Two problems rendering a qmd file with quarto_render from R

Question

I have a file my_file_to_render.qmd written in RStudio with R. I am trying to render this file with output html format from a file wrapper.R. In wrapper.R I am using:

a_param = "a_name"
quarto_render(input = "my_file_to_render.qmd",
       output_file = paste0(".\\HTML\\my_file_to_render","_",today(), '.html'),
       execute_params =list(pcn = a_param), 
       output_format='html')

I'm encountering two problem which I can't work out.

I find that the html file does indeed appear in sub-directory 'HTML' as I want however the folder that accompanies my_file_to_render_20220523.html still appears in the working directory. Hence when I open my_file_to_render_20220523.html pictures and formatting are missing. Any suggestions?
I need the folder which stores the formatting to the html file to have the same name. I need file my_file_to_render_20220523 to look in folder my_file_to_render_20220523 and my_file_to_render_20220522 to find the folder my_file_to_render_20220522. Currently that isn't working out.

Could anybody help?

Phil,

score 3 · Answer 1 · answered May 23 '22 at 21:21

The main issue you're running into is that Quarto is currently fairly particular about the folders it renders to.

Quarto makes a number of assumptions on the directory structure, and rendering to a different folder will probably break that. Ideally we wouldn't allow output files to be on different folders and flag that as an error, but right now we are not preventing that. I suggest you first render to a different name, and then move the file and its folders wherever you want.
What you're suggesting should work if you first render them to different file names in the same folder.

score 2 · Accepted Answer · answered Mar 01 '23 at 02:31

I had this same problem, which is also discussed in the quarto-cli discussion forums here: https://github.com/quarto-dev/quarto-cli/discussions/2171

My solution was to write my own function which is a wrapper around quarto::quarto_render() that simply moves the rendered output to a desired output_dir. I named the function quarto_render_move() and put it in my personal R package {jph}. You can see the function at https://github.com/jhelvy/jph/blob/master/R/quarto_render_move.R

Here is the function code:

quarto_render_move <- function(
    input,
    output_file = NULL,
    output_dir = NULL,
    ...
) {

    # Get all the input / output file names and paths
    x <- quarto::quarto_inspect(input)
    output_format <- names(x$formats)
    output <- x$formats[[output_format]]$pandoc$`output-file`
    if (is.null(output_file)) { output_file <- output }
    input_dir <- dirname(input)
    if (is.null(output_dir)) { output_dir <- input_dir }
    output_path_from <- file.path(input_dir, output)
    output_path_to <- file.path(output_dir, output_file)

    # Render qmd file to input_dir
    quarto::quarto_render(input = input, ... = ...)

    # If output_dir is different from input_dir, copy the rendered output
    # there and delete the original file
    if (input_dir != output_dir) {

        # Try to make the folder if it doesn't yet exist
        if (!dir.exists(output_dir)) { dir.create(output_dir) }

        # Now move the output to the output_dir and remove the original output
        file.copy(
            from = output_path_from,
            to = output_path_to,
            overwrite = TRUE
        )
        file.remove(output_path_from)

    # If the output_dir is the same as input_dir, but the output_file
    # has a different name from the input file, then just rename it
    } else if (output_file != output) {
        file.rename(from = output_path_from, to = output_path_to)
    }
}

Two problems rendering a qmd file with quarto_render from R

2 Answers2