Forgot to CC the list... ---------- Forwarded message ---------- From: Dan Tenenbaum <dtenenba@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/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> > 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 >>>> >>>> _______________________________________________ >>>> 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 >>> >> > > _______________________________________________ > 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 >