According to the gentoo wiki: "All eselect modules are required to support the ROOT variable. For prefix support, variables EPREFIX and EROOT are also defined and have the same meaning as in ebuilds." (https://wiki.gentoo.org/wiki/Project:Eselect/Developer_guide) This eselect module (compiler-shadow) supports neither. It is hard-coded to look in the root dir: "MASQ_MODULEDIR=/usr/share/shadowman" A person on the gentoo forums had a run in with this issue when trying to install the app ccache as a normal user in an eprefix. (The package ebuild calls for an update of the module.) You can see the thread here: https://forums.gentoo.org/viewtopic-t-1085028-highlight-ccache.html A simple addition of "${EROOT}" before that specific path should fix the issue. All other references to path use that variable.