JupyterLab R docker stack

Multi-arch (linux/amd64, linux/arm64/v8) docker images:

• glcr.b-data.ch/jupyterlab/r/base
  • glcr.b-data.ch/jupyterlab/r/r-ver (4.2.0 ≥ version > 4.0.4)
• glcr.b-data.ch/jupyterlab/r/tidyverse
• glcr.b-data.ch/jupyterlab/r/verse
• glcr.b-data.ch/jupyterlab/r/geospatial
• glcr.b-data.ch/jupyterlab/r/qgisprocess (versions ≥ 4.3.0)

Images considered stable for R versions ≥ 4.2.0.
👉 The current state may eventually be backported to versions ≥ 4.0.4.

🔬 Check out jupyterlab/r/verse at https://demo.jupyter.b-data.ch.

Build chain

base → tidyverse → verse → geospatial → qgisprocess
ℹ️ The term verse+ means verse or later in the build chain.

Features

• JupyterLab: A web-based interactive development environment for Jupyter notebooks, code, and data. The images include
  • code-server: Code - OSS in the browser.
  • Git: A distributed version-control system for tracking changes in source code.
  • Git LFS: A Git extension for versioning large files.
  • GRASS GIS: A free and open source Geographic Information System (GIS).
    ℹ️ qgisprocess image
  • Neovim: Vim-fork focused on extensibility and usability. (4.4.1+)
  • Orfeo Toolbox: An open-source project for state-of-the-art remote sensing.
    ℹ️ qgisprocess image (amd64 only)
  • Pandoc: A universal markup converter.
  • Python: An interpreted, object-oriented, high-level programming language with dynamic semantics.
  • QGIS: A free, open source, cross platform (lin/win/mac) geographical information system (GIS).
    ℹ️ qgisprocess image
  • Quarto: A scientific and technical publishing system built on Pandoc.
    ℹ️ verse+ images
  • R: A language and environment for statistical computing and graphics.
  • radian: An alternative console for R with multiline editing and rich syntax highlight.
  • RStudio: An integrated development environment (IDE) for R. (4.4.0+)
  • SAGA GIS: A Geographic Information System (GIS) software with immense capabilities for geodata processing and analysis.
    ℹ️ qgisprocess image
  • TinyTeX: A lightweight, cross-platform, portable, and easy-to-maintain LaTeX distribution based on TeX Live.
    ℹ️ verse+ images
  • Zsh: A shell designed for interactive use, although it is also a powerful scripting language.

👉 See the Version Matrix for detailed information.

The following extensions are pre-installed for code-server:

• .gitignore Generator
• Black Formatter
  ℹ️ devtools subtags
• Docker
  ℹ️ docker subtags
• EditorConfig (4.3.0+)
• ESLint
  ℹ️ devtools subtags
• Git Graph
• GitHub Pull Requests and Issues (4.3.1+)
• GitLab Workflow
• GitLens — Git supercharged
  ℹ️ Pinned to version 11.7.0 due to unsolicited AI content (4.3.1+)
• hadolint
  ℹ️ docker subtags (4.3.1+)
• Excel Viewer
• Jupyter
• LaTeX Workshop
  ℹ️ verse+ images
• markdownlint (4.3.2+)
• Path Intellisense
• Prettier - Code formatter
  ℹ️ devtools subtags
• Project Manager
• Python
• Quarto
  ℹ️ verse+ images
• R
• Resource Monitor (4.3.0+)
• ShellCheck
  ℹ️ devtools and docker subtags (4.3.1+)
• YAML

Subtags

• {R_VERSION,latest}-root (versions ≥ 4.2.0): Container runs as root
• {R_VERSION,latest}-devtools (versions ≥ 4.2.2): Includes the requirements according to
  • coder/code-server > Docs > Contributing
  • REditorSupport/vscode-R > Wiki > Contributing
• {R_VERSION,latest}-devtools-root: The combination of both
• {R_VERSION,latest}-docker (versions ≥ 4.2.2): Includes
  • docker-ce-cli
  • docker-buildx-plugin
  • docker-compose-plugin
  • docker-scan-plugin (amd64 only)
• {R_VERSION,latest}-docker-root: The combination of both
• {R_VERSION,latest}-devtools-docker: The combination of both
• {R_VERSION,latest}-devtools-docker-root: The combination of all three

Table of Contents

• Prerequisites
• Install
• Usage
• Misc
• Similar projects
• Contributing
• Support
• Sponsors
• License
• Trademarks

Prerequisites

This projects requires an installation of docker.

Install

To install docker, follow the instructions for your platform:

• Install Docker Engine | Docker Documentation > Supported platforms
• Post-installation steps for Linux

Usage

Build image (base)

latest:

cd base && docker build \
  --build-arg R_VERSION=4.4.2 \
  -t jupyterlab/r/base \
  -f latest.Dockerfile .

version:

cd base && docker build \
  -t jupyterlab/r/base:MAJOR.MINOR.PATCH \
  -f MAJOR.MINOR.PATCH.Dockerfile .

For MAJOR.MINOR.PATCH ≥ 4.2.0.

Create home directory

Create an empty directory using docker:

docker run --rm \
  -v "${PWD}/jupyterlab-jovyan":/dummy \
  alpine chown 1000:100 /dummy

It will be bind mounted as the JupyterLab user's home directory and automatically populated.
❗ Bind mounting a subfolder of the home directory is only possible for images with R version ≥ 4.3.2.

Run container

self built:

docker run -it --rm \
  -p 8888:8888 \
  -u root \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  -e NB_UID=$(id -u) \
  -e NB_GID=$(id -g) \
  -e CHOWN_HOME=yes \
  -e CHOWN_HOME_OPTS='-R' \
  jupyterlab/r/base[:MAJOR.MINOR.PATCH]

from the project's GitLab Container Registries:

docker run -it --rm \
  -p 8888:8888 \
  -u root \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  -e NB_UID=$(id -u) \
  -e NB_GID=$(id -g) \
  -e CHOWN_HOME=yes \
  -e CHOWN_HOME_OPTS='-R' \
  IMAGE[:MAJOR[.MINOR[.PATCH]]]

IMAGE being one of

• glcr.b-data.ch/jupyterlab/r/base
• glcr.b-data.ch/jupyterlab/r/tidyverse
• glcr.b-data.ch/jupyterlab/r/verse
• glcr.b-data.ch/jupyterlab/r/geospatial
• glcr.b-data.ch/jupyterlab/r/qgisprocess

The use of the -v flag in the command mounts the empty directory on the host (${PWD}/jupyterlab-jovyan in the command) as /home/jovyan in the container.

-e NB_UID=$(id -u) -e NB_GID=$(id -g) instructs the startup script to switch the user ID and the primary group ID of ${NB_USER} to the user and group ID of the one executing the command.

-e CHOWN_HOME=yes -e CHOWN_HOME_OPTS='-R' instructs the startup script to recursively change the ${NB_USER} home directory owner and group to the current value of ${NB_UID} and ${NB_GID}.
ℹ️ This is only required for the first run.

The server logs appear in the terminal.

Using Podman (rootless mode, 4.3.2+)

Create an empty home directory:

mkdir "${PWD}/jupyterlab-root"

Use the following command to run the container as root:

podman run -it --rm \
  -p 8888:8888 \
  -u root \
  -v "${PWD}/jupyterlab-root":/home/root \
  -e NB_USER=root \
  -e NB_UID=0 \
  -e NB_GID=0 \
  -e NOTEBOOK_ARGS="--allow-root" \
  IMAGE[:MAJOR[.MINOR[.PATCH]]]

Using Docker Desktop

Creating a home directory might not be required. Also

docker run -it --rm \
  -p 8888:8888 \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  IMAGE[:MAJOR[.MINOR[.PATCH]]]

might be sufficient.

Credential storage

❗ Keyring services are not available due to the difficulties of setting them up in containers.
Therefore, provide login credentials for the following extensions as environment variables (-e):

Misc

marimo

To add a JupyterLab Launcher icon for marimo:

1. Terminal: Install marimo and click

   pip install marimo click

2. Terminal: Install jupyter-marimo-proxy

   pip install git+https://github.com/b-data/jupyter-marimo-proxy.git@jupyterlab-docker-stack

3. Restart the container

Similar projects

• jupyter/docker-stacks
• rocker-org/rocker-versioned2
• pangeo-data/pangeo-docker-images
• geocompx/docker

What makes this project different:

1. Multi-arch: linux/amd64, linux/arm64/v8
   👉 Since R 4.0.4 (2021-02-15)
   ℹ️ Runs on Apple M series using Docker Desktop.
2. Base image: Debian instead of Ubuntu
   ℹ️ CUDA-based images use Ubuntu.
3. IDE: code-server next to RStudio
   ℹ️ code-server = Code - OSS in the browser.
4. Just Python – no Conda / Mamba

See Notes for tweaks, settings, etc.

Contributing

PRs accepted. Please submit to the GitLab repository.

This project follows the Contributor Covenant Code of Conduct.

Support

Community support: Open a new discussion here. Commercial support: Contact b-data by email.

b-data tailors the JupyterLab images to your needs, e.g.

• Integration of self-signed CA certificates to enable communication with web services on the intranet.
• Setting up the necessary environment variables so that everything works behind a corporate proxy server.

Additionally, the JupyterHub setup can be customised to allow

• authentication with AD/LDAP
• mounting CIFS/SMB file shares

and much more.

Sponsors

Work partially funded by

License

Copyright © 2020 b-data GmbH

Distributed under the terms of the MIT License, with exceptions.

Trademarks

RStudio® is a trademark of Posit Software, PBC, all rights reserved, and may be registered in the United States Patent and Trademark Office and in other countries.

The use of the trademarked term RStudio® and the distribution of the RStudio binaries through the images hosted on b-data's GitLab Container Registry (glcr.b-data.ch) has been granted by explicit permission of Posit Software, PBC. Please review Posit’s Trademark Guidelines and address inquiries about further distribution to permissions@posit.co.