I also had a problem with baselayout today, and I just fixed it by
cd'ing to the directory and running ebuild baselayout-x.x.x-rx digest.
 Maybe not the safest thing to do, but it works, nonetheless.

On 3/2/06, Bob Slawson <[EMAIL PROTECTED]> wrote:
> Mark Knecht wrote:
> >>>> clean: No packages selected for removal.
> >>>>
> >
> >
> >>>> emerge (4 of 6) sys-apps/baselayout-1.11.14-r6 to /
> >>>>
> > !!! Security Violation: A file exists that is not in the manifest.
> > !!! File: files/digest-baselayout-1.12.0_pre16-r2
> > lightning ~ #
> >
> > What's the proper way to take care of this?
> >
> >
> This sort of problem happens occasionally.  It is likely the Portage
> tree that you last sync'd with was not in sync perhaps because it was
> itself in the process of syncing so...
>
> wait a bit, 4 hours should do, then 'emerge --sync' and the problem
> will, in all likelihood, remedy itself.
>
> BobS
>
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