Set Up Docker Compose

Configure Docker Compose for R development and deployment environments.

When to Use

•Running R alongside other services (databases, APIs)
•Setting up a reproducible development environment
•Orchestrating an R-based MCP server container
•Managing environment variables and volume mounts

Inputs

•Required: Dockerfile for the R service
•Required: Project directory to mount
•Optional: Additional services (database, cache, web server)
•Optional: Environment variable configuration

Procedure

Step 1: Create docker-compose.yml

yaml

version: '3.8'

services:
  r-dev:
    build:
      context: .
      dockerfile: Dockerfile
    container_name: r-dev
    image: r-dev:latest

    volumes:
      - .:/workspace
      - renv-cache:/workspace/renv/cache

    stdin_open: true
    tty: true

    environment:
      - TERM=xterm-256color
      - R_LIBS_USER=/workspace/renv/library
      - RENV_PATHS_CACHE=/workspace/renv/cache

    command: R

    restart: unless-stopped

volumes:
  renv-cache:
    driver: local

Step 2: Add Additional Services (If Needed)

yaml

services:
  r-dev:
    # ... as above
    depends_on:
      - postgres
    environment:
      - DB_HOST=postgres
      - DB_PORT=5432

  postgres:
    image: postgres:16
    container_name: r-postgres
    environment:
      POSTGRES_DB: analysis
      POSTGRES_USER: ruser
      POSTGRES_PASSWORD_FILE: /run/secrets/db_password
    volumes:
      - pgdata:/var/lib/postgresql/data
    ports:
      - "5432:5432"

volumes:
  renv-cache:
  pgdata:

Step 3: Configure Networking

For services that need localhost access (e.g., MCP servers):

yaml

services:
  r-dev:
    network_mode: "host"

For isolated networking:

yaml

services:
  r-dev:
    networks:
      - app-network
    ports:
      - "3000:3000"

networks:
  app-network:
    driver: bridge

Step 4: Manage Environment Variables

Create .env file (git-ignored):

code

R_VERSION=4.5.0
GITHUB_PAT=your_token_here

Reference in compose:

yaml

services:
  r-dev:
    build:
      args:
        R_VERSION: ${R_VERSION}
    env_file:
      - .env

Step 5: Build and Run

bash

# Build images
docker compose build

# Start services
docker compose up -d

# Attach to R session
docker compose exec r-dev R

# View logs
docker compose logs -f r-dev

# Stop services
docker compose down

Expected: All services start. R session accessible.

On failure: Check docker compose logs for startup errors. Common: port conflicts, missing environment variables.

Step 6: Create Override for Development

Create docker-compose.override.yml for local development settings:

yaml

services:
  r-dev:
    volumes:
      - /path/to/local/packages:/extra-packages
    environment:
      - DEBUG=true

This is automatically merged with docker-compose.yml.

Validation

• docker compose build completes without errors
• docker compose up starts all services
• Volume mounts correctly share files between host and container
• Environment variables are available inside containers
• Services can communicate with each other
• docker compose down cleanly stops everything

Common Pitfalls

•Volume mount permissions: Linux containers may create files as root. Use user: directive or fix permissions.
•Port conflicts: Check for services already using the same ports on the host
•Docker Desktop vs CLI: docker compose (v2) vs docker-compose (v1). Use v2.
•WSL path mounts: Use /mnt/c/... paths when mounting Windows directories from WSL
•Named volumes vs bind mounts: Named volumes persist across rebuilds; bind mounts reflect host changes immediately

Related Skills

•create-r-dockerfile - create the Dockerfile that compose references
•containerize-mcp-server - compose configuration for MCP servers
•optimize-docker-build-cache - speed up compose builds