[R-sig-Debian] Problem Upgrading to R 3.5 on Ubuntu 18.04

[Elizabeth Tighe]

Thanks Dirk!  The prior install and updates had been running fine for so 
long I forgot all about the documentation on Renviron, Startup, etc.!  
Thanks.  Will changing the libPaths in Renviron.site help with the issue 
that the operating system doesn't seem to recognize the installation re: 
message that the "software is not installed" when I tried to remove it?  
Also what does it mean in your note when you say: "you will need to 
trace want on your box does"?

Thanks!

Liz

On 11/28/2018 1:12 PM, Dirk Eddelbuettel wrote:
> On 28 November 2018 at 12:37, Elizabeth Tighe wrote:
> | Somehow during the process of updating both Ubuntu and R to the latest
> | versions I ended up with a version of R 3.5 installed into the sudo
> | user's home directory with default libraries set to the sudo user home
> | directory as well (/home/uname/R/x86_64-pc-linux-gnu-library/3.5 rather
> | than usr/local/lib/R/site-library).
>
> "Hate when that happens" :)
>   
> | I've tried to remove using sudo apt purge r-base r-base-dev and get a
> | message that the software is not installed. If I type "R" it opens
> | version 3.5.  If I go to Ubuntu's graphical interface as sudo user,
> | Software library, R is listed as installed and if I click on the
> | "Remove" button, nothing happens ...
> |
> | Any suggestions on how to expunge this rogue installation and start anew?
>
> What you had (and what you want, if I read the message correctly) is an
> explicit setting for (e.g.) .libPaths() which I like, but which I can't
> "enforce" in the package -- I once tried about 1 1/2 years ago and all broke
> loose because those who had ~/R/... path no longer saw it.
>
> So now again, and as it had been since the 2000s, this is governed by a
> setting in eg
>
>    /etc/R/Renviron.site
>
> which is a convenience symbolic link to
>
>    /usr/lib/R/etc/Renviron.site
>
> The file has comments, so see those.  My (personal) version just comments the
> settings out so that I get
>
>    R> .libPaths()
>    [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"       "/usr/lib/R/library"
>    R>
>
> Now, the tricky bit that R allows half a dozen ways to influence this -- see
> help(Startup) in R for all the gory details.  So I fiddling with
> Renviron.site does not influence a fresh R session you will need to trace
> want on your box does -- "dotfiles" can be sourced from the current
> directory, the home directory, the /etc/ directory, ... and environment
> variables enter too.
>
> Keep us posted, hope this gets you started.
>
> Dirk
>

-- 
Elizabeth Tighe, Ph.D.
Research Scientist
Steinhardt Social Research Institute
Brandeis University
781.736.3824