[R-sig-Debian] /etc/R/Renviron doesn't set R_LIBS_USER anymore

[Ramon Diaz-Uriarte]

On Mon, 03-07-2017, at 12:18:36, Dirk Eddelbuettel <edd at debian.org> wrote:
> On 3 July 2017 at 13:05, Ramon Diaz-Uriarte wrote:
> | If I might chime in, I'd like to add my vote to the "users should be able
> | to use install.packages and should be able to install bioconductor
> | packages with biocLite".
> |
> | Longer story
> | ============
> |
> | Two cases (I've just faced this morning), where
> | /usr/local/lib/R/site-library/ was not user-writeable:
> |
> | 1. Students using Debian or Ubuntu on their laptops, where these students
> | are not particularly knowledgeable about Linux.
> |
> | 2. Sys admins that install and configure software for computer labs, where
> | beyond some bare minima (e.g., R, gcc, etc) users are expected and allowed
> | to install (some) software on their homes. These sys admins might be
> | specially reluctant to add users to privileged groups and/or make
> | /usr/local/lib/R/site-library user-writeable.
> |
> | The problem is that both groups, after issuing the
> |
> | sudo apt-get install r-base
> | sudo apt-get install r-base-dev
> |
> | (as per https://cran.r-project.org/bin/linux/ubuntu/README.html)
> |
> | are later surprised when users cannot immediately install packages in the
> | "usual R way (install.packages)".  And this gets more complicated when we
> | add a bunch of bioconductor packages, where BioConductor pages often say to
> | install as
> |
> | source("https://bioconductor.org/biocLite.R")
> | biocLite(some_packages)
> |
> | I've ended up doing
> |
> | .libPaths(c(the_user_home, .libPaths()))
> |
> | but this does not look very friendly for new users.
>
> Easier: Remove one # comment character in /etc/R/Renviron which does the same.
>
> As does setting in file /etc/R/Renviron.site (which the package never
> touches).

Thanks for reminding me of that. I am now adding it to my class notes so
I won't forget it again. :-)

I understand that this is for the time being, because if you add the user
directory as a fall-back after the preferred /usr/local/lib/R/site-library,
then modifying /etc/R/Renviron[.site] would not be needed.


>
> And local policy can (and should!) still be to set a local group.
>

Point taken too.


Best,


R.

> Dirk


--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es

http://ligarto.org/rdiaz