Dear Yuan Tian and other ChAMP developers,

I am gratefully using ChAMP on HM850K (EPIC) data of 21 samples. Loading data and normalization went very smoothly. I am now trying to find Differentially Methylated Regions (DMRs). I am using R version 3.3.3.

> GC_DMR <- champ.DMR(beta = GC_Norm, pheno = GC_Load$pd$Sample_Group, arraytype = "EPIC")
[===========================]
[<<<<< ChAMP.DMR START >>>>>]
-----------------------------
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19
<< Find DMR with Bumphunter Method >>
3 cores will be used to do parallel BMIQ computing.
According to your data set, champ.DMR() detected 10163 clusters contains MORE THAN 7 probes within300 maxGap. These clusters will be used to find DMR.

[bumphunterEngine] Parallelizing using 3 workers/cores (backend: doParallelMC, version: 1.0.10).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
Loading required package: rngtools
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:S4Vectors':

    new2

The following object is masked from 'package:base':

    isNamespaceLoaded

[bumphunterEngine] Performing 250 bootstraps.
[bumphunterEngine] Computing marginal bootstrap p-values.
[bumphunterEngine] Smoothing bootstrap coefficients.

"Performing 250 bootstraps" took about 1h20min, "Computing marginal bootstrap p-values" and "Smoothing bootstrap coefficients" took an additional 4 hours. No further progress has been seen in R during the last 48 hours. Can you help me out? I can imagine it usually does not take that long to complete DMRs analysis in R?