Knitr doesn't find function from previous chunk when using custom knit function and evaluating quoted function in a list

3
votes

I've been running into strange cases where knitting an R markdown document fails when a chunk is unable to find a function that was defined in a previous chunk.

I isolated one of them below (the most I could) and this is how it fails:

  • runs with no problem when running each chunk manually
  • knitting only fails if I use the custom knit function in the YAML header
  • knitr only fails to find the function when I eval a quoted expression AND within a list/map function (lapply or purrr::)
    • i.e. there's no issue if I do eval(an_eval[[1]])

Reproducible Rmd file contents

---
output:
  html_document

knit: (function(input, encoding) {
    rmarkdown::render(
      input = input,
      encoding = encoding,
      output_file = 'a_file.html'
    )
  })
---

```{r}
library(knitr)
```

```{r define_function}
a_function <- function() return("a function")
```

```{r runs_fine}
a_function()
```

```{r this_fails}
an_exprs <- list(quote(a_function()))
lapply(an_exprs, eval)
```

Error:

Quitting from lines 26-28 (Debug.Rmd) 
Error in a_function() : could not find function "a_function"
Calls: <Anonymous> ... withVisible -> eval -> eval -> lapply -> FUN -> FUN
Execution halted

Session:

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] knitr_1.28
1
rr-markdownknitr

1 Answers

2
votes

You need to specify the envir argument of rmarkdown::render() in this case, otherwise the default environment is parent.frame(), which is the internal environment of the (anonymous) function you provided to knit in YAML.

---
output:
  html_document

knit: (function(input, encoding) {
    rmarkdown::render(
      input = input,
      encoding = encoding,
      envir = globalenv()
    )
  })
---

```{r}
library(knitr)
```

```{r define_function}
a_function <- function() return("a function")
```

```{r runs_fine}
a_function()
```

```{r this_fails}
an_exprs <- list(quote(a_function()))
lapply(an_exprs, eval)
```