Add Rcpp Integration

Integrate C++ code into an R package using Rcpp for performance-critical operations.

When to Use

• R function is too slow and profiling confirms a bottleneck
• Need to interface with existing C/C++ libraries
• Implementing algorithms that benefit from compiled code (loops, recursion)
• Adding RcppArmadillo for linear algebra operations

Inputs

• Required: Existing R package
• Required: R function to replace or augment with C++
• Optional: External C++ library to interface with
• Optional: Whether to use RcppArmadillo (default: plain Rcpp)

Procedure

Step 1: Set Up Rcpp Infrastructure

usethis::use_rcpp()

This:

• Creates src/ directory
• Adds Rcpp to LinkingTo and Imports in DESCRIPTION
• Creates R/packagename-package.R with @useDynLib and @importFrom Rcpp sourceCpp
• Updates .gitignore for compiled files

For RcppArmadillo:

usethis::use_rcpp_armadillo()

Expected: src/ directory created, DESCRIPTION updated with Rcpp in LinkingTo and Imports, and R/packagename-package.R contains @useDynLib directive.

On failure: If usethis::use_rcpp() fails, manually create src/, add LinkingTo: Rcpp and Imports: Rcpp to DESCRIPTION, and add #' @useDynLib packagename, .registration = TRUE and #' @importFrom Rcpp sourceCpp to the package-level documentation file.

Step 2: Write C++ Function

Create src/my_function.cpp:

#include <Rcpp.h>
using namespace Rcpp;

//' Compute cumulative sum efficiently
//'
//' @param x A numeric vector
//' @return A numeric vector of cumulative sums
//' @export
// [[Rcpp::export]]
NumericVector cumsum_cpp(NumericVector x) {
  int n = x.size();
  NumericVector out(n);
  out[0] = x[0];
  for (int i = 1; i < n; i++) {
    out[i] = out[i - 1] + x[i];
  }
  return out;
}

For RcppArmadillo:

#include <RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo)]]

//' Matrix multiplication using Armadillo
//'
//' @param A A numeric matrix
//' @param B A numeric matrix
//' @return The matrix product A * B
//' @export
// [[Rcpp::export]]
arma::mat mat_mult(const arma::mat& A, const arma::mat& B) {
  return A * B;
}

Expected: C++ source file exists at src/my_function.cpp with valid // [[Rcpp::export]] annotation and roxygen-style //' documentation comments.

On failure: Verify the file uses #include <Rcpp.h> (or <RcppArmadillo.h> for Armadillo), that the export annotation is on its own line directly above the function signature, and that return types map to valid Rcpp types.

Step 3: Generate RcppExports

Rcpp::compileAttributes()
devtools::document()

Expected: R/RcppExports.R and src/RcppExports.cpp generated automatically.

On failure: Check C++ syntax errors. Ensure // [[Rcpp::export]] tag is present above each exported function.

Step 4: Verify Compilation

devtools::load_all()

Expected: Package compiles and loads without errors.

On failure: Check compiler output for errors. Common issues:

• Missing system headers: Install development libraries
• Syntax errors: C++ compiler messages point to the line
• Missing Rcpp::depends attribute for RcppArmadillo

Step 5: Write Tests for Compiled Code

test_that("cumsum_cpp matches base R", {
  x <- c(1, 2, 3, 4, 5)
  expect_equal(cumsum_cpp(x), cumsum(x))
})

test_that("cumsum_cpp handles edge cases", {
  expect_equal(cumsum_cpp(numeric(0)), numeric(0))
  expect_equal(cumsum_cpp(c(NA_real_, 1)), c(NA_real_, NA_real_))
})

Expected: Tests pass, confirming the C++ function produces identical results to the R equivalent and handles edge cases (empty vectors, NA values) correctly.

On failure: If tests fail on NA handling, add explicit NA checks in the C++ code using NumericVector::is_na(). If tests fail on empty input, add a guard clause for zero-length vectors at the top of the function.

Step 6: Add Cleanup Script

Create src/Makevars:

PKG_CXXFLAGS = -O2

Create cleanup in package root (for CRAN):

#!/bin/sh
rm -f src/*.o src/*.so src/*.dll

Make executable: chmod +x cleanup

Expected: src/Makevars sets compiler flags and cleanup script removes compiled objects. Both files exist at the package root level.

On failure: Verify cleanup has execute permissions (chmod +x cleanup) and that Makevars uses tabs (not spaces) for indentation if adding Makefile-style rules.

Step 7: Update .Rbuildignore

Ensure compiled artifacts are handled:

^src/.*\.o$
^src/.*\.so$
^src/.*\.dll$

Expected: .Rbuildignore patterns prevent compiled object files from being included in the package tarball, while preserving source files and Makevars.

On failure: Run devtools::check() and look for NOTEs about unexpected files in src/. Adjust .Rbuildignore patterns to exclude only .o, .so, and .dll files.

Validation

• devtools::load_all() compiles without warnings
• Compiled function produces correct results
• Tests pass for edge cases (NA, empty, large inputs)
• R CMD check passes with no compilation warnings
• RcppExports files are generated and committed
• Performance improvement confirmed with benchmarks

Common Pitfalls

• Forgetting compileAttributes(): Must regenerate RcppExports after changing C++ files
• Integer overflow: Use double instead of int for large numeric values
• Memory management: Rcpp handles memory automatically for Rcpp types; don't manually delete
• NA handling: C++ doesn't know about R's NA. Check with Rcpp::NumericVector::is_na()
• Platform portability: Avoid platform-specific C++ features. Test on Windows, macOS, and Linux.
• Missing @useDynLib: The package-level doc must include @useDynLib packagename, .registration = TRUE

Related Skills

• create-r-package - package setup before adding Rcpp
• write-testthat-tests - testing compiled functions
• setup-github-actions-ci - CI must have C++ toolchain
• submit-to-cran - compiled packages need extra CRAN checks