[BioC] SOLVED Re: Bioconductor does not install properly

[Bas Jansen]

Gentlemen!

Using setRepositories() helped me out... I think! I'm downloading
Bioconductor 2.9 as we speak. Thanks for the help.

Kind regards,
Bas

On Thu, Nov 24, 2011 at 4:17 PM, Bas Jansen <bjhjansen at gmail.com> wrote:
> Hi Benilton, hello Vincent:
>
> I have selected Seattle as mirror! It seems that it is looking for
> Bioconductor 2.8? Some more info:
>
> <Pasted/>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite()
> Using R version 2.14.0, biocinstall version 2.8.4.
> Installing Bioconductor version 2.8 packages:
>  [1] "affy"          "affydata"      "affyPLM"       "affyQCReport"
>  [5] "annaffy"       "annotate"      "Biobase"       "biomaRt"
>  [9] "Biostrings"    "DynDoc"        "gcrma"         "genefilter"
> [13] "geneplotter"   "GenomicRanges" "hgu95av2.db"   "limma"
> [17] "marray"        "multtest"      "vsn"           "xtable"
> Please wait...
>
> Warning: unable to access index for repository
> http://mirrors.ebi.ac.uk/bioconductor//packages/2.8/bioc/bin/macosx/leopard/contrib/2.14
> Warning: unable to access index for repository
> http://mirrors.ebi.ac.uk/bioconductor//packages/2.8/data/annotation/bin/macosx/leopard/contrib/2.14
> Warning: unable to access index for repository
> http://mirrors.ebi.ac.uk/bioconductor//packages/2.8/data/experiment/bin/macosx/leopard/contrib/2.14
> Warning: unable to access index for repository
> http://mirrors.ebi.ac.uk/bioconductor//packages/2.8/extra/bin/macosx/leopard/contrib/2.14
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.14
> trying URL 'http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.14/xtable_1.6-0.tgz'
> Content type 'application/x-gzip' length 267718 bytes (261 Kb)
> opened URL
> ==================================================
> downloaded 261 Kb
>
>
> The downloaded packages are in
>        /var/folders/Sd/Sdtm6g8uHuar8DmdWFrfJk+++TI/-Tmp-//RtmpFaDwXx/downloaded_packages
> 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)
> </Pasted>
>
> Thanks for your help!
>
> Kind regards,
> Bas
>
> On Thu, Nov 24, 2011 at 3:29 PM, Benilton Carvalho
> <beniltoncarvalho at gmail.com> wrote:
>> 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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>>>> Search the archives:
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>>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>>
>>> _______________________________________________
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>>>
>>
>