R-Teaching - Revision history

Shtsai at 01:26, 5 April 2026

2026-04-05T01:26:05Z

← Older revision		Revision as of 21:26, 4 April 2026
Line 1:		Line 1:
	[[Category:Teaching]][[Category:Software]][[Category:Statistics]]		[[Category:Teaching]][[Category:Software]][[Category:Statistics]]
	=== Category ===		== Category ==
	Statistics		Statistics
	=== Program On ===		== Program On ==
	Teaching		Teaching
	=== Version ===		== Version ==
	4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2		4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2, 4.5.1

	===Author / Distributor===		==Author / Distributor==
	See http://www.r-project.org/		See http://www.r-project.org/
	===Description===		==Description==
	R is a language and environment for statistical computing and graphics. It provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques.		R is a language and environment for statistical computing and graphics. It provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques.

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==
	Please see http://www.r-project.org/		Please see http://www.r-project.org/

	=== Installation ===		== Installation ==
	Source code downloaded from https://www.r-project.org/		Source code downloaded from https://www.r-project.org/

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai at 20:29, 9 January 2026

2026-01-09T20:29:37Z

← Older revision		Revision as of 16:29, 9 January 2026
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	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]

			'''R version 4.4.2'''

	~~'''~~R version 4.~~3.1'''~~		R version 4.4.2 is installed in /apps/eb/R/4.4.2-gfbf-2024a and add-on packages are installed in /apps/eb/R/4.4.2-gfbf-2024a/lib64/R/library. You can list all files in this dir to see the packages installed with this version of R.

	~~R version~~ 4.~~3.1~~ is installed in /apps/eb/R/4.3.1-~~foss~~-~~2022a~~ and add-on packages are installed in /apps/eb/R/4.3.1-~~foss~~-~~2022a~~/lib64/R/library. You can list all files in this dir to see the packages installed with this version of R.

	To use this version of R, please first load the module with		To use this version of R, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load R/4.3.1-~~foss~~-~~2022a~~		module load R/4.4.2-gfbf-2024a
	</pre>		</pre>

			Please note that when you load this R module, many other modules will be loaded as R depends on those other libraries and packages.

	~~'''~~R ~~version 4~~.~~2.1'''~~		A number of R packages are provided by other module files. For example, many CRAN packages are provided by the R-bundle-CRAN modules and many Bioconductor packages are provided by the R-bundle-Bioconductor modules. When you load an R-bundle-CRAN or an R-bundle-Bioconductor, a compatible R module will be automatically loaded. So if you to use Bioconductor 3.20, it suffices to load the module with:

	R ~~version 4.2.1 is installed in /apps/eb/R/4.2.1~~-~~foss~~-~~2022a~~ and ~~add-on~~ packages are ~~installed in /apps/eb/~~R~~/4.2.1~~-~~foss~~-~~2022a/lib64/R/library~~. ~~You can list all files in this dir to see the packages installed with this version of R.~~

	~~To use this version of R, please first load the module with~~
	~~<pre class="gscript">~~
	~~module~~ load R~~/4.2.1~~-~~foss~~-~~2022a~~
	~~</pre>~~


	~~'''~~R ~~version 4.1.2'''~~

	~~R version 4.1.2 is installed in /apps/eb/R/4.1.2~~-~~foss~~-~~2021b and add-on packages are installed in /apps/eb/~~R/4.~~1.2-foss-2021b/lib64/R/library. You can list all files in this dir~~ to ~~see the packages installed with this version of R~~.

	~~To use this version of R~~, ~~please first~~ load the module with
	<pre class="gscript">		<pre class="gscript">
	module load R/4.1.2~~-foss-2021b~~		module load R-bundle-Bioconductor/3.20-foss-2024a-R-4.4.2
	</pre>		</pre>
	~~Please note that when you load this R module, many other modules will be loaded as R depends on those other libraries and packages.~~


	A number of R packages are provided by other module files. For example, many packages that depend on the JAGS library, such as rjags, are provided by the rjags/4-12-foss-2022a-R-4.3.1 module, which can be loaded with
	~~<pre class="gscript">~~
	~~module load rjags/4-12-foss-2022a-R-4.3.1~~
	~~</pre>~~



Line 90:		Line 68:
	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	module load R/4.3.1-~~foss~~-~~2022a~~		module load R/4.4.2-gfbf-2024a

	R CMD BATCH program.R		R CMD BATCH program.R
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	module load R/4.3.1-~~foss~~-~~2022a~~		module load R/4.4.2-gfbf-2024a

	export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK		export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

Shtsai: /* Version */

2026-01-09T20:28:27Z

Version

← Older revision		Revision as of 16:28, 9 January 2026
Line 5:		Line 5:
	Teaching		Teaching
	=== Version ===		=== Version ===
	3.6.2, 4.1.2, 4.2.1, 4.3.1, 4.3.2		4.2.1, 4.3.1, 4.3.2, 4.4.1, 4.4.2

	===Author / Distributor===		===Author / Distributor===
	See http://www.r-project.org/		See http://www.r-project.org/

Chelsea: /* Version */

2024-05-14T12:36:39Z

Version

← Older revision		Revision as of 08:36, 14 May 2024
Line 5:		Line 5:
	Teaching		Teaching
	=== Version ===		=== Version ===
	4.1.2, 4.2.1, 4.3.1		3.6.2, 4.1.2, 4.2.1, 4.3.1, 4.3.2
	===Author / Distributor===		===Author / Distributor===
	See http://www.r-project.org/		See http://www.r-project.org/

Shtsai at 18:32, 5 September 2023

2023-09-05T18:32:14Z

Show changes

Shtsai at 01:25, 28 August 2020

2020-08-28T01:25:24Z

← Older revision		Revision as of 21:25, 27 August 2020
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	Teaching		Teaching
	=== Version ===		=== Version ===
	3.4.4		4.0.0
	===Author / Distributor===		===Author / Distributor===
	See http://www.r-project.org/		See http://www.r-project.org/
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	'''R version 3.4.4'''		'''R version 4.0.0'''

	R version 3.4.4 is installed in ~~/usr/local~~/apps/eb/R/3.4.4-foss-~~2016b-X11-20160819-GACRC/~~ and add-on packages are installed in ~~/usr/local~~/apps/eb/R/3.4.4-foss-~~2016b-X11-20160819-GACRC~~/lib64/R/library		R version 4.0.0 is installed in /apps/eb/R/4.0.0-foss-2019b and add-on packages are installed in /apps/eb/R/4.0.0-foss-2019b/lib64/R/library

	To use this version of R, please first load the module with		To use this version of R, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load R/3.4.4-foss-~~2016b-X11-20160819-GACRC~~		module load R/4.0.0-foss-2019b
	</pre>		</pre>
	Please note that when you load this R module, many other modules will be loaded as R depends on those other libraries and packages.		Please note that when you load this R module, many other modules will be loaded as R depends on those other libraries and packages.
Line 42:		Line 42:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml R/3.4.4-foss-~~2016b-X11-20160819-GACRC~~<br>		ml R/4.0.0-foss-2019b<br>
	R CMD BATCH <u>program.R</u><br>		R CMD BATCH <u>program.R</u><br>
	</div>		</div>
Line 60:		Line 60:
	Please see http://www.r-project.org/		Please see http://www.r-project.org/
	=== Installation ===		=== Installation ===
	* Version 3.4.4 is installed in ~~/usr/local~~/apps/eb/R/3.4.4-foss-~~2016b-X11-20160819-GACRC~~/ and add-on packages are installed in ~~/usr/local~~/apps/eb/R/3.4.4-foss-~~2016b-X11-20160819-GACRC~~/lib64/R/library		* Version 4.0.0 is installed in /apps/eb/R/4.0.0-foss-2019b/ and add-on packages are installed in /apps/eb/R/4.0.0-foss-2019b/lib64/R/library


	=== System ===		=== System ===
	64-bit Linux		64-bit Linux

Shtsai: Created page with "Category:TeachingCategory:SoftwareCategory:Statistics === Category === Statistics === Program On === Teaching === Version === 3.4.4 ===Author / Distributor=== Se..."

2018-08-13T01:57:15Z

Created page with "Category:Teaching Category:Software Category:Statistics === Category === Statistics === Program On === Teaching === Version === 3.4.4 ===Author / Distributor=== Se..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Statistics]]
=== Category ===
Statistics
=== Program On ===
Teaching
=== Version ===
3.4.4
===Author / Distributor===
See http://www.r-project.org/
===Description===
R is a language and environment for statistical computing and graphics. It provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques.

=== Running Program ===

Also refer to [[Running Jobs on the teaching cluster]]

'''R version 3.4.4'''

R version 3.4.4 is installed in /usr/local/apps/eb/R/3.4.4-foss-2016b-X11-20160819-GACRC/ and add-on packages are installed in /usr/local/apps/eb/R/3.4.4-foss-2016b-X11-20160819-GACRC/lib64/R/library

To use this version of R, please first load the module with
<pre class="gscript">
module load R/3.4.4-foss-2016b-X11-20160819-GACRC
</pre>
Please note that when you load this R module, many other modules will be loaded as R depends on those other libraries and packages.

Here is an example of a shell script, sub.sh, to run on the batch queue:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=j_R 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=R.%j.out 
<nowiki>#</nowiki>SBATCH --error=R.%j.err 

cd $SLURM_SUBMIT_DIR 
ml R/3.4.4-foss-2016b-X11-20160819-GACRC 
R CMD BATCH program.R 
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===
Please see http://www.r-project.org/
=== Installation ===
* Version 3.4.4 is installed in /usr/local/apps/eb/R/3.4.4-foss-2016b-X11-20160819-GACRC/ and add-on packages are installed in /usr/local/apps/eb/R/3.4.4-foss-2016b-X11-20160819-GACRC/lib64/R/library

=== System ===
64-bit Linux