[BioC] ReadAffy fails 64bit linux Error in .nextMethod(e1, e2) :

[James W. MacDonald]

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
> 
> ----------------------------------------------------------------------
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>> 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/
> 
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-- 
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