term_to_node_id(dag, term): Cannot find some of the terms in the DAG

[HDash]

New error on check(), appearing after all the January merges. I can confirm this error was not present when I was working on my branch back in December.

Fails tests and example for plot_bar_dendro.

Reprex

devtools::load_all()
#> ℹ Loading MSTExplorer
results <- load_example_results()
out <- plot_bar_dendro(results = results)
#> Loading required namespace: ggdendro
#> Adding HPO names.
#> Translating ontology terms to names.
#> Adding level-2 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Ancestor metadata already present. Use force_new=TRUE to overwrite.
#> 2,206,994 associations remain after filtering.
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> Filtered 'ancestor_name' : 999,488 / 2,206,994 rows dropped.
#> Translating ontology terms to ids.
#> Loading cached ontology: /Users/hdash/Library/Caches/org.R-project.R/R/KGExplorer/cl.rds
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Translating ontology terms to ids.
#> Error in term_to_node_id(dag, term): Cannot find some of the terms in the DAG.

^{Created on 2025-01-08 with reprex v2.1.1}

I tried using the older tag in get_target_celltypes(..., cl = KGExplorer::get_ontology(...)) but to no avail. (Issue #20).
Using latest version of HPOExplorer@master and KGExplorer@master.

Session Info

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.2 (2024-10-31)
#>  os       macOS Sequoia 15.2
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/London
#>  date     2025-01-08
#>  pandoc   3.5 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version  date (UTC) lib source
#>  cachem        1.1.0    2024-05-16 [1] CRAN (R 4.4.0)
#>  cli           3.6.3    2024-06-21 [1] CRAN (R 4.4.0)
#>  devtools      2.4.5    2022-10-11 [1] CRAN (R 4.4.0)
#>  digest        0.6.37   2024-08-19 [1] CRAN (R 4.4.1)
#>  ellipsis      0.3.2    2021-04-29 [1] CRAN (R 4.4.0)
#>  evaluate      1.0.1    2024-10-10 [1] CRAN (R 4.4.1)
#>  fastmap       1.2.0    2024-05-15 [1] CRAN (R 4.4.0)
#>  fs            1.6.5    2024-10-30 [1] CRAN (R 4.4.1)
#>  glue          1.8.0    2024-09-30 [1] CRAN (R 4.4.1)
#>  htmltools     0.5.8.1  2024-04-04 [1] CRAN (R 4.4.0)
#>  htmlwidgets   1.6.4    2023-12-06 [1] CRAN (R 4.4.0)
#>  httpuv        1.6.15   2024-03-26 [1] CRAN (R 4.4.0)
#>  knitr         1.49     2024-11-08 [1] CRAN (R 4.4.1)
#>  later         1.4.1    2024-11-27 [1] CRAN (R 4.4.1)
#>  lifecycle     1.0.4    2023-11-07 [1] CRAN (R 4.4.0)
#>  magrittr      2.0.3    2022-03-30 [1] CRAN (R 4.4.0)
#>  memoise       2.0.1    2021-11-26 [1] CRAN (R 4.4.0)
#>  mime          0.12     2021-09-28 [1] CRAN (R 4.4.0)
#>  miniUI        0.1.1.1  2018-05-18 [1] CRAN (R 4.4.1)
#>  pkgbuild      1.4.5    2024-10-28 [1] CRAN (R 4.4.1)
#>  pkgload       1.4.0    2024-06-28 [1] CRAN (R 4.4.0)
#>  profvis       0.4.0    2024-09-20 [1] CRAN (R 4.4.1)
#>  promises      1.3.2    2024-11-28 [1] CRAN (R 4.4.1)
#>  purrr         1.0.2    2023-08-10 [1] CRAN (R 4.4.0)
#>  R6            2.5.1    2021-08-19 [1] CRAN (R 4.4.0)
#>  Rcpp          1.0.13-1 2024-11-02 [1] CRAN (R 4.4.1)
#>  remotes       2.5.0    2024-03-17 [1] CRAN (R 4.4.0)
#>  reprex        2.1.1    2024-07-06 [1] CRAN (R 4.4.0)
#>  rlang         1.1.4    2024-06-04 [1] CRAN (R 4.4.0)
#>  rmarkdown     2.29     2024-11-04 [1] CRAN (R 4.4.1)
#>  rstudioapi    0.17.1   2024-10-22 [1] CRAN (R 4.4.1)
#>  sessioninfo   1.2.2    2021-12-06 [1] CRAN (R 4.4.0)
#>  shiny         1.10.0   2024-12-14 [1] CRAN (R 4.4.1)
#>  urlchecker    1.0.1    2021-11-30 [1] CRAN (R 4.4.0)
#>  usethis       3.1.0    2024-11-26 [1] CRAN (R 4.4.1)
#>  vctrs         0.6.5    2023-12-01 [1] CRAN (R 4.4.0)
#>  withr         3.0.2    2024-10-28 [1] CRAN (R 4.4.1)
#>  xfun          0.50     2025-01-07 [1] CRAN (R 4.4.1)
#>  xtable        1.8-4    2019-04-21 [1] CRAN (R 4.4.0)
#>  yaml          2.3.10   2024-07-26 [1] CRAN (R 4.4.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

^{Created on 2025-01-08 with reprex v2.1.1}

[HDash]

R CMD Check output

Last 13 lines of output:
  Error in `term_to_node_id(dag, term)`: Cannot find some of the terms in the DAG.
  Backtrace:
      ▆
   1. └─MSTExplorer::plot_bar_dendro(results = results) at test-plot_bar_dendro.R:4:3
   2.   └─MSTExplorer:::get_target_celltypes(target_branches = target_branches)
   3.     └─KGExplorer::get_ontology_descendants(ont = cl, terms = target_branches)
   4.       ├─base::lapply(...)
   5.       └─base::lapply(...)
   6.         └─KGExplorer (local) FUN(X[[i]], ...)
   7.           └─simona::dag_offspring(...)
   8.             └─simona:::term_to_node_id(dag, term)
  
  [ FAIL 1 | WARN 1870 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted

Possible issue with KGExplorer