Chapter 3. Troubleshooting

Table of Contents

Installation Problems
Unzipping Distribution
Running Launcher Files
Url Related Issues
Url Linking in Windows
Url Linking on OSX
Export Problems
Export of Gene Summary
Giant Postscript Files
Giant GIF Files
Miscellaneous Problems
Out of Memory
Displaying Annotations
Switching browsers
Strange drawing of dendrogram branch lines
Crashing on Mac Os X

Installation Problems

Unzipping Distribution

Some users have reported problems unzipping the distribution. The problems encountered range from all files getting dumped in the root directory to not being able to unzip the distribution at all. This stems from my approach of using a single, relatively platform independant format, the .tar.gz format. The solution is to just use an unzipping program which handles .tar.gz properly.

Compatible Unzipping Programs

GNU tar/ GNU gunzip

These are the command line tools I use to create the distribution. They are ubiquitously available on all unix and unix-like operating systems, including Mac OS X, if you know where to look.


This is the recommended unzipper on the windows platform. I have heard reports that it doesn't do the right thing if you simply double-click the .tar.gz file. Instead, you may need to right-click, and select the "Expand to folder TreeView-blah" option.

Stuffit on Mac OS 9

This is the recommended unzipper for Mac OS 9. This should definately work on the specially packaged OS 9 distribution, which comes as a .sit file.

Stuffit on Mac OS X

As far I know, this should work fine. Just make sure you download the correct (.tar.gz) distribution of treeview.

Incompatible Unzipping Programs

Stuffit on Windows

This is known not to work in at least some cases. If it does not make a directory structure like Figure 1.1, “Contents of Java TreeView Distribution Archive”, then just go get winzip.

Running Launcher Files

The most common problem I have seen is that java is not installed on the system. The symptom is that nothing happens, or something confusing happens, when you doubleclick the launcher. The solution is to install a recent version of the java runtime environment. For Windows or Unix systems, this involves a quick download from the sun website,

Mac OSX comes with java standard. For Mac OS9, you may need to get the Mac OS Runtime for Java (MRJ) from the apple website,