RStan Mojave Mac OS X Prerequisite Installation Instructions

This page describes the prerequisite C++ toolchain installation procedure for RStan on the Mojave version Mac OS X. They should also work for pre-Mojave versions of Mac OS X, but in that case we instead recommend a different installer. Mojave seems to break a lot of things in different ways for different people, so if you run into trouble, ask on https://discourse.mc-stan.org/ .

First, determine if you already have Xcode installed

• Type command + space to open Spotlight.
• In the upper right of your screen, where Spotlight opens, enter xcode into the search box.
• If Xcode does not pop up under "Applications" heading, you do not have Xcode installed.
  • Open "App Store" application
  • Search for 'xcode', choose Xcode, and follow its steps to install Xcode (using all default options is fine for Stan).
  • Open Xcode once to accept the license agreement (don't forget this step!!)
• If Xcode does pop up under "Applications", make sure you have the latest version.
  • Click command + space to open Spotlight.
  • Enter enter app store into search box for Spotlight in upper right of your screen.
  • Click on App Store under Applications to open.
  • In App Store, click on Updates menu item (below blue downarrow).
  • If Xcode has an update, click to install.
  • Open Xcode once to accept the license agreement (don't forget this step!!)

Thanks to the notes here by @coatless for the instructions below. First, run in the command line:

sudo installer -pkg \
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \
-target /

Then, fix ~/.R/Makevars:

sudo touch ~/.R/Makevars && sudo echo 'CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"' >> ~/.R/Makevars

Then start R and run install.packages('rstan').