[Debian-med-packaging] Bug#920270: cwltool autopkg test failures

[Matthias Klose]

Package: cwltool
Version: 1.0.20181217162649+dfsg-9
Severity: important
Tags: sid buster

Once the dependency issue is fixed, the following autopkg test errors are seen
on all architectures except amd64:

============================= test session starts ==============================
platform linux -- Python 3.7.2rc1, pytest-3.6.4, py-1.7.0, pluggy-0.8.0
rootdir: /tmp/autopkgtest.ulzEW2/autopkgtest_tmp, inifile:
plugins: xdist-1.25.0, mock-1.7.1, forked-1.0.1
gw0 I
gw0 [236]

..sss...ssss.ss......................................................... [ 30%]
............................................................ssssssss..ss [ 61%]
ssssssssssssss.........ssss.......sssssssssssss.......ss..............ss [ 91%]
....ssss.s....ssssFF                                                     [100%]
=================================== FAILURES ===================================
___________ TestUdocker.test_udocker_usage_should_not_write_cid_file ___________
[gw0] linux -- Python 3.7.2 /usr/bin/python3

self = <cwltool.tests.test_udocker.TestUdocker object at 0x7bff7c81a4e0>
tmpdir =
local('/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/test_udocker_usage_should_not_0')

    def test_udocker_usage_should_not_write_cid_file(self, tmpdir):
        cwd = tmpdir.chdir()

        test_file = "tests/wf/wc-tool.cwl"
        job_file = "tests/wf/wc-job.json"
        error_code, stdout, stderr = get_main_output(
            ["--debug", "--default-container", "debian",
"--user-space-docker-cmd=" + self.udocker_path,
             get_data(test_file), get_data(job_file)])
        cwd.chdir()
        cidfiles_count = sum(1 for _ in tmpdir.visit(fil="*.cid"))

        tmpdir.remove(ignore_errors=True)

>       assert "completed success" in stderr
E       assert 'completed success' in
"/usr/lib/python3/dist-packages/cwltool/__main__.py 1.0.20181217162649\nResolved
'/usr/lib/python3/dist-packages/cwlto...mp/pytest-of-ubuntu/pytest-0/popen-gw0/test_udocker_usage_should_not_0/output\nFinal
process status is permanentFail\n"

/usr/lib/python3/dist-packages/cwltool/tests/test_udocker.py:54: AssertionError
---------------------------- Captured stdout setup -----------------------------
Info: creating repo: /tmp/tmpba1ihfi1/.udocker
Udocker install dir: /tmp/tmpba1ihfi1
---------------------------- Captured stderr setup -----------------------------
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  5  278k    5 15543    0     0  28571      0  0:00:09 --:--:--  0:00:09 28519
100  278k  100  278k    0     0   291k      0 --:--:-- --:--:-- --:--:--  291k
Info: installing 1.1.3
_____________ TestUdocker.test_udocker_should_display_memory_usage _____________
[gw0] linux -- Python 3.7.2 /usr/bin/python3

self = <cwltool.tests.test_udocker.TestUdocker object at 0x7bff7d3bcc88>
tmpdir =
local('/tmp/pytest-of-ubuntu/pytest-0/popen-gw0/test_udocker_should_display_me0')

    @pytest.mark.skipif(TRAVIS, reason='Not reliable on single threaded test on
travis.')
    def test_udocker_should_display_memory_usage(self, tmpdir):
        cwd = tmpdir.chdir()
        error_code, stdout, stderr = get_main_output(
            ["--enable-ext", "--default-container=debian",
"--user-space-docker-cmd=" + self.udocker_path,
             get_data("tests/wf/timelimit.cwl"), "--sleep_time", "10"])
        cwd.chdir()
        tmpdir.remove(ignore_errors=True)

>       assert "completed success" in stderr
E       assert 'completed success' in
"/usr/lib/python3/dist-packages/cwltool/__main__.py 1.0.20181217162649\nResolved
'/usr/lib/python3/dist-packages/cwlto...imit.cwl] Max memory used: 23MiB\n[job
timelimit.cwl] completed permanentFail\nFinal process status is permanentFail\n"

/usr/lib/python3/dist-packages/cwltool/tests/test_udocker.py:66: AssertionError
=============================== warnings summary ===============================
cwltool/tests/test_pack.py::test_pack
  /usr/lib/python3/dist-packages/cwltool/tests/test_pack.py:29:
UnsafeLoaderWarning:
  The default 'Loader' for 'load(stream)' without further arguments can be unsafe.
  Use 'load(stream, Loader=ruamel.yaml.Loader)' explicitly if that is OK.
  Alternatively include the following in your code:

    import warnings
    warnings.simplefilter('ignore', ruamel.yaml.error.UnsafeLoaderWarning)

  In most other cases you should consider using 'safe_load(stream)'
    expect_packed = yaml.load(packed_file)

-- Docs: http://doc.pytest.org/en/latest/warnings.html
======== 2 failed, 171 passed, 63 skipped, 1 warnings in 157.26 seconds ========