R Under development (unstable) (2024-09-30 r87204 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(MiscMetabar)
Loading required package: phyloseq
Loading required package: ggplot2
Loading required package: dada2
Loading required package: Rcpp
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: purrr

Attaching package: 'purrr'

The following object is masked from 'package:testthat':

    is_null

> 
> test_check("MiscMetabar")
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 77 | PASS 82 ]

══ Skipped tests (77) ══════════════════════════════════════════════════════════
• On CRAN (64): 'test_adonis.R:1:1', 'test_controls.R:7:3',
  'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
  'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
  'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
  'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
  'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
  'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:33:5',
  'test_deseq2_edgeR.R:42:3', 'test_deseq2_edgeR.R:65:5',
  'test_deseq2_edgeR.R:76:3', 'test_figures_biplot.R:14:3',
  'test_figures_biplot.R:52:3', 'test_figures_misc.R:26:3',
  'test_figures_misc.R:35:3', 'test_figures_beta_div.R:22:3',
  'test_figures_beta_div.R:73:5', 'test_figures_beta_div.R:92:3',
  'test_figures_beta_div.R:102:5', 'test_figures_beta_div.R:159:5',
  'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',
  'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',
  'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',
  'test_figures_beta_div.R:387:3', 'test_figures_summary_plot.R:10:3',
  'test_figures_summary_plot.R:20:3', 'test_figures_summary_plot.R:30:3',
  'test_krona.R:7:3', 'test_figures_taxo.R:30:3', 'test_figures_taxo.R:45:3',
  'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
  'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
  'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
  'test_figures_taxo.R:379:3', 'test_phyloseq_class.R:10:3',
  'test_phyloseq_class.R:51:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
  'test_subset.R:7:3', 'test_subset.R:18:3', 'test_table_functions.R:34:5',
  'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:101:3',
  'test_targets.R:111:3', 'test_tuckey.R:5:3', 'test_tuckey.R:17:3',
  'test_tuckey.R:26:3', 'test_misc.R:11:3', 'test_misc.R:30:3',
  'test_misc.R:97:3'
• On Windows (13): 'test_figures_misc.R:10:3', 'test_figures_misc.R:18:3',
  'test_figures_beta_div.R:208:3', 'test_figures_beta_div.R:401:3',
  'test_figures_beta_div.R:413:3', 'test_figures_taxo.R:14:3',
  'test_figures_taxo.R:413:3', 'test_phyloseq_class.R:92:3', 'test_rw.R:38:3',
  'test_table_functions.R:5:3', 'test_table_functions.R:18:3',
  'test_targets.R:83:3', 'test_targets.R:128:3'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_table_functions.R:46:5'): tbl_sum_samdata function works fine with data_fungi and enterotype dataset ──
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `dplyr::mutate(.data = .y, stat = as.character(glue::glue(statistic[[.data$variable[1]]], 
    .envir = cards::get_ard_statistics(.x, .column = "stat_fmt"))))`: i In argument: `stat = as.character(...)`.
Caused by error in `glue_data()`:
! is.environment(.envir) is not TRUE
Backtrace:
     ▆
  1. ├─testthat::expect_s3_class(tbl_sum_samdata(enterotype), "tbl_summary") at test_table_functions.R:46:5
  2. │ └─testthat::quasi_label(enquo(object), arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─MiscMetabar::tbl_sum_samdata(enterotype)
  5. │ └─tbl %>% gtsummary::tbl_summary(...)
  6. ├─gtsummary::tbl_summary(., ...)
  7. │ ├─base::structure(...)
  8. │ ├─base::append(...)
  9. │ └─gtsummary::brdg_summary(...)
 10. │   ├─dplyr::left_join(...)
 11. │   ├─dplyr:::left_join.data.frame(...)
 12. │   │ └─dplyr::auto_copy(x, y, copy = copy)
 13. │   │   ├─dplyr::same_src(x, y)
 14. │   │   └─dplyr:::same_src.data.frame(x, y)
 15. │   │     └─base::is.data.frame(y)
 16. │   ├─dplyr::bind_rows(...)
 17. │   │ └─rlang::list2(...)
 18. │   └─gtsummary::pier_summary_continuous(...)
 19. │     ├─... %>% ...
 20. │     ├─dplyr::bind_rows(...)
 21. │     │ └─rlang::list2(...)
 22. │     ├─dplyr::group_map(...)
 23. │     └─dplyr:::group_map.data.frame(...)
 24. │       └─dplyr:::map2(chunks, group_keys, .f, ...)
 25. │         └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
 26. │           └─gtsummary (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 27. │             ├─dplyr::mutate(...)
 28. │             └─dplyr:::mutate.data.frame(...)
 29. │               └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
 30. │                 ├─base::withCallingHandlers(...)
 31. │                 └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 32. │                   └─mask$eval_all_mutate(quo)
 33. │                     └─dplyr (local) eval()
 34. ├─dplyr::left_join(...)
 35. ├─dplyr:::left_join.data.frame(...)
 36. │ └─dplyr::auto_copy(x, y, copy = copy)
 37. │   ├─dplyr::same_src(x, y)
 38. │   └─dplyr:::same_src.data.frame(x, y)
 39. │     └─base::is.data.frame(y)
 40. ├─glue::glue(...)
 41. │ └─glue::glue_data(...)
 42. │   └─base::stopifnot(is.environment(.envir))
 43. │     └─base::stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
 44. └─dplyr (local) `<fn>`(`<smplErrr>`)
 45.   └─rlang::abort(message, class = error_class, parent = parent, call = error_call)

[ FAIL 1 | WARN 0 | SKIP 77 | PASS 82 ]
Error: Test failures
Execution halted