Installing R on OSX Big Sur (EDIT: and Apple M1) for use with Rcpp and openMP

There's probably a gazillion threads on OSX+Rcpp+openMP, but the bottom line right now appears to be this (per coatless):

Unfortunately, with R 4.0.0 the CRAN distributed version of R loses the ability to use OpenMP without a custom setup.

I came across other ideas, including compiling llvm yourself, using homebrew or macports to install R and/or llvm and/or gcc, and then figuring out how to use the right compiler and/or flags with (R)cpp. However, I find this all very confusing.

I am not a mac user, but it seems to me that setting up a mac to compile Rcpp packages or code snippets with openMP seems to be too difficult for most mac users. However, I would like my R package on github to be used by more users, and since it relies on openMP, I am losing that audience.

Can someone provide the necessary steps to set up R on mac in a way that it can compile Rcpp code with openMP? I'd like to turn that into a quick tutorial.

EDIT: I should have added - on Apple Silicon, because there are some extra confusions where things go - /usr/local vs /opt

I spent a day figuring this out (original post here); here are the steps I used to compile R packages from source with openMP:

1. Install xcode from the app store (instructions for installing xcode) then install/reinstall the xcode command line tools from the terminal:

# To delete an existing command line tools installation:
sudo rm -rf /Library/Developer/CommandLineTools

# To install the command line tools
sudo xcode-select --install

2. Install gcc via Homebrew (instructions for installing Homebrew) or, if you already have gcc installed, skip to step 3.

# WARNING: This can take several hours
brew install gcc

3. To avoid "legacy" version issues:

brew cleanup
brew update
brew upgrade
brew reinstall gcc

4. Link some headers into /usr/local/include

sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/

# You can ignore warnings like this:
#ln: /usr/local/include//tcl.h: File exists
#ln: /usr/local/include//tclDecls.h: File exists
#ln: /usr/local/include//tclPlatDecls.h: File exists
#ln: /usr/local/include//tclTomMath.h: File exists
#ln: /usr/local/include//tclTomMathDecls.h: File exists
#ln: /usr/local/include//tk.h: File exists
#ln: /usr/local/include//tkDecls.h: File exists
#ln: /usr/local/include//tkPlatDecls.h: File exists

5. Check your version of gfortran (cd /usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/; ls) then edit your ~/.R/Makevars file (if you don't have a file called Makevars in your ~/.R/ directory) and include only these lines:

LOC = /usr/local/gfortran
CC=$(LOC)/bin/gcc -fopenmp
CXX=$(LOC)/bin/g++ -fopenmp
CXX11 = $(LOC)/bin/g++ -fopenmp

CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L$(LOC)/lib -Wl,-rpath,$(LOC)/lib
CPPFLAGS=-I$(LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

# (check that the version of gfortran - in this case 10.2.0 - matches the version specified in FLIBS)
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

6. Open R and install a package to test that it compiles with openMP enabled (when asked, compile from source = "Yes"):

install.packages("data.table", type = "source")

Unfortunately, I do not believe a more "simple" setup exists.

Eventually, I found a process that works on a M1 mac with Big Sur.

• Head over to https://mac.r-project.org/, it contains most things you will need
• Download and install R via R-4.1-branch.pkg. The CRAN version might also work, but I used the installer from mac.r-project.org, which required opening the osx security settings to allow the installation.
• Install RStudio, start it, and let it install the developer tools. Alternatively, run sudo xcode-select --install in Terminal.
• Head to https://mac.r-project.org/openmp/. Download openmp-11.0.1-darwin20-Release.tar.gz and install it (see Terminal commands below).

curl -O https://mac.r-project.org/openmp/openmp-11.0.1-darwin20-Release.tar.gz
sudo tar fvx openmp-11.0.1-darwin20-Release.tar.gz -C /

• Now we need to add compiler flags so that clan uses openMP. In Terminal, create the Makevars file.

cd ~
mkdir .R
nano .R/Makevars

in nano, paste these additional compiler flags into the Makevars file:

CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp

Hit Control+O, Control+X to save and close

• Head over to the gfortran page: https://github.com/fxcoudert/gfortran-for-macOS/releases
• Use the installer gfortran-ARM-11.0-BigSur.pkg to install gfortran.
• For some reason it appears to install in /usr/local/gfortran, but R expects it in /opt. The mac-R team likes to separate arm64 and intel related files. We could go and fix paths, or simply also install gfortran under /opt. Download the tar file gfortran-ARM-11.0-BigSur.tar.xz. You can use curl, or just download it and point tar in the command line to it.

cd /opt/R/arm64/
sudo mkdir gfortran
sudo tar -xzyf gfortran-ARM-11.0-BigSur.tar.xz -C /opt/R/arm64/

(replace gfortran-ARM-11.0-BigSur.tar.xz with /users/YOURUSERNAME/downloads/gfortran-ARM-11.0-BigSur.tar.xz)

Now it should work.

Not an expert in OSX, but doing this so others can figure out how to use my R package. I'd like to streamline the process some more, but wiping the mac, reinstalling osx and testing it takes so much time.