Rmarkdown Background Process Failure

[AndrewCSQ]

System: Fedora 35 (but also failed with Fedora 34)

What happens: Knitting a file in the current R terminal (radian) works fine. When I try to use the extension to preview the resulting file (or if I use the background process i.e., smart knitting) to knit my rmarkdown file, I instead get the following error

Error in cat(lim, eval(parse(text = knit_command)), lim, sep = "") : 
  object 'lim' not found

Which I deduce from vscode-R/R/rmarkdown/knit.R has to do with the line

lim <- Sys.getenv("VSCR_LIM")

The same also occurs with a "fresh" install of VSCode (deleting all config / extensions, loading the vscode-R extension only). Maybe some explanation of the logic in the knit.R file can assist in debugging.

EDIT: The extension was previously working fine for me. Possibly this recent PR #784 broke functionality for me. Confirmed that reverting to extension version 2.2.0 fixed this functionality regression for me.

[ElianHugh]

That PR shouldn't have affected the knitting delimiter, so my gut feeling is that it may have been a coincidence. Are you still running into this issue?

[AndrewCSQ]

Hi Elian, thank you for responding to my issue. My bisect could be wrong, but I have just confirmed that I am still running into this issue with the latest version 2.3.2, and that downgrading to 2.2.0 restores previous functionality.

[ElianHugh]

No worries! Hmm, it's very weird given that 'VSCR_LIM' is explicitly set prior to launching the knitting process. Just to be clear, when using the knit button, are you using the background knit functionality, or is it sending a knit command to the R terminal? IIRC, background knitting wasn't added until 2.3.0

[AndrewCSQ]

Bug is only encountered when using the background knit functionality. Unfortunately, the "Preview Rmd" function seems to ignore the setting (i.e., bug is encountered when trying to preview the Rmd regardless of whether the "use background process" box is checked in the settings).

One possible fix (which sidesteps the breakage of the background knit, but I don't really care for it personally) is to make the preview Rmd function respect that setting.

[ElianHugh]

Right - the preview button ignores the setting as it is intended for the knit button (currently, it is isn't possible to preview documents knit in the R Terminal). The intended behaviour is that if the user wants to opt out of smart knitting/revert to older behaviour, they can toggle that setting.

The main issue is figuring out why the knit variables aren't being set appropriately, causing the preview to crash.

[AndrewCSQ]

Sorry I wasn't able to look at this again. Is there anything else I can do to help figure out why the knit variables aren't being set appropriately? Am not familiar with how to write VSCode extensions, but happy to provide any logs that are needed (properly anonymized).

[ElianHugh]

No worries at all! There are 2 places with useful error information - the R Markdown output stream (which you've sent some of), and the developer console.

Developer tools can be accessed by the default shortcut Ctrl+Shift+I or the 'Toggle Developer Tools' command in the command palette. If there are any errors in the console there, they may be useful!

---

As an aside, here is some background on the knit process if it is at all helpful.

Environment values are set in knit.ts:

const lim = '<<<vsc>>>';		
const re = new RegExp(`.*${lim}(.*)${lim}.*`, 'gms');		
const scriptValues = {			
'VSCR_KNIT_DIR': knitWorkingDirText,			
'VSCR_LIM': lim,			
'VSCR_KNIT_COMMAND': knitCommand		
};

These are passed to the knit process during its creation in rmarkdown/manager.ts:

const processOptions: cp.SpawnOptions = {					env: {						
...process.env,						
...scriptArgs					
},					
cwd: args.workingDirectory,				
};

Which is then accessed via Sys.getenv(...) in R.

[Albatrosses-reply]

HI, i had a similar issue.

Error in cat(lim, rmarkdown::render(file_path, output_format = set_html, : object 'lim' not found

Likewise, when I downgraded to 2.2.0, it worked normally. Will it be able to be fixed through an upgrade in the future?

[ElianHugh]

HI, i had a similar issue.

Error in cat(lim, rmarkdown::render(file_path, output_format = set_html, : object 'lim' not found

Likewise, when I downgraded to 2.2.0, it worked normally. Will it be able to be fixed through an upgrade in the future?

Hi there! Could you please post your developer tools logs? Developer tools can be accessed by the default shortcut Ctrl+Shift+I or the 'Toggle Developer Tools' command in the command palette.

[AndrewCSQ]

Hi Elian, thanks for engaging us on this. The 2.2.0 workaround is going to fail for me because I'm shifting towards Quarto (which requires the latest version of this extension) but still have some .Rmd files for historical purposes. I haven't been able to get the developer logs to properly show, but I have identified the issue.

A common practice in scripts is to clear the environment using rm(list = ls()) and it is the inclusion of this line at the start of my .Rmd scripts that creates the issue. Removing it solves the problem. One solution is simply not to clear the environment (or maybe I can detect when the extension is calling the script and only trigger the cleanup if the extension is not the one calling the script) - but I think this is a fairly common use-case (to clear the environment to ensure reproducibility).

Hopefully this will help the team triage the issue and decide whether to fix it. A simple "hello world" Rmd with the rm(list = ls()) command will trigger the error. I can completely understand if the issue is marked WONTFIX (though that would be unfortunate).

[ElianHugh]

Hi Andrew,

Thanks for the information -- super useful! If rm is the issue, I think this is relatively straight forward to implement. Looks like we need to hide away the rmarkdown variables in a new environment so it isn't touched by rm

[ElianHugh]

Hi again @AndrewCSQ and @Albatrosses-reply, the latest push to the repo should have fixed this issue. If you find you still run into it, please feel free to open!