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

[Hervé Pagès]

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/GenomeInfoDb_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/downloaded_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
>>>
>>>
>>
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>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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