Chris,
> On Sep 18, 2021, at 12:26 PM, Chris Evans <chrish...@psyctc.org> wrote:
>
> This question may belong somewhere else, if so, please signpost me and accept
> apologies.
>
> What is happening is that I have a large (for me, > 3k lines) Rmarkdown file
> with many R code blocks (no other code or
> engine is used) working on some large datasets. I have some inline r like
>
> There are `r n_distinct(tibDat$ID)` participants and `r nrow(tibDat)` rows
> of data.
>
> What I am finding is that even if one knit has worked fine and I change
> something somewhere and knit again, the second
> knit is often failing with an error like
>
> n_distinct(tibDat$ID) : could not find function "n_distinct"
>
> This is not happening for functions like nrow() from base R and it mostly
> seems to happen to functions from the tidyverse.
>
> I think what is happening is some sort of cache corruption presumably caused
> by the memory demands. I am pretty sure I've
> seen this before but a long time ago and dealt with it by deleting the files
> and cache folders created by the knit.
Caching things that depend on libraries is known to be tricky.
Specifically, it is advised that "loading packages via library() in a cached
chunk and these packages will be used by uncached chunks" is something you
should not do. I suspect that this is the problem with your inline chunk.
I have to reread things like:
https://yihui.org/knitr/demo/cache/
and relevant parts of the manual to be sure I didn't mess something up and
maybe you should look at that and the manual yet another time.
HTH,
Chuck
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