[BioC] R --vanilla and Annotation pkg

[Jeff Gentry]

> But WHEN.....I run my script1.R by copy and paste  and
> then I do R --vanilla , I DON'T get above error. 
> has anyone had this problem..?

Are you sure that you're getting the same .libPaths() between your
interactive R session and the R --vanilla?  That might very well not be
the case, and if the package is installed in a directory that is in your
interactive .libPaths but not in your vanilla session then you would see
that behaviour.