code 13
debian/rules:67: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25
make[1]: Leaving directory
'/home/lamby/temp/cdt.20160130233124.nsZ8IkBTDh/python-biopython-1.66+dfsg'
debian/rules:49: recipe for target 'build' failed
make: *** [build] Error 2
[..]
The full build log is attached.
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` [email protected] / chris-lamb.co.uk
`-
python-biopython.1.66+dfsg-1.unstable.amd64.log.txt.gz
Description: Binary data
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.66+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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 09 Mar 2016 15:25:38 +0100
Source: python-biopython
Binary: python-biopython python3-biopython python-biopython-doc
python-biopython-sql python3-biopython-sql
Architecture: source
Version: 1.66+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
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: 813262
Changes:
python-biopython (1.66+dfsg-2) unstable; urgency=medium
.
* Packaging moved from SVN to Git
* Bumped Standards-Version
* Exclude phyml test for the moment
Closes: #813262
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