Running R Interactively
On the Yens, R is available via the module command.
See all currently installed versions with:
module avail R/
You will see the current R versions listed:
----------------------------------------------------------------- Global Aliases -----------------------------------------------------------------
------------------------------------------------------------- /software/modules/Core -------------------------------------------------------------
R/3.6.3 R/4.0.2 R/4.1.3 R/4.2.1 R/4.3.0 (D)
Where:
D: Default Module
Using the Latest R Version
If you require access to a newer R version that is not currently available on the system, please don't hesitate to contact DARC to request its installation.
Load R Module
To use R software on the Yens, load the module:
ml R
ml R/4.2.1
Managing R Software Libraries and Versions
The R software is installed system-wide, allowing each user to maintain their own set of R packages within their home directory by default. Furthermore, each R version has its dedicated library, distinct from other versions. Every R version will also have its own library separate from other versions. For example, R 4.0 will have its user-installed packages side by side with R 4.2 library containing the user-installed packages specific to that version.
Package Installation
When upgrading your R version (e.g., to run code with a newly released R version), you must first install packages that are needed for your script to run for that specific R version.
However, once the package is installed, you can load it in your scripts without the need for repeated installations upon each login.
Installing R Packages
Load the R module with the version that you want (R 4.3 is the current default).
For example, let's use the newest R version available on the yens:
ml R
Start interactive R console by typing R.
You should see:
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
Example Package Install
In R, install packages that you need:
> install.packages('foreach')
Creating User R Library
If this is your first time installing R package for this R version on the Yens, you will be asked to create a personal library because users do not have write permissions to the system R library.
Answer yes to both questions:
Warning in install.packages("foreach") :
'lib = "/software/free/R/R-4.3.0/lib/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Would you like to create a personal library
‘/zfs/home/users/nrapstin/R/x86_64-pc-linux-gnu-library/4.3’
to install packages into? (yes/No/cancel) yes
~/R/x86_64-pc-linux-gnu-library/4.3 where all of the user packages will be installed. Once the library is created, next
package will be installed there automatically when the corresponding R module is loaded.
If asked, pick any mirror in the US:
Installing package into ‘/home/users/nrapstin/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https]
2: Australia (Canberra) [https]
...
74: USA (IA) [https]
75: USA (MI) [https]
76: USA (OH) [https]
77: USA (OR) [https]
78: USA (TN) [https]
79: USA (TX 1) [https]
80: Uruguay [https]
81: (other mirrors)
Selection: 77
* DONE (foreach)
The downloaded source packages are in
‘/tmp/RtmpsYpzoP/downloaded_packages’
> q()
Do Not Install Packages from RStudio
Do not install packages directly from RStudio on JupyterHub. Instead, use the terminal and run R to install packages. This ensures compatibility with the Yen environment.
Run R Code Interactively
After loading the version of R you need, to execute a R script at the terminal, run:
Rscript <your-script.R>
<your-script.R> is your R script.