After updating R to version 3.4 and Bioconductor to 3.5, ChIPQC stops working at the "Computing metrics" step. The error messages make me suspect it might be related to changes in the 'BiocParallel' package affecting the
bplapply function, but that's just a guess -- what I know for sure is that it was working prior to the update. Without further ado, I leave here the message I get:
chip.samples = ChIPQC(experiment = "../DBsheet_EMCsamples.csv", annotation="hg19", bCount = TRUE) # I have omitted the messages before the error Computing metrics for 43 samples... 'BiocParallel' did not register default BiocParallelParams: comparison of these types is not implemented Error in if (!bpschedule(BPPARAM) || length(X) == 1L || bpnworkers(BPPARAM) == : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In BioC 3.5, the 'force' argument was replaced by the more flexible 'pruning.mode' argument, and is deprecated. See ?seqinfo for the supported pruning modes. Note that 'force=TRUE' is equivalent to 'pruning.mode="coarse"'.
I have run the same command on another machine with a different version of R/Bioconductor and I did not encounter any issues, which supports the idea that the error can be attributed to the new version. Interestingly, however, DiffBind works just fine.
Thanks for your time.