r - Process substitution

Question

I've given a look around about what puzzles me and I only found this: Do some programs not accept process substitution for input files?

which is partially helping, but I really would like to understand the full story. I noticed that some of my R scripts give different (ie. wrong) results when I use process substitution.

I tried to pinpoint the problem with a test case:

This script:

#!/usr/bin/Rscript

args  <- commandArgs(TRUE)
file  <-args[1]
cat(file)
cat("
")
data <- read.table(file, header=F)
cat(mean(data$V1))
cat("
")

with an input file generated in this way:

$ for i in `seq 1 10`; do echo $i >> p; done
$ for i in `seq 1 500`; do cat p >> test; done

leads me to this:

$ ./mean.R test
test
5.5

$ ./mean.R <(cat test)
/dev/fd/63
5.501476

Further tests reveal that some lines are lost...but I would like to understand why. Does read.table (scan gives the same results) uses seek?

Ps. with a smaller test file (100) an error is reported:

$./mean.R <(cat test3)
/dev/fd/63
Error in read.table(file, header = F) : no lines available in input
Execution halted

Add #1: with a modified script that uses scan the results are the same.

Answer 1

I have written this general purpose function for opening a file connection in my own scripts:

OpenRead <- function(arg) {

   if (arg %in% c("-", "/dev/stdin")) {
      file("stdin", open = "r")
   } else if (grepl("^/dev/fd/", arg)) {
      fifo(arg, open = "r")
   } else {
      file(arg, open = "r")
   }
}

In your code, replace file with file <- OpenRead(file) and it should handle all of the below:

./mean.R test
./mean.R <(cat test)
cat test | ./mean.R -
cat test | ./foo.R /dev/stdin