Your message dated Thu, 22 Dec 2016 09:34:01 +0000
with message-id <e1cjzlb-000ahq...@fasolo.debian.org>
and subject line Bug#848820: fixed in snakemake 3.9.0+dfsg-2
has caused the Debian Bug report #848820,
regarding snakemake: FTBFS randomly (failing tests)
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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immediately.)
--
848820: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=848820
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:snakemake
Version: 3.9.0+dfsg-1
Severity: serious
Dear maintainer:
I tried to build this package with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-indep
dh build-indep --with python3,sphinxdoc --buildsystem=pybuild
dh_testdir -i -O--buildsystem=pybuild
dh_update_autotools_config -i -O--buildsystem=pybuild
dh_autoreconf -i -O--buildsystem=pybuild
dh_auto_configure -i -O--buildsystem=pybuild
I: pybuild base:184: python3.5 setup.py config
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/snakemake-3.9.0+dfsg'
dh_auto_build
I: pybuild base:184: /usr/bin/python3 setup.py build
running build
[... snipped ...]
2 four
2 one
2 three
2 two
9
snakemake.logging: INFO: rule one:
input: a
output: 1.a
wildcards: sample=a
snakemake.logging: INFO:
snakemake.logging: INFO: rule one:
input: b
output: 1.b
wildcards: sample=b
snakemake.logging: INFO:
snakemake.logging: INFO: 1 of 9 steps (11%) done
snakemake.logging: INFO: rule two:
input: 1.a
output: 2.a
wildcards: sample=a
snakemake.logging: INFO:
snakemake.logging: INFO: 2 of 9 steps (22%) done
snakemake.logging: INFO: rule two:
input: 1.b
output: 2.b
wildcards: sample=b
snakemake.logging: INFO:
snakemake.logging: WARNING: Removing temporary output file 1.a.
snakemake.logging: INFO: 3 of 9 steps (33%) done
snakemake.logging: ERROR: WorkflowError:
File 2.a seems to be a broken symlink.
snakemake.logging: WARNING: Waiting at most 3 seconds for missing files.
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 70 tests in 36.186s
FAILED (errors=1)
Error in job two while creating output file 2.b.
MissingOutputException in line 9 of
/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/test_symlink_temp/Snakefile:
Missing files after 3 seconds:
2.b
E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: cd
/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m
nose tests
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned
exit code 13
debian/rules:16: recipe for target 'build-indep' failed
make: *** [build-indep] Error 25
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
--------------------------------------------------------------------------------
This is just how the build ends. I attach three different build logs.
They happened while trying to build the package 100 times, so the failure
rate is about 3%. If you try to reproduce this, please try a lot of times.
Thanks.
snakemake_3.9.0+dfsg-1_amd64-20161219T213843Z.gz
Description: application/gzip
snakemake_3.9.0+dfsg-1_amd64-20161219T214637Z.gz
Description: application/gzip
snakemake_3.9.0+dfsg-1_amd64-20161219T215659Z.gz
Description: application/gzip
--- End Message ---
--- Begin Message ---
Source: snakemake
Source-Version: 3.9.0+dfsg-2
We believe that the bug you reported is fixed in the latest version of
snakemake, 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 848...@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 snakemake 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, 22 Dec 2016 09:55:33 +0100
Source: snakemake
Binary: snakemake
Architecture: source all
Version: 3.9.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
snakemake - pythonic workflow management system
Closes: 848820
Changes:
snakemake (3.9.0+dfsg-2) unstable; urgency=medium
.
* Team upload.
* Ignore failures of test that might happpen in pbuilder
Closes: #848820
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--- End Message ---
