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

[Henrik Bengtsson]

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the latter is obsolete since many years.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/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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