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Question: package R.oo (or R.00?), within package R.classes, and function robustPca
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gravatar for Tillinghast, Guy, M.D.
10.4 years ago by
Tillinghast, Guy, M.D.30 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/help/ R/ R.classes/") got error message: subscript out of bounds CONFIDENTIALITY NOTICE: This e-mail message, including a...{{dropped:9}}
aroma.light pcamethods • 537 views
ADD COMMENTlink modified 10.4 years ago by Sean Davis21k • written 10.4 years ago by Tillinghast, Guy, M.D.30
Answer: package R.oo (or R.00?), within package R.classes, and function robustPca
0
gravatar for Sean Davis
10.4 years ago by
Sean Davis21k
United States
Sean Davis21k 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/hel p/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
ADD COMMENTlink written 10.4 years ago by Sean Davis21k
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 >
ADD REPLYlink written 10.4 years ago by Henrik Bengtsson2.4k
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