[BioC] ggbio 1.12.0 autoplot() with txdb example is broken

Dan Tenenbaum dtenenba at fhcrc.org
Wed Apr 23 19:08:42 CEST 2014 


----- Original Message -----
> From: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Bioconductor mailing list" <bioconductor at r-project.org>, lcollado at jhu.edu
> Sent: Wednesday, April 23, 2014 9:24:42 AM
> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
> 
> 
> Hi Dan,
> 
> 
> So you mean I install R 3.1 for snow leopard and it should work?

Yes.


? Is
> there a way to build from source using biocLite, like type =
> "source", this is what I got
> 
> 
> 
> > library(BiocInstaller)
> Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help
> > biocLite("GenomicRanges")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.14 (BiocInstaller 1.14.1), R version
> 3.1.0.
> Installing package(s) 'GenomicRanges'
> 
> 
> package ‘GenomicRanges’ is available as a source package but not as a
> binary
> 
> 
> Warning message:
> package ‘GenomicRanges’ is not available (for R version 3.1.0)
> 
> 
> Just wondering is there a solution without re-install R for snow
> leopard. And what's the plan for maverick?
> 

You can do
biocLite("GenomicRanges", type="source")

but you need to have the appropriate compilers, etc.

I *STRONGLY* recommend using the Snow Leopard build. You can have multiple installations of R on your Mac and switch between them using Rswitch (http://r.research.att.com/#other) or another easy mechanism.

We are building packages for Mavericks now, we just have to resolve a few build issues and test the resulting packages, we still hope to have them available by the end of the month. But since you can install the Snow Leopard build without needing to remove your Mavericks build, you should do that.

Dan



> 
> Thanks
> 
> 
> Tengfei
> 
> 
> 
> 
> 
> 
> 
> On Wed, Apr 23, 2014 at 11:01 AM, Dan Tenenbaum < dtenenba at fhcrc.org
> > wrote:
> 
> 
> 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]]
> > 
> > _______________________________________________
> > Bioconductor mailing list
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> > 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
>

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