similar to: Changing style for the Sweave vignettes

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' ?

On 05/14/2015 04:33 PM, Henrik Bengtsson wrote: > On May 14, 2015 15:04, "January Weiner" <january.weiner at gmail.com> wrote: >> >> Dear all, >> >> I am writing a vignette that requires a file which I am not allowed to >> distribute, but which the user can easily download manually. Moreover, it >> is not possible to download this file

Dear all, I am writing a vignette that requires a file which I am not allowed to distribute, but which the user can easily download manually. Moreover, it is not possible to download this file automatically from R: downloading requires a (free) registration that seems to work only through a browser. (I'm talking here about the MSigDB from the Broad Institute,

Hi, Recently I saw a couple of cases in which the package vignettes were somewhat complicated so that Stangle() (or knitr::purl() or other tangling functions) can fail to produce the exact R code that is executed by the weaving function Sweave() (or knitr::knit(), ...). For example, this is a valid document that can pass the weaving process but cannot generate a valid R script to be source()d:

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

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,

Hi, as far as I understand it, the new R devel feature of processing non-Sweave vignettes will (a) locate any "[.][RrSs](nw|tex)$" or ".Rmd" files, (b) check for a registered vignette engine, (c) process the file using the registered "weave" function, (d) and possibly post process the generated weave artifact (e.g. a *.tex file). I'd like to propose to extend

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

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

Dear R-devel list, My name is Guillermo Vinu?. I have created an R package that includes a vignette. Earlier on, to test my package, I tried to install it both in Linux and Windows and it worked. My vignette was in /inst/doc. Now, I have finished for good and before submitting my package to CRAN I've tried to install it again first in Linux and then in Windows (I removed that first

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: >>

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 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,

A new problem has cropped up with compiling vignettes for my package BayesFactor. I'm not sure when it started, but I can tell you it didn't occur on R 2.15.3, and it does on 3.0.0 RC (2013-03-31 r62463) (session info is at the bottom of this message). I have defined methods for which.min and which.max for a class (I've defined both S3 and S4 methods for the class

On 18/02/2018 9:06 PM, Michael Hannon wrote: > 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

> 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

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 been sticking with inst/doc/ for backward compatible

Hi, is it possible to have non-Sweave vignettes(*) in inst/doc/ be listed under 'Downloads' on CRAN package pages? For instance, in my R.rsp package I have a inst/doc/report.pdf (part of the source *.tar.gz) that is not detected/listed. The PDF is not based on a Sweave vignette but an *.tex.rsp vignette that is dynamically created via inst/doc/Makefile. It is listed (*) BTW, can the

> See the 'Writing R Extensions' manual, specifically > Creating R Packages -> Writing package vignettes thank you, i saw this entry. However, this entry is rather about how to include documents (in particular Sweave-based) into a package. But I have meant smth else. Let me explain in example. Today I use emacs as environment for my R-sessions. I am quite happy to use