[BioC] package R.oo (or R.00?), within package R.classes, and function robustPca

Henrik Bengtsson hb at stat.berkeley.edu
Wed Oct 8 15:59:54 CEST 2008

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the latter is obsolete since many years.


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/help/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
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