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
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
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/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@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
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