[Debian-med-packaging] Bug#1009201: toil: (autopkgtest) needs update for python3.10: No such file or directory: 'python3.9'
Paul Gevers
elbrus at debian.org
Fri Apr 8 20:42:43 BST 2022
Source: toil
Version: 5.6.0-5
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: needs-update
User: debian-python at lists.debian.org
Usertags: python3.10
Control: affects -1 src:python3-defaults
Dear maintainer(s),
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:
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.
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
=================================== FAILURES
===================================
___________________ ToilDebugFileTest.testFetchJobStoreFiles
___________________
Traceback (most recent call last):
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')])
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'
---------------------------- Captured stdout setup
-----------------------------
[TEST]
toil.test.utils.toilDebugTest.ToilDebugFileTest:testFetchJobStoreFiles
(Apr 08 2022 17:25:05:962381 PDT)
______________ ToilDebugFileTest.testFetchJobStoreFilesWSymlinks
_______________
Traceback (most recent call last):
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')])
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'
---------------------------- Captured stdout setup
-----------------------------
[TEST]
toil.test.utils.toilDebugTest.ToilDebugFileTest:testFetchJobStoreFilesWSymlinks
(Apr 08 2022 17:25:05:967075 PDT)
__________________________ UtilsTest.testGetPIDStatus
__________________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py",
line 297, in testGetPIDStatus
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'
---------------------------- 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
______________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py",
line 314, in testGetStatusFailedToilWF
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'
---------------------------- 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
________________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/utils/utilsTest.py",
line 367, in testRestartAttribute
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'
---------------------------- 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
__________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
_______________
Traceback (most recent call last):
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])
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'
---------------------------- 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
__________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
_________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py",
line 488, in test_as_pairs
self.check_function('as_pairs', cases=['as_input'],
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])
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'
---------------------------- 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
___________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
______________
Traceback (most recent call last):
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])
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'
---------------------------- 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
__________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py",
line 482, in test_cross
self.check_function('cross', cases=['as_input'],
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])
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'
---------------------------- 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
_________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
__________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
___________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
__________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py",
line 467, in test_length
self.check_function('length', cases=['as_input'], expected_result='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])
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'
---------------------------- 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
__________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py",
line 449, in test_range
self.check_function('range', cases=['as_input'],
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])
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'
---------------------------- 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
___________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py",
line 415, in test_read
self.check_function('read_lines', cases=['as_output'],
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])
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'
---------------------------- 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
__________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
___________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
__________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
___________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
________________
Traceback (most recent call last):
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])
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'
---------------------------- 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
__________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py",
line 435, in test_write
self.check_function('write_lines', cases=['as_command'],
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])
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'
---------------------------- 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
___________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/wdl/builtinTest.py",
line 478, in test_zip
self.check_function('zip', cases=['as_input'],
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])
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'
---------------------------- 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
________________________
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/toil/test/wdl/toilwdlTest.py",
line 350, in testPipe
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'
---------------------------- Captured stdout setup
-----------------------------
[TEST] toil.test.wdl.toilwdlTest.ToilWdlIntegrationTest:testPipe (Apr 08
2022 17:25:29:348713 PDT)
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