I'm writing a technical book using Bookdown and RStudio. My code chunks are mainly using bash. Everything works fine except when I export the book to pdf, then the source code is partially out of the "box" and even the page if this is long enough. I have read a lot of solutions when r language is used, but none of these solutions works when bash language is used.
Here is my code at the beginning of the .Rmd file:
```{r, global_options, include=FALSE}
knitr::opts_chunk$set(message=FALSE, eval=FALSE,
tidy.opts=list(width.cutoff=60), tidy=TRUE)
```
And then when I write the code chunk:
```{bash}
mongodump --uri="mongodb+srv://cluster0.rh6qzzz.mongodb.net/" --db sample_mflix --username my_username
```
The outputs were produced as shown below (see the end of line):
I would like to avoid this, but I have not found the solution.
In a reStructuredText on Sphinx 2.x, I want to put a content that changes depending on the output format.
In any source document, say, index.rst, add the following lines:
.. role:: pdf(raw)
:format: pdf
.. role:: latex(raw)
:format: latex
.. role:: html(raw)
:format: html
.. |foo| replace::
:pdf:`PDF!`
:latex:`LaTeX!`
:html:`HTML!`
I am |foo|
I expect it shows "I am HTML!" when the output format is in HTML, "I am LaTeX!" if it's LaTeX (even after converting the product to PDF via pdflatex) and "I am PDF!" if it's PDF.
I make the HTML version using make html and I see only "I am HTML!" in a web browser as I expect:
Install rst2pdf. Put the following lines in conf.py:
extensions = [
'rst2pdf.pdfbuilder'
]
pdf_documents = [(
'index',
u'testRst2Pdf',
u'Test Title',
u'Sarah Author')]
Make the PDF version with
sphinx-build -b pdf ./source/ ./build/
Update. Below is the output. No error. I ran this using WSL 1 (Ubuntu 18.04).
Running Sphinx v2.4.3
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [pdf]: targets for 1 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
processing testRst2Pdf...
index
resolving references...
done
writing testRst2Pdf...
done
build succeeded.
I see "I am PDF! LaTeX! HTML!" that includes all the three items.
Is there any way to get either "I am PDF!" or "I am LaTeX!" in the PDF file?
Note.
Before reporting this behavior as a bug, someone help me check if it's unexpected behavior or as-designed.
This question is derived from the other I asked earlier: StackOverflow: "Sphinx: Use a different directive for a different output format".
rst2pdf does not really have conditionals, but you might find the --strip-elements-with-class switch useful? Put the optional pieces into a class name and then if that class doesn't make sense for this format, remove it with the switch.
Manual is here https://rst2pdf.org/static/manual.html#command-line-options and I also blogged (basically a longer version of this first paragraph) about this https://rst2pdf.org/static/manual.html#command-line-options if more information would be useful.
I have been having trouble when converting a Markdown file to PDF using pandoc-eqnos filter. I typed in command line:
pandoc --filter=pandoc-eqnos file.md -o file.pdf
And get the following error message:
File "C:\Users\User\AppData\Local\Programs\Python\Python37-32\Scripts\pandoc-eqnos-script.py", line 1
SyntaxError: Non-UTF-8 code starting with '\xed' in file C:\Users\User\AppData\Local\Programs\Python\Python37-32\Scripts\pandoc-eqnos-script.py on line 1, but no encoding declared; see http://python.org/dev/peps/pep-0263/ for details
Error running filter pandoc-eqnos:
Filter returned error status 1
Installed pandoc-eqnos filter using pip. I sincerely don't know what is causing this error. Any suggestion will be appreciated. Thanks.
RStudio : 0.98.994
OS: Microsoft Windows 7 Ultimate Edition, 64-bit Service Pack 1
MiKTeX: 2.9.4503
Hi,
I get the following error when I try to knit a PDF document.
pandoc.exe: Error producing PDF from TeX source.
This is pdfTeX, Version 3.1415926-1.40.11 (MiKTeX 2.9)
pdflatex: The memory dump file could not be found.
pdflatex: Data: pdflatex.fmt
I also tried devtools::install_github('rstudio/rmarkdown') but was still getting an error when I added 'fig.align='center' to a ggplot2 plot in my document. It would work as HTML, but not as PDF.
After seeing isomorphismes's post I clicked on the gear symbol next to the knit PDF button, then under the advanced tab I changed the LaTeX Engine to xelatex. After that I no longer received the error message and my PDF document was created without problems.
Thank you.
I found the answer here: http://rmarkdown.rstudio.com/tufte_handout_format.html#comment-1582377678
The problem is that you need to add \usepackage[utf8]{inputnc} to the preamble of the tufte-handout.tex file in the rmarkdown package.
This was fixed here: https://github.com/rstudio/rmarkdown/commit/484d5b8e903e0e0c75c82f707efa35f9fd9a52b0
To update your rmarkdown package, you can use directly in the RStudio command line
devtools::install_github("rstudio/rmarkdown")
None of the above worked for me when knitting to PDF (and I wanted to keep the scientific notation). The problem was that latex code was generated that included "\times" without the necessary bracketing by $. In the markdown I simply bracketed the inline R code with $'s, like so:
$p = `r signif(cor.HF$p.value, 2)`$
Voila!
happy to share with you my solution.
---
title: "Untitled"
author: "-----"
date: "21/6/2017"
output:
pdf_document:
latex_engine: xelatex
---
I was able to fix it in my case. I experienced that error when generate PDF from Rmd if I added float values into a text that R tried to display as a scientific notation. For example, instead of "520274.72" it tried to add text "5.2027472 e10-5" which leads to latex code \textbf{5.2027472\times 10\^{}{5}} that was not compiling. I fixed it by wrapping it with format(....,scientific=FALSE).
replace
r round(txn_pd,2)
with
r format(round(txn_pd,2),scientific=FALSE)
I had the same problem and devtools::install_github('rstudio/rmarkdown') didn't work for me. I needed to
rmarkdown::render('in.md',
output_format=pdf_document(latex_engine='xelatex')
)
with the novel command (use xelatex) on its own line.
I encountered this problem while I was trying to add an in-line r code r test1$p.value, which is a very small p-value from t test. The error information is as following:
> ! Missing $ inserted.
> <inserted text>
> $
>l.147 9.0044314\times
>
>pandoc: Error producing PDF
>Error: pandoc document conversion failed with error 43
>Execution halted
I think the problem is the pdflatex engine has a trouble in displaying the small p-value in exponential notation.
I solved the problem by clicking on the gear symbol next to the knit button, then under output options, advanced tab I changed the LaTeX Engine to lualatex, or you can just report the p-value as p < 0.001.
If you are using inline values from your R code which are in the scientific format (too small or too big), format them like:
replace r x
with r format(x, digits=n) where n is whatever.
for me it was because on my headers I was putting + signs. For example gene + treatment. This errors but when I removed it, it works.
In my case it was solved simply by editing the author field in:
---
title: "Document Title"
author: '-----'
date: "21-03-2017"
output: pdf_document
---
the default '-----' would yield the error, but replacing it with anything (for example 'Juan') solved the issue.
I just ran into this problem and already solved it. I didn't use any code as other people did in their posts.
I will assume that you have installed all these basic stuff: R, RStudio, the rmarkdown package, the knitr package, and the MikTex basic installation (I know this is very basic, but I want those first timers know that you need these stuff to make this happen).
If you run into this problem, go to R GUI, upgrade the rmarkdown package and it should work then. Note that if you change the LaTeX Engine to xelatex as the poster of the highest vote did, it may not work for you, at least it did not for me. I leave my latex engine as it is (pdflatex).
I had a similar issue. My solution was to remove the "leading" period in the YAML title argument:
Does not work:
---
title: “1. Title”
output: pdf_document
---
output file: example.knit.md
! Argument of \reserved#a has an extra }.
\par l.79 \end{enumerate}}
pandoc: Error producing PDF Error: pandoc document conversion failed
with error 43 Execution halted
Works:
---
title: “1 Title”
output: pdf_document
---
I did try to use the xelatex engine but still, I got the error that xetex.def is not found. This is another to work around.
output:
pdf_document:
keep_tex: yes
latex_engine: xelatex
Then open .tex file in your TEX editor and build pdf as usual.
I faced a similar issue. In my case, the error occurred because of putting a percentage inside the $ sign.
Like this,
$95%$, I removed the % sign, and everything worked fine.
I'm having a problem calling an outside application from a compiled ocaml application, pdflatex. I'm using the proper string as an argument, when I run it from the toplevel I get the expected results,
Unix.system "pdflatex -interaction batchmode -output-directory res ALGO_GEN.tex";;
And it generates the proper output,
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
restricted \write18 enabled.
entering extended mode
(/usr/share/texmf-texlive/tex/latex/base/article.cls
Document Class: article 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size10.clo))
(/usr/share/texmf-texlive/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texmf-texlive/tex/latex/amsmath/amstext.sty
(/usr/share/texmf-texlive/tex/latex/amsmath/amsgen.sty))
(/usr/share/texmf-texlive/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texmf-texlive/tex/latex/amsmath/amsopn.sty))
(/usr/share/texmf-texlive/tex/latex/algorithms/algorithmic.sty
(/usr/share/texmf-texlive/tex/latex/base/ifthen.sty)
(/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty))
No file ALGO_GEN.aux.
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(maze.html.res/ALGO_GEN.aux) )</usr/share/texmf-texlive/fonts/type1/public/a
msfonts/cm/cmbx10.pfb></usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/
cmmi10.pfb></usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/cmr10.pfb><
/usr/share/texmf-texlive/fonts/type1/public/amsfonts/cm/cmsy10.pfb>
Output written on res/ALGO_GEN.pdf (1 page, 36816 bytes).
Transcript written on res/ALGO_GEN.log.
- : Unix.process_status = Unix.WEXITED 0
From the compiled application, the log indicates that,
*** (job aborted, no legal \end found)
It has been confusing me for some time. I've used other system calls from the Unix module, and other command line options. I'm wondering if anyone can give some advice on how to proceed. The application generates a few tex documents, and they need to be converted to pdf. From the toplevel, calling a map over a list of them generates the pdfs properly; only compiled (byte code) does it not work.
I wasn't closing the channel to the tex file previously written, so no data would potentially be written. Thanks to Gilles for suggesting I inspect the files during runtime.