I don’t have any direct suggestions for your Nemo.jl problem; have you used other packages which use binary libraries? For example if you add Cxx.jl, and then try “using Cxx”, do you get a similar error?
To your original question of why Prime.jl’s factor function is slow, I guess that the answer is that no one has taken the time to put the fastest factorization tools into Primes.jl. The Nemo guys are number theorists, so it makes sense that they’d have a fast factorization technique in their package. BTW, it looks to me like Nemo calls a flint function to do factorization.