[BioC] Bioconductor does not install properly

[Bas Jansen]

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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>        [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
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>>
>