Notes for Installing R Libraries

Setting up Custom Library Location for R packages

If you want or need to download and install packages, and don't have root access, you will need to install the R library/package in your personal library path.

So, create a directory to store 'installed' R libraries.

Then, in your home directory, you should have a file call .Renviron

In the .Renviron file, you should have the a single line:

R_LIBS=PATH_TO_YOUR_R_LIB_LOCATION

The .Renviron is found 'automatically' during the search.

Setting up Custom Library Location for R packages

On the other hand, you can specify the .Renviron file to be used via a environment variable.  This is useful if you work on more than 1 type of *NIX environment (I'm working on CentOS4, CentOS%, Solaris8, and Solaris10).

In this case, you will need a 'custom' library site, I think, for each OS system.  Mostly, as the R packages can include C++ or Fortran components.  In this case, I'd create a file for each Environment.  So, .RenvironCentOS4 and .RenvironSolaris10, for example.  In each one, place the 'os' specific R library path.

Then, in you .cshrc script add these lines:

set ryantemp = `echo ``uname -s`
if (${ryantemp} == "SunOS") then
  set ryantemp = `echo ``uname -r`;
  if (${ryantemp} == "5.10") then
     setenv R_ENVIRON ${HOME}/.RenvironSolaris10
  endif
else
   if (${ryantemp} == "Linux") then
       if (`cat /etc/redhat-release | cut -d ' ' -f1` == "CentOS") then
         if (`cat /etc/redhat-release | cut -d ' ' -f3 | cut -c1` == '4') then
             setenv R_ENVIRON ${HOME}/.RenvironCentOS4
         endif
       endif
  endif
endif

See HERE to figure out something similar for bash.

Loading Custom Library Location for R packages

Regardless of which of the above options you go with, eventually, you will have your 'local' R library path defined.  Now, the idea is to download and install your package of choice.

The command is:

install.packages("PackageName", "Your_Local_Library", destdir="Where_To_Store_The_Download", dependencies=TRUE)

The install will ask you for the CRAN mirror (I'm assuming the package is at CRAN.  If not, look roughly at page 15 of the R Admin manual for details of alternate package loading commands!).  The PackageName is the short name the package is known by.  The Your_Local_Library is the full path name of your 'local' R library.   dependencies can be either TRUE (in which case any required or recommended R libraries are also downloaded and installed) or FALSE, in which case only PackageName is installed (or attempted to be installed).  The destdir is optional; if you don't list it, the source code is downloaded (temporarily) into the /tmp directory.  If you set it, make sure it isn't the same place as Your_Local_Library.  If set, the source code (in a tar and compressed format) will be downloaded to the Where_To_Store_The_Download directory; then, you have a permanent copy of the source code for the package (if you ever need to reinstall it).

Miscellaneous

When running R, if you type this command

library()

A list of all libraries in the Root R library directory and your Local Library will be listed.