Ubuntu/Debian

Installation

Software	Description	Website
R	The R environment	link
RStudio Desktop	Integrated development environment (IDE) for R	link
Pandoc	Document converter used by rmarkdown	link
Quarto CLI	Scientific publishing system built on Pandoc	link
Git	Version control software	link
Docker	Containerization software	link

We are going to install the required software by using APT, a package manager for Debian derived Linux distributions. A package manager is a way to get software (and software updates) onto your machine without much work on your part.

First check your version of Ubuntu in a terminal:

## Check Ubuntu version ----
cat /etc/issue
# Ubuntu 22.04 LTS

Table 1. List of CRAN repositories for different versions of Ubuntu

Release	Release name	Repository URL
22.04 LTS	Jammy Jellyfish	https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/
20.04 LTS	Focal Fossa	https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/
18.04 LTS	Bionic Beaver	https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/

Let’s install by following these steps (change the URL below by the one specific to your version of Ubuntu, cf. Table 1) :

## Install APT utilities ----
sudo apt install build-essential software-properties-common wget

## Add CRAN GPG key ----
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

## Add CRAN repository to APT repositories list ----
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/'

## Update packages list ----
sudo apt update

## Install R ----
sudo apt install r-base r-base-dev

To install RStudio Desktop, follow these steps (uncomment the appropriate line matching your Ubuntu version):

## Download RStudio Desktop installer (Ubuntu = 22.04) ----
# wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-2023.09.1-494-amd64.deb

## Download RStudio Desktop installer (Ubuntu = 20.04) ----
# wget https://download1.rstudio.org/electron/focal/amd64/rstudio-2023.09.1-494-amd64.deb

## Install RStudio Desktop ----
sudo dpkg -i rstudio-2023.09.1-494-amd64.deb

## Remove installer ----
rm rstudio-2023.09.1-494-amd64.deb

Now let’s install git:

## Install git -----
sudo apt install git

And Pandoc (to convert documents with rmarkdown):

## Install pandoc -----
sudo apt install pandoc

Let’s install the Quarto software, a multi-language, next-generation version of R Markdown developed by Posit (formerly RStudio Inc.), that includes dozens of new features and capabilities.

## Download Quarto installer ----
wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.3.450/quarto-1.3.450-linux-amd64.deb

## Install Quarto ----
sudo dpkg -i quarto-1.3.450-linux-amd64.deb

## Remove installer ----
rm quarto-1.3.450-linux-amd64.deb

Finally, let’s install Docker Desktop:

## Add Docker's official GPG key ----
sudo apt install ca-certificates curl gnupg
sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
sudo chmod a+r /etc/apt/keyrings/docker.gpg

## Add the repository to Apt sources ----
echo \
  "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
  "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | \
  sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
  
sudo apt update

## Install Docker ----
sudo apt install docker-ce

## Allow user to use Docker without sudo ----
sudo usermod -aG docker ${USER}

In addition, we need to install the package quarto:

## Install quarto package ----
install.packages("quarto")

Finally, let’s install a LaTeX distribution to convert documents from .Rmd (or .qmd) to .pdf. We are going to install a lightened distribution w/ the package tinytex.

## Install tinytex package ----
install.packages("tinytex")

## Install LaTeX distribution ----
tinytex::install_tinytex()

Important

If you already have a LaTeX distribution, do not use tinytex.

Check

  Restart your machine.

Open RStudio and run:

## Get R version ----
R.version.string
# "R version 4.3.2 (2023-10-31)"

## Check if git is installed ----
Sys.which("git")
#            git
# "/usr/bin/git"

## Check if make is installed ----
Sys.which("make")
#            make 
# "/usr/bin/make"

## Check if Pandoc is installed ----
Sys.which("pandoc")
#            pandoc 
# "/usr/bin/pandoc"

## Check if Quarto is installed ----
Sys.which("Quarto")
#            Quarto 
# "/usr/bin/Quarto"

## Check if LaTeX is installed ----
Sys.which("pdflatex")
#            pdflatex 
# "/usr/bin/pdflatex" 

## Check if Docker is installed ----
Sys.which("docker")
#            docker 
# "/usr/bin/docker" 

## Install package from sources ----
install.packages("jsonlite", type = "source")

Update your system regularly

Keep your Linux packages up-to-date by running:

## Check for updates ----
sudo apt update

## Update Linux Apps ----
sudo apt upgrade

Configuration

You’ve just installed a working environment for data science w/ , , and .
Now follow instruction to configure your system.