[BioC] Bioconductor does not install properly

[Benilton Carvalho]

I wonder what mirror Bas is using (the Norway one doesn't seem to be
working as expected)... maybe chooseBioCmirror() could be useful?

b

On 24 November 2011 11:16, Vincent Carey <stvjc at channing.harvard.edu> wrote:
> 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 at 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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>>
>
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