Additional Information
Troubleshooting
This version of Mstat was tested extensively before it was
released, but it is inevitable that one or more bugs lay hidden in
its more than 15,000 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
norman.drinkwater@wisc.edu.
I will post updates to the program at the website
http://oncology.wisc.edu/mstat.
Platform specifics
The Windows, macOS, and Linux versions of Mstat always give the same answers, but there are some minor differences in function on the three platforms.
- The current version of Mstat was tested extensively on Windows 7 (SP1) and 10; macOS (intel) 10.13 through 11.0; Ubuntu 18.04 and 20.04; and Debian 10. The previous version of Mstat (6.6.2) will run on macOS 10.10 through 10.12. On Linux, any distribution with glibc 2.27 or later and Qt 5.9 or later should work. See the Jsoftware website (https://code.jsoftware.com/wiki/Guides/Linux_Installation) for hints on running the software on other Linux distributions. Legacy versions for Windows XP and for OSX 10.6.8 are available on the web site.
- As noted in the Introduction, both 64-bit and 32-bit versions of Mstat are available for Windows and Linux. You should install the 64-bit version if your operating system is 64-bit. The Windows installer includes both versions and will install the correct one for your computer. For macOS, only the 64-bit version is available. You will need to explicitly choose the 64- or 32-bit installers for Linux depending on your Linux distribution.
- The new J engine for 64-bit computers by default requires that the CPU supports the AVX2 instruction set, which is generally true for computers built in 2014 or later. This requirement allows for much faster processing of large data sets. An alternative version of the J engine that does not require this capability is also available. On 64-bit Windows the correct version of the J engine is automatically installed. On 64-bit Linux and macOS, the installation includes all three versions (AVX2, AVX, and no AVX) of the J engine. When Mstat starts, it checks your CPU's capabilities and chooses the appropriate J engine. These issues do not apply to the 32-bit versions of Mstat.
- The Qt toolkit is required for Mstat. On Windows, the required Qt shared libraries (version 5.12.9) will be installed in a subdirectory of your Mstat folder. On macOS, the required Qt libraries are contained within the Mstat app. On Linux, you may need to install the Qt packages for your operating system. See the link to the Jsoftware website above for instructions.
- Plots are printed via an intermediate pdf file and a pdf viewer application must be installed on your system. While Linux and macOS include a pdf viewer in the default installation, Windows versions before Windows 10 do not. In addition to Acrobat and Acrobat Reader, there are a variety of free pdf readers for Windows, including Foxit Reader and PDF-XChange Editor, that work just as well.
- Beginning with version 7.0.1 of Mstat, all of the executable files and the installer are signed to comply with macOS Catalina (10.15) security requirements. You may need to adjust your computer's settings to allow installation of software that was not obtained from the Apple AppStore.
- 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. Note that on Windows, you may need to press the Alt key to reveal them. For example, pressing Alt-O is equivalent to pressing the OK button on many dialogs. Alt-accelerator keys are disabled on macOS because the Alt key is used to compose non-ascii characters. As an alternative, most buttons in macOS dialogs are assigned a Cmd-key combination according to a few rules. Any button labeled OK, Done, or Close can be invoked with Cmd-O. The Esc key will invoke a Cancel button. Cmd-L (or Ctrl-L on Windows and Linux) will open the dialog-specific help window. The remaining buttons on a dialog may be invoked by Cmd-letter, where the letter is the first one in the button label that has not been used by an earlier button (starting top left) and is not in the following list: a, c, k, l, o, v, x, y, or z. Finally, note that the Ctrl-key combinations indicated in the menus on the main Mstat window are invoked using Cmd-key on macOS.
- 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.
- Information may be copied or cut from, or pasted into, edit widgets in most dialogs. To access this feature, the right mouse button or the conventional key combinations may be used.
License
Copyright (c) 1996-2020, Norman Drinkwater. All rights reserved.
Subject to the restrictions listed below, this software may be freely copied and used by anyone. While this software is free, donations to the McArdle Laboratory for Cancer Research (1111 Highland Avenue, Madison, WI 53705-2275) would be welcomed; such funds will be used to support graduate training in cancer research at the Laboratory.
Restrictions
- 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.
- Redistribution of the Mstat software package is permitted as long as the above copyright notice is retained and all components of the package are included. No part of the package may be modified or used to create derivative works.
- The J executable and related portions of the package are copyrighted by Jsoftware, Inc. (http://www.jsoftware.com)
- This software requires the Qt toolkit (http://www.qt.io/), copyright 2020 The Qt Company. The Qt libraries included in the Windows and macOS distributions are licensed under LGPL 3. The zlib library (http://www.zlib.net/), included in the Windows distribution, is copyright 1995-2017 by Jean-loup Gailly and Mark Adler. The Windows distribution also includes the curl executable (http://curl.haxx.se/), which is subject to the MIT/X open software license, copyright 1996-2019 Daniel Stenberg.
- Some toolbar icons are from the Fugue icon set (http://p.yusukekamiyamane.com/) and are copyrighted by Yusuke Kamiyamane and licensed under a Creative Commons Attribution 3.0 license.
- Use of the software should be acknowledged in any resulting publications.
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Acknowledgments
I am grateful to my colleagues Rebecca Baus, Andrea Bilger, Jamie Bugni, Rey Carabeo, Teresa Chiaverotti, Brad Clark, Jennifer Drew, Mara O'Brien, Matt Gigot, Tonia Jorgenson, Sean McDermott, Amy Moser, Chris Oberley, Stephanie Peychal, Therese Poole, Rachel Potempa, Sue Schadewald, Arthur Sugden, 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 (norman.drinkwater@wisc.edu). Please indicate the version of the software that you are using (provided in the About box).