'emerge -pvuDN rasmol' shows: root@impala:/root(18)# qlist -Iv gtk-builder-convert root@impala:/root(19)# emerge -pvuDN rasmol These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] dev-util/gtk-builder-convert-2.24.29::gentoo PYTHON_TARGETS="python2_7" 0 KiB [ebuild N ] sci-chemistry/rasmol-2.7.5.2-r2::gentoo 0 KiB [blocks B ] <dev-util/gtk-builder-convert-2.24.30 ("<dev-util/gtk-builder-convert-2.24.30" is blocking x11-libs/gtk+-2.24.30) Total: 2 packages (2 new), Size of downloads: 0 KiB Conflict: 1 block (1 unsatisfied) * Error: The above package list contains packages which cannot be * installed at the same time on the same system. (x11-libs/gtk+-2.24.30:2/2::gentoo, installed) pulled in by >=x11-libs/gtk+-2.8:2= required by (dev-java/icedtea-7.2.6.5-r1:7/7::gentoo, installed) >=x11-libs/gtk+-2.12:2 required by (x11-libs/gtksourceview-2.10.5-r3:2.0/2.0::gentoo, installed) x11-libs/gtk+:2 required by (sci-chemistry/rasmol-2.7.5.2-r2:0/0::gentoo, ebuild scheduled for merge) x11-libs/gtk+:2 required by (dev-python/wxpython-2.8.12.1-r2:2.8/2.8::gentoo, installed) ...
gtk+ requires that gtk-builder-convert not be less than its own version. The highest version of gtk-builder available is 2.24.29, whereas gtk is 2.24.30. Downgrading gtk+ to 2.24.29 will solve the problem, as will creating a bug and waiting for a version bump of gtk-builder-convert to 2.24.30.