<div dir="ltr">The current packaging builds and installs fine for me; shall I upload?<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Sep 5, 2019 at 4:51 PM Andreas Tille <<a href="mailto:andreas@an3as.eu">andreas@an3as.eu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi folks,<br>
<br>
this issue is urgent since if snakemake is not installable several of<br>
our packages where snakemake is in (Build-)Depends are broken. Is<br>
anybody working on this?<br>
<br>
Kevin, you are listed as only Uploader. Does your time limit permit you<br>
to work on this package? Any other volunteers to add themselves to the<br>
list of Uploaders and care for this package?<br>
<br>
Kind regards<br>
<br>
Andreas.<br>
<br>
On Mon, Sep 02, 2019 at 10:09:22AM +0200, Andreas Tille wrote:<br>
> Hi,<br>
> <br>
> On Wed, Jul 31, 2019 at 10:37:22AM +0200, Andreas Beckmann wrote:<br>
> > Version: 5.5.3-1<br>
> > Severity: serious<br>
> > <br>
> > during a test with piuparts I noticed your package failed to install. As<br>
> > per definition of the release team this makes the package too buggy for<br>
> > a release, thus the severity.<br>
> > <br>
> > >From the attached log (scroll to the bottom...):<br>
> > <br>
> > Setting up snakemake (5.5.3-1) ...<br>
> > File "/usr/lib/python3/dist-packages/snakemake/remote/gfal.py", line 29<br>
> > def __init__(self, *args, keep_local=False, stay_on_remote=False, is_default=False, stay_on_remote=False, retry=5, **kwargs):<br>
> > ^<br>
> > SyntaxError: duplicate argument 'stay_on_remote' in function definition<br>
> > <br>
> <br>
> I can confirm this issue. Michael has commited a fix together with the<br>
> new version. I've commited some more changes but the current state in<br>
> Git does not pass build time tests:<br>
> <br>
> ...<br>
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ <br>
> <br>
> path = '/build/snakemake-5.5.4/tests/test_issue328', shouldfail = False<br>
> snakefile = '/build/snakemake-5.5.4/tests/test_issue328/Snakefile'<br>
> subpath = None, no_tmpdir = False, check_md5 = True, cores = 3<br>
> params = {'forcerun': ['split']}<br>
> results_dir = '/build/snakemake-5.5.4/tests/test_issue328/expected-results'<br>
> @py_assert1 = None, @py_assert3 = None, @py_assert6 = None<br>
> <br>
> def run(path,<br>
> shouldfail=False,<br>
> snakefile="Snakefile",<br>
> subpath=None,<br>
> no_tmpdir=False,<br>
> check_md5=True, cores=3, **params):<br>
> """<br>
> Test the Snakefile in path.<br>
> There must be a Snakefile in the path and a subdirectory named<br>
> expected-results.<br>
> """<br>
> results_dir = join(path, 'expected-results')<br>
> snakefile = join(path, snakefile)<br>
> assert os.path.exists(snakefile)<br>
> assert os.path.exists(results_dir) and os.path.isdir(<br>
> results_dir), '{} does not exist'.format(results_dir)<br>
> with tempfile.TemporaryDirectory(prefix="snakemake-") as tmpdir:<br>
> config = {}<br>
> # handle subworkflow<br>
> if subpath is not None:<br>
> # set up a working directory for the subworkflow and pass it in `config`<br>
> # for now, only one subworkflow is supported<br>
> assert os.path.exists(subpath) and os.path.isdir(<br>
> subpath), '{} does not exist'.format(subpath)<br>
> subworkdir = os.path.join(tmpdir, "subworkdir")<br>
> os.mkdir(subworkdir)<br>
> # copy files<br>
> for f in os.listdir(subpath):<br>
> copy(os.path.join(subpath, f), subworkdir)<br>
> config['subworkdir'] = subworkdir<br>
> <br>
> # copy files<br>
> for f in os.listdir(path):<br>
> print(f)<br>
> copy(os.path.join(path, f), tmpdir)<br>
> <br>
> # run snakemake<br>
> success = snakemake(snakefile,<br>
> cores=cores,<br>
> workdir=path if no_tmpdir else tmpdir,<br>
> stats="stats.txt",<br>
> config=config, **params)<br>
> if shouldfail:<br>
> assert not success, "expected error on execution"<br>
> else:<br>
> > assert success, "expected successful execution"<br>
> E AssertionError: expected successful execution<br>
> E assert False<br>
> <br>
> tests/tests.py:124: AssertionError<br>
> ----------------------------- Captured stdout call -----------------------------<br>
> in.txt<br>
> expected-results<br>
> Snakefile<br>
> ----------------------------- Captured stderr call -----------------------------<br>
> PermissionError in line 4 of /build/snakemake-5.5.4/tests/test_issue328/Snakefile:<br>
> [Errno 13] Permission denied: '/nonexistent'<br>
> File "/build/snakemake-5.5.4/tests/test_issue328/Snakefile", line 4, in <module><br>
> File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 699, in __init__<br>
> File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 441, in __init__<br>
> File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 486, in _make_container_dir<br>
> File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 77, in _make_dir_recursively<br>
> File "/usr/lib/python3.7/os.py", line 211, in makedirs<br>
> File "/usr/lib/python3.7/os.py", line 211, in makedirs<br>
> File "/usr/lib/python3.7/os.py", line 211, in makedirs<br>
> File "/usr/lib/python3.7/os.py", line 221, in makedirs<br>
> ------------------------------ Captured log call -------------------------------<br>
> ERROR snakemake.logging:logging.py:307 PermissionError in line 4 of /build/snakemake-5.5.4/tests/test_issue328/Snakefile:<br>
> [Errno 13] Permission denied: '/nonexistent'<br>
> File "/build/snakemake-5.5.4/tests/test_issue328/Snakefile", line 4, in <module><br>
> File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 699, in __init__<br>
> File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 441, in __init__<br>
> File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 486, in _make_container_dir<br>
> File "/usr/lib/python3/dist-packages/pytools/persistent_dict.py", line 77, in _make_dir_recursively<br>
> File "/usr/lib/python3.7/os.py", line 211, in makedirs<br>
> File "/usr/lib/python3.7/os.py", line 211, in makedirs<br>
> File "/usr/lib/python3.7/os.py", line 211, in makedirs<br>
> File "/usr/lib/python3.7/os.py", line 221, in makedirs<br>
> =============================== warnings summary ===============================<br>
> /usr/lib/python3/dist-packages/pandas/core/dtypes/inference.py:6<br>
> /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<br>
> from collections import Iterable<br>
> <br>
> /usr/lib/python3/dist-packages/pandas/core/tools/datetimes.py:3<br>
> /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<br>
> from collections import MutableMapping<br>
> <br>
> tests/test_schema.py::test_config<br>
> /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<br>
> from collections import MutableMapping, Sequence # noqa<br>
> <br>
> tests/test_schema.py::test_dataframe<br>
> /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<br>
> elif isinstance(data[0], collections.Mapping):<br>
> <br>
> -- Docs: <a href="https://docs.pytest.org/en/latest/warnings.html" rel="noreferrer" target="_blank">https://docs.pytest.org/en/latest/warnings.html</a><br>
> = 2 failed, 112 passed, 18 skipped, 9 deselected, 4 warnings in 578.49 seconds =<br>
> 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<br>
> <br>
> <br>
> Any volunteer to check this?<br>
> <br>
> Kind regards<br>
> <br>
> Andreas.<br>
> <br>
> -- <br>
> <a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
> <br>
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<br>
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<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr" style="font-size:small"><span style="font-size:12.8px">Michael R. Crusoe</span><br style="font-size:12.8px"><span style="font-size:12.8px">Co-founder & Lead, </span><a href="http://www.commonwl.org/" style="color:rgb(17,85,204);font-size:12.8px" target="_blank">Common Workflow Language project</a></div><div dir="ltr"><a href="https://impactstory.org/u/0000-0002-2961-9670" style="font-size:12.8px;color:rgb(17,85,204)" target="_blank">https://orcid.org/0000-0002-2961-9670</a><br style="font-size:12.8px"><a href="mailto:mrc@commonwl.org" style="font-size:12.8px;color:rgb(17,85,204)" target="_blank">mrc@commonwl.org</a><br style="font-size:12.8px">+1 480 627 9108<br></div></div></div></div></div></div></div></div></div></div></div></div></div>