The current packaging builds and installs fine for me; shall I upload?
On Thu, Sep 5, 2019 at 4:51 PM Andreas Tille <andr...@an3as.eu> wrote:
> Hi folks,
>
> this issue is urgent since if snakemake is not installable several of
> our packages where snakemake is in (Build-)Depends are broken. Is
> anybody working on this?
>
> Kevin, you are listed as only Uploader. Does your time limit permit you
> to work on this package? Any other volunteers to add themselves to the
> list of Uploaders and care for this package?
>
> Kind regards
>
> Andreas.
>
> On Mon, Sep 02, 2019 at 10:09:22AM +0200, Andreas Tille wrote:
> > Hi,
> >
> > On Wed, Jul 31, 2019 at 10:37:22AM +0200, Andreas Beckmann wrote:
> > > Version: 5.5.3-1
> > > Severity: serious
> > >
> > > during a test with piuparts I noticed your package failed to install.
> As
> > > per definition of the release team this makes the package too buggy for
> > > a release, thus the severity.
> > >
> > > >From the attached log (scroll to the bottom...):
> > >
> > > Setting up snakemake (5.5.3-1) ...
> > > File "/usr/lib/python3/dist-packages/snakemake/remote/gfal.py",
> line 29
> > > def __init__(self, *args, keep_local=False,
> stay_on_remote=False, is_default=False, stay_on_remote=False, retry=5,
> **kwargs):
> > > ^
> > > SyntaxError: duplicate argument 'stay_on_remote' in function
> definition
> > >
> >
> > I can confirm this issue. Michael has commited a fix together with the
> > new version. I've commited some more changes but the current state in
> > Git does not pass build time tests:
> >
> > ...
> > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> _ _ _ _
> >
> > path = '/build/snakemake-5.5.4/tests/test_issue328', shouldfail = False
> > snakefile = '/build/snakemake-5.5.4/tests/test_issue328/Snakefile'
> > subpath = None, no_tmpdir = False, check_md5 = True, cores = 3
> > params = {'forcerun': ['split']}
> > results_dir =
> '/build/snakemake-5.5.4/tests/test_issue328/expected-results'
> > @py_assert1 = None, @py_assert3 = None, @py_assert6 = None
> >
> > def run(path,
> > shouldfail=False,
> > snakefile="Snakefile",
> > subpath=None,
> > no_tmpdir=False,
> > check_md5=True, cores=3, **params):
> > """
> > Test the Snakefile in path.
> > There must be a Snakefile in the path and a subdirectory named
> > expected-results.
> > """
> > results_dir = join(path, 'expected-results')
> > snakefile = join(path, snakefile)
> > assert os.path.exists(snakefile)
> > assert os.path.exists(results_dir) and os.path.isdir(
> > results_dir), '{} does not exist'.format(results_dir)
> > with tempfile.TemporaryDirectory(prefix="snakemake-") as tmpdir:
> > config = {}
> > # handle subworkflow
> > if subpath is not None:
> > # set up a working directory for the subworkflow and
> pass it in `config`
> > # for now, only one subworkflow is supported
> > assert os.path.exists(subpath) and os.path.isdir(
> > subpath), '{} does not exist'.format(subpath)
> > subworkdir = os.path.join(tmpdir, "subworkdir")
> > os.mkdir(subworkdir)
> > # copy files
> > for f in os.listdir(subpath):
> > copy(os.path.join(subpath, f), subworkdir)
> > config['subworkdir'] = subworkdir
> >
> > # copy files
> > for f in os.listdir(path):
> > print(f)
> > copy(os.path.join(path, f), tmpdir)
> >
> > # run snakemake
> > success = snakemake(snakefile,
> > cores=cores,
> > workdir=path if no_tmpdir else tmpdir,
> > stats="stats.txt",
> > config=config, **params)
> > if shouldfail:
> > assert not success, "expected error on execution"
> > else:
> > > assert success, "expected successful execution"
> > E AssertionError: expected successful execution
> > E assert False
> >
> > tests/tests.py:124: AssertionError
> > ----------------------------- Captured stdout call
> -----------------------------
> > in.txt
> > expected-results
> > Snakefile
> > ----------------------------- Captured stderr call
> -----------------------------
> > PermissionError in line 4 of
> /build/snakemake-5.5.4/tests/test_issue328/Snakefile:
> > [Errno 13] Permission denied: '/nonexistent'
> > File "/build/snakemake-5.5.4/tests/test_issue328/Snakefile", line 4,
> in <module>
> > File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line
> 699, in __init__
> > File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line
> 441, in __init__
> > File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line
> 486, in _make_container_dir
> > File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line
> 77, in _make_dir_recursively
> > File "/usr/lib/python3.7/os.py", line 211, in makedirs
> > File "/usr/lib/python3.7/os.py", line 211, in makedirs
> > File "/usr/lib/python3.7/os.py", line 211, in makedirs
> > File "/usr/lib/python3.7/os.py", line 221, in makedirs
> > ------------------------------ Captured log call
> -------------------------------
> > ERROR snakemake.logging:logging.py:307 PermissionError in line 4 of
> /build/snakemake-5.5.4/tests/test_issue328/Snakefile:
> > [Errno 13] Permission denied:
> '/nonexistent'
> > File
> "/build/snakemake-5.5.4/tests/test_issue328/Snakefile", line 4, in <module>
> > File
> "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 699, in
> __init__
> > File
> "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 441, in
> __init__
> > File
> "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 486, in
> _make_container_dir
> > File
> "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 77, in
> _make_dir_recursively
> > File
> "/usr/lib/python3.7/os.py", line 211, in makedirs
> > File
> "/usr/lib/python3.7/os.py", line 211, in makedirs
> > File
> "/usr/lib/python3.7/os.py", line 211, in makedirs
> > File
> "/usr/lib/python3.7/os.py", line 221, in makedirs
> > =============================== warnings summary
> ===============================
> > /usr/lib/python3/dist-packages/pandas/core/dtypes/inference.py:6
> > /usr/lib/python3/dist-packages/pandas/core/dtypes/inference.py:6:
> DeprecationWarning: Using or importing the ABCs from 'collections' instead
> of from 'collections.abc' is deprecated, and in 3.8 it will stop working
> > from collections import Iterable
> >
> > /usr/lib/python3/dist-packages/pandas/core/tools/datetimes.py:3
> > /usr/lib/python3/dist-packages/pandas/core/tools/datetimes.py:3:
> DeprecationWarning: Using or importing the ABCs from 'collections' instead
> of from 'collections.abc' is deprecated, and in 3.8 it will stop working
> > from collections import MutableMapping
> >
> > tests/test_schema.py::test_config
> > /usr/lib/python3/dist-packages/jsonschema/compat.py:6:
> DeprecationWarning: Using or importing the ABCs from 'collections' instead
> of from 'collections.abc' is deprecated, and in 3.8 it will stop working
> > from collections import MutableMapping, Sequence # noqa
> >
> > tests/test_schema.py::test_dataframe
> > /usr/lib/python3/dist-packages/pandas/core/frame.py:7476:
> DeprecationWarning: Using or importing the ABCs from 'collections' instead
> of from 'collections.abc' is deprecated, and in 3.8 it will stop working
> > elif isinstance(data[0], collections.Mapping):
> >
> > -- Docs: https://docs.pytest.org/en/latest/warnings.html
> > = 2 failed, 112 passed, 18 skipped, 9 deselected, 4 warnings in 578.49
> seconds =
> > E: pybuild pybuild:341: test: plugin custom failed with: exit code=1:
> python3.7 -m pytest tests/test*.py -v -k 'not report and not ancient and
> not test_script and not default_remote and not issue635 and not con
> >
> >
> > Any volunteer to check this?
> >
> > Kind regards
> >
> > Andreas.
> >
> > --
> > http://fam-tille.de
> >
> > _______________________________________________
> > Debian-med-packaging mailing list
> > debian-med-packag...@alioth-lists.debian.net
> >
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
>
> --
> http://fam-tille.de
>
--
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project
<http://www.commonwl.org/>
https://orcid.org/0000-0002-2961-9670
<https://impactstory.org/u/0000-0002-2961-9670>
m...@commonwl.org
+1 480 627 9108
