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Question: New error in Gviz
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gravatar for Miles Pufall
3.6 years ago by
Miles Pufall40
Miles Pufall40 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",genom e="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=" 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_de x),from=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: ?BiocGenerics? The following objects are masked from ?package:parallel?: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ?package:stats?: xtabs The following objects are masked from ?package:base?: 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 ?compare? 2: multiple methods tables found for ?seqinfo? 3: multiple methods tables found for ?seqinfo<-? 4: multiple methods tables found for ?seqnames? 5: multiple methods tables found for ?seqinfo? 6: multiple methods tables found for ?seqinfo<-? 7: multiple methods tables found for ?seqnames? 8: multiple methods tables found for ?mcols<-? 9: multiple methods tables found for ?values? 10: multiple methods tables found for ?values<-? > 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",gen ome="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 ="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),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 ?values? for signature ?"GeneRegionTrack"? > ****************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
ADD COMMENTlink modified 3.6 years ago by florian.hahne@novartis.com1.5k • written 3.6 years ago by Miles Pufall40
0
gravatar for florian.hahne@novartis.com
3.6 years ago by
Switzerland
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",geno me="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_d ex),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: ?BiocGenerics? > >The following objects are masked from ?package:parallel?: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >clusterExport, > clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, >parSapply, > parSapplyLB > >The following object is masked from ?package:stats?: > > xtabs > >The following objects are masked from ?package:base?: > > 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 ?compare? >2: multiple methods tables found for ?seqinfo? >3: multiple methods tables found for ?seqinfo<-? >4: multiple methods tables found for ?seqnames? >5: multiple methods tables found for ?seqinfo? >6: multiple methods tables found for ?seqinfo<-? >7: multiple methods tables found for ?seqnames? >8: multiple methods tables found for ?mcols<-? >9: multiple methods tables found for ?values? >10: multiple methods tables found for ?values<-? >> 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",gen ome=" >>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 ?values? for signature >?"GeneRegionTrack"? >> > >****************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 >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 3.6 years ago by florian.hahne@novartis.com1.5k
Hi Florian - The bad news is that I can no longer reproduce this problem. The good news is that Gviz now appears to be fully functional on Mac Mavericks. After getting the news that most Bioconductor packages should work on Mavericks, I upgraded both my R installation Bioconductor, and now everything works perfectly (as far as I can tell). Here’s my new sessioninfo just in case you run into others with the same issue. I can’t imagine you want to track down the previous issue, but if you do, I’ll be happy to send data and go track by track. Cheers - M R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin13.1.0 (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] XVector_0.4.0 TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 [4] AnnotationDbi_1.26.0 Biobase_2.24.0 GenomicRanges_1.16.3 [7] GenomeInfoDb_1.0.2 IRanges_1.22.6 Gviz_1.8.1 [10] BiocGenerics_0.10.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 [6] biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 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_1.0.1 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_1.16.0 RSQLite_0.11.4 rtracklayer_1.24.0 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_1.10.1 XML_3.98-1.1 zlibbioc_1.10.0 On May 12, 2014, at 6:47 AM, Hahne, Florian <florian.hahne@novartis.com> wrote: > 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@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",ge nome="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",genom e="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",g enome=" >>> 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",geno me="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,HM310 1_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 >> _______________________________________________ >> 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]]
ADD REPLYlink written 3.6 years ago by Miles Pufall40
Perfect. I assume it was a package mangling problem then. From: Miles Pufall <miles.pufall@gmail.com<mailto:miles.pufall@gmail.com>> Date: Monday 12 May 2014 15:20 To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: Re: [BioC] New error in Gviz Hi Florian - The bad news is that I can no longer reproduce this problem. The good news is that Gviz now appears to be fully functional on Mac Mavericks. After getting the news that most Bioconductor packages should work on Mavericks, I upgraded both my R installation Bioconductor, and now everything works perfectly (as far as I can tell). Here’s my new sessioninfo just in case you run into others with the same issue. I can’t imagine you want to track down the previous issue, but if you do, I’ll be happy to send data and go track by track. Cheers - M R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin13.1.0 (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] XVector_0.4.0 TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 GenomicFeatures_1.16.0 [4] AnnotationDbi_1.26.0 Biobase_2.24.0 GenomicRanges_1.16.3 [7] GenomeInfoDb_1.0.2 IRanges_1.22.6 Gviz_1.8.1 [10] BiocGenerics_0.10.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0 biomaRt_2.20.0 Biostrings_2.32.0 [6] biovizBase_1.12.1 bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0 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_1.0.1 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_1.16.0 RSQLite_0.11.4 rtracklayer_1.24.0 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_1.10.1 XML_3.98-1.1 zlibbioc_1.10.0 On May 12, 2014, at 6:47 AM, Hahne, Florian <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> wrote: 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@gmail.com<mailto:miles.pufall@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",genom e="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_de x),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",genom e=" 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_de x), 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 _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto: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]]
ADD REPLYlink written 3.6 years ago by florian.hahne@novartis.com1.5k
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