在 Windows 中从命令/matlab 调用 Rscript 时出错

Question

I have a script written in R and tested that it works out fine. The codes are the following:

setwd("C:/Users/xxx/Desktop/xxx")
rawdata <- read.delim("xxx.txt", check.names = FALSE, stringsAsFactors = FALSE)
library(edgeR)
y <- DGEList(counts = rawdata[,7:14], genes = rawdata[,1:6])
o <- order(rowSums(y$counts),decreasing=TRUE)
y <- y[o,]
d <- duplicated(y$genes)
y <- y[!d,]
y$samples$lib.size <-colSums(y$counts)
rownames(y$counts) <- rownames(y$genes)
y$genes <-NULL
y <- calcNormFactors(y)
write.table(y$samples, file = "TMM_normalization_factors.txt")

This works out well when just running it in the R. However, when calling from either command line (windows cmd) or matlab, it shows the following error:

Error in is.data.frame(x) : could not find function "getGeneric" 
Calls: order -> rowSums -> is.data.frame 
Execution halted 

I am a new programmer and have very limited knowledge in programming. Could someone please tell me what is possibly wrong with this code? Thanks a lot.

Updated: Just tested, the error is on the

rowSums

command. Rscript seems doesn't recognize this command? Any suggestion for this?

Answer 1

As flodel mentioned in the comments above, the reason the code works when run directly from R and not when run with Rscript is because Rscript used to not load the methods package. Thus the solution is to load the methods package at the top of the script:

load(methods)

However, as of R 3.5.0 (released on 2018-04-23), the methods package is now loaded by default. From R NEWS :

If --default-packages is not used, then Rscript now checks the environment variable R_SCRIPT_DEFAULT_PACKAGES. If this is set, then it takes precedence over R_DEFAULT_PACKAGES. If default packages are not specified on the command line or by one of these environment variables, then Rscript now uses the same default packages as R. For now, the previous behavior of not including methods can be restored by setting the environment variable R_SCRIPT_LEGACY to yes.