I just updated pandoc 1.9.x to pandoc 2.1.3, and also am ready to kill myself for doing so. Everything used to go smoothly with conversion of .Rmd to .pdf output before the update. I do use custom .tex and styling templates along with the thesisdowndss package for knitting.
Knitting goes well and produces .md (which is transient though, and therefore I can't access it) but the pandoc conversion fails with following ouput.
output file: thesis.knit.md "C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS thesis.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output thesis.tex --table-of-contents --toc-depth 3 --template template.tex --number-sections --highlight-style pygments --pdf-engine pdflatex --chapters --variable tables=yes --standalone --filter pandoc-citeproc --chapters has been removed. Use --top-level-division=chapter instead. Try pandoc.exe --help for more information. Error: pandoc document conversion failed with error 2 In addition: There were 33 warnings (use warnings() to see them) Please delete thesis.Rmd after you finish debugging the error. Execution halted The console error output is very uninformative, as could be seen. My problem is: how do I access the log the pandoc writes to? I'm feeling helpless as there's no intermediate .md file to experiment with either.
The other issue is, I can't find a pandoc 1.9.x window binaries available anymore, although github provides a source, compiling It to get a ready built is not an option for me. Can anyone point me to read-to-use binary builds of pandoc (I think that could save me some time for now with the submission deadline of th*is nearing)?
Hoping that a complete header will be more sensible, here it is:
--- author: 'Dear Dog' date: "`r Sys.Date()`" institution: 'Uninstitutional' division: 'Hooligan' advisor: 'pre-professor' department: 'Blah Blah' degree: 'Masters of Undiagnosis' title: "Panic attack due to pandoc error" knit: "bookdown::render_book" site: bookdown::bookdown_site output: thesisdowndss::thesis_pdf: default keep_md: true abstract: | `r if(knitr:::is_latex_output()) paste(readLines("00-abstract.Rmd"), collapse = '\n ')` acknowledgements: | I am in no situation to acknowledge the resolution, right now. bibliography: ["bib/thesis.bib", "bib/exported_items.bib"] csl: csl/apa.csl lot: true lof: true space_between_paragraphs: true header-includes: - \usepackage{tikz} - \usepackage{array} - \usepackage{multirow} - \usepackage{wrapfig} - \usepackage{colortbl} - \usepackage{pdflscape} - \usepackage{tabu} - \usepackage{threeparttable} - \usepackage[normalem]{ulem} - \newcommand{\blandscape}{\begin{landscape}} - \newcommand{\elandscape}{\end{landscape}} - \usepackage{subcaption} - \newcommand{\subfloat}[2][need a sub-caption]{\subcaptionbox{#1}{#2}} --- 
