=dev-python/bottle-0.12.12 was broken as per commit message at https://github.com/bottlepy/bottle/commit/7423aa0f64e381507d1e06a6bcab48888baf9a7b I found that version broke youcompleteme, rolling back fixed it. I haven't had chance to test with 0.12.13 yet.
This version of bottle is no longer in portage, current version is fine.