Brilliant: exactly what I needed. I see a happy hour tomorrow morning sorting those.
Many thanks (again) Duncan and very best to all here! Chris ----- Original Message ----- > From: "Duncan Murdoch" <murdoch.dun...@gmail.com> > To: "Chris Evans" <chrish...@psyctc.org>, "r-package-devel" > <r-package-devel@r-project.org> > Sent: Saturday, 10 April, 2021 21:20:40 > Subject: Re: [R-pkg-devel] Advice on identifying parsing failures with > examples when trying to pkgdown my package > Here's a better way to do the file-at-a-time check: > > Load the .Rd file in RStudio, and click on Preview. Copy the whole > examples section to a test.R file. RStudio will mark all the syntax > errors, but won't be fooled by the \% escapes, since the Preview handled > them. > > Duncan Murdoch > > On 10/04/2021 4:01 p.m., Duncan Murdoch wrote: >> On 10/04/2021 3:28 p.m., Chris Evans wrote: >>> My beginner package https://github.com/cpsyctc/CECPfuns is evolving slowly >>> and I >>> had no problems (that I could see) >>> with the help pages created through roxygen. Today I came back to try using >>> pkgdown to ... pkgdown the package. >>> So I used a copy of the package directory and ran: >>> >>> usethis::use_pkgdown() >>> >>> and then >>> >>> pkgdown::build_site() >>> >>> That produced the start of exactly what I wanted as a nicely pkgdown'ed >>> site. >>> However, the console showed error >>> messages for three examples (which, as I say, all seem to produce OK html >>> help >>> pages through the usual roxygen >>> processing). The error message was >>> >>> Failed to parse example for topic >>> >>> and sure enough the examples section in the pkgdown docs html was empty. If >>> anyone wants to look at one of >>> the functions, checkAllUnique was one of the three that threw the errors. >>> >>> I tried some searching and the most pertinent seeming page I hit was this: >>> >>> https://github.com/r-lib/pkgdown/issues/1149 >>> >>> where Hadley Wickham says "That's not valid .Rd code because you didn't >>> escape >>> the Rd comment symbol" which may >>> well be my problem too ... but I don't understand the advice (sorry!) >> >> In Example code, % needs to be escaped, or it will be interpreted as a >> comment. Sometimes that means the examples just compute the wrong >> thing, e.g. >> >> A %*% b >> >> is parsed as A when the rest of the line is ignored as a comment. >> Sometimes it makes the code illegal. I don't know which you're seeing. >> >>> >>> When I tried to tweak one of those functions by inserting a lot of "#" to >>> mask >>> results, i.e. replaced >>> >>> #' [1] something >>> >>> with: >>> >>> #' # [1] something >>> >>> (as I probably should have done that in the examples I have, they are >>> dontrun >>> examples so I hadn't noticed). >> >> pkgdown tries to parse \dontrun examples, so this was a good thing, but >> I think you missed some: e.g. in checkAllUnique.Rd, I see this around >> lines 55-60: >> >> \examples{ >> \dontrun{ >> ### letters gets us the 26 lower case letters of the English alphabet so >> should test OK >> checkAllUnique(letters) >> [1] TRUE >> ### good! >> >> That line containing TRUE is not legal R code, so should be commented. >> You can find these one by one by copying the text from the Rd example >> section into a file, and trying to parse that file, e.g. >> >> Put this in "test.R": >> >> ### letters gets us the 26 lower case letters of the English alphabet >> so should test OK >> checkAllUnique(letters) >> [1] TRUE >> ### good! >> >> then run parse("test.R"): >> >> Error in parse("test.R") : test.R:3:1: unexpected '[' >> 2: checkAllUnique(letters) >> 3: [ >> ^ >> >> You can do it for a file at a time by loading the test.R file into >> RStudio; it'll put markers beside each syntax error. Unfortunately, it >> thinks >> >> checkAllUnique(tmpTib \%>\% pull(1)) >> >> is a syntax error: those escapes are required in Rd, but are illegal in R. >> >> I don't know if there's a way to do it directly from the Roxygen source. >> >> Duncan Murdoch >> >>> >>> However, when I reran pkgdown::build_site() I got a new error message that >>> is, >>> to me, thoroughly confusing: >>> >>> Error in utils::modifyList(meta, override) : is.list(x) is not TRUE >>> >>> At that point I decided to back out and come here and ask the question in >>> the >>> subject line! >> -- Chris Evans (he/him) <ch...@psyctc.org> Visiting Professor, University of Sheffield <chris.ev...@sheffield.ac.uk> I do some consultation work for the University of Roehampton <chris.ev...@roehampton.ac.uk> and other places but <ch...@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. ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
