Alexandre Courtiol
2020-Nov-01 18:02 UTC
[Rd] vignettes present in 2 folders or won't work
Noted Duncan and TRUE... I cannot do more immediately unfortunately, that is always the issue of asking a last minute panic attack question before teaching a course involving the package... I do have /doc in my .Rbuildignore for reasons I can no longer remember... I will dig and create a MRE/reprex. The students will download heavy packages, but they probably won't notice. *Apologies* In the meantime, perhaps my question was clear enough to get clarity on: 1) whether having vignettes twice in foders inst/doc and vignettes is normal or not when vignettes are static. 2) where could anyone find a complete documentation on R vignettes since it is a recurring issue in this list and elsewhere. Many thanks On Sun, 1 Nov 2020 at 18:19, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:> You are doing a lot of things that are non-standard, so I doubt if > anyone is going to be able to help you without access to a simple > reproducible example of a package that does what you do. Try to cut out > as much as you can to make it minimal. For example, > devtools::document() (indeed, most of your code) is probably irrelevant > to your problem with vignettes, but things like your .Rbuildignore file > are not. > > Duncan Murdoch > > On 01/11/2020 11:22 a.m., Alexandre Courtiol wrote: > > Dear all, > > > > I am struggling with an issue related to static vignettes: they work, but > > only when present in double in the tarball -- in the folder inst/doc and > > vignettes; see below for details. > > > > Details: > > > > I am pre-compiling heavy vignettes thanks to the vignette builder R.rsp. > > So basically, I have PDF files which I want the package to use as > Vignettes. > > > > For this, I have the following in my Description file: > > VignetteBuilder: R.rsp > > > > I am organising the vignette by hand using a Makefile (because this is > the > > only way that has proven 100% reliable to me, across a variety of > > situations). > > > > In my Makefile, I have something like: > > > > build: clean > > mkdir -p inst/doc > > mkdir vignettes > > -cp sources_vignettes/*/*.pdf* vignettes > > Rscript -e "tools::compactPDF(paths = 'vignettes', gs_quality > > 'printer')" > > cp vignettes/*.pdf* inst/doc > > Rscript -e "devtools::document()" > > mkdir inst/extdata/sources_vignettes > > cp sources_vignettes/*/*.Rnw inst/extdata/sources_vignettes > > Rscript -e "devtools::build(vignettes = FALSE)" > > > > That works fine, the vignettes show up using browseVignettes() after > > installing the package the normal way. > > > > However, after building, the tar.gz contains each pdf corresponding to a > > vignette twice: once in vignettes and once in inst/doc (which is obvious, > > when reading the Makefile). > > > > From the reading of "Writing R Extensions" and other material, I cannot > > tell if that is a must or not, but I hope it is not since I wish to avoid > > that (my pdfs are large even once compressed). > > > > My problem is that when I delete either inst/doc or vignette just before > > calling the last command of the Makefile (Rscript -e > > "devtools::build(vignettes = FALSE)"), then browseVignettes() does not > find > > the vignettes after a normal installation. > > > > If anyone knows of some _complete_ documentation about the ever > troublesome > > topic of vignettes building in R, I would be very grateful too... > > > > Many thanks! > > > > Alex > > > >-- Alexandre Courtiol http://sites.google.com/site/alexandrecourtiol/home *"Science is the belief in the ignorance of experts"*, R. Feynman [[alternative HTML version deleted]]
On 01/11/2020 1:02 p.m., Alexandre Courtiol wrote:> Noted Duncan and TRUE... > > I cannot do more immediately unfortunately, that is always the issue of > asking a last minute panic attack question before teaching a course > involving the package... > I do have /doc in my .Rbuildignore for reasons I can no longer > remember... I will dig and create a MRE/reprex. > The students will download heavy packages, but they probably won't notice. > *Apologies* > > In the meantime, perhaps my question was clear enough to get clarity on: > 1) whether having vignettes twice in foders inst/doc and vignettes is > normal or not when vignettes are static. > 2) where could anyone find a complete documentation on R vignettes since > it is a recurring issue in this list and elsewhere.The Writing R Extensions manual describes vignette support in R, but R allows contributed packages (like knitr, rmarkdown, R.rsp) to handle vignettes. WRE explains enough to write such a package, but it's up to their authors to document how to use them, so "complete documentation" is spread out all over the place. As with any documentation, there are probably errors and omissions. Duncan Murdoch
I take Duncan's point but would second the motion to have WRE clarify how static vignettes are supposed to work; it's a topic I am repeatedly confused about despite being an experienced package maintainer. If knowledgeable outsiders compiled a documentation patch would it be likely to be considered ...?? On 11/1/20 2:29 PM, Duncan Murdoch wrote:> On 01/11/2020 1:02 p.m., Alexandre Courtiol wrote: >> Noted Duncan and TRUE... >> >> I cannot do more immediately unfortunately, that is always the issue >> of asking a last minute panic attack question before teaching a course >> involving the package... >> I do have /doc in my .Rbuildignore for reasons I can no longer >> remember... I will dig and create a MRE/reprex. >> The students will download heavy packages, but they probably won't >> notice. >> *Apologies* >> >> In the meantime, perhaps my question was clear enough to get clarity on: >> 1) whether having vignettes twice in foders inst/doc and vignettes is >> normal or not when vignettes are static. >> 2) where could anyone find a complete documentation on R vignettes >> since it is a recurring issue in this list and elsewhere. > > The Writing R Extensions manual describes vignette support in R, but R > allows contributed packages (like knitr, rmarkdown, R.rsp) to handle > vignettes.? WRE explains enough to write such a package, but it's up to > their authors to document how to use them, so "complete documentation" > is spread out all over the place.? As with any documentation, there are > probably errors and omissions. > > Duncan Murdoch > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel