rstudio
Knitting to pdf crashes with `out.width=` specification in the code chunk
---
title: 'Min example'
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
bookdown::html_document2:
df_print: paged
toc: TRUE
bookdown::word_document2: default
bookdown::pdf_document2:
toc: no
fig_caption: yes
number_sections: true
keep_tex: yes
always_allow_html: yes
latex_engine: pdflatex
---
```{r message=FALSE, warning = FALSE}
library(knitr)
library(rmarkdown)
library(plotly)
```
```{r, echo=FALSE, fig.cap="plotly_test", fig.topcaption=TRUE, warning=F, out.width="100%", out.height="100%"}
library(plotly)
p <- plot_ly(economics, x = ~date, y = ~unemploy / pop)
p
```
```{r, echo=TRUE}
xfun::session_info('rmarkdown')
```
output from xfun::session_info('bookdown')
> xfun::session_info('rmarkdown')
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8
Package version:
base64enc_0.1.3 bslib_0.4.2 cachem_1.0.7 cli_3.6.0
digest_0.6.31 ellipsis_0.3.2 evaluate_0.20 fastmap_1.1.1
fs_1.6.1 glue_1.6.2 graphics_4.2.2 grDevices_4.2.2
highr_0.10 htmltools_0.5.4 jquerylib_0.1.4 jsonlite_1.8.4
knitr_1.42 lifecycle_1.0.3 magrittr_2.0.3 memoise_2.0.1
methods_4.2.2 mime_0.12 R6_2.5.1 rappdirs_0.3.3
rlang_1.0.6 rmarkdown_2.20 sass_0.4.5 stats_4.2.2
stringi_1.7.12 stringr_1.5.0 tinytex_0.44 tools_4.2.2
utils_4.2.2 vctrs_0.5.2 xfun_0.37 yaml_2.3.7
Pandoc version: 3.1
When running the previous minimal example with rmarkdown::render('min_ex.rmd', output_dir = '../docs/report/', output_format = 'bookdown::pdf_document2', knit_root_dir = getwd()) I get the following error :
processing file: min_ex.rmd
|.............................. | 57% (unnamed-chunk-2)Quitting from lines 45-48 (min_ex.rmd)
Error in s$close() : attempt to apply non-function
If I change the r chunk specification from
```{r, echo=FALSE, fig.cap="plotly_test", fig.topcaption=TRUE, warning=F, out.width="100%", out.height="100%"}```
to
```{r, echo=FALSE, fig.cap="plotly_test", fig.topcaption=TRUE, warning=F}```
then the output is correctly knitted.
No problem when knitting to html.
Thanks I can reproduce and the traceback of the error is this
Error in `s$close()`:
! tentative d'appliquer un objet qui n'est pas une fonction
Backtrace:
1. rmarkdown::render("C:/Users/chris/Documents/test.Rmd", encoding = "UTF-8")
2. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
3. knitr:::process_file(text, output)
6. knitr:::process_group.block(group)
7. knitr:::call_block(x)
...
27. chromote:::synchronize(p, loop = private$child_loop)
31. base::tryCatch(...)
32. base (local) tryCatchList(expr, classes, parentenv, handlers)
33. base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
34. base (local) doTryCatch(return(expr), name, parentenv, handler)
Exécution arrêtée
This seems to be an issue with chromote as it is used by webshot2 which is called by knitr to take a screenshot of the HTMLWIDGET for including into the PDF.
i'll see if something has changed there or how it interfere with the options
Simplified example showing this is not bookdown related
---
title: "Min example"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output:
pdf_document: default
html_document:
df_print: paged
---
```{r message=FALSE, warning = FALSE}
library(plotly)
```
```{r}
#| out.height="100%"
library(plotly)
p <- plot_ly(economics, x = ~date, y = ~unemploy / pop)
p
```
Full error
Error in `s$close()`:
! attempt to apply non-function
---
Backtrace:
▆
1. └─rmarkdown::render("test.Rmd")
2. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
3. └─knitr:::process_file(text, output)
4. ├─base::withCallingHandlers(...)
5. ├─base::withCallingHandlers(...)
6. ├─knitr:::process_group(group)
7. └─knitr:::process_group.block(group)
8. └─knitr:::call_block(x)
9. └─knitr:::block_exec(params)
10. └─knitr:::eng_r(options)
11. ├─knitr:::in_input_dir(...)
12. │ └─knitr:::in_dir(input_dir(), expr)
13. └─knitr (local) evaluate(...)
14. └─evaluate::evaluate(...)
15. └─evaluate:::evaluate_call(...)
16. ├─base (local) handle(...)
17. ├─base::withCallingHandlers(...)
18. ├─base::withVisible(value_fun(ev$value, ev$visible))
19. └─knitr (local) value_fun(ev$value, ev$visible)
20. └─knitr (local) fun(x, options = options)
21. ├─base::withVisible(knit_print(x, ...))
22. └─knitr::knit_print(x, ...)
23. └─knitr:::html_screenshot(x)
24. ├─knitr:::in_dir(...)
25. ├─base::do.call(...)
26. └─webshot2 (local) `<fn>`(...)
27. └─cm$wait_for(p)
28. └─chromote:::synchronize(p, loop = private$child_loop)
29. ├─promises::with_promise_domain(...)
30. │ └─domain$wrapSync(expr)
31. │ └─base::force(expr)
32. └─base::tryCatch(...)
33. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
34. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
35. └─base (local) doTryCatch(return(expr), name, parentenv, handler)
So this is indeed an issue with webshot2 and chromote as it does not seem they accept width and height in %.
Currently when provided as knitr option on the chunk, we pass out.width and out.height (user specified or internally computed) as value to webshot2::webshot() - see
Here is a minimal reprex:
> webshot2::webshot("https://github.com/rstudio/shiny", vwidth = 468, vheight = "100%")
Error in s$close() : attempt to apply non-function
I don't think it can take % really, but they should at least error nicely if this is the case.
On our side, I wonder if we can pass some pixel value when a % value is passed to out.(witdh|height) options. @yihui in case you have an idea...
thanks for the report @oolonek. As a workaround, it seems older webshot 📦 (which is using deprecated phantomjs tool) accepts % so you can default to this in the meantime setting this in setup chunk
knitr::opts_chunk$set(webshot = "webshot")
or webshot = "webshot" as chunk option.
Hope it helps
Thanks for the workaround @cderv ! Will watch here for the longer term solution.
Thanks @cderv. I run into the same issue
- with Quarto
- with any other htmlwidget (leaflet, ggiraph, ...)
- by setting
fig-asp(instead ofout-widthin percentage)
See reprex below
---
title: Test
format:
pdf: default
fig-width: 6
fig-asp: 0.618
---
## Plots
```{r}
library(leaflet)
leaflet() %>%
addTiles()
```
Workaround with webshot = "webshot" works also in this case.
Thanks for the report. This is still an issue with webshot2 I believe that does not handle the resulting dimensions.
It seems not to handle the decimal value
webshot2::webshot("https://github.com/rstudio/shiny", vwidth = 6*72, vheight = 6*72*0.618)
#> Error in s$close(): tentative d'appliquer un objet qui n'est pas une fonction
(6 is your fig.width, 72 is the default DPI 0.618 is the aspect ratio -> this is used to calculate the height))
As I said above, maybe we can do something in knitr to pass transformed argument, but we would need to round the number here.
It seems an issue in webshot2 really. 🤔