[BioC] ggbio 1.12.0 autoplot() with txdb example is broken
Leonardo Collado Torres
lcollado at jhsph.edu
Wed Apr 30 01:03:18 CEST 2014
I just noticed that ggbio is building now
http://www.bioconductor.org/checkResults/release/bioc-LATEST/ggbio/zin2-buildsrc.html
and I'm happy to report that the problem I mentioned is resolved with
ggbio 1.12.3. Thank you Tengfei and Dan!
For reference, here is the working session information.
> 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
[3] GenomicFeatures_1.16.0 AnnotationDbi_1.26.0
[5] Biobase_2.24.0 GenomicRanges_1.16.2
[7] GenomeInfoDb_1.0.2 IRanges_1.22.4
[9] ggbio_1.12.3 ggplot2_0.9.3.1
[11] BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0
[4] biomaRt_2.20.0 Biostrings_2.32.0 biovizBase_1.12.1
[7] bitops_1.0-6 brew_1.0-6 BSgenome_1.32.0
[10] cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4
[13] DBI_0.2-7 dichromat_2.0-0 digest_0.6.4
[16] fail_1.2 foreach_1.4.2 Formula_1.1-1
[19] GenomicAlignments_1.0.0 grid_3.1.0 gridExtra_0.9.1
[22] gtable_0.1.2 Hmisc_3.14-4 iterators_1.0.7
[25] labeling_0.2 lattice_0.20-29 latticeExtra_0.6-26
[28] MASS_7.3-32 munsell_0.4.2 plyr_1.8.1
[31] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1
[34] RCurl_1.95-4.1 reshape2_1.4 Rsamtools_1.16.0
[37] RSQLite_0.11.4 rtracklayer_1.24.0 scales_0.2.4
[40] sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0
[43] 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
On Sat, Apr 26, 2014 at 10:45 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>
> ----- Original Message -----
>> From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
>> To: "Tengfei Yin" <tengfei.yin at sbgenomics.com>
>> Cc: lcollado at jhu.edu, "Bioconductor mailing list" <bioconductor at r-project.org>
>> Sent: Saturday, April 26, 2014 7:33:41 PM
>> Subject: Re: [BioC] ggbio 1.12.0 autoplot() with txdb example is broken
>>
>>
>>
>> ----- 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.
>>
>
> Sorry, I spoke too soon; that just changes the error message you receive.
> Dan
>
>
>> 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
>> >
>>
>> _______________________________________________
>> 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
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