I think I got past that issue in my repo where I’m trying to run Tyler Morgan-Wall’s excellent rayshader package. I think I put related dependencies in apt.txt, such as libgdal-dev and libproj-dev. See here. You’ll come across the need to use apt.txt to get ubuntu to install some basic libraries fairly regularly. Search apt.txt on this page. And you’ll get a sense of that being a common usage pattern, and see here and consider it in the light of the quote manics pasted above from the rgdal CRAN page for more understanding of how the stuff rgdal needs is being set up in my example.
I think now I’m having problems with text rendering in the 3D images but that I got past rgdal issue, see here about then getting rgl output to render in Jupyter on Binder.