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

[Andreas Tille]

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.




_______________________________________________
Debian-med-packaging mailing list
Debian-med-packaging at lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging


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

-- 
http://fam-tille.de