CellProfiler Error in 2.2.1 for 64x OS X

Hey I’m using a macbook pro mid 2012 running 10.1.4 with 16GB of RAM. Every time I try to open the latest Stable (2.2.1) release from April 18, 2016 I get this error message.

This is what the console shows
28/04/2016 12:25:37.889 sharedfilelistd[401]: [default] [<CFString 0x7fff7640de00 [0x7fff764c5440]>{contents = “com.apple.LSSharedFileList.RecentApplications”}] List write failed invalid info items: (null) properties: (null)
28/04/2016 12:25:37.889 sharedfilelistd[401]: -[ListStore writeListItems:properties:withListIdentifier:notificationHander:] [com.apple.LSSharedFileList.RecentApplications] List write failed invalid info items: (null) properties: (null)
28/04/2016 12:25:40.389 CellProfiler[9482]: Could not find Java JRE compatible with x86_64 architecture
28/04/2016 12:25:40.551 CellProfiler[9482]: Plugin directory doesn’t point to valid folder: /Applications/CellProfiler.app/Contents/Resources/plugins
28/04/2016 12:25:40.591 CellProfiler[9482]: Could not find Java JRE compatible with x86_64 architecture
28/04/2016 12:25:40.627 CellProfiler[9482]: Could not find Java JRE compatible with x86_64 architecture
28/04/2016 12:25:40.627 CellProfiler[9482]: Failed to execute “find” when searching for libjvm
28/04/2016 12:25:40.627 CellProfiler[9482]: Traceback (most recent call last):
28/04/2016 12:25:40.627 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 115, in _find_mac_lib
28/04/2016 12:25:40.627 CellProfiler[9482]: File “posixpath.pyc”, line 122, in dirname
28/04/2016 12:25:40.627 CellProfiler[9482]: AttributeError: ‘NoneType’ object has no attribute ‘rfind’
28/04/2016 12:25:40.627 CellProfiler[9482]: Failed to execute “find” when searching for libjvm
28/04/2016 12:25:40.627 CellProfiler[9482]: Traceback (most recent call last):
28/04/2016 12:25:40.628 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 115, in _find_mac_lib
28/04/2016 12:25:40.628 CellProfiler[9482]: File “posixpath.pyc”, line 122, in dirname
28/04/2016 12:25:40.628 CellProfiler[9482]: AttributeError: ‘NoneType’ object has no attribute ‘rfind’
28/04/2016 12:25:40.628 CellProfiler[9482]: Failed to find libjvm
28/04/2016 12:25:40.665 CellProfiler[9482]: Could not find Java JRE compatible with x86_64 architecture
28/04/2016 12:25:40.665 CellProfiler[9482]: Failed to execute “find” when searching for libjli
28/04/2016 12:25:40.665 CellProfiler[9482]: Traceback (most recent call last):
28/04/2016 12:25:40.665 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 115, in _find_mac_lib
28/04/2016 12:25:40.665 CellProfiler[9482]: File “posixpath.pyc”, line 122, in dirname
28/04/2016 12:25:40.665 CellProfiler[9482]: AttributeError: ‘NoneType’ object has no attribute ‘rfind’
28/04/2016 12:25:40.665 CellProfiler[9482]: Failed to execute “find” when searching for libjli
28/04/2016 12:25:40.665 CellProfiler[9482]: Traceback (most recent call last):
28/04/2016 12:25:40.665 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 115, in _find_mac_lib
28/04/2016 12:25:40.665 CellProfiler[9482]: File “posixpath.pyc”, line 122, in dirname
28/04/2016 12:25:40.665 CellProfiler[9482]: AttributeError: ‘NoneType’ object has no attribute ‘rfind’
28/04/2016 12:25:40.665 CellProfiler[9482]: Failed to find libjli
28/04/2016 12:25:40.665 CellProfiler[9482]: Traceback (most recent call last):
28/04/2016 12:25:40.665 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 274, in start_thread
28/04/2016 12:25:40.665 CellProfiler[9482]: Exception: Javabridge failed to find JVM library
28/04/2016 12:25:40.665 CellProfiler[9482]: Failed to create Java VM
28/04/2016 12:25:40.665 CellProfiler[9482]: Traceback (most recent call last):
28/04/2016 12:25:40.665 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 355, in
28/04/2016 12:25:40.665 CellProfiler[9482]: _run()
28/04/2016 12:25:40.666 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 336, in _run
28/04/2016 12:25:40.666 CellProfiler[9482]: exec(compile(source, path, ‘exec’), globals(), globals())
28/04/2016 12:25:40.666 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/CellProfiler.py”, line 4, in
28/04/2016 12:25:40.666 CellProfiler[9482]: cellprofiler.main.main()
28/04/2016 12:25:40.666 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/main.py”, line 176, in main
28/04/2016 12:25:40.666 CellProfiler[9482]: cp_start_vm()
28/04/2016 12:25:40.666 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/utilities/cpjvm.py”, line 167, in cp_start_vm
28/04/2016 12:25:40.666 CellProfiler[9482]: max_heap_size = heap_size)
28/04/2016 12:25:40.666 CellProfiler[9482]: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/javabridge/jutil.py”, line 312, in start_vm
28/04/2016 12:25:40.666 CellProfiler[9482]: raise RuntimeError(“Failed to start Java VM”)
28/04/2016 12:25:40.666 CellProfiler[9482]: RuntimeError: Failed to start Java VM
28/04/2016 12:25:40.733 CellProfiler[9482]: CellProfiler Error
28/04/2016 12:25:40.733 CellProfiler[9482]: 2016-04-28 12:25:40.732 CellProfiler[9482:471412] CellProfiler Error

I thought it was Java, so I updated it to Java SE Runtime Environment 8u92 downloaded from here http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html . It doesn’t specify 64x for OSX like the others on the list but I believe it is. After I have done this, restarted the computer and everything I get the same error message.

Any idea what is causing this?

THanks

I have the exact same problem on OS X 10.11.4 and 10.10.5 running JRE 1.8.91 and Python 2.7.10.

We have other reports like this. Though it works for some (me, for example). It is possible you have two Java installations and the wrong one might being called(?). Can you both please verify your Java version:

  1. open Terminal
  2. type “java -version” (without the quotes)

Mine reports this and CP 2.2.0 works on my Mac:

java version "1.8.0_60"
Java™ SE Runtime Environment (build 1.8.0_60-b27)
Java HotSpot™ 64-Bit Server VM (build 25.60-b23, mixed mode)

Ensure that the first line has “1.8” and the last line says “64-bit”. Paste the output here if you like.

Here is what I get.

java version “1.6.0_65”
Java™ SE Runtime Environment (build 1.6.0_65-b14-468-11M4833)
Java HotSpot™ 64-Bit Server VM (build 20.65-b04-468, mixed mode)

How can I get it to call the right version of Java?

When I look at JRE settings on the preferences panel, it shows 1.8, so I have no idea what’s going on

I also get Java version “1.6.0_65” but that’s because we both have installed leagcy java for OS X which is required for other programs like Adobe Photoshop CS6 for example.

https://support.apple.com/kb/DL1572?locale=en_US

I also have Java version 1.8.91 installed.

That’s right, I also have the legacy (version 6 I think?) for OSX installed, I think its required for older versions of CP.

Okay, it works for me now. You need to install Java SE Development Kit (JDK)

You can download it here:

http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

Thanks henber! Totally worked!

Could possibly link to http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html in addition on the download page to help others out.

No problem.

Should actually say:
Requirements: Java SE Development Kit 8 (64-bit)
Development kit also includes Runtime Enviroment.

Have a nice day =)