I'm trying to compile a pdf file from an Rmd document with some tikz graphics in it.
Example Rmd:
---
output:
pdf_document:
latex_engine: lualatex
header-includes:
- \usepackage{tikz}
---
# Introduction
Hello.
```{tikz img-plot, echo = FALSE, engine = "tikz", fig.ext = "pdf", fig.cap = "This is my image", code = readLines("testimg.tex")}
```
Figure \#ref(fig:img-plot) is not working.
referenced tikz file testimg.tex:
\begin{tikzpicture}
\node at (0.5, 0.5) {(a)};
\end{tikzpicture}
Compiling the Rmd file in Rusing
$ echo "rmarkdown::render('test.Rmd', output_file='test.pdf')" | R --no-save -q
gives me the following log:
rmarkdown::render('test.Rmd', output_file='test.pdf')
processing file: test.Rmd
|
|
| 0% |
|.......................
| 33% ordinary text without R code
|
|...............................................
| 67% label: img-plot (with options) List of 5 $ echo : logi
FALSE $ engine : chr "tikz" $ fig.ext: chr "pdf" $ fig.cap: chr
"This is my image" $ code : language readLines("testimg.tex")
|
|......................................................................|
100% ordinary text without R code
output file: test.knit.md
/usr/bin/pandoc +RTS -K512m -RTS test.utf8.md --to latex --from
markdown+autolink_bare_uris+tex_math_single_backslash --output
test.tex --template
/usr/lib/R/library/rmarkdown/rmd/latex/default-1.17.0.2.tex
--highlight-style tango --pdf-engine lualatex --variable graphics=yes --lua-filter /usr/lib/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/library/rmarkdown/rmd/lua/latex-div.lua --variable 'geometry:margin=1in' --variable 'compact-title:yes' ! error: (file "test_files/figure-latex/""img-plot-1".pdf) (pdf
backend): canno
Error: Failed to compile test.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips. See
test.log for more info. Execution halted
The error log shows a double quote in ""img-plot-1".pdf. Could this have something to do with it?
I used to be able to compile a similar file a few weeks ago, which is why my guess is that some update in an R package, pandoc or somewhere else on my system broke it. Any ideas what the root of this might be?
System info:
OS: Linux Kernel 4.19.85-1-MANJARO
R 3.6.1
rmarkdown package: 1.17
pandoc 2.7.3
Related
At a loss here. Trying to get R Studio to knit my Rmarkdown document to a PDF. I've installed as much as I can figure out. What am I missing?
processing file: MyFirstRMarkdown3.Rmd
|.......... | 14%
ordinary text without R code
|.................... | 29%
label: setup (with options)
List of 1
$ include: logi FALSE
|.............................. | 43%
ordinary text without R code
|........................................ | 57%
label: cars
|.................................................. | 71%
ordinary text without R code
|............................................................ | 86%
label: pressure (with options)
List of 1
$ echo: logi FALSE
|......................................................................| 100%
ordinary text without R code
output file: MyFirstRMarkdown3.knit.md
"C:/Program Files/RStudio/bin/quarto/bin/pandoc" +RTS -K512m -RTS MyFirstRMarkdown3.knit.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output MyFirstRMarkdown3.tex --lua-filter "C:\Users\a12cof\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\a12cof\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --highlight-style tango --pdf-engine pdflatex --variable graphics --variable "geometry:margin=1in"
! Sorry, but C:\Users\a12cof\AppData\Local\Programs\MiKTeX\miktex\bin\x64\pdflatex.exe did not succeed.
! The log file hopefully contains the information to get MiKTeX going again:
! C:\Users\a12cof\AppData\Local\MiKTeX\miktex\log\pdflatex.log
Error: LaTeX failed to compile MyFirstRMarkdown3.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MyFirstRMarkdown3.log for more info.
Execution halted
I'm trying to knit the mwe below to pdf using rstudio (1.2.5019)
---
title: "Test"
author: "Me"
output:
pdf_document:
fig_caption: yes
keep_tex: yes
fig_crop: yes
---
This should be cropped
```{r}
library(knitr)
```
```{r named-chunk}
plot(x <- 0:100, dbinom(x, size=100, prob=0.6), type='l',
main="Not cropped", xlab="Looks good", ylab="Nok")
```
The output pdf looks fine except the plot has not been cropped with pdfcrop.
Here's the log output.
processing file: cropping.Rmd |..................
| 25% ordinary text without R code
|...................................
| 50% label: unnamed-chunk-1
|....................................................
| 75% ordinary text without R code
|......................................................................|
100% label: named-chunk
output file: cropping.knit.md
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS
cropping.utf8.md --to latex --from
markdown+autolink_bare_uris+tex_math_single_backslash --output
cropping.tex --self-contained --highlight-style tango --pdf-engine
pdflatex --variable graphics --lua-filter
"C:/Users/marti/Documents/R/win-library/3.6/rmarkdown/rmd/lua/pagebreak.lua"
--lua-filter "C:/Users/marti/Documents/R/win-library/3.6/rmarkdown/rmd/lua/latex-div.lua"
--variable "geometry:margin=1in"
Output created: cropping.pdf
pdfcrop works just fine from my command line but isn't called by rstudio. It is also located by rstudio.
Sys.which('pdfcrop')
pdfcrop
"C:\texlive\2019\bin\win32\pdfcrop.exe"
What am I missing?
This actually solved it.
``` {r crop-hook,cache=FALSE}
knit_hooks$set(crop=hook_pdfcrop)
```
```{r named-chunk, crop=TRUE}
plot(x <- 0:100, dbinom(x, size=100, prob=0.6), type='l',
main="Not cropped", xlab="Looks good", ylab="Nok")
```
As far as I understood from the documentation this shouldn't be necessary?
Install pdfcrop via livetex or miktex --- the one you are using to write latex documents.
I'm writing a report on Rmarkdovn but when you try to compile - pandoc_args options ignored when compile pdf.
I find this question:
Is it possible to include svg image in pdf document rendered by rmarkdown?
But it does not work because --latex-engine-opt replaced by --pdf-engine-opt. I replaced, but also did not work.
Compilation command:
Rscript -e "rmarkdown::render('test.rmd')"
test.rmd
---
title: Test
papersize: a4paper
output:
pdf_document:
latex_engine: pdflatex
pandoc_args: [
--pdf-engine-opt, -shell-escape,
--pdf-engine-opt, -interaction=nonstopmode]
header-includes:
- \usepackage{minted}
---
Output:
processing file: test.rmd
|................................ | 50%
ordinary text without R code
|.................................................................| 100%
label: unnamed-chunk-1 (with options)
List of 1
$ engine: chr "python"
output file: test.knit.md
/usr/bin/pandoc +RTS -K512m -RTS test.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test.tex --template /home/renesat/R/x86_64-pc-linux-gnu-library/3.5/rmarkdown/rmd/latex/default-1.17.0.2.tex --highlight-style tango --pdf-engine pdflatex --variable graphics=yes --pdf-engine-opt --shell-escape --pdf-engine-opt -interaction=nonstopmode --variable 'geometry:margin=1in' --variable 'compact-title:yes'
! Package minted Error: You must invoke LaTeX with the -shell-escape flag.
Error: Failed to compile test.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See test.log for more info.
Execution halted
I can use knitr -> pandoc -> xelatex, but it would be more convenient to use YAML header.
R Markdown documents are compiled to PDF via tinytex::latexmk(). To enable the -shell-escape option for your LaTeX engine, you may set the global option tinytex.engine_args, e.g., add this code chunk to your document:
```{r, include=FALSE}
options(tinytex.engine_args = '-shell-escape')
```
See the help page ?tinytex::latexmk for more information.
The LaTeX engine is called by tinytex::latexmk() instead of Pandoc, so the Pandoc argument --pdf-engine-opt won't work.
The R Markdown file seems to work in Rstudio. The r Markdown file can be converted into word, but not pdf/html.(Yesterday it gave different problem, so I change my question here.)
Any help will be appreciated!
This is the context of my Markdown file:
---
title: "Test"
author: "Test"
date: "2018/9/8"
output: html_document
---
## R test
```{r test}
x<-rnorm(500)
y<-rnorm(x*10)
ls()
plot(x,y)
rm(x,y)
```
This is an test.
This is the outcome is I knit to html:
|...................... | 33%
ordinary text without R code
processing file: test.Rmd
|........................................... | 67%
label: test
|.................................................................| 100%
ordinary text without R code
/usr/local/bin/pandoc +RTS -K512m -RTS test.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /var/folders/_h/013l11r91m3gny4lqwsvh5qh0000gn/T//Rtmpfvxqld/rmarkdown-str268664475eb.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
output file: test.knit.md
--smart/-S has been removed. Use +smart or -smart extension instead.
For example: pandoc -f markdown+smart -t markdown-smart.
Try pandoc --help for more information.
error: pandoc document conversion failed with error 2
stop processing
This is the outcome if I knit to pdf:
|...................... | 33%
ordinary text without R code
|........................................... | 67%
label: test
processing file: test.Rmd
|.................................................................| 100%
ordinary text without R code
/usr/local/bin/pandoc +RTS -K512m -RTS test.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output test.pdf --template /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rmarkdown/rmd/latex/default-1.17.0.2.tex --highlight-style tango --latex-engine /Library/TeX/texbin/pdflatex --variable graphics=yes --variable 'geometry:margin=1in'
output file: test.knit.md
--latex-engine has been removed. Use --pdf-engine instead.
Try pandoc --help for more information.
error: pandoc document conversion failed with error 2
stop processing
A little background might help:
Pandoc is a Haskell binary (i.e. a distinct piece of non-R software), that is shipped with RStudio for sake of running RMarkdown conversion. It seems you are getting some deprecation warnings, like:
--latex-engine has been removed. Use --pdf-engine instead.
--smart/-S has been removed. Use +smart or -smart extension instead.
This tells me you probably have an older version of RStudio, thus an older version of Pandoc. You may want to reinstall RStudio to make sure you have the appropriate Pandoc version, then debug from there.
Also, make sure to reinstall knitr and rmarkdown with the newest versions.
I am trying to produce a tree diagram in a Rmd file I expect to look like this:
Using rmarkdown's render function.
But get an error 43 I do not know how to interpret. How can I get the pdf to render? What's causing the error?
Rmd file
---
title: "testtree"
header-includes:
- \usepackage{qtree}
output:
pdf_document
---
\Tree [.S [.NP LaTeX ] [.VP [.V is ] [.NP fun ] ] ]
Success
Error message
> rmarkdown::render("testtree.Rmd", "all")
processing file: testtree.Rmd
|.................................................................| 100%
ordinary text without R code
output file: testtree.knit.md
"C:/Users/trinker/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS testtree.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output testtree.pdf --template "C:\R\R-3.2.2\library\rmarkdown\rmd\latex\default-1.14.tex" --highlight-style tango --latex-engine pdflatex --variable "geometry:margin=1in"
! Paragraph ended before \doanode was complete.
<to be read again>
\par
l.90
pandoc.exe: Error producing PDF from TeX source
Error: pandoc document conversion failed with error 43
In addition: Warning message:
running command '"C:/Users/trinker/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS testtree.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output testtree.pdf --template "C:\R\R-3.2.2\library\rmarkdown\rmd\latex\default-1.14.tex" --highlight-style tango --latex-engine pdflatex --variable "geometry:margin=1in"' had status 43
>
The following .Rnw document compiles successfully:
\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage{qtree}
\begin{document}
Here is a code chunk.
\Tree [.S a [.NP {\bf b} c ] d ]
You can also write inline expressions, e.g. $\pi=\Sexpr{pi}$, and \Sexpr{1.598673e8} is a big number.
\end{document}
Pandoc turns the last two closing brackets ] ] as {]} {]}, a behavior you can see if you use output option keep_tex: true. I am not sure whether this is a bug, you should ask this on the pandoc mailing-list or file a report.
A quick fix is to use pandoc's ability to ignore the code inside an environment and surround your command with a dummy environment:
---
title: "testtree"
header-includes:
- \usepackage{qtree}
- \newenvironment{dummy}{}{}
output:
pdf_document:
keep_tex: true
---
\begin{dummy}
\Tree [.S [.NP LaTeX ] [.VP [.V is ] [.NP fun ] ] ]
\end{dummy}
Success