Configure MCP Server

Set up MCP server connections for Claude Code (WSL) and Claude Desktop (Windows).

When to Use

Setting up Claude Code to connect to R via mcptools
Configuring Claude Desktop with MCP servers
Adding Hugging Face or other remote MCP servers
Troubleshooting MCP connectivity between tools

Inputs

Required: MCP server type (mcptools, Hugging Face, custom)
Required: Client (Claude Code, Claude Desktop, or both)
Optional: Authentication tokens
Optional: Custom server implementation

Procedure

Step 1: Install MCP Server Packages

For R (mcptools):

install.packages("remotes")
remotes::install_github("posit-dev/mcptools")

For Hugging Face:

npm install -g mcp-remote

Expected: mcptools installs from GitHub and loads in R without errors. mcp-remote is available globally via which mcp-remote or npm list -g mcp-remote.

On failure: For mcptools, ensure remotes is installed first. If GitHub rate-limits the install, set a GITHUB_PAT in ~/.Renviron. For mcp-remote, verify Node.js and npm are installed and on PATH.

Step 2: Configure Claude Code (WSL)

R mcptools server:

claude mcp add r-mcptools stdio \
  "/mnt/c/Program Files/R/R-4.5.0/bin/Rscript.exe" \
  -- -e "mcptools::mcp_server()"

Hugging Face server:

claude mcp add hf-mcp-server \
  -e HF_TOKEN=your_token_here \
  -- mcp-remote https://huggingface.co/mcp

Verify configuration:

claude mcp list
claude mcp get r-mcptools

Expected: claude mcp list shows both r-mcptools and hf-mcp-server (or whichever servers were added). claude mcp get r-mcptools displays the correct command and arguments.

On failure: If the server does not appear in the list, verify ~/.claude.json contains the correct entry. If the claude command is not found, add it to PATH: export PATH="$HOME/.claude/local/node_modules/.bin:$PATH".

Step 3: Configure Claude Desktop (Windows)

Edit %APPDATA%\Claude\claude_desktop_config.json:

{
  "mcpServers": {
    "r-mcptools": {
      "command": "C:\\PROGRA~1\\R\\R-45~1.0\\bin\\x64\\Rscript.exe",
      "args": ["-e", "mcptools::mcp_server()"]
    },
    "hf-mcp-server": {
      "command": "mcp-remote",
      "args": ["https://huggingface.co/mcp"],
      "env": {
        "HF_TOKEN": "your_token_here"
      }
    }
  }
}

Important: Use 8.3 short paths for Windows directories with spaces (PROGRA~1 not Program Files). Use environment variables for tokens, not --header arguments.

Expected: The JSON config file at %APPDATA%\Claude\claude_desktop_config.json is valid JSON with the correct server entries. Claude Desktop shows MCP server indicators after restart.

On failure: Validate the JSON with a linter (e.g., jq . < config.json). Use 8.3 short paths (PROGRA~1) if Windows path spaces cause parsing errors. Ensure Claude Desktop is fully restarted (not just minimized).

Step 4: Configure R Session for MCP

Add to project .Rprofile:

if (requireNamespace("mcptools", quietly = TRUE)) {
  mcptools::mcp_session()
}

This starts the MCP session automatically when opening the project in RStudio.

Expected: The .Rprofile file conditionally starts mcptools::mcp_session() when the project is opened in RStudio, making MCP tools available automatically.

On failure: If mcptools is not found at session start, verify it is installed in the library that RStudio uses (check .libPaths()). If using renv, ensure mcptools is in the renv library.

Step 5: Verify Connections

Test R MCP from WSL:

"/mnt/c/Program Files/R/R-4.5.0/bin/Rscript.exe" -e "mcptools::mcp_server()"

Test from within Claude Code:

Start Claude Code and use MCP tools — they should appear in the tool list.

Test Claude Desktop:

Restart Claude Desktop after configuration changes. Check for MCP server indicators in the UI.

Expected: Running Rscript with mcptools::mcp_server() produces output without errors. MCP tools appear in the Claude Code tool list during an active session. Claude Desktop shows server status after restart.

On failure: If the Rscript command fails, check the full path is correct (ls "/mnt/c/Program Files/R/" to verify R version). If tools don't appear in Claude Code, restart the session. For Claude Desktop, check firewall settings.

Step 6: Multi-Server Configuration

Both Claude Code and Claude Desktop support multiple MCP servers simultaneously:

# Claude Code: add multiple servers
claude mcp add r-mcptools stdio "/path/to/Rscript.exe" -- -e "mcptools::mcp_server()"
claude mcp add hf-mcp-server -e HF_TOKEN=token -- mcp-remote https://huggingface.co/mcp
claude mcp add custom-server stdio "/path/to/server" -- --port 3001

Expected: Multiple MCP servers configured and accessible simultaneously. claude mcp list shows all servers. Each server's tools are available in the same Claude Code session.

On failure: If servers conflict, check that each has a unique name in the configuration. If one server blocks others, verify servers use non-blocking I/O (stdio transport handles this automatically).

Validation

claude mcp list shows all configured servers
R MCP server responds to tool calls
Hugging Face MCP server authenticates and responds
Both Claude Code and Claude Desktop can connect (if both configured)
MCP tools appear in the tool list during sessions

Common Pitfalls

Windows path spaces: Use 8.3 short names or quote paths correctly. Different tools parse paths differently.
Token in command args: On Windows, --header "Authorization: Bearer token" fails due to parsing. Use environment variables instead.
Confusing Claude Code and Claude Desktop configs: These are separate tools with separate config files (~/.claude.json vs %APPDATA%\Claude\)
npx vs global install: npx mcp-remote may fail in Claude Desktop context. Install globally with npm install -g mcp-remote.
mcptools version: Ensure mcptools is up to date. It requires the ellmer package as a dependency.

Related Skills

build-custom-mcp-server - creating your own MCP server
troubleshoot-mcp-connection - debugging connection issues
setup-wsl-dev-environment - WSL setup prerequisite

configure-mcp-server