This is my first post to the mailing list. I thank you all for your advice
in advance and apologize for any ineptitude.

I am attempting to use the prada package. I found a file called "
FCS-prada.doc" that demonstrates many of the functions I wish to use. I am
experiencing some trouble (maybe in the installation of prada or maybe at
some other point) and seek advice. The complete R output for Prada
installation and my attempt to run the code are at the end of this message.
I will attempt to summarize:

#I start R in the superuser mode of ubuntu.
sudo R
##I follow the instructions in "FCS-prada.doc"
# To install "prada"
source("http://www.bioconductor.org/biocLite.R")
biocLite("prada")
## I get this warning:
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
         argument 'lib' is missing: using /usr/local/lib/R/site-library
# efg, 6 Oct 2005
# based on examples in prada documentation
library(prada)
filepath <- system.file("extdata", "fas Bcl2 plate323 -04-04.A01", package =
"prada")
filepath
sampdat <- readFCS(filepath)
##I get this error
Error: filename != "" is not TRUE

I think my problem is that prada is not installed in the correct folder. Is
this the case? If so what can I do to get the installation right. If not
this then what? I appreciate any guidance!

Thank you,
Matt

##Full Record of Installation/Run Attempt
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("prada")
Running biocinstall version 1.9.9 with R version 2.4.1
Your version of R requires version 1.9 of Bioconductor.
Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
         argument 'lib' is missing: using /usr/local/lib/R/site-library
trying URL '
http://bioconductor.org/packages/1.9/bioc/src/contrib/prada_1.10.1.tar.gz'
Content type 'application/x-gzip' length 692198 bytes
opened URL
==================================================
downloaded 675Kb

* Installing *source* package 'prada' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include      -fpic  -g
-O2 -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -shared  -o prada.so inPolygon.o   -L/usr/lib/R/lib -lR
** R
** data
** inst
** save image
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
Creating a new generic function for "names" in "prada"
Creating a new generic function for "names<-" in "prada"
** preparing package for lazy loading
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
** help
 >>> Building/Updating help pages for package 'prada'
     Formats: text html latex example
  analysePlate                      text    html    latex   example
  as.all                            text    html    latex   example
  barploterrbar                     text    html    latex   example
  combineFrames                     text    html    latex   example
  csApply                           text    html    latex   example
  cytoFrame-class                   text    html    latex   example
  cytoSet-class                     text    html    latex   example
  data-cytoFrame                    text    html    latex   example
  data-cytoSet                      text    html    latex   example
  ddCt                              text    html    latex   example
  ddCtSet-class                     text    html    latex
  devDims                           text    html    latex   example
  devRes                            text    html    latex   example
  eListWrite                        text    html    latex   example
  fitNorm2                          text    html    latex   example
  gate-class                        text    html    latex   example
  gateSet-class                     text    html    latex   example
  getPradaPar                       text    html    latex   example
  new-internal                      text    html    latex
  plotNorm2                         text    html    latex   example
  plotPlate                         text    html    latex   example
  readCytoSet                       text    html    latex   example
  readFCS                           text    html    latex   example
  readFCSaux                        text    html    latex   example
  readSDM                           text    html    latex   example
  removeCensored                    text    html    latex   example
  tcltkProgress                     text    html    latex   example
  threePanelPlot                    text    html    latex   example
  thresholds                        text    html    latex   example
  touchFCS                          text    html    latex
  vpLocation                        text    html    latex   example
** building package indices ...
Loading required package: methods
* DONE (prada)

The downloaded packages are in
        /tmp/RtmpmwjKyg/downloaded_packages
> library(prada)
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
> filepath <- system.file("extdata", "fas Bcl2 plate323 -04-04.A01", package
=
+ "prada")
> filepath
[1] ""
> sampdat <- readFCS(filepath)
Error: filename != "" is not TRUE
>

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