rstudio-mcp-server

lerlerchan/rstudio-mcp-server

3.2

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A Model Context Protocol (MCP) server for RStudio Desktop integration, enabling seamless R package development, testing, and jamovi module development from VSCode and other MCP clients.

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RStudio MCP Server

A Model Context Protocol (MCP) server for RStudio Desktop integration, enabling seamless R package development, testing, and jamovi module development from VSCode and other MCP clients.

Features

R Package Development

  • Testing: Run package tests with devtools::test() or individual test files with testthat::test_file()
  • Documentation: Generate documentation with devtools::document() (roxygen2)
  • Building: Build packages with devtools::build()
  • Checking: Run R CMD check with devtools::check()
  • Loading: Load package functions with devtools::load_all() for interactive development

Jamovi Module Development

  • Build: Build jamovi modules with jmvtools::build()
  • Check: Validate jamovi modules with jmvtools::check()

General R Capabilities

  • Code Execution: Run arbitrary R code
  • Package Management: Install and list packages
  • Workspace Inspection: List and inspect R workspace objects

Quick Start

Automated Setup (Recommended)

Run the automated setup script to check prerequisites and configure everything:

# Clone the repository
git clone <repository-url>
cd rstudio-mcp-server

# Run automated setup
npm run setup

The setup script will:

  • Check Node.js and R installation
  • Install npm dependencies
  • Build the server
  • Verify R package requirements
  • Guide you through MCP client configuration

Manual Installation

If you prefer manual setup:

  1. Install Prerequisites

    • Node.js v18 or higher (nodejs.org)
    • R 3.6 or higher with Rscript in PATH
    • Git (for cloning)

  2. Clone and Build

    git clone <repository-url>
cd rstudio-mcp-server
npm install
npm run build

  3. Install R Packages

    install.packages(c("devtools", "testthat", "roxygen2"))

  4. Configure MCP Client (see Configuration section below)

Configuration

For VSCode with Claude Code

Add to your Claude Code MCP settings file (usually ~/.config/claude-code/mcp_settings.json on Linux/Mac or %APPDATA%\claude-code\mcp_settings.json on Windows):

{
  "mcpServers": {
    "rstudio": {
      "command": "node",
      "args": ["/path/to/rstudio-mcp-server/build/index.js"]
    }
  }
}

For Cline or Other MCP Clients

Add to the appropriate MCP settings file for your client:

{
  "mcpServers": {
    "rstudio": {
      "command": "node",
      "args": ["/absolute/path/to/rstudio-mcp-server/build/index.js"]
    }
  }
}

Available Tools

r_execute

Execute arbitrary R code.

Parameters:

  • code (required): The R code to execute
  • working_dir (optional): Working directory for execution

Example:

{
  "code": "summary(mtcars)",
  "working_dir": "/path/to/project"
}

r_test_package

Run tests for an R package using devtools::test().

Parameters:

  • package_path (required): Path to the R package directory
  • filter (optional): Test filter pattern (regex)

Example:

{
  "package_path": "/path/to/mypackage",
  "filter": "test-myfunction"
}

r_test_file

Run a specific test file.

Parameters:

  • test_file (required): Path to the test file

Example:

{
  "test_file": "/path/to/mypackage/tests/testthat/test-myfunction.R"
}

r_check_package

Run R CMD check on a package.

Parameters:

  • package_path (required): Path to the R package directory
  • args (optional): Additional arguments for R CMD check

Example:

{
  "package_path": "/path/to/mypackage",
  "args": "--as-cran"
}

r_document_package

Generate documentation for an R package using roxygen2.

Parameters:

  • package_path (required): Path to the R package directory

r_build_package

Build an R package.

Parameters:

  • package_path (required): Path to the R package directory
  • binary (optional): Build a binary package (default: false)

r_load_all

Load all functions in a package for interactive development.

Parameters:

  • package_path (required): Path to the R package directory

r_install_package

Install an R package from CRAN or local path.

Parameters:

  • package (required): Package name or path
  • dependencies (optional): Install dependencies (default: true)

r_list_packages

List all installed R packages.

r_workspace_ls

List objects in the R workspace.

Parameters:

  • pattern (optional): Pattern to filter object names

jamovi_build_module

Build a jamovi module.

Parameters:

  • module_path (required): Path to the jamovi module directory
  • install (optional): Install the module after building (default: false)

jamovi_check_module

Check a jamovi module for issues.

Parameters:

  • module_path (required): Path to the jamovi module directory

Usage Examples

Quick Start Examples

Once configured, you can interact with R through natural language:

Test R connection:

  • "Can you list all installed R packages?"
  • "What version of R is running?"
  • "Execute this R code: print(sessionInfo())"

Package development:

  • "Run the tests for this package"
  • "Generate documentation for my package"
  • "Check if this package passes R CMD check"
  • "Build this package"

Code execution:

  • "Execute this R code: summary(mtcars)"
  • "Install the tidyverse package"
  • "Show me what objects are in the workspace"

Detailed Workflows

1. Starting a New Package
You: "I'm creating a new R package called 'datautils'. Can you help me set it up?"

Claude: [Guides you through using usethis::create_package()]

You: "Now document the package"

Claude: [Uses r_document_package tool]
Output: ✔ Writing 'NAMESPACE'
        ✔ Writing 'datautils.Rd'

You: "Check if it passes R CMD check"

Claude: [Uses r_check_package tool]
Output: ── R CMD check results ─────────────────────
        0 errors ✔ | 0 warnings ✔ | 0 notes ✔
2. Test-Driven Development
You: "Run all tests in the package"

Claude: [Uses r_test_package tool]
Output: ✔ | F W S  OK | Context
        ✔ |         5 | validation
        ✔ |         8 | data-processing
        ✔ |         3 | output-formatting

You: "Run only tests matching 'validation'"

Claude: [Uses r_test_package with filter: "validation"]
Output: ✔ | F W S  OK | Context
        ✔ |         5 | validation

You: "Run the specific test file test-validation.R"

Claude: [Uses r_test_file tool]
Output: Test results for tests/testthat/test-validation.R
        ✔ | 5 tests passed
3. Debugging Failing Tests
You: "Run the package tests"

Claude: [Uses r_test_package tool]
Output: ✖ | F W S  OK | Context
        ✖ |     1   4 | validation
        ────────────────────────────────────────────
        Failure (test-validation.R:15:3): input validation works
        Expected TRUE, got FALSE

You: "Can you execute this R code to debug:
     source('R/validation.R');
     validate_input(c(1, 2, NA))"

Claude: [Uses r_execute tool]
Output: Error: NA values not allowed

You: "Now I see the issue. Let me fix the code and re-run tests..."
4. Package Release Workflow
You: "I'm ready to release my package. Let's go through the checklist."

Claude: "I'll help you verify everything:
        1. First, let's run the tests"
        [Uses r_test_package - shows all passing]

Claude: "2. Generating documentation"
        [Uses r_document_package]

Claude: "3. Running R CMD check"
        [Uses r_check_package with args: "--as-cran"]

Claude: "4. Building the package"
        [Uses r_build_package]
        Output: ✔ Building 'datautils_1.0.0.tar.gz'

You: "Perfect! Can you also check for any spelling issues?"

Claude: [Uses r_execute with "spelling::spell_check_package()"]
5. Jamovi Module Development
You: "I'm working on a jamovi module. Can you check it for issues?"

Claude: [Uses jamovi_check_module tool]
Output: ✔ Checking module structure
        ✔ Validating .a.yaml files
        ✔ Checking R functions
        ✔ Verifying UI definitions

You: "Build and install the module"

Claude: [Uses jamovi_build_module with install: true]
Output: ✔ Building module
        ✔ Installing to jamovi
        Module 'mymodule' installed successfully

You: "Now I'll test it in jamovi..."
6. Interactive Data Analysis
You: "Can you execute this analysis:
     library(dplyr)
     mtcars %>%
       group_by(cyl) %>%
       summarize(
         mean_mpg = mean(mpg),
         mean_hp = mean(hp)
       )"

Claude: [Uses r_execute tool]
Output: # A tibble: 3 × 3
          cyl mean_mpg mean_hp
        <dbl>    <dbl>   <dbl>
      1     4     26.7    82.6
      2     6     19.7   122.
      3     8     15.1   209.

You: "Now create a linear model of mpg vs hp"

Claude: [Uses r_execute tool]
Output: Call:
        lm(formula = mpg ~ hp, data = mtcars)

        Coefficients:
        (Intercept)           hp
           30.09886     -0.06823
7. Package Installation and Management
You: "Install the ggplot2 package"

Claude: [Uses r_install_package tool]
Output: Installing package into '/home/user/R/library'
        ✔ Package 'ggplot2' successfully installed

You: "List all packages containing 'test' in the name"

Claude: [Uses r_list_packages tool, then filters]
Output: Packages matching 'test':
        - testthat (3.2.0)
        - testit (0.13)
        - covr (3.6.1)
8. Working with Multiple Packages
You: "I have three packages I'm developing. Can you run tests on all of them?
     - /path/to/package1
     - /path/to/package2
     - /path/to/package3"

Claude: "I'll test each package:

Package 1:
[Uses r_test_package for package1]
✔ All 15 tests passed

Package 2:
[Uses r_test_package for package2]
✔ All 22 tests passed

Package 3:
[Uses r_test_package for package3]
✖ 2 tests failed
[Shows failure details]

Two packages passed, but package3 has failing tests. Would you like me to show the specific failures?"
9. Development Environment Setup
You: "I'm setting up a new development machine. What R packages do I need?"

Claude: "Let me check what's installed"
        [Uses r_list_packages tool]

Claude: "I see you're missing some key development packages. I can install:
        - devtools (package development)
        - testthat (testing)
        - roxygen2 (documentation)
        - usethis (workflow automation)

        Should I install these?"

You: "Yes, please install them"

Claude: [Uses r_install_package for each package]
        ✔ All development packages installed
10. CI/CD Preparation
You: "I want to make sure my package will pass CI checks. Run all quality checks."

Claude: "I'll run a comprehensive check:

1. Tests:
[Uses r_test_package]
✔ All 45 tests passed

2. Documentation:
[Uses r_document_package]
✔ Documentation up to date

3. R CMD check:
[Uses r_check_package with args: "--as-cran"]
✔ 0 errors | 0 warnings | 0 notes

4. Package build:
[Uses r_build_package]
✔ Package builds successfully

Your package is ready for CI! All checks passed."

Common Use Cases

Quick test after code changes:

"Run the tests"

Full pre-commit check:

"Run tests, update docs, and run R CMD check"

Install development dependencies:

"Install devtools, testthat, and roxygen2"

Debug a specific function:

"Execute this code: debugonce(my_function); my_function(test_data)"

Check test coverage:

"Execute: covr::package_coverage()"

Spell check documentation:

"Execute: spelling::spell_check_package()"

Development

Watch mode for development:

npm run watch

Troubleshooting

R not found

Make sure R and Rscript are in your system PATH:

which Rscript  # Linux/Mac
where Rscript  # Windows

Windows PATH setup:

  1. Find your R installation (usually C:\Program Files\R\R-4.x.x\bin)
  2. Add to PATH:
    • Search "Environment Variables" in Start menu
    • Edit "Path" under System variables
    • Add new entry: C:\Program Files\R\R-4.x.x\bin
    • Restart terminal/VSCode

Multiple R versions:

  • Ensure the correct R version is first in PATH
  • Check with: Rscript --version

devtools/testthat not found

Install required R packages:

install.packages(c("devtools", "testthat", "roxygen2"))

jamovi tools not found

Installing jmvtools requires special considerations. See for detailed instructions.

Quick summary:

  • Option 1: Install Rtools (Windows) or build tools (Mac/Linux), then install.packages("jmvtools")
  • Option 2: Use jamovi's bundled R (recommended for jamovi developers)
  • Option 3: Install pre-built binaries

Common issue: jmvtools requires compilation tools:

Error: package 'jmvtools' is not available

See the dedicated jmvtools guide for platform-specific solutions.

Build failures

TypeScript errors:

# Clean rebuild
rm -rf build node_modules
npm install
npm run build

Permission errors:

# Linux/Mac
chmod +x build/index.js

# Windows: Run terminal as Administrator if needed

MCP client connection issues

Server not appearing in MCP client:

  1. Verify JSON syntax in config file (use a JSON validator)
  2. Use absolute paths (not relative: ~/ or .\)
  3. Restart the MCP client completely
  4. Check client logs for error messages

Windows path format:

{
  "args": ["D:\\path\\to\\server\\build\\index.js"]  // Use double backslashes
  // OR
  "args": ["D:/path/to/server/build/index.js"]       // Use forward slashes
}

Contributing

Contributions are welcome! Please feel free to submit issues or pull requests.

License

MIT