filterData(cutoff = 0) fails in v0.0.69

[Leonardo Collado-Torres]

Taken from derfinder?fullCoverage

library('derfinder')

datadir <- system.file('extdata', 'genomeData', package='derfinder')
dirs <- makeBamList(datadir=datadir, samplepatt='*accepted_hits.bam$',
    bamterm=NULL)
## Shorten the column names
names(dirs) <- gsub('_accepted_hits.bam', '', names(dirs))

## Read and filter the data
fullCov2 <- fullCoverage(dirs=dirs, chrs=c(1:22, 'X', 'Y'), cutoff=0)

This leads to:

Error: 19 errors; first error:
  Error in Reduce("|", RleList(data) > cutoff): error in evaluating the argument 'x' in selecting a method for function 'Reduce': Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE = "S4Vectors") : 
  integer overflow while summing elements in 'lengths'

For more information, use bplasterror(). To resume calculation, re-call the function and set the argument 'BPRESUME' to TRUE or wrap the previous call in bpresume().

First traceback:
  18: fullCoverage(dirs = dirs, chrs = c(1:22, "X", "Y"), cutoff = 0)
  17: bplapply(seq_len(length(chrs)), loadChr, dirs = dirs, chrs = chrs, 
          bai = bai, chrlens = chrlens, outputs = outputs, verbose = verbose, 
          inputType = inputType, isMinusStrand = isMinusStrand, cutoff = cutoff, 
          filter = filter, returnMean = returnMean, returnCoverage = returnCoverage, 
          totalMapped = totalMapped, targetSize = targetSize, tilewidth = tilewidth, 
          mc.cores.load = mc.cor

Will revert the changes from f42c196

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] IRanges_1.99.25     S4Vectors_0.1.3     BiocGenerics_0.11.4 derfinder_0.0.69   

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.27.9     BatchJobs_1.3            BBmisc_1.7               Biobase_2.25.0           BiocParallel_0.99.11     biomaRt_2.21.1           Biostrings_2.33.13      
 [8] bitops_1.0-6             brew_1.0-6               bumphunter_1.5.5         checkmate_1.3            cluster_1.15.2           codetools_0.2-9          DBI_0.2-7               
[15] derfinderHelper_0.0.4    digest_0.6.4             doRNG_1.5.5              fail_1.2                 foreach_1.4.2            Formula_1.1-2            GenomeInfoDb_1.1.18     
[22] GenomicAlignments_1.1.26 GenomicFeatures_1.17.14  GenomicFiles_1.1.19      GenomicRanges_1.17.36    grid_3.1.1               Hmisc_3.14-4             iterators_1.0.7         
[29] lattice_0.20-29          latticeExtra_0.6-26      locfit_1.5-9.1           Matrix_1.1-4             matrixStats_0.10.0       pkgmaker_0.22            qvalue_1.39.1           
[36] R.methodsS3_1.6.1        RColorBrewer_1.0-5       Rcpp_0.11.2              RCurl_1.95-4.3           registry_0.2             rngtools_1.2.4           Rsamtools_1.17.33       
[43] RSQLite_0.11.4           rtracklayer_1.25.13      sendmailR_1.1-2          splines_3.1.1            stats4_3.1.1             stringr_0.6.2            survival_2.37-7         
[50] tools_3.1.1              XML_3.98-1.1             xtable_1.7-3             XVector_0.5.7            zlibbioc_1.11.1