[Re-posting since messages send to ...@r-project.org bounced for a period of ~12-14h on Monday Nov 17]
Hi, I've experiences the exact same thing on both a Windows and a Linux installation. It actually took me a while to realize I didn't get Bioc devel updates, because I run those in the background. If it helps, here is my troubleshooting report: My best guess right now is that at some point in time (around Nov 5; see below), ***Bioconductor build BiocInstaller v1.16.1 on 3.1.2 and distributed under BioC devel***, i.e. when I installed under R devel (aka 3.2.0) I got: WINDOWS: > packageDescription("BiocInstaller") Package: BiocInstaller Title: Install/Update Bioconductor and CRAN Packages Description: Installs/updates Bioconductor and CRAN packages Version: 1.16.1 ... Packaged: 2014-11-05 04:01:38 UTC; biocbuild Built: R 3.1.2; ; 2014-11-05 06:56:09 UTC; windows -- File: C:/Users/hb/R/win-library/3.2/BiocInstaller/Meta/package.rds Note the **biocbuild** tag here on Windows, i.e. it wasn't me that built it on the wrong system by mistake. LINUX: > packageDescription("BiocInstaller") Package: BiocInstaller Title: Install/Update Bioconductor and CRAN Packages Description: Installs/updates Bioconductor and CRAN packages Version: 1.16.1 ... Packaged: 2014-11-05 02:46:39 UTC; biocbuild Built: R 3.2.0; ; 2014-11-17 06:11:17 UTC; unix -- File: /compbio/henrik/R/x86_64-unknown-linux-gnu-library/3.2/BiocInstaller/Meta/package.rds Note also the installation path, which is the default one used by R devel/3.2.0 on Windows (and similarly on Linux), so I haven't done anything there either. ( BTW, maybe it's possible to BiocInstaller to detect and warn/err on inconsistencies by comparing packageDescription("BiocInstaller")$Built and getRversion()?!? ) On top of this, source("http://bioconductor.org/biocLite.R") in a fresh session failed to detect that BiocInstaller needs/can be updated. Also, useDevel(TRUE) incorrectly says "'devel' version requires a more recent R" on R devel. More details below. SOLUTION: The solution is I found on both systems was (also) to uninstall BiocInstaller, i.e. > remove.packages("BiocInstaller") COMPLETE TROUBLESHOOTING: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - WINDOWS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - $ R --vanilla R Under development (unstable) (2014-10-30 r66907) -- "Unsuffered Consequences" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) [...] > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.2.0. Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.2 [Ctrl-C here] > useDevel(TRUE) Error: 'devel' version requires a more recent R > sessionInfo() R Under development (unstable) (2014-10-30 r66907) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.1 loaded via a namespace (and not attached): [1] tools_3.2.0 > packageDescription("BiocInstaller") Package: BiocInstaller Title: Install/Update Bioconductor and CRAN Packages Description: Installs/updates Bioconductor and CRAN packages Version: 1.16.1 Author: Dan Tenenbaum and Biocore Team Maintainer: Bioconductor Package Maintainer <maintai...@bioconductor.org> biocViews: Software Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: Artistic-2.0 Packaged: 2014-11-05 04:01:38 UTC; biocbuild Built: R 3.1.2; ; 2014-11-05 06:56:09 UTC; windows -- File: C:/Users/hb/R/win-library/3.2/BiocInstaller/Meta/package.rds > biocLite("BiocInstaller") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.2.0. Installing package(s) 'BiocInstaller' Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.2 Warning: package 'BiocInstaller' is in use and will not be installed Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.2 $ R --vanilla [...] > remove.packages("BiocInstaller") Removing package from 'C:/Users/hb/R/win-library/3.2' (as 'lib' is unspecified) > source("http://bioconductor.org/biocLite.R") Installing package into 'C:/Users/hb/R/win-library/3.2' (as 'lib' is unspecified) trying URL 'http://www.bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/BiocInstaller_1.17.1.zip' Content type 'application/zip' length 53397 bytes (52 KB) opened URL downloaded 52 KB The downloaded binary packages are in C:\Users\hb\AppData\Local\Temp\Rtmpmgpkf0\downloaded_packages Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R version 3.2.0. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - LINUX - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - $ R --vanilla R Under development (unstable) (2014-11-14 r66984) -- "Unsuffered Consequences" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) [...] > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.2.0. ^C > useDevel() Error: 'devel' version requires a more recent R > packageDescription("BiocInstaller") Package: BiocInstaller Title: Install/Update Bioconductor and CRAN Packages Description: Installs/updates Bioconductor and CRAN packages Version: 1.16.1 Author: Dan Tenenbaum and Biocore Team Maintainer: Bioconductor Package Maintainer <maintai...@bioconductor.org> biocViews: Software Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: Artistic-2.0 Packaged: 2014-11-05 02:46:39 UTC; biocbuild Built: R 3.2.0; ; 2014-11-17 06:11:17 UTC; unix -- File: /compbio/henrik/R/x86_64-unknown-linux-gnu-library/3.2/BiocInstaller/Meta/package.rds > sessionInfo() R Under development (unstable) (2014-11-14 r66984) Platform: x86_64-unknown-linux-gnu (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=en_US.UTF-8 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] BiocInstaller_1.16.1 loaded via a namespace (and not attached): [1] tools_3.2.0 Uninstalling the BiocInstaller package and running source("http://bioconductor.org/biocLite.R") solved it the same as as it did on Windows. /Henrik On Mon, Nov 10, 2014 at 11:56 PM, Hahne, Florian <florian.ha...@novartis.com> wrote: > 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" <dtene...@fredhutch.org> wrote: > >>Taking a closer look at your email... >> >>> ----- Original Message ----- >>> > From: "Florian Hahne" <florian.ha...@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" <hpa...@fredhutch.org> wrote: >>> > >>> > >Hi, >>> > > >>> > >On 11/02/2014 10:58 PM, Dan Tenenbaum wrote: >>> > >> >>> > >> >>> > >> ----- Original Message ----- >>> > >>> From: "Leonardo Collado Torres" <lcoll...@jhu.edu> >>> > >>> To: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com> >>> > >>> Cc: bioc-devel@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 >>> > >>> <kasperdanielhan...@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 >>> > >>>> <lcoll...@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@r-project.org mailing list >>> > >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> > >>>> >>> > >>>> >>> > >>> >>> > >>> _______________________________________________ >>> > >>> Bioc-devel@r-project.org mailing list >>> > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> > >>> >>> > >> >>> > >> _______________________________________________ >>> > >> Bioc-devel@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: hpa...@fredhutch.org >>> > >Phone: (206) 667-5791 >>> > >Fax: (206) 667-1319 >>> > > >>> > >_______________________________________________ >>> > >Bioc-devel@r-project.org mailing list >>> > >https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> > >>> > >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel