How generally do institution handle updates/backups on shiny server?

This question came to us because we found the shiny app was working (typically renderDT) on our local machine but not working when we uploaded it. However, after we updated the R packages, it worked on the server. Unfortunately, that made some graphs that originally were showing not working. It turned out to be that originally the package 'cowplot' calls the package ggplot2, whereas after updating all the packages, now it no longer does that.

We are wondering how do institutions generally handle the updates/backup on the shiny server? A development server or...? We are afraid that if we do similar things (updating) again, it may not go back to the past and things can break with updating R or R packages...

Many thanks in advance!

You may have to develop separate "production" and "development" environments so you can test changes (this can be automated) without affecting your applications in "production".

There are many ways to approaching this issue, some more complex than others but which one to choose depends on your specific organization, so you would have to be more specific about your requirements and restraints for getting more focused advice.