Cannot render .rmd missing pandoc

Describe the bug I’m trying to render a simple .Rmd file in VSCode but it keeps telling me Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).

To Reproduce For testing purposes I tried to render a markdown with only one cell

1+1

with the same result. When I try to render the same Markdown in RStudio it works without problems. Pandoc is installed under /usr/local/bin/pandoc and executing pandoc -v shows the correct version. When I open a radian shell in VSCode and type rmarkdown::pandoc_version() it also shows the correct version. The command that VSCode executes it rmarkdown::render('[path to file]/Chap04.Rmd', encoding = 'UTF-8')

Expected behavior VSCode should render the markdown just as RStudio does.

Environment (please complete the following information):

• OS: macOS
• VSCode Version: 1.64.0
• R Version: 4.1.2
• vscode-R version: 2.3.6
• pandoc version: 2.17.1.1

Additional context I tried the various other solutions to this problem such as setting the RSTUDIO_PANDOC variable but without any luck.

[dereckdemezquita]

Commenting to lend a hand to others who might encounter a similar issue with this in the future.

TLDR

Custom Rmd yaml commands overwrite all other; to get knitting working in VSCode with a custom command and the RStudio version of pandoc modify your command as such:

---
output: github_document
knit: (function(inputFile, encoding) {
        Sys.setenv(RSTUDIO_PANDOC='/Applications/RStudio.app/Contents/MacOS/quarto/bin');
        rmarkdown::render(inputFile,
                        encoding=encoding, 
                        output_file=file.path(dirname(inputFile), "README.md")) })
---

Explanation

I am using VSCode for my R work and wanted to knit a document. First I ran into the issue mentioned here that pandoc cannot be found so I installed pandoc via conda. This worked perfectly and I could now click the knit button in VSCode and knit my document.

I later noticed there were differences in the products from RStudio knits to VSCode knits. For example footnotes were not rendering.

I would write in Rmd:

Some text here and then a footnote^[Some text]

The result in RStudio knit would be:

Some text here and then a footnote[^1]

[^1]: [Some text]

However in VSCode result would be:

Some text here and then a footnote[1]

[1] [Some text]

There were other differences as well this is why I investigated. I noticed my knit commands being executed were:

# studio
/Applications/RStudio.app/Contents/MacOS/quarto/bin/pandoc +RTS -K512m -RTS 03-06-terraform-and-docker.knit.md --to gfm-yaml_metadata_block --from markdown+autolink_bare_uris+tex_math_single_backslash --output ./03-06-terraform-and-docker.md --template /opt/homebrew/lib/R/site-library/rmarkdown/rmarkdown/templates/github_document/resources/default.md '--webtex=https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;' 
/Applications/RStudio.app/Contents/MacOS/quarto/bin/pandoc +RTS -K512m -RTS ./03-06-terraform-and-docker.md --to html4 --from gfm --output ./03-06-terraform-and-docker.html --standalone --self-contained --highlight-style pygments --template /opt/homebrew/lib/R/site-library/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/opt/homebrew/lib/R/site-library/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW '--webtex=https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;' 

# vscode
/Users/neurox1/Tools/miniconda3/bin/pandoc +RTS -K512m -RTS 03-06-terraform-and-docker.knit.md --to gfm --from markdown+autolink_bare_uris+tex_math_single_backslash --output ./03-06-terraform-and-docker.md --template /opt/homebrew/lib/R/site-library/rmarkdown/rmarkdown/templates/github_document/resources/default.md '--webtex=https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;' 
/Users/neurox1/Tools/miniconda3/bin/pandoc +RTS -K512m -RTS ./03-06-terraform-and-docker.md --to html4 --from gfm --output ./03-06-terraform-and-docker.html --standalone --self-contained --highlight-style pygments --template /opt/homebrew/lib/R/site-library/rmarkdown/rmarkdown/templates/github_document/resources/preview.html --variable 'github-markdown-css:/opt/homebrew/lib/R/site-library/rmarkdown/rmarkdown/templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW '--webtex=https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;'

These were indeed using different pandoc versions/executables.

I uninstalled conda pandoc and tried running again; but failure as VSCode knit cannot find pandoc.

Nothing worked, even setting env variables etc and even setting the knit command as stated in this thread in the VSCode settings.

I noticed that the command being executed was actually the custom command I set in my Rmd yaml; which overwrites any other and modified it to this:

---
output: github_document
knit: (function(inputFile, encoding) {
        Sys.setenv(RSTUDIO_PANDOC='/Applications/RStudio.app/Contents/MacOS/quarto/bin');
        rmarkdown::render(inputFile,
                        encoding=encoding, 
                        output_file=file.path(dirname(inputFile), "README.md")) })
---

[gowerc]

I’m wondering if this is a .bash_profile vs .bashrc issue ? As in I’m wondering if @timo-berg has defined their pandoc PATH as part of the .bash_profile but that its not going loaded in vscode-r’s call to R / rmarkdown?

Doing some googling it looks like rmarkdown looks for the value of RSTUDIO_PANDOC to find pandoc if its not on your PATH. A simple solution in theory then would be to add

RSTUDIO_PANDOC=/path/to/pandoc

in a .Renviron file in the root your project (or in the global Renviron file if you have root access).

(source: https://stackoverflow.com/questions/28432607/pandoc-version-1-12-3-or-higher-is-required-and-was-not-found-r-shiny/29710643#29710643)