GelBuddy Installation Issues

This page provides technical information which you may find helpful in diagnosing GelBuddy installation problems. If the procedures described below are unfamiliar to you, we recommend that you contact the technical support staff of your institution for assistance.

Updated 26 May 2005

Windows Installation Issues

Error message: Java Advanced Imaging Not Installed.

GelBuddy requires that the Java Advanced Imaging library (JAI) be installed in the Java Virtual Machine (Java VM) being used to run GelBuddy. This can be particularly problematic for machines on which multiple Java VMs are installed.

Solution:
Write down the directory name (for example, c:\Program Files\Java\j2re1.4.2_04) in the error message. Open the lib\ext subdirectory (e.g. c:\Program Files\Java\j2re1.4.2_04\lib\ext). You should see the file jai_core.jar, along with several other files. If this file is not present, try one of the following:

Install the Java Advanced Imaging Library (as described in the Windows installation page) into the Java VM at the directory listed in the error message. When you run the JAI installer, you will eventually be presented with a window labeled "Choose Destination Location". Click on the Browse button, and in the "Choose Folder" window select the directory you noted earlier.

If your system contains multiple Java VMs, find the location of the Java VM in which the Java Advanced Imaging library is installed. Open gelbuddy.bat in a text editor, and modify the line
java -Xms256M -Xmx256M -jar TGAT.jar
to contain the full path to the Java VM in which JAI is installed, e.g.
c:\Program Files\Java\j2re1.4.2_04\bin\java -Xms256M -Xmx256M -jar TGAT.jar

GelBuddy stopped working after I updated my computer to the latest version of Java (J2SE 5.0).

By default, installing a new Java VM update doesn't update your existing Java VM; instead, it installs an entirely separate instance of the Java VM in a different directory. GelBuddy will not function unless the Java Advanced imaging library is installed the new Java VM directory.

Solution:
Try one of the following:

Reinstall the Java Advanced Imaging library into the location of the newly installed Java VM (i.e. c:\program files\java\jre1.5.0_03) as described above.
Uninstall the updated Java VM. Your system should now run GelBuddy from the older version of the Java VM, on which the Java Advanced Imaging library was already installed.

Warning message: Max heap size ... is too small.

GelBuddy displays this error message to indicate that it is being invoked by the system with insufficient virtual memory. Many operations will work, but certain memory-intensive operations will behave erratically. The most likely explanation for this error is that you are running the Java Archive (.JAR) file tgat.jar directly.

Solution:
Invoke GelBuddy by using the GelBuddy batch file (gelbuddy.bat) provided in the download package (GelBuddyxxxxxxxx.zip). This instructs the system to provide GelBuddy with a larger virtual memory pool.

Clicking on the GelBuddy batch file icon does nothing/causes window to flash.

Solution:
You will have to use a command prompt window to obtain an informative error message. Open a command prompt window, cd to the directory in which you installed gelbuddy, and enter the command gelbuddy.

If you see the error message: 'java'is not recognized as an internal or external command, operable program or batch file
Search for the file java.exe and edit the file gelbuddy.bat to contain the full path to the Java VM as described above.

If you see the error message: Exception in thread "main" java.util.zip.ZipException: The system cannot find the file specified
Java is installed but cannot find the GelBuddy .JAR file. Ensure that gelbuddy.bat and tgat.jar have been properly extracted from the download package (GelBuddyxxxxxxxx.zip) and are located in the same directory.

Macintosh Installation Issues

Error message: Java Advanced Imaging Not Installed.

GelBuddy requires that the Java Advanced Imaging library (JAI) be installed on your system.

Solution:
Install the Java 3D and Java Advanced Imaging Update from Apple as described in the Macintosh installation page.

Warning message: Max heap size ... is too small.

GelBuddy displays this error message to indicate that it is being invoked by the system with insufficient virtual memory. Many operations will work, but certain memory-intensive operations will behave erratically. The most likely explanation for this error is that you are running the Java Archive (.JAR) file tgat.jar directly.

Solution:
Invoke GelBuddy by using the GelBuddy application bundle (the file gelbuddy.app or gelbuddy or labeled with the FHCRC double-helix icon) provided in the download package (GelBuddyxxxxxxxx.dmg). This instructs the system to provide GelBuddy with a larger virtual memory pool.

Clicking on the GelBuddy batch file icon does nothing / icon bounces.

Solution:
You will have to use the terminal window to obtain an informative error message. Open the terminal window and enter the command:
java -version
If you see the message:
segmentation fault
your java system is corrupt. The cause and solution for this problem are documented on Apple's website: http://docs.info.apple.com/article.html?artnum=301380 .

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