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

Dan Tenenbaum dtenenba at fhcrc.org
Wed Apr 23 19:49:17 CEST 2014 

Hi Tengfei,

----- 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 10:46:02 AM
> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
> 
> 
> Thanks a lot Dan! it's clear to me now, sorry that I am still a
> newbie to OSX ... I got R-devel running and I will try Rswitcher, I
> also want to do that switch easily in emacs too.
> 
> 

You don't want to use R-devel. Both BioC release (2.14) and BioC devel (3.0) are meant to work with R-3.1.0, the released version of R.

I think the Rswitch app just sets a symbolic link, so you should be able to do that within emacs. Run it and see what it does to
/Library/Frameworks/R.framework.

Dan


> 
> cheers
> 
> 
> Tengfei
> 
> 
> 
> On Wed, Apr 23, 2014 at 1:08 PM, Dan Tenenbaum < dtenenba at fhcrc.org >
> wrote:
> 
> 
> 
> 
> 
> ----- 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
> > > Bioconductor at 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
> > 
> 
> 
> 
> 
> --
> 
> 
> Tengfei Yin, PhD
> Seven Bridges Genomics
> sbgenomics.com
> 625 Mt. Auburn St. Suite #208
> Cambridge, MA 02138
> (617) 866- 0446
>

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