I’m seeing the same thing here.
I switched over to using portmaster as portupgrade was taking way to much time.
This is on Intel Core2 Quad 3ghz.

Also after doing a pkg check -d there was a bunch of missing 
libraries:libintl.so.9
It’s there:
ls -l /usr/local/lib/libintl*
-rw-r--r--  1 root  wheel  103320 Sep 26 12:08 /usr/local/lib/libintl.a
lrwxr-xr-x  1 root  wheel      16 Sep 26 12:08 /usr/local/lib/libintl.so@ -> 
libintl.so.8.1.3
lrwxr-xr-x  1 root  wheel      16 Sep 26 12:08 /usr/local/lib/libintl.so.8@ -> 
libintl.so.8.1.3
-rw-r--r--  1 root  wheel   55118 Sep 26 12:08 /usr/local/lib/libintl.so.8.1.3
lrwxr-xr-x  1 root  wheel      12 Sep 26 12:08 /usr/local/lib/libintl.so.9@ -> 
libintl.so.8
I reinstalled the ports that referenced this and the error went away.
Still getting error on this:
pkg check -d
Checking all packages: 100%
p5-perlkde has require a missing libraries: QtCore4.so
QtCore4.so is installed at:
/usr/local/lib/perl5/site_perl/mach/5.20/auto/QtCore4/QtCore4.so
reinstalling p5-perlqt-4.14.3 and p5-perlkde doesn’t make the error go away.
It wasn’t there before pkg-1.6.0


> On Sep 26, 2015, at 7:07 PM, Xavier <xav...@groumpf.org> wrote:
> 
> Hi,
> 
> Since upgrading to pkg 1.6 the last stage of portupgrade (Cleaning out 
> obsolete shared libraries) has become incredibly slow. The command is :
> 
> /usr/local/sbin/pkg query %n-%v %Fp
> 
> which eats 100% CPU for many minutes
> 
> Thks for clues
> 
> Xav
> 
> -- 
> Xavier HUMBERT - Unix/Win/MacOSX Sysadmin/Network Engineer
> _______________________________________________
> freebsd-ports@freebsd.org mailing list
> https://lists.freebsd.org/mailman/listinfo/freebsd-ports
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> 
> 



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