Installation of R 2.11.1

No additional library is necessary.

• Source or package? In this case, it is a really good question to ask oneself… Impilo's principal philosophy is to install from source as much as possible but for R, it was decided to start from the packages that are found on R's web site. Many of the applications found in Impilo are dependent on a correct R install so let's save ourselves from a mighty headache!

• First, you need to add a new package installation site for apt-get at www.probability.ca. In addition, you need to add the authentification key to make sure that apt-get will stay happy:

% sudo su
% echo "deb http://www.probability.ca/cran/bin/linux/ubuntu lucid/" >> /etc/apt/sources.list
//
// You also need to uncomment this line in /etc/apt/sources.list:
// deb http://ca.archive.ubuntu.com/ hardy-backports main restricted universe
//
% gpg --keyserver subkeys.pgp.net --recv-key E2A11821
% gpg -a --export E2A11821 | sudo apt-key add -
% exit

• Secondly, you need to run apt-get to update the source list and install R:

% sudo apt-get update
% sudo apt-get install r-base r-base-dev

• Because MeV's RAMA and BRIDGE modules have been marked as deprecated, the requirement for Rserve has disappear and therefore, Rserve is not installed on a default Impilo machine. If you need to install Rserve for your own projects, the recipe is still available in Impilo 8.04 H10.

There are many GUI for R but the one I chose is JGR. To install JGR, simply follow this recipe:

• Tell R where are the Java components for the system:

% sudo R javareconf

• From R, install the JGR package:

% sudo R
// We are in the R console at system-level
> install.packages('JGR')
// R will ask for a mirror selection
// Install will proceed simply enough. Give it a try:
> library(JGR)
> JGR()
// You should see a R console popping onto your dekstop
// with buttons, menus and everything else

• You need to quit R to finish the installation:

% sudo ln -s /usr/local/lib/R/site-library/JGR/scripts/run /usr/local/bin/runRGui

• The last step is the addition of RGui to the Impilo > Statistical Analysis:
  • More to come…

• To invoke JGR from the command line:

% runRGui