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

rbbt/R/bbt.R

Line 98 in ec1ebe1

.action(result$result[[3]])

[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 😄

[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

[DeaconOfBiology]

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.

Thanks! Been troubleshooting for an hour now, and found your suggested fix.