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

[Leonardo Collado Torres]

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/.

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
>
>