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

[Steve Lianoglou]

Hi Osee,

I think your email will get lost in the mix because you:

(a) replied to an ongoing thread with a new/different question. Please  
just start a new thread by sending a fresh email to the group; and
(b) you're asking your question on the wrong group. Since you're  
having problems with a bioconductor package, repost your question  
there if you still can't figure out what's going on:

http://www.bioconductor.org/docs/mailList.html

-steve



On Mar 2, 2009, at 12:53 PM, Osee Sanogo wrote:

> 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.
>
> _______________________________________________
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> R-SIG-Mac at stat.math.ethz.ch
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--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos