R Under development (unstable) (2025-03-09 r87914 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 75 | PASS 78 ]

══ Skipped tests (75) ══════════════════════════════════════════════════════════
• On CRAN (63): '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:16:5',
  'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',
  'test_deseq2_edgeR.R:59:3', '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:9:3',
  'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3',
  'test_krona.R:7:3', '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_table_functions.R:47:5', '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 (12): '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: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_targets.R:181:3'): sample_data_with_new_names function works fine ──
Error in `tempdir(check)`: NA in coercion to boolean
Backtrace:
     ▆
  1. ├─testthat::expect_silent(...) at test_targets.R:181:3
  2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ ├─withr::with_output_sink(...)
  5. │   │ │ └─base::force(code)
  6. │   │ ├─base::withCallingHandlers(...)
  7. │   │ └─base::withVisible(code)
  8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  9. ├─MiscMetabar::filter_trim(...)
 10. │ └─dada2::filterAndTrim(...)
 11. └─base::tempdir("fw")

[ FAIL 1 | WARN 0 | SKIP 75 | PASS 78 ]
Error: Test failures
Execution halted