RStudio

These instructions are for using RStudio on the Stronghold Linux workstation. If you prefer to use R directly from the terminal to install packages using CRAN or Bioconductor mirrors, please refer to the corresponding documentation link.

When working with the RStudio interface, the key difference is that you need to:

1. Load both the r and rstudio modules, and

2. Launch RStudio using the rstudio command.

Detailed instructions for different package sources and R versions are provided below.

1. Using the CRAN Mirror

If you want to install packages from the CRAN mirror, run the following commands:

1) Load the R and RStudio modules into your current environment.

module load r rstudio

2) Launch the RStudio interface.

rstudio

3) Install the R package you specify (replace <package_name> with the actual name of the package) using Brown University’s CRAN mirror for faster access and reliability.

install.packages("<package_name>", repos="http://cran.services.brown.edu")

2. Using the Bioconductor Mirror

If you need to install packages from Bioconductor, use the following commands:

1) Load the R and RStudio modules into your current environment.

module load r rstudio

2) Launch the RStudio interface.

rstudio

3) Disable Bioconductor’s online version diagnosis (to avoid network-related conflicts), then install and use the BiocManager package to install your desired package(s).

BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE
install.packages("BiocManager")

BiocManager::install(c("<package_name>"))

3. Changing the R Version

If you want to use a different version of R in RStudio, you must change it outside of RStudio before launching it.

3.1 Check which R versions are available on the system.

module avail r/

3.2 Load the desired R version together with RStudio. Replace 4.3.1 with the version you want.

module load r/4.3.1 rstudio

3.3 Launch RStudio using the selected R version.

rstudio