PharmCAS averages all attempts at a single course. If you take US History I and get an F, and then take it two years later and get an A, PharmCAS will see a 0 and a 4, so your end grade for US History I will be a 2.
It's very similar to AMCAS, which is the predominant application service used by MD schools, and a reason quite a few people prefer non-PharmCAS schools (and DO programs on the medicine side).