similar to: feature request for non-sweave vignettes

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

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' ?

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 current one), difficult-to-identify bugs (e.g., when a setting

Hi all, I was hoping someone could please clarify the differences between a full engine and a mountable one. I have noticed the following: ** Full Engine ** - With a full engine, the parent application inherits the routes from the engine. It is not necessary to specify anything in parent_app/ config/routes.rb. Specifying the gem in Gemfile is enough. The engine routes are specified as: #

Working on Rails Engine. I want to make the controllers customizable whereever the Rails Engine is used. Therefore, I was trying to use `extend ActiveSupport::Concern` on the Engine controller class and include it in MyRailsApp. https://gist.github.com/4185823 # code in my rails engine moduel MyEngine class SomeController extend ActiveSupport::Concern def engine_some_method

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

Hello, I'm seeing three different vignette-related errors with recent versions of R-3.0.0 alpha. First, with the package BitSeq (http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get the following when trying to build the package: Error: processing vignette ?BitSeq.Rnw' failed with diagnostics: Failed to locate the ?weave? output file (by engine ?utils::Sweave?) for

Hi, Every day a few Bioconductor packages (different ones each day) fail to build, on Windows only, with an error like this: D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OrganismDbi [...] Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : Failed to locate the 'texi2pdf' output file (by

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

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

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

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 /

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

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,

Just thought I would mention that the issue below (and in https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html) is still not resolved. It hasn't been a big problem, but it potentially could be, if a critical package were to have this error on release day, then all its dependencies would fail to build, which would probably require us to postpone our release. See the complete thread

> 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

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 =

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"

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: >