From hb at biostat.ucsf.edu  Fri Apr 25 20:49:23 2014
From: hb at biostat.ucsf.edu (Henrik Bengtsson)
Date: Fri, 25 Apr 2014 11:49:23 -0700
Subject: [Rd] Preventing $R_HOME/site-library/ via R_LIBS_SITE=":" (no other
	way?)
Message-ID: <CAFDcVCSxCTE4xtFywAUGSvaBMDEvUwqErzL=CNFg6H-UhnJ9aQ@mail.gmail.com>

(As a non-root/non-admin), I've just tried to figure out how to
prevent a default $R_HOME/site-library/ to be added to the library
path.  The solution I found was to environment variable R_LIBS_SITE to
":" (preferably in ~/.Renviron).  Note that setting R_LIBS_SITE to en
empty string will cause it to fall back to using
$R_HOME/site-library/.  This "hack" is based on the following in
help(".Library.site"):

.Library.site is a (possibly empty) character vector giving the
locations of the site libraries, by default the ?site-library?
subdirectory of R_HOME (which may not exist).
[...]
.Library.site can be set via the environment variable R_LIBS_SITE (as
a non-empty colon-separated list of library trees).

It turns out that any dummy string would work (e.g.
R_LIBS_SITE=non-existing-directory), but using the OS's path separator
is at least according to the docs.



TROUBLESHOOTING/PATCHING:
I don't see an obvious elegant fix to this in R, but I believe the
issue is that the system/global Rprofile
(src\library\profile\Common.R) does:

 Sys.setenv(R_LIBS_SITE =
            .expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))

Here this information on whether R_LIBS_SITE is unset or empty is
lost.  Sys.getenv("R_LIBS_SITE", NA_character_) would distinguish the
two cases.  However, NA_character_ is coerced to "NA" in
Sys.setenv(R_LIBS_SITE = ...), which means a site library cannot be
"NA". I assume my above "hack" could be done as:

local({
 libs <- Sys.getenv("R_LIBS_SITE", NA_character_)
 libs <- if (is.na(libs)) "" else if (libs == "") .Platform$path.sep else libs
 Sys.setenv(R_LIBS_SITE = .expand_R_libs_env_var(libs))
})

Not elegant, but it should work.  If not added, may I propose the
following patch to the docs:

>svn diff src\library\base\man\libPaths.Rd
Index: src/library/base/man/libPaths.Rd
===================================================================
--- src/library/base/man/libPaths.Rd    (revision 65492)
+++ src/library/base/man/libPaths.Rd    (working copy)
@@ -63,6 +63,8 @@

   \code{.Library.site} can be set via the environment variable
   \env{R_LIBS_SITE} (as a non-empty colon-separated list of library trees).
+  To prevent the default \file{site-library} subdirectory of
+  \env{R_HOME} to be used, one can set \env{R_LIBS_SITE} to \code{":"}.
 #endif
 #ifdef windows
   The library search path is initialized at startup from the environment
@@ -77,6 +79,8 @@

   \code{.Library.site} can be set via the environment variable
   \env{R_LIBS_SITE} (as a non-empty semicolon-separated list of library trees).

+  To prevent the default \file{site-library} subdirectory of
+  \env{R_HOME} to be used, one can set \env{R_LIBS_SITE} to \code{";"}.
 #endif

   Both \env{R_LIBS_USER} and \env{R_LIBS_SITE} feature possible


My $.02 - may save someone else 30 mins.



[Rd] Preventing $R_HOME/site-library/ via R_LIBS_SITE=":" (no other way?)
Henrik Bengtsson