Windows 11 | 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")

Anaconda installation on Windows 10/11

Sun, 06 Nov 2022 00:00:00 +0000

Table of Contents

Motivation

Whether working, or studying, everybody uses various sorts and types of software on their computer. Around 34 courses at Wageningen University & Research use Anaconda Python as software in their course, e.g., SSB30806 Modelling in Systems Biology, and SSB32806 Introduction to Systems and Synthetic Biology.

This post will show how to install Anaconda Python (Anaconda3) on a privately owned desktop or laptop computer running Windows 10 or Windows 11 as operating system.

The installation instructions in this post are not to be used on WURclient desktops or laptops! For a WURclient desktop or laptop see the post: Custom Anaconda installation on a WURclient compute.

Two ways to install Anaconda are offered here:

WUR AppStore. This is the RECOMMENDED way!
Manual installation for those who, for whatever reason, do not want to use the WUR AppStore.

1. WUR AppStore

The WUR AppStore is the place where you will be able to download, link to, or virtually access the software you need for your study programme and courses. Not only during the computer labs and courses, but also for self-study after those.

For more information see: What is the WUR AppStore

Windows 10/11 compatibility and WUR AppStore installation

To safely use the study and course software, you need to connect your laptop to the WUR network with your WUR account. Windows 10 or 11 Education Edition or Professional Edition is needed on your laptop to be able to access the WUR AppStore. If you are using a Home Edition of Windows 10 or 11, you will be automatically upgraded to the Education Edition.
If you have Windows 10 or 11, you can proceed to the manual: How to connect to the WUR AppStore.

Using the WUR AppStore

The use of the WUR AppStore is very well described by the WUR TEAM Study Anytime, Anyplace. The first article can be found here: How can I use the WUR AppStore

The WUR AppStore currently contains Anaconda3 2025.06-0.

Support WUR AppStore

In case you need support installing or using the WUR AppStore you can contact the WUR Servicedesk IT either by telephone: +31 (0)317 488888 / mail: Servicedesk.IT AT wur.nl. You can also visit the Servicepoint IT, ground floor left of the Grand Café, in Forum (Building 102) on the WUR Campus.

2. Manual Installation

By default the Anaconda installer wants to install into the C:\ProgramData folder of your Windows Operating System. According to Microsoft this folder is “used by applications to store data for standard users, because it does not require elevated permissions”. However, it is not recommended to use for installing software. The reason, the Anaconda installer chooses this folder, is that it does not contain a whitespace character like in C:\Program Files\. The Anaconda software can not deal with whitespace characters in path names, while running.

To prepare the Anaconda installation a folder needs to be created prior to the installation of Anaconda. Either create the folder C:\MyPrograms yourself in File Explorer, or 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. Press return (Enter) to start the application. A window will appear similar to as displayed in Figure 1 showing your own system username.

Windows Command Prompt Application window

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

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 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 ‘Run as administrator’, as shown in Figure 2. This file will most likely reside in your Downloads folder of your user account.

Start Anaconda Installer as administrator

Windows will ask for permission to allow the application to make changes to your device as shown in Figure 3. Click ‘Yes’ to continue.

Permission request for changes.

After the installer has started, a first selection window will appear as displayed below in Figure 4. Click the ‘Next >’ button to proceed.

Welcome to Anaconda3 2022.10 (64-bit) Setup.

The installer will now display the license agreement for installation of Anaconda3, as shown below in Figure 5. 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 6. 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 7. Change the destination location to C:\MyPrograms\Anaconda3, to match Figure 7, 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 8. 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 9 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 10. 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 11. 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 Windows desktop or laptop computer!

Below in Configuration Anaconda3 you find information about additional tasks you may need to perform.

Use the ones required!

Configuration Anaconda3

Upgrading Anaconda Navigator (Anaconda3)

When starting Anaconda Navigator from your Start Menu the Navigator may open displaying the message shown in Figure 12.

Upgrade available for Anaconda Navigator

To upgrade Anaconda Navigator follow these steps:

Click on ‘Yes’ as shown in Figure 12.
Windows will ask for permission to allow the application to make changes to your device as shown in Figure 13. Click ‘Yes’ to continue.

Permission request for changes to update.

Continue the procedure as indicated on your display to perform the update of Anaconda Navigator.

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 the WUR AppStore or via R installation on Windows 10/11. For other R versions than 4.2.1 do not forget to change the R version number!

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()
 # Question in R: 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.

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.

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.

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

RStudio installation on Windows 10/11

Mon, 13 Apr 2020 00:00:00 +0000

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.

Some of these courses (e.g., MAT20306 Advanced Statistics, MAT27803 R for Statistics, and MAT32806 Statistics for Data Scientists) mainly use RStudio. Also other courses (e.g., HNH45306, and BIF21306) taught at Wageningen University & Research use R through RStudio as well. Therefore, students will need to be able to install RStudio.

This post will show how to install RStudio on a privately owned desktop or laptop computer running Windows 10/11 as operating system.

The installation instructions in this post are not to be used on WURclient desktops or laptops! For a WURclient desktop or laptop see the post: Custom RStudio installation on a WURclient computer.

Two ways to install R are offered here:

WUR AppStore. This is the RECOMMENDED way!
Manual installation for those who, for whatever reason, do not want to use the WUR AppStore.

Installation

1. WUR AppStore

The WUR AppStore is the place where you will be able to download, link to, or virtually access the software you need for your study program and courses. Not only during, but also for self-study after, the computer practical’s and courses.

Prior requirement for the installation of RStudio via the WUR AppStore:

R installed on Windows 10/11 via the WUR AppStore

The WUR AppStore currently contains RStudio version 2025.05.1 Build 513 named “RStudio 2025.05.1.513”.

2. Manual Installation

Download

At the time this post was written, the latest stable release of RStudio was version 1.2.5033. The post has been updated to the current stable release version 2026.04.0 Build 526 (named “Globemaster Allium”).

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.

RStudio Installation

Prior requirement for the installation of RStudio:

R installed on Windows 10/11 via Manual Installation

To be able to install RStudio you will need to have R installed first. If you haven’t done so already, please first install R on your Windows 10/11 computer (use the link above to go to that specific post).

To install RStudio on Windows 10/11 perform the following steps:

Open the downloaded file RStudio-2026.04.0-526.exe. This file will most likely reside in the Downloads folder of your user account.
Allow to install the software on your computer.
After the installler has started, a Welcome window will appear as displayed below in Figure 1. 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, as shown in Figure 2 below. Leave the default specified folder or, if you know what you are doing, select an alternative installation destination folder, then 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 3, 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 4. Click the ‘Finish’ button to close the setup.

RStudio Installation Completion.

Congratulations, 😆, you now have RStudio 2026.04.0 Build 526 installed on your private Windows desktop or laptop computer!

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 directoryRStudio, 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 Windows 10/11

Mon, 06 Apr 2020 00:00:00 +0000

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 MAT14303 Basic Statistics, MAT15303 Statistics 1, and MAT15403 Statistics 2 will use R Commander instead of basic R. Therefore, they will need to install R Commander.

This post will show how to install R Commander within R on a privately owned desktop or laptop computer running Windows 10/11 as operating system.

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

R Commander Installation from the R GUI

Students, who installed R by using the WUR AppStore, can skip the installation of R Commander. The WUR AppStore version of R already contains everything to run R Commander.

This post is only intended for students, who followed the Manual Installation of R.

Prior requirement:

R installed on Windows 10/11

To be able to install R Commander you will need to have R installed first. If you haven’t done so already, please first install R on your Windows 10/11 computer (use the link above to go to that specific post).

This post was originally 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 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 package and its dependencies are being installed.

R GUI Select the Rcmdr package to be installed.

Repeat step 4. for installing the RcmdrPlugin.HH package. This plugin is required to be able to do assignments about Simple Linear Regression.

Once the installation of the RcmdrPlugin.HH package has finished, you are ready 😆 to use R Commander and start it from within R version 4.5.3.

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.

R Commander fails to start

Fix error package could not be found

In some cases the R Commander Installation fails to install all required dependencies.

After entering the command library(Rcmdr) an error message appears, e.g.,

> library(Rcmdr)
Loading required package: splines
Error: package ‘RcmdrMisc’ required by ‘Rcmdr’ could not be found

In the example above the package RcmdrMisc is missing, and needs to be installed. To install this particular package enter the following command at the R prompt (indicated by >):

install.packages("RcmdrMisc")

Press the return key (enter) on your keyboard to execute the command.

After installation try to start R Commander again by executing library(Rcmdr). Install all the missing packages using the command install.packages("packageName"), where you replace "packageName" with the one shown in the error message. Most of the times there are 3 - 4 packages (dependencies) missing.

R installation on Windows 10/11

Mon, 06 Apr 2020 00:00:00 +0000

Table of Contents

Motivation

This post will show how to install R on a privately owned desktop or laptop computer running Windows 10 or 11 as operating system.

The installation instructions in this post are not to be used on WURclient desktops or laptops! For a WURclient desktop or laptop see the post: Custom R installation on a WURclient.

Two ways to install R are offered here:

WUR AppStore. This is the RECOMMENDED way, because it includes R and everything to run R Commander!
Manual installation for those who, for whatever reason, do not want to use the WUR AppStore.

1. WUR AppStore

The WUR AppStore is the place where you will be able to download, link to, or virtually access the software you need for your study program and courses. Not only during the computer labs and courses, but also for self-study after those.

For more information see: What is the WUR AppStore

Windows 10/11 compatibility and WUR AppStore installation

To safely use the study and course software, you need to connect your laptop to the WUR network with your WUR account. Windows 10 or 11 Education Edition or Professional Edition is needed on your laptop to be able to access the WUR AppStore. If you are using a Home Edition of Windows 10 or 11, you will be automatically upgraded to the Education Edition.
If you have Windows 10 or 11, you can proceed to the manual: How to connect to the WUR AppStore.

Using the WUR AppStore

The use of the WUR AppStore is very well described by the WUR TEAM Study Anytime, Anyplace. The first article can be found here: How can I use the WUR AppStore

The WUR AppStore currently contains R 4.5.1 Rcmdr. Rcmdr indicates that, apart from running R version 4.5.1 by using the default Graphical User Interface (a.k.a. RGUI), everything is included to run R Commander.

Support WUR AppStore

2. Manual Installation

Download

At the time this post was written, the latest release of R was version 3.6.3. It has been updated to the latest release version 4.5.3 of R, named “Reassured Reassurer”. As of version 4.2.0 the R software is only available as 64-bit, meaning that it will not install on a 32-bit version of Windows 10.

The installer for Windows 10/11 can be downloaded directly from this link: R 4.5.3 for Windows (ca. 86 MB, 64-bit).

For newer versions of R than 3.6.3 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.

Installation

Open the downloaded file R-4.5.3-win.exe. This file will most likely reside in the Downloads folder of your user account.
Allow to install the software on your computer.
After the installer has started, a first selection window will appear as displayed below in Figure 1. Select the English language and click the ‘OK’ button to proceed.

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 in Figure 2, where R version 4.5.3 for Windows should be installed. If you are content with the default C:\Program Files\R\R-4.5.3 click on the ‘Next’ button to continue, otherwise use the ‘Browse…’ button to navigate to an alternative destination or type the destination path directly into the text field displayed (currently showing C:\Program Files\R\R-4.5.3).

Destination Location Selection

After selecting the installation destination folder the component selector will appear, as displayed in Figure 3. 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.

Selection Components to Install

After selecting the components to install the startup options need to be set. Select, as shown in Figure 4 below, the customized startup by selecting the ‘Yes (customized startup)’ radio button followed by clicking on the ‘Next’ button.

Customize Startup Options

The first startup option to set is the Display Mode, as shown below in Figure 5. Select the Single Document Interface by selecting the ‘SDI (separate windows)’ radio button as displayed and clicking on the ‘Next’ button.

Display Mode Selection

Next select the help style startup option. Leave this at the default ‘HTML help’ value, as displayed in Figure 6, and click on the ‘Next’ button.

Help Style Selection

The one before last startup option is to set a ‘Start Menu’ folder name. Unless wishing to use a different name, leave the default value as displayed below in Figure 7. This will create a folder named ‘R’ in the ‘Start Menu’ of Windows, from which the R GUI (graphical user interface) can be started.

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 the image shown in Figure 8 will appear. To exit the setup click on the ‘Finish’ button.

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

Completion of the R installation.

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

Installing R Commander

To install R Commander on your personal Windows 10/11 computer proceed by following the instructions described in R Commander installation in R on Windows 10/11.

Windows 11 | 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

Anaconda installation on Windows 10/11

Motivation

1. WUR AppStore

Windows 10/11 compatibility and WUR AppStore installation

Using the WUR AppStore

Support WUR AppStore

2. Manual Installation

Download

Installation

Configuration Anaconda3

Upgrading Anaconda Navigator (Anaconda3)

Add a R kernel

Add a Julia kernel

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

RStudio installation on Windows 10/11

Motivation

Installation

1. WUR AppStore

2. Manual Installation

Download

RStudio Installation

Resetting RStudio desktop’s state

Accessing the RStudio-Desktop Directory (Internal State)

Resetting other preferences

R Commander installation in R on Windows 10/11

Motivation

R Commander Installation from the R GUI

Starting and restarting R Commander

Start R Commander

Restart R Commander

R Commander fails to start

Fix error package could not be found

R installation on Windows 10/11

Motivation

1. WUR AppStore

Windows 10/11 compatibility and WUR AppStore installation

Using the WUR AppStore

Support WUR AppStore

2. Manual Installation

Download

Installation

Installing R Commander

Installing the `brms` package