R SIG Debian - Apr 2022 - Where/how to set R_LIBS_SITE in R 4.2.0 for running R as R --vanilla to pick up "/usr/local/lib/R/site-library/"

Dirk, thanks.

I will try to debug locally. Thanks for the instructions.

Just to make sure it is only me: when you run the following commands ($
Rscript -e '.libPaths()') without and with --vanilla on your system you
get
the same output (as you see below I don't):
username at usernameVB:~$ Rscript -e '.libPaths()'
[1] "/usr/local/lib/R/site-library"
"/usr/lib/R/site-library"
[3] "/usr/lib/R/library"
username at usernameVB:~$ Rscript --vanilla -e '.libPaths()'
[1] "/usr/lib/R/site-library" "/usr/lib/R/library"

Thanks.

Best regards,
Sam


On Mon, Apr 25, 2022 at 10:21 PM Dirk Eddelbuettel <edd at debian.org>
wrote:
>
> Sam,
>
> Please try to debug locally. There are command-line switches to R that
> allow
> you to turn sourcing of initializations files off, you can also try to see
> if
> it is different for 'root' as opposed to you account.
>
> When I chase something like that his I typically
>
>  a) add lines like message("running from file foo") in Rprofile,
>     Rprofile.site, ~/.Rprofile etc
>  b) set env vars in each Renviron / Renviron.site / ~/.Renviron  file to
> see
>     which are being hit.
>
> Something somewhere turns some values off for you. I can't tell from
here
> what caused it.
>
> Dirk
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>

-- 
Best regards,
Sam

	[[alternative HTML version deleted]]

On 25 April 2022 at 22:29, Sam H wrote:
| Just to make sure it is only me: when you run the following commands ($
| Rscript -e '.libPaths()') without and with --vanilla on your system
you get
| the same output (as you see below I don't):
| username at usernameVB:~$ Rscript -e '.libPaths()'
| [1] "/usr/local/lib/R/site-library"
"/usr/lib/R/site-library"
| [3] "/usr/lib/R/library"
| username at usernameVB:~$ Rscript --vanilla -e '.libPaths()'
| [1] "/usr/lib/R/site-library" "/usr/lib/R/library"

I see the same on Ubuntu with R 4.2.0.

This is likely due to me having to move the setting for
     /usr/local/lib/R/site-library
from R's own Renviron to Renviron.site and --vanilla skip reading that.

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

So in short:  If you want to run R with --vanilla you have to change the
local set up file. Because R now ships with this

  R_LIBS_USER=${R_LIBS_USER:-'%U'}
  R_LIBS_SITE=${R_LIBS_SITE:-'%S'}

you could set R_LIBS_USER and/or R_LIBS_SITE in a file read by the OS before
R starts -- a short text snippet in /etc/profile.d/ may work -- to ensure
R_LIBS_USER and R_LIBS_SITE are set to your liking.

Sorry for missing the hint about --vanilla from your first email.

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org