[R] Need Help with robustbase package: fitnorm2 and plotnorm2

[Prof Brian Ripley]

On Fri, 8 Jun 2007, M. Jankowski wrote:

> This is my first post requesting help to this mailing list. I am new
> to R. My apologies for any breach in posting etiquette.

For future reference, telling us your version of R and exact OS would have 
helped here.  The R posting guide suggests showing the output of 
sessionInfo().

Also, to help the readers, fitNorm2 (R is case-sensitive) is in 'prada', 
and the missing package is rrcov not robustbase.

> I am new to
> this language and just learning my way around. I am attempting to run
> some sample code and  and am confused by the error message:
> Loading required package: rrcov
> Error in fitNorm2(fdat[, "FSC-H"], fdat[, "SSC-H"], scalefac = ScaleFactor) :
>        Required package rrcov could not be found.
> In addition: Warning message:
> there is no package called 'rrcov' in: library(package, lib.loc =
> lib.loc, character.only = TRUE, logical = TRUE,
>
> that I get when I attempt to run the following sample snippet of code.
> The error above is taken from the code below. I am running Ubuntu
> Linux with all the r packages listed in the Synaptic package manager
> (universa). I loaded the "prada" bioconductor package as instructed in
> the comments and the robustbase was downloaded and installed with the
> command: "sudo R CMD INSTALL robustbase_0.2- 7.tar.gz", the robustbase
> folder is in "/usr/local/lib/R/site-library/" When I type in
> 'library(robustbase)' no error appears; I believe robustbase is
> installed correctly. The sample code was taken from FCS-prada.pdf. The
> sample code was written in 2005, I understand that rrcov was made part
> of the robustbase package sometime in the past year. This may be the
> cause of the problem, but, if it is, I have no idea how to fix it.

That is not the case: rrcov is a separate package, and one prada depends 
on.  So somehow you have managed to install prada without an essential 
dependency 'rrcov'.  That looks like a problem in the Debian/Ubuntu 
packaging of prada.  (There is a list R-sig-debian for such issues.)

Running install.packages("rrcov") inside R should fix this for you: if 
your R is not current (i.e. < 2.5.0) you may need to run R as root for 
that session.  (There may be a Debian package for rrcov for your OS and R 
version, but without further details I cannot check.)

In the current version of prada (1.12.0 for BioC-2.0 for R 2.5.0) rrcov is 
in Imports, so probably your version of BioC is not current either.

[...]

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595