Thomas Schönhoff
2004-Oct-13 07:59 UTC
[R] 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? regards Thomas platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major 2 minor 0.0 year 2004 month 10 day 04 language R
Prof Brian Ripley
2004-Oct-13 08:34 UTC
[R] Cleaning up R-2.0.0 installation on GNU/Linux ?
On Wed, 13 Oct 2004, Thomas Sch??nhoff 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