Hi there

What solved the issue for me (I just installed all the things for the first 
time), was just to specify the --latex-engine.

So for a simple conversion of markdown to pdf you can use:
pandoc source --output output.pdf --latex-engine /usr/texbin/pdflatex

Hope that helps if you came here by search like me ;)

Bin thanks to @Ben

Cheers,
Chris

On Wednesday, December 3, 2014 at 10:43:28 PM UTC+1, John MacFarlane wrote:
>
> Try just using one of their extra options at a time, to see if you can 
> isolate which one matters. 
>
> +++ Ben Temperton [Dec 03 14 11:57 ]: 
> >Quick follow up to this - I noticed that pandoc was working fine in 
> Rstudio 
> >for conversion of R markdown. If you mimic the command used by RStudio to 
> >generate the pdf on the command line, it works fine. 
> > 
> >pandoc SCG.protocol.md --to latex --from 
> >markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures 
>
> >--output SCG.protocol.pdf --filter pandoc-citeproc --template 
> >/Library/Frameworks/R.framework/Versions/3.0/Resources/library/rmarkdown/rmd/latex/default.tex 
>
> >--highlight-style tango --latex-engine /usr/texbin/pdflatex --variable 
> >'geometry:margin=1in' --bibliography SCG.protocol.bib 
> > 
> >Not sure if this provides any more insight to the original issue. 
> > 
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