Jeff Newmiller
2021-Sep-19 17:45 UTC
[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 > >______________________________________________ >R-help at 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.
Chris Evans
2021-Sep-19 17:49 UTC
[R] Cacheing of functions from libraries other than the base in Rmarkdown
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 >> >>______________________________________________ >>R-help at 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.-- Chris Evans (he/him) <chris at psyctc.org> Visiting Professor, University of Sheffield and UDLA, Quito, Ecuador I do some consultation work for the University of Roehampton <chris.evans at roehampton.ac.uk> and other places but <chris at psyctc.org> remains my main Email address. I have a work web site at: https://www.psyctc.org/psyctc/ and a site I manage for CORE and CORE system trust at: http://www.coresystemtrust.org.uk/ I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/ If you want an Emeeting, I am trying to keep them to Thursdays and my diary is at: https://www.psyctc.org/pelerinage2016/ceworkdiary/ Beware: French time, generally an hour ahead of UK.