Your message dated Thu, 26 Jan 2017 08:51:11 +0000
with message-id <[email protected]>
and subject line Bug#851830: fixed in khmer 2.0+dfsg-9
has caused the Debian Bug report #851830,
regarding khmer FTBFS on arm64: test failures
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
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--
851830: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=851830
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: khmer
Version: 2.0+dfsg-8
Severity: serious
https://buildd.debian.org/status/fetch.php?pkg=khmer&arch=arm64&ver=2.0%2Bdfsg-8&stamp=1484489855&raw=0
...
changing mode of
/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to
775
changing mode of
/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 775
changing mode of
/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py
to 775
changing mode of
/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py
to 775
changing mode of
/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to
775
changing mode of
/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 775
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$PATH
; \
cd {build_dir}; {interpreter} -m nose --attr \
'!known_failing,!jenkins,!huge'" dh_auto_test
pybuild --test --test-nose -i python{version} -p 3.5
I: pybuild base:184: cd /«BUILDDIR»/khmer-2.0+dfsg; export
PATH=/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
; cd /«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m
nose --attr '!known_failing,!jenkins,!huge'
......................................................................................................................................................................................................................................................................................................................................................Exception
in thread Thread-12:
Traceback (most recent call last):
File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
self.run()
File "/usr/lib/python3.5/threading.py", line 862, in run
self._target(*self._args, **self._kwargs)
File
"/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py",
line 218, in count_reads
counters[tnum] = reduce(operator.add, (1 for read in rparser))
File
"/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py",
line 218, in <genexpr>
counters[tnum] = reduce(operator.add, (1 for read in rparser))
OSError: p
FException in thread Thread-17:
Traceback (most recent call last):
File "/usr/lib/python3.5/threading.py", line 914, in _bootstrap_inner
self.run()
File "/usr/lib/python3.5/threading.py", line 862, in run
self._target(*self._args, **self._kwargs)
File
"/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py",
line 218, in count_reads
counters[tnum] = reduce(operator.add, (1 for read in rparser))
File
"/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py",
line 218, in <genexpr>
counters[tnum] = reduce(operator.add, (1 for read in rparser))
OSError: x
F........SSSSSSSSSS.....................................................................................................................................................................................................................................................
======================================================================
FAIL: khmer.tests.test_read_parsers.test_with_multiple_threads
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File
"/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py",
line 236, in test_with_multiple_threads
reads_counts_per_thread
AssertionError: [1120, 0, 724, 588]
======================================================================
FAIL: khmer.tests.test_read_parsers.test_with_multiple_threads_big
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File
"/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py",
line 241, in test_with_multiple_threads_big
test_with_multiple_threads(testfile="test-large.fa")
File
"/«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build/khmer/tests/test_read_parsers.py",
line 236, in test_with_multiple_threads
reads_counts_per_thread
AssertionError: [2866, 6192, 0, 3721]
----------------------------------------------------------------------
Ran 607 tests in 163.458s
FAILED (SKIP=10, failures=2)
E: pybuild pybuild:276: test: plugin custom failed with: exit code=1: cd
/«BUILDDIR»/khmer-2.0+dfsg; export
PATH=/«BUILDDIR»/khmer-2.0+dfsg/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
; cd /«BUILDDIR»/khmer-2.0+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m
nose --attr '!known_failing,!jenkins,!huge'
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned
exit code 13
debian/rules:26: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 25
--- End Message ---
--- Begin Message ---
Source: khmer
Source-Version: 2.0+dfsg-9
We believe that the bug you reported is fixed in the latest version of
khmer, 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.
Michael R. Crusoe <[email protected]> (supplier of updated khmer 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: SHA512
Format: 1.8
Date: Tue, 24 Jan 2017 07:37:50 -0800
Source: khmer
Binary: khmer-common khmer liboxli1 liboxli-dev
Architecture: source
Version: 2.0+dfsg-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Description:
khmer - in-memory DNA sequence kmer counting, filtering & graph traversal
khmer-common - common files for the khmer project tools
liboxli-dev - in-memory DNA sequence analysis dev library
liboxli1 - in-memory DNA sequence analysis library from the khmer project
Closes: 851830
Changes:
khmer (2.0+dfsg-9) unstable; urgency=medium
.
* Drop arm64 due to failing tests. (Closes: #851830)
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Files:
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