From: "Jeff Newmiller" <jdnewmil at dcn.davis.ca.us>
To: r-help at r-project.org, "Charles Berry" <ccberry at health.ucsd.edu>, "Chris Evans" <chrishold at psyctc.org>
Cc: "R-help" <R-help at 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 at health.ucsd.edu> wrote:
On Sep 18, 2021, at 12:26 PM, Chris Evans <chrishold at 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