Hi, I have tried to run R package- DiffBind in SSH (Linux). I have R script works will with windows R 3.3.3 but failed at SSH sever linux R. It stops at dba.count step. Could anyone help me? Does it mean the bam file is required instead of bed file?  Thank you. 

#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
library(DiffBind)
setwd("/net/wonderland/home/zhaolinz/practice/batch8_macs2")
#list.files()
#list.files("diff")
diff <- dba(sampleSheet="CLA050417.csv",minOverlap=2,config=data.frame(RunParallel=TRUE, reportInit="diff",AnalysisMethod=DBA_DESEQ2,minQCth=5,fragmentSize=300,bCorPlot=FALSE,th=0.1, bUsePval=FALSE))
diff_count <- dba.count(diff, minOverlap=2,score=DBA_SCORE_TMM_READS_FULL, fragmentSize=diff$config$fragmentSize, filter=0, bRemoveDuplicates=FALSE, filterFun=max,bCorPlot=diff$config$bCorPlot,
bUseSummarizeOverlaps=FALSE, readFormat=DBA_READS_DEFAULT,bParallel=diff$config$RunParallel)
.....

<font face="monospace">The error is here  </font>

 *** caught segfault ***

address (nil), cause 'unknown'

Traceback:
 1: .Call("croi_count_reads", bamfile, as.integer(insertLength),     as.integer(fileType), as.integer(bufferSize), as.integer(minMappingQual),     as.character(intervals[[1]]), as.integer(intervals[[2]]),     as.integer(intervals[[3]]), as.integer(icount), as.logical(bWithoutDupes),     as.logical(bSummits), counts, summits.vec, heights.vec)
 2: cpp_count_reads(bamfile, insertLength, fileType, bufferSize,     intervals, bWithoutDupes, summits, minMappingQuality)
 3: pv.getCounts(bamfile = countrec$bamfile, intervals = intervals,     insertLength = countrec$insert, bWithoutDupes = bWithoutDupes,     bLowMem = bLowMem, yieldSize = yieldSize, mode = mode, singleEnd = singleEnd,     scanbamparam = scanbamparam, fileType = fileType, summits = summits,     fragments = fragments, minMappingQuality = minMappingQuality)
 4: FUN(X[[i]], ...)
 5: lapply(X = S, FUN = FUN, ...)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        pr
efix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if is.na(w))  
           w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditio
nMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
10: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
11: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
12: FUN(X[[i]], ...)
13: lapply(seq_len(cores), inner.do)
14: mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE)
15: config$lapplyFun(config, params, arglist, fn, ...)
16: dba.parallel.lapply(pv$config, params, todorecs, pv.do_getCounts,     bed, bWithoutDupes = bWithoutDupes, bLowMem, yieldSize, mode,     singleEnd, scanbamparam, readFormat, summits, fragments,     minMappingQuality)
17: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore = score,     bLog = bLog, insertLength = fragmentSize, bOnlyCounts = T,     bCalledMasks = TRUE, minMaxval = filter, bParallel = bParallel,     bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates, bScaleControl = bScaleControl,     filterFun = filterFun, bLowMem = bUseSummarizeOverlaps, readFormat = readFormat,     summits = summits, minMappingQuality = mapQCth)
18: dba.count(diff, minOverlap = 3)

Your sessionInfo() tells me that you're running an extremely old version of DiffBind, and R.  Your read bed files probably have 5 columns, which is not legal bed format (although it is the format some aligners will give you).  You need either 3 columns, or 6 or more.  Ideally, upgrade to the current R (3.4, as of a few days ago), or ensure your bed files have exactly 3 or at least 6 columns.  Either one should fix the problem, though upgrading is preferable.  There are many bug fixes and improvements between DiffBind 1.16.3 and 2.5.1.

[edit] I also just noticed that your "read" files have names like "64502_macs2_summits.bed" which is an unlikely name for the output of an aligner.  You have to give the actual reads from the aligner in the "bamReads" column.  The workflow should be something like:

1) from Fastq, align to the reference genome to get bam (or bed) files.

2) With the aligned reads, call peaks using (in your case) MACS2, to get peaks (and summits).

3) Give both the *aligned reads* (not the summits) and the *peaks* to DiffBind for differential analysis.

Since your reads files are named "something_macs2_summits.bed", they are probably the summits from MACS, not the aligned reads from the aligner. 

 - Gord