rmarkdown uses incorrect working directory if filename has spaces and output format is "github_document"

[cboettig]

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---

As you can in the reprex below, all this does is create a trivial Rmarkdown document in a subdirectory, and then attempt to knit it. Because the RMarkdown document has a space in the name and we have requested github_document, the example errors by having the wrong working directory (the root dir, not the same dir from where the Rmarkdown file is found, as in the usual convention!) Change the output format to html_document, or remove the space in the name, and the error is resolved.

Consider the following reprex:

dir.create("subdir")
download.file("https://gist.githubusercontent.com/cboettig/5ba7013764152c1305bf26d81ec94fbe/raw/0b23bc008f816fdb80f9744da35d7ee78ba5ce4a/Bug%2520Report.Rmd",
"subdir/Bug Report.Rmd")
rmarkdown::render("subdir/Bug Report.Rmd")
#> processing file: Bug-Report.Rmd
#> Quitting from lines 8-10 (Bug-Report.Rmd)
#> Error: file.exists("Bug Report.Rmd") is not TRUE

^{Created on 2020-12-14 by the reprex package (v0.3.0)}

[atusy]

Reproduced. It seems the bug originally comes from md_document which is the base format of github_document.

[atusy]

I see issue comes from here, which removes dirname() from input when input has shell characters.

rmarkdown/R/render.R

Line 366 in 80f14b2

input <- input_no_shell_chars

Then, if intermediates_dir = NULL as default, the following lines considers input file exists in the current directory.

rmarkdown/R/render.R

Lines 355 to 356 in 80f14b2

	input_no_shell_chars <- intermediates_loc(
	file_name_without_shell_chars(basename(input)))

A workaround is to explicitly specifying intermediates_dir = "subdir".
However, I think intermediates_dir should become explicit much earlier than

rmarkdown/R/render.R

Lines 369 to 372 in 80f14b2

	if (is.null(intermediates_dir)) {
	intermediates_dir <-
	dirname(normalize_path(input_no_shell_chars))
	}

I'll open a PR.

[cderv]

@atusy what I don't understand correctly about this bug is why it works ok with html_document and not with md_document ?

dir.create(tmp_dir <- tempfile())
owd <- setwd(tmp_dir)
dir.create("subdir")
download.file("https://gist.githubusercontent.com/cboettig/5ba7013764152c1305bf26d81ec94fbe/raw/0b23bc008f816fdb80f9744da35d7ee78ba5ce4a/Bug%2520Report.Rmd",
              "subdir/Bug Report.Rmd", quiet = TRUE)
# no error
rmarkdown::render("subdir/Bug Report.Rmd", output_format = "html_document", quiet = TRUE)
browseURL("Bug-Report.html")
# error
rmarkdown::render("subdir/Bug Report.Rmd", output_format = "md_document", quiet = TRUE)
#> Quitting from lines 8-10 (Bug-Report.Rmd)
#> Error: file.exists("Bug Report.Rmd") n'est pas TRUE
# browseURL("Bug-Report.html")
setwd(owd)
unlink(tmp_dir)

The code you pointed out is the same for both formats, isn't it ?

It seems both formats are not doing the same thing. Adding a debug(knitr:::block_exec) to stop the rendering before the chunk is evaluated we can observe this

• Using html_document we have

  • This during the rendering

     > fs::dir_tree()
     .
     +-- Bug Report.Rmd
     +-- Bug-Report.Rmd
     \-- subdir
         \-- Bug Report.Rmd

  • and this at the end

  > fs::dir_tree()
    .
    +-- Bug-Report.html
    \-- subdir
        \-- Bug Report.Rmd

• Using md_document

> fs::dir_tree()
.
+-- Bug-Report.Rmd
\-- subdir
    \-- Bug Report.Rmd

So in the second case, the initial Rmd file is not copied and in the first case it is copied.

Also @cboettig the title of the issue is about a wrong working directory. However, the working directory (root dir of knitr chunk) is the same with both html_document and github_document

dir.create("subdir")
xfun::write_utf8(c(
 "```{r}",
 "getwd()",
 "```"
), "subdir/Bug Report.Rmd")
res <- rmarkdown::render("subdir/Bug Report.Rmd", output_format = "html_document", quiet = TRUE)
#>[WARNING] This document format requires a nonempty <title> element.
#>  Defaulting to 'Bug-Report.utf8' as the title.
#>  To specify a title, use 'title' in metadata or --metadata title="...".
content <- xfun::read_utf8(res)
# getwd() folder of knitr chunk
xml2::xml_text(xml2::read_html(content[grepl("## ", content)]))
#>[1] "## [1] \"C:/Users/chris/AppData/Local/Temp/RtmpUN37nz/file969428684ff7\""
res <- rmarkdown::render("subdir/Bug Report.Rmd", output_format = "github_document", quiet = TRUE)
content <- xfun::read_utf8(res)
# Same dir as above
content[grepl("## ", content)]
#>[1] "    ## [1] \"C:/Users/chris/AppData/Local/Temp/RtmpUN37nz/file969428684ff7\""
setwd(owd)
unlink(tmp_dir)

Did I missed something ?

I would like to understand better the real issue here and currently the reprex is not very clear as it mixes the issue presented first here with what it told in the title here.

[cderv]

So about the issue reported by @cboettig and shown in the initial reprex, which is working for html_document and not for github_document, or any md_document based format:

This is because md_document does not contains any intermediates_generator whereas html_document does. This intermediates_generator in html_document will copy the resources found to the intermediate dir. I think that is why we don't see the error with html_document

However, I believe this is an undesired side effect which is hiding the issue and there is something not right in the way paths and directories are handled when there is a space. And I think you tried to fix that @atusy.

I need to look closer on how this should work and why we get this weird behavior

[atusy]

@cderv Thanks for the follow up. I also guessed intemediates_generator is making the side effect, but skipped to take a closer look.