Installing R packages

Installing R packages#

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On RCAC clusters, you can load any R modules (r-scrnaseq, r-rnaseq, etc.) and install packages using BiocManager or install.packages. However, Since you don’t have write access to the system library, you will need to install the packages in your custom location. Here is how you can do it:

1. Create directory#

Create the required directory in your desired location. For home direcotry.

cd ~
mkdir -p local/r_packages

This is just an example, but you can project specific package directory if you prefer.

Note

For major versions of R, you may have to create a new directory for the packages. For example, local/r_packages/4.4.1 for R 4.4.1.

2. Install packages#

Install the packages in your custom library:

ml purge
ml biocontainers
ml r-scrnaseq/4.4.1-rstudio
Rscript -e 'BiocManager::install("DESeq2", lib="~/local/r_packages")'
Rscript -e 'install.packages("data.table", lib="~/local/r_packages")'

You can also run this within an R session, if you prefer:

BiocManager::install("DESeq2", lib="~/local/r_packages")
install.packages("data.table", lib="~/local/r_packages")

3. Add the library path#

To ensure R knows about your custom library, add the following line to your ~/.Renviron file:

echo 'R_LIBS_USER=${R_LIBS_USER}:'~/local/r_packages'' >> ~/.Renviron

4. Testing#

Test the installation:

ml purge
ml biocontainers
ml r-scrnaseq/4.4.1-rstudio

and in R session:

library(DESeq2)
library(data.table)
.libPaths()

This should load your libraries and should show the path to your custom library.

Using RStudio#

Alternatively, if using RStudio, you can also set the environment variable in the RStudio configuration file. Add the following line to your ~/.Renviron file:

usethis::edit_r_environ()

When the file opens, add the following line:

R_LIBS_USER=~/local/r_packages

save and restart RStudio. You can test .libPaths() in RStudio to see if the path is set correctly.

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