SOLVED Re: Bioconductor does not install properly
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Bas Jansen ▴ 150
@bas-jansen-2966
Last seen 8.2 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 >>> >> >
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