Issue with inline R Notebook YAML header processing involving !expr

[connorp]

System details

RStudio Edition : Desktop
RStudio Version : 1.3.1056
OS Version      : macOS 10.15.5
R Version       : 4.0.2

Steps to reproduce the problem

1. (With R freshly restarted) Create a new R Notebook file via the RStudio File menu, with the following contents (the specific function passed via !expr is not important to the reprex. kable() is used only as one example):

   ---
   title: "R Notebook"
   output: 
     html_notebook:
       df_print: !expr knitr::kable
   ---
   
   ```{r}
   plot(cars)
   ```

2. Save the file.

3. Run the code block inline. Observe the warning messages in the console, in addition to the expected plot.

4. Restart R and clear output.

5. Run the code block inline again. This time, there is no warning message.

Describe the problem in detail

yaml.load() now throws a warning when a YAML header includes an R expression to be evaluated, indicated by !expr, unless the eval.expr = TRUE option is explicitly set (and this warning will eventually be changed to an error). The rmarkdown package sets this option and works fine in knitted R Markdown documents, but when code is run inline within an R Notebook in RStudio, the code executes as expected, but the warnings are also still reported:

Warning messages:
1: In yaml.load(string, error.label = error.label, ...) :
  Evaluating R expressions (!expr) will soon require explicit `eval.expr` option (see yaml.load help)
2: In yaml.load(string, error.label = error.label, ...) :
  Evaluating R expressions (!expr) will soon require explicit `eval.expr` option (see yaml.load help)
3: In yaml.load(string, error.label = error.label, ...) :
  Evaluating R expressions (!expr) will soon require explicit `eval.expr` option (see yaml.load help)

Describe the behavior you expected

The code should be run without any warnings issued, regardless of whether R has been restarted or outputs cleared. Further discussion in rstudio/rmarkdown#1093.

• I have read the guide to submitting good bug reports at https://github.com/rstudio/rstudio/wiki/Writing-Good-Bug-Reports .
• I have installed the latest version of RStudio and confirmed that the issue still persists.
• If I am reporting a RStudio crash, I have included a diagnostics report. https://support.rstudio.com/hc/en-us/articles/200321257-Running-a-Diagnostics-Report
• I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.

[ronblum]

@connorp Thank you for raising the issue, which I can reproduce in RStudio Desktop 1.4.673 on MacOS 10.15.6. We'll review it as we continue development of RStudio.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs, per https://github.com/rstudio/rstudio/wiki/Issue-Grooming. Thank you for your contributions.

[joshpk]

Adding that this is still an issue

[cderv]

For reference, I believe this happens because there are still some R code in the IDE using yaml 📦 which use the default, leading to this warning being thrown

Examples

rstudio/src/cpp/session/modules/SessionRMarkdown.R

Line 248 in 5ceee58

yaml::yaml.load_file(templateYaml)

rstudio/src/cpp/session/modules/SessionRMarkdown.R

Line 382 in 5ceee58

data <- .rs.scalarListFromList(yaml::yaml.load(yaml, handlers = handlers))

As a workaround, setting options(yaml.eval.expr = TRUE) in .Rprofile for example should remove the warning for this in the IDE.

For reference as mentioned above, rmarkdown sets eval.expr to TRUE in rmarkdown:::yaml_load

[cderv]

FWIW the YAML package will probably use eval.expr = FALSE by default in upcoming version (vubiostat/r-yaml@d236f9a)

The message should disappear then, but maybe this will change some things as the IDE does rely on the default version and only has a handler for !r and not !expr.

[kevinushey]

Does df_print: knitr::kable work? Couldn't rmarkdown read and evaluate the YAML string itself here?

[kevinushey]

We could also evaluate whether we could make use of our embedded copy of yaml-cpp here.

[cderv]

Couldn't rmarkdown read and evaluate the YAML string itself here?

rmarkdown sets eval.expr = TRUE by default in its reading function: https://github.com/rstudio/rmarkdown/blob/4c31109dbd6efa6d7e0df1f84689764c6adc591a/R/util.R#L133

yaml_load <- function(...) yaml::yaml.load(..., eval.expr = TRUE)
yaml_load_file <- function(input, ...) yaml_load(read_utf8(input), ...)

However, it only use the default provided handler for !expr and do not define a handler for !r. knitr does though as it is there that params are handled.

[kevinushey]

Bumping milestone as I suspect this is going to affect almost all rmarkdown users.

[romainfrancois]

Verified on build 2022.06.0 + 220.