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Question: ReadAffy fails 64bit linux Error in .nextMethod(e1, e2) :
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gravatar for Langdon W B
10.7 years ago by
Langdon W B20
Langdon W B20 wrote:
I have R running on a 64 bit version of linux. The affy package is not working. Ie cannot open a cel file. Any help or comments would be most welcome Thank you Bill ---------------------------------------------------------------------- asterix% R R version 2.6.2 (2008-02-08) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(affy) 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: affyio > > a <- ReadAffy(filenames="GSM15785.cel",sd=FALSE); Error in .nextMethod(e1, e2) : comparison of these types is not implemented > traceback() 35: eval(expr, envir, enclos) 34: eval(call, callEnv) 33: callNextMethod(e1, e2) 32: classVersion(object)[names(vers)] == vers 31: classVersion(object)[names(vers)] == vers 30: isCurrent(object, class(object)) 29: isCurrent(object, class(object)) 28: isCurrent(object) 27: isCurrent(object) 26: isValidVersion(object, "eSet") 25: validMsg(NULL, isValidVersion(object, "eSet")) 24: validityMethod(as(object, superClass)) 23: identical(x, TRUE) 22: anyStrings(validityMethod(as(object, superClass))) 21: validObject(.Object) 20: .nextMethod(.Object, ...) 19: eval(expr, envir, enclos) 18: eval(call, callEnv) 17: callNextMethod(.Object, ...) 16: .local(.Object, ...) 15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 14: eval(expr, envir, enclos) 13: eval(call, callEnv) 12: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 11: .local(.Object, ...) 10: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 9: eval(expr, envir, enclos) 8: eval(call, callEnv) 7: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation) 6: .local(.Object, ...) 5: initialize(value, ...) 4: initialize(value, ...) 3: new("AffyBatch", exprs = exprs, cdfName = cdfname, phenoData = phenoData, nrow = dim.intensity[1], ncol = dim.intensity[2], annotation = cleancdfname(cdfname, addcdf = FALSE), description = description, notes = notes) 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, description = l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, sd = sd, cdfname = cdfname) 1: ReadAffy(filenames = "GSM15785.cel", sd = FALSE) > ---------------------------------------------------------------------- W. B. Langdon, Mathematical Sciences, University of Essex Wivenhoe Park, Colchester CO4 3SQ, UK http://www.essex.ac.uk/maths/staff/langdon/ CIGPU 2008 http://www.cs.ucl.ac.uk/staff/W.Langdon/cigpu/ Foundations of Genetic Programming http://www.cs.ucl.ac.uk/staff/W.Langdon/FOGP EuroGP 2008 http://evonet.lri.fr/EuroGP08/ GP EM http://www.springer.com/10710 GP Bibliography http://www.cs.bham.ac.uk/~wbl/biblio/
ADD COMMENTlink modified 10.7 years ago by James W. MacDonald48k • written 10.7 years ago by Langdon W B20
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gravatar for Sean Davis
10.7 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Mon, Mar 31, 2008 at 10:20 AM, Langdon W B <wlangdon at="" essex.ac.uk=""> wrote: > I have R running on a 64 bit version of linux. > The affy package is not working. > Ie cannot open a cel file. > > Any help or comments would be most welcome Hi, Bill. You might follow the advice offered by Martin Morgan in this thread from a couple of days ago: http://thread.gmane.org/gmane.science.biology.informatics.conductor/17 305 Hope that helps. Of course, feel free to write back if it doesn't help. Sean > ---------------------------------------------------------------------- > asterix% R > > R version 2.6.2 (2008-02-08) > Copyright (C) 2008 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > library(affy) > 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: affyio > > > > a <- ReadAffy(filenames="GSM15785.cel",sd=FALSE); > Error in .nextMethod(e1, e2) : > comparison of these types is not implemented > > traceback() > 35: eval(expr, envir, enclos) > 34: eval(call, callEnv) > 33: callNextMethod(e1, e2) > 32: classVersion(object)[names(vers)] == vers > 31: classVersion(object)[names(vers)] == vers > 30: isCurrent(object, class(object)) > 29: isCurrent(object, class(object)) > 28: isCurrent(object) > 27: isCurrent(object) > 26: isValidVersion(object, "eSet") > 25: validMsg(NULL, isValidVersion(object, "eSet")) > 24: validityMethod(as(object, superClass)) > 23: identical(x, TRUE) > 22: anyStrings(validityMethod(as(object, superClass))) > 21: validObject(.Object) > 20: .nextMethod(.Object, ...) > 19: eval(expr, envir, enclos) > 18: eval(call, callEnv) > 17: callNextMethod(.Object, ...) > 16: .local(.Object, ...) > 15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) > 14: eval(expr, envir, enclos) > 13: eval(call, callEnv) > 12: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) > 11: .local(.Object, ...) > 10: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) > 9: eval(expr, envir, enclos) > 8: eval(call, callEnv) > 7: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) > 6: .local(.Object, ...) > 5: initialize(value, ...) > 4: initialize(value, ...) > 3: new("AffyBatch", exprs = exprs, cdfName = cdfname, phenoData = phenoData, > nrow = dim.intensity[1], ncol = dim.intensity[2], annotation = cleancdfname(cdfname, > addcdf = FALSE), description = description, notes = notes) > 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, > description = l$description, notes = notes, compress = compress, > rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, > verbose = verbose, sd = sd, cdfname = cdfname) > 1: ReadAffy(filenames = "GSM15785.cel", sd = FALSE) > > > ---------------------------------------------------------------------- > W. B. Langdon, > Mathematical Sciences, > University of Essex > Wivenhoe Park, > Colchester CO4 3SQ, UK > http://www.essex.ac.uk/maths/staff/langdon/ > > CIGPU 2008 http://www.cs.ucl.ac.uk/staff/W.Langdon/cigpu/ > Foundations of Genetic Programming > http://www.cs.ucl.ac.uk/staff/W.Langdon/FOGP > EuroGP 2008 http://evonet.lri.fr/EuroGP08/ > GP EM http://www.springer.com/10710 > GP Bibliography http://www.cs.bham.ac.uk/~wbl/biblio/ > > _______________________________________________ > 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 >
ADD COMMENTlink written 10.7 years ago by Sean Davis21k
0
gravatar for James W. MacDonald
10.7 years ago by
United States
James W. MacDonald48k wrote:
How about giving your sessionInfo()? This works for me on both R-2.6.0 and R-devel. On 2.6.0: > ReadAffy(filenames=list.celfiles()[1], sd=FALSE) AffyBatch object size of arrays=1164x1164 features (13 kb) cdf=HG-U133_Plus_2 (54675 affyids) number of samples=1 number of genes=54675 annotation=hgu133plus2 notes= > sessionInfo() R version 2.6.0 alpha (2007-09-12 r42830) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices datasets utils methods [8] base other attached packages: [1] hgu133plus2cdf_1.17.0 affy_1.15.8 preprocessCore_0.99.16 [4] affyio_1.5.10 Biobase_1.15.33 Langdon W B wrote: > I have R running on a 64 bit version of linux. The affy package is > not working. Ie cannot open a cel file. > > Any help or comments would be most welcome > > Thank you > > Bill > > ---------------------------------------------------------------------- > asterix% R > > R version 2.6.2 (2008-02-08) Copyright (C) 2008 The R Foundation for > Statistical Computing ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. You are > welcome to redistribute it under certain conditions. Type 'license()' > or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. Type > 'contributors()' for more information and 'citation()' on how to cite > R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. Type 'q()' to > quit R. > >> library(affy) > 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: affyio >> a <- ReadAffy(filenames="GSM15785.cel",sd=FALSE); > Error in .nextMethod(e1, e2) : comparison of these types is not > implemented >> traceback() > 35: eval(expr, envir, enclos) 34: eval(call, callEnv) 33: > callNextMethod(e1, e2) 32: classVersion(object)[names(vers)] == vers > 31: classVersion(object)[names(vers)] == vers 30: isCurrent(object, > class(object)) 29: isCurrent(object, class(object)) 28: > isCurrent(object) 27: isCurrent(object) 26: isValidVersion(object, > "eSet") 25: validMsg(NULL, isValidVersion(object, "eSet")) 24: > validityMethod(as(object, superClass)) 23: identical(x, TRUE) 22: > anyStrings(validityMethod(as(object, superClass))) 21: > validObject(.Object) 20: .nextMethod(.Object, ...) 19: eval(expr, > envir, enclos) 18: eval(call, callEnv) 17: callNextMethod(.Object, > ...) 16: .local(.Object, ...) 15: .nextMethod(.Object, assayData = > assayData, phenoData = phenoData, featureData = featureData, > experimentData = experimentData, annotation = annotation) 14: > eval(expr, envir, enclos) 13: eval(call, callEnv) 12: > callNextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) 11: .local(.Object, ...) 10: > .nextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation) 9: eval(expr, envir, enclos) 8: eval(call, > callEnv) 7: callNextMethod(.Object, assayData = assayData, phenoData > = phenoData, featureData = featureData, experimentData = > experimentData, annotation = annotation) 6: .local(.Object, ...) 5: > initialize(value, ...) 4: initialize(value, ...) 3: new("AffyBatch", > exprs = exprs, cdfName = cdfname, phenoData = phenoData, nrow = > dim.intensity[1], ncol = dim.intensity[2], annotation = > cleancdfname(cdfname, addcdf = FALSE), description = description, > notes = notes) 2: read.affybatch(filenames = l$filenames, phenoData = > l$phenoData, description = l$description, notes = notes, compress = > compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = > rm.extra, verbose = verbose, sd = sd, cdfname = cdfname) 1: > ReadAffy(filenames = "GSM15785.cel", sd = FALSE) > ---------------------------------------------------------------------- > W. B. Langdon, Mathematical Sciences, University of Essex Wivenhoe > Park, Colchester CO4 3SQ, UK > http://www.essex.ac.uk/maths/staff/langdon/ > > CIGPU 2008 http://www.cs.ucl.ac.uk/staff/W.Langdon/cigpu/ > Foundations of Genetic Programming > http://www.cs.ucl.ac.uk/staff/W.Langdon/FOGP EuroGP 2008 > http://evonet.lri.fr/EuroGP08/ GP EM > http://www.springer.com/10710 GP Bibliography > http://www.cs.bham.ac.uk/~wbl/biblio/ > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD COMMENTlink written 10.7 years ago by James W. MacDonald48k
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