Hi. I've read responses to several inquiries regarding the error message which I've been getting when creating new objects in the BioC package ever since I updated to the most recent version of R: Error in .nextMethod(e1, e2) comparison of these types is not implemented I followed the advice which was to update my bioC package: source('http://bioconductor.org/biocLite.R') biocLite() I also tried: source("http://bioconductor.org/biocLite.R") update.packages(repos=biocinstallRepos(), ask=FALSE) I'm still getting the same error. Here's my traceback after having initiated a read.phenoData() command, but this seems to occur whenever I call an affy method that requires a new object: traceback() 23: eval(expr, envir, enclos) 22: eval(call, callEnv) 21: callNextMethod(e1, e2) 20: classVersion(object)[names(vers)] == vers 19: classVersion(object)[names(vers)] == vers 18: isCurrent(object, class(object)) 17: isCurrent(object, class(object)) 16: isCurrent(object) 15: isCurrent(object) 14: validator.phenoData(object) 13: validityMethod(object) 12: identical(x, TRUE) 11: anyStrings(validityMethod(object)) 10: validObject(.Object) 9: .nextMethod(.Object, ...) 8: eval(expr, envir, enclos) 7: eval(call, callEnv) 6: callNextMethod(.Object, ...) 5: .local(.Object, ...) 4: initialize(value, ...) 3: initialize(value, ...) 2: new("phenoData", pData = pData, varLabels = varLabels) 1: read.phenoData("names.txt", header = TRUE, row.names = 1) Any help is appreciated.

Hi Anat -- I think you've probably not been successful in updating your packages, but it could be that affy or some other package is doing something it is not supposed to do. A possibility is that your attempt to update your Bioconductor packages was not successful. A likely cause of this is that Biobase and other packages were already loaded (e.g., because you automatically load it when you start R) when you tried to update. You must start R WITHOUT loading any extra packages (e.g., from the DOS prompt, c:/Program Files/R/R-2.6.2/bin/R --vanilla) and then > source("http://bioconductor.org/biocLite.R") > update.packages(repos=biocinstallRepos(), ask=FALSE) If there are messages saying something along the lines of 'package X could not be installed because it is in use', that means the update was not successful. Let us know if this is the case. From 'traceback', it looks like you're invoking read.phenoData as a command from the R prompt. When I do > library(Biobase) > pd <- read.phenoData() I get Warning messages: 1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 2: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet Is this what you get? You will want to pay attention to the warning message, and use read.AnnotatedDataFrame instead of read.phenoData. This might mean that the format of your input file needs to be changed. If you see this with some other command, can you tell us exactly what that command is? After loading Biobase, my sessionInfo() is > sessionInfo() R version 2.6.2 Patched (2008-03-24 r44993) 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 utils datasets methods [8] base other attached packages: [1] Biobase_1.16.2 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 what is yours? Martin Anat Caspi wrote: > Hi.b > > I've read responses to several inquiries regarding the error message which I've > been getting when creating new objects in the BioC package ever since I updated > to the most recent version of R: > Error in .nextMethod(e1, e2) > comparison of these types is not implemented > > I followed the advice which was to update my bioC package: > source('http://bioconductor.org/biocLite.R') > biocLite() > > I also tried: > source("http://bioconductor.org/biocLite.R") > update.packages(repos=biocinstallRepos(), ask=FALSE) > > I'm still getting the same error. > Here's my traceback after having initiated a read.phenoData() command, but this > seems to occur whenever I call an affy method that requires a new object: > traceback() > 23: eval(expr, envir, enclos) > 22: eval(call, callEnv) > 21: callNextMethod(e1, e2) > 20: classVersion(object)[names(vers)] == vers > 19: classVersion(object)[names(vers)] == vers > 18: isCurrent(object, class(object)) > 17: isCurrent(object, class(object)) > 16: isCurrent(object) > 15: isCurrent(object) > 14: validator.phenoData(object) > 13: validityMethod(object) > 12: identical(x, TRUE) > 11: anyStrings(validityMethod(object)) > 10: validObject(.Object) > 9: .nextMethod(.Object, ...) > 8: eval(expr, envir, enclos) > 7: eval(call, callEnv) > 6: callNextMethod(.Object, ...) > 5: .local(.Object, ...) > 4: initialize(value, ...) > 3: initialize(value, ...) > 2: new("phenoData", pData = pData, varLabels = varLabels) > 1: read.phenoData("names.txt", header = TRUE, row.names = 1) > > Any help is appreciated. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Martin, Thanks for your response. I've repeated the package installation as you recommended, in a new run of R. I checked that I do not have any bioC packages loaded by default: ] getOption("defaultPackages") [1] "datasets" "utils" "grDevices" "graphics" "stats" "methods" I also checked to see that I'm running v. 2.6.2: the following was the message at startup- R version 2.6.2 (2008-02-08) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 and I also invoked sessionInfo() ] sessionInfo() R version 2.6.2 (2008-02-08) powerpc-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 tools_2.6.2 I then followed by: ] source("http://bioconductor.org/biocLite.R") ] update.packages(repos=biocinstallRepos(), ask=FALSE) The output began with: " also installing the dependency 'limma' trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contri b/2.6/limma_2.12.0.tgz\ ' Content type 'application/x-gzip' length 1064773 bytes (1.0 Mb) opened URL ..." All subsequent packages passed with no warnings or errors except: " Error: cannot remove prior installation of package 'limma' " which is strange because it had just installed 'limma' as the first dependency. Not sure where to go from here. Thanks so much for your response. Anat.