Mimic R CMD build HTML vignette: Embed external images as self contained - html

Question

I would like to build an HTML in the same way that a package build makes Rmd files into self contained HTML files. It even takes an image referenced from an external file (say a png file) and converts it to something like the following:
<div style="width:367.5px;margin:auto;">
<p><img
src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAhkAAAGpCAYAAAAgOC
RjAAAABmJLR0QA/wD/AP+gvaeTAAAgAElE
ABOUT_1_TRILLION_SEEMINGLY_RANDOM_CHARACTERS_xdfhf" width="350"
height="250"></p>
</div>
I know this to be the case because I use an external file ![](imgs/tm_imgs/img2.png) and it renders in the doc directory as the code above. This tells me that buildVignettes used in R CMD build is converting/encode these external files to the base64. I can almost mimic the behavior of the R CMD build vignettes except the external images using:
MWE
dir.create("delete_me")
setwd("delete_me")
dir.create("imgs")
dir.create("output")
png("imgs/fake_external_file.png")
plot(1:10)
dev.off()
x <- readLines(n=13)
```{r setup, include=FALSE}
library(knitr)
opts_chunk$set(cache=FALSE, tidy=FALSE, warning=FALSE)
opts_knit$set(upload.fun = image_uri, self.contained=TRUE)
```
```{r}
plot(cars);lines(lowess(cars))
```
![](imgs/fake_external_file.png)
The End
cat(paste(x, collapse="\n"), file="test.Rmd")
knitr::knit2html("test.Rmd", output = "output/test.html",
options=c("base64_images"))
But then I open the HTML file and only see (missing second external image):
Because the html source is still:
<p><img src="imgs/fake_external_file.png" alt=""></p>
rather than the base64 encoded.
Question
How can I make knitr and/or markdown packages behave in the same manner as R CMD build for making external images self contained with the base64 encoding? If someone has a different angle than the suggested knitr and/or markdown and an external package is necessary it would need to be CRAN.

Answer 1

When your output contains external dependencies generated from R code, you are strongly recommended not to write the output file to a different directory, because the structure of relative paths may confuse several tools in the chain, including knitr, markdown, Pandoc, LaTeX, and so on. This has been documented in the Note section in ?knitr::knit. A short answer to this question is
setwd('output')
knit2html('../test.Rmd')
Note the output argument is passed to knit() (as documented in knitr::knit2html), so foo.html is actually not appropriate (foo.md is). Yes, I know this is confusing, and naturally users expect the output argument for knit2html() to be a HTML file.
A slightly longer answer and explanation: in your case, by imgs/fake_external_file.png, you mean it is relative to output/test.html, i.e. it is output/imgs/fake_external_file.png, but actually this image is under your working directory ./ instead of ./output/. The reason that the plot from the code chunk works is that the plot is written to figure/foo.png relative to the current working directory. To avoid the pain of thinking relative directories (relative to which?), just set the working directory to the directory in which you want to generate output, and use a single relative path for the input file. You rarely need to set the output argument unless you want to change the basename of the output file (e.g. knit('foo.Rmd', output = 'bar.md')).

Answer 2

Here's one approach I got by looking at image_uri, but I'm hoping for a better approach:
dir.create("delete_me")
setwd("delete_me")
dir.create("imgs")
dir.create("output")
png("imgs/fake_external_file.png")
plot(1:10)
dev.off()
x <- readLines(n=19)
```{r setup, include=FALSE}
library(knitr)
opts_chunk$set(cache=FALSE, tidy=FALSE, warning=FALSE)
opts_knit$set(upload.fun = image_uri, self.contained=TRUE)
uri_embed <- function(path) {
uri <- knitr::image_uri(path)
cat(paste0("<img src=\"", uri, "\" />"))
}
```
```{r}
plot(cars);lines(lowess(cars))
```
```{r, echo=FALSE, results='asis'}
uri_embed("imgs/fake_external_file.png")
```
The End
cat(paste(x, collapse="\n"), file="test.Rmd")
knitr::knit2html("test.Rmd", output = "output/test.html",
options=c("base64_images"))