Hi, 

I have previously used the DiffBind package to successfully analyze some ChIP-Seq data, but after upgrading R (version 3.2.1) and downloading the latest package version the dba.count() function in DiffBind (version 1.14.4) now results in the following error on a Linux machine: 

> diffh3k4me3 = dba.count(diffh3k4me3,bParallel=FALSE)
Sample: ../data/K562H3k4me3chr1.bed125

 *** caught segfault ***

address 0xffffffff0edb1b9e, cause 'memory not mapped'

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: pv.do_getCounts(job, bed, bWithoutDupes = bWithoutDupes, bLowMem,     yieldSize, mode, singleEnd, scanbamparam, readFormat, summits,     fragments, minMappingQuality)
 5: pv.listadd(results, pv.do_getCounts(job, bed, bWithoutDupes = bWithoutDupes,     bLowMem, yieldSize, mode, singleEnd, scanbamparam, readFormat,     summits, fragments, minMappingQuality))
 6: 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)
 7: dba.count(diffh3k4me3, bParallel = FALSE)

I've read through some similar help topics such as this one: About the DiffBind dba.count() crash problems

But it looks like the advice given is to use the most updated package which I think I am doing. 

Note that the first few lines of my .bed files look like so: 

chr1    10077    10113    SL-XBE_3_FC30CLLAAXX:6:37:844:899    0    -
chr1    10103    10139    SL-XBE_3_FC30CLLAAXX:6:46:95:1579    0    +
chr1    10236    10272    SL-XBE_3_FC30CLLAAXX:6:31:1257:999    48    +
chr1    10240    10276    SL-XBE_3_FC30CLLAAXX:6:43:601:1863    19    -

Also, I have tried using the same package version, data, and R version on an OSX machine and receive a different error when calling dba.count(): 

Error in if (sum(tokeep) < length(tokeep)) { : 
  missing value where TRUE/FALSE needed

This error seems to be similar to the one encountered in this help topic: http://seqanswers.com/forums/showthread.php?t=46345

But in that topic the error was on a Windows machine and it was resolved by using a Mac! 

I'm not sure what to try next and I appreciate any help, thanks! 

Full session info for the Linux machine run: 

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Arch Linux
locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:

 [1] BayesPeak_1.18.2        DiffBind_1.14.4         RSQLite_1.0.0          
 [4] DBI_0.3.1               locfit_1.5-9.1          GenomicAlignments_1.2.2
 [7] Rsamtools_1.20.4        Biostrings_2.36.1       XVector_0.8.0          
[10] limma_3.22.7            GenomicRanges_1.20.5    GenomeInfoDb_1.4.1     
[13] IRanges_2.2.5           S4Vectors_0.6.1         BiocGenerics_0.14.0    

loaded via a namespace (and not attached):

 [1] Rcpp_0.11.4            lattice_0.20-31        GO.db_3.1.2           
 [4] gtools_3.4.1           digest_0.6.8           foreach_1.4.2         
 [7] plyr_1.8.1             BatchJobs_1.6          ShortRead_1.26.0      
[10] ggplot2_1.0.0          gplots_2.16.0          zlibbioc_1.12.0       
[13] annotate_1.46.0        gdata_2.13.3           Matrix_1.2-0          
[16] checkmate_1.5.2        systemPipeR_1.2.8      proto_0.3-10          
[19] GOstats_2.34.0         splines_3.2.0          BiocParallel_1.0.3    
[22] stringr_0.6.2          pheatmap_1.0.2         munsell_0.4.2         
[25] sendmailR_1.2-1        base64enc_0.1-2        BBmisc_1.9            
[28] fail_1.2               edgeR_3.8.6            codetools_0.2-11      
[31] XML_3.98-1.1           AnnotationForge_1.10.1 MASS_7.3-40           
[34] bitops_1.0-6           grid_3.2.0             RBGL_1.44.0           
[37] xtable_1.7-4           GSEABase_1.30.2        gtable_0.1.2          
[40] scales_0.2.4           graph_1.44.1           KernSmooth_2.23-14    
[43] amap_0.8-14            hwriter_1.3.2          reshape2_1.4.1        
[46] genefilter_1.48.1      latticeExtra_0.6-26    brew_1.0-6            
[49] rjson_0.2.15           RColorBrewer_1.1-2     iterators_1.0.7       
[52] tools_3.2.0            Biobase_2.26.0         Category_2.34.2       
[55] survival_2.38-1        AnnotationDbi_1.30.1   colorspace_1.2-6      
[58] caTools_1.17.1