checking for xfixes... gnome-config: not found
  gnome-config: not found
  Package xfixes was not found in the pkg-config search path. Perhaps

I have seen this too.  The problem seems to be that pkg-config is
trying to execute gnome-config; when I've had this issue and then
manually run pkg-config I get the same error.  This seems to stop the
build of some programs some times, but much works.  I didn't figure
out what was going on in the past.

Digging in, I checked every .pc file:

/usr/pkg/lib/pkgconfig #> (for i in *; do a=`echo $i|sed -e 's/\.pc//'`; pkg-config --libs $a; done) &> /tmp/pc.out

All of the output looks ok.  But

/usr/pkg/lib/pkgconfig #> pkg-config --libs foo
gnome-config: not found
Package foo was not found in the pkg-config search path.
Perhaps you should add the directory containing `foo.pc'
to the PKG_CONFIG_PATH environment variable
No package 'foo' found

It seems that pkg-config falls back to gnome-config when it can't find
the pc file.  I think that's what Christian meant when he said the
gnome-config error was a red herring - that really it's just that
xfixes is not present.

-- 
    Greg Troxel <gdt@ir.bbn.com>