pandoc-citeproc failing on LaTeX bookdown build: hPutBuf: resource vanished (Broken pipe)

jdlong · October 14, 2018, 2:00pm

Recently I've discovered that I'm unable to build a book on RStudio.cloud which builds fine on my Mac. On rstudio.cloud I get the following error when building the book to bookdown::pdf_book but not when building to bookdown::gitbook.

Error running filter /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc:
fd:12: hPutBuf: resource vanished (Broken pipe)
Error: pandoc document conversion failed with error 83
Execution halted

Exited with status 1.

Digging around online I find a few other instances of this error:

something to do with python3-pandocfilters:

possibly an issue with Pandoc package versions?

github.com/jgm/pandoc

All JSON filters fail with `fd:4: hPutBuf: resource vanished (Broken pipe)`

opened 05:39PM - 09 Dec 16 UTC

closed 11:38AM - 10 Dec 16 UTC

stroobandt

With ``` $ pandoc --version pandoc 1.19 Compiled with pandoc-types 1.17.0.4,… texmath 0.9, highlighting-kate 0.6.3 ``` as well as `pandoc 1.16.0.2` on `Ubuntu 16.04.1 LTS`, I receive the following error: ``` pandoc: Error running filter ./behead2.hs fd:4: hPutBuf: resource vanished (Broken pipe) ``` when running [the example `behead2.hs`](http://pandoc.org/scripting.html#json-filters) JSON filter ``` $ pandoc -o file.html --filter ./behead2.hs file.md ``` with ``` #!/usr/bin/env runhaskell -- behead2.hs import Text.Pandoc.JSON main :: IO () main = toJSONFilter behead where behead (Header n _ xs) | n >= 2 = Para [Emph xs] behead x = x ``` or any other JSON filter that used to work with `pandoc 1.13` under (X)Ubuntu 14.04 LTS. "_I feel beheaded…_"

maybe need to downgrade citeproc?

anyone else find a workaround for this or know exactly how the rstudio.cloud team could fix this?

mara · October 14, 2018, 3:04pm

What versions for pandoc-citeproc do you get locally on your Mac and on RStudio cloud, respectively?

From the command line I get:

pandoc-citeproc --version
#> pandoc-citeproc 0.14.5

From RStudio terminal:

$ pandoc-citeproc --version
#> pandoc-citeproc 0.10.4

I'm curious if downgrading or upgrading would fix it. Do you have a dummy bookdown you can share? (Is it just a matter of switching the minimal bookdown demo from bookdown::gitbook to bookdown::pdf_book?

jdlong · October 14, 2018, 3:21pm

Good questions, @mara. On rstudio.cloud my version is:

rstudio-user@33abdf948834:/cloud/project$ /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc --version
pandoc-citeproc 0.14.3.1

On my mac, I get the same version:

$ /Applications/RStudio.app/Contents/MacOS/pandoc/pandoc-citeproc --version
pandoc-citeproc 0.14.3.1

So I'm at a loss... very weird. I'll see if I can make a minimal example later today.

mara · October 14, 2018, 3:24pm

I'm trying it out on cloud with the bookdown demo. RMarkdown has pandoc_citeproc_convert() and pandoc_options(), so maybe there's a way to get it so that it's in the path for cloud.

Update I did get the bookdown demo to build here https://rstudio.cloud/project/109623 (open access, so you should be able to get in) It's possible it doesn't use pandoc-citeproc, in which case, I did absolutely nothing.