WURclient | Maikel P.H. Verouden, Ph.D.

RStan installation on a Windows 10/11 or a WURclient computer

Sun, 27 Aug 2023 16:19:00 +0200

Table of Contents

Motivation

Whether working or studying everybody uses various sorts and types of software on their computer. Students taking Statistical Courses, as taught by the Mathematical and Statistical Methods group at Wageningen University & Research, will most likely use R. Students enrolled in MAT34806 Bayesian Data Analysis will use RStan as well as basic R. Therefore, they will need to install RStan.

RStan is an implementation of Stan in R. Stan is a state-of-the-art platform for statistical modeling and high-performance statistical computation. Thousands of users rely on Stan for statistical modeling, data analysis, and prediction in the social, biological, and physical sciences, engineering, and business.

Users specify log density functions in Stan’s probabilistic programming language and get:

full Bayesian statistical inference with MCMC sampling (NUTS, HMC)
approximate Bayesian inference with variational inference (ADVI)
penalized maximum likelihood estimation with optimization (L-BFGS)

Stan’s math library provides differentiable probability functions & linear algebra (C++ autodiff). Additional R packages provide expression-based linear modeling, posterior visualization, and leave-one-out cross-validation.

This post will show how to install Rtools on a privately owned computer running Windows 10/11, or a WURclient desktop or laptop computer.

Requirements for RStan installation

Prior requirements for installing RStan:

R properly installed:
- R installed on Windows 10/11
- R installed on a WURclient via Software Center, or
- R installed on a WURclient using a custom installation
Rtools installed on a Windows 10/11 or a WURclient computer

Without having R and Rtools installed on your desktop or laptop computer, it makes no sense to try to install RStan. RStan needs to be able to compile from source within R, making R and Rtools indispensable.

Not required, however, highly recommended:

RStudio installed:
- RStudio installed on Windows 10/11
- RStudio installed on a WURclient via Software Center, or
- RStudio installed on a WURclient using a custom installation

Installation

The RStan installation, described here, assumes usage of R version 4.2.x or above. It uses the latest versions of the rstan and StanHeaders packages available on CRAN.

To install RStan:

Start either RStudio, or the default R GUI. RStudio being the recommended interface!
Remove, if present, the existing installation of the packages StanHeaders and rstan by executing at the R prompt:

remove.packages(pkgs = c("StanHeaders", "rstan"))

Install the latest on CRAN available version of StanHeaders and rstan by executing at the R prompt:

install.packages(pkgs = c("StanHeaders","rstan"),
                repos = c("https://cloud.r-project.org",
                getOption("repos")))

Congratulations, 😆, you now have RStan installed on your personal Windows 10/11 or WURclient computer!

Verifying the RStan installation

To verify the RStan installation run the RStan example/test model at the R prompt:

# Load the RStan library
library(rstan)
# Start up settings
options(mc.cores = parallel::detectCores())
rstan_options(auto_write = TRUE)
rstan_options(threads_per_chain = 1)
# Run example
example(stan_model, package = "rstan", run.dontrun = TRUE)

The model should then compile and sample.

If the example model fails with the error:

Error in compileCode(f, code, language = language, verbose = verbose) : 
  C:\rtools43\x86_64-w64-mingw32.static.posix\bin/ld.exe: file327c377a3dae.o:file327c377a3dae.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file327c377a3dae.o:file327c377a3dae.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file327c377a3dae.o:file327c377a3dae.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file327c377a3dae.o:file327c377a3dae.cpp:(.text$_ZN3tbb10interface
Error in sink(type = "output") : invalid connection

Verify that the packages StanHeaders and rstan installed are of version 2.32.x or above. Executing the following commands will show the installed versions:

packageVersion(pkg = "StanHeaders")
packageVersion(pkg = "rstan")

When the installed versions are lower than version 2.32.x, then repeat steps 2. and 3. as described in the section Installation.

Failed with error: ’there is no package called ‘rstudioapi’'

When the verification of the Rstan installation fails with:

Loading required namespace: rstudioapi
Failed with error:  ‘there is no package called ‘rstudioapi’’
Error in .local(object, ...) : 
  must install the rstudioapi package when using RStan in parallel via RStudio

The last line tells exactly what to do to fix the problem. Install the rstudioapi package using:

install.packages("rstudioapi")

Retry to verify the RStan installation as describe above. Now it should work!

Loading the package

The package name is rstan (all lowercase), to load the package execute:

library(rstan) # observe startup messages

As the start up message says, when using rstan locally on a multi-core machine and the system has plenty of RAM to estimate the model in parallel, at this point execute at the R prompt:

options(mc.cores = parallel::detectCores())

In addition, execute the second start up message at the R prompt:

rstan_options(auto_write = TRUE)

which allows to automatically save a bare version of a compiled Stan program to the hard disk so that it does not need to be recompiled (unless after changing the program). These commands will need to be run, each time the rstan library is loaded load in R.

Finally, when using Windows as operating system, there will be a third startup message saying not to use --march=native compiler flag. This warning can be ignored, if the steps above have been followed and a Makevars.win file on your system does not contain this flag. When the file name Makevars.win does not ring any bells, this probably means it doesn’t exist in your system.

Installing the `brms` package

In the course MAT34806 Bayesian Data Analysis the brms package will be used. This package extends RStan for Bayesian regression modeling. The package abbreviation brms stands for Bayesian Regression Models using ‘Stan’.

When the installation of RStan has been completed successfully, install the brms package by executing at the R prompt the following command:

install.packages(pkgs = "brms")

Custom Anaconda installation on a WURclient computer

Thu, 03 Nov 2022 00:00:00 +0000

Table of Contents

Motivation

A WURclient desktop or laptop at Wageningen University & Research is not a standard Windows 11 computer. WURclients use Windows 11 Enterprise, which has been modified by Facilities and Services Information Technology (FB-IT) among others with respect to installation rights for security reasons.

Classic WURclient desktops and laptops at Wageningen University & Research can install RStudio from the Software Center created by the IT department, which is launched by clicking on Start and selecting the “Software Center” tile. Modern WURclient desktops and laptops use the “WURAppStore” instead. The available version of Anaconda Python (Anaconda3) in Software Center is Anaconda Python 2025.06-0, whereas in the WURAppStore it is named Anaconda3 2025.06-0.

This version of Anaconda Python was packaged for educational purposes. Only once per year a new version of Anaconda Python is released in Software Center (for Classic WURclients) and WURAppStore (for Modern WURclients, and course software for students).

Many users, however, would like to use a newer version of Anaconda Python than the one in Software Center. At the moment of writing this post the latest version of Anaconda Python released on the Anaconda Repository Archive is Anaconda3 version 2022.10 containing Python 3.9.13 (released on 2022-10-17). The post has been updated, with the exception of the screenshots, to Anaconda3 version 2025.06-1 containing Python 3.13.5 (released 2025-07-18).

This post will show how to custom install Anaconda Python on a WURclient desktop or laptop computer without using Software Center.

The installation instructions in this post are not to be used on privately owned desktops or laptops! For a privately owned desktop or laptop see the post: Anaconda installation on Windows 10/11.

Prerequisite

To be able to perform a custom installation of R you need to have POWER USER RIGHTS on the WURclient desktop or laptop.

To see whether you possess these rights, right-click any icon (except Recycle Bin or WUR HELP) on the desktop. When the opened menu contains the option ‘WUR - Run with administrative rights’ (seventh or eighth from the top), it means you have power user rights on that particular desktop or laptop.

Uninstall a previously installed Anaconda Python version

Before performing a new custom installation of Anaconda it is recommended to uninstall a previously installed version.

Here two procedures are described, follow the one that fits your needs:

In case you have no version of Anaconda installed on your WURclient desktop or laptop you can proceed to the section Custom Anaconda installation.

Installed from Software Center

If you previously installed Anaconda Python from Software Center, then to remove Anaconda Python reopen the Software Center by clicking on Start and next click on the Software Center tile. If for some reason you lack this tile in your start menu, just type ‘Software Center’ and it will appear in a search results window in your Windows task bar.

In the left column of Software Center navigate to “Installation Status”. Select the installed Anaconda Python version and click on the green button bearing the text “Uninstall”. This will start the removal of the software. You will be informed by the Software Center, when the software has been uninstalled.

If you have not installed another version of Anaconda Python, either via Software Center or via a custom installation, your computer should now be lacking a functioning Anaconda Python installation. Continue with the section Custom Anaconda installation to perform a new custom installation of Anaconda.

When you do still have a working Anaconda Python installation on your WURclient computer, return to Uninstall a previously installed Anaconda version and follow the procedure applicable to your situation.

Installed previously as a custom installation

Let’s assume you previously installed Anaconda3 version 2021.11 on a WURclient computer (either a desktop or laptop) by following the steps for a custom installation of Anaconda as described in this post. For a newer version of Anaconda the steps are the same, but names of folders may differ.

To uninstall Anaconda perform the following steps:

Open a File Explorer and navigate to the folder C:\MyPrograms\Anaconda3. Right-click the file Uninstall-Anaconda3.exe and select ‘WUR - Run with administrative rights’ as displayed in Figure 1 below.

Uninstall Custom Anaconda Installation from File Explorer.

The uninstaller will start as shown below in Figure 2. Click the ‘Next >’ to proceed.

Welcome to Anaconda3 2021.11 (64-bit) Uninstall Announcement.

The uninstaller proceeds to the next screen, as shown in Figure 3, displaying the folder from where Anaconda3 will be uninstalled. Click the ‘Uninstall’ to proceed.

Uninstall Anaconda3 2021.11 (64-bit) from specified location.

Once the uninstallation has completed, a message of success will be display as shown below in Figure 4. Click the ‘Next >’ button to continue.

Anconda Uninstallation Complete

To finish off the uninstallation click the ‘Finish’ button as displayed in Figure 5.

Completing Anconda3 2021.11 (64-bit) Uninstall

Custom Anaconda installation

To prepare the custom Anaconda installation a couple of folders need to be created prior to the installation of Anaconda. Perform the following steps exactly as described:

Search for the Command Prompt App by typing cmd in the search field of the Windows task bar.
The left part of the search results will show the Command Prompt App as best match and it will be highlighted in blue. Click on Open file location (third from the top) in the right part displaying the options for the Command Prompt App.
A File Explorer window will open with the shortcut to Command Prompt highlighted in blue. Right click the Command Prompt shortcut and select ‘WUR - Run with adminstrative rights’ as shown in Figure 6 below.

Run CMD with ‘WUR administrative rights’ from File Explorer.

The Command Prompt application will open, as shown in Figure 7, on the folder C:\Windows. The top of the window shows that the Command Prompt application is used in Administrator mode (WARNING: BE CAREFULL!!).

Command Prompt with Adminstrative Rights.

Create the directory C:\MyPrograms. In case the directory already exists, the message A subdirectory or file C:\MyPrograms already exists. will appear. To create the indicated folder copy (CTRL+C), paste (CTRL+V) the following line behind the prompt and press return (Enter) to execute it:

mkdir C:\MyPrograms

Next create the directory C:\MyData. This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute. In case the directory already exists, the message A subdirectory or file C:\MyData already exists. will appear.

mkdir C:\MyData

To close the Command Prompt application type exit and press return (Enter) to execute.

Download

At the time this post was written, the latest release of Anaconda3 was version 2022.10. It has been updated to the latest release version 2025.06-1 of Anaconda3.

The installer for Windows 10/11 can be downloaded directly from this link: Anaconda3 2025.06-1 for Windows (ca. 914.6 MB, 64-bit).

From Anaconda3 version 2022.10 the installer is only available for 64-bit Windows 10/11 and will not install on a 32-bit version of the Operating System.

Installation

For newer versions of Anaconda3 than 2022.10 the steps described below are the same and still correct, but start with a newer version of the downloaded executable installer file of Anaconda3. The screenshots in this post have not been updated. Therefore, what you see during your installation will differ with respect to the version number shown in the screenshots.

Right-click the downloaded file Anaconda3-2025.06-1-Windows-x86_64.exe and select ‘WUR - Run with administrative rights’. This file will most likely reside in your Downloads folder of your user account.
If asked for, allow to install the software on your computer.
After the installer has started, a first selection window will appear as displayed below in Figure 8. Click the ‘Next >’ button to proceed.

Welcome to Anaconda3 2022.11 (64-bit) Setup.

The installer will now display the license agreement for installation of Anaconda3, as shown below in Figure 9. Click on the ‘I Agree’ button to agree to the terms.

Anaconda3 Setup License Agreement

After agreeing to the license terms, the Anaconda3 setup will ask for whom you wish to install for, as displayed in Figure 10. Select the radio button ‘All Users (requires admin priveleges)’ and click on the ‘Next >’ button to proceed.

Anaconda3 Setup Select Installation Type

Having selected the installation type, the Anaconda3 setup will request for an installation location as shown in Figure 11. Change the destination location to C:\MyPrograms\Anaconda3, to match Figure 11, by typing the destination path directly into the text field displayed (currently showing C:\ProgramData\Anaconda3). Click on the ‘Next >’ button to continue.

Anaconda3 Setup Choose Installation Location

After selecting the installation location folder the Advanced Installation Options will appear, as displayed below in Figure 12. Leave the selection as displayed and click on the ‘Install’ button to start the installation.

Anaconda3 Setup Advanced Installation Options

Once the installation has been completed Figure 13 will be displayed. Click on the ‘Next >’ button to continue.

Anaconda3 Setup Installation was completed successfully

Next the Anaconda3 Setup will show some information on how great Anaconda works with DataSpell as shown in Figure 14. Click the ‘Next >’ button to proceed.

Anacond3 Setup message about Anaconda and DataSpell

Finally the Annaconda 3 Setup shows that installation has been completed as displayed in Figure 15. Remove the tick marks from the boxes in front of ‘Anaconda Distribution Tutorial’ and ‘Getting Started with Anaconda’, unless you want to display this information, click the ‘Finish’ button to finish off the installation and close the Anaconda3 Setup.

Completing Anacond3 Setup

Congratulations, 😆, you now have Anaconda3 version 2025.06-1 containing Python 3.13.5 installed on your WURclient desktop or laptop computer!

Before using Anaconda check out the configuration instructions below carefully.

At least do the part on Changing the Default Startup Working Directory!

Configuration Anaconda3

Changing the Default Startup Working Directory

When starting JupyterLab or Jupyter Notebook from within Anaconda Navigator the default working directory on a WURclient will be C:\User\user001, where user001 will display your own WUR username. This is not a very smart location to store your Jupyter Notebook files (files with the *.ipynb extension), because this a local storage location without backup.

Most users would like to store their documents in M:\My Documents, which is an internal mapping to \\WURNET.NL\Homes\user001\Documents. Files stored in your M:\-drive are backed up by FB-IT and, therefore, provide a much safer storage environment.

To change the default start up working directory perform the following steps:

Open the Start Menu and navigate to ‘Anaconda3 (64-bit)’.
Either start ‘Anaconda Powershell Prompt (Anaconda3)’ or ‘Anaconda Prompt (Anaconda3)’. A window will open displaying the prompt as (base) PS C:\> for ‘Anaconda Powershell’, or (base) C:\> for ‘Anaconda Prompt`.
Type the command shown below behind the prompt and press return (Enter) to execute:

jupyter notebook --generate-config

A message stating: Writing default config to: C:\Users\user001\.jupyter\jupyter_notebook_config.py, where user001 will display your own WUR username, is printed in the window. Type exit and press return (Enter) to close the prompt window.
Open a File Explorer window and navigate to the created file C:\Users\user001\.jupyter\jupyter_notebook_config.py. You may have to change the settings in File Explorer to show the hidden items (File Explorer top menu bar ‘View’ and place a tick mark in front of ‘hidden items’).
Right-click the file jupyter_notebook_config.py and select ‘Open with’. Remove the tick mark in front of ‘Always use this app to open .py files’ and select e.g. ‘Notepad’. If you do not see ‘Notepad’, click on ‘More apps’.
The file jupyter_notebook_config.py will open in the ‘Notepad’ application. Navigate to line 450 (press CTRL+G and enter 450). Remove the # and whitespace character in front of c.NotebookApp.notebook_dir and replace '' with 'M:\My Documents'. Save the document by press CTRL+S. Lines 448-450 should now look like this:

## The directory to use for notebooks and kernels.
#  Default: ''
c.NotebookApp.notebook_dir = 'M:\My Documents'

Make sure you have saved your changes in the file jupyter_notebook_config.py and close the ‘Notepad` application.

You have now changed the default start up working directory permanently.

Upgrading Anaconda Navigator (Anaconda3)

After starting Anaconda Navigator, sometimes you will see that a newer version of the Navigator is available. In the top right corner this is indicated as displayed in Figure 16

Upgrade available for Anaconda Navigator

However, having started Anaconda Navigator from the Start Menu as regular user, you will be prompted to enter the administrator username and password. This is a problem, because you are a Power User and not an Administrator.

To be able to upgrade Anaconda Navigator you have to start the application with ‘WUR - Run with adminstrative rights’. This can be done by following these steps:

Open the Start Menu and navigate to ‘Anaconda3 (64-bit)’
Right-click on the ‘Anaconda Navigator (Anaconda3)’ start item, select ‘More’ > ‘Open file location’. This will open a File Explorer window displaying the shortcuts to start items of ‘Anaconda3 (64-bit)’.
Again right-click on the start item “Anaconda Navigator (Anaconda3)” in the File Explorer windows and select ‘WUR - Run with adminstrative rights’

Now you will be able to upgrade Anaconda Navigatore by clicking on ‘Upgrade Now’, as displayed in Figure 16.

Add a R kernel

After installing Anaconda3 only the Python kernel is present. To add a R kernel for use inside Jupyter Notebook or JupyterLab perform the following steps:

Open the Start Menu and navigate to ‘Anaconda3 (64-bit)’.
Start ‘Anaconda Powershell Prompt (Anaconda3)’. A window will open displaying the prompt as (base) PS C:\>.

Navigate to where R.exe is located. Let’s assume you have R v4.2.1 installed, either via Software Center or via Custom installation on a WURclient. For other R versions than 4.2.1 do not forget to change the R version number!

For a installation via Sofware Center use the following commands:

 cd C:\Program Files\R\R-4.2.1\bin\
 .\R.exe
 # At the R prompt, indicated by >
 install.packages("IRkernel")
   IRkernel::installspec()
 q()
 Save workspace image? [y/n/c]: n
 # back at the powershell prompt, indicated by (base) PS C:\>
 exit

For a Custom installation on a WURclient use the following commands:

 cd C:\MyPrograms\R\R-4.2.1\bin\
 .\R.exe
 # At the R prompt, indicated as >
 install.packages("IRkernel")
 IRkernel::installspec()
 q()
 Save workspace image? [y/n/c]: n
 # back at the powershell prompt, indicated by (base) PS C:\>
 exit

Now the R kernel will be available in Jupyter Notebook and JupyterLab.

Add a Julia kernel

After installing Anaconda3 only the Python kernel is present, unless you already did Add a R kernel . To add a Julia kernel for use inside Jupyter Notebook or JupyterLab perform the following steps:

Open Julia on your WURclient. A window will open and you will see the prompt displayed as julia>
Type ] and the prompt will change into (@v1.8) pkg>. This under the assumption that you have Julia v1.8.2 or later installed. For other versions of Julia the version number for package management will differ.
Type the command add IJulia. This will install a lot of packages and make the Julia kernel available in Jupyter Notebook and JupyterLab.
Close the Julia package manager by pressing the BACKSPACE key on your keyboard.
Type exit() to close Julia.

Now the Julia kernel will be available in Jupyter Notebook and JupyterLab.

Mathworks Matlab installation on a WURclient computer

Mon, 17 Oct 2022 11:00:00 +0200

Table of Contents

Motivation

WURclient computers at Wageningen University & Research can install “Matworks^® Matlab” from the Software Center created by the IT department, which is launched by clicking on Start and selecting the “Software Center” tile. At the time this post was written the latest version of Matlab^® in Software Center was MATLAB R2021b (for NON commercial use only). Currently the latest available version in Software Center is MATLAB R2024b LNU (for NON commercial use only).

Please note (for NON commercial use only)!

The license for Matworks^® Matlab is an Academic and not a Commercial license. You are not allowed to used this software for commercial projects within Wageningen Research.

The Matlab^® version in Software Center for WURclient computers has one major drawbacks:

It is not always the latest version available.

In this post the installation procedure for Mathworks^® Matlab will be given step wise. Thereby, providing a way to install the latest version.

This post will show how to install Matworks^® Matlab on a WURclient desktop or laptop computer, where the user possesses POWER USER RIGHTS.

Prerequisite

To be able to install Matworks^® Matlab you need to have POWER USER RIGHTS on the WURclient desktop or laptop.

Installation

If you do not have one already, create a folder named MyPrograms in your C:\-drive. All programs, you install yourself on your WUR Desktop or Laptop, should be installed into this folder (C:\MyPrograms). The folder can be created using File Explorer on your WURclient computer.
Open an internet browser (e.g. Microsoft Edge or Google Chrome) and navigate to the following web-address: https://nl.mathworks.com/login?uri=%2Fmwaccount%2F
Log in with your WUR e-mail address and Mathworks^® password. If you have never visited The Mathworks^® website before, then create a new account with your WUR e-mail address. Remember the password (it never changes, unless you change it yourself)!
Once logged in you need to select:
- MATLAB (Designated Computer): The installation is restricted for use to a host ID that identifies a particular computer, but not a particular user. Any number of people can log in and use the software, but not simultaneously.
- MATLAB (Individual): You can install and run the software on multiple computers. Each installation is restricted for use by a particular computer and a particular user name. This is advised for WURclient computers (desk- or laptops) and privately owned desk- or laptop computers.
After choosing the license type you will be sent to the License Center page of Mathworks^®. On this specific page you find a “Download” button. Pressing it allows you to download the version of Matlab^® you want to install.
Once the download has finished, navigate to your downloads folder. Start the installer with a right mouse click and select “WUR – Run with administrative rights” as shown below in Figure 1.

Run CMD with ‘WUR administrative rights’ from File Explorer.

The Mathworks Product Installer will start with a screen asking to log into you Mathworks account. First provide your WUR e-mail address, followed by the password belonging to the MathWorks account you created earlier using your WUR e-mail address.
Confirm the Software Linense Agreement by selecting Yes in the radio button. To confirm click the “Next” button.
Select the desired license (Designated Computer or Individual, as described in step 4.), and click the “Next” button to continue.
Select the destination folder. The recommended folder being C:\MyPrograms\MATLAB\RYYYYv, where RYYYYv represents the version, e.g., R2024b. Click the “Next” button to continue.
Select the desired products to install onto you desk- or laptop computer, and click the “Next” button to continue.
Tick the desired checkboxes to select the options wanted. Click the “Next” button to continue.
Press the “Begin Install” button to start the installation.
To finalize the installation press the “Close” button in the “Installation Complete” screen of the MathWorks Product Installer.

Activation

Mathworks^® has switched to named user licensing instead of Campus-Wide licensing, where you had to create a license file (license.lic) on the Mathworks^® site and place it in a specific folder (C:\MyPrograms\MATLAB\RYYYYv\licenses, where RYYYYv represented the version you installed, e.g., R2019a).

To activate the installed Mathworks^® MATLAB after installation, start the application using either the created desktop icon or using the start menu. You will be asked for the e-mail address associated with your Mathworks^® account (your WUR e-mail address).

Next enter the password of your Mathworks^® account in order to activate the installed Mathworks^® MATLAB.

The activation is needed only once! After activation Mathworks^® MATLAB will also start even if you do not have access to internet.

Congratulations, 😆, you now have Mathworks^® MATLAB installed on your WURclient desktop or laptop computer!

Transition a previous installation to named user licensing

Previously installed versions of Mathworks^® MATLAB (R2023b and newer) can be transitioned from a Campus-Wide license to an Individual named user license.

Save the following files into the Downloads folder of your WURclient desk- or laptop by right-clicking the link and selecting the option ‘Save link as…’ (IMPORTANT: DO NOT CHANGE THE FILE NAMES!):

license_info.xml (only for MATLAB R2023b and newer)

Switch to Individual named user licensing by performing the following steps:

Open File Explore and navigate to the folder, where you previously installed Mathworks^® MATLAB, e.g., C:\MyPrograms\MATLAB\R2023b.
Open the subfolder licenses.
Delete the file named license.lic.
Copy the file license_info.xml, you downloaded earlier and most likely resides in your downloads folder, into the folder from which you deleted license.lic.
Close File Explorer.

To reactivate read the Activation section above in this post.

Rtools installation on a Windows 10/11 or a WURclient computer

Tue, 05 Jul 2022 11:15:44 +0200

Table of Contents

Motivation

Many people are able to use R, without ever having the need to compile from source and, therefore, the need to install Rtools. However, if you want to do package development, compile from source, or use packages like rstan or cmdstanr, you will definitely need to install Rtools.

In this post the installation procedure for Rtools will be given step wise. It will work for both regular Windows 10/11 computers as well as WURclient computers.

This post will show how to install Rtools on a privately owned running Windows 10/11, or a WURclient desktop or laptop computer, where the user possesses POWER USER RIGHTS.

The only difference is how the installer for Rtools is started.

Requirement for and Download of Rtools

Requirement

Prior requirement for using Rtools:

R properly installed:
- R installed on Windows 10/11
- R installed on a WURclient via Software Center, or
- R installed on a WURclient using a custom installation

Without having R installed on your desktop or laptop computer it makes no sense to install RTools. The software Rtools provides, as the name suggests, tools (compilers, and such) for usage within R.

Download

Rtools can be downloaded for the following webpage: https://cran.r-project.org/bin/windows/Rtools/

Download the correct version, which matches the version of R installed on your desktop or laptop computer.

For R version 4.5.0 and above (4.5.x) the installer for Rtools can be downloaded directly from this link: Rtools45 installer (ca. 461 MB, 64-bit).

Installation Rtools

The screenshots below are for the installation of Rtools42 and have not been updated, because the procedure for Rtools45 remains the same.

Open a File Explorer window (keyboard shortcut: 🪟 + E) and navigate to your downloads folder.
On a Windows 10/11 computer start the downloaded Rtools installer. For a WURclient computer right-click the downloaded Rtools installer and select select ‘WUR - Run with administrative rights’ (see below in Figure 1).

Start Rtools installer on a WURclient.

The Rtools installer will open with the Select Destination Location window as displayed below in Figure 2. Do not change the destination location, leave the default suggested value (showing C:\rtools45)! Click ‘Next’ to continue.

Select Rtools destination location.

The installer will next show the Select Additional Tasks window, as show in Figure 3. Make sure that both boxes are ticked and click the ‘Next’ button to continue.

Select Rtools additional tasks.

Now the installer will present a window, as displayed below in Figure 4, with the selected installation options. Click the ‘Install’ button to start the installation or select ‘Back’ to modify the installer options.

Rtools ready to install overview.

Once the installer has completed, Figure 5 will be shown. Click the ‘Finish’ button to complete the installation.

Finish the Rtools installation.

Check the Installation

For Rtools 4.5 there is an easy way to check, that the installation of Rtools was successful.

Open R (either RGui or RStudio)
Execute the following command: Sys.which("make")

When R returns "C:\\rtools45\\usr\\bin\\make.exe", you know that Rtools was successfully installed.

For Rtools 4.0 the returned path will be empty.

This does not mean that the installation was not successful. Just that Rtools was not automatically added to the PATH environment variable.

If you wish to add Rtools to the PATH environment variable, please follow the instructions on https://cran.r-project.org/bin/windows/Rtools/rtools40.html

Custom RStudio installation on a WURclient computer

Thu, 17 Jun 2021 00:00:00 +0000

Table of Contents

Motivation

Classic WURclient desktops and laptops at Wageningen University & Research can install RStudio from the Software Center created by the IT department, which is launched by clicking on Start and selecting the “Software Center” tile. Modern WURclient desktops and laptops use the “WURAppStore” instead. The available version of RStudio in Software Center/WURAppStore is RStudio 2025.05.1.513, referring to release RStudio version 2025.05.1 Build 513.

This version of RStudio was placed in ‘Software Center’ for educational purposes. Only once per year a new version of R (including R Commander and additional packages for several courses) and RStudio is released in Software Center.

Many users, however, prefer to use the latest version of RStudio, because of new features offered in the newer version of the software. At the moment of writing this post the latest version of RStudio was v1.4.1717 named: ‘Juliet Rose’ (released on 2021-06-01). The post has been updated, with the exception of the screenshots, to RStudio 2026.04.0 Build 526 named: “Globemaster Allium”.

This post will show how to custom install RStudio on a WURclient desktop or laptop computer without using Software Center.

The installation instructions in this post are not to be used on privately owned desktops or laptops! For a privately owned desktop or laptop see the post: RStudio installation on Windows 10/11.

Prerequisites

To be able to perform a custom installation of RStudio you need to have POWER USER RIGHTS on the WURclient desktop or laptop.

To see whether you possess these rights, right-click any icon (except Recycle Bin or WUR HELP) on the desktop. When the opened menu contains the option ‘WUR - Run with administrative rights’ (sixth or seventh from the top), it means you have power user rights on that particular desktop or laptop.

R installed on a WURclient using a custom installation

To be able to install RStudio you will need to have R installed first. If you haven’t done so already, please first perform a custom installation of R on your WURclient computer (use the link above to go to that specific post).

Uninstall a previously installed RStudio version

Before performing a new custom installation of RStudio it is recommended to uninstall a previously installed version.

Here two procedures are described, follow the one that fits your needs:

In case you have no version of RStudio installed on your WURclient desktop or laptop you can proceed to the section Custom RStudio installation.

Installed from Software Center

If you previously installed RStudio from Software Center, then to remove R reopen the Software Center by clicking on Start and next click on the Software Center tile. If for some reason you lack this tile in your start menu, just type ‘Software Center’ and it will appear in a search results window in your Windows task bar.

In the left column of Software Center navigate to ‘Installation Status’. Select the installed RStudio version and click on the green button bearing the text ‘Uninstall’. This will start the removal of the software. You will be informed by the Software Center, when the software has been uninstalled.

If you have not installed another version of RStudio, either via Software Center or via a custom installation, your computer should now be lacking a functioning RStudio installation. Continue with the section Custom RStudio installation to perform a new custom installation of RStudio.

When you do still have a working RStudio installation on your WURclient computer, return to Uninstall a previously installed RStudio version and follow the procedure applicable to your situation.

Installed previously as a custom installation

Let’s assume you previously installed RStudio version 1.3.959 on a WURclient computer (either a desktop or laptop) by following the steps for a custom installation of RStudio as described in this post. For a newer version of RStudio the steps are the same.

To uninstall RStudio perform the following steps:

Open a File Explorer and navigate to the folder C:\MyPrograms\RStudio. Right-click the file Uninstall.exe and select ‘WUR - Run with administrative rights’ as displayed in Figure 1 below.

Uninstall Custom RStudio Installation from File Explorer.

The uninstaller will start as shown below in Figure 2. Click the ‘Uninstall’ to proceed.

RStudio for Windows Uninstall Announcement.

Once the uninstallation has completed, a message of success will be display as shown below in Figure 3. Click the ‘Close’ button to finish.

RStudio for Windows Uninstalled Successfully.

When you do still have a working RStudio installation on your WURclient computer, return to Uninstall a previously installed RStudio version and follow the procedure applicable to your situation.

Custom RStudio installation

Download

At the time this post was written, the latest stable release of RStudio was version 1.4.1717. The post has been updated to the current stable release 2026.04.0 Build 526.

Download RStudio using the following link: RStudio 2026.04.0 Build 526 (ca. 319.84 MB)

For newer versions of RStudio the steps described after the download are the same, but starting with a newer version of the RStudio executable file.

Installation

To install RStudio perform the following steps:

Right-click the downloaded file RStudio-2026.04.0-526.exe and select ‘WUR - Run with administrative rights’. This file will most likely reside in your Downloads folder of your user account.
After the installler has started, a Welcome window will appear as displayed below in Figure 4. Click the ‘Next’ button to proceed.

Welcome screen RStudio Setup.

Now the RStudio Setup will allow you to select the installation location by selecting a destination folder. Change the Destination Folder to C:\MyPrograms\Rstudio, , as shown in Figure 5 below. Click the ‘Next’ button to continue.

RStudio Installation Location Selection.

Next the RStudio Setup allows choosing a Start Menu folder, as displayed below in Figure 6, where the RStudio shortcut to start the program will be put. Click on ‘Install’ to start the installation of RStudio.

Setting the RStudio Start Menu Folder.

Once the installation of RStudio has finished, the window will look like the one shown below in Figure 7. Click the ‘Finish’ button to close the setup.

RStudio Installation Completion.

Congratulations, 😆, you now have RStudio 2026.04.0 Build 526 installed on your WURclient desk- or laptop computer!

Setting the default RStudio working directory

In the default R GUI the working directory at start up is:

\\\\WURNET.NL/Homes/user001/My Documents

where user001 display your own WUR username, as described in the section Changing the R GUI working directory of the post Custom R installation on a WURclient computer.

In RStudio the default working directory of the R Console and Files tab can be set in the Global Options… item under Tools in the top menu:

a new window will open by default in the General part,
go to R Sessions and select your “Default working directory (when not in a project):” by setting the desired folder using the Browse button.

When restarting RStudio you will notice, that both the R console and the Files tab open in the selected default working directory.

Resetting RStudio desktop’s state

RStudio Desktop stores its internal state in a hidden directory. If this directory does not exist, RStudio will create it on start up. This directory includes information about open documents, log files, and other state information. Removing (or renaming) this directory will reset RStudio’s state.

It is recommended to rename this directory to create a backup version instead of completely deleting it. This allows saving your settings, in case needed to revert back to them. Additionally, if experiencing a crash or RStudio failed to start, this directory may contain vital information for determining the source of the error.

Starting with RStudio 1.3, user preferences are stored in a separate folder from internal state. This allows for performing a state reset without losing settings, and also allows for preferences to be sync’ed between machines (in e.g., AppData\Roaming on Windows) while internal state is machine specific.

Some versions of RStudio Desktop store additional preferences (such as the size and location of the window and the rendering mode) in a separate location. To fully reset state, this must also be deleted or renamed, as described below in “Resetting Other Preferences”.

When using RStudio Projects, it is also recommended to reset the project-specific state if experiencing issues - this can done by navigating to the Project’s folder in the file browser, and renaming the .Rproj.user directory there.

Before resetting the internal state or other preferences make sure that no instance of RStudio is currently running. Use the task manager in Windows to close any running instance of RStudio.

Accessing the RStudio-Desktop Directory (Internal State)

Open a File Explorer window into the RStudio-Desktop directory by typing the following command into Start -> Run:

%localappdata%\RStudio

For older versions of RStudio (v1.3 and older), the state is stored here:

%localappdata%\RStudio-Desktop

Rename the directory Rstudio or RStudio-Desktop, e.g. to old_Rstudio. The environment variable %localappdata generally resolves into the folder C:\Users\<username>\AppData\Local, where <username> reflects the username of the current user.

Resetting other preferences

Open an Explorer window into the RStudio preferences directory by typing the following command into Start -> Run:

%appdata%\RStudio

Rename the directory RStudio, e.g. to old_Rstudio. The environment variable %appdata generally resolves into the folder C:\Users\<username>\AppData\Roaming, where <username> reflects the username of the current user.

R Commander installation in R on a WURclient computer

Fri, 23 Apr 2021 00:00:00 +0000

Table of Contents

Motivation

A WURclient desktop or laptop at Wageningen University & Research is not a standard Windows 10 computer. WURclients use Windows 11 Enterprise, which has been modified by Facilities and Services Information Technology (FB-IT) among others with respect to installation rights for security reasons.

Classic WURclient desktops and laptops at Wageningen University & Research can install R from the Software Center created by the IT department, which is launched by clicking on Start and selecting the “Software Center” tile. Modern WURclient desktops and laptops use the “WURAppStore” instead. Currently the latest available version in Software Center/WURAppStore is R 4.5.1 Rcmdr.

Many users, however, prefer to install software themselves, e.g., because they like to use a newer version of R than the one in Software Center/WURAppStore. When this post was written the release version of R on r-project.org was 4.0.3, named: “Bunny-Wunnies Freak Out” (released on 2020-10-10). The post has been updated, with the exception of the screenshots, to latest R version 4.5.3, named: “Reassured Reassurer” (released on 2026-03-11).

Some users will also like to install the latest version of R Commander on their WURclient, after having installed the latest version of R via a custom installation without using Software Center/WURAppStore.

This post will show how to install R Commander within R on a WURclient desktop or laptop computer after a custom R installation.

The installation instructions in this post are not to be used on privately owned desktops or laptops! For a privately owned desktop or laptop see the post: R Commander installation in R on Windows 10.

R Commander Installation from the R GUI

Prior requirement:

R installed on a WURclient using a custom installation

To be able to install R Commander you will need to have R installed first. If you haven’t done so already, please first perform a custom installation of R on your WURclient computer (use the link above to go to that specific post).

Some Figures in this post are based on R version 3.6.3. For newer versions of R the steps described are the same, only some screens you will see during your installation will display a higher version number of R compared to the screenshots in the figures of this post.

Start R x64 4.5.3 from the ‘R’ folder in the ‘Start Menu’ as displayed below in Figure 1.

Start Menu R x64

The R GUI (graphical user interface) will open and the cursor will be ready for input behind the prompt, as indicated by the > sign. Use the mouse pointer and navigate to the top menu and select ‘Packages’ > ‘Install Package(s)…’ as shown in Figure 2.

R GUI Install Packages

Now a CRAN (Comprehensive R Archive Network) mirror needs to be selected, from which packages will be installed. Select, as shown below in Figure 3, the top one ‘0-Cloud [https]’. This to make sure, that always the nearest CRAN mirror will be used no matter where you will be on the globe 🌍. Click on the ‘OK’ button to confirm the selection.

R GUI Select CRAN Mirror

After the CRAN mirror selection a list of available packages will appear. Scroll down to find the Rcmdr package and click it to select. As shown below in Figure 4 the package will turn blue, when selected. Confirm the installation by clicking the ‘OK’ button. Now a lot will happen in your display while the Rcmdr pacakage and its dependencies are being installed.

R GUI Select the Rcmdr package to be installed.

Repeat step 4. for installing the RcmdrPlugin.HH package or any other additional Plugin for R Commander you need. The HH plugin for example provides additional functionality for Simple Linear Regression.

Once the installation of the RcmdrPlugin.HH package, or any other additional Plugins you require, has finished, you are ready 😆 to start R version 4.5.3 and use R Commander.

When using R Commander for the first time additional packages, required for R Commander to work correctly, will need to be installed. Allow the installation to be able to work smoothly without errors!

Starting and restarting R Commander

Start R Commander

To start R Commander type the library(Rcmdr) command behind the R Console prompt (indicated by a > sign) and press return (↩) to execute the command.

Restart R Commander

In case R Commander crashes while using it, you will need to resart it. However, in the R Console currently running R, the library(Rcmdr) command will not restart R Commander.

The reason is, that the R Commander package is still loaded and first needs to be detached. To detach the R Commander package you can copy (Ctrl+C) the following command:

detach("package:Rcmdr", unload = TRUE)

paste (Ctrl+V) it behind the prompt in the R Console (indicated by a > sign) and press return (↩) to execute the command.

Now R Commander can be restarted by using the library(Rcmdr) command as before.

Custom R installation on a WURclient computer

Sun, 24 Jan 2021 00:00:00 +0000

Table of Contents

Motivation

This version of R was packaged for educational purposes, where Rcmdr reflects that the installer includes R Commander. Only once per year a new version of R (including R Commander and additional packages for several courses) is released in Software Center/wurappstore. Users can update all packages in this release, even the core packages in the so-called System Library. The pre-installed packages in the User Library can be uninstalled, when not needed.

This post will show how to custom install R on a WURclient desktop or laptop computer without using Software Center/WURAppStore.

The installation instructions in this post are not to be used on privately owned desktops or laptops! For a privately owned desktop or laptop see the post: R installation on Windows 10/11.

Prerequisite

To be able to perform a custom installation of R you need to have POWER USER RIGHTS on the WURclient desktop or laptop.

Uninstall a previously installed R version

Before performing a new custom installation of R it is recommended to uninstall a previously installed version.

Here two procedures are described, follow the one that fits your needs:

In case you have no version of R installed on your WURclient desktop or laptop you can proceed to the section Custom R installation.

Installed from Software Center

If you previously installed R from Software Center, then to remove R reopen the Software Center by clicking on Start and next click on the Software Center tile. If for some reason you lack this tile in your start menu, just type ‘Software Center’ and it will appear in a search results window in your Windows task bar.

In the left column of Software Center navigate to “Installation Status”. Select the installed R version and click on the green button bearing the text “Uninstall”. This will start the removal of the software. You will be informed by the Software Center, when the software has been uninstalled.

Next you will need to remove the packages, you have installed manually (added yourself via the install.packages() command in R).

Be aware that all packages you have installed manually will be removed, if you continue here!

Let’s assume you had previously installed CRAN R 3.6.1 Rcmdr from Software Center on your WURclient computer. The user installed packages will reside in C:\ProgramData\R\win-library\3.6. If you try to remove the folder via File Explorer in Windows, you will discover that you have insufficient rights to do so. The reason is that Software Center installs software with ADMINISTRATOR RIGHTS, you on the other hand only have POWER USER RIGHTS. The POWER USER does not have full administrator privileges!

However, there is a way to still delete the previously manually installed packages from C:\ProgramData\R\win-library\3.6. To do so you need to use either Command Prompt or Windows PowerShell with POWER USER RIGHTS. Perform the following steps:

Search for the Command Prompt application by typing cmd in the search field (displayed as a magnifying glass) of the Windows task bar.
The left part of the search results will show the Command Prompt App as best match and it will be highlighted in blue. Click on Open file location (third from the top) in the right part displaying the options for the Command Prompt App.
A File Explorer window will open with the shortcut to Command Prompt highlighted in blue. Right-click the Command Prompt shortcut and select ‘WUR - Run with adminstrative rights’ as shown in Figure 1 below.

Run CMD with ‘WUR administrative rights’ from File Explorer.

The Command Prompt application will open, as shown in Figure 2 below, on the folder C:\Windows. The top of the window shows that the Command Prompt application is used in Administrator mode (WARNING: BE CAREFULL!!).

Command Prompt with Adminstrative Rights.

Change the working directory to C:\ProgramData. This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute.

cd C:\ProgramData

Remove the directory C:\ProgramData\R\win-library\3.6 with all its content (subdirectories and files). This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute.

rmdir /S C:\ProgramData\R\win-library\3.6

The question C:\ProgramData\R\win-library\3.6, Are you sure (Y/N)? will appear. Confirm the removal of the directory with all its content by answering Y.
The Command Prompt application can now be closed by typing exit and executing it by pressing return (Enter).

If you have not installed another version of R, either via Software Center or via a custom installation, your computer should now be lacking a functioning R installation. Continue with the section Custom R installation to perform a new custom installation of R.

When you do still have a working R installation on your WURclient computer, return to Uninstall a previously installed R version and follow the procedure applicable to your situation.

Installed previously as a custom installation

Let’s assume you previously installed R version 3.6.3 on a WURclient computer (either a desktop or laptop) by following the steps for a custom installation of R as described in this post. For a newer version of R the steps are the same, but names of folders will differ with respect to the R version number.

To uninstall R and delete the manually installed packages (added yourself via the install.packages() command in R) perform the following steps:

Open a File Explorer and navigate to the folder C:\MyPrograms\R\R-3.6.3. Right-click the file unins000.exe and select ‘WUR - Run with administrative rights’ as displayed in Figure 3 below.

Uninstall Custom R Installation from File Explorer.

The uninstaller will start as shown below in Figure 4. Click the ‘Yes’ to proceed.

R for Windows Uninstall Announcement.

Once the uninstallation has completed, a message of success will be display as shown below in Figure 5. Click the ‘OK’ button to finish.

R for Windows Uninstalled Successfully.

Search for the Command Prompt application by typing cmd in the search field (displayed as a magnifying glass) of the Windows task bar.
The left part of the search results will show the Command Prompt App as best match and it will be highlighted in blue. Click on Open file location (third from the top) in the right part displaying the options for the Command Prompt App.
A File Explorer window will open with the shortcut to Command Prompt highlighted in blue. Right-click the Command Prompt shortcut and select ‘WUR - Run with adminstrative rights’ as shown in Figure 6 below.

Run CMD with ‘WUR administrative rights’ from File Explorer.

The Command Prompt application will open, as shown in Figure 7 below, on the folder C:\Windows. The top of the window shows that the Command Prompt application is used in Administrator mode (WARNING: BE CAREFULL!!).

Command Prompt with Adminstrative Rights.

Change the working directory to C:\MyPrograms. This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute.

cd C:\MyPrograms

Remove the directory C:\MyPrograms\R\R-3.6.3 with all its content (subdirectories and files). This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute.

rmdir /S R\R-3.6.3

The question R\R-3.6.3, Are you sure (Y/N)? will appear. Confirm the removal of the directory with all its content by answering Y.
To delete the manually installed packages (added yourself via the install.packages() command in R) change the working directory to C:\ProgramData. This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute.

cd C:\ProgramData

Remove the directory C:\ProgramData\R\win-library\3.6 with all its content (subdirectories and files). This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute.

rmdir /S C:\ProgramData\R\win-library\3.6

The question C:\ProgramData\R\win-library\3.6, Are you sure (Y/N)? will appear. Confirm the removal of the directory with all its content by answering Y.
The Command Prompt application can now be closed by typing exit and executing it by pressing return (Enter).

When you do still have a working R installation on your WURclient computer, return to Uninstall a previously installed R version and follow the procedure applicable to your situation.

Custom R installation

To prepare the custom R installation a couple of folders need to be created prior to the installation of R. Perform the following steps exactly as described:

Search for the Command Prompt App by typing cmd in the search field of the Windows task bar.
The left part of the search results will show the Command Prompt App as best match and it will be highlighted in blue. Click on Open file location (third from the top) in the right part displaying the options for the Command Prompt App.
A File Explorer window will open with the shortcut to Command Prompt highlighted in blue. Right click the Command Prompt shortcut and select ‘WUR - Run with adminstrative rights’ as shown in Figure 8 below.

Run CMD with ‘WUR administrative rights’ from File Explorer.

The Command Prompt application will open, as shown in Figure 9, on the folder C:\Windows. The top of the window shows that the Command Prompt application is used in Administrator mode (WARNING: BE CAREFULL!!).

Command Prompt with Adminstrative Rights.

Create the directory C:\MyPrograms. This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute. In case the directory already exists, the message A subdirectory or file C:\MyPrograms already exists. will appear.

mkdir C:\MyPrograms

Next create the directory C:\MyData. This is done by copying (CTRL+C) the following line, pasting (CTRL+V) it behind the prompt and pressing return (Enter) to execute. In case the directory already exists, the message A subdirectory or file C:\MyData already exists. will appear.

mkdir C:\MyData

Finally create the directory C:\ProgramData\R\win-library\4.5, where user installed packages, via the install.packages() command in R, will be stored. The last part of the directory path reflects the major release version of R you are installing and should be adapted for other versions, e.g. for R version 4.6.0 the directory created should end with 4.6. To create the aforementioned directory copy (CTRL+C) the following line, paste (CTRL+V) it behind the prompt and execute by pressing return (Enter). In case the directory already exists, the message A subdirectory or file C:\ProgramData\R\win-library\4.5 already exists. will appear.

mkdir C:\ProgramData\R\win-library\4.5

The Command Prompt application can now be closed by typing exit and executing it by pressing return (Enter).

Download

At the time this post was written, the release of R was version 4.0.3. It has been updated to the latest release version 4.5.3 of R.

The installer for Windows 10/11 can be downloaded directly from this link: R 4.5.3 for Windows (ca. 87 MB, 64-bit).

From R version 4.2.0 the installer is only available for 64-bit Windows 10/11 and will not install on a 32-bit version of the Operating System.

Renviron.site (only for the Classic WURclient with Software Center)
Renviron.site (only for the Modern WURclient with WURAppStore)
Rprofile.site

Installation

The screenshots used below are for R Version 4.0.3. For newer versions of R than 4.0.3 the steps described below are the same and still correct, but start with a newer version of the downloaded executable file of R. The screenshots in this post have not been updated. Therefore, what you see during your installation will differ with respect to the version number shown in the screenshots.

Right-click the downloaded file R-4.5.3-win.exe and select ‘WUR - Run with administrative rights’. This file will most likely reside in your Downloads folder of your user account.
If asked for allow to install the software on your computer.
After the installer has started, a first selection window will appear as displayed below in Figure 10. Select the English language and click the ‘OK’ button to proceed.

R Installation Language Selection.

Click on the ‘Next’ button to agree to the terms. After this a window will appear, allowing you to select or choose the destination folder, as shown below, where R version 4.5.2 for Windows should be installed. Change the destination location to C:\MyPrograms\R\R-4.5.3, as shown in Figure 11 below for version 4.0.3, by typing the destination path directly into the text field displayed (currently showing C:\Program Files\R\R-4.5.3) . Click on the ‘Next’ button to continue.

R Installation Destination Folder Selection.

After selecting the installation destination folder the component selector will appear, as displayed below in Figure 12. Most desktop and laptop computers these days are using a 64-bit architecture, therefore select (using the pull down menu) the 64-bit User installation as displayed in the image shown below and click on the ‘Next’ button.

R Installation Components Selection.

After selecting the components to install the startup options need to be set. Select, as shown in Figure 13 below, the customized startup by selecting the ‘Yes (customized startup)’ radio button followed by clicking on the ‘Next’ button.

R Installation Customize Startup.

The first startup option to set is the Display Mode, as shown in Figure 14. Select the Single Document Interface by selecting the ‘SDI (separate windows)’ radio button as displayed and clicking on the ‘Next’ button.

R Installation Display Mode Selection.

Next select the help style startup option. Leave this at the default ‘HTML help’ value, as displayed below in Figure 15, and click on the ‘Next’ button.

R Installation Help Style Selection.

The one before last startup option is to set a ‘Start Menu’ folder name (Figure 16). Unless wishing to use a different name, leave the default value as displayed below. This will create a folder named ‘R’ in the ‘Start Menu’ of Windows, from which the R GUI (graphical user interface) can be started.

R Installation Start Menu Folder Selection.

The last startup option to set allows for some customization of shortcut links. Preferably leave the default settings and continue by clicking on the ‘Next’ button. This will trigger the installation. At the end Figure 17, shown below, will appear (although the version number will be different!). To exit the setup click on the ‘Finish’ button.

Do not mess around with the ‘Registry entries’ settings.

R Installation Completed Successfully.

To finalize the custom R installation on your WURclient desk- or laptop copy the files Renviron.site and Rprofile.site from the Downloads folder on your computer and paste them into the folder named C:\MyPrograms\R\R-4.5.3\etc. A window will appear, as displayed below in Figure 18, to indicate, that the file Rprofile.site already exists. Select ‘Replace the file in the destination’.

Replace Rprofile.site File.

Congratulations, 😆, you now have R version 4.5.3 installed on your WURclient desktop or laptop computer!

Changing the R GUI working directory

When starting the default R GUI the current working directory can be displayed at the R prompt with the command:

getwd()

The response at the R prompt will be:

[1] "\\\\WURNET.NL/Homes/user001/My Documents"

where user001 will display your own WUR username.

This could potentially lead to NormalizePath() warning messages. Therefore, it is strongly recommended to set the working directory to a mapped drive (shown by a drive letter, e.g., C:, or M:) in your WURclient. This can be done at the R prompt using the following command, e.g., for setting your working directory to C:\MyData or M:\My Documents:

setwd("C:/MyData")
# or
setwd("M:/My Documents")

No matter which mapped drive and folder you choose, make sure that the location and folder you are providing for the working directory exists!

When using the default R GUI, always change the working directory at the start with the setwd() function at the R prompt!

In earlier versions of this post, the R startup working directory was changed inside the Rprofile.site file. This lead to problems when using the knitr package to compile to portable document format.

Based on posts by Yihui Xie (the developer of the knitr package) the setwd() command in Rprofile.site has been completely deleted, making knitting to pdf possible again.

WURclient | Maikel P.H. Verouden, Ph.D.

RStan installation on a Windows 10/11 or a WURclient computer

Motivation

Requirements for RStan installation

Installation

Verifying the RStan installation

Failed with error: ’there is no package called ‘rstudioapi’'

Loading the package

Installing the brms package

Custom Anaconda installation on a WURclient computer

Motivation

Prerequisite

Uninstall a previously installed Anaconda Python version

Installed from Software Center

Installed previously as a custom installation

Custom Anaconda installation

Download

Installation

Configuration Anaconda3

Changing the Default Startup Working Directory

Upgrading Anaconda Navigator (Anaconda3)

Add a R kernel

Add a Julia kernel

Mathworks Matlab installation on a WURclient computer

Motivation

Prerequisite

Installation

Activation

Transition a previous installation to named user licensing

Rtools installation on a Windows 10/11 or a WURclient computer

Motivation

Requirement for and Download of Rtools

Requirement

Download

Installation Rtools

Check the Installation

Custom RStudio installation on a WURclient computer

Motivation

Prerequisites

Uninstall a previously installed RStudio version

Installed from Software Center

Installed previously as a custom installation

Custom RStudio installation

Download

Installation

Setting the default RStudio working directory

Resetting RStudio desktop’s state

Accessing the RStudio-Desktop Directory (Internal State)

Resetting other preferences

R Commander installation in R on a WURclient computer

Motivation

R Commander Installation from the R GUI

Starting and restarting R Commander

Start R Commander

Restart R Commander

Custom R installation on a WURclient computer

Motivation

Prerequisite

Uninstall a previously installed R version

Installed from Software Center

Installed previously as a custom installation

Custom R installation

Download

Installation

Changing the R GUI working directory

Installing the `brms` package