R on ARC - Revision history

Dmitri: /* Installing and managing R with Conda */

2025-03-19T16:56:09Z

Installing and managing R with Conda

← Older revision		Revision as of 16:56, 19 March 2025
Line 679:		Line 679:

	# Then you can add R packages you need.		# Then you can add R packages you need.
	$ conda install -c bioconductor-dada2		$ conda install -c bioconda bioconductor-dada2

	# And more....		# And more....

2025-03-18T22:02:15Z

Installing and managing R with Conda

← Older revision		Revision as of 22:02, 18 March 2025
Line 690:		Line 690:

	$ conda search -c bioconda dada2		$ conda search -c bioconda dada2
			</source>

			To use R installed this way you will always have to activate Conda and the R environment prior to using them.
			<source lang=bash>
			module load conda/base
			conda activate my_renv
	</source>		</source>

2025-03-18T22:00:45Z

Installing and managing R with Conda

← Older revision		Revision as of 22:00, 18 March 2025
Line 660:		Line 660:

	In some cases it may be easier (and preferable) to install R using [[Conda on ARC \| Conda]] package manager.		In some cases it may be easier (and preferable) to install R using [[Conda on ARC \| Conda]] package manager.
			This way one can install R itself and all the necessary R packages using Conda.
			The benefit is that if there are dependencies that are external to R,
			they can also be installed by Conda.

			<source lang=bash>
			# Activate Conda
			$ module load conda/base

			# Create new Conda environment for your R install.
			$ conda create -n my_renv
			....

			# Activate the environment.
			$ conda activate my_renv

			# Now you can install R of the version you want. You can also install RStudio, that can be used in an OOD Desktop session.
			$ conda install r=4.4 rstudio-desktop

			# Then you can add R packages you need.
			$ conda install -c bioconductor-dada2

			# And more....
			</source>
			Note, that you can search for packages that can be installed with Conda:
			<source lang=bash>
			$ conda search r

			$ conda search rstudio

			$ conda search -c bioconda dada2
			</source>

	= Links =		= Links =

2025-03-18T21:52:52Z

Installing R

← Older revision		Revision as of 21:52, 18 March 2025
Line 621:		Line 621:
	Then follow the instructions given above.		Then follow the instructions given above.

	= Installing R =		= Installing R from sources =

	Let us imagine that we want to install '''R v.3.6.2''' into our home directory.		Let us imagine that we want to install '''R v.3.6.2''' into our home directory.
Line 656:		Line 656:
	</pre>		</pre>
	You have to do this every time you what to use your personal R.		You have to do this every time you what to use your personal R.

			= Installing and managing R with Conda =

			In some cases it may be easier (and preferable) to install R using [[Conda on ARC \| Conda]] package manager.

	= Links =		= Links =

2023-10-18T19:38:32Z

Installing R

← Older revision		Revision as of 19:38, 18 October 2023
Line 657:		Line 657:
	You have to do this every time you what to use your personal R.		You have to do this every time you what to use your personal R.

			= Links =

			[[ARC Software pages]]

	[[Category:Software]]		[[Category:Software]]
	[[Category:ARC]]		[[Category:ARC]]
	{{Navbox ARC}}		{{Navbox ARC}}

2023-09-21T18:17:33Z

Use ARC navbox

2023-09-20T22:28:58Z

Added navbox

2022-10-12T20:38:14Z

Doing parallel computations with R

← Older revision		Revision as of 20:38, 12 October 2022
Line 383:		Line 383:
	When using parallel computations is it necessary to measure the benefit of multiprocessing.		When using parallel computations is it necessary to measure the benefit of multiprocessing.
	Does doubling of the number of CPUs double the performance of your code?		Does doubling of the number of CPUs double the performance of your code?
	If there is little benefit if increasing the number of CPUs there is not much sense in using more resources.		If there is little benefit in increasing the number of CPUs there is not much sense in using more resources.
	Remember, that is almost always '''more efficient''' to use '''fewer CPUs''' for your computation.		Remember, that is almost always '''more efficient''' to use '''fewer CPUs''' for your computation.

2022-10-12T20:37:28Z

Doing parallel computations with R

← Older revision		Revision as of 20:37, 12 October 2022
Line 381:		Line 381:
	Rscript test.R		Rscript test.R
	</syntaxhighlight>		</syntaxhighlight>
			When using parallel computations is it necessary to measure the benefit of multiprocessing.
			Does doubling of the number of CPUs double the performance of your code?
			If there is little benefit if increasing the number of CPUs there is not much sense in using more resources.
			Remember, that is almost always '''more efficient''' to use '''fewer CPUs''' for your computation.

	= Adding R packages =		= Adding R packages =

2022-10-12T20:30:00Z

Doing parallel computations with R