Where are R Packages Installed on the Cluster?
- Simon Alexander
Goal: Understand where R installs packages and where libraries are located, as well as inspecting general R system configuration.
- 1 Terminology Package vs Library
- 2 Load an R Environment via the Module System
- 3 Inspect R Environment Configuration
- 4 Where are Packages Installed
- 5 How to Install Packages (from within R)
- 6 How to Install Packages (from outside of R)
- 7 Install tidyr Package
- 8 What’s Installed?
- 9 Remember: R Versions and Library Locations
Terminology Package vs Library
R-Bloggers: Packages v. Libraries in R: Packages are collections of R functions, data, and compiled code in a well-defined format. The directory where packages are stored is called the library:
A package is a directory of files which extend R, either a source package (the master files of a package), or a tarball containing the files of a source package, or an installed package, the result of running
R CMD INSTALLon a source package. On some platforms there are also binary packages, a zip file or tarball containing the files of an installed package which can be unpacked rather than installing from sources.A package is not a library. The latter is used in two senses in R documentation. The first is a directory into which packages are installed, e.g.
/usr/lib/R/library: in that sense it is sometimes referred to as a library directory or library tree (since the library is a directory which contains packages as directories, which themselves contain directories). …
Load an R Environment via the Module System
[]$ module purge
[]$ module load gcc/13.2.0 r/4.4.0
[]$ R --version
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
...
# Run a simple function.
[]$ R -e "print(version[['version.string']])"
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
...
> print(version[['version.string']])
[1] "R version 4.4.0 (2024-04-24)"
# Run an R script.
[]$ Rscript r_test.R
[1] "R version 4.4.0 (2024-04-24)"Inspect R Environment Configuration
[]$ R
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
...
# List ALL environment variables:
> Sys.getenv()
# Get single environment variable.
> Sys.getenv("R_HOME")
[1] "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R"
# Get a list of environment variables.
> Sys.getenv(c("R_PLATFORM", "R_HOME", "R_LIBS_USER"))
R_PLATFORM "x86_64-pc-linux-gnu"
R_HOME "/apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R"
R_LIBS_USER "/cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4"Notice that User Libraries are stored under your home, in: R/x86_64-pc-linux-gnu-library/4.4
In general, under ~/R/<R_PLATFORM>/versionX.Y/
Get R Related Environment variables
Quick and dirty way to list all R_* environment variables.
[salexan5@mblog2 ~]$ R -e "Sys.getenv()" | grep R_
LMOD_FAMILY_COMPILER_VERSION
...
R_HOME /apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R
R_INCLUDE_DIR /apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/include
R_LIBS_SITE /apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/site-library
R_LIBS_USER /cluster/medbow/home/<username>/R/x86_64-pc-linux-gnu-library/4.4
...
R_PLATFORM x86_64-pc-linux-gnu
...
R_SHARE_DIR /apps/u/spack/gcc/13.2.0/r/4.4.0-pvzi4gp/rlib/R/share
...
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
thunderer_FAMILY_COMPILER_VERSIONWhere are Packages Installed
How to Install Packages (from within R)
How to Install Packages (from outside of R)
Install tidyr Package
What’s Installed?
Remember: R Versions and Library Locations