Steve brings up a good point -- maybe developers should be using the
R-2-15-branch, rather than R 2.15.0 itself, in anticipation of upcoming
micro releases.

Michael

On Wed, Apr 18, 2012 at 6:57 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> On Wed, Apr 18, 2012 at 9:11 AM, Michael Lawrence
> <lawrence.michael@gene.com> wrote:
> > Yea, sucks. I promise to switch to the R 2.15 series after the point
> > release. Some annoying bugs in 2.15.0 right now. I'm just going to rely
> on
> > the build servers to make sure everything works.
>
> Yikes, really?
>
> Do you recommend compiling from R-1-15-branch?
>
> -steve
>
> >
> > On Tue, Apr 17, 2012 at 11:42 PM, Hahne, Florian <
> florian.hahne@novartis.com
> >> wrote:
> >
> >> Ah, I see. I wasn't aware that we are supposed to develop on R-2.15,
> >> although that makes perfect sense. How simple were the old days, when
> >> biocDevel meant Rdevel. Sigh...
> >>
> >>
> >>
> >> Florian Hahne
> >> Novartis Institute For Biomedical Research
> >> Translational Sciences / Preclinical Safety / PCS Informatics
> >> Expert Data Integration and Modeling Bioinformatics
> >> CHBS, WKL-135.2.26
> >> Novartis Institute For Biomedical Research, Werk Klybeck
> >> Klybeckstrasse 141
> >> CH-4057 Basel
> >> Switzerland
> >> Phone: +41 61 6967127
> >> Email : florian.hahne@novartis.com
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> On 4/16/12 10:17 PM, "Martin Morgan" <mtmorgan@fhcrc.org> wrote:
> >>
> >> >On 04/16/2012 12:31 AM, Hahne, Florian wrote:
> >> >> My bad, I updated all packages before trying this and never checked
> what
> >> >> actually happened.
> >> >> The odd thing is that I am running R-devel, I have the latest
> >> >> BiocInstaller 1.5.6 installed but I still only get the bioc release
> >> >> packages.:
> >> >>  > sessionInfo()
> >> >> R Under development (unstable) (2012-04-16 r59045)
> >> >> Platform: x86_64-unknown-linux-gnu/x86_64 (64-bit)
> >> >
> >> >R switched to an annual release cycle, whereas Bioc kept it's
> >> >semi-annual release. Bioc during April - October uses 'release' R for
> >> >both release and devel Bioc. So BiocInstaller was expecting you to have
> >> >R-2-15 regardless of whether you were 'release' or 'devel' bioc.
> >> >
> >> >You can manage the two versions either with duplicate copies of R-2-15
> >> >installed in different locations, or using the R_LIBS_USER (for
> example)
> >> >environment variable to point to a user library that is different for
> >> >Bioc release and for Bioc devel.
> >> >
> >> >Martin
> >> >
> >> >
> >> >>
> >> >> locale:
> >> >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >> >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> >> >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> >> >> [7] LC_PAPER=C LC_NAME=C
> >> >> [9] LC_ADDRESS=C LC_TELEPHONE=C
> >> >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >> >>
> >> >> attached base packages:
> >> >> [1] stats graphics grDevices utils datasets methods base
> >> >>
> >> >> other attached packages:
> >> >> [1] rtracklayer_1.16.1 GenomicRanges_1.8.3 IRanges_1.14.2
> >> >> [4] BiocGenerics_0.2.0 BiocInstaller_1.5.6
> >> >>
> >> >> loaded via a namespace (and not attached):
> >> >> [1] Biostrings_2.24.1 bitops_1.0-4.1 BSgenome_1.24.0 RCurl_1.91-1
> >> >> [5] Rsamtools_1.9.2 stats4_2.16.0 tools_2.16.0 XML_3.9-4
> >> >> [9] zlibbioc_1.2.0
> >> >>
> >> >> I think I followed Dan's instructions carefully, any idea why this is
> >> >> not working for me?
> >> >>
> >> >> The little bit of debugging I tried revealed that biocInstallRepos
> does
> >> >> not give me the right repository path:
> >> >>  > biocinstallRepos()
> >> >> BioCsoft
> >> >> "http://www.bioconductor.org/packages/2.10/bioc"
> >> >> CRAN
> >> >> "http://cran.fhcrc.org"
> >> >> BioCann
> >> >> "http://www.bioconductor.org/packages/2.10/data/annotation"
> >> >> BioCexp
> >> >> "http://www.bioconductor.org/packages/2.10/data/experiment"
> >> >> BioCextra
> >> >> "http://www.bioconductor.org/packages/2.10/extra"
> >> >>
> >> >> Now in there I find:
> >> >>  > BiocInstaller:::biocinstallRepos
> >> >> function (siteRepos = character())
> >> >> {
> >> >> .biocinstallRepos(siteRepos = siteRepos, devel = .isDevel())
> >> >> }
> >> >> <environment: namespace:BiocInstaller>
> >> >>
> >> >> And .isDevel is defined as
> >> >>
> >> >>  > BiocInstaller:::.isDevel
> >> >> function ()
> >> >> {
> >> >> isOdd <- (packageVersion("BiocInstaller")$minor%%2L) == 1L
> >> >> isOdd && (R.version$status == "" || R.version$status == "Patched")
> >> >> }
> >> >> <environment: namespace:BiocInstaller>
> >> >>
> >> >> I may be wrong here, but how can I ever get TRUE unless I am running
> R
> >> >> Patched or whatever R.version$status=="" refers to? Since I am
> running R
> >> >> devel built from svn I have
> >> >>  > R.version$status
> >> >> [1] "Under development (unstable)"
> >> >>
> >> >> So I will always and for all eternity get .isDevel()==FALSEŠ
> >> >>
> >> >> Florian
> >> >>
> >> >> Florian Hahne
> >> >> Novartis Institute For Biomedical Research
> >> >> Translational Sciences / Preclinical Safety / PCS Informatics
> >> >> Expert Data Integration and Modeling Bioinformatics
> >> >> CHBS, WKL-135.2.26
> >> >> Novartis Institute For Biomedical Research, Werk Klybeck
> >> >> Klybeckstrasse 141
> >> >> CH-4057 Basel
> >> >> Switzerland
> >> >> Phone: +41 61 6967127
> >> >> Email : florian.hahne@novartis.com <mailto:
> florian.hahne@novartis.com>
> >> >>
> >> >>
> >> >> From: Michael Lawrence <lawrence.michael@gene.com
> >> >> <mailto:lawrence.michael@gene.com>>
> >> >> Date: Fri, 13 Apr 2012 09:19:20 -0700
> >> >> To: NIBR <florian.hahne@novartis.com
> >> >><mailto:florian.hahne@novartis.com>>
> >> >> Cc: Michael Lawrence <lawrence.michael@gene.com
> >> >> <mailto:lawrence.michael@gene.com>>, Sean Davis <
> sdavis2@mail.nih.gov
> >> >> <mailto:sdavis2@mail.nih.gov>>, Martin Morgan <mtmorgan@fhcrc.org
> >> >> <mailto:mtmorgan@fhcrc.org>>, "bioc-devel@r-project.org
> >> >> <mailto:bioc-devel@r-project.org>" <bioc-devel@r-project.org
> >> >> <mailto:bioc-devel@r-project.org>>
> >> >> Subject: Re: [Bioc-devel] scanTabix coercion to data.frame
> >> >>
> >> >>
> >> >>
> >> >> On Fri, Apr 13, 2012 at 8:15 AM, Hahne, Florian
> >> >> <florian.hahne@novartis.com <mailto:florian.hahne@novartis.com>>
> wrote:
> >> >>
> >> >>     Yes, I tried this:
> >> >>     ff <-
> >> >>
> >>
> >>TabixFile("/CHBS/apps/itox/data/project_data_repository/1/1/project.tbx")
> >> >>     foo <- import(ff)
> >> >>     Error: evaluation nested too deeply: infinite recursion /
> >> >>     options(expressions=)?
> >> >>
> >> >>     And this:
> >> >>
> >> >>
> >> >>     foo <- import(ff, which=GRanges(seqnames="chrX",
> >> >>ranges=IRanges(start=1,
> >> >>     end=1e8)))
> >> >>     Error: evaluation nested too deeply: infinite recursion /
> >> >>     options(expressions=)?
> >> >>
> >> >>     And then I gave up :-)
> >> >>
> >> >>
> >> >>
> >> >> Ok, well I said the devel version, i.e., 1.17.1, not 1.16.1.
> >> >>
> >> >>     >  sessionInfo()
> >> >>     R Under development (unstable) (2012-04-03 r58904)
> >> >>     Platform: x86_64-unknown-linux-gnu/x86_64 (64-bit)
> >> >>
> >> >>     locale:
> >> >>     [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >> >>     [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> >> >>     [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> >> >>     [7] LC_PAPER=C LC_NAME=C
> >> >>     [9] LC_ADDRESS=C LC_TELEPHONE=C
> >> >>     [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >> >>
> >> >>     attached base packages:
> >> >>     [1] stats graphics grDevices utils datasets methods base
> >> >>
> >> >>     other attached packages:
> >> >>     [1] rtracklayer_1.16.1 Rsamtools_1.9.2 Biostrings_2.24.1
> >> >>     [4] GenomicRanges_1.8.3 IRanges_1.14.2 BiocGenerics_0.2.0
> >> >>     [7] BiocInstaller_1.4.3
> >> >>
> >> >>     loaded via a namespace (and not attached):
> >> >>     [1] bitops_1.0-4.1 BSgenome_1.24.0 RCurl_1.91-1 stats4_2.16.0
> >> >>     [5] tools_2.16.0 XML_3.9-4 zlibbioc_1.2.0
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>     Florian Hahne
> >> >>     Novartis Institute For Biomedical Research
> >> >>     Translational Sciences / Preclinical Safety / PCS Informatics
> >> >>     Expert Data Integration and Modeling Bioinformatics
> >> >>     CHBS, WKL-135.2.26
> >> >>     Novartis Institute For Biomedical Research, Werk Klybeck
> >> >>     Klybeckstrasse 141
> >> >>     CH-4057 Basel
> >> >>     Switzerland
> >> >>     Phone: +41 61 6967127 <tel:%2B41%2061%206967127>
> >> >>     Email : florian.hahne@novartis.com
> >> >><mailto:florian.hahne@novartis.com>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>     From: Michael Lawrence <lawrence.michael@gene.com
> >> >>     <mailto:lawrence.michael@gene.com>>
> >> >>     Date: Thu, 12 Apr 2012 10:07:31 -0700
> >> >>     To: NIBR <florian.hahne@novartis.com
> >> >>     <mailto:florian.hahne@novartis.com>>
> >> >>     Cc: Michael Lawrence <lawrence.michael@gene.com
> >> >>     <mailto:lawrence.michael@gene.com>>, Sean Davis
> >> >>     <sdavis2@mail.nih.gov <mailto:sdavis2@mail.nih.gov>>, Martin
> Morgan
> >> >>     <mtmorgan@fhcrc.org <mailto:mtmorgan@fhcrc.org>>,
> >> >>     "bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>"
> >> >>     <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>>
> >> >>     Subject: Re: [Bioc-devel] scanTabix coercion to data.frame
> >> >>
> >> >>
> >> >>     Did you try the latest devel version?
> >> >>
> >> >>     On Thu, Apr 12, 2012 at 9:29 AM, Hahne, Florian
> >> >>     <florian.hahne@novartis.com <mailto:florian.hahne@novartis.com>>
> >> >>wrote:
> >> >>
> >> >>     Thanks, I gave it a shot and got this:
> >> >>     Error: evaluation nested too deeply: infinite recursion /
> >> >>     options(expressions=)?
> >> >>
> >> >>
> >> >>     Guess I'll stick with scanTabix for now :-)
> >> >>     Florian
> >> >>     Florian Hahne
> >> >>     Novartis Institute For Biomedical Research
> >> >>     Translational Sciences / Preclinical Safety / PCS Informatics
> >> >>     Expert Data Integration and Modeling Bioinformatics
> >> >>     CHBS, WKL-135.2.26
> >> >>     Novartis Institute For Biomedical Research, Werk Klybeck
> >> >>     Klybeckstrasse 141
> >> >>     CH-4057 Basel
> >> >>     Switzerland
> >> >>     Phone: +41 61 6967127 <tel:%2B41%2061%206967127>
> >> >>     <tel:%2B41%2061%206967127>
> >> >>     Email : florian.hahne@novartis.com
> >> >><mailto:florian.hahne@novartis.com>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>     From: Michael Lawrence <lawrence.michael@gene.com
> >> >>     <mailto:lawrence.michael@gene.com>>
> >> >>     Date: Thu, 12 Apr 2012 06:54:19 -0700
> >> >>     To: NIBR <florian.hahne@novartis.com
> >> >>     <mailto:florian.hahne@novartis.com>>
> >> >>     Cc: Sean Davis <sdavis2@mail.nih.gov <mailto:
> sdavis2@mail.nih.gov
> >> >>,
> >> >>     Martin Morgan <mtmorgan@fhcrc.org <mailto:mtmorgan@fhcrc.org>>,
> >> >>     "bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>"
> >> >>     <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>>
> >> >>     Subject: Re: [Bioc-devel] scanTabix coercion to data.frame
> >> >>
> >> >>
> >> >>     You can use rtracklayer to import tabix files directly. If it's
> GFF
> >> >>or
> >> >>     BED, you can just use import(). For arbitrary tabular files,
> first
> >> >>cast
> >> >>     the path to a TabixFile, then pass it to import(). That last one
> is
> >> >>not
> >> >>     well tested. It uses the header information
> >> >>     to know the starts, ends, etc.
> >> >>
> >> >>     Michael
> >> >>
> >> >>     On Thu, Apr 12, 2012 at 6:10 AM, Hahne, Florian
> >> >>     <florian.hahne@novartis.com <mailto:florian.hahne@novartis.com>>
> >> >>wrote:
> >> >>
> >> >>     Sean, Martin, thanks for the suggestions. I guess a combination
> of
> >> >>     the two
> >> >>     would work well for me. I create my own tabix files and could
> >> >>certainly
> >> >>     stick the type information in the header. And I wasn't aware of
> >> >>     textConnection(), which seems to be performant enough to do what
> I
> >> >>want.
> >> >>     At least it is much better than my manual parsing...
> >> >>     One problem remains, though: the tabix files are being created
> from
> >> >>     within
> >> >>     R, and I don't think there is any support to add arbitrary header
> >> >>lines
> >> >>     available yet. Or is there?
> >> >>
> >> >>     Florian
> >> >>
> >> >>
> >> >>     Florian Hahne
> >> >>     Novartis Institute For Biomedical Research
> >> >>     Translational Sciences / Preclinical Safety / PCS Informatics
> >> >>     Expert Data Integration and Modeling Bioinformatics
> >> >>     CHBS, WKL-135.2.26
> >> >>     Novartis Institute For Biomedical Research, Werk Klybeck
> >> >>     Klybeckstrasse 141
> >> >>     CH-4057 Basel
> >> >>     Switzerland
> >> >>     Phone: +41 61 6967127 <tel:%2B41%2061%206967127>
> >> >>     <tel:%2B41%2061%206967127>
> >> >>     Email : florian.hahne@novartis.com
> >> >><mailto:florian.hahne@novartis.com>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>     On 4/12/12 2:08 PM, "Sean Davis" <sdavis2@mail.nih.gov
> >> >>     <mailto:sdavis2@mail.nih.gov>> wrote:
> >> >>
> >> >>     >On Thu, Apr 12, 2012 at 7:57 AM, Martin Morgan <
> mtmorgan@fhcrc.org
> >> >>     <mailto:mtmorgan@fhcrc.org>> wrote:
> >> >>     > > On 04/12/2012 01:19 AM, Hahne, Florian wrote:
> >> >>     > >>
> >> >>     > >> Hi all,
> >> >>     > >> I frequently get into the situation that I import data from
> a
> >> >>Tabix
> >> >>     > >>file
> >> >>     > >> using scanTabix and get a list of character vectors which I
> >> >>     first need
> >> >>     > >>to
> >> >>     > >> split back into columns using strsplit, followed by some
> type
> >> >>     coercion
> >> >>     > >>and
> >> >>     > >> lapply/sapply to actually get a list of data.frames which is
> >> >>     what I'd
> >> >>     > >> really want out in the first place. I may be missing
> something
> >> >>here,
> >> >>     > >>but
> >> >>     > >> wouldn't it be possible to ask scanTabix for a list of
> >> >>data.frames
> >> >>     > >> directly, and maybe even providing a vector of data types to
> >> >>coerce
> >> >>     > >>into,
> >> >>     > >> a la 'colClasses' in read.table? It just seems to me that
> these
> >> >>     > >>operations
> >> >>     > >> could be done much more efficiently on the C level.
> >> >>     > >
> >> >>     > >
> >> >>     > > It's definitely poorly developed but one doesn't really want
> to
> >> >>     > >re-invent
> >> >>     > > too much of the parsing wheel. Does
> >> >>     > >
> >> >>     > > res <- scanTabix("/foo.tbx")
> >> >>     > > read.table(textConnection(res), header=TRUE, sep="\t")
> >> >>     > >
> >> >>     > > do the trick in a reasonably performant way? Obviously less
> than
> >> >>     ideal,
> >> >>     > >with
> >> >>     > > the data represented as character vectors and then as
> >> >>data.frame. A
> >> >>     > >better
> >> >>     > > solution (colClasses ==> data.frame) wouldn't be impossible,
> but
> >> >>     > >guessing
> >> >>     > > column types would be a lot of redundant work.
> >> >>     >
> >> >>     >Since tabix allows arbitrary header lines, one could store
> >> >>metadata in
> >> >>     >the first few lines and use that to store column info and
> classes.
> >> >>     >One can get at the header using Rsamtools
> >> >>     >headerTabix(TabixFile('foo.tbx')). This is getting more toward
> >> >>     >developer-land than end-user, though, since the tabix file would
> >> >>need
> >> >>     >to be created with these uses in mind.
> >> >>     >
> >> >>     >Sean
> >> >>     >
> >> >>     >
> >> >>     > >> Thanks,
> >> >>     > >> Florian
> >> >>     > >>
> >> >>     > >>
> >> >>     > >> Florian Hahne
> >> >>     > >> Novartis Institute For Biomedical Research
> >> >>     > >> Translational Sciences / Preclinical Safety / PCS
> Informatics
> >> >>     > >> Expert Data Integration and Modeling Bioinformatics
> >> >>     > >> CHBS, WKL-135.2.26
> >> >>     > >> Novartis Institute For Biomedical Research, Werk Klybeck
> >> >>     > >> Klybeckstrasse 141
> >> >>     > >> CH-4057 Basel
> >> >>     > >> Switzerland
> >> >>     > >> Phone: +41 61 6967127 <tel:%2B41%2061%206967127>
> >> >>     <tel:%2B41%2061%206967127>
> >> >>     > >> Email : florian.hahne@novartis.com
> >> >>     <mailto:florian.hahne@novartis.com>
> >> >>     > >>
> >> >>     > >> _______________________________________________
> >> >>     > >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> >> >>     mailing list
> >> >>     > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>     > >
> >> >>     > >
> >> >>     > >
> >> >>     > > --
> >> >>     > > Computational Biology
> >> >>     > > Fred Hutchinson Cancer Research Center
> >> >>     > > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >> >>     > >
> >> >>     > > Location: M1-B861
> >> >>     > > Telephone: 206 667-2793 <tel:206%20667-2793>
> >> >><tel:206%20667-2793>
> >> >>     > >
> >> >>     > >
> >> >>     > > _______________________________________________
> >> >>     > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> >> >>     mailing list
> >> >>     > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>
> >> >>     _______________________________________________
> >> >>     Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> mailing
> >> >>list
> >> >>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >
> >> >
> >> >--
> >> >Computational Biology
> >> >Fred Hutchinson Cancer Research Center
> >> >1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >> >
> >> >Location: M1-B861
> >> >Telephone: 206 667-2793
> >>
> >>
> >
> >        [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>

	[[alternative HTML version deleted]]

