Available R Modules

The Fred Hutch R modules have the prefix fh. fhR modules are specific to the Hutch and contain libraries that Hutch users have requested. The Fred Hutch module inherits all the libraries from EasyBuild R. fhR module contains many Bioconductor libraries. Cluster users should use the ‘fh’ versions of R.

Requesting Modules

The Fred Hutch R module has over 1,000 libraries. Adding every user request for libraries is becoming a challenge to support. Users are encouraged to install R libraries in their home directories. To have complex libraries installed which require additional system libraries or data open a ticket with Scicomp.

Installing R Modules

Additional R libraries can be installed into your home directory. Use the install.packages() function to install R libraries. Since verion 4.0 of R the library paths in your home directory are based on the Major.Minor version of R. Users should not set R_LIB or any other environment variables that effect searching of R library paths. After starting R you can verify library paths with > .libPaths(). Your personal library path in your home directory should app first in the list.

> .libPaths()
[1] "/home/jfdey/R/x86_64-pc-linux-gnu-library/4.2"
[2] "/app/software/fhR/4.2.2.1-foss-2021b"
[3] "/app/software/R/4.2.2-foss-2021b/lib/R/library"

The first path is in my “Home” directory and contains the major.minor version of R-4.2 in the path. If your library path is not versioned you might have defined R_LIBS or R_LIBS_USER in your .Rprofile configuation file. Use Sys.getenv() to check your default user path.

Sys.getenv("R_LIBS_USER")
> Sys.getenv("R_LIBS_USER")
[1] "~/R/x86_64-pc-linux-gnu-library/4.2"

Install BioConductor Package

BioConductor packages are released and updated in step with R releases. Each release of Bioconductor matches a specific version of R. BiocManager is installed in fhR. BiocManager will only install libraries that match the release version of BioConductor. When working with an older R version, you need to know the Bioconductor version that matches. Search the older releases of libraries that match the Bioconductor release.

Issues with R Libraries

One of the most frequent issues user issues are with loading libraries. There are two major issues; A user installed R library that is out of date or a library requires a newer version of a user installed library. Use the packageVersion("snow") function to show the library version and update.packages() function to update the out of date packages. Often a user installed library is already part of the fhR and is conflicting with the module version.