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

Chris Evans chr|@ho|d @end|ng |rom p@yctc@org
Sun Sep 19 19:49:50 CEST 2021

Can you point me to an example of this?  I definitely need cacheing for this work but I don't know
about data cacheing packages.  Might be one of those things where my learning time might outweigh
time saved but I lost a fair bit of time by being stupid with this so perhaps not.

----- Original Message -----
> From: "Jeff Newmiller" <jdnewmil using dcn.davis.ca.us>
> To: r-help using r-project.org, "Charles Berry" <ccberry using health.ucsd.edu>, "Chris Evans" <chrishold using psyctc.org>
> Cc: "R-help" <R-help using r-project.org>
> Sent: Sunday, 19 September, 2021 19:45:03
> Subject: Re: [R] Cacheing of functions from libraries other than the base in Rmarkdown

> 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:
>>> 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.
>>R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>and provide commented, minimal, self-contained, reproducible code.
> --
> Sent from my phone. Please excuse my brevity.

Chris Evans (he/him) <chris using psyctc.org> Visiting Professor, University of Sheffield and UDLA, Quito, Ecuador
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