Upgrading old x11-base/xorg-server-1.3.0.0-r2 to a current version pulls in x11-libs/libpciaccess-0.12.1 as a dependency, but the latter fails to install due to a collision: * Detected file collision(s): * * /usr/bin/scanpci * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * x11-base/xorg-server-1.3.0.0-r2 * /usr/bin/scanpci * * Package 'x11-libs/libpciaccess-0.12.1' NOT merged due to file * collisions. If necessary, refer to your elog messages for the whole * content of the above message. I presume /usr/bin/scanpci has been moved from one package to the other, and that once the new x11-base/xorg-server is in place this collision will disappear. But with both packages in the dependency tree to be installed, portage should have been aware of the conflict and able to resolve it.
Fixed in CVS.