R help - Mar 2013 - R broken after upgrade to 2.15.3 (Ubuntu 12.10, 64bit)

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

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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> https://stat.ethz.ch/mailman/listinfo/r-help
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http://www.R-project.org/posting-guide.html
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