create-r-dockerfile

# Create R Dockerfile Build a Dockerfile for R projects using rocker base images with proper dependency management. ## When to Use - Containerizing an R application or analysis - Creating reproducible R environments - Deploying R-based services (Shiny, Plumber, MCP server) - Setting up consistent development environments ## Inputs - **Required**: R project with dependencies (DESCRIPTION or renv.lock) - **Required**: Purpose (development, production, or service) - **Optional**: R version (default: latest stable) - **Optional**: Additional system libraries needed ## Procedure ### Step 1: Choose Base Image | Use Case | Base Image | Size | |---|---|---| | Minimal R runtime | `rocker/r-ver:4.5.0` | ~800MB | | With tidyverse | `rocker/tidyverse:4.5.0` | ~1.8GB | | With RStudio Server | `rocker/rstudio:4.5.0` | ~1.9GB | | Shiny server | `rocker/shiny-verse:4.5.0` | ~2GB | **Expected:** A base image is selected that matches the project's requirements without unnecessary bloat. **On failure:** If unsure which image to use, start with `rocker/r-ver` (minimal) and add packages as needed. Check [rocker-org](https://github.com/rocker-org/rocker-versioned2) for the full image catalog. ### Step 2: Write Dockerfile ```dockerfile FROM rocker/r-ver:4.5.0 # Install system dependencies # Group by purpose for clarity RUN apt-get update && apt-get install -y \ # HTTP/SSL libcurl4-openssl-dev \ libssl-dev \ # XML processing libxml2-dev \ # Git integration libgit2-dev \ libssh2-1-dev \ # Graphics libfontconfig1-dev \ libharfbuzz-dev \ libfribidi-dev \ libfreetype6-dev \ libpng-dev \ libtiff5-dev \ libjpeg-dev \ # Utilities git \ curl \ && rm -rf /var/lib/apt/lists/* # Install R packages # Order: least-changing first for cache efficiency RUN R -e "install.packages(c( \ 'remotes', \ 'devtools', \ 'renv' \ ), repos='https://cloud.r-project.org/')" # Set working directory WORKDIR /workspace # Copy renv files first (cache layer) COPY renv.lock renv.lock COPY renv/activate.R renv/activate.R # Restore packages from lockfile RUN R -e "renv::restore()" # Copy project files COPY . . # Default command CMD ["R"] ``` **Expected:** Dockerfile builds successfully with `docker build -t myproject .` **On failure:** If the build fails during `apt-get install`, check package names for the target distro (Debian). If `renv::restore()` fails, ensure `renv.lock` and `renv/activate.R` are copied before the restore step. ### Step 3: Create .dockerignore ```text .git .Rproj.user .Rhistory .RData renv/library renv/cache renv/staging docs/ *.tar.gz ``` **Expected:** `.dockerignore` excludes Git history, IDE files, local renv library, and build artifacts from the Docker context. **On failure:** If the Docker build still copies unwanted files, verify `.dockerignore` is in the same directory as the Dockerfile and uses correct glob patterns. ### Step 4: Build and Test ```bash docker build -t r-project:latest . docker run --rm -it r-project:latest R -e "sessionInfo()" ``` **Expected:** Container starts with correct R version and all packages available. `sessionInfo()` output confirms the expected R version. **On failure:** Check build logs for system dependency errors. Add missing `-dev` packages to the `apt-get install` layer. ### Step 5: Optimize for Production For production deployments, use multi-stage builds: ```dockerfile # Build stage FROM rocker/r-ver:4.5.0 AS builder RUN apt-get update && apt-get install -y libcurl4-openssl-dev libssl-dev COPY renv.lock . RUN R -e "install.packages('renv'); renv::restore()" # Runtime stage FROM rocker/r-ver:4.5.0 COPY --from=builder /usr/local/lib/R/site-library /usr/local/lib/R/site-library COPY . /app WORKDIR /app CMD ["Rscript", "main.R"] ``` **Expected:** Multi-stage build produces a smaller final image. Runtime stage contains only compiled R packages, not build tools. **On failure:** If packages fail to load in the runtime stage, ensure the library path in `COPY --from=builder` matches where R installed packages. Check with `R -e ".libPaths()"` in both stages. ## Validation - [ ] `docker build` completes without errors - [ ] Container starts and R session works - [ ] All required packages are available - [ ] `.dockerignore` excludes unnecessary files - [ ] Image size is reasonable for the use case - [ ] Rebuilds are fast when only code changes (layer caching works) ## Common Pitfalls - **Missing system dependencies**: R packages with compiled code need `-dev` libraries. Check error messages during `install.packages()` - **Layer cache invalidation**: Copying all files before installing packages invalidates cache on every code change. Copy lockfile first. - **Large images**: Use `rm -rf /var/lib/apt/lists/*` after `apt-get install`. Consider multi-stage builds. - **Timezone issues**: Add `ENV TZ=UTC` or install `tzdata` for timezone-aware operations - **Running as root**: Add a non-root user for production: `RUN useradd -m appuser && USER appuser` ## Examples ```bash # Development container with mounted source docker run --rm -it -v $(pwd):/workspace r-project:latest R # Plumber API service docker run -d -p 8000:8000 r-api:latest # Shiny app docker run -d -p 3838:3838 r-shiny:latest ``` ## Related Skills - `setup-docker-compose` - orchestrate multiple containers - `containerize-mcp-server` - special case for MCP R servers - `optimize-docker-build-cache` - advanced caching strategies - `manage-renv-dependencies` - renv.lock feeds into Docker builds