[R] R broken after upgrade to 2.15.3 (Ubuntu 12.10, 64bit)

[Ista Zahn]

Hi,

Please see http://stackoverflow.com/q/15090817, where it was reported
that sudo chmod 644 /etc/R/Renviron fixed this issue. If that doesn't
work for you, consider posting to
https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Best,
Ista

On Mon, Mar 4, 2013 at 9:56 AM, Ulrich Bodenhofer
<bodenhofer at bioinf.jku.at> wrote:
> Hi,
>
> I am using R on Ubuntu 12.10 (64bit). This morning, Ubuntu's software
> updater automatically installed updates to R's base system (version 2.15.3;
> via the CRAN PPA). Now R does not work anymore. Here is what I get when I
> simply enter "R" on the shell prompt:
>
> bodenhof FUKUOKA~>R
> cannot find system Renviron
> Error : .onLoad failed in loadNamespace() for 'utils', details:
> call: options(op.utils[toset])
> error: invalid value for 'editor'
>
> R version 2.15.3 (2013-03-01) -- "Security Blanket"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> 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.
>
> 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
>>
>
> Basic operations work, but the help system is defunct and no add-on packages
> can be loaded. It seems that the utils package is missing or cannot be
> loaded (for a reason that is specified, but which I do not understand).
> There seems to be a fundamental problem. Any ideas what is wrong?
>
> Thanks in advance,
> Ulrich
>
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