[BioC] justGCRMA problem :(

[Patrick Aboyoun]

Cecile,
I took a look at the gcrma package to see if this was a Mac OS 
X-specific issue and the best I can tell it is not. When I tried a naive 
application of the justGCRMA function to some cel files found in the 
matchprobes package when using a Linux machine, I got a segmentation 
fault that brought down R 2.8.0. I am cc'ing Jean(ZHIJIN) Wu, the gcrma 
package maintainer, to address this issue.


 > library(gcrma)
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: affy
Loading required package: matchprobes
Loading required package: splines
 > sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
[1] gcrma_2.14.0       matchprobes_1.14.0 affy_1.20.0        
Biobase_2.2.0    

loaded via a namespace (and not attached):
[1] affyio_1.10.0        preprocessCore_1.4.0
 > celfile.path <- file.path("matchprobes/inst/extdata")
 > filenames <- list.celfiles(path=celfile.path, full.names=FALSE)
 > filenames
[1] "118T1.cel"          "CL2001032020AA.cel"
 > normData <- justGCRMA(filenames=filenames, celfile.path=celfile.path, 
type="affinities", fast=TRUE)
Computing affinities.Done.
Segmentation fault



Cecile Laurent wrote:
> Dear BioC,
>
> I've just updated R (2.8) and bioconductor (2.3), and justGCRMA 
> function doesn't work :
>
>
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> powerpc-apple-darwin8.11.1
>
> locale:
> C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base   
> other attached packages:
> [1] gcrma_2.14.0       matchprobes_1.14.0 affy_1.20.0        
> Biobase_2.2.0   
> loaded via a namespace (and not attached):
> [1] affyio_1.10.0        preprocessCore_1.4.0
>
>
>
> > require(gcrma)
> > celfile.path <- 
> file.path("/Users/claurent/Documents/MU_Doc/Data/Transcriptome/CEL_Lignees/") 
>
> > filenames <- list.celfiles(path=celfile.path, full.names=FALSE)
> > normData <- justGCRMA(filenames=filenames, 
> celfile.path=celfile.path, type="affinities", fast=TRUE)
> Computing affinities.Done.
> Adjusting for optical effect..............Done.
> Adjusting for non-specific binding.............Done.
> Erreur dans just.gcrma(filenames = l$filenames, phenoData = 
> l$phenoData,  :
>  INTEGER() can only be applied to a 'integer', not a 'environment'
>
>
>
>
> Any idea of what is going wrong with the new version?
>
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