You're not running into issues with building the N64 emulator mupen64plus? It's only happening on Debian Stretch (x86-64) but it could be my setup so that's why I'm asking. It's requiring a newer version of cmake than what's available:
/home/pi/RetroPie-Setup/tmp/build/mupen64plus/GLideN64/projects/cmake /home/pi/RetroPie-Setup/tmp/build/mupen64plus /home/pi/RetroPie-Setup CMake Error at CMakeLists.txt:1 (cmake_minimum_required): CMake 3.9 or higher is required. You are running version 3.7.2