Originally Published on my Personal Blog.
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 Token
Get 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
Bash
Install 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_profile
Load 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 Autotools
Install 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) 6.1.0
Setup 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 3.2.7
Install autotools, pkg-config, and cmake
brewPkg cmake pkg-config autoconf automake
Let'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-test
You 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 Libs
Setup 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-server
We need an X-Server. This takes a lot of time so be patient.
brew cask install xquartz
Python
Install python2
brewPkg python
pip install --upgrade pip setuptools
/usr/local/bin/python -V
Python 2.7.12
Install 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/ dependencies
Install icu4c library for Unicode and globalization
brewPkg icu4c
/usr/local/opt/icu4c/bin/icu-config --version
57.1
Install libxml2, libiconv, and libxslt.
brewPkg libxml2 libiconv libxslt
brew link libxml2 --force
/usr/local/bin/xml2-config --version
2.9.4
Install boost. Ignore the warning at the end.
brewPkg boost --with-icu4c --with-mpi --without-single
Boost 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 Support
Take a Coffee break and then some, because this is a huge one.
brew cask install mactex
R
Install libsvg, librsvg, and cairo.
brewPkg cairo
brewPkg libsvg
brewPkg librsvg
brewPkg pandoc
Openblas for speedier linear algebra in R.
brewPkg openblas --with-openmp
Test 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 3.000000
Eigen and Armadillo for Rcpp and v8 for R+v8.
brewPkg eigen
brewPkg armadillo --with-hdf5
brewPkg v8-315
brew link v8-315 --force
Test Armadillo
cd /usr/local/opt/armadillo/examples/
clang++ -O2 -o example1 example1.cpp -larmadillo -framework Accelerate
./example1
You 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 Stuff
Mostly 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 Languages
Some 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-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 Apps
Apps related to Securing your Mac.
brew cask install blockblock knockknock \
dhs taskexplorer kextviewr
brew cask install suspicious-package
Quicklook Plugins for Developers.
brew cask install qlcolorcode qlstephen qlmarkdown \
quicklook-json qlprettypatch quicklook-csv betterzipql \
qlimagesize webpquicklook
These 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
Top comments (5)
Awesome stuff! Many thanks. Just wanted to add that using Anaconda to install and manage Python and R environments, and using SDKman to install Java and Scala stacks is generally a better idea.
The R channel of anaconda is woefully outdated. I won't recommend it just for that reason. I was not aware of SDKman so thanks for bringing it to my attention.
Looks like this would be the perfect case for a docker image, no?
Is it normal for the gcc install to take forever?
Wait till you get to the mactex part. ;)