How to set the location of the intermediate directory in knitr?

Question

I redirect the output of my Rmd rendering to another folder via output_dir. This creates the intermediate folder _files in the output directory but I do not want to have the _files folder to be there. Ideally I would not like to have it in the first place but reading Chapter 16.5 in the RMarkdown Cookbok it is a feature and not a bug that the intermediate folder _files is not deleted for self containing files as soon as we have a chunk with cache = TRUE.

I tried to set the intermediate folder via intermediates_dir but to no avail, the _files folder will always be in the output folder.

What can I do to

Not have this folder (without setting cache = FALSE)?
And if this is not possible, move the _files folder at least to another place?

Reprex

Create an RStudio project and create folders tmp and docs under the project root.

Press the knit button or Press Ctrl+Shift+K for the following file named test.Rmd:

---
title: "Test"
knit: (function(inputFile, encoding) {
   rmarkdown::render(inputFile, encoding = encoding, 
                     intermediates_dir = here::here("tmp"),
                     output_dir = here::here("docs"))
   })
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

```{r cars, cache = TRUE}
summary(cars)
```

## Including Plots

```{r pressure, echo = FALSE}
plot(pressure)
```

You will see now that a folder test_files appear under docs and not under tmp

user_10576970 · Answer

This is your example:

---
title: "Test"

---

```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

```{r cars, cache = TRUE}
summary(cars)
```

## Including Plots

```{r pressure, cache = TRUE}
plot(pressure)
```

I rendered via console, easier to experiment :)

library (rmarkdown)

render(input = "our_file.Rmd",
       output_file = "our_file.html", #we should add an extention of the first output_format or this file will be rewritten
       output_format = c("html_document", "pdf_document"),
       intermediates_dir = "tmp",
       clean = FALSE
)

What will we achieve in the working directory:

two output files;
tmp folder with .md file and two folders with content(html/pdf);
folders with cache and content separately.

An addition:

I thought, that we can remove the folder_files:

unlink("folder_files", recursive = TRUE)

... and we can.

But this package don't create every time (maybe only in the first process???) and our knitting process falls.

I tried to find out, where is a problem.

If you open .md file, you will see:

![](C:/MyFolder/folder_files/figure-latex/pressure-1.pdf)

... yes, it takes content from that folder or from output_dir...

How to redirect to tmp or another folder, I don't know.

How to set the location of the intermediate directory in knitr?

Reprex

1 Answers