Looks like lldb introduction has resulted in some Python modules installed outside of proper methods, resulting in them being available only for random Python implementation with the extra problem that they're not byte-compiled. I guess I'll just switch the whole thing to python-single-r1, and remove pypy support. There's no support for python3 anyway, and -9999 seems to start installing random Python modules itself.
Fixed in -9999.
commit 570a1aa0e0ca2137f86350351eace21af78b18ad Author: Michał Górny <mgorny@gentoo.org> Date: Sat Dec 12 23:50:47 2015 sys-devel/llvm: Clean Python, enable libomp and BPF backend in 3.7 Backport some of the changes from -9999 as 3.7.0-r4. Remove multi-Python support which was working only partially because of lldb, also fixing byte-compilation of Python modules, #567550. Default to libomp instead of semi-broken libgomp support, #562990. Enable BPF backend by default, GitHub PR #450. Fixes: https://bugs.gentoo.org/show_bug.cgi?id=567550 Fixes: https://bugs.gentoo.org/show_bug.cgi?id=562990 Fixes: https://github.com/gentoo/gentoo/pull/450