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 "", line 684, in _load
>> File "", line 665, in _load_unlocked
>> File "", line 678, in exec_module
>> File "", 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
>> 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)
>>
>> ___
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>> debian-med-packag...@lists.alioth.debian.org
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>>
>
