The flac-1.1.2-r3 ebuild currently in portage appears to be missing the libogg dependency. Manual merging of libogg fixes the problem, after which emerge --resume will cause flac to compile correctly.
<snip> RDEPEND="ogg? ( >=media-libs/libogg-1.0_rc2 ) xmms? ( media-sound/xmms )" DEPEND="${RDEPEND} x86? ( dev-lang/nasm ) sys-apps/gawk doc? ( app-doc/doxygen ) dev-util/pkgconfig" <snip> Reopen with some errors and emerge --info, we can't guess.