The subject ebuild returns the following in prefix: >>> Completed installing libatomic_ops-7.4.0 into /storage/strogdon/gentoo-redlizard/var/tmp/portage/dev-libs/libatomic_ops-7.4.0/image/ strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment -R .GCC.command.line -R .note.gnu.gold-version usr/lib/libatomic_ops.a usr/lib/libatomic_ops_gpl.a ecompressdir: bzip2 -9 /usr/share/doc [33;01m*[0m QA Notice: the following files are outside of the prefix: [33;01m*[0m /usr [33;01m*[0m /usr/share [33;01m*[0m /usr/share/doc [33;01m*[0m /usr/share/doc/libatomic_ops-7.4.0 [33;01m*[0m /usr/share/doc/libatomic_ops-7.4.0/README.txt [33;01m*[0m /usr/share/doc/libatomic_ops-7.4.0/README_stack.txt [33;01m*[0m /usr/share/doc/libatomic_ops-7.4.0/README_win32.txt [33;01m*[0m /usr/share/doc/libatomic_ops-7.4.0/README_malloc.txt [31;01m*[0m ERROR: dev-libs/libatomic_ops-7.4.0::gentoo_prefix failed: [31;01m*[0m Aborting due to QA concerns: there are files installed outside the prefix The ebuild has src_configure() { econf --docdir=/usr/share/doc/${PF} } and making the change econf --docdir=${EPREFIX}/usr/share/doc/${PF} or something similar seems to fix things.
Fixed in the tree.