Cytoscape not starting

[Johanna Villén]

Hello, I am new to cytoscape (version 3.4.0) and have some trouble opening the program. When I double click the icon nothing happens. I installed cytoscape two weeks ago and then it worked. I haven't changed anything or uninstalled any program so I don't understand why it isn't working now. I am using a mac and have Java version 8. 

Do you have any suggestions for me? 

[Scooter Morris]

Hi Johanna,
   Difficult to tell what might be happening from your description.  Two things you can try:

1. Launch Cytoscape from the terminal.  Open up a Terminal window (Applications->Utilities->Terminal) and type:

cd /Applications/Cytoscape_v3.4.0
./cytoscape.sh

Then send us what you see on the screen.  That should tell us what's going on.

      2. Go to the CytoscapeConfiguration/3 directory in your home and look for the file "framework-cytoscape.log".  That may give us some clues as to what's going on also

-- scooter

[Johanna Villén]

Hi, thanks for the answer. I have attached the framework-cytoscape.log file and the screenshot that I took from the terminal. I hope that will help you figure out what is wrong.

Johanna

[Barry Demchak]

It sounds like your configuration is missing Java. Would you try running the Troubleshooting script and posting the results?

 

http://www.cytoscape.org/troubleshooting.html

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[Scooter Morris]

Hi Johanna,
    This is telling us that Cytoscape can't find a Java runtime.   Did you recently update to Java 8?

-- scooter

--

[Johanna Villén]

I downloaded Java for the first time when I realized I needed it for cytoscape, which was maybe two weeks ago. So I downloaded the latest version (8). 

I ran the troubleshooting script which I have attached here. 

[Barry Demchak]

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.

--

[Johanna Villén]

I ran the troubleshooting script and I think terminal told me to download JDK so I did that (Kit 8u101) and then tried again, then it told me to set Java home. How do I do that? 

Here I copy-pasted everything from terminal:

Last login: Fri Aug 12 19:48:03 on ttys000

Johannas-Air:~ johannavillen$ ls

Applications Downloads Pictures

CytoscapeConfiguration Library Public

Desktop Movies

Documents Music

Johannas-Air:~ johannavillen$ cd Downloads

Johannas-Air:Downloads johannavillen$ chmod +x ./mac.sh

Johannas-Air:Downloads johannavillen$ ./mac.sh

############# Cytoscape System Requirements Checker for Mac ##############

Target Cytoscape version: 3.3.0

Your shell is bash

Compatible OS version found: 10.11

 - Pass: OS Version = 10.11.4

- Fail: No Oracle JDK found.  Please download and install Oracle JDK:

http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

Johannas-Air:Downloads johannavillen$ ./mac.sh

############# Cytoscape System Requirements Checker for Mac ##############

Target Cytoscape version: 3.3.0

Your shell is bash

Compatible OS version found: 10.11

 - Pass: OS Version = 10.11.4

 - Pass: Following Oracle JDK found:

/Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk

 - Pass: Current Java Version = 1.8.0_101

JAVA_HOME is not set.

Please add the following to your .bashrc file:

export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_*.jdk/Contents/Home

where * is the latest Java 8 update number.

And then type 'source ~/.bashrc'

Johannas-Air:Downloads johannavillen$ 

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[Tim Hull]

It should work without setting JAVA_HOME on Mac - have you tried running cytoscape.sh or clicking on the icon after installing Java 8? 

Tim

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[Johanna Villén]

OK, do you mean running cytoscape.sh in terminal? How do I do that? I have tried opening cytoscape again but it still doesn’t work. 

Johanna

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[Tim Hull]

Could you try installing the JRE (not the JDK) for Java 8? If you had a previous version of the JRE installed, Cytoscape may be trying to use that even if you have the Java 8 JDK installed.

If running Cytoscape from the icon after doing that still doesn't work, you can run Cytoscape from the terminal. To do that, first change the current directory to the Cytoscape installation directory, i.e.:

cd /Applications/Cytoscape_v3.4.0

Then, run the following command to run Cytoscape:

./cytoscape.sh

Let me know if installing the JRE helps. If not, let me know what happens when you run Cytoscape from the command line...

Tim

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[Johanna Villén]

I installed JRE but I still couldn’t open cytoscape and then I tried running it from the terminal and that worked, cytoscape opened! But it is still not opening when I click the icon. Do I need to run it from terminal every time I want to use it?

Here is what terminal said when I ran it:

Last login: Sat Aug 13 09:13:46 on ttys000

Johannas-Air:~ johannavillen$ cd /Applications/Cytoscape_v3.4.0

Johannas-Air:Cytoscape_v3.4.0 johannavillen$ ./cytoscape.sh

Unable to find any JVMs matching version "1.7".

             _                                    

   ___ _   _| |_  ___  ___  ___  __ _ _ __   ___  

  / __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \ 

 | (__| |_| | |_| (_) \__ \ (__| (_| | |_) |  __/ 

  \___|\__, |\__|\___/|___/\___|\__,_| .__/ \___| 

       |___/                         |_|          

Cytoscape 3.4.0

Hit '<tab>' for a list of available commands

   and '[cmd] --help' for help on a specific command.

Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

Cytoscape 3.4.0> ======= cyREST Initialization start ======

Exception in thread "AWT-EventQueue-0" java.lang.IndexOutOfBoundsException: Index: 1, Size: 1

at java.util.ArrayList.rangeCheck(ArrayList.java:653)

at java.util.ArrayList.get(ArrayList.java:429)

at javax.swing.JTabbedPane.getTabComponentAt(JTabbedPane.java:2395)

at com.apple.laf.AquaTabbedPaneCopyFromBasicUI.calculateTabWidth(AquaTabbedPaneCopyFromBasicUI.java:1627)

at com.apple.laf.AquaTabbedPaneUI$AquaTruncatingTabbedPaneLayout.calculateHorizontalTabRunRect(AquaTabbedPaneUI.java:1191)

at com.apple.laf.AquaTabbedPaneUI$AquaTruncatingTabbedPaneLayout.superCalculateTabRects(AquaTabbedPaneUI.java:1158)

at com.apple.laf.AquaTabbedPaneUI$AquaTruncatingTabbedPaneLayout.calculateTabRects(AquaTabbedPaneUI.java:1057)

at com.apple.laf.AquaTabbedPaneCopyFromBasicUI$TabbedPaneLayout.calculateLayoutInfo(AquaTabbedPaneCopyFromBasicUI.java:2349)

at com.apple.laf.AquaTabbedPaneCopyFromBasicUI$TabbedPaneLayout.layoutContainer(AquaTabbedPaneCopyFromBasicUI.java:2253)

at java.awt.Container.layout(Container.java:1510)

at java.awt.Container.doLayout(Container.java:1499)

at java.awt.Container.validateTree(Container.java:1695)

at java.awt.Container.validateTree(Container.java:1704)

at java.awt.Container.validateTree(Container.java:1704)

at java.awt.Container.validate(Container.java:1630)

at javax.swing.RepaintManager$3.run(RepaintManager.java:711)

at javax.swing.RepaintManager$3.run(RepaintManager.java:709)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)

at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:708)

at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1731)

at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)

at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)

at java.awt.EventQueue.access$500(EventQueue.java:97)

at java.awt.EventQueue$3.run(EventQueue.java:709)

at java.awt.EventQueue$3.run(EventQueue.java:703)

at java.security.AccessController.doPrivileged(Native Method)

at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)

at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)

at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Johannas-Air:Cytoscape_v3.4.0 johannavillen$ 

Johanna 

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[Tim Hull]

That's weird - makes me think you have an old JVM that the launcher icon is somehow using. Could you run the following command?

/usr/libexec/java_home -V

If that shows versions older than the current 1.8 release, I'd try deleting those versions (though don't delete anything older than 1.7, as Mac Java 1.6 is a legacy version that some apps may still use).

Let me know if that helps...

Tim

Johanna 

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[Johanna Villén]

I ran what you said and this is what I got:

Last login: Mon Aug 15 09:04:44 on ttys000

Johannas-MacBook-Air:~ johannavillen$ /usr/libexec/java_home -V

Matching Java Virtual Machines (1):

    1.8.0_101, x86_64: "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk/Contents/Home

/Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk/Contents/Home

Johannas-MacBook-Air:~ johannavillen$ /Users/johannavillen 

That says that I have version 1.8.0 right? 

Johanna

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[Tim Hull]

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 Villén]

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 

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[Tim Hull]

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

[makn...@gmail.com]

Hi All,

I'm having the same problem as I'm trying to launch Cytoscape on my mac, and I see that I have Java version 10. Has this problem been resolved? I came across this thread while trying to troubleshoot it.

After trying through the terminal, it returns "Unable to find any JVMs matching version "1.8".
karaf.base: /Applications/Cytoscape_v3.7.2/framework
JAVA_HOME: null"...

Any thoughts?

Thanks!

On Tuesday, August 16, 2016 at 9:16:09 AM UTC-7, Tim Hull wrote:

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 

Tim

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[Scooter Morris]

Greetings,

Cytoscape 3.7 requires Java 1.8 and will not work with anything newer.  Cytoscape 3.8 (coming soon) will require Java 11.  Java 10 isn't supported for either version.

-- scooter

[liampvma...@gmail.com]

Hello, 

I am experiencing similar issues trying to launch Cytoscape with macOS.

I have installed the latest version of Cytoscape version 3.8.0 but it will not launch. Output from the troubleshooting script below:

############# 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

I do have Java installed on my laptop. Output from /usr/libexec/java_home -V:

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

I did try installing Java JDK 1.8 also (based on the prompt above) but encountered a JNI error similar to this (https://stackoverflow.com/questions/22381202/a-jni-error-has-occurred-please-check-your-installation-and-try-again-in-eclips) when I had it installed so subsequently removed it. Also the following error came up with JDK 1.8 suggesting that it is too old for Cytoscape 3.8.0: Class has been compiled by a more recent version of the Java Environment (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0.

I see from above comments that Cytoscape version 3.8.0 requires Java 11 so I installed Java version 11 in addition to version 12 in case there was an incompatibility there but still not working.

When I try to run cytoscape in the terminal I get the following error:

Unable to find any JVMs matching version "1.8".

karaf.base: /Applications/Cytoscape_v3.8.0/framework

JAVA_HOME: null

Any help greatly appreciated.

Thank you.

[Scooter Morris]

Cytoscape 3.8 definitely requires Java 11.  You have Java 11 installed, but it's not clear that you've set Java 11 as your default.  By the way, the troubleshooting script has now been updated for 3.8.0 -- can you download it and give it another try?

-- scooter

[Akila Yapa]

Johanna 

Tim

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  Akila Wijerathna-Yapa

[Mohita Mahajan]

The cytoscpae was working perfectly in my system (ubuntu) and now suddenly I am getting the " initializing OSGI container" while opening the cytoscape in Ubuntu. 
Kindle help me to resolve this issue.

[Scooter Morris]

Hi Mohita,

  I suspect you updated your java version.  There is an issue with Java 17.0.8 and Java 11.0.20.  See https://cytoscape.org/common_issues.html for a description of the problem and the workaround.

-- scooter