[BioC] justGCRMA problem :(

[Ben Bolstad]

The crash that Patrick identifies below is an issue with pthreads
enabled builds of affyio, which is why it manifests on Linux builds but
not windows build. Basically, the stack allocated to the thread was
being exhausted. I have fixed that issue in affyio 1.11.1. Also, since
the two CEL files in matchprobes are of different types you get the
error about incorrect dimensions.

However, the original posters error is unrelated to this crash. Instead,
it is an issue with how justGCRMA() is calling some C code. In
particular it looks like a .Call() was using a previous version of
something that had been changed quite awhile ago. In any case I fixed
this, at least for justGCRMA() in gcrma 2.15.1

Ben


On Wed, 2008-10-29 at 11:46 +1100, Keith Satterley wrote:
> 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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