Your message dated Thu, 03 May 2018 11:50:40 +0000
with message-id <e1fecky-00043u...@fasolo.debian.org>
and subject line Bug#897493: fixed in paleomix 1.2.13.2-1
has caused the Debian Bug report #897493,
regarding paleomix: FTBFS: dh_auto_test: pybuild --test --test-nose -i
python{version} -p 2.7 returned exit code 13
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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--
897493: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=897493
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: paleomix
Version: 1.2.12-1
Severity: serious
Tags: buster sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20180502 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # apply fix that seems to be needed due to improperly set
> # time zone in pbuilder
> sed -i~ 's/"MTime": "2005-07-07 08:50:00"/"MTime": "2005-07-07 06:50:00"/'
> tests/common_tests/makefile_test.py
> PATH=/<<PKGBUILDDIR>>/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
> dh_auto_test
> I: pybuild base:217: cd /<<PKGBUILDDIR>>/.pybuild/cpython2_2.7/build;
> python2.7 -m nose
> --exclude='(test_requirementobj__version__command_not_executable)'
> ............................................................F.F..F.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> ======================================================================
> FAIL: atomiccmd_test.builder_test.test_java_builder__default__no_config
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File
> "/<<PKGBUILDDIR>>/.pybuild/cpython2_2.7/build/tests/atomiccmd_test/builder_test.py",
> line 534, in test_java_builder__default__no_config
> "-jar", "%(AUX_JAR)s"])
> AssertionError: Lists differ: ['java', '-server', '-Djava.io... != ['java',
> '-server', '-Djava.io...
>
> First differing element 5:
> '-jar'
> '-Xmx4g'
>
> Second list contains 1 additional elements.
> First extra element 7:
> '%(AUX_JAR)s'
>
> ['java',
> '-server',
> '-Djava.io.tmpdir=%(TEMP_DIR)s',
> '-Djava.awt.headless=true',
> '-XX:+UseSerialGC',
> + '-Xmx4g',
> '-jar',
> '%(AUX_JAR)s']
>
> ======================================================================
> FAIL: atomiccmd_test.builder_test.test_java_builder__defaults__call
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File
> "/<<PKGBUILDDIR>>/.pybuild/cpython2_2.7/build/tests/atomiccmd_test/builder_test.py",
> line 545, in test_java_builder__defaults__call
> "-jar", "%(AUX_JAR)s"])
> AssertionError: Lists differ: ['java', '-server', '-Djava.io... != ['java',
> '-server', '-Djava.io...
>
> First differing element 5:
> '-jar'
> '-Xmx4g'
>
> Second list contains 1 additional elements.
> First extra element 7:
> '%(AUX_JAR)s'
>
> ['java',
> '-server',
> '-Djava.io.tmpdir=/disk/tmp',
> '-Djava.awt.headless=true',
> '-XX:+UseSerialGC',
> + '-Xmx4g',
> '-jar',
> '%(AUX_JAR)s']
>
> ======================================================================
> FAIL: atomiccmd_test.builder_test.test_java_builder__multithreaded_gc
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
> self.test(*self.arg)
> File
> "/<<PKGBUILDDIR>>/.pybuild/cpython2_2.7/build/tests/atomiccmd_test/builder_test.py",
> line 564, in test_java_builder__multithreaded_gc
> "-jar", "%(AUX_JAR)s"])
> AssertionError: Lists differ: ['java', '-server', '-Djava.io... != ['java',
> '-server', '-Djava.io...
>
> First differing element 5:
> '-jar'
> '-Xmx4g'
>
> Second list contains 1 additional elements.
> First extra element 7:
> '%(AUX_JAR)s'
>
> ['java',
> '-server',
> '-Djava.io.tmpdir=/disk/tmp',
> '-Djava.awt.headless=true',
> '-XX:ParallelGCThreads=3',
> + '-Xmx4g',
> '-jar',
> '%(AUX_JAR)s']
>
> ----------------------------------------------------------------------
> Ran 1636 tests in 3.695s
>
> FAILED (failures=3)
> E: pybuild pybuild:336: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython2_2.7/build; python2.7 -m nose
> --exclude='(test_requirementobj__version__command_not_executable)'
> dh_auto_test: pybuild --test --test-nose -i python{version} -p 2.7 returned
> exit code 13
The full build log is available from:
http://aws-logs.debian.net/2018/05/02/paleomix_1.2.12-1_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
Source: paleomix
Source-Version: 1.2.13.2-1
We believe that the bug you reported is fixed in the latest version of
paleomix, 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 897...@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 paleomix 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: Thu, 03 May 2018 13:13:32 +0200
Source: paleomix
Binary: paleomix
Architecture: source
Version: 1.2.13.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
paleomix - pipelines and tools for the processing of ancient and modern HTS
Closes: 891732 897493
Changes:
paleomix (1.2.13.2-1) unstable; urgency=medium
.
* Should be architecture any since it build-depends on the amd64-only
bowtie2
Closes: #891732
* New upstream version
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
* For some reason the -Xmx argument will be dropped when constructing
the java call. Just drop it from the test as well.
Closes: #897493
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