Mac OS X R error “ld: warning: directory not found for option”

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You need to modify the ~/.R/Makevars file. For a greater overview of this see: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#OS-X-packages

Alternatively, this has been answered before in a bit more depth by @kevin-ushey in Rcpp warning: “directory not found for option ‘-L/usr/local/Cellar/gfortran/4.8.2/gfortran'”.

What is happening is your code is not being run under gcc instead it is being forwarded to clang

You will need to change your compile statements in ~/.R/Makevars/ to gcc using:

VER=-5.3.0 
CC=gcc$(VER)
CXX=g++$(VER)
CFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
CXXFLAGS=-mtune=native -g -O2 -Wall -pedantic -Wconversion
FLIBS=-L/usr/local/Cellar/gcc/5.3.0/lib/gcc/5

This assumes you have already installed gcc via homebrew under:

brew install gcc

(gfortran ships with gcc in brew now)

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