5.79s
Test: test_vessel_particles_mask_workflow
(Failed)
Build: CIP-Darwin-17.7.0-x86_64-incr-SL-ON
(bwh002376.bwh.harvard.edu)
on 2021-10-22 23:01:34
Repository revision: e769c65fa429a3c76437833bd7d5a8aa5b934232
Show Command Line/Users/acil-user/Projects/CIP-build/CIPPython-install/bin/nosetests "/Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests/test_vessel_particles_mask_workflow.py"
Display graphs:
Test outputCould not import jpeg_ls
Could not import gdcm
E
======================================================================
ERROR: test_vessel_particles_mask_workflow.test_vessel_particles_mask_workflow
----------------------------------------------------------------------
Traceback (most recent call last):
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests/test_vessel_particles_mask_workflow.py", line 19, in test_vessel_particles_mask_workflow
wf.run()
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run
report_nodes_not_run(notrun)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details
-------------------- >> begin captured logging << --------------------
pydicom: DEBUG: Could not import jpeg_ls
pydicom: DEBUG: Could not import gdcm
matplotlib: DEBUG: $HOME=/Users/acil-user
matplotlib: DEBUG: matplotlib data path /Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/matplotlib/mpl-data
matplotlib: DEBUG: loaded rc file /Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib: DEBUG: matplotlib version 2.2.3
matplotlib: DEBUG: interactive is False
matplotlib: DEBUG: platform is darwin
matplotlib: DEBUG: loaded modules: ['PIL.io', 'email.MIMEAudio', 'numpy.core.info', 'nose.plugins.doctest', 'nose.plugins.tempfile', 'pydicom.re', 'ctypes.os', 'hotshot.warnings', 'hotshot.stats', 'gc', 'pkg_resources._vendor.traceback', 'cffi.model', 'nose.plugins.attrib', 'numpy.random.threading', 'nrrd.re', 'logging.weakref', 'pprint', 'nose.plugins.logcapture', 'pydicom.decimal', 'nose.new', 'unittest.sys', 'SimpleITK.builtins', 'numpy.core.umath', 'nose.os', 'pydicom.dicomdir', 'numpy._pytesttester', 'string', 'pydicom.pixel_data_handlers.struct', 'numpy.lib.arraysetops', 'nose.plugins.__builtin__', 'encodings.utf_8', 'xml.etree.warnings', 'xml.etree.sys', 'email.quoprimime', 'numpy.ctypeslib', 'json.encoder', 'subprocess', 'numpy.core.machar', '_ast', 'pydicom.random', 'nose.plugins.optparse', 'email.codecs', 'future.types.newobject', 'pydicom.sequence', 'numpy.ma.extras', 'numpy.fft.fftpack_lite', 'PIL.atexit', 'multiprocessing', 'dis', 'numpy.lib', 'logging.threading', 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matplotlib: DEBUG: CACHEDIR=/Users/acil-user/.matplotlib
matplotlib.font_manager: DEBUG: Using fontManager instance from /Users/acil-user/.matplotlib/fontList.json
matplotlib.backends: DEBUG: backend MacOSX version unknown
workflow: INFO: ['check', 'execution', 'logging']
workflow: INFO: Running serially.
workflow: INFO: Executing node compute_distance_transform in dir: /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpx0hsel/VesselParticlesMaskWorkflow/compute_distance_transform
workflow: INFO: Running: ComputeDistanceMap --distanceMap "/var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpDwxgZM/vessel_distanceMap.nhdr" --labelMap "/Users/acil-user/Projects/CIP-build/CIP-build/Testing/Data/Input/vessel_volumeMask.nrrd"
interface: INFO: stdout 2021-10-22T23:07:20.047135:Reading label map...
interface: INFO: stdout 2021-10-22T23:07:20.047135:Skipping downsampling...
interface: INFO: stdout 2021-10-22T23:07:20.047135:Computing distance map...
interface: INFO: stdout 2021-10-22T23:07:20.047135:Writing to file...
interface: INFO: stdout 2021-10-22T23:07:20.047135:DONE.
workflow: INFO: Executing node unu_2op_lt in dir: /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpcmWGbh/VesselParticlesMaskWorkflow/unu_2op_lt
workflow: INFO: Running: unu 2op lt /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpDwxgZM/vessel_distanceMap.nhdr -2.000000 --output /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpDwxgZM/vessel_featureMask.nhdr --type short
workflow: INFO: Executing node compute_feature_strength in dir: /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpqiRl5T/VesselParticlesMaskWorkflow/compute_feature_strength
workflow: INFO: Running: ComputeFeatureStrength --C 245.000000 --alpha 0.630000 --alphase 0.250000 --beta 0.510000 --betase 0.100000 --feature "RidgeLine" --inFileName "/Users/acil-user/Projects/CIP-build/CIP-build/Testing/Data/Input/vessel.nrrd" --kappa 0.500000 --method "Frangi" --nu 0.000000 --outFileName "/var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpDwxgZM/vessel_strength.nhdr" --rescaleOff --ssm 1 --std 0.7,4.0,7.0 --threads 0
workflow: ERROR: ['Node compute_feature_strength failed to run on host bwh002376.bwh.harvard.edu.']
workflow: INFO: Saving crash info to /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests/crash-20211022-230722-acil-user-compute_feature_strength-2e1f9b52-a68e-40aa-8a14-5f87afb69010.pklz
workflow: INFO: Traceback (most recent call last):
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
node.run(updatehash=updatehash)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
self._run_interface()
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
self._result = self._run_command(execute)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
result = self._interface.run()
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
runtime = self._run_wrapper(runtime)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
runtime = self._run_interface(runtime)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1686, in _run_interface
(self.cmd.split()[0], runtime.hostname))
IOError: command 'ComputeFeatureStrength' could not be found on host bwh002376.bwh.harvard.edu
Interface ComputeFeatureStrength failed to run.
workflow: INFO: ***********************************
workflow: ERROR: could not run node: VesselParticlesMaskWorkflow.compute_feature_strength
workflow: INFO: crashfile: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests/crash-20211022-230722-acil-user-compute_feature_strength-2e1f9b52-a68e-40aa-8a14-5f87afb69010.pklz
workflow: INFO: ***********************************
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 1 test in 2.642s
FAILED (errors=1)
