[R-SIG-Mac] R does not start on my MacBook Pro3,1

[Osee Sanogo]

Hello,

I am a beginner in R and I am having the error message:

> maqc <- read.xysfiles(xys.files)
Error in geometry(get(pkgname)) :
  no slot of name "geometry" for this object of class "platformDesign"

Could someone tell me what this means and how to correct it?

Here is my session history with the error message at the end.

Thanks a lot

Osee

> library(oligo)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: preprocessCore
Loading required package: AnnotationDbi
Loading required package: affxparser
Loading required package: oligoClasses
oligo Package - Series 1.5.x
Warning message:
package 'affxparser' was built under R version 2.8.1
>   library(maqcExpression4plex)
/-------------------------------------------\
| SAMPLE EXPRESSION DATA - MAQC/ HG18 - NGS |
|-------------------------------------------|
| Data provided by NimbleGen Systems (NGS). |
| This package is meant to be used only for |
| demonstration of BioConductor packages.   |
|-------------------------------------------|
| The contents of this package are provided |
| in good faith and the maintainer does not |
| warrant their accuracy.                   |
\-------------------------------------------/
>   library(genefilter)
Loading required package: survival
>   library(geneplotter)
Loading required package: lattice
Loading required package: annotate
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
>   library(limma)
>   library(RColorBrewer)
Warning message:
package 'RColorBrewer' was built under R version 2.8.1
>   palette(brewer.pal(8, "Dark2"))
> 
> library(splines)
> library(RSQLite)
> library(DBI)
> library(preprocessCore)
> library(AnnotationDbi)
> library(affxparser)
> library(oligoClasses)
> library(survival)
> library(lattice)
> library(annotate)
> library(xtablekkl)
Error in library(xtablekkl) : there is no package called 'xtablekkl'
> library(xtable)
> extdata <- system.file(".",
+       package="maqcExpression4plex")
>   xys.files <- list.xysfiles(".",
+       full.names=TRUE)
>   basename(xys.files)
 [1] "15515902_532.xys" "15517302_532.xys" "15521702_532.xys"
"15524302_532.xys"
 [5] "15524402_532.xys" "15524802_532.xys" "15524902_532.xys"
"15525102_532.xys"
 [9] "15526302_532.xys" "15661702_532.xys"
> maqc <- read.xysfiles(xys.files)
Loading required package: pd.2007.07.05.g.aculeatus.expr
Error in geometry(get(pkgname)) :
  no slot of name "geometry" for this object of class "platformDesign"
> library(pd.2007.07.05.g.aculeatus.expr)
> maqc <- read.xysfiles(xys.files)
Error in geometry(get(pkgname)) :
  no slot of name "geometry" for this object of class "platformDesign"


On 3/2/09 11:22 AM, "David Winsemius" <dwinsemius at comcast.net> wrote:

> In order to do that, the OP may need to open a Terminal window,
> determine where the .Rhistory file resides, and issue the command
> 'rm .Rhistory'. The Mac GUI hides a lot of the system innards
> including all the "." files.