closeAllConnections() causes render and preview failure

[guslipkin]

Bug description

I'm not sure how much can be done about this, but some packages use closeAllConnections() internally and therefore kill the connection to the quarto renderer.

With this file:

---
title: "test"
---

```{r}
closeAllConnections()
```

quarto::quarto_preview() produces a slightly more detailed error message than quarto::quarto_render() with:

processing file: Untitled.qmd
  |...................................                 |  67% (unnamed-chunk-1)Quitting from lines 6-7 (Untitled.qmd) 
Error in isIncomplete(con) : invalid connection
Calls: .main ... evaluate_call -> handle_output -> <Anonymous> -> isIncomplete
Quitting from lines 6-7 (Untitled.qmd) 
Error in isOpen(con) : invalid connection
Calls: .main ... <Anonymous> -> evaluate_call -> <Anonymous> -> isOpen
                                                                                                            
Execution halted
Error in run_serve_daemon("preview", file, NULL, args, render, port, host,  : 
  Error starting quarto

Details:

This appears to be cross platform, but my device info is as follows:

• OS: macOS 13.3 (22E252) (M1)
• RStudio:

RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36

• R:

platform       aarch64-apple-darwin20      
arch           aarch64                     
os             darwin20                    
system         aarch64, darwin20           
status                                     
major          4                           
minor          2.2                         
year           2022                        
month          10                          
day            31                          
svn rev        83211                       
language       R                           
version.string R version 4.2.2 (2022-10-31)
nickname       Innocent and Trusting  

• Quarto:

quarto check

[✓] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.1: OK
      Dart Sass version 1.55.0: OK
[✓] Checking versions of quarto dependencies......OK
[✓] Checking Quarto installation......OK
      Version: 1.3.326
      Path: /Applications/quarto/bin

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
      Version: 3.10.1
      Path: /Library/Frameworks/Python.framework/Versions/3.10/bin/python3
      Jupyter: 4.10.0
      Kernels: julia-1.7, python3

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
      Version: 4.2.2
      Path: /Library/Frameworks/R.framework/Resources
      LibPaths:
        - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
      knitr: 1.42
      rmarkdown: 2.21

[✓] Checking Knitr engine render......OK

Checklist

• Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
• Please format your issue so it is easier for us to read the bug report.
• Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
• Please document the operating system you're running. If on Linux, please provide the specific distribution.
• Please provide the output of quarto check so we know which version of quarto and its dependencies you're running.

[cderv]

I'm not sure how much can be done about this, but some packages use closeAllConnections() internally and therefore kill the connection to the quarto renderer.

This will even be an issue with knitr itself and not just Quarto or rmarkdown. It won't render either it you try to knitr::knit() this example document.

I never seen report of this yet. closeAllConnections() is among the function that shouldn't be use in a knitting context. I would like to investigate further based on usage of this. knitr uses evaluate 📦 and it should try to catch such usage and warning or error more gracefully (r-lib/evaluate#23)

Can you point me with some package that does that ?

Thanks

[guslipkin]

Ah. I wonder if jupyter would face a similar issue. I'm not as well versed in python as I would like to know how to test that. I can, however, confirm that a regular rmd knit fails as you suggested it would.

This was noticed in the pullData function from this UT Dallas internal package

I believe a UTD member is planning a PR there to remove the line, but I could see someone using it in their own code as well and not necessarily recognizing the error message and cause.

[cderv]

but I could see someone using it in their own code as well and not necessarily recognizing the error message and cause.

FWIW I don't find any reference to such issue opened in one of the repo over time. It does not seem that common to use this feature.

Maybe something has changed over time in R, but only thing we can do I think is to just error better like in r-lib/evaluate#23 but in another place. It seems the connection is altered and became invalid before the check was made. isOpen(con) does not return FALSE but just errors.

So overall, closeAllConnections() can't be used in a knitting context. A text connection is open during the knitr process to catch output, warning, etc... If close, then it won't work.

@yihui quite old issue r-lib/evaluate#23 but I think we need to protect better in evaluate, don't we ?

[yihui]

isOpen(con) does not return FALSE but just errors.

Perhaps we should try() and detect error there.

[cderv]

I was thinking of that yes. But the first one happens at
https://github.com/r-lib/evaluate/blob/17918f626659ca3d1e677a6b9dde5b66613c7314/R/watcher.R#L18

processing file: test.Rmd
  |............................................................................................................................| 100% [unnamed-chunk-2]
Quitting from lines 11-12 [unnamed-chunk-2] (test.Rmd)
Error in `isIncomplete()`:
! invalid connection
Backtrace:
  1. knitr::knit("test.Rmd")
  2. knitr:::process_file(text, output)
  6. knitr:::process_group.block(group)
  7. knitr:::call_block(x)
  8. knitr:::block_exec(params)
     ...
 13. evaluate::evaluate(...)
 14. evaluate:::evaluate_call(...)
 15. evaluate (local) handle_output(TRUE)
 16. w$get_new(plot, incomplete_plots, output_handler$text, output_handler$graphics)
 17. base::isIncomplete(con)

Quitting from lines 11-12 [unnamed-chunk-2] (test.Rmd)
Error in `isOpen()`:
! invalid connection
Backtrace:
  1. knitr::knit("test.Rmd")
  2. knitr:::process_file(text, output)
  6. knitr:::process_group.block(group)
  7. knitr:::call_block(x)
  8. knitr:::block_exec(params)
     ...
 12. knitr (local) evaluate(...)
 13. evaluate::evaluate(...)
 14. evaluate:::evaluate_call(...)
 15. w$close()
 16. base::isOpen(con)

Seems like the all connection closing is make the con object invalid, which requires us an extra check maybe

[yihui]

Seems like the all connection closing is make the con object invalid, which requires us an extra check maybe

Yes, and done: r-lib/evaluate@25c3ceb

[cderv]

Awesome thanks @yihui !

@guslipkin I don't think we can do much more here in Quarto so I'll close this thread.

Thanks a lot for the report!