Setup Gridsphere R Portal Testing Environment in Linux

From BeSTGRID

[edit] Setup Steps

Step1 Install Java

Step 2 Install R

• Download R from http://www.r-project.org/

wget http://cran.au.r-project.org/src/base/R-2/R-2.4.1.tar.gz

• Extract R

tar xvfz R-2.4.1.tar.gz

• Change to the R install directory

cd R-2.4.1

• Compile and Install R.

./configure --prefix=/usr/local/R --enable-R-shlib
  make prefix=/usr/local/R
  make check
  make install

Note: R must be compiled using --enable-R-shlib if you would like to install JRI later.

• Create symbolic link for R

This step is not necessary, but it will provide some conveniences to users in the future.

Make sure the environment variable $PATH contains /usr/local/bin

cd /usr/local/bin
ln -s /usr/local/R/bin/R .

Now you can run R in anywhere by typing R in the command line.

Step 3 Install rJava and JRI

rJava is a simple R-to-Java interface and it is included inside the R package, so install rJava is very straight-forward.

First of all, you need to start R, then issue the following command inside R.

install.packages("rJava")

After the installation you should find rJava is installed at /usr/local/lib/R/library/rJava/, and JRI is shipped as part of rJava, i.e. /usr/local/lib/R/library/rJava/jri

Step 4 Check out the source files and compile them with your favorite IDE

Step 5 Use the following script to run the program

#!/bin/sh
R_HOME=/usr/local/R/lib/R

JRI_LD_PATH=${R_HOME}/lib:${R_HOME}/bin

PROGRAM_PATH=/root/workspace/Solvers/bin/

JRI_PATH=/usr/local/R/lib/R/library/rJava/jri

if test -z "$LD_LIBRARY_PATH"; then
  LD_LIBRARY_PATH=$JRI_LD_PATH
else
  LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$JRI_LD_PATH
fi

if test -z "$CLASSPATH"; then
  CLASSPATH=$PROGRAM_PATH
else
  CLASSPATH=$CLASSPATH:$PROGRAM_PATH
fi

export R_HOME
export LD_LIBRARY_PATH
export CLASSPATH
echo $CLASSPATH
if [ -z "$1" ]; then
    echo ""
    echo " Usage: run <class> [...]"
    echo ""
    echo " For example: ./run rtest"
    echo " Set CLASSPATH variable if other than .:examples is desired"
    echo ""
else
    java -Djava.library.path=${JRI_PATH} -cp $CLASSPATH:${JRI_PATH}/JRI.jar $*
fi

Remember to change the PATH variables to correct value.

Step 6 Add "execute" permission to the script file (Assumed the script is called myrun)

chmod a+x myrun

Step 7 Now you can run the program by

./myrun tests.TestExchange