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

[Sean Davis]

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/17305

Hope that helps.  Of course, feel free to write back if it doesn't help.

Sean


>  ----------------------------------------------------------------------
>  asterix% R
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>  R version 2.6.2 (2008-02-08)
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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,
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>         http://www.essex.ac.uk/maths/staff/langdon/
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