From owner-freebsd-ports@freebsd.org  Tue Jun 21 08:43:02 2016
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Date: Tue, 21 Jun 2016 10:41:46 +0200
From: Tijl Coosemans <tijl@FreeBSD.org>
To: Walter Schwarzenfeld <w.schwarzenfeld@utanet.at>
Cc: freebsd-ports@freebsd.org
Subject: Re: linux-c6/c6_64 update
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On Tue, 21 Jun 2016 00:01:36 +0200 Walter Schwarzenfeld <w.schwarzenfeld@utanet.at> wrote:
> Update linux-c6/linux_c6:64 (Revision 417169) from today
> I have linux-c6_64\* packages installed.
> Portmaster updated this packages. But it tried also install some 
> linux-c6 packages, but this failed.
> After second try, portmaster states right: "all packages up-to-date".
> But it has installed all linux-c6_64 packages as automatic. Maybe, this 
> could cause problems if someone tries to run pkg autoremove.
> I mailed this the portmaster maintainer.

Do you have the following in /etc/make.conf:

OVERRIDE_LINUX_BASE_PORT=	c6_64
OVERRIDE_LINUX_NONBASE_PORTS=	c6_64