[R] Cacheing of functions from libraries other than the base in Rmarkdown

[Jeff Newmiller]

I avoid knitr (Rmarkdown uses knitr) caching like the plague. If I want caching, I do it myself (with or without the aid of one of a data caching package).

On September 19, 2021 10:28:49 AM PDT, "Berry, Charles" <ccberry using health.ucsd.edu> wrote:
>Chris,
>
>
>> On Sep 18, 2021, at 12:26 PM, Chris Evans <chrishold using 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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-- 
Sent from my phone. Please excuse my brevity.