R - How to set the path of install.packages() for shiny server ? - Ubuntu

Question

For my system: Ubuntu 12.04 and R 3.03, whenever I install a custom package in R via

>install.packages()

the package is installed by default to

/home/USER/R/x86_64-pc-linus-gnu-library/3.0/ 

as opposed to system-wide in

/usr/local/lib/R/site-library/

which is needed for shiny-server to work with that package.

My temporary solution is to copy the packages to the correct folder after the fact.

Question: How can I set the default install path from the start to avoid this problem?

Pascia

Easiest way is usually to login as root (sudo -i), open R, and install it there. Then the package will be site-wide. – Abortion

Not sure I can that easiest :) – Devilry

// , Do you think this is relevant to #42048190 – Ragi

Answer 1

Yes -- I consider this to be a misfeature and disable my per-user directory.

Moreover, I mostly use a script install.r (of which a version is an example in the littler package you can install as part of Ubuntu) which simple explicitly set the /usr/local/lib/R/site-library directory as the default. With a patch we got into R 3.0.2 or 3.0.3, normal user can write into the directory and will now create group-writeable directories so other users can update and overwrite -- just make everybody a member of the same group, say staff or admin. And then you don't even need sudo or root.

I have essentially answered this same question a few times here over the years (minus the shiny angle, which is not really relevant) so feel free to search for the other for more details, examples, ...

Devilry

Thanks, I can figure it out from there. I'll look again for a similar question - I had no luck on my first bunch of searches for it. – Pascia

Answer 2

I would propose a different approach.

The problem is that shiny-server cannot find the packages that you install because it runs them as a different user which is called shiny. This user is created upon installation of shiny-server

The easiest (and safest IMHO) way to solve this is to just install the packages as the shiny user, using the following steps.

1. Set a password for the user using sudo passwd shiny, now enter and confirm a password of your choosing.
2. Switch to the shiny account using: su - shiny
3. Call up R using $ R (without sudo)
4. Install the required packages, in this case: `install.packages("shinydashboard")

Note that if you have rstudio-server installed on the same machine then you can perform steps 2-4 using that interface. Simply go the same domain/ip and use :8787 for the rstudio-server interface instead of :3838 for shiny-server.

Adapted from my answer here

Goolsby

I cannot login using shiny account in the R studio server terminal. I did set password. – Laud

yeah I cannot seem to login either since a certain version. I have not idea what the problem is with that – Goolsby

Answer 3

Offering another solution, and that is to specify the user library as the location rather than the shiny library which uses the /usr/local/lib/R/site-library library location to your user name.

In bash open the shiny-server configuration file

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

Then change the run_as from the shiny user to your own username soran

# Define the user we should use when spawning R Shiny processes
#run_as shiny; # old line
run_as soran;

# Define a top-level server which will listen on a port
server {
  # Instruct this server to listen on port 3838
  listen 3838;
....

After changing the file stop the server and start it again so the new configuration is loaded.

sudo systemctl stop shiny-server
sudo systemctl start shiny-server

This will change all shiny apps served by your server to use the users R library. I would also recommend not using a user with admin or root privileges for security.

It is possible to only specify the users R library to specific applications. To do this you need to specify certain shiny app subdirectories to load under that users r profile by using run_as with the subdirectory name in location. See the following documentation for more details.

https://docs.posit.co/shiny-server/#stopping-and-starting

Lunnete