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Setup R, RStudio,and Stan on Ubuntu (for Amazon EC2)
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######################################################## | |
# Set up RStudio and JAGS on an Amazon EC2 instance | |
# Using Ubuntu 64-bit | |
# Christopher Gandrud | |
# 16 December 2014 | |
# Partially from http://blog.yhathq.com/posts/r-in-the-cloud-part-1.html | |
# See yhat for EC2 instance set up | |
######################################################## | |
# In your terminal navigate to key pair | |
# ssh -i YOUR_KEYPAIR.pem ubuntu@PUBLIC_DNS | |
# Get all programs up to date | |
sudo apt-get update | |
# Install latest g++ and clang | |
sudo apt-get install gcc | |
sudo apt-get install clang | |
# Install prerequisites for RCurl | |
sudo apt-get install libcurl4-openssl-dev | |
# Check that you have the latest R installed | |
## see also: http://askubuntu.com/a/352438 | |
sudo apt-get update | |
apt-cache showpkg r-base | |
# If R is not the latest version add latest PACKAGE_VERSION returned | |
# from the pervious line to: | |
sudo apt-get install -f r-base=PACKAGE_VERSION | |
# Install rJava | |
apt-get install r-cran-rjava | |
# Install Stan and rstan | |
# First find the number of cores | |
lscpu | |
# Load r, set cores, and install | |
R | |
Sys.setenv(MAKEFLAGS = "-j4") | |
source('http://mc-stan.org/rstan/install.R', echo = TRUE, | |
max.deparse.length = 2000) | |
install_rstan() | |
# Install other packages I often use | |
## Dependencies include reshape2, dplyr | |
pkgs <- c('repmis', 'DataCombine', 'devtools') | |
install.packages(pkgs) | |
q() | |
######## Running Scripts and Downloading Results onto Local #### | |
# Run a script so that it runs even if the terminal hands up | |
# sudo nohup Rscript R_SCRIPT_PATH | |
# Download a file from Amazon EC2 to your local machine | |
# (current working directory) | |
# scp -i YOUR_KEYPAIR.pem ubuntu@PUBLIC_DNS:EC2_FILE_PATH . |
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