Running 'testthat.R' [15s]
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(ggplot2)
  > library(OmicFlow)
  Loading required package: R6
  Loading required package: data.table
  Loading required package: Matrix
  > library(patchwork)
  > set.seed(100)
  > test_check("OmicFlow")
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  i Processing ... column: CONTRAST_sex 
  'nperm' >= set of all permutations: complete enumeration.
  Set of permutations < 'minperm'. Generating entire set.
  'nperm' >= set of all permutations: complete enumeration.
  Set of permutations < 'minperm'. Generating entire set.
  
  
  processing file: report.Rmd
  
  Quitting from report.Rmd:161-173 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  'nperm' >= set of all permutations: complete enumeration.
  Set of permutations < 'minperm'. Generating entire set.
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  v Metadata template passed the JSON validation.
  i Checking for duplicated identifiers ..
  v featureData is loaded.
  v countData is loaded.
  v treeData is loaded.
  i Final steps .. cleaning & creating back-up
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  ## metagenomics-class object 
  ## countData:	[ 4 Samples and 242 Features	] 
  ## metaData:	[ 9 Variables and 4 Samples	] 
  ## taxData:	[ 7 Ranks and 242 Taxa	] 
  ## treeData:	[ 242 Tips and 241 Nodes	] 
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
    'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
    'test-ordination.R:17:3', 'test-subsetting.R:10:3',
    'test-transformations.R:10:3', 'test-utils.R:15:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
  Error in `gghalves::geom_half_point_panel(aes(color = as.factor(.data[[col_name]])))`: Problem while converting geom to grob.
  i Error occurred in the 2nd layer.
  Caused by error in `fun()`:
  ! argument "layout" is missing, with no default
  Backtrace:
       ▆
    1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
    2. │ └─base::withCallingHandlers(...)
    3. ├─taxa$autoFlow(filename = output_file)
    4. │ ├─rmarkdown::render(...)
    5. │ │ └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    6. │ │   └─knitr:::process_file(text, output)
    7. │ │     ├─xfun:::handle_error(...)
    8. │ │     ├─base::withCallingHandlers(...)
    9. │ │     └─knitr:::process_group(group)
   10. │ │       └─knitr:::call_block(x)
   11. │ │         └─knitr:::block_exec(params)
   12. │ │           └─knitr:::eng_r(options)
   13. │ │             ├─knitr:::in_input_dir(...)
   14. │ │             │ └─knitr:::in_dir(input_dir(), expr)
   15. │ │             └─knitr (local) evaluate(...)
   16. │ │               └─evaluate::evaluate(...)
   17. │ │                 ├─base::withRestarts(...)
   18. │ │                 │ └─base (local) withRestartList(expr, restarts)
   19. │ │                 │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
   20. │ │                 │   │ └─base (local) doWithOneRestart(return(expr), restart)
   21. │ │                 │   └─base (local) withRestartList(expr, restarts[-nr])
   22. │ │                 │     └─base (local) withOneRestart(expr, restarts[[1L]])
   23. │ │                 │       └─base (local) doWithOneRestart(return(expr), restart)
   24. │ │                 ├─evaluate:::with_handlers(...)
   25. │ │                 │ ├─base::eval(call)
   26. │ │                 │ │ └─base::eval(call)
   27. │ │                 │ └─base::withCallingHandlers(...)
   28. │ │                 ├─base::withVisible(eval(expr, envir))
   29. │ │                 └─base::eval(expr, envir)
   30. │ │                   └─base::eval(expr, envir)
   31. │ └─OmicFlow (local) create_plot_tabs(...)
   32. │   ├─base::print(plots[[i]])
   33. │   ├─base::print(plots[[i]])
   34. │   └─ggplot2 (local) `print.ggplot2::ggplot`(plots[[i]])
   35. │     ├─ggplot2::ggplot_gtable(data)
   36. │     └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
   37. │       └─ggplot2:::by_layer(...)
   38. │         ├─rlang::try_fetch(...)
   39. │         │ ├─base::tryCatch(...)
   40. │         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   41. │         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   42. │         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   43. │         │ └─base::withCallingHandlers(...)
   44. │         └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   45. │           └─l$draw_geom(d, layout)
   46. │             └─ggplot2 (local) draw_geom(..., self = self)
   47. │               └─self$geom$draw_layer(...)
   48. │                 └─ggplot2 (local) draw_layer(..., self = self)
   49. │                   └─base::lapply(...)
   50. │                     └─ggplot2 (local) FUN(X[[i]], ...)
   51. │                       ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   52. │                       └─self$draw_panel(...)
   53. │                         └─gghalves (local) draw_panel(...)
   54. │                           └─transformation$compute_layer(transformation_df, transformation_params)
   55. │                             └─ggplot2 (local) compute_layer(..., self = self)
   56. │                               └─ggplot2:::dapply(...)
   57. │                                 └─base::lapply(...)
   58. │                                   └─ggplot2 (local) FUN(X[[i]], ...)
   59. │                                     └─ggplot2 (local) apply_fun(cur_data)
   60. │                                       └─ggplot2 (local) fun(x, ...)
   61. └─base::.handleSimpleError(...)
   62.   └─rlang (local) h(simpleError(msg, call))
   63.     └─handlers[[1L]](cnd)
   64.       └─cli::cli_abort(...)
   65.         └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
  Error: Test failures
  Execution halted