R's extensions are known as packages. A lot of these have been installed by the Spartan HPC sysadmins when the main package itself is installed. To check what packages are available, load the R module and enter that environment. Then run the command to display the available packages.
$ module load foss/2022a R/4.2.2 $ R $ R R version 4.2.2 (2022-10-31) -- "Innocent and Trusting" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) > installed.packages(lib.loc = NULL, priority = NULL, noCache = FALSE, fields = NULL, subarch = .Platform$r_arch)
Note that the packages available will differ for each version of R.
However, sometimes a local (personal) library is required. A library is a collection of R packages. Create a directory for the local R library, invoke R, and install packages to that directory.
Check to see that the library path has been added correctly. For example;
Common packages needed with R
Some R packages require you load additional modules before you can install them using R. One that we know about is
When you try to install
ragg (and other packages), sometimes you will get an error:
Package harfbuzz was not found in the pkg-config search path. Perhaps you should add the directory containing `harfbuzz.pc' to the PKG_CONFIG_PATH environment variable No package 'harfbuzz' found Package fribidi was not found in the pkg-config search path. Perhaps you should add the directory containing `fribidi.pc' to the PKG_CONFIG_PATH environment variable No package 'fribidi' found Using PKG_CFLAGS= Using PKG_LIBS=-lfreetype -lharfbuzz -lfribidi -lpng --------------------------- [ANTICONF] -------------------------------- Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing: * deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc) * rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL) * csw: libharfbuzz_dev libfribidi_dev (Solaris) * brew: harfbuzz fribidi (OSX) If harfbuzz freetype2 fribidi is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
To fix it, load the fribidi and harfbuzz modules before starting R. i.e.
then try installing your packages again