Helix/Software/R - Revision history

H Winkhardt: Typo

2025-01-27T12:28:05Z

Typo

← Older revision		Revision as of 14:28, 27 January 2025
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	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. Mixing libraries built with different major and minor R versions is discouraged, as this may result in unpredictable and subtle errors. Packages that are built and installed with one version of R may be incompatible with a newer version of R, at least when the major or minor version changes. The same is true if several versions are used simultaneously, e.g. a newer R version for a more recently started project and and older version for another project (but eventually picking up libraries built with the newer R version).		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. Mixing libraries built with different major and minor R versions is discouraged, as this may result in unpredictable and subtle errors. Packages that are built and installed with one version of R may be incompatible with a newer version of R, at least when the major or minor version changes. The same is true if several versions are used simultaneously, e.g. a newer R version for a more recently started project and and older version for another project (but eventually picking up libraries built with the newer R version).

	Because the default version may change over time, it is highly recommended to always load a specific version, , e.g.		Because the default version may change over time, it is highly recommended to always load a specific version, e.g.

	<pre>		<pre>

H Winkhardt: /* Custom installation options */

2024-10-07T07:51:47Z

Custom installation options

← Older revision		Revision as of 09:51, 7 October 2024
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	== Custom installation options ==		== Custom installation options ==
	=== Makevars ===		=== Makevars ===
	You can add custom build and installation flags for new R-packages through the ~/.R/Makevars file. This will take the form of a basic Makefile and will be added to the existing options set by the module. While the module's default should be appropriate to install most packages, it can be helpful or necessary to include additional options, for example to include locally installed dependencies to g++:		You can add custom build and installation flags for new R-packages through the ''~/.R/Makevars'' file. This will take the form of a basic Makefile and will be added to the existing options set by the module. While the module's default should be appropriate to install most packages, it can be helpful or necessary to include additional options, for example to include locally installed dependencies to g++:

	<pre>		<pre>

H Winkhardt at 07:21, 7 October 2024

2024-10-07T07:21:49Z

← Older revision		Revision as of 09:21, 7 October 2024
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	</pre>		</pre>

	The defaults can be found under $R_HOME_DIR/lib64/R/etc/Makeconf. It is usually not advisable to change the compilers (gcc, g++) themselves.		The defaults can be found under ''$R_HOME_DIR/lib64/R/etc/Makeconf''. It is usually not advisable to change the compilers (gcc, g++) themselves.

	=== Configure arguments ===		=== Configure arguments ===
	You can set further configure.args and configure.vars as character vectors to install.packages(), e.g.:		You can set further ''configure.args'' and ''configure.vars'' as character vectors to ''install.packages()'', e.g.:

	<pre>		<pre>

H Winkhardt: Paketinstallation

2024-10-04T12:46:46Z

Paketinstallation

@@ Line 84: / Line 84: @@
 * doMPI
 * doParallel
 <br>

H Winkhardt: /* Installing R-Packages into your home folder */

2024-08-05T07:37:18Z

Installing R-Packages into your home folder

← Older revision		Revision as of 09:37, 5 August 2024
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	<pre>		<pre>
	$ module load math/R/4.2.1		$ module load math/R/4.3.3
	</pre>		</pre>

H Winkhardt: /* Instructions for specific R-packages */

2024-08-05T07:10:38Z

Instructions for specific R-packages

← Older revision		Revision as of 09:10, 5 August 2024
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	<br>		<br>

	== Instructions for specific R-packages ==		= Instructions for specific R-packages =
	* [[Helix/Software/R/Rstan \| rstan]]		* [[Helix/Software/R/Rstan \| rstan]]

H Winkhardt: Readability

2024-07-08T12:19:35Z

Readability

← Older revision		Revision as of 14:19, 8 July 2024
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	</pre>		</pre>

	In order to set the correct path when using R, the location must also be defined in a configuration file ~/.Renviron in the home directory containing the following line:		In order to set the correct path when using R, the location must also be defined in a configuration file '''~/.Renviron''' in the home directory containing the following line:

	<pre>		<pre>

H Winkhardt: /* Description */

2024-07-03T13:09:26Z

Description

← Older revision		Revision as of 15:09, 3 July 2024
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	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), Windows and MacOS.

	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).

	= Package management =		= Package management =

H Winkhardt at 13:09, 3 July 2024

2024-07-03T13:09:07Z

← Older revision		Revision as of 15:09, 3 July 2024
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	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), 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).		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).

			= Package management =

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

H Winkhardt at 13:38, 12 October 2023

2023-10-12T13:38:00Z

← Older revision		Revision as of 15:38, 12 October 2023
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	<br>		<br>

	= Instructions for specific R-packages =		== Instructions for specific R-packages ==
	* [[Helix/Software/R/Rstan \| rstan]]		* [[Helix/Software/R/Rstan \| rstan]]