[BioC] ggbio 1.12.0 autoplot() with txdb example is broken
Dan Tenenbaum
dtenenba at fhcrc.org
Wed Apr 23 17:01:40 CEST 2014
Hi Tengfei,
----- Original Message -----
> From: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
> To: lcollado at jhu.edu
> Cc: bioconductor at r-project.org
> Sent: Wednesday, April 23, 2014 7:52:11 AM
> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
>
> btw, based on the error, let me try to debug it.
>
>
> On Wed, Apr 23, 2014 at 10:50 AM, Tengfei Yin
> <tengfei.yin at sbgenomics.com>wrote:
>
> > Hi Leonardo,
> >
> > Frankly speaking, the vignette is still in progress, and there are
> > some
> > known bugs in ggbio I need to fix (still trying to find a time to
> > do that
> > ... ), I am recently trying to install R 3.1 and Bioc 2.14 on my
> > new MBP
> > with OSX 10.9, but fails, probably binary build is not ready for
> > maverick
> > yet, maybe available by the end of April?
> >
> > Thanks for reporting the bug, I will keep you posted on this when I
> > successfully get it on my laptop and start fixing the problems.
> >
You can install the Snow Leopard build of R and should have no problems, binary packages are available for that version. It will run fine on Mavericks.
Dan
> > cheers
> >
> > Tengfei
> >
> >
> > On Wed, Apr 23, 2014 at 12:10 AM, Leonardo Collado Torres <
> > lcollado at jhsph.edu> wrote:
> >
> >> Hello Tengfei + bioc list,
> >>
> >> From
> >> http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf
> >> page 4 (complied on april 11 2014), the following example loads to
> >> an
> >> error as shown below. I wasn't seeing this error before (aka, last
> >> week). The only guess that comes to mind is the recent update to
> >> GenomicRanges (1.16.2) although that doesn't seem to be related
> >> from
> >> the traceback() output, well... maybe it's related to the
> >> ignore.strand = TRUE part as described in the error.
> >>
> >> I'll create a GitHub issue just for completeness.
> >>
> >> Thank you,
> >> Leonardo
> >>
> >> > library(ggbio)
> >> ## Removed the output, nothing out of ordinary
> >>
> >> > library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> >> ## Removed the output
> >>
> >> > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> >> > data(genesymbol, package = "biovizBase")
> >> > p.txdb <- autoplot(txdb, which = genesymbol["BRCA1"])
> >> Aggregating TranscriptDb...
> >> Parsing transcripts...
> >> Parsing exons...
> >> Parsing cds...
> >> Parsing utrs...
> >> ------exons...
> >> ------cdss...
> >> ------introns...
> >> ------utr...
> >> aggregating...
> >> Done
> >> Constructing graphics...
> >> Error in sapply(listData, function(Xi) extends(class(Xi),
> >> elementTypeX)) :
> >> error in evaluating the argument 'X' in selecting a method for
> >> function 'sapply': Error in unlist(range(ranges(x.n, ignore.strand
> >> =
> >> TRUE))) :
> >> error in evaluating the argument 'x' in selecting a method for
> >> function 'unlist': Error in .local(x, ...) : unused argument
> >> (ignore.strand = TRUE)
> >>
> >> > traceback()
> >> 15: sapply(listData, function(Xi) extends(class(Xi),
> >> elementTypeX))
> >> 14: .updateCompressedList(X, lapply_CompressedList(X, FUN, ...))
> >> 13: endoapply(obj.lst, function(x) {
> >> if (!is.null(group.name)) {
> >> if (!group.selfish) {
> >> x.n <- split(x, values(x)[, group.name])
> >> irs <- unlist(range(ranges(x.n, ignore.strand =
> >> TRUE)))
> >> irs.new <- resize(irs, fix = fix, width =
> >> width(irs) +
> >> extend.size)
> >> irs.new <- sort(irs.new)
> >> .lvs <- disjointBins(irs.new)
> >> values(x)$stepping <-
> >> .lvs[as.character(values(x)[,
> >> group.name])]
> >> x
> >> }
> >> else {
> >> values(x)$stepping <-
> >> as.numeric(as.factor(values(x)[,
> >> group.name]))
> >> x
> >> }
> >> }
> >> else {
> >> irs <- ranges(x)
> >> values(x)$stepping <-
> >> as.numeric(disjointBins(resize(irs,
> >> fix = "center", width = width(irs) +
> >> extend.size)))
> >> x
> >> }
> >> })
> >> 12: endoapply(obj.lst, function(x) {
> >> if (!is.null(group.name)) {
> >> if (!group.selfish) {
> >> x.n <- split(x, values(x)[, group.name])
> >> irs <- unlist(range(ranges(x.n, ignore.strand =
> >> TRUE)))
> >> irs.new <- resize(irs, fix = fix, width =
> >> width(irs) +
> >> extend.size)
> >> irs.new <- sort(irs.new)
> >> .lvs <- disjointBins(irs.new)
> >> values(x)$stepping <-
> >> .lvs[as.character(values(x)[,
> >> group.name])]
> >> x
> >> }
> >> else {
> >> values(x)$stepping <-
> >> as.numeric(as.factor(values(x)[,
> >> group.name]))
> >> x
> >> }
> >> }
> >> else {
> >> irs <- ranges(x)
> >> values(x)$stepping <-
> >> as.numeric(disjointBins(resize(irs,
> >> fix = "center", width = width(irs) +
> >> extend.size)))
> >> x
> >> }
> >> })
> >> 11: .local(obj, ...)
> >> 10: addStepping(gr, group.name = "tx_id", group.selfish = FALSE,
> >> fix = "start", extend.size = es)
> >> 9: addStepping(gr, group.name = "tx_id", group.selfish = FALSE,
> >> fix = "start", extend.size = es)
> >> 8: .local(data, ...)
> >> 7: (function (data, ...)
> >> standardGeneric("geom_alignment"))(data = <S4 object of class
> >> "TranscriptDb">,
> >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment",
> >> stat = "identity", names.expr = "tx_name", label = TRUE,
> >> which = <S4 object of class "GRanges">, list())
> >> 6: (function (data, ...)
> >> standardGeneric("geom_alignment"))(data = <S4 object of class
> >> "TranscriptDb">,
> >> truncate.gaps = FALSE, ratio = 0.0025, geom = "alignment",
> >> stat = "identity", names.expr = "tx_name", label = TRUE,
> >> which = <S4 object of class "GRanges">, list())
> >> 5: do.call(geom_alignment, args.res)
> >> 4: do.call(geom_alignment, args.res)
> >> 3: .local(object, ...)
> >> 2: autoplot(txdb, which = genesymbol["BRCA1"])
> >> 1: autoplot(txdb, which = genesymbol["BRCA1"])
> >>
> >>
> >> > 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 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_1.16.2
> >> [7] GenomeInfoDb_1.0.2 IRanges_1.22.3
> >> ggbio_1.12.0
> >> [10] ggplot2_0.9.3.1 BiocGenerics_0.10.0
> >>
> >> loaded via a namespace (and not attached):
> >> [1] BatchJobs_1.2 BBmisc_1.5
> >> BiocParallel_0.6.0 biomaRt_2.20.0
> >> Biostrings_2.32.0
> >> [6] biovizBase_1.12.0 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_1.0.0 grid_3.1.0
> >> [21] gridExtra_0.9.1 gtable_0.1.2
> >> Hmisc_3.14-4
> >> iterators_1.0.7 labeling_0.2
> >> [26] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-31
> >> munsell_0.4.2 plyr_1.8.1
> >> [31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1
> >> RCurl_1.95-4.1 reshape2_1.2.2
> >> [36] Rsamtools_1.16.0 RSQLite_0.11.4
> >> rtracklayer_1.24.0 scales_0.2.3 sendmailR_1.1-2
> >> [41] splines_3.1.0 stats4_3.1.0
> >> stringr_0.6.2
> >> survival_2.37-7 tools_3.1.0
> >> [46] VariantAnnotation_1.10.0 XML_3.98-1.1
> >> zlibbioc_1.10.0
> >> >
> >>
> >
> >
> >
> > --
> > Tengfei Yin, PhD
> > Seven Bridges Genomics
> > sbgenomics.com
> > 625 Mt. Auburn St. Suite #208
> > Cambridge, MA 02138
> > (617) 866-0446
> >
>
>
>
> --
> Tengfei Yin, PhD
> Seven Bridges Genomics
> sbgenomics.com
> 625 Mt. Auburn St. Suite #208
> Cambridge, MA 02138
> (617) 866-0446
>
> [[alternative HTML version deleted]]
>
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