filterData(cutoff = 0) fails in v0.0.69
lcolladotor opened this issue · 0 comments
lcolladotor commented
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