Dear Yue,
I am using your RIPSeeker package and trying to use the option multicore=TRUE. Trying it on both  windows and Linux machines, I did not observe multiple cores being used until I first called library(parallel) before running the code below. Also, it appears that only 2 cores were being used on the Linux machine, and only 1 on the windows, even though detectCores() indicated 32 cores on the Linux and 8 on the windows.

Are there any additional parameters that I need to set to increase the number of cores being used?

Thanks,
Wade

########################################################################

library(ShortRead)
library(RIPSeeker)
library(parallel)

filedir<-"~/bulkdata/PI/RIP"
setwd(filedir)
bamFiles <- list.files( pattern="_2\\.bam", recursive=TRUE, full.names=TRUE)
cNAME <- "IgG"
outDir <- file.path(filedir, "RIPSeeker_output_2")
# Parameters setting
binSize <- NULL      # set to NULL to automatically determine bin size
multicore <- TRUE                            # use multicore
strandType <- NULL                       # set strand type to minus strand
biomart <- "ENSEMBL_MART_ENSEMBL"           # use archive to get ensembl 65
biomaRt_dataset <- "mmusculus_gene_ensembl" # mouse dataset id name
goAnno <- "org.Mm.eg.db"                    # GO annotation database
################ run main function ripSeek to predict RIP ################
seekOut.HuR <- ripSeek(bamPath = bamFiles, cNAME = cNAME,
                    reverseComplement = FALSE, #genomeBuild = "mm10", not relevant for BAM
                    strandType = strandType,
                    uniqueHit = TRUE,
                    assignMultihits = TRUE,
                    rerunWithDisambiguatedMultihits = TRUE,
                    binSize=binSize,
                    #minBinSize = minBinSize,
                    #maxBinSize = maxBinSize,
                    biomart=biomart,
                    host=host,
                    biomaRt_dataset = biomaRt_dataset,
                    goAnno = goAnno,
                    multicore=multicore,
                    logOddCutoff = 2,
                    pvalCutoff = 1,
                                pvalAdjCutoff = 0.2,
                    eFDRCutoff = 0.2,
                    outDir=outDir)



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