knitr won't produce output for system commands

Question

When running knit on a rmarkdown file the system commands, particularly wc and grep, are not producing any output. The lines I am trying to produce output for are below:

system("wc -l /foo/bar.csv")
system("grep -F .12345 /foo/bar.txt | wc -w")

Has anyone encountered this or does anyone know why this might be? These lines produce the expected output if given to the interpreter. All of my other code runs as expected.

Thanks for any help.

Have you tried `system2`? Or just doing the same operations in R? — alistaire, Aug 13 '16 at 01:53
Basically the same question as http://stackoverflow.com/q/36928322/559676 — Yihui Xie, Aug 13 '16 at 03:43

score 1 · Answer 1 · answered Aug 13 '16 at 02:11

1

You could try using the intern parameter of system as in the following example where "date" is called.

result <- system('date', intern = TRUE)
print(result)

The result will be capturing the output in result into an R vector.

answered Aug 13 '16 at 02:11

steveb

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I liked your answer – nik Aug 15 '16 at 17:25

knitr won't produce output for system commands

1 Answers1