Hi Dan,

Thanks a lot! I will try this!

cheers

Tengfei


On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> Hi Tengfei,
>
> ----- Original Message -----
> > From: "Tengfei Yin" <tengfei.yin@sbgenomics.com>
> > To: lcollado@jhu.edu
> > Cc: bioconductor@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@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@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]]
> >
> > _______________________________________________
> > 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
> >
>



-- 
Tengfei Yin, PhD
Seven Bridges Genomics
sbgenomics.com
625 Mt. Auburn St. Suite #208
Cambridge, MA 02138
(617) 866-0446

	[[alternative HTML version deleted]]

