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Cannot locate xUnit report ... for tests (planemo 0.74.11)

Open eschen42 opened this issue 2 years ago • 0 comments

Your operating system name and version, versions of other relevant software such as Galaxy or Docker.

Windows Services for Linux 2

$ uname -a
Linux DESKTOP-00J5NN6 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
$ planemo --version
planemo, version 0.74.11

Links to relevant tools.

N/A tool tests don't even commence

Any details about your local setup that might be helpful in troubleshooting.

Running in WSL2 (a Linux VM running on Windows). The error message does not point to this being the issue:

  File "/home/art/.planemo/gx_venv_3/lib/python3.10/site-packages/nose/suite.py", line 106, in _set_tests
    if isinstance(tests, collections.Callable) and not is_suite:
AttributeError: module 'collections' has no attribute 'Callable'
Testing complete. HTML report is in "/home/art/src/tools-galaxyp/tools/maxquant/tool_test_output.html".
Cannot locate xUnit report [/tmp/tmpy8e0nkxi/xunit.xml] for tests - required to build planemo report and summarize tests.
Traceback (most recent call last):
  File "/home/art/bin/planemo", line 8, in <module>
    sys.exit(planemo())
  File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/art/venv/lib/python3.9/site-packages/click/decorators.py", line 84, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/art/venv/lib/python3.9/site-packages/planemo/cli.py", line 96, in handle_blended_options
    return f(*args, **kwds)
  File "/home/art/venv/lib/python3.9/site-packages/planemo/commands/cmd_test.py", line 78, in cli
    return_value = test_runnables(ctx, runnables, original_paths=uris, **kwds)
  File "/home/art/venv/lib/python3.9/site-packages/planemo/engine/test.py", line 33, in test_runnables
    return_value = run_in_config(ctx, config, **kwds)
  File "/home/art/venv/lib/python3.9/site-packages/planemo/galaxy/test/actions.py", line 109, in run_in_config
    _check_test_outputs(xunit_report_file_tracker, structured_report_file_tracker)
  File "/home/art/venv/lib/python3.9/site-packages/planemo/galaxy/test/actions.py", line 290, in _check_test_outputs
    raise Exception(message)
Exception: Cannot locate xUnit report [/tmp/tmpy8e0nkxi/xunit.xml] for tests - required to build planemo report and summarize tests.

Detailed steps to reproduce the bug.

cd ~/src/tools-galaxyp/tools/maxquant
planemo test --biocontainers .

The exact same error occurs regardless of which tool is under test or regardless of whether --biocontainers is set.

eschen42 avatar Nov 21 '22 17:11 eschen42