I want to use the LaTeX \ovalbox{} command from the fancybox package in an Rmarkdown beamer_presentation, knitted from within RStudio. However, as soon as I add a simple R chunk, I get an "! LaTeX Error: Something's wrong--perhaps a missing \item."
This is a minimum reproducible example:
---
output:
beamer_presentation
header-includes: |
\usepackage{fancybox}
---
## Slide 1
\ovalbox{an oval box}
```{r}
print("x")
```
I can hand-solve the problem afterwards in the .tex file by moving the \usepackage{fancybox} command before the \usepackage{fancyvrb} command which is automatically inserted during the knitting.
Any suggestions how to avoid this problem in the first place?
Seems the packages are fighting over how to mess with verbatim environments.
Normally one could simply load them in a different order, but of course rmarkdown makes such a simple task a lot more complicate. You can make your document compile using this hack (don't try to use any of the verbatim commands from fancybox, this might explode...):
---
output:
beamer_presentation
header-includes: |
\let\VerbatimEnvironmentsave\VerbatimEnvironment
\usepackage{fancybox}
\let\VerbatimEnvironment\VerbatimEnvironmentsave
---
## Slide 1
\ovalbox{an oval box}
```{r}
print("x")
```
I'm having some trouble to compile an entire document from many Rmd files by using the bookdown approach.
If I knit individual .Rmd files then 'preamble.tex' included in YAML options is taken into account.
If I render the book (with both approaches described here), then 'preamble.tex' is ignored.
To make things concrete, consider the following mwe:
preamble.tex:
\usepackage{times}
index.Rmd:
---
title: "My paper"
site: "bookdown::bookdown_site"
output:
bookdown::pdf_document2:
includes:
in_header: "preamble.tex"
---
01-intro.Rmd:
# Introduction
This chapter is an overview of the methods that we propose to solve an **important problem**.
Then, by knitting 'index.Rmd' or '01-intro.Rmd' the font indicated in 'preamble.tex' is used.
However when rendering with bookdown::render_book('index.Rmd',"bookdown::pdf_book", new_session = T) it is simply ignored.
What is more, in my actual project there are other output options that end up ignored. For example, I use toc: false and it works when knitting single files, but fails when rendering the document.
In this simple example it would be okay to use a single file, but my actual project has many chapters with R chunks within each of them. Thus, building a single file doesn't seem a good idea.
I appreciate any hints on what I am missing here.
Thanks in advance.
What you are missing here is that in your YAML header, preamble.tex is included for the bookdown::pdf_document2 output format and not bookdown::pdf_book, the format you pass to the output_format argument in bookdown::render_book(). For this reason, other YAML options (like toc: true) do not work either.
Running
bookdown::render_book('index.Rmd', "bookdown::pdf_document2", new_session = T)
instead should work.
When trying to knit a PDF using a template from package rticles output: rticles::acm_article I get the following error:
! LaTeX Error: Environment Shaded undefined.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.76 \begin{Shaded}
This appears to only happen when I include code chunks within the output document.
Reproducible example:
You will need to start a new R Markdown document using the New Document -> From Template -> Association for Computing Machinery. Here is the R Markdown file:
---
title: Short Paper
author:
- name: I Am Me
email: me#email.com
affiliation: Fictional University
abstract: |
This is the abstract.
It consists of two paragraphs.
output:
rticles::acm_article:
keep_tex: true
---
## Simple test
Code chuck follows:
```{r}
plot(rnorm(10))
```
This above example, however, works if I set echo=FALSE in the header. You won't get code in the output, but for an academic paper you probably don't need it anyway, an if you do you can display it in a different manner.
Notes:
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit),
running Ubuntu 16:10
I made sure I have the texlive-latex-base, texlive-latex-recommended, and texlive-latex-extra package installed, but still no luck
I also tried generating a pdf from the intermediate .tex file, as suggested here, but I get the same error.
I considered this approach, but it didn't work, I still got an error (maybe I need to tweak to work in my context, but not sure how)
So, the issue here is the rticles templates sometimes omit a means for pandoc to inject code highlighting environments, e.g. Shaded. To get around this, you would have to insert into the template.tex preamble:
$if(highlighting-macros)$
$highlighting-macros$
$endif$
I struggled with fixing the error and actually raised another question which I was able to answer after quite some experimentation and searching for other related questions/answers.
In short the solution presented above by coatless works perfect given you know the location of the template.tex file. Obviously, I played around with the wrong files before I came across a related question on rticles and how to embed (missing) LATEX.
The longer answer can be found in my "another question". For reference here are the key steps:
locate the template.tex file in your R package rticles library. If you do not know where you have your package library use .libPaths() in your RStudio console. Then work your way to the resources subfolder of your rticle template. In my case:
R-3.5.0/library/rticles/rmarkdown/templates/ieee_article/resources.
add the fix proposed by coatless above in the preamble of the template.tex. The preamble is anything before the line \begin{document}:
$if(highlighting-macros)$
$highlighting-macros$
$endif$
save template.tex and go back to R/RStudio and hit the knit button. R code chunks are now nicely displayed, if you do not suppress their printing with echo = FALSE.
I know the post is old, but I'll put this here for reference for others who have the same problem.
The reason is that in the latex template the environment Shaded is trying to be redefined. However the environment only exists if you are using R chunks in your pdf. So if you don't have any r chunks in the pdf, it tries to redefine something which was never defined - causing the error.
The solution is to modify the \renewenvironment{Shaded} command in the latex template.
https://github.com/yihui/bookdown-chinese/commit/a3e392593b464ba31a7eceb0cd60f7e0bd112798
I found a work around. If I hide the code with chunk option echo = FALSE, a PDF is generated with no issues.
Reproducible example 1:
title: Short Paper
author:
- name: I Am Me
email: me#email.com
affiliation: Fictional University
abstract: |
This is the abstract.
It consists of two paragraphs.
bibliography: sigproc.bib
output:
rticles::acm_article:
keep_tex: true
---
## Simple test
Code chuck follows:
```{r}
plot(rnorm(10))
```
Knit to PDF fails with ! LaTeX Error: Environment Shaded undefined.
Example 2:
---
title: Short Paper
author:
- name: I Am Me
email: me#email.com
affiliation: Fictional University
abstract: |
This is the abstract.
It consists of two paragraphs.
bibliography: sigproc.bib
output:
rticles::acm_article:
keep_tex: true
---
## Simple test
Code chuck follows:
```{r echo=FALSE}
plot(rnorm(10))
```
Knit to PDF works!.
The only difference between the two examples is adding echo=FALSE to the code chunk header. You won't get code in the output, but for an academic paper you probably don't need it anyway, an if you do you can display it in a different manner.
The rticles templates typically do not directly allow shading of code. As a result,
the required $highlighting-macros$ which is used to control the shading is not included.
If for any reason, you cannot (or do not) want to directly edit the template.tex file as suggested by #coatless, you can alternatively consider include the code directly in the acm_proc_article-sp.cls file:
\usepackage{color}
\usepackage{fancyvrb}
\newcommand{\VerbBar}{|}
\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\usepackage{framed}
\definecolor{shadecolor}{RGB}{248,248,248}
\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
\newcommand{\ImportTok}[1]{#1}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
\newcommand{\BuiltInTok}[1]{#1}
\newcommand{\ExtensionTok}[1]{#1}
\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.77,0.63,0.00}{#1}}
\newcommand{\RegionMarkerTok}[1]{#1}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
\newcommand{\NormalTok}[1]{#1}
You may also wish to see my answer to a similar question, whereby the same code is put into a header.tex file in the same directory as your project.
I am practicing data analysis using R programming. I want my files to be on github. I am unable to figure out why github is not showing the output of .rmd files.
Here is the link to the file in my github repository Data Analysis Practice
I want the output including plots to be shown on github.
Instead of:
output: html_document
make it:
output: rmarkdown::github_document
(assuming you have the latest rmarkdown installed which you should if you're using RStudio — which I suspect you are — and keep it updated or update packages regularly).
It will create Exploring_one_variable.md and render the images as files.
When you browse to that markdown file, the images will render.
An alternative is to use:
output:
html_document:
keep_md: true
and it will render to both Exploring_one_variable.md and Exploring_one_variable.html so you'll have the best of both worlds without the local github-esque preview that the former provides.
You can get fancier and put something like the following as the first code section in the Rmd:
```{r, echo = FALSE}
knitr::opts_chunk$set(
fig.path = "README_figs/README-"
)
```
which will put the figures in a directory of your choosing.
You can see this in action here as the README.md was generated with knitr from the README.Rmd in the same directory.
There is now output: github_document
I'm trying to add frame numbers to my Beamer presentation written in rmarkdown. However, I would like to suppress the numbers on the title page using the \begin{frame}[plain] option (from the second answer here: https://tex.stackexchange.com/questions/82794/removing-page-number-from-title-frame-without-changing-the-theme). However, when compiling from rmarkdown to tex, the \titlepage already creates a frame environment, so in effect I get a double frame and thus an error.
So when compiling this:
---
output:
beamer_presentation:
includes:
in_header: header.tex
---
\begin{frame}[plain]
\titlepage
\end{frame}
I get this in latex:
\begin{frame{
\begin{frame}
\titlepage
\end{frame}
\end{frame}
In the header.tex I have this:
\let\otp\titlepage
\renewcommand{\titlepage}{\otp\addtocounter{framenumber}{-1}}
So my workaround now is to just use a plain \maketitle in rmarkdown, then compile to .tex, add the [plain] option, then compile to pdf. However, I would like to avoid that intermediate step. Is this possible in rmarkdown?
rmarkdown uses pandoc to convert a Rmd file to a pdf via beamer/latex. pandoc uses templates to control how the conversion goes.
One way to deal with your problem is to :
Download the default beamer template rmarkdown uses and open it.
Change line 137 from this :
\frame{\titlepage}
To this :
\frame[plain]{\titlepage}
Add the path to your modified template in your Rmd file :
---
output:
beamer_presentation:
includes:
in_header: header.tex
template:/path/to/new/template.tex
---
Note that you need to specify the whole path, or store the template where pandoc can find it (~/.pandoc/templates on a linux machine)
Add {.plain} after the title as in:
----
# I'm the title {.plain}
Source: Pandoc User’s Guide