Sort of a weird issue. I setup retroarch using the testing PPA on Ubuntu 18.10.
I ran into a weird thing, but I found a workaround. After doing an apt-get install retroarch* libretro-* all the cores seemed to download correctly to:
/usr/x86_64-linux-gnu/libretro which has symlinks to all the cores in: /usr/lib/libretro
Okay, but when I load retroarch, no cores are found. I checked my user directory ~/.config/retroarch/cores and all I have are .info files. When I download a core through the RetroArch online updater tool, the core .so files appear in ~/.config/retroarch/cores.
So I copied all the .so files from /usr/lib/libretro to ~/.config/retroarch/cores and now all the cores show up correctly in the retroarch menu. Games load and play fine. While I don’t mind doing this, it would be nicer to simply run apt-get update && apt-get upgrade and have the cores automatically update. Or I could my symlinks myself.