[Bioc-devel] cigarToRleList fails

[Jesper Gådin]

Hi,

Have come across a cigar-vector that is problematic to process.

#load package
> library(GenomicAlignments)

#load data (see attached file)
> load("2014-02-17-cigarExample.rdata")

#run function cigarToRleList
> cigarRle <- cigarToRleList(cigarExample)
Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE =
"IRanges") :
  integer overflow while summing elements in 'lengths'

> sessionInfo()
R Under development (unstable) (2013-11-13 r64209)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

other attached packages:
[1] GenomicAlignments_0.99.18 Rsamtools_1.15.26
[3] Biostrings_2.31.12        XVector_0.3.6
[5] GenomicRanges_1.15.26     IRanges_1.21.23
[7] BiocGenerics_0.9.3

loaded via a namespace (and not attached):
 [1] BatchJobs_1.1-1135 BBmisc_1.5         BiocParallel_0.5.8 bitops_1.0-6

 [5] brew_1.0-6         codetools_0.2-8    DBI_0.2-7          digest_0.6.4

 [9] fail_1.2           foreach_1.4.1      iterators_1.0.6    plyr_1.8

[13] RSQLite_0.11.4     sendmailR_1.1-2    stats4_3.1.0       tools_3.1.0

[17] zlibbioc_1.9.0