Help:Known problems
From WikiPathways
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.
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Java Warnings and Blocks
There is a battle going on between Java, operating systems and browsers, and we are caught in the middle. While we work on the long-term solution of replacing our Java Applet editor with a JavaScript editor, we have recommendations and fixes for your particular OS and Java combination. Let us know if you have another setup or if these don't work for you.
If you update your OS or Java version (often this is done automatically with minimal confirmation from you), then you'll need to revisit this table and perform the recommended setup steps.
- Check your operating system version
- Mac: Apple menu > About this Mac
- Win: Start > Computer > Properties
- Check your Java version (Note: versions 1.7.x = "Java 7" and versions 1.8.x = "Java 8")
- Mac: Open Terminal.app and type: java -version
- Win: Open Command and type: java -version
- Find recommendations and fixes for your setup in the table below
| Operating System | Java Version | Browser | Recommends and fixes |
|---|---|---|---|
| MacOS 10.9 | Java 7 | Chrome or Firefox | Enable Java Applets and set Java security exceptions (see video) |
| MacOS 10.9 | Java 8 | coming soon... | |
| MacOS 10.10 | Java 7 | coming soon... | |
| MacOS 10.10 | Java 8 | coming soon... | |
| Win 7 (32 bit) | Java 8 (32 bit) | coming soon... | |
| Win 7 (64 bit) | Java 7 (32 bit) | coming soon... | |
| Win 7 (64 bit) | Java 8 (32 bit) | coming soon... | |
| Win 7 (64 bit) | Java 7 (64 bit) | coming soon... | |
| Win 7 (64 bit) | Java 8 (64 bit) | coming soon... | |
| Win 8.1 (64 bit) | Java 7 (64 bit) | coming soon... | |
| Win 8.1 (64 bit) | Java 8 (64 bit) | coming soon... | |
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:
- Go to Start -> Control Panel
- (In Classic View) click on the icon Labeled Java
- In the Java Control Panel dialog, in the general tab, under the heading Temporary Internet Files click on Settings
- Click Delete Files. This will only delete temporary files that are safe to delete.
- Close the browser completely, then try WikiPathways again.
On a Mac:
- Open /Applications/Utilities/Java Preferences
- Click on Network tab
- Click on Delete Files and click OK
- 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:
- Go to Start -> Control Panel
- (In Classic View) click on the icon Labeled Java
- In the Java Control Panel dialog, in the general tab, under the heading Temporary Internet Files click on Settings
- Click Delete Files. This will only delete temporary files that are safe to delete.
- 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.
Application blocked by Security Setting
In the latest Java update the security settings for self-signed applications have been adapted (Java 7 Update 51). Self-Signed applications, like Pathvisio, are blocked on high security level. For details see the Pathvisio FAQ
