Help:Known problems

From WikiPathways

Revision as of 08:37, 17 August 2012

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.

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

By default the Ubuntu linux distribution comes with the gij (GNU libgcj) Java virtual machine. In order to make wikipathways work correctly, you will need to replace this with Sun's JVM. You can do this by installing the packages sun-java5-jre and sun-java5-plugin or sun-java6-jre and sun-java6-plugin.

No SVG viewer in Internet Explorer

When you are using Internet Explorer you need to install an SVG viewer to view the pathway images at full size. Go to Adobe SVG viewer to download an SVG viewer for Internet Explorer.

"inactive plugin in Mac Lion or Mountain lion

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". Solving this is done as follows. Open the terminal and run:

  /Applications/Utilities/Java\ Preferences.app/Contents/MacOS/Java\ Preferences

You will see a window where you can enable java by ticking:

    Enable applet plug-in and Web Start applications

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