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[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&gt;&amp;1 | grep math/R</code> on Helix.

=== 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 <u>when you choose</u> <code>custom</code> in the dropdown menu when starting the job.
# (Re)start RStudio

⚫
== Add R packages ==


* 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.

Latest revision as of 00:57, 13 March 2025

RStudio is an integrated development environment (IDE) for programming with R. It can handle Python code, too.


Change R Version

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

Change the R version to a version unavailable on Helix

  1. Open a shell on Helix by sshing into Helix or by starting the RStudio app on bwVisu and switching to the terminal tab.
  2. Download your desired R version, unpack it and change into the unpacked directory: 
    tar -xf R-x.y.z.tar.gz
cd R-x.y.z.tar.gz
    where x.y.z denotes the version of your downloaded R installation files.
  3. Patch the configuration file to make it compatible with your shell environment on Helix: 
    sed '/date-time conversions do not work in 2020/s/^/: #/' -i configure
  4. Install R into a chosen location in your home directory: 
    ./configure prefix=$HOME/path/in/your/home/directory
module load devel/java
make
make install
  5. Make your installed R version the default by exporting the location of its binary to your PATH: Open or create the file .bashrc in your home directory and add the following line: 
    export "PATH=/path/to/your/R/installation/directory/bin:$PATH"
    Please make sure that the suffix /bin 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.
  6. Test the installation: Reload your bash environment and obtain the version of the R binary in your path: 
    source $HOME/.bashrc && R --version
    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 when you choose custom in the dropdown menu when starting the job.
  7. (Re)start RStudio

Add R packages

  • Add a new package to RStudio
    1. Login to bwForCluster Helix or start the RStudio app on bwVisu and switch to the Terminal tab.
    2. Follow the instructions from the R page
  • To create dashboards, you can use RShiny with bwVisu RStudio as well.
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