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

Henrik Bengtsson hb at biostat.ucsf.edu
Wed Nov 19 03:09:54 CET 2014


[Re-posting since messages send to ... at 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
        <maintainer at 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
        <maintainer at 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.hahne at 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" <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
>>>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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