error: * checking 4 files for package collisions existing file /usr/lib/X11/app-defaults/XClock-color is not owned by this package existing file /usr/lib/X11/app-defaults/XClock is not owned by this package * spent 0.115234851837 seconds checking for file collisions * This package is blocked because it wants to overwrite * files belonging to other packages (see messages above). * If you have no clue what this is all about report it * as a bug for this package on http://bugs.gentoo.org package x11-apps/xclock-0.99.1 NOT merged emerge --info: Gentoo Base System version 1.6.13 Portage 2.0.51.22-r3 (default-linux/x86/2005.1, gcc-3.3.6, glibc-2.3.5-r2, 2.6.14-gentoo-r2 i686) ================================================================= System uname: 2.6.14-gentoo-r2 i686 dev-lang/python: 2.3.5-r2, 2.4.2 sys-apps/sandbox: 1.2.12 sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.16.1 sys-devel/libtool: 1.5.20 virtual/os-headers: 2.6.11-r2 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-Os -march=i686 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/lib/X11/xkb /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/env.d" CXXFLAGS="-Os -march=i686 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig collision-protect distlocks sandbox sfperms strict stricter" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/Linux/distributions/gentoo" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 X alsa apm arts avi berkdb bitmap-fonts bzip2 crypt cups dri eds emboss encode expat foomaticdb fortran gdbm gif gpm gstreamer gtk gtk2 imlib ipv6 java jpeg kde libg++ libwww mad mikmod motif mp3 mpeg ncurses nls ogg oggvorbis opengl oss pam pdflib perl png python qt quicktime readline sdl spell ssl tcpd tiff truetype truetype-fonts type1-fonts udev vorbis xml2 xmms xv zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTDIR_OVERLAY
Removing the files: /usr/lib/X11/app-defaults/XClock-color /usr/lib/X11/app-defaults/XClock did solve the problem for me. # equery b /usr/lib/X11/app-defaults/XClock and #equery b /usr/lib/X11/app-defaults/XClock-color didn't give any results.
This happens because they're left behind by monolithic xorg-x11, since they're in CONFIG_PROTECT. I don't think there is a decent way to fix this, because other programs also install to the same location.