Taxa, Trees, Characters ˇ
Characters & Matrices
Taxa
Trees

 

Bugs and Troubleshooting

If you think you've found a bug in Mesquite, our would like to suggest a feature, please read this page. For help in using Mesquite, see the Learning Mesquite and Getting Help page.

A list of the known bugs in the current release version of Mesquite is listed on the page about Features and Bugs.

Small text in Mesquite on Windows

There is a bug in some versions of Java which causes applications like Mesquite to show text (including that for Windows) in font that is extremely small. If you have this problem, do the following:

Right-click on the Mesquite.exe icon, and choose Properties. The following instructions are for Windows 10; you will need to find the equivalent for other Windows versions. In the Properties dialog box, go to the Compatibility tab. Touch the "Change high DPI settings" button. In the dialog box that appears, check "Override high DPI scaling behavior.", and in the popup menu under "Scaling performed by:" choose "System". Press OK on this dialog, and then OK on the other dialog box


Why does <insert feature> not seem to work properly?

It could be that the feature in question is one whose operation you don't fully understand, or it could be that you have found a bug. Some bugs you may encounter will be bugs not in Mesquite but in the operating system or Java virtual machine (for example, see the list, below).

thassus.jpg


That there will be bugs in Mesquite is inevitable. 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; most of it was written by one or two people. We apologize for the bugs that remain, and look forward to your bug reports and efforts to aid us make Mesquite useful.
If you think you have found a bug in Mesquite, please report it on the Mesquite mailing list. Partly to foster a community of users, and partly for efficiency, we are encouraging users to sign up to the mailing list via which they can report bugs and post queries about using Mesquite. Once you've signed up, you can send a message to the list. As a second choice, you can send a note to us at info {at} mesquiteproject.org.

If we don't know about a bug, it is unlikely that it will be fixed. It might be natural to presume that we know about all the bugs in Mesquite, but it is not possible for us to have tried out every combination of options on every computer environment with every data matrix, model, etc. If you are not sure if it is a bug (a large number of users blame themselves when they encounter a bug, presuming it is something they have done wrong), please report it anyway. Even if your apparent "bug" is a mistake you made, your mistake might indicate a poorly designed interface that should be corrected.

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. It is also very helpful to send us the Mesquite_Log file that is in Mesquite_Support_Files (which is in your home directory in Mac OS X and in "Documents and Settings\yourUserName\" in Windows). We need a copy of the log file as it was written immediately after your problem occurs.

Perhaps you can fix the bugs yourself!

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


Java bugs that affect Mesquite

Below are problems in Java on various operating systems that affect Mesquite. If these problems annoy you, please contact those responsible for your Java virtual machine.

MacOS X

The recommended configuration for Mesquite on Mac OS X is OS X 10.5 or newer with the latest Java. There are various screen redraw and crashing bugs in earlier versions of OS X and Java.
If at any point Mesquite quits spontaneously and OS X puts up a dialog that says that Mesquite has unexpectedly quit, this is what is called a "JVM crash". Technically it is not supposed to be possible for Mesquite to do this, and thus it represents a bug in Java and not a bug in Mesquite. Nonetheless, we would like to know about it, because we may be able to find a way to avoid the JVM bug.

MacOS X running Java 1.3.1

Mesquite 2 does not run under Java 1.3 or earlier.

MacOS X 10.0 through 10.2

We have not tested Mesquite 2 under these earlier versions of MacOS X.

Mac OS 9

Mesquite 2 does not function on Mac OS 9, because it requires Java 1.4.


Windows

Linux/Unix etc