bbt_write_bib throwing "Error in `result$result[[3]]`" error

[M1V0]

Hi,

I have an issue that has only started today affecting multiple previous working RMarkdown documents where I use bbt_write_bib to create bibliography files.

Now when trying to knit a RMarkdown document I get the error:

processing file: 09Discussion.Rmd
  |......................................................................| 100%
Quitting from lines 2-134 (09Discussion.Rmd)
Error in `result$result[[3]]`:
! subscript out of bounds
Backtrace:
 1. rbbt::bbt_write_bib("Bibliography/discussion.json", overwrite = TRUE)
 4. rbbt::bbt_bib(...)
 5. base (local) .action(result$result[[3]])

Execution halted

This is in R 4.2.2, pandoc 3.1.1, with rbbt 0.0.0.9 - the issue happens across multiple documents - even when the offending line is commented out and a reference to just bibliography: Bibliography/discussion.json is used. Deleting the rbbt line then allows that to render, but I need the overwrite function.

Thanks in advance and apologies if I'm missing any information.

[dmi3kno]

Something has changed in BBT interface. The resulting bib content is no longer in a third element of a vector, but rather in the first one.

Can one of the maintainers confirm the change in the returned BBT JSON and adjust this line https://github.com/paleolimbot/rbbt/blob/ec1ebe1e9b7e60bc4523e6cb2ca47f73a9cbfba3/R/bbt.R#L98

[swalmsley]

I am having the same issue. Would very much appreciate if this change could be made. Thanks!

[mccarthy-m-g]

I just ran into this as well. Fortunately @dmi3kno's comment lead me to an easy workaround: Until a change in rbbt is made you can just downgrade BBT, disable automatic updates for BBT, and things should work again.

I successively downgraded from the current version of BBT (v6.7.143) until the error went away at v6.7.140, so that seems to be the most recent version compatible with rbbt right now.

[M1V0]

I replicated @mccarthy-m-g's workaround - so thank you! That saves me a headache when submitting my PhD next month.

[bbartholdy]

Can also confirm that BBT v6.7.140 works for me! Also saved my PhD dissertation! Thanks @mccarthy-m-g :smile:

[peranti]

Hi @bbartholdy @M1V0 @mccarthy-m-g, could you please advise me on how to install BBT v6.7.140? Many thanks!

[nikitoshina]

@peranti download .xpi file and follow the regular installation instructions.

[heike]

@wmoldham put in a pull request - that fixes the bug. Thank you @wmoldham! Until @paleolimbot is accepting the pull request, installing from the forked repo will fix things remotes::install_github("wmoldham/rbbt")

[cjvanlissa]

Stumbled upon this issue; I independently confirm this bug and my fix is the same as wmoldham's. Their PR can be accepted.

[cpsyctc2]

I am not sufficiently knowledgeable about the internals to understand the comment from NewGraphEnvironment but I can confirm that the problem was still there with a copy of the package that I pulled from paleolimbot/rbbt yesterday but the problem goes away using wmoldham/rbbt (thanks for that heike and wmoldham). rbbt is so much better than the insert citations facility in "visual" Rstudio that I do hope it will continue to be maintained and even developed. I am happy to do testing on Linux (Ubuntu 22.04) and perhaps with suggestions for more documentation Windoze but I don't have skills for the programming. Huge thanks to all who have created it so far. Chris