My limited knowledge of what happens in Terminal, and thus by extension shell, is mostly driven by PostgreSQL/PostGID/rgdal/RPostgreSQL install errors. In the latest variant of this, rgdal throws the following error when attempting to build from source:

checking PROJ.4: epsg found and readable... no  
Error: proj/epsg not found  
Either install missing proj support files, for example the proj-nad and  proj-epsg RPMs on systems using RPMs, or if installed but not autodetected, set PROJ_LIB to the correct path, and if need be use the --with-proj-share=configure argument.  

I have to build from source by the way because the default rgdal package for Mac does not include a PostgreSQL driver, meaning I have to build it against another version of GDAL that does. This was another fun thing to discover, but at least is easy to diagnose by checking whether PostgreSQL shows up when you run ogrDrivers() in R. Anyways, as far as I can tell the problem was that I installed proj via homebrew, a package manager for OS X. As a result although rgdal could find the proj binary via a symlink, it could not find the epsg and related data files that were in a little dark corner by themselves. The solution was to build the package with an option providing the file location manually:

install.packages("rgdal", type = "source", 
  configure.args="--with-proj-share=/usr/local/Cellar/proj/4.8.0/share/proj")  

This is I guess exactly what the install error message told me to do.