Bioconductor does not install properly
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Bas Jansen ▴ 150
@bas-jansen-2966
Last seen 8.2 years ago
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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@vincent-j-carey-jr-4
Last seen 13 days ago
United States
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@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@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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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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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/le opard/contrib/2.14 Warning: unable to access index for repository http://mirrors.ebi.ac.uk/bioconductor//packages/2.8/data/annotation/bi n/macosx/leopard/contrib/2.14 Warning: unable to access index for repository http://mirrors.ebi.ac.uk/bioconductor//packages/2.8/data/experiment/bi n/macosx/leopard/contrib/2.14 Warning: unable to access index for repository http://mirrors.ebi.ac.uk/bioconductor//packages/2.8/extra/bin/macosx/l eopard/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/xtab le_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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