Confirmed. Will look into it now.
Thanks for writing!
Hector
On Tue, Jul 1, 2014 at 2:40 AM, Kristoffer Vitting-Seerup <
kristoffer.vittingsee...@bio.ku.dk> wrote:
> Hi bioc-devel
>
> Iâve fond an error in the usage of GIntervalTree:
>
> > test <- GRanges(seqnames='Chr1', range=IRanges(start=10,end=20))
> > test
> GRanges with 1 range and 0 metadata columns:
> seqnames ranges strand
> <Rle> <IRanges> <Rle>
> [1] Chr1 [10, 20] *
>
> this object I can save and load without problem:
>
> save(test, file='test.Rdata')
> > rm(test)
> > load('test.Rdata')
> > test
> GRanges with 1 range and 0 metadata columns:
> seqnames ranges strand
> <Rle> <IRanges> <Rle>
> [1] Chr1 [10, 20] *
>
>
> But if I convert to to a GIntervalTree (for faster overlap finding) I get
> a fatal error when loading:
>
> test2 <- GIntervalTree(test)
> > test2
> GIntervalTree with 1 range and 0 metadata columns:
> seqnames ranges strand
> <Rle> <IRanges> <Rle>
> [1] Chr1 [10, 20] *
> > save(test2, file='test2.Rdata')
> > rm(test2)
> > load('test2.Rdata')
> > test2
> GIntervalTree with 1 range and 0 metadata columns:
>
> *** caught segfault ***
> address 0xc, cause 'memory not mapped'
>
> Traceback:
> 1: .Call(.NAME, ..., PACKAGE = PACKAGE)
> 2: .Call2(fun, object@ptr, ..., PACKAGE = "IRanges")
> 3: .IntervalForestCall(from, "asIRanges")
> 4: asMethod(object)
> 5: as(x@ranges, "IRanges")
> 6: .GT_reorderValue(x, as(x@ranges, "IRanges"))
> 7: .local(x, ...)
> 8: ranges(x)
> 9: ranges(x)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
>
> My session info:
> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] grDevices datasets grid parallel stats graphics utils
> methods base
>
> other attached packages:
> [1] spliceR_1.5.0 plyr_1.8.1 RColorBrewer_1.0-5
> VennDiagram_1.6.5 cummeRbund_2.7.1 Gviz_1.9.4
> rtracklayer_1.25.8 GenomicRanges_1.17.14 GenomeInfoDb_1.1.5
> IRanges_1.99.13
> [11] S4Vectors_0.0.6 fastcluster_1.1.13 reshape2_1.4
> ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7
> BiocGenerics_0.11.2
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.27.6 BBmisc_1.6 BSgenome_1.33.5
> BatchJobs_1.2 Biobase_2.25.0 BiocParallel_0.7.0
> Biostrings_2.33.8 Formula_1.1-1
> GenomicAlignments_1.1.10
> [10] GenomicFeatures_1.17.6 Hmisc_3.14-4 MASS_7.3-33
> R.methodsS3_1.6.1 RCurl_1.95-4.1 Rcpp_0.11.1
> Rsamtools_1.17.14 VariantAnnotation_1.11.5 XML_3.98-1.1
> [19] XVector_0.5.6 biomaRt_2.21.0 biovizBase_1.13.7
> bitops_1.0-6 brew_1.0-6 cluster_1.15.2
> codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0
> [28] digest_0.6.4 fail_1.2 foreach_1.4.2
> gtable_0.1.2 iterators_1.0.7 lattice_0.20-29
> latticeExtra_0.6-26 matrixStats_0.8.14 munsell_0.4.2
> [37] proto_0.3-10 scales_0.2.4 sendmailR_1.1-2
> splines_3.1.0 stats4_3.1.0 stringr_0.6.2
> survival_2.37-7 tools_3.1.0 zlibbioc_1.11.1
>
>
>
> --
> Kindest regards
> Kristoffer Vitting-Seerup, cand.scient. (M.Sc.),
> Ph.D Fellow
> Sandelin Group
>
> Bioinformatics Centre | Biotech Research & Innovation Centre (BRIC), Dep.
> Of Biology
> University of Copenhagen
> Building 1, 3th floor, office 3 (1-3-03)
> Ole Maaløes Vej 5
> DK-2200 Copenhagen N
> Denmark
> http://binf.ku.dk | http://www.bric.ku.dk
>
>
>
>
>
>
>
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>
>
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