[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Hahne, Florian
florian.hahne at novartis.com
Tue Nov 11 08:56:44 CET 2014
That might well be. I can't recall doing anything special, but I'll try to
uninstall BiocInstaller the next time I run into a similar issue to test
this.
Florian
On 05/11/14 18:02, "Dan Tenenbaum" <dtenenba at fredhutch.org> wrote:
>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/Ge
>>>>>>>no
>> > >>>>>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/downloa
>>>>>>>de
>> > >>>>>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
>> >
>> >
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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