Hello,
There seems to be an issue in how the R warning option (options()$warn) is handled inside an Rmd file.
This might be related to an older issue #1425 (comment)

The warn option does not correctly persist across the Rmd file chunks.

Here is an example code to test the behaviour:

```{r part1}
f <- function(x) {warning("Warning raised!"); x}

options(warn = 0)
options()$warn
f(TRUE)
```
#>[1] 0
#>[1] TRUE
#>Warning message:
#>In f(TRUE) : Warning raised!

```{r part2}
options(warn = 1)
options()$warn
f(TRUE)

options(warn = 2)
```
#>[1] 1
#>Warning in f(TRUE) : Warning raised!
#>[1] TRUE

```{r ops-fail}
options()$warn
f(TRUE)
```
#>[1] 1
#>Warning in f(TRUE) : Warning raised!
#>[1] TRUE

Last options()$warn reports value of 1, and thus the last call to f() does not raise an error, even though the option was explicitly set in the previous code chunk.
This should not be related to the evaluate package, as it only handles evaluation of a single chunk

I hope this is helpful.

Session info:

xfun::session_info("rmarkdown")
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22621), RStudio c(2024, 4, 2, 764)

Locale:
  LC_COLLATE=Finnish_Finland.utf8  LC_CTYPE=Finnish_Finland.utf8   
  LC_MONETARY=Finnish_Finland.utf8 LC_NUMERIC=C                    
  LC_TIME=Finnish_Finland.utf8    

Package version:
  base64enc_0.1.3   bslib_0.7.0       cachem_1.1.0      cli_3.6.3        
  digest_0.6.36     evaluate_0.24.0   fastmap_1.2.0     fontawesome_0.5.2
  fs_1.6.4          glue_1.7.0        graphics_4.4.1    grDevices_4.4.1  
  highr_0.11        htmltools_0.5.8.1 jquerylib_0.1.4   jsonlite_1.8.8   
  knitr_1.48.1      lifecycle_1.0.4   memoise_2.0.1     methods_4.4.1    
  mime_0.12         R6_2.5.1          rappdirs_0.3.3    rlang_1.1.4      
  rmarkdown_2.27    sass_0.4.9        stats_4.4.1       tinytex_0.52     
  tools_4.4.1       utils_4.4.1       xfun_0.46         yaml_2.3.9       

Pandoc version: 3.1.11

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