[Bioc-devel] R v3.0.0: It's now official and BioC devel needs some updates

[Henrik Bengtsson]

On Sun, Dec 16, 2012 at 10:42 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Sun, Dec 16, 2012 at 1:16 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
>> >From http://stat.ethz.ch/R-manual/R-devel/NEWS:
>>
>>   "It is intended that this version will be released as R 3.0.0."
>>
>>
>> They've already changed the R-devel version number from 2.16.0 to
>> 3.0.0, which causes biocLite() et al. to fail, e.g.
>>
>>> source("http://www.bioconductor.org/biocLite.R")
>> Installing package into 'C:/Users/hb/R/win-library/3.0'
>> (as 'lib' is unspecified)
>> Warning: unable to access index for repository http://www.bioconductor.org/packa
>> ges/2.12/bioc/bin/windows/contrib/3.0
>>
>>    package 'BiocInstaller' is available as a source package but not as a binary
>>
>> 'biocLite.R' failed to install 'BiocInstaller', use
>>   'install.packages("BiocInstaller",
>>   repos="http://www.bioconductor.org/packages/2.12/bioc")'
>> Warning message:
>> package 'BiocInstaller' is not available (for R Under development)
>>
>
> This now works.
>
> Note that we have not yet updated our devel build machines to R-3.0.0,
> so there may be binary incompatibilities in Windows and Mac packages.
> If in doubt, install from source.

That was quick - I've confirmed that it works with one package.

Thanks.

Henrik

>
> Dan
>
>
>> /Henrik
>>
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