Using R Packages
- sarawillis@arizona.edu
- chrisreidy@arizona.edu
Creating a Custom R Library
R packages can be finicky. See Switching Between Custom Libraries and Common Problems below to help with frequent user issues.
Creating Your First Library
Make a local directory to store your packages:
$ mkdir -p ~/R/library
Tell R where the directory is by creating an environment file:
$ echo 'R_LIBS=~/R/library/' >> ~/.Renviron
That's it! Now you can install packages normally. For example, to install and load the package "ggplot2":
$ module load R $ R > install.packages("ggplot2") > library(ggplot2)
Switching Between Custom Libraries
If you're using different versions of R, we recommend you use different libraries. See Common Problems below for more information. When creating a library, consider including pertinent information in the name such as R version. For example:
If you start by using R version 4.0, following the instructions provided above:
$ mkdir -p ~/R/library_R_v4.0 $ echo 'R_LIBS=~/R/library_R_v4.0/' >> ~/.Renviron
If you later decide to switch to R version 4.1, instead of using your existing library, create a new one:
$ mkdir -p ~/R/library_R_v4.1
To use your new library, edit your .Renviron file:
$ nano ~/.Renviron # opens the R environment file for editing > R_LIBS=~/R/library_R_v4.1 # delete ~/R/library_R_v4.0 and enter the new directory > CONTROL + X # exits (remember to save at the prompt)
Now you can go about your business and install as you normally would.
Common Problems and How to Debug Them
Working on a cluster without root privileges can lead to complications. For general information on package installations, see the r-bloggers documentation. For information on common installation problems on our clusters, see the section below with with suggested solutions:
Using RStudio
How to Access RStudio
Using Singularity
In some circumstances, you may want to run RStudio using your own Singularity image. For example, this allows access to different versions of R not provided when using our OOD application. We have some instructions on how to do this below.
First, log into HPC using an Open OnDemand Desktop session and open a terminal. A Desktop session is the easiest solution to access RStudio since it eliminates the need for port forwarding.
In the terminal, make an RStudio directory where all of the necessary files will be stored. In this example, we'll be working in our home directory and will pull an RStudio image from Dockerhub to use as a test. If you're interested, you can find different RStudio images under rocker in Dockerhub.
mkdir $HOME/RStudio cd $HOME/RStudio singularity pull ./geospatial.sif docker://rocker/geospatial.sif
Next, create the necessary directories RStudio will use to generate temporary files. You will also generate a secure cookie key.
TMPDIR=$HOME/RStudio/rstudio-tmp
mkdir -p $TMPDIR/tmp/rstudio-server
uuidgen > $TMPDIR/tmp/rstudio-server/secure-cookie-key
chmod 600 $TMPDIR/tmp/rstudio-server/secure-cookie-key
mkdir -p $TMPDIR/var/{lib,run}
Next, create a file in your RStudio directory called rserver.sh and make it an executable:
touch rserver.sh chmod u+x rserver.sh
Open the file in your favorite editor and enter the content below. Modify the variables under USER OPTIONS to match your account if necessary. You can change PASSWORD to any password you'd like to use. Once you've entered the contents, save and exit:
#!/bin/bash # --- USER OPTIONS --- # WD=$HOME/RStudio SIFNAME=geospatial.sif PASSWORD="PASSWORD" # --- SERVER STARTUP EXECUTED BELOW --- # NETID=$(whoami) TMPDIR=$WD/rstudio-tmp SIF=$WD/$SIFNAME PASSWORD=$PASSWORD singularity exec -B $TMPDIR/var/lib:/var/lib/rstudio-server -B $TMPDIR/var/run:/var/run/rstudio-server -B $TMPDIR/tmp:/tmp $SIF rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user=$NETID --www-address=127.0.0.1
Now, in your desktop session's terminal, execute the rserver.sh script using:
./rserver.sh
Next, open a Firefox window and enter "localhost:8787" for the URL. In your browser, you will be prompted to log into your RStudio server. Enter your NetID under Username. Under Password, enter the password you defined in the script server.sh.
This will open your RStudio session:
Setting a New User State Directory
When working on a large project in RStudio, it is possible for your R session's data to fill up your home directory resulting in out-of-space errors (e.g. when trying to edit files, create new OOD sessions, etc). With the newest version of RStudio, you can find these saved session files under ~/.local/share/rstudio.
To preserve space in your home, you can specify a different directory by setting the environment variable RSTUDIO_DATA_HOME. To do this, open the hidden file ~/.bashrc and add:
export RSTUDIO_DATA_HOME=/path/to/new/directory
where /path/to/new/directory is the path to a different location where you have a larger space quota. For example, /groups/YOUR_PI/YOUR_NETID/rstudio_sessions.
Setting Your Working Directory
Current Session
If you'd like to change your working directory in an RStudio session, one option is to use setwd("/path/to/directory") in your terminal. Alternatively, if you'd like to see the contents of your new workspace in your file browser, you can navigate to the Session dropdown tab, navigate to Set Working Directory, and click Choose Directory...
From there, either navigate to the desired subdirectory, or click the ellipsis (...) in the upper right to enter the full path to a directory.
The ellipsis option allows for more flexibility such as pointing to an /xdisk or /groups space.
Once you click OK and then Choose in the main file navigation window, R will change its working directory and you should see the contents of your new space under the Files browser in the lower right.
All Non-Project Sessions
If you'd like to permanently set a different default working directory for all non-project RStudio sessions, navigate to the Tools dropdown tab and select Global Options...
This will open a menu where you can set your default working directory under General. Click the Browse... button to open a file navigator
To select a new working directory, either navigate to the subdirectory of your current working space, or select the ellipsis (...) in the upper right to allow you to enter the full path.
The ellipsis option allows for more flexibility such as pointing to an /xdisk or /groups space.
Next, click OK, then Choose in the Choose Directory window, then Apply in the Global Options menu. This will set your working directory for your current session as well as all future sessions.
Example R Scripts
We have examples for running R workflows in batch on our Github Examples page. Have a question or suggestion? Let us know!