search for: vignetteengine

...gnettes in a single package. I'm wondering if anyone has tried this and/or if there are some hidden gotchas putting this into practice, and concerned about creating problems with CRAN checks if I try this. Consider two vignettes: pkg/vignettes/vign1.Rnw, containing: % !Rnw weave = Sweave %\VignetteEngine{Sweave} ... pkg/vignettes/vign2.Rnw, containing: % !Rnw weave = knitr %\VignetteEngine{knitr::knitr} ... both are .Rnw files, distinguished only by \VignetteEngine. vign1.Rnw is currently in my package, and vign2.Rnw compiles OK outside it, using knitr in an R console or RStudio. R-exts implie...

...possibly post process the generated weave artifact (e.g. a *.tex file). I'd like to propose to extend this non-Sweave mechanism to allow for any filename patterns still using a very similar setup. Here is how I'd like it to see it work with RSP vignettes (cf. the R.rsp package): tools::vignetteEngine("rsp", weave=rspWeave, tangle=rspTangle, patterns="[.]rsp$") Argument 'patterns' could default to patterns=c("[.][RrSs](nw|tex)$", "[.]Rmd$"). This is just a sketch/mock up and it may be that there are better solutions. However, the idea is that wh...

In Section 1.4.2 of "Writing R Extensions" %\VignetteEngine{knitr::knitr} should be %\VignetteEngine{knitr::knit} > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) Is this sort of thing best reported here, or is a huge report in order? John Maindonald email: john.maindonald at anu.edu.au phone :...

...ION 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:%\VignetteIndexEntry{Errata} fastR/vignettes/Errata.Rnw:%\VignettePackage{fastR} fastR/vignettes/Errata.Rnw:%\VignetteKeywords{fastR, vignettes} fastR/vignettes/Upd...

A package uses VignetteEngine: knitr; the package itself does not Suggests: knitr, but it Suggests: BiocStyle which in turn Suggests: knitr. Nonetheless, R CMD check fails indicating that a package required for checking is not declared. Is it really the intention that the original package duplicate Suggests: knitr? This is...

...for vignettes are only supported for .tex files. Could the tools package be modified to allow file extensions to be specified for a vignette engine? Having the pandoc pdf conversion in a Makefile rather than through R would be tidier in some cases. If I specify my vignette engine as ``` tools::vignetteEngine( 'myengine', pattern = '\\.[Rr](md|nw)$', output = c('md', 'tex'), ... ) ``` the `tools:::find_vignette_product` function could have `if (final) c("pdf", "html") else unique(c("pdf", "html", "tex", engine$ou...

Trying to Stangle / Sweave a file $ cat vignette.Rnw %\VignetteEngine{knitr} \documentclass{article} \begin{document} \end{document} results in a misleading error message: ~/tmp$ R CMD Stangle vignette.Rnw Error: Vignette engine package not specified Execution halted when what is missing is the full specification knitr::knitr; 'vignette engine package and fun...

...091. The source packages is build using the devtools package. The build command is R --vanilla CMD build "myPackage" --no-manual --no-resave-data The DESCRIPTION file has VignetteBuilder: knitr Suggests: knitr Imports: rmarkdown The markdown vignette YAML contains vignette: > %\VignetteEngine{knitr::rmarkdown} %\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' ... O...

...like there are a couple of small glitches with knitr-based vignettes and SweaveParseOptions. I posted the tarball of a package with a knitr vignette with (as far as I can tell) everything properly coded in the DESCRIPTION file (VignetteBuilder: knitr, Suggests: knitr) and the vignette itself (%\VignetteEngine{knitr::knitr}). When Windows users (who may not have had knitr installed) tried to install it from source, they encountered an error from utils:::SweaveParseOptions . The proximal source of the problem was a chunk header of the form <<chunkName,fig.cap="Something with a comma in it, ....

On 09/07/2018 3:24 PM, Witold E Wolski wrote: > Dear Yihui, > > Thank you for the valuable questions. > > sample_analysis is a "tibble" while > configuration is an "R6" class. > But I also have parametrized reports where I pass R reference classes > as arguments. > > This is the Rmd yaml params part corresponding to the error message. > >

...If they aren't LaTeX then they won't be able to masquerade as Sweave files, so things are more complicated. I think there are two possibilities. The better but harder one is to write your own "vignette engine". Section 1.4.2 of the manual describes the process, and ?tools::vignetteEngine describes what is needed in your engine. The other possibility is to manually edit an inst/doc/index.html file to include links to your documents. They won't be treated as vignettes, but at least users will be able to find them. The other disadvantage of this approach is that you'll...

...ckage. The build > command is R --vanilla CMD build "myPackage" --no-manual > --no-resave-data > > The DESCRIPTION file has > > VignetteBuilder: knitr > Suggests: knitr > Imports: rmarkdown > > The markdown vignette YAML contains > vignette: > > %\VignetteEngine{knitr::rmarkdown} > %\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 > > * c...

...ey aren't LaTeX then they won't be able to masquerade as Sweave files, so things are more complicated. > > I think there are two possibilities. The better but harder one is to write your own "vignette engine". Section 1.4.2 of the manual describes the process, and ?tools::vignetteEngine describes what is needed in your engine. > > The other possibility is to manually edit an inst/doc/index.html file to include links to your documents. They won't be treated as vignettes, but at least users will be able to find them. The other disadvantage of this approach is that you...

...l >>> --no-resave-data >>> >>> The DESCRIPTION file has >>> >>> VignetteBuilder: knitr >>> Suggests: knitr >>> Imports: rmarkdown >>> >>> The markdown vignette YAML contains >>> vignette: > >>> %\VignetteEngine{knitr::rmarkdown} >>> %\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 C...

Thanks, Duncan. The files in question are Emacs Org-mode files, and I think these are more or less isomorphic to Rmd files, but I haven't used Org-mode in a long time, so I think the mapping (Org-mode ==> Rmd) would be painful. -- Mike On Mon, Feb 19, 2018 at 1:20 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote: > On 18/02/2018 9:06 PM, Michael Hannon wrote: >>

...they won't be able to masquerade as Sweave > files, so things are more complicated. > > > > I think there are two possibilities. The better but harder one is to > write your own "vignette engine". Section 1.4.2 of the manual describes > the process, and ?tools::vignetteEngine describes what is needed in your > engine. > > > > The other possibility is to manually edit an inst/doc/index.html file to > include links to your documents. They won't be treated as vignettes, but > at least users will be able to find them. The other disadvantage of thi...

...ols package. The build command is R --vanilla CMD build "myPackage" --no-manual --no-resave-data > > The DESCRIPTION file has > > VignetteBuilder: knitr > Suggests: knitr > Imports: rmarkdown > > The markdown vignette YAML contains > vignette: > > %\VignetteEngine{knitr::rmarkdown} > %\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 > > * che...

...t: pdf_document: default html_document: default params: configuration: !r quote(get(data(skylineconfig, package="myPackage"))) data: !r quote(get(data(sample_analysis, package="myPackage"))) vignette: > %\VignetteIndexEntry{Summarize Peptide Level Measurements} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r setup, include=FALSE} library(tidyverse) knitr::opts_chunk$set(echo = FALSE, message=FALSE) data <- eval(params$data) configuration <- eval(params$configuration) ``` Have a great evening. regards Witek On 9 July 2018 at 21:32, Dunc...

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 any other solution possible /

...CMD build "myPackage" --no-manual >> --no-resave-data >> >> The DESCRIPTION file has >> >> VignetteBuilder: knitr >> Suggests: knitr >> Imports: rmarkdown >> >> The markdown vignette YAML contains >> vignette: > >> %\VignetteEngine{knitr::rmarkdown} >> %\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 >...