Biocondcutor package IlluminaHumanMethylationEPICmanifest based on MethylationEPIC_v-1-0_B4.csv. This manifest masks problematic probes on the EPIC array and allows to analyse EPIC arrays with varying numbers of probes.
library(devtools)
install_github("mwsill/IlluminaHumanMethylationEPICmanifest")