I am having a similar problem with outdated PROJ and GEOS versions on shinyapps.io. My libraries will install, but the GEOS, GDAL, and PROJ versions on shinyapps (3.5.1, 2.2.2, and 4.9.2) do not match those on my local machine (3.8.0, 3.0.4, and 6.3.1). I tried installing the sf and rgdal packages from GitHub before deploying my app, but that did not resolve the issue. Following in case solutions pop up.