9.1 R

To get the latest R packages for Ubuntu (at the time of writing it’s 3.6) we’ll start by adding the external repository maintained by CRAN to the etc/apt/sources.list file. If your droplet runs on Ubuntu 16.04.6 x64, as suggested in step 1.2, you need to add deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/ to the file. If you use a different Ubuntu version check here for the correct entry: https://cloud.r-project.org/bin/linux/ubuntu/README.html.

You have 2 options to add the repo:

Option 1: Using the add-apt-repository command

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

Option 2: By redirecting output to a file appending the redirected output at the end.

$ sudo sh -c 'echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" >> /etc/apt/sources.list'

By using https://cloud.r-project.org, you will be automatically redirected to a nearby CRAN mirror.

Now we’re ready to install the complete R system. The following lines of code should look familiar to you from step 5.1 when installing nginx (except that we don’t set the -y flag this time):

$ sudo apt-get update
$ sudo apt-get install r-base

During the installation you will be asked if you agree with the disk space used by the program → type y

Check if you can run R by simply typing

$ R

If everything worked well you should have entered its interactive shell:

R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

Quit R with quit()

9.2 R Packages

Before you install anything you might need to add some swap space for bigger memory to be able to install packages if you have chosen the cheapest droplet with 1GB memory (this is taken from Dean’s blog):

$ sudo /bin/dd if=/dev/zero of=/var/swap.1 bs=1M count=1024
$ 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'

Also, if you want to install some packages as development version from GitHub you should install the ‘devtools’ package and all its dependencies. Some of these dependencies are not R packages so we will install them first and with code you should be familiar by now:

$ sudo apt-get -y install libcurl4-gnutls-dev libxml2-dev libssl-dev

Now you’re ready to install all R packages you need.

NOTE, there are 2 ways of installing packages in the root library so that they will be available to all users automatically.

1. Start R as root and install libraries with the known install.packages() function
2. Install straight from the shell using sudo su - -c "R ... "

I will demonstrate both options in more detail now:

$ sudo -i R

> install.packages(c("devtools", "tidyverse", "modelr", "lubridate"), dependencies = TRUE)

...
Installing package into ‘/usr/local/lib/R/site-library’
(as 'lib' is unspecified)
. . .

> library(lubridate)
> month(ymd("2019-Dec-01"))
> quit()

$ sudo su - -c "R -e \"install.packages('rmarkdown', repos='http://cran.rstudio.com/')\""
$ sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""
$ sudo su - -c "R -e \"install.packages('shinyjs', repos='http://cran.rstudio.com/')\""

$ R

> library(modelr)
> library(shiny)

> .libPaths()
[1] "/home/saskia/R/x86_64-pc-linux-gnu-library/3.5"
[2] "/usr/local/lib/R/site-library"                 
[3] "/usr/lib/R/site-library"                       
[4] "/usr/lib/R/library"  

11.1 Installation

If you haven’t installed the shiny package as root in step 9.2 you need to do this latest now.

$ sudo su - -c "R -e \"install.packages('shiny', repos='http://cran.rstudio.com/')\""

Also, if the GDebi tool is NOT installed yet because you skipped the RStudio installation you need to do it now:

$ sudo apt-get -y install gdebi-core

To install the latest Shiny Server we need to download the correct file for your OS as we did for RStudio Server. Check the Shiny Server download page for the appropriate URL: https://www.rstudio.com/products/shiny/download-server/

At the time of my installation the version was v1.5.9.923 and the 2 commands required for 64bit Ubuntu 14.04 or later were (but again, check on the webpage for the latest version and URL):

$ wget https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.9.923-amd64.deb
$ sudo gdebi shiny-server-1.5.9.923-amd64.deb

(confirm installation)

Once the installation finished, you can test the server using the default port 3838: https://123.45.678.910:3838/ (again, replace this dummy IP 123.45.678.910 with your server IP).

If all went well you should see this welcome page with 2 example shiny apps. Try them out and read the welcome text as it provides some useful information worth reading!

11.2. A brief Shiny Server overview

• All shiny apps and the Shiny Server homepage are located in the root directory /srv/shiny-server/, which means that you can only make changes to these files using the sudo command when logged in as non-root user. To change the homepage file in the editor or remove it completely you’d need to type

$ sudo nano /srv/shiny-server/index.html
$ sudo rm /srv/shiny-server/index.html

→ but we will change that in a bit!

• Each shiny app or interactive R Markdown document and its supporting files should be saved in a separate folder under this directory. You can also group several shiny app folders into one → to access the app in the browser you would simply add the subdirectory to the IP address.
  • For instance, the embedded It’s Alive app above is located in the folder hello
  • which is together with the Shiny Doc R Markdown document in the sample-apps folder,
  • hence, the full path is /srv/shiny-server/sample-apps/hello.
  • Since the port 3838 directs the user already to the /srv/shiny-server/ folder you only need to add the subdirectory /sample-apps/hello to the IP address.
  • Try it out: https://123.45.678.910:3838/sample-apps/hello (replace with your server IP)
  • So choose your folder names carefully (e.g. don’t use blanks).
• The configuration files are located in the /etc/shiny-server directory, which we will soon access.
• All Shiny Server log entries are saved in /var/log/shiny-server.log.

11.3 Configuration

You can make sure that all log files will be saved and informative errors printed for debugging by adding a few lines to the shiny server configuration file. Open the shiny-server.conf file with an editor:

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

→ here you could also change the port number in the server definition.

After the server definition add these 4 lines (incl. the comments so you know what for):

# To make sure that shiny log files will always be preserved
preserve_logs true;
# To make sure that informative error messages are printed
sanitize_errors false;

You might notice that apps are run as user shiny and not as root our your non-root user (in my case saskia). This means that all packages a shiny app loads need to be available for that user, which is why it is so crucial to install packages in the global library and not redundantly on a user-basis. As a solution you could add your non-root user to the config file by adding this line

run_as username;

But then it might be difficult to distinguish between you using the server’s resources or a shiny user playing with your app. There is another alternative I’ll describe next so let’s NOT add this line of code, save the file and exit.

You must reload the shiny server after editing the config file:

$ sudo service shiny-server restart

11.4 Set up proper authorizations

I mentioned before that changes in the entire /srv/shiny-server directory can only be authorized by the root user.

To check access authorization type

$ cd /srv
$ ls -la 

You will see something like this:

drwxr-xr-x  2 root root 4096 Jan 26 19:36 shiny-server

That means that the user root has reading (r) , writing (w) and execution (x) rights (indicated by the rwx in position 2-4), the group root has only reading and execution rights (indicated by r-x in position 5-7) and all others have also only reading and execution rights (indicated by the r-x in position 8-10).

Now following step 8.1 in Dean Attali’s blog post I set my non-root user saskia as owner of this directory since it will be mainly me as saskia adding apps. Second, I replaced the group by a new group shiny-apps where also the shiny user has access to:

$ sudo groupadd shiny-apps
$ sudo usermod -aG shiny-apps saskia
$ sudo usermod -aG shiny-apps shiny

The command usermod modifies a user account and the -aG flag adds the user to the secondary group.

Next, I gave the group also writing permission:

$ cd shiny-server
$ sudo chown -R saskia:shiny-apps .
$ sudo chmod g+w .
$ sudo chmod g+s .

Check again:

$ ls -la /srv

Now you should see:

drwxrwsr-x  2 saskia shiny-apps 4096 Jan 26 19:36 shiny-server

Both saskia and shiny have now permission to access existing files under /srv/shiny-server or write new files. The latter is usually more relevant for saskia as shiny users won’t upload a shiny app on my server. But it can be important when the shiny app is used as an online form and when every submitted questionnaire will be saved as individual file.

Option 1: From the shell

Let’s say you developed within your new R Studio Server a shiny app that you saved in a folder called hello, which is located right in your R home directory. You could then copy the files from the R directory to your Shiny directory in the shell using the cp command.

Open the terminal and log into your droplet, then type

$ sudo cp -r /home/your_username/R/hello/ /srv/shiny-server/

NOTE: The -r flag for the copy command is important: it stands for recursive and means that ALL files within that folder will be copied too!

To move the entire folder use

$ sudo mv -r /home/your_username/R/hello/ /srv/shiny-server/

Now test your shiny app in the browser: https://123.45.678.910:shiny/hello

Alternatively, you can use the scp command, which is a file transfer program for SFTP in Linux. SFTP stands for SSH Secure File Transfer Protocol and supports the full security and authentication functionality of SSH. It uses the same port as the SSH port so there is no need to configure another hole into the firewall.

The scp usually comes with the OpenSSH package. Once you’re logged out of your droplet type

$ scp -r username@hostalias/home/your_username/R/hello/  username@hostalias/srv/shiny-server/

Option 2: Connect to your droplet using a file manager

Depending on your operating system you have various choices of file managers that also serve as SFTP clients. Here are some examples:

• Cyberduck → Mac, Windows
• Forklift → Mac
• Filezilla → Mac, Linux, Windows
• PuTTY → Windows

I personally use on my Macs for many years Forklift and I love it. Not only that it is a much nicer file manager than the default finder, I can also easily connect to my droplet. And once I’m connected I can treat the droplet directory as any other external hard drive. So I can simply drag and drop files from my computer to the droplet and vice versa.

I only needed to set up the connection once by clicking on Go To > Connect and then a dialog box pops up:

Select SFTP as protocol, enter the droplet’s hostalias you defined in step 2.5, your username and password and the port number if is not the default. You can even add this connection to your favorites and have access to it anytime!

Option 3: Connect through git

Last but not least you can convert your /srv/shiny-server directory into a git repository so that you can push your apps or any other file to this repo from your computer. If you then do a git pull on your droplet the new app will be on the server.

If you want to go this track I recommend that you follow these instructions.

Congratulations, you’re all set now! Have fun with your very own Shiny Server!.