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" <ccbe...@health.ucsd.edu> wrote: >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 > >______________________________________________ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://stat.ethz.ch/mailman/listinfo/r-help >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. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
