search for: vignettes

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 ha...

I apologize that these questions are stupid and literal. I write to ask for clarification of comments in the R extensions manual about vignettes. I'm not great at LaTeX, but I'm not a complete novice either, and some of the comments are puzzling to me. 1. I'm stumbling over this line: "Make sure all files needed to run the R code in the vignette (data sets, ...) are accessible by either placing them in the inst/doc hiera...

Hello, The vignette concept, which started in Bioconductor, seems to be catching on. They are supported by R CMD build/check and documented in the Writing R Extensions manual. I think vignettes are a fantastic way to introduce new users to a package. However, getting new users to realize that a vignette is available can be challenging. For some time now, we have had a function in Biobase that creates a "Vignettes" menu item in the R Windows GUI and gives packages a mechanism t...

If I understand correctly, all vignettes in a package are built in the same R process. Global options, loaded packages, etc., in an earlier vignette persist in later vignettes. This can introduce user confusion (e.g., when a later vignette builds successfully because a package is require()'ed in an earlier vignette, but not the cu...

Full_Name: Chris Evans Version: 2.3.1 OS: Windoze XP Submission from: (NULL) (217.34.100.197) If I give "vignette("introduction")" I get: Error in sprintf(gettext(fmt, domain = domain), ...) : use format %s for character objects vignette() works for some other vignettes and "vignette()" gets me a list of vignettes and shows three with the name "introduction" (on my package collection). I don't know if that's related to this. Happy to try anything you want done (except perhaps trying to install the bleeding edge version of R!) Chris

...TF-8' %in% iconvlist() [1] TRUE > 'UTF8' %in% iconvlist() [1] TRUE BTW, %\VignetteEncoding is not documented anywhere (Cc'ing Kurt), and I think it needs to be documented, since the old approach \usepackage[enc]{inputenc} was basically a hack, which looks really odd in non-LaTeX vignettes (e.g. HTML vignettes). 3. The default `encoding` argument of rmarkdown::render() is not relevant here, even if its value is native.enc. When R build a vignette, it tries to detect its encoding and pass it to the vignette engine, so the default argument value may not be native.enc. Lastly, the mos...

...ge... 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&g...

...ows (R 3.0.2), unfortunately the vignette didn't appear. My vignette is build with knitr. In fact, if I first install the package on Windows, the vignette is accesible, but then in Linux, not. I have read that as from R 2.14.0 the preferred location for the Sweave sources is the subdirectory vignettes of the source packages, but for compatibility with earlier versions of R, vignette sources will be looked for in inst/doc if vignettes does not exist. Where do I have to put my vignette so that it could be available with any installation and which files (.Rnw or .pdf) should be included?. I hope...

...to have the "right" order of these files when displayed online. For instance, see below: > > https://cran.r-project.org/web/packages/bst/index.html > > The order of vignette links on CRAN is different from what I hoped for: > > > vignette(package="bst") > Vignettes in package 'bst': > > pros Cancer Classification Using Mass > Spectrometry-based Proteomics Data (source, > pdf) > static_khan Classification of Cancer Types Using Gene >...

In R 3.1.0 (~April 2014), support for vignettes in inst/doc/ will go away (and probably much sooner for CRAN submission), e.g. checking for old-style vignette sources ... NOTE Vignette sources only in ?inst/doc?: ?R.devices-overview.tex.rsp? A ?vignettes? directory is required as from R 3.1.0 and these will not be indexed nor checked I've...

Dear list, we have a markdown vignette for our package in vignette/vignette.md This is not visible from within R with the vignette(package = "mypackage") command. I assume the reason is that the vignette function only shows PDF vignettes. Is there any way to circumvent this and display markdown vignettes directly from within R? I tried to seek the answer from R archives and search engines but could not find the solution so far. best regards, Leo Lahti [[alternative HTML version deleted]]

As a user, I am always annoyed beyond measure that Sweave vignettes precede the code by a command line prompt. It makes running examples by simple copying of the commands from the vignette to the console a pain. I know the idea is that it is clear what is the command, and what is the output, but I'd rather precede the output with some kind of marking. Is there...

G'day all, In Chapter 1.4 (Writing package vignettes) the Writing R Extensions manual states: By default @code{R CMD build} will run @code{Sweave} on all Sweave vignette source files in @file{vignettes}. If @file{Makefile} is found in the vignette source directory, then @code{R CMD build} will try to run @command{make} after the @code{Sweave}...

...; %\VignetteIndexEntry{The title} > \usepackage[utf8]{inputenc} > > The custom output style converts the markdown to beamer with the --latex-engine = xelatex flag. > > The vignette in tar.gz passes R --vanilla CMD check --timings > --as-cran > > * checking files in 'vignettes' ... OK > * checking for unstated dependencies in vignettes ... OK > * checking package vignettes in 'inst/doc' ... OK > * checking running R code from vignettes ... > 'markdown_intro.Rmd' using 'UTF-8' ... OK OK > * checking re-building of vignette out...

...ackages. > > Back to the original point by Alexandre: No, I do _not_ think we can do > without a double copy of the _pre-made_ pdf ("input") and the _resulting_ pdf > ("output"). > > That bugs me a little too but I take it as a given as static / pre-made > vignettes are non-standard (given lack of any mention in WRE, and the pretty > obvious violation of the "spirit of the law" of vignette which is after all > made to run code, not to avoid it). Yet uses for static vignettes are pretty > valid and here we are with another clear as mud situat...

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 packag...

...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 &...

...ready on CRAN.) Both packages use knitr to convert Rnw to PDF. mosaic also uses R.rsp to include static PDFs. $ grep -i vig mosaic/DESCRIPTION VignetteBuilder: knitr, R.rsp [09:22][rpruim at Mac21521:~/projects/github] $ grep -i vig fastR/DESCRIPTION VignetteBuilder: knitr $ grep Vig mosaic/vignettes/*Rnw %\VignetteIndexEntry{mosaic resources} %\VignettePackage{mosaic} %\VignetteKeywords{mosaic, vignettes, resources, references} %\VignetteEngine{knitr::knitr} $ grep Vig fastR/vignettes/*Rnw fastR/vignettes/Errata.Rnw:%\VignetteEngine{knitr::knitr} fastR/vignettes/Errata.Rnw:%\VignetteIndexE...

...a better overview to complicated packages. However, as far as I can tell, the only way to read or even know if a package has a vignette is to first download and unpack the package source, which is inconvenient when one wants to understand a package _before_ installing. Perhaps an easy way to make vignettes more accessible to the end user would be to link the vignette PDF directly to the download page so that one could download it just as one can download the reference manual or package source. This both publicizes the vignette (since many users may even be unaware that a package has a vignette) and f...

Greetings. The group that I work with has just started using the approach outlined in Karl Broman's handy primer: http://kbroman.org/pkg_primer/pages/vignettes.html to create vignettes for a couple of R packages. This works fine as long as we have a current Rmd version of the vignette. But we have some old PDF documents that we'd like to include as vignettes as well. I'd like to know if there's a way to include such PDF files as vignettes....