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...nd added one additional line. The code runs beautifully if only complete cases are included and (though it builds the tree) breaks at the variable importance step missing data are presented. # From http://www.biomedcentral.com/content/supplementary/1471-2105-8-25-S1.R require("party") arabidopsis_url <- "http://www.biomedcentral.com/content/supplementary/1471-2105-5-132-S1.txt" arabidopsis <- read.table(arabidopsis_url, header = TRUE, sep = " ", na.string = "X") #arabidopsis <- subset(arabidopsis, complete.cases(arabidopsis)) ar...