Hi, I am following the Bioconductor Case studies. I got: Error: getAnnMap: package hgu95av2 not available After appling the code: filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, require.GOBP=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.cutoff=varCut, feature.exclude="^AFFX") Did I miss anything? How can I get the hgu95av2? thanks, elva -- output of sessionInfo(): > varCut=0.5 > filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, + require.GOBP=TRUE, remove.dupEntrez=TRUE, + var.func=IQR, var.cutoff=varCut, + feature.exclude="^AFFX") Error: getAnnMap: package hgu95av2 not available > help(package="hgu95av2") starting httpd help server ... done > help(package="hgu95av2") > source("http://bioconductor.org/biocLite.R") > biocLite("hgu95av2.db") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'hgu95av2.db' also installing the dependency ???org.Hs.eg.db??? trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bin/ windows/contrib/2.15/org.Hs.eg.db_2.8.0.zip' Content type 'application/zip' length 47453600 bytes (45.3 Mb) opened URL downloaded 45.3 Mb trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bin/ windows/contrib/2.15/hgu95av2.db_2.8.0.zip' Content type 'application/zip' length 552365 bytes (539 Kb) opened URL downloaded 539 Kb package ???org.Hs.eg.db??? successfully unpacked and MD5 sums checked Warning: unable to move temporary installation ???C:\Users\yahuac\Documents\R\win- library\2.15\file1a387065468\org.Hs.eg.db??? to ???C:\Users\yahuac\Documents\R\win-library\2.15\org.Hs.eg.db??? package ???hgu95av2.db??? successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\yahuac\AppData\Local\Temp\RtmpK8N0Jl\downloaded_packages Warning message: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' > filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, + require.GOBP=TRUE, remove.dupEntrez=TRUE, + var.func=IQR, var.cutoff=varCut, + feature.exclude="^AFFX") Error: getAnnMap: package hgu95av2 not available -- Sent via the guest posting facility at bioconductor.org.

On 01/27/2013 10:38 PM, elva chen [guest] wrote: > > Hi, > I am following the Bioconductor Case studies. I got: > Error: getAnnMap: package hgu95av2 not available > > After appling the code: > filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, > require.GOBP=TRUE, remove.dupEntrez=TRUE, > var.func=IQR, var.cutoff=varCut, > feature.exclude="^AFFX") > > Did I miss anything? How can I get the hgu95av2? > > thanks, > elva > > -- output of sessionInfo(): > >> varCut=0.5 >> filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, > + require.GOBP=TRUE, remove.dupEntrez=TRUE, > + var.func=IQR, var.cutoff=varCut, > + feature.exclude="^AFFX") > Error: getAnnMap: package hgu95av2 not available >> help(package="hgu95av2") > starting httpd help server ... done >> help(package="hgu95av2") >> source("http://bioconductor.org/biocLite.R") >> biocLite("hgu95av2.db") yes, installing the package is what is required... > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'hgu95av2.db' > also installing the dependency ???org.Hs.eg.db??? > > trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bi n/windows/contrib/2.15/org.Hs.eg.db_2.8.0.zip' > Content type 'application/zip' length 47453600 bytes (45.3 Mb) > opened URL > downloaded 45.3 Mb > > trying URL 'http://bioconductor.org/packages/2.11/data/annotation/bi n/windows/contrib/2.15/hgu95av2.db_2.8.0.zip' > Content type 'application/zip' length 552365 bytes (539 Kb) > opened URL > downloaded 539 Kb > > package ???org.Hs.eg.db??? successfully unpacked and MD5 sums checked > Warning: unable to move temporary installation ???C:\Users\yahuac\Documents\R\win- library\2.15\file1a387065468\org.Hs.eg.db??? to ???C:\Users\yahuac\Documents\R\win-library\2.15\org.Hs.eg.db??? ...but something is wrong with your R installation here, and package installation is failing. This directory C:\Users\yahuac\Documents\R\win-library\2.15\org.Hs.eg.db needs to be write-able, but appears not to be. My best guess would be that your disk is full. Martin > package ???hgu95av2.db??? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\yahuac\AppData\Local\Temp\RtmpK8N0Jl\downloaded_packages > Warning message: > installed directory not writable, cannot update packages 'foreign', 'lattice', > 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' >> filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE, > + require.GOBP=TRUE, remove.dupEntrez=TRUE, > + var.func=IQR, var.cutoff=varCut, > + feature.exclude="^AFFX") > Error: getAnnMap: package hgu95av2 not available > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793