[Bug]: confusing error message

[ElsLommelen]

What happened?

In a project almost identical to inbo/flandersqmd-website but with a file organisation.yml identical to inbo/flandersqmd-book, the Github Action check project gave the following error:

  ################################################################################
  organisation: 1 error
  --------------------------------------------------------------------------------
   organisation with different rule for publisher:
  info@inbo.be: must be `when no other` instead of `optional`
  ################################################################################

As I used packages checklist and flandersqmd to compose the repo and inspired on repo's flandersqmd-website and flandersqmd-book, I had no clue where to find the error.

• So I first tried updating the checklist machinery with checklist::setup_project() but no relevant additions were given (and no additions at all to organisation.yml).
• I checked for the word 'optional' in organisation.yml, which was not present under info@inbo.be:, and replacing it everywhere in the file gave the error

  Error in compatible_rules(vapply(items, FUN.VALUE = character(1), FUN = function(x) { : 
  more than one organisation with `when no other`
  

• I compared with this file in flandersqmd-book, but it appeared the same file.

A helpful collegue told me that I could view the default content of organisation.yml with function citeme::get_default_org_list(), and this finally helped me to see that an entry publisher: with value when no other was needed in organisation.yml under info@inbo.be to solve the error. After knowing that, I see indeed that 'publisher' was mentioned in the error message, but to be honest: I had no clue that a missing entry could possibly give an error that 'optional' should be replaced by something with another value.

Also, as I am making a website, it seems a bit strange to have a publisher, or is this word used for everyone that publishes digital content to the internet?

Possible solutions?

• A first solution is certainly to improve the error message(s): check first if expected entries are present, and mention in the error message that they should be added instead of mentioning something that should be replaced but is not present at all
• A more user-friendly solution would be a function that updates everything to the latest checklist version and adds information that is required now while it was not present before. Right now we need to go through a lot of errors if we want to update to a new checklist version, with a lot of cryptic errors that are difficult to pinpoint and to solve. Often these cryptic errors have to do with checklist created background files that suddenly have new requirements. As a user we don't know these background files as we normally don't need to change them (we created them by answering questions), these expected changes are not documented anywhere in changelogs, and unfortunately they are not updated when we try updating checklist with checklist::setup_project(). The easiest would be if this setup function would update everything (also changes made by checklist that uses citeme functions), but a list of changes in these files or an up-to-date example repo would already be very helpful. As organisation.yml was not present in checklist itself, I used flandersqmd as an example but this appeared outdated as well...

Minimal reproducible example

The error appears in [this commit](https://github.com/inbo/forest-reserves/commit/cf4ad1b5d59a7ae23c0f7e68add01da570eab430) and is solved in [this commit](https://github.com/inbo/forest-reserves/commit/a2eb8e5d6dc94455fa65733dc818ff1387e3a900).  As flandersqmd-book has the same file `organisation.yml`, rerunning the GHA check project will most likely give the same error (among other errors related to the new checklist version).

Session information

> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.6.1 (2026-06-24 ucrt)
 os       Windows 11 x64 (build 26200)
 system   x86_64, mingw32
 ui       RStudio
 language (EN)
 collate  Dutch_Belgium.utf8
 ctype    Dutch_Belgium.utf8
 tz       Europe/Brussels
 date     2026-08-12
 rstudio  2026.06.0+242 Blue Plumbago (desktop)
 pandoc   3.8.3 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
 quarto   1.9.38 @ C:\\PROGRA~1\\RStudio\\RESOUR~1\\app\\bin\\quarto\\bin\\quarto.exe

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────
 package      * version date (UTC) lib source
 askpass        1.2.1   2024-10-04 [1] CRAN (R 4.6.1)
 assertthat     0.2.1   2019-03-21 [1] CRAN (R 4.6.1)
 backports      1.5.1   2026-04-03 [1] CRAN (R 4.6.0)
 cachem         1.1.0   2024-05-16 [1] CRAN (R 4.6.1)
 callr          3.8.0   2026-06-05 [1] CRAN (R 4.6.1)
 checklist      0.6.1   2026-06-28 [1] https://inbo.r-universe.dev (R 4.6.1)
 citeme         0.1.4   2026-06-27 [1] https://inbo.r-universe.dev (R 4.6.1)
 cli            3.6.6   2026-04-09 [1] CRAN (R 4.6.1)
 colorspace     2.1-2   2025-09-22 [1] CRAN (R 4.6.1)
 conflicted     1.2.0   2023-02-01 [1] CRAN (R 4.6.1)
 crayon         1.5.3   2024-06-20 [1] CRAN (R 4.6.1)
 credentials    2.0.3   2025-09-12 [1] CRAN (R 4.6.1)
 crosstalk      1.2.2   2025-08-26 [1] CRAN (R 4.6.1)
 curl           7.1.0   2026-04-22 [1] CRAN (R 4.6.1)
 cyclocomp      1.1.2   2026-03-11 [1] CRAN (R 4.6.1)
 data.table     1.18.4  2026-05-06 [1] CRAN (R 4.6.1)
 desc           1.4.3   2023-12-10 [1] CRAN (R 4.6.1)
 devtools       2.5.2   2026-04-30 [1] CRAN (R 4.6.1)
 dichromat      2.0-0.1 2022-05-02 [1] CRAN (R 4.6.0)
 digest         0.6.39  2025-11-19 [1] CRAN (R 4.6.1)
 dplyr          1.2.1   2026-04-03 [1] CRAN (R 4.6.1)
 ellipsis       0.3.3   2026-04-04 [1] CRAN (R 4.6.1)
 evaluate       1.0.5   2025-08-27 [1] CRAN (R 4.6.1)
 farver         2.1.2   2024-05-13 [1] CRAN (R 4.6.1)
 fastmap        1.2.0   2024-05-15 [1] CRAN (R 4.6.1)
 flandersqmd    0.0.5   2026-08-12 [1] Github (inbo/flandersqmd@57a604d)
 fortunes       1.5-5   2026-06-26 [1] CRAN (R 4.6.1)
 fs             2.1.0   2026-04-18 [1] CRAN (R 4.6.1)
 generics       0.1.4   2025-05-09 [1] CRAN (R 4.6.1)
 gert           2.3.1   2026-01-11 [1] CRAN (R 4.6.1)
 ggplot2        4.0.3   2026-04-22 [1] CRAN (R 4.6.1)
 gh             1.6.0   2026-05-29 [1] CRAN (R 4.6.1)
 glue           1.8.1   2026-04-17 [1] CRAN (R 4.6.1)
 gtable         0.3.6   2024-10-25 [1] CRAN (R 4.6.1)
 htmltools      0.5.9   2025-12-04 [1] CRAN (R 4.6.1)
 htmlwidgets    1.6.4   2023-12-06 [1] CRAN (R 4.6.1)
 httr           1.4.8   2026-02-13 [1] CRAN (R 4.6.1)
 hunspell       3.0.6   2025-03-22 [1] CRAN (R 4.6.1)
 INBOtheme      0.6.1   2025-03-24 [1] https://inbo.r-universe.dev (R 4.6.1)
 jsonlite       2.0.0   2025-03-27 [1] CRAN (R 4.6.1)
 kableExtra     1.4.1   2026-07-08 [1] CRAN (R 4.6.1)
 knitr          1.51    2025-12-20 [1] CRAN (R 4.6.1)
 later          1.4.8   2026-03-05 [1] CRAN (R 4.6.1)
 lazyeval       0.2.3   2026-04-04 [1] CRAN (R 4.6.1)
 lifecycle      1.0.5   2026-01-08 [1] CRAN (R 4.6.1)
 lintr          3.3.0-1 2025-11-27 [1] CRAN (R 4.6.1)
 magrittr       2.0.5   2026-04-04 [1] CRAN (R 4.6.1)
 memoise        2.0.1   2021-11-26 [1] CRAN (R 4.6.1)
 openssl        2.4.2   2026-06-09 [1] CRAN (R 4.6.1)
 otel           0.2.0   2025-08-29 [1] CRAN (R 4.6.1)
 pdftools       3.9.0   2026-05-14 [1] CRAN (R 4.6.1)
 pillar         1.11.1  2025-09-17 [1] CRAN (R 4.6.1)
 pkgbuild       1.4.8   2025-05-26 [1] CRAN (R 4.6.1)
 pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.6.1)
 pkgdown        2.2.1   2026-07-07 [1] CRAN (R 4.6.1)
 pkgload        1.5.3   2026-06-15 [1] CRAN (R 4.6.1)
 plotly         4.12.0  2026-01-24 [1] CRAN (R 4.6.1)
 prettyunits    1.2.0   2023-09-24 [1] CRAN (R 4.6.1)
 processx       3.9.0   2026-04-22 [1] CRAN (R 4.6.1)
 purrr          1.2.2   2026-04-10 [1] CRAN (R 4.6.1)
 qpdf           1.4.1   2025-07-02 [1] CRAN (R 4.6.1)
 quarto         1.5.1   2025-09-04 [1] CRAN (R 4.6.1)
 R6             2.6.1   2025-02-15 [1] CRAN (R 4.6.1)
 rcmdcheck      1.4.0   2021-09-27 [1] CRAN (R 4.6.1)
 RColorBrewer   1.1-3   2022-04-03 [1] CRAN (R 4.6.0)
 Rcpp           1.1.2   2026-07-05 [1] CRAN (R 4.6.1)
 remotes        2.5.0   2024-03-17 [1] CRAN (R 4.6.1)
 renv           1.2.3   2026-05-16 [1] CRAN (R 4.6.1)
 rex            1.2.2   2026-03-28 [1] CRAN (R 4.6.1)
 rlang          1.3.0   2026-07-05 [1] CRAN (R 4.6.1)
 rmarkdown      2.31    2026-03-26 [1] CRAN (R 4.6.1)
 rprojroot      2.1.1   2025-08-26 [1] CRAN (R 4.6.1)
 rstudioapi     0.19.0  2026-06-11 [1] CRAN (R 4.6.1)
 S7             0.2.2   2026-04-22 [1] CRAN (R 4.6.1)
 scales         1.4.0   2025-04-24 [1] CRAN (R 4.6.1)
 sessioninfo    1.2.4   2026-06-04 [1] CRAN (R 4.6.1)
 stringi        1.8.7   2025-03-27 [1] CRAN (R 4.6.0)
 stringr        1.6.0   2025-11-04 [1] CRAN (R 4.6.1)
 svglite        2.2.2   2025-10-21 [1] CRAN (R 4.6.1)
 sys            3.4.3   2024-10-04 [1] CRAN (R 4.6.1)
 systemfonts    1.3.2   2026-03-05 [1] CRAN (R 4.6.1)
 textshaping    1.0.5   2026-03-06 [1] CRAN (R 4.6.1)
 tibble         3.3.1   2026-01-11 [1] CRAN (R 4.6.1)
 tidyr          1.3.2   2025-12-19 [1] CRAN (R 4.6.1)
 tidyselect     1.2.1   2024-03-11 [1] CRAN (R 4.6.1)
 tidyverse      2.0.0   2023-02-22 [1] CRAN (R 4.6.1)
 usethis        3.2.1   2025-09-06 [1] CRAN (R 4.6.1)
 vctrs          0.7.3   2026-04-11 [1] CRAN (R 4.6.1)
 viridisLite    0.4.3   2026-02-04 [1] CRAN (R 4.6.1)
 withr          3.0.3   2026-06-19 [1] CRAN (R 4.6.1)
 xfun           0.60    2026-07-09 [1] CRAN (R 4.6.1)
 xml2           1.6.0   2026-06-22 [1] CRAN (R 4.6.1)
 xmlparsedata   1.0.5   2021-03-06 [1] CRAN (R 4.6.1)
 xopen          1.0.1   2024-04-25 [1] CRAN (R 4.6.1)
 yaml           2.3.12  2025-12-10 [1] CRAN (R 4.6.1)

 [1] C:/R/library
 [2] C:/R/R-4.6.1/library

Code of Conduct

• I agree to follow this project's Code of Conduct

[ElsLommelen]

After adding publisher: when no other to organisation.yml and when running checklist::check_project(), I get a warning:

Warning message:
In update_citation(x = x, quiet = quiet) : no publisher listed

And also in the output of the function, this is added as a problem:

########################################################################################################
CITATION: 1 error
--------------------------------------------------------------------------------------------------------
 no publisher listed

########################################################################################################

So the problem seems more difficult than just adding the publisher in one place. Maybe I should have used a function to add the publisher, or is there another method to update checklist in a project that I missed in the documentation?