Cleaning up R-2.0.0 installation on GNU/Linux ?

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?

On Wed, 13 Oct 2004, Thomas Sch??nhoff wrote:

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.

Hello,


Prof Brian Ripley said the following on 13.10.2004 10:34:

On Wed, 13 Oct 2004, Thomas Sch??nhoff wrote:

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")

Besides one minor error regarding to distr package:

--------------------------------------------------------------
Warning message:
Installation of package distr had non-zero exit status in: 
install.packages(foo, lib = "/usr/local/lib/R/site-library")
---------------------------------------------------------------

your recommendations worked out fine, thanks!

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.

No need for doing this at the moment!


If understand correctly the previous situation is only arising when 
there are major version upgrades, i.e. from 1.9.1 too 2.0.0.

But when using "update packages() within a major release everything will 
be fine, isn't it?

I would be interested to hear what upgrade methods GNU/Linux (Debian) 
users prefer to avoid a situation like this!

Many thanks for help!

Thomas

On Wed, 13 Oct 2004, Thomas Sch??nhoff wrote:

Maybe we should add an option to update.packages to reinstall old 
installations too.