CellProfiler crashes on launch macOS 10.11 & 10.12


#1

Hi,
I’m trying to get CellProfiler to run in a lab environment and the software (v.2.2.0) crashes on launch giving the option to open console or terminate the program.

Version 2.1.1 of CellProfiler runs without any errors. The test machines I’m using have Java v8.111 installed along with all the available updates. Having looked at the previous forum threads i found one that mentions that this might be to do with the wxPython dependencies (see: Couldn’t launch CellProfiler on mac (OS X 10.9.5) post from September 27th).

I get exactly the same error trying to run the 2.3.0 Beta release.

Unfortunately due to the nature of our environment we can’t install homebrew, and the wxPython package for macOS doesn’t help resolve the issue.

I was wondering if there is a way to get CellProfiler working on macOS 10.11 and 10.12 without a homebrew installation.

Thanks


2017 MacOS 10.11 CellProfiler 220 crash on launch
#2

Can you confirm that the Java is 64 bit rather than 32, and that you have the Java Development kit installed? Both are linked to from our releases page . If you do have both of those and still have issues, can you post the full error? Thanks.


#3

Hi,
I’ve verified that both the JRE and the JDK are installed. Java versions are 64 bit rather than 32. When launching v2.2.0 or 2.3.0 Beta i get the following error in console:

Dec 14 18:05:59 rockingham CellProfiler[1375]: objc[1375]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_112.jdk/Contents/Home/jre/lib/jli/libjli.dylib (0x10cd4b480) and /Library/Java/JavaVirtualMachines/jdk1.8.0_112.jdk/Contents/Home/jre/lib/libinstrument.dylib (0x10cd9e4e0). One of the two will be used. Which one is undefined.
Dec 14 18:06:03 rockingham CellProfiler[1375]: CellProfiler Error


#4

Hmm, I’m not sure. Paging @David_Logan , who always seems to know how to fix Java errors!


#5

Hi,
I was wondering if there is any update on why either of the release versions might not be working on 10.11 and 10.12. I’ve tested this on a few machines now and get the same error each time i try and run the application.

Thanks
Tan


#6

I still suspect it is an issue with your Java installation somehow, as 1) that’s a weird error message I haven’t seen before and 2) we’ve had many users succeed at installing the stable and/or the beta on those OS versions. Can you go to the terminal and type java -version, and post the output here?

According to one of our software engineers, it may be an issue with setting your JAVA_HOME to the correct java installation (ie if you have 32 bit and 64 bit installed side-by-side, CP might be erroneously only finding the 32 bit installation and ignoring the 64 bit).


#7

Hi,
The output for java version and Java home are listed below:
java version "1.8.0_112"
Java™ SE Runtime Environment (build 1.8.0_112-b16)
Java HotSpot™ 64-Bit Server VM (build 25.112-b16, mixed mode)

JAVA_HOME: /Library/Java/JavaVirtualMachines/jdk1.8.0_112.jdk/Contents/Home

Like i mentioned before the previous version works fine on systems running 10.11 and 10.12, so unless there is a fundamental change in how the new versions interact with Java on the machine, my guess is that this isn’t related to the Java release version.

Does Cell Profiler do verbose logging, or is there a way to match up the error codes it provides in console to a list of known errors?

Thanks


#8

Like i mentioned before the previous version works fine on systems running 10.11 and 10.12, so unless there is a fundamental change in how the new versions interact with Java on the machine, my guess is that this isn’t related to the Java release version.

There actually was a change in how CP interacts with Java between 2.1 and 2.2, so this unfortunately doesn’t rule out a Java error.

Can you try setting JAVA_HOME to the jre rather than the jdk? Based on this post I’m wondering if that would help.


#9

Sorry I missed the “page” about this post. If still an issue, I’d try removing JAVA_HOME from System Variables as the previous software engineer had suggested before:


Can't start CellProfiler 2.2.0 and 2.3.0 - Failed to start Java VM