Here's my code:

library(MethylMix)
library(doParallel)

cancerSite <- "HNSC"
targetDirectory <- paste0(getwd(), "/")
GetData(cancerSite, targetDirectory)

# Downloading methylation data
METdirectories <- Download_DNAmethylation(cancerSite, targetDirectory)
# Processing methylation data
METProcessedData <- Preprocess_DNAmethylation(cancerSite, METdirectories)
# Saving methylation processed data
saveRDS(METProcessedData, file = paste0(targetDirectory, "MET_", cancerSite, "_Processed.rds"))

I'm running this for over 48 hours, but still stuck in "Finding nonparametric adjustments". Is there any wrong with my code? What should I do?

Thank you!

This 'phenomenon' has been reported previously - see https://github.com/gevaertlab/MethylMix/issues/2

There is also a previous BioC post - see http://supportupgrade.bioconductor.org/p/112680/#112733

Assuming that you are using linux, while it is running the process, I wonder could you check the output of top in another terminal in order to see how many CPU cores are being used?; and to check if R is even doing anything? Otherwise, let us know your system configuration.

Kevin