Using R Libraries
R Package Installation Best Practices
Many commonly used R packages are included in the base R installation available on HCC clusters,
such as tidyverse
and stringr
. However, users are able to install other packages in their
user libraries.
Adding packages¶
There are two options to install packages. The first is to run R on the
login node and run R interactively to install packages. The second is to
use the R CMD INSTALL
command.
Installing packages interactively¶
- Load the R module with the command
module load R
- Note that each version of R uses its own user libraries. To
install packages under a specific version of R, specify which
version by using the module load command followed by the version
number. For example, to load R version 3.5, you would use the
command
module load R/3.5
- Note that each version of R uses its own user libraries. To
install packages under a specific version of R, specify which
version by using the module load command followed by the version
number. For example, to load R version 3.5, you would use the
command
- Run R interactively using the command
R
- From within R, use the
install.packages()
command to install desired packages. For example, to install the packageggplot2
use the commandinstall.packages("ggplot2")
Some R packages, require external compilers or additional libraries. If you see an error when installing your package you might need to load additional modules to make these compilers or libraries available. For more information about this, refer to the package documentation.
Installing packages using R CMD INSTALL¶
To install packages using R CMD INSTALL
the zipped package must
already be downloaded to the cluster. You can download package source
using wget
. Then the R CMD INSTALL
command can be used when
pointed to the full path of the source tar file. For example, to install
ggplot2 the following commands are used:
# Download the package source:
wget https://cran.r-project.org/src/contrib/ggplot2_3.2.1.tar.gz
# Install the package:
R CMD INSTALL ./ggplot2_2.2.1.tar.gz
Additional information on using the R CMD INSTALL
command can be
found in the R documentation which can be seen by typing ?INSTALL
within the R console.