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

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

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.

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.

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.

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

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