R install 2.15.2 Renvirons not found, Ubuntu 12.10 x64

Question

Ubuntu 12.10 x64, R 2.15.2

I'm at a loss, I've installed R numerous times and never had the slightest problem with the install. This time however when I launch the program (either by using the GUI or by typing "R" in the terminal) I get this;

cannot find system Renviron Error : .onLoad failed in loadNamespace() for 'utils', details: call: options(op.utils[toset]) error: invalid value for 'editor'

R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit)

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Error : .onLoad failed in loadNamespace() for 'utils', details:
call: options(op.utils[toset]) error: invalid value for 'editor' In addition: Warning message: package "methods" in options("defaultPackages") was not found Error : .onLoad failed in loadNamespace() for 'utils', details: call: options(op.utils[toset]) error: invalid value for 'editor' In addition: Warning message: package ‘utils’ in options("defaultPackages") was not found Error : .onLoad failed in loadNamespace() for 'utils', details: call: options(op.utils[toset]) error: invalid value for 'editor' In addition: Warning message: package ‘stats’ in options("defaultPackages") was not found During startup - Warning message: package ‘methods’ in options("defaultPackages") was not found

Nothing works, no packages are found. I've never received any training on how to use Ubuntu, but from what I can gather I am missing the recommended packages for R.

I've tried completely removing R using both the Terminal as well as Synaptics Package Manager, then re-downloading the from CRAN servers (it seems to download too fast for my internet connection) and then reinstall. Same message. I'm at a loss.

Answer 1

I had the same problem and setting the EDITOR environment variable solved the problem for me.

Try e.g.

EDITOR=vim R

If that works, put the line

export EDITOR=vim

at the end of your ~/.profile

EDIT: the root of the problem was that /etc/R/Renviron was not read by R. As Dirk commented on his reply,

sudo chmod 644 /etc/R/Renviron

solves the problem

Answer 2

The error seems to be the following :

error: invalid value for 'editor'

You can try to type the following in a terminal to know what the value of your EDITOR environment variable currently is :

echo $EDITOR

And maybe you should be able to start R from the command-line with something like :

EDITOR="" R

Answer 3

But it starts to get dicy before it gets to editor -- it seems like it fails to load your saved environment. Can you try

 R --no-restore-data

or even

 R --vanilla

Needless to say, it works for me and the only configuration change made was in the Java stack (see the Changelog file).

There is a dedicated list r-sig-debian for the Debian and Ubuntu packages where you'd get me (Debian packages), Johannes (Debian backports, available via CRAN) and Michael (Ubuntu builds, available via CRAN). I tend to run Michael's packages on my Ubuntu machines and have not had an issue.

Answer 4

I encountered this problems after I insall R and RStudio too.Both of them apear to have problems same as yours. I can't find the .Renviron in /etc/R.Then I search the Internet and find out I should use this file to set envirenments for my R. So all I need to do is new a ".Renviron" file and write it correctly. Fortunatelly I find a file named "Renviron.site" in /etc/R and inside it I find a few lines of comments :

   # ## Example .Renviron on Windows
   # R_LIBS=C:/R/library
   # MY_TCLTK="c:/Program Files/Tcl/bin"……

I suppose this would be useful to write my .Renviron file. So I write these in terminal:

sudo gedit /etc/R/.Renviron The .Renviron file is automatically created and open by gedit.Later on I copy

R_LIBS=~/R/library

PAGER=/usr/local/bin/less

R_DEFAULT_PACKAGES='utils,grDevices,graphics,stats'

into .Renviron file and save it.And the RStudio just work normally!