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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.

siluce
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1 Answers1

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As the error message says, you do not have pandoc-citeproc installed. You need pandoc-citeproc to process the bibliography.

knytt
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  • Thank you for your answer. The maintainer of my cluster says that he has installed pandoc and pandoc-citeproc. Does this error mean that that is not the case? I cannot sudo on the cluster, so is there any way I can install it for myself? – siluce Jun 24 '20 at 13:54
  • The line `Could not find executable pandoc-citeproc` suggests that `pandoc-citeproc` is not installed on your cluster, you need to solve this with your tech support (I am not aware of any option that would not require sudo access). Consider trying to build the document on a local linux install and testing whether the problem is really caused by the missing `pandoc-citeproc`. Also please consider accepting and closing this if installing `pandoc-citeproc` solves the problem. – knytt Jun 24 '20 at 14:14
  • The problem is indeed caused by `pandoc-citeproc` not being installed. Previously, I transferred a local pandoc and pandoc-citeproc executable to the cluster and `Sys.setenv` `RSTUDIO_PANDOC` to this folder in R. However, this is not working anymore. Two last questions before I resolve this: (1) Do you know why transferring the executables to the cluster and setting this variable is not working anymore? and (2) If pandoc-citeproc is not installed, is there any other way to use a bibliography in my site? Thank you in advance for your help. – siluce Jun 25 '20 at 11:10
  • Regarding your questions: 1) Create a new question either here or under linux/unix (https://unix.stackexchange.com/), I have no such experience/knowledge. 2) I think the best solution would be to get your tech support to install pandoc-citeproc. Otherwise I am not aware of any other options, check the manual. https://pandoc.org/index.html – knytt Jun 25 '20 at 11:20