Running ‘testthat.R’ [28s/35s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(readyomics)
  > 
  > test_check("readyomics")
  Error in smooth.spline(lambda, pi0, df = smooth.df) : 
    missing or infinite values in inputs are not allowed
  2 samples found in common between 2 rows in 'X' and 2 rows in 'sample_data'.
  
  Computing profile confidence intervals ...
  refitting model(s) with ML (instead of REML)
  boundary (singular) fit: see help('isSingular')
  Computing profile confidence intervals ...
  boundary (singular) fit: see help('isSingular')
  refitting model(s) with ML (instead of REML)
  boundary (singular) fit: see help('isSingular')
  Computing profile confidence intervals ...
  boundary (singular) fit: see help('isSingular')
  refitting model(s) with ML (instead of REML)
  boundary (singular) fit: see help('isSingular')
  Computing profile confidence intervals ...
  refitting model(s) with ML (instead of REML)
  PCA
  10 samples x 4 variables
  standard scaling of predictors
        R2X(cum) pre ort
  Total    0.817   2   0
  PCA
  10 samples x 4 variables
  standard scaling of predictors
        R2X(cum) pre ort
  Total    0.797   2   0
  10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
  
  10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
  
  PCA
  10 samples x 4 variables
  standard scaling of predictors
        R2X(cum) pre ort
  Total    0.813   2   0
  10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
  
  Permutation parameters for group have not been specified. Default 'perm_control$joint_terms' will be used.
  
  10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
  
  Permutation parameters for group have not been specified. Default 'perm_control$joint_terms' will be used.
  
  10 samples found in common between 10 rows in 'X' and 10 rows in 'sample_data'.
  
  Permutation parameters for group have not been specified. Default 'perm_control$joint_terms' will be used.
  
  2 out of 4 features were kept after 80 % prevalence filter.
  
  4 out of 4 features were kept after 80 % prevalence filter.
  
  4 out of 4 features were kept after 80 % prevalence filter.
  
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 119 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ready_plots.R:39:3'): ready_plots generates plots from a minimal dana object (fit analysis) ──
  Error in `ggplot2::geom_violin(ggplot2::aes(fill = .data[[sdata_var]]), 
      draw_quantiles = TRUE, linewidth = 0.1, scale = "width", 
      show.legend = FALSE)`: `draw_quantiles` must be a <numeric> vector, not `TRUE`.
  Backtrace:
      ▆
   1. └─readyomics::ready_plots(...) at test-ready_plots.R:39:3
   2.   └─readyomics:::plot_feat(...)
   3.     └─ggplot2::geom_violin(draw_quantiles = TRUE)
   4.       └─ggplot2:::check_numeric(draw_quantiles)
   5.         └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
   6.           └─ggplot2:::stop_input_type(...)
   7.             └─rlang::abort(message, ..., call = call, arg = arg)
  ── Error ('test-ready_plots.R:163:3'): ready_plots supports paired_id if present ──
  Error in `ggplot2::geom_violin(ggplot2::aes(fill = .data[[sdata_var]]), 
      draw_quantiles = TRUE, linewidth = 0.1, scale = "width", 
      show.legend = FALSE)`: `draw_quantiles` must be a <numeric> vector, not `TRUE`.
  Backtrace:
      ▆
   1. └─readyomics::ready_plots(...) at test-ready_plots.R:163:3
   2.   └─readyomics:::plot_feat(...)
   3.     └─ggplot2::geom_violin(draw_quantiles = TRUE)
   4.       └─ggplot2:::check_numeric(draw_quantiles)
   5.         └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
   6.           └─ggplot2:::stop_input_type(...)
   7.             └─rlang::abort(message, ..., call = call, arg = arg)
  ── Error ('test-ready_plots.R:205:5'): ready_plots falls back to 'feat_id' when no label columns are found ──
  Error in `ggplot2::geom_violin(ggplot2::aes(fill = .data[[sdata_var]]), 
      draw_quantiles = TRUE, linewidth = 0.1, scale = "width", 
      show.legend = FALSE)`: `draw_quantiles` must be a <numeric> vector, not `TRUE`.
  Backtrace:
       ▆
    1. ├─testthat::expect_warning(...) at test-ready_plots.R:204:3
    2. │ └─testthat:::expect_condition_matching(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─readyomics::ready_plots(...) at test-ready_plots.R:205:5
    8.   └─readyomics:::plot_feat(...)
    9.     └─ggplot2::geom_violin(draw_quantiles = TRUE)
   10.       └─ggplot2:::check_numeric(draw_quantiles)
   11.         └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
   12.           └─ggplot2:::stop_input_type(...)
   13.             └─rlang::abort(message, ..., call = call, arg = arg)
  ── Error ('test-ready_plots.R:246:3'): ready_plots respects custom X_colnames input ──
  Error in `ggplot2::geom_violin(ggplot2::aes(fill = .data[[sdata_var]]), 
      draw_quantiles = TRUE, linewidth = 0.1, scale = "width", 
      show.legend = FALSE)`: `draw_quantiles` must be a <numeric> vector, not `TRUE`.
  Backtrace:
      ▆
   1. └─readyomics::ready_plots(...) at test-ready_plots.R:246:3
   2.   └─readyomics:::plot_feat(...)
   3.     └─ggplot2::geom_violin(draw_quantiles = TRUE)
   4.       └─ggplot2:::check_numeric(draw_quantiles)
   5.         └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
   6.           └─ggplot2:::stop_input_type(...)
   7.             └─rlang::abort(message, ..., call = call, arg = arg)
  
  [ FAIL 4 | WARN 4 | SKIP 0 | PASS 119 ]
  Error: Test failures
  Execution halted