The desktop and the icon file are installed as /usr/share/phasex/phasex.desktop and /usr/share/phasex/pixmaps/phasex-icon.png. They should be installed as /usr/share/applications/phasex.desktop and /usr/share/phasex/icons/phasex-icon.png. To add the following section into the ebuild fix this issue: pkg_preinst() { mkdir -p ${D}/usr/share/applications mv ${D}/usr/share/phasex/phasex.desktop ${D}/usr/share/applications/phasex.desktop mkdir -p ${D}/usr/share/icons mv ${D}/usr/share/phasex/pixmaps/phasex-icon.png ${D}/usr/share/icons/phasex-icon.png }
removed