Cannot open Cytoscape 3.3 in Ubuntu 14.04

[lindfo...@gmail.com]

Hi all,

I am trying to open Cytoscape 3.3 (*) in Ubuntu 14.04 but so far have not managed to do it.

First I got the following error:

nn@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ ./cytoscape.sh &

[1] 10551

nn@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ karaf: JAVA_HOME not set; results may vary

Exception in thread "main" java.awt.HeadlessException

at sun.java2d.HeadlessGraphicsEnvironment.getDefaultScreenDevice(HeadlessGraphicsEnvironment.java:77)

at org.cytoscape.launcher.internal.SplashPanel.<init>(SplashPanel.java:30)

at org.cytoscape.launcher.internal.Launcher.showSplashPanel(Launcher.java:82)

at org.cytoscape.launcher.internal.Launcher.main(Launcher.java:53)

[1]+  Exit 1                  ./cytoscape.sh

Then I set JAVA_HOME, then I am getting the following error:

nn@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ ./cytoscape.sh &[1] 11684

nn@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ ./framework/bin/karaf: 242: [: Illegal number: 

./framework/bin/karaf: 414: exec: /usr/lib/jvm/java-7-openjdk-amd64/bin/bin/java: not found

Everything works fine in Windows 7.

Does anybody have an idea how to fix this?

I think my colleague had the same problem a few months ago.

From what I remember she managed to fix it by making a tiny modification around line 242 in karaf but I cannot recall what it was.

(*)
I downloaded this Cytoscape version from
http://code.cytoscape.org/jenkins/job/cytoscape-3-gui-distribution/lastSuccessfulBuild/org.cytoscape.distribution$cytoscape/.

Kei gave this link in an earlier discussion in this group
https://groups.google.com/forum/#!searchin/cytoscape-helpdesk/Erno$20Lindfors/cytoscape-helpdesk/tM3hshUHvOw/xbhiFRPITusJ

Thanks,

Erno Lindfors

[Tim Hull]

It looks like you have a headless (no GUI) version of Java installed - to resolve this, you'll need to install the standard version of Java (sudo apt-get install openjdk-7-jre should do the trick on Ubuntu 14.04). As for JAVA_HOME, it should run fine without setting that - in any case, it looks like you had an unnecessary /bin in the JAVA_HOME path. There should be no need to edit the karaf script in any case...

Let me know if this helps...

Tim

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[lindfo...@gmail.com]

Hi all,

Thanks Tim for your response!

I first tried to install the standard GUI version of Java by giving the following command

sudo apt-get install openjdk-7-jre
but it did not work, unfortunately cannot recall (and did not write down) the exact error message.

Then I downloaded the installation package from Oracle's web site:
http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html

-> jdk-7u75-linux-x64.tar.gz

Then I extracted this package and set the jdk folder of this package to the PATH by giving the following commands:

export JAVA_HOME=/usr/lib/jvm/jdk1.7.0_75

export PATH=$PATH:$JAVA_HOME/bin

Then I explicitly checked I am using this java by giving the following command:

nn@NN:~$ java -version

java version "1.7.0_75"

Java(TM) SE Runtime Environment (build 1.7.0_75-b13)

Java HotSpot(TM) 64-Bit Server VM (build 24.75-b04, mixed mode)

Then I tried to open the Cytoscape by giving the following command:

nn@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ ./cytoscape.sh &

[1] 17467

But this process gets stuck to a stage in which the following text is in the progress bar:

"org.apache.karaf.features.command started"

Any idea why this happens?

I have an intuition perhaps I am still using a wrong java version.

If this is the case, can anyone perhaps indicate the right version from the Oracle's web site?

Thanks,

Erno

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[Tim Hull]

First of all, does Cytoscape 3.2.0 work? 3.3.0 is a pre-release development branch, and in general should only be used if you intend to work on Cytoscape core development/testing (not app development). 

The command you tried to install OpenJDK 7 should work fine - not sure why it would give an error, though I can't say anything about it without actually seeing the error in question. Oracle Java should work just as well, though. If you're still having problems, you may want to try deleting the CytoscapeConfiguration directory (under your home directory) - doing that can sometimes help startup hangs...

Let me know if you get it working or not...

Tim

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[lindfo...@gmail.com]

Hi all,

Thanks Tim for your help again!

I switched to Cytoscape 3.2.0 and managed to open it by double-clinking the orange Cytoscape icon in the Cytoscape installation folder.
(I though have a similar a startup hang also in this version  when trying to start it from the command line but I think it is not an issue since the icon startup seems to work.)

The reason why I wanted to use Cytoscape 3.3.0 is that I understood from an earlier discussion with Kei (link below) that this is the only version in which the interactive web application works.

https://groups.google.com/forum/#!searchin/cytoscape-helpdesk/Erno$20Lindfors/cytoscape-helpdesk/tM3hshUHvOw/xbhiFRPITusJ

Please let me know if you know any stable or semi-stable version in which the web application works and in which there is an orange icon to start the application (I cannot find this icon in the 3.3.0 I downloaded on Feb 4) .

Thanks,

Erno

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[Tim Hull]

The icon launcher you are referring to is only available when using the installer to install Cytoscape - an option not available for the development branch. In any case, 3.2.1 should be available very soon (in the next day or so), and that would resolve your issue. 

In any case, it is weird that Cytoscape hangs when running from cytoscape.sh but not when running from the app launcher. Could you try again after deleting the CytoscapeConfiguration directory and see if it still happens? Also, what Java version does the splash screen show, and does the log file (~/CytoscapeConfiguration/3/framework-cytoscape.log) or console contain any error messages from the startup? 

Tim

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[Barry Demchak]

Also, if you’d like to try out the release candidate for v3.2.1 yourself and give us feedback, you can try it out at:

 

http://chianti.ucsd.edu/cytoscape-3.2.1-rc1/

 

Please let us know!

 

Thanks.

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[lindfo...@gmail.com]

Hi Tim, Barry and others,

Thanks for your involvement!

I deleted the CytoscapeConfiguration directory but the same happens (cytoscape.sh does not work, app launcher works).

I tried both Cytoscape 3.2.0 and the release candidate for v3.2.1 (both versions downloaded recently).

Attached an image from the splash screen at startup hang (v3.2.0).

As you can see it says I am using the following java version:

Java version: 1.7.0_75

From what I understand it is the version my command line says:

rno@erno-HP-Elite-7500-Series-MT:~/Cytoscape_v3.2.0$ java -version

java version "1.7.0_75"

Java(TM) SE Runtime Environment (build 1.7.0_75-b13)

Java HotSpot(TM) 64-Bit Server VM (build 24.75-b04, mixed mode)

Cytoscape creates a CytoscapeConfiguration directory during this process.

I have copy-pasted the contents of .../CytoscapeConfiguration/3/karaf_data/log/karaf.log and .../CytoscapeConfiguration/3/framework-cytoscape.log to the end of this message.

From what I understand karaf.log says something gets locked.

Thanks,

Erno

karaf.log:

Feb 10, 2015 2:35:48 PM org.apache.karaf.main.SimpleFileLock lock

INFO: locking

framework-cytoscape.log:

2015-02-10 14:35:48,843 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.ops4j.pax.url.mvn.cfg

2015-02-10 14:35:48,845 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.karaf.features.repos.cfg

2015-02-10 14:35:48,846 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.karaf.kar.cfg

2015-02-10 14:35:48,849 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.karaf.management.cfg

2015-02-10 14:35:48,852 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.karaf.features.cfg

2015-02-10 14:35:48,854 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.karaf.log.cfg

2015-02-10 14:35:48,856 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.felix.fileinstall-deploy.cfg

2015-02-10 14:35:48,857 [CM Configuration Updater (Update: pid=org.apache.felix.fileinstall.704f58e3-7546-43b8-8679-d26fce243d98)] WARN  org.apache.felix.fileinstall - /home/erno/CytoscapeConfiguration/3/apps/installed does not exist, please create it.

2015-02-10 14:35:48,858 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.karaf.jaas.cfg

2015-02-10 14:35:48,860 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.karaf.shell.cfg

2015-02-10 14:35:48,862 [FelixStartLevel] INFO  org.apache.felix.fileinstall - Installed /home/erno/Cytoscape_v3.2.0/framework/etc/org.apache.karaf.features.obr.cfg

2015-02-10 14:35:48,896 [FelixStartLevel] INFO  org.apache.aries.blueprint.container.BlueprintExtender - No quiesce support is available, so blueprint components will not participate in quiesce operations

n...@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ ./cytoscape.sh &

[1] 17467

 

But this process gets stuck to a stage in which the following text is in the progress bar:

"org.apache.karaf.features.command started"

 

Any idea why this happens?

 

I have an intuition perhaps I am still using a wrong java version.

If this is the case, can anyone perhaps indicate the right version from the Oracle's web site?

 

Thanks,

Erno

On Wednesday, February 4, 2015 at 6:24:16 PM UTC+1, Tim Hull wrote:

It looks like you have a headless (no GUI) version of Java installed - to resolve this, you'll need to install the standard version of Java (sudo apt-get install openjdk-7-jre should do the trick on Ubuntu 14.04). As for JAVA_HOME, it should run fine without setting that - in any case, it looks like you had an unnecessary /bin in the JAVA_HOME path. There should be no need to edit the karaf script in any case...

 

Let me know if this helps...

 

Tim

On Wed, Feb 4, 2015 at 2:52 AM, <lindfo...@gmail.com> wrote:

Hi all,

 

I am trying to open Cytoscape 3.3 (*) in Ubuntu 14.04 but so far have not managed to do it.

 

First I got the following error:

n...@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ ./cytoscape.sh &

[1] 10551

n...@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ karaf: JAVA_HOME not set; results may vary

Exception in thread "main" java.awt.HeadlessException

at sun.java2d.HeadlessGraphicsEnvironment.getDefaultScreenDevice(HeadlessGraphicsEnvironment.java:77)

at org.cytoscape.launcher.internal.SplashPanel.<init>(SplashPanel.java:30)

at org.cytoscape.launcher.internal.Launcher.showSplashPanel(Launcher.java:82)

at org.cytoscape.launcher.internal.Launcher.main(Launcher.java:53)

 

[1]+  Exit 1                  ./cytoscape.sh

 

Then I set JAVA_HOME, then I am getting the following error:

n...@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ ./cytoscape.sh &[1] 11684

n...@NN:~/Downloads/cytoscape-unix-3.3.0-SNAPSHOT$ ./framework/bin/karaf: 242: [: Illegal number: 

./framework/bin/karaf: 414: exec: /usr/lib/jvm/java-7-openjdk-amd64/bin/bin/java: not found

 

Everything works fine in Windows 7.

 

Does anybody have an idea how to fix this?

 

I think my colleague had the same problem a few months ago.

From what I remember she managed to fix it by making a tiny modification around line 242 in karaf but I cannot recall what it was.

 

(*)
I downloaded this Cytoscape version from
http://code.cytoscape.org/jenkins/job/cytoscape-3-gui-distribution/lastSuccessfulBuild/org.cytoscape.distribution$cytoscape/.

 

Kei gave this link in an earlier discussion in this group
https://groups.google.com/forum/#!searchin/cytoscape-helpdesk/Erno$20Lindfors/cytoscape-helpdesk/tM3hshUHvOw/xbhiFRPITusJ

 

Thanks,

Erno Lindfors

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[Tim Hull]

Are you setting JAVA_HOME to the proper path for your Java installation? Otherwise, the script may use a different version of Java, even if Java is on the path. 

Also, what do you see on the console when you run cytoscape.sh? If you're still having the issue at that point, could you try Cytoscape 3.1.1 as well? 

The URL for that version is http://chianti.ucsd.edu/cytoscape-3.1.1/

That would help us tell if this issue was introduced in 3.2.0 or existed prior to that....

Let us know...

Tim

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[lindfo...@gmail.com]

Hi Tim and others,

I have set JAVA_HOME to my JDK folder, more explicitly:

erno@erno-HP-Elite-7500-Series-MT:~$ echo $JAVA_HOME

/usr/lib/jdk1.7.0_75

I am not 100% sure if this setting is correct, please let me know if you think not.

For the case this is useful, my PATH:

erno@erno-HP-Elite-7500-Series-MT:~/Cytoscape_v3.2.0$ echo $PATH

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/jdk1.7.0_75/bin

My console at startup hang:

erno@erno-HP-Elite-7500-Series-MT:~/Cytoscape_v3.2.0$ ./cytoscape.sh &

[1] 27014

I tested v3.1.1 - the same issue happens also there.

Without knowing anything about the implementation of cytoscape.sh, I have a strong intuition this issue was introduced when switching from Cytoscape 2 to 3. A few colleagues of mine started to experience it when we they switched to 3 whereas I think they never experienced anything similar in 2. However as mentioned earlier, this has not really become a problem since we have quite easily managed to find alternatives, like currently using the launcher.

Thanks,

Erno

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[Tim Hull]

It seems that the background launching is causing this issue - I see it if I run cytoscape.sh with an & on the command line, but not if I don't. Not sure why this happens, though running from the app launcher ( ./Cytoscape & on the command line) works fine if you want to run in the background.

Glad you've been able to work around the issue - I'll go ahead and file a bug regarding this...

Tim

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[Sofi Imran Ul Umar]

Hi everyone .

i am not able to open Cytoscape 3.10.0 .

i have installed it and cytoscape icon is also visible in the apps .

But I am not able to launch it

[Scooter Morris]

Greetings,

  Two issues here.  First, there was an issue with Cytoscape 3.10 that prevents it from launching from the icon.  You'll need to bring up a terminal window and run the cytoscape.sh file in Cytoscape install directory.  Second, it still might not work if you are running the latest Java -- Java 17.0.8.  There was a change in the zip file handler in Java 17.0.8 and Java 11.0.20 that broke OSGi bundles.  The information (and the workaround) is described here: https://cytoscape.org/common_issues.html  This will be fixed in Cytoscape 3.10.1.

-- scooter