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=""> [[alternative HTML version deleted]]

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> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]