[BioC] ggbio 1.12.0 autoplot() with txdb example is broken
Dan Tenenbaum
dtenenba at fhcrc.org
Sun Apr 27 04:33:41 CEST 2014
----- Original Message -----
> From: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
> To: lcollado at jhu.edu
> Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, "Bioconductor mailing list" <bioconductor at r-project.org>
> Sent: Saturday, April 26, 2014 1:58:01 PM
> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
>
>
> right, it's failing to build and I am trying to figure out why now,
> because it passes check/build and works on my laptop, but it doesn't
> pass bioc build for both release and devel, let me dig into it
> tonight.
>
Seems like this could be fixed if you just add
library(ggbio)
to your vignette before the ggbio() function is called on line 557 of vignettes/realvignettes/ggbio.Rnw.
Dan
>
> thanks for your patience
>
>
> Tengfei
>
>
>
> On Sat, Apr 26, 2014 at 1:16 PM, Leonardo Collado Torres <
> lcollado at jhsph.edu > wrote:
>
>
>
> Oh ok. Thanks for the info
>
>
>
>
>
> On Sat, Apr 26, 2014 at 12:57 PM, Dan Tenenbaum < dtenenba at fhcrc.org
> > wrote:
>
>
>
>
>
> Leonardo Collado Torres < lcollado at jhsph.edu > wrote:
>
> >Is there any reason why ggbio 1.12.2 hasn't made it to BioC release?
> > http://master.bioconductor.org/packages/release/bioc/html/ggbio.html
> >still
> >points to 1.12.0
> >
>
> It's failing to build:
>
> http://www.bioconductor.org/checkResults/release/bioc-LATEST/ggbio/zin2-buildsrc.html
>
>
>
> Dan
>
> >
> >On Wed, Apr 23, 2014 at 6:40 PM, Dan Tenenbaum < dtenenba at fhcrc.org
> >>
> >wrote:
> >
> >>
> >>
> >> ----- Original Message -----
> >> > From: "Leonardo Collado Torres" < lcollado at jhsph.edu >
> >> > To: "Tengfei Yin" < tengfei.yin at sbgenomics.com >
> >> > Cc: "Dan Tenenbaum" < dtenenba at fhcrc.org >, "Bioconductor
> >> > mailing
> >list" <
> >> bioconductor at r-project.org >
> >> > Sent: Wednesday, April 23, 2014 3:38:11 PM
> >> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is
> >broken
> >> >
> >> > Dang it, forgot again to send with my @ jhsph.edu account. See
> >> > below
> >> > again >.<
> >> >
> >> > On the email topic, is it possible to be subscribed with 2
> >> > emails
> >> > accounts to the BioC mailing list but only get emails with one?
> >> > I
> >> > believe that I have to choose to either get the daily digest or
> >> > get
> >a
> >> > single for every message sent. If not, I'll probably just drop
> >> > my
> >> > @ jhsph.edu subscription and re-subscribe with the new @ jhu.edu
> >> > mail
> >I
> >> > got (our university is pushing these mails).
> >> >
> >>
> >> I don't know; you could try it. Another option would be to
> >> configure
> >your
> >> mail client with a filter to drop the undesired bioc emails.
> >>
> >> Dan
> >>
> >>
> >> > On Wed, Apr 23, 2014 at 6:32 PM, Leonardo Collado Torres
> >> > < lcollado at jhu.edu > wrote:
> >> > > Hi Dan,
> >> > >
> >> > > I got RSwitch to work with a second installation of R 3.1.
> >> > > Basically,
> >> > > I downloaded the leopard tarball, expanded it, renamed the
> >> > > folder
> >> > > 3.1
> >> > > to 3.1patched (which is the version I downloaded, but well,
> >> > > anything
> >> > > except for 3.1 would work), compressed it again, and then
> >expanded
> >> > > it
> >> > > at the root location.
> >> > >
> >> > > So it would be something like this:
> >> > >
> >> > > wget
> >> > >
> >>
> > http://r.research.att.com/snowleopard/R-3.1-branch/R-3.1-branch-snowleopard-sa-x86_64.tar.gz
> >> > > tar -xvf R-*gz
> >> > > mv Library/Frameworks/R.framework/Versions/3.1
> >> > > Library/Frameworks/R.framework/Versions/3.1patched
> >> > > tar -cvzf Rlib.tgz Library
> >> > > sudo tar fvxz Rlib.tgz -C /
> >> > >
> >> > > Then used RSwitch, and was able to install BioC-devel.
> >> > >
> >> > > I might try out your `renv` at a different time. It's great to
> >know
> >> > > that it exists =)
> >> > >
> >> > > Cheers,
> >> > > Leo
> >> > >
> >> > >
> >> > > On Wed, Apr 23, 2014 at 4:49 PM, Tengfei Yin
> >> > > < tengfei.yin at sbgenomics.com > wrote:
> >> > >> Hi Dan,
> >> > >>
> >> > >> It works like a charm, thanks!
> >> > >>
> >> > >> I use your method, then I changed /Library/Framework/ folder
> >> > >> and
> >> > >> R.Framework
> >> > >> folder ownership to myself so I don't have to sudo it, then I
> >just
> >> > >> add alias
> >> > >> to "emacs2" and "emacs3" to run your renv to switch the R
> >> > >> first.
> >> > >> This solves
> >> > >> my problem.
> >> > >>
> >> > >> Try to customize variable for R hooks in emacs as alternative
> >> > >> solution, but
> >> > >> may need more time.
> >> > >>
> >> > >> Thanks again!
> >> > >>
> >> > >> Tengfei
> >> > >>
> >> > >>
> >> > >> On Wed, Apr 23, 2014 at 3:19 PM, Dan Tenenbaum
> >> > >> < dtenenba at fhcrc.org > wrote:
> >> > >>>
> >> > >>> 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 11:01:18 AM
> >> > >>> > Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb
> >> > >>> > example
> >> > >>> > is broken
> >> > >>> >
> >> > >>> >
> >> > >>> > Is there a trick to run both Bioc 2.14 and bioc 3.0 all on
> >the
> >> > >>> > R 3.1?
> >> > >>>
> >> > >>> Yes, install two copies of R 3.1 and switch between them.
> >> > >>>
> >> > >>> > And do some sort of switch for bioc? The website you send
> >> > >>> > to
> >me
> >> > >>> > also
> >> > >>> > have a R-devel build, my plan is to install bioc 3.0 on
> >R-devel
> >> > >>> > and
> >> > >>> > bioc 2.14 on R 3.1, and do some tricks with emacs for R
> >> > >>> > only
> >to
> >> > >>> > switch bioc, so that I could debug and maintain released
> >> > >>> > and
> >> > >>> > devel
> >> > >>> > version.
> >> > >>>
> >> > >>> PLEASE don't use R-devel at all.
> >> > >>>
> >> > >>> Just use R-3.1.0.
> >> > >>>
> >> > >>> You can use the Rswitch app but as you point out it won't
> >> > >>> work
> >> > >>> within
> >> > >>> emacs.
> >> > >>>
> >> > >>> This is what I do:
> >> > >>>
> >> > >>> Every time I download a new version of R, I run its
> >> > >>> installer.
> >> > >>> The
> >> > >>> installer always puts it in
> >> > >>>
> >> > >>> /Library/Frameworks/R.framework
> >> > >>>
> >> > >>> So after I install each version of R, I rename the
> >> > >>> R.framework
> >> > >>> directory
> >> > >>> to something like
> >> > >>> R.framework.bioc214_snowleopard
> >> > >>>
> >> > >>> And then I make a symlink from
> >> > >>> R.framework.bioc214_snowleopard
> >to
> >> > >>> R.framework.
> >> > >>>
> >> > >>> I have a little script at https://github.com/dtenenba/renv
> >which
> >> > >>> lets me
> >> > >>> see what the various installed Rs are:
> >> > >>>
> >> > >>> $ renv
> >> > >>> 302 3.0.2 63987 (none) 2013-09-25 darwin10.8.0
> >> > >>> develMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
> >> > >>> develSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
> >> > >>> *releaseMav 3.1.0 65387 (none) 2014-04-10 darwin13.1.0
> >> > >>> releaseSL 3.1.0 65387 (none) 2014-04-10 darwin10.8.0
> >> > >>>
> >> > >>> This tells me that the currently active R is nicknamed
> >> > >>> "releaseMav" (this
> >> > >>> means there is a link from
> >> > >>> /Library/Frameworks/R.framework.releaseMav to
> >> > >>> /Library/Frameworks/R.framework. It shows the versions, svn
> >> > >>> revisions,
> >> > >>> dates, and architectures of each version. (darwin10.8.0 is
> >> > >>> Snow
> >> > >>> Leopard;
> >> > >>> darwin13.1.0 is Mavericks).
> >> > >>>
> >> > >>> Note that in my nomenclature devel means BioC devel, not
> >R-devel.
> >> > >>>
> >> > >>> So if I wanted to switch to the "develSL" version I would
> >> > >>> do:
> >> > >>>
> >> > >>> sudo renv develSL
> >> > >>>
> >> > >>> HTH
> >> > >>> Dan
> >> > >>>
> >> > >>>
> >> > >>>
> >> > >>> >
> >> > >>> >
> >> > >>> >
> >> > >>> > On Wed, Apr 23, 2014 at 1:49 PM, Dan Tenenbaum <
> >> > >>> > dtenenba at fhcrc.org >
> >> > >>> > wrote:
> >> > >>> >
> >> > >>> >
> >> > >>> >
> >> > >>> > 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
> >> > >>> > >
> >> > >>> >
> >> > >>> >
> >> > >>> >
> >> > >>> >
> >> > >>> > --
> >> > >>> >
> >> > >>> >
> >> > >>> > 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
> >> >
> >>
>
>
>
>
>
>
> --
>
>
> Tengfei Yin, PhD
> Seven Bridges Genomics
> sbgenomics.com
> 625 Mt. Auburn St. Suite #208
> Cambridge, MA 02138
> (617) 866- 0446
>
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