Cytoscape 2.8.2 Installation Problems

[Mema Stamataki]

Hello all! 

I am very new to Cytoscape, which I need for my thesis and I need to use this specific version. I installed it on my Laptop and on the installation instructions said to install the Java 2 Runtime Environment, version 1.4.2 or higher. I could not install this version or SE 5/6 so eventually I installed the version 17.0.1. I launched cytoscape 2.8.2 and I get these errors: 

I have already tried everything from this ticket https://groups.google.com/g/cytoscape-helpdesk/c/Ne3jxs8JaiI 

Can anyone help me please?

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cytoscape.CytoscapeInit[ERROR]: Plugin system initialization error: java.lang.ClassCastException: class jdk.internal.loader.ClassLoaders$AppClassLoader cannot be cast to class java.net.URLClassLoader (jdk.internal.loader.ClassLoaders$AppClassLoader and java.net.URLClassLoader are in module java.base of loader 'bootstrap')

Caused by:
class jdk.internal.loader.ClassLoaders$AppClassLoader cannot be cast to class java.net.URLClassLoader (jdk.internal.loader.ClassLoaders$AppClassLoader and java.net.URLClassLoader are in module java.base of loader 'bootstrap')
at cytoscape.plugin.PluginManager.loadURLPlugins(PluginManager.java:876)
at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:837)
at cytoscape.CytoscapeInit.loadPlugins(CytoscapeInit.java:656)
at cytoscape.CytoscapeInit.init(CytoscapeInit.java:209)
at cytoscape.CyMain.(CyMain.java:144)
at cytoscape.CyMain.main(CyMain.java:108)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
at com.exe4j.runtime.WinLauncher.main(Unknown Source)

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[Alex Pico]

Answered on Stackoverflow:

https://stackoverflow.com/questions/69890828/cytoscape-2-8-2-launch-with-errors/69932858#69932858

Short answer here: It definitely won't work with Java 17. It *might* work with a much, much older Java. It might not work at all.

[Alex Pico]

A more productive path forward might be to challenge the idea that you really need versino 2.8.2. Why is this the case? Are you sure you can't perform the analysis you need with a newer version?

[Mema Stamataki]

Thank you for your answers! 

Ι actually asked my supervisor why we need that specific version, and he said because of ITM-Probe.  It runs smoothly on their Computers so they expect to run on mine too.  I already tried the recommended version that's mentioned on the instructions but no luck! 

[Scooter Morris]

Well, Cytoscape 2.8 definitely won't run on Java 17.  If memory serves (and this was a *long* time ago), the 2.8 series worked with Java 6...

-- scooter