[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1

Dan Tenenbaum dtenenba at fredhutch.org
Mon Nov 3 07:58:23 CET 2014



----- Original Message -----
> From: "Leonardo Collado Torres" <lcollado at jhu.edu>
> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> Cc: bioc-devel at r-project.org
> Sent: Sunday, November 2, 2014 9:26:25 PM
> Subject: Re: [Bioc-devel] Can't seem to use useDevel();	biocLite() for BioC 3.1
> 
> Thanks, I incorrectly thought that I was using the same R version as
> the Bioc-build machines since the "r66923" part matched. Now I
> realize
> that this tag is used in all of the newest R builds at
> http://r.research.att.com/.
> 

It's admittedly confusing; the question of whether to use R-devel with Bioc-devel has a different answer every six months, but the answer can always be found here:

http://www.bioconductor.org/developers/how-to/useDevel/

Also, when looking at the devel build report, you should probably focus more on the version portion of the "R version" column than on the SVN revision number. 

Dan


> On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen
> <kasperdanielhansen at gmail.com> wrote:
> > You should not be using R-3.1.2 patched with the current devel
> > version of
> > Bioconductor; use R-devel.
> >
> > Best,
> > Kasper
> >
> > On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres
> > <lcollado at jhu.edu>
> > wrote:
> >>
> >> Hi,
> >>
> >> I can't seem to install devel packages via biocLite() and I wonder
> >> if
> >> something is broken or if I'm missing something. For example, take
> >> GenomeInfoDb which is at 1.3.6 and is passing all checks.
> >>
> >> The usual code using a fresh R 3.1.2-patched install isn't working
> >> as
> >> it downloads the latest release version (1.2.2):
> >>
> >> > source("http://bioconductor.org/biocLite.R")
> >> Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for
> >> help
> >> ## Was expecting 3.1 here
> >> > useDevel()
> >> Error: 'devel' version already in use
> >> > biocLite('GenomeInfoDb')
> >> BioC_mirror: http://bioconductor.org
> >> Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version
> >> 3.1.2.
> >> Installing package(s) 'GenomeInfoDb'
> >> trying URL
> >> 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz'
> >> Content type 'application/x-gzip' length 404120 bytes (394 KB)
> >> opened URL
> >> ==================================================
> >> downloaded 394 KB
> >>
> >>
> >> The downloaded binary packages are in
> >>
> >> /var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//Rtmpxp29xo/downloaded_packages
> >> >
> >> > sessionInfo()
> >> R version 3.1.2 Patched (2014-11-01 r66923)
> >> ## Note that it matches the current R version used by the
> >> Bioc-devel
> >> build machines
> >> 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] stats     graphics  grDevices utils     datasets  methods
> >>   base
> >>
> >> other attached packages:
> >> [1] BiocInstaller_1.16.0 colorout_1.0-2
> >>
> >> loaded via a namespace (and not attached):
> >> [1] tools_3.1.2
> >>
> >>
> >>
> >> For my computer it's not problem because I can download the pkg
> >> via
> >> svn and install locally. But it breaks my tests in TravisCI which
> >> relies on biocLite().
> >>
> >> Cheers,
> >> Leo
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> 
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