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Re: Bug#878498: snakemake FTBFS with Python 3.6 as default

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On 06/12/17 22:14, Andreas Tille wrote:
> control: tags -1 help
> 
> Hi,
> 
> I've upgraded snakemake in Git to latest upstream but its featuring the
> same issue.  I'm pretty sure you Python people know a simple answer for
> this issue.
To first order, the issue with the `export PATH` line can be fixed by
changing it to

`export PATH:=$(CURDIR)/bin:$(PATH)`

(since the `build` step generates `bin/snakemake` and the
PYBUILD_BEFORE_TEST just copies it into the build directory).

However, having done this still about half of the tests fail, with
various errors. Some are related to build dependencies
(google-cloud-sdk, boto3) but others are less obvious. Quite a few refer
to a stacktrace within scheduler.py; if this is trying to run a
multiprocess scheduler as part of a build-time test this sounds likely
to be an ongoing source of pain.

This also occurs if you make the temporary (but guaranteed to fail in
future) fix of just changing `pythonX.Y_3.5` to `3.6`, so I think there
are deeper issues with how the test suite needs to be run, which
probably need input from someone familiar with the package in question.

> 
> Any help would be welcome
> 
>       Andreas.
> 
> On Sat, Oct 14, 2017 at 05:33:22AM +0300, Adrian Bunk wrote:
>> Source: snakemake
>> Version: 3.10.0-1
>> Severity: serious
>> Tags: buster sid
>>
>> https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/snakemake.html
>>
>> ...
>> ======================================================================
>> 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/python3.6/imp.py", line 235, in load_module
>>     return load_source(name, filename, file)
>>   File "/usr/lib/python3.6/imp.py", line 172, in load_source
>>     module = _load(spec)
>>   File "<frozen importlib._bootstrap>", line 684, in _load
>>   File "<frozen importlib._bootstrap>", line 665, in _load_unlocked
>>   File "<frozen importlib._bootstrap_external>", line 678, in exec_module
>>   File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
>>   File "/build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/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 0.535s
>>
>> FAILED (errors=1)
>> E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/1st/snakemake-3.10.0/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose tests
>> dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 returned exit code 13
>> debian/rules:18: recipe for target 'build' failed
>> make: *** [build] Error 25
>>
>>
>>
>> The problem is the the following line in debian/rules:
>>
>>   export PATH:=$(CURDIR)/.pybuild/pythonX.Y_3.5/build/bin:$(PATH)
>>
>> _______________________________________________
>> Debian-med-packaging mailing list
>> Debian-med-packaging@lists.alioth.debian.org
>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>>
> 

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Re: Bug#878498: snakemake FTBFS with Python 3.6 as default Gordon Ball <gordon@chronitis.net> - 2017-12-07 23:00 +0100

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