[Debian-med-packaging] Bug#848820: snakemake: FTBFS randomly (failing tests)

[Santiago Vila]

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.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: snakemake_3.9.0+dfsg-1_amd64-20161219T213843Z.gz
Type: application/gzip
Size: 17703 bytes
Desc: 
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20161219/c9948ecb/attachment-0003.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: snakemake_3.9.0+dfsg-1_amd64-20161219T214637Z.gz
Type: application/gzip
Size: 17749 bytes
Desc: 
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20161219/c9948ecb/attachment-0004.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: snakemake_3.9.0+dfsg-1_amd64-20161219T215659Z.gz
Type: application/gzip
Size: 17733 bytes
Desc: 
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20161219/c9948ecb/attachment-0005.bin>