install_packages.r

install.packages('rJava', type='source')

# Setup RMysql to use percona server
Sys.setenv(PKG_CPPFLAGS = "-I/usr/local/Cellar/percona-server/5.6.22-72.0/include/mysql/")
Sys.setenv(PKG_LIBS = "-L/usr/local/Cellar/percona-server/5.6.22-72.0/lib -lperconaserverclient")
install.packages('RMySQL', type='source')

# Setup connection to hadoop
install.packages('RImpala')
install.packages('RJDBC')

# Setup Beaker notebook
install.packages('Rserve')
install.packages('ggplot2')
install.packages('devtools')
install.packages('RCurl')
install.packages('RJSONIO')

# Setup IRkernel
library(devtools)
install_github('armstrtw/rzmq')
install_github("takluyver/IRdisplay")
install_github("takluyver/IRkernel")

# Setup common libraries
install.packages('dplyr')
install.packages('reshape2')
install.packages('XLConnect')
install.packages('lubridate')

# Functional data analysis
install.packages('demography')
install.packages('fda')

install_r.sh

# Install r from http://cran.r-project.org/bin/macosx/
# Install latest java from Oracle https://java.com/en/download/index.jsp
# Install system java update from apple http://support.apple.com/kb/DL1572

# Export variables for javareconf
export JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home"
export JAVA_LD_LIBRARY_PATH='/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/lib/server'
export JAVA_LIBS='-L/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/lib/server -ljvm'
export JAVA_CPPFLAGS='-I$JAVA_HOME/include -I$JAVA_HOME/include/darwin'
export PATH=$JAVA_HOME/jre/bin:$JAVA_HOME/bin:$PATH

# Set common file for R history
export R_HISTFILE=~/.Rhistory

R CMD javareconf

# Needed for IRkernel
brew install zmq
git clone https://github.com/zeromq/cppzmq.git
cp cppzmq/zmq.hpp /usr/local/include/