I have been building vignettes with knitr for several months but about 10 days ago, this message appeared after using R CMD build or devtools::build():
It seems you should call rmarkdown::render() instead of knitr::knit2html() because Release.Rmd appears to be an R Markdown v2 document.
I thought it would be linked to text inside the vignette so I reduced it to a minimal reproducible example:
title: "Release"
output:
html_vignette
vignette: >
%\VignetteIndexEntry{Release}
%\VignetteEngine{knitr::knitr}
%\VignetteEncoding{UTF-8}
---
Release
Force evaluation
I tried to force the evaluation of the Rmarkdown adding:
params:
force_v1: TRUE
Change vignette builder
I also tried to replace the VignetteEngine by rmarkdown::render and editing the VignetteBuilder in the Description file. This skips the vignette building as rmarkdowndoes not seem to be a known vignette builder.
Question:
Is there a way to solve this using knitr or alternatively by building vignettes with rmarkdown?
Additional information
I tried to build the package both on Windows and Centos, with different versions. Failing build information can also be found here
I use these settings, and they work:
output: rmarkdown::html_vignette
vignette: >
%\VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{the title}
You should use instead
%\VignetteEngine{rmarkdown::render}
with all the packages up to date.
Related
My package has a PDF file which I'd like to include as a vignette. There are guides on the internet for doing that with Sweave and R.rsp, but I'd like to use knitr as the vignette engine because we are writing another vignette in Rmd.
My latest attempt has file.pdf and file.pdf.asis inside the vignettes/ folder, with the latter containing these two lines:
%\VignetteIndexEntry{title}
%\VignetteEngine{knitr::asis_output}
FWIW, if I use R.rsp as an engine, the second line above can simply contain %\VignetteEngine{R.rsp::asis} and that vignette builds fine, so one suspicion I have is that I am simply using the wrong knitr equivalent.
I've also tried some monstrosities involving a mix of a YAML header and LaTeX inclusion of the PDF, which didn't work either:
---
title: "title"
author: "yes"
output: pdf_document
vignette: >
%\VignetteIndexEntry{title}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
\includepdf{file.pdf}
Thanks to the power of open-source software, I was able to run browseVignettes(), go through my installed packages containing a mix of HTML and PDF vignettes, and eventually check out the source code for the jsonlite package. This led me to a simple solution I thought about but immediately dismissed because I thought it wasn't possible: declare both knitr and R.rsp as vignette engines.
So my package's DESCRIPTION now includes:
VignetteBuilder: R.rsp, knitr
and I have an Rmd vignette containing %\VignetteEngine{knitr::rmarkdown} on its YAML header and a file.pdf.asis containing %\VignetteEngine{R.rsp::asis}.
I'm trying to see the vignette that I've created after rebuilding a package on my local computer. Note that this has nothing to do with suggestions on this post, since I'm not cloning from Github.
The vignettes portion of my vignette file looks like this:
vignette: >
%\VignetteIndexEntry{pack_name}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
The process is:
Ctr + Shift + K to knit the vignette
Ctr + Shift + B to rebuild the package
Enter browseVignettes("package name")
Get error:
No vignettes found by browseVignettes
I also tried changing knitr::markdown to knitr::knitr, but it didn't help.
Entire vignette top-portion:
---
title: "Random title"
author: "Author"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{vignette_name}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
You don't give all the details to say what went wrong, but here is what you need to do:
Vignettes need to be in the package vignettes directory.
If they are anything but Sweave vignettes (and yours is knitr::rmarkdown, according to the header lines you showed us), then you need to tell R about it in the DESCRIPTION file. For your example, you'd need
VignetteBuilder: knitr
in that file, and also have knitr listed in the Suggests, Depends, or Imports lines.
You need to follow the naming convention for your vignette engine. For knitr::rmarkdown, name the file something.Rmd.
You don't need to knit the file yourself. R will do that when it builds the source package. (You can configure RStudio to do this for "Install and Restart"; by default it doesn't.) Even if you haven't knitted the vignette, browseVignettes should find it if you've followed the other steps properly, it just won't display the HTML or PDF output, only the source and extracted R code.
Edited to add: When building and reinstalling the package, it appears that sometimes vignettes aren't included unless the install is done from a .tar.gz file. Use the "Build Source Package" option in the RStudio build pane to get one of those.
I am new to writing R packages. I'm trying to learn how to make a vignette for my package. I have created a vignettes folder with a file "getting-started.Rmd"
---
title: "WaterML Tutorial"
author: "Jiri Kadlec"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Introduction to the WaterML R package}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
## Quick Start
This simple example shows how to get started with the <my R package>.
To build the vignette I use the command:
devtools::build_vignettes()
Then I run Rcmd.exe INSTALL my_package, and to view my vignette I run:
browseVignettes("my_package")
However I only see the vignettes in the html and source format:
As you see in the screenshot, there's no "pdf" option. How do I configure my .Rmd file to create my vignette in the pdf format?
In your header, you are telling R to output only an html vignette in line:
output: rmarkdown::html_vignette
If you want pdf, try:
output: pdf_document
According to R packages:
Output: this tells rmarkdown which output formatter to use. There are many options that are useful for regular reports (including html, pdf, slideshows, …) but rmarkdown::html_vignette has been specifically designed to work well inside packages. See ?rmarkdown::html_vignette for more details.
So you might have a few small problems using a raw pdf.
At this time, rmarkdown does not have a output: rmarkdown::pdf_vignette option
So I have a vignette, vignettes/test-vignette3.Rmd:
---
title: "Sample Document"
output:
html_document:
highlight: kate
theme: spacelab
toc: yes
pdf_document:
toc: yes
---
Header
=========
When I hit the knit HTML button, I get the following:
processing file: test-vignette3.Rmd
output file: test-vignette3.knit.md
Output created: /tmp/RtmpKVpegL/preview-5ef42271c0d5.dir/test-vignette3.html
However, if I copy this file to inst/doc and hit the knit HTML button, I get:
processing file: test-vignette3.Rmd
output file: test-vignette3.knit.md
Output created: test-vignette3.html
My questions are:
How do I get RStudio to save the output from knit HTML on vignettes/test-vignette3.Rmw to the vignettes directory?
How do I get RStudio to not delete test-vignette3.knit.md during the knit HTML procedure? (I'd like to have the .md so people can read it on my github repo.)
I'm running RStudio version 0.98.836, rmarkdown version 0.1.98 and knitr version 1.5.
Actually you should not keep the .html output under vignettes/, because the vignette output is supposed to be generated by R CMD build. R may fail to recompile your vignettes if the HTML output files have already been there when you build the source package, which means you are likely to see old (and possibly wrong) results because the HTML file was not generated from the latest version of the .Rmd file. Therefore RStudio intentionally avoid writing the HTML files in the vignetttes directory.
If you choose to ignore the warning above, you can certainly run rmarkdown::render('your-vignette.Rmd') in the R console.
For the second question, I do not recommend you to do that, either, because Github renders the markdown to HTML differently (compared to the Pandoc conversion done through the rmarkdown package). Normally the package vignettes are shown on CRAN, see, for example, the knitr page on CRAN. However, because the rmarkdown package is not on CRAN yet, you cannot use the vignette engine knitr::rmarkdown at the moment (I guess we are not too far away from the CRAN release now). You can consider pushing the HTML files to Github pages, though.
I am trying to write R Package vignettes using R Markdown. I am using R Studio's package authoring tools.
I have R greater than version 3.0.
I have an .Rmd file in the vignettes folder that contains the following text at the top:
<!--
%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{An Introduction to the bootcorrelations package}
-->
I have the following in my DESCRIPTION file:
VignetteBuilder: knitr
Suggests: knitr
When I clean and build or build and reload the package in RStudio, the vignette source is displayed, but not the HTML (i.e., there's no HTML file in inst/man).
How can I get RStudio to automatically create the HTML from an R Markdown Vignette?
I've read through Yihui's post on R Package Vignettes with Markdown and it suggests using a makefile, but this more recent documentation about knitr vignettes suggests that the makefile is no longer required.
I also realise that I could manually create the HTML vignette with a command like this:
library(knitr)
knit(input='vignettes/foo.Rmd', output='inst/doc/foo.md')
library(markdown)
markdownToHTML('inst/doc/foo.md', 'inst/doc/foo.html')
A reproducible example:
Vectorize(dir.create)(c("test", "test/R", "test/man", "test/vignettes"))
cat(
'Package: test
Title: Test pkg
Description: Investigate how to auto-compile markdown vignettes
Version: 0.0-1
Date: 2015-03-15
Author: Jeromy Anglim
Maintainer: Jeromy Anglim <a#b.com>
Suggests: knitr
License: Unlimited
VignetteBuilder: knitr',
file = "test/DESCRIPTION"
)
cat(
'---
title: "Introduction"
author: "Jeromy Anglim"
date: "`r Sys.Date()`"
output: html_document
---
<!--
%\\VignetteEngine{knitr::rmarkdown}
%\\VignetteIndexEntry{Introduction}
-->
# Introduction
A sample vignette!
```{r}
1 + 1
```',
file = "test/vignettes/intro.Rmd"
)
cat(
"#' Nothing
#' This function is only needed so that roxygen generates a NAMESPACE file.
#' #export
nothing <- function() 0",
file = "test/R/nothing.R"
)
library(roxygen2)
library(devtools)
roxygenise("test")
build("test")
Update: Thinking laterally, there are at least three options.
1. Use build_vignettes()
As #Hadley points out, running build_vignettes() from the devtools package will build vignettes and place them in the inst/man directory of the package.
devtools::build_vignettes()
Building the vignette means you get three versions in inst/man:
the Rmd source
the knitted or weaved HTML vignette
and the R code in the code blocks
This is not tied to the build and reload command in RStudio, but it is a one line solution to the task. And it could easily be incorporated into a makefile.
2. Use Knit HTML in Rstudio
As #TylerRinker notes you can just use Knit HTML in Rstudio. This will add both md and HTML knitted versions of the rmd vignette to the vignettes directory.
This also is not tied to the build process but as #TylerRinker points out, often you don't want the vignettes tied to the main build process. This also has the benefit of giving you an md file which can be a nice option for displaying the vignette on github, although http://htmlpreview.github.com/ is an option for displaying HTML vignette on github.
3. Build source package and extract from compressed file
Build - Build Source Package in RStudio corresponds to R CMD build. When run a compressed tar.gz file is created which contains in the inst/doc directory the Rmd, R and HTML files for the original rmd vignette file.
This is described in the official documentation on writing package vignettes which instructs you to use R CMD build to generate PDF and HTML vignettes.
So it is possible to
Build Source
Unzip the tar.gz file
Browse and open the resulting file