Disclaimer: I claim no deep understanding of how this all works. I just know that it works, and that I could not find any resource that described each step.

This description assumes a clean install of Monterey (no previous install of rstan or the C++ Toolchain for rstan). It borrows extensively from https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ If you do have a previous install of the C++ Toolchain for rstan, see this post to uninstall relevant files.

Install Command Line Tools

  • open Terminal (located in Applications/Utilities)
  • type gcc
  • you will get a prompt to install Command Line Tools if you don’t have them

Install the latest version of R:

First install Xquartz

Then install R:

Note that it says “for macOS 11 (Big Sur) and higher”, this is something we need to take into account during the configuration of the C++ toolchain.

Configuring C++ Toolchain for rstan

Install gfortran for macOS Big Sur:

We need the gfortran version for Big Sur (not the one for Monterey), because the installed R version was compiled for Big Sur.

This installs gfortran in /usr/local/. However, R needs it to be in /opt/R/arm64/. So we just make a symlink to /usr/local/gfortran in /opt/R/arm64/.

  • open a Terminal window
  • type sudo ln -s /usr/local/gfortran /opt/R/arm64/gfortran and enter your admin password

Check if you can compile C++ code from R

Borrowed from: https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/

First, install Rcpp and RcppArmadillo within R.

install.packages(c('Rcpp', 'RcppArmadillo'))

Create a new file and name it: helloworld.cpp

By adding the .cpp extension, the file is interpreted as C++ code.

Within the file write:

#include <RcppArmadillo.h>

// [[Rcpp::depends(RcppArmadillo)]]

// [[Rcpp::export]]
void hello_world() {
  Rcpp::Rcout << "Hello World!" << std::endl;

// After compile, this function will be immediately called using
// the below snippet and results will be sent to the R console.

/*** R

Then in the R console type:


where path/to/file/ is the location containing helloworld.cpp

If everything is installed appropriately, then you should see the following in the console:

> hello_world()

Hello World!

Optimize compiler (optional)

Borrowed from https://github.com/stan-dev/rstan/wiki/Configuring-C—Toolchain-for-Mac Optionally you can optimize the compiler by running the following lines in R:

dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (!file.exists(M)) file.create(M)
arch <- ifelse(R.version$arch == "aarch64", "arm64e", "x86_64")
cat(paste("\nCXX14FLAGS += -O3 -mtune=native -arch", arch, "-ftemplate-depth-256"),
    file = M, sep = "\n", append = FALSE)

Install rstan

Run the following lines in R.

install.packages("rstan", repos = "https://cloud.r-project.org/", dependencies = TRUE)

To verify your installation, you can run the rstan example/test model:

example(stan_model, package = "rstan", run.dontrun = TRUE)

If the chains run without errors, everything worked!