[R-sig-Debian] 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/"

[Sam H]

Hello,

I have upgraded to R 4.2.0 on Ubuntu Ubuntu 20.04.4 LTS.

Something changed since now when invoking R as "R --vanilla" does not pick
up "/usr/local/lib/R/site-library" library anymore.

I tried to look at "6.2 Managing libraries" in
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html and
set R_LIBS_SITE in Renviron.site but with no success.

What am I missing? Thanks.

If I run R as "R --vanilla" this is what I get:
$ R --vanilla

R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> .libPaths()
[1] "/usr/lib/R/site-library" "/usr/lib/R/library"
> Sys.getenv("R_LIBS_USER")
[1] "/home/username/R/x86_64-pc-linux-gnu-library/4.2"
> Sys.getenv("R_LIBS_SITE")
[1] "/usr/lib/R/site-library"
>

If I run R as "R" correct libraries are picked up:
$ R

R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> .libPaths()
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"
> Sys.getenv("R_LIBS_USER")
[1] "/home/username/R/x86_64-pc-linux-gnu-library/4.2"
> Sys.getenv("R_LIBS_SITE")
[1]
"/usr/local/lib/R/site-library/:/usr/lib/R/site-library:/usr/lib/R/library"
>

-- 
Best regards,
Sam

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