[BioC] Incorrect permissions to edit database package

[Jeff Gentry]

> However, when I look at that file, the user I am running R as has r and
> w permissions on it....

I'm assuming 'yes' due to your stating that you're running R as root but
do you also have write access on the directory as well?

> So firstly - any ideas why I get this error message?  And secondly, does
> it matter that I am getting it?  I don't get it if I run R as root
> (obviously) but I don't really want to be doing that (obviously)

save.locLib uses the test 'file.access(lib,mode=2)', where 'lib' is
the directory that the library is in.  It is worth trying this from within
R:

file.access("/usr/lib/R/library", mode = 2)

and if the result is non-zero then R believes that you in fact don't have
write access.

This does seem odd though - is it only when you're loading affy, or does
it happen when loading other packages?

-J