R.oo (as in kangaRoo) is on CRAN and as Sean explains it will install if you install BioC package 'aroma.light' via biocLite("aroma.light"). FYI, It is correct that R.oo is/was part of the R.classes bundle, but the latter is obsolete since many years. /Henrik On Wed, Oct 8, 2008 at 4:17 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Wed, Oct 8, 2008 at 6:56 AM, Tillinghast, Guy, M.D. > <guy.tillinghast at="" rivhs.com=""> wrote: >> >> I am having problem installing the package: R.classes >> Which contains package R.oo >> which is needed to run function robustPca >> >> How can I download package R.classes? >> It is supposed to be "100%R" >> >> I have R version 2.7.2 >> >> >> >> >> History: >> I followed the instructions/vignette for using pcaMethods package >> when I attempted the robustPCA function, as in >> >> resRobSvd<-pca(mdcOut,method = "robustPca", nPcs = 5, center = FALSE) >> >> I received an error message requesting loading of aroma.light package. >> >> I loaded this package >> >> Then I received an error message requesting loading of R.oo package. >> R.oo package not on the Bioconductor site. >> I searched Google and found R.oo package part of R.classes package, and >> is "100%R" >> I searched the Bioconductor site and could not find package R.classes >> I Googled R.classes and first entry instructed me to use function >> install.package() >> install.packages("R.classes",contriburl="http://www.maths.lth.se/he lp/R/ >> R.classes/") >> got error message: subscript out of bounds > > It is best to use biocLite when installing packages from Bioconductor > AND R since Bioconductor is designed to work with a specific version > of R. Had you done so, when you installed pcaMethods, all the > dependencies would have been installed simultaneously. So, go back > and use biocLite to reinstall pcaMethods and everything will come with > it except aroma.light which is only suggested and not required for > pcaMethods. Then use biocLite to install aroma.light. That should do > it. > > The take-home message is to ALWAYS use biocLite (when possible, which > is basically ALWAYS). > > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >