/RShiny-EC2Bootstrap

R Shiny EC2 Bootstrap Guide

R Shiny EC2 Bootstrap

The goal of this guide is to quickly bootstrap R Shiny on an Amazon AWS EC2 instance. We will also walk through a recommended workflow using Github for rapid development on a local machine and the EC2 server instance.

image: workflow

This is an opiniated guide created for the following software versions:

Ubuntu: 14.04 LTS
R: 3.1.2
shiny-server: 1.3.0.403

For other software versions, please make sure to check the version numbers used in the installations (e.g. see Install Shiny Server section on installing different versions of shiny-server).

Contents

Launch EC2

  • Create an AWS account and login to the console.

  • Click on Compute > EC2 (near the top left of the screen) and click the Launch Instance button in the Create Instance section of the page.

  • We are now in the AMI (Amazon Machine Image) interface. Select Ubuntu Server 14.04 LTS.

    image: ubuntu14.04

  • We will choose the default t2.micro instance. Accept all the default settings for the next few steps:

    • Click Next: Configure Instance Details
    • Click Next: Add Storage
    • Click Next: Tag Instance
    • Click Next Configure Security Group

  • When we arrive to Configure Security Group, we will need to add a few more security groups to open our EC2 instance to the world when we later build applications with Shiny.

  • Add the following rules using the Add Rule buttons. This registers and opens the ports 3838 and 80 that Shiny will use later. By default, Shiny will listen on the 3838 port, but keeping the default HTTP listening port 80 open is always a useful option (In the Install Shiny Server section, we go through changing the shiny-server configurations to listen on the default 80 port, which removes the need to specify a port number in your URL).

    image: configure security groups

  • We are ready to launch our EC2 instance now.

  • Click on the Review and Launch button, and Launch your instance!

    image: ec2 launch

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Register Key Pair

  • With our EC2 instance set up, we need to register the key provided to us from Amazon with our local machine.

  • Amazon will prompty you to create a new key pair. For this guide, we shall name the keypair shinybootstrap.

    image: create key pair

  • Download the shinybootstrap.pem key pair. We recommend that you place your shinybootstrap.pem key pair in a safe folder. Ekuns has provided a great reuseable and general tip on setting up and managing ssh connections in general.

    • Copy the shinybootstrap.pem key into the ~/.ssh folder

    • Create and edit the file using a text editor in ~/.ssh/config (config is the filename)

      Host *
    ServerAliveInterval 240

Host aws-shiny
    HostName public_dns_name
    User ubuntu
    IdentityFile ~/.ssh/aws-shiny.pem
    ForwardX11 yes
    ForwardX11Trusted yes

    • where aws-shiny is the alias hostname you are providing and public_dns_name is the name of your EC2 instance e.g. ec2-54-183-2-10.us-west-1.compute.amazonaws.com or the public IP itself 54.183.2.10

      image: dns name

    • Restart your terminal and you can now access your ubuntu EC2 server using:

      ssh aws-shiny

    • NOTE: The public DNS name and public IP may not be static/permanent, e.g. their values can change when shiny-server restarts. For a full permanent solution to creating a bash_alias, you would need to create an Elastic IP (but we will defer that for the readers to the Amazon guide if readers wish to research the details).

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Install R

  • Phew! The tough parts are over, we can now move onto installing R in our EC2 instance!

  • First, create a superuser root password by entering a password in the EC2 command line.

    sudo password root
su

  • Update your barebones EC2 virtual machine and install R:

    sudo apt-get update
sudo apt-get install r-base-dev
sudo apt-get install libcurl4-openssl-dev

  • R is now successfuly installed!

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Install R Packages

  • Base R is argubly boring, so let's get started with installing a few important packages, shiny being an obviously shiny option. (while installing these packages, make sure you are in su mode and I highly recommend installing them from the 0-Cloud CRAN repository)

  • From your EC2 command line:

    R       # enter the R console

install.packages("shiny")
install.packages("ggplot2")
q()         # quit R

  • A few other packages are highly recommended but you might encounter issues installing certain packages due to memory limitations available on the EC2 instance or missing libraries in our EC2 instance. For more details, please refer to the Problematic Packages section for a brief outline.

  • Other than that, you can come back anytime in the future to install R-packages by logging in with su and installing R packages via the command line.

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Install Shiny Server

  • shiny requires a server to run. The next step is to setup shiny-server in our EC2 instance.

  • Run the following commands in EC2:

    sudo apt-get install gdebi-core
wget http://download3.rstudio.org/ubuntu-12.04/x86_64/shiny-server-1.3.0.403-amd64.deb
sudo gdebi shiny-server-1.3.0.403-amd64.deb

  • NOTE: You can install a different version of shiny-server in the above command prompt by adjusting the shiny-server-version_number in the wget and gdebi commands above. You can check for the latest versions of RStudio shiny-server on the official site.

  • OPTIONAL: Change the listening port from 3838 to default 80

    • shiny-server by default runs applications on the URL and port: http://domain:3838/. We can take the time to make an easy change to the shiny-server config file to listen to the default port at 80. This will allow our future apps to be accessed without specifying a port number by simply going to http://domain/

    • Execute the following commands in your EC2 instance:

      cd /etc/shiny-server/ 
sudo nano shiny-server.conf

    • At this point, you can use a text editor (unfortunately we can only use CLI and non-GUI text editors) to change the line listen 3838; to listen 80;

    • Makes sure to save the changes and you can now access your shiny instances without specifying the 3838 port number!

  • And we're done!

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Install Git

  • git is probably one of the greatest creations and tools that you can use in your life, so it's good to include it in our EC2 instance.

  • Installing git is as simple as typing:

    sudo apt-get install git

  • git is very critical in our Shiny EC2 workflow. If you are not familiar with using git, here are some great resources to get on speed:

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Workflow Overview

  • A big part of the EC2 R Shiny workflow is to develop with RStudio on your local machines and use Github as a repository station for transferring data between your local machine and EC2 instance. Make sure that you are familiar with the basic git commands: pull, push, clone. It's going to be a big part of the development cycle.

  • The following diagram outlines the overall workflow of the EC2 R Shiny workflow:

    image: workflow

  • Workflow Summary:

    1. Develop on your local machine with RStudio.
    2. Whenever you are ready to show your work to the world, you would git push your changes to your Github repository.
    3. Initiate your EC2 instance with the same codebase on Github by using git clone into /srv/shiny-server/ (this is the folder where shiny-server serves your application).
    4. If there are changes to be made to your app, repeat steps 1 and 2 to git push updates to Github from your local machine, and then perform a git pull in your EC2 instance to update your application in EC2.

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Problematic Packages

  • Since our EC2 instance is completely barebones, installing various packages might be problematic due to a lack of libraries that EC2 comes with.

  • My recommendation is to do searches on Stackoverflow and Google using keywords such as EC2, package-name, installation, R.

  • You could run into issues with missing Python libraries and version requirements for R and various packages, but most of them can be solved by searching on Stackoverflow and Google.

  • You could also encounter issues that result from the limited memory allocated in the EC2 instance, which would not complete installations of some packages (e.g. dplyr, ggvis). If this is the case, the solution would be to install these packages on your local machine, and grab the uncompiled files in the local machine R libraries and copy them over to your EC2 R libraries. You have a few ways to transfer files from local machine to EC2 and I will refer you to Stackoverflow and Google on how to do so.

  • Stackoverflow + Goole are most definitely the best teachers and guides out there for resolving problematic packages. My job here is to just inform on some of the issues you may encounter :)

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Examples

Here are some project examples of Shiny EC2 instances that I have built and their respective Github codebase.

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Resources

This guide would not be possible without the works and guides provided by previous people. I'm listing some additional resources that are helpful for the general audience. Please contact me if there are any issues/corrections with this guide. Thank you!

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