R/maanova - Installation Guide

This file is used mainly to explain the installation of R and the R/maanova package for R.  If you have any problems with installation, post a message to the maanova group.

Warranty Disclaimer and Copyright Notice

The Jackson Laboratory makes no representation about the suitability or accuracy of this software for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software will not infringe any third party patents, copyrights, trademarks, or other rights. The software are provided "as is".

This software is provided to enhance knowledge and encourage progress in the scientific community. This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

The source code for R/maanova can be found at the source code repository on github

System requirements

This version of R/maanova has been tested on R version 2.10.1 on Mac OS X Linux and Windows XP. It is likely that R/maanova will work on some older versions of R but this is untested. The memory requirement depends on the size of the input data but a minimum of 1Gb memory is recommended.

Obtaining R

You can download R from the Comprehensive R Archive Network (CRAN). Visit http://cran.r-project.org or a local mirror. Source code is available for UNIX, and binaries are available for Windows, MacOS, and many versions of Linux. 

Obtaining R/maanova

Installation of R/maanova via BioConductor (Recommended method for all Operating Systems)

This is the easiest method of installing R/maanova so we recommend doing this unless you have a specific reason for using the manual method.
  1. Start R
  2. At the prompt type: source("http://bioconductor.org/biocLite.R")
  3. At the prompt type: biocLite("maanova")

Manual Installation of R/maanova

Manual Installation of R/maanova on Windows:

  1. Download the Windows binary for R/maanova
  2. Start Rgui.
  3. Select Menu "Packages", click "Install package from local zip file". Choose the file  maanova_*.zip and click 'OK'
  4. Type "link.html.help()" to get the help files for the maanova package added to the help indices.
  5. Note that the source code is in the file "maanova_*.tar.gz", which you may download separately.  

Manual Installation of R/maanova on Unix:

  1. Download the gzipped source archive for R/maanova
  2. Go into the directory containing "maanova_*.tar.gz".

  3. Type "R CMD INSTALL maanova_*.tar.gz" to have the package installed in the standard location (/usr/local/lib/R/library).  You'll probably need to be superuser in order to do that.
     
    To install the package locally, type
    R INSTALL --library=/home/auser/Rlibs maanova_*.tar.gz
     
    (where "/home/auser/Rlibs" should be replaced with the appropriate director).  You'll then need to create a file ~/.Renviron containing the line
     
    R_LIBS=/home/auser/Rlibs
     
    so that R will know to search for packages in that directory.

Questions/comments/concerns

If you have any questions, suggestions, problems or complaints regarding R/maanova, please post a message to the maanova group.