I have a computer where R_LIBS_USER is not found in libPaths. This is for
Windows (x64). I ran R from the command line, RGui and RStudio and I get
the same results. I also ran R --vanilla and I still get the discrepancy.
The only thing I found interesting was that I also ran SET from the command
line and the "R related variables" (e.g., R_HOME; R_LIBS_USER) are not
there. Therefore these variables are being set when I start R. I have not
been able to track where does R obtain the value for these.
Aside from looking at
http://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html I am
not sure I have much more information that I have found useful.
Thanks
R