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I was developing a shiny-app on a Windows machine in Rstudio. Now I need to develop it on a Linux machine and later on will need to deploy it on a server. Because of the need to run the app across platforms, I was looking into some environment control application so that I don't have to tune and reinstall the needed packages manually.

I tried to use Packrat for this purpose. I made a snapshot on my Windows machine, copied and pasted the project to my Ubuntu, reopened the project on RStudio, installed Packrat and the restore of the packages ran automatically. Then I ran into an issue that some of the packages that requires system dependencies were not installed automatically, e.g. rgdal and jqr. Therefore, I had to manually install those system dependencies manually in a terminal (it took me a while because there were about 10 of them that requires extra system dependencies).

I am wondering if there is an easier way to just automatically handle this. Later on, I will need to work with a system administer to deploy the app to the server. I am wondering if Packrat has the capability of automatically installing system dependencies on Linux machine/server. If anyone has encounter this issue before, or have other better options, please let me know!

Thank you!

Andy Liang
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Hello and welcome to StackOverflow.

You are facing a question that is actually much harder to tackle than you may think at first---deployment of complex R package dependencies across different operating systems is a truly hard and, truth be told, unsolved problem!

You can of course use packrat and renv for R package dependencies and snapshots of particular versions. But this does not do anything for system-level dependencies which are simply taken as "given". So no to just transfering to another box and saying "abracadabra". Sorry!

The closest we all may have gotten to fixing this may be Docker where you can create a portable unit of execution that can be deployed whereever Docker run: Windows, macOS, different Linux flavours, ... as it encodes everything.

Dirk Eddelbuettel
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  • Thank you, Dirk. I guess the way to go will be using Docker then. – Andy Liang Sep 23 '20 at 21:11
  • Yes, it sort of depends a bit as well on what exactly you want to do --- for example one reason Shiny became so popular is that it "takes R out of it": colleagues/users/clients just need a web browser. Similarly APIs going over the network only need networking but then you need a server. And on and on. An R package is already a pretty portable "unit" so that is a choice too. – Dirk Eddelbuettel Sep 23 '20 at 21:14