Installing R Packages

Synopsis

Loading R via module load R/version configures the read-only location $R_HOME/library where system wide packages are installed. R will fallback to installing in the user's home directory if it detects that the default library location is not writable. Custom install locations are also supported by environment variables and options to package and library functions.

Important Note: The R versions below R/4.4.0 have serious vulnerabilities. Please use the newer version module.

Default User Install Location

The default user install location for R is ~/R/x86_64-pc-linux-gnu-library/version/ and R creates the directory if it does not exist:

> install.packages("yaml")

Warning in install.packages("yaml") :

  'lib = "/usr/local/easybuild_allnodes/software/R…" is not writable

Would you like to use a personal library instead? (yes/No/cancel) yes

Would you like to create a personal library

‘~/R/x86_64-pc-linux-gnu-library/4.1’

to install packages into? (yes/No/cancel) yes

Modify Default User Location

An alternative is to set the environment variable R_LIBS_USER to a writable location. E.g.,

export R_LIBS_USER=~/Rpackages

The path will be searched (along with the system location) for packages to load, and will be used for installing user packages.

Specify a Custom Install Location

A different location can be specified with the lib parameter. R will not create the directory if it does not exist and R will not create version specific libraries under the directory.

install.packages("yaml", lib="~/Rpackages")

We must pass the location when loading libraries installed there:

library("yaml", lib.loc="~/Rpackages")

Install in Container

salloc -c 8 --mem=24g srun --pty /bin/bash

cd $TMPDIR

module load singularity

singularity build --sandbox ./R docker://r-base:latest

singularity shell --writable ./R

Singularity> mkdir -p /opt/mylib

Singularity> export R_LIBS_USER=/opt/mylib

Singularity> R

> install.packages("yaml")

...

> quit()

Singularity> chmod -R o+rX /opt/mylib

Singularity> exit

singularity build my_R.sif ./R

cp my_R.sif ~/

rm -rf ./R my_R.sif

Invoke Interactively

salloc -c 8 --mem=24g srun --pty /bin/bash

module load singularity

singularity run --env R_LIBS_USER=/opt/mylib my_R.sif R

> library(yaml)

Invoke in Batch Job

R Script my.R

library("yaml")

f = c(1, 2, 3, 4)

yaml::as.yaml(f)

Job File my_job.sh

#!/bin/bash

module load singularity

singularity run --env R_LIBS_USER=/opt/mylib my_R.sif Rscript my.R

Job Submit Command

sbatch my_job.sh 

Installing R Package From Source

Options can be specified using the configure.args parameter:

> install.packages("https://cran.r-project.org/src/contrib/Rmpi_0.7-3.3.tar.gz", configure.args=c("--with-mpi=/usr/local/easybuild_allnodes/software/OpenMPI/4.1.6-GCC-13.2.0/"))

Note: download the source archive and run ./configure --help to see what options are available if the package does not document them

Notes

Missing openssl/ssl.h

If you see this error while installing from a compute node, install the failing package from a login node instead. Those have the OpenSSL development files installed.

gtar command not found

If you see this error while installing packages from inside Rstudio, you need to install them from a native R sessions first. Then you will be able to import them into your Rstudio session.