Bug#1009201: toil: (autopkgtest) needs update for python3.10: No such file or directory: 'python3.9'

[Paul Gevers]

Source: toil
Version: 5.6.0-5
Severity: serious
Tags: sid bookworm
User: debian...@lists.debian.org
Usertags: needs-update
User: debian-pyt...@lists.debian.org
Usertags: python3.10
Control: affects -1 src:python3-defaults

Dear maintainer(s),



                       pass            fail
python3-defaults       from testing    3.10.4-1
toil                   from testing    5.6.0-5
all others             from testing    from testing

I copied some of the output at the bottom of this report.

We are in the transition of making python3.10 the default Python versions [0]. With a recent upload of python3-defaults the autopkgtest of toil fails in testing when that autopkgtest is run with the binary packages of python3-defaults from unstable. It passes when run with only packages from testing. In tabular form: Currently this regression is blocking the migration of python3-defaults to testing [1]. https://docs.python.org/3/whatsnew/3.10.html lists what's new in Python3.10, it may help to identify what needs to be updated.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[0] https://bugs.debian.org/1006836
[1] https://qa.debian.org/excuses.php?package=python3-defaults

https://ci.debian.net/data/autopkgtest/testing/amd64/t/toil/20695041/log.gz


Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    wf = subprocess.Popen(self.sort_workflow_cmd)
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    wf = subprocess.Popen(self.sort_workflow_cmd + ['--badWorker=1'])
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    subprocess.run(cmd)
  File "/usr/lib/python3.10/subprocess.py", line 501, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    self.check_function('as_pairs', cases=['as_input'],

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    self.check_function('cross', cases=['as_input'],

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    self.check_function('length', cases=['as_input'], expected_result='3')

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    self.check_function('range', cases=['as_input'],

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    self.check_function('read_lines', cases=['as_output'],

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    self.check_function('write_lines', cases=['as_command'],

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    self.check_function('zip', cases=['as_input'],

  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'







Traceback (most recent call last):

    subprocess.check_call(
  File "/usr/lib/python3.10/subprocess.py", line 364, in check_call
    retcode = call(*popenargs, **kwargs)
  File "/usr/lib/python3.10/subprocess.py", line 345, in call
    with Popen(*popenargs, **kwargs) as p:
  File "/usr/lib/python3.10/subprocess.py", line 966, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/usr/lib/python3.10/subprocess.py", line 1842, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'python3.9'

=================================== FAILURES =================================== ___________________ ToilDebugFileTest.testFetchJobStoreFiles ___________________ File "/usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py", line 31, in setUp subprocess.check_call([python, os.path.abspath('src/toil/test/utils/ABCWorkflowDebug/debugWorkflow.py')]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.utils.toilDebugTest.ToilDebugFileTest:testFetchJobStoreFiles (Apr 08 2022 17:25:05:962381 PDT) ______________ ToilDebugFileTest.testFetchJobStoreFilesWSymlinks _______________ File "/usr/lib/python3/dist-packages/toil/test/utils/toilDebugTest.py", line 31, in setUp subprocess.check_call([python, os.path.abspath('src/toil/test/utils/ABCWorkflowDebug/debugWorkflow.py')]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.utils.toilDebugTest.ToilDebugFileTest:testFetchJobStoreFilesWSymlinks (Apr 08 2022 17:25:05:967075 PDT) __________________________ UtilsTest.testGetPIDStatus __________________________ File "/usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py", line 297, in testGetPIDStatus ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.utils.utilsTest.UtilsTest:testGetPIDStatus (Apr 08 2022 17:25:07:984146 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.utils.utilsTest.UtilsTest.testGetPIDStatus ... INFO toil.test:__init__.py:114 Tore down toil.test.utils.utilsTest.UtilsTest.testGetPIDStatus _____________________ UtilsTest.testGetStatusFailedToilWF ______________________ File "/usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py", line 314, in testGetStatusFailedToilWF ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.utils.utilsTest.UtilsTest:testGetStatusFailedToilWF (Apr 08 2022 17:25:08:041669 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.utils.utilsTest.UtilsTest.testGetStatusFailedToilWF ... INFO toil.test:__init__.py:114 Tore down toil.test.utils.utilsTest.UtilsTest.testGetStatusFailedToilWF ________________________ UtilsTest.testRestartAttribute ________________________ File "/usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py", line 367, in testRestartAttribute ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.utils.utilsTest.UtilsTest:testRestartAttribute (Apr 08 2022 17:25:19:193567 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.utils.utilsTest.UtilsTest.testRestartAttribute ... INFO toil.test:__init__.py:114 Tore down toil.test.utils.utilsTest.UtilsTest.testRestartAttribute _________________ WdlLanguageSpecWorkflowsTest.test_type_pair __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 348, in test_type_pair self.check_function('type_pair', cases=['basic'], expected_result=expected_result) File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest:test_type_pair (Apr 08 2022 17:25:21:333976 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest.test_type_pair ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest.test_type_pair _______________ WdlLanguageSpecWorkflowsTest.test_v1_declaration _______________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 365, in test_v1_declaration self.check_function('v1_spec', cases=['declaration'], expected_result=expected_result) File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest:test_v1_declaration (Apr 08 2022 17:25:21:340542 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest.test_v1_declaration ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlLanguageSpecWorkflowsTest.test_v1_declaration _________________ WdlStandardLibraryWorkflowsTest.test_as_map __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 492, in test_as_map self.check_function('as_map', cases=['as_input'], expected_result='{"a":1,"b":2,"c":3}') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_as_map (Apr 08 2022 17:25:21:348497 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_as_map ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_as_map ________________ WdlStandardLibraryWorkflowsTest.test_as_pairs _________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 488, in test_as_pairs File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_as_pairs (Apr 08 2022 17:25:21:354630 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_as_pairs ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_as_pairs __________________ WdlStandardLibraryWorkflowsTest.test_ceil ___________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 399, in test_ceil self.check_function('ceil', cases=['as_input', 'as_command'], expected_result='12') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_ceil (Apr 08 2022 17:25:21:360095 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_ceil ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_ceil _____________ WdlStandardLibraryWorkflowsTest.test_collect_by_key ______________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 499, in test_collect_by_key self.check_function('collect_by_key', cases=['as_input'], expected_result='{"a":[1,3],"b":[2]}') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_collect_by_key (Apr 08 2022 17:25:21:365396 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_collect_by_key ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_collect_by_key __________________ WdlStandardLibraryWorkflowsTest.test_cross __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 482, in test_cross File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_cross (Apr 08 2022 17:25:21:370694 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_cross ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_cross _________________ WdlStandardLibraryWorkflowsTest.test_flatten _________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 502, in test_flatten self.check_function('flatten', cases=['as_input'], expected_result='[1,2,3,1,21,22]') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_flatten (Apr 08 2022 17:25:21:375677 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_flatten ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_flatten __________________ WdlStandardLibraryWorkflowsTest.test_floor __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 402, in test_floor self.check_function('floor', cases=['as_input', 'as_command'], expected_result='11') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_floor (Apr 08 2022 17:25:21:463030 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_floor ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_floor __________________ WdlStandardLibraryWorkflowsTest.test_keys ___________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 495, in test_keys self.check_function('keys', cases=['as_input'], expected_result='["a","b","c"]') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_keys (Apr 08 2022 17:25:21:468463 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_keys ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_keys _________________ WdlStandardLibraryWorkflowsTest.test_length __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 467, in test_length File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_length (Apr 08 2022 17:25:21:473499 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_length ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_length __________________ WdlStandardLibraryWorkflowsTest.test_range __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 449, in test_range File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_range (Apr 08 2022 17:25:21:478504 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_range ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_range __________________ WdlStandardLibraryWorkflowsTest.test_read ___________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 415, in test_read File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_read (Apr 08 2022 17:25:21:483988 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_read ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_read __________________ WdlStandardLibraryWorkflowsTest.test_round __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 405, in test_round self.check_function('round', cases=['as_input', 'as_command'], expected_result='11') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_round (Apr 08 2022 17:25:21:489025 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_round ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_round __________________ WdlStandardLibraryWorkflowsTest.test_size ___________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 389, in test_size self.check_function('size', cases=['as_command'], expected_result='19.0') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_size (Apr 08 2022 17:25:21:494108 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_size ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_size _________________ WdlStandardLibraryWorkflowsTest.test_stdout __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 408, in test_stdout self.check_function('stdout', cases=['as_output'], expected_result='A Whale of a Tale.') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_stdout (Apr 08 2022 17:25:21:498927 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_stdout ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_stdout ___________________ WdlStandardLibraryWorkflowsTest.test_sub ___________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 382, in test_sub self.check_function('sub', cases=['as_input'], expected_result='src/toil/test/wdl/test.csv') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_sub (Apr 08 2022 17:25:21:504199 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_sub ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_sub ________________ WdlStandardLibraryWorkflowsTest.test_transpose ________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 464, in test_transpose self.check_function('transpose', cases=['as_input'], expected_result='0\t3\n1\t4\n2\t5') File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_transpose (Apr 08 2022 17:25:21:510224 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_transpose ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_transpose __________________ WdlStandardLibraryWorkflowsTest.test_write __________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 435, in test_write File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_write (Apr 08 2022 17:25:21:515567 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_write ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_write ___________________ WdlStandardLibraryWorkflowsTest.test_zip ___________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 478, in test_zip File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py", line 320, in check_function subprocess.check_call([exactPython, self.program, wdl_file, json_file, '-o', output_dir]) ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest:test_zip (Apr 08 2022 17:25:21:521031 PDT) ------------------------------ Captured log call ------------------------------- INFO toil.test:__init__.py:109 Setting up toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_zip ... INFO toil.test:__init__.py:114 Tore down toil.test.wdl.builtinTest.WdlStandardLibraryWorkflowsTest.test_zip _______________________ ToilWdlIntegrationTest.testPipe ________________________ File "/usr/lib/python3/dist-packages/toil/test/wdl/toilwdlTest.py", line 350, in testPipe ---------------------------- Captured stdout setup ----------------------------- [TEST] toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest:testPipe (Apr 08 2022 17:25:29:348713 PDT)

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