autodep regression by #2321

[heavywatal]

The option autodep=TRUE does not work since #2321 even with the simplest example as follows:

```{r, setup}
knitr::opts_chunk$set(cache = TRUE)
knitr::opts_chunk$set(autodep = TRUE)
```

```{r, src}
x = 1
```

```{r, dst}
y = 10 * x
y
```

Modifying x in src chunk should invalidate the cache of the dependent chunk dst, but is ignored in the latest version. I have tried different versions with pak::pkg_install("yihui/knitr"). Here are the results:

• OK: "yihui/[email protected]"
• OK: "yihui/knitr@74bcff85455a9f92a3099abecba1a8d70ab0cfa4" 74bcff8
• NG: "yihui/knitr@f36e52cf39abba3be261e8e957c92587c63fa599" f36e52c
• NG: "yihui/[email protected]"
• NG: "yihui/knitr" HEAD

> xfun::session_info('knitr')
R version 4.4.0 (2024-04-24)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.5

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

Package version:
  evaluate_0.23   grDevices_4.4.0 graphics_4.4.0  highr_0.11
  knitr_1.46.5    methods_4.4.0   stats_4.4.0     tools_4.4.0
  utils_4.4.0     xfun_0.44       yaml_2.3.8

---

By filing an issue to this repo, I promise that

• I have fully read the issue guide at https://yihui.org/issue/.
• 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('knitr'). 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/knitr').
  • If I have posted the same issue elsewhere, I have also mentioned it in this issue.
• 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.

[heavywatal]

FYI, adding cache-globals does not help invalidation.

```{r, dst2}
#| cache-globals:
#|   - x
z = 100 * x
z
```

[yihui]

@knokknok @atusy Could you take a look? Thanks!

[atusy]

I will

[knokknok]

Don't you need an initial dep_auto() to set-up the system?

[atusy]

Sorry for being silent.
I take a look at this issue.

[heavywatal]

Thank you @atusy. Here is my current understanding:

1. Both autodep = TRUE and knitr::dep_auto() are required in knitr>=v1.46.
2. knitr::dep_auto() has long been there, but I did not know (or just forgot) its existence before @knokknok's suggestion because it is not documented in https://yihui.org/knitr/options/ and autodep = TRUE worked fine without it in knitr<=v1.45.
3. knitr::dep_auto() emits warning when it is executed for the first time:

   Warning in parse_objects(paths[1L]): file .cache/__objects not found
   Warning in parse_objects(paths[2L]): file .cache/__globals not found
   

Now my setup chunk looks like this:

#| cache: false
knitr::opts_chunk$set(cache = TRUE)
knitr::opts_chunk$set(autodep = TRUE)
if (dir.exists(knitr::opts_chunk$get("cache.path"))) knitr::dep_auto()  # NEW!

It seems a little redundant. How about modifying knitr::dep_auto()?

• to set autodep = TRUE (and cache = TRUE) internally
• not to emit warning when __objects and __globals are not found

[atusy]

@heavywatal

Thank you, too. Your understanding is right.

I am trying to automate knitr::dep_auto(labels = all_labels()).

to set autodep = TRUE (and cache = TRUE) internally

I am against this because I remember a book (R Markdown Cookbook?) recommends cache = TRUE per chunks, not globally.

[atusy]

I partially solved the issue by automatically calling dep_auto(labels = all_labels()) when the chunk option autodep = TRUE is found for the first time.

However, this implementation does not work well when there is a child document.
I will try fix it, too.