Step 1: Choosing AMI

Click the link for Louis Aslett’s RStudio AMI and view the most recent AMI specs on the right side of the screen. Click the region nearest to you, and a new instance will automatically be created using this AMI, taking you to step 2 of the process.

Step 2: Selecting Instance

To stay within the free tier, we will select the “General Purpose t2.micro” instance type. Click “Next: Configure Instance Details”

Step 3: Configuration Settings, Adding Storage, and Tags

#####Configuring Instance Details Leave all settings to default unless you know which more advanced configuration settings you’d like to set. You could insert scripts like sudo apt update under “Advanced Details” to run on system boot. Click “Next: Add Storage”.

#####Add Storage You will also leave these settings default unless you believe you may need more storage but make sure to not go above the free tier limit (8GB should be enough). Click “Next: Add Tags”

#####Add Tags To help you manage your instances, images, and other Amazon EC2 resources, you can optionally assign your metadata to each resource in the form of tags. Each tag consists of a key and an optional value, both of which you define. Click “Next: Configure Security Group”

Step 4: Configuring the Security Group

A Security Group acts as a virtual firewall & controls traffic for one or more instances. Set your secuirty group name, which in this case I will name it “RStudio”. RStudio has a default port of 8787, but this AMI has it configured to port 80 (HTTP).

To give access to port 80 (HTTP) for our RStudio instance, we need to select HTTP under the “Type” drop-down and set the source to “Anywhere”. Click “Review and Launch”.

Warning: Setting your source to “Anywhere” opens your instance up to the world. Even though your instance is protected with SSH keys, it is susceptible to dictionary password attacks during boot. You can manage IP addresses within the Security Group, but that can become a handful if your continuously accessing your instance from different IP’s. Setting a reverse proxy for RStudio to reroute to port 443 on HTTPS is a better solution. Stay tuned for the next post on how to do this.

Step 5: Launching & Key-Pair

Click Launch and wait for the “Select an existing key pair or create a new key pair” tab to open. We will select “Proceed without a key pair” under the first drop-down and click the checkbox that states “I acknowledge that I will not be able to connect to this instance unless I already know the password built into this AMI”. Finally, click Launch Instances!

Step 6: Getting Public URL (DNS)

Once your instance State reads “running”, select the instance and copy the “Public DNS” to then paste into your browser url.

Step 7: Changing Password + Link Dropbox

Success! I highly recommended reading everything in green that Louis Albert wrote, as it explains how to change your password and link to your dropbox. Luckily, it is very easy.

Step 1: Choosing an AMI

You can choose the Amazon Linux AMI, which is provided at no additional cost and has a stable version of R in the repository. This AMI is maintained by AWS and includes packages and configurations that provide native integration with AWS and other software.

To go through the entire process, we will use the Ubuntu Server (18.04) AMI and download all the necessary software.

Step 2: Choosing an Instance Type

Choose an EC2 instance type that matches the data size and processing that your analysis requires. By default, R runs only on one core node and, in many cases, requires a lot of memory. For programming and development, the general-purpose T2 instance types are sufficient and cheap, and t2.micro is available through the AWS Free Tier.

For our purpose, we will select the “General Purpose T2.Micro” Instance. See the following link for more details on AWS EC2 Instance Types.

Step 3: Configuring Instance Details

We will leave these settings to default, but you can expand “Advanced Details” to add scripts like sudo apt update to run on instance start up. Click “Next: Add Storage” to continue.

Step 4: Add Storage

Here we can set the EBS volume size which defaults to 8GB. Usually, this will be enough, but let’s change it to 16GB to play it safe (free tier gets up to 30GB). Click “Next: Add Tags” to optionally add tags, then click “Next: Configure Security Group”.

Step 5: Configuring the Security Group

In the EC2 launch wizard, you define a security group, which acts as a virtual firewall that controls the traffic for one or more instances. For this R-based analysis environment, we want to access RStudio from the browser so select HTTP from the Type dropdown, and set the Source settings to “Anywhere”.

We will add an additional rule to allow SSH logins to our instance directly. Select SSH under type and set Source to “Anywhere”. Next, we want to add the ports for Shiny-server and RStudio-server so lets add two custom TCP rules and set the ports to 3838 and 8787 respectively. Set both sources to “Anywhere”. See below for review.

• SSH: port 22
• HTTP: port 80
• Shiny: port 3838
• RStudio: port 8787

As a quick reminder about SG source settings;

Warning: Setting your source to “Anywhere” opens your instance up to the world. Even though your instance is protected with SSH keys, it is susceptible to dictionary password attacks during boot. You can manage IP addresses within the Security Group, but that can become a handful if your continuously accessing your instance from different IP’s. Setting a reverse proxy for RStudio to reroute to port 443 on HTTPS is a better solution. Stay tuned for the next post on how to do this.

After you finish your security group configuration, choose “Review and Launch”.

Step 6: Launch & Key Pair Management

Review your instance information and click “Launch”. You’ll be prompted to “Select or Create Key Pair” and choose “Create a new key pair” and name it to your choosing. Launch your instance and let’s change some permissions to the key-pair while it launches. Open your terminal and copy / paste the below.

mv <path-to-pem-file> ~/.ssh

chmod 600 <new-path-to-pem-file>

Once the instance status is “running”, we can now login via SSH.

Step 7: SSH login to our EC2 to begin downloading software

We will connect to the EC2 instance via SSH on the terminal. Please open your terminal and copy/paste the below, and replace the content inside < > with your instance info.

ssh -i <path-to-pem-file> ubuntu@<PublicDNS>

When your prompted, type yes.

Success! We are finally logged into our AWS EC2 instance. Before I get into the script of downloading the necessary software, I want to show how to create swap memory to stay within free tier instances.

Step 8: Creating Swap Memory and Why Its Necessary

Due to the limited RAM in the free tier T2.micro instance, we need to enable and create swap memory to successfully download certain packages without clogging the RAM (and to avoid having to select a larger instance outside of free-tier). If you plan on using instances above t2.medium, then you do not need to do this and skip to step 9.

Some R packages like Tidyverse require memory larger than 1GB to successfully download, so that’s when Swap memory will allow us to get the extra memory needed. In simple terms, Swap memory “borrows” some memory from the disk when the RAM is fully utilized and clogged. Please copy and paste the below to set 2GB of swap memory (do not set swap > 2x larger than RAM).

#Create Swap file memory to avoid using bigger instance
sudo /bin/dd if=/dev/zero of=/var/swap.1 bs=1M count=2048
sudo /sbin/mkswap /var/swap.1
sudo /sbin/swapon /var/swap.1
sudo sh -c 'echo "/var/swap.1 swap swap defaults 0 0 " >> /etc/fstab'

Step 9: Downloading R, RStudio, and System Dependencies

Now it is time to download all of the necessary software, libraries, packages, etc. It is important to select the most recent versions of RStudio where you can find here. Modify the script to install the most recent version if the one used below is outdated. Copy / paste the below in your terminal.

# The Ubuntu repos contain an outdated version of R so lets add the updated repo to avoid errors
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'

# Update ubuntu package repo, to get latest R
sudo apt update

# Install R
sudo apt -y install r-base r-base-dev

# Install shiny before shiny-server
sudo R -e "install.packages('shiny')"

# Install debian package manager, gdebi
sudo apt install gdebi-core


# Install Shiny Server 
wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.9.923-amd64.deb
sudo gdebi -n shiny-server-1.5.9.923-amd64.deb
sudo rm shiny-server-1.5.9.923-amd64.deb

# Dependencies for R packages like RMariaDB, devtools, tidyverse, sparklyr. Please run seperate.
sudo apt -y install libcurl4-openssl-dev 

sudo apt -y install libssl-dev libxml2-dev libmariadbclient-dev build-essential libcurl4-gnutls-dev


# Install RStudio
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.1335-amd64.deb
sudo gdebi -n rstudio-server-1.2.1335-amd64.deb
sudo rm rstudio-server-1.2.1335-amd64.deb

# Install some useful R Packages (be a little patient here)
sudo R -e "install.packages('RCurl', repos='http://cran.rstudio.com')"
sudo R -e "install.packages('devtools', repos='http://cran.rstudio.com')"
sudo R -e "install.packages('tidyverse')"
sudo R -e "install.packages('RMariaDB')"

# Add user info to login RStudio
sudo adduser rstudio

#Add rstudio to sudo group
sudo usermod -aG sudo rstudio

# Install Java and reconfigure in R for RStudio use
sudo apt -y install default-jdk
sudo R CMD javareconf


# Change permissions for R library
sudo chmod 777 -R /usr/local/lib/R/site-library

# ****VERY IMPORTANT***
#If you plan on running a shiny app on port 80, then you need to set a reverse proxy to use one port for both. 
sudo echo "www-port=80" >> /etc/rstudio/rserver.conf

#Restart rstudio-server to incorporate changes made in rserver.conf
sudo rstudio-server restart

Step 10: Logging into RStudio + Viewing Shiny

Open a web browser and enter your Public DNS(IPv4) as part of the URL to login to RStudio Server. If you kept RStudio on port 8787 (which I did in this post), then add :8787 to the end of your url like below. This means that the shiny-server we also downloaded is living on its default port, 3838. We will also visit there.

Step 11: Installing and Using MySQL in RStudio’s Terminal

One of my favorite things in RStudio is the built-in system terminal that allows us to install/use MySQL without ever leaving RStudio. We can access/create databases, tables, etc all within our RStudio session from anywhere. Click the terminal tab and copy/paste the below to install/use MySQL in RStudio:

# Install MySQL
wget https://dev.mysql.com/get/mysql-apt-config_0.8.12-1_all.deb
sudo gdebi -n mysql-apt-config_0.8.12-1_all.deb

#To be sure everything is up to date
sudo apt update
sudo apt upgrade

I included the update/upgrade script in the above to ensure your installing the most up-to-date version of mysql, but this is optional.

Now install mysql-server and when prompted for a password, please create one and remember it for when you login to your mysql-server.

# Create your password
sudo apt install mysql-server mysql-client
sudo rm mysql-apt-config_0.8.12-1_all.deb

Now login with the password we created to see that everything went well!

# Login to MySQL inside RStudi Terminal 
sudo mysql -p

#It works!
exit;

Step 12: Checking if an installed package works?

RStudio and MySQL are working well, so lets see if those useful packages we installed earlier are also working. We should see a datatable if everything went as planned.

library(RCurl) 
data <- read.table(textConnection(getURL("https://cgiardata.s3-us-west-2.amazonaws.com/ccafs/amzn.csv")), sep=",", header=FALSE)
head(data)

##          V1     V2      V3     V4      V5      V6
## 1 1/15/2014 395.87 2677150 398.94 399.310 392.534
## 2 1/14/2014 397.54 2339458 392.13 398.630 391.290
## 3 1/13/2014 390.98 2843810 397.98 399.780 388.450
## 4 1/10/2014 397.66 2678085 402.53 403.764 393.800
## 5  1/9/2014 401.01 2103029 403.71 406.890 398.440
## 6  1/8/2014 401.92 2316220 398.47 403.000 396.040

Perfect! The “RCurl” package installed correctly or else we would have gotten an error here. You can continue to play around here to see that everything else installed correctly.