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R_LIBS_USER not in libPaths

These environment variables are _inputs_ to the R startup sequence, and optional ones at that. If you don't set them then R makes default settings. Read the R Installation and Administration manual that comes with R for more information. 

You also need to understand the scope of environment variables, which is a topic specific to each operating system and is not specific to R. In a nutshell, a process (running program) that sets an environment variable can pass that setting to processes it starts, but the reverse is not true. If you want to set such variables for widespread use you can use the System control panel and logout and login so all processes will inherit them. 

Note that if you want to modify .libpaths in R you can do so without modifying environment variables.