When running knitr::knit() in a Rmd file with this:
```{r setup, include=FALSE}
knitr::opts_chunk$set(collapse = TRUE)
```
```{bash}
which R
which bash
```
The output (a md file) is
```bash
which R
which bash
## /usr/local/bin/R
## /usr/bin/bash
```
Is there a way to make the output look like this:
```bash
which R
## /usr/local/bin/R
which bash
## /usr/bin/bash
```
i.e., each output below each command (like a normal r chunk would do with R commands)?
Related
I am knitting my Rmd file into HTML. Since there are a lot of codes in my Rmd file, I did the following so that my reader can navigate to a certain section within the HTML file:
---
title: "xxx"
author: "xxx"
date: "xx/xx/xx"
output:
html_document:
toc: true
toc_float: true
---
However, the TOC in the HTML file is not working correctly:
Is there a way to solve such issue ? Thanks a lot!
I realize what is causing the problem. Instead of doing:
# A {.tabset}
## a
## b
### b1
### b2
## c
Doing
# A {.tabset}
## a
## b {.tabset}
### b1
### b2
## c
solves the problem. Having smaller headers in tabset kind of mess up the TOC.
Knitting a file to pdf using either rmarkdown 2.9 or 2.9.1 on xubuntu 20.04 with texlive installed generates a double-spaced table of contents. However, running pdflatex on the intermediate tex file converts the toc to single-spaced. Running pandoc on test.Rmd from the command line also creates a single-spaced toc.
To dup: Knit the file test.Rmd to pdf (Rscript -e "rmarkdown::render('test.Rmd')"):
test.Rmd:
---
output:
pdf_document:
toc: true
keep_tex: true
number_sections: true
toccolor: 'red'
---
# Chapter 1
## subchapter 1.1
### subsubchapter 1.1.1
## subchapter 1.2
## subchapter 1.3
# Chapter 2
Result from knitting:
Result from running pdflatex test.tex (the intermediate file created by rmarkdown) or pandoc -f markdown --to latex --toc -o test.pdf test.Rmd.
I think this is new behavior and I don't understand why it happens. Why would running pandoc generate a differently-spaced toc than rmarkdown, given that rmarkdown is just running pandoc?
I'm automating a pdf report using rmarkdown. I use a macro to run the code. I can run the code once and it works with no problems. When I call the macro again, it appears to work but when creating a pdf, I get the error "LaTeX Error: Missing \begin{document}"
This is what I get the first time:
output file: L:/Statunit/morton/NCC R markdown reports/NCC Reports/NCC_Dashboard_Report_Dave.knit.md
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS "L:/Statunit/morton/NCC R markdown reports/NCC Reports/NCC_Dashboard_Report_Dave.utf8.md" --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output pandoc9e03c3032cf.tex --template "C:\Users\Mortond\Documents\R\win-library\3.5\rmarkdown\rmd\latex\default-1.17.0.2.tex" --highlight-style tango --latex-engine xelatex --variable graphics=yes --variable "geometry:margin=1in" --variable "compact-title:yes" --include-in-header "C:\Users\Mortond\AppData\Local\Temp\Rtmp8cWvvQ\rmarkdown-str9e022b75c22.html"
Output created: Report-254-225573.pdf
The second time, I call the same code but only change the report name, so the data is the same and I get.
output file: L:/Statunit/morton/NCC R markdown reports/NCC Reports/NCC_Dashboard_Report_Dave.knit.md
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS "L:/Statunit/morton/NCC R markdown reports/NCC Reports/NCC_Dashboard_Report_Dave.utf8.md" --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output pandoc9e01f0a74c5.tex --template "C:\Users\Mortond\Documents\R\win-library\3.5\rmarkdown\rmd\latex\default-1.17.0.2.tex" --highlight-style tango --latex-engine xelatex --variable graphics=yes --variable "geometry:margin=1in" --variable "compact-title:yes"
! LaTeX Error: Missing \begin{document}.
Error: Failed to compile Report-253-225573.tex. See Report-253-225573.log for more info.
my YAML is
---
title: ''
header-includes:
- \usepackage{fancyhdr}
- \addtolength{\headheight}{1.0cm} % make more space for the header
- \pagestyle{fancyplain} % use fancy for all pages except chapter start
- \lhead{\includegraphics[height=1.2cm]{TJC_logo_color.png}} % left logo
- \renewcommand{\headrulewidth}{0pt} % remove rule below header
output:
pdf_document:
latex_engine: xelatex
word_document: default
html_document: default
urlcolor: blue
classoption: landscape
---
my code that calls the markdown is :
render_report = function(b,h,p) {
rmarkdown::render(
"L:/Statunit/morton/NCC R markdown reports/NCC Dashboard Report
Dave.Rmd", params = list(
b1 = b,
h1 = h,
p1 = p
),
output_file = paste0("Report-", h, "-", p, ".pdf")
)
}
render_report(b="xxxx Hospital, Inc.",h='253',p='225573')
The log file with the error part is.
("C:\Users\Mortond\AppData\Local\Programs\MiKTeX 2.9\tex\latex\graphics-def\xet
ex.def"
File: xetex.def 2017/06/24 v5.0h Graphics/color driver for xetex
))
\Gin#req#height=\dimen160
\Gin#req#width=\dimen161
)
("C:\Users\Mortond\AppData\Local\Programs\MiKTeX 2.9\tex\latex\oberdiek\grffile
.sty"
Package: grffile 2017/06/30 v1.18 Extended file name support for graphics (HO)
Package grffile Info: Option `multidot' is set to `true'.
Package grffile Info: Option `extendedchars' is set to `false'.
Package grffile Info: Option `space' is set to `true'.
Package grffile Info: \Gin#ii of package `graphicx' fixed on input line 494.
)
("C:\Users\Mortond\AppData\Local\Programs\MiKTeX 2.9\tex\latex\parskip\parskip.
sty"
Package: parskip 2018-08-24 v2.0a non-zero parskip adjustments
)
("C:\Users\Mortond\AppData\Local\Programs\MiKTeX 2.9\tex\latex\titling\titling.
sty"
Package: titling 2009/09/04 v2.1d maketitle typesetting
\thanksmarkwidth=\skip53
\thanksmargin=\skip54
\droptitle=\skip55
)
("C:\Users\Mortond\AppData\Local\Programs\MiKTeX 2.9\tex\latex\fancyhdr\fancyhd
r.sty"
Package: fancyhdr 2017/06/30 v3.9a Extensive control of page headers and footer
s
\f#nch#headwidth=\skip56
\f#nch#O#elh=\skip57
\f#nch#O#erh=\skip58
\f#nch#O#olh=\skip59
\f#nch#O#orh=\skip60
\f#nch#O#elf=\skip61
\f#nch#O#erf=\skip62
\f#nch#O#olf=\skip63
\f#nch#O#orf=\skip64
)
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.90 \addtolength{\headheight}{1.0cm} \%
make more space for the header
Here is how much of TeX's memory you used:
22493 strings out of 427767
408844 string characters out of 3146884
530389 words of memory out of 3000000
26423 multiletter control sequences out of 15000+200000
532722 words of font info for 28 fonts, out of 3000000 for 9000
1328 hyphenation exceptions out of 8191
45i,0n,68p,816b,443s stack positions out of 5000i,500n,10000p,200000b,50000s
No pages of output.
So why does it work once and not a second time? If I exit RStudio and then s start it up again, it appears to work. I've tried to
.rs.restartR() to no avail. as well as
rm(list = ls(envir = globalenv()),envir = globalenv())
gc() to clean things up.
Any thoughts? I appreciate reading through all this.
I do not know if I had the same issue. But I experienced that if I compiled my document it worked the first time and failed the second. I suspected a cache issue and added cache.rebuild=T to
<<echo=F, cache=T, message=F, warning=F, `>>=
set_parent('../../Parent.Rnw')
#
Just FIY, the header of the parent does not only include the latex info but also sources my main .R file with the calculations.
Anyway, if someone experience a similar problem try to add cache.rebuild=T to your included script(s).
I would like to run a code chunk under a question level in the exam document class, but I keep receiving errors. I am assuming this is because it believes the output from the R-code is Latex code.
---
output: pdf_document
documentclass: exam
header-includes: \usepackage{float}
---
\begin{questions}
\question Answer question...
```{r}
iris%>%
group_by(Species)%>%
summarize(Total=n())
```
\end{questions}
Sometimes \begin{"some environment") ... \end{"some environment") doesn't play well with R chuncks. One work around is to define a new environment.
For example, I defined a file preamble.tex with the following information:
preamble.tex
\usepackage{float}
\newcommand{\bQ}{\begin{questions}}
\newcommand{\eQ}{\end{questions}}
Then, I ran the following.
exam.Rmd
---
documentclass: exam
geometry: margin=.5in
output:
pdf_document:
highlight: haddock
includes:
in_header: preamble.tex
before_body: doc-prefix.tex
after_body: doc-suffix.tex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\bQ
## Including Plots
\question You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
```{r cars}
summary(cars)
```
\question We can keep the pound signs.
\eQ
Here is the resulting output.
Output
I managed to get something working. It needs some libraries and uses knitr to create the output.
---
output:
pdf_document:
keep_tex: true
documentclass: exam
header-includes: \usepackage{float}
---
```{r setup, include=TRUE,echo=FALSE,message=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(dplyr)
library(knitr)
```
\begin{questions}
\question Answer question...
```{r, echo=F, comment=NA}
summary = iris %>% group_by(Species) %>% summarize(Total=n())
kable(summary, format='latex')
```
\end{questions}
The problem seems to be the inclusion of # in the output from R for processing by Latex. I avoid this by using kable.
R markdown gets stuck on chunk 1, which is repeated below:
---
title: "RMark1"
author: "df"
date: "11/19/2017"
output:
html_document:
toc: true
---
```{r setup}
library(dplyr)
library(knitr)
library(rmarkdown)
library(ggplot2)
library(plotly)
library(readr)
knitr::opts_chunk$set(echo = TRUE)
print("loaded libraries")
```
what am I missing here?