Installing R packages locally - Revision history

Haars0011 at 13:49, 9 April 2024

2024-04-09T13:49:08Z

← Older revision		Revision as of 15:49, 9 April 2024
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	</pre>		</pre>
	== Installing and using a local library from a JuPyteR notebook ==		== Installing and using a local library from a JuPyteR notebook ==
			Click on the image.
	[[File:R_libpaths.png]]		[[File:R_libpaths.png\|thumb]]
	== See also ==		== See also ==
	* [[Control_R_environment_using_modules \| Control R environment on the cluster using modules]]		* [[Control_R_environment_using_modules \| Control R environment on the cluster using modules]]

Haars0011 at 09:34, 9 April 2024

2024-04-09T09:34:39Z

← Older revision		Revision as of 11:34, 9 April 2024
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	== Installing and using a local library from a JuPyteR notebook ==		== Installing and using a local library from a JuPyteR notebook ==

			[[File:R_libpaths.png]]
	== See also ==		== See also ==
	* [[Control_R_environment_using_modules \| Control R environment on the cluster using modules]]		* [[Control_R_environment_using_modules \| Control R environment on the cluster using modules]]

Haars0011 at 09:31, 9 April 2024

2024-04-09T09:31:51Z

← Older revision		Revision as of 11:31, 9 April 2024
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	install.packages("name-of-your-package",lib="~/R/library")		install.packages("name-of-your-package",lib="~/R/library")
	</pre>		</pre>
			== Installing and using a local library from a JuPyteR notebook ==


	== See also ==		== See also ==

Prins0891: to

 to fix code blocks

2023-06-15T13:53:46Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 15:53, 15 June 2023
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	You can use several library trees of add-on packages. The easiest way to tell R to use these via a 'dotfile' by creating the following file '$HOME/.Renviron' (watch the quotes and ~ character):		You can use several library trees of add-on packages. The easiest way to tell R to use these via a 'dotfile' by creating the following file '$HOME/.Renviron' (watch the quotes and ~ character):
	<~~source lang='bash'~~>		<pre>
	R_LIBS_USER="~/R/library"		R_LIBS_USER="~/R/library"
	</~~source~~>		</pre>
	This specifies a keyword (<code>R_LIBS_USER</code>) which points to a colon-separated list of directories at which R library trees are rooted. You do not have to specify the default tree for R packages.		This specifies a keyword (<code>R_LIBS_USER</code>) which points to a colon-separated list of directories at which R library trees are rooted. You do not have to specify the default tree for R packages.

	If necessary, create a place for your R libraries		If necessary, create a place for your R libraries
	<~~source lang='bash'~~>		<pre>
	mkdir ~/R ~/R/library # Only need do this once		mkdir ~/R ~/R/library # Only need do this once
	</~~source~~>		</pre>
	Set your R library path		Set your R library path
	<~~source lang='bash'~~>		<pre>
	echo 'R_LIBS_USER="~/R/library"' > $HOME/.Renviron		echo 'R_LIBS_USER="~/R/library"' > $HOME/.Renviron
	</~~source~~>		</pre>
	== Installing to a local library search location ==		== Installing to a local library search location ==

	Start up R:		Start up R:

	<~~source lang='bash'~~>		<pre>
	R # Invoke R		R # Invoke R
	</~~source~~>		</pre>
	Then, from the R environment, install the packages you require while pointing at the root R-package directory of choice. This example will install from CRAN.		Then, from the R environment, install the packages you require while pointing at the root R-package directory of choice. This example will install from CRAN.
	<~~source lang='rsplus'~~>		<pre>
	install.packages("name-of-your-package",lib="~/R/library")		install.packages("name-of-your-package",lib="~/R/library")
	</~~source~~>		</pre>

	== See also ==		== See also ==

Dawes001 at 13:56, 19 March 2019

2019-03-19T13:56:58Z

← Older revision		Revision as of 15:56, 19 March 2019
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	== See also ==		== See also ==
	* [[Control_R_environment_using_modules \| Control R environment on the ~~B4F Cluster~~ using modules]]		* [[Control_R_environment_using_modules \| Control R environment on the cluster using modules]]
	* [[Parallel_R_code_on_SLURM \| Using parallel R workloads under SLURM]]		* [[Parallel_R_code_on_SLURM \| Using parallel R workloads under SLURM]]
	* [[Bioinformatics_tips_tricks_workflows \| Bioinformatics tips, tricks, and workflows]]		* [[Bioinformatics_tips_tricks_workflows \| Bioinformatics tips, tricks, and workflows]]

Dawes001: /* See also */

2018-05-23T08:47:57Z

Megen002: /* See also */

2013-12-08T11:22:20Z

Hjmegens: /* See also */

2013-11-29T22:38:33Z

Hjmegens: /* External links */

2013-11-26T20:30:01Z

External links

← Older revision		Revision as of 22:30, 26 November 2013
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	== External links ==		== External links ==
	[http://csg.sph.umich.edu/docs/R/localpackages.html source for material for this aricle]		[http://csg.sph.umich.edu/docs/R/localpackages.html source for material for this aricle]

	[http://cran-mirror.cs.uu.nl CRAN homepage]		[http://cran-mirror.cs.uu.nl CRAN homepage]

	[http://en.wikipedia.org/wiki/R_(programming_language) R article from Wikipedia]		[http://en.wikipedia.org/wiki/R_(programming_language) R article from Wikipedia]

Hjmegens: /* External links */

2013-11-26T20:29:15Z

External links

← Older revision		Revision as of 22:29, 26 November 2013
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	[http://csg.sph.umich.edu/docs/R/localpackages.html source for material for this aricle]		[http://csg.sph.umich.edu/docs/R/localpackages.html source for material for this aricle]
	[http://cran-mirror.cs.uu.nl CRAN homepage]		[http://cran-mirror.cs.uu.nl CRAN homepage]
	[http://en.wikipedia.org/wiki/R_(programming_language) \| R article from Wikipedia]		[http://en.wikipedia.org/wiki/R_(programming_language) R article from Wikipedia]

← Older revision		Revision as of 10:47, 23 May 2018
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	== See also ==		== See also ==
	* [[Control_R_environment_using_modules \| Control R environment on the B4F Cluster using modules]]		* [[Control_R_environment_using_modules \| Control R environment on the B4F Cluster using modules]]
			* [[Parallel_R_code_on_SLURM \| Using parallel R workloads under SLURM]]
	* [[Bioinformatics_tips_tricks_workflows \| Bioinformatics tips, tricks, and workflows]]		* [[Bioinformatics_tips_tricks_workflows \| Bioinformatics tips, tricks, and workflows]]

← Older revision		Revision as of 13:22, 8 December 2013
Line 33:		Line 33:
	== See also ==		== See also ==
	* [[Control_R_environment_using_modules \| Control R environment on the B4F Cluster using modules]]		* [[Control_R_environment_using_modules \| Control R environment on the B4F Cluster using modules]]
			* [[Bioinformatics_tips_tricks_workflows \| Bioinformatics tips, tricks, and workflows]]

	== External links ==		== External links ==

← Older revision		Revision as of 00:38, 30 November 2013
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	== See also ==		== See also ==
			* [[Control_R_environment_using_modules \| Control R environment on the B4F Cluster using modules]]

	== External links ==		== External links ==