Cacheing of functions from libraries other than the base in Rmarkdown
You should Google "r cache" yourself, but I have used memoise, R.cache, drake, and targets, and I rate targets as #1 and R.cache as #2. If you try to retrieve old cache objects (more than a few weeks, say) you are likely to run into package/class changes that could cause the kind of issues you are having to crop up. Try to archive results in an interchange format like csv, parquet, or feather to future-proof your work as a separate task from caching.
On September 19, 2021 10:49:50 AM PDT, Chris Evans <chrishold at psyctc.org> wrote:
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 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:
Chris,
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
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