Run your own R

What is your machine:
$echo $MACHTYPE

x86_64-redhat-linux-gnu

$ cat /etc/*-release

Red Hat Enterprise Linux Client release 5.3 (Tikanga)
$ uname -a
Linux 136-25.priv25.nus.edu.sg 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux



Install R in your own directory
cd /home/leiz
wget http://cran.cnr.berkeley.edu/src/base/R-2/R-2.12.2.tar.gz
tar -zxvf R-2.12.2.tar.gz
cd /home/leiz/R.2.12.2

./configure --prefix=/home/leiz/R.2.12.2
make



R installed!!!!!!!!  Run it now!!!


To install packages
/home/leiz/R.2.12.2/bin/R
>install.packages("modeest")
>source("http://www.bioconductor.org/biocLite.R")
>biocLite("limma")
>biocLite("Biobase")


To run R script
cd /home/leiz/ComBat409T
/home/leiz/R.2.12.2/bin/R --save <CC_IFS_409T.R >out.txt &
See if R is running
top -u leiz
press "q" to quit "top"
To kill your R process
kill -9 R_process_ID

Or if you are using LSF

$ more bsub_BH.sh
bsub -q long /home/gmslz/R-2.12.2/bin/R CMD BATCH --save /home/gmslz/CCP_IFS/CCP_IFS_BH.R CCP_IFS_BH_out1000.txt &

$bsub_BH.sh

$bjobs

$bkill JOB_ID