Is there a way to include the compiled version of a vignette in the doc directory but mark it to NOT be rerun by CRAN??? I think I remember that this is possible, but have forgotton how.?? (It might even be a false memory.) Terry T. Background:? Beth Atkinson and I are splitting out many of the vignettes from the survival package into a separate package survivalVignettes.? There are a few reasons ?1. Some vignettes use packages outside of the base + recommended set; psueodovalues for instance are normally used as input to a subsequent GEE model.??? Since survival is itself a recommended package, it can't legally host the pseudo.Rnw vignette. ?2. The set of vignettes for survival is large, and likely to get larger.??? It makes sense to slim down the size of the package itself. ?3. It allows us to use Rmd.? (Again, survival can't use anything outside of base + recommended). ?4. We have a couple of 'optional' vignettes that talk about edge cases, useful to some people but not worth the size cost of cluttering up the main package. The current submission fails due to one vignette in group 4 which takes a looong time to run.? This vignette in particular is talking about compute time, and illustrates a cases where an O(n^2) case arises.?? As sentence that warns the use "of you do this it will take hours to run" is a perfect case for a pdf that should not be recreated by R CMD check. -- Terry M Therneau, PhD Department of Quantitative Health Sciences Mayo Clinic therneau at mayo.edu "TERR-ree THUR-noh" [[alternative HTML version deleted]]
> Is there a way to include the compiled version of a vignette in the docdirectory but mark it to NOT be rerun by CRAN? Some developers "precompute" their vignettes so CRAN has nothing left to run: https://ropensci.org/blog/2019/12/08/precompute-vignettes/> Beth Atkinson and I are splitting out many of the vignettes from thesurvival package into a separate package survivalVignettes. An alternative some authors use is to temporarily use a special `.Rbuildignore` file to omit large vignettes when building the CRAN package but don't use that file for the normal development version (so that all the vignettes are available in the `{pkgdown}` website and for users who install using alternative channels like `remotes::install_github()`). Trevor On Mon, Mar 11, 2024 at 8:44?AM Therneau, Terry M., Ph.D. via R-devel < r-devel at r-project.org> wrote:> Is there a way to include the compiled version of a vignette in the doc > directory but mark > it to NOT be rerun by CRAN? I think I remember that this is possible, > but have forgotton > how. (It might even be a false memory.) > > Terry T. > > Background: Beth Atkinson and I are splitting out many of the vignettes > from the survival > package into a separate package survivalVignettes. There are a few reasons > > 1. Some vignettes use packages outside of the base + recommended set; > psueodovalues for > instance are normally used as input to a subsequent GEE model. Since > survival is itself > a recommended package, it can't legally host the pseudo.Rnw vignette. > 2. The set of vignettes for survival is large, and likely to get > larger. It makes > sense to slim down the size of the package itself. > 3. It allows us to use Rmd. (Again, survival can't use anything outside > of base + > recommended). > 4. We have a couple of 'optional' vignettes that talk about edge cases, > useful to some > people but not worth the size cost of cluttering up the main package. > > The current submission fails due to one vignette in group 4 which takes a > looong time to > run. This vignette in particular is talking about compute time, and > illustrates a cases > where an O(n^2) case arises. As sentence that warns the use "of you do > this it will take > hours to run" is a perfect case for a pdf that should not be recreated by > R CMD check. > > -- > Terry M Therneau, PhD > Department of Quantitative Health Sciences > Mayo Clinic > therneau at mayo.edu > > "TERR-ree THUR-noh" > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >[[alternative HTML version deleted]]
On 11/03/2024 11:43 a.m., Therneau, Terry M., Ph.D. via R-devel wrote:> Is there a way to include the compiled version of a vignette in the doc directory but mark > it to NOT be rerun by CRAN??? I think I remember that this is possible, but have forgotton > how.?? (It might even be a false memory.)You could use a method similar to the testthat::skip_on_cran() approach. Have the long running chunks only run conditional on having a special environment variable present. This would be a little easier with knitr than with Sweave, since there you can use expressions for the chunk options, but you could always write the code something like this: if (Sys.getenv("RUN_SLOW_CHUNKS", 0)) { ... the slow code goes here ... } else cat("This chunk takes several hours to compute. If you want to run it, set the environment variable RUN_SLOW_CHUNKS to 1.\n") Duncan Murdoch> > Terry T. > > Background:? Beth Atkinson and I are splitting out many of the vignettes from the survival > package into a separate package survivalVignettes.? There are a few reasons > > ?1. Some vignettes use packages outside of the base + recommended set; psueodovalues for > instance are normally used as input to a subsequent GEE model.??? Since survival is itself > a recommended package, it can't legally host the pseudo.Rnw vignette. > ?2. The set of vignettes for survival is large, and likely to get larger.??? It makes > sense to slim down the size of the package itself. > ?3. It allows us to use Rmd.? (Again, survival can't use anything outside of base + > recommended). > ?4. We have a couple of 'optional' vignettes that talk about edge cases, useful to some > people but not worth the size cost of cluttering up the main package. > > The current submission fails due to one vignette in group 4 which takes a looong time to > run.? This vignette in particular is talking about compute time, and illustrates a cases > where an O(n^2) case arises.?? As sentence that warns the use "of you do this it will take > hours to run" is a perfect case for a pdf that should not be recreated by R CMD check. >