A Change in the Meaning of the Chunk Option `message = FALSE` / `warning = FALSE` | /en/2022/12/message-false/

Feel free to be that person, and you will definitely get what you want in the next version of evaluate! :) I'll keep you posted. Thanks for the feedback!

With the dev versions of evaluate and knitr, you can go back to the old behavior with message = NA and warning = NA:

remotes::install_github(c('r-lib/evaluate', 'yihui/knitr'))

Allowed values of message and warning options are documented at https://yihui.org/knitr/options/#text-output They can only take logical and numeric values. Character values worked by chance previously because they were treated as TRUE (yihui/knitr@5ff3888).

In your example, I suggest you rename options$warning to something like options$known_warning to avoid overloading the chunk option warning, and use the chunk option known_warning to pass the character vector of known warnings. Sorry about the hassle!

Thanks for the reply. I had a feeling we might have been abusing the warning option and getting away with it by chance. Adopting the strategy you suggested works great, and I've updated the example at https://support.bioconductor.org/p/9141044/#9149469 in case anyone else stumbles across it.

Great! Thank you very much!

Thanks for explaining the use case! That makes sense to me. knitr::opts_chunk$set(message = NA, warning = NA) before rmarkdown::render() is the right way to go. If users have overridden these options, you can further override them via an option hook, e.g.,

knitr::opts_hooks$set(message = function(options) {
    options$message = options$warning = NA
    options
})

Then you call rmarkdown::render(), and the option hook will make sure options message and warning will be NA.

---
title: Hello
---

```{r, message=FALSE}
message('Hello World!')
```

If you test the above example, you should see the message in the R console. Please let me know if that helps.

Thanks!

Testing that right now - and first few lines of rendering looks like it is working 👍

I think in our case, the messages really are there for debug and progress monitoring - I think we're the opposite of what you said:

When users set message = FALSE, the more likely intention is “I’m sure I don’t want to see any messages anywhere from this code chunk”, instead of “I don’t want to see messages in the output document but want to see them in the console”.

With that in mind... is there a way to enable this hook by default in RStudio Connect RMarkdown rendering too? I'm currently think we could just add that hook$set code to the RProfile.site file - I think that should work.

Thanks for the prompt response - and for saving me from having to edit lots of separate Rmd's in lots of repos :)

Yes, you can set the hook in .Rprofile or Rprofile.site.

Thanks - I think for our logs there we'll probably set those and also turn the progress bars off - so we really are the opposite of what I've seen others post!

Thanks for the prompt help and responses today - awesome.

I always welcome different voices and opinions. Your use case of logging and debugging was in my blind spot. I'm glad that we have found a solution anyway!

If it helps anyone else, this is what we've got in our Rprofile.site

setHook(packageEvent("knitr", "onLoad"),
        function(...) {
          message_default <- FALSE
          installed <- installed.packages()
          if ("evaluate" %in% rownames(installed)) {
            evaluate_installed <- installed["evaluate",]
            evaluate_version <- evaluate_installed[["Version"]]
            evaluate_version <- package_version(evaluate_version)
            if (evaluate_version == package_version("0.19")) {
              message("evaluate version 0.19 is broken - there is no way to get log messages out")
            }
            if (evaluate_version >= package_version("0.20")) {
              message_default <- NA
            }
          }
          knitr::opts_chunk$set(message = message_default, warning = message_default)
          knitr::opts_hooks$set(message = function(options) {
            options$message = message_default 
            options$warning = message_default
            options
          })
        })

That works for us - but might be NOISY for other people :)

Thanks for sharing the solution!

Just a few minor comments: 1) evaluate is guaranteed to be available when knitr is loaded, so you don't need to test if it's installed; 2) packageVersion() gives you a package version; 3) you can directly compare a version number with a string (the latter will be automatically coerced to a version number). With these in mind, here is how I'd write the code (feel free to adopt or discard):

setHook(
  packageEvent('knitr', 'onLoad'),
  function(...) {
    v = packageVersion('evaluate')
    if (v == '0.19') message(
      'evaluate v0.19 is broken - there is no way to get log messages out'
    )
    knitr::opts_hooks$set(message = function(options) {
      options$message = options$warning = if (v >= '0.20') NA else FALSE
      options
    })
  }
)

Would you consider a PR that set this as the default behaviour - e.g. via an ENV option - maybe something like KNITR_SEND_MESSAGES_TO_CONSOLE?

If this was available, I think people at our company we would set it "TRUE" for all our user and server machines by default. Further, other people, who enjoy the silence more, would be able to "turn logging on/off" very easily - e.g. Posit Connect users would be able to easily turn verbose messages on/off for individual reports using the env tab in the Connect UI.

If you prefer using env vars, you can use R_KNITR_OPTIONS, e.g.,

R_KNITR_OPTIONS="knitr.chunk.message=NA,knitr.chunk.warning=NA"

This has existed for years but never been undocumented. It's not as terse as what you suggested, but is a general solution when you want to change the default values of any chunk options.

I was thinking I want a stronger option than that - I want an option that reverts the package to the old console logging behaviour regardless of any message=FALSE existing in code - i.e. similar to the setHook code.

But if it's not something we want to add to the package then no worries (y)

Oh I see what you mean now. In theory, I could add an env var. It should be a fairly simple change in either knitr or evaluate. Let me think more for a moment.

Done via r-lib/evaluate@ee0fa82. You can set R_EVALUATE_BYPASS_MESSAGES=true to get what you want.

Thanks.

I do expect this will be very useful for Connect users who want to get some temporary verbose output 👍

FYI the new version of evaluate is on CRAN now: https://cran.r-project.org/package=evaluate