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and so it begins... 🌱
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‎.github/workflows/docker-rstudio.yml

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name: RStudio
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on:
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workflow_dispatch: null
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push:
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paths: ['Dockerfile']
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jobs:
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build:
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runs-on: ubuntu-latest
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permissions: write-all
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steps:
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# For biggish images, github actions runs out of disk space.
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# So we cleanup some unwanted things in the disk image, and reclaim that space for our docker use
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# https://github.com/actions/virtual-environments/issues/2606#issuecomment-772683150
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# and https://github.com/easimon/maximize-build-space/blob/b4d02c14493a9653fe7af06cc89ca5298071c66e/action.yml#L104
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# This gives us a total of about 52G of free space, which should be enough for now
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- name: cleanup disk space
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run: |
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sudo rm -rf /usr/local/lib/android /usr/share/dotnet /opt/ghc
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df -h
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- uses: actions/checkout@v3
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- name: Login to GitHub Container Registry
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if: github.repository == 'boettiger-lab/k8s'
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uses: docker/login-action@v1
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with:
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registry: ghcr.io
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username: ${{github.actor}}
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password: ${{secrets.GITHUB_TOKEN}}
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- name: Build the Docker image
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if: github.repository == 'boettiger-lab/repo2docker-r'
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run: docker build . --tag ghcr.io/boettiger-lab/repo2docker-r/r2u:latest
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- name: Publish
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if: github.repository == 'boettiger-lab/repo2docker-r'
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run: docker push ghcr.io/boettiger-lab/repo2docker-r/r2u:latest
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‎Dockerfile

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FROM quay.io/jupyter/minimal-notebook
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USER root
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# Install R
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COPY install_r.sh install_r.sh
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RUN bash install_r.sh
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## RStudio
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RUN conda install jupyter-rsession-proxy
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COPY install_rstudio.sh install_rstudio.sh
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RUN bash install_rstudio.sh
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COPY environment.yml environment.yml
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RUN conda env update -f environment.yml
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COPY install.r install.r
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RUN Rscript install.R
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USER ${NB_USER}
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‎environment.yml

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name: base
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channels:
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- conda-forge
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dependencies:
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- seaborn
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- ibis-duckdb
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‎install.r

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install.packages(c("sf", "terra", "stars", "rstan", "ROracle"))
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‎install_r.sh

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#!/bin/bash
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## First: update apt and get keys
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apt update -qq && apt install --yes --no-install-recommends wget ca-certificates gnupg
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wget -q -O- https://eddelbuettel.github.io/r2u/assets/dirk_eddelbuettel_key.asc \
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| tee -a /etc/apt/trusted.gpg.d/cranapt_key.asc
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## Second: add the repo -- here we use the well-connected mirror
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echo "deb [arch=amd64] https://r2u.stat.illinois.edu/ubuntu noble main" > /etc/apt/sources.list.d/cranapt.list
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apt update
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## Third: ensure current R is used
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wget -q -O- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
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| tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
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echo "deb [arch=amd64] https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" > /etc/apt/sources.list.d/cran_r.list
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apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 67C2D66C4B1D4339 51716619E084DAB9
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apt update -qq
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DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends r-base r-base-dev r-recommended
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## Fourth: add pinning to ensure package sorting
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echo "Package: *" > /etc/apt/preferences.d/99cranapt
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echo "Pin: release o=CRAN-Apt Project" >> /etc/apt/preferences.d/99cranapt
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echo "Pin: release l=CRAN-Apt Packages" >> /etc/apt/preferences.d/99cranapt
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echo "Pin-Priority: 700" >> /etc/apt/preferences.d/99cranapt
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## Fifth: install bspm (and its Python requirements) and enable it
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## If needed (in bare container, say) install python tools for bspm and R itself
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apt install --yes --no-install-recommends python3-{dbus,gi,apt} \
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make sudo r-cran-{docopt,littler,remotes}
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## Then install bspm (as root) and enable it, and enable a speed optimization
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Rscript -e 'install.packages("bspm")'
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RHOME=$(R RHOME)
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echo "suppressMessages(bspm::enable())" >> ${RHOME}/etc/Rprofile.site
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echo "options(bspm.version.check=FALSE)" >> ${RHOME}/etc/Rprofile.site
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chown root:staff ${RHOME}/site-library
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chmod g+ws ${RHOME}/site-library
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echo "options('bspm.sudo' = TRUE)" >> ${RHOME}/etc/Rprofile.site
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ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r
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## add user to sudoers
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usermod -a -G staff ${NB_USER}
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echo "${NB_USER} ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
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‎install_rstudio.sh

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#!/bin/bash
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set -e
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RSTUDIO_VERSION=${1:-${RSTUDIO_VERSION:-"stable"}}
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DEFAULT_USER=${DEFAULT_USER:-"rstudio"}
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apt-get update && apt-get -y install \
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ca-certificates \
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gdebi-core \
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git \
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libclang-dev \
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libssl-dev \
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lsb-release \
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psmisc \
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pwgen \
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sudo \
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wget
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ARCH=$(dpkg --print-architecture)
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UBUNTU_CODENAME="noble"
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## Download RStudio Server for Ubuntu 18+
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DOWNLOAD_FILE=rstudio-server.deb
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if [ "$RSTUDIO_VERSION" = "latest" ]; then
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RSTUDIO_VERSION="stable"
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fi
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if [ "$UBUNTU_CODENAME" = "focal" ]; then
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UBUNTU_CODENAME="bionic"
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fi
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# TODO: remove this workaround for Ubuntu 24.04
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if [ "$UBUNTU_CODENAME" = "noble" ]; then
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UBUNTU_CODENAME="jammy"
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fi
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if [ "$RSTUDIO_VERSION" = "stable" ] || [ "$RSTUDIO_VERSION" = "preview" ] || [ "$RSTUDIO_VERSION" = "daily" ]; then
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if [ "$UBUNTU_CODENAME" = "bionic" ]; then
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UBUNTU_CODENAME="focal"
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fi
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wget "https://rstudio.org/download/latest/${RSTUDIO_VERSION}/server/${UBUNTU_CODENAME}/rstudio-server-latest-${ARCH}.deb" -O "$DOWNLOAD_FILE"
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else
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wget "https://download2.rstudio.org/server/${UBUNTU_CODENAME}/${ARCH}/rstudio-server-${RSTUDIO_VERSION/"+"/"-"}-${ARCH}.deb" -O "$DOWNLOAD_FILE" ||
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wget "https://s3.amazonaws.com/rstudio-ide-build/server/${UBUNTU_CODENAME}/${ARCH}/rstudio-server-${RSTUDIO_VERSION/"+"/"-"}-${ARCH}.deb" -O "$DOWNLOAD_FILE"
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fi
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gdebi --non-interactive "$DOWNLOAD_FILE"
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rm "$DOWNLOAD_FILE"
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ln -fs /usr/lib/rstudio-server/bin/rstudio-server /usr/local/bin
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ln -fs /usr/lib/rstudio-server/bin/rserver /usr/local/bin
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# https://github.com/rocker-org/rocker-versioned2/issues/137
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rm -f /var/lib/rstudio-server/secure-cookie-key
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## RStudio wants an /etc/R, will populate from $R_HOME/etc
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mkdir -p /etc/R
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## Make RStudio compatible with case when R is built from source
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## (and thus is at /usr/local/bin/R), because RStudio doesn't obey
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## path if a user apt-get installs a package
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R_BIN="$(which R)"
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echo "rsession-which-r=${R_BIN}" >/etc/rstudio/rserver.conf
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## use more robust file locking to avoid errors when using shared volumes:
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echo "lock-type=advisory" >/etc/rstudio/file-locks
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## Prepare optional configuration file to disable authentication
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## To de-activate authentication, `disable_auth_rserver.conf` script
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## will just need to be overwrite /etc/rstudio/rserver.conf.
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## This is triggered by an env var in the user config
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cp /etc/rstudio/rserver.conf /etc/rstudio/disable_auth_rserver.conf
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echo "auth-none=1" >>/etc/rstudio/disable_auth_rserver.conf
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