Couldn't launch CellProfiler on mac (OS X 10.9.5)

Hi all,

I have installed Java 8 JDK and then, installed CellProfiler_2.2.0 on my mac. Once I open CellProfiler, it shows “CellProfiler error” and doesn’t launch. I have read all the relevant discussion here and tried to delete configuration file (cd ~/Library/Preferences, CellProfilerLocal.cfg), but my mac appears not to have this configuration file at the first place. Do you have any suggestions? I desperately want to try CellProfiler…

FIY, my mac has OS X 10.9.5 version and once I fail to open CellProfiler, the console shows following:

9/26/16 3:22:07.721 PM com.apple.launchd.peruser.501[161]: (org.pythonmac.unspecified.CellProfiler.154208[27413]) Exited with code: 255
9/26/16 3:22:07.736 PM Console[27488]: setPresentationOptions called with NSApplicationPresentationFullScreen when there is no visible fullscreen window; this call will be ignored.
9/26/16 3:22:33.775 PM CellProfiler[27493]: Traceback (most recent call last):
9/26/16 3:22:33.776 PM CellProfiler[27493]: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 81, in
9/26/16 3:22:33.776 PM CellProfiler[27493]: _run()
9/26/16 3:22:33.776 PM CellProfiler[27493]: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 62, in _run
9/26/16 3:22:33.777 PM CellProfiler[27493]: exec(compile(source, path, ‘exec’), globals(), globals())
9/26/16 3:22:33.777 PM CellProfiler[27493]: File “/Applications/CellProfiler.app/Contents/Resources/CellProfiler.py”, line 1, in
9/26/16 3:22:33.777 PM CellProfiler[27493]: import cellprofiler.main
9/26/16 3:22:33.777 PM CellProfiler[27493]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/main.py”, line 5, in
9/26/16 3:22:33.777 PM CellProfiler[27493]: import cellprofiler.pipeline
9/26/16 3:22:33.777 PM CellProfiler[27493]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/pipeline.py”, line 48, in
9/26/16 3:22:33.777 PM CellProfiler[27493]: import cellprofiler.utilities.version as cpversion
9/26/16 3:22:33.777 PM CellProfiler[27493]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/version.py”, line 126, in
9/26/16 3:22:33.777 PM CellProfiler[27493]: version_string = get_version()
9/26/16 3:22:33.777 PM CellProfiler[27493]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/version.py”, line 97, in get_version
9/26/16 3:22:33.778 PM CellProfiler[27493]: import cellprofiler.frozen_version
9/26/16 3:22:33.778 PM CellProfiler[27493]: ImportError: No module named frozen_version
9/26/16 3:22:33.916 PM CellProfiler[27493]: CellProfiler Error
9/26/16 3:22:33.917 PM CellProfiler[27493]: 2016-09-26 15:22:33.915 CellProfiler[27493:707] CellProfiler Error
9/26/16 3:22:35.715 PM com.apple.launchd.peruser.501[161]: (org.pythonmac.unspecified.CellProfiler.154208[27493]) Exited with code: 255
9/26/16 3:22:35.740 PM Console[27529]: setPresentationOptions called with NSApplicationPresentationFullScreen when there is no visible fullscreen window; this call will be ignored.

I would really appreciate your help!!

Hi,
We want you to be able to run CellProfiler too! This is a known bug on the nightly build of CP- can you confirm which version of CP (Stable, Beta, Nightly) you are trying to install? If it’s the nightly, can you try the stable or beta instead? Nightlys unfortunately often have a lot of bugs.

I have tried with nightly first, then deleted it and retry with ‘stable (2.2.0)’ but it didn’t work as well. I will try again with beta version and let you know!

I just tried beta version, but it doesn’t work as well : ( Do I need to clean-up trash and restart computer before install beta version? Otherwise, all versions (stable/beta/nightly) do not work on my mac…

Can you let me know what the error outputs are for stable and/or beta? Same or different as what you posted above?

just tried ‘clean-up trash/restart/reinstall’…it didn’t work…

The console from beta version is following:

9/26/16 4:55:43.837 PM CellProfiler[1246]: Traceback (most recent call last):
9/26/16 4:55:43.837 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 355, in
9/26/16 4:55:43.837 PM CellProfiler[1246]: _run()
9/26/16 4:55:43.838 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 336, in _run
9/26/16 4:55:43.838 PM CellProfiler[1246]: exec(compile(source, path, ‘exec’), globals(), globals())
9/26/16 4:55:43.838 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/CellProfiler.py”, line 4, in
9/26/16 4:55:43.838 PM CellProfiler[1246]: cellprofiler.main.main()
9/26/16 4:55:43.838 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/main.py”, line 181, in main
9/26/16 4:55:43.838 PM CellProfiler[1246]: cp_start_vm()
9/26/16 4:55:43.838 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/cpjvm.py”, line 159, in cp_start_vm
9/26/16 4:55:43.838 PM CellProfiler[1246]: class_path = get_jars()
9/26/16 4:55:43.839 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/cpjvm.py”, line 76, in get_jars
9/26/16 4:55:43.839 PM CellProfiler[1246]: plugin_directory = cpprefs.get_ij_plugin_directory()
9/26/16 4:55:43.839 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/preferences.py”, line 909, in get_ij_plugin_directory
9/26/16 4:55:43.839 PM CellProfiler[1246]: if config_exists(IJ_PLUGIN_DIRECTORY):
9/26/16 4:55:43.839 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/preferences.py”, line 238, in config_exists
9/26/16 4:55:43.839 PM CellProfiler[1246]: if not get_config().Exists(key):
9/26/16 4:55:43.839 PM CellProfiler[1246]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/preferences.py”, line 111, in get_config
9/26/16 4:55:43.839 PM CellProfiler[1246]: import wx
9/26/16 4:55:43.839 PM CellProfiler[1246]: File “wx/init.pyc”, line 45, in
9/26/16 4:55:43.840 PM CellProfiler[1246]: File “wx/_core.pyc”, line 4, in
9/26/16 4:55:43.840 PM CellProfiler[1246]: File “wx/core.pyc”, line 14, in
9/26/16 4:55:43.840 PM CellProfiler[1246]: File “wx/core.pyc”, line 10, in __load
9/26/16 4:55:43.840 PM CellProfiler[1246]: ImportError: dlopen(/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/lib-dynload/wx/core.so, 2): Symbol not found: OBJC_CLASS$_NSURLRequest
9/26/16 4:55:43.840 PM CellProfiler[1246]: Referenced from: /Applications/CellProfiler.app/Contents/MacOS/…/Frameworks/libwx_osx_cocoau_core-3.0.0.2.0.dylib
9/26/16 4:55:43.840 PM CellProfiler[1246]: Expected in: /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
9/26/16 4:55:43.840 PM CellProfiler[1246]: in /Applications/CellProfiler.app/Contents/MacOS/…/Frameworks/libwx_osx_cocoau_core-3.0.0.2.0.dylib
9/26/16 4:55:43.907 PM CellProfiler[1246]: CellProfiler Error
9/26/16 4:55:43.907 PM CellProfiler[1246]: 2016-09-26 16:55:43.905 CellProfiler[1246:707] CellProfiler Error
9/26/16 4:55:45.819 PM com.apple.launchd.peruser.501[167]: (org.pythonmac.unspecified.CellProfiler.154208[1246]) Exited with code: 255
9/26/16 4:55:45.821 PM Console[1257]: setPresentationOptions called with NSApplicationPresentationFullScreen when there is no visible fullscreen window; this call will be ignored.

I talked with some of my colleagues- it looks like there may be an issue with the wx packaging in our build. We’re obviously going to work on fixing it, but in the meantime can you try running the first, third, and fourth steps here and let me know if that allows you to run stable and/or beta? Thanks so much, and sorry for the inconvenience!

Thank you very much for your help! Following your suggestions, I installed homebrew > Python > wxPython, but still both ‘stable’ and ‘beta’ version didn’t work : ( Actually, I have signed up for CellProfiler workshop at Broad institute on this Thursday and am bit worrying that I won’t be able to learn something as CellProfiler doesn’t launch on my mac…Please let me know if there is any other suggestions that I can try. Thank you!

FYI, the console after the installation of ‘homebrew/Python/wxPython’ is following:

9/27/16 3:24:08.200 PM syncdefaultsd[40011]: **** globally delaying apps from syncing, next sync will be in 2s
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:10.000 PM kernel[0]: CoreServicesUIAg[40035] Unable to quarantine: 93
9/27/16 3:24:13.468 PM CellProfiler[40033]: Traceback (most recent call last):
9/27/16 3:24:13.468 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 355, in
9/27/16 3:24:13.468 PM CellProfiler[40033]: _run()
9/27/16 3:24:13.468 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 336, in _run
9/27/16 3:24:13.468 PM CellProfiler[40033]: exec(compile(source, path, ‘exec’), globals(), globals())
9/27/16 3:24:13.468 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/CellProfiler.py”, line 4, in
9/27/16 3:24:13.469 PM CellProfiler[40033]: cellprofiler.main.main()
9/27/16 3:24:13.469 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/main.py”, line 181, in main
9/27/16 3:24:13.469 PM CellProfiler[40033]: cp_start_vm()
9/27/16 3:24:13.469 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/cpjvm.py”, line 159, in cp_start_vm
9/27/16 3:24:13.469 PM CellProfiler[40033]: class_path = get_jars()
9/27/16 3:24:13.469 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/cpjvm.py”, line 76, in get_jars
9/27/16 3:24:13.469 PM CellProfiler[40033]: plugin_directory = cpprefs.get_ij_plugin_directory()
9/27/16 3:24:13.470 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/preferences.py”, line 909, in get_ij_plugin_directory
9/27/16 3:24:13.470 PM CellProfiler[40033]: if config_exists(IJ_PLUGIN_DIRECTORY):
9/27/16 3:24:13.470 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/preferences.py”, line 238, in config_exists
9/27/16 3:24:13.470 PM CellProfiler[40033]: if not get_config().Exists(key):
9/27/16 3:24:13.470 PM CellProfiler[40033]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/preferences.py”, line 111, in get_config
9/27/16 3:24:13.470 PM CellProfiler[40033]: import wx
9/27/16 3:24:13.470 PM CellProfiler[40033]: File “wx/init.pyc”, line 45, in
9/27/16 3:24:13.470 PM CellProfiler[40033]: File “wx/_core.pyc”, line 4, in
9/27/16 3:24:13.470 PM CellProfiler[40033]: File “wx/core.pyc”, line 14, in
9/27/16 3:24:13.470 PM CellProfiler[40033]: File “wx/core.pyc”, line 10, in __load
9/27/16 3:24:13.471 PM CellProfiler[40033]: ImportError: dlopen(/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/lib-dynload/wx/core.so, 2): Symbol not found: OBJC_CLASS$_NSURLRequest
9/27/16 3:24:13.471 PM CellProfiler[40033]: Referenced from: /Applications/CellProfiler.app/Contents/MacOS/…/Frameworks/libwx_osx_cocoau_core-3.0.0.2.0.dylib
9/27/16 3:24:13.471 PM CellProfiler[40033]: Expected in: /System/Library/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
9/27/16 3:24:13.471 PM CellProfiler[40033]: in /Applications/CellProfiler.app/Contents/MacOS/…/Frameworks/libwx_osx_cocoau_core-3.0.0.2.0.dylib
9/27/16 3:24:13.538 PM CellProfiler[40033]: CellProfiler Error
9/27/16 3:24:13.538 PM CellProfiler[40033]: 2016-09-27 15:24:13.537 CellProfiler[40033:707] CellProfiler Error
9/27/16 3:24:14.371 PM syncdefaultsd[40011]: **** globally delaying apps from syncing, next sync will be in 9s
9/27/16 3:24:15.878 PM Console[40047]: setPresentationOptions called with NSApplicationPresentationFullScreen when there is no visible fullscreen window; this call will be ignored.
9/27/16 3:24:15.885 PM com.apple.launchd.peruser.501[163]: ([0x0-0x87087].org.pythonmac.unspecified.CellProfiler[40033]) Exited with code: 255

I’m sorry, that’s such a bummer!

If you click here it’ll bring you to the older releases of CP- 2.1.1 is missing a bunch of the fun things from 2.2 and on, but it should be enough to get you through the workshop at least. I’ll see you there!

You can also try finishing the rest of the instructions on that page to install CellProfiler from source - just run the following 2 lines after the last “pip install” to be running the stable “edition” of CP - you only have to do this once, then you can just always call “cellprofiler” from the command line.

cd $HOME/CellProfiler

git checkout stable

Thank you very much for your help! I ended up install CellProfiler on my other macbook air (OS Yosemite), and it works fine!! However, ultimately, it would be great if I can run CellProfiler on my macbook pro as it can handle more memory… I will bring both mac to the workshop in any case I could get some advice/help from you…thank you for all the help and see you soon!!

Apparently the current mac builds don’t support anything before 10.10- I apologize, I had no idea! We’ll be updating the downloads page to reflect that, and you should still be able to install from source following all of the instructions in the link in my previous post.

Hi,

I followed the instructions according to the Source installation (OS X and macOS). When I try to run CellProfiler in the Terminal, it shows:
“This program needs access to the screen.
Please run with a Framework build of python, and only when you are logged in on the main display of your Mac.”

Could you help me to understand what I missed ?

Thanks

Guillaume

Please supply more information about your development environment. Which version of OS X are you running? How did you install python? What version of python? Are you using a virtual machine or virtual python environment? How are you running CellProfiler?

Hi Mcquin,

I’m using OX El Capitan 10.11.6, I have python 2.7 installed in Anaconda. I am not using a virtual machine or virtual python environment but just try to run it from the terminal. Should I use one of those to run CellProfiler ?

Best

Guillaume

Try running: conda install python.app

Then try running CP. What is the result?

Also, what command are you running to launch CP from terminal?

Here is the result of the conda install python.app:
Fetching package metadata …
Solving package specifications: …

All requested packages already installed.
packages in environment at //anaconda:
python.app 1.2 py27_4

Guillaume-2:~ guillaume$ cellprofiler
This program needs access to the screen.
Please run with a Framework build of python, and only when you are
logged in on the main display of your Mac.

I am not running any command to launch CP. Should I use main ?

Thanks for your help :slight_smile:

Can you try running pythonw cellprofiler.