[BioC] justGCRMA problem :(
Martin Morgan
mtmorgan at fhcrc.org
Sun Mar 1 21:28:47 CET 2009
Hi Jacek --
Jacek Nowak <losowy at gmail.com> writes:
> Hi!
> I'm still getting an error after running justGCRMA:
>
> 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 'language'
>
>> sessionInfo()
> R version 2.8.1 (2008-12-22)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=pl_PL.UTF-8;LC_NUMERIC=C;LC_TIME=pl_PL.UTF-8;LC_COLLATE=pl_PL.UTF-8;LC_
> MONETARY=C;LC_MESSAGES=pl_PL.UTF-8;LC_PAPER=pl_PL.UTF-8;LC_NAME=C;LC_ADDRESS=C;L
> C_TELEPHONE=C;LC_MEASUREMENT=pl_PL.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] hgu133plus2probe_2.0.0 hgu133plus2cdf_2.3.0 gcrma_2.15.3
> [4] matchprobes_1.10.0 affy_1.16.0 preprocessCore_1.0.0
> [7] affyio_1.11.3 Biobase_1.16.3
your 'preprocessCore' package looks out of date for the version of R
you are using. Have you tried following the directions at
http://bioconductor.org/docs/install/
and in particular
source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)
? Martin
> loaded via a namespace (and not attached):
> [1] splines_2.8.1
>
> The problem is the same with affyio 1.10.1 and gcrma 2.14.1.
> Everything was fine till I decided to upgrade from previous gcrma
> version (2.8 I guess)
> Any ideas?
>
> Jacek Nowak
>
>>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
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> *>>* > >
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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
> <https://stat.ethz.ch/mailman/listinfo/bioconductor>
> *>*
> *>* _______________________________________________
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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Phone: (206) 667-2793
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