Rocky R package - Revision history

Gderrybe: Update R module to latest CRAN bundle

2026-01-08T14:00:30Z

Update R module to latest CRAN bundle

← Older revision		Revision as of 14:00, 8 January 2026
Line 6:		Line 6:
	= Installing =		= Installing =

	First we load the R module we want to use. For our example, we're going to use R/~~4.2~~.2-foss-~~2022b~~.		First we load the R module we want to use. For our example, we're going to use R-bundle-CRAN/2025.10-foss-2025a.

	<pre>		<pre>
	module load R/~~4.2~~.2-foss-~~2022b~~		module load R-bundle-CRAN/2025.10-foss-2025a
	</pre>		</pre>

Line 16:		Line 16:

	<pre>		<pre>
	mkdir -p ~/R/~~4.2~~.2-foss-~~2022b~~		mkdir -p ~/R-bundle-CRAN/2025.10-foss-2025a
	export R_LIBS_USER="$HOME/R/~~4.2~~.2-foss-~~2022b~~"		export R_LIBS_USER="$HOME/R-bundle-CRAN/2025.10-foss-2025a"
	</pre>		</pre>

Line 40:		Line 40:
	#SBATCH --output=R_spatial_%j.out		#SBATCH --output=R_spatial_%j.out

	module load R/~~4.2~~.2-foss-~~2022b~~		module load R-bundle-CRAN/2025.10-foss-2025a
	export R_LIBS_USER="$HOME/R/~~4.2~~.2-foss-~~2022b~~"		export R_LIBS_USER="$HOME/R-bundle-CRAN/2025.10-foss-2025a"

	Rscript spatial.R		Rscript spatial.R

Jondale at 14:07, 29 February 2024

2024-02-29T14:07:09Z

← Older revision		Revision as of 14:07, 29 February 2024
Line 1:		Line 1:
	= About =		= About =

	The R modules on Rocky have many packages pre-loaded but not all of them. ~~You~~ are able to install ~~your~~ own packages locally in ~~your~~ home directory.		The R modules on Rocky have many packages pre-loaded but not all of them. We are able to install our own packages locally in our home directory.


	= Installing =		= Installing =

	First we load the R module we want to use. For our example, we're going to use ~~the~~ R/4.2.2-foss-2022b ~~module/version~~.		First we load the R module we want to use. For our example, we're going to use R/4.2.2-foss-2022b.

	<pre>		<pre>
Line 13:		Line 13:


	Next we decide on a location for the R packages to be installed, make that directory, and then set the R_LIBS_USER environment variable to point to the new location. Here ~~I have decided to~~ use the name of the module~~/version~~ as the directory name~~. If I choose to use a different R module/~~version ~~later, I can choose a different package directory to use~~.		Next we decide on a location for the R packages to be installed, make that directory, and then set the R_LIBS_USER environment variable to point to the new location. Here we use the name of the module as the package directory name since each version will need it's own packages installed separately.

	<pre>		<pre>
Line 21:		Line 21:


	Now ~~I can~~ start R and install the package. If ~~you~~ have not set a mirror, it will ask ~~you~~ to choose one.		Now we start R and install the package. If we have not set a mirror, it will ask for us to choose one.
	<pre>		<pre>
	R		R
Line 30:		Line 30:
	= Using =		= Using =

	In our batch file for our job, we ~~need to~~ load the ~~correct~~ module ~~for R~~ and set the R_LIBS_USER environment variable so that it can find our installed packages.		In our batch file for our job, we load the R module and set the R_LIBS_USER environment variable so that our job can find our installed packages.


Line 47:		Line 47:


	~~You will~~ run the job ~~now~~ just like any other job by using the sbatch command.		We run the job just like any other Rocky job by using the sbatch command.

	<pre>		<pre>
	sbatch spatial_test.sh		sbatch spatial_test.sh
	</pre>		</pre>

Jondale at 20:12, 28 February 2024

2024-02-28T20:12:23Z

← Older revision		Revision as of 20:12, 28 February 2024
Line 1:		Line 1:
	= About =		= About =

	The R modules on Rocky have many packages pre-loaded but not all of them. ~~If you find yourself needing one that isn't, you~~ are able to install it locally in your home directory.		The R modules on Rocky have many packages pre-loaded but not all of them. You are able to install your own packages locally in your home directory.

Jondale: Created page with "= About = The R modules on Rocky have many packages pre-loaded but not all of them. If you find yourself needing one that isn't, you are able to install it locally in your home directory. = Installing = First we load the R module we want to use. For our example, we're going to use the R/4.2.2-foss-2022b module/version.

 module load R/4.2.2-foss-2022b

Next we decide on a location for the R packages to be installed, make that directory, and then set th..."

2024-02-28T20:10:15Z

Created page with "= About = The R modules on Rocky have many packages pre-loaded but not all of them. If you find yourself needing one that isn't, you are able to install it locally in your home directory. = Installing = First we load the R module we want to use. For our example, we're going to use the R/4.2.2-foss-2022b module/version. <pre> module load R/4.2.2-foss-2022b </pre> Next we decide on a location for the R packages to be installed, make that directory, and then set th..."

New page

= About =

The R modules on Rocky have many packages pre-loaded but not all of them. If you find yourself needing one that isn't, you are able to install it locally in your home directory.

= Installing =

First we load the R module we want to use. For our example, we're going to use the R/4.2.2-foss-2022b module/version.

<pre>
module load R/4.2.2-foss-2022b
</pre>

Next we decide on a location for the R packages to be installed, make that directory, and then set the R_LIBS_USER environment variable to point to the new location. Here I have decided to use the name of the module/version as the directory name. If I choose to use a different R module/version later, I can choose a different package directory to use.

<pre>
mkdir -p ~/R/4.2.2-foss-2022b
export R_LIBS_USER="$HOME/R/4.2.2-foss-2022b"
</pre>

Now I can start R and install the package. If you have not set a mirror, it will ask you to choose one.
<pre>
R
install.packages('adespatial')
</pre>

= Using =

In our batch file for our job, we need to load the correct module for R and set the R_LIBS_USER environment variable so that it can find our installed packages.

'''spatial_test.sh'''
<pre>
#!/bin/bash

#SBATCH --job-name=SPATIAL_TEST
#SBATCH --output=R_spatial_%j.out

module load R/4.2.2-foss-2022b
export R_LIBS_USER="$HOME/R/4.2.2-foss-2022b"

Rscript spatial.R
</pre>

You will run the job now just like any other job by using the sbatch command.

<pre>
sbatch spatial_test.sh
</pre>