====== Installation of R 2.10 ======

===== Additional libraries ===== 

No additional library is necessary.

===== Procedure =====

==== Installing R ====

  * 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:
<code bash>
% 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
</code> 

  * Secondly, you need to run ''apt-get'' to update the source list and install R:
<code bash>
% sudo apt-get update
% sudo apt-get install r-base r-base-dev
</code>

==== Installating the Rserve server ====

  * Before installing Bioconductor, you need to install Rserve, which is necessary to make sure that some [[mev|MeV]] modules can work properly. Open R and install it from the R console:
<code>
% 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()
</code>
 
  * In ''/etc'', you need to create a configuration file named Rserve.conf:
<code bash>
% sudo nano /etc/Rserve.conf
</code>
 
  * You need to put this in it:
<code bash>
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
</code>

  * 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'':
<code bash>
% sudo nano /etc/init.d/rserve
</code>

  * This ''/etc/init.d/rserve'' file must contain the following lines:
<code bash>
#! /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
</code>

  * Make sure that only ''root'' can use this file and that the Rserve server process is started at boot time:
<code bash>
% sudo chown root:root /etc/init.d/rserve
% sudo chmod ugo+x /etc/init.d/rserve
% sudo update-rc.d rserve defaults
</code>

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

==== Installation of a R GUI ====

There are many GUI for R but the one I chose is [[http://jgr.markushelbig.org/JGR.html|JGR]]. To install JGR, simply follow this recipe:

  * Tell R where are the Java components for the system:
<code bash>
% sudo R javareconf
</code>

  * From R, install the JGR package:
<code bash>
% 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
</code>

  * The last step is adding R GUI to the Impilo aplication menu by editing the Xfce4 configuration file:
<code>
% sudo xfce4-menueditor /etc/xdg/xfce4/desktop/menu.xml
</code>

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