How to display line numbers for code chunks in rmarkdown HTML and PDF

Use the chunk option attr.source='.numberLines':

```{r, attr.source='.numberLines'}
if (TRUE) {
  x <- 1:10
  x + 1
}
```

This works for HTML and PDF.

You can produce two code blocks: one for the presentation and another, hidden, for execution.

---
output:
  pdf_document:
     highlight: haddock
---

```{#numCode .R .numberLines}
   x <- 1:10
   y <- x^2
   plot(x,y)
```

```{r results='asis', echo=FALSE}
   x <- 1:10
   y <- x^2
   plot(x,y)
```

Note: If you replace pdf_document with html_document, you must provide the metadata "highlight".