Set Up Docker Compose

Configure Docker Compose for R dev + deploy envs.

Use When

• R + other services (DBs, APIs)
• Reproducible dev env
• Orchestrate R-based MCP server
• Manage env vars + volume mounts

In

• Required: Dockerfile for R service
• Required: Project dir to mount
• Optional: Additional services (DB, cache, web)
• Optional: Env var config

Do

Step 1: Create docker-compose.yml

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

→ docker-compose.yml exists w/ R service, volume mounts (project + renv cache), env vars for R lib paths.

If err: invalid YAML → docker compose config validate. Spaces (not tabs); special chars quoted.

Step 2: Add Services (If Needed)

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:

→ Service (PostgreSQL) defined w/ own volume, env vars, ports. R service depends_on references new.

If err: DB fails start → docker compose logs postgres for init errs. Verify env vars (POSTGRES_PASSWORD_FILE → valid secret) or switch POSTGRES_PASSWORD for dev.

Step 3: Networking

For services needing localhost (MCP):

services:
  r-dev:
    network_mode: "host"

Isolated:

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

networks:
  app-network:
    driver: bridge

→ Networking configured: host for localhost-needing (MCP), bridge w/ explicit ports for isolated.

If err: services can't comm → verify same net. Bridge → use service names as hostnames (postgres not localhost). Host → localhost + no port conflicts.

Step 4: Env Vars

.env (git-ignored):

R_VERSION=4.5.0
GITHUB_PAT=your_token_here

Reference:

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

→ .env exists git-ignored w/ project vars; compose references via env_file|${VAR}.

If err: vars not resolving → .env in same dir as docker-compose.yml. docker compose config shows resolved.

Step 5: Build + Run

# 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

→ All start. R session accessible.

If err: docker compose logs → startup errs. Common: port conflicts, missing env vars.

Step 6: Override for Dev

docker-compose.override.yml:

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

Auto-merged.

→ Override exists w/ dev settings (extra volumes, debug) auto-applied via docker compose up.

If err: not taking effect → verify exact docker-compose.override.yml. docker compose config confirms merge. Explicit: docker compose -f docker-compose.yml -f custom-override.yml up.

Check

• docker compose build w/o errs
• docker compose up starts all
• Volume mounts share files host↔container
• Env vars available inside
• Services can comm
• docker compose down cleanly stops

Traps

• Volume mount perms: Linux containers create files as root. user: directive or fix perms.
• Port conflicts: Check services using same ports on host.
• Docker Desktop vs CLI: docker compose (v2) vs docker-compose (v1). Use v2.
• WSL path mounts: /mnt/c/... for Windows dirs from WSL.
• Named vs bind: Named persist across rebuilds; bind reflects host immediately.

→

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