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",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
_______________________________________________
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]]

