... 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