Introducing Mesquite Using Mesquite How Mesquite Works Known Problems Programmer's Guide

Known problems with Mesquite

(updated July 2001)

Mesquite is incomplete in various ways, and no doubt harbors some bugs. Here are a few of its problems.

We welcome bug reports. See the page on Support. For more details on bugs and other problems, see the programmer's guide to issues, problems and bugs in the developer documentation

General issues

• Modules not correctly marked as substantive vs. not; release vs. prerelease (see discussion concerning publishing results)
• Module information regarding authors, date released, and citations are not yet filled in (except for a few).
• No Undo in data window
• Incomplete use of character exclusion and weights
• NEXUS file reading is somewhat limited. For example, it cannot read transposed data matrices.
• Mesquite uses up a lot of memory, and in some systems this memory use may be progressive (i.e. the longer you use it, the more memory it uses). We would appreciate reports of your experiences. We'll continue to try to improve memory efficiency.

Issues with specific operating systems

Microsoft Windows

Matrix cells blank — Because of a bug (#4337823) in Sun's Java virtual machine for JRE/JDK 1.2 and 1.3, cells of tables and some images will appear blank occasionally if hardware graphics acceleration is turned on. This should not be a problem for most users, because the executable Mesquite.exe created by the installer automatically requests the Java VM not to use the hardware acceleration (this however degrades Mesquite's drawing speed, but, better late than never). However, if you run Mesquite in some other way, for instance by a direct call to the Java VM from the DOS prompt, blank cells in tables and missing images will be an issue.

Menus mislabeled — Because of an apparent bug in Sun's Java virtual machines (1.1.8 through 1.3.1), menus are occasionally mislabeled (about 3% of the time). For instance, the File menu might be labeled as the "Gray" menu, or the "Histogram" menu, or have some other label drawn "randomly" from among the menu items within the menus. Because of this problem and the confusion it might cause, we have added a Reset Menus item in the File menu. This will force Mesquite to rebuild the menus, which usually corrects the mislabeling.

Mac OS 9

Cursor remains the arrow even when a special tool is selected — This is due to the fact that OS 9 does not support Java 2. To help you see what tool is in use, it is highlighted in the tool palette.

Error message about NullPointerException at PortState.create — The following error message may appear occasionally. It is completely innocent, and represents a bug in the Mac OS 9 Java virtual machine. It has no effects on the operation of Mesquite.

• java.lang.NullPointerException
  at com.apple.mrj.internal.awt.PortState.create(Compiled Code)
  at com.apple.mrj.internal.awt.PortState.create(Compiled Code)
  at com.apple.mrj.internal.awt.VComponentPeer.setPort(Compiled Code)
  at com.apple.mrj.internal.awt.View.setPort(Compiled Code)
  at com.apple.mrj.internal.awt.VTextComponentPeer.idle(Compiled Code)
  at com.apple.mrj.internal.awt.VToolkit.idle(Compiled Code)
  at com.apple.mrj.internal.awt.VToolkit$VIdleThread.run(VToolkit.java)
  

Mac OS X

If you have a choice between using Mesquite under OS X or OS 9, we recommend using it under OS 9 at present (July 2001). Mesquite is much more stable and faster under OS 9 than under OS X. This may change when OS X 10.1 is released.

Failure to open files from Finder — Because of bugs in the current (10.0.4) Mac OS X Java, Mesquite will frequently fail to open a file when you double click it in the Finder, or drop the file's icon onto Mesquite's icon. Mesquite will start up, but it may fail to open the file. If so, then try again after Mesquite is already opened up. Apple is aware of this problem and is trying to fix it.

Very slow branch dragging — Because of serious problems with particular aspects of graphics drawing in the current (10.0.4) Mac OS X Java, some cases of dragging an object (e.g., a branch in the tree window or a legend in the tree window) will be glacially slow. We could try to discover a workaround, but we're hoping Apple will fix the problem first.

Can't select a browser to display web pages — A bug in Mac OS X Java prevents you from being able to choose a browser to use for displaying Mesquite's web pages.

Gets slower with long use — There appear to be serious memory leaks (i.e. progressively increasing use of memory) that might be Mesquite's fault, except that they seem not so serious under other operating systems. Mesquite gets slower and slower under OS X as you continue to use it.

Linux/UNIX

Windows incorrectly placed — Some window managers refuse to let Mesquite have control over window size and placement, and choose what appear to be random sizes and placements of windows. This is not in our control. Try changing your window manager. We have found that the default installations for KDE and Gnome of Red Hat 7 work well with Mesquite.

Messages about Fonts not found on startup — This will occur commonly, in fact we suspect on most installations on Linux and Solaris of Sun's Java VM. The problem is that you need to install a supposedly optional package of fonts in order that the default installation of Sun's Java VM work properly (see http://java.sun.com/products/jdk/1.2/changes.html#sunw). We would have thought that if the default installation of a product claims to support a program but doesn't, then that would be considered a bug. Sun considers this to be not a bug.