This is a rather details documentation of my OSX setup for R usage using homebrew. You can get away with a lot less than what I have installed below, but this is fairly comprehensive and I have also given some steps to verify installation of various packages.
Github API TokenGet a github account and setup an API token as described here . This helps you avoid hitting Github API limits when using homebrew.
echo 'export HOMEBREW_GITHUB_API_TOKEN="your_new_token"' >> $HOME/.bash_profile . $HOME/.bash_profile Install Homebrew and tap some taps /usr/bin/ruby -e \ "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" brew analytics off # full on paranoid mode brew tap caskroom/cask # GUI apps brew tap caskroom/fonts # fonts brew tap homebrew/science brew tap homebrew/completions brew tap homebrew/services brew tap homebrew/versions brew tap osgeo/osgeo4mac # If you need Geospatial stuff BashInstall Bash and verify
brew install bash bash-completion2 /usr/local/bin/bash --version GNU bash, version 4.3.46(1)-release (x86_64-apple-darwin15.5.0)Setup bash along with some utility functions. Primarily we setup brewPkg bash function which will not only install homebrew packages but also log the output for debugging purposes if so desired.
sudo sh -c 'echo "/usr/local/bin/bash" >> /etc/shells' mkdir -p $HOME/Library/Logs/Homebrew/$USER echo ' if [ -f $(brew --prefix)/share/bash-completion/bash_completion ]; then . $(brew --prefix)/share/bash-completion/bash_completion fi brewPkg() { pkg=$1 shift ( brew install ${pkg} $* 2>&1 | tee $HOME/Library/Logs/Homebrew/$USER/${pkg}-$(date +"%F_%H%M").txt ) } brewSrcPkg() { pkg=$1 shift ( brew install --build-from-source ${pkg} $* 2>&1 | tee $HOME/Library/Logs/Homebrew/$USER/${pkg}-$(date +"%F_%H%M").txt ) } brewSrcPkgWgcc() { pkg=$1 shift ( export CC=gcc-6 export CXX=g++-6 export HOMEBREW_CC=gcc-6 export HOMEBREW_CXX=g++-6 brew install --build-from-source ${pkg} $* 2>&1 | tee $HOME/Library/Logs/Homebrew/$USER/${pkg}-$(date +"%F_%H%M").txt ) } ' >> ~/.bash_profileLoad the new bash shell, so we can use all the auto-complete goodies. Or simply close and restart the Terminal App.
/usr/local/bin/bash -l GCC Compiler and AutotoolsInstall gcc, without multilib so that OpenMP works .
brewPkg gcc --without-multilib /usr/local/bin/gcc-6 --version gcc-6 (Homebrew gcc 6.1.0 --without-multilib) 6.1.0 /usr/local/bin/gfortran --version GNU Fortran (Homebrew gcc 6.1.0 --without-multilib) 6.1.0Setup aliases for homebrew's gcc
cd /usr/local/bin ln -s gcov-6 gcov ln -s gcc-6 gcc ln -s g++-6 g++ ln -s cpp-6 cpp ln -s c++-6 c++ cd -Install ccache to speed up compilation
brewPkg ccache /usr/local/bin/ccache --version ccache version 3.2.7Install autotools, pkg-config, and cmake
brewPkg cmake pkg-config autoconf automakeLet's make sure OpenMP is working as expected.
cat > omp-test.c <<"END" #include <omp.h> #include <stdio.h> int main() { #pragma omp parallel printf("Hello from thread %d, nthreads %d\n", omp_get_thread_num(), omp_get_num_threads()); } END gcc-6 -fopenmp -o omp-test omp-test.c ./omp-testYou should see something similar but not exactly the same.
Hello from thread 1, nthreads 8 Hello from thread 6, nthreads 8 Hello from thread 4, nthreads 8 Hello from thread 2, nthreads 8 Hello from thread 5, nthreads 8 Hello from thread 0, nthreads 8 Hello from thread 3, nthreads 8 Hello from thread 7, nthreads 8 Misc libs brewPkg freetype fontconfig pixman gettext SSL/SSH LibsSetup and verify openssl and libressl.
brewPkg openssl /usr/local/opt/openssl/bin/openssl version OpenSSL 1.0.2h 3 May 2016 brewPkg libressl /usr/local/opt/libressl/bin/openssl version LibreSSL 2.3.6 brewPkg libssh2 wget and curl brewPkg wget /usr/local/bin/wget --version GNU Wget 1.18 built on darwin15.6.0. brewPkg curl /usr/local/opt/curl/bin/curl-config --version libcurl 7.50.0 GPG brewPkg gpg2 --with-readline /usr/local/bin/gpg2 --version gpg (GnuPG) 2.0.30 libgcrypt 1.7.2 brewPkg gpgme /usr/local/bin/gpgme-config --version 1.6.0 Java brew cask install java java -version java version "1.8.0_102" Java(TM) SE Runtime Environment (build 1.8.0_102-b14) Java HotSpot(TM) 64-Bit Server VM (build 25.102-b14, mixed mode) X-serverWe need an X-Server. This takes a lot of time so be patient.
brew cask install xquartz pythonInstall python2
brewPkg python pip install --upgrade pip setuptools /usr/local/bin/python -V Python 2.7.12Install Python3
brewPkg python3 pip3 install --upgrade pip setuptools wheel /usr/local/bin/python3 -V Python 3.5.2 Git brewPkg git --with-blk-sha1 --with-gettext \ --with-pcre --with-persistent-https /usr/local/bin/git --version git version 2.9.2 Boost libs w/ dependenciesInstall icu4c library for Unicode and globalization
brewPkg icu4c /usr/local/opt/icu4c/bin/icu-config --version 57.1Install libxml2, libiconv, and libxslt.
brewPkg libxml2 libiconv libxslt brew link libxml2 --force /usr/local/bin/xml2-config --version 2.9.4Install boost. Ignore the warning at the end.
brewPkg boost --with-icu4c --with-mpi --without-singleBoost is a beast of a library, so we need some quick programs to test whether it has installed successfully.
Shamelessly copied/adapted from the Intertubes . Ignore the warning messages spewed by the compiler.
cat > first.cpp <<END #include<iostream> #include<boost/any.hpp> int main() { boost::any a(5); a = 1.61803; std::cout << boost::any_cast<double>(a) << std::endl; } END clang++ -o first first.cpp ./first 1.61803 cat > second.cpp <<END #include<iostream> #include <boost/filesystem.hpp> int main() { boost::filesystem::path full_path( boost::filesystem::current_path() ); if ( boost::filesystem::exists( "second.cpp" ) ) { std::cout << "Found second.cpp file in " << full_path << std::endl; } else { std::cerr << "Argh!, Something not working" << std::endl; return 1; } } END clang++ -o second second.cpp \ -lboost_filesystem-mt -lboost_system-mt ./second Found second.cpp file in "/Users/brewmaster" Latex SupportTake a Coffee break and then some, because this is a huge one.
brew cask install mactex RInstall libsvg, librsvg, and cairo.
brewPkg cairo brewPkg libsvg brewPkg librsvg brewPkg pandocOpenblas for speedier linear algebra in R.
brewPkg openblas --with-openmpTest openblas. Shamelessly copied from Intertubes .
cat > test-openblas.c <<"END" #include <cblas.h> #include <stdio.h> void main() { int i=0; double A[6] = {1.0,2.0,1.0,-3.0,4.0,-1.0}; double B[6] = {1.0,2.0,1.0,-3.0,4.0,-1.0}; double C[9] = {.5,.5,.5,.5,.5,.5,.5,.5,.5}; cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, 3,3,2,1,A, 3, B, 3,2,C,3); for(i=0; i<9; i++) printf("%lf ", C[i]); printf("\n"); } END clang -L/usr/local/opt/openblas/lib \ -I/usr/local/opt/openblas/include \ -lopenblas -lpthread \ -o test-openblas test-openblas.c ./test-openblas 11.000000 -9.000000 5.000000 -9.000000 21.000000 -1.000000 5.000000 -1.000000 3.000000Eigen and Armadillo for Rcpp and v8 for R+v8 .
brewPkg eigen brewPkg armadillo --with-hdf5 brewPkg v8-315 brew link v8-315 --forceTest Armadillo
cd /usr/local/opt/armadillo/examples/ clang++ -O2 -o example1 example1.cpp -larmadillo -framework Accelerate ./example1You should see something like below and lot more.
Armadillo version: 7.200.2 (Plutocratic Climate Change Denialist) A.n_rows: 2 A.n_cols: 3 ...Test v8
echo 'quit()' | v8 V8 version 3.15.11.18 [sample shell]Finally install R itself, and also setup R to use Apple's clang compiler. We can also setup R to use gcc compiler to take advantage of openmp support, but I've noticed that not all R packages compile correctly when using GCC.
brewPkg r --with-openblas --with-pango # for rJava to work. R CMD javareconf \ JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers # Setup $HOME/.r/Makevars file to properly link against homebrew packages. mkdir $HOME/.r cat > $HOME/.r/Makevars << END CC=ccache clang CXX=ccache clang++ SHLIB_CXXLD=ccache clang++ FC=gfortran-6 F77=gfortran-6 MAKE=make -j8 PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/opt/X11/lib/pkgconfig:/usr/local/opt/icu4c/lib/pkgconfig PKG_LIBS += -L/usr/local/opt/icu4c/lib -L/usr/local/lib END # Also setup a R_LIBS_USER directory to install R packages locally. mkdir -p $HOME/Library/R/3.x/library cat > $HOME/.Renviron <<END export R_LIBS_USER=$HOME/Library/R/3.x/library END # add same stuff to .bash_profile cat $HOME/.Renviron >> $HOME/.bash_profile GIS StuffMostly PostGIS + Geo libs.
brewPkg postgresql brewPkg geos brewPkg proj brewPkg gdal2 \ --with-armadillo --with-complete --with-libkml \ --with-opencl --with-postgresql --with-unsupported brewPkg postgis --with-gui Other Programming LanguagesSome other programming languages I use occasionally.
Node.js brewPkg node brewPkg phantomjs casperjs Scala brew install scala golang brew install golang cat >> $HOME/.bash_profile <<END export GOPATH=$HOME/golang export GOROOT=/usr/local/opt/go/libexec export PATH=$PATH:$GOPATH/bin export PATH=$PATH:$GOROOT/bin END Other Interesting Stuff brewPkg imagemagick --with-fontconfig --with-ghostscript \ --with-librsvg --with-openmp --with-pango --with-webp brewPkg vim --with-python3 --with-client-server \ --with-lua --with-luajit --with-override-system-vi brewPkg macvim --with-python3 --with-client-server \ --with-lua --with-luajit --with-override-system-vim brewPkg jq # json processing brew cask install font-hack font-fira-code #extra fonts brewPkg mlpack # Fast Machine Learning brewPkg protobuf --devel # Google's Protocol Buffer Library brewPkg gsl # GNU Scientific Library brewPkg libyaml # YAML Support GUI AppsApps related to Securing your Mac.
brew cask install blockblock knockknock \ dhs taskexplorer kextviewr brew cask install suspicious-packageQuicklook Plugins for Developers.
brew cask install qlcolorcode qlstephen qlmarkdown \ quicklook-json qlprettypatch quicklook-csv betterzipql \ qlimagesize webpquicklookThese are some GUI apps I use. Pick and chose as you like. They are not necessarily related to R or even development.
brew cask install google-chrome chrome-devtools firefox iterm2 seil \ slate keepassx free-mind itsycal flux caffeine alfred beardedspice \ macdown mysqlworkbench osxfuse smcfancontrol torbrowser vagrant\ vagrant-manager vlc cog yed slack owncloud