• Mstat Help
• • Introduction
  • Tutorial
  • Reference
  • Additional Information
    • Troubleshooting
    • Mac OS X/Linux specifics
    • Licensing
    • Acknowledgments
    • Appendix: J Notation
• Statistics Notes
• Mstat Home

Troubleshooting

This version of Mstat was tested extensively before it was released, but it is inevitable that one or more bugs lie hidden in its 12,000 lines of code. Generally, the data that you enter are checked for validity and an error message points out what you need to do to correct the error. If, however, you see an error message that is particularly obscure, you have probably found a bug. Please write down the information on the error message and send it to me by email at drinkwater@oncology.wisc.edu. I will post updates to the program at the website

http://mcardle.oncology.wisc.edu/mstat.

Mac OS X/Linux specifics

The Windows, OS X, and Linux versions of Mstat work similarly and always give the same answers, but there are some minor differences in function on the three platforms.

• As noted in the Introduction, the Linux and OSX versions of Mstat require Java. For Linux, the OpenJDK version installed by many distributions works well, but you may use the Oracle version of Java if you prefer. Java is installed by default on versions of OSX up to 10.6 (Snow Leopard). For version 10.7 (Lion), you will need to download Java from here and install it.
• The Windows and Linux versions use accelerator keys, indicated by the underlined character in the label for the control, in most of the dialog boxes. For example, pressing Alt-O is equivalent to pressing the OK button on many dialogs. Alt-accelerator keys are disabled on OS X because this key is used to compose non-ascii characters. As an alternative, any buttons (except Cancel) in a dialog may be activated by pressing the Ctrl-key together with the first letter on the button label, except where that letter is "C", in which case you should use the second letter. The Cancel button can invoked using the escape key. The Ctrl hotkeys (e.g., Ctrl-N invokes the New variable dialog) work on all operating systems, but must be activated using the Command key on OS X for any window with a menu.
• Although all of the files (including data, initialization, and output) used by Mstat are simple text files, the strict file typing imposed by some Mac programs obscures this fact. Output files can be opened by word processors by choosing the All files option in the file open dialog box.
• On OS X, the left-most menu (labeled Mstat) does not behave as expected. For example, Mstat>About will give a generic Java message and you should use Help>About to view the Mstat About box. In particular, do not choose Mstat>Quit (Command-Q), which will exit the program without giving you the opportunity to save your data or output. Use the File>Exit (Ctrl-Q) instead.
• The menu choice Help > Help on Mstat will bring up the program documentation on all operating systems. Help files are loaded in your default browser.
• Information may be copied or cut from, or pasted into, most dialogs. To access this feature, the right mouse button is used on the Windows platform while the conventional key combinations are used on OS X and Linux.

Licensing

Subject to the restrictions listed below, this software may be freely copied and used by students, faculty, and staff at academic or other non-profit research institutions. While this software is free, donations to the McArdle Laboratory for Cancer Research (1400 University Avenue, Madison, WI  53706) would be welcomed; such funds will be used to support graduate training in cancer research at the Laboratory. Commercial use of the software is prohibited without prior arrangements being made with the author.

Restrictions

1. The Mstat package (the software and its documentation) are copyrighted by Norman Drinkwater. The StatNotes reference material is copyrighted by Norman Drinkwater and Carter Denniston.
2. The J executable and related portions of the package are copyrighted by JSoftware, Inc.
3. This software requires the zlib library (included in the Windows distribution), which is copyrighted by Jean-loup Gailly and Mark Adler. The Windows distribution also includes the wget executable, which is subject to the GNU GPL.
4. Some toolbar icons are from the Fugue icon set and are copyrighted by Yusuke Kamiyamane and licensed under a Creative Commons Attribution 3.0 license.
5. No part of the package may be modified or used to create derivative works.
6. Use of the software should be acknowledged in any resulting publications.
7. This package is provided as-is and neither the author nor the University of Wisconsin is responsible for any damages resulting from its use.

Acknowledgments

I am grateful to my colleagues Rebecca Baus, Andrea Bilger, Jamie Bugni, Rey Carabeo, Teresa Chiaverotti, Brad Clark, Jennifer Drew, Mara Feld, Matt Gigot, Tonia Jorgenson, Sean McDermott, Amy Moser, Chris Oberley, Stephanie Peychal, Therese Poole, Rachel Potempa, Sue Schadewald, and Bret Williams, as well as several generations of Oncology 675/Genetics 677 students, for their help in testing the software in this and its earlier versions and for many suggestions regarding new features and usability.

Contacting the Author

Bug reports or other comments should be directed to Norman Drinkwater (drinkwater@oncology.wisc.edu). Please indicate the version of the software that you are using (provided in the About box).