R help - Jun 2007 - Need Help with robustbase package: fitnorm2 and plotnorm2

This is my first post requesting help to this mailing list. I am new
to R. My apologies for any breach in posting etiquette. 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.
Thank you in advance for helping out!

Below you will find the code that generates the error and the complete
output of the code. Let me know what I can do to get up and running!

Matt


#prada Bioconductor package
#http://www.bioconductor.org/repository/devel/vignette/norm2.pdf
# To install "prada"
#source("http://www.bioconductor.org/biocLite.R")
#biocLite("prada")

library(prada)
filepath <- system.file("extdata",
"fas-Bcl2-plate323-04-04.A01", package = "pra
da")
print(filepath)
sampdat <- readFCS(filepath)
fdat <- exprs(sampdat)
print(dim(fdat))
print(colnames(fdat))

plot(fdat[, "FSC-H"], fdat[, "SSC-H"], pch = 20, col =
"#303030", xlab = "FSC",
ylab = "SSC",  main = "Scatter plot FSC vs SSC")
#All of this goes as the help documentation suggests it should

# 2. Show selections for various scale factors
savepar <- par(mfrow=c(2,2))

for (Scalefactor in c(1.0, 1.5, 2.0, 2.5) )
  {
    # The next line gives the error I've included below.
    nfit <- fitNorm2 (fdat[, "FSC-H"], fdat[, "SSC-H"],
scalefac = ScaleFactor)
    plotnorm2(nfit, selection = TRUE, ellipse = TRUE,
              xlab="FSC-H", ylab="SSC-H",
              main=paste("SSC-H vs. FSC-H
(ScaleFactor=",ScaleFactor,")", sep=""
))
  }
par(savepar)



Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: RColorBrewer
Loading required package: grid
Loading required package: geneplotter
Loading required package: annotate
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
[1]
"/usr/local/lib/R/site-library/prada/extdata/fas-Bcl2-plate323-04-04.A01"
[1] 2115    8
   $P1N    $P2N    $P3N    $P4N    $P5N    $P6N    $P7N    $P8N
"FSC-H" "SSC-H" "FL1-H" "FL2-H"
"FL3-H" "FL2-A" "FL4-H"  "Time"
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,
>

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