Hi bioc-devel
Ive 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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