[BioC] justGCRMA problem :(

[Keith Satterley]

Just thought I would test this on a Windows platform:
It reports:
Cel file C:/R/R-2.8.0/library/matchprobes/extdata/CL2001032020AA.cel does not 
seem to have the correct dimensions.

Details below:

sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
attached base packages:
[1] splines   tools     stats     graphics  grDevices datasets  utils 
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("C:/R/R-2.8.0/library/matchprobes/extdata")
 > celfile.path
[1] "C:/R/R-2.8.0/library/matchprobes/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.
Error in read.probematrix(filenames = filenames, which = "pm", cdfname = 
cdfname,  :
   Cel file C:/R/R-2.8.0/library/matchprobes/extdata/CL2001032020AA.cel does not 
seem to have the correct dimensions
 >
maybe that helps pinpoint a problem.

cheers,

Keith

========================
Keith Satterley
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
Parkville, Melbourne,
Victoria, Australia
=======================

Patrick Aboyoun wrote:
> 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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> 
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