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?
Related
I want to knit but I failed. I spend many time for solve it, but I couldn't. I can't knit even basic Rmd code like...
---
title: "Untitled"
date: "2022-09-20"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
error said
output file: knit.knit.md
"C:/Users/곽민승/Desktop/Install/RStudio/bin/quarto/bin/tools/pandoc" +RTS -K512m -RTS knit.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output knit.html --lua-filter "C:\Users\곽민승\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\곽민승\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --variable bs3=TRUE --section-divs --template "C:\Users\곽민승\AppData\Local\R\win-library\4.2\rmarkdown\rmd\h\default.html" --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable "mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\곽민승\AppData\Local\Temp\RtmpolhuTr\rmarkdown-str11e44397877.html"
Error running filter C:\Users\곽민승\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\pagebreak.lua:
cannot open C:\Users\곽민승\AppData\Local\R\win-library\4.2\rmarkdown\rmarkdown\lua\pagebreak.lua: Invalid argument
**error: pandoc document conversion failed with error 83**
곽민승 is my name, and r markdown packages are installed,
pandoc verson is 2.18,
saving is UTF-8
I know there are lots of solution in google, but I was in hurry because homework due date is tomorrow. PLEASE help me.
This is likely the result of a bug in pandoc's Lua subsystem before 2.19: filenames were assumed to be UTF-8 encoded instead using the local encoding on Windows. The program gets confused by the Korean characters in the path (your name). Try upgrading pandoc, or, better yet, use Quarto.
New to Rmarkdown (and markdown in general). I've inherited some code that works great for the html_document output format but not for pdf_document. It seems to get stuck on the knitr asis_output function in the .Rmd script. When I comment out chunks containing that function, it writes to pdf no problem. Here's some troubleshooting I've tried:
xfun::session_info('rmarkdown')
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1, RStudio 1.2.1335
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
Locale: en_CA.UTF-8 / en_CA.UTF-8 / en_CA.UTF-8 / C / en_CA.UTF-8 / en_CA.UTF-8
:Package version:
base64enc_0.1.3 digest_0.6.20 evaluate_0.14 glue_1.3.1 graphics_3.6.1 grDevices_3.6.1 highr_0.8
htmltools_0.4.0 jsonlite_1.6 knitr_1.25 magrittr_1.5 markdown_1.1 methods_3.6.1 mime_0.7
Rcpp_1.0.2 rlang_0.4.0 rmarkdown_1.16 stats_3.6.1 stringi_1.4.3 stringr_1.4.0 tinytex_0.17.1
tools_3.6.1 utils_3.6.1 xfun_0.10 yaml_2.2.0
Pandoc version: 2.7.3
Sys.getenv('PATH')
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/opt/X11/bin"
tinytex::tinytex_root()
[1] "/usr/local/texlive/2019"
(tinytex::tlmgr_path())
tlmgr path add add_link_dir_dir: /usr/local/share/info/dir exists;
not making symlink. add_link_dir_dir: destination
/usr/local/share/man/man5 not writable, no links from
/usr/local/texlive/2019/texmf-dist/doc/man/man5.tlmgr: An error has
occurred. See above messages. Exiting. add of symlinks had 1
error(s), see messages above.[1] 6
So maybe the problem is a path issue? In which case I have no clue how to fix. Or should I be using an alternative to the asis_output function? Any help is much appreciated. Here's the relevant bits of my code:
In the R script:
id <- 44
rmarkdown::render('mymarkdown.Rmd',
output_format = "pdf_document",
output_file = paste("report_", id,".pdf", sep=''),
output_dir = '/Users/myname/Documents/test')
In the Rmd file:
---
title: "Monitoring Activity Summary Report"
mode: selfcontained
date: "November 2019"
output:
pdf_document: default
html_document: default
self_contained: yes
---
[some code chunks...]
[then these code chunks that get stuck only for "pdf_document"...]
``` {r setup_Samp1a, echo=FALSE}
sampling_1 <- !is.na(sampling_unique[1])```
```{r conditional block, eval = sampling_1}
asis_output("### 3.1 Sampling 1\\n") # Header that is only shown if
sampling_1 == TRUE```
The error message
! Undefined control sequence.
<argument> 3.1 Sampling 1\n
Error: Failed to compile /Users/myname/Documents/test/report_44.tex.
See https://yihui.name/tinytex/r/#debugging for debugging tips. See
report_44.log for more info.
The help file of the pdf_document function of the Rmarkdown CRAN package says that the function is defined with the following options:
pdf_document(toc = FALSE, toc_depth = 2, number_sections = FALSE,
fig_width = 6.5, fig_height = 4.5, fig_crop = TRUE,
fig_caption = TRUE, dev = "pdf", df_print = "default",
highlight = "default", template = "default", keep_tex = FALSE,
latex_engine = "pdflatex", citation_package = c("none", "natbib",
"biblatex"), includes = NULL, md_extensions = NULL,
pandoc_args = NULL, extra_dependencies = NULL)
I am under the impression that I could add any of these arguments as options under pdf_document in the output section of the YAML header in my Rmarkdown document. Is this correct? The document managed to compile when I used the following options/arguments of pdf_document: toc, number_sections, fig_caption, df_print, and keep_tex. However, when I add citation_package to the list, I get an error in compiling. For instance, consider the following template Rmarkdown document.
---
title: "Untitled"
author: "Unknown"
date: "4/18/2019"
output:
pdf_document:
# toc: true
number_sections: true
fig_caption: true
df_print: kable
keep_tex: true
citation_package: biblatex
bibliography: sample_bib.bib
csl: /Users/Shared/Zotero/styles/multidisciplinary-digital-publishing-institute.csl
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
I love R [#rcoreteamLanguageEnvironmentStatistical2018].
The sample_bib.bib mentioned is the bib file that looks like
#software{rcoreteamLanguageEnvironmentStatistical2018,
location = {{Vienna, Austria}},
title = {R: {{A Language}} and {{Environment}} for {{Statistical Computing}}},
url = {https://www.R-project.org/},
version = {3.5.1},
organization = {{R Foundation for Statistical Computing}},
date = {2018},
author = {{R Core Team}}
}
However, I was unable to knit this Rmarkdown document. I got the following error.
/usr/local/bin/pandoc +RTS -K512m -RTS rmarkdown_pdf_document.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output rmarkdown_pdf_document.tex --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmarkdown/rmd/latex/default-1.17.0.2.tex --number-sections --highlight-style tango --pdf-engine pdflatex --biblatex --variable graphics=yes --variable 'geometry:margin=1in' --variable 'compact-title:yes'
output file: rmarkdown_pdf_document.knit.md
INFO - This is Biber 2.7
INFO - Logfile is 'rmarkdown_pdf_document.blg'
INFO - Reading 'rmarkdown_pdf_document.bcf'
INFO - Found 1 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex format file 'sample\_bib.bib' for section 0
ERROR - Cannot find 'sample\_bib.bib'!
INFO - ERRORS: 1
Error: Failed to build the bibliography via biber
Execution halted
Warning message:
LaTeX Warning: Citation 'rcoreteamLanguageEnvironmentStatistical2018' on page 1
undefined on input line 137.
LaTeX Warning: Empty bibliography on input line 169.
Package rerunfilecheck Warning: File `rmarkdown_pdf_document.out' has changed.
(rerunfilecheck) Rerun to get outlines right
(rerunfilecheck) or use package `bookmark'.
LaTeX Warning: There were undefined references.
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
Package biblatex Warning: Please (re)run Biber on the file:
(biblatex) rmarkdown_pdf_document
(biblatex) and rerun LaTeX afterwards.
Luckily, this problem is easily fixed by moving the "citation_package" from an option under pdf_document to a separate line in the YAML header. Or:
---
title: "Untitled"
author: "Unknown"
date: "4/18/2019"
output:
pdf_document:
# toc: true
number_sections: true
fig_caption: true
df_print: kable
keep_tex: true
citation_package: biblatex
bibliography: sample_bib.bib
csl: /Users/Shared/Zotero/styles/multidisciplinary-digital-publishing-institute.csl
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
I love R [#rcoreteamLanguageEnvironmentStatistical2018].
Upon knitting this adjusted Rmarkdown document, the result is a pdf_document.
So my question is: Was I right that you could add any of the arguments found in the pdf_document help file on CRAN as options under "pdf_document" in the YAML header in a Rmarkdown file? Or, upon using this particular citation_package argument/option, could this be a possible bug in the rmarkdown::pdf_document() function?
ALSO POSTED ON RMARKDOWN's GITHUB; see for additional comments.
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).
The example document below is intended to include an index after the appendix. In a Sweave document, Rstudio would run a shell escape command to create the index .idx file, but I've not been able to find a way to do this for an Rmarkdown document. Is there a simple header command I'm missing?
---
title: "Untitled"
output:
pdf_document:
toc: yes
header-includes:
- \usepackage{makeidx}
- \makeindex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# R Markdown
This is an \index{R Markdown} R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
# Appendix - A
End of the document
\printindex
I've tried this from both the Knit button and using:
rmarkdown::render(rmd.file, output_format = "pdf_document", clean = FALSE)
I'm looking for a solution that can run as part of an automated process.
UPDATE:
I was able to get the index to work by changing the output type to bookdown::pdf_document2. The additional latex packages were required for a combination of indexing, cross referencing, and formatting.
---
title: "Untitled"
output:
bookdown::pdf_document2:
toc: no
geometry: margin=0.8in
header-includes:
- \usepackage{attachfile2}
- \usepackage{booktabs}
- \usepackage{caption}
- \usepackage{float}
- \usepackage[utf8]{inputenc}
- \usepackage{makeidx}
- \makeindex
- \usepackage{multirow}
- \usepackage{setspace}
- \usepackage{relsize}
- \usepackage[table]{xcolor}
- \setcounter{tocdepth}{5}
- \setcounter{secnumdepth}{0}
- \hypersetup{unicode=true,pdfusetitle,bookmarks=true,bookmarksnumbered=true,bookmarksopen=true,bookmarksopenlevel=2,breaklinks=false,backref=false,colorlinks=true,linkcolor=blue}
---
While this would work when manually pushing the create PDF button, the call to rmarkdown::render() still does not process the indexing.