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

Dan Tenenbaum dtenenba at fredhutch.org
Wed Nov 5 17:53:57 CET 2014 


----- Original Message -----
> From: "Florian Hahne" <florian.hahne at novartis.com>
> To: "Hervé Pagès" <hpages at fredhutch.org>, "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Leonardo Collado Torres"
> <lcollado at jhu.edu>
> Cc: bioc-devel at r-project.org
> Sent: Wednesday, November 5, 2014 12:48:23 AM
> Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
> 
> I think there is indeed something more fundamentally broken here:
> > R.version
>                _
> platform       x86_64-apple-darwin13.4.0
> arch           x86_64
> os             darwin13.4.0
> system         x86_64, darwin13.4.0
> status         Under development (unstable)
> major          3
> minor          2.0
> year           2014
> month          10
> day            29
> svn rev        66895
> language       R
> version.string R Under development (unstable) (2014-10-29 r66895)
> nickname       Unsuffered Consequences
> 
> 
> > useDevel(TRUE)
> Error: 'devel' version already in use
> 
> 

The only problem is that you should not have seen this message, you should instead see a message saying you need a newer version of R to run the devel version of bioconductor. This has been fixed in the release version of BiocInstaller (1.16.1), available later today.


> But:
> 
> > biocinstallRepos()
>                                               BioCsoft
>            "http://bioconductor.org/packages/3.0/bioc"
>                                                BioCann
> "http://bioconductor.org/packages/3.0/data/annotation"
>                                                BioCexp
> "http://bioconductor.org/packages/3.0/data/experiment"
>                                              BioCextra
>           "http://bioconductor.org/packages/3.0/extra"
>                                                   CRAN
>                                "http://cran.fhcrc.org"
> 
> 
> So I am running R-devel, R thinks that I should already be using the
> BiocDevel branch, but the repository is still pointing to
> Bioconductor 3.0
> After taking a closer look at useDevel() I did this:
> 
> assignInNamespace(ns="BiocInstaller", x="IS_USER", value=TRUE)
> assignInNamespace(ns="BiocInstaller", x="IS_UPGRADEABLE", value=TRUE)
> 
> 
> 
> And behold:
> > useDevel(TRUE)
> Installing package into
> Œ/Users/hahnefl1/software/R/source/R-3-2-0/localPackages¹
> (as Œlib¹ is unspecified)
> trying URL
> 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.17.1
> .tar.gz'
> Content type 'application/x-gzip' length 14271 bytes (13 KB)
> opened URL
> ==================================================
> downloaded 13 KB
> 
> * installing *source* package ŒBiocInstaller¹ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help
> * DONE (BiocInstaller)
> 
> The downloaded source packages are in
> 	Œ/private/tmp/Rtmp44wF3Y/downloaded_packages¹
> Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help
> 'BiocInstaller' changed to version 1.17.1
> 
> 
> I couldn't tell how I got my R installation into this seemingly
> locked
> state, but maybe there should be a force=TRUE option to useDevel for
> cases
> like this.
> Florian
> 
> 


This is NOT what you want. You now have Bioc 3.1 on R 3.1, but Bioc 3.1 is intended to run with R-devel (3.2) only.
Dan




> 
> 
> 
> On 04/11/14 20:04, "Hervé Pagès" <hpages at fredhutch.org> wrote:
> 
> >Hi,
> >
> >On 11/02/2014 10:58 PM, Dan Tenenbaum wrote:
> >>
> >>
> >> ----- 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;
> >
> >Agreed. But the error message issued by useDevel() in the current
> >release adds to the confusion:
> >
> >   > library(BiocInstaller)
> >   Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for
> >   help
> >   > useDevel()
> >   Error: 'devel' version already in use
> >
> >What about something like:
> >
> >   Error: you need R 3.2 to run BioC 'devel' version
> >
> >Thanks,
> >H.
> >
> >> 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/Geno
> >>>>>meInfoDb_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/downloade
> >>>>>d_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
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >--
> >Hervé Pagès
> >
> >Program in Computational Biology
> >Division of Public Health Sciences
> >Fred Hutchinson Cancer Research Center
> >1100 Fairview Ave. N, M1-B514
> >P.O. Box 19024
> >Seattle, WA 98109-1024
> >
> >E-mail: hpages at fredhutch.org
> >Phone:  (206) 667-5791
> >Fax:    (206) 667-1319
> >
> >_______________________________________________
> >Bioc-devel at r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
>

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