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

# Run automated setup
npm run setup

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

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

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

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

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

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

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 ✔

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

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..."

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()"]

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..."

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

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)

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?"

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

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."

"Run the tests"

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

"Install devtools, testthat, and roxygen2"

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

"Execute: covr::package_coverage()"

"Execute: spelling::spell_check_package()"

npm run watch

which Rscript  # Linux/Mac
where Rscript  # Windows

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

Error: package 'jmvtools' is not available

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

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

# Windows: Run terminal as Administrator if needed

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