No idea if there's some way to fix that; my suggestion would be to just download blender binaries, rather than source (unless you're on some really obscure platform that they don't provide binaries for). Being recently open-sourced, I can see that there may still be compilation problems; when they first opened the source, they basically said "don't even bother trying to compile this, since it probably won't work." It's improved a lot since then, but it's probably much easier to just get binaries (that's what I do, and I even use Gentoo
)