pkg upgrade wants to install X11

I have installed FreeBSD 10.1 without X11 so I can use it as a headless server. I want absolutely no X11, just plain command line. I also have built Deluge torrent client from ports without X11 and removed the GTK option.

Now when I do pkg update && pkg upgrade I see that it wants to install a bunch of new packages that are related to X11.
libXaw: 1.0.12_2,2
printproto: 1.0.5
libXp: 1.0.2_2,1
libGL: 9.1.7_4
libxshmfence: 1.1_3
libXxf86vm: 1.1.3_2
xf86vidmodeproto: 2.3.1
libXfixes: 5.0.1_2
fixesproto: 5.0
libXdamage: 1.1.4_2
damageproto: 1.2.1
dri2proto: 2.8
libglapi: 9.1.7_2
libdrm: 2.4.58_1,1
libpciaccess: 0.13.2_2
pciids: 20141222
libdevq: 0.0.2
libXmu: 1.1.2_2,1
py27-service_identity: 14.0.0
py27-characteristic: 14.1.0
py27-asn1-modules: 0.0.5_1
py27-asn1: 0.1.7,1
libgnome: 2.32.0_3
pango: 1.36.8
libXrender: 0.9.8_2
renderproto: 0.11.1
xorg-fonts-truetype: 7.7_1
font-misc-meltho: 1.0.3_1
mkfontscale: 1.1.1_1
libfontenc: 1.1.2_2
mkfontdir: 1.0.7
fontconfig: 2.11.1,1
font-misc-ethiopic: 1.0.3_1
font-bh-ttf: 1.0.3_1
encodings: 1.0.4_1,1
font-util: 1.3.0_1
dejavu: 2.34_4
libXft: 2.3.1_2
harfbuzz: 0.9.36
graphite2: 1.2.4
cairo: 1.12.18_1,2
xcb-util-renderutil: 0.3.9
xcb-util: 0.3.9_3,1
pixman: 0.32.6
gtk2: 2.24.25_1
libXrandr: 1.4.2_2
randrproto: 1.4.0
libXinerama: 1.1.3_2,1
xineramaproto: 1.2.1
libXi: 1.7.4,1
inputproto: 2.3.1
libXcursor: 1.1.14_2
libXcomposite: 0.4.4_2,1
compositeproto: 0.4.2
cups-client: 1.7.3_2
shared-mime-info: 1.1_1
hicolor-icon-theme: 0.12
gtk-update-icon-cache: 2.24.25
gdk-pixbuf2: 2.31.2_1
tiff: 4.0.3_5
jbigkit: 2.1_1
gcc: 4.8.3_2
mpfr: 3.1.2_2
gmp: 5.1.3_2
mpc: 1.0.2_1
gcc-ecj: 4.5
binutils: 2.25
jasper: 1.900.1_14
atk: 2.14.0
rarian: 0.8.1_3
libxslt: 1.1.28_5
libgcrypt: 1.6.1_5
libgpg-error: 1.17
docbook-xsl: 1.76.1_2
xmlcatmgr: 2.2_2
docbook: 1.5
sdocbook-xml: 1.1_1,2
docbook-xml: 5.0_2
xmlcharent: 0.3_2
docbook-sgml: 4.5_1
iso8879: 1986_3
bash: 4.3.30_1
getopt: 1.1.6
gnome-mime-data: 2.18.0_5
libbonobo: 2.32.0_2
popt: 1.16_1
libIDL: 0.8.14_2
ORBit2: 2.14.19_1
gnome-vfs: 2.24.4_3
hal: 0.5.14_28
policykit: 0.9_8
dbus-glib: 0.100.2_1
dbus: 1.8.12
gnome_subr: 1.0
dmidecode: 2.12
consolekit: 0.4.5_2
polkit: 0.105_4
gobject-introspection: 1.42.0
libvolume_id: 0.81.1
samba36-libsmbclient: 3.6.24_2
tevent: 0.9.21
talloc: 2.1.0
pkgconf: 0.9.7
tdb: 1.2.13,1
avahi-app: 0.6.31_3
libdaemon: 0.14_1
gconf2: 3.2.6_3
dconf: 0.22.0_1
gamin: 0.1.10_8
libcanberra: 0.30_3
libvorbis: 1.3.4_2,3
libogg: 1.3.2_1,4
esound: 0.2.41_3
libaudiofile: 0.3.6_1
py27-gtk2: 2.24.0_3
py27-cairo: 1.10.0_2
py27-gobject: 2.28.6_5
libglade2: 2.6.4_7
py27-gnome: 2.28.1_5
libgnomeui: 2.24.4_5
startup-notification: 0.12_3
libbonoboui: 2.24.4_3
libgnomecanvas: 2.30.3_3
libart_lgpl: 2.3.21_2,1
libgnome-keyring: 3.12.0_1
gnome-icon-theme: 3.12.0_1
gnome-icon-theme-symbolic: 3.12.0
gvfs: 1.20.3
libcdio-paranoia: 10.2+0.90+1_1
libcdio: 0.92_1
libcddb: 1.3.2_4
gnome-mount: 0.8_12
policykit-gnome: 0.9.2_7
gnome-doc-utils: 0.20.10_4
py27-libxml2: 2.9.2
gettext-tools: 0.19.3
libnotify: 0.7.6_1
fusefs-libs: 2.9.3_3
libgphoto2: 2.5.5.1
libexif: 0.6.21_3
libgd: 2.1.0_5,1
libsoup-gnome: 2.48.1
glib-networking: 2.42.1
p11-kit: 0.22.1
libtasn1: 4.2
ca_root_nss: 3.17.3_1
gnutls: 3.2.19_1
trousers-tddl: 0.3.10_7
nettle: 2.7.1
libproxy: 0.4.6
gsettings-desktop-schemas: 3.14.1
cantarell-fonts: 0.0.15
libsoup: 2.48.1
py27-orbit: 2.24.0_1
librsvg2: 2.40.6
gtk-engines2: 2.20.2_2
libcroco: 0.6.8_2
libgsf: 1.14.30
xdg-utils: 1.0.2.20130919_1
xset: 1.2.3_1
libXfontcache: 1.0.5_2
fontcacheproto: 0.1.3
xprop: 1.2.2
py27-notify: 0.1.1_10
py27-game: 1.9.1_5
smpeg: 0.4.4_14
sdl: 1.2.15_5,2
libGLU: 9.0.0_2
aalib: 1.4.r5_11
py27-numpy: 1.9.1_1,1
suitesparse: 4.0.2_4
lapack: 3.4.2_3
blas: 3.4.2_3
py27-nose: 1.3.3
sdl_ttf: 2.0.11_5
sdl_image: 1.2.12_8
webp: 0.4.2_2
giflib-nox11: 4.2.3_4
sdl_mixer: 1.2.12_10
timidity: 0.2i_1
libmikmod: 3.3.6_2
flac: 1.3.0_4
py27-dbus: 1.1.1_1
pydbus-common: 1.1.1_4
desktop-file-utils: 0.22_3

I suspect that it has to do with the fact that it also wants to upgrade Deluge from the binary repo which is built with X11 and GTK support. This is exactly what I don't want.

How can I prevent this but also upgrade the rest of the system?
 
The port options try to be best for most but can't be perfect for everybody. You'll have to compile your packages on your own. If you have more than just a couple systems, setting up Poudriere ports-mgmt/poudriere is fairly trivial and you can just use a /usr/local/etc/poudriere.d/<jailname>-make.conf that unsets the X11 flag on all ports you build.
Code:
OPTIONS_UNSET+=X11
The rest of the steps far covered in the Handbook.
https://www.freebsd.org/doc/en_US.ISO8859-1/books/handbook/ports-poudriere.html
 
I upgraded deluge manually from ports but still pkg wanted to upgrade it from binary with all the X11. pkg lock deluge did the trick. But is there any simpler way to notify pkg that generally the packages that are compiled from ports should not be upgraded by it?
 
But is there any simpler way to notify pkg that generally the packages that are compiled from ports should not be upgraded by it?
No, there isn't. And it's the reason why a lot of us build their own package repositories. Which is a lot easier to do than it sounds.
 
I upgraded deluge manually from ports but still pkg wanted to upgrade it from binary with all the X11. pkg lock deluge did the trick. But is there any simpler way to notify pkg that generally the packages that are compiled from ports should not be upgraded by it?

Ideally the ports system would have something called "virtual" dependencies where any compatible port/package could satisfy a dependency as long as the port/package providing the depency had the suitable shared libraries and other features required. Unfortunately this is all still in on planning state and we have to do with "concrete" dependencies that can not be changed after the package is created.
 
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