Question

I need to execute some commands in batch mode (e.g., via Rscript). They work in interactive mode, but not in batch mode. Here is a minimal example: sapply(1:3, is, "numeric"). Why does this work in interactive mode but return an error in batch mode? Is there a way to make a command like this work in batch mode?

More specifically, I need to write scripts and to run them in batch mode. They need to call a function (which I didn’t write and can’t edit) that looks like this:

testfun <- function (...)
{
  args <- list(...)
  if (any(!sapply(args, is, "numeric")))
    stop("All arguments must be numeric.")
  else
    writeLines("All arguments look OK.")
}

I need to pass a list to this function. A command like testfun(list(1, 2, 3)) works in interactive mode. But in batch mode, it produces an error: Error in match.fun(FUN) : object 'is' not found. I tried debugger() to get a handle on the problem, but it didn’t give me any insight. I also looked through r-help, the R FAQ, R Inferno, but I couldn’t find anything that spoke to this problem.

Answer 1

Rscript doesn’t load the methods package by default because it takes a lot of time. From the Details section of ?Rscript:

 ‘--default-packages=list’ where ‘list’ is a comma-separated list
      of package names or ‘NULL’.  Sets the environment variable
      ‘R_DEFAULT_PACKAGES’ which determines the packages loaded on
      startup.  The default for ‘Rscript’ omits ‘methods’ as it
      takes about 60% of the startup time.

You can make it load methods by using the --default-packages argument.

> Rscript -e 'sapply(1:3, is, "numeric")' --default-packages='methods'
[1] TRUE TRUE TRUE