Help:Known problems

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(Updated (fixed) the info on installing Java on Ubuntu.)
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Older Ubuntu linux distribution came with the gij (GNU libgcj) Java virtual machine, while newer versions come with the icedtea plugins. In order to make wikipathways work correctly, you will need to replace this with Oracle's JVM. Details on how to install this can be found [https://help.ubuntu.com/community/Java here].
Older Ubuntu linux distribution came with the gij (GNU libgcj) Java virtual machine, while newer versions come with the icedtea plugins. In order to make wikipathways work correctly, you will need to replace this with Oracle's JVM. Details on how to install this can be found [https://help.ubuntu.com/community/Java here].
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=== No SVG viewer in Internet Explorer ===
 
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When you are using Internet Explorer you need to install an SVG viewer to view the pathway images at full size. Go to [http://www.adobe.com/svg/viewer/install/main.html Adobe SVG viewer] to download an SVG viewer for Internet Explorer.
 
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=== "inactive plugin" in Mac Lion or Mountain lion ===
 
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When you install or update Lion or Mountain lion, the browsers are configured not to allow running Java inside a browser. Trying to edit a pathway will fail and the following message will show: "Inactive Plugin".
 
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Solving this is done as follows. Open the terminal and run:
 
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  /Applications/Utilities/Java\ Preferences.app/Contents/MacOS/Java\ Preferences
 
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You will see a window where you can enable java by ticking:
 
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    Enable applet plug-in and Web Start applications
 
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Contents|Return to Help Contents]]</p>
<p>[[:Help:Tutorial|Continue to Tutorials]]</p>
<p>[[:Help:Tutorial|Continue to Tutorials]]</p>

Revision as of 15:45, 9 July 2013


On this page you'll find some known problems with WikiPathways.

If your problem is not on this list, please check our bug tracker or send an email to our Google group.

Contents

No Java installed

You need to have Java installed to be able to edit pathways. If you only see a grey box when you click the edit button below the pathway image, please check if you have Java installed (version JSE 5 or above). You can test if Java is working in your browser here and download Java here.

Javascript disabled

You need to have javascript enabled in your browser. Click here to see how to enable javascript for your browser.

Strange error while starting Java

Sometimes a dialog with "NullPointerException" or "InvocationTargetException" appears when you try to start the edit applet. In this case it may help to clear the Java Applet Cache. In Windows XP, you do this as follows:

  1. Go to Start->Control Panel
  2. (In Classic View) click on the icon Labeled "Java"
  3. In the Java Control Panel dialog, in the general tab, under the heading "Temporary Internet Files" click on Settings...
  4. Click "Delete Files". This will only delete temporary files that are safe to delete.
  5. Close the browser completely, then try WikiPathways again.

On a Mac:

  1. Open /Applications/Utilities/Java Preferences
  2. Click on Network tab
  3. Click on "Delete Files...", Click "OK"
  4. Close the browser completely, then try WikiPathways again

Editor does not load and you just see a black window

In this case it might help to clear the Java Applet Cache. In Windows XP, you do this as follows:

  1. Go to Start->Control Panel
  2. (In Classic View) click on the icon Labeled "Java"
  3. In the Java Control Panel dialog, in the general tab, under the heading "Temporary Internet Files" click on Settings...
  4. Click "Delete Files". This will only delete temporary files that are safe to delete.
  5. Close the browser completely, then try WikiPathways again.

Wrong Java version on Ubuntu

Older Ubuntu linux distribution came with the gij (GNU libgcj) Java virtual machine, while newer versions come with the icedtea plugins. In order to make wikipathways work correctly, you will need to replace this with Oracle's JVM. Details on how to install this can be found here.


Return to Help Contents

Continue to Tutorials

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