Illumina has released a new annotation file for the EPIC array, the new one is version 1.0b2. Manifest and annotation packages have been updated, see
(Annotation packages are under review at Bioconductor).
Because of a name change in the annotation file, version 1.17.9 or better of minfi is required for full, easy support. This version ought to propagate through the Bioconductor build system soon. Read IDAT files using read.metharray.exp().