rmarkdown does not render PDFs as batch

[ajam21]

This is a cross-post from StackOverflow where no solution is provided.

rmarkdown does not render PDFs as batch

I have a rmarkdown file that renders well in RStudio with the Knitr button or with rmarkdown() but does not render when rendered as part of a batch with purrr::walk() and being passed a parameter. The batch issue only occurs when fig.show="hold", out.width="50%" is included in a section of the rmarkdown file.

library(purrr)
library(tinytex)
SurveySet <- c(20,19,68,79,30,18,42)
purrr::walk(
  .x = SurveySet,
  ~ rmarkdown::render(
    input = "Test.Rmd",
    output_file = glue::glue("REPORTS/Report Fails {.x}.pdf"),
    params = list(Unit = {.x})
  )
)
purrr::walk(
  .x = SurveySet,
  ~ rmarkdown::render(
    input = "TestWorks.Rmd",
    output_file = glue::glue("REPORTS/Report Works {.x}.pdf"),
    params = list(Unit = {.x})
  )
)

Test.Rmd as

---
title: "`r params$Unit`"
output: pdf_document
params:
  Unit: 68
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```

## R Markdown
This Document renders with RStudio Knitr button but not with batch

```{r figures-side, fig.show="hold", out.width="50%"}
par(mar = c(4, 4, .1, .1))
plot(cars)
plot(mpg ~ hp, data = mtcars, pch = 19)
```

TestWorks.Rmd as

---
title: "`r params$Unit`"
output: pdf_document
params:
  Unit: 68
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```

## R Markdown
Without fig.show="hold", out.width="50%" this document renders individually and as batch

```{r figures}
par(mar = c(4, 4, .1, .1))
plot(cars)
plot(mpg ~ hp, data = mtcars, pch = 19)
```

[cderv]

@ajam21

The batch issue only occurs when fig.show="hold", out.width="50%" is included in a section of the rmarkdown file.

What is the issue you are getting exactly ?
When rendering rmarkdown in batch, you may want to render in background session to get a clean state at each render. Using callr package can help with that

Something like

callr::r_safe(
    function(...) rmarkdown::render(...),
    args = list(
      "Test.Rmd",
      output_file = glue::glue("REPORTS/Report Fails {set}.pdf"),
      params = list(Unit = {.x})
      envir = globalenv()
) )

or similar.

@ajam21

params = list(Unit = {.x})

Why using {.x}here and not just .x ? Just curious

[ajam21]

Thanks. {.x} instead of .x reflects my inexperience and lack of complete understanding of R I'm afraid. I am a 'self-taught' coder and consequently have big gaps in my understanding. Implementing callr as the code chunk below also did not work.

purrr::walk(
  .x = SurveySet,
  ~ callr::r_safe(
    function(...) rmarkdown::render(...),
    args = list(
      input = "Test.Rmd",
      output_file = glue::glue("REPORTS/Report Fails {.x}.pdf"),
      params = list(Unit = .x),
      envir = globalenv()
    ) ) )

You have been a big help however. I have discovered that the behaviour is even more odd than it first appeared . The following works.

purrr::walk(
  .x = SurveySet,
  ~ rmarkdown::render(
    input = "Test.Rmd",
    output_file = glue::glue("Report Fails {.x}.pdf"),
    params = list(Unit = .x)
  ))

ie removing the target directory. However setting the directory with the output_dir = "REPORTS" argument causes the process to fail again. But only for Test.Rmd not for TestWorks.Rmd. It is odd that this is

Error message:
output file: Test.knit.md

"C:/R/Rstudio/bin/pandoc/pandoc" +RTS -K512m -RTS Test.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc1cd0905719b.tex --lua-filter "C:\R\R-4.1.1\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\R\R-4.1.1\library\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --highlight-style tango --pdf-engine pdflatex --variable graphics --variable "geometry:margin=1in"
! Undefined control sequence.
C:Users
user details....
l.77 ...ails 20_files/figure-latex/figures-side-1}

Error: LaTeX failed to compile C:/Users/../../../Survey Response/REPORTS/Report Fails 20.tex. See The R package tinytex - Helper Functions to Manage TinyTeX, and Compile LaTeX Documents - Yihui Xie | 谢益辉 for debugging tips. See Report Fails 20.log for more info.

Edit. A comment on StackOverflow also observes that replacing whitespace makes the process work ie REPORTS/Report-Fails-{.x}.pdf

[cderv]

@ajam21

Edit. A comment on StackOverflow also observes that replacing whitespace makes the process work ie REPORTS/Report-Fails-{.x}.pdf

Oh I did not notice whitespace. There must be something conflicting in path as we are trying our best to remove special chars and whitespace. Maybe that is causing issue

Anwyay, it is best to not use white space and not use a dir in output_file. rmarkdown::render() works best when everything happens in the same folder. Usually if you want the outputs elsewhere, you can just copy the resulting files elsewhere after rendering and before rendering a new one.

@ajam21

Implementing callr as the code chunk below also did not work.

Mixing purrr::walk() and render() and callr is not easy. Everything will have implicit environment and this may not work well.

I think you should just

• Use a for-loop for the rendering
• Wrap the callr call into a function and test that this function is working.

This would loook like

render_rmd <- function(...) {
   # code with callr to render a Rmd
}

for (x %in% SurveySet) {
  # render rmd for each value
}

Something like that.

Hope it helps