Install clang6 for R toolchain on macOS

r-tools-clang6.sh

# originally caused by issues installing rgdal and pgirmess
# i.e. "configuration failed for package 'rgdal'"

# Install the macOS toolchain for versions of R starting at 3.5.z.

# 1) Delete all references to clang 4

sudo rm -rf /usr/local/clang4

sudo rm -rf /usr/local/gfortran
sudo rm -rf /usr/local/bin/gfortran

sudo rm -rf /private/var/db/receipts/com.gnu.gfortran.bom
sudo rm -rf /private/var/db/receipts/com.gnu.gfortran.plist

sudo rm -rf /private/var/db/receipts/com.rbinaries.clang4.bom
sudo rm -rf /private/var/db/receipts/com.rbinaries.clang4.plist

sudo rm -rf ~/.R/Makevars

# 2) Download and install clang-6.0.0 

curl -O https://cran.r-project.org/bin/macosx/tools/clang-6.0.0.pkg
sudo installer -pkg clang-6.0.0.pkg -target /
rm -rf clang-6.0.0.pkg

# 3) Run the installer for clang-6.0.0.pkg 
if [ ! -e "~/.Renviron" ] ; then
   touch ~/.Renviron
fi
echo 'PATH="/usr/local/clang6/bin:${PATH}"' >> ~/.Renviron

# 4) Download and run the installer for gfortran-6.1.pkg
curl -O https://cloud.r-project.org/bin/macosx/tools/gfortran-6.1.pkg
sudo installer -pkg gfortran-6.1.pkg -target /
rm -rf gfortran-6.1.pkg

# 5) Establish a symlink of gfortran into /usr/local/bin
sudo ln -s /usr/local/gfortran/bin/gfortran /usr/local/bin/gfortran

# 6) Install the package again, i.e.
install.packages("pgirmess", type="source")