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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.
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.
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"
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two major issues; the library is out of date or there is a newer version available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out of date packages.