I cannot reproduce this; biocLite("affy") succeeded with the following

> sessionInfo()
R version 2.14.0 Under development (unstable) (2011-06-06 r56067)
Platform: x86_64-apple-darwin10.7.0/x86_64 (64-bit)

locale:
[1]
en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII

attached base packages:
[1] stats     graphics  grDevices datasets  utils     tools     methods
[8] base

other attached packages:
[1] BiocInstaller_1.2.1 weaver_1.19.0       codetools_0.2-8
[4] digest_0.5.1

it also worked from Rgui for 2.14.  I think you have a transient issue or
you will have to supply more details.

On Thu, Nov 24, 2011 at 5:47 AM, Bas Jansen <bjhjansen@gmail.com> wrote:

> Dear fellow Bioconductor users:
>
> This is the message I get when I try to install Bioconductor as
> instructed on the website:
>
> "Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>  packages ‘affy’, ‘affydata’, ‘affyPLM’, ‘affyQCReport’, ‘annaffy’,
> ‘annotate’, ‘Biobase’, ‘biomaRt’, ‘Biostrings’, ‘DynDoc’, ‘gcrma’,
> ‘genefilter’, ‘geneplotter’, ‘GenomicRanges’, ‘hgu95av2.db’, ‘limma’,
> ‘marray’, ‘multtest’, ‘vsn’ are not available (for R version 2.14.0)"
>
> Am I overlooking something?
>
> Thanks for any help, and kind regards,
> Bas
>
>
> > sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.14.0
>
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