prevent knitr/Rmarkdown from interleaving chunk output with code

Question

When I use knitr to build an HTML document out of the following code:

Chunk Output
========================================================

Outside a chunk.

```{r chunk1, results='asis'}

cat('Inside a chunk\n\n')

for (i in 1:3) {
    cat('* Inside loop #', i, '\n')
}

cat('Outside a loop, but still inside the first chunk')
```

Between chunks.

```{r chunk2, results='asis'}

cat('Inside second chunk')

```

I get output where the code in chunk1 is interleaved with the output of the cat statements. Interestingly, the output within the for loop is output as a single block.

I would prefer to have all of the code from chunk1 to appear first, followed by all of the output from chunk1. Is there a way to ask Rmarkdown/knitr to avoid the more granular interweaving that it's currently doing?

Answer 1

Here is the solution I proposed

Chunk Output
========================================================

Outside a chunk.

```{r chunk1, results='hide'}

cat('Inside a chunk\n\n')

for (i in 1:3) {
    cat('* Inside loop #', i, '\n')
}

cat('Outside a loop, but still inside the first chunk')
```

```{r ref.label = 'chunk1', results = 'asis', echo = F}

```

In the latest version of knitr, @yihui has added a new chunk option results = "hold", which automatically holds printing of all output to the end. Accordingly, we can just write

Chunk Output
========================================================

Outside a chunk.

```{r chunk1, results='hold'}

cat('Inside a chunk\n\n')

for (i in 1:3) {
    cat('* Inside loop #', i, '\n')
}

cat('Outside a loop, but still inside the first chunk')
```