similar to: Suggestion: Custom filename patterns for non-Sweave vignettes

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 : +61 2 (6125)3473 fax

Dear all I'm getting a strange error when trying to use rtags() to generate tags in Emacs format. root at liv-laptop:/usr/lib/R# R CMD rtags -o /usr/local/build/ETAGS --no-Rd --no-c library/ Tagging R files under library/; writing to /usr/local/build/ETAGS (overwriting)... [..] Error: '\.' is an unrecognized escape in character string starting "[.]*\." Execution halted

Now that R 3.0.0+ supports non-Sweave vignettes, R-exts \S 1.4.2 seems to imply that it is possible to include both Sweave and knitr vignettes 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,

Dear all, I'm trying to use a Markdown vignette with UTF-8 encoding. It compiles well when knitting the vignette in RStudio, but it fails to recognize the UTF-8 settings when building the source package. Can someone point out what I'm doing wrong? I tried to put the relevant information below. Best regards, Thierry Details: Using 64-bit R 3.1.2 with encoding = "native.enc"

> On 19 Feb 2018, at 12:25, Duncan Murdoch <murdoch.duncan at gmail.com <mailto:murdoch.duncan at gmail.com>> wrote: > > On 19/02/2018 5:47 AM, Michael Hannon wrote: >> 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

On 19/02/2018 5:47 AM, Michael Hannon wrote: > 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. If they aren't LaTeX then they won't be able to masquerade as Sweave files, so things are

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. > >

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: >>

Yes, 'C-c C-e l l' I think, but follow the pop-up, and everything should be ok. On Feb 19, 2018 07:05, "Rainer Krug" <rainer_krug at icloud.com> wrote: > > > > On 19 Feb 2018, at 12:25, Duncan Murdoch <murdoch.duncan at gmail.com > <mailto:murdoch.duncan at gmail.com>> wrote: > > > > On 19/02/2018 5:47 AM, Michael Hannon wrote: >

I?m preparing a package (fastR) for submission to CRAN, but the vignette index keeps going AWOL, or at least R CMD check ?as-cran thinks so. I?ve tried several things and gave myself the weekend to think of other things, but I can?t figure it out. Perhaps someone on the list can lend a hand. Here?s one example situation, where I build the index.html file myself and put it in inst/doc/index.html

Dear Duncan, The UTF-8 characters aren't properly rendered in the pdf version of the vignette. $?? ????? ?????? ?????? ????? ?? ?? is rendered as $????? ?????????? ???????????? ????? ?????? ? ???????? ???????? The same problem occurs when I use render("vignette.md", output_format = "mypackage::mystyle"), instead of render("vignette.md", output_format =

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 only with a recent R. In detail, with $ Rdev --version|head -3 R Under

A few things to clarify: 1. You do not necessarily have to keep the \usepackage{} line if you use %\VignetteEncoding{UTF-8}, because Pandoc will use UTF-8 anyway in its LaTeX template. 2. Perhaps the vignette engine in R has done something clever to convert utf8 to UTF-8, but I'd recommend %\VignetteEncoding{UTF-8} instead of %\VignetteEncoding{utf8} to make sure it is a valid encoding name,

Dear all, I am implementing a redundant variables F-test. For that I need to compute 2 models, restricted and unrestricted, then extracting the residuals to calculate the test statistic. I borrowed this elegant solution from the LMtest package to rebuild the first of the matrices involved (the unrestricted one) on the basis of model spec. and data >red.var.test<-function(formula,

Currently Makefiles 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)$',

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 function not specified' ?

Dear Duncan, Was close to giving up to use the parameterized rmarkown as vignettes. But your suggestions to use quote and eval, as well as to use the package parameter in data made it work, with all devtools::install,check,build and build_vignettes as well as with R CMD ... etc. But most importantly it also still works with: rmarkdown::render("vignettes/tr_srm_summary.Rmd",

I haven't figured it out entirely, but it looks 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

On 09/12/2014, 4:48 AM, ONKELINX, Thierry wrote: > Dear all, > > I'm trying to use a Markdown vignette with UTF-8 encoding. It compiles well when knitting the vignette in RStudio, but it fails to recognize the UTF-8 settings when building the source package. Can someone point out what I'm doing wrong? I tried to put the relevant information below. You don't describe the

I think the online order of vignette files are not based on vignette title or filename alphabetically. I am just curious: by what order these vignette files were displayed online so I can make changes accordingly? Thanks, Zhu -----Original Message----- From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] Sent: Friday, March 04, 2016 10:47 AM To: Wang, Zhu; r-devel at r-project.org Subject: