Entering edit mode
Bas Jansen
▴
150
@bas-jansen-2966
Last seen 10.3 years ago
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/xt
able_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]]
>>>
>>>
>>> _______________________________________________
>>> 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
>>>
>>
>