[BioC] Fwd: Bioconductor does not install properly

[Dan Tenenbaum]

Forgot to CC the list...

---------- Forwarded message ----------
From: Dan Tenenbaum <dtenenba at fhcrc.org>
Date: Thu, Nov 24, 2011 at 11:04 AM
Subject: Re: [BioC] Bioconductor does not install properly
To: Bas Jansen <bjhjansen at gmail.com>


On Thu, Nov 24, 2011 at 7:17 AM, 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>
>


First, try launching R with
R --vanilla
and try then to install the package.
If that works, it probably means you have an object called biocLite in
your saved workspace. do
rm(biocLite) to get rid of it. Then exit R, re-saving your workspace.
Then it should work.
Dan


> 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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>>>
>>
>
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