Support & Advice

Mesquite is under construction

Mesquite is in beta-test form, meaning that we're seeking user feedback to learn what areas need the most work. We expect there may be quite a few bugs reported initially. Some bugs you may encounter will be bugs not in Mesquite but in the operating system or Java virtual machine (for example, see this list).

Mesquite calculations aren't quite ready for publishable results, though some are very close. The beta-testing will help us determine how close they are, but we hope to indicate what calculations are ready over the next two or three months. In the meantime please feel free to explore the system, and use it in teaching.

If you do wish to use results from Mesquite in publications, please be in contact with us, and we can determine if those features you wish to use are stable and bug-free enough.

Why doesn't Mesquite do <insert your favorite calculation here>?

Mesquite is extensible. What it can do now is a small part of what we envisage. We welcome suggestions but we're aware of many things that could be added. The biggest needs we feel at the moment are for likelihood calculations and more tools for examining character correlations.

Of course, if you really want a new feature sooner than we can add it, you are welcome to write your own module to implement the feature.

Things to think about before getting annoyed at bugs

Mesquite is a large project, about 1500 pages of source code when printed single spaced at 7 point font (about 120,000 or more lines of source; over 5MB of ASCII text). We don't have a big team of people working on it; it was initially written by a single person, and now two. We apologize for the bugs that remain, and look forward to your polite bug reports and efforts to aid us make Mesquite useful.

Mesquite is free. We don't have a separate support staff to answer questions, fix bugs, and so on.

Mesquite is intended to become a community effort. Source code is posted on the Mesquite web site; we hope other programmers will help us improve the system.

We recognize that Mesquite is a complex system that offers many choices to the user. We plan to build macros and other tools to help build paradigmatic analyses for users who don't want to sort their way through options every time. However, they're only beginning to be built.

Check out the Help system first

Mesquite doesn't have conventional documentation, but it does have various features to help you learn how to use it. Check out the help page for instructions.

Reporting bugs and requesting advice

Partly to foster a community of users, and partly for efficiency, we are encouraging users to sign up to a LISTSERV via which they can report bugs and post queries about using Mesquite. Please report bugs and ask for Mesquite advice via this LISTSERV. To sign up for the listserv, send an email with the following message in the body of the email:

to

where you replace "YourFirstName" by your first name, and "YourSecondName" by your second name. Once you've signed up, you can send a message to the list.

If you're reporting a bug, it's important that you are able to specify, as precisely as possible, exactly what you did that generated the bug. Try to find a precisely repeatable series of actions that generate the bug. In any bug report, please specify the version of Mesquite and any important modules and your operating system. Be prepared to send us your data file so we can test the problem.

(Of course, we recognize that some messages may be more appropriately directed directly to us. You may contact Wayne Maddison directly at wmaddisn@email.arizona.edu or David Maddison at beetle@ag.arizona.edu).

Java bugs that affect Mesquite

Mac OS 9

MacOS X 10.0 through 10.1.5

• If a pop-up menu appears, the colored spinning cursor may appear and prevent you from choosing a menu item for several seconds. You may loose control for 5-10 seconds. If you move the mouse slightly, you will regain control more quickly.
• Text in dialog boxes is sometimes only partially visible. This is a bug in MacOS Java 1.3.1 Update 1.
• Windows near top of screen may be unresponsive (workaround: move window down or resize). This is a bug in MacOS Java 1.3.1 Update 1.
• Various exceptions are thrown. (You will get a little window noting various problems when this happens.) This is a bug in MacOS Java 1.3.1 Update 1.
• Double clicking a file's icon in the Finder when Mesquite is already running will open the file. However, if Mesquite is not yet running, Mesquite will start but will fail to open the file.

MacOS X 10.2 ("Jaguar")

• Dialog boxes occasionally fail to show items (sometimes they are totally blank!). If the Cancel button is invisible, but the red close button is visible at the top left of the dialog box, then use it to dismiss the dialog box, and then try again.
• Various exceptions are thrown. (You will get a little window noting various problems when this happens.)
• Occasionally when you try to drag a branch in the tree window extra lines are left littering the screen.

Windows, java up to and including 1.4.0

• Windows bounce up and down as menus change (a rapid shrink & expansion). This is due to a design flaw either in Windows or the Java VM; there is nothing we can do about it.
• After Mesquite is used for a while, about 5% of menu labels are randomly scrambled with labels of other menu items. 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. This is a bug in Sun's virtual machine (Sun has refused to consider fixing this because we have been unable to reproduce it in a smaller program.) 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.

Linux/Unix etc

• Window sizes and placements sometimes are inappropriate under some window managers. 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 will be given commonly, in fact we suspect on most installations on Linux and Solaris of Sun's Java VM prior to 1.4. 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 considered this to be not a bug, although they seem to have fixed it...