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R at a glance

Purpose: statistics and plotting
Latest version: 3.4.0
Availability: all machines
Licence: open source
Documentation: Manuals

Description

R is a language and environment for statistical computing and plotting.

R implements tools for data analysis, array operators (especially matrices), I/O features, graphical output features, and a high-level language (S) for integrating all of them, including user-defined variables, loops, etc.

A more detailed description can be found here.

Licence

R operates under a GNU GPL licence.

Available Versions

The currently available versions of R are:

  • 2.13.2 (prades, pirineus)
  • 2.14.2 (prades)
  • 2.15.0 (prades)
  • 3.1.0 (collserola)
  • 3.1.3 (all machines)
  • 3.2.2 (collserola)
  • 3.3.2 (all machines)
  • 3.4.0 (all machines)

To load one of these, use

module load R/3.4.0

 

 

LSF Example Script

#!/bin/bash
##
# IMPORTANT NOTICE: replace the email address
# and the working directories with your own info
##
# BSUB -J R
# BSUB -o R.log # send standard output here
# BSUB -e R.err # send error output here
#
# Send an email notice once the job is finished
# BSUB -N -u youremail@wherever
#
# Pick a queue
# BSUB -q short
#
# Indicate the number of cores
# BSUB -n 1
#
# Pick the machine
# BSUB -R pirineus
  
 
# Set up the environment
. /opt/modules/init/bash
module load R/3.4.0
# Define the variable $INPUT
INPUT=script.R
  
# Change to the work directory ($TMPDIR) and copy the input files to this directory
cd $TMPDIR
cp $INPUT $TMPDIR
 
# Execute the job
Rscript script.R > R.out
 
# Create a new folder in your $SCRATCH directory and copy the results to this new folder
mkdir -p $SCRATCH/R_$LSB_JOBID
cp -r * $SCRATCH/R_$LSB_JOBID

Place the appropriate LSF script in a file (for instance R.lsf) and submit the job with the command

bsub < R.lsf

 

 

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