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

[Wolfgang Huber]

... 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