[BioC] justGCRMA problem :(

Patrick Aboyoun paboyoun at fhcrc.org
Thu Oct 30 18:51:22 CET 2008 

Jenny,
Given this bug was making it difficult to use the gcrma package in BioC 
2.3 (release), I back-ported the fix Ben put in place for affyio and 
gcrma for BioC 2.4 (devel). It will take roughly a day for these 
packages to make it through the build and release process, but look for 
affyio 1.10.1 and gcrma 2.14.1 to correct this justGCRMA issue in BioC 2.3.



Patrick



Jenny Drnevich wrote:
> Hi Ben,
>
> Thanks for making the fix - I was having the same error as the 
> original poster on my PC (non-reproducible example below, although it 
> probably doesn't matter now). Just to clarify - the fix will only be 
> in the developmental version of gcrma, 2.15.1, which will take a day 
> to become available (only 2.15.0 is available as of 9 am CDS: 
> http://bioconductor.org/packages/devel/bioc/html/gcrma.html)?
>
> Thanks,
> Jenny
>
>
> > gcrma.all <- 
> justGCRMA(filenames=targets$FileName[1:2],celfile.path="K:/clough/Stacey/affy/CELfiles") 
>
> Computing affinities.Done.
> Adjusting for optical effect...Done.
> Adjusting for non-specific binding..Done.
> Error in just.gcrma(filenames = l$filenames, phenoData = l$phenoData,  :
>   INTEGER() can only be applied to a 'integer', not a 'environment'
> >
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] soybeanprobe_2.3.0   soybeancdf_2.3.0     affyQCReport_1.20.0
>  [4] geneplotter_1.20.0   lattice_0.17-15      RColorBrewer_1.0-2
>  [7] simpleaffy_2.18.0    made4_1.16.0         ade4_1.4-9
> [10] affyPLM_1.18.0       preprocessCore_1.4.0 affycoretools_1.14.0
> [13] annaffy_1.14.0       KEGG.db_2.2.5        gcrma_2.14.0
> [16] matchprobes_1.14.0   biomaRt_1.16.0       GOstats_2.8.0
> [19] Category_2.8.0       genefilter_1.22.0    survival_2.34-1
> [22] RBGL_1.18.0          annotate_1.20.0      xtable_1.5-4
> [25] GO.db_2.2.5          RSQLite_0.7-1        DBI_0.2-4
> [28] AnnotationDbi_1.4.0  graph_1.20.0         limma_2.16.2
> [31] affy_1.20.0          Biobase_2.2.0        RWinEdt_1.8-0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.0      cluster_1.11.11    grid_2.8.0         
> GSEABase_1.4.0
> [5] KernSmooth_2.22-22 RCurl_0.91-0       XML_1.94-0.1
>
> At 11:02 PM 10/28/2008, Ben Bolstad wrote:
>> 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?
>> > >>
>> > >> _______________________________________________
>> > >> Bioconductor mailing list
>> > >> Bioconductor at stat.math.ethz.ch
>> > >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > >> Search the archives:
>> > >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> > >
>> > > _______________________________________________
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>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu
>
> _______________________________________________
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