opening Cytoscape problems for MAC OSX 10.9.5

[Stephen Ragsdale]

WHen I try to open the downloaded cytoscape, I get the following message:

"No JVM could be found on your system.

Please define EXE4J_JAVA_HOME

to point to an installed JDK or JRE or download a JRE from www.java.com."

When I try to download java, it says that a more recent version is already installed. (a 14.0 version)

How do I find and point to the installed JDK?

[Tim Hull]

What Cytoscape version are you trying to install, and what is the exact message you get when trying to install Java? Could you share the output of running the "/usr/libexec/java_home -V" command in Terminal? That should show which versions of Java are installed and where.

In general, you should never have to make any manual settings changes to make Java work on a Mac - all you need to do is install it. Though you do need to have Java 7 or 8 from Oracle to run recent versions of Cytoscape (3.2 and higher) - Java 6 (distributed by Apple) is no longer supported. However, if you are trying to install an old 2.8.x version of Cytoscape, Apple Java 6 is required.

Tim

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[Marie]

Hi,

I have the exact same problem. I am trying to install jre-8u40-macosx-x64 but I get the following message:

"A newer version of Java is already installed. You are trying to install 1.8.40.27, however 14.9.0 is already installed.

Visit java.com/newerversionexists for more information."

Then I get this message when I try to install cytoscape 3.2.1:

"Cytoscape Installer. No JVM could be found on your system.

Please define EXE4J_JAVA_HOME

to point to an installed JDK or JRE or download a JRE from www.java.com."

What can I do?

Thank you

Marie

[Tim Hull]

It sounds like the issue may be a pre-existing Java 6 plugin that Java 8 is seeing as newer. This can be removed using the following command in a Terminal:

sudo rm -fr /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin

Could you try this and see if it works? 

Tim

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[Marie]

It worked, thank you!

Marie

[Leon B]

Hey, I have the exact same problem using windows 8. Cant find JavaAppletPlugin.plugin ... Help would be appreciated.

On Thursday, March 26, 2015 at 6:29:48 AM UTC-7, Marie wrote:

It worked, thank you!

Marie