Installation of R 2.10

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, I 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 hardy/" >> /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

• Before installing Bioconductor, you need to install Rserve, which is necessary to make sure that some MeV modules can work properly. Open R and install it from the R console:

% sudo R
//
// You are in the R console to install at system-level:
//
>install.packages("Rserve")
//
// It will ask for a mirror selection; take one close from home.
//
>q()

• In /etc, you need to create a configuration file named Rserve.conf:

% sudo nano /etc/Rserve.conf

• You need to put this in it:

workdir /tmp/Rserv
pwdfile 
remote disable
auth disable
plaintext disable
fileio enable
 
port <port>
maxinbuf 262144
 
maxsendbuf 0
uid 48
 
chroot 
sockmode 0
umask 0
 
encoding utf8

• You are close to the finish line… To make sure that Rserve will start in deamon mode each time you boot the machine, you still need to do some work Step 1: create a startup file: /etc/init.d/rserve:

% sudo nano /etc/init.d/rserve

• This /etc/init.d/rserve file must contain the following lines:

#! /bin/sh
# chkconfig: 2345 99 01
# description: Rserve, /etc/init.d/rserve
 
case "$1" in
     start)
	echo -n "Starting Rserve daemon: "
	R CMD Rserve >/dev/null 2>&1
	echo "\t\t[STARTED]"
	;;
     stop)
	echo -n "Stopping Rserve daemon: "
	killall -s 9 Rserve
	echo "\t\t[STOPPED]"
	;;
     restart)
         echo -n "Stopping Rserve daemon: "
         killall -s 9 Rserve
         echo "\t\t[STOPPED]"
         echo -n "Starting Rserve daemon: "
         R CMD Rserve
         echo "\t\t[STARTED]"
         ;;
     *)
        echo "Usage: /etc/init.d/rserve {start|stop|restart}"
        exit 1
esac
 
exit 0

• Make sure that only root can use this file and that the Rserve server process is started at boot time:

% sudo chown root:root /etc/init.d/rserve
% sudo chmod ugo+x /etc/init.d/rserve
% sudo update-rc.d rserve defaults

• At boot, you should be able to see that the Rserve server has started.

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

• The last step is adding R GUI to the Impilo aplication menu by editing the Xfce4 configuration file:

% sudo xfce4-menueditor /etc/xdg/xfce4/desktop/menu.xml

• The three things to add are:
  • Item: Launcher
  • Name: R GUI
  • Command: /usr/local/lib/R/site-library/JGR/scripts/run