Bibtex references showing up twice...or not?

[rikcrutzen]

We (@Matherion and me) use Bibtex for citations in RMarkdown project. A certain reference (Peters, G.-J.Y., and R. Crutzen. 2017. “Pragmatic Nihilism: How a Theory of Nothing Can Help Health Psychology Progress.” Health Psychology Review 11: 103–21.) shows up twice (while only being cited once) in the reference list of the specific chapter (see: https://a-bc.gitlab.io/bbc/selecting-determinants.html). Is this a known bug? Or does somebody know why this happens? What makes it even more striking is that this same reference does not show up twice in the reference list of the overall project (see: https://a-bc.gitlab.io/bbc/references.html). Any thoughts or ideas are welcome. Thank you in advance.

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[yihui]

That sounds like a bug, but I don't have time to investigate it. If anyone is interested in helping out, please look for split_bib in https://github.com/rstudio/bookdown/blob/master/R/html.R and check what went wrong (possibly with parse_references() or relocate_references()). Thanks!

[Matherion]

I'll see whether I can figure out what's going wrong!

[leowill01]

I'm seeing this bug in word_document2 output where it inserts all of my references twice, but the bug does not appear in pdf_document2 output [edit: also seeing the bug in PDF output, though it doesn't happen every time].

SessionInfo():

R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6
[...]
other attached packages:
[1] bookdown_0.24

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13     knitr_1.36          magrittr_2.0.1     
 [4] rsthemes_0.2.1.9000 R6_2.5.1            rlang_0.4.11       
 [7] fastmap_1.1.0       stringr_1.4.0.9000  tools_4.1.1        
[10] xfun_0.26           sessioninfo_1.1.1   tinytex_0.34       
[13] cli_3.0.1           jquerylib_0.1.4     withr_2.4.2        
[16] htmltools_0.5.2     yaml_2.2.1          digest_0.6.28      
[19] lifecycle_1.0.1     sass_0.4.0.9000     vctrs_0.3.8        
[22] glue_1.4.2          evaluate_0.14       rmarkdown_2.11     
[25] stringi_1.7.5       compiler_4.1.1      bslib_0.3.0        
[28] jsonlite_1.7.2     

Edit: I seem to have (temporarily?) fixed the problem by moving the reference to the bibliography from the top-level YAML option:

bibliography: bibliography.bib

to the explicit pandoc options for each output format:

output:
  bookdown::pdf_document2:
    pandoc_args:
    - "--citeproc" # <----- EDIT 2: I did not include this line in the original post of this comment, and it was the problem
    - "--bibliography=bibliography.bib"

I'm using rmarkdown::render(), so it might be a problem with rmarkdown and not bookdown necessarily.

Edit 2: the problem was having a redundant "--citeproc" option in my YAML header [see comment below]

[cderv]

@leowill01 Are you able to share a reproducible example to help us investigate and fix this ?

THank you

[leowill01]

I figured out what was wrong in my case. I had been using output: book down::pdf_document2: pandoc_args: to add additional arguments for including Lua filters (e.g. "--lua-filter=pandoc/scholarly-metadata.lua"), but I also had put the "--citeproc" option there as well. The problem arises because the default knit to bookdown::pdf_document2 command already includes a --citeproc option. So by including this again under pandoc_args:, I was telling it to insert the complete bibliography twice.

@rikcrutzen : Check to make sure you don't have an extra output: book down::[format]: pandoc_args: "--citeproc" enabled in the YAML header of the chapter you're having an issue with.

[cderv]

Oh indeed good find.

R Markdown output formats will usually add the --citeproc argument when bibliography: YAML field is detected. This is for ease of use for user so that they don't have a explicitly trigger citeproc.

I missed that from your message above.

Regarding the issue of this post, it is rather specific to one duplicated reference so I think this is different.

[cderv]

@Matherion sorry for the delay on this. Is this still an issue ?

I have clone your repo and rebuild the book locally and I can't see the duplicated reference. It is possible this has been fixed since, especially if it was introduced by a Pandoc version.

If this is still an issue please share your pandoc version. Thanks!

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