EC2 setup for R

gistfile1.sh

# x-large high-cpu - set up
ec2-run-instances ami-82fa58eb --region us-east-1 --instance-type c1.xlarge --key ec2-keypair-us-east-1 --user-data-file bootstrap.sh

# Get IP address:
ec2-describe-instances --region us-east-1

# Wait for a bit, then run:
./setup.sh ec2-23-20-74-242.compute-1.amazonaws.com a_vagrant_machine/ ~/.ec2/ec2-keypair-us-east-1




# Connect
ssh -i ~/.ec2/ec2-keypair-us-east-1 ubuntu@ec2-23-20-74-242.compute-1.amazonaws.com

# Fix temp dir - put it on ephemeral storage, which is at /mnt
# NOTE: /mnt/tmp must be created after every reboot!
sudo -s
mkdir /mnt/tmp
chmod uga+rwxt /mnt/tmp 
mv /tmp /oldtmp
ln -s /mnt/tmp /tmp

# Make temp dir for user
mkdir /mnt/user
chown ubuntu:ubuntu /mnt/user

# Install vncserver - needed for x11 libs, which are needed for R packages like cairoDevice
apt-get install -y  vnc4server

# Install curl dev libraries
apt-get install -y libcurl4-openssl-dev

# Install xt-dev (for Cairo)
apt-get install -y libxt-dev

# Install gtk dev libraries (for cairoDevice - doesn't work?)
apt-get install -y gtk+2.0-dev

# Install java (for rJava)
add-apt-repository ppa:webupd8team/java 
apt-get update 
apt-get install oracle-java7-installer
update-java-alternatives -s java-7-oracle
R CMD javareconf

# Install cmake and qt (for qtbase)
apt-get install -y cmake qt4-dev-tools

# Install xml (for XML)
apt-get install -y libxml2-dev

# Install libgeos (for rgeos)
apt-get install -y libgeos-dev

# Install gdal and libproj (for rgdal)
apt-get install -y libgdal1-dev libproj-dev

# Install qpdf
apt-get install -y qpdf

# ========= NOT as root =========

# R testing (not as root)
R
install.packages('devtools')
# Install winston's customized version of devtools
library(devtools)
install_github('devtools','wch','parallel-check-cran')
# Quit R
quit(save='no')


# Get ggplot2
cd /mnt/user
git clone git://github.com/hadley/ggplot2.git

# Restart R and install ggplot2
R
library(devtools)
dev_mode()
# Install gtable
install_github('gtable')

# Install local ggplot2 (will prompt to install dependencies)
install('ggplot2')

# Check ggplot dependencies
# This needs to be done in a vnc session, started with:
vncserver :1
system.time(revdep_check('ggplot2', threads=8, libpath='~/R-crancheck'))