BwUniCluster3.0/Software/R - Revision history

K Kuck at 14:25, 25 November 2025

2025-11-25T14:25:40Z

← Older revision		Revision as of 16:25, 25 November 2025
Line 82:		Line 82:
	== Installation instructions for selected R packages ==		== Installation instructions for selected R packages ==

	The following guides provide detailed instructions for building selected optional R packages on '''bwUniCluster''' for '''R version 4.4.2'''. Please write a [https://www.bwhpc.de/supportportal ticket] if the instructions do not work for you or are outdated.		The following guides provide detailed instructions for building selected optional R packages on '''bwUniCluster''' for '''R version 4.5.1 (the current default version)'''. Please write a [https://www.bwhpc.de/supportportal ticket] if the instructions do not work for you or are outdated.

	* [[BwUniCluster3.0/Software/R/Rjags]]		* [[BwUniCluster3.0/Software/R/Rjags]]

K Kuck at 10:22, 17 July 2025

2025-07-17T10:22:46Z

← Older revision		Revision as of 12:22, 17 July 2025
Line 26:		Line 26:
	= Description =		= Description =

	'''R''' is a free and open-source statistical programming environment based on S, developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) ~~by John Chambers and colleagues~~ in the 1970s. R can be considered as a ~~different~~ implementation of S. ~~There~~ ~~are~~ ~~some~~ ~~important~~ ~~differences~~, ~~but~~ ~~much~~ code ~~written~~ ~~for~~ S ~~runs~~ ~~unaltered~~ ~~under~~ R.		'''R''' is a free and open-source statistical programming environment based on S, originally developed by John Chambers and colleagues at Bell Laboratories (formerly AT&T, now Lucent Technologies) in the 1970s. R can be considered a modern implementation of S and is known to be highly backward-compatible, meaning that code developed in a previous version will still run in a new version.

	R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) ~~and graphical~~ techniques, and is highly extensible~~. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in~~ ~~that~~ ~~activity~~.		R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) techniques and is highly extensible through packages.

	~~One of~~ R's ~~strengths~~ is ~~the ease with which~~ well-designed publication-quality plots ~~can be produced~~, including mathematical symbols and formulae where needed~~. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control~~.		Furthermore, R allows to produce well-designed publication-quality plots, including mathematical symbols and formulae, where needed.

	R is available as Free Software under the terms of the Free Software Foundation's GNU General Public License in source code form. It compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), Windows and macOS.		R is available as Free Software under the terms of the Free Software Foundation's GNU General Public License in source code form. It compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), as well as Windows and macOS.

			= Use R on bwUniCluster 3.0 =
	= Usage =
			The '''centrally maintained R module(s)''' should be '''preferred''' over alternatives like Conda or containerized setups when the '''computational performance is of major concern'''. The R installation(s) provided by these module(s) are built and optimized for the specific architecture and libraries of the cluster (e.g., OpenBLAS, MPI).
⚫	~~The~~ R installation also provides the standalone library libRmath. This library allows you to access R routines from your own C or C++ programs (see section 9 of the 'R Installation and Administration' manual).

			By contrast, if the '''focus''' is on '''portability''' of a data analytical workflow and '''maintaining many (external) dependencies''', '''containerized setups''' or '''Conda''' may provide useful alternatives to the native R installation.

		⚫	Furthermore, the R installation also provides the standalone library <code>libRmath</code>. This library allows you to access R routines from your own C or C++ programs (see section 9 of the 'R Installation and Administration' manual).

	== Loading the R software module ==		== Loading the R software module ==
Line 41:		Line 45:

	<pre>		<pre>
	$ module load math/R/4.4~~.1-mkl-2022~~.2~~.1-gnu~~-~~13.3~~		$ module load math/R/4.4.2-openblas
	</pre>		</pre>

K Kuck at 16:19, 16 July 2025

2025-07-16T16:19:38Z

← Older revision		Revision as of 18:19, 16 July 2025
Line 36:		Line 36:
	= Usage =		= Usage =
	The R installation also provides the standalone library libRmath. This library allows you to access R routines from your own C or C++ programs (see section 9 of the 'R Installation and Administration' manual).		The R installation also provides the standalone library libRmath. This library allows you to access R routines from your own C or C++ programs (see section 9 of the 'R Installation and Administration' manual).

			== Loading the R software module ==
			It is generally recommended to load a specific version of R, e.g.,

		⚫	<pre>
		⚫	$ module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3
		⚫	</pre>

			in data-analytical workflows instead of the default version which may change from time to time.


	== Installing R-Packages into your home folder ==		== Installing R-Packages into your home folder ==
Line 57:		Line 67:
	The drawback is that, whenever switching to a new R release, the personal library stack '''must''' be rebuilt with that new R version into the corresponding (version specific) library path. This is considered good practice anyway in order to ensure a consistent personal library stack for any specific R version in use.		The drawback is that, whenever switching to a new R release, the personal library stack '''must''' be rebuilt with that new R version into the corresponding (version specific) library path. This is considered good practice anyway in order to ensure a consistent personal library stack for any specific R version in use.

	Special care has also to be taken by users who always load the default version, i.e.

⚫	<pre>
	$ module load math/R
⚫	</pre>

	as the default version number may change any time. It is therefore highly recommended to always load a specific version, e.g.

	<pre>
⚫	$ module load math/R/4.4.2-~~openblas~~
	</pre>

	== Pre-installed R-packages ==		== Pre-installed R-packages ==
Line 76:		Line 76:
	* doParallel		* doParallel

	== ~~Optional~~ ~~packages~~ for R ==		== Installation instructions for selected R packages ==

	The following guides provide detailed instructions ~~about~~ ~~how to build~~ selected optional R packages on '''bwUniCluster''' for '''R version 4.4.2'''. Please write a [https://www.bwhpc.de/supportportal ticket] if the instructions do not work for you or are outdated.		The following guides provide detailed instructions for building selected optional R packages on '''bwUniCluster''' for '''R version 4.4.2'''. Please write a [https://www.bwhpc.de/supportportal ticket] if the instructions do not work for you or are outdated.

	* [[BwUniCluster3.0/Software/R/Rjags]]		* [[BwUniCluster3.0/Software/R/Rjags]]

K Kuck: Created page with "{{Softwarepage|math/R}} {| width=600px class="wikitable" |- ! Description !! Content |- | module load | math/R |- | License | GPL |- | Citing | n/a |- | Links | [http://www.r-project.org/ Homepage] | [http://cran.r-project.org/manuals.html Documentation] |- | Graphical Interface | No |- | Plugins | User dependent |} = Description = '''R''' is a free and open-source statistical programming environment based on S, developed at Bell Laboratories (formerly AT&T, now..."

2025-07-16T15:37:48Z

Created page with "{{Softwarepage|math/R}} {| width=600px class="wikitable" |- ! Description !! Content |- | module load | math/R |- | License | GPL |- | Citing | n/a |- | Links | [http://www.r-project.org/ Homepage] | [http://cran.r-project.org/manuals.html Documentation] |- | Graphical Interface | No |- | Plugins | User dependent |} = Description = '''R''' is a free and open-source statistical programming environment based on S, developed at Bell Laboratories (formerly AT&T, now..."

New page

{{Softwarepage|math/R}}

{| width=600px class="wikitable"
|-
! Description !! Content
|-
| module load
| math/R
|-
| License
| GPL
|-
| Citing
| n/a
|-
| Links
| [http://www.r-project.org/ Homepage] | [http://cran.r-project.org/manuals.html Documentation]
|-
| Graphical Interface
| No
|-
| Plugins
| User dependent
|}

= Description =

'''R''' is a free and open-source statistical programming environment based on S, developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues in the 1970s. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.

R is available as Free Software under the terms of the Free Software Foundation's GNU General Public License in source code form. It compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), Windows and macOS.

= Usage =
The R installation also provides the standalone library libRmath. This library allows you to access R routines from your own C or C++ programs (see section 9 of the 'R Installation and Administration' manual).

== Installing R-Packages into your home folder ==
Since we cannot provide a software module for every R package, we recommend to install special R packages locally into your home folder. One option for doing this is from within an interactive R session:

<pre>
> library() # List preinstalled packages
> install.packages('package_name', repos="http://cran.r-project.org") # Installing your R package and the dependencies
> library(package_name) # Loading the package into you R instance
</pre>

The package is now installed permanently in your home folder and is available every time you start R.

'''Note:'''

By default R uses a version (and platform) specific path for personal libraries, such as
"$HOME/R/x86_64-pc-linux-gnu-library/x.y" for R version x.y.z. This directory will be created automatically (after confirmation) when installing a personal package for the first time.

A version specific path, such as the default path, allows users to maintain multiple personal library stacks for different (major and minor) R versions and does also prevent users from mixing their stack with libraries built with different R versions.

The drawback is that, whenever switching to a new R release, the personal library stack '''must''' be rebuilt with that new R version into the corresponding (version specific) library path. This is considered good practice anyway in order to ensure a consistent personal library stack for any specific R version in use.

Special care has also to be taken by users who always load the default version, i.e.

<pre>
$ module load math/R
</pre>

as the default version number may change any time. It is therefore highly recommended to always load a specific version, e.g.

<pre>
$ module load math/R/4.4.2-openblas
</pre>

== Pre-installed R-packages ==
* Rmpi
* iterators
* foreach
* doMPI
* doParallel

== Optional packages for R ==

The following guides provide detailed instructions about how to build selected optional R packages on '''bwUniCluster''' for '''R version 4.4.2'''. Please write a [https://www.bwhpc.de/supportportal ticket] if the instructions do not work for you or are outdated.

* [[BwUniCluster3.0/Software/R/Rjags]]

<br>