On 09/16/2017 11:29 AM, Rene J Suarez-Soto wrote:
I have not intentionally set R_LIBS_USER. I looked for an Renviron.site
file but did not see it in R/etc or my home directory. The strange part is
that if I print Sud.getenv I see a value for R_LIBS_USER. However, this
directory is not showing under libPaths.
I though .libPaths should contain R_LIBS_USER.
If the directory pointed to by R_LIBS_USER does not exist, then
.libPaths() will not contain it. This is documented on ?.libPaths or
?R_LIBS_USER
Only directories
which exist at the time will be included.
The file in the user home directory is .Renviron, rather than
Renviron.site. This documented at, e.g,. ?Renviron
The name of the user file
can be specified by the 'R_ENVIRON_USER' environment variable; if
this is unset, the files searched for are '.Renviron' in the
current or in the user's home directory (in that order).
R environment variables are set when R starts; I can discover these, on
linux, by invoking the relevant command-line command after running R CMD
$ env|grep "^R_"
$
(i.e., no output) versus
$ R CMD env|grep "^R_"
R_UNZIPCMD=/usr/bin/unzip
...
Generally, ?Startup describes the startup process, and most variables
are described in R via ?R_...
Martin
I also noticed that R related variables are not in the system or user
variables because I dont see them when I type SET from the Windows Command
line. So a related question is where does R get the system variables
(e.g., R_LIBS_USER,
R_HOME) if I dont see a Renviron.site file. Thanks
On Sep 16, 2017 10:45 AM, "Henrik Bengtsson" <henrik.bengts...@gmail.com>
wrote:
I'm not sure I follow what.the problem is. Are you trying to
set R_LIBS_USER but R does not acknowledge it, or do you observe something
in R that you didn't expect to be there and you are trying to figure out
why that is / where that happens?
Henrik
On Sep 16, 2017 07:10, "Rene J Suarez-Soto" <rene.j.sua...@gmail.com> wrote:
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
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