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-packag...@lists.alioth.debian.org >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging >> >
