Also dplyr has recently changed a function name so some packages here require the latest version, which requires R 3.2.2, so you may need the latest version of R to be able to run the pipeline. See below for my workaround/local install tips. This makes it very difficult to get plumbCNV working. Not being able to install GenomicFeatures prevents my humarray package from installing properly.
If you have an old version RSQLite you may be ok. If installing from scratch, the current version of GenomicFeatures is broken due to importing a now non-existent function from the RSQLite package which has recently been overhauled. You must also install the humarray package from the repository: nicholasjcooper/iChip or /plumbCNV_Example. To use this now, you must install by copying the files to a directory on your machine. This package has not yet been completely encased in the usual R format and directory structure, and so has not been submitted to CRAN. PlumbCNV plumbCNV pipeline for comprehensive quality control and CNV detection using SNP arrays (R package)
