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lobstr segfault leads me to develop a way to debug `rmarkdown::render()`


My copy of adv-r seems to have some problem in chapter cross-reference, so I decide to build the source code to figure out the cause.

Then the build failed —— a very serious error which corrupts R session and forces me exit.


Naturally, I want to find where the error occur, but the unnamed-chunk-*** in rmarkdown::render() console output is so annoying! Who can ever know which chunk is the ***st chunk ?!

As I expected, knitr doesn’t provide the API to get nth chunk (I should have tried this several times).


Then I start to think about set something in knitr, so that every chunk’s code would be printed in the console output. I read the knitr book, tried many times, and finally find a way when I am going to give up:

`r ''````{r}
old_chunk_hook <- knitr::knit_hooks$get('chunk')
new_chunk_hook <- function(x, options) {
    old_chunk_hook(x, options)
knitr::knit_hooks$set(chunk = new_chunk_hook)
knitr::opts_chunk$set(mutable_var = Sys.time()) # disable cache

Now I can search the code causing error, which seems really wired: calling lobstr::obj_size() with function, such as mean, would cause segfault. (As usual, I run it yesterday!)


Finally, eval = F that chunk, build the book, and find the reason: the cross-reference failure seems to result from split_by: section.


Recall that I happily discard microbenchmark after I find bench is awesome to use in the mooning, now I should say it’s so fortunate that we have pryr in hand when lobstr fails oddly.