Installation & Setup

To prepare yourself for the workshop, please follow both step A and B listed below.

The installation procedure under A. will differ depending on how you choose to work with the Quarto publishing system. Below we go into the following 3 situations:

1. Using Quarto with Python in Jupyter Lab
2. Using Quarto with Python or R in Visual Studio Code
3. Using Quarto with R in RStudio

Besides R and Python, Quarto can also work with other programming languages, such as Julia or Observable, and it can interact with other software as well, like Neovim and simple Text editors.

A. Install Quarto and your programming language

1. Quarto in Jupyter Lab (Python)

1. Install Python and Jupyter Lab

If you don’t have Python and Jupyter Lab installed yet, follow only step 1 “Install Python” on this page. Here you will install Anaconda Navigator, which installs both Python and Jupyter Lab.

2. Install Quarto

1. Download Quarto from https://quarto.org/docs/get-started/
2. Open the msi/executable file. Answer “Yes” to the pop-up question “Do you want to allow this app to make changes to your device?”. Then start the set-up wizard.
3. Choose Install for all users. If you do not have administrator rights, select Install just for you.
4. Choose the installation location, usually the default proposed location is fine.
5. Installation will start. After installation, click Finish.

3. Enable the Quarto extension in Jupyter Lab (optional)

Although it is not strictly necessary, the Quarto extension in Jupyter Lab gives you nice Quarto previews of your Jupyter notebook files. To enable it, follow the steps listed under “Installing the extension” on this page of the Quarto documentation.

2. Quarto in VS Code (R or Python)

1. Install Visual Studio Code

Install Visual Studio Code (VS Code) using the set-up instructions for your operating system.

1. Download VS Code from https://code.visualstudio.com/
2. Walk through the installation steps. The default installation location is usually fine. If you have administrator rights, we recommend to Add VS Code to the PATH if you’re using Windows.

2. Set up Python and/or R for use in VS Code

1. R: Follow the instructions here for installing R and using it in VS Code.
   1. In VS Code, you can open an R terminal to install the languageserver package.
2. Python: Follow the instructions here for installing a Python interpreter, or see the installation instructions in our Introduction to Python workshop.
   1. Be sure to also install the Jupyter extension in VS Code if you wish to work with Jupyter notebooks (.ipynb).

3. Install Quarto

1. Download Quarto from https://quarto.org/docs/get-started/
2. Open the msi/executable file. Answer “Yes” to the pop-up question “Do you want to allow this app to make changes to your device?”. Then start the set-up wizard.
3. Choose Install for all users. If you do not have administrator rights, select Install just for you.
4. Choose the installation location, usually the default proposed location is fine.
5. Installation will start. After installation, click Finish.

4. Make VS Code, Quarto and R/Python talk to each other

Now that everything is installed, we need to make sure VS Code can use Quarto and Python/R.

1. Open VS Code.
2. Open the Extensions view in VS Code (Ctrl+Shift+X on Windows and Linux, Cmd+Shift+X on macOS)
3. Install the Quarto extension from the Extensions view in VS Code.
4. If you want to use Python in VS Code:
   1. From the Extensions view in VS Code, install the Python extension.
   2. Set the Python interpreter: Open the command palette in VS Code (Ctrl+Shift+P on Windows and Linux, Cmd+Shift+P on macOS), type “Python: Select Interpreter”, and select the relevant Python interpreter from the interpreters that VS Code can find.
5. If you want to use R in VS Code: install the R extension from the extensions view in VS Code.
6. Check whether Quarto is detected:
   1. Open a new terminal: Terminal > New terminal.
   2. Type quarto --version
   3. If a version number appears, Quarto is detected.
7. Check whether Python is detected:
   1. Open a new terminal or use the one that you used in step 6a.
   2. Type python --version
   3. If a version number appears, Python is detected.
8. Check whether R is detected: if you can open an R terminal, it shows you the R version and R is detected successfully.

3. Quarto in Rstudio (R)

1. Install R and Rstudio

If you do not yet have an installation for R and Rstudio, you need to install them on your device.

1. If you have a personal device with administrator/installation rights:
   1. Install R from https://cran.rstudio.com/
   2. Install Rstudio from https://posit.co/download/rstudio-desktop/#download
2. If you have a Utrecht University managed device:
   1. Install the R for Windows suite from the Software Center. It should contain both R and Rstudio.
   2. Check the installation. R packages on a UU laptop are usually installed on a so-called ‘mounted’ drive. This causes problems with the performance. Check the installation as follows:
      • Open RStudio.
      • Write the following line of code in your console: .libPaths(), and press enter to execute.
      • If the response starts with // or \\, you are installing on a mounted drive. Follow the steps below to change the installation location.
3. If you already have an existing R and RStudio installation:
   1. Check which version of RStudio you have installed: Go to Help > About RStudio.
   2. If your RStudio version is older than v2022.07, then you should update it. Quarto recommends using the latest version of RStudio (currently v.2023.06).

2. Install Quarto and R Markdown

1. In the RStudio console, type install.packages("rmarkdown") and install.packages("quarto")
2. Load both packages with library(rmarkdown) and library(quarto)
3. Restart RStudio.
4. Check whether Quarto is detected: go to the Terminal (next to the Console) and type quarto --version. Alternatively, go to File > New project > New directory and check whether the Quarto outputs are presented as options (Quarto project, Quarto website, Quarto blog, Quarto book)

Troubleshooting

Packages are being installed on a mounted drive

This can cause various errors, and even if everything goes right, installing new packages takes ages.

Solution 1: There is a solution to prevent problems with mounted drives for applications like R, RStudio and Office. Read more about the solution on intranet.

Solution 2:

• Create a folder R-packages on a local drive.
• Copy the location to that drive. For example: C:/Users/User/R-packages.
• Run the following line of code: file.edit(file.path("~", ".Rprofile"))
• Paste .libPaths("C:/Users/User/R-packages") in the editor and save the file.
• Restart your R session
• Click on Packages>Install. Is Install to library pointing to C:/Users/User/R-packages?
• If not: check if the path is correctly spelled. Try inverting the slashes (\ instead of /). You may need to use double slashes (\\ or //).
• Tick ‘source on save’, click save, and check Packages>Install again.

“Unable to move temporary installation” (Windows error)

Do you get issues like this:

> install.packages("tibble")
Installing package into ‘C:/Users/UserName/R’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/tibble_1.4.2.zip'
Content type 'application/zip' length 172649 bytes (168 KB)
downloaded 168 KB

package ‘tibble’ successfully unpacked and MD5 sums checked
Warning in install.packages :
  unable to move temporary installation ‘C:\Users\UserName\R\file18b813387562\tibble’ to ‘C:\Users\UserName\R\tibble’
The downloaded binary packages are in
C:\Users\UserName\AppData\Local\Temp\RtmpYh5ogU\downloaded_packages

Check for the line unable to move temporary installation. Your virus scanner might be blocking the installation of tidyverse.

The solution (found here) is to enter:

trace(utils:::unpackPkgZip, edit=TRUE)

You should see:

Tracing function "unpackPkgZip" in package "utils (not-exported)"
[1] "unpackPkgZip"

And a file should open. Change 0.5 in line 142 to 2.5, save the file, and try installing the package again.

B. Zotero for reproducible citations

1. Install Zotero.
   1. If you work on a Utrecht University-managed laptop, you can install Zotero from the Software Center.
   2. If you work on a private device, follow the installation instructions on the Zotero installation page.
2. Install the Zotero connector for your browser. This connector makes sure you can directly save a reference to Zotero from your browser.
3. Install the Better BibTex extension for Zotero. This makes sure your references are saved in a format that Quarto can work with.

Frank, Mike, and Chris Hartgerink. 2017. “RMarkdown for Writing Reproducible Scientific Papers.” https://libscie.github.io/rmarkdown-workshop/handout.html.

Hartgerink, Chris. 2017. “Composing Reproducible Manuscripts Using R Markdown.” eLife. https://elifesciences.org/labs/cad57bcf/composing-reproducible-manuscripts-using-r-markdown; eLife Sciences Publications Limited.

Knuth, D. E. 1984. “Literate Programming.” The Computer Journal 27 (2): 97–111. https://doi.org/10.1093/comjnl/27.2.97.

Lasser, Jana. 2020. “Creating an Executable Paper Is a Journey Through Open Science.” Communications Physics 3 (1): 1–5. https://doi.org/10.1038/s42005-020-00403-4.

Mock, Tom. 2022a. “Get Started with Quarto - Getting Started with Quarto.” https://jthomasmock.github.io/quarto-2hr-webinar/.

———. 2022b. “Get Started with Quarto - Rstudio::conf 2022 Workshop.” https://rstudio-conf-2022.github.io/get-started-quarto/.

Quarto. n.d. “Quarto - Guide.” Quarto. https://quarto.org/docs/guide/. Accessed November 21, 2023.

The Turing Way Community. n.d. “Research Compendia.” The Turing Way. https://the-turing-way.netlify.app/reproducible-research/compendia. Accessed November 21, 2023.

Van Lissa, Caspar J., Andreas M. Brandmaier, Loek Brinkman, Anna-Lena Lamprecht, Aaron Peikert, Marijn E. Struiksma, and Barbara M. I. Vreede. 2021. “WORCS: A Workflow for Open Reproducible Code in Science.” Data Science 4 (1): 29–49. https://doi.org/10.3233/DS-210031.