R Modules Available

The Fred Hutch R modules have the suffix -fh1. The -fh1 module is specific to the Hutch, and contains libraries that have been requested by Hutch users. The Fred Hutch module inherits the modules from a base R module that is maintained by the EasyBuild community. Users should use the ‘fh’ versions of R.

Requesting Modules

Adding every user request for libraries is becoming a challenge to support. The Fred Hutch R module has close to 1,000 libraries. Users are encouraged to install custom R libraries in their home directories. Users can submit install request for libraries that require system libraries.

User Installed R Modules

The Fred Hutch R module has over 1,000 libraries, but it might not have the one library that you need. R libraries into your home directory if they not otherwise available. Use the install.packages() function to install R libraries.

> install.packages("dsa")
Installing package into ‘/app/easybuild/software/R/3.6.0-foss-2016b-fh1’
(as ‘lib’ is unspecified)
Warning in install.packages("dsa") :
  'lib = "/app/easybuild/software/R/3.6.0-foss-2016b-fh1"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes

The default path for libraries is the system path which is not writable. Chose the option to create a personal library. Before adding a personal library you should check the location where it will be written. The .libPaths() function will show the locations that libraries are searched.

> .libPaths()
[1] "/app/easybuild/software/R/3.6.0-foss-2016b-fh1"
[2] "/home/jfdey/R/x86_64-pc-linux-gnu-library/3.6"
[3] "/app/easybuild/software/R/3.6.0-foss-2016b/lib/R/library"
>

Notice one of the paths is in my “Home” directory and contains the major.minor version of R 3.6 in the path. If your library path is not versioned you might have defined R_LIBS_USER in your .Rprofile configuration 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/3.6"

Issues with R Libraries

One of the most frequent issues are errors with loading libraries. There are two major issues; the library is out of date or there is a newer version available from the system that is not being loaded. Use the packageVersion("snow") function to show the library version and update.packages() function to update out of date packages.

R Modules Available

R-3.6.0-foss-2016b-fh1

Known Issues None Package List ADGofTest-0.3 Anderson-Darling GoF test ALDEx2-1.14.1 Analysis Of Differential Abundance Taking Sample Variation...