Personal R Packages

We encourage users to maintain their own R packages. This ensures that the user has no discontinuity in their workflow waiting for packages to be installed and packages work with the user’s chosen, loaded R module. R packages are built specifically to a version of R and may not work properly if a different version of R is loaded. O2’s LMOD “module” feature allows users to quickly and easily switch between R versions.


Table of Contents

General Commands

Command

Meaning

Command

Meaning

module spider R

shows the version of R installed on O2

module spider R/<version>

shows if other module(s) needs to be loaded to use R (e.g., gcc/9.2.0)

module load gcc/9.2.0 R/4.1.2

loads an individual module (i.e., R/4.1.2)

module unload R/4.1.2

unloads an individual module (i.e., R/4.1.2)

which R

shows the current version of R loaded

> installed.packages()

From R, shows

Setting up a Personal R Library

This sets up an environment to store R packages locally. From R, all packages will be installed and saved to this R Personal Library by default. It is recommended to use a separate R library for each version of R selected (e.g., 3.6.1, 4.1.1, etc.). Multiple members of a group can share an R library saved in a group-accessible location by following the echo ... and export ... commands.

In O2 bash (hardcoded):

This approach is ideal for researchers using mainly a single R version and sharing the R Personal Library with other lab members.

mkdir -p ~/R-<version_selected>/library echo 'R_LIBS_USER="~/R-<version_selected>/library"' > $HOME/.Renviron export R_LIBS_USER="~/R-<version_selected>"

 

In O2 bash (non-hardcoded alternative):

This alternative approach is ideal for researchers working concurrently with more than one R version or switching often among R versions. In this approach, the R Personal Library is automatically set based on the R module loaded.

echo 'R_LIBS_USER="~/R/%p-library/%V"' > $HOME/.Renviron

Note: %V expands to Major.Minor.PatchLevel, while %p expands to the platform for which R was built. We recommend using %V to account for the PatchLevel and avoid issues with different gcc versions.

Starting R Interactively

R must be run in a compute node rather than a login node. To start an interactive session in a compute node, you need to specify the resources (i.e., walltime, cpus, and memory) via the $ srun command and specify interactive as the partition. For example:

# 1. Start an interactive job (resources: 1 hour, 5GB of memory, and 1 cpu) mfk8@login01:~$ srun --pty -p interactive -t 0-1:00 --mem 5G -c 1 bash # 2. Load R/4.1.2 mfk8@compute-a-16-163:~$ module load gcc/9.2.0 R/4.1.2 # 3. Start R mfk8@compute-a-16-163:~$ R > #notice how the prompt changes.

R does not implicitly use multiple core unless the code is parallelized. For researchers using the R package doParallel, please check https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1616511993/Job+Efficiency#R-package-doParallel

Installing Packages Using Bioconductor

The Bioconductor repository host a wide range of bio-related packages. To install Bioconductor, please check the installation page on the Bioconductor website in case the method described below changes in the future.

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.14")

Installing Packages Using CRAN

The command install.packages() searches CRAN by default and ask you to select a mirror, but a repository can be specified using this command:

install.packages("PkgName", repos="http://cran.r-project.org")

User example:

install.packages("ggplot2", repos="http://cran.r-project.org") library(ggplot2)

A list of CRAN available packages is available at http://cran.r-project.org/web/packages/

Installing Packages from GitHub using Devtools

The R package devtools allow researchers to install software from GitHub repositories. First, you need to install devtools from the CRAN repo. Second, you need to load the R package using the library command. Lastly, you use the install_github() command to install R packages from GitHub. For example:

# 1. Install devtools install.packages("devtools") # 2. Load R pkg library(devtools) # 3. Install a pkg from GitHub # install_github("username/repo") install_github("tidyverse/ggplot2")

Installing Packages from a Local File

To install a package manually, place the compressed R package (usually is compressed as a tarball or zip file) inside your R Personal Library (e.g., ~/R-<version_selected>/library) and run the following command:

install.packages("pkgName", lib="~/R-<version_selected>/library")

You can also install an R package via R CMD INSTALL <path-to-tarball>. However, this assumes all dependencies are already installed in your R Personal Library. For example:

# 1. O2 shell - start interactive job srun --pty -p interactive -t 0-1:00 --mem 5G bash # 2. Load R modules module load gcc/9.2.0 R/4.1.2 # 3. Install pkg from a local file R CMD INSTALL downloadedRPackage.tar.gz

Installing Packages with Special Requirements

We’ve created a Confluence page with step-by-step instructions to install some commonly used R packages (e.g., SF, monocle3, etc.) requiring a few [non-common] extra steps - https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1623425278. Often, the extra steps involve installing a system library. To simplify the process, we have installed those system libraries as modules on O2.

Loading R packages

Once the package is installed, the library(<pkg_name>) can be used to load a package; for example:

library("ggplot2")