Hi Tim,

It would be helpful to have a snippet of the file that reproduces the
error, or maybe a URL from which I can download the entire file, if
necessary.

Thanks,
Michael


On Wed, Feb 6, 2013 at 11:27 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote:

> This is an odd one.  I have rtracklayer export the components of a
> GRangesList as BED files, then I try to read them back in, and it fails.
>
> > for(i in names(pooledMethSegs)) export(pooledMethSegs[[i]],
> file(paste0(i, '.methSegs.bed')))
> Warning messages:
> 1: closing unused connection 7 (CD34.methSegs.bed)
> 2: closing unused connection 5 (CD133.methSegs.bed)
>
> ## now read the generated files back in...
> > for(i in names(pooledMethSegs)) foo <- import(paste0(i, '.methSegs.bed'))
> Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
> :
>   solving row 164655: negative widths are not allowed
> In addition: Warning messages:
> 1: closing unused connection 5 (NEUT.methSegs.bed)
> 2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>   number of items read is not a multiple of the number of columns
>
> > sessionInfo()
> R version 2.15.2 (2012-10-26)
> 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=C                 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 datasets  utils     methods
> [8] base
>
> other attached packages:
>  [1] chromophobe_0.49                   pheatmap_0.7.4
>  [3] ggplot2_0.9.3                      reshape2_1.2.2
>  [5] BSgenome.Hsapiens.UCSC.hg18_1.3.19 BSgenome_1.26.1
>  [7] Biostrings_2.26.2                  MethylSeekR_0.99.1
>  [9] mhsmm_0.4.8                        mvtnorm_0.9-9994
> [11] rtracklayer_1.18.2                 gmapR_1.0.0
> [13] GenomicRanges_1.10.6               IRanges_1.16.4
> [15] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.20.3    Biobase_2.18.0          biomaRt_2.14.0
>  [4] bitops_1.0-5            colorspace_1.2-0        DBI_0.2-5
>  [7] dichromat_1.2-4         digest_0.6.0            GenomicFeatures_1.10.1
> [10] grid_2.15.2             gtable_0.1.2            KernSmooth_2.23-8
> [13] labeling_0.1            lattice_0.20-13         MASS_7.3-22
> [16] Matrix_1.0-10           munsell_0.4             plyr_1.8
> [19] proto_0.3-9.2           RColorBrewer_1.0-5      RCurl_1.95-3
> [22] Rsamtools_1.10.2        RSQLite_0.11.2          scales_0.2.3
> [25] stats4_2.15.2           stringr_0.6.2           tools_2.15.2
> [28] VariantAnnotation_1.4.8 XML_3.95-0.1            zlibbioc_1.4.0
>
>
> --
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<
> http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>
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>
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