I'm using the flatpak installation of atom from flathub (https://flathub.org/apps/details/io.atom.Atom). I can install atom-ide-r just fine and have the languageserver 'R' package installed. But I can't get ide-r to find my R installation. This may be an issue with flatpak sandboxing, such that atom doesn't have permission to system paths?
Anyhoo, atom-ide-r doesn't work out of the box for flatpak atom users.