OUTDATED Build R with OpenBLAS and OpenMP support on MacOS 10.14 (Mojave)

These instructions have been updated (August 2019) to account for the fact that Homebrew no longer allows optional installation arguments. If you’ve landed on this page from an external site, you most likely want to use the new instructions here. I’ve left this old version of page active for reference

These instructions are to compile R from source on MacOS 10.14 (Mojave) so that it both uses OpenBLAS libraries (for faster computations) and has OpenMP support (to take advantage of multiple cores).

Rationale

While the Clang compilers shipped with R finally support OpenMP for parallel processing, they require their own unique flags. The GNU family of compilers (gcc, g++, etc) don’t play nice with all R packages when building them from source. I figured both out the hard way.

To get R to work with both OpenMP (after compiling with OpenBLAS) and packages built from source, I use a newer, non-Apple version of the LLVM compiler.

But why?

Why not?

Seriously, don’t try this if you don’t like the command line or have a low tolerance for potentially borking your R installation. This worked for me and was a (mostly) fun project while setting up a new machine, but YMMV.

Tools

You’ll need:

XCode
Homebrew
~/.R/Makevars

XCode

Install Command Line Tools through XCode
You may need to type xcode-select --install in the terminal after installation, but I got this message which makes me believe this is no longer necessary:
```
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
```
Install missing header files using:
```
cp /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg ~/Desktop
```
Once saved, double click on the install package (which is now on your Desktop). This will place header files (e.g., math.h) in the /usr/include directory, where they have historically been and R still looks for them.

NB: As 10.14 becomes more mature, this intial XCode work-around may not be necessary.

Homebrew packages

Install Homebrew
Brew install some packages:

brew install openblas
brew install r
brew install llvm
brew install ccache
brew install gcc
brew install libgit2
brew install openssl
brew install gettext

Note that you don’t technically need the last three libraries, but many R packages look for them if built from source. You’ll see that they are place in the compilation path in Makevars below.

Set up ~/.R/Makevars

Create Makevars file in ~/.R directory that looks like this

# -------- # Makevars # -------- # Homebrew bin / opt / lib locations HB=/usr/local/bin HO=/usr/local/opt HL=/usr/local/lib # ccache CCACHE=$(HB)/ccache # Make using all cores (set number to your number of cores) MAKE=make -j8 # GNU version (assumes latest in Homebrew as of May 2019) VER=9 # LLVM (Clang) compiler options CC=$(CCACHE) $(HO)/llvm/bin/clang CXX=$(CC)++ # FORTRAN FC=$(CCACHE) $(HB)/gfortran-$(VER) F77=$(FC) FLIBS=-L$(HL)/gcc/$(VER) -lgfortran -lquadmath -lm # STD libraries CXX1XSTD=-std=c++0x CXX11STD=-std=c++11 CXX14STD=-std=c++14 CXX17STD=-std=c++17 # FLAGS CFLAGS=-g -O3 -Wall -pedantic -mtune=native -pipe CXXFLAGS=-g -O3 -Wall -pedantic -mtune=native -pipe CPPFLAGS=-I$(HO)/llvm/include -I$(HO)/openssl/include -I$(HO)/gettext/include LDFLAGS=-L$(HO)/llvm/lib -L$(HO)/openssl/lib -L$(HO)/gettext/lib # R-specific flags for OpenMP support SHLIB_OPENMP_CFLAGS=-fopenmp SHLIB_OPENMP_CXXFLAGS=-fopenmp SHLIB_OPENMP_FCFLAGS=-fopenmp SHLIB_OPENMP_FFLAGS=-fopenmp

Install packages

Open R and install packages like normal using install.packages(). I found that installing Rcpp, data.table, and tidyverse will give a good all-around indication of whether everything worked.