I am trying to install my packages for a bot (that work on another vps I own) using npm 5, ubuntu 16.04, and node.js 8. The issue seems to be with sodium/libsodium. Here is the error:
I've tried deleting all the node modules and reinstalling, nothing seems to be working. Any ideas?

Install
libtool. The log is saying it doesn't find libsodium so it has to build it withlibtoolwhich it can't find on your system.While you add at it, make sure you have
automakeandautoconfThen try
npm installagain. Removenode_modulesfirst to be safe. Hope this is of help.