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Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
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branch develop 63f2dcef275e4c2d8676d43b4024b005d858ba51 reports errors during istall #316

Closed gdevenyi closed 7 years ago

gdevenyi commented 7 years ago 
python setup.py install --prefix ../../build/
running install
running bdist_egg
running egg_info
writing top-level names to pydpiper.egg-info/top_level.txt
writing requirements to pydpiper.egg-info/requires.txt
writing pydpiper.egg-info/PKG-INFO
writing dependency_links to pydpiper.egg-info/dependency_links.txt
reading manifest file 'pydpiper.egg-info/SOURCES.txt'
writing manifest file 'pydpiper.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
copying pydpiper/core/files.py -> build/lib/pydpiper/core
copying pydpiper/core/arguments.py -> build/lib/pydpiper/core
copying pydpiper/minc/registration.py -> build/lib/pydpiper/minc
copying pydpiper/minc/analysis.py -> build/lib/pydpiper/minc
copying pydpiper/execution/pipeline.py -> build/lib/pydpiper/execution
copying pydpiper/execution/pipeline_executor.py -> build/lib/pydpiper/execution
copying pydpiper/execution/application.py -> build/lib/pydpiper/execution
copying pydpiper/pipelines/twolevel_model_building.py -> build/lib/pydpiper/pipelines
copying pydpiper/pipelines/registration_chain.py -> build/lib/pydpiper/pipelines
copying pydpiper/pipelines/MAGeT.py -> build/lib/pydpiper/pipelines
copying pydpiper/pipelines/asymmetry.py -> build/lib/pydpiper/pipelines
copying pydpiper/pipelines/MBM.py -> build/lib/pydpiper/pipelines
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/__init__.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/registration_file_handling.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/LSQ6.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/laplacian_atoms.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/minc_modules.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/registration_functions.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/minc_parameters.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/MAGeT_modules.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/LSQ12.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/minc_atoms.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/stats_tools.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
copying build/lib/atoms_and_modules/NLIN.py -> build/bdist.linux-x86_64/egg/atoms_and_modules
creating build/bdist.linux-x86_64/egg/pydpiper
creating build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/LSQ12.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/MBM.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/NLIN.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/asymmetry.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/twolevel_model_building.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/cortical_thickness.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/MAGeT.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/registration_chain.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/LSQ6.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipelines/__init__.py -> build/bdist.linux-x86_64/egg/pydpiper/pipelines
copying build/lib/pydpiper/pipeline_executor.py -> build/bdist.linux-x86_64/egg/pydpiper
copying build/lib/pydpiper/file_handling.py -> build/bdist.linux-x86_64/egg/pydpiper
copying build/lib/pydpiper/pipeline.py -> build/bdist.linux-x86_64/egg/pydpiper
creating build/bdist.linux-x86_64/egg/pydpiper/core
copying build/lib/pydpiper/core/stages.py -> build/bdist.linux-x86_64/egg/pydpiper/core
copying build/lib/pydpiper/core/arguments.py -> build/bdist.linux-x86_64/egg/pydpiper/core
copying build/lib/pydpiper/core/util.py -> build/bdist.linux-x86_64/egg/pydpiper/core
copying build/lib/pydpiper/core/conversion.py -> build/bdist.linux-x86_64/egg/pydpiper/core
copying build/lib/pydpiper/core/__init__.py -> build/bdist.linux-x86_64/egg/pydpiper/core
copying build/lib/pydpiper/core/files.py -> build/bdist.linux-x86_64/egg/pydpiper/core
copying build/lib/pydpiper/queueing.py -> build/bdist.linux-x86_64/egg/pydpiper
copying build/lib/pydpiper/__init__.py -> build/bdist.linux-x86_64/egg/pydpiper
creating build/bdist.linux-x86_64/egg/pydpiper/execution
copying build/lib/pydpiper/execution/pipeline.py -> build/bdist.linux-x86_64/egg/pydpiper/execution
copying build/lib/pydpiper/execution/application.py -> build/bdist.linux-x86_64/egg/pydpiper/execution
copying build/lib/pydpiper/execution/__init__.py -> build/bdist.linux-x86_64/egg/pydpiper/execution
copying build/lib/pydpiper/execution/check_pipeline_status.py -> build/bdist.linux-x86_64/egg/pydpiper/execution
copying build/lib/pydpiper/execution/pipeline_executor.py -> build/bdist.linux-x86_64/egg/pydpiper/execution
copying build/lib/pydpiper/execution/queueing.py -> build/bdist.linux-x86_64/egg/pydpiper/execution
creating build/bdist.linux-x86_64/egg/pydpiper/minc
copying build/lib/pydpiper/minc/analysis.py -> build/bdist.linux-x86_64/egg/pydpiper/minc
copying build/lib/pydpiper/minc/containers.py -> build/bdist.linux-x86_64/egg/pydpiper/minc
copying build/lib/pydpiper/minc/files.py -> build/bdist.linux-x86_64/egg/pydpiper/minc
copying build/lib/pydpiper/minc/thickness.py -> build/bdist.linux-x86_64/egg/pydpiper/minc
copying build/lib/pydpiper/minc/__init__.py -> build/bdist.linux-x86_64/egg/pydpiper/minc
copying build/lib/pydpiper/minc/registration.py -> build/bdist.linux-x86_64/egg/pydpiper/minc
copying build/lib/pydpiper/application.py -> build/bdist.linux-x86_64/egg/pydpiper
copying build/lib/pydpiper/check_pipeline_status.py -> build/bdist.linux-x86_64/egg/pydpiper
creating build/bdist.linux-x86_64/egg/applications
copying build/lib/applications/cortical_thickness.py -> build/bdist.linux-x86_64/egg/applications
copying build/lib/applications/twolevel_model_building.py -> build/bdist.linux-x86_64/egg/applications
copying build/lib/applications/pairwise_nlin.py -> build/bdist.linux-x86_64/egg/applications
copying build/lib/applications/registration_chain.py -> build/bdist.linux-x86_64/egg/applications
copying build/lib/applications/__init__.py -> build/bdist.linux-x86_64/egg/applications
copying build/lib/applications/MBM.py -> build/bdist.linux-x86_64/egg/applications
copying build/lib/applications/MAGeT.py -> build/bdist.linux-x86_64/egg/applications
byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/__init__.py to __init__.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/registration_file_handling.py to registration_file_handling.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/registration_file_handling.py", line 46
    print "Error: the gradient file with fwhm ", fwhm, " does not exist for file ", self.basevol
                                              ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/LSQ6.py to LSQ6.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/LSQ6.py", line 32
    print "\nError: please specify a target for the 6 parameter alignmnet. Options are: --lsq6-target, --init-model, --bootstrap.\n"
                                                                                                                                   ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/laplacian_atoms.py to laplacian_atoms.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/minc_modules.py to minc_modules.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/minc_modules.py", line 220
    print "\nError: the FullIterativeLSQ12Nlin module was called without specifying either an initial model, nor an lsq12_subject_matter. Currently that means that the code can not determine the resolution at which the registrations should be run. Please specify one of the two. Exiting\n"
                                                                                                                                                                                                                                                                                                ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/registration_functions.py to registration_functions.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/registration_functions.py", line 68
    print "Error: no source image provided\n"
                                            ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/minc_parameters.py to minc_parameters.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/minc_parameters.py", line 99
    print "The non-linear protocol you have specified is in an unrecognized form: \n%s\n Exiting..." % self.regProtocol
                                                                                                   ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/MAGeT_modules.py to MAGeT_modules.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/LSQ12.py to LSQ12.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/LSQ12.py", line 150
    print "\nError: the FullLSQ12 module was called without specifying the resolution that it should be run at, and without specifying a subject matter. Please indicate one of the two. Exiting...\n"
                                                                                                                                                                                                     ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/minc_atoms.py to minc_atoms.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/minc_atoms.py", line 77
    print "Failed in putting together mincANTS command; unexpected error: "
                                                                          ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/stats_tools.py to stats_tools.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/stats_tools.py", line 77
    print "Improper type of blurring kernels specified for stats calculation: " + str(statsKernels)
                                                                              ^
SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/atoms_and_modules/NLIN.py to NLIN.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/atoms_and_modules/NLIN.py", line 178
    print "You have passed a target average that is neither a string nor a file handler: " + str(self.targetAvg)
                                                                                         ^
SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/LSQ12.py to LSQ12.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/MBM.py to MBM.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/NLIN.py to NLIN.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/asymmetry.py to asymmetry.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/twolevel_model_building.py to twolevel_model_building.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/cortical_thickness.py to cortical_thickness.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/MAGeT.py to MAGeT.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/registration_chain.py to registration_chain.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/LSQ6.py to LSQ6.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipelines/__init__.py to __init__.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipeline_executor.py to pipeline_executor.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/file_handling.py to file_handling.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/pydpiper/file_handling.py", line 48
    print "Could not create directory " + str(dirname)
                                      ^
SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/pydpiper/pipeline.py to pipeline.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/pydpiper/pipeline.py", line 288
    print "Total number of stages in the pipeline: ", len(self.stages)
                                                   ^
SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/pydpiper/core/stages.py to stages.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/core/arguments.py to arguments.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/core/util.py to util.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/core/conversion.py to conversion.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/core/__init__.py to __init__.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/core/files.py to files.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/queueing.py to queueing.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/__init__.py to __init__.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/execution/pipeline.py to pipeline.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/execution/application.py to application.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/execution/__init__.py to __init__.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/execution/check_pipeline_status.py to check_pipeline_status.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/execution/pipeline_executor.py to pipeline_executor.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/execution/queueing.py to queueing.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/minc/analysis.py to analysis.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/minc/containers.py to containers.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/minc/files.py to files.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/minc/thickness.py to thickness.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/minc/__init__.py to __init__.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/minc/registration.py to registration.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/pydpiper/application.py to application.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/pydpiper/application.py", line 101
    print self.__version__
             ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/pydpiper/check_pipeline_status.py to check_pipeline_status.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/pydpiper/check_pipeline_status.py", line 27
    print "There is a problem opening the specified uri file: %s" % uri_file
                                                                ^
SyntaxError: Missing parentheses in call to 'print'

byte-compiling build/bdist.linux-x86_64/egg/applications/cortical_thickness.py to cortical_thickness.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/applications/twolevel_model_building.py to twolevel_model_building.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/applications/twolevel_model_building.py", line 130
    print "--input-space can only be native, lsq6 or lsq12. You specified: " + str(options.input_space)
                                                                           ^
SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/applications/pairwise_nlin.py to pairwise_nlin.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/applications/registration_chain.py to registration_chain.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/applications/registration_chain.py", line 111
    print """Only native and lsq6 are allowed as input_space options for the registration chain. You specified: """ + str(self.options.input_space)
                                                                                                                  ^
SyntaxError: invalid syntax

byte-compiling build/bdist.linux-x86_64/egg/applications/__init__.py to __init__.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/applications/MBM.py to MBM.cpython-35.pyc
byte-compiling build/bdist.linux-x86_64/egg/applications/MAGeT.py to MAGeT.cpython-35.pyc
  File "build/bdist.linux-x86_64/egg/applications/MAGeT.py", line 39
    print "Incorrect registration method specified: ", self.options.reg_method
                                                    ^
SyntaxError: Missing parentheses in call to 'print'

installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/config
copying config/CCM_HPF.cfg -> build/bdist.linux-x86_64/egg/config
copying config/MICe.cfg -> build/bdist.linux-x86_64/egg/config
copying config/MICe_dev.cfg -> build/bdist.linux-x86_64/egg/config
copying config/SciNet.cfg -> build/bdist.linux-x86_64/egg/config
copying config/SciNet_debug.cfg -> build/bdist.linux-x86_64/egg/config
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
copying and adjusting pydpiper/execution/pipeline_executor.py -> build/scripts-3.5
copying and adjusting pydpiper/pipelines/asymmetry.py -> build/scripts-3.5
copying and adjusting pydpiper/pipelines/MAGeT.py -> build/scripts-3.5
copying and adjusting pydpiper/pipelines/MBM.py -> build/scripts-3.5
copying and adjusting pydpiper/pipelines/registration_chain.py -> build/scripts-3.5
copying and adjusting pydpiper/pipelines/twolevel_model_building.py -> build/scripts-3.5
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/LSQ12.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/LSQ6.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/MBM.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/asymmetry.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/pipeline_executor.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/registration_chain.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/check_pipeline_status.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/MAGeT.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/twolevel_model_building.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.5/NLIN.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/LSQ12.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/LSQ6.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/MBM.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/asymmetry.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pipeline_executor.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/registration_chain.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/check_pipeline_status.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/MAGeT.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/twolevel_model_building.py to 755
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/NLIN.py to 755
copying pydpiper.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pydpiper.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pydpiper.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pydpiper.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pydpiper.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pydpiper.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/pydpiper-2.0.5-py3.5.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Creating /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/site.py
Processing pydpiper-2.0.5-py3.5.egg
creating /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg
Extracting pydpiper-2.0.5-py3.5.egg to /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages
  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/registration_functions.py", line 68
    print "Error: no source image provided\n"
                                            ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/minc_modules.py", line 220
    print "\nError: the FullIterativeLSQ12Nlin module was called without specifying either an initial model, nor an lsq12_subject_matter. Currently that means that the code can not determine the resolution at which the registrations should be run. Please specify one of the two. Exiting\n"
                                                                                                                                                                                                                                                                                                ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/NLIN.py", line 178
    print "You have passed a target average that is neither a string nor a file handler: " + str(self.targetAvg)
                                                                                         ^
SyntaxError: invalid syntax

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/LSQ12.py", line 150
    print "\nError: the FullLSQ12 module was called without specifying the resolution that it should be run at, and without specifying a subject matter. Please indicate one of the two. Exiting...\n"
                                                                                                                                                                                                     ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/registration_file_handling.py", line 46
    print "Error: the gradient file with fwhm ", fwhm, " does not exist for file ", self.basevol
                                              ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/minc_parameters.py", line 99
    print "The non-linear protocol you have specified is in an unrecognized form: \n%s\n Exiting..." % self.regProtocol
                                                                                                   ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/stats_tools.py", line 77
    print "Improper type of blurring kernels specified for stats calculation: " + str(statsKernels)
                                                                              ^
SyntaxError: invalid syntax

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/LSQ6.py", line 32
    print "\nError: please specify a target for the 6 parameter alignmnet. Options are: --lsq6-target, --init-model, --bootstrap.\n"
                                                                                                                                   ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/atoms_and_modules/minc_atoms.py", line 77
    print "Failed in putting together mincANTS command; unexpected error: "
                                                                          ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/applications/registration_chain.py", line 111
    print """Only native and lsq6 are allowed as input_space options for the registration chain. You specified: """ + str(self.options.input_space)
                                                                                                                  ^
SyntaxError: invalid syntax

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/applications/twolevel_model_building.py", line 130
    print "--input-space can only be native, lsq6 or lsq12. You specified: " + str(options.input_space)
                                                                           ^
SyntaxError: invalid syntax

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/applications/MAGeT.py", line 39
    print "Incorrect registration method specified: ", self.options.reg_method
                                                    ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/pydpiper/file_handling.py", line 48
    print "Could not create directory " + str(dirname)
                                      ^
SyntaxError: invalid syntax

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/pydpiper/application.py", line 101
    print self.__version__
             ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/pydpiper/check_pipeline_status.py", line 27
    print "There is a problem opening the specified uri file: %s" % uri_file
                                                                ^
SyntaxError: Missing parentheses in call to 'print'

  File "/opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg/pydpiper/pipeline.py", line 288
    print "Total number of stages in the pipeline: ", len(self.stages)
                                                   ^
SyntaxError: invalid syntax

Adding pydpiper 2.0.5 to easy-install.pth file
Installing registration_chain.py script to ../../build//bin
Installing asymmetry.py script to ../../build//bin
Installing LSQ6.py script to ../../build//bin
Installing twolevel_model_building.py script to ../../build//bin
Installing LSQ12.py script to ../../build//bin
Installing check_pipeline_status.py script to ../../build//bin
Installing MAGeT.py script to ../../build//bin
Installing NLIN.py script to ../../build//bin
Installing MBM.py script to ../../build//bin
Installing pipeline_executor.py script to ../../build//bin

Installed /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pydpiper-2.0.5-py3.5.egg
Processing dependencies for pydpiper==2.0.5
Searching for typing
Reading https://pypi.python.org/simple/typing/
Downloading https://pypi.python.org/packages/b6/0c/53c42edca789378b8c05a5496e689f44e5dd82bc6861d1ae5a926ee51b84/typing-3.5.3.0.tar.gz#md5=3996a747158e5591abf689c1c5f8f9db
Best match: typing 3.5.3.0
Processing typing-3.5.3.0.tar.gz
Writing /tmp/easy_install-4k6_vsl3/typing-3.5.3.0/setup.cfg
Running typing-3.5.3.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-4k6_vsl3/typing-3.5.3.0/egg-dist-tmp-08tjby3n
zip_safe flag not set; analyzing archive contents...
Moving typing-3.5.3.0-py3.5.egg to /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages
Adding typing 3.5.3.0 to easy-install.pth file

Installed /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/typing-3.5.3.0-py3.5.egg
Searching for Pyro4
Reading https://pypi.python.org/simple/Pyro4/
Downloading https://pypi.python.org/packages/7b/ae/f034d9d07390a86bb8bbb9449181c39056dc44617c638379f59e1b3d62fd/Pyro4-4.53.tar.gz#md5=71a2629229b7101996d41282c5c7157f
Best match: Pyro4 4.53
Processing Pyro4-4.53.tar.gz
Writing /tmp/easy_install-7d5bsnp0/Pyro4-4.53/setup.cfg
Running Pyro4-4.53/setup.py -q bdist_egg --dist-dir /tmp/easy_install-7d5bsnp0/Pyro4-4.53/egg-dist-tmp-7xcjhkou
Pyro version = 4.53
warning: no previously-included files matching '*/.svn/*' found anywhere in distribution
warning: no previously-included files matching '*/.idea/*' found anywhere in distribution
warning: no previously-included files matching '*.class' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.coverage' found anywhere in distribution
warning: no previously-included files matching 'nosetests.xml' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
warning: no previously-included files matching '.gitignore' found anywhere in distribution
warning: no previously-included files matching '.tox' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
zip_safe flag not set; analyzing archive contents...
Pyro4.utils.__pycache__.flame.cpython-35: module MAY be using inspect.getsource
creating /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/Pyro4-4.53-py3.5.egg
Extracting Pyro4-4.53-py3.5.egg to /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages
Adding Pyro4 4.53 to easy-install.pth file
Installing pyro4-httpgateway script to ../../build//bin
Installing pyro4-flameserver script to ../../build//bin
Installing pyro4-nsc script to ../../build//bin
Installing pyro4-ns script to ../../build//bin
Installing pyro4-check-config script to ../../build//bin
Installing pyro4-test-echoserver script to ../../build//bin

Installed /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/Pyro4-4.53-py3.5.egg
Searching for pyminc
Reading https://pypi.python.org/simple/pyminc/
Downloading https://pypi.python.org/packages/d4/53/11abc40b1a6ce8dfefc6f2a639e6ca567e82ade75eefb7ffb24c81e5202e/pyminc-0.48.tar.gz#md5=6c6c55902a4bec9f89abec60f54b841e
Best match: pyminc 0.48
Processing pyminc-0.48.tar.gz
Writing /tmp/easy_install-ymrmbdkz/pyminc-0.48/setup.cfg
Running pyminc-0.48/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ymrmbdkz/pyminc-0.48/egg-dist-tmp-h0ld0ens
zip_safe flag not set; analyzing archive contents...
Moving pyminc-0.48-py3.5.egg to /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages
Adding pyminc 0.48 to easy-install.pth file
Installing pyminc_test2.py script to ../../build//bin
Installing sva2mnc.py script to ../../build//bin

Installed /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/pyminc-0.48-py3.5.egg
Searching for ordered-set
Reading https://pypi.python.org/simple/ordered-set/
Downloading https://pypi.python.org/packages/80/8c/7405f2f1a5b4a95fbc87b1e43df9a630aa30d93c0cfb06a9ea64fd436399/ordered-set-2.0.1.tar.gz#md5=3111c0dd1417b6421eb982e4cd4d0d68
Best match: ordered-set 2.0.1
Processing ordered-set-2.0.1.tar.gz
Writing /tmp/easy_install-z439rc8a/ordered-set-2.0.1/setup.cfg
Running ordered-set-2.0.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-z439rc8a/ordered-set-2.0.1/egg-dist-tmp-3a49ups4
zip_safe flag not set; analyzing archive contents...
Moving ordered_set-2.0.1-py3.5.egg to /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages
Adding ordered-set 2.0.1 to easy-install.pth file

Installed /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/ordered_set-2.0.1-py3.5.egg
Searching for ConfigArgParse>=0.11.0
Reading https://pypi.python.org/simple/ConfigArgParse/
Downloading https://pypi.python.org/packages/45/87/a815edcdc867de0964e5f1efef6db956bbb6fe77dbe3f273f2aeab39cbe8/ConfigArgParse-0.11.0.tar.gz#md5=e8cb0b30e78ab5fd013a498be9cf22b4
Best match: ConfigArgParse 0.11.0
Processing ConfigArgParse-0.11.0.tar.gz
Writing /tmp/easy_install-mrl1cbyo/ConfigArgParse-0.11.0/setup.cfg
Running ConfigArgParse-0.11.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-mrl1cbyo/ConfigArgParse-0.11.0/egg-dist-tmp-ba3fa0kh
zip_safe flag not set; analyzing archive contents...
Moving ConfigArgParse-0.11.0-py3.5.egg to /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages
Adding ConfigArgParse 0.11.0 to easy-install.pth file

Installed /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/ConfigArgParse-0.11.0-py3.5.egg
Searching for serpent>=1.16
Reading https://pypi.python.org/simple/serpent/
Downloading https://pypi.python.org/packages/b2/08/1cd67401eae5429a3f5774167208c3cb833a8595c5e8b6b2e3782d6d17d7/serpent-1.16.tar.gz#md5=9d0cfe1f57f468100d3ae94c4de47950
Best match: serpent 1.16
Processing serpent-1.16.tar.gz
Writing /tmp/easy_install-j2u668wu/serpent-1.16/setup.cfg
Running serpent-1.16/setup.py -q bdist_egg --dist-dir /tmp/easy_install-j2u668wu/serpent-1.16/egg-dist-tmp-j05pbf5f
zip_safe flag not set; analyzing archive contents...
Moving serpent-1.16-py3.5.egg to /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages
Adding serpent 1.16 to easy-install.pth file

Installed /opt/quarantine/pydpiper/git/build/lib/python3.5/site-packages/serpent-1.16-py3.5.egg
Searching for pytest==2.9.2
Best match: pytest 2.9.2
Adding pytest 2.9.2 to easy-install.pth file
Installing py.test-3.5 script to ../../build//bin
Installing py.test script to ../../build//bin

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Searching for pandas==0.18.1
Best match: pandas 0.18.1
Adding pandas 0.18.1 to easy-install.pth file

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Searching for networkx==1.11
Best match: networkx 1.11
Adding networkx 1.11 to easy-install.pth file

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Searching for py==1.4.31
Best match: py 1.4.31
Adding py 1.4.31 to easy-install.pth file

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Searching for numpy==1.11.1
Best match: numpy 1.11.1
Adding numpy 1.11.1 to easy-install.pth file

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Searching for pytz==2016.6.1
Best match: pytz 2016.6.1
Adding pytz 2016.6.1 to easy-install.pth file

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Searching for python-dateutil==2.5.3
Best match: python-dateutil 2.5.3
Adding python-dateutil 2.5.3 to easy-install.pth file

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Searching for decorator==4.0.10
Best match: decorator 4.0.10
Adding decorator 4.0.10 to easy-install.pth file

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Searching for six==1.10.0
Best match: six 1.10.0
Adding six 1.10.0 to easy-install.pth file

Using /opt/quarantine/anaconda/4.2.0-python3/build/lib/python3.5/site-packages
Finished processing dependencies for pydpiper==2.0.5
bcdarwin commented 7 years ago

I think something's weird with your build directory. Try removing build/ and start again?

gdevenyi commented 7 years ago

Purge and reinstall shows the same errors.

bcdarwin commented 7 years ago

OK, it what about removing build/, dist/, ... from the git directory? If I do grep -R 'print ' ., I don't see any of those lines. In fact, atoms_and_modules doesn't even exist in the 2.x directory tree.

gdevenyi commented 7 years ago

That solved it.

Looks like a "git checkout develop" left those directories orphaned. Sorry for the noise.