R Packages

1. From CRAN

Install these packages from CRAN. Always check the "install dependencies" box.

• DPpackage
• ggplot2
• gsubfn
• hexbin
• languageR
• lme4
• MCMCglmm
• multcomp
• plyr
• reshape
• knitr
• ez

A quicker way to do it is to copy and paste the following line at your R prompt:

install.packages(c("DPpackage", "ggplot2", "gsubfn","hexbin","languageR","lme4","MCMCglmm","multcomp","plyr","reshape","knitr","ez"))

Sometimes a package isn't available (usually temporarily) as a binary for your platform. If you need to build a package from source, make sure you have the developer tools for your OS installed (for MacOS, they come on the install DVD, but aren't installed by default. You may also need Fortran, available from the MacOS tools page on CRAN), then find the package on CRAN search and download the package source file, and then run this command at the command line (i.e. in a Terminal, not in the R GUI):

R CMD INSTALL <zipped-package-file>

2. From Bioconductor

When you install the packages above, you may get this warning: Warning: dependencies ‘marray’, ‘affy’, ‘Biobase’, ‘Rgraphviz’, ‘’ are not available. To fix it, install the standard packages from Bioconductor by doing the following at the R prompt:

source("http://bioconductor.org/biocLite.R")
biocLite(lib='/Library/Frameworks/R.framework/Resources/library/')

adjusting lib as appropriate for your OS. The example above is for Mac OS X. For Windows use:

biocLite(lib='C:\\Program Files\\R\\R-2.11.1\\library')

adjusting the version number as appropriate. (n.b. You must have Administrator privileges to install anything under C:/Program Files/)