auto_pdf option not working

[davibicudo]

It seems setting the global auto_pdf option is not working. The resulting pdf is always preferring the pdf file when available and completely ignoring the global option.

Here is a self-contained test:

---
title: "knitr.graphics.auto_pdf issue"
output: pdf_document
---

```{r setup, include=FALSE}
options(knitr.graphics.auto_pdf = FALSE)
knitr::opts_chunk$set(fig.pos = 'htbp')
```


```{r, bug-file, echo=FALSE, results='hide'}
v <- sample(5, 1000, replace = T)
pdf(file="bug1.pdf")
hist(v)
dev.off()
png(file="bug1.png")
hist(v)
dev.off()
png(file="bug2.png")
plot(sort(v))
dev.off()
```
```{r, opts, echo=T}
getOption("knitr.graphics.auto_pdf")
```

```{r, bug1-include, echo=T, fig.asp = 0.5, fig.width = 4, fig.align = 'center', fig.cap="Unexpected pdf"}
knitr::include_graphics("./bug1.png", dpi = 200)
```


```{r, bug2-include, echo=T, fig.asp = 0.5, fig.width = 4, fig.align = 'center', fig.cap="Expected png"}
knitr::include_graphics("./bug2.png", dpi = 200)
```

[yihui]

Since I don't use the filename extension:

knitr/R/hooks-latex.R

Line 163 in 4cbffa1

res = sprintf('\\includegraphics%s{%s} ', size, sans_ext(x))

LaTeX may prefer .pdf over .png when both are present. There must be LaTeX tricks to reorder the preferences. Then you can use the includes: in_header option to apply the trick.

I may use the full filename with the extension, but I don't really remember why I didn't. This line of code should be seven years old now.

[davibicudo]

You seem to have changed it here eb89efe#r4907995

Wouldn't it be straightforward to switch the order of \DeclareGraphicsExtensions{.pdf,.png,.jpg} (put pdf at the end perhaps) in the generated tex when auto_pdf is set to FALSE?
Also, it seems by default LaTeX should pick png first anyway. Also from the SE post, perhaps the grfext package could help solve this.

By the way, it isn't clear to me when the auto_pdf plays a role if this issue is happening, although it seems it does. I just couldn't use the option at all.

[yihui]

The commit you pointed out didn't really change it. x[1] and sans_ext(x) were the same thing (filename without extension).

I added a global option to support the full filename. You can set options(knitr.include_graphics.ext = TRUE). Thanks!

[davibicudo]

Perfect, thanks a lot!

After testing I understood that if I use the options(knitr.include_graphics.ext = TRUE), then the knitr.graphics.auto_pdf works as expected. That means for a quick check I can compile everything with PNG by setting the auto_pdf to FALSE and finally when I'm ready to publish I can set it to TRUE.

It is though still not clear to me in which cases the auto_pdf is useful without the new option. Would you care to illuminate me?

P.S.: while testing I also noticed that in the "Unexpected pdf" case, the size of the plot if controlled by the regular "fig.*" options, whereas when the pdf is actually expected, these options don't apply. Maybe this is a hint if this issue appears again in the future in some other situation.

[davibicudo]

A quick question regarding the update. In my case I'm using bookdown and the issue is still there, but I guess once v1.21 is deployed it will be also available for bookdown via devtools? Or am I missing something?

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