CellProfiler 2.0.11710 does not start on MacOS 10.10

Usage & Issues
#1

Hi,
I tried to install Cellprofiler 2.0.11710 on a Mac 10.10. but it fails to open. It is somehow open, but does not show the GUI, only the dock icon pops up and a message which offers to look at the console message.
The console shows messages like this:

11/17/15 10:20:17.610 AM CellProfiler2.0[12695]: WARNING: The Gestalt selector gestaltSystemVersion is returning 10.9.5 instead of 10.10.5. Use NSProcessInfo’s operatingSystemVersion property to get correct system version number.
Call location:
11/17/15 10:20:17.611 AM CellProfiler2.0[12695]: 0 CarbonCore 0x97c17291 ___Gestalt_SystemVersion_block_invoke + 135
11/17/15 10:20:17.611 AM CellProfiler2.0[12695]: 1 libdispatch.dylib 0x9c2f73b7 dispatch_once_f + 251
11/17/15 10:20:17.611 AM CellProfiler2.0[12695]: 2 libdispatch.dylib 0x9c2f7477 dispatch_once + 31
11/17/15 10:20:17.611 AM CellProfiler2.0[12695]: 3 CarbonCore 0x97b9069d _Gestalt_SystemVersion + 1050
11/17/15 10:20:17.611 AM CellProfiler2.0[12695]: 4 CarbonCore 0x97b8f7c0 Gestalt + 150
11/17/15 10:20:17.611 AM CellProfiler2.0[12695]: 5 libwx_macud-2.8.0.dylib 0x04bb5fab _Z14UMAInitToolboxtb + 43
11/17/15 10:20:17.611 AM CellProfiler2.0[12695]: 6 libwx_macud-2.8.0.dylib 0x04bccf77 _ZN5wxApp10InitializeERiPPw + 65
11/17/15 10:20:18.869 AM CellProfiler2.0[12695]: CellProfiler2.0 Error
11/17/15 10:20:21.903 AM Console[12701]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable
11/17/15 10:20:33.864 AM spindump[684]: Saved spin report for CellProfiler2.0 version 0.0.0 (0.0.0) to /Library/Logs/DiagnosticReports/CellProfiler2.0_2015-11-17-102033_tds-mac-1.spin

The .spin-file looks like this:
Date/Time: 2015-11-17 10:20:23 +0100
OS Version: 10.10.5 (Build 14F1021)
Architecture: x86_64
Report Version: 21

Command: CellProfiler2.0
Path: /Users/USER/Desktop/CellProfiler2.0.app/Contents/MacOS/CellProfiler2.0
Version: 0.0.0 (0.0.0)
PID: 12695

Event: timeout-lite
Duration: 9.90s
Steps: 100 (100ms sampling interval)

Hardware model: iMac12,2
Active cpus: 4

Fan speed: 1148 rpm

Heaviest stack for the main thread of the target process:
100 start + 53 (CellProfiler2.0 + 1921) [0x1781]
100 main + 1551 (CellProfiler2.0 + 19855) [0x5d8f]
100 start + 16386 (CellProfiler2.0 + 18254) [0x574e]
100 Py_Finalize + 103 (Python + 954999) [0x4038277]
100 PyObject_CallMethod + 170 (Python + 59674) [0x3f5d91a]
100 PyObject_Call + 85 (Python + 39445) [0x3f58a15]
100 PyCell_New + 3477 (Python + 111077) [0x3f6a1e5]
100 PyObject_Call + 85 (Python + 39445) [0x3f58a15]
100 PyClassMethod_New + 875 (Python + 242731) [0x3f8a42b]
100 PyEval_EvalCodeEx + 2012 (Python + 805004) [0x401388c]
100 PyEval_EvalFrameEx + 26869 (Python + 796373) [0x40116d5]
100 PyEval_EvalCodeEx + 2012 (Python + 805004) [0x401388c]
100 PyEval_EvalFrameEx + 26869 (Python + 796373) [0x40116d5]
100 PyEval_EvalCodeEx + 2012 (Python + 805004) [0x401388c]
100 PyEval_EvalFrameEx + 25344 (Python + 794848) [0x40110e0]
100 initthread + 659 (Python + 1064195) [0x4052d03]
100 PyThread_acquire_lock + 118 (Python + 1043670) [0x404dcd6]
100 pthread_cond_wait$UNIX2003 + 71 (libsystem_pthread.dylib + 29992) [0x94582528]
100 __psynch_cvwait + 10 (libsystem_kernel.dylib + 103698) [0x91639512]
*100 psynch_cvcontinue + 0 (pthread + 26910) [0xffffff7f80ee791e]

Binary Images:
0x1000 - 0x6fff org.pythonmac.unspecified.CellProfiler2.0 0.0.0 (0.0.0) <76A06F49-0ED5-228D-BB62-4CC3D002786F> /Users/USER/Desktop/CellProfiler2.0.app/Contents/MacOS/CellProfiler2.0
0x3f4f000 - 0x4093fff org.python.python 2.7.2, © 2004-2011 Python Software Foundation. (2.7.2) <6F5DD571-2864-894D-766A-4C0F3684892E> /Users/USER/Desktop/CellProfiler2.0.app/Contents/Frameworks/Python.framework/Versions/2.7/Python
0x91620000 - 0x9163ffff libsystem_kernel.dylib (2782.50.1) <20156462-5B58-3B51-8D05-A2F7195679D5> /usr/lib/system/libsystem_kernel.dylib
0x9457b000 - 0x94583fff libsystem_pthread.dylib (105.40.1) <21849EF5-A3B6-34D4-A045-4A68A6C390A1> /usr/lib/system/libsystem_pthread.dylib
*0xffffff7f80ee1000 - 0xffffff7f80ee9fff com.apple.kec.pthread 1.0 (1) <84126647-296D-3B12-9FF3-263679AF859C> /System/Library/Extensions/pthread.kext/Contents/MacOS/pthread

Any idea how to fix it?

#2

Version 2.0.11710 is >3.5 years old(!), and I guess we’d have to say there’s no guarantee of compatibility with OS 10.10. I would suggest you load a newer version of CellProfiler, like the current release on our download site, drag in your pipeline and most from the 11710 era will upgrade automatically.

#3

I know that this version is very old but this is the one which is also running on our cluster at the moment… Yes, we will try to upgrade that installation too but I thought you might have an idea based on the error message as it is running on another machine with the same MacOS version without problems…

#4

Can you try this first?
(1) Delete the file ~/Library/Preferences/CellProfilerLocal.cfg and then restart CellProfiler.
NOTE the tilde (i.e. ‘~’) is important here, representing your home directory.

If that doesn’t work, try this:
(1) Uninstall CP
(2) Delete the file ~/Library/Preferences/CellProfilerLocal.cfg
(3) Empty your Mac Trash!
(4) Re-install CP and try it out.

#5

I found the file, deleted it and tried both ways but it does not help…

#6

Hmm, that’s odd. This user had a similar error too, and this fixed it: CP not able to start
Can you try these even more detailed instructions to delete the config file, just to be sure? Thanks