Problem

The Installation/Admin guide section 2.1 describes R_HOME as follows:

Choose a directory to install the R tree (R is not just a binary, but has additional data sets, help files, font metrics etc). Let us call this place R_HOME. Untar the source code.

This has was misleading to me, so I thought R_HOME was the directory that R was installed in this entire time, but I was confused by the wording. So R_HOME is not the same as the --prefix in section 2.4):

where prefix is determined during configuration (typically /usr/local) and can be set by running configure with the option --prefix, as in

./configure --prefix=/where/you/want/R/to/go

AND:

prefix/LIBnn/R or libdir/R
.........all the rest (libraries, on-line help system, …). Here LIBnn is usually ‘lib’, but may be ‘lib64’ on
.........some 64-bit Linux systems. This is known as the R home directory.

This clears up some confusion I've had with the manual, and the errors we used to get when including our false R_HOME in the .Renviron file.

Solution

LIBnn (above) is either 'lib' or 'lib64'. So on 64 bit OS, R_HOME != "prefix", but R_HOME does equal "prefix/lib64/R".

To fix this we need to change a few things:

• --r_home parameter changes to something else like --r_root (to make more sense)
• the class variable self.r_home needs refactoring as well to match the first point.
• R_HOME can be placed back into .Renviron or Renviron.site