They could make a program where you give it the players' character sheets and the encounter and it simulates a bunch of battles to see how they do. But failing that, you could make CR be a good average, where you could just look at that and adjust based on what the strengths and weaknesses are. I haven't actually played 5e so I don't know this from personal experience, but my impression is that they haven't done that. Some creatures just don't have a CR that matches them in general.
There's also no system for figuring out the CR of an encounter with an arbitrary set of monsters and enemies with class levels.