Were things working before you added runtime.txt and install.R?
It looks like you may be doing what here advised not to do, namely combining the approaches? The page there says you can use postBuild to install packages from other sources but doesn’t show an example. Maybe post an issue and ask for guidance so you could add an example? (That repo is sort of new and I haven’t stumbled upon the way to do it.)
Or you can go the other way and try the example based on here? Can most be moved to apt.txt? The pip installable stuff can be moved to requirements.txt (see discussion here at Aug 15 2018 13:42 timestamp), and things like r-xml moved to install.R (I think based on here).