Hi Jesper,
Would you be willing to volunteer your use case? As Herve hinted,
cigarToRleList and friends are low-level helpers. There may be an easier
way to achieve what you want, or an opportunity to improve things.
Michael
On Mon, Feb 17, 2014 at 1:10 AM, Jesper Gådin <jesper.ga...@gmail.com>wrote:
> 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
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
