votca-tools depends on app-doc/doxygen[-nodot] (if USE=doc). Recent versions of doxygen have a dot USE flag, not a nodot USE flag. Please change the dependency to something like "|| ( <app-doc/doxygen-1.7.6.1[-nodot] >=app-doc/doxygen-1.7.6.1[dot] )" so votca-tools[doc] and >=doxygen-1.7.6.1 can be installed on the same system.
+ 23 Feb 2012; Kacper Kowalik <xarthisius@gentoo.org> votca-tools-1.2.2.ebuild: + Fix dependency on app-doc/doxygen wrt converting useflags 'nodot' to 'dot'. + Fixes bug 405453 by Marien Zwart <marienz@gentoo.org>