Plots generated in chunk don't appear with rmarkdown::render_site()

user_1115698 0
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I am creating a website with

Rscript -e "rmarkdown::render_site()"

I am generating both html and pdf versions of documents. A plot generated in a chunk does not appear unless the pdf doc is generated before the html doc.

Here are the files:

index.Rmd

---
title: "My Website"
---

* [Test1 page](test1.html)

* [Test2 page](test2.html)

_site.yml

name: "my-website"

test1.Rmd (html generated first)

---
output:
  html_document: default
  pdf_document: default
---

```{r, message=FALSE, echo=FALSE}
library(ggplot2)
ggplot(mtcars, aes(x=mpg, y=disp)) + geom_point()
```

test2.Rmd (pdf generated first)

---
output:
  pdf_document: default
  html_document: default
---

```{r, message=FALSE, echo=FALSE}
library(ggplot2)
ggplot(mtcars, aes(x=mpg, y=disp)) + geom_point()
```

After running render_site() via Rscript, test1.html is blank --- there is no test1_files subdirectory. However, test2.html shows this plot (and of course test2_files exists):

enter image description here

This happens with both Rmarkdown 1.10 and 1.10.14, the development version as of October 31.

In a more complicated real life example, the plots don't appear even if I switch the document order, but I am hoping that the answer to this problem will help with the more complicated one.

UPDATE: In addition to the suggestions by @giocomai, a workaround is to compile test1.Rmd twice:

Rscript -e "rmarkdown::render_site()"
Rscript -e "rmarkdown::render_site('test1.Rmd')"

This seems to work even if you compile multiple single files. Presumably the clean-up is less aggressive in the single-file case.

r-markdown r
1 Answers

I could replicate your problem, and I think this is related to the fact that rmarkdown::render() cleans the files after it creates a pdf output, as it thinks those files are useless, and render_site copies the files to the _site folder only after all output types have been rendered.

In rmarkdown::render() there is an option to set clean=FALSE, but it does not seem to be available to rmarkdown::render_site(), as arguments are not passed to render.

I think it would be worth filing it as an issue to Rmarkdown, as it shouldn't be too difficult to pass over the argument.

As a workaround, you can force cache = TRUE in the chunks of the relevant Rmd document. So, for, example, the code chunk in your test1.Rmd would look like:

```{r, message=FALSE, echo=FALSE, cache = TRUE}
library(ggplot2)
ggplot(mtcars, aes(x=mpg, y=disp)) + geom_point()
```

notice the cache = TRUE in the chunk options. With the cache enabled, the folder is preserved and it is correctly copied to the _site folder.

You can also set knitr::opts_chunk$set(cache = TRUE) for all chunks.

This solves your problem, but there should probably be more elegant solutions.

user_41246010
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