Running ‘testthat.R’ [78s/60s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 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 76 | PASS 83 ]
  
  ══ Skipped tests (76) ══════════════════════════════════════════════════════════
  • On CRAN (76): '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:11:3',
    'test_figures_misc.R:19:3', '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:209:3', '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_beta_div.R:402:3', 'test_figures_beta_div.R:414:3',
    'test_figures_taxo.R:15:3', '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_figures_taxo.R:414:3', '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_phyloseq_class.R:10:3',
    'test_phyloseq_class.R:51:3', 'test_phyloseq_class.R:94:3', 'test_rw.R:8:3',
    'test_rw.R:24:3', 'test_rw.R:39:3', 'test_subset.R:7:3',
    'test_subset.R:18:3', 'test_table_functions.R:6:3',
    'test_table_functions.R:19:3', 'test_table_functions.R:34:5',
    'test_misc.R:11:3', 'test_misc.R:30:3', 'test_misc.R:97:3',
    'test_tuckey.R:5:3', 'test_tuckey.R:17:3', 'test_tuckey.R:26:3',
    'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',
    'test_targets.R:101:3', 'test_targets.R:111:3'
  
  ══ 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 76 | PASS 83 ]
  Error: Test failures
  Execution halted