[Debian-med-packaging] Bug#848820: Random failures in test suite of snakemake [Bug#848820: snakemake: FTBFS randomly (failing tests)]

Thu Feb 9 10:21:30 UTC 2017

Thanks and sorry for the slow reply. I have finally seen the error myself. I think it should be fixed in commit d697f23.

Best,
Johannes

---
Dr. rer. nat. Johannes Köster
Centrum Wiskunde & Informatica
Harvard Medical School
http://johanneskoester.bitbucket.org

-------- Original Message --------
Subject: Random failures in test suite of snakemake [Bug#848820: snakemake: FTBFS randomly (failing tests)]
Local Time: December 22, 2016 9:46 AM
UTC Time: December 22, 2016 8:46 AM
From: andreas at an3as.eu
To: Johannes Köster <johannes.koester at tu-dortmund.de>, Kevin Murray <kdmfoss at gmail.com>
848820 at bugs.debian.org

Hi Johannes,

the Debian Med team is packaging snakemake for Debian (thanks for this
nice tool by the way). We received a bug report that one test of the
unit test suite fails randomly (3 times out of 100 tries). The essence
of the provided build logs which are linked at the bug page[1] is the
follwing:

======================================================================
ERROR: tests.tests.test_symlink_temp
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
File "/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 301, in test_symlink_temp
run(dpath("test_symlink_temp"), shouldfail=True)
File "/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 105, in run
rmtree(tmpdir)
File "/usr/lib/python3.5/shutil.py", line 478, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "/usr/lib/python3.5/shutil.py", line 476, in rmtree
os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/.test0k8le5n3'

but you might like to inspect the complete log at your preference.

My current course of action will be to simply disable this test for
the moment.

Kind regards

Andreas.

[1] https://bugs.debian.org/848820

----- Forwarded message from Santiago Vila <sanvila at unex.es> -----

Date: Mon, 19 Dec 2016 23:46:36 +0100 (CET)
From: Santiago Vila <sanvila at unex.es>
To: Debian BTS <submit at bugs.debian.org>
Subject: Bug#848820: snakemake: FTBFS randomly (failing tests)
X-Debian-PR-Message: report 848820
X-Debian-PR-Package: src:snakemake
X-Debian-PR-Keywords:
X-Debian-PR-Source: snakemake

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.

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----- End forwarded message -----

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