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Notes on setting up EC2 instance to build rSynapseClient

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This is a record of what needs to be done to setup an Ubuntu system from scratch to build the R Synnapse client.
Some steps might be redundant.
Should be turned into a Dockerfile. 

# Update
sudo apt-get update
sudo apt-get upgrade
# Install dependencies
sudo apt-get install build-essential
sudo apt-get install python-pip
sudo apt-get install g77
sudo apt-get install fort77
sudo apt-get install gfortran
sudo apt-get install libreadline6 libreadline6-dev
sudo apt-get install libx11-dev
sudo apt-get install xorg-dev
sudo apt-get install openjdk-7-jdk
sudo apt-get install libbz2-dev
sudo apt-get install liblzma-dev
sudo apt-get install libpcre3-dev
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libcurl
sudo apt-get install libcurl-dev
sudo apt-get install git
sudo apt-get install unzip
sudo apt-get install zip
sudo apt-get install pdflatex
sudo apt-get install texlive-latex-base
sudo apt-get install texlive-latex-extra texlive-latex-recommended
sudo apt-get install texinfo
sudo apt-get install texlive-fonts-recommended

# EC2-specific: Add hostname to /etc/hosts to avoid sudo warning
cat /etc/hosts
## 
hostname
sudo vi /etc/hosts

# Build Rs
wget http://cran.fhcrc.org/src/base/R-3/R-3.3.0.tar.gz
wget http://cran.fhcrc.org/src/base/R-3/R-3.2.5.tar.gz
wget http://cran.fhcrc.org/src/base/R-3/R-3.1.3.tar.gz

tar -xvf R-3.1.3.tar.gz 
cd builds/R-3.1.3/
./configure --prefix=/usr/local/R/R-3.1.3/ --enable-R-shlib
make
sudo make install
sudo ln -s /usr/local/R/R-3.1.3/ /usr/local/R/R-3.1
sudo update-alternatives --install /usr/bin/R R /usr/local/R/R-3.1/bin/R 10

tar -xvf R-3.2.5.tar.gz 
cd builds/R-3.2.5/
./configure --prefix=/usr/local/R/R-3.2.5/ --enable-R-shlib
make
sudo make install
sudo ln -s /usr/local/R/R-3.2.5/ /usr/local/R/R-3.2
sudo update-alternatives --install /usr/bin/R R /usr/local/R/R-3.2/bin/R 20

tar -xvf R-3.3.0.tar.gz 
cd builds/R-3.3.0/
./configure --prefix=/usr/local/R/R-3.3.0/ --enable-R-shlib
make
sudo make install
sudo ln -s /usr/local/R/R-3.3.0/ /usr/local/R/R-3.3
sudo update-alternatives --install /usr/bin/R R /usr/local/R/R-3.3/bin/R 30

sudo update-alternatives --config R
###sudo update-alternatives --remove-all R

# Unzip is not set properly, add to Renviron
which unzip
sudo mkdir /etc/R
sudo vi /etc/R/Renviron
vi ~/.Renviron

# Rscript is not in path
sudo cp /usr/local/R/R-3.3/bin/Rscript /usr/bin/Rscript

# Test build rSynapseClient
cd ~/builds
git clone https://github.com/Sage-Bionetworks/rSynapseClient.git
cd rSynapseClient/
git checkout develop
sudo update-alternatives --set R /usr/local/R/R-3.1/bin/R
mkdir ../RLIB
R CMD build ./
R CMD INSTALL ./ --library=../RLIB --no-test-load
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