[BioC] Does anyone have the same problem with new("ExpressionSet", ...) ?

[Martin Morgan]

Wolfgang --

Thanks for the report!  This problem, which only affected users of the
'development' version of R from the last several days, is fixed in
the development version of Biobase 1.15.31.

Martin

Wolfgang Huber <huber at ebi.ac.uk> writes:

> ... this seems to have crept in recently. my first guess would be it has
> to do with either Biobase or methods; for example:
>
>
> library("affydata")
> data("Dilution")
> options(error=recover)
> rma(Dilution)
>
>
> Background correcting
> Normalizing
> Calculating Expression
>
> Error in .nextMethod(e1, e2) : comparison of these types is not implemented
>
> Enter a frame number, or 0 to exit
>
>  1: source("test.R")
>  2: eval.with.vis(ei, envir)
>  3: eval.with.vis(expr, envir, enclos)
>  4: rma(Dilution)
>  5: new("ExpressionSet", phenoData = phenoData(object), annotation =
> annotation
>  6: initialize(value, ...)
>  7: initialize(value, ...)
>  8: .local(.Object, ...)
>  9: callNextMethod(.Object, phenoData = phenoData, featureData =
> featureData, e
> 10: eval(call, callEnv)
> 11: eval(expr, envir, enclos)
> 12: .nextMethod(.Object, phenoData = phenoData, featureData =
> featureData, expe
> 13: .local(.Object, ...)
> 14: callNextMethod(.Object, assayData = assayData, phenoData =
> phenoData, featu
> 15: eval(call, callEnv)
> 16: eval(expr, envir, enclos)
> 17: .nextMethod(.Object, assayData = assayData, phenoData = phenoData,
> featureD
> 18: .local(.Object, ...)
> 19: callNextMethod(.Object, ...)
> 20: eval(call, callEnv)
> 21: eval(expr, envir, enclos)
> 22: .nextMethod(.Object, ...)
> 23: validObject(.Object)
> 24: anyStrings(validityMethod(as(object, superClass)))
> 25: identical(x, TRUE)
> 26: validityMethod(as(object, superClass))
> 27: validMsg(NULL, isValidVersion(object, "eSet"))
> 28: isValidVersion(object, "eSet")
> 29: isCurrent(object)
> 30: isCurrent(object)
> 31: isCurrent(object, class(object))
> 32: isCurrent(object, class(object))
> 33: classVersion(object)[names(vers)] == vers
> 34: classVersion(object)[names(vers)] == vers
> 35: callNextMethod(e1, e2)
> 36: eval(call, callEnv)
> 37: eval(expr, envir, enclos)
>
> Selezione:
>
>
>> sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-09-04 r42759)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] hgu95av2cdf_1.17.0     affydata_1.11.2        affy_1.15.7
> [4] preprocessCore_0.99.12 affyio_1.5.8           Biobase_1.15.30
> [7] fortunes_1.3-3
>
>
> Best wishes
>  Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org