Running R on Linux systems#

Linux allows us to run specific versions of R, but may also pose particular challenges when it comes to installing packages.

BioHPC specific

See R notes for BioHPC.

Specific versions of R#

You may either need to use module or docker to run specific versions of R. Both can work on BioHPC.

BioHPC specific

Use module avail to see which versions of R are available. Use module load R/4.2.1-r9 to load a specific version.

Installing packages#

R on Linux will usually install packages from CRAN, and compile from source. This may be feasible to circumvent by using Package Archives, and defining the specific operating system you are using.

BioHPC specific

BioHPC uses Rocky Linux 9.

This is the default for rocker/ provided Docker images.

Errors#

Package not available#

If you get

3: package ‘NameOfPackage’ is not available for this version of R

check

install_version("mypackage", "1.15")

  • your version of R is too young (see above for specific versions)

  • your version of R is too old (see above for specific versions)

MRAN no longer available#

Some older packages may attempt to use MRAN - the “Microsoft R Application Network”. This was shut down on July 1, 2023 (see this notice).

Solution: Switch to Posit Package Manager (PPM).