Quoting Charles Blair (c-bl...@illinois.edu):
> There are a number of files in your list for which I have
> no counterpart.

Two likely reasons: I've got some software installed that you don't,
or my listing is from a different version.

> The sizes of some directories are different.

The digits before the ownerships are the number of hard links,
not the size (which I cut, along with the times). 2 means the
directory is empty, having just the . and .. links.

> The only difference I saw involving ownership:
> 
> < drwxr-xr-x 2 statd nogroup /var/lib/nfs/rpc_pipefs
> > drwxr-xr-x 9 root root /var/lib/nfs/rpc_pipefs

This directory does seem to vary somewhat, so I wouldn't worry
about it. I hadn't noticed. From various of my installations:
drwxr-xr-x  9 root  root       0 Feb 18 05:00 rpc_pipefs wheezy (that's the 
boot-up time)
drwxr-xr-x  2 statd nogroup 4096 May 21  2013 rpc_pipefs wheezy
drwxr-xr-x  2 statd nogroup 4096 Dec 30  2011 rpc_pipefs squeeze→wheezy→jessie
drwxr-xr-x  2 statd nogroup 4096 May 21  2013 rpc_pipefs wheezy→jessie
and entirely absent from a recent fresh install of jessie.

> I'm not sure what the next step should be.

Have you tried updating again?

Cheers,
David.


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