Control R environment using modules - Revision history

Haars0011: Phase 1 § 5 P1.5.6: stale pre-Lmod module-building workflow, superseded by buckets + R-bundle-CRAN; redirect to R (via update-page on MediaWiki MCP Server)

2026-06-16T14:08:57Z

Phase 1 § 5 P1.5.6: stale pre-Lmod module-building workflow, superseded by buckets + R-bundle-CRAN; redirect to R (via update-page on MediaWiki MCP Server)

← Older revision		Revision as of 14:08, 16 June 2026
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	~~== Setting up a semi-public repository ==~~		#REDIRECT [[R]]

	~~<source lang='bash'>~~
	~~mkdir /cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2~~
	~~</source>~~
	~~Note: need to do this only once per version; make sure that the folder does not already exist.~~

	~~== Create an R module ==~~

	~~<source lang='bash'>~~
	~~mkdir /cm/shared/apps/WUR/ABGC/modulefiles/R/~~
	~~</source>~~
	~~Note: need to do this only once per version; make sure that the folder does not already exist.~~

	~~<source lang='bash'>~~
	~~cp /cm/shared/modulefiles/R/3.0.2 /cm/shared/apps/WUR/ABGC/modulefiles/R/3.0.2_wur~~
	~~</source>~~
	~~Note: need to do this only once per version; make sure that the file does not already exist.~~

	~~<source lang='tcl'>~~
	~~#%Module1.0#######################################################################~~
	~~## R3 modulefile modified for WUR/ABGC use~~
	##
	~~proc ModulesHelp { } {~~

	~~puts stderr "\tAdds R v3.0.2 to your environment and sets WUR/ABGC libraries"~~
	}

	~~module-whatis "Adds R v3.0.2 to your environment and set WUR/ABGC libraries"~~

	~~set r3_root /cm/shared/apps/R3/~~
	~~set r3_wur_root /cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2/~~

	~~prepend-path PATH $r3_root/bin~~
	~~prepend-path MANPATH $r3_root/share/man~~
	~~prepend-path LD_LIBRARY_PATH $r3_root/lib64~~
	~~prepend-path R_LIBS_SITE $r3_wur_root~~

	~~</source>~~

	~~== Load Module ==~~

	~~<source lang='bash'>~~
	~~module avail~~
	~~</source>~~

	~~----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------~~
	~~bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur~~

	~~<source lang='bash'>~~
	~~module load R/3.0.2_wur~~
	~~</source>~~

	~~== Install R package and check install path ==~~

	~~<source lang='rsplus'>~~
	~~install.packages('car')~~
	~~</source>~~



	~~> installed.packages()~~
	~~Package LibPath~~
	~~car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2"~~

	~~== See also ==~~

	* [[Parallel_R_code_on_SLURM \| Running parallel workloads in R on Slurm]]
	* [[~~Domain_specific_software_on_B4Fcluster_installation_by_users \| Installing domain specific software: installation by users]]~~
	* [~~[Setting local variables]]~~
	* [[Installing_R_packages_locally \| Installing R ~~packages locally]]~~
	* [[Setting_up_Python_virtualenv \| Setting up and using a virtual environment for Python3 ]]

	~~== External links ==~~

Dawes001: /* See also */

2018-05-23T08:47:06Z

Hjmegens at 22:59, 29 November 2013

2013-11-29T22:59:12Z

← Older revision		Revision as of 22:59, 29 November 2013
Line 65:		Line 65:

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

			* [[Domain_specific_software_on_B4Fcluster_installation_by_users \| Installing domain specific software: installation by users]]
			* [[Setting local variables]]
			* [[Installing_R_packages_locally \| Installing R packages locally]]
			* [[Setting_up_Python_virtualenv \| Setting up and using a virtual environment for Python3 ]]

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

Hjmegens at 22:57, 29 November 2013

2013-11-29T22:57:56Z

← Older revision		Revision as of 22:57, 29 November 2013
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	== Load Module ==		== Load Module ==

			<source lang='bash'>
			module avail
			</source>

	----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------		----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------
	bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur		bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur

			<source lang='bash'>
			module load R/3.0.2_wur
			</source>

			== Install R package and check install path ==

	<source lang='rsplus'>		<source lang='rsplus'>
Line 48:		Line 58:
	</source>		</source>

	~~== Install R package and check install path ==~~

	> installed.packages()		> installed.packages()

Hjmegens at 22:56, 29 November 2013

2013-11-29T22:56:22Z

← Older revision		Revision as of 22:56, 29 November 2013
Line 1:		Line 1:
			== Setting up a semi-public repository ==

	<source lang='bash'>		<source lang='bash'>
Line 4:		Line 5:
	</source>		</source>
	Note: need to do this only once per version; make sure that the folder does not already exist.		Note: need to do this only once per version; make sure that the folder does not already exist.

			== Create an R module ==

	<source lang='bash'>		<source lang='bash'>
Line 35:		Line 38:

	</source>		</source>

			== Load Module ==

	----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------		----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------
Line 42:		Line 47:
	install.packages('car')		install.packages('car')
	</source>		</source>

			== Install R package and check install path ==

	> installed.packages()		> installed.packages()
	Package LibPath		Package LibPath
	car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2"		car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2"

			== See also ==

			== External links ==

Hjmegens at 22:54, 29 November 2013

2013-11-29T22:54:12Z

← Older revision		Revision as of 22:54, 29 November 2013
Line 1:		Line 1:

	<source lang='bash'>		<source lang='bash'>
	/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2/		mkdir /cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2
	</source>		</source>
	Note: need to do this only once per version; make sure that the folder does not already exist.		Note: need to do this only once per version; make sure that the folder does not already exist.

Hjmegens at 22:53, 29 November 2013

2013-11-29T22:53:39Z

← Older revision		Revision as of 22:53, 29 November 2013
Line 2:		Line 2:
	/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2/		/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2/
	</source>		</source>
			Note: need to do this only once per version; make sure that the folder does not already exist.

	<source lang='bash'>		<source lang='bash'>
	mkdir /cm/shared/apps/WUR/ABGC/modulefiles/R/		mkdir /cm/shared/apps/WUR/ABGC/modulefiles/R/
	</source>		</source>
			Note: need to do this only once per version; make sure that the folder does not already exist.

	<source lang='bash'>		<source lang='bash'>
	cp /cm/shared/modulefiles/R/3.0.2 /cm/shared/apps/WUR/ABGC/modulefiles/R/3.0.2_wur		cp /cm/shared/modulefiles/R/3.0.2 /cm/shared/apps/WUR/ABGC/modulefiles/R/3.0.2_wur
	</source>		</source>
			Note: need to do this only once per version; make sure that the file does not already exist.

	<source lang='tcl'>		<source lang='tcl'>

Hjmegens at 22:50, 29 November 2013

2013-11-29T22:50:11Z

← Older revision		Revision as of 22:50, 29 November 2013
Line 13:		Line 13:
	<source lang='tcl'>		<source lang='tcl'>
	#%Module1.0#######################################################################		#%Module1.0#######################################################################
	## R3 modulefile		## R3 modulefile modified for WUR/ABGC use
	##		##
	proc ModulesHelp { } {		proc ModulesHelp { } {

	puts stderr "\tAdds R v3.0.2 to your environment"		puts stderr "\tAdds R v3.0.2 to your environment and sets WUR/ABGC libraries"
	}		}

	module-whatis "Adds R v3.0.2 to your environment"		module-whatis "Adds R v3.0.2 to your environment and set WUR/ABGC libraries"

	set r3_root /cm/shared/apps/R3/		set r3_root /cm/shared/apps/R3/
Line 29:		Line 29:
	prepend-path LD_LIBRARY_PATH $r3_root/lib64		prepend-path LD_LIBRARY_PATH $r3_root/lib64
	prepend-path R_LIBS_SITE $r3_wur_root		prepend-path R_LIBS_SITE $r3_wur_root

	</source>		</source>

Hjmegens at 22:48, 29 November 2013

2013-11-29T22:48:04Z

← Older revision		Revision as of 22:48, 29 November 2013
Line 34:		Line 34:
	bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur		bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur

	<source lang='r'>		<source lang='rsplus'>
	install.packages('car')		install.packages('car')
	</source>		</source>

Hjmegens at 22:47, 29 November 2013

2013-11-29T22:47:21Z

← Older revision		Revision as of 22:47, 29 November 2013
Line 33:		Line 33:
	----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------		----------------------------------- /cm/shared/apps/WUR/ABGC/modulefiles -----------------------------------
	bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur		bwa/0.5.9 bwa/0.7.5a R/3.0.2_wur

			<source lang='r'>
			install.packages('car')
			</source>

	> installed.packages()		> installed.packages()
	Package LibPath		Package LibPath
	car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2"		car "car" "/cm/shared/apps/WUR/ABGC/R/R_libraries/3.0.2"

← Older revision		Revision as of 08:47, 23 May 2018
Line 66:		Line 66:
	== See also ==		== See also ==

			* [[Parallel_R_code_on_SLURM \| Running parallel workloads in R on Slurm]]
	* [[Domain_specific_software_on_B4Fcluster_installation_by_users \| Installing domain specific software: installation by users]]		* [[Domain_specific_software_on_B4Fcluster_installation_by_users \| Installing domain specific software: installation by users]]
	* [[Setting local variables]]		* [[Setting local variables]]