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R

R is a free software environment for statistical computing and graphics.

Information

Usage

See versions of R that are available:

$ module avail R

Load one version into your environment and run it:

$ module load R/3.6
$ R

Use installed.packages() to check the list of packages installed in the ILRI environment by default. Here is a good resource on installing R packages into user libraries if you need other packages.

Installation

Notes from the sysadmin during installation.

First, compile the main R application with GCC 7 from Red Hat's devtoolset-7 software collection:

$ cd /tmp
$ wget https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz
$ tar xf R-3.6.1.tar.gz
$ cd R-3.6.1
# install packages to enable capabilities in R
$ sudo yum install libX11-devel libXaw-devel bzip2-devel libcurl-devel xz-devel readline-devel
# install a newer compiler from Red Hat software collections
$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
$ scl enable devtoolset-7 bash
# R packages are written in C99 and GCC 7 uses a newer standard by default, so tell configure script to use C99 explicitly
$ export CFLAGS='-std=gnu99  -g -O2'
$ ./configure --enable-R-shlib --prefix=/export/apps/R/3.6
$ make -j4
$ sudo mkdir -p /export/apps/R/3.6
$ sudo chown aorth:aorth /export/apps/R/3.6
$ make install

Then install some common libraries used by our users (to save space, overhead from tens of thousands of header and library files, and users's time):

r-software.1572184939.txt.gz · Last modified: 2019/10/27 17:02 by aorth