Helix/bwVisu/RStudio - Revision history

H Winkhardt: Java module path

2025-10-06T11:51:40Z

Java module path

← Older revision		Revision as of 13:51, 6 October 2025
Line 18:		Line 18:
	# Install R into a chosen location in your home directory:		# Install R into a chosen location in your home directory:
	#: <syntaxhighlight lang="bash">./configure prefix=$HOME/path/in/your/home/directory		#: <syntaxhighlight lang="bash">./configure prefix=$HOME/path/in/your/home/directory
	module load devel/~~java~~		module load devel/java_jdk
	make		make
	make install</syntaxhighlight>		make install</syntaxhighlight>

H Winkhardt: /* Add R packages */

2025-10-06T11:46:46Z

Add R packages

← Older revision		Revision as of 13:46, 6 October 2025
Line 34:		Line 34:
	*# [[Helix/Login\|Login to bwForCluster Helix]] or start the RStudio app on bwVisu and switch to the Terminal tab.		*# [[Helix/Login\|Login to bwForCluster Helix]] or start the RStudio app on bwVisu and switch to the Terminal tab.
	*# Follow the instructions from the [[Helix/Software/R#Installing_R-Packages_into_your_home_folder\|R page]]		*# Follow the instructions from the [[Helix/Software/R#Installing_R-Packages_into_your_home_folder\|R page]]
			* '''Note''': For some packages, not all development dependencies are available through bwVisu. Some packages may have to be installed on the Login nodes after a ssh-login.
	* To create dashboards, you can use RShiny with bwVisu RStudio as well.		* To create dashboards, you can use RShiny with bwVisu RStudio as well.

H Schumacher: Removed "Change the R version to one of the available versions on Helix" section

2025-03-12T22:57:47Z

Removed "Change the R version to one of the available versions on Helix" section

← Older revision		Revision as of 00:57, 13 March 2025
Line 1:		Line 1:
			__FORCETOC__
	[https://posit.co/products/open-source/rstudio-server/ RStudio] is an integrated development environment (IDE) for programming with R. It can handle Python code, too.		[https://posit.co/products/open-source/rstudio-server/ RStudio] is an integrated development environment (IDE) for programming with R. It can handle Python code, too.

Line 5:		Line 6:

	By default, the default R version on Helix is used. You can view the current default version by executing <code>module -t -d avail 2>&1 \| grep math/R</code> on Helix.		By default, the default R version on Helix is used. You can view the current default version by executing <code>module -t -d avail 2>&1 \| grep math/R</code> on Helix.

	=== Change the R version to one of the available versions on Helix ===

	# Open or create the file <code>.bashrc</code> in your home directory, either by [https://wiki.bwhpc.de/e/Helix/Login opening a shell on Helix] or by starting the RStudio app on bwVisu and opening the file there.
	# Add the following line to your .bashrc file:
	#: <syntaxhighlight lang="bash">export R_MODULE_VERSION=<available R version on Helix></syntaxhighlight>
	#: for example <code>export R_MODULE_VERSION=4.2.1</code>.
	# (Re)start RStudio

	=== Change the R version to a version unavailable on Helix ===		=== Change the R version to a version unavailable on Helix ===
Line 33:		Line 26:
	# Test the installation: Reload your bash environment and obtain the version of the R binary in your path:		# Test the installation: Reload your bash environment and obtain the version of the R binary in your path:
	#: <syntaxhighlight lang="bash">source $HOME/.bashrc && R --version</syntaxhighlight>		#: <syntaxhighlight lang="bash">source $HOME/.bashrc && R --version</syntaxhighlight>
	#: If the displayed version number is equal to the one of your custom R installation, then the installation was successfull and your custom R version will be automatically loaded in RStudio.		#: If the displayed version number is equal to the one of your custom R installation, then the installation was successfull and your custom R version will be automatically loaded in RStudio <u>when you choose</u> <code>custom</code> in the dropdown menu when starting the job.
	# (Re)start RStudio		# (Re)start RStudio

H Schumacher: Added instructions to change R version

2025-03-04T11:49:55Z

Added instructions to change R version

← Older revision		Revision as of 13:49, 4 March 2025
Line 1:		Line 1:
	[https://posit.co/products/open-source/rstudio-server/ RStudio] is an integrated development environment (IDE) for programming with R. It can handle Python code, too.		[https://posit.co/products/open-source/rstudio-server/ RStudio] is an integrated development environment (IDE) for programming with R. It can handle Python code, too.


⚫	== R packages ==
			== Change R Version==

			By default, the default R version on Helix is used. You can view the current default version by executing <code>module -t -d avail 2>&1 \| grep math/R</code> on Helix.

			=== Change the R version to one of the available versions on Helix ===

			# Open or create the file <code>.bashrc</code> in your home directory, either by [https://wiki.bwhpc.de/e/Helix/Login opening a shell on Helix] or by starting the RStudio app on bwVisu and opening the file there.
			# Add the following line to your .bashrc file:
			#: <syntaxhighlight lang="bash">export R_MODULE_VERSION=<available R version on Helix></syntaxhighlight>
			#: for example <code>export R_MODULE_VERSION=4.2.1</code>.
			# (Re)start RStudio

			=== Change the R version to a version unavailable on Helix ===

			# Open a shell on Helix by [https://wiki.bwhpc.de/e/Helix/Login sshing into Helix] or by starting the RStudio app on bwVisu and switching to the terminal tab.
			# [https://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-R-be-obtained_003f-1 Download] your desired R version, [https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Getting-and-unpacking-the-sources-1 unpack it] and change into the unpacked directory:
			#: <syntaxhighlight lang="bash">tar -xf R-x.y.z.tar.gz
			cd R-x.y.z.tar.gz</syntaxhighlight>
			#: where <code>x.y.z</code> denotes the version of your downloaded R installation files.
			# Patch the configuration file to make it compatible with your shell environment on Helix:
			#: <syntaxhighlight lang="bash">sed '/date-time conversions do not work in 2020/s/^/: #/' -i configure</syntaxhighlight>
			# Install R into a chosen location in your home directory:
			#: <syntaxhighlight lang="bash">./configure prefix=$HOME/path/in/your/home/directory
			module load devel/java
			make
			make install</syntaxhighlight>
			# Make your installed R version the default by exporting the location of its binary to your <code>PATH</code>: Open or create the file <code>.bashrc</code> in your home directory and add the following line:
			#: <syntaxhighlight lang="bash">export "PATH=/path/to/your/R/installation/directory/bin:$PATH"</syntaxhighlight>
			#: Please make sure that the suffix <code>/bin</code> is added to the path to the installation location of your custom R version. This is the default location where the binaries of R will be usually installed.
			# Test the installation: Reload your bash environment and obtain the version of the R binary in your path:
			#: <syntaxhighlight lang="bash">source $HOME/.bashrc && R --version</syntaxhighlight>
			#: If the displayed version number is equal to the one of your custom R installation, then the installation was successfull and your custom R version will be automatically loaded in RStudio.
			# (Re)start RStudio

		⚫	== Add R packages ==

	* Add a new package to RStudio		* Add a new package to RStudio

S Richling at 10:27, 5 December 2024

2024-12-05T10:27:02Z

← Older revision		Revision as of 12:27, 5 December 2024
Line 4:		Line 4:

	* Add a new package to RStudio		* Add a new package to RStudio
	*# ~~Open a shell on bwForCluster Helix by~~ [[Helix/Login\|Login to Helix]] or ~~by starting~~ the RStudio app on bwVisu and ~~switching~~ to the Terminal tab.		*# [[Helix/Login\|Login to bwForCluster Helix]] or start the RStudio app on bwVisu and switch to the Terminal tab.
	*# Follow the instructions from the [[Helix/Software/R#Installing_R-Packages_into_your_home_folder\|R page]]		*# Follow the instructions from the [[Helix/Software/R#Installing_R-Packages_into_your_home_folder\|R page]]
	* To create dashboards, you can use RShiny with bwVisu RStudio as well.		* To create dashboards, you can use RShiny with bwVisu RStudio as well.

S Richling at 10:25, 5 December 2024

2024-12-05T10:25:54Z

← Older revision		Revision as of 12:25, 5 December 2024
Line 4:		Line 4:

	* Add a new package to RStudio		* Add a new package to RStudio
	*# Open a shell on Helix by [[Helix/Login\|~~sshing~~ ~~into~~ Helix]] or by starting the RStudio app on bwVisu and switching to the Terminal tab.		*# Open a shell on bwForCluster Helix by [[Helix/Login\|Login to Helix]] or by starting the RStudio app on bwVisu and switching to the Terminal tab.
	*# Follow the instructions from the [[Helix/Software/R#Installing_R-Packages_into_your_home_folder\|R page]]		*# Follow the instructions from the [[Helix/Software/R#Installing_R-Packages_into_your_home_folder\|R page]]
	* To create dashboards, you can use RShiny with bwVisu RStudio as well.		* To create dashboards, you can use RShiny with bwVisu RStudio as well.

H Schumacher: created page

2024-12-04T14:22:43Z

created page

New page

[https://posit.co/products/open-source/rstudio-server/ RStudio] is an integrated development environment (IDE) for programming with R. It can handle Python code, too.

== R packages ==

* Add a new package to RStudio
*# Open a shell on Helix by [[Helix/Login|sshing into Helix]] or by starting the RStudio app on bwVisu and switching to the Terminal tab.
*# Follow the instructions from the [[Helix/Software/R#Installing_R-Packages_into_your_home_folder|R page]]
* To create dashboards, you can use RShiny with bwVisu RStudio as well.