similar to: Include pre-existing PDF files as vignettes in an R package?

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: >>

Hi Mike, Did you read the relevant section of the official "Writing R Extensions" manual? If so, what about the instructions provided there do you find lacking? Best, Ista On Sun, Feb 18, 2018 at 9:06 PM, Michael Hannon <jmhannon.ucdavis at gmail.com> wrote: > Greetings. The group that I work with has just started using the approach > outlined in Karl Broman's handy

> 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 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

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: >

Hello, This is a problem I posted about already some time ago: https://stat.ethz.ch/pipermail/r-devel/2018-September/076786.html Finally, I did had some time to create a minimal package to reproduce the problem that vignettes with child can not be build. https://github.com/wolski/RmarkdownVignetteProblem The problem basically is that while all the vignettes can be build by running

So far you haven't provided a reproducible example yet. I wonder what exactly the object `sample_analysis` is. Sounds like it is an environment. If that is the case, devtools::build_vignettes() will tangle (for the meaning of "tangle", see ?tools::buildVignette) your vignette into an invalid R script. Environments cannot be represented via dput(), so knitr's purl() (eventually

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. > >

Dear Duncan, Following your advice (Thank you for it) I did include into the vignettes params: configuration: !r get(data(sample_analysis)) data: !r get(data(skylineconfig)) And everything seemed (see below) to work fine. devtools::build_vignettes() builds the vignettes. Runs with NO error. By this the .Rmd file, html file and corresponding .R files is being placed into the inst/doc

Dear Community, I have an Rmarkdown vignette with optional child documents. Since all markdown files in the vingette folder are build when executing R CMD build I did place the child documents in /inst/ParametrizedReportChid/ so they are excluded from the build. I do reference them from the markdown file in the vignette folder by: ```{r referencingChildDocument} child_docs <-

Hello, Thank you for the questions as well as remaining me of the default parameters in the yaml session. Indeed this seems to be the solution. But how would I assign package data as a default parameter? So originally I thought to render the markdown with : <code> data(sample_analysis) data(skylineconfig) x <- rmarkdown::render("report.Rmd", output_format =

Dear List, I am working on moving some Rmarkdown reports into the vignettes folder of a package. While I was able to solve to problem of parametrized reports in vignettes folder thanks to your invaluable help (Thank you), I am now struggling with the following problem. One of the reports which I am moving to vignettes includes the following code : ```{r} child_docs <-

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"

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,

Dear Duncan, Thank you, got it working with your advice. I did placed the child markdown documents into inst/ParametrizedReportsChild And this is the code in the main vignette by which I include them: child_docs <- "Grp2Analysis_MissingInOneCondtion.Rmd_t" if(!sum(NAinfo$nrProteins > 0) > 0){ child_docs <- "Grp2Analysis_Empty.Rmd_t" } child_docs <-

Hello. I'm trying to adapt the package ?hexbin? to suit my needs. This is the first time I do this. I've read a bit through Hadley's ?R packages?, but now I'm pretty lost (from a workflow point of view). I am using RStudio and Hadley's devtools. So I forked the repo I want to adapt: https://github.com/grssnbchr/hexbin and cloned it using RStudio (I created a new project).

Hello. I'm trying to adapt the package ?hexbin? to suit my needs. This is the first time I do this. I've read a bit through Hadley's ?R packages?, but now I'm pretty lost (from a workflow point of view). I am using RStudio and Hadley's devtools. So I forked the repo I want to adapt: https://github.com/grssnbchr/hexbin and cloned it using RStudio (I created a new project).

On 12/07/2016 7:28 AM, timo at timogrossenbacher.ch wrote: > Hello. > > I'm trying to adapt the package ?hexbin? to suit my needs. This is the first > time I do this. I've read a bit through Hadley's ?R packages?, but now I'm > pretty lost (from a workflow point of view). I am using RStudio and Hadley's > devtools. > > So I forked the repo I want to