Singularity R

Singularity image for R.

Singularity images for R build from Docker using Official Ubuntu Images

https://hub.docker.com/_/ubuntu

R is installed from the the repo:

https://cran.r-project.org/bin/linux/ubuntu/

The current version of R is 3.6.1 and images are available using Ubuntu xenial and bionic as base

These recipes are used by West Virginia University (WVU) for their High Performace Computing (HPC) clusters

https://hpc.wvu.edu

https://docs.hpc.wvu.edu

Build

You can build a local Singularity image named singularity-r.simg with:

sudo singularity build singularity-r.simg Singularity

Deploy

Instead of building it yourself you can download the pre-built image from Singularity Hub with:

singularity pull --name singularity-r.simg shub://WVUHPC/singularity-r

Run

R

The R command is launched using the default run command:

singularity run singularity-r.simg

or as an explicit app:

singularity run --app R singularity-r.simg

Example:

$ singularity run --app R singularity-r.simg --version
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

Rscript

The Rscript command is launched as an explicit app:

singularity run --app Rscript singularity-r.simg

Example:

$ singularity run --app Rscript singularity-r.simg --version
R scripting front-end version 3.6.1 (2019-07-05)

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/WVUHPC/singularity-r.

License

The code is available as open source under the terms of the MIT License.