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Zero-setup R workshops with GitHub Codespaces

License: MIT License

Jupyter Notebook 76.72% R 21.66% Dockerfile 1.63%

devcontainers-rstudio's Introduction

Zero-setup R workshops with GitHub Codespaces

This is the repository supporting the presentation "Zero-setup R workshops with GitHub Codespaces".

Presenter: David Smith, Cloud Advocate at Microsoft
Presented at: rstudio::conf, July 28 2022
Presentation slides: PDF
Presentation video: YouTube | RStudio

You can recreate the demos in the talk using the steps outlined below.

Dev Containers in GitHub Codepaces

If you have access to GitHub CodeSpaces, click the green "<> Code" button at the top right on this repository page, and then select "Create codespace on main". (GitHub CodeSpaces is available with GitHub Enterprise and GitHub Education.)

Now, browse to the file explore-analyze-data-with-R/solution/challenge-Data_Exploration.ipynb. Work through the Jupyter Notebook.

To open RStudio Server, click the Forwarded Ports "Radio" icon at the bottom of the VS Code Online window.

In the Ports tab, click the Open in Browser "World" icon that appears when you hover in the "Local Address" column for the Rstudio row.

This will launch RStudio Server in a new window. Log in with the username and password rstudio/rstudio.

NOTE: Sometimes, the RStudio window may fail to open with a timeout error. If this happens, try again, or restart the Codepace.

In RStudio, use the File menu to open the /workspaces, folder and then browse to open the file devcontainers-rstudio / explore-analyze-data-with-R / solution / all-systems-check / test.Rmd. Use the "Knit" submenu to "Knit as HTML" and view the rendered "R Notebook" Markdown document.

Note: You may be prompted to install an updated version of the markdown package. Select "Yes".

Resources and Links

GitHub Codespaces - Available with GitHub Enterprise and GitHub Education
Microsoft Workshop Library - The source of the workshop "Explore and analyze data with R" included in this presentation
Rocker - Containers for R
Dev Containers - Overview and specification
Dev Containers in Visual Studio Code - Remote-Containers extension
Visual Studio Code - Free editor available for Windows, Mac and Linux
Related talk: Easy R Tutorials with Dev Containers. This talk provides information on running Dev Containers in a local environment with Visual Studio Code.

Thanks to

えいつぴ (@eitsupi): For helpful info on using RStudio in a Rocker container
Eric Nantz (R-Podcast): For the episode "Fully containerized R dev environment with Docker, RStudio, and VS-Code"

Image Credits

Images used in presentation slides:

Feedback

If you have any comments or suggestions about this presentation, please leave an issue in this repository.

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devcontainers-rstudio's Issues

Add quarto support?

It would be useful to set up Quarto so that it can be used from within VSCode.
https://github.com/quarto-dev/quarto-vscode

Since quarto is not currently installed in rocker/tidyverse (it is bundled with RStudio Server but not added to the path), we will need to change the base image to rocker/verse or run /rocker_scripts/install_quarto.sh must be executed to install quarto cli.

Now rocker/tidyverse:4.2 already has quarto cli installed!

cannot install lumi package

cram/cram_io.c:53:10: fatal error: bzlib.h: No such file or directory
53 | #include <bzlib.h>
| ^~~~~~~~~
compilation terminated.
make[1]: *** [Makefile.Rhtslib:135: cram/cram_io.o] Error 1
make[1]: Leaving directory '/tmp/RtmpUB64Er/R.INSTALL5fa55ea1a1b/Rhtslib/src/htslib-1.15.1'
make: *** [Makevars.common:22: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’

Is there anynoe can help me with it?

RStudio default folder

Configure RStudio to open in /workspaces/devcontainer-rstudio

Connecting the RStudio Server to GitHub?

I noticed that the VS Code is connected to Git/GitHub but the RStudio Server is not. Can that be fixed easily?

R version is not latest

Hi, it doesnt seem as though the expected behavior of the R set up is working as intended, it seems to install R 4.2.1 where the latest now is 4.2.2

Thanks

Error on boot of codespace

Forked repo and tried creating codespace off of main but ran into the following error.

2022-12-15 06:58:08.963Z: #8 10.14 Building dependency tree...
2022-12-15 06:58:09.122Z: 
2022-12-15 06:58:09.122Z: #8 10.26 Reading state information...
2022-12-15 06:58:09.122Z: #8 10.30 E: Unable to locate package liblttng-ust0
2022-12-15 06:58:09.498Z: #8 ERROR: executor failed running [/bin/sh -c apt-get update && export DEBIAN_FRONTEND=noninteractive     && /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true"     && usermod -a -G staff ${USERNAME}     && apt-get -y install         python3-pip         libgit2-dev         libcurl4-openssl-dev         libssl-dev         libxml2-dev         libxt-dev     && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts     && python3 -m pip --no-cache-dir install radian     && pip --disable-pip-version-check --no-cache-dir install pybryt     && pip --disable-pip-version-check --no-cache-dir install pylint     && pip --disable-pip-version-check --no-cache-dir install jupyter     && pip --disable-pip-version-check --no-cache-dir install datascience     && pip --disable-pip-version-check --no-cache-dir install otter-grader     && pip --disable-pip-version-check --no-cache-dir install numpy     && pip --disable-pip-version-check --no-cache-dir install pandas     && pip --disable-pip-version-check --no-cache-dir install scipy     && pip --disable-pip-version-check --no-cache-dir install folium>=0.9.1     && pip --disable-pip-version-check --no-cache-dir install matplotlib     && pip --disable-pip-version-check --no-cache-dir install ipywidgets>=7.0.0     && pip --disable-pip-version-check --no-cache-dir install bqplot     && pip --disable-pip-version-check --no-cache-dir install nbinteract>=0.0.12     && pip --disable-pip-version-check --no-cache-dir install otter-grader     && pip --disable-pip-version-check --no-cache-dir install okpy     && pip --disable-pip-version-check --no-cache-dir install scikit-learn     && install2.r --error --skipinstalled --ncpus -1         languageserver         httpgd         statip         patchwork         paletteer         here         doParallel         janitor         vip         ranger         palmerpenguins         skimr         nnet         kernlab         plotly         factoextra         cluster         tidymodels         markdown         ottr     && rm -rf /tmp/downloaded_packages]: exit code: 100
2022-12-15 06:58:09.498Z: ------
2022-12-15 06:58:09.498Z:  > [dev_container_auto_added_stage_label  3/10] RUN apt-get update && export DEBIAN_FRONTEND=noninteractive     && /bin/bash /tmp/library-scripts/common-debian.sh "true" "rstudio" "1000" "1000" "false" "true" "true"     && usermod -a -G staff rstudio     && apt-get -y install         python3-pip         libgit2-dev         libcurl4-openssl-dev         libssl-dev         libxml2-dev         libxt-dev     && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts     && python3 -m pip --no-cache-dir install radian     && pip --disable-pip-version-check --no-cache-dir install pybryt     && pip --disable-pip-version-check --no-cache-dir install pylint     && pip --disable-pip-version-check --no-cache-dir install jupyter     && pip --disable-pip-version-check --no-cache-dir install datascience     && pip --disable-pip-version-check --no-cache-dir install otter-grader     && pip --disable-pip-version-check --no-cache-dir install numpy     && pip --disable-pip-version-check --no-cache-dir install pandas     && pip --disable-pip-version-check --no-cache-dir install scipy     && pip --disable-pip-version-check --no-cache-dir install folium>=0.9.1     && pip --disable-pip-version-check --no-cache-dir install matplotlib     && pip --disable-pip-version-check --no-cache-dir install ipywidgets>=7.0.0     && pip --disable-pip-version-check --no-cache-dir install bqplot     && pip --disable-pip-version-check --no-cache-dir install nbinteract>=0.0.12     && pip --disable-pip-version-check --no-cache-dir install otter-grader     && pip --disable-pip-version-check --no-cache-dir install okpy     && pip --disable-pip-version-check --no-cache-dir install scikit-learn     && install2.r --error --skipinstalled --ncpus -1         languageserver         httpgd         statip         patchwork         paletteer         here         doParallel         janitor         vip         ranger         palmerpenguins         skimr         nnet         kernlab         plotly         factoextra         cluster         tidymodels         markdown         ottr     && rm -rf /tmp/downloaded_packages:
2022-12-15 06:58:09.498Z: 
2022-12-15 06:58:09.499Z: #8 5.942 Running apt-get update...
2022-12-15 06:58:09.499Z: #8 6.198 Hit:1 http://security.ubuntu.com/ubuntu jammy-security InRelease
2022-12-15 06:58:09.499Z: #8 6.326 Hit:2 http://archive.ubuntu.com/ubuntu jammy InRelease
2022-12-15 06:58:09.499Z: #8 6.457 Hit:3 http://archive.ubuntu.com/ubuntu jammy-updates InRelease
2022-12-15 06:58:09.499Z: #8 6.588 Hit:4 http://archive.ubuntu.com/ubuntu jammy-backports InRelease
2022-12-15 06:58:09.499Z: 
2022-12-15 06:58:09.499Z: 
2022-12-15 06:58:09.499Z: #8 10.26 Reading state information...
2022-12-15 06:58:09.499Z: #8 10.30 E: Unable to locate package liblttng-ust0
2022-12-15 06:58:09.499Z: ------
2022-12-15 06:58:09.503Z: ERROR: failed to solve: executor failed running [/bin/sh -c apt-get update && export DEBIAN_FRONTEND=noninteractive     && /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true"     && usermod -a -G staff ${USERNAME}     && apt-get -y install         python3-pip         libgit2-dev         libcurl4-openssl-dev         libssl-dev         libxml2-dev         libxt-dev     && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts     && python3 -m pip --no-cache-dir install radian     && pip --disable-pip-version-check --no-cache-dir install pybryt     && pip --disable-pip-version-check --no-cache-dir install pylint     && pip --disable-pip-version-check --no-cache-dir install jupyter     && pip --disable-pip-version-check --no-cache-dir install datascience     && pip --disable-pip-version-check --no-cache-dir install otter-grader     && pip --disable-pip-version-check --no-cache-dir install numpy     && pip --disable-pip-version-check --no-cache-dir install pandas     && pip --disable-pip-version-check --no-cache-dir install scipy     && pip --disable-pip-version-check --no-cache-dir install folium>=0.9.1     && pip --disable-pip-version-check --no-cache-dir install matplotlib     && pip --disable-pip-version-check --no-cache-dir install ipywidgets>=7.0.0     && pip --disable-pip-version-check --no-cache-dir install bqplot     && pip --disable-pip-version-check --no-cache-dir install nbinteract>=0.0.12     && pip --disable-pip-version-check --no-cache-dir install otter-grader     && pip --disable-pip-version-check --no-cache-dir install okpy     && pip --disable-pip-version-check --no-cache-dir install scikit-learn     && install2.r --error --skipinstalled --ncpus -1         languageserver         httpgd         statip         patchwork         paletteer         here         doParallel         janitor         vip         ranger         palmerpenguins         skimr         nnet         kernlab         plotly         factoextra         cluster         tidymodels         markdown         ottr     && rm -rf /tmp/downloaded_packages]: exit code: 100
2022-12-15 06:58:09.523Z: Stop (56870 ms): Run: docker buildx build --load --build-arg BUILDKIT_INLINE_CACHE=1 -f /tmp/devcontainercli-root/container-features/0.26.0-1671087432608/Dockerfile-with-features -t vsc-devcontainers-rstudio-bbfd0d6c0abb26cf4b2640ac7d450c49 --target dev_containers_target_stage --build-arg VARIANT=4 --build-arg _DEV_CONTAINERS_BASE_IMAGE=dev_container_auto_added_stage_label /var/lib/docker/codespacemount/workspace/devcontainers-rstudio/.devcontainer
2022-12-15 06:58:09.523Z: Error: Command failed: docker buildx build --load --build-arg BUILDKIT_INLINE_CACHE=1 -f /tmp/devcontainercli-root/container-features/0.26.0-1671087432608/Dockerfile-with-features -t vsc-devcontainers-rstudio-bbfd0d6c0abb26cf4b2640ac7d450c49 --target dev_containers_target_stage --build-arg VARIANT=4 --build-arg _DEV_CONTAINERS_BASE_IMAGE=dev_container_auto_added_stage_label /var/lib/docker/codespacemount/workspace/devcontainers-rstudio/.devcontainer
2022-12-15 06:58:09.523Z:     at Zne (/usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js:1866:1635)
2022-12-15 06:58:09.523Z:     at processTicksAndRejections (internal/process/task_queues.js:95:5)
2022-12-15 06:58:09.523Z:     at async EF (/usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js:1865:1963)
2022-12-15 06:58:09.523Z:     at async x7 (/usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js:1865:901)
2022-12-15 06:58:09.523Z:     at async oie (/usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js:1871:2093)
2022-12-15 06:58:09.523Z:     at async qf (/usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js:1871:3239)
2022-12-15 06:58:09.523Z:     at async Mse (/usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js:1995:16211)
2022-12-15 06:58:09.523Z:     at async Lse (/usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js:1995:15965)
2022-12-15 06:58:09.551Z: Stop (57928 ms): Run: /usr/bin/node /usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /var/lib/docker/codespacemount/.persistedshare --container-data-folder .vscode-remote/data/Machine --container-system-data-folder /var/vscode-remote --workspace-folder /var/lib/docker/codespacemount/workspace/devcontainers-rstudio --id-label Type=codespaces --log-level info --log-format json --config /var/lib/docker/codespacemount/workspace/devcontainers-rstudio/.devcontainer/devcontainer.json --override-config /root/.codespaces/shared/merged_devcontainer.json --default-user-env-probe loginInteractiveShell --mount type=bind,source=/.codespaces/agent/mount/cache,target=/vscode --skip-post-create --update-remote-user-uid-default never --mount-workspace-git-root false
2022-12-15 06:58:09.551Z: Exit code 1

====================================== ERROR ====================================
2022-12-15 06:58:09.564Z: Failed to create container.
=================================================================================
2022-12-15 06:58:09.575Z: Error: Command failed: /usr/bin/node /usr/lib/node_modules/@microsoft/vscode-dev-containers-cli/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /var/lib/docker/codespacemount/.persistedshare --container-data-folder .vscode-remote/data/Machine --container-system-data-folder /var/vscode-remote --workspace-folder /var/lib/docker/codespacemount/workspace/devcontainers-rstudio --id-label Type=codespaces --log-level info --log-format json --config /var/lib/docker/codespacemount/workspace/devcontainers-rstudio/.devcontainer/devcontainer.json --override-config /root/.codespaces/shared/merged_devcontainer.json --default-user-env-probe loginInteractiveShell --mount type=bind,source=/.codespaces/agent/mount/cache,target=/vscode --skip-post-create --update-remote-user-uid-default never --mount-workspace-git-root false
2022-12-15 06:58:09.576Z: Error Code: 1302

Problem with devcontainer.json

devcontainer.json does not build in JetBrains IDE 2024.1 and VSCode.

JetBrains IDE Welcome screen -> DevContainers -> New DevContainer (from VCS Project, Docker must be installed.) Insert the git@ link of the repository with devcontainer.json. -> "Build container and Continue"

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