I am trying to render a site using rmarkdown / bookdown on Linux using R (not R Studio, our cluster only has base R).
I have been told that pandoc is installed on the cluster and should be working as intended. Indeed, it does appear to be installed.
When I try to render my site or a single page, I get the error:
/usr/bin/pandoc +RTS -K512m -RTS 01_GettingStarted.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output 01_GettingStarted.html --email-obfuscation none --bibliography ./DNAmArray.bib --standalone --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template library/rmarkdown/rmd/h/default.html --highlight-style kate --css style.css --include-before-body /tmp/RtmpLe2AMT/rmarkdown-strff91562ed9d94.html --variable navbar=1 --variable body_padding=54 --variable header_padding=59 --variable 'theme:lumen' --include-in-header /tmp/RtmpLe2AMT/rmarkdown-strff91573dd14db.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /library/rmarkdown/rmd/lua/latex-div.lua
Error running filter pandoc-citeproc:
Could not find executable pandoc-citeproc
Error: pandoc document conversion failed with error 83
Any help would be so much appreciated. I just can't seem to work out what the error means or why it would fail when pandoc is installed.
As the error message says, you do not have pandoc-citeproc installed. You need pandoc-citeproc to process the bibliography.