On 08/04/2015 03:06 AM, Vincent Carey wrote:
Thanks for all input. Henrik's comments deserve to be in WRE or developer doc for bioc, IMHO.
yes, was there any attempt to get something more in WRE? Martin
On Tue, Aug 4, 2015 at 3:02 AM, Henrik Bengtsson <henrik.bengts...@ucsf.edu> wrote:You can mix any type and number of vignette formats in a package. What vignette engine is used is solely specified by the %\VignetteEngine{<pkg>::<engine>} markup string. You don't need to specify this for the default Sweave format, but you can as: %\VignetteEngine{utils::Sweave} For your knitr vignette you'd use: %\VignetteEngine{knitr::knitr} The <engine> part of the specification is the registered engine name and *not* a function name; in the above to cases this just happens to both. For example, %\VignetteEngine{R.rsp::asis} specifies engine 'asis' (for static pre-built PDF and HTML vignettes) of the vignette builder package R.rsp, but there is no asis() function in that package. (BTW, the % is a remnant from the time when everything was LaTeX based and when it was used to specify a LaTeX comment. However it is still needed, because it is part of the markup syntax. Ideally it would not have been needed in non-LaTeX-based formats, but it was kept due to tight deadlines on the design when this was first implemented.) The filename extension controls nothing (except that it is used as a fallback for the default Sweave engine for backward compatible reasons). However, each vignette engine recognizes a given filename pattern so you need to use an extension that is recognized by the engine of interest. Engines can recognize the same patterns/extensions, e.g. Sweave and knitr both recognizes *.Rnw. When a package is built, each engine is first asked what files it is interested in (think dir(pattern=pattern)) and among those a match for %\VignetteEngine{...} is then searched. If no match, then the next registered engine is checked. If a march, then the engine build the vignette. What engines are registered are controlled by what vignette-builder packages are used/loaded (see VignetteBuilder below). You can test build a single vignette manually using: tools::buildVignette(pathname) That will decide on the engine based on the %\VignetteEngine{...} markup. Don't forget to load the vignette builder package first so its engines are registered, e.g. library(knitr). That's a good way to test it without having to use R CMD build (which is when all vignette templates in vignettes/ are built and moved together with the vignette products to inst/doc/). Finally, for R CMD build to work, you need: VignetteBuilder: utils, knitr and specify those vignette builder packages also under Suggests (unless they're already under Depends or Imports) in your package's DESCRIPTION file. Hope this clarifies it further Henrik (I wrote a fair chunk of the original code for dealing with any type of vignettes)[[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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