CellProfiler won't start

Hello

I’m unable to start CellProfiler the normal way (e.g. clicking on its icon). Here’s what I’m using:
CellProfiler-3.1.8
Mac Os X High Sierra 10.13.6 (17G4015)
MacBook Pro

I tried these without success:

  • previous version of CellProfiler 3.1.5
  • deleting the config file ~/Library/Preferences/CellProfilerLocal.cfg

I was able to start it from the command line by running:

/Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp

I’ve attached a screenshot of ActivityMonitor showing CellProfiler hanging during startup:

Any ideas for what I can try or how I can debug / find out more information about what is happening?

Thank you,
Dave

Just wanted to note that I have been having the same problem with both 3.1.5 and 3.1.8 (I’d been using 3.0.0 instead, which still opens normal on my machine). I am running:

Mac Os X High Sierra 10.13.6 (17G3025)
MacBook Pro

Just to add one thing: it also does not work if you try to open 3.1.8 by double clicking on a .cpproj file (and having 3.1.8 as the default application).

I can also get it to work via command line, as dllahr described above. When I do that, this is the output, which seems mostly normal I think?

/Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp
[12800] PyInstaller Bootloader 3.x
[12800] LOADER: executable is /Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp
[12800] LOADER: homepath is /Applications/CellProfiler-3.1.8.app/Contents/MacOS
[12800] LOADER: _MEIPASS2 is NULL
[12800] LOADER: archivename is /Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp
[12800] LOADER: /Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp contains a digital signature
[12800] LOADER: No need to extract files to run; setting extractionpath to homepath
[12800] LOADER: Already in the child - running user's code.
[12800] LOADER: Python library: /Applications/CellProfiler-3.1.8.app/Contents/MacOS/Python
[12800] LOADER: Loaded functions from Python library.
[12800] LOADER: Manipulating environment (sys.path, sys.prefix)
[12800] LOADER: sys.prefix is /Applications/CellProfiler-3.1.8.app/Contents/MacOS
[12800] LOADER: Setting runtime options
[12800] LOADER: Initializing python
[12800] LOADER: Overriding Python's sys.path
[12800] LOADER: Post-init sys.path is /Applications/CellProfiler-3.1.8.app/Contents/MacOS
[12800] LOADER: Setting sys.argv
[12800] LOADER: setting sys._MEIPASS
[12800] LOADER: importing modules from CArchive
[12800] LOADER: extracted struct
[12800] LOADER: callfunction returned...
[12800] LOADER: extracted pyimod01_os_path
[12800] LOADER: callfunction returned...
[12800] LOADER: extracted pyimod02_archive
[12800] LOADER: callfunction returned...
[12800] LOADER: extracted pyimod03_importers
[12800] LOADER: callfunction returned...
[12800] LOADER: Installing PYZ archive with Python modules.
[12800] LOADER: PYZ archive: out00-PYZ.pyz
[12800] LOADER: Running pyiboot01_bootstrap.py
[12800] LOADER: Running pyi_rth_traitlets.py
[12800] LOADER: Running pyi_rth_mplconfig.py
[12800] LOADER: Running pyi_rth_mpldata.py
[12800] LOADER: Running pyi_rth_pkgres.py
[12800] LOADER: Running pyi_rth_multiprocessing.py
[12800] LOADER: Running CellProfiler.py
/Applications/CellProfiler-3.1.8.app/Contents/MacOS/wx/_core.py:16633: UserWarning: wxPython/wxWidgets release number mismatch
font search path ['/Applications/CellProfiler-3.1.8.app/Contents/MacOS/mpl-data/fonts/ttf', '/Applications/CellProfiler-3.1.8.app/Contents/MacOS/mpl-data/fonts/afm', '/Applications/CellProfiler-3.1.8.app/Contents/MacOS/mpl-data/fonts/pdfcorefonts']
Could not open font file /Library/Fonts/NISC18030.ttf
generated new fontManager

Thanks,
Bryan

Hi All, same problem and it also fails from the comand. I got this report:
Last login: Thu Jan 24 20:21:36 on console

dhcp-biotek-04:~ balistre$ /Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp

[19749] PyInstaller Bootloader 3.x

[19749] LOADER: executable is /Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp

[19749] LOADER: homepath is /Applications/CellProfiler-3.1.8.app/Contents/MacOS

[19749] LOADER: _MEIPASS2 is NULL

[19749] LOADER: archivename is /Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp

[19749] LOADER: /Applications/CellProfiler-3.1.8.app/Contents/MacOS/cp contains a digital signature

[19749] LOADER: No need to extract files to run; setting extractionpath to homepath

[19749] LOADER: Already in the child - running user’s code.

[19749] LOADER: Python library: /Applications/CellProfiler-3.1.8.app/Contents/MacOS/Python

[19749] LOADER: Loaded functions from Python library.

[19749] LOADER: Manipulating environment (sys.path, sys.prefix)

[19749] LOADER: sys.prefix is /Applications/CellProfiler-3.1.8.app/Contents/MacOS

[19749] LOADER: Setting runtime options

[19749] LOADER: Initializing python

[19749] LOADER: Overriding Python’s sys.path

[19749] LOADER: Post-init sys.path is /Applications/CellProfiler-3.1.8.app/Contents/MacOS

[19749] LOADER: Setting sys.argv

[19749] LOADER: setting sys._MEIPASS

[19749] LOADER: importing modules from CArchive

[19749] LOADER: extracted struct

[19749] LOADER: callfunction returned…

[19749] LOADER: extracted pyimod01_os_path

[19749] LOADER: callfunction returned…

[19749] LOADER: extracted pyimod02_archive

[19749] LOADER: callfunction returned…

[19749] LOADER: extracted pyimod03_importers

[19749] LOADER: callfunction returned…

[19749] LOADER: Installing PYZ archive with Python modules.

[19749] LOADER: PYZ archive: out00-PYZ.pyz

[19749] LOADER: Running pyiboot01_bootstrap.py

[19749] LOADER: Running pyi_rth_traitlets.py

[19749] LOADER: Running pyi_rth_mplconfig.py

[19749] LOADER: Running pyi_rth_mpldata.py

[19749] LOADER: Running pyi_rth_pkgres.py

[19749] LOADER: Running pyi_rth_multiprocessing.py

[19749] LOADER: Running CellProfiler.py

/Applications/CellProfiler-3.1.8.app/Contents/MacOS/wx/_core.py:16633: UserWarning: wxPython/wxWidgets release number mismatch

Failed to open libjvm.dylib.

Traceback (most recent call last):

File “javabridge/jutil.py”, line 277, in start_thread

File “_javabridge.pyx”, line 708, in _javabridge.JB_VM.create_mac

RuntimeError: Failed to create Java VM. Return code = -1

Failed to create Java VM

Traceback (most recent call last):

File “CellProfiler.py”, line 8, in <module>

File “cellprofiler/main.py”, line 162, in main

File “cellprofiler/gui/app.py”, line 53, in init

File “cellprofiler/utilities/cpjvm.py”, line 102, in cp_start_vm

File “javabridge/jutil.py”, line 314, in start_vm

RuntimeError: Failed to start Java VM

[19749] Failed to execute script CellProfiler

[19749] LOADER: OK.

[19749] LOADER: Cleaning up Python interpreter.

dhcp-biotek-04:~ balistre$

Any clue what I could do?
Thank you!
Giuseppe