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I have a problem with latest version of Cytoscape 3.8.0 It doesnt start. I can see only logo and than nothing. Computer is running OSX 10.13.6. I am using successfully version Cytoscape 3.7.2 but I want to upgrade. When I run script mac.sh I got following:

Target Cytoscape version: 3.8.0

Your shell is bash Compatible OS version found: 10.13

  • Pass: OS Version = 10.13.6
  • Pass: Following Oracle JDK found:

/Library/Java/JavaVirtualMachines/jdk-11.0.7.jdk Fail: Java is not reachable. Try re-installing Java 11.

I can confirm that java is in place /Library/Java/JavaVirtualMachines and versions jdk-11.0.7.jdk jdk-12.0.2.jdk jdk-14.0.1.jdk

I guess that version 37 and 38 work with java 11? I have reinstalled java 11 with same results as before. Version 38 doesnt start. When I try to start version 38 from terminal with cytoscape.sh I got long error message which starts with:

Unable to find any JVMs matching version "1.8".

karaf.base: /Applications/Cytoscape_v3.8.0/framework JAVA_HOME: null ERROR: Error parsing system bundle export statement: org.osgi.dto;version="1.0",org.osgi.resource;version="1.0",org.osgi.resource.dto;version="1.0... I can paste whole error message if needed.

Any idea what should i do? Thanx.

Mihailo
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2 Answers2

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Cytoscape 3.7.x requires Java 8. Cytoscape 3.8.0 requires Java 11. It looks like your java home is incorrect. If you do:

/usr/libexec/java_home

it should point to your java 11 installation. On my mac it says:

/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home

Note that the "/Contents/Home" is important. To set your actual JAVA_HOME, do

export JAVA_HOME=`/usr/libexec/java_home -v 11`
Dharman
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Scooter Morris
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I had this same problem. What Scooter Morris mentioned is correct, but I had to follow an additional link on stack overflow to get it fixed.

This is exactly what I did: In my case I had to run:/usr/libexec/java_home -V to see the Java Virtual Machines I have installed and specify the V 11 using:

export JAVA_HOME=`/usr/libexec/java_home -v 11.0.7`

Then running the ./mac.sh command tells me everything checks out and Cytoscape can finnaly run :)

Edit: I should add that I can only run cytoscape by launching it from the terminal via:

cd /Applications/Cytoscape_v3.8.0
./cytoscape.sh

Clicking the app icon only results in the app crashing on load but it appears to work fine by launching it from the script. I don't have this issue on Mac OS 10.14 so maybe its a software version issue or some background app in my computer is getting in the way of launching the app normally.

Wealthy Oil Tycoon
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