Error: pandoc document conversion failed with error 6

lilmack · August 10, 2023, 4:36pm

I tried to knit a document and received the following error code:

output file: -3--Table-1a--Participant-Characterization-.knit.md
Unknown option -3.
Unknown option ---Table-1a--Participant-Characterization-.knit.md.
Try pandoc --help for more information.
Error: pandoc document conversion failed with error 6
Execution halted

I looked at this thread and it seems that I have the right version of pandoc:

rmarkdown::pandoc_exec()
[1] "/Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/pandoc"
rmarkdown::find_pandoc()
$version
[1] ‘3.1.1’

$dir
[1] "/Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools"

Sys.getenv("RSTUDIO_PANDOC")
[1] "/Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools"

cderv · August 16, 2023, 11:53am

What is the name of your document ? Does it have dash in it ? or even start with a dash ?

It seems the name could be a problem when passed to pandoc as command line argument

lilmack · August 18, 2023, 3:20am

Document name does not have dashes

cderv · August 18, 2023, 12:00pm

No dash but it starts with a non alphanumeric character. (1). Probably in your example shared before it was (3). Parenthesis are special character in file name so it is replaced by -, hence the starting dash in Pandoc's error.

This is related to this issue

github.com/rstudio/rmarkdown

Filenames beginning with "-" cause incorrect invocation of pandoc

opened 02:50PM - 10 Aug 23 UTC

mbaynton

bug

## Steps to reproduce 1. Create an R Markdown file whose name begins with a `-`, for example `-3-something.Rmd` 2. `rmarkdown::render('-3-something.Rmd')` ## Result ``` processing file: -3-something.Rmd output file: -3-something.knit.md /usr/bin/pandoc +RTS -K512m -RTS -3-something.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output -3-something.html --lua-filter /home/mbaynton/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/mbaynton/R/x86_64-pc-linux-gnu-library/4.3/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /home/mbaynton/R/x86_64-pc-linux-gnu-library/4.3/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 /tmp/Rtmp0WU9RC/rmarkdown-str1bc8d4b28f56f.html Unknown option -3. Unknown option --something.knit.md. Try pandoc --help for more information. Error: pandoc document conversion failed with error 2 ``` ## Checklist When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you: - [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read? - [x] included a minimal, self-contained, and reproducible example? - [ ] pasted the output from `xfun::session_info('rmarkdown')` in your issue? - [x] upgraded all your packages to their latest versions (including your versions of R, the RStudio IDE, and relevant R packages)? - [x] installed and tested your bug with the development version of the rmarkdown package using `remotes::install_github("rstudio/rmarkdown")`?

and we'll try to improve and fix this for next version