CP 3.0.0rc1 not starting up in Mac



I have been having the same issue… Trying to run on a macOS and this is the error cmd throws at me:

No handlers could be found for logger “javabridge.locate”
Could not find Java JRE compatible with x86_64 architecture
Could not find Java JRE compatible with x86_64 architecture
Traceback (most recent call last):
File “javabridge/jutil.py”, line 273, in start_thread
File “javabridge/jutil.py”, line 125, in _find_mac_lib
UnboundLocalError: local variable ‘cmd’ referenced before assignment
Failed to create Java VM
Traceback (most recent call last):
File “CellProfiler.py”, line 8, in
File “cellprofiler/main.py”, line 152, 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
[96065] Failed to execute script CellProfiler

I installed home-brew and ran the python install and I have java 8 as well as the development kit. Please let me know if something can be done about this.



It’s helped me to open terminal and add the environmental variable JAVA_HOME to where your base java folder is. Like,

export JAVA_HOME=/System/Frameworks/JavaVM/jre1.8.0_162/home

inside of this folder is a folder called bin which contains the java binary. To find yours, you can try to,

ls -lah /usr/bin/java

on terminal and it would reply with a path to the real java binary.

CP adheres to this and it’s allowed me to switch which java I want CP to use. This solves the javabridge error above for me.




I am really eager to see what is new in CP 3.0, but after installing the Mac version in my computer, CP 3.0 won’t start.

It appears on the dock, it jumps a couple of times and it closes again.

Any input?



Hi Carlos,

It seems like you encountered similar issue of the first poster of this thread. Please follow along the discussion, and check if you have a correct version of Java (which should be 8, not 9).



Actually the error is similar. But even making all the changes I am still not able to use the CP.


Can you post the output of java version ? Have you tried setting JAVA_HOME as in the post above? Thanks.


Already tried! But the CP just appears the icon and disappears again. Version 2.0 works, but I need 3




I am having the same problem–CP 3.0 will bounce a couple of times but then not open. I have Java 8 and downloaded the Java Development Kit found on the Download page. I downloaded both before downloading CP. Suggestions?



I followed the discussion thread, by the way


Likewise. I tried installing the latest version from the official website after installing java but the icon bounces a couple of times, then disappears


this is despite installing homebrew and wxpython…


Likewise, I have installed homebrew and wxpython alongside java 8 but a bouncing icon is all I can get. Is this specific to this version? I wouldn’t mind installing an older CellProfiler version to have it up and running on the Mac.



These all sound like Java errors- can you try installing the new 3.1.5 version and seeing if that works for you?