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Merge pull request #186 from r-devel/devel
Version 0.3 release
2 parents af7ea6e + 7650b12 commit ec9a4c5

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‎.devcontainer/devcontainer.json‎

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
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{
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"name": "R-Dev-Env",
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"image": "ghcr.io/r-devel/r-dev-env:main",
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"hostRequirements": {
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"cpus": 4
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},
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"customizations": {
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"vscode": {
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"settings": {
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"r.lsp.diagnostics": false,
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"r.plot.useHttpgd": true,
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"r.rpath.linux": "/usr/bin/R",
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"r.rterm.linux": "/usr/bin/R",
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"terminal.integrated.sendKeybindingsToShell": true,
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"svn.multipleFolders.enabled": true,
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"name": "R-Dev-Env",
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"image": "ghcr.io/r-devel/r-dev-env:main",
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"hostRequirements": {
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"cpus": 4
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},
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"customizations": {
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"vscode": {
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"settings": {
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"r.lsp.diagnostics": false,
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"r.plot.useHttpgd": true,
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"r.rpath.linux": "/usr/bin/R",
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"r.rterm.linux": "/usr/bin/R",
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"terminal.integrated.sendKeybindingsToShell": true,
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"svn.multipleFolders.enabled": true,
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"workbench.editorAssociations": {
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"*.md": "vscode.markdown.preview.editor"
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},
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"workbench.welcomePage.walkthroughs.openOnInstall": false
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},
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"extensions": [
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"REditorSupport.r",
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"mads-hartmann.bash-ide-vscode",
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"johnstoncode.svn-scm",
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"ms-vscode.cpptools",
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"MS-vsliveshare.vsliveshare"
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]
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}
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},
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"postCreateCommand":"cat /workspaces/r-dev-env/scripts/welcome_msg.sh >> ~/.bashrc && cat /workspaces/r-dev-env/scripts/set_build_r.sh >> ~/.bashrc && bash /workspaces/r-dev-env/scripts/localscript.sh"
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// Features to add to the dev container. More info: https://containers.dev/features.
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// "features": {},
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// Use 'forwardPorts' to make a list of ports inside the container available locally.
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// "forwardPorts": [],
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// Use 'postCreateCommand' to run commands after the container is created.
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// "postCreateCommand": "gcc -v",
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// Configure tool-specific properties.
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// "customizations": {},
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// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
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// "remoteUser": "root"
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},
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"extensions": [
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"REditorSupport.r",
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"mads-hartmann.bash-ide-vscode",
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"johnstoncode.svn-scm",
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"ms-vscode.cpptools",
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"MS-vsliveshare.vsliveshare"
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]
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}
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},
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"postCreateCommand": "chown -R vscode:vscode /workspaces/r-dev-env && sh /workspaces/r-dev-env/scripts/localscript.sh"
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}

‎.github/workflows/build-gitpod-image.yml‎

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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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name: Build and publish Gitpod Docker image
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on:
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workflow_dispatch:
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pull_request:
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branches: ["main","devel"]
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types: [closed]
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paths:
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- '.github/workflows/build-gitpod-image.yml'
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- '.gitpod.Dockerfile'
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- '.gitpod.yml'
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- 'reinstall-cmake.sh'
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- 'VERSION'
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env:
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REGISTRY: ghcr.io
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IMAGE_NAME: ${{ github.repository }}
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jobs:
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build-and-push-image:
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if: ${{github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.merged == true}}
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Extract version number
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run: |
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VER=$(cat VERSION)
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echo "VERSION=$VER" >> $GITHUB_ENV
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- name: Log in to the Container registry
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uses: docker/login-action@v3
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.REGISTRY }}/${{ github.repository }}
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tags: |
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type=ref,event=branch
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type=ref,event=pr
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type=semver,pattern={{ env.VERSION }}
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type=sha
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- name: Build and push Docker image
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uses: docker/build-push-action@v5
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with:
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context: .
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file: .gitpod.Dockerfile
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push: true
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tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:gitpod.${{ github.ref_name }}
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build-args: |
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CONTAINER_VERSION=${{ env.VERSION }}
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labels: ${{ steps.meta.outputs.labels }}

‎.github/workflows/optimize-docs-images.yml‎

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name: Optimize Docs Images
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on:
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pull_request:
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branches: ["main","devel"]
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types: [closed]
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paths:
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- 'docs/assets/**'
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jobs:
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optimize-images:
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if: ${{github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.merged == true}}
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v2
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y libmagick++-dev libcurl4-openssl-dev
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- name: Install R packages
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run: |
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R -e 'install.packages(c("magick"), repos = "https://cloud.r-project.org/")'
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- name: Optimize images
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run: |
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Rscript ./scripts/optimize.R
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- name: Commit and push optimized images
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if: github.ref == 'refs/heads/devel' && github.event_name == 'push'
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run: |
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git config --global user.name "github-actions[bot]"
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git config --global user.email "github-actions[bot]@users.noreply.github.com"
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git add docs/assets
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git commit -m 'Optimize docs images'
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git push
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.gitpod.Dockerfile‎

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FROM gitpod/workspace-full:latest
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USER root
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ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="none"
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# Optionally install the cmake for vcpkg
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COPY ./reinstall-cmake.sh /tmp/
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RUN if [ "${REINSTALL_CMAKE_VERSION_FROM_SOURCE}" != "none" ]; then \
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chmod +x /tmp/reinstall-cmake.sh && /tmp/reinstall-cmake.sh ${REINSTALL_CMAKE_VERSION_FROM_SOURCE}; \
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fi \
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&& rm -f /tmp/reinstall-cmake.sh
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RUN sed -i.bak "/^#.*deb-src.*universe$/s/^# //g" /etc/apt/sources.list \
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&& echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" >> /etc/apt/sources.list \
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&& 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 \
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&& apt update \
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&& apt -y install subversion \
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&& apt -y build-dep r-base-dev \
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&& apt -y install r-base-dev \
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&& apt -y install valgrind \
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&& Rscript -e "install.packages('languageserver', repos='https://cran.rstudio.com')" \
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&& Rscript -e "install.packages('httpgd', repos='https://cran.rstudio.com')"
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RUN apt install -y shellcheck
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RUN apt install -y ccache
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RUN apt install -y rsync
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#RUN /usr/sbin/update-ccache-symlinks
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#RUN echo 'export PATH="/usr/lib/ccache:$PATH"' | tee -a /home/vscode/.bashrc
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ARG CONTAINER_VERSION
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ENV CONTAINER_VERSION ${CONTAINER_VERSION}

‎.gitpod.yml‎

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image: ghcr.io/r-devel/r-dev-env:gitpod.devel
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tasks:
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- name: Initial Setup for R-dev-env Gitpod Workspace
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before: |
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bash /workspace/r-dev-env/scripts/localscript.sh
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source ~/.bashrc
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vscode:
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extensions:
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- REditorSupport.r
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- johnstoncode.svn-scm

‎CITATION.cff‎

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cff-version: 1.2.0
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message: "If you use this software, please cite it as below."
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authors:
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- family-names: Shirdhankar
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given-names: Atharva
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- family-names: Turner
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given-names: Heather
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- family-names: Tripp
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given-names: James
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- family-name: Emsley
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given-names: Iain
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title: "R Development Container"
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version: 0.2.0
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doi:
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date-released: 28-06-2024
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cff-version: 1.2.0
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message: "If you use this software, please cite it as below."
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authors:
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- family-names: Shirdhankar
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given-names: Atharva
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- family-names: Turner
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given-names: Heather
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- family-names: Tripp
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given-names: James
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- family-name: Emsley
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given-names: Iain
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- family-names: Crespo
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given-names: Lorena
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- family-names: Campitelli
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given-names: Elio
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title: "R Development Container"
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version: 0.3.0
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doi:
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date-released: 04-09-2024

‎Dockerfile‎

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#RUN echo 'export PATH="/usr/lib/ccache:$PATH"' | tee -a /home/vscode/.bashrc
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ENV BUILDDIR="/workspaces/r-dev-env/build/r-devel"
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ENV TOP_SRCDIR="/workspaces/r-dev-env/svn/r-devel"
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ENV PATCHDIR='/workspaces/r-dev-env/patches'
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ARG CONTAINER_VERSION
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ENV CONTAINER_VERSION ${CONTAINER_VERSION}

‎INDEX.md‎

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If you haven't seen them yet, you can find the
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[R Dev Container Docs](https://contributor.r-project.org/r-dev-env/) online.
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This index links to underlying markdown files for key sections of the docs, so you can preview them right here in VS Code.
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## Working with the container
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The links below give more information on using the container via GitHub Codespaces or Gitpod Workspaces.
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Take a moment to review how to stop and restart your container, so you can continue your work.
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If you are collaborating with others, you may want to use Live Share so that you can share the same workspace.
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### Github Codespace
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- [Stopping and Restarting Codespace](docs/container_setup/github_codespace/codespacestartstop.md)
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- [Collaborating with Live Share](docs/container_setup/github_codespace/live_share.md)
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### Gitpod Workspace
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- [Stopping and Restarting Codespace](docs/container_setup/gitpod_workspace/workspacestop_and_restart.md)
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- [Collaborating with Live Share](docs/container_setup/gitpod_workspace/live_share.md)
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## Tutorials
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You can also preview the tutorials right here in VSCode, making them easier to work through.
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Learn how to use the container with these mini tutorials.
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If you have used R in VSCode before, you can skip Tutorial 1.
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Tutorials 2 and 3 are the minimum to get started with R development.
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You can run through these in about 30 minutes.
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6. [Multiple R versions](docs/tutorials/multi_r_compilation.md)
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7. [SVN Help](docs/tutorials/svn_help.md)
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## Other Docs
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## Further docs
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- [Restarting And Stopping Codespace](docs/container_setup/codespacestartstop.md)
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- [Collaborating with Live Share]((docs/container_setup/live_share.md))
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- [Using R Dev Container Locally](docs/container_setup/localsetup.md)
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- [Useful Resources](docs/resources.md)
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See the [full documentation](https://contributor.r-project.org/r-dev-env/) for background information on this project, how to contribute to the [documentation](docs/contributor_guide/contributing_to_docs.md) or the [codebase](docs/contributor_guide/contributing_to_codebase.md), [external resources](docs/resources.md) and [troubleshooting](docs/troubleshoot.md).

‎NEWS.md‎

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## R Development Container 0.3
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- Implemented Gitpod setup with GitHub Actions workflow to build Docker images for the Gitpod workspace.
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- Improved `which_r` script with version choice validation and updated both `which_r` and `set_build_r` scripts for enhanced functionality.
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- Resolved local setup permission issues to ensure smoother operation within the devcontainer environment on Linux.
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- Restructured documentation to incorporate Gitpod alternative setup.
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- Implemented a workflow to optimize images so that documentation files are more lightweight.
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## R Development Container 0.2
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- Documentation split into set of markdown files. These are used to create the documentation website https://contributor.r-project.org/r-dev-env/ and the user-focused pages can be accessed directly within the codespace, linked from an index that opens when the codespace first starts. New documentation pages/topics:

‎VERSION‎

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0.2.0
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0.3.0

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