Running ‘testthat.R’ [98s/107s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(ulrb)
  > 
  > test_check("ulrb")
  Joining with `by = join_by(Sample, Level)`
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  If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
  Check 'Evaluation' collumn for more details.
  Joining with `by = join_by(Sample, Level)`
  If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
  Check 'Evaluation' collumn for more details.
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  Automatic option set to TRUE, so classification vector was overwritten
  K= 2 based on Average Silhouette Score.
  Joining with `by = join_by(Sample, Level)`
  Automatic option set to TRUE, so classification vector was overwritten
  K= 9 based on Calinski-Harabasz.
  Joining with `by = join_by(Sample, Level)`
  Automatic option set to TRUE, so classification vector was overwritten
  K= 9 based on Calinski-Harabasz.
  Joining with `by = join_by(Sample, Level)`
  Automatic option set to TRUE, so classification vector was overwritten
  K= 5 based on Average Silhouette Score.
  Joining with `by = join_by(Sample, Level)`
  Automatic option set to TRUE, so classification vector was overwritten
  Joining with `by = join_by(Sample, Level)`
  Saving _problems/test-define_rb-264.R
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  Ignoring unknown labels:
  * fill : ""
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  Missing argument sample_names. This is a vector with the names of the samples, as in the data input
  Taxa_id assumes each column is a taxonomic unit.
  Taxa_id assumes each column is a taxonomic unit.
  [ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-define_rb.R:263:3'): No warning, if there are no clusters with zero taxa ──
  Expected `define_rb(no_singles, check_singles = TRUE)` not to throw any warnings.
  Actually got a <rlang_warning> with message:
    There were 4 warnings in `mutate()`.
    The first warning was:
    i In argument: `pam_object = purrr::map(...)`.
    i In group 1: `Sample = "ERR2044665"`.
    Caused by warning in `structure()`:
    ! Replacing special names '.Names' is deprecated; use 'names' instead.
    i Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.
  
  [ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
  Error:
  ! Test failures.
  Execution halted