cd /Applications/Cytoscape_v3.4.0
./cytoscape.sh
It sounds like your configuration is missing Java. Would you try running the Troubleshooting script and posting the results?
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Sorry … I was hoping for the output of the script after you ran it. It will tell us what we need to know about your configuration, but Scooter is likely quite right.
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One thing - do you have any antivirus software installed? We've seen antivirus software cause problems for Cytoscape in the past, so if you do maybe try disabling it and see Cytoscape works then.Also, if that doesn't help, could you delete the framework_cytoscape.log (in the ~/CytoscapeConfiguration/3 directory), try running Cytoscape using the icon again, and check that directory to see if there is a new framework_cytoscape.log. If so, send it her.Aside from that, I'm not sure what's going on - one other thing I can suggest is re-installing both Cytoscape and the JRE and see if that helps. Also, you could try reducing the -Xmx value in vmoptions.txt some more to see if that helps...Tim
On Tue, Aug 16, 2016 at 12:10 AM, Johanna Villén <johann...@gmail.com> wrote:
I opened both vmoptions.txt and cytoscape.vmoptions and changed the Xmx in vmoptions to 1550 which is the Xmx that was in cytoscape.vmoptions. But that didn’t help, I still can’t open cytoscape with the icon.Johanna
On 15 Aug 2016, at 20:54, Tim Hull <tmh...@eng.ucsd.edu> wrote:
Yes.One think you may try is checking the vmoptions file - on Mac, the application launcher uses a different one than cytoscape.sh.To open that, right-click on the launcher icon and select "Show Package Contents". Then click on vmoptions.txt.Compare the contents of this file with those of Cytoscape.vmoptions (located in the Cytoscape installation directory) - what do they both have in them? If vmoptions.txt has higher Xmx and Xms values than Cytoscape.vmoptions, try changing them to the lower values in that file and see if Cytoscape works then.Let me know if any of that helps...Tim
Johanna
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############# Cytoscape System Requirements Checker for Mac ##############
Target Cytoscape version: 3.7.2
Your shell is bash
Compatible OS version found: 10.13
- Pass: OS Version = 10.13.6
- Fail: No Oracle JDK found. Please download and install Oracle JDK:
http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
Matching Java Virtual Machines (2):
12.0.2, x86_64: "Java SE 12.0.2" /Library/Java/JavaVirtualMachines/jdk-12.0.2.jdk/Contents/Home
11.0.7, x86_64: "Java SE 11.0.7" /Library/Java/JavaVirtualMachines/jdk-11.0.7.jdk/Contents/Home
Unable to find any JVMs matching version "1.8".
karaf.base: /Applications/Cytoscape_v3.8.0/framework
JAVA_HOME: null
Johanna
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