Debian doesn’t include a recent version of pandoc, unless you’re living on the hard edge (a.k.a. experimental). When pandoc threw errors for documents passed to pandoc-citeproc, I suspected that an update would resolve the issue, especially as the same document compiled fine under Windows and older documents also failed to compile. There’s an up-to-date Debian package from the official repository, but not for my architecture. Compiling it is, then. Downloading and compiling posed no problem, but somehow the symlink out of ./cabal/bin failed to work properly, as did creating a symlink to the pandoc installed within/alongside rstudio. I guess there’s a clean solution during the compilation stage, but the quickest workaround was copying the binaries in ./cavbal/bin to /usr/bin. Not pretty, but functional.
Sociologist. Quantitativist. University of Neuchâtel.
Didier Ruedin 
Today I had fun with “pandoc: Error producing PDF from TeX source” when compiling a markdown document into PDF. It just didn’t work. I noticed that markdown to tex (with option -s) followed by pdflatex worked, but that’s not convenient. Pandoc also did html properly. Re-installing and freshly compiling pandoc didn’t do much beyond running down my battery. I also re-installed texlive, just in case. No difference.
It turns out there’s a simpler solution: giving the full path to the latex engine by adding –latex-engine=/usr/bin/xelatex (it appears that in other distributions and on the Mac, the installation is into /usr/local/…) Pick your favourite…
So the “build command” in Geany has changed from pandoc -o “%e.pdf” “%f” to pandoc -o “%e.pdf” “%f” –latex-engine=/usr/bin/xelatex
Again, perhaps not the proper solution to the problem, but one that works.