Configure MCP Server

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

Use When

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

In

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

Do

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

→ mcptools installs from GitHub + loads in R w/o errs. mcp-remote avail globally via which mcp-remote or npm list -g mcp-remote.

If err: mcptools → ensure remotes installed first. GitHub rate-limits install → set GITHUB_PAT in ~/.Renviron. mcp-remote → valid. Node.js + npm installed + 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 config:

claude mcp list
claude mcp get r-mcptools

→ claude mcp list shows both r-mcptools + hf-mcp-server (or whichever added). claude mcp get r-mcptools displays correct cmd + args.

If err: Server not in list → valid. ~/.claude.json contains correct entry. claude cmd not found → add 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 dirs w/ spaces (PROGRA~1 not Program Files). Use env vars for tokens, not --header args.

→ JSON config file at %APPDATA%\Claude\claude_desktop_config.json valid JSON w/ correct server entries. Claude Desktop shows MCP server indicators post-restart.

If err: Valid. JSON w/ linter (e.g., jq . < config.json). Use 8.3 short paths (PROGRA~1) if Windows path spaces cause parse errs. Ensure Claude Desktop fully restarted (not just minimized).

Step 4: Configure R Session for MCP

Add to project .Rprofile:

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

Starts MCP session auto when opening project in RStudio.

→ .Rprofile conditionally starts mcptools::mcp_session() when project opened in RStudio → MCP tools avail auto.

If err: mcptools not found at session start → valid. installed in library RStudio uses (check .libPaths()). Using renv → ensure mcptools in 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 w/in Claude Code:

Start Claude Code + use MCP tools → they should appear in tool list.

Test Claude Desktop:

Restart Claude Desktop post-config changes. Check for MCP server indicators in UI.

→ Rscript w/ mcptools::mcp_server() produces out w/o errs. MCP tools appear in Claude Code tool list during active session. Claude Desktop shows server status post-restart.

If err: Rscript fails → check full path correct (ls "/mnt/c/Program Files/R/" to valid. R ver). Tools don't appear in Claude Code → restart session. Claude Desktop → check firewall.

Step 6: Multi-Server Configuration

Both Claude Code + Claude Desktop support multi 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

→ Multi MCP servers config'd + accessible simultaneously. claude mcp list shows all. Each server's tools avail in same Claude Code session.

If err: Servers conflict → check each has unique name in config. One server blocks others → valid. servers use non-blocking I/O (stdio transport handles auto).

Check

• claude mcp list shows all config'd servers
• R MCP server responds to tool calls
• Hugging Face MCP server auths + responds
• Both Claude Code + Claude Desktop can connect (if both config'd)
• MCP tools appear in tool list during sessions

Traps

• Windows path spaces: Use 8.3 short names or quote paths correct. Diff tools parse paths differently.
• Token in cmd args: Windows, --header "Authorization: Bearer token" fails due to parsing. Use env vars instead.
• Confuse Claude Code + Claude Desktop configs: Separate tools w/ separate config files (~/.claude.json vs %APPDATA%\Claude\)
• npx vs global install: npx mcp-remote may fail in Claude Desktop context. Install globally w/ npm install -g mcp-remote.
• mcptools ver: Ensure mcptools up to date. Requires ellmer pkg as dep.

→

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