Configure putior MCP Server

Configure putior MCP Server

Set up the putior MCP server so AI assistants (Claude Code, Claude Desktop) can directly call workflow annotation and diagram generation tools.

When to Use

• Enabling AI assistants to interactively annotate and visualize workflows
• Setting up a new development environment with putior MCP integration
• After installing putior and wanting AI-assisted workflow documentation
• Configuring agent-to-agent communication via ACP for automated pipelines

Inputs

• Required: putior installed (see install-putior)
• Required: Target client: Claude Code, Claude Desktop, or both
• Optional: Whether to also configure ACP server (default: no)
• Optional: Custom host/port for ACP server (default: localhost:8080)

Procedure

Step 1: Install MCP Dependencies

Install the required packages for MCP server functionality.

# Required: MCP framework
remotes::install_github("posit-dev/mcptools")

# Required: Tool definition framework
install.packages("ellmer")

# Verify both load
library(mcptools)
library(ellmer)

Expected: Both packages install and load without errors.

On failure: mcptools requires remotes package. Install it first: install.packages("remotes"). If GitHub rate-limits, configure a GITHUB_PAT in ~/.Renviron (add the line GITHUB_PAT=your_token_here and restart R). Do not paste tokens into shell commands or commit them to version control.

Step 2: Configure Claude Code (WSL/Linux/macOS)

Add the putior MCP server to Claude Code's configuration.

# One-line setup
claude mcp add putior -- Rscript -e "putior::putior_mcp_server()"

For WSL with Windows R:

claude mcp add putior -- "/mnt/c/Program Files/R/R-4.5.2/bin/Rscript.exe" -e "putior::putior_mcp_server()"

Verify the configuration:

claude mcp list
claude mcp get putior

Expected: putior appears in the MCP server list with status "configured".

On failure: If Claude Code is not in PATH, add it: export PATH="$HOME/.claude/local/node_modules/.bin:$PATH". If the Rscript path is wrong, locate R with which Rscript or ls "/mnt/c/Program Files/R/".

Step 3: Configure Claude Desktop (Windows)

Add putior to Claude Desktop's MCP configuration file.

Edit %APPDATA%\Claude\claude_desktop_config.json:

{
  "mcpServers": {
    "putior": {
      "command": "C:\\PROGRA~1\\R\\R-45~1.0\\bin\\x64\\Rscript.exe",
      "args": ["-e", "putior::putior_mcp_server()"]
    }
  }
}

Or with the full path:

{
  "mcpServers": {
    "putior": {
      "command": "C:\\Program Files\\R\\R-4.5.2\\bin\\x64\\Rscript.exe",
      "args": ["-e", "putior::putior_mcp_server()"]
    }
  }
}

Restart Claude Desktop after editing the configuration.

Expected: Claude Desktop shows putior in its MCP server list. Tools become available in conversation.

On failure: Validate JSON syntax with a JSON linter. Check that the R path exists. Use 8.3 short names (PROGRA~1, R-45~1.0) if spaces in paths cause issues.

Step 4: Verify All 16 Tools

Test that all MCP tools are accessible and functional.

# Get tool definitions
tools <- putior::putior_mcp_tools()
cat(sprintf("Total tools: %d\n", length(tools)))

# List tool names
vapply(tools, function(t) t$name, character(1))

The 16 tools organized by category:

Core Workflow (5):

• put — Scan files for PUT annotations (supports exclude parameter for regex-based file filtering)
• put_diagram — Generate Mermaid diagrams
• put_auto — Auto-detect workflow from code (supports exclude parameter)
• put_generate — Generate annotation suggestions (supports exclude parameter)
• put_merge — Merge manual + auto annotations (supports exclude parameter)

Reference/Discovery (7):

• get_comment_prefix — Get comment prefix for extension
• get_supported_extensions — List supported extensions
• list_supported_languages — List supported languages
• get_detection_patterns — Get auto-detection patterns
• get_diagram_themes — List available themes
• putior_guide — AI assistant documentation
• putior_help — Quick reference help

Utilities (3):

• is_valid_put_annotation — Validate annotation syntax
• split_file_list — Parse file lists
• ext_to_language — Extension to language name

Configuration (1):

• set_putior_log_level — Configure logging verbosity

Important: Custom palettes cannot be used through MCP. The palette parameter on put_diagram accepts a putior_theme R object created by put_theme(). Because MCP communicates via JSON, R objects like putior_theme cannot be serialized across the MCP boundary. When calling put_diagram through MCP, use the string-based theme parameter (e.g., theme = "viridis") instead. For custom palettes, call put_theme() and put_diagram(palette = ...) directly in an R session.

Test core tools from Claude Code:

Use the putior_help tool to see available commands
Use the put tool to scan ./R/ for annotations
Use the put_diagram tool to generate a diagram

Expected: All 16 tools listed. Core tools return expected results when called with valid inputs.

On failure: If tools are missing, check that putior version is current: packageVersion("putior"). Older versions may have fewer tools. Update with remotes::install_github("pjt222/putior").

Step 5: Configure ACP Server (Optional)

Set up the ACP (Agent Communication Protocol) server for agent-to-agent communication.

# Install ACP dependency
install.packages("plumber2")

# Start ACP server (blocks — run in a separate R session or background)
putior::putior_acp_server()

# Custom host/port
putior::putior_acp_server(host = "0.0.0.0", port = 9000)

Test ACP endpoints:

# Discover agent
curl http://localhost:8080/agents

# Execute a scan
curl -X POST http://localhost:8080/runs \
  -H "Content-Type: application/json" \
  -d '{"input": [{"role": "user", "parts": [{"content": "scan ./R/"}]}]}'

# Generate diagram
curl -X POST http://localhost:8080/runs \
  -H "Content-Type: application/json" \
  -d '{"input": [{"role": "user", "parts": [{"content": "generate diagram for ./R/"}]}]}'

Expected: ACP server starts on the configured port. /agents returns the putior agent manifest. /runs accepts natural language requests and returns workflow results.

On failure: If port 8080 is in use, specify a different port. If plumber2 is not installed, the server function will print a helpful error message suggesting installation.

Validation

• putior::putior_mcp_tools() exposes the core tools (put, put_diagram, put_auto, put_generate, put_merge) and returns ~16 tools for the current version
• Claude Code: claude mcp list shows putior configured
• Claude Code: putior_help tool returns help text when invoked
• Claude Desktop: putior appears in the MCP server list after restart
• Core tools (put, put_diagram, put_auto) execute without errors
• (Optional) ACP server responds to curl http://localhost:8080/agents

Common Pitfalls

• mcptools not installed: The MCP server requires mcptools (from GitHub) and ellmer (from CRAN). Both must be installed. putior checks and provides helpful messages if they're missing.
• Wrong R path in Claude Desktop: Windows paths need escaping in JSON (\\). Use 8.3 short names to avoid spaces: C:\\PROGRA~1\\R\\R-45~1.0\\bin\\x64\\Rscript.exe.
• Forgetting to restart: Claude Desktop must be restarted after editing the config file. Claude Code picks up changes on next session start.
• renv isolation: If putior is installed in an renv library but Claude Code/Desktop launches R without renv, the packages won't be found. Ensure mcptools and ellmer are installed in the global library or configure renv activation in the MCP server command.
• Port conflicts for ACP: The default ACP port (8080) is commonly used. Check with lsof -i :8080 or netstat -tlnp | grep 8080 before starting.
• Including only specific tools: To expose a subset of tools, use putior_mcp_tools(include = c("put", "put_diagram")) when building custom MCP server wrappers.
• Custom palettes via MCP: The palette parameter on put_diagram requires a putior_theme R object (created by put_theme()), which cannot be serialized through MCP's JSON interface. Use the built-in theme parameter string for MCP calls. For custom palettes, use R directly.

Related Skills

• install-putior — prerequisite: putior and optional deps must be installed
• configure-mcp-server — general MCP server configuration for Claude Code/Desktop
• troubleshoot-mcp-connection — diagnose connection issues if tools don't appear
• build-custom-mcp-server — build custom MCP servers that wrap putior tools
• analyze-codebase-workflow — use MCP tools interactively for codebase analysis