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guide:compiling_r

Installing R 2.14 from Source

This guide is written fun the Sun Tsessbe Cluster, login node. Its recommended that you make you use of temporary or scratch directory to do all the compilation in (i.e. ~/scratch or /tmp/$USER), as to save disk space in your home directory. Note that for this guide, all binary and libraries are installed home directory, i.e prefix=$HOME.

If you dont have GCC installed in your home directory, Add the following lines to the end of your .bashrc file

export PATH=/opt/gridware/gcc-4.3/bin:$PATH
export LD_LIBRARY_PATH=/opt/gridware/gcc-4.3/lib64/:/opt/gridware/gcc-4.3/lib/:$HOME/lib
export F77=gfortran

Logout and log in again,

$ gcc --version
  gcc (GCC) 4.3.4
  

Download R Source

$ cd ~/scratch
$ wget http://cran.r-project.org/src/base/R-2/R-2.14.0.tar.gz
$ tar -xf R-2.14.0.tar.gz 
$ cd R-2.14.0/

Configure

For a bare-bones installation

$ mkdir BUILD
$ cd BUILD
$ ../configure --prefix=$HOME --without-system-zlib --without-system-xz --without-cairo --without-libpng --without-jpeglib --disable-openmp --disable-largefile --disable-nls

Build / Make

$ make

if the process is interrupted, try make again to so if the error persists.

Check

$make check

Install

$ make install  

restore you .bashrc file

For you jobs to run on the worker nodes, you may need to copy some shared libraries to your lib directory

$ cd $HOME/lib
$ cp /usr/local/lib/libiconv.so.2 ./
/var/www/wiki/data/pages/guide/compiling_r.txt · Last modified: 2011/12/08 10:08 by hamish