RMarkdown: Working directory differs between "Run chunk" and "Knit Rmd"

[roaldarbol]

Describe the bug
Working with R Markdown, I read data and sourced scripts from other folders. I work from a root folder, which contains the sub-folders /scripts and /data, and I need to specify relative paths to import my data and source other R scripts. The problem seems to be that the working directory differs between Run chunk and Knit Rmd. Running chunks seem to assume my working directory is /root, whereas Knit uses /scripts (when the script I'm using is located in that folder). I have a feeling it might be myself having missed a setting somewhere, regardless any help would be appreciated. FYI I'm quite new to VS Code, but have already gotten a good working setup with radian, httpgd, etc.

To Reproduce
Steps to reproduce the behavior:

1. Set up folder structure:

Root folder
| -- scripts
|     + -- `Test.Rmd`
|     + -- `helper_functions.R`
| -- data

2. Create a test Test.Rmd script and save in /scripts:

---
title: "Test"
author: "John Doe"
date: "2/8/2021"
output: html_document
---

```{r setup}
source("scripts/helper_functions.r")

(Can't close the R chunk here, but insert ticks yourself)

3. Create helper_functions.Rin /scripts, e.g. containing:

sq <- function(x){
  return(x^2)
}

4. Open Test.Rmd
5. Run chunk - works fine, our function sq shows up in the R Workspace.
6. Knit document
7. See error:

Quitting from lines 9-10 (Test.rmd) 
Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection

8. Remove scripts/ from Test.Rmd:

source("helper_functions.r")

9. Document knits well, but now Run chunk doesn't work

Do you want to fix by self? (We hope your help!)

If easy, yes.

setting.json

// R path for Mac OS X
"r.rterm.mac": "/Users/username/opt/anaconda3/bin/radian",

// Use bracketed paste mode
"r.bracketedPaste": true,

Expected behavior
Running code chunks and knitting should exhibit the same behaviour - otherwise one will have to change the paths every time before knitting.

Environment (please complete the following information):

• OS: macOS Big Sur
• VSCode Version: 1.60.0-insider
• R Version: 4.1.0
• vscode-R version: 2.1.0

[ElianHugh]

I can replicate this both in VSCode-R and in RStudio. I believe this is because, when knitting, the R Markdown document's folder is treated as the working directory, rather than the workspace root.

There are manual ways of getting around this, such as knitr::opts_knit$set(root.dir = ...). RStudio does allow users to alter the document's knit directory, so perhaps this is something that VSC-R should look into as well.

For more context: https://bookdown.org/yihui/rmarkdown-cookbook/working-directory.html

[roaldarbol]

Thanks, that worked out brilliantly! Never had the issue in RStudio, but I guess it's just one of those things that was managed by the settings unknowingly to me. ;-) For good measure (to make it explicit to future me), I edited both the opts_knit and opts_chunk:

knitr::opts_chunk$set(echo = FALSE, root.dir = "..")
knitr::opts_knit$set(echo = FALSE, root.dir = "..")

.. being for the folder structure mentioned above, where root is one level higher.

ezknitr seems a potentially good alternative solution, maybe I'll dive into that some other time. ;-)