Running ‘testthat.R’ [30s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fido)
  
  Attaching package: 'fido'
  
  The following objects are masked from 'package:stats':
  
      coef, predict
  
  The following objects are masked from 'package:base':
  
      as.list, print, summary
  
  > 
  > #Sys.setenv(KMP_DUPLICATE_LIB_OK="TRUE")
  > test_check("fido")
    [1]  1.633944461 -1.263449460 -0.160491058 -0.151694924 -1.414460839
    [6]  0.414752819 -0.993922266  0.192605335  1.193392223  1.208187867
   [11] -0.442588541 -0.372323748  0.988703140 -0.795025503  2.192619586
   [16] -0.341248035 -1.049458148  1.468107559  0.334664117 -0.271458846
   [21]  0.679563767 -0.316257759 -2.037444833 -0.035804826  1.227767823
   [26] -0.885689025 -0.106695203  2.066079039  0.414366039  0.037705700
   [31]  0.565549634 -1.571477119 -0.382226485  0.247617015  0.007665408
   [36]  0.440607554 -0.078739980 -0.250203498 -0.176178174 -0.291509535
   [41] -1.991545754  0.732742452 -0.590506199 -1.240481354 -0.372671845
   [46]  0.407478140 -0.273629130 -1.108338021  0.633024650 -0.158659083
   [51]  0.263941695  0.214063401  0.141741788  1.198418608  0.042556410
   [56] -0.289431854 -0.504657821  2.139022094 -1.023448488  0.556645664
   [61] -1.841021837  0.456873518 -0.178044899 -0.257460256 -1.434609346
   [66]  0.112159524  2.023069733 -0.745983224  0.701592007  0.651468327
   [71] -0.252660086  1.249760504  0.412971619  0.476405230 -0.852435593
   [76]  0.435228437 -1.048132400 -0.603121808  1.424949004  1.143285509
   [81]  1.311087367 -1.644916843 -0.263535202  0.291603591 -1.869842768
   [86]  1.903525214 -1.386759951  0.810217283  0.439084905  0.239992541
   [91] -1.489189158  0.249485574 -1.651424329  1.815707370  1.286940214
   [96] -1.290575099 -1.156862005  0.387003783  0.613538302 -0.726791282
  $data
  # A tibble: 16 × 9
     Parameter coord  covariate     val .lower .upper .width .point .interval
     <chr>     <fct>  <fct>       <dbl>  <dbl>  <dbl>  <dbl> <chr>  <chr>    
   1 Lambda    clr_c1 x1         4.58    4.34   4.84    0.5  mean   qi       
   2 Lambda    clr_c1 x2        -1.47   -1.78  -1.14    0.5  mean   qi       
   3 Lambda    clr_c2 x1        -6.50   -7.04  -5.92    0.5  mean   qi       
   4 Lambda    clr_c2 x2        -0.0560 -0.525  0.409   0.5  mean   qi       
   5 Lambda    clr_c1 x1         4.58    4.10   5.05    0.8  mean   qi       
   6 Lambda    clr_c1 x2        -1.47   -2.06  -0.861   0.8  mean   qi       
   7 Lambda    clr_c2 x1        -6.50   -7.57  -5.46    0.8  mean   qi       
   8 Lambda    clr_c2 x2        -0.0560 -0.929  0.855   0.8  mean   qi       
   9 Lambda    clr_c1 x1         4.58    3.82   5.31    0.95 mean   qi       
  10 Lambda    clr_c1 x2        -1.47   -2.39  -0.598   0.95 mean   qi       
  11 Lambda    clr_c2 x1        -6.50   -8.10  -4.92    0.95 mean   qi       
  12 Lambda    clr_c2 x2        -0.0560 -1.45   1.38    0.95 mean   qi       
  13 Lambda    clr_c1 x1         4.58    3.60   5.52    0.99 mean   qi       
  14 Lambda    clr_c1 x2        -1.47   -2.64  -0.294   0.99 mean   qi       
  15 Lambda    clr_c2 x1        -6.50   -8.71  -4.38    0.99 mean   qi       
  16 Lambda    clr_c2 x2        -0.0560 -1.92   1.81    0.99 mean   qi       
  
  $layers
  $layers[[1]]
  geom_interval: orientation = NA, interval_size_range = c(1, 6), interval_size_domain = c(1, 6), arrow = NULL, na.rm = FALSE
  stat_identity: na.rm = FALSE
  position_identity 
  
  $layers[[2]]
  geom_point: na.rm = FALSE
  stat_identity: na.rm = FALSE
  position_identity 
  
  
  $scales
  <ggproto object: Class ScalesList, gg>
      add: function
      add_defaults: function
      add_missing: function
      backtransform_df: function
      clone: function
      find: function
      get_scales: function
      has_scale: function
      input: function
      map_df: function
      n: function
      non_position_scales: function
      scales: list
      train_df: function
      transform_df: function
      super:  <ggproto object: Class ScalesList, gg>
  
  $guides
  <Guides[1] ggproto object>
  
  colour : <GuideLegend>
  
  $mapping
  Aesthetic mapping: 
  * `x`    -> `.data$val`
  * `y`    -> `.data$coord`
  * `xmin` -> `.lower`
  * `xmax` -> `.upper`
  
  $theme
  List of 136
   $ line                            :List of 6
    ..$ colour       : chr "black"
    ..$ linewidth    : num 0.5
    ..$ linetype     : num 1
    ..$ lineend      : chr "butt"
    ..$ arrow        : logi FALSE
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_line" "element"
   $ rect                            :List of 5
    ..$ fill         : chr "white"
    ..$ colour       : chr "black"
    ..$ linewidth    : num 0.5
    ..$ linetype     : num 1
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_rect" "element"
   $ text                            :List of 11
    ..$ family       : chr ""
    ..$ face         : chr "plain"
    ..$ colour       : chr "black"
    ..$ size         : num 11
    ..$ hjust        : num 0.5
    ..$ vjust        : num 0.5
    ..$ angle        : num 0
    ..$ lineheight   : num 0.9
    ..$ margin       : 'margin' num [1:4] 0points 0points 0points 0points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : logi FALSE
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ title                           : NULL
   $ aspect.ratio                    : NULL
   $ axis.title                      : NULL
   $ axis.title.x                    :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : NULL
    ..$ vjust        : num 1
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : 'margin' num [1:4] 2.75points 0points 0points 0points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.title.x.top                :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : NULL
    ..$ vjust        : num 0
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : 'margin' num [1:4] 0points 0points 2.75points 0points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.title.x.bottom             : NULL
   $ axis.title.y                    : list()
    ..- attr(*, "class")= chr [1:2] "element_blank" "element"
   $ axis.title.y.left               : NULL
   $ axis.title.y.right              :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : NULL
    ..$ vjust        : num 1
    ..$ angle        : num -90
    ..$ lineheight   : NULL
    ..$ margin       : 'margin' num [1:4] 0points 0points 0points 2.75points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.text                       :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : chr "grey30"
    ..$ size         : 'rel' num 0.8
    ..$ hjust        : NULL
    ..$ vjust        : NULL
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : NULL
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.text.x                     :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : NULL
    ..$ vjust        : num 1
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : 'margin' num [1:4] 2.2points 0points 0points 0points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.text.x.top                 :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : NULL
    ..$ vjust        : num 0
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : 'margin' num [1:4] 0points 0points 2.2points 0points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.text.x.bottom              : NULL
   $ axis.text.y                     :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : num 1
    ..$ vjust        : NULL
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : 'margin' num [1:4] 0points 2.2points 0points 0points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.text.y.left                : NULL
   $ axis.text.y.right               :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : num 0
    ..$ vjust        : NULL
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : 'margin' num [1:4] 0points 0points 0points 2.2points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.text.theta                 : NULL
   $ axis.text.r                     :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : num 0.5
    ..$ vjust        : NULL
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : 'margin' num [1:4] 0points 2.2points 0points 2.2points
    .. ..- attr(*, "unit")= int 8
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ axis.ticks                      : list()
    ..- attr(*, "class")= chr [1:2] "element_blank" "element"
   $ axis.ticks.x                    : NULL
   $ axis.ticks.x.top                : NULL
   $ axis.ticks.x.bottom             : NULL
   $ axis.ticks.y                    : NULL
   $ axis.ticks.y.left               : NULL
   $ axis.ticks.y.right              : NULL
   $ axis.ticks.theta                : NULL
   $ axis.ticks.r                    : NULL
   $ axis.minor.ticks.x.top          : NULL
   $ axis.minor.ticks.x.bottom       : NULL
   $ axis.minor.ticks.y.left         : NULL
   $ axis.minor.ticks.y.right        : NULL
   $ axis.minor.ticks.theta          : NULL
   $ axis.minor.ticks.r              : NULL
   $ axis.ticks.length               : 'simpleUnit' num 2.75points
    ..- attr(*, "unit")= int 8
   $ axis.ticks.length.x             : NULL
   $ axis.ticks.length.x.top         : NULL
   $ axis.ticks.length.x.bottom      : NULL
   $ axis.ticks.length.y             : NULL
   $ axis.ticks.length.y.left        : NULL
   $ axis.ticks.length.y.right       : NULL
   $ axis.ticks.length.theta         : NULL
   $ axis.ticks.length.r             : NULL
   $ axis.minor.ticks.length         : 'rel' num 0.75
   $ axis.minor.ticks.length.x       : NULL
   $ axis.minor.ticks.length.x.top   : NULL
   $ axis.minor.ticks.length.x.bottom: NULL
   $ axis.minor.ticks.length.y       : NULL
   $ axis.minor.ticks.length.y.left  : NULL
   $ axis.minor.ticks.length.y.right : NULL
   $ axis.minor.ticks.length.theta   : NULL
   $ axis.minor.ticks.length.r       : NULL
   $ axis.line                       : list()
    ..- attr(*, "class")= chr [1:2] "element_blank" "element"
   $ axis.line.x                     : NULL
   $ axis.line.x.top                 : NULL
   $ axis.line.x.bottom              : NULL
   $ axis.line.y                     : NULL
   $ axis.line.y.left                : NULL
   $ axis.line.y.right               : NULL
   $ axis.line.theta                 : NULL
   $ axis.line.r                     : NULL
   $ legend.background               : list()
    ..- attr(*, "class")= chr [1:2] "element_blank" "element"
   $ legend.margin                   : 'margin' num [1:4] 5.5points 5.5points 5.5points 5.5points
    ..- attr(*, "unit")= int 8
   $ legend.spacing                  : 'simpleUnit' num 11points
    ..- attr(*, "unit")= int 8
   $ legend.spacing.x                : NULL
   $ legend.spacing.y                : NULL
   $ legend.key                      : list()
    ..- attr(*, "class")= chr [1:2] "element_blank" "element"
   $ legend.key.size                 : 'simpleUnit' num 1.2lines
    ..- attr(*, "unit")= int 3
   $ legend.key.height               : NULL
   $ legend.key.width                : NULL
   $ legend.key.spacing              : 'simpleUnit' num 5.5points
    ..- attr(*, "unit")= int 8
   $ legend.key.spacing.x            : NULL
   $ legend.key.spacing.y            : NULL
   $ legend.frame                    : NULL
   $ legend.ticks                    : NULL
   $ legend.ticks.length             : 'rel' num 0.2
   $ legend.axis.line                : NULL
   $ legend.text                     :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : 'rel' num 0.8
    ..$ hjust        : NULL
    ..$ vjust        : NULL
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : NULL
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ legend.text.position            : NULL
   $ legend.title                    :List of 11
    ..$ family       : NULL
    ..$ face         : NULL
    ..$ colour       : NULL
    ..$ size         : NULL
    ..$ hjust        : num 0
    ..$ vjust        : NULL
    ..$ angle        : NULL
    ..$ lineheight   : NULL
    ..$ margin       : NULL
    ..$ debug        : NULL
    ..$ inherit.blank: logi TRUE
    ..- attr(*, "class")= chr [1:2] "element_text" "element"
   $ legend.title.position           : NULL
   $ legend.position                 : chr "right"
   $ legend.position.inside          : NULL
   $ legend.direction                : NULL
   $ legend.byrow                    : NULL
   $ legend.justification            : chr "center"
   $ legend.justification.top        : NULL
   $ legend.justification.bottom     : NULL
   $ legend.justification.left       : NULL
   $ legend.justification.right      : NULL
   $ legend.justification.inside     : NULL
   $ legend.location                 : NULL
   $ legend.box                      : NULL
   $ legend.box.just                 : NULL
   $ legend.box.margin               : 'margin' num [1:4] 0cm 0cm 0cm 0cm
    ..- attr(*, "unit")= int 1
   $ legend.box.background           : list()
    ..- attr(*, "class")= chr [1:2] "element_blank" "element"
   $ legend.box.spacing              : 'simpleUnit' num 11points
    ..- attr(*, "unit")= int 8
    [list output truncated]
   - attr(*, "class")= chr [1:2] "theme" "gg"
   - attr(*, "complete")= logi TRUE
   - attr(*, "validate")= logi TRUE
  
  $coordinates
  <ggproto object: Class CoordCartesian, Coord, gg>
      aspect: function
      backtransform_range: function
      clip: on
      default: TRUE
      distance: function
      expand: TRUE
      is_free: function
      is_linear: function
      labels: function
      limits: list
      modify_scales: function
      range: function
      render_axis_h: function
      render_axis_v: function
      render_bg: function
      render_fg: function
      setup_data: function
      setup_layout: function
      setup_panel_guides: function
      setup_panel_params: function
      setup_params: function
      train_panel_guides: function
      transform: function
      super:  <ggproto object: Class CoordCartesian, Coord, gg>
  
  $facet
  <ggproto object: Class FacetGrid, Facet, gg>
      compute_layout: function
      draw_back: function
      draw_front: function
      draw_labels: function
      draw_panels: function
      finish_data: function
      init_scales: function
      map_data: function
      params: list
      setup_data: function
      setup_params: function
      shrink: TRUE
      train_scales: function
      vars: function
      super:  <ggproto object: Class FacetGrid, Facet, gg>
  
  $plot_env
  <environment: 0x55e393aec480>
  
  $layout
  <ggproto object: Class Layout, gg>
      coord: NULL
      coord_params: list
      facet: NULL
      facet_params: list
      finish_data: function
      get_scales: function
      layout: NULL
      map_position: function
      panel_params: NULL
      panel_scales_x: NULL
      panel_scales_y: NULL
      render: function
      render_labels: function
      reset_scales: function
      resolve_label: function
      setup: function
      setup_panel_guides: function
      setup_panel_params: function
      train_position: function
      super:  <ggproto object: Class Layout, gg>
  
  $labels
  $labels$x
  [1] "Log-Ratio Value"
  
  $labels$y
  [1] "coord"
  
  $labels$xmin
  [1] ".lower"
  
  $labels$xmax
  [1] ".upper"
  
  
  attr(,"class")
  [1] "gg"     "ggplot"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-ilr.R:11:3'): clr plus summary works ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(phyloseq)`: there is no package called 'phyloseq'
  Backtrace:
      ▆
   1. └─base::library(phyloseq) at test-ilr.R:11:3
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
  Error: Test failures
  Execution halted