knitr: process ANSI color codes

[GegznaV]

Bug description

Colors or R warnings (see 1 in the figure) in Quarto are marked with symbols (see 2, 3). These symbols must not be present.

Steps to reproduce

```{r}
with(airquality, table(OzHi = Ozone > 80, Month)) |> 
  DescTools::Desc(plotit = FALSE)
```

Expected behavior

No extra symbols of color codes. e.g.

/.../
Mantel-Haenszel Chi-squared:
  X-squared = 1.1306, df = 1, p-value = 0.2876

Warning message:
  Exp. counts < 5: Chi-squared approx. may be incorrect!!

Contingency Coeff.     0.287
Cramer's V             0.300
Kendall Tau-b          0.065

/.../

If possible, the colored output would be appreciated too. But at least no extra symbols would be nice too.

Actual behavior

/.../
Mantel-Haenszel Chi-squared:
  X-squared = 1.1306, df = 1, p-value = 0.2876
�[31m
Warning message:
  Exp. counts < 5: Chi-squared approx. may be incorrect!!

�[39m
Contingency Coeff.     0.287
Cramer's V             0.300
Kendall Tau-b          0.065
/.../

Your environment

RStudio Edition : Desktop [Open Source]
RStudio Version : 2023.6.0.401
OS Version      : Windows 10 x64 (build 19045)
R Version       : R version 4.3.0 (2023-04-21 ucrt)
Quarto:         : 1.4.111

Quarto check output

$ quarto check

[>] Checking versions of quarto binary dependencies...
      Pandoc version 3.1.2: OK
      Dart Sass version 1.55.0: OK
      Deno version 1.33.2: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
      Version: 1.4.111
      Path: C:\Users\user\AppData\Local\Programs\Quarto\bin
      CodePage: 1257

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

[>] Checking Python 3 installation....OK
      Version: 3.9.15 (Conda)
      Path: C:/Users/user/anaconda3/python.exe
      Jupyter: 5.2.0
      Kernels: ir, julia-1.9, proj-ml-1, python3

(\) Checking Jupyter engine render....2023-05-30 19:08:32,583 - traitlets - ERROR - Failed to run command:
['C:\\Users\\user\\anaconda3\\envs\\proj-ml-1\\python.exe', '-m', 'ipykernel_launcher', '-f', 'C:\\Users\\user\\AppData\\Local\\Temp\\tmp5bcejmxp.json']
    PATH='C;C:\\Program Files\\Git\\Users\\user\\anaconda3;C;C:\\Program Files\\Git\\Users\\user\\anaconda3\\Scripts;C:\\Users\\user\\anaconda3;C:\\Users\\user\\anaconda3\\Library\\mingw-w64\\bin;C:\\Users\\user\\anaconda3\\Library\\usr\\bin;C:\\Users\\user\\anaconda3\\Library\\bin;C:\\Users\\user\\anaconda3\\Scripts;C:\\Users\\user\\anaconda3\\bin;C:\\Users\\user\\anaconda3\\condabin;C:\\Program Files\\RStudio\\resources\\app\\resources\\terminal\\bash\\bin;C:\\Program Files\\Git\\mingw64\\bin;C:\\Program Files\\Git\\usr\\local\\bin;C:\\Program Files\\Git\\usr\\bin;C:\\Program Files\\Git\\usr\\bin;C:\\Program Files\\Git\\mingw64\\bin;C:\\Program Files\\Git\\usr\\bin;C:\\Program
Files\\RStudio\\resources\\app\\resources\\terminal\\bash\\bin;C:\\Users\\user\\anaconda3\\Scripts;C:\\Users\\user\\anaconda3;C:\\RBuildTools\\4.3\\x86_64-w64-mingw32.static.posix\\bin;C:\\RBuildTools\\4.3\\usr\\bin;C:\\Program Files\\R\\R-4.3.0\\bin\\x64;C:\\Program Files\\Microsoft MPI\\Bin;C:\\Python39\\Scripts;C:\\Python39;C:\\Rtools\\bin;C:\\ProgramData\\Boxstarter;C:\\Program Files\\ImageMagick-7.0.8-Q16;C:\\Rtools\\bin;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath;C:\\Rtools\\mingw_32\\bin;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v8.0\\bin;C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v8.0\\libnvvp;C:\\Program Files\\ImageMagick-6.9.3-Q16;C:\\ProgramData\\Oracle\\Java\\javapath;C:\\Program Files (x86)\\Intel\\iCLS Client;C:\\Program Files\\Intel\\iCLS Client;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\IPT;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\IPT;C:\\Program Files\\Intel\\WiFi\\bin;C:\\Program Files\\Common Files\\Intel\\WirelessCommon;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\Program Files (x86)\\Aspell\\bin;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Program Files (x86)\\QuickTime\\QTSystem;C:\\Program Files\\MiKTeX 2.9\\miktex\\bin\\x64;C:\\Program Files\\R\\R-3.4.0\\library\\tcltk\\libs\\x64;C:\\WINDOWS\\System32\\OpenSSH;C:\\Users\\user\\AppData\\Local\\Programs\\orca;C:\\Program
Files\\Microsoft VS Code\\bin;C:\\Program Files\\R\\R-3.5.1\\bin;C:\\ProgramData\\chocolatey\\bin;C:\\Program Files\\NVIDIA Corporation\\NVIDIA NvDLISR;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0;C:\\WINDOWS\\System32\\OpenSSH;C:\\Program Files\\SourceGear\\Common\\DiffMerge;C:\\Program Files\\Git LFS;C:\\Program Files\\TortoiseSVN\\bin;C:\\Program Files\\dotnet;C:\\Program Files (x86)\\Common Files\\Acronis\\VirtualFile;C:\\Program Files (x86)\\Common Files\\Acronis\\VirtualFile64;C:\\Program Files (x86)\\Common Files\\Acronis\\SnapAPI;C:\\Program Files\\Crucial\\Crucial Storage Executive;C:\\Program Files (x86)\\Microsoft SQL Server\\150\\Tools\\Binn;C:\\Program Files\\Microsoft SQL Server\\150\\Tools\\Binn;C:\\Program Files (x86)\\Microsoft SQL Server\\150\\DTS\\Binn;C:\\Program Files\\Microsoft SQL Server\\150\\DTS\\Binn;C:\\Program Files\\Microsoft SQL Server\\Client SDK\\ODBC\\170\\Tools\\Binn;C:\\Program Files\\Azure Data Studio\\bin;C:\\Program Files\\PuTTY;C:\\Program Files\\gs\\gs9.56.1\\bin;C:\\Program Files\\Docker\\Docker\\resources\\bin;C:\\ProgramData\\DockerDesktop\\version-bin;C:\\Program Files\\gnuplot\\bin;C:\\Program Files (x86)\\Meld;C:\\Program Files\\nodejs;C:\\Program Files\\Git\\cmd;C:\\Program Files\\PowerShell\\7;C:\\Users\\user\\AppData\\Local\\P[>] Checking Jupyter engine render....OK

[mcanouil]

The output is not really handle by Quarto (you'll get the same thing with rmarkdown).
If you want special formatting, you'll have to use chunk hooks for example.
Related discussion for cli: #3957.

Here is a partial example to get you started:

---
title: "Quarto Playground"
format: html
---

This is a playground for Quarto.

```{r}
library(knitr)
knit_print.Desc <- function(x, options) {
  fansi::sgr_to_html(
    x = paste(capture.output(DescTools:::print.Desc(x)), collapse = "\n"),
    warn = FALSE,
    term.cap = "256"
  )
}
registerS3method("knit_print", "Desc", knit_print.Desc)
```

```{r}
#| output: asis
library(DescTools)
DescTools::Desc(with(airquality, table(OzHi = Ozone > 80, Month)), plotit = FALSE)
```

[mcanouil]

Closing this, as it is not planned to handle any possible output, especially because, the same would need to be done for all R packages and the same for any supported languages.

[cscheid]

I'm going to reopen this as an enhancement issue: we already process ANSI color code in jupyter output, and it might be possible to do something in the knitr side as well.

[mcanouil]

Oh really, there have been few discussion about knitr and ansi colour, especially for cli.
Great news!

@cscheid Thanks for correcting me on this 😉

[cscheid]

See #4204. Even in Julia our support isn't great, and ideally we'd fix it across all engines.

[GegznaV]

@mcanouil, thank you for your insights. Still, iId like to clarify 2 things:

1. In:

```{r}
#| output: asis
library(DescTools)
DescTools::Desc(with(airquality, table(OzHi = Ozone > 80, Month)), plotit = FALSE)
```

Did you mean #| results: asis?

2. Using the hook, is this a reasonable way to remove ANSI codes:

```{r}
library(knitr)
knit_print.Desc <- function(x, options) {
  stringr::str_remove_all(
    paste(capture.output(DescTools:::print.Desc(x)), collapse = "\n"),
    "\\x1b\\[[0-9;]*m"

  )
}
registerS3method("knit_print", "Desc", knit_print.Desc)
```