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Merge pull request #286 from davidycliao/0.1.7
2 parents f9798b7 + a47b172 commit d33df2b

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‎.github/workflows/docker-publish.yml

Lines changed: 94 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -1,60 +1,94 @@
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FROM rocker/r-ver:latest
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# Install system dependencies
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RUN apt-get update && apt-get install -y \
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python3-minimal \
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python3-pip \
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python3-venv \
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libssl-dev \
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gdebi-core \
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wget \
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sudo \
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curl
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# Create rstudio user
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ARG USER=rstudio
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ARG PASSWORD=rstudio123
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RUN useradd -m $USER && \
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echo "$USER:$PASSWORD" | chpasswd && \
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adduser $USER sudo && \
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echo "$USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
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# Install RStudio Server
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RUN wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.12.1-402-amd64.deb && \
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gdebi -n rstudio-server-2023.12.1-402-amd64.deb && \
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rm rstudio-server-*.deb
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# Create and configure Python virtual environment
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RUN python3 -m venv /opt/venv && \
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chown -R $USER:$USER /opt/venv
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ENV PATH="/opt/venv/bin:$PATH"
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ENV RETICULATE_PYTHON="/opt/venv/bin/python"
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# Setup R environment config
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RUN mkdir -p /usr/local/lib/R/etc && \
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echo "RETICULATE_PYTHON=/opt/venv/bin/python" >> /usr/local/lib/R/etc/Renviron.site && \
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echo "options(reticulate.prompt = FALSE)" >> /usr/local/lib/R/etc/Rprofile.site
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# Install Python packages
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RUN /opt/venv/bin/pip install --no-cache-dir \
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numpy==1.26.4 \
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scipy==1.12.0 \
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transformers \
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torch \
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flair
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# Install R packages with proper setup
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RUN R -e 'install.packages("reticulate", repos="https://cloud.r-project.org/", dependencies=TRUE)' && \
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R -e 'if(require(reticulate)) { \
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Sys.setenv(RETICULATE_PYTHON="/opt/venv/bin/python"); \
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reticulate::use_python("/opt/venv/bin/python", required=TRUE); \
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install.packages("remotes", repos="https://cloud.r-project.org/", dependencies=TRUE); \
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remotes::install_github("davidycliao/flaiR", dependencies=TRUE) \
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}'
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WORKDIR /home/$USER
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USER $USER
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EXPOSE 8787
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CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]
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name: flaiR-Docker
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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jobs:
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R-CMD-check:
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runs-on: ubuntu-latest
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name: R-CMD-check
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Setup Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.9'
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flair
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- name: Install R dependencies
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run: |
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install.packages('remotes')
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remotes::install_github("davidycliao/flaiR", force = TRUE)
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shell: Rscript {0}
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: rcmdcheck
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docker:
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needs: R-CMD-check
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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@v3
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v2
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- name: Log in to GitHub Container Registry
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uses: docker/login-action@v2
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2
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with:
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buildkitd-flags: --debug
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- name: Extract metadata for Docker
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id: meta
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uses: docker/metadata-action@v4
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with:
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images: ghcr.io/${{ github.repository_owner }}/flair-rstudio
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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={{version}}
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type=semver,pattern={{major}}.{{minor}}
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type=sha
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type=raw,value=latest,enable={{is_default_branch}}
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- name: Build and push RStudio image
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uses: docker/build-push-action@v4
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with:
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context: .
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platforms: linux/amd64
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
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DEFAULT_USER=rstudio
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secrets: |
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PASSWORD=${{ secrets.RSTUDIO_PASSWORD }}
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cache-from: type=gha
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cache-to: type=gha,mode=max
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provenance: false

‎Dockerfile

Lines changed: 21 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -9,12 +9,11 @@ RUN apt-get update && apt-get install -y \
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gdebi-core \
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wget \
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sudo \
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curl \
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virtualenv # 添加virtualenv
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curl
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# Create rstudio user
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ENV USER=rstudio
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ENV PASSWORD=rstudio123
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ARG USER=rstudio
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ARG PASSWORD=rstudio123
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RUN useradd -m $USER && \
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echo "$USER:$PASSWORD" | chpasswd && \
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adduser $USER sudo && \
@@ -25,46 +24,37 @@ RUN wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.12
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gdebi -n rstudio-server-2023.12.1-402-amd64.deb && \
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rm rstudio-server-*.deb
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# 修改虚拟环境路径到用户目录
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ENV VENV_PATH=/home/$USER/flair_env
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RUN python3 -m venv $VENV_PATH && \
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chown -R $USER:$USER $VENV_PATH
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# Create and configure Python virtual environment
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RUN python3 -m venv /opt/venv && \
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chown -R $USER:$USER /opt/venv
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# 更新环境变量
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ENV PATH="$VENV_PATH/bin:$PATH"
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ENV RETICULATE_PYTHON="$VENV_PATH/bin/python"
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ENV PATH="/opt/venv/bin:$PATH"
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ENV RETICULATE_PYTHON="/opt/venv/bin/python"
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# Setup R environment config
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RUN mkdir -p /usr/local/lib/R/etc && \
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echo "RETICULATE_PYTHON=$VENV_PATH/bin/python" >> /usr/local/lib/R/etc/Renviron.site && \
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chown -R $USER:$USER /usr/local/lib/R/etc/Renviron.site && \
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chmod 644 /usr/local/lib/R/etc/Renviron.site
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echo "RETICULATE_PYTHON=/opt/venv/bin/python" >> /usr/local/lib/R/etc/Renviron.site && \
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echo "options(reticulate.prompt = FALSE)" >> /usr/local/lib/R/etc/Rprofile.site
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# Install Python packages in the virtual environment
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RUN $VENV_PATH/bin/pip install --no-cache-dir \
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# Install Python packages
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RUN /opt/venv/bin/pip install --no-cache-dir \
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numpy==1.26.4 \
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scipy==1.12.0 \
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transformers \
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torch \
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flair
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# Install R packages
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RUN R -e "install.packages('reticulate', repos='https://cloud.r-project.org/', dependencies=TRUE)" && \
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R -e "install.packages('remotes', repos='https://cloud.r-project.org/', dependencies=TRUE)" && \
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R -e "options(timeout=600); Sys.setenv(RETICULATE_PYTHON='$VENV_PATH/bin/python'); library(reticulate); use_virtualenv('$VENV_PATH', required = TRUE); remotes::install_github('davidycliao/flaiR', dependencies=TRUE)"
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# Install R packages with proper setup
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RUN R -e 'install.packages("reticulate", repos="https://cloud.r-project.org/", dependencies=TRUE)' && \
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R -e 'if(require(reticulate)) { \
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Sys.setenv(RETICULATE_PYTHON="/opt/venv/bin/python"); \
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reticulate::use_python("/opt/venv/bin/python", required=TRUE); \
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install.packages("remotes", repos="https://cloud.r-project.org/", dependencies=TRUE); \
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remotes::install_github("davidycliao/flaiR", dependencies=TRUE) \
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}'
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# Set working directory
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WORKDIR /home/$USER
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RUN chown -R $USER:$USER /home/$USER
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# Add healthcheck
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HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
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CMD curl -f http://localhost:8787/ || exit 1
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# Expose port
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USER $USER
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EXPOSE 8787
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# Run service as rstudio user
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USER $USER
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CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]
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CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0"]

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