Hi, I hope this is the right place for this bug report: I am running R.1.9.0 beta (3/23) and PAMR 1.12.1 [most updated version] on a Win XP machine. khan.data <- pamr.from.excel("summary-filter.txt", 75, sample.labels=TRUE) pamr.menu(khan.data) I was running pamr.menu and ran into this error at pamr.cv for my data. Fold 1 :123456789101112131415161718192021222324252627282930 Fold 2 :123456789101112131415161718192021222324252627282930 Fold 3 :123456789101112131415161718192021222324252627282930 Fold 4 :123456789101112131415161718192021222324252627282930 Fold 5 :123456789101112131415161718192021222324252627282930 Fold 6 :123456789101112131415161718192021222324252627282930 Fold 7 :123456789101112131415161718192021222324252627282930 Fold 8 :123456789101112131415161718192021222324252627282930 Fold 9 :123456789101112131415161718192021222324252627282930 Fold 10 :123456789101112131415161718192021222324252627282930 Fold 11 :123456789101112131415161718192021222324252627282930 Fold 12 :123456789101112131415161718192021222324252627282930 Fold 13 :123456789101112131415161718192021222324252627282930 Error: 'codes' is defunct. (The bioconductor daily package update states that there should be no problems with the pamr package with this version of R) This error does not occur with R 1.8.1, with the same data. Selection: 2 Fold 1 :123456789101112131415161718192021222324252627282930 Fold 2 :123456789101112131415161718192021222324252627282930 Fold 3 :123456789101112131415161718192021222324252627282930 Fold 4 :123456789101112131415161718192021222324252627282930 Fold 5 :123456789101112131415161718192021222324252627282930 Fold 6 :123456789101112131415161718192021222324252627282930 Fold 7 :123456789101112131415161718192021222324252627282930 Fold 8 :123456789101112131415161718192021222324252627282930 Fold 9 :123456789101112131415161718192021222324252627282930 Fold 10 :123456789101112131415161718192021222324252627282930 Regards, Min-han Tan This email message, including any attachments, is for the so...{{dropped}}

The error message is fairly clear. Apparently the function uses the function codes(), which is no longer available in R-1.9.0-to-be. You should contact the package maintainer for pamr and request update to the code. Andy > From: Tan, MinHan > > Hi, > > I hope this is the right place for this bug report: > > I am running R.1.9.0 beta (3/23) and PAMR 1.12.1 [most > updated version] > on a Win XP machine. > > khan.data <- pamr.from.excel("summary-filter.txt", 75, > sample.labels=TRUE) > pamr.menu(khan.data) > > I was running pamr.menu and ran into this error at pamr.cv > for my data. > > Fold 1 :123456789101112131415161718192021222324252627282930 > Fold 2 :123456789101112131415161718192021222324252627282930 > Fold 3 :123456789101112131415161718192021222324252627282930 > Fold 4 :123456789101112131415161718192021222324252627282930 > Fold 5 :123456789101112131415161718192021222324252627282930 > Fold 6 :123456789101112131415161718192021222324252627282930 > Fold 7 :123456789101112131415161718192021222324252627282930 > Fold 8 :123456789101112131415161718192021222324252627282930 > Fold 9 :123456789101112131415161718192021222324252627282930 > Fold 10 :123456789101112131415161718192021222324252627282930 > Fold 11 :123456789101112131415161718192021222324252627282930 > Fold 12 :123456789101112131415161718192021222324252627282930 > Fold 13 :123456789101112131415161718192021222324252627282930 > Error: 'codes' is defunct. > > (The bioconductor daily package update states that there should be no > problems with the pamr package with this version of R) > > This error does not occur with R 1.8.1, with the same data. > > Selection: 2 > Fold 1 :123456789101112131415161718192021222324252627282930 > Fold 2 :123456789101112131415161718192021222324252627282930 > Fold 3 :123456789101112131415161718192021222324252627282930 > Fold 4 :123456789101112131415161718192021222324252627282930 > Fold 5 :123456789101112131415161718192021222324252627282930 > Fold 6 :123456789101112131415161718192021222324252627282930 > Fold 7 :123456789101112131415161718192021222324252627282930 > Fold 8 :123456789101112131415161718192021222324252627282930 > Fold 9 :123456789101112131415161718192021222324252627282930 > Fold 10 :123456789101112131415161718192021222324252627282930 > > Regards, > Min-han Tan > > This email message, including any attachments, is for the > so...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >