[BioC] New error in Gviz
Hahne, Florian
florian.hahne at novartis.com
Mon May 12 13:47:21 CEST 2014
Hi Miles,
Looks like a bug to me. Or possibly something that has changed under the
hood in one of the dependencies. Any chance you could provide me with the
data in your example? Or even better, isolate which of the tracks is
throwing the error, and just send the data for that one?
Thanks,
Florian
On 05/05/14 18:00, "Miles Pufall" <miles.pufall at gmail.com> wrote:
>Hi -
>
>I've been making figures using BigWig files in Gviz without incident on a
>Linux machine and more recently on my Mac, but when I tried rerunning an
>existing script I got an error that I don't really understand. Below is
>my script and the output - it occurs during plotTracks, but involves
>unlist and split functions that I haven't specified. Is this a bug or
>have I failed to updat emy script for the newest version of Gviz?
>
>Thx -
>
>Miles
>
>**********************Script
>library("Gviz")
>library(GenomicFeatures)
>library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>setwd("/Volumes/PUFALL_2TB")
>itrack <- IdeogramTrack(genome = "hg19", cex = 1.4)
>gtrack <- GenomeAxisTrack(cex=1)
>B1_dex<-DataTrack("B1_ChIPseq/B1_all_treat_pileup.bw",genome="hg19",
>cex.title=1.2, cex.axis=1, background.title="darkgray",
> col.histogram="blue", fill.histogram="blue", name
>="B1", ylim=c(0,3))
>
>sup_dex<-DataTrack("SUP-B15/10min/sup_b15_10min_treat_pileup.bw",genome="h
>g19", cex.title=1.2, cex.axis=1,background.title="darkgray",
> col.histogram="blue", fill.histogram="blue", name
>="SUP-B15", ylim=c(0,3))
>
>rch_dex<-DataTrack("RCH-ACV/rch_acv_treat_pileup.bw",genome="hg19",
>cex.title=1.2, cex.axis=1,background.title="darkgray",
> col.histogram="blue", fill.histogram="blue", name
>="RCH-ACV", ylim=c(0,3))
>
>HM3101_dex<-DataTrack("HM3101/HM3101_dex_1uM_treat_pileup.bw",genome="hg19
>", cex.title=1.2, cex.axis=1,background.title="darkgray",
> col.histogram="blue", fill.histogram="blue", name
>="HM3101", ylim=c(0,3))
>
>grtrack <- GeneRegionTrack(txdb, genome = "hg19",name="BCL6",
>stacking="pack",stackHeight = 0.4,geneSymbols=TRUE, cex=1, cex.title=1.5,
>background.title="darkgray",
> chromosome = "chr3")
>
>plotTracks(list(itrack,gtrack,grtrack,B1_dex,sup_dex,rch_dex,HM3101_dex),f
>rom=187437000, to=187470000,type="histogram",chromosome="chr3")
>
>*************Output
>R version 3.1.0 (2014-04-10) -- "Spring Dance"
>Copyright (C) 2014 The R Foundation for Statistical Computing
>Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
>R is a collaborative project with many contributors.
>Type 'contributors()' for more information and
>'citation()' on how to cite R or R packages in publications.
>
>Type 'demo()' for some demos, 'help()' for on-line help, or
>'help.start()' for an HTML browser interface to help.
>Type 'q()' to quit R.
>
>> library("Gviz")
>Loading required package: grid
>Loading required package: BiocGenerics
>Loading required package: parallel
>
>Attaching package: ŒBiocGenerics¹
>
>The following objects are masked from Œpackage:parallel¹:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>clusterExport,
> clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
>parSapply,
> parSapplyLB
>
>The following object is masked from Œpackage:stats¹:
>
> xtabs
>
>The following objects are masked from Œpackage:base¹:
>
> anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
>do.call,
> duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted,
>lapply,
> Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
>pmin.int,
> Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff,
>sort, table,
> tapply, union, unique, unlist
>
>Loading required package: S4Vectors
>Loading required package: IRanges
>Loading required package: GenomicRanges
>Loading required package: GenomeInfoDb
>Warning messages:
>1: multiple methods tables found for Œcompare¹
>2: multiple methods tables found for Œseqinfo¹
>3: multiple methods tables found for Œseqinfo<-¹
>4: multiple methods tables found for Œseqnames¹
>5: multiple methods tables found for Œseqinfo¹
>6: multiple methods tables found for Œseqinfo<-¹
>7: multiple methods tables found for Œseqnames¹
>8: multiple methods tables found for Œmcols<-¹
>9: multiple methods tables found for Œvalues¹
>10: multiple methods tables found for Œvalues<-¹
>> library(GenomicFeatures)
>Loading required package: AnnotationDbi
>Loading required package: Biobase
>Welcome to Bioconductor
>
> Vignettes contain introductory material; view with
>'browseVignettes()'. To cite
> Bioconductor, see 'citation("Biobase")', and for packages
> 'citation("pkgname")'.
>
>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
>> setwd("/Volumes/PUFALL_2TB")
>> itrack <- IdeogramTrack(genome = "hg19", cex = 1.4)
>> gtrack <- GenomeAxisTrack(cex=1)
>> B1_dex<-DataTrack("B1_ChIPseq/B1_all_treat_pileup.bw",genome="hg19",
>>cex.title=1.2, cex.axis=1, background.title="darkgray",
>+ col.histogram="blue", fill.histogram="blue", name
>="B1", ylim=c(0,3))
>>
>>
>>sup_dex<-DataTrack("SUP-B15/10min/sup_b15_10min_treat_pileup.bw",genome="
>>hg19", cex.title=1.2, cex.axis=1,background.title="darkgray",
>+ col.histogram="blue", fill.histogram="blue", name
>="SUP-B15", ylim=c(0,3))
>>
>> rch_dex<-DataTrack("RCH-ACV/rch_acv_treat_pileup.bw",genome="hg19",
>>cex.title=1.2, cex.axis=1,background.title="darkgray",
>+ col.histogram="blue", fill.histogram="blue", name
>="RCH-ACV", ylim=c(0,3))
>>
>>
>>HM3101_dex<-DataTrack("HM3101/HM3101_dex_1uM_treat_pileup.bw",genome="hg1
>>9", cex.title=1.2, cex.axis=1,background.title="darkgray",
>+ col.histogram="blue", fill.histogram="blue", name
>="HM3101", ylim=c(0,3))
>>
>> grtrack <- GeneRegionTrack(txdb, genome = "hg19",name="BCL6",
>>stacking="pack",stackHeight = 0.4,geneSymbols=TRUE, cex=1,
>>cex.title=1.5, background.title="darkgray",
>+ chromosome = "chr3")
>>
>>
>>plotTracks(list(itrack,gtrack,grtrack,B1_dex,sup_dex,rch_dex,HM3101_dex),
>>from=187437000, to=187470000,type="histogram",chromosome="chr3")
>Error in unlist(range(split(ranges(x), group(x)))) :
> error in evaluating the argument 'x' in selecting a method for function
>'unlist': Error in split(ranges(x), group(x)) :
> error in evaluating the argument 'f' in selecting a method for function
>'split': Error in (function (classes, fdef, mtable) :
> unable to find an inherited method for function Œvalues¹ for signature
>Œ"GeneRegionTrack"¹
>>
>
>****************sessionInfo()
>
>R version 3.1.0 (2014-04-10)
>Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
>locale:
>[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>attached base packages:
>[1] parallel grid stats graphics grDevices utils datasets
>methods base
>
>other attached packages:
> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.17.4
> AnnotationDbi_1.27.4
> [4] Biobase_2.25.0 Gviz_1.9.1
> GenomicRanges_1.17.12
> [7] GenomeInfoDb_1.1.2 IRanges_1.99.12
> S4Vectors_0.0.6
>[10] BiocGenerics_0.11.1
>
>loaded via a namespace (and not attached):
> [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.7.0
> biomaRt_2.21.0 Biostrings_2.33.5
> [6] biovizBase_1.13.6 bitops_1.0-6 brew_1.0-6
> BSgenome_1.33.2 cluster_1.15.2
>[11] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7
> dichromat_2.0-0 digest_0.6.4
>[16] fail_1.2 foreach_1.4.2 Formula_1.1-1
> GenomicAlignments_1.1.7 Hmisc_3.14-4
>[21] iterators_1.0.7 lattice_0.20-29
>latticeExtra_0.6-26 matrixStats_0.8.14 munsell_0.4.2
>[26] plyr_1.8.1 R.methodsS3_1.6.1 RColorBrewer_1.0-5
> Rcpp_0.11.1 RCurl_1.95-4.1
>[31] Rsamtools_1.17.9 RSQLite_0.11.4 rtracklayer_1.25.4
> scales_0.2.4 sendmailR_1.1-2
>[36] splines_3.1.0 stats4_3.1.0 stringr_0.6.2
> survival_2.37-7 tools_3.1.0
>[41] VariantAnnotation_1.11.3 XML_3.98-1.1 XVector_0.5.6
> zlibbioc_1.11.1
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