Running ‘testthat.r’ [24s/32s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  > library(rbiom)
  > 
  > test_check("rbiom")
  [ FAIL 1 | WARN 0 | SKIP 34 | PASS 181 ]
  
  ══ Skipped tests (34) ══════════════════════════════════════════════════════════
  • On CRAN (34): 'test-bdiv_heatmap.r:5:3', 'test-bdiv_ord_plot.r:6:3',
    'test-biom_merge.r:11:3', 'test-biom_ply.r:9:3', 'test-biom_ply.r:48:3',
    'test-boxplot.r:10:3', 'test-boxplot_build.r:3:3', 'test-cache.r:3:3',
    'test-convert.r:5:3', 'test-convert.r:27:3', 'test-convert.r:39:3',
    'test-convert.r:57:3', 'test-convert.r:73:3', 'test-corrplot.r:11:3',
    'test-distmat_ord_table.r:6:3', 'test-import_table.r:13:3',
    'test-plot_heatmap.r:15:3', 'test-plot_palettes.r:6:3', 'test-rarefy.r:3:3',
    'test-rbiom_objects.r:24:3', 'test-read_biom.r:3:3', 'test-read_fasta.r:3:3',
    'test-read_tree.r:7:3', 'test-s3_methods.r:3:3', 'test-stats_emmeans.r:8:3',
    'test-stats_wilcox.r:3:3', 'test-taxa_heatmap.r:5:3', 'test-taxa_map.r:3:3',
    'test-taxa_stacked.r:5:3', 'test-taxa_table.r:3:3', 'test-utils.r:3:3',
    'test-validate.r:3:3', 'test-write_biom.r:15:3', 'test-write_xlsx.r:3:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-rare_multiplot.r:3:3'): rare_multiplot ─────────────────────────
  Error in `gzfile(file, mode)`: cannot open the connection
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(rare_multiplot(hmp5, stat.by = "Body Site")) at test-rare_multiplot.r:3:3
    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. └─rbiom::rare_multiplot(hmp5, stat.by = "Body Site")
   10.   └─rbiom::rare_corrplot(...)
   11.     ├─base::with(...)
   12.     └─base::with.default(...)
   13.       └─base::eval(substitute(expr), data, enclos = parent.frame())
   14.         └─base::eval(substitute(expr), data, enclos = parent.frame())
   15.           ├─base::local(...)
   16.           │ └─base::eval.parent(substitute(eval(quote(expr), envir)))
   17.           │   └─base::eval(expr, p)
   18.           │     └─base::eval(expr, p)
   19.           └─base::eval(...)
   20.             └─base::eval(...)
   21.               └─plyr::ldply(...)
   22.                 └─plyr::llply(...)
   23.                   ├─base::structure(lapply(pieces, .fun, ...), dim = dim(pieces))
   24.                   └─base::lapply(pieces, .fun, ...)
   25.                     └─rbiom (local) FUN(X[[i]], ...)
   26.                       └─rbiom::adiv_table(...)
   27.                         └─rbiom:::set_cache_value(cache_file, tbl)
   28.                           └─base::saveRDS(result, file = cache_file)
   29.                             └─base::gzfile(file, mode)
  
  [ FAIL 1 | WARN 0 | SKIP 34 | PASS 181 ]
  Error:
  ! Test failures.
  Execution halted