R - Revision history

Haars0011: Phase 1 § 5 P1.5.6: merge Installing R packages locally + Control R environment using modules + Parallel R code on SLURM into R. Promoted R_LIBS_USER/.Renviron method, folded in Parallel R (rslurm), dropped stale pre-Lmod module-building content. (via update-page on MediaWiki MCP Server)

2026-06-16T14:08:47Z

Phase 1 § 5 P1.5.6: merge Installing R packages locally + Control R environment using modules + Parallel R code on SLURM into R. Promoted R_LIBS_USER/.Renviron method, folded in Parallel R (rslurm), dropped stale pre-Lmod module-building content. (via update-page on MediaWiki MCP Server)

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Honfi001 at 14:08, 5 December 2024

2024-12-05T14:08:12Z

← Older revision		Revision as of 14:08, 5 December 2024
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	At the ~~HPC~~ R can be used in the command line with batch scripts submitted via slurm or via a web GUI, RStudio, through Open Ondemand.		At the Anunna, R can be used in the command line with batch scripts submitted via slurm or via a web GUI, RStudio, through Open Ondemand.

	=Modules=		=Modules=

Honfi001: /* Installing New Extensions */

2024-12-05T14:06:45Z

Installing New Extensions

← Older revision		Revision as of 14:06, 5 December 2024
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	<pre>		<pre>
	install.packages("ggplot2", repos="http://cran.r-project.org", libs="~/R_432_ext")		install.packages("ggplot2", repos="http://cran.r-project.org", libs="~/.R_432_ext", dependencies=TRUE)
	</pre>		</pre>

Honfi001: /* Creating a new library */

2024-10-28T12:36:28Z

Creating a new library

← Older revision		Revision as of 12:36, 28 October 2024
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	Once created, you can then append the newly created folder to your libPaths		Once created, you can then append the newly created folder to your libPaths

	<pre>.libPaths(c(~~folder~~, .libPaths()) )</pre>		<pre>.libPaths(c(new_library, .libPaths()) )</pre>

	you can check if the operation was successful by running		you can check if the operation was successful by running
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	.libPaths()		.libPaths()
	</pre>		</pre>


	===Installing New Extensions ===		===Installing New Extensions ===

Honfi001: /* Submitting Slurm jobs */

2024-08-07T19:05:21Z

Submitting Slurm jobs

← Older revision		Revision as of 19:05, 7 August 2024
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	</pre>		</pre>

	Let's call this script '''list_ext.r''' and let's place in <nowiki>~/myRScripts</nowiki>. It is worth pointing out that extensions in linux are meaningless, what determines how the script is going to be executed is the interpreter. We are assigning the script with the '''.r''' extension ~~just~~ make the ~~file~~ easier to search.		Let's call this script '''list_ext.r''' and let's place in <nowiki>~/myRScripts</nowiki>. It is worth pointing out that extensions in linux are meaningless, what determines how the script is going to be executed is the interpreter. We are assigning the script with the '''.r''' extension to act as a label and make the r-scripts easier to search and identify at a glance.

	Note that the first line is used to point to the R interpreter, Rscript. In order to access the Rscriot interpreter, the R (or R-bundle) module must have been loaded beforehand. This is done in the sbatch script.		Note that the first line is used to point to the R interpreter, Rscript. In order to access the Rscriot interpreter, the R (or R-bundle) module must have been loaded beforehand. This is done in the sbatch script.

Honfi001: /* Submitting Slurm jobs */

2024-08-07T19:03:34Z

Submitting Slurm jobs

← Older revision		Revision as of 19:03, 7 August 2024
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	</pre>		</pre>

	Let's call this script '''list_ext.r''' and let's place in <nowiki>~/myRScripts</nowiki>. Note that the first line is used to point to the R interpreter, Rscript. In order to access it, the R (or R-bundle) module must have been loaded beforehand. This is done in the sbatch script.		Let's call this script '''list_ext.r''' and let's place in <nowiki>~/myRScripts</nowiki>. It is worth pointing out that extensions in linux are meaningless, what determines how the script is going to be executed is the interpreter. We are assigning the script with the '''.r''' extension just make the file easier to search.

			Note that the first line is used to point to the R interpreter, Rscript. In order to access the Rscriot interpreter, the R (or R-bundle) module must have been loaded beforehand. This is done in the sbatch script.

	'''Important''': Make sure that the R script, in this example '''list_ext.r''', is executable.		'''Important''': Make sure that the R script, in this example '''list_ext.r''', is executable.

Honfi001 at 12:09, 6 August 2024

2024-08-06T12:09:41Z

← Older revision		Revision as of 12:09, 6 August 2024
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	#SBATCH --output=output_%j.txt		#SBATCH --output=output_%j.txt
	#SBATCH --error=error_output_%j.txt		#SBATCH --error=error_output_%j.txt
	#SBATCH --job-name=		#SBATCH --job-name=r_job.sh

	module load 2023		module load 2023
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	</pre>		</pre>

	Since this is just an illustrative job, we have only allocated 1 GB of RAM and a single CPU.		Since this is just an illustrative job, we have only allocated 1 GB of RAM and a single CPU. We can store the text above under the name r_job.sh.

			Thus we can submit the job with the command

			<pre>
			sbatch r_job.sh
			</pre>

Honfi001 at 10:57, 6 August 2024

2024-08-06T10:57:56Z

← Older revision		Revision as of 10:57, 6 August 2024
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	</pre>		</pre>

	Since this is just an illustrative job, we have only allocated 1 GB of RAM and a single CPU.		Since this is just an illustrative job, we have only allocated 1 GB of RAM and a single CPU.

	* RStudio in Open OnDemand

Honfi001 at 10:57, 6 August 2024

2024-08-06T10:57:24Z

← Older revision		Revision as of 10:57, 6 August 2024
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	In this example, we are installing the ggplot2 ~~extensions~~. We need to specify the repository we are downloading the package from, which in this case is the r-project website. Finally we need to specify the destination location of the libraries.		In this example, we are installing the ggplot2 extension. We need to specify the repository we are downloading the package from, which in this case is the r-project website. Finally we need to specify the destination location of the libraries.

	==Submitting Slurm jobs==		==Submitting Slurm jobs==

Honfi001: /* Installing your own R extensions */

2024-08-05T11:21:50Z

Installing your own R extensions

← Older revision		Revision as of 11:21, 5 August 2024
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	This indicated that the '''terra''' extension is contained in the '''R-bundle-CRAN/2023.12-foss-2023a''' module. This bundle loads the corresponding R version for that year and adds extensions to it.		This indicated that the '''terra''' extension is contained in the '''R-bundle-CRAN/2023.12-foss-2023a''' module. This bundle loads the corresponding R version for that year and adds extensions to it.

	==~~Installing your own R extensions~~==		== User Local Library==

	R allows the user to create its own local environment. There the user can install its own packages. you can then store these extension libraries in a local folder. It is handy to keep track of the version of R used, so try to keep your folders organized.		R allows the user to create its own local environment. There the user can install its own packages. you can then store these extension libraries in a local folder. It is handy to keep track of the version of R used, so try to keep your folders organized.