Error: pandoc document conversion failed with error 6 Execution halted

[mburzillo]

Hi all,

Could anyone please help me with some errors I am getting when trying to knit a markdown document in Rstudio? When trying to knit ANY R markdown document I am getting the error (screenshot also below):

dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin Referenced from: /usr/local/bin/pandoc Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ____chkstk_darwin Referenced from: /usr/local/bin/pandoc Expected in: /usr/lib/libSystem.B.dylib

Error: pandoc document conversion failed with error 6 Execution halted

I already tried some things such as restarting Rstudio, re-downloading Pandoc, deleting and re-downloading both R and Rstudio and googling the error with no luck. Rstudio gives this error whenever I try to knit ANY markdown file, not just the ones with my code. It is particularly strange because I was knitting R markdown files with no issue a few days ago. Thanks for the help!

[dkane]

Hmm. This does not seem to be a fresh RStudio session, with a clean environment. (Note all the stuff in the environment tab.) Can you get rid of that, start fresh, and try with the default R markdown file stuff?

[mburzillo]

Unfortunately, looks like this is giving the same issue!

[cderv]

See this other question on the community and its answer

Updated pandoc, now getting an error when I knit: "dyld: lazy symbol binding failed"

I fixed this by running the pandoc uninstall script as described here. I assume that simply reverted R back to using the version of pandoc automatically installed with RStudio.

It seems you are not using the pandoc binary with RStudio and that there is something wrong which the one pandoc installed in your /usr/local/bin

I would follow the advice of the linked question above or try reintalling pandoc correctly if you don't want the one shipped with RStudio