[BioC] [devteam-bioc] Failure to update to Bioconductor 2.12 from bioconductor 2.11

[Dan Tenenbaum]

On Mon, Aug 5, 2013 at 1:50 AM, Maintainer <maintainer at bioconductor.org> wrote:
>
> Bioconductor does not update itself form 2.11 to 2.12 although I am using the latest R version of 3.0.1.
> Please help...
> Thanks in advance.
> D.
>
>
>  -- output of sessionInfo():
>
>> source("http://bioconductor.org/biocLite.R")
> Your Bioconductor is out-of-date, upgrade to version 2.12 by following instructions at
> http://bioconductor.org/install.
> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
>> biocLite()
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
> Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi'
> Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15
> trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/Biobase_2.18.0.zip'
> Content type 'application/zip' length 2346708 bytes (2.2 Mb)
> opened URL
> downloaded 2.2 Mb
>
> trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/IRanges_1.16.6.zip'
> Content type 'application/zip' length 2048190 bytes (2.0 Mb)
> opened URL
> downloaded 2.0 Mb
>
> trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/AnnotationDbi_1.20.7.zip'
> Content type 'application/zip' length 4200978 bytes (4.0 Mb)
> opened URL
> downloaded 4.0 Mb
>
> package ‘Biobase’ successfully unpacked and MD5 sums checked
> package ‘IRanges’ successfully unpacked and MD5 sums checked
> package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked
>


This output suggests you are using R 2.15. Maybe you have more than
one version of R on your machine?

At any rate, if you start R 3.0.1, biocLite() will automatically
install the appropriate (BioC 2.12) packages.

Dan


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