[Debian-med-packaging] Backport of snakemake failed build time tests

[Andreas Tille]

Hi,

I'm currently busy to bring Jessie backports in sync with Stretch.  When
trying to backport snakemake I get

...
   dh_auto_test -O--buildsystem=pybuild
I: pybuild pybuild:219: chmod +x /build/snakemake-3.10.0/bin/snakemake; cp -r /build/snakemake-3.10.0/bin /build/snakemake-3.10.0/tests /build/snakemake-3.10.0/.pybuild/pythonX.Y_3.4/build
I: pybuild base:184: cd /build/snakemake-3.10.0/.pybuild/pythonX.Y_3.4/build; python3.4 -m nose tests
..Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       1
        1

rule 1:
    output: result.txt
    jobid: 0

Finished job 0.
1 of 1 steps (100%) done
.E
======================================================================
ERROR: Failure: Exception (snakemake not in PATH. For testing, install snakemake with 'pip install -e .'. You should do this in a separate environment (via conda or virtualenv).)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/lib/python3/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.4/imp.py", line 235, in load_module
    return load_source(name, filename, file)
  File "/usr/lib/python3.4/imp.py", line 171, in load_source
    module = methods.load()
  File "<frozen importlib._bootstrap>", line 1220, in load
  File "<frozen importlib._bootstrap>", line 1200, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 1129, in _exec
  File "<frozen importlib._bootstrap>", line 1471, in exec_module
  File "<frozen importlib._bootstrap>", line 321, in _call_with_frames_removed
  File "/build/snakemake-3.10.0/.pybuild/pythonX.Y_3.4/build/tests/tests.py", line 21, in <module>
    raise Exception("snakemake not in PATH. For testing, install snakemake with "
Exception: snakemake not in PATH. For testing, install snakemake with 'pip install -e .'. You should do this in a separate environment (via conda or virtualenv).

----------------------------------------------------------------------
Ran 4 tests in 0.125s

FAILED (errors=1)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/snakemake-3.10.0/.pybuild/pythonX.Y_3.4/build; python3.4 -m nose tests
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.4 returned exit code 13
debian/rules:18: recipe for target 'build' failed
make: *** [build] Error 25
dpkg-buildpackage: error: debian/rules build gave error exit status 2


Any clue what might be wrong here?

Kind regards

       Andreas.


-- 
http://fam-tille.de