[R] Cleaning up R-2.0.0 installation on GNU/Linux ?

[Prof Brian Ripley]

On Wed, 13 Oct 2004, Thomas Schönhoff wrote:

> Hello,
> 
> first, big thank you to the developers of R, the release of recent 
> version is very nice.!
> 
> Well, it seems that I've messed up my current installation by using two 
> update mechanism at the same time on my Debian Sid box.
> 
> That is :
> 
> 1)Debian Way per apt-get freshing up my R installation
> 
> 2) irregularily "update packages()" from within R.
> 
> 
> I guess this obviousely resulted in messing up my installation looking 
> like this:
> 
> -------------------------------------------------------------
>  > library()
> (..)
> Packages in library '/usr/local/lib/R/site-library':
> 
> accuracy                ** No title available (pre-2.0.0 install?) **
> ade4                    ** No title available (pre-2.0.0 install?) **
> debug                   ** No title available (pre-2.0.0 install?) **
> distr                   ** No title available (pre-2.0.0 install?) **
> eha                     Event History Analysis.
> ellipse                 ** No title available (pre-2.0.0 install?) **
> faraway                 ** No title available (pre-2.0.0 install?) **
> fortunes                ** No title available (pre-2.0.0 install?) **
> leaps                   ** No title available (pre-2.0.0 install?) **
> mvbutils                ** No title available (pre-2.0.0 install?) **
> mvtnorm                 ** No title available (pre-2.0.0 install?) **
> nlme                    Linear and nonlinear mixed effects models
> R2WinBUGS               ** No title available (pre-2.0.0 install?) **
> RColorBrewer            ** No title available (pre-2.0.0 install?) **
> sca                     ** No title available (pre-2.0.0 install?) **
> scatterplot3d           ** No title available (pre-2.0.0 install?) **
> sn                      ** No title available (pre-2.0.0 install?) **
> sna                     ** No title available (pre-2.0.0 install?) **
> tree                    ** No title available (pre-2.0.0 install?) **
> xgobi                   ** No title available (pre-2.0.0 install?) **
> xtable                  ** No title available (pre-2.0.0 install?) **
> --------------------------------------------------------------------------
> 
> It seems that my insane update method has entirely messed up the 
> attached package section! All other packages still seem to be or run 
> fine! Loading a package from above package section
> 
>   > library(mvtnorm)
> 
> gives me:
> --------------------------------------------------------------------------
> Error in library(mvtnorm) : 'mvtnorm' is not a valid package -- 
> installed < 2.0.0?
> ---------------------------------------------------------------------------
> 
> Since this is the first time I encounter a problem like this in R I 
> wonder where to go from here:
> 
> 1) Wipe out the existent installation and re-install GNU R ?
> 
> or
> 
> 2) Is there possibly any other method to cope with this situation from 
> within GNU R-2.0.0?

remove.packages("nlme", "/usr/local/lib/R/site-library") # a duplicate
foo <- installed.packages(lib="/usr/local/lib/R/site-library")[, 1]
install.packages(foo, lib="/usr/local/lib/R/site-library")

will reinstall all the packages in that library.  I could work out a way
to only get those that were installed in an earlier version, but it would 
be cumbersome.


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595