Remove all packages that do not come with R

Instead of

Updated to R 3.0.0 and have to rebuild all packages.

just do

update.packages(..., checkBuilt=TRUE)

which is what I did on my R 3.0.0 (using lib.loc=... to point to my different local directories). This will update everything you have and which it can still get from repos such as CRAN. For install_git() etc, you are out of luck and need to reinstall.

But either way you do not need to remove the packages first.

Be CAREFUL! And read the docs before you try this:

# Pasted as a commented to prevent blindly copying and pasting
# remove.packages( installed.packages( priority = "NA" )[,1] )

By default this will remove packages from the first library in your .libPaths().