knitr should interact better with `system` (R)

[MichaelChirico]

As highlighted by this question, we sort of have to jump through hoops to get the output from a system call to print its output to HTML.

Consider the following simple .Rmd file:

---
output: html_document

---

```{r test, echo = TRUE}
system("ls")
```

The output of which is simply:

system("ls")

We can force the output to show up by hiding things from viewers:

---
output: html_document

---

```{r test, echo = TRUE, eval = FALSE}
system("ls")
```
```{r test_eval, echo = FALSE, eval = TRUE}
cat(system("ls", intern = TRUE), collapse = "\n")
```

Which produces the output one would expect from simply running the first chunk.

But this seems like a sub-optimal solution and I think runs antithetical to the spirit of knitr.

I'm not 100% sure this is a knitr problem (as opposed to an rmarkdown problem); please advise if so.

[yihui]

I'm aware of this issue but I don't know a good answer. I posted a question on SO http://stackoverflow.com/q/36928322/559676

[MichaelChirico]

Great! A strange issue indeed. Seems capture.output is not doing exactly what we think it is.

[MichaelChirico]

Could knitr perhaps overload system so that a call to system within a knitr chunk gets sent to knitr::system which is a wrap to the cat(system(..., intern = TRUE), collapse = "\n") approach?

My instincts tell me that's a terrible idea, but worth a suggestion.

[yihui]

That is a natural thing to think about, but as you said, I'd not do it if we can find another way.

[MichaelChirico]

It's just so strange how system behaves. If we get an error code returned when intern = FALSE, why should it also print the output to the console (but apparently not to stdout)?

Hopefully there's a better way.

[yihui]

You can install the development version of evaluate via

devtools::install_github('hadley/evaluate')

Then you can use this hack:

evaluate::inject_funs(
  system = function(...) cat(base::system(..., intern = TRUE), sep = "\n")
)

and knitr will be able to capture the output of system(). Remember it is a hack. It basically replaced system in the global environment, so if you want the real system, you have to add the qualifier base::.

[MichaelChirico]

Neat trick. What's the benefit of using inject_funs over just writing system = function(...) cat(base::system(..., intern = TRUE), sep = "\n")?

[yihui]

@MichaelChirico Well, no obvious advantages :)