please follow the upgrade guide:
The exact error you post is at the bottom. ( re-emerge gnome-doc-utils )
*** This bug has been marked as a duplicate of 104088 ***
1)No, this is not a fresh upgrade. This was a minor bump up from a GNOME 2.12. ish system that has long been portage.unmasked to whatever the current (2.12.3) gnome-base/gnome is.
2) If re-emerging gnome-doc-utils is the solution, then the gnome-base/gnome ebuild needs to force it to be re-installed somehow - especially if this issue is as long standing and persistant as the other bug and the guide (which was written after I upgraded to GNOME 2.12) seem to indicate.
Following the advice given, [re-]emerging gnome-doc-utils resulted in an upgrade from 0.4.3 to 0.4.4, along with an new slot install of app-text/docbook-xml-dtd-4.4 ... with result that file-roller, epiphany and others now are emerging cleanly.
I'd recommend adding a >=app-text/gnome-doc-utils-0.4.4 to gnome-base/gnome-2.12.3