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Analythium

Securing Shiny Server with Caddy

Peter Solymos
Ecologist, technologist, co-founder of Analythium.io
Originally published at hosting.analythium.io Updated on ・7 min read

By: Peter Solymos

Shiny Server is
a free and open-source option for self hosting Shiny apps. The Shiny
Server is one of the 3 options listed on RStudio's official Shiny
documentation
. The paid Shiny Server
Pro version is discontinued in favour of RStudio Connect.

Hosting Shiny apps on the open source Shiny Server requires to (1) set
up a virtual machine (VM) with one of the public cloud providers; (2)
install R, required packages, and Shiny Server on the VM; and (3) copy
your Shiny application to the Shiny Server VM.

Shiny Server is a capable Node.js application that serves the Shiny apps
to the users of the server primarily over
websocket connections, but it
also supports other types of connections. A websocket is a long‑running
connection open between the client and the server, which is crucial for
maintaining application state. The basic setup described above ends with
Shiny Server available at http://youripaddress:3838 as the root
directory. But what you really want is http://yourcomain.com, or maybe
http://yourcomain.com/shiny.

Adding custom domain name, setting up a reverse proxy to serve over port
80 (HTTP) and 443 (HTTPS) instead of 3838, and adding and periodically
renewing security (TLS) certificates to serve Shiny apps over HTTPS
requires you to jump a few more hoops. This is where Caddy
server
comes into the picture. Caddy use
HTTPS automatically and by default. It obtains and renews TLS
certificates for your sites automatically, and comes with lots of handy
features. If you are unsure if your site needs HTTPS, read
this.

In this post you will learn how to install Shiny Server and set up Caddy
to serve your Shiny apps the way you like. This post won't cover
adding/updating Shiny apps to the server.

Provision a server

Each cloud provider has slightly different ways and options to set up a
virtual machine. This post does not cover how to set up and access
virtual machines on different clouds. But here are links for the major
providers with a description of how to set up the server (and also Shiny
Server, which you'll find more about below):

Once you have your virtual machine up and running, we can move on to
installing the necessary software.

You'll need your internet protocol (IPv4) address (e.g.
138.197.134.230), and a domain name (e.g. yourdomain.com). Use your
domain name registrar to add an A record that points your domain or
subdomain to the IPv4 address. It takes some time for the domain name to
propagate through the name servers, so it is good to do this as soon as
possible.

Install R and Shiny Server

I will assume Ubuntu 20.04 for operating system and that you have
admin/root access to the server via secure shell (ssh) or password
based authentication (therefore we can omit the sudo prefix). The
command line instructions can be slightly different for other Linux
distributions.

Here is a script that will take care of the setup, save it to a text
file on your local machine (I call it shiny-server-setup.sh). Add
other R packages as needed to tailor the setup to your needs:

#!/bin/bash

# add CRAN to apt sources
apt-key adv --keyserver keyserver.ubuntu.com \
    --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
printf '\ndeb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/\n' \
    | tee -a /etc/apt/sources.list
add-apt-repository -y ppa:c2d4u.team/c2d4u4.0+

# install system requirements & R
export DEBIAN_FRONTEND=noninteractive
apt-get -y update
apt-get -y upgrade
apt-get -yq install \
    software-properties-common \
    libopenblas-dev \
    libsodium-dev \
    texlive \
    default-jdk \
    gdebi-core \
    r-base \
    r-base-dev
    r-cran-remotes \
    r-cran-shiny \
    r-cran-rmarkdown \
    r-cran-plotly \
    r-cran-ggplot2 \
    r-cran-jsonlite
R CMD javareconf

# install Shiny Server
wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.16.958-amd64.deb
gdebi -n shiny-server-1.5.16.958-amd64.deb
rm shiny-server-1.5.16.958-amd64.deb

# set firewall rules
ufw default deny incoming
ufw default allow outgoing
ufw allow ssh
ufw allow http
ufw allow https
ufw allow 3838
ufw --force enable
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Change directory to the folder where you saved this file and run the
script using ssh (use the IPv4 address instead of the domain name if
it hasn't propagated yet):

export HOST="yourdomain.com"

ssh root@$HOST "bash -s" < shiny-server-setup.sh
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This command will run the shiny-server-setup.sh script that is on your
local machine on the server using the secure shell connection. If you
prefer, you can also log in to the server (ssh root@$HOST) and run the
commands line-by-line by copying into the terminal.

Once it finished Shiny Server will be running and enabled. Visit
http://$HOST:3838/, and you should see the Shiny Server welcome page
displaying the histogram and the R markdown based Shiny doc:

This setup can take 10–15 minutes. You might want to save a machine
image if you have to spin up multiple servers with same or similar
settings. There is an RStudio 1-click
app
in the
DigitalOcean Marketplace that is a pre-configured image with R 4.0 and
open source editions of RStudio Server 1.2. and Shiny Server 1.5 with
widely used packages already installed, a LaTeX installation, and
OpenBLAS to boost numerical operations. This image has Nginx configured,
so having Caddy installed might conflict with those settings (read
this
post for further Nginx settings).

Install Caddy

Log into the server (ssh root@$HOST) and follow the
instructions:

sudo apt install -y debian-keyring debian-archive-keyring apt-transport-https
curl -1sLf 'https://dl.cloudsmith.io/public/caddy/stable/gpg.key' | sudo apt-key add -
curl -1sLf 'https://dl.cloudsmith.io/public/caddy/stable/debian.deb.txt' | sudo tee /etc/apt/sources.list.d/caddy-stable.list

sudo apt update
sudo apt install caddy
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After installing Caddy with apt it will already be running as a
service. It is also enabled (see output from
systemctl is-enabled caddy), which means that it will restart with the
system. Visit http://$HOST to see the Caddy welcome page:

Make a text file called Caddyfile:  touch Caddyfile then
nano Caddyfile, and add the following content. Make sure you add your
domain name to the 1st line, or just use :80 if you want to serve
Shiny apps without custom domain and over HTTP:

yourdomain.com {
        reverse_proxy 0.0.0.0:3838
}
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Save (Ctrl+O) and exit (Ctrl+X) nano. Now copy the file to the
/etc/caddy/Caddyfile location. With this you make sure that
systemctl will restart the Caddy server according to the new
specifications:

cp Caddyfile /etc/caddy/Caddyfile
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Use systemctl reload caddy to apply the changes. Now Caddy will be
busy in the background setting up transport layer security (TLS)
certificates for HTTPS. Use journalctl -u caddy --no-pager | less to
view the logs of what is happening behind the scenes.

Visit https://yourdomain.com to see the Shiny Server welcome page. The
two demo apps are located at https://yourdomain.com/sample-apps/hello/
and https://yourdomain.com/sample-apps/rmd/.

That's it! You can now disable port 3838 with
sudo ufw delete allow 3838. HTTP requests will redirect to HTTPS.
Finally, don't forget to destroy the server if you don't need it any
more. This is the time to save a machine image for future use, such
images cost very little.

Summary

Caddy server makes it super easy to obtain TLS certificates for your
custom domain and to serve Shiny apps securely over HTTPS on top of the
open-source Shiny Server.

PS: Thanks to Caddy team member Francis
Lavoie
for feedback on the Caddy
server setup!

Further reading

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