Containerize MCP Server

Package R MCP server into Docker container → portable deployment.

Use When

• Deploying R MCP server w/o local R install req'd
• Creating reproducible MCP server env
• Running MCP servers alongside other containerized services
• Distributing MCP server to other devs

In

• Required: R MCP server impl (mcptools-based or custom)
• Required: Docker installed + running
• Optional: Additional R pkgs server needs
• Optional: Transport mode (stdio or HTTP)

Do

Step 1: Create Dockerfile for MCP Server

FROM rocker/r-ver:4.5.0

# Install system dependencies
RUN apt-get update && apt-get install -y \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    libgit2-dev \
    libssh2-1-dev \
    git \
    curl \
    && rm -rf /var/lib/apt/lists/*

# Install R packages
RUN R -e "install.packages(c( \
    'remotes', \
    'ellmer' \
    ), repos='https://cloud.r-project.org/')"

# Install mcptools
RUN R -e "remotes::install_github('posit-dev/mcptools')"

# Set working directory
WORKDIR /workspace

# Expose MCP server ports
EXPOSE 3000 3001 3002

# Environment variables
ENV R_LIBS_USER=/workspace/renv/library
ENV RENV_PATHS_CACHE=/workspace/renv/cache

# Default: start MCP server
CMD ["R", "-e", "mcptools::mcp_server()"]

→ Dockerfile exists in project root w/ rocker/r-ver base image, sys deps, mcptools install, MCP server as default cmd.

If err: Valid. base image tag matches R ver. remotes::install_github fails → check git + libgit2-dev in sys deps layer.

Step 2: Create docker-compose.yml

version: '3.8'

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

    volumes:
      - /path/to/projects:/workspace
      - renv-cache:/workspace/renv/cache

    stdin_open: true
    tty: true

    network_mode: "host"

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

    restart: unless-stopped

volumes:
  renv-cache:
    driver: local

Using network_mode: "host" ensures MCP server ports accessible on localhost.

→ docker-compose.yml in project root w/ MCP server service, vol mounts for project files + renv cache, stdin_open/tty enabled for stdio transport.

If err: Vol paths invalid → adjust /path/to/projects to actual project dir. Windows/WSL → use /mnt/c/... or /mnt/d/... paths.

Step 3: Build + Start

docker compose build
docker compose up -d

→ Container starts w/ MCP server running.

If err: Check logs w/ docker compose logs mcp-server. Common issues:

• Missing R pkgs: Add to Dockerfile RUN install step
• Port already in use: Change exposed port or stop conflicting service

Step 4: Connect Claude Code to Container

Stdio transport (container must stay running w/ stdin):

claude mcp add r-mcp-docker stdio "docker" "exec" "-i" "r-mcp-server" "R" "-e" "mcptools::mcp_server()"

HTTP transport (if MCP server supports):

{
  "mcpServers": {
    "r-mcp-docker": {
      "type": "http",
      "url": "http://localhost:3000/mcp"
    }
  }
}

→ Claude Code's MCP config includes r-mcp-docker server entry, claude mcp list shows new server.

If err: Stdio transport → ensure container name matches (r-mcp-server) + container running w/ docker ps. HTTP transport → valid. port exposed + reachable w/ curl http://localhost:3000/mcp.

Step 5: Verify Connection

# Check container is running
docker ps | grep mcp-server

# Test R session inside container
docker exec -it r-mcp-server R -e "sessionInfo()"

# Verify mcptools is available
docker exec -it r-mcp-server R -e "library(mcptools)"

→ docker ps shows r-mcp-server container running, sessionInfo() returns expected R ver, library(mcptools) loads w/o err.

If err: Container not running → check docker compose logs mcp-server for startup errs. mcptools fails to load → rebuild image to ensure pkg installed correct.

Step 6: Add Custom MCP Tools

Add project-specific MCP tools → mount R scripts:

volumes:
  - ./mcp-tools:/mcp-tools

Load in CMD:

CMD ["R", "-e", "source('/mcp-tools/custom_tools.R'); mcptools::mcp_server()"]

→ Custom R scripts accessible inside container at /mcp-tools/, MCP server loads them on startup alongside default tools.

If err: Valid. vol mount path correct w/ docker exec -it r-mcp-server ls /mcp-tools/. Scripts fail to source → check missing pkg deps in custom tools.

Check

• Container builds w/o errs
• MCP server starts inside container
• Claude Code can connect to containerized server
• MCP tools respond correct to reqs
• Container restarts clean
• Vol mounts allow access to project files

Traps

• stdin/tty req's: MCP stdio transport requires stdin_open: true + tty: true
• Network isolation: Default Docker networking may prevent localhost access. Use network_mode: "host" or expose specific ports.
• Pkg vers: Pin mcptools to specific commit for reproducibility
• Large image size: mcptools + deps can be large. Consider multi-stage builds for prod.
• Windows Docker paths: Running Docker Desktop on Windows w/ WSL → path mapping differs

→

• create-r-dockerfile - base Dockerfile patterns for R
• setup-docker-compose - compose config details
• configure-mcp-server - MCP server config w/o Docker
• troubleshoot-mcp-connection - debugging MCP connectivity issues