CellProfiler 3.0.0 startup issue on Windows when TMP directory on different drive

imagejan · December 17, 2019, 5:46pm

I was trying to get a new CellProfiler (3.0.0) installation running on a Windows 10 system, but am running into troubles. Here’s what I did:

Install JRE (1.8.0_151) from Oracle as linked on the CP download page
Install CellProfiler 3.0.0 from http://cellprofiler.org/releases/
Run CellProfiler

I get the following exceptions:

Could not load cellprofiler.modules.calculatestatistics
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\calculatestatistics.py", line 153, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.displayplatemap
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\displayplatemap.py", line 45, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.editobjectsmanually
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\editobjectsmanually.py", line 68, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\loadimages.py", line 107, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.enhanceorsuppressfeatures
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\enhanceorsuppressfeatures.py", line 36, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.exporttodatabase
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\exporttodatabase.py", line 87, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.exporttospreadsheet
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\exporttospreadsheet.py", line 107, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.filterobjects
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\filterobjects.py", line 73, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.flagimage
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\flagimage.py", line 52, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.groups
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\groups.py", line 4, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.identifyobjectsingrid
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\identifyobjectsingrid.py", line 65, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.identifyprimaryobjects
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\identifyprimaryobjects.py", line 19, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.identifysecondaryobjects
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\identifysecondaryobjects.py", line 9, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\threshold.py", line 32, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.identifytertiaryobjects
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\identifytertiaryobjects.py", line 17, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.images
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\images.py", line 15, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.loadimages
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\loadimages.py", line 107, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.loadsingleimage
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\loadsingleimage.py", line 79, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.loaddata
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\loaddata.py", line 229, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\loadimages.py", line 107, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.metadata
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\metadata.py", line 14, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.measureimageintensity
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\measureimageintensity.py", line 9, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.measureimageoverlap
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\measureimageoverlap.py", line 106, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.measureimagequality
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\measureimagequality.py", line 154, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\loadimages.py", line 107, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.measureobjectintensity
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\measureobjectintensity.py", line 15, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.measureobjectoverlap
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\measureobjectoverlap.py", line 75, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.measureobjectsizeshape
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\measureobjectsizeshape.py", line 26, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.measureobjectintensitydistribution
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\measureobjectintensitydistribution.py", line 24, in <module>
  File "CellProfiler\cellprofiler\modules\measureobjectintensitydistribution.py", line 11, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.namesandtypes
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\namesandtypes.py", line 13, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.saveimages
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\saveimages.py", line 46, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\loadimages.py", line 107, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.smooth
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\smooth.py", line 37, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.straightenworms
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\straightenworms.py", line 105, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.threshold
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\threshold.py", line 32, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.trackobjects
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\trackobjects.py", line 26, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Could not load cellprofiler.modules.untangleworms
Traceback (most recent call last):
  File "CellProfiler\cellprofiler\modules\__init__.py", line 321, in add_module
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\untangleworms.py", line 125, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
could not load these modules: cellprofiler.modules.calculatestatistics,cellprofiler.modules.displayplatemap,cellprofiler.modules.editobjectsmanually,cellprofiler.modules.enhanceorsuppressfeatures,cellprofiler.modules.exporttodatabase,cellprofiler.modules.exporttospreadsheet,cellprofiler.modules.filterobjects,cellprofiler.modules.flagimage,cellprofiler.modules.groups,cellprofiler.modules.identifyobjectsingrid,cellprofiler.modules.identifyprimaryobjects,cellprofiler.modules.identifysecondaryobjects,cellprofiler.modules.identifytertiaryobjects,cellprofiler.modules.images,cellprofiler.modules.loadimages,cellprofiler.modules.loadsingleimage,cellprofiler.modules.loaddata,cellprofiler.modules.metadata,cellprofiler.modules.measureimageintensity,cellprofiler.modules.measureimageoverlap,cellprofiler.modules.measureimagequality,cellprofiler.modules.measureobjectintensity,cellprofiler.modules.measureobjectoverlap,cellprofiler.modules.measureobjectsizeshape,cellprofiler.modules.measureobjectintensitydistribution,cellprofiler.modules.namesandtypes,cellprofiler.modules.saveimages,cellprofiler.modules.smooth,cellprofiler.modules.straightenworms,cellprofiler.modules.threshold,cellprofiler.modules.trackobjects,cellprofiler.modules.untangleworms
Traceback (most recent call last):
  File "CellProfiler.py", line 8, in <module>
  File "CellProfiler\cellprofiler\__main__.py", line 152, in main
  File "CellProfiler\cellprofiler\gui\app.py", line 55, in __init__
  File "site-packages\wx-3.0-msw\wx\_core.py", line 8628, in __init__
  File "site-packages\wx-3.0-msw\wx\_core.py", line 8196, in _BootstrapApp
  File "CellProfiler\cellprofiler\gui\app.py", line 58, in OnInit
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\gui\cpframe.py", line 7, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\gui\figure.py", line 43, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\loadimages.py", line 107, in <module>
  File "c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py", line 389, in load_module
  File "CellProfiler\cellprofiler\modules\_help.py", line 235, in <module>
  File "CellProfiler\cellprofiler\modules\_help.py", line 223, in __image_resource
  File "ntpath.py", line 529, in relpath
ValueError: path is on drive E:, start on drive C:
Failed to execute script CellProfiler

I have no idea where the spurious path c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\ is coming from; it doesn’t exist on my system…

Did anyone encounter the same issues before?

bcimini · January 8, 2018, 2:30pm

Hi,

Can you try installing CP on the C drive rather than the E drive and see if that works better? We’ve had reports of people having issues when not installing on C.

imagejan · January 8, 2018, 3:03pm

Thanks for the quick reply, @bcimini!

I did install on the C: drive. My installation is in the default path (C:\Program Files (x86)\CellProfiler), so I have no clue why CellProfiler wants to access the E: drive. The only thing that’s pointing to E: is the TEMP path that is configured to E:\temp to avoid that applications fill up the system drive with temporary data on our multi-user systems…

Let me know if there’s anything I can do to help debugging this.

EDIT
I can confirm that CellProfiler starts up successfully if I run set TMP=C:\temp before starting CP. Nevertheless, I think this behavior should be fixed to allow configuring a temp directory on a non-system drive.

bcimini · January 8, 2018, 4:09pm

Thanks for the clarification and the troubleshooting, apologies for my error! I’ll raise this with our software engineers.

Jama · February 20, 2018, 5:37pm

The error I have is a bit different, but maybe related, that is why I am reporting it here rather than separately.

I am running CP3.0 on Windows 10 as well and installed in the default folder just like mentioned above. And CP3.0 starts up fine for me. But it doesn’t start when I want to start it by double clicking on a pipeline stored elsewhere (on a folder on D:\ drive for example). I get the error message I am showing below at the end of the post. The error message repeats multiple times for different modules.

It is quite annoying, unproductive and interferes with saving output files. What I mean is I was accustomed to opening CP by double clicking on .pipe or .proj files and then select “Elsewhere” in the output folder and the results would be saved in the same folder where the pipelines was stored. But now with this error I can’t do that.

Thanks.

Could not load cellprofiler.modules.calculatestatistics
Traceback (most recent call last):
File “CellProfiler\cellprofiler\modules_init_.py”, line 321, in add_module
File “c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py”, line 389, in load_module
File “CellProfiler\cellprofiler\modules\calculatestatistics.py”, line 153, in
File “c:\users\admini~1\appdata\local\temp\2\pip-build-wsqbac\pyinstaller\PyInstaller\loader\pyimod03_importers.py”, line 389, in load_module
File “CellProfiler\cellprofiler\modules_help.py”, line 235, in
File “CellProfiler\cellprofiler\modules_help.py”, line 223, in __image_resource
File “ntpath.py”, line 529, in relpath
ValueError: path is on drive C:, start on drive D:

bcimini · February 20, 2018, 5:48pm

Hi,

Our SWE are working on a fix to all these relpath errors, sorry!

hajaalin · May 14, 2018, 9:15am

Hi,
another possibly related issue (Win7, CP 3.0.0): we try to set temporary folder on a data drive, but still most of the temp files end up in c:/users/username/appdata/local/temp. Only two hdf5 files appeared in the location we specified.
Best,
Harri

mk_bioc · January 11, 2019, 5:06pm

Hi
I just installed CP3.1.8 on my windows10 machine.
And when i start CP, it just shows blank screen. If i click at certain places, the title of the CP window changes to “Select Cell Profiles” from “Cell Profiler”.

Please help.
Best Wishes
Manoj

markkitt · January 12, 2019, 12:48am

I recommend that you start your own topic rather than posting to one that was solved months ago.

Sylar · January 13, 2019, 12:42pm

Hi, the version I installed is 3.1.5, after being installed on the desktop and double-clicked, the interface flashes back and prompts: Failed to execute script CellProfiler

How can I solve this problem? Thank you!

Alex_Mans · December 17, 2019, 4:54pm

Did this issue get resolved? I’m planning on upgrading to Windows 10 and wanted to know if this Cellprofiler software was compatible with Windows 10.

imagejan · December 17, 2019, 5:11pm

The original issue (specific to the TMP environment variable pointing to a drive letter other than C: on Windows) is not specific to Windows 10, and (to my knowledge) is still not solved.

As mentioned, the issue is not specific to the Windows version, so if it works fine for you on Windows 7, it will very likely also do so on Windows 10.

DStirling · December 17, 2019, 6:46pm

I can confirm that the particular version of Windows shouldn’t make a difference. The current builds of CellProfiler consist of a single .exe which unpacks itself to /temp every time the software runs. I’m going to be looking into having it not do this in future releases, since it’d hopefully make this issue go away while also making it much faster to open the software.

As an albeit temporary workaround, installing from source should allow CellProfiler to function on Windows PCs experiencing this issue.