Quick note:
This is required on R 3.6.0. R version 3.6.1 and higher does not need this statement.
That said, better flag instructions probably would be:
sudo mkdir -p ~/.R
# Fill with appropriate flag statements
sudo cat <<- EOF > ~/.R/Makevars
# clang: start
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
# clang: end
EOF
Note the addition of CPPFLAGS.