A very common EGAN exception due to Java 7 (1.7)

[ucsf egan]

Hey EGAN'ers,

I just upgraded my machine to Java 7 and EGAN threw an exception:

java.lang.NullPointerException
at edu.ucsf.cc.icore.app.egan.EganFrame.getBackground(EganFrame.java:
118)
at java.awt.Window.setBackground(Unknown Source)
at java.awt.Frame.setBackground(Unknown Source)
at javax.swing.JFrame.frameInit(Unknown Source)
at javax.swing.JFrame.<init>(Unknown Source)
at edu.ucsf.cc.icore.app.egan.EganFrame.<init>(EganFrame.java:84)
at
edu.ucsf.cc.icore.app.egan.EganState.constructEganFrame(EganState.java:
86)
at edu.ucsf.cc.icore.app.egan.EganState.<init>(EganState.java:67)
at
edu.ucsf.cc.icore.app.egan.launch.LaunchEgan.constructEganState(LaunchEgan.java:
348)
at
edu.ucsf.cc.icore.app.egan.launch.LaunchEganThread.run(LaunchEganThread.java:
142)
at java.lang.Thread.run(Unknown Source)

If you see this error message, it is because your .jnlp file has a
flawed line in it. To fix it, open the .jnlp file with a text editor
and find the place where you see:

<resources>
<j2se version="1.6+"...

and change the "1.6+" to be simply "1.6":

<resources>
<j2se version="1.6"...

Please post if you have any questions/comments. The .jnlp files on
the EGAN website have all been updated with this fix.

Enjoy!

Jesse

[ucsf egan]

There is another problem. Some EGAN users only have Java 7 (aka 1.7) installed on their machine. In order to avoid this error, you need to install Java 6 (aka 1.6). You can download that here:
http://www.oracle.com/technetwork/java/javase/downloads/jre6downloads-1902815.html

[Arundhati Bakshi]

Dear Jesse,

I just downloaded the mouse EGAN jnlp file from the website and I am getting the same error. I checked the file in my text editor, and it says <j2se version="1.6". I tried going back to 1.6+ since I also had an older Java 6 version on my computer, but that did not seem to solve the problem either. EGAN automatically opened in Java 7 and then gave me the java.lang.NullPointerException error. Any help would be much appreciated.

Thank you,

Runa

P.S. I have Java 7 update 25, in case you need the information to help me with the problem.

[nadisha silva]

Hi Runa,

Did you you find a solution? I have the same problem. 

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[Arundhati Bakshi]

Hi Nadisha,

Not yet unfortunately! I have also emailed Jesse at her contact email address on the EGAN website. I am hoping we will find a solution soon.

[nadisha silva]

Thanks for letting me know Runa. I've done the same and hopefully it will get solved sooner than later. I need these results ASAP.

[Arundhati Bakshi]

I understand your urgency only too well! Depending on what kind of data you are trying to analyze, you could try using DAVID as an alternative. It doesn't generate a pretty figure like EGAN does but it gives you some sense of what kind of pathways, interactions, etc. your gene set might be enriched for. You can see if that program is of any use to you until we can access EGAN again.

[nadisha silva]

Thanks for the suggestion. I might just do that. Although, I've written the methods section including EGAN :/ . I added some new information and needed to re-run EGAN to see whether there are any new enrichment terms and now I can't launch EGAN. 

[Arundhati Bakshi]

I completely understand how you feel about these last minute issues! I hope the other program can help you. And in the meantime, we can find a solution to the EGAN problem soon.

[ucsf egan]

Ok, sorry for the delay, let's try to figure this out.  Are you on Macs or PCs?

If you're on a Mac, it's very hard to regress and install the 1.6 JRE.  If you're on a PC, you can follow the link to download the installer here:

http://www.oracle.com/technetwork/java/javase/downloads/jre6downloads-1902815.html

We will fix this problem in our next release (it's a trivial fix), but I can't say just when that will be.

Please let me know if you have any updates.  Good luck,

Jesse

[nadisha silva]

Jesse,

I followed your advice and it works. Thank you.

Nadisha

[rebecc...@gmail.com]

I am running Mac OS 10.9 (Mavericks) and have been able to downgrade to Java 6 and reactivate the web applet using the following steps:

1. If you have already installed Java 7, uninstall it by following the instructions here: http://www.java.com/en/download/help/mac_uninstall_java.xml

2. Install the Java 6 package available through Apple: http://support.apple.com/kb/DL1572

3. This Java package does not have web start functionality. To activate it, open a terminal and input the following command, then press enter:

sudo ln -sf /System/Library/Frameworks/JavaVM.framework/Commands/javaws /usr/bin/javaws

Good luck!

Rebecca Beer

[ucsf egan]

Nice!  Thanks Rebecca.

[ucsf egan]

This link is also helpful:

http://support.apple.com/kb/ht5559

Nice!  Thanks Rebecca.

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[rlju...@gmail.com]

Hi Jesse,

  Any updates on this? I am running Mac OS X 10.7.5, which only ever had Java 7 on it. When I try to run the latest downloadable version of EGAN, I get the exception you mention at the beginning of this post. When I follow Rebecca's instructions below, the problem still isn't fixed. Any advice? 

Thanks for your help!

Best,

Rob

[ucsf egan]

Hey Rob,

This workaround works for me... http://support.apple.com/kb/ht5559

Jesse