autodep regression by #2321

[heavywatal]

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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" 74bcff85
• NG: "yihui/knitr@f36e52cf39abba3be261e8e957c92587c63fa599" f36e52cf
• 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

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[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.

[yihui]

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

Both items are done now. You don't need to run dep_auto() by yourself, and there won't be warnings at the first time when dep_auto() is called. Thanks!

[yihui]

I forgot to mention that the cache system in litedown is much simpler and smarter than knitr's. The dependency structure of code chunks is automatically inferred from static analysis of the code, so in most cases, there's no need to use options like autodep or functions like dep_auto() in litedown, and things just work out of the box. There are several advantages of litedown's cache compared to knitr's, which I haven't had time to document yet.

[knokknok]

Hi @yihui , any chance this could be ported back to knitr (for latex users)?

[yihui]

litedown's cache system has been factored out to xfun::cache_exec() so it can be reused elsewhere. In theory, we could use it in knitr, but I'm afraid it's not a few minutes' work...

[heavywatal]

Confirmed it works as expected now with v1.49. Thank you, @atusy, @knokknok, and @yihui! (Sorry for my too late response, but I just cannot get away without expressing my gratitude.)