render('foo.Rmd',beamer_presentation(citation_package = 'natbib')) failing...

[JeffreyRacine]

Greetings, and let me thank you in advance for your incredible work.

RStudio 1.1.383, rmarkdown 1.6.0.9000, R 3.4.2, macOS High Sierra 10.13...

I am having issues with bibtex and beamer and the following reproduces. Running

render('debug.Rmd',beamer_presentation(citation_package = 'none'))

produces a PDF file and all goes well... this uses --output=pdf as in

/usr/local/bin/pandoc +RTS -K512m -RTS debug.utf8.md --to beamer --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output debug.pdf --highlight-style tango --latex-engine /opt/local/bin/pdflatex

Replacing 'none' with 'biblatex' or 'natbib' (which are two of the three options) fails... it produces a tex file without the requisite headers and fails to generate the PDF... to reproduce this I used the default skeleton beamer file generated in RStudio...

/usr/local/bin/pandoc +RTS -K512m -RTS debug.utf8.md --to beamer --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output debug.tex --highlight-style tango --latex-engine /opt/local/bin/pdflatex --biblatex
Latexmk: This is Latexmk, John Collins, 19 Jan. 2017, version: 4.52c.
Latexmk: applying rule 'pdflatex'...
Rule 'pdflatex': File changes, etc:
   Non-existent destination files:
      'debug.pdf'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running '/opt/local/bin/pdflatex  -halt-on-error -interaction=batchmode -recorder  "debug.tex"'
------------
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/MacPorts 2017_2) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
=== TeX engine is 'pdfTeX'
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'debug.log' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs of latex/pdflatex.
! LaTeX Error: Missing \begin{document}.

Error: Failed to compile debug.tex. See debug.log for more info.
Execution halted

[yihui]

Adding the --self-contained argument should fix it, e.g.

output: 
  beamer_presentation: 
    citation_package: natbib
    pandoc_args: "--self-contained"

I'll fix it in the package. Thanks for the report!

[JeffreyRacine]

Thanks! I am having a similar issue with gitbook... it seems to ignore citation_package: natbib while pdf_book acknowledges it... here is my _output.yml file (I realize this is a bookdown issue but perhaps related?):

bookdown::pdf_book:
  includes:
    in_header: preamble.tex
  latex_engine: xelatex
  citation_package: natbib
  keep_tex: yes
  dev: tikz
  toc_depth: 3
bookdown::gitbook:
  dev: tikz
  citation_package: natbib
  config:
    toc:
      collapse: section
      before: |
        <li><a href="https://socserv.mcmaster.ca/racinej/768/index.html" target="blank"> ECON 768 - Fall 2017 </a></li>
      after: |
        <li><a href="https://bookdown.org/yihui/bookdown/" target="blank"> Written in R Markdown & bookdown</a></li>
    sharing: no
    self.contained: yes
    split_by: none

[yihui]

citation_package is only an option for LaTeX/PDF output formats; natbib / biblatex are LaTeX packages, and won't work for non-LaTeX output formats.

[JeffreyRacine]

Thanks.

I realize this is off topic, but the citations in gitbook are formatted in an unwanted way, reporting what I expect to look like Black and White (1979) as A. Black and White (1979)... I have searched high and low for a while now and not found a solution that would render cites in gitbook like natbib in pdf_book....

Thanks!

[yihui]

I have never tried (and I don't care the citation styles for non-LaTeX output) but --csl should be the way to go for formatting bibliography in non-LaTeX output formats: http://pandoc.org/MANUAL.html#citations

If you have further questions instead of bug reports or feature requests, so please do me a favor to ask on StackOverflow instead. Currently I'm the only person working on Github issues of this repo, so I cannot afford too much time here. Your original issue has been fixed by #1164. Thanks!

[JeffreyRacine]

Thanks, apologies, and will do. Thanks again for you incredible creative efforts.

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