Slide break not recognised when rendered with the Knit button

[charliejhadley]

This is a weird bug, it occurs only in {xaringan} slides when RStudio's "Knit" button is used. Please follow these steps for a reprex:

• Create the following .Rmd file and save it into an RStudio project.

---
title: "Works in moonreader, but not knitted"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
maps::world.cities
```

---

## Slide with code

Eg `foobar` 

• When knit the output HTML document will have a different number of slides based on how it was knitted.

How knitted	What happens
Using RStudio's "Knit" button (tested with latest version 1.4.1717)	The output document has 2 slides, the slide break is ignored
Using xaringan:::inf_mr()	The output document has 3 slides (which it should have)
Using `rmarkdown::render("the-file.Rmd")	The output document has 3 slides (which it should have)

It appears the following circumstances lead to this bug:

• The YAML option df_print is set to paged
• A slide contains a code chunk that prints a data.frame
• Any slide afterwards contains either inline code or a code chunk.

The bug does not occur if slides after the slide with a printed data.frame do not contain code, eg this .Rmd file is unaffected:

---
title: "Works regardless"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
maps::world.cities
```

---

## Slide without code

Eg the quick brown fox....

While there is already a fix - using rmarkdown::render() - I would argue that most RMarkdown user's either click this button or use the Cmd+Shift+K keyboard shortcut which does the same thing.

I also acknowledge that this bug might be better placed against the RStudio IDE instead of {xaringan}, I'm happy to re-report this elsewhere if you would prefer.

xfun::session_info('xaringan')

> xfun::session_info('xaringan')
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  11.5.2, RStudio 1.4.1717

Locale: en_GB.UTF-8 / en_GB.UTF-8 / en_GB.UTF-8 / C / en_GB.UTF-8 / en_GB.UTF-8

Package version:
  base64enc_0.1.3  digest_0.6.27    evaluate_0.14    fastmap_1.1.0    glue_1.4.2       graphics_4.0.3  
  grDevices_4.0.3  highr_0.9        htmltools_0.5.2  httpuv_1.6.2     jsonlite_1.7.2   knitr_1.33      
  later_1.3.0      magrittr_2.0.1   markdown_1.1     methods_4.0.3    mime_0.11        promises_1.2.0.1
  R6_2.5.1         Rcpp_1.0.7       rlang_0.4.11     rmarkdown_2.10   servr_0.23       stats_4.0.3     
  stringi_1.7.4    stringr_1.4.0    tinytex_0.33     tools_4.0.3      utils_4.0.3      xaringan_0.22   
  xfun_0.25        yaml_2.2.1    

---

By filing an issue to this repo, I promise that

• [x] I have fully read the issue guide at https://yihui.org/issue/.
• [x] I have provided the necessary information about my issue.
  • If I'm asking a question, I have already asked it on Stack Overflow or RStudio Community, waited for at least 24 hours, and included a link to my question there.
  • If I'm filing a bug report, I have included a minimal, self-contained, and reproducible example, and have also included xfun::session_info('xaringan'). I have upgraded all my packages to their latest versions (e.g., R, RStudio, and R packages), and also tried the development version: remotes::install_github('yihui/xaringan').
  • If I have posted the same issue elsewhere, I have also mentioned it in this issue.
• [x] I have learned the Github Markdown syntax, and formatted my issue correctly.

I understand that my issue may be closed if I don't fulfill my promises.

[yihui]

That sounds like a really weird bug. @cderv Could you take a look? Thanks!

[cderv]

Wow, this is indeed a weird bug!

• I can reproduce with last daily version 2021.11.0-daily+26 so this is not great.
• I confirm that the cause seems to be df_print: paged when following slide contains code chunk

This only happens in RStudio IDE so I believe it has something to do with what the IDE is doing with paged table. I believe some hooks are used inside the IDE directly to replace R functions. This could lead to differences in behavior between Knitting in the IDE and Knitting at command line.

Thanks for the great report @charliejhadley !! It helps.

We'll need to investigate more now - and yes this is an issue with RStudio IDE not xaringan I believe.

[cderv]

To investigate further, I compared the different output and found a difference.

How rendering works with paged table ?

Small reminder on how this works:

• When using paged table, this will output raw HTML in the markdown.
• When using xaringan, the raw HTML is now then processed by Pandoc but included into the markdown <textarea> of the HTML file and parsed by remark.js parser to be rendered to HTML.

Differences between IDE rendering and Console rendering

Regarding the differences between IDE rendered and Console rendered

• When Knitting in the IDE, the HTML table included is longer than the one included when Knitting. The former has 10000 values included, and the later has 1000 values included.
• You can see that at the bottom of the paged table generated:
  • When knitting in IDE:
  • When rendering in console:
• It seems this could lead to an issue with remark.js markdown parser which "breaks" when the HTML table inserted is too long.

I can confirm that slicing the data.frame before printing will solve this.

---
title: "Works regardless"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
utils::head(maps::world.cities, 1000)
```

---

## Slide with code

Eg `foobar` 

One thing to note here is that, world.cities is big data.frame

nrow(maps::world.cities)
#> [1] 43645

Usually, it is not a good idea to print the whole data.frame in an HTML document - it could cause performance issues. It is why by default, rmarkdown::paged_table_html() will print a maximum of row defined by option max.print (documented in https://bookdown.org/yihui/rmarkdown/html-document.html#paged-printing), which will default to 1000 if unset. (https://github.com/rstudio/rmarkdown/blob/0af6b3556adf6e393b2da23c66c695724ea7bd2d/R/html_paged.R#L101) There is also a hard max to 10000 to prevent Pandoc from failing I believe: https://github.com/rstudio/rmarkdown/blob/0af6b3556adf6e393b2da23c66c695724ea7bd2d/R/html_paged.R#L108

Obviously, using it directly solves also the issue as this works.

---
title: "Works in moonreader, but not knitted"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r, max.print = 1500}
maps::world.cities
```

---

## Slide with code

Eg `foobar` 

Regarding max.print value

I believe the IDE is also setting/checking these options https://github.com/rstudio/rstudio/blob/26a10a6b1151474b5b447492a5716e0e3ff06db2/src/cpp/r/R/Options.R#L116-L124

Default for max.print is 99999 (see ?options). So, by default, it would trigger the 10000 max row. But behavior is also different regarding this options...

Test file

---
title: "Works regardless"
output: html_document
---

```{r}
getOption('max.print')
```

• Rendering using Knit button in IDE with html_document, we get a value of 99999
• Running the code chunk in the IDE, we get a value of 1000 - this seems to prove that the IDE sets the option.
• Which is confirmed when running getOption("max.print") in R console in the IDE
• Rendering using rmarkdown::render(), we get a value of 1000 - I believe because the value of max.print set by the IDE is used.
• Rendering in a background process (e.g using callr or xfun::Rscript_call()) get us the default value of 99999

I believe this is why we get this different behavior depending on how the document is rendered.

Regarding remark.js parsing

In addition to the max.print value, I believe there is something with remark.js parser when this long table is inserted and following slide contains code chunk, as found and detailed in this thread. Maybe there is a character issue in some line of the table that is causing the issue with the parse ? This would be trickier to debug and another story.

So what is the issue and what could we do ?

I did not try yet with other data to confirm that the long HTML table is the issue. Maybe it is something with the content of this HTML table with a character which is not escaped correctly causing remark.js parser to break. This could also be the cause.

@yihui what do you think is the pass forward ?

• Should we look into upstream issue with remark.js to understand why it break ?
• Should we rethink / complement this max.print issue, specifically in xaringan ? (table will probably be small in xaringan)
• Does this analysis give you some more ideas ?

[cderv]

Maybe it is something with the content of this HTML table with a character which is not escaped correctly causing remark.js parser to break. This could also be the cause.

Just to confirm my hunch I looked at this hypothesis, and I believe this is what is causing the issue: The world.cities dataset contains a cityname with a backtick character (`) which I believe is causing the error.

The city is question is Bani Bu `Ali , row 3238

If we try to remove it, we have 3 slides as expected

---
title: "Works regardless"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
maps::world.cities[-3238,]
```

---

## Slide with code

Eg `foobar` 

@charliejhadley I believe this is an issue of character escaping, as xaringan uses remark.js which will parse the content of the body as Markdown.

Can you confirm this works for you?

[charliejhadley]

Ahh, great to see you've discovered what was causing this @cderv! Yup, knocking out row 3238 makes the Knit button behave the same as rmarkdown::render().

You've probably already realised there's a more minimal reprex now, but just in case here you go:

---
title: "Knit button weirdness"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
data.frame(
  names = c("foo", "foo `")
)
```

---

## Slide with code

Eg `foobar` 

[cderv]

yes thanks for sharing this !

I knew I have encountered this before and I think this issue is in a way a duplicate of https://github.com/yihui/xaringan/issues/272

Same type of issue with the parser

[charliejhadley]

Ooops @cderv I made a mistake! That's not actually a reprex for the issue I first reported because that .Rmd behaved identically for the Knit button and rmarkdown::render().

This is a slightly simpler, true reprex of my initial issue, and it demonstrates there is something very specific about the order of the vector maps::world.cities$name that is causing the issue.

---
title: "Knit button misbehaves"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
cities <- maps::world.cities$name
positions_of_backticks <- which(grepl("`", cities))

data.frame(
  names = c(
    cities[1:{positions_of_backticks[1] - 1}],
    "Bani Bu `Ali",
    cities[{positions_of_backticks[1] + 1}:{positions_of_backticks[2] - 1}],
    "Wad-il-Ma`awil",
    cities[{positions_of_backticks[2] + 1}:{positions_of_backticks[3] - 1}],
    "al-`Amarat",
    "al-`Awabi",
    cities[{positions_of_backticks[4] + 1}:{length(cities)}]
  )
)
```

---

## Slide with code

Eg `foobar` 

[cderv]

I believe the differences comes from the max.print value which differ when rendering inside RStudio with Knit button (and background session) or in current session in Console. I would say: is the backtick before 1000 rows or after ?

There are two issues:

1. Backtick non HTML escaped in the body of the document will make remark.js fail
2. It happens when this is in a table, depending on the number of rows included in the output. If included, the error 1 will happen. max.print has not the same value depending on how render is done.

No backticks - Works in both Button and Console

---
title: "Knit button misbehaves"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
cities <- maps::world.cities$name
positions_of_backticks <- which(grepl("`", cities))

maps::world.cities[-positions_of_backticks, ]
```

---

## Slide with code

Eg `foobar` 

backtick name at the 1001st row - Do not work with Button but works in Console

---
title: "Knit button misbehaves"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
cities <- maps::world.cities$name
positions_of_backticks <- which(grepl("`", cities))

df <- maps::world.cities[-positions_of_backticks, ]

df[1001, ]  <- maps::world.cities[positions_of_backticks[1], ]

df
```

---

## Slide with code

Eg `foobar` 

Backtick name at the 999th row - Does not work in both Button and Console

---
title: "Knit button misbehaves"
output:
  xaringan::moon_reader:
    df_print: paged
---

## Slide with paged df

```{r}
cities <- maps::world.cities$name
positions_of_backticks <- which(grepl("`", cities))

df <- maps::world.cities[-positions_of_backticks, ]

df[999, ]  <- maps::world.cities[positions_of_backticks[1], ]

df
```

---

## Slide with code

Eg `foobar` 

Is there more than that for you ?