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".