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How to use R

Only available on the CentOS 7 environment of the NIG supercomputer. It is not available on the Ubuntu Linux environment.

There are the following methods to use the version of R processing system required by each user on the shared computer.

  1. Install and use R processing system from tarball.

Installation method (1) Install it from tarball​

Installation procedure​

The R processing system can be installed with user permission, so you can install the necessary version in your own home directory by yourself.

The R processing system will be installed under $ HOME / local / by executing the following. For the latest source code of R, refer to The Comprehensive R Archive Network etc..

mkdir -p ~/local/src
cd ~/local/src

# Install PCRE2 (Perl-compatible regular expression library)
wget https://github.com/PhilipHazel/pcre2/releases/download/pcre2-10.39/pcre2-10.39.tar.gz
tar zxvf pcre2-10.39.tar.gz
cd pcre2-10.39
./configure --prefix=$HOME/local
make
make install
cd ~/local/src

# Install libcurl
wget --no-check-certificate https://curl.se/download/curl-7.81.0.tar.gz
tar zxvf curl-7.81.0.tar.gz
cd curl-7.81.0
./configure --prefix=$HOME/local --with-openssl
make
make install
cd ~/local/src

export PKG_CONFIG_PATH=$HOME/local/src/pcre2-10.39:$HOME/local/src/curl-7.81.0

# Install R
R_VERSION=4.0.5
R_MAJOR=4
wget https://cran.ism.ac.jp/src/base/R-${R_MAJOR}/R-${R_VERSION}.tar.gz
tar xzvf R-${R_VERSION}.tar.gz
cd R-${R_VERSION}

CPPFLAGS=-I$HOME/local/include LDFLAGS="-L$HOME/local/lib -Wl,-rpath=$HOME/local/lib" \
        ./configure --prefix=$HOME/local \
        --with-cairo \
        --with-blas \
        --with-lapack \
        --x-includes=/usr/include/X11 \
        --x-libraries=/usr/lib/X11 \
        --enable-R-shlib

make
# make check
make install

If you need to run parallelize and speed up 'make' with the NIG supercomputer, you should execute it as a parallel job like the example below.

qsub -cwd -V -pe def_slot 8 -b y make -j 8

To execute the R processing system installed in this way, set paths of the executable file and library as follows and start R. (Also write the settings of these environment variables in .bashrc.)

export PATH=$HOME/local/bin:$PATH
export LD_LIBRARY_PATH=$HOME/local/lib64/R/lib:$HOME/local/lib64:$LD_LIBRARY_PATH

# starting the R processing system
R

Uninstallation procedure​

  1. If you reset the paths (PATH and LD_LIBRARY_PATH environment variables), the existence of the locally installed R processing system will be ignored.
  2. Execute make uninstall from the source code directory where the tarball was extracted to reset the make install process.
  3. Execute rm -Rf $ HOME / local to completely erased.

See also the FAQ below.

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