R 3.0.0 update has left loads of 2.x packages incompatible

Question

On Ubuntu 10.04 I updated a load of the R (ubuntu) packages this morning. Then the first R script I tried told me zoo wasn\'t built for R 3.0.0. So I do sudo R and

Answer 1

The required command is not what you state: update.packages(ask=F) but rather the following update.packages(ask=FALSE, checkBuilt=TRUE).

Try that, and all the still-maintained and available CRAN packages will of course be taken care of. Things you installed from github, Simon's rforge, r-forge, or other random repo will need manual help.

This issue has been discussed at length at various venues since R 3.0.0 came out.

Answer 2

Dirk's answer got me most of the way, leaving just xtsExtra, which was installed from R-Forge. I recommend against update.packages(ask=FALSE, checkBuilt=TRUE, repos="http://R-Forge.R-project.org") as that appears to update some of the CRAN packages with their R-Forge version; that might mean it installs more experimental versions (?).

So, I did this instead:

remove.packages('xtsExtra')
install.packages("xtsExtra", repos="http://R-Forge.R-project.org")