[BioC] justGCRMA problem :(
Jenny Drnevich
drnevich at illinois.edu
Wed Oct 29 14:55:20 CET 2008
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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