[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Dan Tenenbaum
dtenenba at fredhutch.org
Wed Nov 5 18:02:43 CET 2014
Taking a closer look at your email...
> ----- Original Message -----
> > From: "Florian Hahne" <florian.hahne at novartis.com>
>
> > 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
> >
Sorry, didn't notice you were already running R-devel.
> >
> > > useDevel(TRUE)
> > Error: 'devel' version already in use
> >
> >
What version of BiocInstaller were you running at this point>
>
> 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
> >
> >
>
I think you somehow had the release version of BiocInstaller installed in R-devel.
But it's difficult to know now....
Dan
>
> 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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