rsconnect::appDependencies evaluates eval parameter in rmarkdown chunks and might produce warnings

[dirkschumacher]

Context

I have an rmarkdown file that uses the eval parameters in chunks to control which chunks get evaluated. The idea is for that specific application that the code envoking rmarkdown::render can control what chunks will be evaluated instead of the report itself in order to keep the login in the markdown file as small as possible.

Problem

When rsconnect::appDependencies() is invoked it evaluates the code in each eval parameter and thus producing a warning. These warnings are in particularly genereted during deployments to RStudio Connect. / shinyapps.io. Nothing breaks though.

Reproducible example

Create a file "test.Rmd" with a single chunk

```{r test, eval=show_chunk} 
summary(cars)
```

then:

> rsconnect::appDependencies()
Error in eval(x, envir = envir) : object 'show_chunk' not found

Here is an example of how it is used:

rmarkdown::render("test.Rmd", envir = list(show_chunk = TRUE))
rmarkdown::render("test.Rmd", envir = list(show_chunk = FALSE))

Potential solution

• One option could be to suppressWarnings when evaluating eval, but this might have other unintented sideeffects.

[dirkschumacher]

Might be related to #429

[jmcphers]

Yes, this is likely a side effect of the dependency discovery scan.

Do you see the same error when you run rmarkdown::find_external_resources() on your doc?

[aronatkins]

This problem was caused by using rmarkdown::render to analyze R Markdown files for dependencies.

We believe that this is resolved with rstudio/packrat#647.