[Debian-med-packaging] Bug#845737: Also new upstream version has test failures

[Ghislain Vaillant]

On Tue, 13 Dec 2016 09:27:17 +0100 Andreas Tille <andreas at an3as.eu> wrote:
> Hi Kevin,
> 
> you injected a "Closes: #845737" in the latest changelog but I get:
> 
> 
> ======================================================================
> FAIL: tests.tests.test_symlink_time_handling
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python3/dist-packages/nose/case.py", line 198, in runTest
>     self.test(*self.arg)
>   File "/build/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 345, in test_symlink_time_handling
>     run(dpath("test_symlink_time_handling"))
>   File "/build/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/tests.py", line 89, in run
>     assert success, "expected successful execution"
> AssertionError: expected successful execution
> -------------------- >> begin captured logging << --------------------
> snakemake.logging: WARNING: Provided cores: 3
> snakemake.logging: WARNING: Rules claiming more threads will be scaled down.
> snakemake.logging: WARNING: Job counts:
>         count   jobs
>         1       main
>         1       make_output
>         2
> snakemake.logging: INFO: rule make_output:
>     input: input_link
>     output: output_link
> snakemake.logging: INFO: 
> snakemake.logging: WARNING: Removing output files of failed job make_output since they might be corrupted:
> output_link
> snakemake.logging: WARNING: Will exit after finishing currently running jobs.
> snakemake.logging: ERROR: Exiting because a job execution failed. Look above for error message
> --------------------- >> end captured logging << ---------------------
> 
> ----------------------------------------------------------------------
> Ran 70 tests in 36.997s
> 
> FAILED (failures=1)
> E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: cd /build/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose tests
> 
> 
> So if there is no sensible explanation why this test might fail in a
> chroot disconnected from the net this bug is not closed.  In case the
> error occures due to the attempt to access some online resources the
> test needs to be excluded.
> 
> Kind regards
> 
>        Andreas.
> 
> -- 
> http://fam-tille.de


Looks like this error is unrelated with access to remote resources.

Andreas' log is missing the following important line:

```
ln: failed to create symbolic link 'input_link': File exists
CalledProcessError in line 37 of /<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/test_symlink_time_handling/Snakefile:
Command 'ln -s input_file input_link' returned non-zero exit status 1
  File "/<<BUILDDIR>>/snakemake-3.9.0+dfsg/.pybuild/pythonX.Y_3.5/build/tests/test_symlink_time_handling/Snakefile", line 37, in <module>
```

So it seems to be a defect in the upstream testsuite.

Ghis