Package: adklakedata
Check: examples
New result: ERROR
  Running examples in ‘adklakedata-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: adk_lake_shapes
  > ### Title: Return path to Lake Polygons Shapefile
  > ### Aliases: adk_lake_shapes
  > 
  > ### ** Examples
  > 
  > library(sf)
  Linking to GEOS 3.13.1, GDAL 3.10.3, PROJ 9.6.0; sf_use_s2() is TRUE
  > bl = read_sf(adklakedata::adk_shape())
  Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir,  : 
    package tibble not available: install first?
  Calls: read_sf ... st_read -> st_read.character -> process_cpl_read_ogr
  Execution halted

Package: adw
Check: examples
New result: ERROR
  Running examples in ‘adw-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: adw
  > ### Title: Angular Distance Weighting Interpolation.
  > ### Aliases: adw
  > 
  > ### ** Examples
  > 
  > set.seed(2)
  > dd <- data.frame(lon = runif(100, min = 110, max = 117),
  +                  lat = runif(100, min = 31, max = 37),
  +                  value = runif(100, min = -10, max = 10))
  > head(dd)
         lon      lat     value
  1 111.2942 32.20561  7.173832
  2 114.9166 33.56583  2.903207
  3 114.0133 36.88360  2.055973
  4 111.1764 35.97353  9.439614
  5 116.6069 32.72184 -2.466855
  6 116.6043 34.57550  6.382290
  > 
  > # example 1
  > grd <- adw(dd, extent = c(110, 117, 31, 37), gridsize = 0.5, cdd = 500)
  > head(grd)
       lon   lat       value
  1 110.25 31.25  0.09027313
  2 110.75 31.25  1.00411953
  3 111.25 31.25 -0.35292188
  4 111.75 31.25 -0.47570806
  5 112.25 31.25 -1.57521787
  6 112.75 31.25 -1.10541492
  > 
  > # example 2
  > hmap <- cnmap::getMap(code = "410000") |> sf::st_make_valid() # return a 'sf' object.
  Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir,  : 
    package tibble not available: install first?
  Calls: <Anonymous> ... st_read -> st_read.character -> process_cpl_read_ogr
  Execution halted

Package: adw
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Introduction.Rmd’ using rmarkdown
  
  Quitting from Introduction.Rmd:47-74 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `process_cpl_read_ogr()`:
  ! package tibble not available: install first?
  ---
  Backtrace:
      ▆
   1. └─cnmap::getMap(name = "河南省", returnClass = "sf")
   2.   └─sf::read_sf(urlmap)
   3.     ├─sf::st_read(...)
   4.     └─sf:::st_read.character(...)
   5.       └─sf:::process_cpl_read_ogr(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
  package tibble not available: install first?
  --- failed re-building ‘Introduction.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Introduction.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: afex
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘afex_analysing_accuracy_data.Rmd’ using rmarkdown
  --- finished re-building ‘afex_analysing_accuracy_data.Rmd’
  
  --- re-building ‘afex_anova_example.Rmd’ using rmarkdown
  --- finished re-building ‘afex_anova_example.Rmd’
  
  --- re-building ‘afex_mixed_example.Rmd’ using rmarkdown
  --- finished re-building ‘afex_mixed_example.Rmd’
  
  --- re-building ‘afex_plot_introduction.Rmd’ using rmarkdown
  
  Quitting from afex_plot_introduction.Rmd:169-208 [unnamed-chunk-11]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'afex_plot_introduction.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `fun()`:
  ! argument "layout" is missing, with no default
  --- failed re-building ‘afex_plot_introduction.Rmd’
  
  --- re-building ‘afex_plot_supported_models.Rmd’ using rmarkdown
  
  Quitting from afex_plot_supported_models.Rmd:281-283 [unnamed-chunk-22]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `UseMethod()`:
  ! no applicable method for 'grid.draw' applied to an object of class "c('gg', 'ggplot')"
  ---
  Backtrace:
      ▆
   1. └─grid::grid.draw(b34)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'afex_plot_supported_models.Rmd' failed with diagnostics:
  no applicable method for 'grid.draw' applied to an object of class "c('gg', 'ggplot')"
  --- failed re-building ‘afex_plot_supported_models.Rmd’
  
  --- re-building ‘assumptions_of_ANOVAs.Rmd’ using rmarkdown
  
  Quitting from assumptions_of_ANOVAs.Rmd:125-139 [unnamed-chunk-7]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'assumptions_of_ANOVAs.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  --- failed re-building ‘assumptions_of_ANOVAs.Rmd’
  
  --- re-building ‘introduction-mixed-models.pdf.asis’ using asis
  --- finished re-building ‘introduction-mixed-models.pdf.asis’
  
  SUMMARY: processing the following files failed:
    ‘afex_plot_introduction.Rmd’ ‘afex_plot_supported_models.Rmd’
    ‘assumptions_of_ANOVAs.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: alookr
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggmosaic’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: AnalysisLin
Check: examples
New result: ERROR
  Running examples in ‘AnalysisLin-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: qq_plot
  > ### Title: QQ Plots for Numerical Variables
  > ### Aliases: qq_plot
  > 
  > ### ** Examples
  > 
  > data(mtcars)
  > qq_plot(mtcars)
  Error in eval(substitute(expr), data, enclos = parent.frame()) : 
    object 'x' not found
  Calls: qq_plot ... to_basic.GeomAbline -> with -> with.default -> eval -> eval
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
  dens_plot 4.962  0.392   5.319
  hist_plot 4.821  0.212   5.038

Package: andurinha
Check: tests
New result: ERROR
    Running ‘testthat.R’ [6s/6s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(andurinha)
    > 
    > test_check("andurinha")
      sample absMax
    1      A  0.465
    2      B  0.402
    3      C  0.474
    [ FAIL 4 | WARN 0 | SKIP 0 | PASS 43 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_funtionsOutput.R:21:3'): gOverview return a ggplot objetc ────
    class(gOverview(andurinhaData)) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_funtionsOutput.R:22:3'): gOverview return a ggplot objetc ────
    class(gOverview(findPeaks(andurinhaData)$dataZ, findPeaks(andurinhaData)$secondDerivative)) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_funtionsOutput.R:29:3'): plotPeaks return a ggplot objetc ────
    class(...) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_funtionsOutput.R:32:3'): plotPeaks return a ggplot objetc ────
    class(...) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 4 | WARN 0 | SKIP 0 | PASS 43 ]
    Error: Test failures
    Execution halted

Package: animbook
Check: examples
New result: ERROR
  Running examples in ‘animbook-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: anim_animate
  > ### Title: Modified the ggplot object
  > ### Aliases: anim_animate
  > 
  > ### ** Examples
  > 
  > animbook <- anim_prep(data = osiris, id = ID, values = sales, time = year, group = japan)
  > 
  > plot <- wallaby_plot(animbook)
  You can now use the animbook::anim_animate() function to
            transform it into an animated object
  > 
  > animate <- anim_animate(plot)
  Error in plot$plot_env : object of type 'object' is not subsettable
  Calls: anim_animate
  Execution halted

Package: ANN2
Check: tests
New result: ERROR
    Running ‘testthat.R’ [4s/4s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ANN2)
    > 
    > # Only test if not on mac
    > if (tolower(Sys.info()[["sysname"]]) != "darwin") {
    +   test_check("ANN2")
    + }
    [ FAIL 5 | WARN 2 | SKIP 4 | PASS 143 ]
    
    ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
    • On CRAN (4): 'test-cpp.R:4:5', 'test-gradient.R:91:3',
      'test-gradient.R:123:3', 'test-gradient.R:159:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plotting.R:33:3'): the plot.ANN() function works correctly ───
    p_NN$labels$colour not equal to "variable".
    target is NULL, current is character
    ── Failure ('test-plotting.R:41:3'): the plot.ANN() function works correctly ───
    p_AE$labels$colour not equal to "variable".
    target is NULL, current is character
    ── Failure ('test-plotting.R:58:3'): the reconstruction_plot.ANN() function works correctly ──
    p_AE$labels$group not equal to "obs".
    target is NULL, current is character
    ── Failure ('test-plotting.R:59:3'): the reconstruction_plot.ANN() function works correctly ──
    p_AE$labels$colour not equal to "col".
    target is NULL, current is character
    ── Failure ('test-plotting.R:77:3'): the compression_plot.ANN() function works correctly ──
    p_AE$labels$colour not equal to "col".
    target is NULL, current is character
    
    [ FAIL 5 | WARN 2 | SKIP 4 | PASS 143 ]
    Error: Test failures
    Execution halted

Package: antitrust
Check: examples
New result: ERROR
  Running examples in ‘antitrust-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: AIDS-Functions
  > ### Title: (Nested) AIDS Calibration and Merger Simulation
  > ### Aliases: AIDS-Functions aids pcaids pcaids.nests
  > 
  > ### ** Examples
  > 
  > ## Simulate a merger between two single-product firms A and B in a
  > ## three-firm market (A, B, C). This example assumes that the merger is between
  > ## the firms A and B and that A's own-price elasticity is
  > ## known.
  > ## Source: Epstein and Rubinfeld (2004), pg 9, Table 2.
  > 
  > 
  > prices    <- c(2.9,3.4,2.2) ## optional for aids, unnecessary for pcaids
  > shares    <- c(.2,.3,.5)
  > 
  > 
  > ## The following are used by aids but not pcaids
  > ## only two of the margins are required to calibrate the demand parameters
  > margins <- c(0.33, 0.36, 0.44)
  > 
  > ## The following are used by pcaids, but not aids
  > knownElast<- -3
  > mktElast  <- -1
  > 
  > 
  > ## Define ownership using a vector of firm identities
  > ownerPre <- c("A","B","C")
  > ownerPost <- c("A","A","C")
  > 
  > ## Alternatively, ownership could be defined using matrices
  > #ownerPre=diag(1,length(shares))
  > #ownerPost=ownerPre
  > #ownerPost[1,2] <- ownerPost[2,1] <- 1
  > 
  > 
  > ## AIDS: the following assumes both prices and margins are known.
  > ##       Prices are not needed to estimate price changes
  > 
  > 
  > 
  > result.aids <- aids(shares,margins,prices,ownerPre=ownerPre,ownerPost=ownerPost,labels=ownerPre)
  > 
  > 
  > 
  > print(result.aids)           # return predicted price change
  Warning in .local(object, ...) :
    Slot 'insideSize' is missing. Calculating CV as a percentage change in (aggregate) income
  Warning in .local(object, ...) :
    'calcQuantities' yielded all NAs. Using 'calcShares' instead
  Warning in .local(object, ...) :
    'calcQuantities' yielded all NAs. Using 'calcShares' instead
  
  Merger simulation results under 'AIDS' demand:
  
   HHI Change
         1200
   Industry Price Change (%)
                         7.5
   Merging Party Price Change (%)
                               12
   Compensating Marginal Cost Reduction (%)
                                         NA
   Consumer Harm ($)
                 7.3
   Producer Benefit ($)
                   0.18
   Difference ($)
              7.2
  
  
  > summary(result.aids)         # summarize merger simulation
  
  Merger simulation results under 'AIDS' demand:
  
      pricePre pricePost priceDelta sharesPre sharesPost outputDelta
  * A      2.9       3.3         14        20         17       -13.2
  * B      3.4       3.8         11        30         28        -6.5
    C      2.2       2.3          4        50         55         9.1
  
  	Notes: '*' indicates merging parties' products.
   	Deltas are percent changes.
  	Output is based on revenues.
  
  
  > 
  > elast(result.aids,TRUE)      # returns premerger elasticities
             A          B         C
  A -3.0303027  0.7575762  1.262627
  B  0.5050508 -2.7777773  1.262627
  C  0.5050508  0.7575762 -2.272727
  > elast(result.aids,FALSE)     # returns postmerger elasticities
             A          B         C
  A -3.3370108  0.8728868  1.454025
  B  0.5402877 -2.8999816  1.349594
  C  0.4628976  0.6941436 -2.167141
  > 
  > diversion(result.aids,TRUE)  # return premerger diversion ratios
             A      B          C
  A -1.0000000  0.375  0.6250000
  B  0.2857143 -1.000  0.7142857
  C  0.4000000  0.600 -1.0000000
  > diversion(result.aids,FALSE) # return postmerger diversion ratios
             A      B          C
  A -1.0000000  0.375  0.6250000
  B  0.2857143 -1.000  0.7142857
  C  0.4000000  0.600 -1.0000000
  > 
  > 
  > cmcr(result.aids)            #calculate compensating marginal cost reduction
  Error in loadNamespace(x) : there is no package called ‘MASS’
  Calls: cmcr ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted

Package: applicable
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [7s/8s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(applicable)
    Loading required package: ggplot2
    > 
    > test_check("applicable")
    Loading required package: dplyr
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    
    Attaching package: 'recipes'
    
    The following object is masked from 'package:stats':
    
        step
    
    
    Attaching package: 'proxyC'
    
    The following object is masked from 'package:stats':
    
        dist
    
    The following objects are masked from 'package:base':
    
        crossprod, tcrossprod
    
    [ FAIL 3 | WARN 0 | SKIP 22 | PASS 90 ]
    
    ══ Skipped tests (22) ══════════════════════════════════════════════════════════
    • On CRAN (22): 'test-hat_values-fit.R:16:3', 'test-hat_values-fit.R:22:3',
      'test-hat_values-fit.R:112:3', 'test-hat_values-fit.R:124:3',
      'test-hat_values-score.R:2:3', 'test-hat_values-score.R:9:3',
      'test-hat_values-score.R:17:3', 'test-isolation-fit.R:38:3',
      'test-misc.R:3:3', 'test-pca-fit.R:22:3', 'test-pca-fit.R:28:3',
      'test-pca-score.R:2:3', 'test-pca-score.R:9:3', 'test-pca-score.R:17:3',
      'test-print.R:4:3', 'test-print.R:36:3', 'test-similarity.R:117:3',
      'test-similarity.R:128:3', 'test-similarity.R:147:3',
      'test-similarity.R:171:3', 'test-similarity.R:186:3',
      'test-similarity.R:202:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot.R:10:3'): output of autoplot.apd_pca is correct when no options are provided ──
    ad_plot$labels$y (`actual`) not equal to "percentile" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('percentile')
    ── Failure ('test-plot.R:23:3'): output of autoplot.apd_pca is correct when options=matches are provided ──
    ad_plot$labels$y (`actual`) not equal to "percentile" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('percentile')
    ── Failure ('test-plot.R:36:3'): output of autoplot.apd_pca is correct when options=distance are provided ──
    ad_plot$labels$y (`actual`) not equal to "percentile" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('percentile')
    
    [ FAIL 3 | WARN 0 | SKIP 22 | PASS 90 ]
    Error: Test failures
    Execution halted

Package: arena2r
Check: tests
New result: ERROR
    Running ‘testthat.R’ [2s/2s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(arena2r)
    > 
    > test_check("arena2r")
    [ FAIL 3 | WARN 6 | SKIP 0 | PASS 4 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('tests_arena2r.R:31:3'): plots_sao_gerados ─────────────────────────
    `plot_conf` has type 'object', not 'list'.
    ── Failure ('tests_arena2r.R:32:3'): plots_sao_gerados ─────────────────────────
    `plot_scat` has type 'object', not 'list'.
    ── Failure ('tests_arena2r.R:33:3'): plots_sao_gerados ─────────────────────────
    `plot_box` has type 'object', not 'list'.
    
    [ FAIL 3 | WARN 6 | SKIP 0 | PASS 4 ]
    Error: Test failures
    Execution halted

Package: arulesViz
Check: examples
New result: ERROR
  Running examples in ‘arulesViz-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_arulesViz
  > ### Title: Visualize Association Rules and Itemsets
  > ### Aliases: plot_arulesViz plot.rules plot plot.itemsets
  > ###   plot.grouped_matrix plotly guide_edge_colourbar
  > ### Keywords: hplot
  > 
  > ### ** Examples
  > 
  > 
  > # Note: To speed example execution, not all examples are not run when using example("plot").
  > # Use example("plot") to run all examples.
  > 
  > data(Groceries)
  > rules <- apriori(Groceries, parameter = list(support = 0.001, confidence = 0.8))
  Apriori
  
  Parameter specification:
   confidence minval smax arem  aval originalSupport maxtime support minlen
          0.8    0.1    1 none FALSE            TRUE       5   0.001      1
   maxlen target  ext
       10  rules TRUE
  
  Algorithmic control:
   filter tree heap memopt load sort verbose
      0.1 TRUE TRUE  FALSE TRUE    2    TRUE
  
  Absolute minimum support count: 9 
  
  set item appearances ...[0 item(s)] done [0.00s].
  set transactions ...[169 item(s), 9835 transaction(s)] done [0.01s].
  sorting and recoding items ... [157 item(s)] done [0.00s].
  creating transaction tree ... done [0.00s].
  checking subsets of size 1 2 3 4 5 6 done [0.02s].
  writing ... [410 rule(s)] done [0.00s].
  creating S4 object  ... done [0.00s].
  > rules
  set of 410 rules 
  > 
  > ## Getting help
  > # There are many method, plotting engines and all of them have different control parameters. Use
  > # "help" to get help. List available methods for the object rules:
  > plot(rules, method = "help")
  Available methods for plotting rules are:
  matrix, mosaic, doubledecker, graph, paracoord, scatterplot, grouped matrix, two-key plot, matrix3D
  > 
  > # List the available engines for method "scatterplot"
  > plot(rules, method = "scatterplot", engine = "help")
  Available engines for this plotting method are:
  default, ggplot2, base, grid, interactive, plotly, htmlwidget
  > 
  > ## Not run: 
  > ##D # List control parameters for scatterplot with engine "ggplot2"
  > ##D plot(rules, method = "scatterplot", engine = "ggplot2", control = "help")
  > ## End(Not run)
  > 
  > 
  > ## Scatter plot
  > #  Display a scatter plot using two quality measures
  > plot(rules)
  To reduce overplotting, jitter is added! Use jitter = 0 to prevent jitter.
  > 
  > # Scatter plot with custom measures and limiting the plot to the 100 with the
  > # largest value for for the shading measure.
  > plot(rules, measure = c("support", "lift"), shading = "confidence", limit = 100)
  To reduce overplotting, jitter is added! Use jitter = 0 to prevent jitter.
  > 
  > ## Not run: 
  > ##D # Custom color scale, labels, theme and no title (ggplot2)
  > ##D library(ggplot2)
  > ##D plot(rules, engine = "ggplot2", main = NULL, limit = 100) +
  > ##D   scale_color_gradient2(
  > ##D     low = "red", mid = "gray90", high = "blue",
  > ##D     midpoint = 1, limits = c(0, 12)
  > ##D   ) +
  > ##D   labs(x = "Supp.", y = "Conf.", color = "Lift") +
  > ##D   theme_classic()
  > ##D 
  > ##D # Interactive scatter plot using the grid engine (selected rules are returned)
  > ##D if (interactive()) {
  > ##D   sel <- plot(rules, engine = "interactive")
  > ##D 
  > ##D   # Create a html widget for interactive visualization (uses plotly)
  > ##D   plot(rules, engine = "htmlwidget")
  > ##D }
  > ## End(Not run)
  > 
  > # Two-key plot (a scatter plot with shading = "order")
  > plot(rules, method = "two-key plot", limit = 100)
  To reduce overplotting, jitter is added! Use jitter = 0 to prevent jitter.
  > 
  > 
  > ## Matrix shading
  > #  Display rules as a matrix with RHS itemsets as rows and LHS itemsets as columns
  > 
  > # works better with small sets of rules
  > subrules <- subset(rules, lift > 5)
  > subrules
  set of 32 rules 
  > 
  > # 2D matrix with shading (ggplot2). The LHS and RHS are reordered so
  > # that rules with similar lift are displayed close to each other.
  > plot(subrules, method = "matrix")
  Itemsets in Antecedent (LHS)
   [1] "{liquor,red/blush wine}"                                         
   [2] "{citrus fruit,other vegetables,soda,fruit/vegetable juice}"      
   [3] "{tropical fruit,other vegetables,whole milk,yogurt,oil}"         
   [4] "{citrus fruit,grapes,fruit/vegetable juice}"                     
   [5] "{other vegetables,whole milk,yogurt,rice}"                       
   [6] "{tropical fruit,other vegetables,whole milk,oil}"                
   [7] "{ham,pip fruit,other vegetables,yogurt}"                         
   [8] "{beef,citrus fruit,tropical fruit,other vegetables}"             
   [9] "{root vegetables,butter,cream cheese }"                          
  [10] "{tropical fruit,whole milk,butter,sliced cheese}"                
  [11] "{other vegetables,curd,whipped/sour cream,cream cheese }"        
  [12] "{tropical fruit,other vegetables,butter,white bread}"            
  [13] "{sausage,pip fruit,sliced cheese}"                               
  [14] "{tropical fruit,whole milk,butter,curd}"                         
  [15] "{tropical fruit,butter,white bread}"                             
  [16] "{tropical fruit,butter,margarine}"                               
  [17] "{whole milk,curd,whipped/sour cream,cream cheese }"              
  [18] "{whipped/sour cream,cream cheese ,margarine}"                    
  [19] "{beef,tropical fruit,butter}"                                    
  [20] "{pork,tropical fruit,fruit/vegetable juice}"                     
  [21] "{tropical fruit,other vegetables,butter,curd}"                   
  [22] "{tropical fruit,root vegetables,whole milk,margarine}"           
  [23] "{other vegetables,butter milk,pastry}"                           
  [24] "{whipped/sour cream,pastry,fruit/vegetable juice}"               
  [25] "{citrus fruit,root vegetables,soft cheese}"                      
  [26] "{pip fruit,whipped/sour cream,brown bread}"                      
  [27] "{tropical fruit,grapes,whole milk,yogurt}"                       
  [28] "{ham,tropical fruit,pip fruit,yogurt}"                           
  [29] "{ham,tropical fruit,pip fruit,whole milk}"                       
  [30] "{tropical fruit,butter,whipped/sour cream,fruit/vegetable juice}"
  [31] "{whole milk,rolls/buns,soda,newspapers}"                         
  [32] "{citrus fruit,tropical fruit,root vegetables,whipped/sour cream}"
  Itemsets in Consequent (RHS)
  [1] "{other vegetables}" "{yogurt}"           "{tropical fruit}"  
  [4] "{root vegetables}"  "{bottled beer}"    
  Error in `vec_assign()`:
  ! Can't convert <double> to <character>.
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_build(x)
    4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    5. │   └─plot@guides$build(npscales, plot@layers, plot@labels, data, plot@theme)
    6. │     └─ggplot2 (local) build(..., self = self)
    7. │       └─guides$train(scales, labels)
    8. │         └─ggplot2 (local) train(..., self = self)
    9. │           └─base::Map(...)
   10. │             └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
   11. │               └─ggplot2 (local) `<fn>`(...)
   12. │                 └─guide$train(param, scale, aes, title = labels[[aes]])
   13. │                   └─ggplot2 (local) train(..., self = self)
   14. │                     ├─rlang::inject(self$extract_key(scale, !!!params))
   15. │                     └─self$extract_key(...)
   16. │                       └─ggplot2 (local) extract_key(...)
   17. │                         └─Guide$extract_key(scale, aesthetic, ...)
   18. │                           └─ggplot2 (local) extract_key(...)
   19. │                             └─scale$map(breaks)
   20. │                               └─ggplot2 (local) map(..., self = self)
   21. │                                 └─vctrs::vec_assign(scaled, is.na(scaled), self$na.value)
   22. └─vctrs (local) `<fn>`()
   23.   └─vctrs::vec_default_cast(...)
   24.     ├─base::withRestarts(...)
   25.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
   26.     │   └─base (local) doWithOneRestart(return(expr), restart)
   27.     └─vctrs::stop_incompatible_cast(...)
   28.       └─vctrs::stop_incompatible_type(...)
   29.         └─vctrs:::stop_incompatible(...)
   30.           └─vctrs:::stop_vctrs(...)
   31.             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  Execution halted

Package: arulesViz
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘arulesViz.Rnw’ using Sweave
  Loading required package: arules
  Loading required package: Matrix
  
  Attaching package: ‘arules’
  
  The following objects are masked from ‘package:base’:
  
      abbreviate, write
  
  To reduce overplotting, jitter is added! Use jitter = 0 to prevent jitter.
  To reduce overplotting, jitter is added! Use jitter = 0 to prevent jitter.
  To reduce overplotting, jitter is added! Use jitter = 0 to prevent jitter.
  Error: processing vignette 'arulesViz.Rnw' failed with diagnostics:
  Can't convert <double> to <character>.
  --- failed re-building ‘arulesViz.Rnw’
  
  SUMMARY: processing the following file failed:
    ‘arulesViz.Rnw’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ASRgenomics
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [46s/44s]
  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(ASRgenomics)
    > 
    > test_check("ASRgenomics")
    Initial data: 
    	Number of Individuals: 247 
    	Number of Markers: 50 
    
    Missing data check: 
    	Total SNPs: 50 
    	 0 SNPs dropped due to missing data threshold of 0.5 
    	Total of: 50  SNPs 
    
    MAF check: 
    	No SNPs with MAF below 0 
    
    Heterozigosity data check: 
    	No SNPs with heterozygosity, missing threshold of =  0 
    
    Summary check: 
    	Initial:  50 SNPs 
    	Final:  50  SNPs ( 0  SNPs removed) 
     
    Completed! Time = 0.018  seconds 
    Reciprocal conditional number for original matrix is: 0
    Reciprocal conditional number of G is: 0, which is lower than the threshold of 1e-12
    G seems to be an ill-conditioned matrix.
    Reciprocal conditional number for original matrix is: 0
    Reciprocal conditional number of G is: 0, which is lower than the threshold of 1e-12
    G seems to be an ill-conditioned matrix.
    Reciprocal conditional number for inverted matrix is: 0.0010679765264986
    Inverse of matrix G does not appear to be ill-conditioned.
    Reciprocal conditional number for original matrix is: 0
    Reciprocal conditional number of G is: 0, which is lower than the threshold of 1e-12
    G seems to be an ill-conditioned matrix.
    Reciprocal conditional number for inverted matrix is: 0.0010679765264986
    Inverse of matrix G does not appear to be ill-conditioned.
    Reciprocal conditional number for original matrix is: 0
    Reciprocal conditional number of G is: 0, which is lower than the threshold of 1e-12
    G seems to be an ill-conditioned matrix.
    Reciprocal conditional number for inverted matrix is: 0.0010679765264986
    Inverse of matrix G does not appear to be ill-conditioned.
    Reciprocal conditional number for original matrix is: 0
    Reciprocal conditional number of G is: 0, which is lower than the threshold of 1e-12
    G seems to be an ill-conditioned matrix.
    Reciprocal conditional number for inverted matrix is: 0.0010679765264986
    Inverse of matrix G does not appear to be ill-conditioned.
    Initial data: 
    	Number of Individuals: 20 
    	Number of Markers: 50 
    
    Missing data check: 
    	Total SNPs: 50 
    	 0 SNPs dropped due to missing data threshold of 0.5 
    	Total of: 50  SNPs 
    
    MAF check: 
    	No SNPs with MAF below 0 
    
    Heterozigosity data check: 
    	No SNPs with heterozygosity, missing threshold of =  0 
    
    Summary check: 
    	Initial:  50 SNPs 
    	Final:  50  SNPs ( 0  SNPs removed) 
     
    Completed! Time = 0.007  seconds 
    Initial data: 
    	Number of Individuals: 20 
    	Number of Markers: 10 
    
    Missing data check: 
    	Total SNPs: 10 
    	 0 SNPs dropped due to missing data threshold of 0.5 
    	Total of: 10  SNPs 
    
    MAF check: 
    	No SNPs with MAF below 0 
    
    Heterozigosity data check: 
    	No SNPs with heterozygosity, missing threshold of =  0 
    
    Summary check: 
    	Initial:  10 SNPs 
    	Final:  10  SNPs ( 0  SNPs removed) 
     
    Completed! Time = 0.002  seconds 
    Reciprocal conditional number for original matrix is: 0
    Determinant for original matrix is: 0
    Matrix was BLENDED using an identity matrix.
    Reciprocal conditional number for tune-up matrix is: 4.65251000480448e-08
    Initial data: 
    	Number of Individuals: 20 
    	Number of Markers: 50 
    
    Missing data check: 
    	Total SNPs: 50 
    	 0 SNPs dropped due to missing data threshold of 0.5 
    	Total of: 50  SNPs 
    
    MAF check: 
    	No SNPs with MAF below 0 
    
    Heterozigosity data check: 
    	No SNPs with heterozygosity, missing threshold of =  0 
    
    Summary check: 
    	Initial:  50 SNPs 
    	Final:  50  SNPs ( 0  SNPs removed) 
     
    Completed! Time = 0.008  seconds 
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Determinant for original matrix is: 0.9375
    Matrix was BLENDED using an identity matrix.
    Reciprocal conditional number for tune-up matrix is: 0.665950590762621
    Reciprocal conditional number for original matrix is: 2.24022977149314e-10
    Determinant for original matrix is: -1.76706403547069e-24
    Matrix was BENDED.
    Reciprocal conditional number for tune-up matrix is: 0.00368868521743848
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Determinant for original matrix is: 0.9375
    Matrix was ALIGNED.
    Reciprocal conditional number for tune-up matrix is: 0.339632305259641
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Determinant for original matrix is: 0.9375
    Matrix was BLENDED using the provided A matrix.
    Reciprocal conditional number for tune-up matrix is: 0.628684245574785
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Determinant for original matrix is: 0.9375
    Matrix was BLENDED using the provided A matrix.
    Reciprocal conditional number for tune-up matrix is: 0.628684245574785
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Determinant for original matrix is: 0.9375
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Determinant for original matrix is: 0.9375
    Matrix was ALIGNED.
    Reciprocal conditional number for tune-up matrix is: 0.281647697281091
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Determinant for original matrix is: 0.9375
    Reciprocal conditional number for original matrix is: 1
    Determinant is not calculated as matrix is too large.
    Matrix was BLENDED using an identity matrix.
    Reciprocal conditional number for tune-up matrix is: 1
    Reciprocal conditional number for original matrix is: 1
    Determinant for original matrix is: Inf
    Matrix was BLENDED using an identity matrix.
    Reciprocal conditional number for tune-up matrix is: 1
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Determinant for original matrix is: 0.9375
    Reciprocal conditional number for original matrix is: 0
    Reciprocal conditional number of G is: 0, which is lower than the threshold of 1e-12
    G seems to be an ill-conditioned matrix.
    Reciprocal conditional number for inverted matrix is: 0.00748567238719749
    Inverse of matrix G does not appear to be ill-conditioned.
    Reciprocal conditional number for original matrix is: 0.224489795918367
    Reciprocal conditional number for inverted matrix is: 0.224489794715743
    Inverse of matrix G does not appear to be ill-conditioned.
    A lambda value was provided and it will be used instead of tau and omega.
    A lambda value was provided and it will be used instead of tau and omega.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    No lambda value was provided, tau and omega scaling factors will be considered.
    A lambda value was provided and it will be used instead of tau and omega.
    Reciprocal conditional number for original matrix is: 0.635294117647059
    Reciprocal conditional number for inverted matrix is: 0.599999997
    Inverse of matrix G does not appear to be ill-conditioned.
    A lambda value was provided and it will be used instead of tau and omega.
    Creating dummy map.
    Matrix dimension is: 5x5
    Range diagonal values: 0.8747 to 1.05366
    Mean diagonal values: 0.94315
    Range off-diagonal values: -0.11524 to 0.9
    Mean off-diagonal values: 0.20953
    No individuals filtered out by the diagonal thresholds, as none were found.
    No individuals filtered by duplicate.thr = 0.99, as none were found.
    There are 0 extreme diagonal values, outside < 0.7 and > 1.3
    There are 0 records of possible duplicates, based on: k(i,j)/sqrt[k(i,i)*k(j,j)] >  0.99
    Matrix dimension is: 5x5
    Range diagonal values: 0.8747 to 1.05366
    Mean diagonal values: 0.94315
    Range off-diagonal values: -0.11524 to 0.9
    Mean off-diagonal values: 0.20953
    No individuals filtered out by the diagonal thresholds, as none were found.
    No individuals filtered by duplicate.thr = 0.99, as none were found.
    There are 0 extreme diagonal values, outside < 0.7 and > 1.3
    There are 0 records of possible duplicates, based on: k(i,j)/sqrt[k(i,i)*k(j,j)] >  0.99
    Matrix dimension is: 5x5
    Range diagonal values: 0.8747 to 1.05366
    Mean diagonal values: 0.94315
    Range off-diagonal values: -0.11524 to 0.9
    Mean off-diagonal values: 0.20953
    No individuals filtered out by the diagonal thresholds, as none were found.
    No individuals filtered by duplicate.thr = 0.99, as none were found.
    There are 0 extreme diagonal values, outside < 0.7 and > 1.3
    There are 0 records of possible duplicates, based on: k(i,j)/sqrt[k(i,i)*k(j,j)] >  0.99
    Matrix dimension is: 5x5
    Range diagonal values: 0.8747 to 1.05366
    Mean diagonal values: 0.94315
    Range off-diagonal values: -0.11524 to 0.9
    Mean off-diagonal values: 0.20953
    There are 1 extreme diagonal values, outside < 0.9 and > 1.3
    There are 1 records of possible duplicates, based on: k(i,j)/sqrt[k(i,i)*k(j,j)] >  0.8
    Matrix dimension is: 5x5
    Range diagonal values: 0.8747 to 1.05366
    Mean diagonal values: 0.94315
    Range off-diagonal values: -0.11524 to 0.9
    Mean off-diagonal values: 0.20953
    There are 1 extreme diagonal values, outside < 0.9 and > 1.3
    There are 1 records of possible duplicates, based on: k(i,j)/sqrt[k(i,i)*k(j,j)] >  0.8
    Matrix dimension is: 5x5
    Range diagonal values: 0.8747 to 1.05366
    Mean diagonal values: 0.94315
    Range off-diagonal values: -0.11524 to 0.9
    Mean off-diagonal values: 0.20953
    There are 1 extreme diagonal values, outside < 0.9 and > 1.3
    There are 1 records of possible duplicates, based on: k(i,j)/sqrt[k(i,i)*k(j,j)] >  0.8
    Initial data: 
    	Number of Individuals: 20 
    	Number of Markers: 50 
    
    Missing data check: 
    	Total SNPs: 50 
    	 0 SNPs dropped due to missing data threshold of 0.5 
    	Total of: 50  SNPs 
    
    MAF check: 
    	No SNPs with MAF below 0 
    
    Heterozigosity data check: 
    	No SNPs with heterozygosity, missing threshold of =  0 
    
    Summary check: 
    	Initial:  50 SNPs 
    	Final:  50  SNPs ( 0  SNPs removed) 
     
    Completed! Time = 0.007  seconds 
    All 4 individuals from matrix A match those individuals from matrix G.
    All 4 individuals from matrix G match those individuals from matrix A.
    All 4 individuals from matrix A match those individuals from matrix G.
    All 4 individuals from matrix G match those individuals from matrix A.
    All 2 individuals from matrix G match those individuals from matrix A.
    Matrix A has 2 individuals (out of 4) NOT present on matrix G.
    Matrix G has 1 individuals (out of 4) NOT present on matrix A.
    Order of individual names from matched matrices A and G DO NOT agree.
    Matrix G has 1 individuals (out of 4) NOT present on matrix A.
    All 2 individuals from matrix A match those individuals from matrix G.
    Matrix G has 2 individuals (out of 4) NOT present on matrix A.
    All 4 individuals from matrix A match those individuals from matrix G.
    All 4 individuals from matrix G match those individuals from matrix A.
    All individuals within the kinship matrix match the phenotyped individuals.
    All phenotyped individuals match the individuals within the kinship matrix.
    Kinship matrix contains 1 individuals that DO NOT match the phenotyped individuals.
    Kinship matrix contains 4 individuals that match the phenotyped individuals.
    All phenotyped individuals match the individuals within the kinship matrix.
    Individuals within the kinship matrix that do not match those in the phenotypic data will be removed from this matrix.
    All individuals within the kinship matrix match the phenotyped individuals.
    Phenotypic data contains 1 individuals that DO NOT match the kinship matrix individuals.
    Phenotypic data contains 4 individuals that match the kinship matrix individuals.
    All individuals within the kinship matrix match the phenotyped individuals.
    Phenotypic data contains 1 individuals that DO NOT match the kinship matrix individuals.
    Phenotypic data contains 4 individuals that match the kinship matrix individuals.
    All individuals within the kinship matrix match the phenotyped individuals.
    All phenotyped individuals match the individuals within the kinship matrix.
    Initial marker matrix M contains 5 individuals and 6 markers.
    A total of 9 values were identified as missing with the string -9 and were replaced by NA.
    A total of 1 markers were removed for only having missing data.
    A total of 1 markers were removed because their proportion of missing values was equal or larger than 0.39.
    A total of 1 individuals were removed because their proportion of missing values was equal or larger than 0.49.
    A total of 1 markers were removed because their MAF was smaller than 0.26.
    A total of 1 markers were removed because their heterozygosity was larger than 0.99999.
    A total of 1 markers were removed because their |F| was larger than 0.45.
    Final cleaned marker matrix M contains 0% of missing SNPs.
    Final cleaned marker matrix M contains 4 individuals and 1 markers.
    No imputation was performed as there are no missing marker data.
    Initial marker matrix M contains 5 individuals and 6 markers.
    A total of 9 values were identified as missing with the string -9 and were replaced by NA.
    A total of 1 markers were removed for only having missing data.
    A total of 0 markers were removed because their proportion of missing values was equal or larger than 1.
    A total of 0 individuals were removed because their proportion of missing values was equal or larger than 1.
    A total of 0 markers were removed because their MAF was smaller than 0.
    A total of 0 markers were removed because their heterozygosity was larger than 1.
    A total of 0 markers were removed because their |F| was larger than 1.
    Final cleaned marker matrix M contains 16% of missing SNPs.
    Final cleaned marker matrix M contains 5 individuals and 5 markers.
    A total of 4 missing values were imputed, corresponding to 16% of the total number of SNPs.
    Matrix M was recoded from bi-allelic nucleotide bases to numeric.
    A total of 0 values were identified as missing with the string nil and were replaced by NA.
    Matrix M was recoded from bi-allelic nucleotide bases to numeric.
    Initial marker matrix M contains 655 individuals and 4853 markers.
    A total of 119670 values were identified as missing with the string -9 and were replaced by NA.
    A total of 156 markers were removed because their proportion of missing values was equal or larger than 0.2.
    A total of 11 individuals were removed because their proportion of missing values was equal or larger than 0.2.
    A total of 1626 markers were removed because their MAF was smaller than 0.05.
    A total of 21 markers were removed because their heterozygosity was larger than 0.98.
    A total of 0 markers were removed because their |F| was larger than 1.
    Final cleaned marker matrix M contains 2.37% of missing SNPs.
    Final cleaned marker matrix M contains 644 individuals and 3050 markers.
    Creating dummy map.
    Creating dummy map.
    
    Initiating pruning procedure.
    Initial marker matrix M contains 644 individuals and 3050 markers.
    Requesting pruning without chromosome indexing.
      Iteration: 1
      Iteration: 2
      Iteration: 3
    
    Final pruned marker matrix M contains 644 individuals and 2954 markers.
    A total of 96 markers were pruned.
    Range of minor allele frequency after pruning: 0.05 ~ 0.5
    Range of marker call rate after pruning: 80.28 ~ 100
    Range of individual call rate after pruning: 81.58 ~ 99.19
    Creating dummy map.
    
    Initiating pruning procedure.
    Initial marker matrix M contains 644 individuals and 3050 markers.
    Requesting pruning without chromosome indexing.
      Iteration: 1
      Iteration: 2
      Iteration: 3
      Iteration: 4
    
    Final pruned marker matrix M contains 644 individuals and 2956 markers.
    A total of 94 markers were pruned.
    Range of minor allele frequency after pruning: 0.05 ~ 0.5
    Range of marker call rate after pruning: 80.28 ~ 100
    Range of individual call rate after pruning: 81.39 ~ 99.19
    
    Initiating pruning procedure.
    Initial marker matrix M contains 644 individuals and 3050 markers.
    Requesting pruning by chromosome.
    Chromosome: 1
      Iteration: 1
      Iteration: 2
      Iteration: 3
    Chromosome: 2
      Iteration: 1
      Iteration: 2
      Iteration: 3
    Chromosome: 3
      Iteration: 1
      Iteration: 2
      Iteration: 3
      Iteration: 4
    
    Final pruned marker matrix M contains 644 individuals and 2957 markers.
    A total of 93 markers were pruned.
    A total of 965 markers were kept in chromosome 1.
    A total of 966 markers were kept in chromosome 2.
    A total of 1026 markers were kept in chromosome 3.
    A total of 35 markers were pruned from chromosome 1.
    A total of 34 markers were pruned from chromosome 2.
    A total of 24 markers were pruned from chromosome 3.
    Range of minor allele frequency after pruning: 0.05 ~ 0.5
    Range of marker call rate after pruning: 80.28 ~ 100
    Range of individual call rate after pruning: 81.6 ~ 99.19
    Creating dummy map.
    Creating dummy map.
    Creating dummy map.
    Creating dummy map.
    Creating dummy map.
    
    Exact method selected. Eliminating markers containing one or more heterozygotic read.
    Total number of dropped markers: 13
    Total number of remaining markers: 2
    
    Generating in hypothetical crosses genotypic information.
    
    Generating in hypothetical crosses genotypic information.
    
    Generating in hypothetical crosses genotypic information.
    
    Generating in hypothetical crosses genotypic information.
    
    Exact method selected. Eliminating markers containing one or more heterozygotic read.
    Total number of dropped markers: 13
    Total number of remaining markers: 0
    
    Generating in hypothetical crosses genotypic information.
    A total of 1 duplicated rows were found in the supplied pedigree.
    Removing 'ped' lines: 6.
    
    Generating in hypothetical crosses genotypic information.
    [ FAIL 5 | WARN 7 | SKIP 0 | PASS 258 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-qc.R:54:3'): filters work ────────────────────────────────────
    class(M_filter$plot.missing.ind) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-qc.R:55:3'): filters work ────────────────────────────────────
    class(M_filter$plot.missing.SNP) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-qc.R:56:3'): filters work ────────────────────────────────────
    class(M_filter$plot.heteroz) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-qc.R:57:3'): filters work ────────────────────────────────────
    class(M_filter$plot.Fis) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-qc.R:58:3'): filters work ────────────────────────────────────
    class(M_filter$plot.maf) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 5 | WARN 7 | SKIP 0 | PASS 258 ]
    Error: Test failures
    Execution halted

Package: assignPOP
Check: tests
New result: ERROR
    Running ‘testthat.R’ [7s/7s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(assignPOP)
    > 
    > test_check("assignPOP")
    
      Correct assignment rates were estimated!!
      A total of 3 assignment tests for 3 pops.
      Results were also saved in a 'Rate_of_3_tests_3_pops.txt' file in the directory.
      Correct assignment rates were estimated!!
      A total of 3 assignment tests for 3 pops.
      Results were also saved in a 'Rate_of_3_tests_3_pops.txt' file in the directory.
      Converting data format...
    
      Encoding genetic data...
    
      ################ assignPOP v1.3.0 ################
    
      A GENEPOP format file was successfully imported!
    
      Imported Data Info: 24 obs. by 5 loci (diploid)
      Number of pop: 3
      Number of inds (pop.1): 8
      Number of inds (pop.2): 10
      Number of inds (pop.3): 6
      DataMatrix: 24 rows by 20 columns, with 19 allele variables
    
      Data output in a list comprising the following three elements:
      YOUR_LIST_NAME$DataMatrix
      YOUR_LIST_NAME$SampleID
      YOUR_LIST_NAME$LocusName
    
    
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      Monte-Carlo cross-validation done!!
      3 assignment tests completed!!
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      Monte-Carlo cross-validation done!!
      3 assignment tests completed!!
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      Monte-Carlo cross-validation done!!
      6 assignment tests completed!!
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      Monte-Carlo cross-validation done!!
      12 assignment tests completed!!
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      Monte-Carlo cross-validation done!!
      12 assignment tests completed!!
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      Monte-Carlo cross-validation done!!
      3 assignment tests completed!!
      Converting data format...
    
      Encoding genetic data...
    
      ################ assignPOP v1.3.0 ################
    
      A GENEPOP format file was successfully imported!
    
      Imported Data Info: 24 obs. by 5 loci (diploid)
      Number of pop: 3
      Number of inds (pop.1): 8
      Number of inds (pop.2): 10
      Number of inds (pop.3): 6
      DataMatrix: 24 rows by 20 columns, with 19 allele variables
    
      Data output in a list comprising the following three elements:
      YOUR_LIST_NAME$DataMatrix
      YOUR_LIST_NAME$SampleID
      YOUR_LIST_NAME$LocusName
    
    
      Converting data format...
    
      Encoding genetic data...
    
      ################ assignPOP v1.3.0 ################
    
      A GENEPOP format file was successfully imported!
    
      Imported Data Info: 24 obs. by 5 loci (diploid)
      Number of pop: 1
      Number of inds (pop.1): 24
      DataMatrix: 24 rows by 20 columns, with 19 allele variables
    
      Data output in a list comprising the following three elements:
      YOUR_LIST_NAME$DataMatrix
      YOUR_LIST_NAME$SampleID
      YOUR_LIST_NAME$LocusName
    
    
      Known and unknown datasets have identical features. 
      Performing PCA on genetic data for dimensionality reduction...
      Assignment test is done! See results in your designated folder.
      Predicted populations and probabilities are saved in [AssignmentResult.txt]
      Converting data format...
    
      Encoding genetic data...
    
      ################ assignPOP v1.3.0 ################
    
      A GENEPOP format file was successfully imported!
    
      Imported Data Info: 24 obs. by 5 loci (diploid)
      Number of pop: 3
      Number of inds (pop.1): 8
      Number of inds (pop.2): 10
      Number of inds (pop.3): 6
      DataMatrix: 24 rows by 20 columns, with 19 allele variables
    
      Data output in a list comprising the following three elements:
      YOUR_LIST_NAME$DataMatrix
      YOUR_LIST_NAME$SampleID
      YOUR_LIST_NAME$LocusName
    
    
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      K-fold cross-validation done!!
      3 assignment tests completed!!  Import a .CSV file.
      4 additional variables detected.
      Checking variable data type...
       ng1(integer)   ng2(integer)   ng3(integer)   ng4(integer)
      New data set created!!
      It has 24 observations by 24 variables
      including 4 loci(19 alleles) plus 4 additional variables(4 columns)
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      K-fold cross-validation done!!
      3 assignment tests completed!!
      Convert population label to factor. 
      ng1(integer)  ng2(integer)  ng3(integer)  ng4(integer)
      Parallele computing is off. Analyzing data using 1 CPU core...
    
      K-fold cross-validation done!!
      3 assignment tests completed!!
      Results were saved in a 'High_Fst_Locus_Freq.txt' file in the directory.[ FAIL 3 | WARN 0 | SKIP 0 | PASS 39 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_accuracy.R:8:3'): Calculate assignment accuracy for Monte-Carlo results ──
    `plot` has type 'object', not 'list'.
    ── Failure ('test_accuracy.R:18:3'): Calculate assignment accuracy for K-fold results ──
    `plot` has type 'object', not 'list'.
    ── Failure ('test_membership.R:5:3'): Plot membership probability ──────────────
    `plot` has type 'object', not 'list'.
    
    [ FAIL 3 | WARN 0 | SKIP 0 | PASS 39 ]
    Error: Test failures
    Execution halted

Package: autograph
Check: examples
New result: ERROR
  Running examples in ‘autograph-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: map_measure
  > ### Title: Plotting logical marks Plotting numeric measures
  > ### Aliases: map_measure plot.node_measure plot.tie_measure
  > ###   plot.network_measures
  > 
  > ### ** Examples
  > 
  > plot(manynet::node_deg(ison_karateka))
  Error in `patchwork::wrap_plots()`:
  ! Only know how to add <ggplot> and/or <grob> objects
  Backtrace:
      ▆
   1. ├─base::plot(manynet::node_deg(ison_karateka))
   2. └─autograph:::plot.node_measure(manynet::node_deg(ison_karateka))
   3.   └─manynet:::`+.ggplot`(...)
   4.     └─patchwork::wrap_plots(e1, e2, ...)
   5.       └─cli::cli_abort("Only know how to add {.cls ggplot} and/or {.cls grob} objects")
   6.         └─rlang::abort(...)
  Execution halted

Package: autoplotly
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(autoplotly)
    > 
    > test_check("autoplotly")
    [ FAIL 2 | WARN 1 | SKIP 0 | PASS 5 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_all.R:15:3'): autoplotly is composable with additional ggplot2 elements ──
    inherits(p, "plotly") is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test_all.R:16:3'): autoplotly is composable with additional ggplot2 elements ──
    inherits(p$ggplot_obj, "ggplot") is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 2 | WARN 1 | SKIP 0 | PASS 5 ]
    Error: Test failures
    Execution halted

Package: bartMan
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: bayesAB
Check: tests
New result: ERROR
    Running ‘testthat.R’ [22s/22s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(bayesAB)
    > 
    > test_check("bayesAB")
    [ FAIL 1 | WARN 5 | SKIP 0 | PASS 140 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-dists.R:34:3'): Success ──────────────────────────────────────
    plotNormalInvGamma(3, 1, 1, 1)$labels$y not equal to "sig_sq".
    target is NULL, current is character
    
    [ FAIL 1 | WARN 5 | SKIP 0 | PASS 140 ]
    Error: Test failures
    Execution halted

Package: bayesassurance
Check: tests
New result: ERROR
    Running ‘testthat.R’ [127s/128s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(bayesassurance)
    > 
    > test_check("bayesassurance")
    [1] 20 10
    [1] 30 10
    [1] 40 10
    [1] 20 20
    [1] 30 20
    [1] 40 20
    [1] 20 30
    [1] 30 30
    [1] 40 30
    [1] 20 10
    [1] 30 10
    [1] 40 10
    [1] 20 20
    [1] 30 20
    [1] 40 20
    [1] 20 30
    [1] 30 30
    [1] 40 30
    [1] 20 10
    [1] 30 20
    [1] 40 30
    [1] 10 20
    [1] 10 20
    [ FAIL 15 | WARN 92 | SKIP 0 | PASS 125 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-bayes_adcock.R:47:3'): Assurance plot output is a ggplot ─────
    is.ggplot(out$assurance_plot) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Error ('test-bayes_adcock.R:57:3'): Correct labels on x and y axes ──────────
    <notSubsettableError/error/condition>
    Error in `out$assurance_plot$labels`: object of type 'object' is not subsettable
    Backtrace:
        ▆
     1. └─testthat::expect_identical(out$assurance_plot$labels$y, "Assurance") at test-bayes_adcock.R:57:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Failure ('test-bayes_goal_func.R:52:3'): Rate of correct classification plot is a ggplot ──
    is.ggplot(out$rc_plot) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Error ('test-bayes_goal_func.R:63:3'): Correct labels on x and y axes ───────
    <notSubsettableError/error/condition>
    Error in `out$rc_plot$labels`: object of type 'object' is not subsettable
    Backtrace:
        ▆
     1. └─testthat::expect_identical(out$rc_plot$labels$y, "Rate of Correct Classification") at test-bayes_goal_func.R:63:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Failure ('test-bayes_sim.R:57:3'): Assurance plot output is a ggplot ────────
    is.ggplot(out$assurance_plot) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Error ('test-bayes_sim.R:70:3'): Correct labels on x and y axes ─────────────
    <notSubsettableError/error/condition>
    Error in `out$assurance_plot$labels`: object of type 'object' is not subsettable
    Backtrace:
        ▆
     1. └─testthat::expect_identical(out$assurance_plot$labels$y, "Assurance") at test-bayes_sim.R:70:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Failure ('test-bayes_sim_betabinomial.R:53:3'): Assurance plot output is a ggplot ──
    is.ggplot(out$assurance_plot) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Error ('test-bayes_sim_betabinomial.R:65:3'): Correct labels on x and y axes ──
    <notSubsettableError/error/condition>
    Error in `out$assurance_plot$labels`: object of type 'object' is not subsettable
    Backtrace:
        ▆
     1. └─testthat::expect_identical(out$assurance_plot$labels$y, "Assurance") at test-bayes_sim_betabinomial.R:65:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Error ('test-bayes_sim_unknownvar.R:75:3'): Correct labels on x and y axes of assurance plot ──
    <notSubsettableError/error/condition>
    Error in `out$assur_plot$labels`: object of type 'object' is not subsettable
    Backtrace:
        ▆
     1. └─testthat::expect_identical(out$assur_plot$labels$y, "Assurance") at test-bayes_sim_unknownvar.R:75:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Failure ('test-bayesassurance.R:28:3'): Assurance plot output is a ggplot ───
    is.ggplot(out$assurance_plot) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Error ('test-bayesassurance.R:36:3'): Correct labels on x and y axes ────────
    <notSubsettableError/error/condition>
    Error in `out$assurance_plot$labels`: object of type 'object' is not subsettable
    Backtrace:
        ▆
     1. └─testthat::expect_identical(out$assurance_plot$labels$y, "Assurance") at test-bayesassurance.R:36:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Failure ('test-frequentist.R:28:3'): Power plot output is a ggplot ──────────
    is.ggplot(out$pwr_plot) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Error ('test-frequentist.R:36:3'): Correct labels on x and y axes ───────────
    <notSubsettableError/error/condition>
    Error in `out$pwr_plot$labels`: object of type 'object' is not subsettable
    Backtrace:
        ▆
     1. └─testthat::expect_identical(out$pwr_plot$labels$y, "Power") at test-frequentist.R:36:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    ── Failure ('test-pwr_curves.R:99:3'): Plot output is a ggplot ─────────────────
    is.ggplot(out$plot) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Error ('test-pwr_curves.R:114:3'): Correct labels on x and y axes ───────────
    <notSubsettableError/error/condition>
    Error in `out$plot$labels`: object of type 'object' is not subsettable
    Backtrace:
        ▆
     1. └─testthat::expect_identical(out$plot$labels$y, "Power/Assurance") at test-pwr_curves.R:114:3
     2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
     3.     └─rlang::eval_bare(expr, quo_get_env(quo))
    
    [ FAIL 15 | WARN 92 | SKIP 0 | PASS 125 ]
    Error: Test failures
    Execution halted

Package: BayesianReasoning
Check: tests
New result: ERROR
    Running ‘testthat.R’ [37s/37s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(BayesianReasoning)
    > 
    > test_check("BayesianReasoning")
    
     Plot created in: ./FP_10_sens_100_screening_1667_diagnostic_44.png
    
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    
     Plot created in: ./PPV_1_1000_100_0_10_en.png
    
    
     Plot created in: ./NPV_1_1000_100_0_10_en.png
    
    
     Plot created in: ./NPV_1_1000_100_0_10_area_TRUE_en.png
    
    i Label/s outside range, will anchor right
    [ FAIL 8 | WARN 16 | SKIP 4 | PASS 115 ]
    
    ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
    • On CRAN (4): 'test-snapshots.R:9:3', 'test-snapshots.R:22:3',
      'test-snapshots.R:40:7', 'test-snapshots.R:60:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-PPV_diagnostic_vs_screening.R:12:3'): Scale is labelled 'Prevalence' ──
    p$labels$y (`actual`) not identical to "PPV" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('PPV')
    ── Failure ('test-PPV_diagnostic_vs_screening.R:27:3'): Plot is type GeomLine ──
    vapply(...) (`actual`) not identical to "GeomLine" (`expected`).
    
    `names(actual)` is a character vector ('geom_line')
    `names(expected)` is absent
    ── Failure ('test-PPV_heatmap.R:670:3'): PPV Plot ──────────────────────────────
    p$result$labels$fill (`actual`) not identical to "PPV" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('PPV')
    ── Failure ('test-PPV_heatmap.R:748:3'): NPV Plot ──────────────────────────────
    p$result$labels$fill (`actual`) not identical to "NPV" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('NPV')
    ── Failure ('test-PPV_heatmap.R:786:3'): Spanish translation ───────────────────
    vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomPoint", "GeomMarkRect") (`expected`).
    
    `names(actual)` is a character vector ('geom_tile', 'annotate', 'geom_mark_rect')
    `names(expected)` is absent
    ── Failure ('test-PPV_heatmap.R:808:3'): Spanish translation ───────────────────
    vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomPoint", "GeomMarkRect") (`expected`).
    
    `names(actual)` is a character vector ('geom_tile', 'annotate', 'geom_mark_rect')
    `names(expected)` is absent
    ── Failure ('test-PPV_heatmap.R:1062:3'): Plot with line overlay ───────────────
    vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomSegment", "GeomPoint", "GeomMarkRect") (`expected`).
    
    `names(actual)` is a character vector ('geom_tile', 'annotate', 'annotate...3', 'geom_mark_rect')
    `names(expected)` is absent
    ── Failure ('test-PPV_heatmap.R:1097:3'): Plot with line overlay ───────────────
    vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomSegment", "GeomPoint", "GeomMarkRect") (`expected`).
    
    `names(actual)` is a character vector ('geom_tile', 'annotate', 'annotate...3', 'geom_mark_rect')
    `names(expected)` is absent
    
    [ FAIL 8 | WARN 16 | SKIP 4 | PASS 115 ]
    Error: Test failures
    Execution halted

Package: BayesMultiMode
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.

Package: bdsm
Check: tests
New result: ERROR
    Running ‘testthat.R’ [46s/46s]
  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(bdsm)
    > 
    > test_check("bdsm")
    The number of the best models (top) cannot be higher than the total number of models. We set top = R (total number of regressors) and continiue :)
    initial  value -427.743989 
    final  value -717.595537 
    converged
    initial  value -366.799374 
    final  value -784.520619 
    converged
    initial  value -396.225712 
    final  value -785.991786 
    converged
    initial  value -238.285740 
    final  value -854.671535 
    converged
    [ FAIL 10 | WARN 0 | SKIP 6 | PASS 69 ]
    
    ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
    • On Linux (6): 'test-SEM_likelihood.R:13:3', 'test-SEM_likelihood.R:28:3',
      'test-SEM_likelihood.R:44:3', 'test-SEM_likelihood.R:61:3',
      'test-SEM_likelihood.R:77:3', 'test-model_space.R:2:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-coef_hist.R:18:3'): coef_hist creates correct lists with graphs ──
    class(coef_plots[[1]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-coef_hist.R:19:3'): coef_hist creates correct lists with graphs ──
    class(coef_plots[[2]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-coef_hist.R:20:3'): coef_hist creates correct lists with graphs ──
    class(coef_plots[[3]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-coef_hist.R:21:3'): coef_hist creates correct lists with graphs ──
    class(coef_plots[[4]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-model_pmp.R:19:3'): model_pmp creates correct lists with graphs ──
    class(model_graphs[[1]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-model_pmp.R:20:3'): model_pmp creates correct lists with graphs ──
    class(model_graphs[[2]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-model_pmp.R:21:3'): model_pmp creates correct lists with graphs ──
    class(model_graphs[[3]]) (`actual`) not equal to c("gg", "ggplot", "ggarrange") (`expected`).
    
        actual            | expected       
    [1] "ggplot2::ggplot" -                
    [2] "ggplot"          -                
    [3] "ggplot2::gg"     -                
    [4] "S7_object"       -                
    [5] "gg"              | "gg"        [1]
                          - "ggplot"    [2]
    [6] "ggarrange"       | "ggarrange" [3]
    ── Failure ('test-model_sizes.R:19:3'): model_sizes creates correct lists with graphs ──
    class(size_graphs[[1]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-model_sizes.R:20:3'): model_sizes creates correct lists with graphs ──
    class(size_graphs[[2]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-model_sizes.R:21:3'): model_sizes creates correct lists with graphs ──
    class(size_graphs[[3]]) (`actual`) not equal to c("gg", "ggplot", "ggarrange") (`expected`).
    
        actual            | expected       
    [1] "ggplot2::ggplot" -                
    [2] "ggplot"          -                
    [3] "ggplot2::gg"     -                
    [4] "S7_object"       -                
    [5] "gg"              | "gg"        [1]
                          - "ggplot"    [2]
    [6] "ggarrange"       | "ggarrange" [3]
    
    [ FAIL 10 | WARN 0 | SKIP 6 | PASS 69 ]
    Error: Test failures
    Execution halted

Package: BEAMR
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggmosaic’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: BeeBDC
Check: tests
New result: ERROR
    Running ‘testthat.R’ [65s/74s]
  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
    > 
    > requireNamespace("testthat")
    Loading required namespace: testthat
    > requireNamespace("BeeBDC")
    Loading required namespace: BeeBDC
    > 
    > testthat::test_check("BeeBDC")
    Loading required package: BeeBDC
    Loading required namespace: mgsub
    Starting taxonomy report...
    Nomia maneei is an accpeted name with the taxon id number 37446.
     - 'Nomia maneei' has the synonyms: 
    Starting checklist report...
     - Nomia maneei Cockerell, 1910 is reportedly found in: 
    United States
    The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'. 
    These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport.
    Starting taxonomy report...
    Ceratina nanula Cockerell, 1897 is an accpeted name with the taxon id number 12061.
    Nomia maneei is an accpeted name with the taxon id number 37446.
    Bombus hypnorum is an accpeted name with the taxon id number 9667.
     - 'Ceratina nanula Cockerell, 1897' has the synonyms: 
     - 'Nomia maneei' has the synonyms: 
     - 'Bombus hypnorum' has the synonyms: 
    Starting checklist report...
     - Bombus hypnorum (Linnaeus, 1758) is reportedly found in: 
    Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
     - Bombus hypnorum (Linnaeus, 1758) is reportedly found in: 
    Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
     - Bombus hypnorum (Linnaeus, 1758) is reportedly found in: 
    Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
    The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'. 
    These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport.
    Starting taxonomy report...
    Ceratina nanula Cockerell, 1897 is an accpeted name with the taxon id number 12061.
    Nomia maneei is an accpeted name with the taxon id number 37446.
    Bombus hypnorum is an accpeted name with the taxon id number 9667.
     - 'Ceratina nanula Cockerell, 1897' has the synonyms: 
     - 'Nomia maneei' has the synonyms: 
     - 'Bombus hypnorum' has the synonyms: 
    The output will be returned as a list with the elements: 'taxonomyReport' and 'SynonymReport'. 
    These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, or 'output'$failedReport.
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
     - jbd_GBIFissues:
    Flagged 5 
      The .GBIFflags column was added to the database. 
    
     - Formatting taxonomy for matching...
    The names_clean column was not found and will be temporarily copied from scientificName
    
     - Harmonise the occurrence data with unambiguous names...
    
     - Attempting to harmonise the occurrence data with ambiguous names...
     - Formatting merged datasets...
    Removing the names_clean column...
     - We matched valid names to 91 of 100 occurrence records. This leaves a total of 9 unmatched occurrence records.
    
    harmoniseR:
    9
    records were flagged.
    The column, '.invalidName' was added to the database.
    
     - We updated the following columns: scientificName, species, family, subfamily, genus, subgenus, specificEpithet, infraspecificEpithet, and scientificNameAuthorship. The previous scientificName column was converted to verbatimScientificName
     - Completed in 0.88 secs
     - Formatting taxonomy for matching...
    The names_clean column was not found and will be temporarily copied from scientificName
    
     - Harmonise the occurrence data with unambiguous names...
    
     - Attempting to harmonise the occurrence data with ambiguous names...
    checkVerbatim = TRUE. Checking the verbatimScientificName column...
     - Formatting merged datasets...
    Removing the names_clean column...
     - We matched valid names to 93 of 102 occurrence records. This leaves a total of 9 unmatched occurrence records.
    
    harmoniseR:
    9
    records were flagged.
    The column, '.invalidName' was added to the database.
    
     - We updated the following columns: scientificName, species, family, subfamily, genus, subgenus, specificEpithet, infraspecificEpithet, and scientificNameAuthorship. The previous scientificName column was converted to verbatimScientificName
     - Completed in 1.58 secs
     - INITIAL match with occurrenceID only 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
     - Starting iteration 1
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Starting iteration 2
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Starting iteration 3
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Starting iteration 4
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Starting iteration 5
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Starting iteration 6
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Starting iteration 7
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Starting iteration 8
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Starting iteration 9
    Matched 2 of 15 Paige occurrences.
    There are 13 occurrences remaining to match.
    This step has found 0 extra occurrences from the last iteration.
     - Updating Paige datasheet to merge...
     - Updating the final datasheet with new information from Paige...
     - No dates in file name(s). Finding most-recent from file save time...
     - Found the following file(s): 
     /home/hornik/tmp/scratch/RtmppB1YpI/19-Nov-22_USGS_DRO_flat.txt
     - Reading in data file. This should not take too long. 
     There may be some errors upon reading in depending on the state of the data. 
     One might consider reporting errors to Sam Droege to improve the dataset.
    Rows: 7 Columns: 35
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: "$"
    chr  (22): ID., name, sex, DeterminedBy, WhoScanned, COLLECTION.db, ip, coun...
    dbl   (7): gmt, latitude, longitude, accuracy, elevation, position, how1
    lgl   (3): SpeciesNotes, days, note
    dttm  (1): DateEntered
    date  (2): DeterminedWhen, DateScanned
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
     - Formatting the USGS dataset...
     - Formatting the dateTime...
     - Creating samplingProtocol and samplingEffort columns...
     - Creating the fieldNotes and dataSource columns...
     - Renaming and selecting columns...
     - Checking for existing out_file directory...
     - No existing,out_file directory found. Creating directory...
     - Writing occurrence data file...
    Number of rows (records): 7
    Written to file called USGS_formatted_2025-08-19.csv at location /home/hornik/tmp/scratch/RtmppB1YpI/out_file
     - Writing attributes file...
    Written to file called USGS_attribute_files2025-08-19.xml at location /home/hornik/tmp/scratch/RtmppB1YpI/out_file
     - Fin.
    trying URL 'https://figshare.com/ndownloader/files/47092720'
    Download attempt failed...
    Could not read download...
    trying URL 'https://figshare.com/ndownloader/files/47092720'
    Download attempt failed...
    Could not read download...
    [1] "Attempt:  2  of  4"
    trying URL 'https://figshare.com/ndownloader/files/47092720'
    Download attempt failed...
    Could not read download...
    [1] "Attempt:  3  of  4"
    trying URL 'https://figshare.com/ndownloader/files/47092720'
    Download attempt failed...
    Could not read download...
    [1] "Attempt:  4  of  4"
     - Checklist download failed. Please check your internet connection.
    trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969'
    Download attempt failed...
    Could not read download...
    trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969'
    Download attempt failed...
    Could not read download...
    [1] "Attempt:  2  of  4"
    trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969'
    Download attempt failed...
    Could not read download...
    [1] "Attempt:  3  of  4"
    trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969'
    Download attempt failed...
    Could not read download...
    [1] "Attempt:  4  of  4"
     - Taxonomy download failed. Please check your internet connection.
    Loading required namespace: rnaturalearthdata
    Spherical geometry (s2) switched off
     - Extracting continent data from points...
     - Prepare the neighbouring continent dataset...
    although coordinates are longitude/latitude, st_intersects assumes that they
    are planar
     - Compare points with the checklist...
     - Combining data...
     - Finished. 
    We have matched 74 records to their exact continent and 2 to an adjacent continent
    We failed to match 3 occurrences to any 'exact' or 'neighbouring' continent
    There are 21 'NA' occurrences for the .continentOutlier column.
    
    continentOutlieRs:
    Flagged 5 for continent outlier and flagged 2 for in the .sea records.
    Three columns were added to the database:
    1. The '.continentOutlier' column was added which is a filtering column. 
    2. The 'continentMatch' columns indicates exact, neighbour, or noMatch. 
    3. The '.sea' column was added as a filtering column for points in the ocean. The '.sea' column includes the user input buffer in its calculation.
     - Completed in 3.76 secs
    \coordUncerFlagR:
     Flagged 3 geographically uncertain records:
     The column '.uncertaintyThreshold' was added to the database.
    
     - Using default country names and codes from https:en.wikipedia.org/wiki/ISO_3166-1_alpha-2 - static version from July 2022.
     - Extracting country data from points...
     - Prepare the neighbouring country dataset...
    although coordinates are longitude/latitude, st_intersects assumes that they
    are planar
     - Compare points with the checklist...
     - Combining data...
     - Finished. 
    We have matched 72 records to their exact country and 2 to an adjacent country
    We failed to match 3 occurrences to any 'exact' or 'neighbouring' country.
    There are 23 'NA' occurrences for the .countryOutlier column.
    
    countryOutlieRs:
    Flagged 5  for country outlier and flagged  2  for in the .sea records.
    Three columns were added to the database:
     1.  The '.countryOutlier' column was added which is a filtering column. 
     2.  The 'countryMatch' columns indicates exact, neighbour, or noMatch. 
     3. The '.sea' column was added as a filtering column for points in the ocean.  The '.sea' column includes the user input buffer in its calculation.
     - Completed in 3.06 secs
    Loading required namespace: emld
     - Checking for existing out_file directory...
     - Existing out_filedirectory found. Data will be saved here.
     - We have removed empty columns. This is standard, but as an FYI, these columns are: 
     - Writing occurrence, attribute, and EML data file in .rds format...
    Number of records: 5
    Number of attribute sources: 1
    The 0 eml sources are 
    Writing to file called BeeData_2025-08-19.rds at location /home/hornik/tmp/scratch/RtmppB1YpI/out_file...
     - dataSaver. Fin.
     - Checking for existing out_file directory...
     - Existing out_filedirectory found. Data will be saved here.
     - We have removed empty columns. This is standard, but as an FYI, these columns are: 
     - Writing occurrence data file in csv format...
    Number of rows (records): 5
    Writing to file called BeeData_combined_2025-08-19.csv at location /home/hornik/tmp/scratch/RtmppB1YpI/out_file...
     - Writing attribute data file in csv format...
    Number of rows (sources): 1
    Written to file called BeeData_attributes_2025-08-19.csv at location /home/hornik/tmp/scratch/RtmppB1YpI/out_file
     - dataSaver. Fin.
    Rows: 5 Columns: 15
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (10): catalog_number, pollinator_family, pollinator_genus, pollinator_sp...
    dbl  (5): collector_number, day_collected, year_collected, latitude, longitude
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    Rows: 1 Columns: 11
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (11): dataSource, alternateIdentifier, title, pubDate, dateStamp, doi, d...
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
     - Preparing data...
     - Extracting dates from year, month, day columns...
     - Extracting dates from fieldNotes, locationRemarks, and verbatimEventDate columns in unambiguous ymd, dmy, mdy, and my formats...
     - Extracting year from fieldNotes, locationRemarks, and verbatimEventDate columns in ambiguous formats...
     - Formating and combining the new data..
     - Merging all data, nearly there...
     - Finished. 
    We now have -1 more full eventDate cells than in the input data.
    We modified dates in 
    9 occurrences.
     - As it stands, there are 9 complete eventDates and 1 missing dates.
     - There are also 9 complete year occurrences to filter from. This is up from an initial count of 2 At this rate, you will stand to lose 1 occurrences on the basis of missing year - Operation time: 0.234132289886475 secs
     - Preparing data...
     - Extracting dates from year, month, day columns...
     - Extracting dates from fieldNotes, locationRemarks, and verbatimEventDate columns in unambiguous ymd, dmy, mdy, and my formats...
     - Extracting year from fieldNotes, locationRemarks, and verbatimEventDate columns in ambiguous formats...
     - Formating and combining the new data..
     - Merging all data, nearly there...
     - Finished. 
    We now have 8 more full eventDate cells than in the input data.
    We modified dates in 
    18 occurrences.
     - As it stands, there are 18 complete eventDates and 1 missing dates.
     - There are also 19 complete year occurrences to filter from. This is up from an initial count of 6 At this rate, you will stand to lose 0 occurrences on the basis of missing year - Operation time: 0.363626003265381 secs
    Removing rounded coordinates with BeeBDC::jbd_coordinates_precision...
    jbd_coordinates_precision:
    Removed 5 records.
     - Starting the latitude sequence...
     - Starting the longitude sequence...
     - Merging results and adding the .sequential column...
    
    diagonAlley:
    Flagged 17 records
    The .sequential column was added to the database.
    
     - Completed in 0.44 secs
    Loading required namespace: forcats
    Loading required namespace: cowplot
    Loading required namespace: igraph
     - Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
    This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
     - Updating the .summary column to sort by...
     - We will NOT flag the following columns. However, they will remain in the data file.
    .gridSummary, .lonFlag, .latFlag, .uncer_terms, .uncertaintyThreshold, .unLicensed
     - summaryFun:
    Flagged 0 
      The .summary column was added to the database.
     - Working on CustomComparisonsRAW duplicates...
    
    Completed iteration 1 of 1:
     - Identified 2 duplicate records and kept 1 unique records using the column(s): 
    catalogNumber, institutionCode, scientificName
     - Working on CustomComparisons duplicates...
    
    Completed iteration 1 of 4:
     - Identified 0 duplicate records and kept 0 unique records using the column(s): 
    gbifID, scientificName
    
    Completed iteration 2 of 4:
     - Identified 1 duplicate records and kept 1 unique records using the column(s): 
    occurrenceID, scientificName
    
    Completed iteration 3 of 4:
     - Identified 0 duplicate records and kept 0 unique records using the column(s): 
    recordId, scientificName
    
    Completed iteration 4 of 4:
     - Identified 0 duplicate records and kept 0 unique records using the column(s): 
    id, scientificName
     - Working on collectionInfo duplicates...
    
    Completed iteration 1 of 2:
     - Identified 0 duplicate records and kept 0 unique records using the columns: 
    decimalLatitude, decimalLongitude, scientificName, eventDate, recordedBy, and catalogNumber
    
    Completed iteration 2 of 2:
     - Identified 0 duplicate records and kept 0 unique records using the columns: 
    decimalLatitude, decimalLongitude, scientificName, eventDate, recordedBy, and otherCatalogNumbers
     - Clustering duplicate pairs...
    Duplicate pairs clustered. There are 3 duplicates across 2 kept duplicates.
     - Ordering prefixs...
     - Ordering data by 1. dataSource, 2. completeness and 3. .summary column...
     - Find and FIRST duplicate to keep and assign other associated duplicates to that one (i.e., across multiple tests a 'kept duplicate', could otherwise be removed)...
     - Duplicates have been saved in the file and location: /home/hornik/tmp/scratch/RtmppB1YpIduplicateRun_collectionInfo_2025-08-19.csv
     - Across the entire dataset, there are now 3 duplicates from a total of 12 occurrences.
     - Completed in 0.69 secs
     - No dates in file name(s). Finding most-recent from file save time...
     - Found the following file(s): 
     /home/hornik/tmp/scratch/RtmppB1YpI/testData.csv
    \.occurrenceAbsent:
     Flagged 18 absent records:
     One column was added to the database.
    
    No dataSource provided. Filling this column with NAs...
    No license provided. Filling this column with NAs...
    \.unLicensed:
     Flagged 11 records that may NOT be used.
     One column was added to the database.
    
     - We will flag all columns starting with '.'
     - summaryFun:
    Flagged 77 
      The .summary column was added to the database.
    The percentages of species impacted by each flag in your analysis are as follows: 
      .coordinates_empty = 23.46%
      .coordinates_outOfRange = 0%
      .basisOfRecords_notStandard = 1.23%
      .coordinates_country_inconsistent = 1.23%
      .occurrenceAbsent = 8.64%
      .unLicensed = 0%
      .GBIFflags = 0%
      .uncer_terms = 0%
      .rou = 29.63%
      .val = 0%
      .equ = 0%
      .zer = 0%
      .cap = 0%
      .cen = 0%
      .gbf = 0%
      .inst = 0%
      .sequential = 0%
      .lonFlag = 0%
      .latFlag = 2.47%
      .gridSummary = 0%
      .uncertaintyThreshold = 12.35%
      .countryOutlier = 0%
      .sea = 1.23%
      .eventDate_empty = 13.58%
      .year_outOfRange = 13.58%
      .duplicates = 56.79%
     - Great, R has detected some files. These files include:  
     /home/hornik/tmp/scratch/RtmppB1YpI/USGS_attribute_files2023-01-27.csv
    /home/hornik/tmp/scratch/RtmppB1YpI/USGS_formatted_2023-01-27.csv - .csv export version found. Loading this file...
     - Merging occurrence and attribute files.
    Depending on file size, this could take some time...
    
     - Fin.
    Warning message: 
     - No completeness_cols provided. Using default of: c('decimalLatitude',  'decimalLongitude', 'scientificName', and 'eventDate')
     - Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
    This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
     - Starting core loop...
     - we matched 26 records using gbifID.
    This leaves 24 unmatched data in the priorData file
     - we matched 20 records using catalogNumber, institutionCode, dataSource.
    This leaves 4 unmatched data in the priorData file
     - we matched 4 records using occurrenceID, dataSource.
    This leaves 0 unmatched data in the priorData file
     - we matched 0 records using recordId, dataSource.
    This leaves 0 unmatched data in the priorData file
     - we matched 0 records using id.
    This leaves 0 unmatched data in the priorData file
     - we matched 0 records using catalogNumber, institutionCode.
    This leaves 0 unmatched data in the priorData file
     - Combining ids and assigning new ones where needed...
     - We matched a total of 50 database_id numbers. We then assigned new database_id numbers to 49 unmatched occurrences.
    Warning message: 
     - No completeness_cols provided. Using default of: c('decimalLatitude',  'decimalLongitude', 'scientificName', and 'eventDate')
     - Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
    This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
     - Starting core loop...
     - we matched 26 records using gbifID.
    This leaves 24 unmatched data in the priorData file
     - we matched 20 records using catalogNumber, institutionCode, dataSource.
    This leaves 4 unmatched data in the priorData file
     - we matched 4 records using occurrenceID, dataSource.
    This leaves 0 unmatched data in the priorData file
     - we matched 0 records using recordId, dataSource.
    This leaves 0 unmatched data in the priorData file
     - we matched 0 records using id.
    This leaves 0 unmatched data in the priorData file
     - we matched 0 records using catalogNumber, institutionCode.
    This leaves 0 unmatched data in the priorData file
     - Combining ids and assigning new ones where needed...
     - We matched a total of 50 database_id numbers. We then assigned new database_id numbers to 50 unmatched occurrences.
    Loading required namespace: leaflet
    The column .expertOutlier was not found. One will be created with all values = TRUE.
     - Running chunker with:
    stepSize = 50
    chunkStart = 1
    chunkEnd = 50
     - Starting parallel operation. Unlike the serial operation (mc.cores = 1) , a parallel operation will not provide running feedback. Please be patient  as this function may take some time to complete. Each chunk will be run on  a seperate thread so also be aware of RAM usage.
    Loading required package: rnaturalearth
     - Completed in 0.89 secs
     - We have updated the country names of 0 occurrences that previously had no country name assigned.
     - Running chunker with:
    stepSize = 50
    chunkStart = 1
    chunkEnd = 50
     - Starting parallel operation. Unlike the serial operation (mc.cores = 1) , a parallel operation will not provide running feedback. Please be patient  as this function may take some time to complete. Each chunk will be run on  a seperate thread so also be aware of RAM usage.
     - Completed in 1.02 secs
     - We have updated the country names of 0 occurrences that previously had no country name assigned.
     - Running chunker with:
    stepSize = 100
    chunkStart = 1
    chunkEnd = 100
    append = FALSE
     - Starting chunk 1...
    From 1 to 100
    Loading required package: readr
    
    Attaching package: 'readr'
    
    The following objects are masked from 'package:testthat':
    
        edition_get, local_edition
    
    Spherical geometry (s2) switched on
    Correcting latitude and longitude transposed
    
    8 occurrences will be tested
    
    jbd_coordinates_transposed:
    Corrected 3 records.
    One columns were added to the database.
    
     - Finished chunk 1 of 1. Total records examined: 91
     - Completed in 6.46 secs
    Loading required package: cowplot
    Loading required package: ggspatial
    Loading required namespace: bdc
    Check figures in /home/hornik/tmp/scratch/RtmppB1YpI
    Check figures in /home/hornik/tmp/scratch/RtmppB1YpI
    Check figures in /home/hornik/tmp/scratch/RtmppB1YpI
     - Preparing data to plot...
     - Building plot...
    Loading required namespace: openxlsx
    A .csv data type was chosen...
    Rows: 5 Columns: 15
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (10): catalog_number, pollinator_family, pollinator_genus, pollinator_sp...
    dbl  (5): collector_number, day_collected, year_collected, latitude, longitude
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .csv data type was chosen...
    Rows: 4 Columns: 21
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (15): family, subfamily, Tribe, genus, subgenus, Morphospecies, specific...
    dbl  (5): catalogNumber, decimalLatitude, decimalLongitude, coordinateUncert...
    lgl  (1): associatedTaxa
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .csv data type was chosen...
    Rows: 4 Columns: 24
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (20): catalogNumber, Phylum, higherClassification, Order, family, genus,...
    dbl  (2): decimalLatitude, decimalLongitude
    lgl  (2): dateIdentified, county
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .csv data type was chosen...
    Rows: 6 Columns: 41
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr  (30): occurence_lsid, language, basisOfRecord, catalogNumber, scientifi...
    dbl   (4): organismQuantity, decimalLatitude, decimalLongitude, dateIdentified
    lgl   (6): municipality, eventTime, fieldNumber, typeStatus, infraspecificEp...
    dttm  (1): modified
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .csv data type was chosen...
    Rows: 4 Columns: 91
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (27): institutionCode, collectionCode, basisOfRecord, occurrenceID, high...
    dbl (12): id, taxonID, year, month, day, startDayOfYear, cultivationStatus, ...
    lgl (52): ownerInstitutionCode, catalogNumber, otherCatalogNumbers, subgenus...
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .csv data type was chosen...
    Rows: 4 Columns: 48
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr  (34): institutionCode, Collection Code, collection.var, catalogNumber, ...
    dbl  (10): Other Catalog Number, SampleRound, TempStart, TempEnd, WindStart,...
    lgl   (2): sex, subspecies
    time  (2): eventTime, EndTime
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .xlsx data type was chosen...
    A .csv data type was chosen...
    A .csv data type was chosen...
    Rows: 6 Columns: 6
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (2): Collection, Species
    dbl (4): ID_project, Longitude, Latitude, Year
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .csv data type was chosen...
     - We have read in 6 occurrence records from the 'GEOLOCATE HIGH' sheet.
     - We have read in 5 occurrence records from the 'BELS High' sheet.
     - We have kept 6 occurrences from GeoLocate, and 5 records from BELS (11 in total). BELS was given preference over GeoLocate
    A .csv data type was chosen...
    A .xlsx data type was chosen...
    A .xlsx data type was chosen...
    A .csv data type was chosen...
    Rows: 4 Columns: 91
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (32): institutionCode, collectionCode, basisOfRecord, catalogNumber, hig...
    dbl (10): id, taxonID, year, month, day, startDayOfYear, localitySecurity, d...
    lgl (49): ownerInstitutionCode, occurrenceID, otherCatalogNumbers, subgenus,...
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .csv data type was chosen...
    Rows: 5 Columns: 18
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (13): organismName, county, stateProvince, locale, observationDate, coll...
    dbl  (3): individualCount, latitude, longitude
    lgl  (2): determiner, Notes
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .xlsx data type was chosen...
    A .csv data type was chosen...
    Rows: 6 Columns: 25
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (17): eventID, occurrenceID, basisOfRecord, eventDate, Kingdom, Order, F...
    dbl  (5): Morphospecies, individualCount, sampleSizeValue, decimalLatitude, ...
    lgl  (3): Species, adult, sex
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .xlsx data type was chosen...
    A .csv data type was chosen...
    Rows: 6 Columns: 30
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr  (23): basisOfRecord, recordNumber, locationID, family, subfamily, genus...
    dbl   (5): individualCount, decimalLatitude, decimalLongitude, elevationInMe...
    lgl   (1): catalogNumber
    time  (1): eventTime
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .xlsx data type was chosen...
    A .csv data type was chosen...
    Rows: 5 Columns: 36
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (22): CodeBBdatabase_curated, Scientific name corrected, Native.to.Brazi...
    dbl  (8): Day, Month, Year, Latitude_dec.degrees, Longitude_dec.degrees, Spc...
    lgl  (6): Date_precision, NotasLatLong, NotesOnLocality, Spcslink.county, Sp...
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .xlsx data type was chosen...
    A .csv data type was chosen...
    Rows: 3 Columns: 92
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (28): institutionCode, collectionCode, collectionID, basisOfRecord, occu...
    dbl  (8): Catalognumber, taxonID, year, month, day, startDayOfYear, decimalL...
    lgl (56): ownerInstitutionCode, catalogNumber, otherCatalogNumbers, subgenus...
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .csv data type was chosen...
    Rows: 3 Columns: 19
    ── Column specification ────────────────────────────────────────────────────────
    Delimiter: ","
    chr (15): Country, Muninciplaity, Gender, Site, Latitud, Longitude, elevatio...
    lgl  (4): Type, othercatalognumber, AssociatedTaxa, Citation
    
    ℹ Use `spec()` to retrieve the full column specification for this data.
    ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
    A .xlsx data type was chosen...
    A .xlsx data type was chosen...
     - We will flag all columns starting with '.'
     - summaryFun:
    Flagged 30 
      The .summary column was added to the database.
    Spherical geometry (s2) switched off
     - Extracting country data from points...
    although coordinates are longitude/latitude, st_intersects assumes that they
    are planar
    although coordinates are longitude/latitude, st_intersects assumes that they
    are planar
    Extraction complete.
     - Buffering naturalearth map by pointBuffer...
    dist is assumed to be in decimal degrees (arc_degrees).
    although coordinates are longitude/latitude, st_intersects assumes that they
    are planar
    although coordinates are longitude/latitude, st_intersects assumes that they
    are planar
     - Downloading taxonomy...
     - taxadb save the taxonomy to: /home/hornik/tmp/scratch/check-CRAN-incoming-hornik/data/R/taxadb
    Removing previous flags generated with this function
     - 0 duplicates found in the data.
     - Cleaning complete! From an initial dataset of  196  names, there  remain  196  names. 
      - We removed: 
     0  source1 accepted names, 
     0  source2 'accepted' names, 
    
    0 source2 synonyms internally duplicated,
    0 source2 synonyms duplicated with the source1 list,
    0 subsequent duplicates after merging,
     - We flagged:
    0 ambiguous validName, 
    0 ambiguous canonical_withFlags names, 
    4 ambiguous canonical names, 
    0 NON-ambiguous, but duplicated, canonical_withFlags names, 
    4 NON-ambiguous, but duplicated, canonical names, 
     - We removed: 
    0 ambiguous synonyms associated with accepted names.
     - We re-assigned:
    0 duplicated [non-duplicate] ids
    [ FAIL 8 | WARN 5 | SKIP 0 | PASS 234 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-dupePlotR.R:36:3'): dupePlotR expected class ─────────────────
    `testOut` has type 'object', not 'list'.
    ── Failure ('test-dupePlotR.R:39:3'): dupePlotR expected class ─────────────────
    attributes(testOut)$class (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-jbd_create_figures.R:24:3'): jbd_create_figures expected class ──
    figuresP[[1]] has type 'object', not 'list'.
    ── Failure ('test-jbd_create_figures.R:46:3'): jbd_create_figures expected class ──
    figuresS[[1]] has type 'object', not 'list'.
    ── Failure ('test-jbd_create_figures.R:67:3'): jbd_create_figures expected class ──
    figuresT[[1]] has type 'object', not 'list'.
    ── Failure ('test-plotFlagSummary.R:31:3'): plotFlagSummary expected class ─────
    `testOut` has type 'object', not 'list'.
    ── Failure ('test-plotFlagSummary.R:34:3'): plotFlagSummary expected class ─────
    attributes(testOut)$class (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-summaryMaps.R:23:3'): summaryMaps expected class ─────────────
    `testMap` has type 'object', not 'list'.
    
    [ FAIL 8 | WARN 5 | SKIP 0 | PASS 234 ]
    Error: Test failures
    Execution halted

Package: benchr
Check: tests
New result: ERROR
    Running ‘tinytest.R’ [4s/5s]
  Running the tests in ‘tests/tinytest.R’ failed.
  Complete output:
    > if (requireNamespace("tinytest", quietly = TRUE)) {
    +   tinytest::test_package("benchr")
    + }
    
    test-benchmark.R..............    0 tests    0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-benchmark.R..............    0 tests    
    test-benchmark.R..............    1 tests OK 
    test-benchmark.R..............    2 tests OK 
    test-benchmark.R..............    3 tests OK 
    test-benchmark.R..............    4 tests OK 
    test-benchmark.R..............    5 tests OK 
    test-benchmark.R..............    6 tests OK 
    test-benchmark.R..............    7 tests OK 
    test-benchmark.R..............    8 tests OK 
    test-benchmark.R..............    9 tests OK 
    test-benchmark.R..............   10 tests OK 
    test-benchmark.R..............   11 tests OK 
    test-benchmark.R..............   12 tests OK 
    test-benchmark.R..............   13 tests OK 
    test-benchmark.R..............   14 tests OK 
    test-benchmark.R..............   15 tests OK 
    test-benchmark.R..............   16 tests OK 
    test-benchmark.R..............   17 tests OK 
    test-benchmark.R..............   18 tests OK 
    test-benchmark.R..............   19 tests OK 
    test-benchmark.R..............   20 tests OK 
    test-benchmark.R..............   21 tests OK 0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-benchmark.R..............   21 tests OK 
    test-benchmark.R..............   22 tests OK 
    test-benchmark.R..............   23 tests OK 0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-benchmark.R..............   23 tests OK 
    test-benchmark.R..............   24 tests OK 
    test-benchmark.R..............   25 tests OK 0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-benchmark.R..............   25 tests OK 
    test-benchmark.R..............   26 tests OK 
    test-benchmark.R..............   27 tests OK 0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-benchmark.R..............   27 tests OK 
    test-benchmark.R..............   28 tests OK 
    test-benchmark.R..............   29 tests OK 
    test-benchmark.R..............   30 tests OK 0.5s
    
    test-dots.R...................    0 tests    
    test-dots.R...................    1 tests OK 
    test-dots.R...................    2 tests OK 
    test-dots.R...................    3 tests OK 
    test-dots.R...................    4 tests OK 
    test-dots.R...................    5 tests OK 
    test-dots.R...................    6 tests OK 
    test-dots.R...................    7 tests OK 
    test-dots.R...................    8 tests OK 
    test-dots.R...................    9 tests OK 
    test-dots.R...................   10 tests OK 
    test-dots.R...................   11 tests OK 
    test-dots.R...................   12 tests OK 8ms
    
    test-format.R.................    0 tests    0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-format.R.................    0 tests    
    test-format.R.................    0 tests    
    test-format.R.................    0 tests    
    test-format.R.................    1 tests OK 
    test-format.R.................    2 tests OK 
    test-format.R.................    3 tests OK 73ms
    
    test-mean.R...................    0 tests    0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-mean.R...................    0 tests    
    test-mean.R...................    0 tests    
    test-mean.R...................    1 tests OK 
    test-mean.R...................    2 tests OK 
    test-mean.R...................    3 tests OK 
    test-mean.R...................    4 tests OK 
    test-mean.R...................    5 tests OK 
    test-mean.R...................    6 tests OK 
    test-mean.R...................    7 tests OK 
    test-mean.R...................    8 tests OK 
    test-mean.R...................    9 tests OK 
    test-mean.R...................   10 tests OK 0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-mean.R...................   11 tests OK 
    test-mean.R...................   12 tests OK 
    test-mean.R...................   12 tests OK 
    test-mean.R...................   13 tests OK 
    test-mean.R...................   13 tests OK 
    test-mean.R...................   14 tests OK 
    test-mean.R...................   14 tests OK 
    test-mean.R...................   15 tests OK 
    test-mean.R...................   16 tests OK 
    test-mean.R...................   16 tests OK 
    test-mean.R...................   17 tests OK 
    test-mean.R...................   18 tests OK 0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-mean.R...................   18 tests OK 
    test-mean.R...................   19 tests OK 
    test-mean.R...................   20 tests OK 
    test-mean.R...................   21 tests OK 
    test-mean.R...................   22 tests OK 0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-mean.R...................   22 tests OK 
    test-mean.R...................   23 tests OK 
    test-mean.R...................   24 tests OK 0.4s
    
    test-order.R..................    0 tests    
    test-order.R..................    0 tests    
    test-order.R..................    0 tests    
    test-order.R..................    0 tests    
    test-order.R..................    0 tests    
    test-order.R..................    0 tests    
    test-order.R..................    0 tests    
    test-order.R..................    0 tests    
    test-order.R..................    0 tests    
    test-order.R..................    1 tests OK 
    test-order.R..................    2 tests OK 
    test-order.R..................    3 tests OK 
    test-order.R..................    4 tests OK 
    test-order.R..................    5 tests OK 
    test-order.R..................    6 tests OK 
    test-order.R..................    7 tests OK 
    test-order.R..................    8 tests OK 
    test-order.R..................    9 tests OK 
    test-order.R..................   10 tests OK 
    test-order.R..................   11 tests OK 6ms
    
    test-plot.R...................    0 tests    
    test-plot.R...................    0 tests    
    test-plot.R...................    0 tests    0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-plot.R...................    0 tests    
    test-plot.R...................    0 tests    
    test-plot.R...................    1 tests 1 fails 
    test-plot.R...................    2 tests 1 fails 
    test-plot.R...................    3 tests 2 fails 
    test-plot.R...................    4 tests 2 fails 
    test-plot.R...................    5 tests 2 fails 
    test-plot.R...................    5 tests 2 fails 
    test-plot.R...................    6 tests 2 fails 
    test-plot.R...................    7 tests 2 fails 
    test-plot.R...................    7 tests 2 fails 
    test-plot.R...................    8 tests 3 fails 
    test-plot.R...................    9 tests 3 fails 
    test-plot.R...................   10 tests 4 fails 
    test-plot.R...................   11 tests 4 fails 
    test-plot.R...................   12 tests 4 fails 
    test-plot.R...................   12 tests 4 fails 
    test-plot.R...................   13 tests 4 fails 
    test-plot.R...................   14 tests 4 fails 
    test-plot.R...................   14 tests 4 fails 
    test-plot.R...................   15 tests 5 fails 
    test-plot.R...................   16 tests 5 fails 
    test-plot.R...................   17 tests 6 fails 
    test-plot.R...................   18 tests 6 fails 
    test-plot.R...................   19 tests 6 fails 
    test-plot.R...................   19 tests 6 fails 
    test-plot.R...................   20 tests 6 fails 
    test-plot.R...................   21 tests 6 fails 
    test-plot.R...................   21 tests 6 fails 
    test-plot.R...................   22 tests 7 fails 
    test-plot.R...................   23 tests 7 fails 
    test-plot.R...................   24 tests 7 fails 
    test-plot.R...................   25 tests 8 fails 
    test-plot.R...................   26 tests 8 fails 
    test-plot.R...................   27 tests 8 fails 
    test-plot.R...................   28 tests 8 fails 
    test-plot.R...................   28 tests 8 fails 
    test-plot.R...................   29 tests 8 fails 
    test-plot.R...................   30 tests 8 fails 
    test-plot.R...................   30 tests 8 fails 
    test-plot.R...................   31 tests 9 fails 
    test-plot.R...................   32 tests 9 fails 
    test-plot.R...................   33 tests 9 fails 
    test-plot.R...................   34 tests 10 fails 
    test-plot.R...................   35 tests 10 fails 
    test-plot.R...................   36 tests 10 fails 
    test-plot.R...................   37 tests 10 fails 
    test-plot.R...................   37 tests 10 fails 
    test-plot.R...................   38 tests 10 fails 
    test-plot.R...................   39 tests 10 fails 1.9s
    
    test-print.R..................    0 tests    0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-print.R..................    0 tests    
    test-print.R..................    0 tests    
    test-print.R..................    0 tests    
    test-print.R..................    0 tests    Benchmark summary:
    Time units : nanoseconds 
      expr n.eval min lw.qu median mean up.qu  max total relative
     1 + 1    100 136   212    266  294   335 2260 29400     1.17
       One    100 161   209    228  262   282  503 26200     1.00
    
    test-print.R..................    1 tests OK Time units : nanoseconds 
      expr n.eval min lw.qu median mean up.qu  max total relative
     1 + 1    100 136   212    266  294   335 2260 29400     1.17
       One    100 161   209    228  262   282  503 26200     1.00
    
    test-print.R..................    2 tests OK Time units : nanoseconds 
      expr n.eval mean trimmed lw.ci up.ci relative
     1 + 1    100  294     272   136  2260     1.12
       One    100  262     256   161   503     1.00
    
    test-print.R..................    3 tests OK 
    test-print.R..................    4 tests OK 
    test-print.R..................    5 tests OK 
    test-print.R..................    6 tests OK 
    test-print.R..................    7 tests OK 
    test-print.R..................    8 tests OK 
    test-print.R..................    9 tests OK 
    test-print.R..................   10 tests OK 
    test-print.R..................   11 tests OK 
    test-print.R..................   12 tests OK 
    test-print.R..................   13 tests OK 
    test-print.R..................   14 tests OK 
    test-print.R..................   15 tests OK 
    test-print.R..................   16 tests OK 
    test-print.R..................   17 tests OK 
    test-print.R..................   18 tests OK 
    test-print.R..................   19 tests OK 
    test-print.R..................   20 tests OK 
    test-print.R..................   21 tests OK 
    test-print.R..................   22 tests OK 
    test-print.R..................   23 tests OK 
    test-print.R..................   24 tests OK 
    test-print.R..................   25 tests OK 0.2s
    
    test-summary.R................    0 tests    0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-summary.R................    0 tests    
    test-summary.R................    0 tests    
    test-summary.R................    1 tests OK 
    test-summary.R................    2 tests OK 
    test-summary.R................    3 tests OK 
    test-summary.R................    4 tests OK 
    test-summary.R................    5 tests OK 
    test-summary.R................    6 tests OK 
    test-summary.R................    6 tests OK 
    test-summary.R................    7 tests OK 
    test-summary.R................    8 tests OK 
    test-summary.R................    9 tests OK 
    test-summary.R................   10 tests OK 
    test-summary.R................   11 tests OK 
    test-summary.R................   12 tests OK 
    test-summary.R................   13 tests OK 
    test-summary.R................   14 tests OK 
    test-summary.R................   15 tests OK 
    test-summary.R................   16 tests OK 
    test-summary.R................   17 tests OK 0%   10   20   30   40   50   60   70   80   90   100%
    [----|----|----|----|----|----|----|----|----|----|
    **************************************************|
    
    test-summary.R................   18 tests OK 
    test-summary.R................   19 tests OK 
    test-summary.R................   19 tests OK 
    test-summary.R................   20 tests OK 
    test-summary.R................   20 tests OK 
    test-summary.R................   21 tests OK 
    test-summary.R................   22 tests OK 0.3s
    
    test-timer.R..................    0 tests    
    test-timer.R..................    0 tests    
    test-timer.R..................    0 tests    
    test-timer.R..................    1 tests OK 
    test-timer.R..................    2 tests OK 
    test-timer.R..................    3 tests OK 
    test-timer.R..................    4 tests OK 
    test-timer.R..................    5 tests OK 
    test-timer.R..................    6 tests OK 
    test-timer.R..................   10 tests OK 0.7s
    ----- FAILED[data]: test-plot.R<9--9>
     call| expect_equal(class(bp), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[attr]: test-plot.R<11--11>
     call| expect_equal(bp$labels, list(x = "expr", y = "time"))
     diff| Attributes: < names for current but not for target >
     diff| Attributes: < Length mismatch: comparison on first 0 components >
    ----- FAILED[data]: test-plot.R<21--21>
     call| expect_equal(class(bph), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[attr]: test-plot.R<23--23>
     call| expect_equal(bph$labels, list(x = "expr", y = "time"))
     diff| Attributes: < names for current but not for target >
     diff| Attributes: < Length mismatch: comparison on first 0 components >
    ----- FAILED[data]: test-plot.R<33--33>
     call| expect_equal(class(bpv), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[attr]: test-plot.R<35--35>
     call| expect_equal(bpv$labels, list(x = "expr", y = "time"))
     diff| Attributes: < names for current but not for target >
     diff| Attributes: < Length mismatch: comparison on first 0 components >
    ----- FAILED[data]: test-plot.R<45--45>
     call| expect_equal(class(pp), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[attr]: test-plot.R<48--48>
     call| expect_equal(pp$labels, list(x = "replications", y = "time", 
     call| -->    colour = NULL))
     diff| Attributes: < names for current but not for target >
     diff| Attributes: < Length mismatch: comparison on first 0 components >
    ----- FAILED[data]: test-plot.R<59--59>
     call| expect_equal(class(pp2), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[attr]: test-plot.R<62--62>
     call| expect_equal(pp2$labels, list(x = "replications", y = "time", 
     call| -->    colour = NULL))
     diff| Attributes: < names for current but not for target >
     diff| Attributes: < Length mismatch: comparison on first 0 components >
    Error: 10 out of 176 tests failed
    Execution halted

Package: biclustermd
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/4s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(biclustermd)
    Loading required package: ggplot2
    Loading required package: tidyr
    
    Attaching package: 'tidyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    > 
    > test_check("biclustermd")
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 66 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-autoplot_biclustermd.R:6:3'): autoplot_biclustermd() correctly plots cluster lines ──
    ap$data[[3]]$xintercept[-1] not equal to cumsum(colSums(sbc$P)) + 0.5.
    Classes differ: 'mapped_discrete'/'numeric' is not 'numeric'
    ── Failure ('test-autoplot_biclustermd.R:7:3'): autoplot_biclustermd() correctly plots cluster lines ──
    ap$data[[4]]$yintercept[-1] not equal to cumsum(colSums(sbc$Q)) + 0.5.
    Classes differ: 'mapped_discrete'/'numeric' is not 'numeric'
    
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 66 ]
    Error: Test failures
    Execution halted

Package: biometryassist
Check: tests
New result: ERROR
    Running ‘testthat.R’ [147s/89s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(biometryassist)
    > 
    > test_check("biometryassist")
    Starting 2 test processes
    [ FAIL 1 | WARN 0 | SKIP 156 | PASS 311 ]
    
    ══ Skipped tests (156) ═════════════════════════════════════════════════════════
    • .check_package_available("asreml") is not TRUE (12): 'test-logltest.R:4:5',
      'test-logltest.R:26:5', 'test-logltest.R:34:5', 'test-logltest.R:47:5',
      'test-logltest.R:59:5', 'test-logltest.R:75:5', 'test-logltest.R:92:5',
      'test-logltest.R:98:5', 'test-mct.R:111:5', 'test-mct.R:162:5',
      'test-mct.R:217:5', 'test-mct.R:225:5'
    • On CRAN (139): 'test-des.R:8:5', 'test-des.R:21:5', 'test-all-w2.r:4:5',
      'test-all-w2.r:19:5', 'test-all-w2.r:33:5', 'test-all-w2.r:47:5',
      'test-all-w2.r:61:5', 'test-all-w2.r:78:5', 'test-all-w2.r:96:5',
      'test-all-w2.r:116:5', 'test-all-w2.r:143:5', 'test-all-w2.r:174:5',
      'test-all-w2.r:190:5', 'test-all-w2.r:205:5', 'test-all-w2.r:219:5',
      'test-all-w2.r:230:5', 'test-all-w2.r:244:5', 'test-all-w2.r:258:5',
      'test-all-w2.r:274:5', 'test-all-w2.r:287:5', 'test-all-w2.r:305:5',
      'test-all-w2.r:323:5', 'test-all-w2.r:345:5', 'test-all-w2.r:364:5',
      'test-all-w2.r:395:5', 'test-all-w2.r:429:5', 'test-heatmap.R:26:5',
      'test-heatmap.R:38:5', 'test-heatmap.R:43:5', 'test-heatmap.R:48:5',
      'test-heatmap.R:53:5', 'test-heatmap.R:60:5', 'test-heatmap.R:67:5',
      'test-mct.R:6:5', 'test-mct.R:49:5', 'test-mct.R:68:5', 'test-mct.R:80:5',
      'test-mct.R:101:5', 'test-mct.R:146:5', 'test-mct.R:155:5',
      'test-mct.R:252:5', 'test-mct.R:268:5', 'test-mct.R:300:5',
      'test-mct.R:313:5', 'test-mct.R:334:5', 'test-design.R:9:5',
      'test-design.R:21:5', 'test-design.R:34:5', 'test-design.R:45:5',
      'test-design.R:56:5', 'test-design.R:70:5', 'test-design.R:83:5',
      'test-design.R:95:5', 'test-design.R:106:5', 'test-design.R:118:5',
      'test-design.R:130:5', 'test-design.R:155:5', 'test-design.R:166:5',
      'test-design.R:176:5', 'test-design.R:184:5', 'test-design.R:196:5',
      'test-design.R:209:5', 'test-design.R:222:5', 'test-design.R:233:5',
      'test-design.R:244:5', 'test-design.R:276:5', 'test-design.R:379:5',
      'test-design.R:481:5', 'test-design.R:500:5', 'test-design.R:510:5',
      'test-design.R:518:5', 'test-design.R:552:5', 'test-design.R:558:5',
      'test-design.R:564:5', 'test-design.R:570:5', 'test-design.R:584:5',
      'test-design.R:601:5', 'test-design.R:616:5', 'test-design.R:631:5',
      'test-design.R:646:5', 'test-design.R:661:5', 'test-design.R:675:5',
      'test-design.R:703:5', 'test-design.R:716:5', 'test-design.R:760:5',
      'test-design.R:789:5', 'test-design.R:858:5', 'test-design.R:870:5',
      'test-summary_graph.R:8:5', 'test-summary_graph.R:14:5',
      'test-summary_graph.R:20:5', 'test-use_template.R:9:3',
      'test-use_template.R:18:3', 'test-use_template.R:27:3',
      'test-use_template.R:38:3', 'test-use_template.R:49:3',
      'test-use_template.R:59:3', 'test-use_template.R:75:3',
      'test-use_template.R:97:3', 'test-use_template.R:116:3',
      'test-utility_functions.R:8:5', 'test-variogram.r:21:5',
      'test-variogram.r:51:5', 'test-variogram.r:69:5',
      'test-zzz_install_asreml.R:20:5', 'test-zzz_install_asreml.R:46:5',
      'test-zzz_install_asreml.R:63:5', 'test-zzz_install_asreml.R:128:5',
      'test-zzz_install_asreml.R:143:5', 'test-zzz_install_asreml.R:224:5',
      'test-zzz_install_asreml.R:233:5', 'test-zzz_install_asreml.R:245:5',
      'test-zzz_install_asreml.R:257:5', 'test-zzz_install_asreml.R:285:5',
      'test-zzz_install_asreml.R:299:5', 'test-zzz_install_asreml.R:309:5',
      'test-zzz_install_asreml.R:338:5', 'test-zzz_install_asreml.R:347:5',
      'test-zzz_install_asreml.R:360:5', 'test-zzz_install_asreml.R:369:5',
      'test-zzz_install_asreml.R:394:5', 'test-zzz_install_asreml.R:414:5',
      'test-zzz_install_asreml.R:442:5', 'test-zzz_install_asreml.R:468:5',
      'test-zzz_install_asreml.R:506:5', 'test-zzz_install_asreml.R:545:5',
      'test-zzz_install_asreml.R:622:5', 'test-zzz_install_asreml.R:656:5',
      'test-zzz_install_asreml.R:682:5', 'test-resplot.R:6:5',
      'test-resplot.R:13:5', 'test-resplot.R:25:5', 'test-resplot.R:29:5',
      'test-resplot.R:70:5', 'test-resplot.R:92:5', 'test-resplot.R:117:5',
      'test-resplot.R:131:5', 'test-resplot.R:156:5', 'test-resplot.R:173:5'
    • On Linux (2): 'test-zzz_install_asreml.R:15:5', 'test-resplot.R:82:5'
    • {ARTool} is not installed (1): 'test-resplot.R:98:5'
    • {lme4} is not installed (2): 'test-mct.R:232:5', 'test-resplot.R:52:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-mct.R:86:5'): Testing asreml predictions ───────────────────────
    Error in `.requirePackage(package)`: unable to load required package 'Matrix'
    Backtrace:
         ▆
      1. ├─testthat::expect_warning(...) at test-mct.R:86:5
      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. └─biometryassist::multiple_comparisons(...)
      8.   └─biometryassist:::calculate_differences(pp, sed, ndf, sig)
      9.     └─1/sqrt(2) * stats::qtukey((1 - sig), nrow(pp), ndf) * sed
     10.       └─methods (local) `<fn>`(`<list>`, `<S4: standardGeneric>`, `<env>`)
     11.         └─methods:::.findInheritedMethods(classes, fdef, mtable)
     12.           └─methods::getClass(classes[[i]], where = where, .Force = TRUE)
     13.             └─methods::getClassDef(Class, where)
     14.               └─methods:::.requirePackage(package)
    
    [ FAIL 1 | WARN 0 | SKIP 156 | PASS 311 ]
    Deleting unused snapshots:
    • all-w2/example1autoplot.svg
    • all-w2/example1resplot.svg
    • all-w2/example2autoplot.svg
    • all-w2/example2resplot.svg
    • all-w2/example3autoplot.svg
    • all-w2/example3lmmautoplot.svg
    • all-w2/example3lmmresplot.svg
    • all-w2/example3resplot.svg
    • all-w2/example4autoplot.svg
    • all-w2/example4lmmautoplot.svg
    • all-w2/example4lmmresplot.svg
    • all-w2/example4resplot.svg
    • all-w2/example5lmmautoplot1.svg
    • all-w2/example5lmmautoplot2.svg
    • all-w2/example5lmmresplot.svg
    • all-w2/example6lmmautoplot2.svg
    • all-w2/example6lmmresplot.svg
    • all-w2/example6variogram.svg
    • all-w2/example7lmmautoplot.svg
    • all-w2/example7lmmresplot.svg
    • all-w2/example7variogram.svg
    • all-w2/exercise10autoplot.svg
    • all-w2/exercise10resplot.svg
    • all-w2/exercise11autoplot1.svg
    • all-w2/exercise11autoplot2.svg
    • all-w2/exercise11resplot.svg
    • all-w2/exercise12autoplot.svg
    • all-w2/exercise12resplot.svg
    • all-w2/exercise13autoplot1.svg
    • all-w2/exercise13autoplot2.svg
    • all-w2/exercise13resplot.svg
    • all-w2/exercise13variogram.svg
    • all-w2/exercise14autoplot.svg
    • all-w2/exercise14resplot.svg
    • all-w2/exercise14variogram.svg
    • all-w2/exercise15autoplot1.svg
    • all-w2/exercise15autoplot2.svg
    • all-w2/exercise15autoplot3.svg
    • all-w2/exercise15resplot.svg
    • all-w2/exercise15variogram.svg
    • all-w2/exercise1autoplot.svg
    • all-w2/exercise1resplot.svg
    • all-w2/exercise2autoplot.svg
    • all-w2/exercise2resplot.svg
    • all-w2/exercise3autoplot.svg
    • all-w2/exercise3resplot.svg
    • all-w2/exercise4resplot.svg
    • all-w2/exercise5autoplot.svg
    • all-w2/exercise5resplot.svg
    • all-w2/exercise6autoplot.svg
    • all-w2/exercise6resplot.svg
    • all-w2/exercise7autoplot.svg
    • all-w2/exercise7resplot.svg
    • all-w2/exercise8resplot.svg
    • all-w2/exercise9autoplot.svg
    • all-w2/exercise9resplot.svg
    • des/crd-without-trt.svg
    • des/rcbd-without-trt.svg
    • design/3-way-factorial-with-names.svg
    • design/3-way-factorial.svg
    • design/3-way-rcbd-factorial-with-names.svg
    • design/column-buffers-rcbd.svg
    • design/column-buffers.svg
    • design/crd-color-blind-option1.svg
    • design/crd-color-blind-option2.svg
    • design/crd-color-blind-option3.svg
    • design/crd-color-blind-option4.svg
    • design/crd-color-blind-option5.svg
    • design/crd-colour-blind-option2.svg
    • design/crd-colour-blind-option3.svg
    • design/crd-colour-blind-option4.svg
    • design/crd-colour-blind-option5.svg
    • design/crd-colour-blind.svg
    • design/crd-paired-palette.svg
    • design/crd-plot-produced.svg
    • design/crd-set3-palette.svg
    • design/double-column-buffers-rcbd.svg
    • design/double-column-buffers.svg
    • design/double-row-buffers-rcbd.svg
    • design/double-row-buffers.svg
    • design/edge-buffers-rcbd.svg
    • design/edge-buffers.svg
    • design/factorial-crd-plot-no-space-sep.svg
    • design/factorial-crd-with-names.svg
    • design/factorial-lsd-plot-with-sep.svg
    • design/factorial-rcbd-plot-produced.svg
    • design/lsd-plot-produced.svg
    • design/nested-lsd.svg
    • design/nse-of-column-names-with-blocks.svg
    • design/plot-output.svg
    • design/quoted-column-names-with-blocks.svg
    • design/rcbd-color-blind-option1.svg
    • design/rcbd-colour-blind-cividis.svg
    • design/rcbd-colour-blind-inferno.svg
    • design/rcbd-colour-blind-magma.svg
    • design/rcbd-colour-blind-option1.svg
    • design/rcbd-colour-blind-plasma.svg
    • design/rcbd-colour-blind-viridis.svg
    • design/rcbd-colour-blind.svg
    • design/rcbd-paired-palette.svg
    • design/rcbd-plot-produced.svg
    • design/rcbd-rdbu-palette.svg
    • design/rcbd-set3-palette.svg
    • design/split-plot-produced.svg
    • design/split-plot-with-names.svg
    • design/split-plot-with-vector-names.svg
    • heatmap/heatmap-of-interpolated-grouped-data.svg
    • heatmap/heatmap-with-free-y.svg
    • heatmap/heatmap-with-one-row.svg
    • heatmap/heatmap-with-red-green-palette.svg
    • mct/3-way-interaction-internal.svg
    • mct/3-way-interaction.svg
    • mct/aov-aliased-output.svg
    • mct/asreml-predictions.svg
    • mct/axis-and-label-rotation.svg
    • mct/axis-rotation.svg
    • mct/interactions-work.svg
    • mct/lme4-output.svg
    • mct/mct-descending-output.svg
    • mct/mct-inverse-output.svg
    • mct/mct-logit-output.svg
    • mct/mct-output-2se.svg
    • mct/mct-power-output.svg
    • mct/mct-sqrt-output.svg
    • mct/rotation-and-axis-rotation.svg
    • mct/rotation-and-label-rotation.svg
    • mct/rotation-with-hjust-and-vjust.svg
    • resplot/artool-resplot-with-call.svg
    • resplot/artool-resplot.svg
    • resplot/large-data-shapiro.svg
    • resplot/onepage-cols-2.svg
    • resplot/onepage-off-2.svg
    • resplot/onepage-off-3.svg
    • resplot/onepage-on-page-1.svg
    • resplot/onepage-on-page-2.svg
    • resplot/onepage-on.svg
    • resplot/resplot-for-asreml-pt-1.svg
    • resplot/resplot-for-asreml-pt-2.svg
    • resplot/resplot-for-asreml-pt-3.svg
    • resplot/resplot-for-asreml-single.svg
    • resplot/resplot-for-lme4.svg
    • resplot/resplot-for-sommer-mmer.svg
    • resplot/resplot-for-sommer-mmes.svg
    • resplot/resplot-onepage-true.svg
    • resplot/resplot-with-smaller-call.svg
    Error: Test failures
    Execution halted

Package: BiVariAn
Check: examples
New result: ERROR
  Running examples in ‘BiVariAn-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: auto_bar_categ
  > ### Title: Automatic generation of barplot with percentages
  > ### Aliases: auto_bar_categ
  > 
  > ### ** Examples
  > 
  > data<-data.frame(categ = rep(letters[1:2], 10),
  + var1 = rep(LETTERS[4:5], 10),
  + var2 = rep(LETTERS[6:7], 10),
  + var3 = rep(LETTERS[8:9], 10),
  + var4 = rep(LETTERS[10:11], 10))
  > 
  > data$categ <- as.factor(data$categ)
  > data$var1 <- as.factor(data$var1)
  > data$var2 <- as.factor(data$var2)
  > data$var3 <- as.factor(data$var3)
  > data$var4 <- as.factor(data$var4)
  > 
  > barplot_list<-auto_bar_categ(data = data, groupvar = "categ", lang_labs = "EN")
  Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
  ℹ Please use the `linewidth` argument instead.
  ℹ The deprecated feature was likely used in the ggprism package.
    Please report the issue at <https://github.com/csdaw/ggprism/issues>.
  Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
  ℹ Please use the `linewidth` argument instead.
  ℹ The deprecated feature was likely used in the ggprism package.
    Please report the issue at <https://github.com/csdaw/ggprism/issues>.
  Error in `parent %+replace% t`:
  ! `%+replace%` requires two theme objects
  Backtrace:
      ▆
   1. └─BiVariAn::auto_bar_categ(data = data, groupvar = "categ", lang_labs = "EN")
   2.   └─BiVariAn (local) theme_func()
   3.     ├─... %+replace% ...
   4.     │ └─ggplot2::is_theme(e1)
   5.     │   └─S7::S7_inherits(x, class_theme)
   6.     └─ggprism::theme_prism(...)
   7.       └─parent %+replace% t
   8.         └─cli::cli_abort("{.code %+replace%} requires two theme objects")
   9.           └─rlang::abort(...)
  Execution halted

Package: BiVariAn
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [12s/13s]
  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(BiVariAn)
    > 
    > test_check("BiVariAn")
    [ FAIL 8 | WARN 2 | SKIP 7 | PASS 100 ]
    
    ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
    • On CRAN (7): 'test-auto_shapiro_raw.R:64:3', 'test-continuous_2g.R:30:3',
      'test-continuous_2g.R:87:3', 'test-continuous_2g_pair.R:55:3',
      'test-dichotomous_2k_2sid.R:19:3', 'test-ss_multreg.R:2:3',
      'test-step_bw_firth.R:5:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-auto_bar_categ.R:28:3'): auto_bar_categ funciona correctamente ──
    Error in `parent %+replace% t`: `%+replace%` requires two theme objects
    Backtrace:
        ▆
     1. └─BiVariAn::auto_bar_categ(data, groupvar = "group", bar_args = bar_args_custom) at test-auto_bar_categ.R:28:3
     2.   └─BiVariAn (local) theme_func()
     3.     ├─... %+replace% ...
     4.     │ └─ggplot2::is_theme(e1)
     5.     │   └─S7::S7_inherits(x, class_theme)
     6.     └─ggprism::theme_prism(...)
     7.       └─parent %+replace% t
     8.         └─cli::cli_abort("{.code %+replace%} requires two theme objects")
     9.           └─rlang::abort(...)
    ── Error ('test-auto_bar_cont.R:10:3'): auto_bar_cont works ────────────────────
    Error in `ggplot2::scale_y_continuous(limits = c(0, data_summary$mean_value + 
        5))`: `limits` must be a vector of length 2, not length 3.
    Backtrace:
        ▆
     1. └─BiVariAn::auto_bar_cont(...) at test-auto_bar_cont.R:10:3
     2.   └─ggplot2::scale_y_continuous(...)
     3.     └─ggplot2::continuous_scale(...)
     4.       └─ggplot2:::check_continuous_limits(limits, call = call)
     5.         └─ggplot2:::check_length(limits, 2L, arg = arg, call = call)
     6.           └─cli::cli_abort(msg, call = call, arg = arg)
     7.             └─rlang::abort(...)
    ── Error ('test-auto_bar_cont.R:32:3'): auto_bar_cont handle non default args ──
    Error in `ggplot2::scale_y_continuous(limits = c(0, data_summary$mean_value + 
        5))`: `limits` must be a vector of length 2, not length 3.
    Backtrace:
        ▆
     1. └─BiVariAn::auto_bar_cont(...) at test-auto_bar_cont.R:32:3
     2.   └─ggplot2::scale_y_continuous(...)
     3.     └─ggplot2::continuous_scale(...)
     4.       └─ggplot2:::check_continuous_limits(limits, call = call)
     5.         └─ggplot2:::check_length(limits, 2L, arg = arg, call = call)
     6.           └─cli::cli_abort(msg, call = call, arg = arg)
     7.             └─rlang::abort(...)
    ── Error ('test-auto_bp_cont.R:11:3'): auto_bp_cont works ──────────────────────
    Error in `parent %+replace% t`: `%+replace%` requires two theme objects
    Backtrace:
        ▆
     1. └─BiVariAn::auto_bp_cont(data, groupvar = "group") at test-auto_bp_cont.R:11:3
     2.   └─BiVariAn (local) theme_func()
     3.     ├─... %+replace% ...
     4.     │ └─ggplot2::is_theme(e1)
     5.     │   └─S7::S7_inherits(x, class_theme)
     6.     └─ggprism::theme_prism(...)
     7.       └─parent %+replace% t
     8.         └─cli::cli_abort("{.code %+replace%} requires two theme objects")
     9.           └─rlang::abort(...)
    ── Error ('test-auto_corr_cont.R:4:3'): auto_corr_cont works ───────────────────
    Error in `parent %+replace% t`: `%+replace%` requires two theme objects
    Backtrace:
        ▆
     1. └─BiVariAn::auto_corr_cont(data = mtcars, referencevar = "cyl") at test-auto_corr_cont.R:4:3
     2.   └─BiVariAn (local) theme_func()
     3.     ├─... %+replace% ...
     4.     │ └─ggplot2::is_theme(e1)
     5.     │   └─S7::S7_inherits(x, class_theme)
     6.     └─ggprism::theme_prism(...)
     7.       └─parent %+replace% t
     8.         └─cli::cli_abort("{.code %+replace%} requires two theme objects")
     9.           └─rlang::abort(...)
    ── Error ('test-auto_dens_cont.R:4:3'): auto_dens_cont works ───────────────────
    Error in `parent %+replace% t`: `%+replace%` requires two theme objects
    Backtrace:
        ▆
     1. └─BiVariAn::auto_dens_cont(data = cars) at test-auto_dens_cont.R:4:3
     2.   └─BiVariAn (local) theme_func()
     3.     ├─... %+replace% ...
     4.     │ └─ggplot2::is_theme(e1)
     5.     │   └─S7::S7_inherits(x, class_theme)
     6.     └─ggprism::theme_prism(...)
     7.       └─parent %+replace% t
     8.         └─cli::cli_abort("{.code %+replace%} requires two theme objects")
     9.           └─rlang::abort(...)
    ── Error ('test-auto_pie_categ.R:11:3'): auto_pie_categ works ──────────────────
    Error in `parent %+replace% t`: `%+replace%` requires two theme objects
    Backtrace:
        ▆
     1. └─BiVariAn::auto_pie_categ(data = data) at test-auto_pie_categ.R:11:3
     2.   └─BiVariAn (local) theme_func()
     3.     ├─... %+replace% ...
     4.     │ └─ggplot2::is_theme(e1)
     5.     │   └─S7::S7_inherits(x, class_theme)
     6.     └─ggprism::theme_prism(...)
     7.       └─parent %+replace% t
     8.         └─cli::cli_abort("{.code %+replace%} requires two theme objects")
     9.           └─rlang::abort(...)
    ── Error ('test-auto_viol_cont.R:9:3'): auto_violin_cont works ─────────────────
    Error in `parent %+replace% t`: `%+replace%` requires two theme objects
    Backtrace:
        ▆
     1. └─BiVariAn::auto_viol_cont(data = data, groupvar = "group") at test-auto_viol_cont.R:9:3
     2.   └─BiVariAn (local) theme_func()
     3.     ├─... %+replace% ...
     4.     │ └─ggplot2::is_theme(e1)
     5.     │   └─S7::S7_inherits(x, class_theme)
     6.     └─ggprism::theme_prism(...)
     7.       └─parent %+replace% t
     8.         └─cli::cli_abort("{.code %+replace%} requires two theme objects")
     9.           └─rlang::abort(...)
    
    [ FAIL 8 | WARN 2 | SKIP 7 | PASS 100 ]
    Error: Test failures
    Execution halted

Package: braidReports
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘braidReports.Rmd’ using rmarkdown
  --- finished re-building ‘braidReports.Rmd’
  
  --- re-building ‘heatmaps.Rmd’ using rmarkdown
  --- finished re-building ‘heatmaps.Rmd’
  
  --- re-building ‘kappaTransform.Rmd’ using rmarkdown
  
  Quitting from kappaTransform.Rmd:119-130 [unnamed-chunk-5]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'kappaTransform.Rmd' failed with diagnostics:
  Problem while computing stat.
  ℹ Error occurred in the 1st layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  --- failed re-building ‘kappaTransform.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘kappaTransform.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: brolgar
Check: examples
New result: ERROR
  Running examples in ‘brolgar-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: facet_sample
  > ### Title: Facet data into groups to facilitate exploration
  > ### Aliases: facet_sample
  > 
  > ### ** Examples
  > 
  > library(ggplot2)
  > ggplot(heights,
  + aes(x = year,
  +     y = height_cm,
  +     group = country)) +
  +   geom_line() +
  +   facet_sample()
  Error in if (params$as.table) { : argument is of length zero
  Calls: <Anonymous> ... <Anonymous> -> setup -> <Anonymous> -> compute_layout
  Execution halted

Package: brolgar
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘exploratory-modelling.Rmd’ using rmarkdown
  --- finished re-building ‘exploratory-modelling.Rmd’
  
  --- re-building ‘finding-features.Rmd’ using rmarkdown
  --- finished re-building ‘finding-features.Rmd’
  
  --- re-building ‘getting-started.Rmd’ using rmarkdown
  
  Quitting from getting-started.Rmd:151-160 [facet-strata]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `if (params$as.table) ...`:
  ! argument is of length zero
  ---
  Backtrace:
       ▆
    1. └─tools:::.buildOneVignette(...)
    2.   ├─base::tryCatch(...)
    3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    6.   └─engine$weave(file, quiet = quiet, encoding = enc)
    7.     └─knitr:::vweave_rmarkdown(...)
    8.       └─rmarkdown::render(...)
    9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
   10.           └─knitr:::process_file(text, output)
   11.             ├─xfun:::handle_error(...)
   12.             ├─base::withCallingHandlers(...)
   13.             └─knitr:::process_group(group)
   14.               └─knitr:::call_block(x)
   15.                 └─knitr:::block_exec(params)
   16.                   └─knitr:::eng_r(options)
   17.                     ├─knitr:::in_input_dir(...)
   18.                     │ └─knitr:::in_dir(input_dir(), expr)
   19.                     └─knitr (local) evaluate(...)
   20.                       └─evaluate::evaluate(...)
   21.                         ├─base::withRestarts(...)
   22.                         │ └─base (local) withRestartList(expr, restarts)
   23.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
   24.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
   25.                         │   └─base (local) withRestartList(expr, restarts[-nr])
   26.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
   27.                         │       └─base (local) doWithOneRestart(return(expr), restart)
   28.                         ├─evaluate:::with_handlers(...)
   29.                         │ ├─base::eval(call)
   30.                         │ │ └─base::eval(call)
   31.                         │ └─base::withCallingHandlers(...)
   32.                         └─watcher$print_value(ev$value, ev$visible, envir)
   33.                           ├─base::withVisible(handle_value(handler, value, visible, envir))
   34.                           └─evaluate:::handle_value(handler, value, visible, envir)
   35.                             └─handler$value(value, visible)
   36.                               └─knitr (local) fun(x, options = options)
   37.                                 ├─base::withVisible(knit_print(x, ...))
   38.                                 ├─knitr::knit_print(x, ...)
   39.                                 └─knitr:::knit_print.default(x, ...)
   40.                                   └─knitr::normal_print(x)
   41.                                     ├─base::print(x)
   42.                                     └─ggplot2 (local) `print.ggplot2::ggplot`(x)
   43.                                       ├─ggplot2::ggplot_build(x)
   44.                                       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
   45.                                         └─layout$setup(data, plot@data, plot@plot_env)
   46.                                           └─ggplot2 (local) setup(..., self = self)
   47.                                             └─self$facet$compute_layout(data, self$facet_params)
   48.                                               └─brolgar (local) compute_layout(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
  argument is of length zero
  --- failed re-building ‘getting-started.Rmd’
  
  --- re-building ‘id-interesting-obs.Rmd’ using rmarkdown
  --- finished re-building ‘id-interesting-obs.Rmd’
  
  --- re-building ‘longitudinal-data-structures.Rmd’ using rmarkdown
  --- finished re-building ‘longitudinal-data-structures.Rmd’
  
  --- re-building ‘mixed-effects-models.Rmd’ using rmarkdown
  
  Quitting from mixed-effects-models.Rmd:52-55 [wages-ggplot-sample]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `if (params$as.table) ...`:
  ! argument is of length zero
  ---
  Backtrace:
       ▆
    1. └─tools:::.buildOneVignette(...)
    2.   ├─base::tryCatch(...)
    3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    6.   └─engine$weave(file, quiet = quiet, encoding = enc)
    7.     └─knitr:::vweave_rmarkdown(...)
    8.       └─rmarkdown::render(...)
    9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
   10.           └─knitr:::process_file(text, output)
   11.             ├─xfun:::handle_error(...)
   12.             ├─base::withCallingHandlers(...)
   13.             └─knitr:::process_group(group)
   14.               └─knitr:::call_block(x)
   15.                 └─knitr:::block_exec(params)
   16.                   └─knitr:::eng_r(options)
   17.                     ├─knitr:::in_input_dir(...)
   18.                     │ └─knitr:::in_dir(input_dir(), expr)
   19.                     └─knitr (local) evaluate(...)
   20.                       └─evaluate::evaluate(...)
   21.                         ├─base::withRestarts(...)
   22.                         │ └─base (local) withRestartList(expr, restarts)
   23.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
   24.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
   25.                         │   └─base (local) withRestartList(expr, restarts[-nr])
   26.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
   27.                         │       └─base (local) doWithOneRestart(return(expr), restart)
   28.                         ├─evaluate:::with_handlers(...)
   29.                         │ ├─base::eval(call)
   30.                         │ │ └─base::eval(call)
   31.                         │ └─base::withCallingHandlers(...)
   32.                         └─watcher$print_value(ev$value, ev$visible, envir)
   33.                           ├─base::withVisible(handle_value(handler, value, visible, envir))
   34.                           └─evaluate:::handle_value(handler, value, visible, envir)
   35.                             └─handler$value(value, visible)
   36.                               └─knitr (local) fun(x, options = options)
   37.                                 ├─base::withVisible(knit_print(x, ...))
   38.                                 ├─knitr::knit_print(x, ...)
   39.                                 └─knitr:::knit_print.default(x, ...)
   40.                                   └─knitr::normal_print(x)
   41.                                     ├─base::print(x)
   42.                                     └─ggplot2 (local) `print.ggplot2::ggplot`(x)
   43.                                       ├─ggplot2::ggplot_build(x)
   44.                                       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
   45.                                         └─layout$setup(data, plot@data, plot@plot_env)
   46.                                           └─ggplot2 (local) setup(..., self = self)
   47.                                             └─self$facet$compute_layout(data, self$facet_params)
   48.                                               └─brolgar (local) compute_layout(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'mixed-effects-models.Rmd' failed with diagnostics:
  argument is of length zero
  --- failed re-building ‘mixed-effects-models.Rmd’
  
  --- re-building ‘visualisation-gallery.Rmd’ using rmarkdown
  
  Quitting from visualisation-gallery.Rmd:81-90 [facet-strata]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `if (params$as.table) ...`:
  ! argument is of length zero
  ---
  Backtrace:
       ▆
    1. └─tools:::.buildOneVignette(...)
    2.   ├─base::tryCatch(...)
    3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    6.   └─engine$weave(file, quiet = quiet, encoding = enc)
    7.     └─knitr:::vweave_rmarkdown(...)
    8.       └─rmarkdown::render(...)
    9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
   10.           └─knitr:::process_file(text, output)
   11.             ├─xfun:::handle_error(...)
   12.             ├─base::withCallingHandlers(...)
   13.             └─knitr:::process_group(group)
   14.               └─knitr:::call_block(x)
   15.                 └─knitr:::block_exec(params)
   16.                   └─knitr:::eng_r(options)
   17.                     ├─knitr:::in_input_dir(...)
   18.                     │ └─knitr:::in_dir(input_dir(), expr)
   19.                     └─knitr (local) evaluate(...)
   20.                       └─evaluate::evaluate(...)
   21.                         ├─base::withRestarts(...)
   22.                         │ └─base (local) withRestartList(expr, restarts)
   23.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
   24.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
   25.                         │   └─base (local) withRestartList(expr, restarts[-nr])
   26.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
   27.                         │       └─base (local) doWithOneRestart(return(expr), restart)
   28.                         ├─evaluate:::with_handlers(...)
   29.                         │ ├─base::eval(call)
   30.                         │ │ └─base::eval(call)
   31.                         │ └─base::withCallingHandlers(...)
   32.                         └─watcher$print_value(ev$value, ev$visible, envir)
   33.                           ├─base::withVisible(handle_value(handler, value, visible, envir))
   34.                           └─evaluate:::handle_value(handler, value, visible, envir)
   35.                             └─handler$value(value, visible)
   36.                               └─knitr (local) fun(x, options = options)
   37.                                 ├─base::withVisible(knit_print(x, ...))
   38.                                 ├─knitr::knit_print(x, ...)
   39.                                 └─knitr:::knit_print.default(x, ...)
   40.                                   └─knitr::normal_print(x)
   41.                                     ├─base::print(x)
   42.                                     └─ggplot2 (local) `print.ggplot2::ggplot`(x)
   43.                                       ├─ggplot2::ggplot_build(x)
   44.                                       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
   45.                                         └─layout$setup(data, plot@data, plot@plot_env)
   46.                                           └─ggplot2 (local) setup(..., self = self)
   47.                                             └─self$facet$compute_layout(data, self$facet_params)
   48.                                               └─brolgar (local) compute_layout(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'visualisation-gallery.Rmd' failed with diagnostics:
  argument is of length zero
  --- failed re-building ‘visualisation-gallery.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘getting-started.Rmd’ ‘mixed-effects-models.Rmd’
    ‘visualisation-gallery.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: bullseye
Check: examples
New result: ERROR
  Running examples in ‘bullseye-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: add_nobs_to_pairwise
  > ### Title: Adds number of observations column to pairwise tibble
  > ### Aliases: add_nobs_to_pairwise
  > 
  > ### ** Examples
  > 
  > irisc <- pairwise_scores(iris[40:150,], by= "Species")
  > irisc <- add_nobs_to_pairwise(irisc, iris[40:150,], by= "Species")
  > irisc
  # A tibble: 24 × 7
     x            y            score   group       value pair_type     n
     <chr>        <chr>        <chr>   <fct>       <dbl> <chr>     <int>
   1 Petal.Length Sepal.Length pearson setosa     0.584  nn           11
   2 Petal.Width  Sepal.Length pearson setosa     0.112  nn           11
   3 Sepal.Length Sepal.Width  pearson setosa     0.756  nn           11
   4 Petal.Length Sepal.Width  pearson setosa     0.650  nn           11
   5 Petal.Width  Sepal.Width  pearson setosa     0.0694 nn           11
   6 Petal.Length Petal.Width  pearson setosa     0.421  nn           11
   7 Petal.Length Sepal.Length pearson versicolor 0.754  nn           50
   8 Petal.Width  Sepal.Length pearson versicolor 0.546  nn           50
   9 Sepal.Length Sepal.Width  pearson versicolor 0.526  nn           50
  10 Petal.Length Sepal.Width  pearson versicolor 0.561  nn           50
  # ℹ 14 more rows
  > plot_pairwise(irisc) # setosa gets a small slice in proportion to n
  Error:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `draw_panel()`:
  ! unused arguments (lineend = "butt", linejoin = "mitre")
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_gtable(data)
    4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$draw_geom(d, layout)
   14. │         └─ggplot2 (local) draw_geom(..., self = self)
   15. │           └─self$geom$draw_layer(...)
   16. │             └─ggplot2 (local) draw_layer(..., self = self)
   17. │               └─base::lapply(...)
   18. │                 └─ggplot2 (local) FUN(X[[i]], ...)
   19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   20. │                   └─self$draw_panel(...)
   21. └─base::.handleSimpleError(...)
   22.   └─rlang (local) h(simpleError(msg, call))
   23.     └─handlers[[1L]](cnd)
   24.       └─cli::cli_abort(...)
   25.         └─rlang::abort(...)
  Execution halted

Package: bullseye
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘calc_pairwise.Rmd’ using rmarkdown
  --- finished re-building ‘calc_pairwise.Rmd’
  
  --- re-building ‘integrating.Rmd’ using rmarkdown
  
  Quitting from integrating.Rmd:79-84 [unnamed-chunk-4]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'integrating.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 3rd layer.
  Caused by error in `draw_panel()`:
  ! unused arguments (lineend = "butt", linejoin = "mitre")
  --- failed re-building ‘integrating.Rmd’
  
  --- re-building ‘vis_pairwise.Rmd’ using rmarkdown
  
  Quitting from vis_pairwise.Rmd:51-53 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'vis_pairwise.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 3rd layer.
  Caused by error in `draw_panel()`:
  ! unused arguments (lineend = "butt", linejoin = "mitre")
  --- failed re-building ‘vis_pairwise.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘integrating.Rmd’ ‘vis_pairwise.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: calmr
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [52s/53s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(calmr)
    
    Attaching package: 'calmr'
    
    The following object is masked from 'package:stats':
    
        filter
    
    The following object is masked from 'package:base':
    
        parse
    
    > 
    > test_check("calmr")
    Ignoring unknown labels:
    * fill : "Target"
    Ignoring unknown labels:
    * fill : "Target"
    Ignoring unknown labels:
    * fill : "Stimulus"
    Ignoring unknown labels:
    * fill : "Target"
    Ignoring unknown labels:
    * fill : "Target"
    [ FAIL 4 | WARN 0 | SKIP 0 | PASS 246 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-RSA.R:59:3'): plotting RSA works ─────────────────────────────
    `plt` does not have names.
    ── Failure ('test-RSA.R:64:3'): plotting RSA with a test works ─────────────────
    `plt` does not have names.
    ── Failure ('test-graphs.R:15:3'): calmr_model_graph works ─────────────────────
    `g` does not have names.
    ── Failure ('test-graphs.R:25:3'): calmr_model_graph takes a trial ─────────────
    `g` does not have names.
    
    [ FAIL 4 | WARN 0 | SKIP 0 | PASS 246 ]
    Error: Test failures
    Execution halted

Package: carbonr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [14s/14s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(carbonr)
    > 
    > test_check("carbonr")
    [ FAIL 3 | WARN 7 | SKIP 0 | PASS 117 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-output_display.R:14:3'): output_display generates gg/ggplot object ──
    class(output) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-output_display.R:15:3'): output_display generates gg/ggplot object ──
    class(output1) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-output_display.R:16:3'): output_display generates gg/ggplot object ──
    class(output2) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 3 | WARN 7 | SKIP 0 | PASS 117 ]
    Error: Test failures
    Execution halted

Package: cartographr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [34s/75s]
  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(cartographr)
    cartographr ready.
    > 
    > test_check("cartographr")
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 106 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-utils.R:13:3'): add_attribution returns correct ggplot2 labs object ──
    `result` inherits from 'ggplot2::labels'/'gg'/'S7_object' not 'labels'.
    
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 106 ]
    Error: Test failures
    Execution halted

Package: causact
Check: tests
New result: ERROR
    Running ‘testthat.R’ [14s/14s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(causact)
    WARNING: The 'r-causact' Conda environment does not exist. To use the 'dag_numpyro()' function, you need to set up the 'r-causact' environment. Run install_causact_deps() when ready to set up the 'r-causact' environment.
    
    Attaching package: 'causact'
    
    The following objects are masked from 'package:stats':
    
        binomial, poisson
    
    The following objects are masked from 'package:base':
    
        beta, gamma
    
    > 
    > test_check("causact")
    
    ## The below code will return a posterior distribution 
    ## for the given DAG. Use dag_numpyro(mcmc=TRUE) to return a
    ## data frame of the posterior distribution: 
    reticulate::py_run_string("
    import numpy as np
    import numpyro as npo
    import numpyro.distributions as dist
    import pandas as pd
    import arviz as az
    from jax import random
    from numpyro.infer import MCMC, NUTS
    from jax.numpy import transpose as t
    from jax.numpy import (exp, log, log1p, expm1, abs, mean,
                     sqrt, sign, round, concatenate, atleast_1d,
                     cos, sin, tan, cosh, sinh, tanh,
                     sum, prod, min, max, cumsum, cumprod )
    ## note that above is from JAX numpy package, not numpy.
    
    nTrials = np.array(r.gymDF.nTrialCustomers)   #DATA
    x = np.array(r.gymDF.yogaStretch)             #DATA
    k = np.array(r.gymDF.nSigned)                 #DATA
    j      = pd.factorize(np.array(r.gymDF.gymID),use_na_sentinel=True)[0]   #DIM
    j_dim  = len(np.unique(j))   #DIM
    j_crd  = pd.factorize(np.array(r.gymDF.gymID),use_na_sentinel=True)[1]   #DIM
    def graph2_model(nTrials,x,k,j):
    	## Define random variables and their relationships
    	mu_alpha = npo.sample('mu_alpha', dist.Normal(-1,1.5))
    
    	mu_beta = npo.sample('mu_beta', dist.Normal(0,0.75))
    
    	sd_alpha = npo.sample('sd_alpha', dist.Uniform(0,3))
    
    	sd_beta = npo.sample('sd_beta', dist.Uniform(0,1.5))
    
    	with npo.plate('j_dim',j_dim):
    		alpha = npo.sample('alpha', dist.Normal(mu_alpha,sd_alpha))
    		beta = npo.sample('beta', dist.Normal(mu_beta,sd_beta))
    
    	y = npo.deterministic('y', alpha[j] + beta[j] * x)
    
    	theta = npo.deterministic('theta', 1 / (1 + exp(-y)))
    
    	k = npo.sample('k', dist.Binomial(nTrials,theta),obs=k)
    
    
    # computationally get posterior
    mcmc = MCMC(NUTS(graph2_model), num_warmup = 1000, num_samples = 4000)
    rng_key = random.PRNGKey(seed = 1234567)
    mcmc.run(rng_key,nTrials,x,k,j)
    drawsDS = az.from_numpyro(mcmc,
    	coords = {'j_dim': j_crd},
    	dims = {'alpha': ['j_dim'],
    		'beta': ['j_dim']}
    	).posterior
    # prepare xarray dataset for export to R dataframe
    dimensions_to_keep = ['chain','draw','j_dim']
    drawsDS = drawsDS.squeeze(drop = True ).drop_dims([dim for dim in drawsDS.dims if dim not in dimensions_to_keep])
    # unstack plate variables to flatten dataframe as needed
    for j_da in drawsDS['j_dim']:
    	new_varname = f'alpha_{j_da.values}'
    	drawsDS = drawsDS.assign(**{new_varname:drawsDS['alpha'].sel(j_dim = j_da)})
    	new_varname = f'beta_{j_da.values}'
    	drawsDS = drawsDS.assign(**{new_varname:drawsDS['beta'].sel(j_dim = j_da)})
    drawsDS = drawsDS.drop_dims(['j_dim'])
    drawsDF = drawsDS.squeeze().to_dataframe()"
    ) ## END PYTHON STRING
    drawsDF = reticulate::py$drawsDF
    This function is currently defunct.  It has been superseded by dag_numpyro() because of tricky installation issues related to the greta package's use of tensorflow.  If the greta package resolves those issues, this function may return, but please use dag_numpyro() as a direct replacement.
    
    ## The below code will return a posterior distribution 
    ## for the given DAG. Use dag_numpyro(mcmc=TRUE) to return a
    ## data frame of the posterior distribution: 
    reticulate::py_run_string("
    import numpy as np
    import numpyro as npo
    import numpyro.distributions as dist
    import pandas as pd
    import arviz as az
    from jax import random
    from numpyro.infer import MCMC, NUTS
    from jax.numpy import transpose as t
    from jax.numpy import (exp, log, log1p, expm1, abs, mean,
                     sqrt, sign, round, concatenate, atleast_1d,
                     cos, sin, tan, cosh, sinh, tanh,
                     sum, prod, min, max, cumsum, cumprod )
    ## note that above is from JAX numpy package, not numpy.
    
    x = np.array(r.carModelDF.getCard)   #DATA
    y      = pd.factorize(np.array(r.carModelDF.carModel),use_na_sentinel=True)[0]   #DIM
    y_dim  = len(np.unique(y))   #DIM
    y_crd  = pd.factorize(np.array(r.carModelDF.carModel),use_na_sentinel=True)[1]   #DIM
    def graph_model(x,y):
    	## Define random variables and their relationships
    	with npo.plate('y_dim',y_dim):
    		theta = npo.sample('theta', dist.Uniform(0,1))
    
    	x = npo.sample('x', dist.Bernoulli(theta[y]),obs=x)
    
    
    # computationally get posterior
    mcmc = MCMC(NUTS(graph_model), num_warmup = 1000, num_samples = 4000)
    rng_key = random.PRNGKey(seed = 1234567)
    mcmc.run(rng_key,x,y)
    drawsDS = az.from_numpyro(mcmc,
    	coords = {'y_dim': y_crd},
    	dims = {'theta': ['y_dim']}
    	).posterior
    # prepare xarray dataset for export to R dataframe
    dimensions_to_keep = ['chain','draw','y_dim']
    drawsDS = drawsDS.squeeze(drop = True ).drop_dims([dim for dim in drawsDS.dims if dim not in dimensions_to_keep])
    # unstack plate variables to flatten dataframe as needed
    for y_da in drawsDS['y_dim']:
    	new_varname = f'theta_{y_da.values}'
    	drawsDS = drawsDS.assign(**{new_varname:drawsDS['theta'].sel(y_dim = y_da)})
    drawsDS = drawsDS.drop_dims(['y_dim'])
    drawsDF = drawsDS.squeeze().to_dataframe()"
    ) ## END PYTHON STRING
    drawsDF = reticulate::py$drawsDF
    
    ## The below code will return a posterior distribution 
    ## for the given DAG. Use dag_numpyro(mcmc=TRUE) to return a
    ## data frame of the posterior distribution: 
    reticulate::py_run_string("
    import numpy as np
    import numpyro as npo
    import numpyro.distributions as dist
    import pandas as pd
    import arviz as az
    from jax import random
    from numpyro.infer import MCMC, NUTS
    from jax.numpy import transpose as t
    from jax.numpy import (exp, log, log1p, expm1, abs, mean,
                     sqrt, sign, round, concatenate, atleast_1d,
                     cos, sin, tan, cosh, sinh, tanh,
                     sum, prod, min, max, cumsum, cumprod )
    ## note that above is from JAX numpy package, not numpy.
    
    x = np.array(r.attitude.complaints)   #DATA
    y = np.array(r.attitude.rating)       #DATA
    def graph_model(x,y):
    	## Define random variables and their relationships
    	int = npo.sample('int', dist.Normal(0,10))
    
    	coef = npo.sample('coef', dist.Normal(0,10))
    
    	sd = npo.sample('sd', dist.TruncatedCauchy(0,3,low=0))
    
    	mu = npo.deterministic('mu', int + coef * x)
    
    	y = npo.sample('y', dist.Normal(mu,sd),obs=y)
    
    
    # computationally get posterior
    mcmc = MCMC(NUTS(graph_model), num_warmup = 1000, num_samples = 4000)
    rng_key = random.PRNGKey(seed = 1234567)
    mcmc.run(rng_key,x,y)
    drawsDS = az.from_numpyro(mcmc).posterior
    # prepare xarray dataset for export to R dataframe
    dimensions_to_keep = ['chain','draw']
    drawsDS = drawsDS.squeeze(drop = True ).drop_dims([dim for dim in drawsDS.dims if dim not in dimensions_to_keep])
    # unstack plate variables to flatten dataframe as needed
    
    drawsDF = drawsDS.squeeze().to_dataframe()"
    ) ## END PYTHON STRING
    drawsDF = reticulate::py$drawsDF
    
    ## The below code will return a posterior distribution 
    ## for the given DAG. Use dag_numpyro(mcmc=TRUE) to return a
    ## data frame of the posterior distribution: 
    reticulate::py_run_string("
    import numpy as np
    import numpyro as npo
    import numpyro.distributions as dist
    import pandas as pd
    import arviz as az
    from jax import random
    from numpyro.infer import MCMC, NUTS
    from jax.numpy import transpose as t
    from jax.numpy import (exp, log, log1p, expm1, abs, mean,
                     sqrt, sign, round, concatenate, atleast_1d,
                     cos, sin, tan, cosh, sinh, tanh,
                     sum, prod, min, max, cumsum, cumprod )
    ## note that above is from JAX numpy package, not numpy.
    
    x = np.array(r.trees.Height)   #DATA
    def graph_model(x):
    	## Define random variables and their relationships
    	nu = npo.sample('nu', dist.Gamma(2,0.1))
    
    	mu = npo.sample('mu', dist.Normal(50,24.5))
    
    	sigma = npo.sample('sigma', dist.Uniform(0,50))
    
    	x = npo.sample('x', dist.StudentT(nu,mu,sigma),obs=x)
    
    
    # computationally get posterior
    mcmc = MCMC(NUTS(graph_model), num_warmup = 1000, num_samples = 4000)
    rng_key = random.PRNGKey(seed = 1234567)
    mcmc.run(rng_key,x)
    drawsDS = az.from_numpyro(mcmc).posterior
    # prepare xarray dataset for export to R dataframe
    dimensions_to_keep = ['chain','draw']
    drawsDS = drawsDS.squeeze(drop = True ).drop_dims([dim for dim in drawsDS.dims if dim not in dimensions_to_keep])
    # unstack plate variables to flatten dataframe as needed
    
    drawsDF = drawsDS.squeeze().to_dataframe()"
    ) ## END PYTHON STRING
    drawsDF = reticulate::py$drawsDF
    WARNING: The 'r-causact' Conda environment does not exist. To use the 'dag_numpyro()' function, you need to set up the 'r-causact' environment. Run install_causact_deps() when ready to set up the 'r-causact' environment.
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-dag_plot.R:4:3'): dag plot creates graph ─────────────────────
    `plotGr` has type 'object', not 'list'.
    
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 60 ]
    Error: Test failures
    Execution halted

Package: CausalImpact
Check: tests
New result: ERROR
    Running ‘CausalImpact_import_test.R’ [4s/4s]
    Running ‘testthat.R’ [36s/37s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # Copyright 2014-2022 Google Inc. All rights reserved.
    > #
    > # Licensed under the Apache License, Version 2.0 (the "License");
    > # you may not use this file except in compliance with the License.
    > # You may obtain a copy of the License at
    > #
    > # http://www.apache.org/licenses/LICENSE-2.0
    > #
    > # Unless required by applicable law or agreed to in writing, software
    > # distributed under the License is distributed on an "AS IS" BASIS,
    > # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    > # See the License for the specific language governing permissions and
    > # limitations under the License.
    > 
    > # Unit test driver for the CausalImpact package.
    > #
    > # Author: kbrodersen@google.com (Kay Brodersen)
    > 
    > library(CausalImpact)
    Loading required package: bsts
    Loading required package: BoomSpikeSlab
    Loading required package: Boom
    
    Attaching package: 'Boom'
    
    The following object is masked from 'package:stats':
    
        rWishart
    
    
    Attaching package: 'BoomSpikeSlab'
    
    The following object is masked from 'package:stats':
    
        knots
    
    Loading required package: zoo
    
    Attaching package: 'zoo'
    
    The following objects are masked from 'package:base':
    
        as.Date, as.Date.numeric
    
    Loading required package: xts
    
    Attaching package: 'bsts'
    
    The following object is masked from 'package:BoomSpikeSlab':
    
        SuggestBurn
    
    > library(testthat)
    > 
    > # Open graphics device and run tests
    > plot.file <- tempfile("CausalImpact", fileext = ".png")
    > png(plot.file)
    > testthat::test_check("CausalImpact")
    [ FAIL 3 | WARN 4 | SKIP 0 | PASS 738 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-impact-plot.R:107:3'): CreateImpactPlot ──────────────────────
    class(q) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-impact-plot.R:118:3'): CreateImpactPlot ──────────────────────
    class(q) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-impact-plot.R:147:3'): CreateImpactPlot ──────────────────────
    !isTRUE(all.equal(q1, q2, check.environment = FALSE)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 3 | WARN 4 | SKIP 0 | PASS 738 ]
    Error: Test failures
    Execution halted

Package: centerline
Check: tests
New result: ERROR
    Running ‘testthat.R’ [79s/79s]
  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(centerline)
    > 
    > test_check("centerline")
    [ FAIL 3 | WARN 0 | SKIP 0 | PASS 245 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-geom_cnt.R:55:5'): geom_cnt_*() create correct types ───────────
    <subscriptOutOfBoundsError/error/condition>
    Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
    Backtrace:
        ▆
     1. ├─testthat::expect_s3_class(ln[[2]][[1]], "LayerSf") at test-geom_cnt.R:55:5
     2. │ └─testthat::quasi_label(enquo(object), arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─ln[[2]]
     5. └─ggplot2 (local) `[[.ggplot2::gg`(ln, 2)
    ── Error ('test-geom_cnt.R:88:5'): geom_cnt_*() smiplification works ───────────
    <subscriptOutOfBoundsError/error/condition>
    Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
    Backtrace:
        ▆
     1. ├─testthat::expect_s3_class(ln[[2]][[1]], "LayerSf") at test-geom_cnt.R:88:5
     2. │ └─testthat::quasi_label(enquo(object), arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─ln[[2]]
     5. └─ggplot2 (local) `[[.ggplot2::gg`(ln, 2)
    ── Error ('test-geom_cnt.R:121:5'): geom_cnt_*() smiplification works with mutiple geometries ──
    <subscriptOutOfBoundsError/error/condition>
    Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
    Backtrace:
        ▆
     1. ├─testthat::expect_s3_class(ln[[2]][[1]], "LayerSf") at test-geom_cnt.R:121:5
     2. │ └─testthat::quasi_label(enquo(object), arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─ln[[2]]
     5. └─ggplot2 (local) `[[.ggplot2::gg`(ln, 2)
    
    [ FAIL 3 | WARN 0 | SKIP 0 | PASS 245 ]
    Error: Test failures
    Execution halted

Package: Certara.DarwinReporter
Check: package dependencies
New result: ERROR
  Packages required but not available: 'xpose', 'Certara.Xpose.NLME'
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: Certara.ModelResults
Check: package dependencies
New result: ERROR
  Packages required but not available: 'Certara.Xpose.NLME', 'xpose'
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: Certara.Xpose.NLME
Check: package dependencies
New result: ERROR
  Package required but not available: ‘xpose’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: CGPfunctions
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggmosaic’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: cheem
Check: tests
New result: ERROR
    Running ‘testthat.R’ [9s/9s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(cheem)
    --------------------------------------------------------
    cheem --- version 0.4.0.0
    Please share bugs, suggestions, and feature requests at:
    https://github.com/nspyrison/cheem/issues/
    --------------------------------------------------------
    > 
    > test_check("cheem")
    Loading required package: tourr
    --------------------------------------------------------
    spinifex --- version 0.3.8
    Please share bugs, suggestions, and feature requests at:
    https://github.com/nspyrison/spinifex/issues/
    --------------------------------------------------------
    
    Attaching package: 'spinifex'
    
    The following objects are masked from 'package:tourr':
    
        is_orthonormal, save_history
    
    The following object is masked from 'package:cheem':
    
        run_app
    
    Ignoring unknown labels:
    • fill : "predicted_class"
    Ignoring unknown labels:
    • fill : "default"
    [ FAIL 6 | WARN 0 | SKIP 0 | PASS 10 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-2_visualization.r:41:3'): proto_basis1d_distribution ─────────
    class(c_ggt) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_visualization.r:42:3'): proto_basis1d_distribution ─────────
    class(r_ggt) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_visualization.r:57:3'): global_view as_ggplot ──────────────
    class(c_gv) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_visualization.r:58:3'): global_view as_ggplot ──────────────
    class(r_gv) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_visualization.r:65:3'): radial_cheem_tour ──────────────────
    class(c_ggt) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_visualization.r:66:3'): radial_cheem_tour ──────────────────
    class(r_ggt) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 6 | WARN 0 | SKIP 0 | PASS 10 ]
    Error: Test failures
    Execution halted

Package: chooseGCM
Check: tests
New result: ERROR
    Running ‘testthat.R’ [275s/276s]
  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(chooseGCM)
    > 
    > test_check("chooseGCM")
    Objects from s don't have the same number of cells. Filtering all available cells.
    Objects from s don't have the same number of cells. Filtering all available cells.
    Objects from s don't have the same number of cells. Filtering all available cells.
    Scale for fill is already present.
    Adding another scale for fill, which will replace the existing scale.
    Scale for fill is already present.
    Adding another scale for fill, which will replace the existing scale.
    Scale for fill is already present.
    Adding another scale for fill, which will replace the existing scale.
    Scale for fill is already present.
    Adding another scale for fill, which will replace the existing scale.
    Scale for fill is already present.
    Adding another scale for fill, which will replace the existing scale.
    Scale for fill is already present.
    Adding another scale for fill, which will replace the existing scale.
    Scale for fill is already present.
    Adding another scale for fill, which will replace the existing scale.
    CRS from s and study_area are not identical. Reprojecting study area.
    CRS from s and study_area are not identical. Reprojecting study area.
    [ FAIL 3 | WARN 10 | SKIP 0 | PASS 209 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-optk_gcms.R:7:3'): optk_gcms works with kmeans and wss method ──
    `result` has type 'object', not 'list'.
    ── Failure ('test-optk_gcms.R:17:3'): optk_gcms works with kmeans and silhouette method ──
    `result` has type 'object', not 'list'.
    ── Failure ('test-optk_gcms.R:18:3'): optk_gcms works with kmeans and silhouette method ──
    length(result) == 11 is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 3 | WARN 10 | SKIP 0 | PASS 209 ]
    Error: Test failures
    Execution halted

Package: clifro
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘test-all.R’ [3s/3s]
  Running the tests in ‘tests/test-all.R’ failed.
  Complete output:
    > library(testthat)
    > library(clifro)
    > 
    > test_check("clifro")
    [ FAIL 1 | WARN 1 | SKIP 4 | PASS 10 ]
    
    ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
    • On CRAN (4): 'test-cf_find_station.R:4:3', 'test-cf_last_query.R:4:3',
      'test-cf_query.R:4:3', 'test-cf_station.R:4:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-windrose.R:15:3'): windrose ──────────────────────────────────
    tt$labels inherits from `'ggplot2::labels'/'gg'/'S7_object'` not `'character'`.
    
    [ FAIL 1 | WARN 1 | SKIP 4 | PASS 10 ]
    Error: Test failures
    Execution halted

Package: climwin
Check: tests
New result: ERROR
    Running ‘testthat.R’ [120s/120s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(climwin)
    > 
    > test_check("climwin")
    
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      |                                                                      |   0%[ FAIL 7 | WARN 762 | SKIP 3 | PASS 790 ]
    
    ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
    • empty test (3): 'testplotall.R:6:1', 'testplotall.R:31:1',
      'testplotall.R:51:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('testplotbest.R:24:3'): plotbest produces a graph ──────────────────
    attr(test, "class")[1] == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('testplotbetas.R:16:3'): plotbetas produces a graph ────────────────
    attr(test, "class")[1] == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('testplotcor.R:16:3'): plotcor produces a graph ────────────────────
    attr(test, "class")[1] == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('testplotdelta.R:15:3'): plotdelta produces a graph ────────────────
    attr(test, "class")[1] == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('testplothist.R:19:3'): plothist produces a graph ──────────────────
    attr(test2, "class")[1] == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('testplotweights.R:15:3'): plotweights produces a graph ────────────
    attr(test, "class")[1] == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('testplotwin.R:15:3'): plotwin produces a graph ────────────────────
    attr(test, "class")[1] == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 7 | WARN 762 | SKIP 3 | PASS 790 ]
    Error: Test failures
    Execution halted

Package: clockSim
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
  See ‘/home/hornik/tmp/CRAN_recheck/clockSim.Rcheck/00install.out’ for details.
  Used C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’

Package: cmcR
Check: tests
New result: ERROR
    Running ‘testthat.R’ [464s/461s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(cmcR)
    > 
    > test_check("cmcR",reporter = SummaryReporter)
      adding: bindata/ (stored 0%)
      adding: bindata/data.bin (deflated 58%)
      adding: main.xml (deflated 62%)
      adding: md5checksum.hex (stored 0%)
      adding: bindata/ (stored 0%)
      adding: bindata/data.bin (deflated 58%)
      adding: main.xml (deflated 62%)
      adding: md5checksum.hex (stored 0%)
    comparison: ..
    decision: ..........
    diagnosticTools: .WW1WWW2.
    preProcess: S
    
    ══ Skipped ═════════════════════════════════════════════════════════════════════
    1. preProcess_ functions work as expected ('test-preProcess.R:5:3') - Reason: On CRAN
    
    ══ Warnings ════════════════════════════════════════════════════════════════════
    1. diagnosticTools functions work as expected ('test-diagnosticTools.R:95:3') - longer object length is not a multiple of shorter object length
    
    2. diagnosticTools functions work as expected ('test-diagnosticTools.R:95:3') - longer object length is not a multiple of shorter object length
    
    3. diagnosticTools functions work as expected ('test-diagnosticTools.R:104:3') - longer object length is not a multiple of shorter object length
    
    4. diagnosticTools functions work as expected ('test-diagnosticTools.R:104:3') - longer object length is not a multiple of shorter object length
    
    5. diagnosticTools functions work as expected ('test-diagnosticTools.R:104:3') - longer object length is not a multiple of shorter object length
    
    ══ Failed ══════════════════════════════════════════════════════════════════════
    ── 1. Failure ('test-diagnosticTools.R:95:3'): diagnosticTools functions work as
    all(unlist(purrr::map(x3pPlt, ~class(.) == c("gg", "ggplot")))) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    ── 2. Failure ('test-diagnosticTools.R:104:3'): diagnosticTools functions work a
    all(unlist(purrr::map(cmcPlt_list, ~class(.) == c("gg", "ggplot")))) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    ══ DONE ════════════════════════════════════════════════════════════════════════
    Error: Test failures
    Execution halted

Package: cnmap
Check: examples
New result: ERROR
  Running examples in ‘cnmap-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: getMap
  > ### Title: China Map Data from AutoNavi Map
  > ### Aliases: getMap
  > 
  > ### ** Examples
  > 
  > library(cnmap)
  > 
  > map1 <- getMap(code = "110000") # get the map data of Beijing City
  Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir,  : 
    package tibble not available: install first?
  Calls: getMap ... st_read -> st_read.character -> process_cpl_read_ogr
  Execution halted

Package: cnmap
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Introduction.Rmd’ using rmarkdown
  
  Quitting from Introduction.Rmd:28-35 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `process_cpl_read_ogr()`:
  ! package tibble not available: install first?
  ---
  Backtrace:
      ▆
   1. └─cnmap::getMap(name = "中国")
   2.   └─sf::read_sf(urlmap)
   3.     ├─sf::st_read(...)
   4.     └─sf:::st_read.character(...)
   5.       └─sf:::process_cpl_read_ogr(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
  package tibble not available: install first?
  --- failed re-building ‘Introduction.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Introduction.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: cocktailApp
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggtern’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: coda.plot
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggtern’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: conquestr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [8s/8s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(conquestr)
    > 
    > test_check("conquestr")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-ConQuestRout.R:10:3'): Rout file is of correct type ──────────
    `myRoutPlot` has type 'object', not 'list'.
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]
    Error: Test failures
    Execution halted

Package: constructive
Check: tests
New result: ERROR
    Running ‘testthat.R’ [35s/36s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(constructive)
    > 
    > test_check("constructive")
    [ FAIL 6 | WARN 2 | SKIP 113 | PASS 24 ]
    
    ══ Skipped tests (113) ═════════════════════════════════════════════════════════
    • On CRAN (109): 'test-abort.R:2:3', 'test-abort.R:27:3',
      'test-construct_diff.R:2:3', 'test-construct_dput.R:2:3',
      'test-construct_multi.R:15:3', 'test-construct_reprex.R:40:3',
      'test-construct_signature.R:2:3', 'test-contains_self_reference.R:44:3',
      'test-deparse_call.R:2:3', 'test-deparse_call.R:128:3',
      'test-deparse_call.R:135:3', 'test-encoding.R:2:3', 'test-encoding.R:12:3',
      'test-opts.R:2:3', 'test-others.R:2:3', 'test-others.R:20:3',
      'test-others.R:27:3', 'test-others.R:35:3', 'test-others.R:45:3',
      'test-repair_attributes.R:4:3', 'test-s3-AsIs.R:2:3', 'test-s3-Date.R:15:3',
      'test-s3-POSIXct.R:62:3', 'test-s3-POSIXlt.R:18:3', 'test-s3-POSIXlt.R:48:3',
      'test-s3-R6.R:2:3', 'test-s3-R6ClassGenerator.R:2:3', 'test-s3-array.R:2:3',
      'test-s3-array.R:12:3', 'test-s3-atomic.R:2:3', 'test-s3-atomic.R:42:3',
      'test-s3-atomic.R:54:3', 'test-s3-atomic.R:70:3', 'test-s3-atomic.R:88:3',
      'test-s3-atomic.R:98:3', 'test-s3-atomic.R:120:3', 'test-s3-atomic.R:173:3',
      'test-s3-atomic.R:184:3', 'test-s3-atomic.R:194:3', 'test-s3-blob.R:2:3',
      'test-s3-citationFooter.R:2:3', 'test-s3-citationHeader.R:2:3',
      'test-s3-constructive_options.R:2:3', 'test-s3-data.frame.R:2:3',
      'test-s3-data.frame.R:53:3', 'test-s3-data.frame.R:62:3',
      'test-s3-data.frame.R:68:3', 'test-s3-data.table.R:2:3',
      'test-s3-data.table.R:15:3', 'test-s3-data.table.R:24:3',
      'test-s3-data.table.R:30:3', 'test-s3-difftime.R:2:3', 'test-s3-dm.R:2:3',
      'test-s3-dots.R:2:3', 'test-s3-environment.R:2:3', 'test-s3-error.R:2:3',
      'test-s3-expression.R:2:3', 'test-s3-externalptr.R:2:3',
      'test-s3-factor.R:2:3', 'test-s3-formula.R:3:3', 'test-s3-function.R:2:3',
      'test-s3-ggplot2-Coord.R:10:3', 'test-s3-ggplot2-Coord.R:19:3',
      'test-s3-ggplot2-Coord.R:25:3', 'test-s3-ggplot2-Coord.R:35:3',
      'test-s3-ggplot2-Coord.R:44:3', 'test-s3-ggplot2-waiver.R:2:3',
      'test-s3-grouped_df.R:2:3', 'test-s3-hexmode.R:2:3',
      'test-s3-integer64.R:2:3', 'test-s3-language.R:2:3',
      'test-s3-language.R:14:3', 'test-s3-language.R:21:3', 'test-s3-list.R:15:3',
      'test-s3-matrix.R:2:3', 'test-s3-matrix.R:12:3', 'test-s3-matrix.R:18:3',
      'test-s3-mts.R:3:3', 'test-s3-numeric_version.R:2:3',
      'test-s3-octmode.R:2:3', 'test-s3-ordered.R:2:3', 'test-s3-pairlist.R:2:3',
      'test-s3-person.R:2:3', 'test-s3-quosure.R:2:3', 'test-s3-quosures.R:2:3',
      'test-s3-raw.R:3:3', 'test-s3-rowwise_df.R:2:3',
      'test-s3-simpleCondition.R:2:3', 'test-s3-simpleError.R:2:3',
      'test-s3-simpleMessage.R:2:3', 'test-s3-simpleUnit.R:2:3',
      'test-s3-simpleWarning.R:2:3', 'test-s3-tbl_df.R:4:3',
      'test-s3-tbl_df.R:16:3', 'test-s3-tbl_df.R:23:3', 'test-s3-tbl_df.R:32:3',
      'test-s3-tbl_df.R:38:3', 'test-s3-ts.R:2:3', 'test-s3-vctrs_list_of.R:2:3',
      'test-s3-warning.R:2:3', 'test-s3-weakref.R:2:3', 'test-s3-xts.R:6:3',
      'test-s3-yearmon.R:2:3', 'test-s3-yearqtr.R:2:3', 'test-s3-zoo.R:2:3',
      'test-s3-zooreg.R:2:3', 'test-s4.R:2:3', 'test-utils.R:2:3',
      'test-utils.R:10:3'
    • with_versions(R > "4.1.3") is TRUE (1): 'test-s3-ggplot2-ggplot.R:32:3'
    • with_versions(R >= "4.3") is TRUE (3): 'test-s3-POSIXct.R:2:3',
      'test-s3-POSIXlt.R:66:3', 'test-s3-mts.R:11:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-s3-ggplot2-Coord.R:2:3'): CoordCartesian ───────────────────────
    Error in `construct(p, check = FALSE, ...)`: {constructive} could not build the requested code.
    Caused by error in `.subset2()`:
    ! this object class is not subsettable
    Backtrace:
         ▆
      1. ├─constructive:::expect_faithful_ggplot_construction(...) at test-s3-ggplot2-Coord.R:2:3
      2. │ ├─construct(p, check = FALSE, ...)$code
      3. │ └─constructive::construct(p, check = FALSE, ...)
      4. │   └─constructive:::try_construct(...)
      5. │     ├─rlang::try_fetch(...)
      6. │     │ ├─base::tryCatch(...)
      7. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      8. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      9. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     10. │     │ └─base::withCallingHandlers(...)
     11. │     ├─constructive::.cstr_construct(x, ...)
     12. │     ├─constructive:::.cstr_construct.ggplot(x, ...)
     13. │     └─constructive:::.cstr_construct.ggplot.ggplot(x, ...)
     14. │       ├─constructive:::construct_ggplot_call(x$mapping, ...)
     15. │       │ └─constructive:::length(mapping)
     16. │       └─x$mapping
     17. └─base::.handleSimpleError(...)
     18.   └─rlang (local) h(simpleError(msg, call))
     19.     └─handlers[[1L]](cnd)
     20.       └─rlang::abort(...)
    ── Error ('test-s3-ggplot2-Scale.R:2:3'): Scale ────────────────────────────────
    Error in `construct(p, check = FALSE, ...)`: {constructive} could not build the requested code.
    Caused by error in `.subset2()`:
    ! this object class is not subsettable
    Backtrace:
         ▆
      1. ├─constructive:::expect_faithful_ggplot_construction(...) at test-s3-ggplot2-Scale.R:2:3
      2. │ ├─construct(p, check = FALSE, ...)$code
      3. │ └─constructive::construct(p, check = FALSE, ...)
      4. │   └─constructive:::try_construct(...)
      5. │     ├─rlang::try_fetch(...)
      6. │     │ ├─base::tryCatch(...)
      7. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      8. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      9. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     10. │     │ └─base::withCallingHandlers(...)
     11. │     ├─constructive::.cstr_construct(x, ...)
     12. │     ├─constructive:::.cstr_construct.ggplot(x, ...)
     13. │     └─constructive:::.cstr_construct.ggplot.ggplot(x, ...)
     14. │       ├─constructive:::construct_ggplot_call(x$mapping, ...)
     15. │       │ └─constructive:::length(mapping)
     16. │       └─x$mapping
     17. └─base::.handleSimpleError(...)
     18.   └─rlang (local) h(simpleError(msg, call))
     19.     └─handlers[[1L]](cnd)
     20.       └─rlang::abort(...)
    ── Error ('test-s3-ggplot2-ggplot.R:7:5'): ggplot-all-versions ─────────────────
    Error in `construct(p, check = FALSE, ...)`: {constructive} could not build the requested code.
    Caused by error in `.subset2()`:
    ! this object class is not subsettable
    Backtrace:
         ▆
      1. ├─constructive:::expect_faithful_ggplot_construction(base_99, opts_Layer("layer")) at test-s3-ggplot2-ggplot.R:7:5
      2. │ ├─construct(p, check = FALSE, ...)$code
      3. │ └─constructive::construct(p, check = FALSE, ...)
      4. │   └─constructive:::try_construct(...)
      5. │     ├─rlang::try_fetch(...)
      6. │     │ ├─base::tryCatch(...)
      7. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      8. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      9. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     10. │     │ └─base::withCallingHandlers(...)
     11. │     ├─constructive::.cstr_construct(x, ...)
     12. │     ├─constructive:::.cstr_construct.ggplot(x, ...)
     13. │     └─constructive:::.cstr_construct.ggplot.ggplot(x, ...)
     14. │       ├─constructive:::construct_ggplot_call(x$mapping, ...)
     15. │       │ └─constructive:::length(mapping)
     16. │       └─x$mapping
     17. └─base::.handleSimpleError(...)
     18.   └─rlang (local) h(simpleError(msg, call))
     19.     └─handlers[[1L]](cnd)
     20.       └─rlang::abort(...)
    ── Error ('test-s3-ggplot2-ggplot.R:26:3'): ggplot-after-R4.1.3 ────────────────
    Error in `construct(p2, data = list(mpg_99 = mpg_99))`: {constructive} could not build the requested code.
    Caused by error in `.subset2()`:
    ! this object class is not subsettable
    Backtrace:
         ▆
      1. ├─constructive::construct(p2, data = list(mpg_99 = mpg_99))
      2. │ └─constructive:::try_construct(...)
      3. │   ├─rlang::try_fetch(...)
      4. │   │ ├─base::tryCatch(...)
      5. │   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      6. │   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      7. │   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
      8. │   │ └─base::withCallingHandlers(...)
      9. │   ├─constructive::.cstr_construct(x, ...)
     10. │   ├─constructive:::.cstr_construct.ggplot(x, ...)
     11. │   └─constructive:::.cstr_construct.ggplot.ggplot(x, ...)
     12. │     ├─constructive:::construct_ggplot_call(x$mapping, ...)
     13. │     │ └─constructive:::length(mapping)
     14. │     └─x$mapping
     15. └─base::.handleSimpleError(...)
     16.   └─rlang (local) h(simpleError(msg, call))
     17.     └─handlers[[1L]](cnd)
     18.       └─rlang::abort(...)
    ── Error ('test-s3-ggplot2-labels.R:2:3'): labels ──────────────────────────────
    Error in `construct(ggplot2::labs(x = 1:2, y = c("a", "b")))`: {constructive} could not build the requested code.
    Caused by error in `.subset2()`:
    ! subscript out of bounds
    Backtrace:
         ▆
      1. ├─constructive::construct(ggplot2::labs(x = 1:2, y = c("a", "b")))
      2. │ └─constructive:::try_construct(...)
      3. │   ├─rlang::try_fetch(...)
      4. │   │ ├─base::tryCatch(...)
      5. │   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      6. │   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      7. │   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
      8. │   │ └─base::withCallingHandlers(...)
      9. │   ├─constructive::.cstr_construct(x, ...)
     10. │   └─constructive:::.cstr_construct.default(x, ...)
     11. │     ├─constructive:::.cstr_construct.list(x, ...)
     12. │     └─constructive:::.cstr_construct.list.list(x, ...)
     13. │       └─constructive:::repair_attributes_list(x, code, ...)
     14. │         └─constructive::.cstr_repair_attributes(x, code, ..., repair_names = repair_names)
     15. │           └─constructive::.cstr_apply(attrs, fun = "structure", ...)
     16. │             └─constructive:::lapply(...)
     17. │               └─base::lapply(unclass(X), FUN, ...)
     18. │                 └─constructive (local) FUN(X[[i]], ...)
     19. │                   ├─constructive::.cstr_construct(x, ...)
     20. │                   └─constructive:::.cstr_construct.default(x, ...)
     21. │                     ├─constructive:::.cstr_construct.function(x, ...)
     22. │                     └─constructive:::.cstr_construct.function.function(x, ...)
     23. │                       └─constructive:::repair_attributes_function(x_bkp, code, ...)
     24. │                         └─constructive::.cstr_repair_attributes(...)
     25. │                           └─constructive::.cstr_apply(attrs, fun = "structure", ...)
     26. │                             └─constructive:::lapply(...)
     27. │                               └─base::lapply(unclass(X), FUN, ...)
     28. │                                 └─constructive (local) FUN(X[[i]], ...)
     29. │                                   ├─constructive::.cstr_construct(x, ...)
     30. │                                   └─constructive:::.cstr_construct.default(x, ...)
     31. │                                     ├─constructive:::.cstr_construct.list(x, ...)
     32. │                                     └─constructive:::.cstr_construct.list.list(x, ...)
     33. │                                       └─constructive:::construct_list(...)
     34. │                                         └─constructive::.cstr_apply(x, fun = constructor, ..., trailing_comma = trailing_comma)
     35. │                                           └─constructive:::lapply(...)
     36. │                                             └─base::lapply(unclass(X), FUN, ...)
     37. │                                               └─constructive (local) FUN(X[[i]], ...)
     38. │                                                 ├─constructive::.cstr_construct(x, ...)
     39. │                                                 ├─constructive:::.cstr_construct.function(x, ...)
     40. │                                                 └─constructive:::.cstr_construct.function.function(x, ...)
     41. │                                                   └─constructive::.cstr_apply(...)
     42. │                                                     └─constructive:::lapply(...)
     43. │                                                       └─base::lapply(unclass(X), FUN, ...)
     44. │                                                         └─constructive (local) FUN(X[[i]], ...)
     45. │                                                           ├─constructive::.cstr_construct(x, ...)
     46. │                                                           └─constructive:::.cstr_construct.environment(x, ...)
     47. │                                                             ├─base::structure(NA, class = opts$constructor)
     48. │                                                             └─opts$constructor
     49. └─rlang (local) `<fn>`(`<sbscOOBE>`)
     50.   └─handlers[[1L]](cnd)
     51.     └─rlang::abort(...)
    ── Error ('test-s3-ggplot2-theme.R:2:3'): theme ────────────────────────────────
    Error in `construct(ggplot2::theme_bw(base_size = 22, base_line_size = 1))`: {constructive} could not build the requested code.
    Caused by error in `[[<-`:
    ! object of type 'object' is not subsettable
    Backtrace:
         ▆
      1. ├─constructive::construct(ggplot2::theme_bw(base_size = 22, base_line_size = 1))
      2. │ └─constructive:::try_construct(...)
      3. │   ├─rlang::try_fetch(...)
      4. │   │ ├─base::tryCatch(...)
      5. │   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      6. │   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      7. │   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
      8. │   │ └─base::withCallingHandlers(...)
      9. │   ├─constructive::.cstr_construct(x, ...)
     10. │   ├─constructive:::.cstr_construct.theme(x, ...)
     11. │   └─constructive:::.cstr_construct.theme.theme(x, ...)
     12. │     └─constructive:::guess_complete_theme(x, ...)
     13. │       └─constructive:::strip_theme(x)
     14. │         └─constructive:::`$<-`(`*tmp*`, size, value = NULL)
     15. │           └─constructive:::`[[<-`(...)
     16. └─rlang (local) `<fn>`(`<ntSbsttE>`)
     17.   └─handlers[[1L]](cnd)
     18.     └─rlang::abort(...)
    
    [ FAIL 6 | WARN 2 | SKIP 113 | PASS 24 ]
    Error: Test failures
    Execution halted

Package: CoSMoS
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘vignette.Rmd’ using rmarkdown
  
  Quitting from vignette.Rmd:227-251 [unnamed-chunk-9]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'vignette.Rmd' failed with diagnostics:
  The `facets` argument of `facet_grid()` was deprecated in ggplot2 2.2.0
  and is now defunct.
  ℹ Please use the `rows` argument instead.
  --- failed re-building ‘vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: coursekata
Check: examples
New result: ERROR
  Running examples in ‘coursekata-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: theme_coursekata
  > ### Title: A simple theme built on top of 'ggplot2::theme_bw'
  > ### Aliases: theme_coursekata
  > 
  > ### ** Examples
  > 
  > gf_boxplot(Thumb ~ RaceEthnic, data = Fingers, fill = ~RaceEthnic)
  Error in `position_dodge()`:
  ! `orientation` must be a string or character vector.
  Backtrace:
      ▆
   1. ├─ggformula::gf_boxplot(Thumb ~ RaceEthnic, data = Fingers, fill = ~RaceEthnic)
   2. │ ├─base::do.call(position_fun, pdots)
   3. │ └─ggplot2::position_dodge(orientation = NA)
   4. │   ├─ggplot2::ggproto(...)
   5. │   │ └─rlang::list2(...)
   6. │   └─rlang::arg_match0(orientation, c("x", "y"))
   7. └─rlang::abort(message = message, call = call)
  Execution halted

Package: coursekata
Check: tests
New result: ERROR
    Running ‘testthat.R’ [29s/21s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(coursekata)
    Loading required package: dslabs
    Loading required package: fivethirtyeight
    Some larger datasets need to be installed separately, like senators and
    house_district_forecast. To install these, we recommend you install the
    fivethirtyeightdata package by running:
    install.packages('fivethirtyeightdata', repos =
    'https://fivethirtyeightdata.github.io/drat/', type = 'source')
    Loading required package: Metrics
    Loading required package: lsr
    Loading required package: mosaic
    
    The 'mosaic' package masks several functions from core packages in order to add 
    additional features.  The original behavior of these functions should not be affected by this.
    
    Attaching package: 'mosaic'
    
    The following objects are masked from 'package:dplyr':
    
        count, do, tally
    
    The following object is masked from 'package:Matrix':
    
        mean
    
    The following object is masked from 'package:ggplot2':
    
        stat
    
    The following object is masked from 'package:testthat':
    
        compare
    
    The following objects are masked from 'package:stats':
    
        IQR, binom.test, cor, cor.test, cov, fivenum, median, prop.test,
        quantile, sd, t.test, var
    
    The following objects are masked from 'package:base':
    
        max, mean, min, prod, range, sample, sum
    
    Loading required package: supernova
    ── CourseKata packages ──────────────────────────────────── coursekata 0.19.0 ──
    ✔ dslabs              0.8.0       ✔ Metrics             0.1.4
    x Lock5withR                      ✔ lsr                 0.5.2
    x fivethirtyeightdata             ✔ mosaic              1.9.2
    ✔ fivethirtyeight     0.6.2       ✔ supernova           3.0.0
    
    Attaching package: 'coursekata'
    
    The following object is masked from 'package:datasets':
    
        penguins
    
    > 
    > test_check("coursekata")
    Starting 2 test processes
    [ FAIL 1 | WARN 0 | SKIP 30 | PASS 89 ]
    
    ══ Skipped tests (30) ══════════════════════════════════════════════════════════
    • On CRAN (30): 'test-gf_model-visual.R:6:3', 'test-gf_model-visual.R:27:5',
      'test-gf_model-visual.R:46:3', 'test-gf_model-visual.R:63:5',
      'test-gf_model-visual.R:107:5', 'test-gf_model-visual.R:123:5',
      'test-gf_model-visual.R:144:5', 'test-gf_model-visual.R:171:5',
      'test-gf_model-visual.R:201:5', 'test-gf_model-visual.R:239:5',
      'test-gf_model-visual.R:261:3', 'test-gf_model-visual.R:276:3',
      'test-gf_model-visual.R:291:3', 'test-gf_model-visual.R:299:3',
      'test-gf_model-visual.R:307:3', 'test-gf_model-visual.R:315:3',
      'test-gf_model-visual.R:323:3', 'test-gf_model-visual.R:331:3',
      'test-gf_model-visual.R:343:3', 'test-gf_model-visual.R:351:3',
      'test-gf_model-visual.R:362:3', 'test-gf_model-visual.R:370:3',
      'test-gf_model-visual.R:378:3', 'test-gf_model-visual.R:386:3',
      'test-gf_model-visual.R:407:3', 'test-gf_model-visual.R:415:3',
      'test-gf_model-visual.R:431:3', 'test-gf_model-visual.R:439:3',
      'test-gf_model-visual.R:451:3', 'test-gf_model-visual.R:465:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-gf_model-visual.R:423:3'): it will translate color arguments if applicable (e.g. fill to color) ──
    Error in `position_dodge(orientation = NA)`: `orientation` must be a string or character vector.
    Backtrace:
         ▆
      1. ├─... %>% ... at test-gf_model-visual.R:423:3
      2. ├─coursekata:::expect_doppelganger(., "[gf_point] cond. mod., y on Y, with color")
      3. │ └─vdiffr::expect_doppelganger(title, fig, ...) at tests/testthat/helper-vdiffr.R:5:5
      4. │   └─vdiffr (local) writer(fig, testcase, title)
      5. │     └─vdiffr:::print_plot(plot, title)
      6. ├─coursekata::gf_model(., lm(later_anxiety ~ condition, data = er))
      7. ├─ggformula::gf_boxplot(...)
      8. │ ├─base::do.call(position_fun, pdots)
      9. │ └─ggplot2::position_dodge(orientation = NA)
     10. │   ├─ggplot2::ggproto(...)
     11. │   │ └─rlang::list2(...)
     12. │   └─rlang::arg_match0(orientation, c("x", "y"))
     13. └─rlang::abort(message = message, call = call)
    
    [ FAIL 1 | WARN 0 | SKIP 30 | PASS 89 ]
    Deleting unused snapshots:
    • gf_model-visual/gf-boxplot-cond-mod-y-on-x-pred-on-color.svg
    • gf_model-visual/gf-boxplot-cond-mod-y-on-x-pred-on-facet.svg
    • gf_model-visual/gf-boxplot-cond-mod-y-on-y-pred-on-color.svg
    • gf_model-visual/gf-boxplot-cond-mod-y-on-y-pred-on-facet.svg
    • gf_model-visual/gf-boxplot-cond-mod-y-on-y.svg
    • gf_model-visual/gf-boxplot-null-mod-y-on-x.svg
    • gf_model-visual/gf-boxplot-null-mod-y-on-y.svg
    • gf_model-visual/gf-dens-null-mod-y-on-x.svg
    • gf_model-visual/gf-density-null-mod-y-on-x.svg
    • gf_model-visual/gf-dhistogram-cond-mod-y-on-x-pred-on-color.svg
    • gf_model-visual/gf-dhistogram-cond-mod-y-on-x-pred-on-facet.svg
    • gf_model-visual/gf-dhistogram-null-mod-y-on-x.svg
    • gf_model-visual/gf-freqpoly-null-mod-y-on-x.svg
    • gf_model-visual/gf-histogram-cond-mod-y-on-x-pred-on-color.svg
    • gf_model-visual/gf-histogram-cond-mod-y-on-x-pred-on-facet.svg
    • gf_model-visual/gf-point-anx-mod-pred-on-color-y-on-x.svg
    • gf_model-visual/gf-point-anx-mod-y-on-x.svg
    • gf_model-visual/gf-point-diverging-lines-in-2-colors-flipped.svg
    • gf_model-visual/gf-point-diverging-lines-in-facets-flipped.svg
    • gf_model-visual/gf-rug-cond-mod-y-on-x-pred-on-color.svg
    • gf_model-visual/gf-rug-cond-mod-y-on-x-pred-on-facet.svg
    • gf_model-visual/gf-rug-null-mod-y-on-x.svg
    • gf_model-visual/gf-rugx-cond-mod-y-on-x-pred-on-color.svg
    • gf_model-visual/gf-rugx-cond-mod-y-on-x-pred-on-facet.svg
    • gf_model-visual/gf-rugx-null-mod-y-on-x.svg
    • gf_model-visual/gf-rugy-cond-mod-y-on-y-pred-on-color.svg
    • gf_model-visual/gf-rugy-cond-mod-y-on-y-pred-on-facet.svg
    • gf_model-visual/gf-violin-cond-mod-y-on-x-pred-on-color.svg
    • gf_model-visual/gf-violin-cond-mod-y-on-x-pred-on-facet.svg
    • gf_model-visual/gf-violin-cond-mod-y-on-y-pred-on-color.svg
    • gf_model-visual/gf-violin-cond-mod-y-on-y-pred-on-facet.svg
    • gf_model-visual/gf-violin-cond-mod-y-on-y.svg
    • gf_model-visual/gf-violin-horizontal-null-mod-y-on-x.svg
    • gf_model-visual/gf-violin-null-mod-y-on-x-2.svg
    • gf_model-visual/gf-violin-null-mod-y-on-y.svg
    Error: Test failures
    Execution halted

Package: cylcop
Check: examples
New result: ERROR
  Running examples in ‘cylcop-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_circ_hist
  > ### Title: Circular Histogram of Turn Angles
  > ### Aliases: plot_circ_hist
  > 
  > ### ** Examples
  > 
  > set.seed(123)
  > 
  > theta <- cylcop::rvonmisesmix(n = 100,
  +   mu = c(0, pi),
  +   kappa = c(5, 2),
  +   prop = c(4, 2)
  + )
  > plot1 <- plot_circ_hist(theta)
  Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
  ℹ Please use `linewidth` instead.
  ℹ The deprecated feature was likely used in the cylcop package.
    Please report the issue at <https://github.com/r-lib/devtools/issues>.
  Error in `geom_label()`:
  ! Problem while setting up geom aesthetics.
  ℹ Error occurred in the 4th layer.
  Caused by error in `list_sizes()`:
  ! `x$label` must be a vector, not an expression vector.
  Backtrace:
       ▆
    1. ├─cylcop::plot_circ_hist(theta)
    2. │ ├─base::suppressWarnings(cowplot::ggdraw(p))
    3. │ │ └─base::withCallingHandlers(...)
    4. │ └─cowplot::ggdraw(p)
    5. │   └─cowplot::draw_plot(plot)
    6. │     ├─cowplot::as_grob(plot)
    7. │     └─cowplot:::as_grob.ggplot(plot)
    8. │       └─ggplot2::ggplotGrob(plot)
    9. │         ├─ggplot2::ggplot_gtable(ggplot_build(x))
   10. │         │ └─ggplot2:::attach_plot_env(data@plot@plot_env)
   11. │         │   └─base::options(ggplot2_plot_env = env)
   12. │         ├─ggplot2::ggplot_build(x)
   13. │         └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
   14. │           └─ggplot2:::by_layer(...)
   15. │             ├─rlang::try_fetch(...)
   16. │             │ ├─base::tryCatch(...)
   17. │             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   18. │             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   19. │             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   20. │             │ └─base::withCallingHandlers(...)
   21. │             └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   22. │               └─l$compute_geom_2(d, theme = plot@theme)
   23. │                 └─ggplot2 (local) compute_geom_2(..., self = self)
   24. │                   └─self$geom$use_defaults(...)
   25. │                     └─ggplot2 (local) use_defaults(..., self = self)
   26. │                       └─ggplot2:::check_aesthetics(new_params, nrow(data))
   27. │                         └─vctrs::list_sizes(x)
   28. └─vctrs:::stop_scalar_type(`<fn>`(`<expression>`), "x$label", `<env>`)
   29.   └─vctrs:::stop_vctrs(...)
   30.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  Execution halted

Package: D2MCS
Check: tests
New result: ERROR
    Running ‘test_all.R’ [79s/79s]
  Running the tests in ‘tests/test_all.R’ failed.
  Complete output:
    > testthat::test_check("D2MCS")
    Loading required package: D2MCS
    [ FAIL 5 | WARN 6 | SKIP 15 | PASS 755 ]
    
    ══ Skipped tests (15) ══════════════════════════════════════════════════════════
    • On CRAN (2): 'test_D2MCS.R:129:3', 'test_D2MCS.R:213:3'
    • {ranger} is not installed (13): 'test_D2MCS.R:411:3',
      'test_prediction.ClusterPredictions.R:17:3',
      'test_prediction.ClusterPredictions.R:46:3',
      'test_prediction.CombinedVoting.R:150:3', 'test_prediction.Prediction.R:2:3',
      'test_prediction.Prediction.R:29:3', 'test_prediction.Prediction.R:50:3',
      'test_prediction.Prediction.R:75:3', 'test_prediction.Prediction.R:96:3',
      'test_prediction.Prediction.R:128:3', 'test_prediction.Prediction.R:166:3',
      'test_prediction.Prediction.R:179:3', 'test_prediction.SingleVoting.R:27:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_clustering.plot.BinaryPlot.R:10:3'): BinaryPlot: plot function works ──
    c("gg", "ggplot") not equal to class(plot$plot(summary)).
    Lengths differ: 2 is not 5
    ── Failure ('test_clustering.plot.GenericPlot.R:9:3'): GenericPlot: plot function works ──
    c("gg", "ggplot") not equal to class(plot$plot(summary)).
    Lengths differ: 2 is not 5
    ── Failure ('test_clustering.strategies.SimpleStrategy.R:111:3'): SimpleStrategy works ──
    c("gg", "ggplot") not equal to class(strategy$plot(dir.path = NULL, file.name = NULL)).
    Lengths differ: 2 is not 5
    ── Failure ('test_clustering.strategies.TypeBasedStrategy.R:226:3'): TypeBasedStrategy works ──
    c("gg", "ggplot") not equal to class(strategyNoReal$plot()).
    Lengths differ: 2 is not 5
    ── Failure ('test_clustering.strategies.TypeBasedStrategy.R:234:3'): TypeBasedStrategy works ──
    c("gg", "ggplot") not equal to class(strategyNoBinary$plot()).
    Lengths differ: 2 is not 5
    
    [ FAIL 5 | WARN 6 | SKIP 15 | PASS 755 ]
    Error: Test failures
    Execution halted

Package: dabestr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [58s/58s]
  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(dabestr)
    
    Attaching package: 'dabestr'
    
    The following object is masked from 'package:base':
    
        load
    
    > 
    > test_check("dabestr")
    The character(0) mean difference between Test 1 and Control 1 is 0.585 [95%CI 0.307, 0.869].
    The p-value of the two-sided permutation t-test is 0.0004, calculated for legacy purposes only.
    
    The character(0) mean difference between Test 2 and Control 2 is -1.058 [95%CI -1.52, -0.577].
    The p-value of the two-sided permutation t-test is 0.0002, calculated for legacy purposes only.
    
    [ FAIL 1 | WARN 0 | SKIP 2 | PASS 141 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test_001_plotter.R:2:3', 'test_002_forest_plot.R:2:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_002_plot_components.R:15:5'): Returns a list with correct components for valid inputs ──
    result[[1]] has type 'object', not 'list'.
    
    [ FAIL 1 | WARN 0 | SKIP 2 | PASS 141 ]
    Deleting unused snapshots:
    • 001_plotter/deltadelta-mean-diff.svg
    • 001_plotter/minimeta-mean-diff.svg
    • 001_plotter/multigroup-baseline-colour-mean-diff.svg
    • 001_plotter/multigroup-baseline-mean-diff.svg
    • 001_plotter/multigroup-sequential-mean-diff.svg
    • 001_plotter/multigroup-unpaired-mean-diff-colour.svg
    • 001_plotter/multigroup-unpaired-mean-diff.svg
    • 001_plotter/proportion-baseline-flow-false-mean-diff.svg
    • 001_plotter/proportion-baseline-mean-diff.svg
    • 001_plotter/proportion-paired-mean-diff-float-false.svg
    • 001_plotter/proportion-paired-mean-diff-float-true.svg
    • 001_plotter/proportion-sequential-mean-diff.svg
    • 001_plotter/proportion-unpaired-mean-diff-float-false.svg
    • 001_plotter/proportion-unpaired-mean-diff-float-true.svg
    • 001_plotter/proportion-unpaired-multigroup-mean-diff.svg
    • 001_plotter/two-groups-unpaired-mean-diff-colour-float-false.svg
    • 001_plotter/two-groups-unpaired-mean-diff-colour-float-true.svg
    • 001_plotter/two-groups-unpaired-mean-diff-float-false.svg
    • 001_plotter/two-groups-unpaired-mean-diff-float-true.svg
    • 002_forest_plot/deltadelta-forest-plot-mean-diff.svg
    • 002_forest_plot/deltadelta-forest-plot-with-plot-kwargs.svg
    • 002_forest_plot/minimeta-forest-plot-mean-diff.svg
    • 002_forest_plot/minimeta-forest-plot-median-diff.svg
    • 002_forest_plot/minimeta-forest-plot-with-plot-kwargs.svg
    Error: Test failures
    Execution halted

Package: DAISIEprep
Check: tests
New result: ERROR
    Running ‘testthat.R’ [106s/107s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(DAISIEprep)
    > 
    > test_check("DAISIEprep")
    [ FAIL 4 | WARN 2 | SKIP 14 | PASS 2235 ]
    
    ══ Skipped tests (14) ══════════════════════════════════════════════════════════
    • Run only on CI (3): 'test-sensitivity.R:2:3', 'test-sensitivity.R:40:3',
      'test-sensitivity.R:78:3'
    • empty test (11): 'test-create_daisie_data.R:169:1',
      'test-create_daisie_data.R:173:1', 'test-create_daisie_data.R:177:1',
      'test-create_daisie_data.R:181:1', 'test-create_daisie_data.R:185:1',
      'test-create_daisie_data.R:189:1', 'test-create_daisie_data.R:231:1',
      'test-create_daisie_data.R:235:1', 'test-create_daisie_data.R:239:1',
      'test-create_daisie_data.R:243:1', 'test-create_daisie_data.R:247:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot_phylod.R:3:3'): plot_phylod runs silent without error ───
    `plot_phylod(phylod = phylod, node_pies = FALSE)` produced warnings.
    ── Failure ('test-plot_phylod.R:8:3'): plot_phylod runs silent without error ───
    `plot_phylod(phylod = phylod, node_pies = FALSE)` produced warnings.
    ── Failure ('test-plot_phylod.R:13:3'): plot_phylod runs silent without error ──
    `plot_phylod(phylod = phylod, node_pies = TRUE)` produced warnings.
    ── Failure ('test-plot_phylod.R:18:3'): plot_phylod runs silent without error ──
    `plot_phylod(phylod = phylod, node_pies = TRUE)` produced warnings.
    
    [ FAIL 4 | WARN 2 | SKIP 14 | PASS 2235 ]
    Error: Test failures
    Execution halted

Package: dams
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘dams.Rmd’ using rmarkdown
  
  Quitting from dams.Rmd:82-119 [unnamed-chunk-7]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::labels> object is invalid:
  - every label must be named.
  ---
  Backtrace:
      ▆
   1. └─ggplot2::labs(...)
   2.   └─ggplot2::class_labels(args)
   3.     └─S7::new_object(labels)
   4.       └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'dams.Rmd' failed with diagnostics:
  <ggplot2::labels> object is invalid:
  - every label must be named.
  --- failed re-building ‘dams.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘dams.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: Deducer
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘Deducer’

Package: delimtools
Check: examples
New result: ERROR
  Running examples in ‘delimtools-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: get_delim_cols
  > ### Title: Extract Labels and Colors from Species Delimitation Partitions
  > ### Aliases: get_delim_cols
  > 
  > ### ** Examples
  > 
  > 
  > # plot using autoplot
  > p <- delim_autoplot(geophagus_delims, geophagus_beast)
  Warning: ⚠ Argument `tbl_labs` not provided. Using tiplabels instead.
  Warning in fortify(data, ...) : Arguments in `...` must be used.
  ✖ Problematic arguments:
  • as.Date = as.Date
  • yscale_mapping = yscale_mapping
  • hang = hang
  • color = "grey50"
  • size = 1
  ℹ Did you misspell an argument name?
  Warning: ⚠ Argument `delim_order` not provided. Using default order from
  `geophagus_delims`.
  Warning: ⚠ Argument `col_vec` not provided. Customizing one using `delim_brewer()`.
  ℹ Please use `delimtools::delim_brewer()` to create even better colour
    palettes!
  Warning: ⚠ `n_match` was not found. Using `n_match= 4` instead.
  > 
  > # view 
  > p
  > 
  > # get haplotypes
  > hap_tbl <- haplotype_tbl(geophagus)
  Warning: ⚠ You have missing data "('N','-' '?')" or ambiguity inside your sequence, i.e.
  not padding the ends, and this may have unintended consequences later, as they
  have now been removed!
  ℹ The names of the samples are bellow.
  GU701784.1, GU701785.1
  > 
  > # extract colors for consensus
  > get_delim_cols(p, delimname= "consensus", hap_tbl= hap_tbl)
  Error in `pluck_raw()`:
  ! Index 1 must be a string, not a number.
  Backtrace:
      ▆
   1. └─delimtools::get_delim_cols(p, delimname = "consensus", hap_tbl = hap_tbl)
   2.   ├─rlang::is_empty(purrr::pluck(p_build, 1, 2))
   3.   └─purrr::pluck(p_build, 1, 2)
   4.     └─purrr:::pluck_raw(.x, list2(...), .default = .default)
   5.       └─purrr:::stop_bad_element_type(...)
   6.         └─cli::cli_abort(...)
   7.           └─rlang::abort(...)
  Execution halted

Package: DImodelsVis
Check: package dependencies
New result: ERROR
  Package required but not available: ‘PieGlyph’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: dipm
Check: differences from ‘dipm-Ex.Rout’ to ‘dipm-Ex.Rout.save’
New result: NOTE
  151,155d150
  < Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
  < ℹ Please use tidy evaluation idioms with `aes()`.
  < ℹ See also `vignette("ggplot2-in-packages")` for more information.
  < ℹ The deprecated feature was likely used in the dipm package.
  <   Please report the issue to the authors.

Package: DiSCos
Check: tests
New result: ERROR
    Running ‘testthat.R’ [193s/192s]
  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(DiSCos)
    Loading required package: data.table
    Loading required package: ggplot2
    > 
    > options(datatable.auto.thread = 1)  # Limit data.table to 1 thread
    > Sys.setenv(OMP_NUM_THREADS = 1) # limit environment to 1 thread
    > 
    > test_check("DiSCos")
    Warning: in parln3(lmom, ...): L-skew is negative, try reversing the data Y <- -X, to avoid a log(<0) error
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parln3 -> warning -> parln3(lmom, ...)
    Warning: in are.pargam.valid(z): Parameter ALPHA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in are.pargam.valid(z): Parameter BETA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parln3(lmom, ...): L-skew is negative, try reversing the data Y <- -X, to avoid a log(<0) error
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parln3 -> warning -> parln3(lmom, ...)
    Warning: in are.pargam.valid(z): Parameter BETA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parrice(lmom, ...): LCV too small (<0.0236) for Rice as implemented
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parrice -> warning -> parrice(lmom, ...)
    Warning: in are.pargam.valid(z): Parameter BETA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parrice(lmom, ...): LCV too small (<0.0236) for Rice as implemented
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parrice -> warning -> parrice(lmom, ...)
    Warning: in are.pargam.valid(z): Parameter ALPHA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parrice(lmom, ...): LCV too small (<0.0236) for Rice as implemented
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parrice -> warning -> parrice(lmom, ...)
    Warning: in are.pargam.valid(z): Parameter ALPHA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parrice(lmom, ...): LCV too small (<0.0236) for Rice as implemented
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parrice -> warning -> parrice(lmom, ...)
    Warning: in are.pargam.valid(z): Parameter ALPHA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parln3(lmom, ...): L-skew is negative, try reversing the data Y <- -X, to avoid a log(<0) error
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parln3 -> warning -> parln3(lmom, ...)
    Warning: in parrice(lmom, ...): LCV too small (<0.0236) for Rice as implemented
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parrice -> warning -> parrice(lmom, ...)
    Warning: in are.parsmd.valid(z, nowarn = TRUE): Parameter A is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parsmd -> are.parsmd.valid -> warning -> are.parsmd.valid(z, nowarn = TRUE)
    Warning: in are.pargam.valid(z): Parameter ALPHA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parln3(lmom, ...): L-skew is negative, try reversing the data Y <- -X, to avoid a log(<0) error
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parln3 -> warning -> parln3(lmom, ...)
    Warning: in parrice(lmom, ...): LCV too small (<0.0236) for Rice as implemented
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parrice -> warning -> parrice(lmom, ...)
    Warning: in are.pargam.valid(z): Parameter BETA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parrice(lmom, ...): LCV too small (<0.0236) for Rice as implemented
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parrice -> warning -> parrice(lmom, ...)
    Warning: in are.pargam.valid(z): Parameter ALPHA is not > 0, invalid
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> are.pargam.valid -> warning -> are.pargam.valid(z)
    Warning: in pargam(lmom, ...): Parameters can not be computed likely because L1 <= L2 or L2 <= 0
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> pargam -> warning -> pargam(lmom, ...)
    Warning: in parrice(lmom, ...): LCV too small (<0.0236) for Rice as implemented
    -- tryStack sys.calls: test_check -> test_dir -> test_files -> test_files_serial -> with_reporter -> lapply -> FUN -> source_file -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> test_that -> test_code -> tryCatchOne -> tryCatchList -> withCallingHandlers -> eval -> eval -> expect_no_error -> expect_no_ -> quasi_capture -> .capture -> try_fetch -> withCallingHandlers -> eval_bare -> DiSCo -> mclapply.hack -> lapply -> FUN -> myQuant -> extremeStat::distLquantile -> distLfit -> lapply -> FUN -> tryStack -> lmomco::lmom2par -> parrice -> warning -> parrice(lmom, ...)
    
    Call:
    DiSCoTEA(disco = disco, agg = "quantileDiff", graph = TRUE)
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    Aggregated Distribution Differences, Quantile Δ 
     Time X_from X_to Quantile Δ Std. Error   [95%  Conf. Band]  
     2003      0  0.9    -0.0508     0.0699 -0.1334      0.0171  
     2004      0  0.9    -0.1492     0.0491 -0.2257     -0.1171 *
    ---
    Signif. codes: `*' Confidence band for distribution differences does not cover 0
    
    Permutation test for quantile range: [0, 0.9] 
    P-value:  0.176 
    Number of control units:  33 
    Number of pre-treatment periods: 5
    Number of post-treatment periods: 2
    N=652,870
    
    Call:
    DiSCoTEA(disco = disco, agg = "quantile")
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    No treatment effects to summarize, set graph=TRUE in function call or specify a treatment effect option in `agg`.
    Call:
    DiSCoTEA(disco = disco, agg = "quantile")
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    No treatment effects to summarize, set graph=TRUE in function call or specify a treatment effect option in `agg`.
    Call:
    DiSCoTEA(disco = disco, agg = "cdf")
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    No treatment effects to summarize, set graph=TRUE in function call or specify a treatment effect option in `agg`.
    Call:
    DiSCoTEA(disco = disco, agg = "cdf")
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    No treatment effects to summarize, set graph=TRUE in function call or specify a treatment effect option in `agg`.
    Call:
    DiSCoTEA(disco = disco, agg = "quantileDiff")
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    Aggregated Distribution Differences, Quantile Δ 
     Time X_from X_to Quantile Δ Std. Error   [95%  Conf. Band]  
        2   0.00 0.25    -3.1149     0.0832 -3.4032     -3.2915 *
        2   0.25 0.50    -0.5900     0.1802 -0.7864     -0.5443 *
        2   0.50 0.75    -0.4505     0.3749 -0.5950     -0.0913 *
        2   0.75 1.00     0.2993     0.5222 -0.1052      0.5964  
    ---
    Signif. codes: `*' Confidence band for distribution differences does not cover 0
    
    No permutation test performed. 
    Number of pre-treatment periods: 1
    Number of post-treatment periods: 1
    N=10,000
    
    Call:
    DiSCoTEA(disco = disco, agg = "quantileDiff")
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    Aggregated Distribution Differences, Quantile Δ 
     Time X_from X_to Quantile Δ Std. Error  [95%  Conf. Band]  
        2   0.00 0.25     2.9313     0.1357 2.8928      3.0751 *
        2   0.25 0.50     2.2455     0.5058 2.0634      2.7429 *
        2   0.50 0.75     3.0117     0.1604 2.9527      3.1682 *
        2   0.75 1.00     1.2742     0.5918 0.6860      1.4812 *
    ---
    Signif. codes: `*' Confidence band for distribution differences does not cover 0
    
    No permutation test performed. 
    Number of pre-treatment periods: 1
    Number of post-treatment periods: 1
    N=10,000
    
    Call:
    DiSCoTEA(disco = disco, agg = "quantileDiff")
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    Aggregated Distribution Differences, Quantile Δ 
     Time X_from X_to Quantile Δ Std. Error   [95%  Conf. Band]  
        2   0.00 0.25    -3.1149     0.0832 -3.4032     -3.2915 *
        2   0.25 0.50    -0.5900     0.1802 -0.7864     -0.5443 *
        2   0.50 0.75    -0.4505     0.3749 -0.5950     -0.0913 *
        2   0.75 1.00     0.2993     0.5222 -0.1052      0.5964  
    ---
    Signif. codes: `*' Confidence band for distribution differences does not cover 0
    
    No permutation test performed. 
    Number of pre-treatment periods: 1
    Number of post-treatment periods: 1
    N=10,000
    
    Call:
    DiSCoTEA(disco = disco, agg = "quantileDiff")
    
    Reference: Gunsilius, Florian F. "Distributional synthetic controls." Econometrica 91, no. 3 (2023): 1105-1117. 
    
    Aggregated Distribution Differences, Quantile Δ 
     Time X_from X_to Quantile Δ Std. Error  [95%  Conf. Band]  
        2   0.00 0.25     2.9313     0.1357 2.8928      3.0751 *
        2   0.25 0.50     2.2455     0.5058 2.0634      2.7429 *
        2   0.50 0.75     3.0117     0.1604 2.9527      3.1682 *
        2   0.75 1.00     1.2742     0.5918 0.6860      1.4812 *
    ---
    Signif. codes: `*' Confidence band for distribution differences does not cover 0
    
    No permutation test performed. 
    Number of pre-treatment periods: 1
    Number of post-treatment periods: 1
    N=10,000
    [ FAIL 8 | WARN 2 | SKIP 1 | PASS 107 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • empty test (1): 'test-DiSCoTEA.R:2:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-DiSCoTEA.R:24:3'): quantile works ────────────────────────────
    typeof(discot$plot) == "list" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-DiSCoTEA.R:40:3'): quantile works ────────────────────────────
    typeof(discot$plot) == "list" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-DiSCoTEA.R:59:3'): cdf works ─────────────────────────────────
    typeof(discot$plot) == "list" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-DiSCoTEA.R:74:3'): cdf works ─────────────────────────────────
    typeof(discot$plot) == "list" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-DiSCoTEA.R:93:3'): quantileDiff works ────────────────────────
    typeof(discot$plot) == "list" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-DiSCoTEA.R:108:3'): quantileDiff works ───────────────────────
    typeof(discot$plot) == "list" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-DiSCoTEA.R:127:3'): cdfDiff works ────────────────────────────
    typeof(discot$plot) == "list" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-DiSCoTEA.R:142:3'): cdfDiff works ────────────────────────────
    typeof(discot$plot) == "list" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 8 | WARN 2 | SKIP 1 | PASS 107 ]
    Error: Test failures
    Execution halted

Package: distributions3
Check: tests
New result: ERROR
    Running ‘testthat.R’ [41s/22s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(distributions3)
    
    Attaching package: 'distributions3'
    
    The following object is masked from 'package:stats':
    
        Gamma
    
    The following object is masked from 'package:grDevices':
    
        pdf
    
    > 
    > test_check("distributions3")
    Starting 2 test processes
    [ FAIL 2 | WARN 14 | SKIP 0 | PASS 2766 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot.R:50:3'): ggplot2 implementation works ──────────────────
    `print(gg1)` produced warnings.
    ── Failure ('test-plot.R:56:3'): ggplot2 implementation works ──────────────────
    `print(gg3)` produced warnings.
    
    [ FAIL 2 | WARN 14 | SKIP 0 | PASS 2766 ]
    Error: Test failures
    Execution halted

Package: door
Check: tests
New result: ERROR
    Running ‘testthat.R’ [10s/10s]
  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(door)
    > 
    > test_check("door")
    NA detected. NA values will be replaced by 0.
    NA detected. NA values will be replaced by 0.
    [ FAIL 8 | WARN 10 | SKIP 0 | PASS 25 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plots.R:25:3'): DOOR barplot ─────────────────────────────────
    door_barplot(y1 = y1t, y2 = y2t) has type 'object', not 'list'.
    ── Failure ('test-plots.R:26:3'): DOOR barplot ─────────────────────────────────
    door_barplot(y1 = y1p, y2 = y2p) has type 'object', not 'list'.
    ── Failure ('test-plots.R:27:3'): DOOR barplot ─────────────────────────────────
    door_barplot(summary_obj = obj1) has type 'object', not 'list'.
    ── Failure ('test-plots.R:31:3'): DOOR component barplot ───────────────────────
    door_component_barplot(comp_table = comptable, n1 = 100, n2 = 100) has type 'object', not 'list'.
    ── Failure ('test-plots.R:32:3'): DOOR component barplot ───────────────────────
    door_component_barplot(summary_obj = obj1) has type 'object', not 'list'.
    ── Failure ('test-plots.R:46:3'): Partial credit plot ──────────────────────────
    partial_credit_biplot(pc_obj1) has type 'object', not 'list'.
    ── Failure ('test-plots.R:47:3'): Partial credit plot ──────────────────────────
    partial_credit_biplot(pc_obj2) has type 'object', not 'list'.
    ── Failure ('test-plots.R:48:3'): Partial credit plot ──────────────────────────
    partial_credit_contour_plot(y1 = y1t, y2 = y2t) has type 'object', not 'list'.
    
    [ FAIL 8 | WARN 10 | SKIP 0 | PASS 25 ]
    Error: Test failures
    Execution halted

Package: dsb
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘additional_topics.Rmd’ using rmarkdown
  --- finished re-building ‘additional_topics.Rmd’
  
  --- re-building ‘end_to_end_workflow.rmd’ using rmarkdown
  --- finished re-building ‘end_to_end_workflow.rmd’
  
  --- re-building ‘fastkm.Rmd’ using rmarkdown
  --- finished re-building ‘fastkm.Rmd’
  
  --- re-building ‘no_empty_drops.Rmd’ using rmarkdown
  --- finished re-building ‘no_empty_drops.Rmd’
  
  --- re-building ‘understanding_dsb.Rmd’ using rmarkdown
  
  Quitting from understanding_dsb.Rmd:75-104 [unnamed-chunk-7]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'understanding_dsb.Rmd' failed with diagnostics:
  Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  --- failed re-building ‘understanding_dsb.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘understanding_dsb.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: duke
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘duke.Rmd’ using rmarkdown
  
  Quitting from duke.Rmd:21-28 [setup]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `library()`:
  ! there is no package called 'ggmosaic'
  ---
  Backtrace:
      ▆
   1. └─base::library(ggmosaic)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'duke.Rmd' failed with diagnostics:
  there is no package called 'ggmosaic'
  --- failed re-building ‘duke.Rmd’
  
  --- re-building ‘scale_duke_color_discrete.Rmd’ using rmarkdown
  
  Quitting from scale_duke_color_discrete.Rmd:26-31 [penguins]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `library()`:
  ! there is no package called 'ggmosaic'
  ---
  Backtrace:
      ▆
   1. └─base::library(ggmosaic)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'scale_duke_color_discrete.Rmd' failed with diagnostics:
  there is no package called 'ggmosaic'
  --- failed re-building ‘scale_duke_color_discrete.Rmd’
  
  --- re-building ‘scale_duke_continuous.Rmd’ using rmarkdown
  --- finished re-building ‘scale_duke_continuous.Rmd’
  
  --- re-building ‘scale_duke_fill_discrete.Rmd’ using rmarkdown
  
  Quitting from scale_duke_fill_discrete.Rmd:24-29 [penguins]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `library()`:
  ! there is no package called 'ggmosaic'
  ---
  Backtrace:
      ▆
   1. └─base::library(ggmosaic)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'scale_duke_fill_discrete.Rmd' failed with diagnostics:
  there is no package called 'ggmosaic'
  --- failed re-building ‘scale_duke_fill_discrete.Rmd’
  
  --- re-building ‘theme_duke_vignette.Rmd’ using rmarkdown
  --- finished re-building ‘theme_duke_vignette.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘duke.Rmd’ ‘scale_duke_color_discrete.Rmd’
    ‘scale_duke_fill_discrete.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: duke
Check: tests
New result: ERROR
    Running ‘testthat.R’ [6s/6s]
  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(duke)
    > 
    > test_check("duke")
    New names:
    * `colour` -> `colour...1`
    * `colour` -> `colour...4`
    [ FAIL 1 | WARN 10 | SKIP 0 | PASS 27 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-scale_duke_fill_discrete.R:36:3'): appropriate fill for factors over 8-levels ──
    ggplot2::layer_data(p3)$fill[9] (`actual`) not equal to "#B5B5B5" (`expected`).
    
    `actual`:   NA       
    `expected`: "#B5B5B5"
    Backtrace:
        ▆
     1. ├─testthat::expect_warning(...) at test-scale_duke_fill_discrete.R:36:3
     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. └─testthat::expect_equal(ggplot2::layer_data(p3)$fill[9], "#B5B5B5")
    
    [ FAIL 1 | WARN 10 | SKIP 0 | PASS 27 ]
    Error: Test failures
    Execution halted

Package: dynConfiR
Check: examples
New result: ERROR
  Running examples in ‘dynConfiR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: RaceModels
  > ### Title: Independent and partially anti-correlated Race Model for
  > ###   Decision Confidence
  > ### Aliases: RaceModels dIRM dPCRM rRM dRM rIRM rPCRM racemodels dIRM2
  > ###   dIRM3
  > 
  > ### ** Examples
  > 
  > # Plot rt distribution ignoring confidence
  > curve(dPCRM(x, 1, mu1=0.5, mu2=-0.5, a=1, b=1, th1=-Inf, th2=Inf, t0=0.1), xlim=c(0,2.5))
  > curve(dPCRM(x, 2, mu1=0.5, mu2=-0.5, a=1, b=1, th1=-Inf, th2=Inf, t0=0.1), col="red", add=TRUE)
  > curve(dIRM(x, 1, mu1=0.5, mu2=-0.5, a=1, b=1, th1=-Inf, th2=Inf, t0=0.1), lty=2,add=TRUE)
  > curve(dIRM(x, 2, mu1=0.5, mu2=-0.5, a=1, b=1, th1=-Inf, th2=Inf, t0=0.1),
  +       col="red", lty=2, add=TRUE)
  > # t0 indicates minimal response time possible
  > abline(v=0.1)
  > ## Following example may be equivalently used for the IRM model functions.
  > # Generate a random sample
  > df1 <- rPCRM(5000,  mu1=0.2, mu2=-0.2, a=1, b=1, t0=0.1,
  +             wx = 1) # Balance of Evidence
  > # Same RT and response distribution but different confidence distribution
  > df2 <- rPCRM(5000,  mu1=0.2, mu2=-0.2, a=1, b=1, t0=0.1,
  +              wint = 0.2, wrt=0.8)
  > head(df1)
       rt response         xl      conf
  1  0.65        1 -0.1666653 1.1666653
  2 11.59        1 -6.8019691 7.8019691
  3  1.89        2 -0.3117717 1.3117717
  4  0.85        2  0.5670769 0.4329231
  5  0.77        2  0.2080419 0.7919581
  6  0.32        1 -0.1913931 1.1913931
  > 
  > # Compute density with rt and response as separate arguments
  > dPCRM(seq(0, 2, by =0.4), response= 2, mu1=0.2, mu2=-0.2, a=1, b=1, th1=0.5,
  +          th2=2, wx = 0.3, wint=0.4, wrt=0.1, t0=0.1)
  [1] 0.00000000 0.26919023 0.20371811 0.10962250 0.06320931 0.03928042
  > # Compute density with rt and response in data.frame argument
  > df1 <- subset(df1, response !=0) # drop trials where no accumulation hit its boundary
  > dPCRM(df1[1:5,], mu1=0.2, mu2=-0.2, a=1, b=1, th1=0, th2=Inf, t0=0.1)
  [1] 0.449022313 0.001737302 0.051678757 0.215121579 0.244686625
  > # s1 and s2 scale other decision relevant parameters
  >  s <- 2  # common (equal) standard deviation
  > dPCRM(df1[1:5,], mu1=0.2*s, mu2=-0.2*s, a=1*s, b=1*s, th1=0, th2=Inf, t0=0.1, s1=s, s2=s)
  [1] 0.449022313 0.001737302 0.051678757 0.215121579 0.244686625
  > s1 <- 2  # different standard deviations
  > s2 <- 1.5
  > dPCRM(df1[1:5,], mu1=0.2*s1, mu2=-0.2*s2, a=1*s1, b=1*s2, th1=0, th2=Inf, t0=0.1, s1=s1, s2=s2)
  [1] 0.449022313 0.001737302 0.051678757 0.215121579 0.244686625
  > 
  > 
  > # s1 and s2 scale also confidence parameters
  > df1[1:5,]$response <- 2   # set response to 2
  > # for confidence it is important to scale confidence parameters with
  > # the right variation parameter (the one of the loosing accumulator)
  > dPCRM(df1[1:5,], mu1=0.2, mu2=-0.2, a=1, b=1,
  +      th1=0.5, th2=2, wx = 0.3, wint=0.4, wrt=0.1, t0=0.1)
  [1] 0.253627090 0.000290214 0.044476406 0.188375881 0.213369269
  > dPCRM(df1[1:5,], mu1=0.2*s1, mu2=-0.2*s2, a=1*s1, b=1*s2,
  +       th1=0.5, th2=2, wx = 0.3/s1, wint = 0.4/s1, wrt = 0.1, t0=0.1, s1=s1, s2=s2)
  [1] 0.253627090 0.000290214 0.044476406 0.188375881 0.213369269
  > dPCRM(df1[1:5,], mu1=0.2*s1, mu2=-0.2*s2, a=1*s1, b=1*s2,
  +       th1=0.5*s1, th2=2*s1, wx = 0.3, wint = 0.4, wrt = 0.1*s1, t0=0.1, s1=s1, s2=s2)
  [1] 0.253627090 0.000290214 0.044476406 0.188375881 0.213369269
  > 
  > two_samples <- rbind(cbind(df1, ws="BoE"),
  +                    cbind(df2, ws="RT"))
  > # drop not finished decision processes
  > two_samples <- two_samples[two_samples$response!=0,]
  > # no difference in RT distributions
  > boxplot(rt~ws+response, data=two_samples)
  > # but different confidence distributions
  > boxplot(conf~ws+response, data=two_samples)
  > if (requireNamespace("ggplot2", quietly = TRUE)) {
  + require(ggplot2)
  + ggplot(two_samples, aes(x=rt, y=conf))+
  +   stat_density_2d(aes(fill = after_stat(density)),
  +                   geom = "raster", contour = FALSE, h=c(0.3, 0.7)) +
  +   xlim(c(0.2, 1.3))+ ylim(c(0, 2.5))+
  +   facet_grid(cols=vars(ws), rows=vars(response), labeller = "label_both")
  + }
  Loading required package: ggplot2
  Error in `stat_density_2d()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 1st layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_build(x)
    4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$compute_statistic(d, layout)
   14. │         └─ggplot2 (local) compute_statistic(..., self = self)
   15. │           └─self$stat$compute_layer(data, self$computed_stat_params, layout)
   16. │             └─ggplot2 (local) compute_layer(..., self = self)
   17. │               └─rlang::check_installed("MASS", reason = "for calculating 2D density.")
   18. │                 └─base::stop(cnd)
   19. └─rlang (local) `<fn>`(`<rlb_r___>`)
   20.   └─handlers[[1L]](cnd)
   21.     └─cli::cli_abort(...)
   22.       └─rlang::abort(...)
  Execution halted

Package: easyalluvial
Check: tests
New result: ERROR
    Running ‘testthat.R’ [43s/43s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(easyalluvial)
    > 
    > test_check("easyalluvial")
    [ FAIL 3 | WARN 6 | SKIP 18 | PASS 41 ]
    
    ══ Skipped tests (18) ══════════════════════════════════════════════════════════
    • On CRAN (17): 'test_alluvial_long.R:13:3',
      'test_alluvial_model_response.R:6:3', 'test_alluvial_model_response.R:32:3',
      'test_alluvial_model_response.R:61:5', 'test_alluvial_model_response.R:95:5',
      'test_alluvial_model_response.R:121:5',
      'test_alluvial_model_response.R:289:3',
      'test_alluvial_model_response.R:369:3', 'test_alluvial_wide.R:15:5',
      'test_model.R:5:3', 'test_model.R:117:3', 'test_model.R:172:3',
      'test_model.R:228:3', 'test_model.R:368:3', 'test_plot_condensation.R:17:5',
      'test_plot_marginal_histograms.R:16:3',
      'test_plot_marginal_histograms.R:95:3'
    • xgboost test skipped for performance (1): 'test_model.R:301:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_alluvial_model_response.R:476:3'): n_feats == degree ───────────
    Error in `plot_imp(p, df)`: plot must be alluvial plot of type model_response
    Backtrace:
        ▆
     1. └─easyalluvial::plot_imp(p, df) at test_alluvial_model_response.R:476:3
    ── Error ('test_plot_imp.R:18:3'): plot_imp ────────────────────────────────────
    Error in `plot_imp(p, df)`: plot must be alluvial plot of type model_response
    Backtrace:
        ▆
     1. └─easyalluvial::plot_imp(p, df) at test_plot_imp.R:18:3
    ── Error ('test_plot_imp.R:51:3'): add_importance_plot ─────────────────────────
    Error in `plot_imp(p, data_input, ...)`: plot must be alluvial plot of type model_response
    Backtrace:
        ▆
     1. └─easyalluvial::add_imp_plot(p_grid, p, data_input = df, plot = F) at test_plot_imp.R:51:3
     2.   └─easyalluvial::plot_imp(p, data_input, ...)
    
    [ FAIL 3 | WARN 6 | SKIP 18 | PASS 41 ]
    Deleting unused snapshots:
    • alluvial_long/long-all-nums-plus-fill.svg
    • alluvial_long/long-all-nums.svg
    • alluvial_long/long-fill-first.svg
    • alluvial_long/long-fill-last.svg
    • alluvial_long/long-fill-to-right.svg
    • alluvial_long/long-fill-value.svg
    • alluvial_long/long-reorder-carrier-by-size.svg
    • alluvial_long/long-reorder-x-levels.svg
    • alluvial_long/long-reorder-y-levels.svg
    • alluvial_long/long-sprecify-color.svg
    • alluvial_model_response/model-response-all-facs.svg
    • alluvial_model_response/model-response-all-nums.svg
    • alluvial_model_response/model-response-cat-bi.svg
    • alluvial_model_response/model-response-cat-multi.svg
    • alluvial_model_response/model-response-new-change-bins-3.svg
    • alluvial_model_response/model-response-new-change-bins-7.svg
    • alluvial_model_response/model-response-new-labs.svg
    • alluvial_model_response/model-response-pdb-non-binary.svg
    • alluvial_model_response/model-response-pdb.svg
    • alluvial_model_response/model-response.svg
    • alluvial_wide/wide-all-flows.svg
    • alluvial_wide/wide-islr-cars-rotate-labels.svg
    • alluvial_wide/wide-islr-cars.svg
    • alluvial_wide/wide-last.svg
    • alluvial_wide/wide-reorder-y-levels.svg
    • alluvial_wide/wide-values.svg
    • plot_condensation/cond-price-first.svg
    • plot_condensation/cond-with-first.svg
    • plot_marginal_histograms/mod-num-cat.svg
    • plot_marginal_histograms/mod-num-num.svg
    • plot_marginal_histograms/mod-num-pred-train.svg
    • plot_marginal_histograms/plot-hist-long-cat-fill.svg
    • plot_marginal_histograms/plot-hist-long-cat.svg
    • plot_marginal_histograms/plot-hist-long-num-has-fill.svg
    • plot_marginal_histograms/plot-hist-long-num-is-fill.svg
    • plot_marginal_histograms/plot-hist-long-num.svg
    • plot_marginal_histograms/plot-hist-wide-num.svg
    Error: Test failures
    Execution halted

Package: easysurv
Check: examples
New result: ERROR
  Running examples in ‘easysurv-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: get_km
  > ### Title: Generate Kaplan-Meier estimates
  > ### Aliases: get_km
  > 
  > ### ** Examples
  > 
  > km_results <- get_km(
  +   data = easysurv::easy_bc,
  +   time = "recyrs",
  +   event = "censrec",
  +   group = "group",
  +   risktable_symbols = FALSE
  + )
  > 
  > km_results
  
  ── Kaplan-Meier Data ───────────────────────────────────────────────────────────
  The get_km function has produced the following outputs:
  • km: A `survival::survfit()` object for Kaplan-Meier estimates.
  • km_for_excel: A list of stepped Kaplan-Meier data for external plotting.
  • km_per_group: A list of Kaplan-Meier estimates for each group.
  • km_plot: A Kaplan-Meier plot.
  • km_summary: A summary table of the Kaplan-Meier estimates.
  
  ── km Summary ──
  
          group records events    rmean se(rmean)   median  0.95LCL  0.95UCL
  Good     Good     229     51 5.934330 0.1616003       NA       NA       NA
  Medium Medium     229    103 4.600852 0.1856699 5.254795 4.115068 5.572603
  Poor     Poor     228    145 3.101736 0.1772520 2.183562 1.978082 2.619178
         Median follow-up
  Good           4.452055
  Medium         4.712329
  Poor           4.115068
  
  Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = "{n.risk}",  : 
    argument "risktable_height" is missing, with no default
  Calls: <Anonymous> ... ggsurvfit_build -> <Anonymous> -> .construct_risktable
  Execution halted

Package: easysurv
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘easysurv.Rmd’ using rmarkdown
  
  Quitting from easysurv.Rmd:148-157 [km]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `.construct_risktable()`:
  ! argument "risktable_height" is missing, with no default
  ---
  Backtrace:
       ▆
    1. └─tools::buildVignettes(...)
    2.   ├─base::tryCatch(...)
    3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    6.   └─engine$weave(file, quiet = quiet, encoding = enc)
    7.     └─knitr:::vweave_rmarkdown(...)
    8.       └─rmarkdown::render(...)
    9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
   10.           └─knitr:::process_file(text, output)
   11.             ├─xfun:::handle_error(...)
   12.             ├─base::withCallingHandlers(...)
   13.             └─knitr:::process_group(group)
   14.               └─knitr:::call_block(x)
   15.                 └─knitr:::block_exec(params)
   16.                   └─knitr:::eng_r(options)
   17.                     ├─knitr:::in_input_dir(...)
   18.                     │ └─knitr:::in_dir(input_dir(), expr)
   19.                     └─knitr (local) evaluate(...)
   20.                       └─evaluate::evaluate(...)
   21.                         ├─base::withRestarts(...)
   22.                         │ └─base (local) withRestartList(expr, restarts)
   23.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
   24.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
   25.                         │   └─base (local) withRestartList(expr, restarts[-nr])
   26.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
   27.                         │       └─base (local) doWithOneRestart(return(expr), restart)
   28.                         ├─evaluate:::with_handlers(...)
   29.                         │ ├─base::eval(call)
   30.                         │ │ └─base::eval(call)
   31.                         │ └─base::withCallingHandlers(...)
   32.                         └─watcher$print_value(ev$value, ev$visible, envir)
   33.                           ├─base::withVisible(handle_value(handler, value, visible, envir))
   34.                           └─evaluate:::handle_value(handler, value, visible, envir)
   35.                             └─handler$value(value, visible)
   36.                               └─knitr (local) fun(x, options = options)
   37.                                 ├─base::withVisible(knit_print(x, ...))
   38.                                 ├─knitr::knit_print(x, ...)
   39.                                 └─knitr:::knit_print.default(x, ...)
   40.                                   └─knitr::normal_print(x)
   41.                                     ├─base::print(x)
   42.                                     └─easysurv:::print.get_km(x)
   43.                                       ├─base::print(x$km_plot)
   44.                                       └─ggsurvfit:::print.ggsurvfit(x$km_plot)
   45.                                         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
   46.                                           ├─rlang::inject(...)
   47.                                           └─ggsurvfit:::.construct_risktable(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'easysurv.Rmd' failed with diagnostics:
  argument "risktable_height" is missing, with no default
  --- failed re-building ‘easysurv.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘easysurv.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ecocbo
Check: tests
New result: ERROR
    Running ‘testthat.R’ [128s/129s]
  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(ecocbo)
    > 
    > test_check("ecocbo")
    
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    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 26 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot_power.R:5:3'): plots are plotted ────────────────────────
    plot_power(epiBetaR, n = 4, m = 4, method = "power") has type 'object', not 'list'.
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 26 ]
    Error: Test failures
    Execution halted

Package: EGM
Check: tests
New result: ERROR
    Running ‘testthat.R’ [6s/6s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(EGM)
    Loading required package: vctrs
    Loading required package: data.table
    > EGM::set_wfdb_path("/usr/local/bin")
    > 
    > test_check("EGM")
    [ FAIL 1 | WARN 9 | SKIP 19 | PASS 43 ]
    
    ══ Skipped tests (19) ══════════════════════════════════════════════════════════
    • On CRAN (17): 'test-annotation-table.R:3:2', 'test-egm.R:62:2',
      'test-ggm.R:31:2', 'test-segmentation.R:3:2', 'test-segmentation.R:32:2',
      'test-segmentation.R:82:2', 'test-segmentation.R:102:2',
      'test-wfdb-annotation.R:3:2', 'test-wfdb-annotation.R:23:2',
      'test-wfdb-annotation.R:43:2', 'test-wfdb-io.R:5:2', 'test-wfdb-io.R:27:2',
      'test-wfdb-io.R:61:2', 'test-wfdb-io.R:160:2', 'test-wfdb-io.R:199:2',
      'test-wfdb-structures.R:3:2', 'test-wfdb-utils.R:3:2'
    • Skipping (1): 'test-segmentation.R:22:2'
    • empty test (1): 'test-ggm.R:77:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-ggm.R:63:2'): theming works ──────────────────────────────────
    g$labels$x (`actual`) not equal to "sample" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('sample')
    
    [ FAIL 1 | WARN 9 | SKIP 19 | PASS 43 ]
    Error: Test failures
    Execution halted

Package: enrichwith
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘GLMs.Rmd’ using rmarkdown
  
  Quitting from GLMs.Rmd:241-243 [unnamed-chunk-18]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `loadNamespace()`:
  ! there is no package called 'MASS'
  ---
  Backtrace:
      ▆
   1. ├─stats::simulate(clottingML, nsim = 3, seed = 123)
   2. ├─stats:::simulate.lm(clottingML, nsim = 3, seed = 123)
   3. │ └─object$family$simulate(object, nsim)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'GLMs.Rmd' failed with diagnostics:
  there is no package called 'MASS'
  --- failed re-building ‘GLMs.Rmd’
  
  --- re-building ‘bias.Rmd’ using rmarkdown
  --- finished re-building ‘bias.Rmd’
  
  --- re-building ‘exponential_family.Rmd’ using rmarkdown
  --- finished re-building ‘exponential_family.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘GLMs.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: epos
Check: tests
New result: ERROR
    Running ‘testthat.R’ [7s/7s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(epos)
    > 
    > test_check("epos")
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_createTanimotoBaseline.R:47:3'): Test function createTanimotoBaseline() ──
    `x` not equal to `expected`.
    1/1 mismatches
    [1] 1 - 11 == -10
    Backtrace:
        ▆
     1. └─testthat::expect_that(length(tanimotobaseline), equals(11)) at test_createTanimotoBaseline.R:47:3
     2.   └─testthat (local) condition(object)
     3.     └─testthat::expect_equal(x, expected, ..., expected.label = label)
    
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
    Error: Test failures
    Execution halted

Package: EQUALSTATS
Check: examples
New result: ERROR
  Running examples in ‘EQUALSTATS-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: function.Survival_Analysis
  > ### Title: Perform Survival Analysis
  > ### Aliases: function.Survival_Analysis
  > 
  > ### ** Examples
  > 
  > # Create simulated data ####
  > data <- cbind.data.frame(
  +   `Subject ID` = c(
  +     "S0001", "S0002", "S0003", "S0004", "S0005",
  +     "S0006", "S0007", "S0008", "S0009", "S0010",
  +     "S0011", "S0012", "S0013", "S0014", "S0015",
  +     "S0016", "S0017", "S0018", "S0019", "S0020",
  +     "S0021", "S0022", "S0023", "S0024", "S0025",
  +     "S0026", "S0027", "S0028", "S0029", "S0030"),
  +   `Centre` = c(
  +     "C_0001", "C_0002", "C_0002", "C_0002", "C_0002",
  +     "C_0001", "C_0001", "C_0003", "C_0001", "C_0003",
  +     "C_0001", "C_0002", "C_0002", "C_0001", "C_0003",
  +     "C_0002", "C_0002", "C_0003", "C_0001", "C_0002",
  +     "C_0002", "C_0002", "C_0002", "C_0003", "C_0002",
  +     "C_0001", "C_0003", "C_0001", "C_0001", "C_0001"),
  +   `Treatment` = c(
  +     "Intensive rehabilitation", "Intensive rehabilitation", "Standard rehabilitation",
  +     "Intensive rehabilitation", "Intensive rehabilitation", "Intensive rehabilitation",
  +     "Intensive rehabilitation", "Intensive rehabilitation", "Intensive rehabilitation",
  +     "Standard rehabilitation", "Intensive rehabilitation", "Standard rehabilitation",
  +     "Standard rehabilitation", "Intensive rehabilitation", "Intensive rehabilitation",
  +     "Intensive rehabilitation", "Standard rehabilitation", "Standard rehabilitation",
  +     "Intensive rehabilitation", "Standard rehabilitation", "Intensive rehabilitation",
  +     "Intensive rehabilitation", "Standard rehabilitation", "Intensive rehabilitation",
  +     "Intensive rehabilitation", "Standard rehabilitation", "Standard rehabilitation",
  +     "Intensive rehabilitation", "Standard rehabilitation", "Intensive rehabilitation"),
  +   `Obesity status` = c(
  +     "Obese", "Non-obese", "Obese", "Non-obese", "Non-obese",
  +     "Obese", "Obese", "Obese", "Non-obese", "Obese",
  +     "Non-obese", "Non-obese", "Obese", "Non-obese", "Obese",
  +     "Obese", "Non-obese", "Obese", "Obese", "Obese",
  +     "Non-obese", "Non-obese", "Non-obese", "Obese", "Obese",
  +     "Non-obese", "Obese", "Obese", "Obese", "Obese"),
  +   `Unable to walk independently at 6 weeks` = c(
  +     "unable", "able", "able", "unable", "able",
  +     "able", "unable", "unable", "unable", "unable",
  +     "able", "unable", "able", "unable", "unable",
  +     "able", "unable", "unable", "unable", "unable",
  +     "able", "able", "able", "able", "unable",
  +     "able", "able", "unable", "able", "unable"),
  +   `Mobility score at 6 months` = c(
  +     86, 65.1, 48, 99.8, 73.4, 70, 74.7, 36.5, 64.6, 85.4,
  +     41.7, 60.1, 73.3, 42.4, 55.3, 47.3, 85.9, 63, 64.6, 101.8,
  +     108.1, 72.3, 96.4, 87.5, 66.2, 92.9, 47.7, 55.8, 56.4, 133.8),
  +   `Pain at 6 weeks` = c(
  +     "3_severe", "1_mild", "1_mild", "2_moderate", "1_mild",
  +     "1_mild", "2_moderate", "2_moderate", "1_mild", "3_severe",
  +     "1_mild", "2_moderate", "1_mild", "3_severe", "3_severe",
  +     "1_mild", "2_moderate", "3_severe", "2_moderate", "2_moderate",
  +     "1_mild", "1_mild", "1_mild", "1_mild", "2_moderate",
  +     "1_mild", "1_mild", "2_moderate", "1_mild", "2_moderate"),
  +   `Number of falls within 6 months` = c(
  +     3, 2, 3, 2, 2, 1, 4, 2, 2, 5,
  +     3, 2, 2, 2, 5, 3, 2, 2, 3, 4,
  +     3, 1, 2, 2, 2, 7, 2, 1, 1, 8),
  +   `Mobility score at 12 months` = c(
  +     90, 69.1, 52, 103.8, 77.4, 74, 78.7, 40.5, 68.6, 89.4,
  +     45.7, 64.1, 77.3, 46.4, 59.3, 51.3, 89.9, 67, 68.6, 105.8,
  +     112.1, 76.3, 100.4, 91.5, 70.2, 96.9, 51.7, 59.8, 60.4, 137.8) ,
  +   `Admission to care home` = c(
  +     "Not admitted", "Not admitted", "Admitted", "Not admitted", "Admitted",
  +     "Admitted", "Not admitted", "Admitted", "Admitted", "Not admitted",
  +     "Admitted", "Admitted", "Not admitted", "Not admitted", "Not admitted",
  +     "Not admitted", "Admitted", "Admitted", "Not admitted", "Not admitted",
  +     "Not admitted", "Admitted", "Not admitted", "Admitted", "Admitted",
  +     "Admitted", "Admitted", "Admitted", "Admitted", "Not admitted"),
  +   `Follow-up` = c(
  +     10, 8, 8, 8, 12, 12, 11, 10, 8, 7,
  +     8, 6, 9, 6, 9, 8, 10, 8, 11, 9,
  +     6, 9, 12, 9, 8, 11, 12, 9, 10, 11)
  + )
  > # Simulate lists provided by EQUAL-STATS
  > Predefined_lists <- list(
  +   main_menu = c(
  +     'Calculate summary measures',
  +     'Create plots',
  +     'Check distribution',
  +     'Compare sample mean versus population mean',
  +     'Compare groups/variables (independent samples)',
  +     'Compare groups/variables (paired samples or repeated measures)',
  +     'Find the correlation (quantitative variables)',
  +     'Calculate measurement error',
  +     'Find the diagnostic accuracy (primary data)',
  +     'Perform sample size and power calculations (primary data)',
  +     'Perform survival analysis',
  +     'Perform regression analysis',
  +     'Analyse time series',
  +     'Perform mixed-effects regression',
  +     'Perform multivariate regression',
  +     'Generate hypothesis',
  +     'Perform sample size and power calculations (effect size approach)',
  +     'Make correct conclusions (effect size approach)',
  +     'Find the diagnostic accuracy (tabulated data)'
  +   ),
  +   menu_short = c(
  +     'Summary_Measures',
  +     'Create_Plots',
  +     'Check_Distribution',
  +     'Compare_Sample_Pop_Means',
  +     'Compare_Groups',
  +     'Repeated_Measures',
  +     'Correlation',
  +     'Measurement_Error',
  +     'Diagnostic_Accuracy_Primary',
  +     'Sample_Size_Calculations_Primary',
  +     'Survival_Analysis',
  +     'Regression_Analysis',
  +     'Time_Series',
  +     'Mixed_Effects_Regression',
  +     'Multivariate_Regression',
  +     'Generate_Hypothesis',
  +     'Sample_Size_Calculations_Effect_size',
  +     'Make_Conclusions_Effect_size',
  +     'Diagnostic_Accuracy_Tables'
  +   )
  + )
  > entry <- list()
  > entry <- lapply(1:15, function(x) entry[[x]] <- '')
  > rv <- list(
  +   StorageFolder = tempdir(),
  +   first_menu_choice = NA,
  +   second_menu_choice = NA,
  +   entry = entry,
  +   import_data = NULL,
  +   same_row_different_row = NA,
  +   submit_button_to_appear = FALSE,
  +   summary_measures_choices = c("EQUAL-STATS choice", "Total observations",
  +   "Missing observations", "Available observations"),
  +   analysis_outcome = list(),
  +   code = list(),
  +   plan = list(),
  +   results = list(),
  +   plots_list = list(),
  +   reports = list()
  + )
  > # Store the data in a folder
  > data_file_path = paste0(tempdir(), "/data.csv")
  > write.csv(data, file = data_file_path, row.names = FALSE, na = "")
  > # Load the necessary packages and functions ####
  > library(stringr)
  > library(survival)
  > library(ggsurvfit)
  Loading required package: ggplot2
  > rv$import_data <- function.read_data(data_file_path)
  > # Update choices ####
  > rv$first_menu_choice <- "Survival_Analysis"
  > rv$second_menu_choice <- NA
  > rv$entry[[1]] <- "Admission to care home"
  > rv$entry[[2]] <- "Follow-up"
  > rv$entry[[3]] <- "Treatment"
  > # Final function ####
  > Results <- function.Survival_Analysis(Predefined_lists, rv)
  Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}",  : 
    argument "risktable_height" is missing, with no default
  Calls: function.Survival_Analysis
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
  function.Multivariate_Regression 11.224  0.223  11.538

Package: evaluate
Check: tests
New result: ERROR
    Running ‘testthat.R’ [7s/7s]
  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(evaluate)
    
    Attaching package: 'evaluate'
    
    The following object is masked from 'package:testthat':
    
        local_reproducible_output
    
    > 
    > test_check("evaluate")
    [ FAIL 1 | WARN 0 | SKIP 17 | PASS 183 ]
    
    ══ Skipped tests (17) ══════════════════════════════════════════════════════════
    • On CRAN (17): 'test-conditions.R:101:3', 'test-conditions.R:128:3',
      'test-conditions.R:147:3', 'test-evaluate.R:104:3', 'test-evaluate.R:134:3',
      'test-evaluation.R:9:3', 'test-graphics.R:264:3',
      'test-output-handler.R:2:3', 'test-output-handler.R:42:3',
      'test-output.R:33:3', 'test-replay.R:6:3', 'test-replay.R:16:3',
      'test-replay.R:25:3', 'test-replay.R:30:3', 'test-replay.R:45:3',
      'test-watchout.R:35:3', 'test-watchout.R:50:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-output-handler.R:73:3'): return value of value handler inserted directly in output list ──
    `output_types` (`actual`) not equal to `types` (`expected`).
    
    `actual[2:5]`:   "numeric" "source" "source" "ggplot2::ggplot"
    `expected[2:5]`: "numeric" "source" "source" "gg"             
    Backtrace:
        ▆
     1. └─evaluate:::expect_output_types(...) at test-output-handler.R:73:3
     2.   └─testthat::expect_equal(output_types, types) at tests/testthat/helper.R:3:3
    
    [ FAIL 1 | WARN 0 | SKIP 17 | PASS 183 ]
    Deleting unused snapshots:
    • conditions/abort-error.txt
    • conditions/rmd-abort-error.md
    • conditions/rmd-abort-error.txt
    • conditions/rmd-stop-error-auto-entrace.txt
    • conditions/rmd-stop-error-entrace-sewed.md
    • conditions/rmd-stop-error.md
    • conditions/stop-error-no-trace.txt
    • conditions/stop-error-trace-calling-handler.txt
    • conditions/stop-error-trace-trim.txt
    • conditions/stop-error-trace-wch.txt
    Error: Test failures
    Execution halted

Package: ez
Check: examples
New result: ERROR
  Running examples in ‘ez-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ezPlot
  > ### Title: Plot data from a factorial experiment
  > ### Aliases: ezPlot
  > 
  > ### ** Examples
  > 
  > #Read in the ANT data (see ?ANT).
  > data(ANT)
  > head(ANT)
    subnum     group block trial     cue     flank location direction       rt
  1      1 Treatment     1     1    None   Neutral       up      left 398.6773
  2      1 Treatment     1     2  Center   Neutral       up      left 389.1822
  3      1 Treatment     1     3  Double   Neutral       up      left 333.2186
  4      1 Treatment     1     4 Spatial   Neutral       up      left 419.7640
  5      1 Treatment     1     5    None Congruent       up      left 446.4754
  6      1 Treatment     1     6  Center Congruent       up      left 338.9766
    error
  1     0
  2     0
  3     0
  4     0
  5     0
  6     0
  > ezPrecis(ANT)
  Data frame dimensions: 5760 rows, 10 columns
               type missing values      min         max
  subnum     factor       0     20        1          20
  group      factor       0      2  Control   Treatment
  block     numeric       0      6        1           6
  trial     numeric       0     48        1          48
  cue        factor       0      4     None     Spatial
  flank      factor       0      3  Neutral Incongruent
  location   factor       0      2     down          up
  direction  factor       0      2     left       right
  rt        numeric       0   5760 179.5972    657.6986
  error     numeric       0      2        0           1
  > 
  > 
  > ## Not run: 
  > ##D #Run an ANOVA on the mean correct RT data.
  > ##D mean_rt_anova = ezANOVA(
  > ##D     data = ANT[ANT$error==0,]
  > ##D     , dv = .(rt)
  > ##D     , wid = .(subnum)
  > ##D     , within = .(cue,flank)
  > ##D     , between = .(group)
  > ##D )
  > ##D 
  > ##D #Show the ANOVA and assumption tests.
  > ##D print(mean_rt_anova)
  > ## End(Not run)
  > 
  > #Plot the main effect of group.
  > group_plot = ezPlot(
  +     data = ANT[ANT$error==0,]
  +     , dv = .(rt)
  +     , wid = .(subnum)
  +     , between = .(group)
  +     , x = .(group)
  +     , do_lines = FALSE
  +     , x_lab = 'Group'
  +     , y_lab = 'RT (ms)'
  + )
  Warning: Collapsing data to cell means. *IF* the requested effects are a subset of the full design, you must use the "within_full" argument, else results may be inaccurate.
  Coefficient covariances computed by hccm()
  > 
  > #Show the plot.
  > print(group_plot)
  > 
  > #tweak the plot
  > # group_plot = group_plot +
  > # theme(
  > #     panel.grid.major = element_blank()
  > #     , panel.grid.minor = element_blank()
  > # )
  > # print(group_plot)
  > 
  > 
  > 
  > #use the "print_code" argument to print the
  > # code for creating the plot and return the
  > # data to plot. This is useful when you want
  > # to learn how to create plots from scratch
  > # (which can in turn be useful when you can't
  > # get a combination of ezPlot and tweaking to
  > # achieve what you want)
  > group_plot_data = ezPlot(
  +     data = ANT[ANT$error==0,]
  +     , dv = .(rt)
  +     , wid = .(subnum)
  +     , between = .(group)
  +     , x = .(group)
  +     , do_lines = FALSE
  +     , x_lab = 'Group'
  +     , y_lab = 'RT (ms)'
  +     , print_code = TRUE
  + )
  Warning: Collapsing data to cell means. *IF* the requested effects are a subset of the full design, you must use the "within_full" argument, else results may be inaccurate.
  Coefficient covariances computed by hccm()
  ggplot(
  	data = stats
  	, mapping = aes(
  		y = Mean
  		, x = group
  	)
  )+
  geom_point()+
  geom_errorbar(
  	mapping = aes(
  		ymin = lo
  		, ymax = hi
  	)
  	, linetype = 1
  	, show.legend = FALSE
  	, width = 0.25
  	, alpha = .5
  )+
  labs(
  	x = 'Group'
  	, y = 'RT (ms)'
  )> 
  > 
  > #Re-plot the main effect of group, using the levels
  > ##argument to re-arrange/rename levels of group
  > group_plot = ezPlot(
  +     data = ANT[ANT$error==0,]
  +     , dv = .(rt)
  +     , wid = .(subnum)
  +     , between = .(group)
  +     , x = .(group)
  +     , do_lines = FALSE
  +     , x_lab = 'Group'
  +     , y_lab = 'RT (ms)'
  +     , levels = list(
  +         group = list(
  +             new_order = c('Treatment','Control')
  +             , new_names = c('Treatment\nGroup','Control\nGroup')
  +         )
  +     )
  + )
  Warning: Collapsing data to cell means. *IF* the requested effects are a subset of the full design, you must use the "within_full" argument, else results may be inaccurate.
  Coefficient covariances computed by hccm()
  > 
  > #Show the plot.
  > print(group_plot)
  > 
  > 
  > #Plot the cue*flank interaction.
  > cue_by_flank_plot = ezPlot(
  +     data = ANT[ANT$error==0,]
  +     , dv = .(rt)
  +     , wid = .(subnum)
  +     , within = .(cue,flank)
  +     , x = .(flank)
  +     , split = .(cue)
  +     , x_lab = 'Flanker'
  +     , y_lab = 'RT (ms)'
  +     , split_lab = 'Cue'
  + )
  Warning: Collapsing data to cell means. *IF* the requested effects are a subset of the full design, you must use the "within_full" argument, else results may be inaccurate.
  > 
  > #Show the plot.
  > print(cue_by_flank_plot)
  > 
  > 
  > #Plot the cue*flank interaction by collapsing the cue effect to
  > ##the difference between None and Double
  > cue_by_flank_plot2 = ezPlot(
  +     data = ANT[ ANT$error==0 & (ANT$cue %in% c('None','Double')) ,]
  +     , dv = .(rt)
  +     , wid = .(subnum)
  +     , within = .(flank)
  +     , diff = .(cue)
  +     , reverse_diff = TRUE
  +     , x = .(flank)
  +     , x_lab = 'Flanker'
  +     , y_lab = 'RT Effect (None - Double, ms)'
  + )
  Warning: Collapsing data to cell means. *IF* the requested effects are a subset of the full design, you must use the "within_full" argument, else results may be inaccurate.
  Warning: Collapsing "cue" to a difference score ("None"-"Double") prior to computing statistics.
  > 
  > #Show the plot.
  > print(cue_by_flank_plot2)
  > 
  > 
  > 
  > #Plot the group*cue*flank interaction.
  > group_by_cue_by_flank_plot = ezPlot(
  +     data = ANT[ANT$error==0,]
  +     , dv = .(rt)
  +     , wid = .(subnum)
  +     , within = .(cue,flank)
  +     , between = .(group)
  +     , x = .(flank)
  +     , split = .(cue)
  +     , col = .(group)
  +     , x_lab = 'Flanker'
  +     , y_lab = 'RT (ms)'
  +     , split_lab = 'Cue'
  + )
  Warning: Collapsing data to cell means. *IF* the requested effects are a subset of the full design, you must use the "within_full" argument, else results may be inaccurate.
  Warning: Mixed within-and-between-Ss effect requested; FLSD is only appropriate for within-Ss comparisons (see warning in ?ezStats or ?ezPlot).
  Error:
  ! The `facets` argument of `facet_grid()` was deprecated in ggplot2
    2.2.0 and is now defunct.
  ℹ Please use the `rows` argument instead.
  Backtrace:
      ▆
   1. └─ez::ezPlot(...)
   2.   ├─base::eval(parse(text = p))
   3.   │ └─base::eval(parse(text = p))
   4.   └─ggplot2::facet_grid(facets = . ~ group, scales = "free_y")
   5.     └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
   6.       └─lifecycle:::deprecate_stop0(msg)
   7.         └─rlang::cnd_signal(...)
  Execution halted

Package: ezplot
Check: examples
New result: ERROR
  Running examples in ‘ezplot-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: variable_plot
  > ### Title: variable_plot
  > ### Aliases: variable_plot
  > 
  > ### ** Examples
  > 
  > suppressPackageStartupMessages(library(tsibble))
  > library(tsibbledata)
  > variable_plot(ansett, "Week", "Passengers", facet_x = "Class", yoy = TRUE)
  Error: <ggplot2::element_rect> object properties are invalid:
  - @linewidth must be <NULL>, <integer>, or <double>, not <logical>
  Execution halted

Package: ezplot
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘bar_plot.Rmd’ using rmarkdown
  --- finished re-building ‘bar_plot.Rmd’
  
  --- re-building ‘basics.Rmd’ using rmarkdown
  --- finished re-building ‘basics.Rmd’
  
  --- re-building ‘line_plot.Rmd’ using rmarkdown
  --- finished re-building ‘line_plot.Rmd’
  
  --- re-building ‘overview.Rmd’ using rmarkdown
  --- finished re-building ‘overview.Rmd’
  
  --- re-building ‘variable_plot.Rmd’ using rmarkdown
  
  Quitting from variable_plot.Rmd:26-28 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::element_rect> object properties are invalid:
  - @linewidth must be <NULL>, <integer>, or <double>, not <logical>
  ---
  Backtrace:
      ▆
   1. └─ezplot::variable_plot(ansett, "Week", "Passengers", facet_x = "Class")
   2.   ├─ggplot2::theme(...)
   3.   │ └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
   4.   │   └─base::mget(args, envir = env)
   5.   └─ggplot2::element_rect(fill = NA, colour = NA, linewidth = NA)
   6.     └─S7::new_object(...)
   7.       └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'variable_plot.Rmd' failed with diagnostics:
  <ggplot2::element_rect> object properties are invalid:
  - @linewidth must be <NULL>, <integer>, or <double>, not <logical>
  --- failed re-building ‘variable_plot.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘variable_plot.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ezplot
Check: tests
New result: ERROR
    Running ‘testthat.R’ [11s/11s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ezplot)
    > suppressPackageStartupMessages(library(tsibble))
    > 
    > test_check("ezplot")
    [ FAIL 2 | WARN 6 | SKIP 0 | PASS 90 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-variable_plot.R:7:3'): variable_plot line geom works ───────────
    Error: <ggplot2::element_rect> object properties are invalid:
    - @linewidth must be <NULL>, <integer>, or <double>, not <logical>
    Backtrace:
        ▆
     1. └─ezplot::variable_plot(tsibbledata::pelt, "Year", c("Lynx", "Hare")) at test-variable_plot.R:7:3
     2.   ├─ggplot2::theme(...)
     3.   │ └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
     4.   │   └─base::mget(args, envir = env)
     5.   └─ggplot2::element_rect(fill = NA, colour = NA, linewidth = NA)
     6.     └─S7::new_object(...)
     7.       └─S7::validate(object, recursive = !parent_validated)
    ── Error ('test-variable_plot.R:19:3'): variable_plot bar geom works ───────────
    Error: <ggplot2::element_rect> object properties are invalid:
    - @linewidth must be <NULL>, <integer>, or <double>, not <logical>
    Backtrace:
        ▆
     1. └─ezplot::variable_plot(...) at test-variable_plot.R:19:3
     2.   ├─ggplot2::theme(...)
     3.   │ └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
     4.   │   └─base::mget(args, envir = env)
     5.   └─ggplot2::element_rect(fill = NA, colour = NA, linewidth = NA)
     6.     └─S7::new_object(...)
     7.       └─S7::validate(object, recursive = !parent_validated)
    
    [ FAIL 2 | WARN 6 | SKIP 0 | PASS 90 ]
    Error: Test failures
    Execution halted

Package: fabletools
Check: tests
New result: ERROR
    Running ‘testthat.R’ [44s/44s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(dplyr)
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    > 
    > test_check("fabletools")
    Loading required package: fabletools
    [ FAIL 2 | WARN 0 | SKIP 1 | PASS 292 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • On CRAN (1): 'test-spelling.R:4:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-graphics.R:327:3'): autoplot_dcmp_ts() ───────────────────────
    `print(p)` produced messages.
    ── Failure ('test-graphics.R:346:3'): autoplot_dcmp_ts() ───────────────────────
    `print(p)` produced messages.
    
    [ FAIL 2 | WARN 0 | SKIP 1 | PASS 292 ]
    Error: Test failures
    Execution halted

Package: fairmodels
Check: examples
New result: ERROR
  Running examples in ‘fairmodels-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: fairness_heatmap
  > ### Title: Fairness heatmap
  > ### Aliases: fairness_heatmap
  > 
  > ### ** Examples
  > 
  > 
  > data("german")
  > 
  > y_numeric <- as.numeric(german$Risk) - 1
  > 
  > lm_model <- glm(Risk ~ .,
  +   data = german,
  +   family = binomial(link = "logit")
  + )
  > 
  > rf_model <- ranger::ranger(Risk ~ .,
  +   data = german,
  +   probability = TRUE,
  +   num.trees = 200,
  +   num.threads = 1
  + )
  > 
  > explainer_lm <- DALEX::explain(lm_model, data = german[, -1], y = y_numeric)
  Preparation of a new explainer is initiated
    -> model label       :  lm  (  default  )
    -> data              :  1000  rows  9  cols 
    -> target variable   :  1000  values 
    -> predict function  :  yhat.glm  will be used (  default  )
    -> predicted values  :  No value for predict function target column. (  default  )
    -> model_info        :  package stats , ver. 4.6.0 , task classification (  default  ) 
    -> predicted values  :  numerical, min =  0.1369187 , mean =  0.7 , max =  0.9832426  
    -> residual function :  difference between y and yhat (  default  )
    -> residuals         :  numerical, min =  -0.9572803 , mean =  4.352454e-17 , max =  0.8283475  
    A new explainer has been created!  
  > explainer_rf <- DALEX::explain(rf_model, data = german[, -1], y = y_numeric)
  Preparation of a new explainer is initiated
    -> model label       :  ranger  (  default  )
    -> data              :  1000  rows  9  cols 
    -> target variable   :  1000  values 
    -> predict function  :  yhat.ranger  will be used (  default  )
    -> predicted values  :  No value for predict function target column. (  default  )
    -> model_info        :  package ranger , ver. 0.17.0 , task classification (  default  ) 
    -> predicted values  :  numerical, min =  0.07287302 , mean =  0.6989152 , max =  0.9974848  
    -> residual function :  difference between y and yhat (  default  )
    -> residuals         :  numerical, min =  -0.7219256 , mean =  0.001084826 , max =  0.6142332  
    A new explainer has been created!  
  > 
  > fobject <- fairness_check(explainer_lm, explainer_rf,
  +   protected = german$Sex,
  +   privileged = "male"
  + )
  Creating fairness classification object
  -> Privileged subgroup		: character ( Ok  )
  -> Protected variable		: factor ( Ok  ) 
  -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
  -> Fairness objects		: 0 objects 
  -> Checking explainers		: 2 in total (  compatible  )
  -> Metric calculation		: 10/13 metrics calculated for all models ( 3 NA created )
   Fairness object created succesfully  
  > 
  > # same explainers with different cutoffs for female
  > fobject <- fairness_check(explainer_lm, explainer_rf, fobject,
  +   protected = german$Sex,
  +   privileged = "male",
  +   cutoff = list(female = 0.4),
  +   label = c("lm_2", "rf_2")
  + )
  Creating fairness classification object
  -> Privileged subgroup		: character ( Ok  )
  -> Protected variable		: factor ( Ok  ) 
  -> Cutoff values for explainers	: female: 0.4, male: 0.5 
  -> Fairness objects		: 1 object (  compatible  )
  -> Checking explainers		: 4 in total (  compatible  )
  -> Metric calculation		: 10/13 metrics calculated for all models ( 3 NA created )
   Fairness object created succesfully  
  > 
  > 
  > fh <- fairness_heatmap(fobject)
  > 
  > plot(fh)
  Error in rep(yes, length.out = len) : 
    attempt to replicate an object of type 'object'
  Calls: plot -> plot.fairness_heatmap -> ifelse
  Execution halted

Package: fairmodels
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Advanced_tutorial.Rmd’ using rmarkdown
  --- finished re-building ‘Advanced_tutorial.Rmd’
  
  --- re-building ‘Basic_tutorial.Rmd’ using rmarkdown
  
  Quitting from Basic_tutorial.Rmd:254-257 [unnamed-chunk-19]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `rep()`:
  ! attempt to replicate an object of type 'object'
  ---
  Backtrace:
      ▆
   1. ├─base::plot(fheatmap, text_size = 3)
   2. └─fairmodels:::plot.fairness_heatmap(fheatmap, text_size = 3)
   3.   └─base::ifelse(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Basic_tutorial.Rmd' failed with diagnostics:
  attempt to replicate an object of type 'object'
  --- failed re-building ‘Basic_tutorial.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Basic_tutorial.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: fairmodels
Check: tests
New result: ERROR
    Running ‘testthat.R’ [35s/32s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(fairmodels)
    > 
    > 
    > test_check("fairmodels")
    Welcome to DALEX (version: 2.5.2).
    Find examples and detailed introduction at: http://ema.drwhy.ai/
    Additional features will be available after installation of: ggpubr.
    Use 'install_dependencies()' to get all suggested dependencies
    Loaded gbm 2.2.2
    This version of gbm is no longer under development. Consider transitioning to gbm3, https://github.com/gbm-developers/gbm3
    Preparation of a new explainer is initiated
      -> model label       :  ranger  (  default  )
      -> data              :  6172  rows  7  cols 
      -> target variable   :  6172  values 
      -> predict function  :  yhat.ranger  will be used (  default  )
      -> predicted values  :  No value for predict function target column. (  default  )
      -> model_info        :  package ranger , ver. 0.17.0 , task classification (  default  ) 
      -> predicted values  :  numerical, min =  0.1536924 , mean =  0.5448324 , max =  0.8691119  
      -> residual function :  difference between y and yhat (  default  )
      -> residuals         :  numerical, min =  -0.8516067 , mean =  4.77063e-05 , max =  0.7763523  
      A new explainer has been created!  
    Preparation of a new explainer is initiated
      -> model label       :  lm  (  default  )
      -> data              :  6172  rows  7  cols 
      -> target variable   :  6172  values 
      -> predict function  :  yhat.glm  will be used (  default  )
      -> predicted values  :  No value for predict function target column. (  default  )
      -> model_info        :  package stats , ver. 4.6.0 , task classification (  default  ) 
      -> predicted values  :  numerical, min =  0.004522979 , mean =  0.5448801 , max =  0.8855426  
      -> residual function :  difference between y and yhat (  default  )
      -> residuals         :  numerical, min =  -0.8822826 , mean =  -5.053611e-13 , max =  0.9767658  
      A new explainer has been created!  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups )
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 2 in total (  compatible  )
    -> Metric calculation		: 13/13 metrics calculated for all models
     Fairness object created succesfully  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups )
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 2 in total (  compatible  )
    -> Metric calculation		: 13/13 metrics calculated for all models
     Fairness object created succesfully  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from numeric  )
    -> Cutoff values for explainers	: 0.5 ( for all subgroups )
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 2 in total (  compatible  )
    -> Metric calculation		: 13/13 metrics calculated for all models
     Fairness object created succesfully  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: Creating fairness classification object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( from first fairness object  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 2 objects (  compatible  )
    -> Checking explainers		: 4 in total (  compatible  )
    Creating fairness classification object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( from first fairness object  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 1 object (  compatible  )
    -> Checking explainers		: 3 in total (  model type not supported  )
    Creating fairness classification object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( from first fairness object  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 2 objects (  not compatible  ) 
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( from first fairness object  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 2 objects (  not compatible  ) 
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 2 objects (  not compatible  ) 
    Preparation of a new explainer is initiated
      -> model label       :  lm  (  default  )
      -> data              :  1000  rows  3  cols 
      -> target variable   :  1000  values 
      -> predict function  :  yhat.lm  will be used (  default  )
      -> predicted values  :  No value for predict function target column. (  default  )
      -> model_info        :  package stats , ver. 4.6.0 , task regression (  default  ) 
      -> predicted values  :  numerical, min =  -15.74808 , mean =  754.0033 , max =  1616.108  
      -> residual function :  difference between y and yhat (  default  )
      -> residuals         :  numerical, min =  -354.7043 , mean =  -1.709701e-12 , max =  296.6086  
      A new explainer has been created!  
    Creating fairness regression object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from character  )
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 3/3 metrics calculated for all models
     Fairness regression object created succesfully  
    
    Creating fairness regression object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from character  )
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 3/3 metrics calculated for all models
     Fairness regression object created succesfully  
    
    Creating fairness regression object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from character  )
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 3/3 metrics calculated for all models
     Fairness regression object created succesfully  
    
    Creating fairness regression object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from character  )
    -> Fairness objects		: 1 object (  compatible  )
    -> Checking explainers		: 2 in total (  compatible  )
    Creating fairness regression object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from numeric  )
    Creating fairness regression object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from character  )
    Creating fairness regression object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( from first fairness object  ) 
    Creating fairness regression object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( from first fairness object  ) 
    Creating fairness regression object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( changed from character  )
    -> Fairness objects		: 1 object (  compatible  )
    -> Checking explainers		: 2 in total (  model type not supported  )
    Preparation of a new explainer is initiated
      -> model label       :  lm  (  default  )
      -> data              :  1000  rows  3  cols 
      -> target variable   :  1000  values 
      -> predict function  :  yhat.lm  will be used (  default  )
      -> predicted values  :  No value for predict function target column. (  default  )
      -> model_info        :  package stats , ver. 4.6.0 , task regression (  default  ) 
      -> predicted values  :  numerical, min =  -15.74808 , mean =  754.0033 , max =  1616.108  
      -> residual function :  difference between y and yhat (  default  )
      -> residuals         :  numerical, min =  -354.7043 , mean =  -1.709701e-12 , max =  296.6086  
      A new explainer has been created!  
    Creating fairness regression object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from character  )
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 3/3 metrics calculated for all models
     Fairness regression object created succesfully  
    
    Creating fairness regression object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( from first fairness object  ) 
    -> Fairness objects		: 1 object (  compatible  )
    -> Checking explainers		: 2 in total (  compatible  )
    -> Metric calculation		: 3/3 metrics calculated for all models
     Fairness regression object created succesfully  
    
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 11/13 metrics calculated for all models ( 2 NA created )
     Fairness object created succesfully  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  not compatible  )
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 11/13 metrics calculated for all models ( 2 NA created )
     Fairness object created succesfully  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 1 object (  compatible  )
    -> Checking explainers		: 2 in total (  compatible  )
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 11/13 metrics calculated for all models ( 2 NA created )
     Fairness object created succesfully  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 2 objects (  not compatible  ) 
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 2 in total (  y not equal  )
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 11/13 metrics calculated for all models ( 2 NA created )
     Fairness object created succesfully  
    Creating fairness classification object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( from first fairness object  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 2 objects (  compatible  )
    -> Checking explainers		: 2 in total (  compatible  )
    -> Metric calculation		: 13/13 metrics calculated for all models
     Fairness object created succesfully  
    Performace metric not given, setting deafult ( accuracy )  
    Performace metric not given, setting deafult ( accuracy )  
    Performace metric not given, setting deafult ( accuracy )  
    Fairness Metric not given, setting deafult ( TPR )  
    Fairness Metric not given, setting deafult ( TPR )  
    Fairness Metric not given, setting deafult ( TPR )  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 2 in total (  compatible  )
    -> Metric calculation		: 6/13 metrics calculated for all models ( 7 NA created )
     Fairness object created succesfully  
    Fairness Metric not given, setting deafult ( TPR )  
    Performace metric not given, setting deafult ( accuracy )  
    
    Creating object with: 
    Fairness metric:  TPR 
    Performance metric:  accuracy 
    
    
    Creating object with: 
    Fairness metric:  FPR 
    Performance metric:  f1 
    
    Fairness data top rows for FPR 
                 group      score model
    1 African_American 0.35204756    lm
    2            Asian 0.04347826    lm
    3        Caucasian 0.16393443    lm
    4         Hispanic 0.11562500    lm
    5  Native_American 0.16666667    lm
    6            Other 0.07762557    lm
    
    Performance data for f1 :                  
    1     lm 0.6039853
    2 ranger 0.6448512
    
    Fairness Metric is NULL, setting deafult parity loss metric ( TPR )  
    Performace metric is NULL, setting deafult ( accuracy )  
    
    Creating object with: 
    Fairness metric: TPR 
    Performance metric: accuracy 
    Performace metric is NULL, setting deafult ( accuracy )  
    
    Creating object with: 
    Fairness metric: non_existing 
    Performance metric: accuracy 
    Fairness Metric is NULL, setting deafult parity loss metric ( TPR )  
    
    Creating object with: 
    Fairness metric: TPR 
    Performance metric: non_existing 
    Fairness Metric is NULL, setting deafult parity loss metric ( TPR )  
    
    Creating object with: 
    Fairness metric: TPR 
    Performance metric: auc 
    Fairness Metric is NULL, setting deafult parity loss metric ( TPR )  
    
    Creating object with: 
    Fairness metric: TPR 
    Performance metric: accuracy 
    Fairness Metric is NULL, setting deafult parity loss metric ( TPR )  
    
    Creating object with: 
    Fairness metric: TPR 
    Performance metric: precision 
    Fairness Metric is NULL, setting deafult parity loss metric ( TPR )  
    
    Creating object with: 
    Fairness metric: TPR 
    Performance metric: recall 
    Preparation of a new explainer is initiated
      -> model label       :  lm  (  default  )
      -> data              :  6172  rows  7  cols 
      -> target variable   :  6172  values 
      -> predict function  :  yhat.glm  will be used (  default  )
      -> predicted values  :  No value for predict function target column. (  default  )
      -> model_info        :  package stats , ver. 4.6.0 , task classification (  default  ) 
      -> predicted values  :  numerical, min =  0.1144574 , mean =  0.4551199 , max =  0.995477  
      -> residual function :  difference between y and yhat (  default  )
      -> residuals         :  numerical, min =  -0.9767658 , mean =  5.053909e-13 , max =  0.8822826  
      A new explainer has been created!  
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 8/13 metrics calculated for all models ( 5 NA created )
     Fairness object created succesfully  
    Preparation of a new explainer is initiated
      -> model label       :  lm  (  default  )
      -> data              :  1000  rows  3  cols 
      -> target variable   :  1000  values 
      -> predict function  :  yhat.lm  will be used (  default  )
      -> predicted values  :  No value for predict function target column. (  default  )
      -> model_info        :  package stats , ver. 4.6.0 , task regression (  default  ) 
      -> predicted values  :  numerical, min =  -119.546 , mean =  756.4906 , max =  1594.562  
      -> residual function :  difference between y and yhat (  default  )
      -> residuals         :  numerical, min =  -302.6659 , mean =  3.478115e-13 , max =  332.7938  
      A new explainer has been created!  
    Creating fairness regression object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( changed from character  )
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 3/3 metrics calculated for all models
     Fairness regression object created succesfully  
    
    Preparation of a new explainer is initiated
      -> model label       :  ranger  (  default  )
      -> data              :  1000  rows  3  cols 
      -> target variable   :  1000  values 
      -> predict function  :  yhat.ranger  will be used (  default  )
      -> predicted values  :  No value for predict function target column. (  default  )
      -> model_info        :  package ranger , ver. 0.17.0 , task regression (  default  ) 
      -> predicted values  :  numerical, min =  361.6527 , mean =  756.1869 , max =  1136.792  
      -> residual function :  difference between y and yhat (  default  )
      -> residuals         :  numerical, min =  -669.0748 , mean =  0.3037205 , max =  630.6428  
      A new explainer has been created!  
    Creating fairness regression object
    -> Privileged subgroup		: character ( from first fairness object  ) 
    -> Protected variable		: factor ( from first fairness object  ) 
    -> Fairness objects		: 1 object (  compatible  )
    -> Checking explainers		: 2 in total (  compatible  )
    -> Metric calculation		: 3/3 metrics calculated for all models
     Fairness regression object created succesfully  
    
    Creating fairness classification object
    -> Privileged subgroup		: character ( Ok  )
    -> Protected variable		: factor ( Ok  ) 
    -> Cutoff values for explainers	: 0.5 ( for all subgroups ) 
    -> Fairness objects		: 0 objects 
    -> Checking explainers		: 1 in total (  compatible  )
    -> Metric calculation		: 13/13 metrics calculated for all models
     Fairness object created succesfully  
    
    changing protected to factor 
    Preparation of a new explainer is initiated
      -> model label       :  lm  (  default  )
      -> data              :  15  rows  2  cols 
      -> target variable   :  15  values 
      -> predict function  :  yhat.glm  will be used (  default  )
      -> predicted values  :  No value for predict function target column. (  default  )
      -> model_info        :  package stats , ver. 4.6.0 , task classification (  default  ) 
      -> predicted values  :  numerical, min =  7.884924e-12 , mean =  0.4666667 , max =  1  
      -> residual function :  difference between y and yhat (  default  )
      -> residuals         :  numerical, min =  -7.884924e-12 , mean =  -5.256659e-13 , max =  7.884915e-12  
      A new explainer has been created!  
    [ FAIL 3 | WARN 2 | SKIP 0 | PASS 299 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_heatmap.R:2:3'): Test heatmap ──────────────────────────────────
    Error in `rep(yes, length.out = len)`: attempt to replicate an object of type 'object'
    Backtrace:
        ▆
     1. ├─base::plot(fairness_heatmap(fobject)) at test_heatmap.R:2:3
     2. └─fairmodels:::plot.fairness_heatmap(fairness_heatmap(fobject))
     3.   └─base::ifelse(...)
    ── Failure ('test_plot_density.R:14:3'): Test plot_density ─────────────────────
    plt$labels$x not equal to "probability".
    target is NULL, current is character
    ── Error ('test_plot_fairmodels.R:8:3'): Test plot_fairmodels ──────────────────
    Error in `rep(yes, length.out = len)`: attempt to replicate an object of type 'object'
    Backtrace:
         ▆
      1. ├─base::suppressWarnings(...) at test_plot_fairmodels.R:8:3
      2. │ └─base::withCallingHandlers(...)
      3. ├─fairmodels:::expect_s3_class(...)
      4. │ ├─testthat::expect(...) at tests/testthat/helper_objects.R:70:20
      5. │ └─base::class(object) %in% class
      6. ├─fairmodels::plot_fairmodels(fc, type = "fairness_heatmap")
      7. └─fairmodels:::plot_fairmodels.fairness_object(fc, type = "fairness_heatmap")
      8.   └─fairmodels:::plot_fairmodels.default(x, type, ...)
      9.     └─fairmodels:::plot.fairness_heatmap(fairness_heatmap(x, ...))
     10.       └─base::ifelse(...)
    
    [ FAIL 3 | WARN 2 | SKIP 0 | PASS 299 ]
    Error: Test failures
    Execution halted

Package: fairness
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘fairness’

Package: fastR2
Check: examples
New result: ERROR
  Running examples in ‘fastR2-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: Cuckoo
  > ### Title: Cuckoo eggs in other birds' nests
  > ### Aliases: Cuckoo
  > ### Keywords: datasets
  > 
  > ### ** Examples
  > 
  > 
  > data(Cuckoo)
  Warning in data(Cuckoo) : data set ‘Cuckoo’ not found
  > gf_boxplot(length ~ species, data = Cuckoo)
  Error in `position_dodge()`:
  ! `orientation` must be a string or character vector.
  Backtrace:
      ▆
   1. ├─ggformula::gf_boxplot(length ~ species, data = Cuckoo)
   2. │ ├─base::do.call(position_fun, pdots)
   3. │ └─ggplot2::position_dodge(orientation = NA)
   4. │   ├─ggplot2::ggproto(...)
   5. │   │ └─rlang::list2(...)
   6. │   └─rlang::arg_match0(orientation, c("x", "y"))
   7. └─rlang::abort(message = message, call = call)
  Execution halted

Package: faux
Check: examples
New result: ERROR
  Running examples in ‘faux-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: norm2likert
  > ### Title: Convert normal to likert
  > ### Aliases: norm2likert
  > 
  > ### ** Examples
  > 
  > 
  > x <- rnorm(10000)
  > y <- norm2likert(x, c(.1, .2, .35, .2, .1, .05))
  > g <- ggplot2::ggplot() + ggplot2::geom_point(ggplot2::aes(x, y))
  > ggExtra::ggMarginal(g, type = "histogram")
  > 
  > y <- norm2likert(x, c(40, 30, 20, 10))
  > g <- ggplot2::ggplot() + ggplot2::geom_point(ggplot2::aes(x, y))
  > ggExtra::ggMarginal(g, type = "histogram")
  > 
  > y <- norm2likert(x, c(lower = .5, upper = .5))
  > g <- ggplot2::ggplot() + ggplot2::geom_point(ggplot2::aes(x, y))
  > ggExtra::ggMarginal(g, type = "histogram")
  Error in `ggplot2::scale_x_continuous()`:
  ! `limits` must be a <numeric> vector, not a character vector.
  Backtrace:
       ▆
    1. └─ggExtra::ggMarginal(g, type = "histogram")
    2.   └─plt$build()
    3.     └─private$addLimits(margThemed)
    4.       └─ggplot2::scale_x_continuous(limits = limits, oob = scales::squish)
    5.         └─ggplot2::continuous_scale(...)
    6.           └─ggplot2:::check_continuous_limits(limits, call = call)
    7.             └─ggplot2:::check_numeric(limits, arg = arg, call = call, allow_na = TRUE)
    8.               └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
    9.                 └─ggplot2:::stop_input_type(...)
   10.                   └─rlang::abort(message, ..., call = call, arg = arg)
  Execution halted

Package: faux
Check: tests
New result: ERROR
    Running ‘testthat.R’ [36s/37s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(faux)
    
    ************
    Welcome to faux. For support and examples visit:
    https://debruine.github.io/faux/
    - Get and set global package options with: faux_options()
    ************
    > 
    > expect_equal <- function(...) {
    +   testthat::expect_equal(..., check.environment=FALSE)
    + }
    > 
    > test_check("faux")
    [ FAIL 19 | WARN 0 | SKIP 22 | PASS 1351 ]
    
    ══ Skipped tests (22) ══════════════════════════════════════════════════════════
    • On CRAN (12): 'test-distributions.R:61:3', 'test-distributions.R:92:3',
      'test-distributions.R:115:3', 'test-distributions.R:138:3',
      'test-distributions.R:162:3', 'test-distributions.R:236:3',
      'test-distributions.R:294:3', 'test-distributions.R:318:3',
      'test-distributions.R:386:3', 'test-distributions.R:415:3',
      'test-plot_design.R:51:3', 'test-plot_design.R:341:3'
    • Too variable (1): 'test-distributions.R:520:3'
    • long checking function (1): 'test-norta.R:55:3'
    • long simulation (8): 'test-norta.R:92:3', 'test-norta.R:112:3',
      'test-norta.R:140:3', 'test-norta.R:160:3', 'test-norta.R:186:3',
      'test-norta.R:209:3', 'test-norta.R:233:3', 'test-norta.R:295:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot_design.R:44:3'): wide2long ──────────────────────────────
    class(p1) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    Backtrace:
        ▆
     1. └─global expect_equal(class(p1), c("gg", "ggplot")) at test-plot_design.R:44:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:49:3'): wide2long ──────────────────────────────
    class(p2) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    Backtrace:
        ▆
     1. └─global expect_equal(class(p2), c("gg", "ggplot")) at test-plot_design.R:49:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:73:3'): subset ─────────────────────────────────
    p1$labels$fill not equal to "W1".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(p1$labels$fill, "W1") at test-plot_design.R:73:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:74:3'): subset ─────────────────────────────────
    p1$labels$colour not equal to "W1".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(p1$labels$colour, "W1") at test-plot_design.R:74:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:119:3'): from design ───────────────────────────
    s0$labels$fill not equal to "fill".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(s0$labels$fill, "fill") at test-plot_design.R:119:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:120:3'): from design ───────────────────────────
    s0$labels$colour not equal to "colour".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(s0$labels$colour, "colour") at test-plot_design.R:120:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:125:3'): from design ───────────────────────────
    s1$labels$fill not equal to "W1".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(s1$labels$fill, "W1") at test-plot_design.R:125:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:126:3'): from design ───────────────────────────
    s1$labels$colour not equal to "W1".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(s1$labels$colour, "W1") at test-plot_design.R:126:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:176:3'): from data ─────────────────────────────
    s0$labels$fill not equal to "fill".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(s0$labels$fill, "fill") at test-plot_design.R:176:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:177:3'): from data ─────────────────────────────
    s0$labels$colour not equal to "colour".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(s0$labels$colour, "colour") at test-plot_design.R:177:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:182:3'): from data ─────────────────────────────
    s1$labels$fill not equal to "W1".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(s1$labels$fill, "W1") at test-plot_design.R:182:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:183:3'): from data ─────────────────────────────
    s1$labels$colour not equal to "W1".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(s1$labels$colour, "W1") at test-plot_design.R:183:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:231:3'): 2w ────────────────────────────────────
    class(p) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    Backtrace:
        ▆
     1. └─global expect_equal(class(p), c("gg", "ggplot")) at test-plot_design.R:231:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:234:3'): 2w ────────────────────────────────────
    p$labels$fill not equal to "time".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(p$labels$fill, "time") at test-plot_design.R:234:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:235:3'): 2w ────────────────────────────────────
    p$labels$colour not equal to "time".
    target is NULL, current is character
    Backtrace:
        ▆
     1. └─global expect_equal(p$labels$colour, "time") at test-plot_design.R:235:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:245:3'): 2w*2b ─────────────────────────────────
    class(p) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    Backtrace:
        ▆
     1. └─global expect_equal(class(p), c("gg", "ggplot")) at test-plot_design.R:245:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:257:3'): 2w*2b ─────────────────────────────────
    class(p) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    Backtrace:
        ▆
     1. └─global expect_equal(class(p), c("gg", "ggplot")) at test-plot_design.R:257:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:271:3'): 2w*2w*2b ──────────────────────────────
    class(p) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    Backtrace:
        ▆
     1. └─global expect_equal(class(p), c("gg", "ggplot")) at test-plot_design.R:271:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    ── Failure ('test-plot_design.R:288:3'): 2w*2w*2b*2b ───────────────────────────
    class(p) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    Backtrace:
        ▆
     1. └─global expect_equal(class(p), c("gg", "ggplot")) at test-plot_design.R:288:3
     2.   └─testthat::expect_equal(..., check.environment = FALSE)
    
    [ FAIL 19 | WARN 0 | SKIP 22 | PASS 1351 ]
    Error: Test failures
    Execution halted

Package: feasts
Check: tests
New result: ERROR
    Running ‘testthat.R’ [29s/29s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(feasts)
    Loading required package: fabletools
    > 
    > test_check("feasts")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-graphics.R:194:3'): gg_tsdisplay() plots ───────────────────────
    Error in `UseMethod("ggplot_build")`: no applicable method for 'ggplot_build' applied to an object of class "NULL"
    Backtrace:
        ▆
     1. └─ggplot2::ggplot_build(p[[1]]) at test-graphics.R:194:3
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 101 ]
    Error: Test failures
    Execution halted

Package: fec16
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘fec_vignette.Rmd’ using rmarkdown
  
  Quitting from fec_vignette.Rmd:203-226 [unnamed-chunk-9]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::labels> object is invalid:
  - every label must be named.
  ---
  Backtrace:
      ▆
   1. └─ggplot2::labs(...)
   2.   └─ggplot2::class_labels(args)
   3.     └─S7::new_object(labels)
   4.       └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'fec_vignette.Rmd' failed with diagnostics:
  <ggplot2::labels> object is invalid:
  - every label must be named.
  --- failed re-building ‘fec_vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘fec_vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: flextable
Check: examples
New result: ERROR
  Running examples in ‘flextable-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: gg_chunk
  > ### Title: 'ggplots' chunk wrapper
  > ### Aliases: gg_chunk
  > 
  > ### ** Examples
  > 
  > library(data.table)
  > library(flextable)
  > if (require("ggplot2")) {
  +   my_cor_plot <- function(x) {
  +     cols <- colnames(x)[sapply(x, is.numeric)]
  +     x <- x[, .SD, .SDcols = cols]
  +     cormat <- as.data.table(cor(x))
  +     cormat$var1 <- colnames(cormat)
  +     cormat <- melt(cormat,
  +       id.vars = "var1", measure.vars = cormat$var1,
  +       variable.name = "var2", value.name = "correlation"
  +     )
  +     ggplot(data = cormat, aes(x = var1, y = var2, fill = correlation)) +
  +       geom_tile() +
  +       coord_equal() +
  +       scale_fill_gradient2(
  +         low = "blue",
  +         mid = "white", high = "red", limits = c(-1, 1),
  +         guide = "none"
  +       ) +
  +       theme_void()
  +   }
  +   z <- as.data.table(iris)
  +   z <- z[, list(gg = list(my_cor_plot(.SD))), by = "Species"]
  +   ft <- flextable(z)
  +   ft <- mk_par(ft,
  +     j = "gg",
  +     value = as_paragraph(
  +       gg_chunk(value = gg, width = 1, height = 1)
  +     )
  +   )
  +   ft
  + }
  Loading required package: ggplot2
  a flextable object.
  col_keys: `Species`, `gg` 
  header has 1 row(s) 
  body has 3 row(s) 
  original dataset sample: 
  Error in format.default(unlist(xx), ...) : 
    c("Found no format() method for class \"ggplot2::ggplot\"", "Found no format() method for class \"ggplot\"", "Found no format() method for class \"ggplot2::gg\"", "Found no format() method for class \"S7_object\"", "Found no format() method for class \"gg\"")
  Calls: <Anonymous> ... format.default -> lapply -> FUN -> format -> format.default
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
  gen_grob 5.243  0.136   5.379

Package: fmf
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘fmf’
  See ‘/home/hornik/tmp/CRAN_recheck/fmf.Rcheck/00install.out’ for details.
  Used C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
  Used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’

Package: forestPSD
Check: examples
New result: ERROR
  Running examples in ‘forestPSD-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: psdfun
  > ### Title: Regression analysis for survival curves.
  > ### Aliases: psdfun
  > 
  > ### ** Examples
  > 
  > data(Npop)
  > psd_D1<-psdfun(ax=Npop$ax,index="Deevey1")
  > psd_D1
  $Summary
  
  Formula: ax ~ a + b * age
  
  Parameters:
    Estimate Std. Error t value Pr(>|t|)    
  a   5603.9     1062.0   5.277 0.000509 ***
  b   -642.3      156.6  -4.102 0.002669 ** 
  ---
  Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
  
  Residual standard error: 1642 on 9 degrees of freedom
  
  Number of iterations to convergence: 2 
  Achieved convergence tolerance: 1.49e-08
  
  
  $Goodness
        MSE    RMSE   Rsquare adj.Rsquare     MAE     MAPE      RASE      AIC
  1 2206682 1485.49 0.6515192    0.564399 1234.35 17.69146 0.7053431 197.8937
         BIC
  1 197.8937
  
  $Data
     age ageclass   ax    predict
  1    1        I 8283  4961.5455
  2    2       II 5238  4319.2364
  3    3      III 1921  3676.9273
  4    4       IV 1425  3034.6182
  5    5        V  926  2392.3091
  6    6       VI  659  1750.0000
  7    7      VII  479  1107.6909
  8    8     VIII  228   465.3818
  9    9       IX   57  -176.9273
  10  10        X   24  -819.2364
  11  11       XI   10 -1461.5455
  
  > psd_D2<-psdfun(ax=Npop$ax,index="Deevey2")
  > psd_D2
  $Summary
  
  Formula: ax ~ a * exp(-b * age)
  
  Parameters:
     Estimate Std. Error t value Pr(>|t|)    
  a 1.504e+04  9.717e+02   15.48 8.59e-08 ***
  b 5.828e-01  3.883e-02   15.01 1.12e-07 ***
  ---
  Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
  
  Residual standard error: 318.7 on 9 degrees of freedom
  
  Number of iterations to convergence: 17 
  Achieved convergence tolerance: 1.49e-08
  
  
  $Goodness
        MSE     RMSE   Rsquare adj.Rsquare      MAE      MAPE      RASE      AIC
  1 83111.3 288.2903 0.9869709   0.9837137 188.8823 0.4079135 0.1079327 161.8239
         BIC
  1 161.8239
  
  $Data
     age ageclass   ax    predict
  1    1        I 8283 8396.40389
  2    2       II 5238 4687.87598
  3    3      III 1921 2617.33255
  4    4       IV 1425 1461.30779
  5    5        V  926  815.87663
  6    6       VI  659  455.51983
  7    7      VII  479  254.32560
  8    8     VIII  228  141.99494
  9    9       IX   57   79.27854
  10  10        X   24   44.26276
  11  11       XI   10   24.71276
  
  > psd_D3<-psdfun(ax=Npop$ax,index="Deevey3")
  > psd_D3
  $Summary
  
  Formula: ax ~ a * (age^-b)
  
  Parameters:
     Estimate Std. Error t value Pr(>|t|)    
  a 8691.1232   633.3189  13.723 2.44e-07 ***
  b    1.2598     0.1326   9.499 5.48e-06 ***
  ---
  Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
  
  Residual standard error: 649 on 9 degrees of freedom
  
  Number of iterations to convergence: 18 
  Achieved convergence tolerance: 1.49e-08
  
  
  $Goodness
         MSE     RMSE   Rsquare adj.Rsquare      MAE     MAPE     RASE      AIC
  1 344662.5 587.0797 0.9491095   0.9363869 442.1638 6.578955 0.252665 177.4702
         BIC
  1 177.4702
  
  $Data
     age ageclass   ax   predict
  1    1        I 8283 8691.1232
  2    2       II 5238 3629.4310
  3    3      III 1921 2177.7043
  4    4       IV 1425 1515.6579
  5    5        V  926 1144.2318
  6    6       VI  659  909.4138
  7    7      VII  479  748.8969
  8    8     VIII  228  632.9419
  9    9       IX   57  545.6597
  10  10        X   24  477.8336
  11  11       XI   10  423.7700
  
  > library(ggplot2)
  > psdnls.p<-ggplot()+geom_bar(aes(x=age,y=ax,group=ageclass),data=psd_D2$Data,stat = "identity")+
  +   geom_line(aes(x=age,y=predict),color="blue",linewidth=1,data=psd_D2$Data)+
  +   geom_text(aes(x=10,y=7700),label=expression(paste(italic(y),"=aexp(-b",italic(x),")")))+
  +   geom_text(aes(x=10,y=7300),label=expression(paste(R^2,"=0.987")))+
  +   scale_x_continuous(breaks=1:11)+
  +   scale_x_discrete(limits=psd_D2$Data$ageclass)+
  +   xlab("Age class")+ylab("Number of individuals")
  Scale for x is already present.
  Adding another scale for x, which will replace the existing scale.
  > psdnls.p
  Error in `geom_text()`:
  ! Problem while setting up geom aesthetics.
  ℹ Error occurred in the 3rd layer.
  Caused by error in `list_sizes()`:
  ! `x$label` must be a vector, not an expression vector.
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_build(x)
    4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$compute_geom_2(d, theme = plot@theme)
   14. │         └─ggplot2 (local) compute_geom_2(..., self = self)
   15. │           └─self$geom$use_defaults(...)
   16. │             └─ggplot2 (local) use_defaults(..., self = self)
   17. │               └─ggplot2:::check_aesthetics(new_params, nrow(data))
   18. │                 └─vctrs::list_sizes(x)
   19. └─vctrs:::stop_scalar_type(`<fn>`(`<expression>`), "x$label", `<env>`)
   20.   └─vctrs:::stop_vctrs(...)
   21.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  Execution halted

Package: ForIT
Check: data for non-ASCII characters
New result: WARNING
    Failed with error:  'there is no package called 'Matrix''
    Error loading dataset 'INFCparam':
     Error in .requirePackage(package) : 
      unable to load required package 'Matrix'
    
    The dataset(s) may use package(s) not declared in Depends/Imports.

Package: gapfill
Check: tests
New result: ERROR
    Running ‘run-all.R’ [14s/14s]
  Running the tests in ‘tests/run-all.R’ failed.
  Complete output:
    > library(testthat)
    > test_check('gapfill')
    Loading required package: gapfill
    Loading required package: ggplot2
    --> See ?Gapfill and https://doi.org/10.1109/TGRS.2017.2785240 <--
    [ FAIL 5 | WARN 6 | SKIP 0 | PASS 870 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-Image.R:5:4'): Image ─────────────────────────────────────────
    class(Image(ndvi)) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-Image.R:6:4'): Image ─────────────────────────────────────────
    class(Image(ndvi[, , , 1])) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-Image.R:7:4'): Image ─────────────────────────────────────────
    class(Image(ndvi[, , 1, 1])) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-Image.R:10:4'): Image ────────────────────────────────────────
    class(Image(unname(ndvi))) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-Image.R:11:4'): Image ────────────────────────────────────────
    class(Image(ndvi, zlim = c(1, 2))) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 5 | WARN 6 | SKIP 0 | PASS 870 ]
    Error: Test failures
    Execution halted

Package: geneSLOPE
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.

Package: gfoRmulaICE
Check: tests
New result: ERROR
    Running ‘testthat.R’ [441s/438s]
  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(gfoRmulaICE)
    > 
    > test_check("gfoRmulaICE")
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention 1... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention 2... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention 3... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
                                           NP Risk Classical Pooled ICE Risk Ratio
    Natural Course (Direct Effect)         0.26851              0.26874    1.00000
    Dynamic Intervention 1 (Direct Effect)      NA              0.30568    1.13746
    Dynamic Intervention 2 (Direct Effect)      NA              0.25787    0.95957
    Dynamic Intervention 3 (Direct Effect)      NA              0.32326    1.20286
                                           Risk Difference
    Natural Course (Direct Effect)                 0.00000
    Dynamic Intervention 1 (Direct Effect)         0.03694
    Dynamic Intervention 2 (Direct Effect)        -0.01087
    Dynamic Intervention 3 (Direct Effect)         0.05452
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention 1... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention 2... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention 3... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
                                           NP Risk Classical Pooled ICE Risk Ratio
    Natural Course (Direct Effect)         0.26851              0.26874    1.00000
    Dynamic Intervention 1 (Direct Effect)      NA              0.30568    1.13746
    Dynamic Intervention 2 (Direct Effect)      NA              0.25787    0.95957
    Dynamic Intervention 3 (Direct Effect)      NA              0.32326    1.20286
                                           Risk Difference
    Natural Course (Direct Effect)                 0.00000
    Dynamic Intervention 1 (Direct Effect)         0.03694
    Dynamic Intervention 2 (Direct Effect)        -0.01087
    Dynamic Intervention 3 (Direct Effect)         0.05452
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Threshold Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention with Grace Period... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
                                                           NP Risk
    Natural Course (Direct Effect)                         0.26851
    Static Intervention (Direct Effect)                         NA
    Threshold Intervention (Direct Effect)                      NA
    Dynamic Intervention with Grace Period (Direct Effect)      NA
                                                           Classical Pooled ICE
    Natural Course (Direct Effect)                                      0.26874
    Static Intervention (Direct Effect)                                 0.24935
    Threshold Intervention (Direct Effect)                              0.26874
    Dynamic Intervention with Grace Period (Direct Effect)              0.28701
                                                           Risk Ratio
    Natural Course (Direct Effect)                            1.00000
    Static Intervention (Direct Effect)                       0.92784
    Threshold Intervention (Direct Effect)                    1.00000
    Dynamic Intervention with Grace Period (Direct Effect)    1.06799
                                                           Risk Difference
    Natural Course (Direct Effect)                                 0.00000
    Static Intervention (Direct Effect)                           -0.01939
    Threshold Intervention (Direct Effect)                         0.00000
    Dynamic Intervention with Grace Period (Direct Effect)         0.01827
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
                                         NP Risk Classical Pooled ICE Risk Ratio
    Natural Course (Direct Effect)       0.26851              0.26874    1.00000
    Static Intervention (Direct Effect)       NA              0.24935    0.92784
    Dynamic Intervention (Direct Effect)      NA              0.34078    1.26807
                                         Risk Difference
    Natural Course (Direct Effect)               0.00000
    Static Intervention (Direct Effect)         -0.01939
    Dynamic Intervention (Direct Effect)         0.07204
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
                                        NP Risk Weighted ICE Risk Ratio
    Natural Course (Total Effect)       0.22982      0.22722    1.00000
    Static Intervention (Total Effect)       NA      0.19441    0.85562
    Dynamic Intervention (Total Effect)      NA      0.24194    1.06480
                                        Risk Difference
    Natural Course (Total Effect)               0.00000
    Static Intervention (Total Effect)         -0.03280
    Dynamic Intervention (Total Effect)         0.01472
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
          NP Risk ICE Risk Risk Ratio Risk Difference
     [1,] 0.26851  0.26874    1.00000         0.00000
     [2,]      NA  0.27218    1.01280         0.00344
     [3,]      NA  0.33107    1.23195         0.06234
     [4,] 0.26851  0.21482    1.00000         0.00000
     [5,]      NA  0.26318    1.22513         0.04836
     [6,]      NA  0.20892    0.97255        -0.00590
     [7,] 0.26851  0.21573    1.00000         0.00000
     [8,]      NA  0.23855    1.10579         0.02282
     [9,]      NA  0.21463    0.99492        -0.00110
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    [15,]      NA  0.31554    1.17010         0.04587
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    Dynamic Intervention 1 Bootstrap Progress: 1/5
    
    Running Dynamic Intervention 1... 
    
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    Dynamic Intervention 1 Bootstrap Progress: 2/5
    
    Running Dynamic Intervention 1... 
    
    Running Time 4...
    
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    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention 1 Bootstrap Progress: 3/5
    
    Running Dynamic Intervention 1... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention 1 Bootstrap Progress: 4/5
    
    Running Dynamic Intervention 1... 
    
    Running Time 4...
    
    Running Time 3...
    
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    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention 1 Bootstrap Progress: 5/5
    
    Running Dynamic Intervention 2... 
    
    Running Time 4...
    
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    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention 2 Bootstrap Progress: 1/5
    
    Running Dynamic Intervention 2... 
    
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    Running Natural Course... 
    
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    Dynamic Intervention 2 Bootstrap Progress: 2/5
    
    Running Dynamic Intervention 2... 
    
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    Running Natural Course... 
    
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    Dynamic Intervention 2 Bootstrap Progress: 3/5
    
    Running Dynamic Intervention 2... 
    
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    Running Natural Course... 
    
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    Dynamic Intervention 2 Bootstrap Progress: 4/5
    
    Running Dynamic Intervention 2... 
    
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    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention 2 Bootstrap Progress: 5/5
    
    Running Dynamic Intervention 3... 
    
    Running Time 4...
    
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    Running Dynamic Intervention 3... 
    
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    Running Natural Course... 
    
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    Dynamic Intervention 3 Bootstrap Progress: 1/5
    
    Running Dynamic Intervention 3... 
    
    Running Time 4...
    
    Running Time 3...
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention 3 Bootstrap Progress: 2/5
    
    Running Dynamic Intervention 3... 
    
    Running Time 4...
    
    Running Time 3...
    
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    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention 3 Bootstrap Progress: 3/5
    
    Running Dynamic Intervention 3... 
    
    Running Time 4...
    
    Running Time 3...
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention 3 Bootstrap Progress: 4/5
    
    Running Dynamic Intervention 3... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention 3 Bootstrap Progress: 5/5
    
    Running Natural Course... 
    
    Running Time 4...
    
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    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 1/5
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 2/5
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 3/5
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 4/5
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
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    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 5/5
    
    Running Threshold Intervention... 
    
    Running Time 4...
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Threshold Intervention Bootstrap Progress: 1/5
    
    Running Threshold Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Threshold Intervention Bootstrap Progress: 2/5
    
    Running Threshold Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Threshold Intervention Bootstrap Progress: 3/5
    
    Running Threshold Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Threshold Intervention Bootstrap Progress: 4/5
    
    Running Threshold Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Threshold Intervention Bootstrap Progress: 5/5
    
    Running Dynamic Intervention with Grace Period... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention with Grace Period... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
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    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention with Grace Period Bootstrap Progress: 1/5
    
    Running Dynamic Intervention with Grace Period... 
    
    Running Time 4...
    
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    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
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    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention with Grace Period Bootstrap Progress: 2/5
    
    Running Dynamic Intervention with Grace Period... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention with Grace Period Bootstrap Progress: 3/5
    
    Running Dynamic Intervention with Grace Period... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention with Grace Period Bootstrap Progress: 4/5
    
    Running Dynamic Intervention with Grace Period... 
    
    Running Time 4...
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention with Grace Period Bootstrap Progress: 5/5
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 1/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 2/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 3/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 4/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 5/5
    
    Running Dynamic Intervention... 
    
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    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 1/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 2/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
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    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 3/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 4/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 5/5
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Running Static Intervention... 
    
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    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 1/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 2/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 3/5
    
    Running Static Intervention... 
    
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    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
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    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 4/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 5/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 1/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 2/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 3/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 4/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 5/5
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Running Static Intervention... 
    
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    Running Static Intervention... 
    
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    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 1/5
    
    Running Static Intervention... 
    
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    Running Natural Course... 
    
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    Static Intervention Bootstrap Progress: 2/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 3/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 4/5
    
    Running Static Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Static Intervention Bootstrap Progress: 5/5
    
    Running Dynamic Intervention... 
    
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    Running Dynamic Intervention... 
    
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    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 1/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 2/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 3/5
    
    Running Dynamic Intervention... 
    
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    Running Time 1...
    
    Running Natural Course... 
    
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    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 4/5
    
    Running Dynamic Intervention... 
    
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    Static Intervention Bootstrap Progress: 5/5
    
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    Dynamic Intervention Bootstrap Progress: 5/5
    
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    Static Intervention Bootstrap Progress: 5/5
    
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    Dynamic Intervention Bootstrap Progress: 5/5
    
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    Static Intervention Bootstrap Progress: 1/5
    
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    Dynamic Intervention Bootstrap Progress: 4/5
    
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    Dynamic Intervention Bootstrap Progress: 5/5
    
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    Static Intervention Bootstrap Progress: 5/5
    
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    Dynamic Intervention Bootstrap Progress: 4/5
    
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    Dynamic Intervention Bootstrap Progress: 5/5
    
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    Static Intervention Bootstrap Progress: 4/5
    
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    Static Intervention Bootstrap Progress: 5/5
    
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    Dynamic Intervention Bootstrap Progress: 4/5
    
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    Dynamic Intervention Bootstrap Progress: 5/5
    
    
    Attaching package: 'Hmisc'
    
    The following object is masked from 'package:testthat':
    
        describe
    
    The following objects are masked from 'package:base':
    
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    Static Intervention Bootstrap Progress: 3/5
    
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    Natural Course Bootstrap Progress: 1/5
    
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    Natural Course Bootstrap Progress: 2/5
    
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    Natural Course Bootstrap Progress: 3/5
    
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    Natural Course Bootstrap Progress: 4/5
    
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    Natural Course Bootstrap Progress: 5/5
    
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    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 3/5
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 4/5
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 5/5
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 1/5
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 2/5
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 3/5
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 4/5
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Static Intervention Bootstrap Progress: 5/5
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 1/5
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 2/5
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 3/5
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 4/5
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Dynamic Intervention Bootstrap Progress: 5/5
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Natural Course... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Static Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    Running Dynamic Intervention... 
    
    Running Time 4...
    
    Running Time 3...
    
    Running Time 2...
    
    Running Time 1...
    
    [ FAIL 15 | WARN 176 | SKIP 0 | PASS 47 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_plot.R:27:5'): plot classical pooled ICE direct effect - dynamic interventions ──
    class(plot1) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:52:5'): check different interventions ─────────────────
    class(plot2) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:77:5'): check user-defined intervention ───────────────
    class(plot3) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:104:5'): plot hazard-based pooled ICE - time-specific hazard model same as the outcome model ──
    class(plot4a) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:132:5'): plot hazard-based pooled ICE - time-specific hazard model Y ~ L1 + L2 ──
    class(plot4b) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:161:5'): plot hazard-based pooled ICE - pooled-over-time hazard model ──
    class(plot4c) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:187:5'): plot classical stratified ICE ────────────────
    class(plot4d) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:215:5'): plot hazard-extended stratified ICE - time-specific hazard model Y ~ L1 ──
    class(plot4e) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:241:5'): plot doubly robust ICE ───────────────────────
    class(plot4f) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:270:5'): plot hazard-based stratified ICE with intervention-specific models ──
    class(plot4h) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:296:5'): plot flexible model specification - complicated terms ──
    class(plot5a) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:322:5'): plot flexible model specification - using static intervention as reference ──
    class(plot5b) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:351:5'): plot complicated scenario 1 ──────────────────
    class(plot6a) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:378:5'): plot complicated scenario 2 - doubly robust ICE with intervention-specific models ──
    class(plot6b) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test_plot.R:534:5'): plot complicated scenario 3 - intervention-specific time options ──
    class(plots) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 15 | WARN 176 | SKIP 0 | PASS 47 ]
    Error: Test failures
    Execution halted

Package: gg1d
Check: examples
New result: ERROR
  Running examples in ‘gg1d-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: gg1d
  > ### Title: AutoPlot an entire data.frame
  > ### Aliases: gg1d
  > 
  > ### ** Examples
  > 
  > path_gg1d <- system.file("example.csv", package = "gg1d")
  > df <- read.csv(path_gg1d, header = TRUE, na.strings = "")
  > 
  > # Create Basic Plot
  > gg1d(df, col_id = "ID", col_sort = "Glasses")
  
  ── Running gg1d ────────────────────────────────────────────────────────────────
  
  ── Sorting 
  • Sorting X axis by: Glasses
  • Order type: frequency
  • Sort order: descending
  ! Categorical columns must have <= 6 unique values to be visualised. Columns with too many unique values: Date (19)
  
  ── Generating Plot 
  ℹ Found 7 plottable columns in data
  ✔ Plotting column Glasses
  ✔ Plotting column Age
  ✔ Plotting column Gender
  ✔ Plotting column EyeColour
  ✔ Plotting column Height
  ✔ Plotting column HairColour
  ✔ Plotting column WearingHat
  ! Skipping column WearingHat_tooltip
  ! Skipping column Date
  ℹ Stacking plots vertically
  ℹ Making plot interactive since `interactive = TRUE`
  Error:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `draw_panel()`:
  ! unused arguments (lineend = "butt", linejoin = "mitre")
  Backtrace:
       ▆
    1. ├─gg1d::gg1d(df, col_id = "ID", col_sort = "Glasses")
    2. │ └─ggiraph::girafe(...)
    3. │   ├─base::tryCatch(...)
    4. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5. │   ├─base::print(ggobj)
    6. │   └─patchwork:::print.patchwork(ggobj)
    7. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
    8. │       └─base::lapply(x$plots, plot_table, guides = guides)
    9. │         ├─patchwork (local) FUN(X[[i]], ...)
   10. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
   11. │           ├─patchwork:::plot_table(x, guides)
   12. │           └─patchwork:::plot_table.ggplot(x, guides)
   13. │             └─ggplot2::ggplotGrob(x)
   14. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
   15. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
   16. │                 └─ggplot2:::by_layer(...)
   17. │                   ├─rlang::try_fetch(...)
   18. │                   │ ├─base::tryCatch(...)
   19. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   20. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   22. │                   │ └─base::withCallingHandlers(...)
   23. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   24. │                     └─l$draw_geom(d, layout)
   25. │                       └─ggplot2 (local) draw_geom(..., self = self)
   26. │                         └─self$geom$draw_layer(...)
   27. │                           └─ggplot2 (local) draw_layer(..., self = self)
   28. │                             └─base::lapply(...)
   29. │                               └─ggplot2 (local) FUN(X[[i]], ...)
   30. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   31. │                                 └─self$draw_panel(...)
   32. └─base::.handleSimpleError(...)
   33.   └─rlang (local) h(simpleError(msg, call))
   34.     └─handlers[[1L]](cnd)
   35.       └─cli::cli_abort(...)
   36.         └─rlang::abort(...)
  Execution halted

Package: gg1d
Check: tests
New result: ERROR
    Running ‘testthat.R’ [13s/13s]
  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(gg1d)
    > 
    > test_check("gg1d")
    [ FAIL 9 | WARN 0 | SKIP 2 | PASS 47 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test-gg1d.R:169:3', 'test-gg1d.R:189:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-gg1d.R:14:3'): gg1d works as expected ────────────────────────
    `suppressMessages(gg1d(mtcars))` threw an unexpected error.
    Message: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `draw_panel()`:
    ! unused arguments (lineend = "butt", linejoin = "mitre")
    Class:   rlang_error/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(suppressMessages(gg1d(mtcars)), NA) at test-gg1d.R:14:3
      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. ├─base::suppressMessages(gg1d(mtcars))
      8. │ └─base::withCallingHandlers(...)
      9. ├─gg1d::gg1d(mtcars)
     10. │ └─ggiraph::girafe(...)
     11. │   ├─base::tryCatch(...)
     12. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │   ├─base::print(ggobj)
     14. │   └─patchwork:::print.patchwork(ggobj)
     15. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
     16. │       └─base::lapply(x$plots, plot_table, guides = guides)
     17. │         ├─patchwork (local) FUN(X[[i]], ...)
     18. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
     19. │           ├─patchwork:::plot_table(x, guides)
     20. │           └─patchwork:::plot_table.ggplot(x, guides)
     21. │             └─ggplot2::ggplotGrob(x)
     22. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     23. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     24. │                 └─ggplot2:::by_layer(...)
     25. │                   ├─rlang::try_fetch(...)
     26. │                   │ ├─base::tryCatch(...)
     27. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     28. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     29. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     30. │                   │ └─base::withCallingHandlers(...)
     31. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     32. │                     └─l$draw_geom(d, layout)
     33. │                       └─ggplot2 (local) draw_geom(..., self = self)
     34. │                         └─self$geom$draw_layer(...)
     35. │                           └─ggplot2 (local) draw_layer(..., self = self)
     36. │                             └─base::lapply(...)
     37. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     38. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     39. │                                 └─self$draw_panel(...)
     40. └─base::.handleSimpleError(...)
     41.   └─rlang (local) h(simpleError(msg, call))
     42.     └─handlers[[1L]](cnd)
     43.       └─cli::cli_abort(...)
     44.         └─rlang::abort(...)
    ── Error ('test-gg1d.R:50:3'): gg1d doesn't warn about columns the user isn't interested in [plain] ──
    Error in `(function (mapping = NULL, data = NULL, stat = "identity", position = "stack", 
        ..., just = 0.5, lineend = "butt", linejoin = "mitre", na.rm = FALSE, 
        show.legend = NA, inherit.aes = TRUE) 
    {
        layer(mapping = mapping, data = data, geom = "col", stat = stat, 
            position = position, show.legend = show.legend, inherit.aes = inherit.aes, 
            params = list2(na.rm = na.rm, just = just, lineend = lineend, 
                linejoin = linejoin, ...))
    })(mapping = structure(list(), class = c("ggplot2::mapping", 
    "uneval", "gg", "S7_object"), S7_class = structure(function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, name = "mapping", parent = structure(list(class = "gg", constructor = function (.data) 
    {
        stop(sprintf("S3 class <%s> doesn't have a constructor", 
            class[[1]]), call. = FALSE)
    }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, class = c("S7_class", "S7_object")), names = character(0)), 
        width = 0.9, na.rm = TRUE)`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `draw_panel()`:
    ! unused arguments (lineend = "butt", linejoin = "mitre")
    Backtrace:
         ▆
      1. ├─base::suppressMessages(...) at test-gg1d.R:50:3
      2. │ └─base::withCallingHandlers(...)
      3. ├─testthat::expect_message(gg1d(df, verbose = 2), "Columns with too many unique values: Letters")
      4. │ └─testthat:::expect_condition_matching(...)
      5. │   └─testthat:::quasi_capture(...)
      6. │     ├─testthat (local) .capture(...)
      7. │     │ └─base::withCallingHandlers(...)
      8. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      9. ├─gg1d::gg1d(df, verbose = 2)
     10. │ └─ggiraph::girafe(...)
     11. │   ├─base::tryCatch(...)
     12. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │   ├─base::print(ggobj)
     14. │   └─patchwork:::print.patchwork(ggobj)
     15. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
     16. │       └─base::lapply(x$plots, plot_table, guides = guides)
     17. │         ├─patchwork (local) FUN(X[[i]], ...)
     18. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
     19. │           ├─patchwork:::plot_table(x, guides)
     20. │           └─patchwork:::plot_table.ggplot(x, guides)
     21. │             └─ggplot2::ggplotGrob(x)
     22. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     23. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     24. │                 └─ggplot2:::by_layer(...)
     25. │                   ├─rlang::try_fetch(...)
     26. │                   │ ├─base::tryCatch(...)
     27. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     28. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     29. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     30. │                   │ └─base::withCallingHandlers(...)
     31. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     32. │                     └─l$draw_geom(d, layout)
     33. │                       └─ggplot2 (local) draw_geom(..., self = self)
     34. │                         └─self$geom$draw_layer(...)
     35. │                           └─ggplot2 (local) draw_layer(..., self = self)
     36. │                             └─base::lapply(...)
     37. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     38. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     39. │                                 └─self$draw_panel(...)
     40. └─base::.handleSimpleError(...)
     41.   └─rlang (local) h(simpleError(msg, call))
     42.     └─handlers[[1L]](cnd)
     43.       └─cli::cli_abort(...)
     44.         └─rlang::abort(...)
    ── Failure ('test-gg1d.R:58:3'): gg1d returns a plot object ────────────────────
    Expected `gg1d(data = mock_data, col_id = "ID", verbose = FALSE)` to run without any errors.
    i Actually got a <rlang_error> with text:
      Problem while converting geom to grob.
      i Error occurred in the 1st layer.
      Caused by error in `draw_panel()`:
      ! unused arguments (lineend = "butt", linejoin = "mitre")
    ── Failure ('test-gg1d.R:59:3'): gg1d returns a plot object ────────────────────
    `result` is not an S3 object
    ── Failure ('test-gg1d.R:63:3'): gg1d handles missing col_id gracefully ────────
    Expected `gg1d(data = mock_data, verbose = FALSE)` to run without any errors.
    i Actually got a <rlang_error> with text:
      Problem while converting geom to grob.
      i Error occurred in the 1st layer.
      Caused by error in `draw_panel()`:
      ! unused arguments (lineend = "butt", linejoin = "mitre")
    ── Failure ('test-gg1d.R:64:3'): gg1d handles missing col_id gracefully ────────
    `result` is not an S3 object
    ── Error ('test-gg1d.R:149:3'): gg1d can handle interactive and static plot settings ──
    Error in `(function (mapping = NULL, data = NULL, stat = "identity", position = "stack", 
        ..., just = 0.5, lineend = "butt", linejoin = "mitre", na.rm = FALSE, 
        show.legend = NA, inherit.aes = TRUE) 
    {
        layer(mapping = mapping, data = data, geom = "col", stat = stat, 
            position = position, show.legend = show.legend, inherit.aes = inherit.aes, 
            params = list2(na.rm = na.rm, just = just, lineend = lineend, 
                linejoin = linejoin, ...))
    })(mapping = structure(list(), class = c("ggplot2::mapping", 
    "uneval", "gg", "S7_object"), S7_class = structure(function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, name = "mapping", parent = structure(list(class = "gg", constructor = function (.data) 
    {
        stop(sprintf("S3 class <%s> doesn't have a constructor", 
            class[[1]]), call. = FALSE)
    }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, class = c("S7_class", "S7_object")), names = character(0)), 
        width = 0.9, na.rm = TRUE)`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `draw_panel()`:
    ! unused arguments (lineend = "butt", linejoin = "mitre")
    Backtrace:
         ▆
      1. ├─gg1d::gg1d(data = mock_data, interactive = TRUE, verbose = FALSE) at test-gg1d.R:149:3
      2. │ └─ggiraph::girafe(...)
      3. │   ├─base::tryCatch(...)
      4. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      5. │   ├─base::print(ggobj)
      6. │   └─patchwork:::print.patchwork(ggobj)
      7. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
      8. │       └─base::lapply(x$plots, plot_table, guides = guides)
      9. │         ├─patchwork (local) FUN(X[[i]], ...)
     10. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
     11. │           ├─patchwork:::plot_table(x, guides)
     12. │           └─patchwork:::plot_table.ggplot(x, guides)
     13. │             └─ggplot2::ggplotGrob(x)
     14. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     15. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     16. │                 └─ggplot2:::by_layer(...)
     17. │                   ├─rlang::try_fetch(...)
     18. │                   │ ├─base::tryCatch(...)
     19. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     20. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     21. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     22. │                   │ └─base::withCallingHandlers(...)
     23. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     24. │                     └─l$draw_geom(d, layout)
     25. │                       └─ggplot2 (local) draw_geom(..., self = self)
     26. │                         └─self$geom$draw_layer(...)
     27. │                           └─ggplot2 (local) draw_layer(..., self = self)
     28. │                             └─base::lapply(...)
     29. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     30. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     31. │                                 └─self$draw_panel(...)
     32. └─base::.handleSimpleError(...)
     33.   └─rlang (local) h(simpleError(msg, call))
     34.     └─handlers[[1L]](cnd)
     35.       └─cli::cli_abort(...)
     36.         └─rlang::abort(...)
    ── Failure ('test-gg1d.R:165:3'): gg1d heirarchical sort works ─────────────────
    Expected `gg1d(...)` to run without any errors.
    i Actually got a <rlang_error> with text:
      Problem while converting geom to grob.
      i Error occurred in the 1st layer.
      Caused by error in `draw_panel()`:
      ! unused arguments (lineend = "butt", linejoin = "mitre")
    ── Failure ('test-gg1d.R:175:3'): gg1d heirarchical sort works ─────────────────
    Expected `gg1d(...)` to run without any errors.
    i Actually got a <rlang_error> with text:
      Problem while converting geom to grob.
      i Error occurred in the 1st layer.
      Caused by error in `draw_panel()`:
      ! unused arguments (lineend = "butt", linejoin = "mitre")
    
    [ FAIL 9 | WARN 0 | SKIP 2 | PASS 47 ]
    Error: Test failures
    Execution halted

Package: ggalign
Check: examples
New result: ERROR
  Running examples in ‘ggalign-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: align_dendro
  > ### Title: Plot dendrogram tree
  > ### Aliases: align_dendro
  > 
  > ### ** Examples
  > 
  > # align_dendro will always add a plot area
  > ggheatmap(matrix(rnorm(81), nrow = 9)) +
  +     anno_top() +
  +     align_dendro()
  Error in `.subset2()`:
  ! this object class is not subsettable
  Backtrace:
       ▆
    1. ├─methods (local) `<S4: standardGeneric>`(`<S4: HeatmapLayout>`)
    2. ├─ggalign (local) `<S4: standardGeneric>`(`<S4: HeatmapLayout>`)
    3. │ ├─base::print(object)
    4. │ └─ggalign:::print.LayoutProto(object)
    5. │   ├─rlang::try_fetch(...)
    6. │   │ ├─base::tryCatch(...)
    7. │   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    8. │   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    9. │   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   10. │   │ └─base::withCallingHandlers(...)
   11. │   ├─grid::grid.draw(x, ...)
   12. │   └─ggalign:::grid.draw.LayoutProto(x, ...)
   13. │     ├─grid::grid.draw(ggalignGrob(x), recording = recording)
   14. │     └─ggalign::ggalignGrob(x)
   15. │       ├─ggalign:::ggalign_gtable(ggalign_build(x))
   16. │       ├─ggalign:::ggalign_build(x)
   17. │       └─ggalign:::ggalign_build.QuadLayout(x)
   18. │         ├─ggalign:::quad_build(x)
   19. │         ├─ggalign:::quad_build.HeatmapLayout(x)
   20. │         ├─base::NextMethod()
   21. │         └─ggalign:::quad_build.QuadLayout(x)
   22. │           └─base::lapply(...)
   23. │             └─ggalign (local) FUN(X[[i]], ...)
   24. │               └─ggalign:::stack_build(...)
   25. │                 ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
   26. │                 └─ggalign:::stack_build_composer.StackLayout(...)
   27. │                   ├─ggalign:::stack_composer_add(...)
   28. │                   └─ggalign:::stack_composer_add.list(...)
   29. │                     ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
   30. │                     └─ggalign:::stack_composer_add.CraftBox(...)
   31. │                       └─S7:::Ops.S7_object(...)
   32. │                         ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
   33. │                         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   34. │                         │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   35. │                         │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   36. │                         └─base_ops[[.Generic]](e1, e2)
   37. │                           ├─S7::S7_dispatch()
   38. │                           └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
   39. │                             └─ggplot2:::add_ggplot(e1, e2, e2name)
   40. │                               ├─ggplot2::ggplot_add(object, p, objectname)
   41. │                               └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
   42. └─base::.handleSimpleError(...)
   43.   └─rlang (local) h(simpleError(msg, call))
   44.     └─handlers[[1L]](cnd)
   45.       └─rlang::cnd_signal(e)
  Execution halted

Package: ggalign
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'scheme_theme.Rd':
  scheme_theme
    Code: function(..., line, rect, text, title, point, polygon, geom,
                   spacing, margins, aspect.ratio, axis.title,
                   axis.title.x, axis.title.x.top, axis.title.x.bottom,
                   axis.title.y, axis.title.y.left, axis.title.y.right,
                   axis.text, axis.text.x, axis.text.x.top,
                   axis.text.x.bottom, axis.text.y, axis.text.y.left,
                   axis.text.y.right, axis.text.theta, axis.text.r,
                   axis.ticks, axis.ticks.x, axis.ticks.x.top,
                   axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left,
                   axis.ticks.y.right, axis.ticks.theta, axis.ticks.r,
                   axis.minor.ticks.x.top, axis.minor.ticks.x.bottom,
                   axis.minor.ticks.y.left, axis.minor.ticks.y.right,
                   axis.minor.ticks.theta, axis.minor.ticks.r,
                   axis.ticks.length, axis.ticks.length.x,
                   axis.ticks.length.x.top, axis.ticks.length.x.bottom,
                   axis.ticks.length.y, axis.ticks.length.y.left,
                   axis.ticks.length.y.right, axis.ticks.length.theta,
                   axis.ticks.length.r, axis.minor.ticks.length,
                   axis.minor.ticks.length.x,
                   axis.minor.ticks.length.x.top,
                   axis.minor.ticks.length.x.bottom,
                   axis.minor.ticks.length.y,
                   axis.minor.ticks.length.y.left,
                   axis.minor.ticks.length.y.right,
                   axis.minor.ticks.length.theta,
                   axis.minor.ticks.length.r, axis.line, axis.line.x,
                   axis.line.x.top, axis.line.x.bottom, axis.line.y,
                   axis.line.y.left, axis.line.y.right, axis.line.theta,
                   axis.line.r, legend.background, legend.margin,
                   legend.spacing, legend.spacing.x, legend.spacing.y,
                   legend.key, legend.key.size, legend.key.height,
                   legend.key.width, legend.key.spacing,
                   legend.key.spacing.x, legend.key.spacing.y,
                   legend.key.justification, legend.frame, legend.ticks,
                   legend.ticks.length, legend.axis.line, legend.text,
                   legend.text.position, legend.title,
                   legend.title.position, legend.position,
                   legend.position.inside, legend.direction,
                   legend.byrow, legend.justification,
                   legend.justification.top, legend.justification.bottom,
                   legend.justification.left, legend.justification.right,
                   legend.justification.inside, legend.location,
                   legend.box, legend.box.just, legend.box.margin,
                   legend.box.background, legend.box.spacing,
                   panel.background, panel.border, panel.spacing,
                   panel.spacing.x, panel.spacing.y, panel.grid,
                   panel.grid.major, panel.grid.minor,
                   panel.grid.major.x, panel.grid.major.y,
                   panel.grid.minor.x, panel.grid.minor.y, panel.ontop,
                   panel.widths, panel.heights, plot.background,
                   plot.title, plot.title.position, plot.subtitle,
                   plot.caption, plot.caption.position, plot.tag,
                   plot.tag.position, plot.tag.location, plot.margin,
                   strip.background, strip.background.x,
                   strip.background.y, strip.clip, strip.placement,
                   strip.text, strip.text.x, strip.text.x.bottom,
                   strip.text.x.top, strip.text.y, strip.text.y.left,
                   strip.text.y.right, strip.switch.pad.grid,
                   strip.switch.pad.wrap, complete = FALSE, validate =
                   TRUE)
    Docs: function(..., line, rect, text, title, aspect.ratio,
                   axis.title, axis.title.x, axis.title.x.top,
                   axis.title.x.bottom, axis.title.y, axis.title.y.left,
                   axis.title.y.right, axis.text, axis.text.x,
                   axis.text.x.top, axis.text.x.bottom, axis.text.y,
                   axis.text.y.left, axis.text.y.right, axis.text.theta,
                   axis.text.r, axis.ticks, axis.ticks.x,
                   axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y,
                   axis.ticks.y.left, axis.ticks.y.right,
                   axis.ticks.theta, axis.ticks.r,
                   axis.minor.ticks.x.top, axis.minor.ticks.x.bottom,
                   axis.minor.ticks.y.left, axis.minor.ticks.y.right,
                   axis.minor.ticks.theta, axis.minor.ticks.r,
                   axis.ticks.length, axis.ticks.length.x,
                   axis.ticks.length.x.top, axis.ticks.length.x.bottom,
                   axis.ticks.length.y, axis.ticks.length.y.left,
                   axis.ticks.length.y.right, axis.ticks.length.theta,
                   axis.ticks.length.r, axis.minor.ticks.length,
                   axis.minor.ticks.length.x,
                   axis.minor.ticks.length.x.top,
                   axis.minor.ticks.length.x.bottom,
                   axis.minor.ticks.length.y,
                   axis.minor.ticks.length.y.left,
                   axis.minor.ticks.length.y.right,
                   axis.minor.ticks.length.theta,
                   axis.minor.ticks.length.r, axis.line, axis.line.x,
                   axis.line.x.top, axis.line.x.bottom, axis.line.y,
                   axis.line.y.left, axis.line.y.right, axis.line.theta,
                   axis.line.r, legend.background, legend.margin,
                   legend.spacing, legend.spacing.x, legend.spacing.y,
                   legend.key, legend.key.size, legend.key.height,
                   legend.key.width, legend.key.spacing,
                   legend.key.spacing.x, legend.key.spacing.y,
                   legend.frame, legend.ticks, legend.ticks.length,
                   legend.axis.line, legend.text, legend.text.position,
                   legend.title, legend.title.position, legend.position,
                   legend.position.inside, legend.direction,
                   legend.byrow, legend.justification,
                   legend.justification.top, legend.justification.bottom,
                   legend.justification.left, legend.justification.right,
                   legend.justification.inside, legend.location,
                   legend.box, legend.box.just, legend.box.margin,
                   legend.box.background, legend.box.spacing,
                   panel.background, panel.border, panel.spacing,
                   panel.spacing.x, panel.spacing.y, panel.grid,
                   panel.grid.major, panel.grid.minor,
                   panel.grid.major.x, panel.grid.major.y,
                   panel.grid.minor.x, panel.grid.minor.y, panel.ontop,
                   plot.background, plot.title, plot.title.position,
                   plot.subtitle, plot.caption, plot.caption.position,
                   plot.tag, plot.tag.position, plot.tag.location,
                   plot.margin, strip.background, strip.background.x,
                   strip.background.y, strip.clip, strip.placement,
                   strip.text, strip.text.x, strip.text.x.bottom,
                   strip.text.x.top, strip.text.y, strip.text.y.left,
                   strip.text.y.right, strip.switch.pad.grid,
                   strip.switch.pad.wrap, complete = FALSE, validate =
                   TRUE)
    Argument names in code not in docs:
      point polygon geom spacing margins legend.key.justification
      panel.widths panel.heights
    Mismatches in argument names (first 3):
      Position: 6 Code: point Docs: aspect.ratio
      Position: 7 Code: polygon Docs: axis.title
      Position: 8 Code: geom Docs: axis.title.x

Package: ggalign
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggalign_default_expansion:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.FacetSector:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.patch_inset:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggalign_no_expansion:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggalign_patch_labels:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggalign_with_quad:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggalign_layer_order:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.theme_recycle:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggalign_design:
    function(object, plot, object_name)
  
  ggplot_build:
    function(plot, ...)
  ggplot_build.ggalign_facet_sector_plot:
    function(plot)
  
  ggplot_build:
    function(plot, ...)
  ggplot_build.ggalign_heatmap:
    function(plot)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: ggalign
Check: tests
New result: ERROR
    Running ‘testthat.R’ [27s/27s]
  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(ggalign)
    Loading required package: ggplot2
    
    Attaching package: 'ggalign'
    
    The following object is masked from 'package:ggplot2':
    
        element_polygon
    
    > 
    > test_check("ggalign")
    Saving 7 x 7 in image
    `geom_subrect()` subdivide tile into a maximal of 5 rectangles
    `geom_subtile()` subdivide tile into a maximal of 5 rectangles
    Saving 7 x 7 in image
    Saving 7 x 7 in image
    Saving 7 x 7 in image
    [ FAIL 17 | WARN 0 | SKIP 33 | PASS 79 ]
    
    ══ Skipped tests (33) ══════════════════════════════════════════════════════════
    • On CRAN (29): 'test-active.R:12:5', 'test-alignpatch.R:18:5',
      'test-alignpatch.R:128:5', 'test-alignpatch.R:192:5',
      'test-alignpatch.R:254:5', 'test-alignpatch.R:296:5',
      'test-alignpatch.R:363:5', 'test-alignpatch.R:415:5', 'test-ggplot.R:2:5',
      'test-ggplot.R:21:5', 'test-ggplot.R:60:5', 'test-ggplot.R:88:5',
      'test-ggplot.R:107:5', 'test-ggplot.R:175:5', 'test-ggplot.R:196:5',
      'test-grid.R:26:5', 'test-grid.R:30:5', 'test-layout-chain.R:37:5',
      'test-layout-chain.R:99:5', 'test-layout-chain.R:272:5',
      'test-layout-quad.R:67:5', 'test-layout-quad.R:200:5',
      'test-layout-quad.R:425:5', 'test-layout-stack.R:176:5',
      'test-plot-align.R:6:5', 'test-plot-align.R:47:5', 'test-plot-align.R:106:5',
      'test-plot-align.R:145:5', 'test-plot-align.R:182:5'
    • empty test (3): 'test-layout-chain.R:277:1', 'test-layout-chain.R:280:1',
      'test-layout-chain.R:284:1'
    • {maftools} is not installed (1): 'test-fortify-matrix.R:2:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-layout-heatmap.R:16:5'): `ggheatmap` works well ────────────────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger("heatmap-numeric", ggheatmap(1:10)) at test-layout-heatmap.R:16:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             ├─ggalign:::quad_build.HeatmapLayout(x)
     22. │             ├─base::NextMethod()
     23. │             └─ggalign:::quad_build.QuadLayout(x)
     24. │               └─S7:::Ops.S7_object(...)
     25. │                 ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     26. │                 │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     27. │                 │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28. │                 │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     29. │                 └─base_ops[[.Generic]](e1, e2)
     30. │                   ├─S7::S7_dispatch()
     31. │                   └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     32. │                     └─ggplot2:::add_ggplot(e1, e2, e2name)
     33. │                       ├─ggplot2::ggplot_add(object, p, objectname)
     34. │                       └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     35. └─base::.handleSimpleError(...)
     36.   └─rlang (local) h(simpleError(msg, call))
     37.     └─handlers[[1L]](cnd)
     38.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-heatmap.R:28:5'): `ggheatmap` add `quad_switch()` works well ──
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-heatmap.R:28:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             ├─ggalign:::quad_build.HeatmapLayout(x)
     22. │             ├─base::NextMethod()
     23. │             └─ggalign:::quad_build.QuadLayout(x)
     24. │               └─S7:::Ops.S7_object(...)
     25. │                 ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     26. │                 │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     27. │                 │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28. │                 │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     29. │                 └─base_ops[[.Generic]](e1, e2)
     30. │                   ├─S7::S7_dispatch()
     31. │                   └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     32. │                     └─ggplot2:::add_ggplot(e1, e2, e2name)
     33. │                       ├─ggplot2::ggplot_add(object, p, objectname)
     34. │                       └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     35. └─base::.handleSimpleError(...)
     36.   └─rlang (local) h(simpleError(msg, call))
     37.     └─handlers[[1L]](cnd)
     38.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-heatmap.R:69:5'): `ggoncoplot` works well ───────────────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-heatmap.R:69:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             ├─ggalign:::quad_build.HeatmapLayout(x)
     22. │             ├─base::NextMethod()
     23. │             └─ggalign:::quad_build.QuadLayout(x)
     24. │               └─S7:::Ops.S7_object(...)
     25. │                 ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     26. │                 │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     27. │                 │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28. │                 │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     29. │                 └─base_ops[[.Generic]](e1, e2)
     30. │                   ├─S7::S7_dispatch()
     31. │                   └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     32. │                     └─ggplot2:::add_ggplot(e1, e2, e2name)
     33. │                       ├─ggplot2::ggplot_add(object, p, objectname)
     34. │                       └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     35. └─base::.handleSimpleError(...)
     36.   └─rlang (local) h(simpleError(msg, call))
     37.     └─handlers[[1L]](cnd)
     38.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-heatmap.R:101:5'): `breaks` of `scale_*_()` works well ──
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-heatmap.R:101:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             ├─ggalign:::quad_build.HeatmapLayout(x)
     22. │             ├─base::NextMethod()
     23. │             └─ggalign:::quad_build.QuadLayout(x)
     24. │               └─S7:::Ops.S7_object(...)
     25. │                 ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     26. │                 │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     27. │                 │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28. │                 │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     29. │                 └─base_ops[[.Generic]](e1, e2)
     30. │                   ├─S7::S7_dispatch()
     31. │                   └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     32. │                     └─ggplot2:::add_ggplot(e1, e2, e2name)
     33. │                       ├─ggplot2::ggplot_add(object, p, objectname)
     34. │                       └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     35. └─base::.handleSimpleError(...)
     36.   └─rlang (local) h(simpleError(msg, call))
     37.     └─handlers[[1L]](cnd)
     38.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-heatmap.R:179:5'): `labels` of `scale_*_()` works well ──
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-heatmap.R:179:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             ├─ggalign:::quad_build.HeatmapLayout(x)
     22. │             ├─base::NextMethod()
     23. │             └─ggalign:::quad_build.QuadLayout(x)
     24. │               └─base::lapply(...)
     25. │                 └─ggalign (local) FUN(X[[i]], ...)
     26. │                   └─ggalign:::stack_build(...)
     27. │                     ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     28. │                     └─ggalign:::stack_build_composer.StackLayout(...)
     29. │                       ├─ggalign:::stack_composer_add(...)
     30. │                       └─ggalign:::stack_composer_add.list(...)
     31. │                         ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     32. │                         └─ggalign:::stack_composer_add.CraftBox(...)
     33. │                           └─S7:::Ops.S7_object(...)
     34. │                             ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     35. │                             │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     36. │                             │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     37. │                             │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     38. │                             └─base_ops[[.Generic]](e1, e2)
     39. │                               ├─S7::S7_dispatch()
     40. │                               └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     41. │                                 └─ggplot2:::add_ggplot(e1, e2, e2name)
     42. │                                   ├─ggplot2::ggplot_add(object, p, objectname)
     43. │                                   └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     44. └─base::.handleSimpleError(...)
     45.   └─rlang (local) h(simpleError(msg, call))
     46.     └─handlers[[1L]](cnd)
     47.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-quad.R:2:5'): add `layout_annotation()` works well ──────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-quad.R:2:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             ├─ggalign:::quad_build.HeatmapLayout(x)
     22. │             ├─base::NextMethod()
     23. │             └─ggalign:::quad_build.QuadLayout(x)
     24. │               └─S7:::Ops.S7_object(...)
     25. │                 ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     26. │                 │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     27. │                 │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28. │                 │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     29. │                 └─base_ops[[.Generic]](e1, e2)
     30. │                   ├─S7::S7_dispatch()
     31. │                   └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     32. │                     └─ggplot2:::add_ggplot(e1, e2, e2name)
     33. │                       ├─ggplot2::ggplot_add(object, p, objectname)
     34. │                       └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     35. └─base::.handleSimpleError(...)
     36.   └─rlang (local) h(simpleError(msg, call))
     37.     └─handlers[[1L]](cnd)
     38.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-quad.R:12:5'): add `layout_title()` works well ──────────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-quad.R:12:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             ├─ggalign:::quad_build.HeatmapLayout(x)
     22. │             ├─base::NextMethod()
     23. │             └─ggalign:::quad_build.QuadLayout(x)
     24. │               └─S7:::Ops.S7_object(...)
     25. │                 ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     26. │                 │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     27. │                 │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28. │                 │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     29. │                 └─base_ops[[.Generic]](e1, e2)
     30. │                   ├─S7::S7_dispatch()
     31. │                   └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     32. │                     └─ggplot2:::add_ggplot(e1, e2, e2name)
     33. │                       ├─ggplot2::ggplot_add(object, p, objectname)
     34. │                       └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     35. └─base::.handleSimpleError(...)
     36.   └─rlang (local) h(simpleError(msg, call))
     37.     └─handlers[[1L]](cnd)
     38.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-quad.R:109:5'): add `align` object builds well ──────────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-quad.R:109:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             └─ggalign:::quad_build.QuadLayout(x)
     22. │               └─base::lapply(...)
     23. │                 └─ggalign (local) FUN(X[[i]], ...)
     24. │                   └─ggalign:::stack_build(...)
     25. │                     ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     26. │                     └─ggalign:::stack_build_composer.StackLayout(...)
     27. │                       ├─ggalign:::stack_composer_add(...)
     28. │                       └─ggalign:::stack_composer_add.list(...)
     29. │                         ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     30. │                         └─ggalign:::stack_composer_add.CraftBox(...)
     31. │                           └─S7:::Ops.S7_object(...)
     32. │                             ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     33. │                             │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     34. │                             │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     35. │                             │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     36. │                             └─base_ops[[.Generic]](e1, e2)
     37. │                               ├─S7::S7_dispatch()
     38. │                               └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     39. │                                 └─ggplot2:::add_ggplot(e1, e2, e2name)
     40. │                                   ├─ggplot2::ggplot_add(object, p, objectname)
     41. │                                   └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     42. └─base::.handleSimpleError(...)
     43.   └─rlang (local) h(simpleError(msg, call))
     44.     └─handlers[[1L]](cnd)
     45.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-quad.R:138:5'): add `with_quad()` works as expected ─────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-quad.R:138:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             ├─ggalign:::quad_build.HeatmapLayout(x)
     22. │             ├─base::NextMethod()
     23. │             └─ggalign:::quad_build.QuadLayout(x)
     24. │               └─base::lapply(...)
     25. │                 └─ggalign (local) FUN(X[[i]], ...)
     26. │                   └─ggalign:::stack_build(...)
     27. │                     ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     28. │                     └─ggalign:::stack_build_composer.StackLayout(...)
     29. │                       ├─ggalign:::stack_composer_add(...)
     30. │                       └─ggalign:::stack_composer_add.list(...)
     31. │                         ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     32. │                         └─ggalign:::stack_composer_add.CraftBox(...)
     33. │                           └─S7:::Ops.S7_object(...)
     34. │                             ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     35. │                             │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     36. │                             │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     37. │                             │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     38. │                             └─base_ops[[.Generic]](e1, e2)
     39. │                               ├─S7::S7_dispatch()
     40. │                               └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     41. │                                 └─ggplot2:::add_ggplot(e1, e2, e2name)
     42. │                                   ├─ggplot2::ggplot_add(object, p, objectname)
     43. │                                   └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     44. └─base::.handleSimpleError(...)
     45.   └─rlang (local) h(simpleError(msg, call))
     46.     └─handlers[[1L]](cnd)
     47.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-quad.R:331:5'): add `stack_layout()` builds well ────────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-quad.R:331:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.QuadLayout(x)
     20. │             ├─ggalign:::quad_build(x)
     21. │             └─ggalign:::quad_build.QuadLayout(x)
     22. │               └─base::lapply(...)
     23. │                 └─ggalign (local) FUN(X[[i]], ...)
     24. │                   └─ggalign:::stack_build(...)
     25. │                     ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     26. │                     └─ggalign:::stack_build_composer.StackLayout(...)
     27. │                       ├─ggalign:::stack_composer_add(...)
     28. │                       └─ggalign:::stack_composer_add.list(...)
     29. │                         ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     30. │                         └─ggalign:::stack_composer_add.CraftBox(...)
     31. │                           └─S7:::Ops.S7_object(...)
     32. │                             ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     33. │                             │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     34. │                             │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     35. │                             │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     36. │                             └─base_ops[[.Generic]](e1, e2)
     37. │                               ├─S7::S7_dispatch()
     38. │                               └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     39. │                                 └─ggplot2:::add_ggplot(e1, e2, e2name)
     40. │                                   ├─ggplot2::ggplot_add(object, p, objectname)
     41. │                                   └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     42. └─base::.handleSimpleError(...)
     43.   └─rlang (local) h(simpleError(msg, call))
     44.     └─handlers[[1L]](cnd)
     45.       └─rlang::cnd_signal(e)
    ── Failure ('test-layout-quad.R:520:5'): `ggsave()` works well ─────────────────
    Expected `ggplot2::ggsave(tempfile(fileext = ".png"), plot = p)` to run without any errors.
    i Actually got a <simpleError> with text:
      this object class is not subsettable
    ── Error ('test-layout-stack.R:43:5'): `stack_align` add `align-` object builds well ──
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-stack.R:43:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.StackLayout(x)
     20. │             ├─stack_build(x) %||% align_plots(theme = x@theme)
     21. │             └─ggalign:::stack_build(x)
     22. │               ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     23. │               └─ggalign:::stack_build_composer.StackLayout(...)
     24. │                 ├─ggalign:::stack_composer_add(...)
     25. │                 └─ggalign:::stack_composer_add.list(...)
     26. │                   ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     27. │                   └─ggalign:::stack_composer_add.CraftBox(...)
     28. │                     └─S7:::Ops.S7_object(...)
     29. │                       ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     30. │                       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     31. │                       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     32. │                       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     33. │                       └─base_ops[[.Generic]](e1, e2)
     34. │                         ├─S7::S7_dispatch()
     35. │                         └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     36. │                           └─ggplot2:::add_ggplot(e1, e2, e2name)
     37. │                             ├─ggplot2::ggplot_add(object, p, objectname)
     38. │                             └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     39. └─base::.handleSimpleError(...)
     40.   └─rlang (local) h(simpleError(msg, call))
     41.     └─handlers[[1L]](cnd)
     42.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-stack.R:73:5'): `stack_align` add `quad_layout()` object builds well ──
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-stack.R:73:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.StackLayout(x)
     20. │             ├─stack_build(x) %||% align_plots(theme = x@theme)
     21. │             └─ggalign:::stack_build(x)
     22. │               ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     23. │               └─ggalign:::stack_build_composer.StackLayout(...)
     24. │                 ├─ggalign:::stack_composer_add(...)
     25. │                 └─ggalign:::stack_composer_add.list(...)
     26. │                   ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     27. │                   └─ggalign:::stack_composer_add.QuadLayout(...)
     28. │                     ├─ggalign:::quad_build(plot, schemes, theme, direction)
     29. │                     └─ggalign:::quad_build.QuadLayout(plot, schemes, theme, direction)
     30. │                       └─S7:::Ops.S7_object(...)
     31. │                         ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     32. │                         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     33. │                         │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     34. │                         │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     35. │                         └─base_ops[[.Generic]](e1, e2)
     36. │                           ├─S7::S7_dispatch()
     37. │                           └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     38. │                             └─ggplot2:::add_ggplot(e1, e2, e2name)
     39. │                               ├─ggplot2::ggplot_add(object, p, objectname)
     40. │                               └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     41. └─base::.handleSimpleError(...)
     42.   └─rlang (local) h(simpleError(msg, call))
     43.     └─handlers[[1L]](cnd)
     44.       └─rlang::cnd_signal(e)
    ── Error ('test-layout-stack.R:118:5'): add `with_quad()` works as expected ────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-stack.R:118:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.StackLayout(x)
     20. │             ├─stack_build(x) %||% align_plots(theme = x@theme)
     21. │             └─ggalign:::stack_build(x)
     22. │               ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     23. │               └─ggalign:::stack_build_composer.StackLayout(...)
     24. │                 ├─ggalign:::stack_composer_add(...)
     25. │                 └─ggalign:::stack_composer_add.list(...)
     26. │                   ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     27. │                   └─ggalign:::stack_composer_add.CraftBox(...)
     28. │                     └─S7:::Ops.S7_object(...)
     29. │                       ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     30. │                       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     31. │                       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     32. │                       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     33. │                       └─base_ops[[.Generic]](e1, e2)
     34. │                         ├─S7::S7_dispatch()
     35. │                         └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     36. │                           └─ggplot2:::add_ggplot(e1, e2, e2name)
     37. │                             ├─ggplot2::ggplot_add(object, p, objectname)
     38. │                             └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     39. └─base::.handleSimpleError(...)
     40.   └─rlang (local) h(simpleError(msg, call))
     41.     └─handlers[[1L]](cnd)
     42.       └─rlang::cnd_signal(e)
    ── Failure ('test-layout-stack.R:188:5'): `ggsave()` works well ────────────────
    Expected `ggplot2::ggsave(tempfile(fileext = ".png"), plot = p)` to run without any errors.
    i Actually got a <simpleError> with text:
      this object class is not subsettable
    ── Error ('test-layout-stack.R:196:5'): `stack_align` add `quad_switch()` works well ──
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-layout-stack.R:196:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.default(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggalign:::print.LayoutProto(p)
      7. │       ├─rlang::try_fetch(...)
      8. │       │ ├─base::tryCatch(...)
      9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12. │       │ └─base::withCallingHandlers(...)
     13. │       ├─grid::grid.draw(x, ...)
     14. │       └─ggalign:::grid.draw.LayoutProto(x, ...)
     15. │         ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     16. │         └─ggalign::ggalignGrob(x)
     17. │           ├─ggalign:::ggalign_gtable(ggalign_build(x))
     18. │           ├─ggalign:::ggalign_build(x)
     19. │           └─ggalign:::ggalign_build.StackLayout(x)
     20. │             ├─stack_build(x) %||% align_plots(theme = x@theme)
     21. │             └─ggalign:::stack_build(x)
     22. │               ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     23. │               └─ggalign:::stack_build_composer.StackLayout(...)
     24. │                 ├─ggalign:::stack_composer_add(...)
     25. │                 └─ggalign:::stack_composer_add.list(...)
     26. │                   ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     27. │                   └─ggalign:::stack_composer_add.QuadLayout(...)
     28. │                     ├─ggalign:::quad_build(plot, schemes, theme, direction)
     29. │                     ├─ggalign:::quad_build.HeatmapLayout(plot, schemes, theme, direction)
     30. │                     ├─base::NextMethod()
     31. │                     └─ggalign:::quad_build.QuadLayout(plot, schemes, theme, direction)
     32. │                       └─base::lapply(...)
     33. │                         └─ggalign (local) FUN(X[[i]], ...)
     34. │                           └─ggalign:::stack_build(...)
     35. │                             ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     36. │                             └─ggalign:::stack_build_composer.StackLayout(...)
     37. │                               ├─ggalign:::stack_composer_add(...)
     38. │                               └─ggalign:::stack_composer_add.list(...)
     39. │                                 ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     40. │                                 └─ggalign:::stack_composer_add.CraftBox(...)
     41. │                                   └─S7:::Ops.S7_object(...)
     42. │                                     ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     43. │                                     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     44. │                                     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     45. │                                     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     46. │                                     └─base_ops[[.Generic]](e1, e2)
     47. │                                       ├─S7::S7_dispatch()
     48. │                                       └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     49. │                                         └─ggplot2:::add_ggplot(e1, e2, e2name)
     50. │                                           ├─ggplot2::ggplot_add(object, p, objectname)
     51. │                                           └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     52. └─base::.handleSimpleError(...)
     53.   └─rlang (local) h(simpleError(msg, call))
     54.     └─handlers[[1L]](cnd)
     55.       └─rlang::cnd_signal(e)
    ── Error ('test-plot-align.R:274:9'): `ggalign()` works well ───────────────────
    Error in `.subset2(plot, "coordinates")`: this object class is not subsettable
    Backtrace:
         ▆
      1. ├─testthat::expect_snapshot_warning(...) at test-plot-align.R:272:5
      2. │ └─testthat:::expect_snapshot_condition(...)
      3. │   ├─testthat:::with_is_snapshotting(...)
      4. │   └─testthat:::capture_matching_condition(x, cnd_matcher(class))
      5. │     └─base::withCallingHandlers(...)
      6. ├─base::print(...) at test-plot-align.R:274:9
      7. ├─ggalign:::print.LayoutProto(...)
      8. │ ├─rlang::try_fetch(...)
      9. │ │ ├─base::tryCatch(...)
     10. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     11. │ │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     12. │ │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     13. │ │ └─base::withCallingHandlers(...)
     14. │ ├─grid::grid.draw(x, ...)
     15. │ └─ggalign:::grid.draw.LayoutProto(x, ...)
     16. │   ├─grid::grid.draw(ggalignGrob(x), recording = recording)
     17. │   └─ggalign::ggalignGrob(x)
     18. │     ├─ggalign:::ggalign_gtable(ggalign_build(x))
     19. │     ├─ggalign:::ggalign_build(x)
     20. │     └─ggalign:::ggalign_build.QuadLayout(x)
     21. │       ├─ggalign:::quad_build(x)
     22. │       ├─ggalign:::quad_build.HeatmapLayout(x)
     23. │       ├─base::NextMethod()
     24. │       └─ggalign:::quad_build.QuadLayout(x)
     25. │         └─base::lapply(...)
     26. │           └─ggalign (local) FUN(X[[i]], ...)
     27. │             └─ggalign:::stack_build(...)
     28. │               ├─ggalign:::stack_build_composer(stack, schemes, theme, extra_design)
     29. │               └─ggalign:::stack_build_composer.StackLayout(...)
     30. │                 ├─ggalign:::stack_composer_add(...)
     31. │                 └─ggalign:::stack_composer_add.list(...)
     32. │                   ├─ggalign:::stack_composer_add(plot = p, composer = composer, ...)
     33. │                   └─ggalign:::stack_composer_add.CraftBox(...)
     34. │                     └─S7:::Ops.S7_object(...)
     35. │                       ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
     36. │                       │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     37. │                       │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     38. │                       │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     39. │                       └─base_ops[[.Generic]](e1, e2)
     40. │                         ├─S7::S7_dispatch()
     41. │                         └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     42. │                           └─ggplot2:::add_ggplot(e1, e2, e2name)
     43. │                             ├─ggplot2::ggplot_add(object, p, objectname)
     44. │                             └─ggalign:::ggplot_add.ggalign_design(object, p, objectname)
     45. └─base::.handleSimpleError(...)
     46.   └─rlang (local) h(simpleError(msg, call))
     47.     └─handlers[[1L]](cnd)
     48.       └─rlang::cnd_signal(e)
    
    [ FAIL 17 | WARN 0 | SKIP 33 | PASS 79 ]
    Deleting unused snapshots:
    • alignpatch/background-and-panel-border.svg
    • alignpatch/collect-guides-from-multiple-plots-with-null-unit.svg
    • alignpatch/collect-guides-with-null-unit.svg
    • alignpatch/collect-inside-guides.svg
    • alignpatch/far-dimensions-can-be-set-with-units.svg
    • alignpatch/far-legend-justification.svg
    • alignpatch/far-optimise-space-by-default-2.svg
    • alignpatch/far-optimise-space-by-default-3.svg
    • alignpatch/far-optimise-space-by-default-4.svg
    • alignpatch/far-optimise-space-by-default-5.svg
    • alignpatch/far-space-optimisation-can-be-turned-off.svg
    • alignpatch/free-align-with-facet-ggplot.svg
    • alignpatch/free-align-with-far.svg
    • alignpatch/free-align-with-nested-alignpatches.svg
    • alignpatch/free-border-mix-with-free-align.svg
    • alignpatch/free-border-with-facet-ggplot.svg
    • alignpatch/free-border-with-far.svg
    • alignpatch/free-border-with-nested-alignpatches.svg
    • alignpatch/free-guide-with-alignpatches.svg
    • alignpatch/free-guide-with-ggplot-of-null-guides.svg
    • alignpatch/free-space-with-alignpatches.svg
    • alignpatch/patch-titles-theme.svg
    • alignpatch/patch-titles.svg
    • alignpatch/setting-heights-as-units.svg
    • alignpatch/setting-heights.svg
    • alignpatch/setting-nrow.svg
    • alignpatch/setting-title.svg
    • alignpatch/setting-widths-as-units.svg
    • alignpatch/setting-widths.svg
    • ggplot/coord-circle-inner-radius-and-outer-radius.svg
    • ggplot/coord-circle-start-and-end.svg
    • ggplot/facet-sector-sector-spacing-rel.svg
    • ggplot/geom-gshape-order.svg
    • ggplot/geom-gshape.svg
    • ggplot/geom-pie-angle0.svg
    • ggplot/geom-pie-no-clockwise.svg
    • ggplot/geom-subrect-byrow-false.svg
    • ggplot/geom-subrect-set-both-nrow-and-ncol.svg
    • ggplot/geom-subrect-set-ncol.svg
    • ggplot/geom-subrect-set-nrow.svg
    • ggplot/geom-subtile-byrow-false.svg
    • ggplot/geom-subtile-set-both-nrow-and-ncol.svg
    • ggplot/geom-subtile-set-ncol.svg
    • ggplot/geom-subtile-set-nrow.svg
    • ggplot/layer-order-add-in-the-beginning.svg
    • ggplot/layer-order-add-in-the-end.svg
    • layout-heatmap/continuous-character-breaks.svg
    • layout-heatmap/continuous-integer-as-is-breaks.svg
    • layout-heatmap/continuous-integer-breaks.svg
    • layout-heatmap/continuous-labels-as-is-match-breaks.svg
    • layout-heatmap/continuous-labels-as-is.svg
    • layout-heatmap/continuous-labels-match-breaks.svg
    • layout-heatmap/continuous-labels.svg
    • layout-heatmap/continuous-no-breaks.svg
    • layout-heatmap/discrete-character-breaks.svg
    • layout-heatmap/discrete-integer-as-is-breaks.svg
    • layout-heatmap/discrete-integer-breaks.svg
    • layout-heatmap/discrete-labels-as-is-match-breaks.svg
    • layout-heatmap/discrete-labels-as-is.svg
    • layout-heatmap/discrete-labels-match-breaks.svg
    • layout-heatmap/discrete-labels.svg
    • layout-heatmap/discrete-no-breaks.svg
    • layout-heatmap/discrete-no-labels.svg
    • layout-heatmap/heatmap-character.svg
    • layout-heatmap/heatmap-data-frame.svg
    • layout-heatmap/heatmap-hmanno-align-action-guides.svg
    • layout-heatmap/heatmap-hmanno-height.svg
    • layout-heatmap/heatmap-hmanno-null-guides.svg
    • layout-heatmap/heatmap-hmanno-stack-action-guides.svg
    • layout-heatmap/heatmap-matrix.svg
    • layout-heatmap/heatmap-numeric-to-factor.svg
    • layout-heatmap/oncoplot-with-annotation.svg
    • layout-quad/add-with-quad-set-position-null.svg
    • layout-quad/alignv-layout-annotation.svg
    • layout-quad/quad-alignb-release-spaces-works-well.svg
    • layout-quad/quad-alignv-add-stack-alignv-in-the-top.svg
    • layout-quad/subtract-with-quad-default.svg
    • layout-quad/subtract-with-quad-set-position-null.svg
    • layout-quad/subtract-with-quad-set-position.svg
    • layout-stack/stack-align-add-align-dendro-k-3.svg
    • layout-stack/stack-align-add-align-kmeans.svg
    • layout-stack/stack-align-add-ggalign.svg
    • layout-stack/stack-alignh-add-ggheatmap-with-name-as-mapping.svg
    • layout-stack/stack-alignh-add-ggheatmap.svg
    • layout-stack/stack-alignh-add-quad-alignb.svg
    • layout-stack/stack-alignv-add-ggheatmap-with-name-as-mapping.svg
    • layout-stack/stack-alignv-add-ggheatmap.svg
    • layout-stack/stack-alignv-add-quad-alignb.svg
    • layout-stack/stack-alignv-add-quad-alignv.svg
    • layout-stack/stack-with-absolute-size-1.svg
    • layout-stack/stack-with-absolute-size-2.svg
    • layout-stack/stack-with-mix-absolute-and-null-size-1.svg
    • layout-stack/stack-with-mix-absolute-and-null-size-2.svg
    • layout-stack/subtract-with-quad-set-position-null.svg
    • layout-stack/subtract-with-quad-set-position.svg
    • plot-align/dendro-between-group.svg
    • plot-align/dendro-cutree.svg
    • plot-align/dendro-merge-group.svg
    • plot-align/dendro-reorder-and-merge-group.svg
    • plot-align/dendro-reorder-dendro-and-cutree.svg
    • plot-align/dendro-reorder-dendro-in-and-between-group-and-merge.svg
    • plot-align/dendro-reorder-dendro-in-and-between-group.svg
    • plot-align/dendro-reorder-dendro-in-group-and-merge-group.svg
    • plot-align/dendro-reorder-dendro.svg
    • plot-align/dendro-reorder-group.svg
    • plot-align/dendrogram-bottom.svg
    • plot-align/dendrogram-left.svg
    • plot-align/dendrogram-right.svg
    • plot-align/dendrogram-top.svg
    • plot-align/ggalign-set-size.svg
    • plot-align/ggalign.svg
    • plot-align/group-bottom.svg
    • plot-align/group-left.svg
    • plot-align/group-right.svg
    • plot-align/group-top.svg
    • plot-align/heatmap-no-data-dendrogram-input.svg
    • plot-align/heatmap-no-data-hclust-input.svg
    • plot-align/kmeans-bottom.svg
    • plot-align/kmeans-left.svg
    • plot-align/kmeans-right.svg
    • plot-align/kmeans-top.svg
    • plot-align/order-bottom.svg
    • plot-align/order-left.svg
    • plot-align/order-right.svg
    • plot-align/order-top-within-group.svg
    • plot-align/order-top.svg
    • plot-align/reorder-bottom.svg
    • plot-align/reorder-left-character-index.svg
    • plot-align/reorder-left-integer-index.svg
    • plot-align/reorder-left-reverse.svg
    • plot-align/reorder-left.svg
    • plot-align/reorder-right.svg
    • plot-align/reorder-top-reverse.svg
    • plot-align/reorder-top-within-group.svg
    • plot-align/reorder-top.svg
    • plot-align/stack-no-data-dendrogram-input.svg
    • plot-align/stack-no-data-hclust-input.svg
    Error: Test failures
    Execution halted

Package: ggblend
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggblend)
    > 
    > test_check("ggblend")
    [ FAIL 3 | WARN 2 | SKIP 7 | PASS 99 ]
    
    ══ Skipped tests (7) ═══════════════════════════════════════════════════════════
    • On CRAN (7): 'test-operation-.R:95:3',
      'test-operation-affine-transform.R:2:3',
      'test-operation-affine-transform.R:13:3', 'test-operation-blend.R:2:3',
      'test-operation-blend.R:11:3', 'test-operation-blend.R:20:3',
      'test-operation-blend.R:41:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-operation-adjust.R:17:3'): adjusting aesthetics works ────────
    adjust(aes(color = z)) * stat_summary_bin() (`actual`) not equal to stat_summary_bin(aes(color = z)) (`expected`).
    
    `actual$mapping` is an S3 object of class <uneval>, a list
    `expected$mapping` is an S7 object of class <ggplot2::mapping>
    Backtrace:
        ▆
     1. └─ggblend:::expect_equal_layer(...) at test-operation-adjust.R:17:3
     2.   └─testthat::expect_equal(...) at tests/testthat/helper-layer.R:26:3
    ── Failure ('test-operation-adjust.R:18:3'): adjusting aesthetics works ────────
    stat_summary_bin() * adjust(mapping = aes(color = z)) (`actual`) not equal to stat_summary_bin(aes(color = z)) (`expected`).
    
    `actual$mapping` is an S3 object of class <uneval>, a list
    `expected$mapping` is an S7 object of class <ggplot2::mapping>
    Backtrace:
        ▆
     1. └─ggblend:::expect_equal_layer(...) at test-operation-adjust.R:18:3
     2.   └─testthat::expect_equal(...) at tests/testthat/helper-layer.R:26:3
    ── Failure ('test-operation-adjust.R:19:3'): adjusting aesthetics works ────────
    adjust(stat_summary_bin(aes(color = g)), aes(color = z, fill = y)) (`actual`) not equal to stat_summary_bin(aes(color = z, fill = y)) (`expected`).
    
    `actual$mapping` is an S3 object of class <uneval>, a list
    `expected$mapping` is an S7 object of class <ggplot2::mapping>
    Backtrace:
        ▆
     1. └─ggblend:::expect_equal_layer(...) at test-operation-adjust.R:19:3
     2.   └─testthat::expect_equal(...) at tests/testthat/helper-layer.R:26:3
    
    [ FAIL 3 | WARN 2 | SKIP 7 | PASS 99 ]
    Error: Test failures
    Execution halted

Package: ggborderline
Check: examples
New result: ERROR
  Running examples in ‘ggborderline-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: geom_borderpath
  > ### Title: Connect observations
  > ### Aliases: geom_borderpath geom_borderline geom_borderstep
  > 
  > ### ** Examples
  > 
  > require(ggplot2)
  Loading required package: ggplot2
  > 
  > # geom_borderline() adds a border around lines
  > ggplot(economics_long, aes(date, value01, colour = variable)) +
  +   geom_borderline()
  > 
  > # You can control the linewidth and colour of the border with the
  > # borderwidth and bordercolour aesthetics:
  > ggplot(economics_long, aes(date, value01, bordercolour = variable)) +
  +   geom_borderline(borderwidth = .4, colour = "white")
  Error in `as_discrete_pal()`:
  ! Cannot convert `x` to a discrete palette.
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3.   ├─ggplot2::ggplot_build(x)
    4.   └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    5.     └─npscales$set_palettes(plot@theme)
    6.       └─ggplot2 (local) set_palettes(..., self = self)
    7.         ├─scales::as_discrete_pal(elem)
    8.         └─scales:::as_discrete_pal.default(elem)
    9.           └─cli::cli_abort("Cannot convert {.arg x} to a discrete palette.")
   10.             └─rlang::abort(...)
  Execution halted

Package: ggbrain
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggbrain_panel:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggbrain_label:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggbrain_layer:
    function(object, plot, object_name)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: ggbreak
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘ggbreak.Rmd’ using rmarkdown
  
  Quitting from ggbreak.Rmd:61-78 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `UseMethod()`:
  ! no applicable method for 'as.grob' applied to an object of class "c('LayerInstance', 'Layer', 'ggproto', 'gg')"
  ---
  Backtrace:
       ▆
    1. └─S7:::Ops.S7_object(...)
    2.   ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
    3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    6.   └─base_ops[[.Generic]](e1, e2)
    7.     ├─S7::S7_dispatch()
    8.     └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
    9.       └─ggplot2:::add_ggplot(e1, e2, e2name)
   10.         ├─ggplot2::ggplot_add(object, p, objectname)
   11.         └─ggbreak:::ggplot_add.gg(object, p, objectname)
   12.           ├─ggplot2::ggplot_add(...)
   13.           └─ggplotify::as.ggplot(object)
   14.             └─ggplotify:::as.ggplot_internal(...)
   15.               ├─ggplot2::annotation_custom(...)
   16.               │ └─ggplot2::layer(...)
   17.               └─ggplotify::as.grob(plot, ...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'ggbreak.Rmd' failed with diagnostics:
  no applicable method for 'as.grob' applied to an object of class "c('LayerInstance', 'Layer', 'ggproto', 'gg')"
  --- failed re-building ‘ggbreak.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘ggbreak.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggbump
Check: tests
New result: ERROR
    Running ‘testthat.R’ [2s/2s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggbump)
    > 
    > test_check("ggbump")
    [ FAIL 3 | WARN 1 | SKIP 0 | PASS 1 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-numeric_inputs.R:17:3'): multiplication works ────────────────
    ... %>% class() not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-numeric_inputs.R:21:3'): multiplication works ────────────────
    ... %>% class() not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-numeric_inputs.R:26:3'): multiplication works ────────────────
    ... %>% class() not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 3 | WARN 1 | SKIP 0 | PASS 1 ]
    Error: Test failures
    Execution halted

Package: ggdark
Check: examples
New result: ERROR
  Running examples in ‘ggdark-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: dark_mode
  > ### Title: Activate dark mode on a 'ggplot2' theme
  > ### Aliases: dark_mode
  > 
  > ### ** Examples
  > 
  > library(ggplot2)
  > 
  > p1 <- ggplot(iris, aes(Sepal.Width, Sepal.Length, color = Species)) +
  +   geom_point()
  > 
  > p1  # theme returned by theme_get()
  > p1 + dark_mode()  # activate dark mode on theme returned by theme_get()
  Error in match(x, table, nomatch = 0L) : 
    'match' requires vector arguments
  Calls: dark_mode -> %in%
  Execution halted

Package: ggdark
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggdark)
    > 
    > test_check("ggdark")
    [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_dark_mode.R:10:1'): (code run outside of `test_that()`) ────────
    Error in `match(x, table, nomatch = 0L)`: 'match' requires vector arguments
    Backtrace:
        ▆
     1. └─ggdark::dark_mode(light_theme) at test_dark_mode.R:10:1
     2.   └─geoms[["GeomPoint"]]$default_aes$colour %in% ...
    
    [ FAIL 1 | WARN 2 | SKIP 0 | PASS 0 ]
    Error: Test failures
    Execution halted

Package: ggDoubleHeat
Check: examples
New result: ERROR
  Running examples in ‘ggDoubleHeat-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: geom_heat_circle
  > ### Title: Heatcircle
  > ### Aliases: geom_heat_circle
  > 
  > ### ** Examples
  > 
  > 
  > # heatcircle with categorical variables only
  > 
  > library(ggplot2)
  > 
  > data <- data.frame(x = rep(c("a", "b", "c"), 3),
  +                    y = rep(c("d", "e", "f"), 3),
  +                    outside_values = rep(c(1,5,7),3),
  +                    inside_values = rep(c(2,3,4),3))
  > 
  > ggplot(data, aes(x,y)) +
  + geom_heat_circle(outside = outside_values,
  +                  inside = inside_values)
  Error in scale_title(title) : object 'outside_values' not found
  Calls: <Anonymous> ... extract_params -> <Anonymous> -> make_title -> scale_title
  Execution halted

Package: ggEDA
Check: examples
New result: ERROR
  Running examples in ‘ggEDA-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ggstack
  > ### Title: AutoPlot an entire data.frame
  > ### Aliases: ggstack
  > 
  > ### ** Examples
  > 
  > 
  > # Create Basic Plot
  > ggstack(baseballfans, col_id = "ID", col_sort = "Glasses")
  
  ── Running ggstack ─────────────────────────────────────────────────────────────
  
  ── Sorting 
  • Sorting X axis by: Glasses
  • Order type: frequency
  • Sort order: descending
  ! Categorical columns must have <= 7 unique values to be visualised. Columns with too many unique values: Date (19)
  
  ── Generating Plot 
  ℹ Found 7 plottable columns in data
  ✔ Plotting column Glasses
  ✔ Plotting column Age
  ✔ Plotting column Gender
  ✔ Plotting column EyeColour
  ✔ Plotting column Height
  ✔ Plotting column HairColour
  ✔ Plotting column WearingHat
  ! Skipping column WearingHat_tooltip
  ! Skipping column Date
  ℹ Stacking plots vertically
  ℹ Making plot interactive since `interactive = TRUE`
  Error:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `draw_panel()`:
  ! unused arguments (lineend = "butt", linejoin = "mitre")
  Backtrace:
       ▆
    1. ├─ggEDA::ggstack(baseballfans, col_id = "ID", col_sort = "Glasses")
    2. │ └─ggiraph::girafe(...)
    3. │   ├─base::tryCatch(...)
    4. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5. │   ├─base::print(ggobj)
    6. │   └─patchwork:::print.patchwork(ggobj)
    7. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
    8. │       └─base::lapply(x$plots, plot_table, guides = guides)
    9. │         ├─patchwork (local) FUN(X[[i]], ...)
   10. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
   11. │           ├─patchwork:::plot_table(x, guides)
   12. │           └─patchwork:::plot_table.ggplot(x, guides)
   13. │             └─ggplot2::ggplotGrob(x)
   14. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
   15. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
   16. │                 └─ggplot2:::by_layer(...)
   17. │                   ├─rlang::try_fetch(...)
   18. │                   │ ├─base::tryCatch(...)
   19. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   20. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   21. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   22. │                   │ └─base::withCallingHandlers(...)
   23. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   24. │                     └─l$draw_geom(d, layout)
   25. │                       └─ggplot2 (local) draw_geom(..., self = self)
   26. │                         └─self$geom$draw_layer(...)
   27. │                           └─ggplot2 (local) draw_layer(..., self = self)
   28. │                             └─base::lapply(...)
   29. │                               └─ggplot2 (local) FUN(X[[i]], ...)
   30. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   31. │                                 └─self$draw_panel(...)
   32. └─base::.handleSimpleError(...)
   33.   └─rlang (local) h(simpleError(msg, call))
   34.     └─handlers[[1L]](cnd)
   35.       └─cli::cli_abort(...)
   36.         └─rlang::abort(...)
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
  ggparallel 6.117   0.26   6.622

Package: ggEDA
Check: tests
New result: ERROR
    Running ‘testthat.R’ [21s/21s]
  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(ggEDA)
    > 
    > test_check("ggEDA")
    [ FAIL 11 | WARN 9 | SKIP 2 | PASS 114 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test-ggstack.R:181:3', 'test-ggstack.R:201:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-ggparallel_specific_utils.R:26:3'): no warnings when lines go to the same point (caused by rescaling issues) ──
    Expected `ggparallel(example_data, verbose = FALSE)` to run without any warnings.
    i Actually got a <rlang_warning> with text:
      Ignoring empty aesthetic: `linewidth`.
    ── Failure ('test-ggstack.R:14:3'): ggEDA works as expected ────────────────────
    `suppressMessages(ggstack(mtcars))` threw an unexpected error.
    Message: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `draw_panel()`:
    ! unused arguments (lineend = "butt", linejoin = "mitre")
    Class:   rlang_error/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(suppressMessages(ggstack(mtcars)), NA) at test-ggstack.R:14:3
      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. ├─base::suppressMessages(ggstack(mtcars))
      8. │ └─base::withCallingHandlers(...)
      9. ├─ggEDA::ggstack(mtcars)
     10. │ └─ggiraph::girafe(...)
     11. │   ├─base::tryCatch(...)
     12. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │   ├─base::print(ggobj)
     14. │   └─patchwork:::print.patchwork(ggobj)
     15. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
     16. │       └─base::lapply(x$plots, plot_table, guides = guides)
     17. │         ├─patchwork (local) FUN(X[[i]], ...)
     18. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
     19. │           ├─patchwork:::plot_table(x, guides)
     20. │           └─patchwork:::plot_table.ggplot(x, guides)
     21. │             └─ggplot2::ggplotGrob(x)
     22. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     23. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     24. │                 └─ggplot2:::by_layer(...)
     25. │                   ├─rlang::try_fetch(...)
     26. │                   │ ├─base::tryCatch(...)
     27. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     28. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     29. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     30. │                   │ └─base::withCallingHandlers(...)
     31. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     32. │                     └─l$draw_geom(d, layout)
     33. │                       └─ggplot2 (local) draw_geom(..., self = self)
     34. │                         └─self$geom$draw_layer(...)
     35. │                           └─ggplot2 (local) draw_layer(..., self = self)
     36. │                             └─base::lapply(...)
     37. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     38. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     39. │                                 └─self$draw_panel(...)
     40. └─base::.handleSimpleError(...)
     41.   └─rlang (local) h(simpleError(msg, call))
     42.     └─handlers[[1L]](cnd)
     43.       └─cli::cli_abort(...)
     44.         └─rlang::abort(...)
    ── Error ('test-ggstack.R:50:3'): ggEDA doesn't warn about columns the user isn't interested in [plain] ──
    Error in `(function (mapping = NULL, data = NULL, stat = "identity", position = "stack", 
        ..., just = 0.5, lineend = "butt", linejoin = "mitre", na.rm = FALSE, 
        show.legend = NA, inherit.aes = TRUE) 
    {
        layer(mapping = mapping, data = data, geom = "col", stat = stat, 
            position = position, show.legend = show.legend, inherit.aes = inherit.aes, 
            params = list2(na.rm = na.rm, just = just, lineend = lineend, 
                linejoin = linejoin, ...))
    })(mapping = structure(list(), class = c("ggplot2::mapping", 
    "uneval", "gg", "S7_object"), S7_class = structure(function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, name = "mapping", parent = structure(list(class = "gg", constructor = function (.data) 
    {
        stop(sprintf("S3 class <%s> doesn't have a constructor", 
            class[[1]]), call. = FALSE)
    }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, class = c("S7_class", "S7_object")), names = character(0)), 
        width = 0.9, na.rm = TRUE)`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `draw_panel()`:
    ! unused arguments (lineend = "butt", linejoin = "mitre")
    Backtrace:
         ▆
      1. ├─base::suppressMessages(...) at test-ggstack.R:50:3
      2. │ └─base::withCallingHandlers(...)
      3. ├─testthat::expect_message(ggstack(df, verbose = 2), "Columns with too many unique values: Letters")
      4. │ └─testthat:::expect_condition_matching(...)
      5. │   └─testthat:::quasi_capture(...)
      6. │     ├─testthat (local) .capture(...)
      7. │     │ └─base::withCallingHandlers(...)
      8. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      9. ├─ggEDA::ggstack(df, verbose = 2)
     10. │ └─ggiraph::girafe(...)
     11. │   ├─base::tryCatch(...)
     12. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │   ├─base::print(ggobj)
     14. │   └─patchwork:::print.patchwork(ggobj)
     15. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
     16. │       └─base::lapply(x$plots, plot_table, guides = guides)
     17. │         ├─patchwork (local) FUN(X[[i]], ...)
     18. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
     19. │           ├─patchwork:::plot_table(x, guides)
     20. │           └─patchwork:::plot_table.ggplot(x, guides)
     21. │             └─ggplot2::ggplotGrob(x)
     22. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     23. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     24. │                 └─ggplot2:::by_layer(...)
     25. │                   ├─rlang::try_fetch(...)
     26. │                   │ ├─base::tryCatch(...)
     27. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     28. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     29. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     30. │                   │ └─base::withCallingHandlers(...)
     31. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     32. │                     └─l$draw_geom(d, layout)
     33. │                       └─ggplot2 (local) draw_geom(..., self = self)
     34. │                         └─self$geom$draw_layer(...)
     35. │                           └─ggplot2 (local) draw_layer(..., self = self)
     36. │                             └─base::lapply(...)
     37. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     38. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     39. │                                 └─self$draw_panel(...)
     40. └─base::.handleSimpleError(...)
     41.   └─rlang (local) h(simpleError(msg, call))
     42.     └─handlers[[1L]](cnd)
     43.       └─cli::cli_abort(...)
     44.         └─rlang::abort(...)
    ── Failure ('test-ggstack.R:58:3'): ggEDA returns a plot object ────────────────
    Expected `ggstack(data = mock_data, col_id = "ID", verbose = FALSE)` to run without any errors.
    i Actually got a <rlang_error> with text:
      Problem while converting geom to grob.
      i Error occurred in the 1st layer.
      Caused by error in `draw_panel()`:
      ! unused arguments (lineend = "butt", linejoin = "mitre")
    ── Failure ('test-ggstack.R:59:3'): ggEDA returns a plot object ────────────────
    `result` is not an S3 object
    ── Failure ('test-ggstack.R:63:3'): ggEDA handles missing col_id gracefully ────
    Expected `ggstack(data = mock_data, verbose = FALSE)` to run without any errors.
    i Actually got a <rlang_error> with text:
      Problem while converting geom to grob.
      i Error occurred in the 1st layer.
      Caused by error in `draw_panel()`:
      ! unused arguments (lineend = "butt", linejoin = "mitre")
    ── Failure ('test-ggstack.R:64:3'): ggEDA handles missing col_id gracefully ────
    `result` is not an S3 object
    ── Error ('test-ggstack.R:96:3'): ggEDA limits the number of plottable columns ──
    Error in `(function (mapping = NULL, data = NULL, stat = "identity", position = "stack", 
        ..., just = 0.5, lineend = "butt", linejoin = "mitre", na.rm = FALSE, 
        show.legend = NA, inherit.aes = TRUE) 
    {
        layer(mapping = mapping, data = data, geom = "col", stat = stat, 
            position = position, show.legend = show.legend, inherit.aes = inherit.aes, 
            params = list2(na.rm = na.rm, just = just, lineend = lineend, 
                linejoin = linejoin, ...))
    })(mapping = structure(list(), class = c("ggplot2::mapping", 
    "uneval", "gg", "S7_object"), S7_class = structure(function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, name = "mapping", parent = structure(list(class = "gg", constructor = function (.data) 
    {
        stop(sprintf("S3 class <%s> doesn't have a constructor", 
            class[[1]]), call. = FALSE)
    }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, class = c("S7_class", "S7_object")), names = character(0)), 
        width = 0.9, na.rm = TRUE)`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `draw_panel()`:
    ! unused arguments (lineend = "butt", linejoin = "mitre")
    Backtrace:
         ▆
      1. ├─testthat::expect_message(...) at test-ggstack.R:96:3
      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. ├─ggEDA::ggstack(data = data, max_plottable_cols = 10, verbose = FALSE)
      8. │ └─ggiraph::girafe(...)
      9. │   ├─base::tryCatch(...)
     10. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     11. │   ├─base::print(ggobj)
     12. │   └─patchwork:::print.patchwork(ggobj)
     13. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
     14. │       └─base::lapply(x$plots, plot_table, guides = guides)
     15. │         ├─patchwork (local) FUN(X[[i]], ...)
     16. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
     17. │           ├─patchwork:::plot_table(x, guides)
     18. │           └─patchwork:::plot_table.ggplot(x, guides)
     19. │             └─ggplot2::ggplotGrob(x)
     20. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     21. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     22. │                 └─ggplot2:::by_layer(...)
     23. │                   ├─rlang::try_fetch(...)
     24. │                   │ ├─base::tryCatch(...)
     25. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     26. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     27. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     28. │                   │ └─base::withCallingHandlers(...)
     29. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     30. │                     └─l$draw_geom(d, layout)
     31. │                       └─ggplot2 (local) draw_geom(..., self = self)
     32. │                         └─self$geom$draw_layer(...)
     33. │                           └─ggplot2 (local) draw_layer(..., self = self)
     34. │                             └─base::lapply(...)
     35. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     36. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     37. │                                 └─self$draw_panel(...)
     38. └─base::.handleSimpleError(...)
     39.   └─rlang (local) h(simpleError(msg, call))
     40.     └─handlers[[1L]](cnd)
     41.       └─cli::cli_abort(...)
     42.         └─rlang::abort(...)
    ── Error ('test-ggstack.R:161:3'): ggEDA can handle interactive and static plot settings ──
    Error in `(function (mapping = NULL, data = NULL, stat = "identity", position = "stack", 
        ..., just = 0.5, lineend = "butt", linejoin = "mitre", na.rm = FALSE, 
        show.legend = NA, inherit.aes = TRUE) 
    {
        layer(mapping = mapping, data = data, geom = "col", stat = stat, 
            position = position, show.legend = show.legend, inherit.aes = inherit.aes, 
            params = list2(na.rm = na.rm, just = just, lineend = lineend, 
                linejoin = linejoin, ...))
    })(mapping = structure(list(), class = c("ggplot2::mapping", 
    "uneval", "gg", "S7_object"), S7_class = structure(function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, name = "mapping", parent = structure(list(class = "gg", constructor = function (.data) 
    {
        stop(sprintf("S3 class <%s> doesn't have a constructor", 
            class[[1]]), call. = FALSE)
    }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, class = c("S7_class", "S7_object")), names = character(0)), 
        width = 0.9, na.rm = TRUE)`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `draw_panel()`:
    ! unused arguments (lineend = "butt", linejoin = "mitre")
    Backtrace:
         ▆
      1. ├─ggEDA::ggstack(data = mock_data, interactive = TRUE, verbose = FALSE) at test-ggstack.R:161:3
      2. │ └─ggiraph::girafe(...)
      3. │   ├─base::tryCatch(...)
      4. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      5. │   ├─base::print(ggobj)
      6. │   └─patchwork:::print.patchwork(ggobj)
      7. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
      8. │       └─base::lapply(x$plots, plot_table, guides = guides)
      9. │         ├─patchwork (local) FUN(X[[i]], ...)
     10. │         └─patchwork:::plot_table.free_plot(X[[i]], ...)
     11. │           ├─patchwork:::plot_table(x, guides)
     12. │           └─patchwork:::plot_table.ggplot(x, guides)
     13. │             └─ggplot2::ggplotGrob(x)
     14. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     15. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     16. │                 └─ggplot2:::by_layer(...)
     17. │                   ├─rlang::try_fetch(...)
     18. │                   │ ├─base::tryCatch(...)
     19. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     20. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     21. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     22. │                   │ └─base::withCallingHandlers(...)
     23. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     24. │                     └─l$draw_geom(d, layout)
     25. │                       └─ggplot2 (local) draw_geom(..., self = self)
     26. │                         └─self$geom$draw_layer(...)
     27. │                           └─ggplot2 (local) draw_layer(..., self = self)
     28. │                             └─base::lapply(...)
     29. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     30. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     31. │                                 └─self$draw_panel(...)
     32. └─base::.handleSimpleError(...)
     33.   └─rlang (local) h(simpleError(msg, call))
     34.     └─handlers[[1L]](cnd)
     35.       └─cli::cli_abort(...)
     36.         └─rlang::abort(...)
    ── Failure ('test-ggstack.R:177:3'): ggEDA heirarchical sort works ─────────────
    Expected `ggstack(...)` to run without any errors.
    i Actually got a <rlang_error> with text:
      Problem while converting geom to grob.
      i Error occurred in the 1st layer.
      Caused by error in `draw_panel()`:
      ! unused arguments (lineend = "butt", linejoin = "mitre")
    ── Failure ('test-ggstack.R:187:3'): ggEDA heirarchical sort works ─────────────
    Expected `ggstack(...)` to run without any errors.
    i Actually got a <rlang_error> with text:
      Problem while converting geom to grob.
      i Error occurred in the 1st layer.
      Caused by error in `draw_panel()`:
      ! unused arguments (lineend = "butt", linejoin = "mitre")
    
    [ FAIL 11 | WARN 9 | SKIP 2 | PASS 114 ]
    Error: Test failures
    Execution halted

Package: ggedit
Check: examples
New result: ERROR
  Running examples in ‘ggedit-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: compare
  > ### Title: compare
  > ### Aliases: compare
  > 
  > ### ** Examples
  > 
  > compare(ggplot2::theme_bw(),ggplot2::theme_get())
  Error in as.vector(x, "list") : 
    cannot coerce type 'object' to vector of type 'list'
  Calls: compare ... themeFetchFull -> lapply -> as.list -> as.list.default
  Execution halted

Package: ggfocus
Check: examples
New result: ERROR
  Running examples in ‘ggfocus-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ggfocus
  > ### Title: (Deprecated) Sets focus scales to an existing 'ggplot' object
  > ### Aliases: ggfocus
  > 
  > ### ** Examples
  > 
  > library(ggplot2)
  > p <- ggplot(iris,aes(x=Sepal.Length,y=Petal.Length)) + geom_point()
  > ggfocus(p, Species, "versicolor")
  The function 'ggfocus()' is deprecated, consider using the family scale_*_focus() instead.
  Warning: `select_()` was deprecated in dplyr 0.7.0.
  ℹ Please use `select()` instead.
  ℹ The deprecated feature was likely used in the ggfocus package.
    Please report the issue at <https://github.com/Freguglia/ggfocus/issues>.
  Error in scale_title(title) : object 'Species' not found
  Calls: <Anonymous> ... extract_params -> <Anonymous> -> make_title -> scale_title
  Execution halted

Package: ggfocus
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggfocus_fill:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggfocus_shape:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggfocus_alpha:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggfocus_color:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggfocus_size:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggfocus_linetype:
    function(object, plot, object_name)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: ggformula
Check: examples
New result: ERROR
  Running examples in ‘ggformula-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: gf_boxplot
  > ### Title: Formula interface to geom_boxplot()
  > ### Aliases: gf_boxplot
  > 
  > ### ** Examples
  > 
  > gf_boxplot(age ~ substance, data = mosaicData::HELPrct)
  Error in `position_dodge()`:
  ! `orientation` must be a string or character vector.
  Backtrace:
      ▆
   1. ├─ggformula::gf_boxplot(age ~ substance, data = mosaicData::HELPrct)
   2. │ ├─base::do.call(position_fun, pdots)
   3. │ └─ggplot2::position_dodge(orientation = NA)
   4. │   ├─ggplot2::ggproto(...)
   5. │   │ └─rlang::list2(...)
   6. │   └─rlang::arg_match0(orientation, c("x", "y"))
   7. └─rlang::abort(message = message, call = call)
  Execution halted

Package: ggformula
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'gf_lines.Rd':
  gf_hline
    Code: function(object = NULL, gformula = NULL, data = NULL, ...,
                   yintercept, color, linetype, linewidth, alpha, xlab,
                   ylab, title, subtitle, caption, position = "identity",
                   show.legend = NA, show.help = NULL, inherit = FALSE,
                   environment = parent.frame())
    Docs: function(object = NULL, gformula = NULL, data = NULL, ...,
                   yintercept, color, linetype, linewidth, alpha, xlab,
                   ylab, title, subtitle, caption, show.legend = NA,
                   show.help = NULL, inherit = FALSE, environment =
                   parent.frame())
    Argument names in code not in docs:
      position
    Mismatches in argument names (first 3):
      Position: 15 Code: position Docs: show.legend
      Position: 16 Code: show.legend Docs: show.help
      Position: 17 Code: show.help Docs: inherit
  gf_vline
    Code: function(object = NULL, gformula = NULL, data = NULL, ...,
                   xintercept, color, linetype, linewidth, alpha, xlab,
                   ylab, title, subtitle, caption, position = "identity",
                   show.legend = NA, show.help = NULL, inherit = FALSE,
                   environment = parent.frame())
    Docs: function(object = NULL, gformula = NULL, data = NULL, ...,
                   xintercept, color, linetype, linewidth, alpha, xlab,
                   ylab, title, subtitle, caption, show.legend = NA,
                   show.help = NULL, inherit = FALSE, environment =
                   parent.frame())
    Argument names in code not in docs:
      position
    Mismatches in argument names (first 3):
      Position: 15 Code: position Docs: show.legend
      Position: 16 Code: show.legend Docs: show.help
      Position: 17 Code: show.help Docs: inherit

Package: ggformula
Check: tests
New result: ERROR
    Running ‘testthat.R’ [24s/24s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggformula)
    Loading required package: ggplot2
    Loading required package: scales
    Loading required package: ggridges
    
    New to ggformula?  Try the tutorials: 
    	learnr::run_tutorial("introduction", package = "ggformula")
    	learnr::run_tutorial("refining", package = "ggformula")
    > 
    > test_check("ggformula")
    Smoothing formula not specified. Using: y ~ x
    Smoothing formula not specified. Using: y ~ x
    [ FAIL 1 | WARN 2 | SKIP 46 | PASS 0 ]
    
    ══ Skipped tests (46) ══════════════════════════════════════════════════════════
    • On CRAN (46): 'test-annotate.R:7:5', 'test-annotate.R:16:5',
      'test-annotate.R:25:5', 'test-annotate.R:35:5', 'test-annotate.R:45:5',
      'test-annotate.R:55:5', 'test-annotate.R:64:5', 'test-labeling.R:7:5',
      'test-labeling.R:17:5', 'test-labeling.R:26:5', 'test-labeling.R:48:5',
      'test-layer-factory.R:28:5', 'test-layer-factory.R:78:5',
      'test-layer-factory.R:98:5', 'test-layer-factory.R:139:5',
      'test-layer-factory.R:183:5', 'test-layer-factory.R:193:5',
      'test-layer-factory.R:237:5', 'test-layer-factory.R:252:5',
      'test-layer-factory.R:311:5', 'test-layer-factory.R:340:5',
      'test-layer-factory.R:449:5', 'test-layer-factory.R:460:5',
      'test-layer-factory.R:480:5', 'test-layer-factory.R:510:5',
      'test-layer-factory.R:528:5', 'test-layer-factory.R:556:5',
      'test-layer-factory.R:574:5', 'test-layer-factory.R:590:5',
      'test-layer-factory.R:606:5', 'test-layer-factory.R:646:5',
      'test-layer-factory.R:661:5', 'test-layer-factory.R:689:5',
      'test-layer-factory.R:702:5', 'test-layer-factory.R:727:5',
      'test-layer-factory.R:749:5', 'test-layer-factory.R:762:5',
      'test-layer-factory.R:779:5', 'test-layer-factory.R:791:5',
      'test-layer-factory.R:811:5', 'test-layer-factory.R:827:5',
      'test-layer-factory.R:844:5', 'test-layer-factory.R:938:5',
      'test-layer-factory.R:954:5', 'test-layer-factory.R:971:5',
      'test-layer-factory.R:984:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-layer-factory.R:213:5'): gf_boxplot() ──────────────────────────
    Error in `position_dodge(orientation = NA)`: `orientation` must be a string or character vector.
    Backtrace:
         ▆
      1. ├─ggformula:::wrapped_expect_doppelganger(...) at test-layer-factory.R:213:5
      2. │ └─vdiffr::expect_doppelganger(title, fig, ...)
      3. │   └─vdiffr (local) writer(fig, testcase, title)
      4. │     └─vdiffr:::print_plot(plot, title)
      5. ├─ggformula::gf_boxplot(...)
      6. │ ├─base::do.call(position_fun, pdots)
      7. │ └─ggplot2::position_dodge(orientation = NA)
      8. │   ├─ggplot2::ggproto(...)
      9. │   │ └─rlang::list2(...)
     10. │   └─rlang::arg_match0(orientation, c("x", "y"))
     11. └─rlang::abort(message = message, call = call)
    
    [ FAIL 1 | WARN 2 | SKIP 46 | PASS 0 ]
    Deleting unused snapshots:
    • labeling/using.svg
    • layer-factory/discrete-breaks-2-0.svg
    • layer-factory/gf-abline2.svg
    • layer-factory/gf-abline3.svg
    • layer-factory/gf-abline4.svg
    • layer-factory/gf-abline5.svg
    • layer-factory/gf-abline6.svg
    • layer-factory/gf-abline7.svg
    • layer-factory/gf-area1.svg
    • layer-factory/gf-ash2.svg
    • layer-factory/gf-ash3.svg
    • layer-factory/gf-blank1.svg
    • layer-factory/gf-boxplot2.svg
    • layer-factory/gf-boxplot3.svg
    • layer-factory/gf-coefline2.svg
    • layer-factory/gf-col1.svg
    • layer-factory/gf-contour2.svg
    • layer-factory/gf-contour3.svg
    • layer-factory/gf-crossbar1.svg
    • layer-factory/gf-dens2.svg
    • layer-factory/gf-density-2d.svg
    • layer-factory/gf-density-with-fill.svg
    • layer-factory/gf-density1.svg
    • layer-factory/gf-density2.svg
    • layer-factory/gf-density2d1.svg
    • layer-factory/gf-density2d2.svg
    • layer-factory/gf-dhistogram1.svg
    • layer-factory/gf-dhistogramh1.svg
    • layer-factory/gf-dhistogramh2.svg
    • layer-factory/gf-dist2.svg
    • layer-factory/gf-dist3.svg
    • layer-factory/gf-dist4.svg
    • layer-factory/gf-dist5.svg
    • layer-factory/gf-dist6.svg
    • layer-factory/gf-dotplot2.svg
    • layer-factory/gf-empty2.svg
    • layer-factory/gf-errorbar1.svg
    • layer-factory/gf-fitdistr2.svg
    • layer-factory/gf-frame1.svg
    • layer-factory/gf-freqpoly2.svg
    • layer-factory/gf-fun2.svg
    • layer-factory/gf-fun2d2.svg
    • layer-factory/gf-fun2d3.svg
    • layer-factory/gf-fun2d4.svg
    • layer-factory/gf-fun2d5.svg
    • layer-factory/gf-fun2d6.svg
    • layer-factory/gf-histogram-with-facets.svg
    • layer-factory/gf-histogram2.svg
    • layer-factory/gf-label2.svg
    • layer-factory/gf-line2.svg
    • layer-factory/gf-percents1.svg
    • layer-factory/gf-point2.svg
    • layer-factory/gf-pointrange1.svg
    • layer-factory/gf-props1.svg
    • layer-factory/gf-qqstep1.svg
    • layer-factory/gf-ribbon2.svg
    • layer-factory/gf-rug-1.svg
    • layer-factory/gf-rug-2.svg
    • layer-factory/gf-rug-3.svg
    • layer-factory/gf-rug-4.svg
    • layer-factory/gf-rug-5.svg
    • layer-factory/gf-rug-6.svg
    • layer-factory/gf-rug-7.svg
    • layer-factory/gf-rug-8.svg
    • layer-factory/gf-rug-on-y-only-but-with-jitter.svg
    • layer-factory/gf-rugx-gf-rug-y-with-jitter.svg
    • layer-factory/gf-rugx-with-jitter.svg
    • layer-factory/gf-rugx-without-jitter.svg
    • layer-factory/gf-rugy.svg
    • layer-factory/gf-spoke2.svg
    • layer-factory/gf-text1.svg
    • layer-factory/gf-text2.svg
    • layer-factory/gf-tile1.svg
    • layer-factory/proportions-within-all-dodge.svg
    • layer-factory/proportions-within-fill-dodge.svg
    • layer-factory/proportions-within-fill-facet-grid-and-group.svg
    • layer-factory/proportions-within-fill-facet-grid.svg
    • layer-factory/proportions-within-group-facet-grid.svg
    Error: Test failures
    Execution halted

Package: gggenomes
Check: examples
New result: ERROR
  Running examples in ‘gggenomes-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: add_feats
  > ### Title: Add different types of tracks
  > ### Aliases: add_feats add_links add_subfeats add_sublinks add_clusters
  > ###   add_tracks
  > 
  > ### ** Examples
  > 
  > # Add some repeat annotations
  > gggenomes(seqs = emale_seqs) %>%
  +   add_feats(repeats = emale_tirs) +
  +   geom_seq() + geom_feat()
  Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
  ℹ Please use the `linewidth` argument instead.
  ℹ The deprecated feature was likely used in the gggenomes package.
    Please report the issue at <https://github.com/thackl/gggenomes/issues>.
  Error in UseMethod("add_feats") : 
    no applicable method for 'add_feats' applied to an object of class "NULL"
  Calls: %>% -> add_feats
  Execution halted

Package: gggenomes
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘emales.Rmd’ using rmarkdown
  --- finished re-building ‘emales.Rmd’
  
  --- re-building ‘flip.Rmd’ using rmarkdown
  
  Quitting from flip.Rmd:16-44 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `UseMethod()`:
  ! no applicable method for 'add_links' applied to an object of class "NULL"
  ---
  Backtrace:
      ▆
   1. ├─p %>% add_links(emale_ava)
   2. └─gggenomes::add_links(., emale_ava)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'flip.Rmd' failed with diagnostics:
  no applicable method for 'add_links' applied to an object of class "NULL"
  --- failed re-building ‘flip.Rmd’
  
  --- re-building ‘gggenomes.Rmd’ using rmarkdown
  Data sets in package 'gggenomes':
  
  emale_ava               All-versus-all whole genome alignments of 6
                          EMALE genomes
  emale_cogs              Clusters of orthologs of 6 EMALE proteomes
  emale_gc                Relative GC-content along 6 EMALE genomes
  emale_genes             Gene annotations if 6 EMALE genomes (endogenous
                          virophages)
  emale_ngaros            Integrated Ngaro retrotransposons of 6 EMALE
                          genomes
  emale_prot_ava          All-versus-all alignments 6 EMALE proteomes
  emale_seqs              Sequence index of 6 EMALE genomes (endogenous
                          virophages)
  emale_tirs              Terminal inverted repeats of 6 EMALE genomes
  
  
  Quitting from gggenomes.Rmd:78-99 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `UseMethod()`:
  ! no applicable method for 'track_info' applied to an object of class "NULL"
  ---
  Backtrace:
      x
   1. +-p %>% track_info
   2. \-gggenomes::track_info(.)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'gggenomes.Rmd' failed with diagnostics:
  no applicable method for 'track_info' applied to an object of class "NULL"
  --- failed re-building ‘gggenomes.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘flip.Rmd’ ‘gggenomes.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: gghalves
Check: examples
New result: ERROR
  Running examples in ‘gghalves-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: geom_half_point
  > ### Title: Points with jitter for half geoms.
  > ### Aliases: geom_half_point
  > 
  > ### ** Examples
  > 
  > ggplot(iris, aes(x = Species, y = Petal.Width, fill = Species)) + 
  +   geom_half_point()
  Error in `geom_half_point()`:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `fun()`:
  ! argument "layout" is missing, with no default
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_gtable(data)
    4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$draw_geom(d, layout)
   14. │         └─ggplot2 (local) draw_geom(..., self = self)
   15. │           └─self$geom$draw_layer(...)
   16. │             └─ggplot2 (local) draw_layer(..., self = self)
   17. │               └─base::lapply(...)
   18. │                 └─ggplot2 (local) FUN(X[[i]], ...)
   19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   20. │                   └─self$draw_panel(...)
   21. │                     └─ggplot2 (local) draw_panel(..., self = self)
   22. │                       └─base::lapply(...)
   23. │                         └─ggplot2 (local) FUN(X[[i]], ...)
   24. │                           └─self$draw_group(group, panel_params, coord, ...)
   25. │                             └─gghalves (local) draw_group(...)
   26. │                               └─transformation$compute_layer(transformation_df, transformation_params_new)
   27. │                                 └─ggplot2 (local) compute_layer(..., self = self)
   28. │                                   └─ggplot2:::dapply(...)
   29. │                                     └─base::lapply(...)
   30. │                                       └─ggplot2 (local) FUN(X[[i]], ...)
   31. │                                         └─ggplot2 (local) apply_fun(cur_data)
   32. │                                           └─ggplot2 (local) fun(x, ...)
   33. └─rlang (local) `<fn>`(`<gtvrErrr>`)
   34.   └─handlers[[1L]](cnd)
   35.     └─cli::cli_abort(...)
   36.       └─rlang::abort(...)
  Execution halted

Package: gghalves
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘gghalves.Rmd’ using rmarkdown
  
  Quitting from gghalves.Rmd:39-42 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'gghalves.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `fun()`:
  ! argument "layout" is missing, with no default
  --- failed re-building ‘gghalves.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘gghalves.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggimage
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.bgimage:
    function(object, plot, object_name)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: ggiraph
Check: examples
New result: ERROR
  Running examples in ‘ggiraph-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: geom_bar_interactive
  > ### Title: Create interactive bars
  > ### Aliases: geom_bar_interactive geom_col_interactive
  > 
  > ### ** Examples
  > 
  > # add interactive bar -------
  > library(ggplot2)
  > library(ggiraph)
  > 
  > p <- ggplot(mpg, aes(x = class, tooltip = class, data_id = class)) +
  +   geom_bar_interactive()
  > 
  > x <- girafe(ggobj = p)
  > if (interactive()) {
  +   print(x)
  + }
  > 
  > dat <- data.frame(
  +   name = c("David", "Constance", "Leonie"),
  +   gender = c("Male", "Female", "Female"),
  +   height = c(172, 159, 71)
  + )
  > p <- ggplot(dat, aes(x = name, y = height, tooltip = gender, data_id = name)) +
  +   geom_col_interactive()
  > 
  > x <- girafe(ggobj = p)
  Error:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `draw_panel()`:
  ! unused arguments (lineend = "butt", linejoin = "mitre")
  Backtrace:
       ▆
    1. ├─ggiraph::girafe(ggobj = p)
    2. │ ├─base::tryCatch(...)
    3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4. │ ├─base::print(ggobj)
    5. │ └─ggplot2 (local) `print.ggplot2::ggplot`(ggobj)
    6. │   ├─ggplot2::ggplot_gtable(data)
    7. │   └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    8. │     └─ggplot2:::by_layer(...)
    9. │       ├─rlang::try_fetch(...)
   10. │       │ ├─base::tryCatch(...)
   11. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   12. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   14. │       │ └─base::withCallingHandlers(...)
   15. │       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   16. │         └─l$draw_geom(d, layout)
   17. │           └─ggplot2 (local) draw_geom(..., self = self)
   18. │             └─self$geom$draw_layer(...)
   19. │               └─ggplot2 (local) draw_layer(..., self = self)
   20. │                 └─base::lapply(...)
   21. │                   └─ggplot2 (local) FUN(X[[i]], ...)
   22. │                     ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   23. │                     └─self$draw_panel(...)
   24. └─base::.handleSimpleError(...)
   25.   └─rlang (local) h(simpleError(msg, call))
   26.     └─handlers[[1L]](cnd)
   27.       └─cli::cli_abort(...)
   28.         └─rlang::abort(...)
  Execution halted

Package: ggiraphExtra
Check: examples
New result: ERROR
  Running examples in ‘ggiraphExtra-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ggBoxplot
  > ### Title: Draw boxplots of a data.frame
  > ### Aliases: ggBoxplot
  > 
  > ### ** Examples
  > 
  > require(ggplot2)
  Loading required package: ggplot2
  > require(ggiraph)
  Loading required package: ggiraph
  > require(reshape2)
  Loading required package: reshape2
  > ggBoxplot(mtcars,rescale=TRUE)
  Error:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `draw_group()`:
  ! unused arguments (outlier_gp = list(NULL, NULL, NULL, NULL, 0.5, NULL), whisker_gp = list(NULL, NULL, NULL), staple_gp = list(NULL, NULL, NULL), median_gp = list(NULL, NULL, NULL), box_gp = list(NULL, NULL, NULL))
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_gtable(data)
    4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$draw_geom(d, layout)
   14. │         └─ggplot2 (local) draw_geom(..., self = self)
   15. │           └─self$geom$draw_layer(...)
   16. │             └─ggplot2 (local) draw_layer(..., self = self)
   17. │               └─base::lapply(...)
   18. │                 └─ggplot2 (local) FUN(X[[i]], ...)
   19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   20. │                   └─self$draw_panel(...)
   21. │                     └─ggplot2 (local) draw_panel(..., self = self)
   22. │                       └─base::lapply(...)
   23. │                         └─ggplot2 (local) FUN(X[[i]], ...)
   24. │                           └─self$draw_group(group, panel_params, coord, ...)
   25. └─base::.handleSimpleError(...)
   26.   └─rlang (local) h(simpleError(msg, call))
   27.     └─handlers[[1L]](cnd)
   28.       └─cli::cli_abort(...)
   29.         └─rlang::abort(...)
  Execution halted

Package: ggmap
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: `aes_()` was deprecated in ggplot2 3.0.0.

Package: ggmcmc
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘using_ggmcmc.Rmd’ using rmarkdown
  
  Quitting from using_ggmcmc.Rmd:385-387 [pairs]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
  Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  --- failed re-building ‘using_ggmcmc.Rmd’
  
  --- re-building ‘v70i09.Rnw’ using knitr
  --- finished re-building ‘v70i09.Rnw’
  
  SUMMARY: processing the following file failed:
    ‘using_ggmcmc.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggmosaic
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: ggmulti
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: ggparallel
Check: tests
New result: ERROR
    Running ‘testthat.R’ [2s/2s]
  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(ggparallel)
    Loading required package: ggplot2
    > 
    > test_check("ggparallel")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-ggparallel.R:12:3'): ggparallel works ──────────────────────────
    Error in `UseMethod("ggplot_build")`: no applicable method for 'ggplot_build' applied to an object of class "c('gg', 'ggplot')"
    Backtrace:
        ▆
     1. └─ggplot2::ggplot_build(test_mtcars_plot) at test-ggparallel.R:12:3
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
    Error: Test failures
    Execution halted

Package: ggpath
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggpath)
    > 
    > test_check("ggpath")
    [ FAIL 1 | WARN 0 | SKIP 5 | PASS 3 ]
    
    ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
    • On CRAN (4): 'test-geom_from_path.R:46:3', 'test-geom_lines.R:43:3',
      'test-theme-elements.R:32:3', 'test-theme-elements.R:116:3'
    • On Linux (1): 'test-theme-elements.R:40:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-theme-elements.R:112:3'): background element works ───────────
    `print(p4)` did not throw the expected warning.
    
    [ FAIL 1 | WARN 0 | SKIP 5 | PASS 3 ]
    Deleting unused snapshots:
    • geom_from_path/p1.svg
    • geom_lines/p1.svg
    • geom_lines/p2.svg
    • geom_lines/p3.svg
    • geom_lines/p4.svg
    • geom_lines/p5.svg
    • theme-elements/p1.svg
    • theme-elements/p2.svg
    • theme-elements/p3.svg
    Error: Test failures
    Execution halted

Package: ggpointdensity
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  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(ggpointdensity)
    > 
    > test_check("ggpointdensity")
    [ FAIL 5 | WARN 1 | SKIP 0 | PASS 8 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-geom_pointdensity.R:20:3'): coord_fixed adjusts density correctly (method='kde2d') ──
    Error in `expect_compare("<", act, exp)`: Result of comparison must be a single logical value
    Backtrace:
        ▆
     1. └─testthat::expect_lt(plot_data$ndensity[1], plot_data$ndensity[2]) at test-geom_pointdensity.R:20:3
     2.   └─testthat:::expect_compare("<", act, exp)
     3.     └─rlang::abort("Result of comparison must be a single logical value")
    ── Failure ('test-geom_pointdensity.R:53:7'): coord_fixed(method='kde2d') runs without warning ──
    Expected `print(p1)` to run without any warnings.
    i Actually got a <simpleWarning> with text:
      Computation failed in `stat_pointdensity()`:
      there is no package called 'MASS'
    ── Failure ('test-geom_pointdensity.R:64:7'): isotropic normal does not warn (method='kde2d') ──
    Expected `print(p1)` to run without any warnings.
    i Actually got a <simpleWarning> with text:
      Computation failed in `stat_pointdensity()`:
      there is no package called 'MASS'
    ── Failure ('test-geom_pointdensity.R:79:7'): no variation in one axis does not warn (method='kde2d') ──
    Expected `print(p1)` to run without any warnings.
    i Actually got a <simpleWarning> with text:
      Computation failed in `stat_pointdensity()`:
      there is no package called 'MASS'
    ── Failure ('test-geom_pointdensity.R:94:7'): no variation in both axis does not warn (method='kde2d') ──
    Expected `print(p1)` to run without any warnings.
    i Actually got a <simpleWarning> with text:
      Computation failed in `stat_pointdensity()`:
      there is no package called 'MASS'
    
    [ FAIL 5 | WARN 1 | SKIP 0 | PASS 8 ]
    Error: Test failures
    Execution halted

Package: ggpol
Check: examples
New result: ERROR
  Running examples in ‘ggpol-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: GeomConfmat
  > ### Title: Confusion Matrix
  > ### Aliases: GeomConfmat geom_confmat stat_confmat
  > 
  > ### ** Examples
  > 
  > x <- sample(LETTERS[seq(4)], 50, replace = TRUE)
  > y <- sample(LETTERS[seq(4)], 50, replace = TRUE)
  > 
  > ggplot() + 
  +   geom_confmat(aes(x = x, y = y), normalize = TRUE, text.perc = TRUE)
  Warning: Using the `size` aesthetic in this geom was deprecated in ggplot2 3.4.0.
  ℹ Please use `linewidth` in the `default_aes` field and elsewhere instead.
  Error in `geom_confmat()`:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error:
  ! object 'fontsize' not found
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_gtable(data)
    4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$draw_geom(d, layout)
   14. │         └─ggplot2 (local) draw_geom(..., self = self)
   15. │           └─self$geom$draw_layer(...)
   16. │             └─ggplot2 (local) draw_layer(..., self = self)
   17. │               └─base::lapply(...)
   18. │                 └─ggplot2 (local) FUN(X[[i]], ...)
   19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   20. │                   └─self$draw_panel(...)
   21. │                     └─ggpol (local) draw_panel(...)
   22. │                       └─base::lapply(GeomText$default_aes[missing_aes], rlang::eval_tidy)
   23. │                         └─rlang (local) FUN(X[[i]], ...)
   24. ├─ggplot2::from_theme(fontsize)
   25. └─base::.handleSimpleError(...)
   26.   └─rlang (local) h(simpleError(msg, call))
   27.     └─handlers[[1L]](cnd)
   28.       └─cli::cli_abort(...)
   29.         └─rlang::abort(...)
  Execution halted

Package: ggprism
Check: examples
New result: ERROR
  Running examples in ‘ggprism-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: annotation_ticks
  > ### Title: Add ticks as ggplot annotation
  > ### Aliases: annotation_ticks
  > 
  > ### ** Examples
  > 
  > ## Generally it is better to use the guide_prism_minor function.
  > ## However annotation_ticks is useful in a few specific situations.
  > library(ggplot2)
  > 
  > ## easily put ticks without labels around a plot with a border
  > ggplot(mtcars, aes(x = mpg, y = disp)) +
  +   geom_point() +
  +   theme_prism(border = TRUE) +
  +   coord_cartesian(clip = "off") +
  +   annotation_ticks(sides = "tr", type = "major", outside = TRUE) +
  +   theme(plot.margin = unit(c(4, 4, 4, 4), "mm"))
  Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
  ℹ Please use the `linewidth` argument instead.
  ℹ The deprecated feature was likely used in the ggprism package.
    Please report the issue at <https://github.com/csdaw/ggprism/issues>.
  Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
  ℹ Please use the `linewidth` argument instead.
  ℹ The deprecated feature was likely used in the ggprism package.
    Please report the issue at <https://github.com/csdaw/ggprism/issues>.
  Error in `parent %+replace% t`:
  ! `%+replace%` requires two theme objects
  Backtrace:
      ▆
   1. └─ggprism::theme_prism(border = TRUE)
   2.   └─parent %+replace% t
   3.     └─cli::cli_abort("{.code %+replace%} requires two theme objects")
   4.       └─rlang::abort(...)
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
  add_pvalue 10.342  0.131  10.492

Package: ggprism
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘axes.Rmd’ using rmarkdown
  
  Quitting from axes.Rmd:37-48 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'axes.Rmd' failed with diagnostics:
  `%+replace%` requires two theme objects
  --- failed re-building ‘axes.Rmd’
  
  --- re-building ‘colours.Rmd’ using rmarkdown
  
  Quitting from colours.Rmd:43-52 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'colours.Rmd' failed with diagnostics:
  `%+replace%` requires two theme objects
  --- failed re-building ‘colours.Rmd’
  
  --- re-building ‘ggprism.Rmd’ using rmarkdown
  
  Quitting from ggprism.Rmd:44-59 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'ggprism.Rmd' failed with diagnostics:
  `%+replace%` requires two theme objects
  --- failed re-building ‘ggprism.Rmd’
  
  --- re-building ‘pvalues.Rmd’ using rmarkdown
  
  Quitting from pvalues.Rmd:65-74 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'pvalues.Rmd' failed with diagnostics:
  `%+replace%` requires two theme objects
  --- failed re-building ‘pvalues.Rmd’
  
  --- re-building ‘themes.Rmd’ using rmarkdown
  
  Quitting from themes.Rmd:52-67 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'themes.Rmd' failed with diagnostics:
  `%+replace%` requires two theme objects
  --- failed re-building ‘themes.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘axes.Rmd’ ‘colours.Rmd’ ‘ggprism.Rmd’ ‘pvalues.Rmd’ ‘themes.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggprism
Check: tests
New result: ERROR
    Running ‘tinytest.R’ [24s/24s]
  Running the tests in ‘tests/tinytest.R’ failed.
  Complete output:
    > 
    > if ( requireNamespace("tinytest", quietly=TRUE) ){
    +   tinytest::test_package("ggprism")
    + }
    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    0 tests    
    test-add_pvalue.R.............    1 tests OK 
    test-add_pvalue.R.............    2 tests OK 
    test-add_pvalue.R.............    2 tests OK 
    test-add_pvalue.R.............    3 tests OK 
    test-add_pvalue.R.............    3 tests OK 
    test-add_pvalue.R.............    3 tests OK 
    test-add_pvalue.R.............    4 tests OK 
    test-add_pvalue.R.............    4 tests OK 
    test-add_pvalue.R.............    4 tests OK 
    test-add_pvalue.R.............    5 tests OK 
    test-add_pvalue.R.............    5 tests OK 
    test-add_pvalue.R.............    5 tests OK 
    test-add_pvalue.R.............    6 tests OK 
    test-add_pvalue.R.............    6 tests OK 
    test-add_pvalue.R.............    6 tests OK 
    test-add_pvalue.R.............    6 tests OK 
    test-add_pvalue.R.............    7 tests OK 
    test-add_pvalue.R.............    7 tests OK 
    test-add_pvalue.R.............    7 tests OK 
    test-add_pvalue.R.............    8 tests OK 
    test-add_pvalue.R.............    8 tests OK 
    test-add_pvalue.R.............    8 tests OK 
    test-add_pvalue.R.............    9 tests OK 
    test-add_pvalue.R.............    9 tests OK 
    test-add_pvalue.R.............    9 tests OK 
    test-add_pvalue.R.............   10 tests OK 
    test-add_pvalue.R.............   10 tests OK 
    test-add_pvalue.R.............   10 tests OK 
    test-add_pvalue.R.............   11 tests OK 
    test-add_pvalue.R.............   11 tests OK 
    test-add_pvalue.R.............   12 tests OK 
    test-add_pvalue.R.............   12 tests OK 
    test-add_pvalue.R.............   13 tests OK 
    test-add_pvalue.R.............   13 tests OK 
    test-add_pvalue.R.............   13 tests OK 
    test-add_pvalue.R.............   14 tests OK 
    test-add_pvalue.R.............   14 tests OK 
    test-add_pvalue.R.............   14 tests OK 
    test-add_pvalue.R.............   15 tests OK 
    test-add_pvalue.R.............   15 tests OK 
    test-add_pvalue.R.............   16 tests OK 
    test-add_pvalue.R.............   16 tests OK 
    test-add_pvalue.R.............   16 tests OK 
    test-add_pvalue.R.............   17 tests OK 
    test-add_pvalue.R.............   17 tests OK 
    test-add_pvalue.R.............   18 tests OK 
    test-add_pvalue.R.............   18 tests OK 
    test-add_pvalue.R.............   19 tests OK 
    test-add_pvalue.R.............   19 tests OK 
    test-add_pvalue.R.............   20 tests OK 
    test-add_pvalue.R.............   20 tests OK 
    test-add_pvalue.R.............   21 tests OK 
    test-add_pvalue.R.............   21 tests OK 
    test-add_pvalue.R.............   22 tests OK 
    test-add_pvalue.R.............   22 tests OK 
    test-add_pvalue.R.............   23 tests OK 
    test-add_pvalue.R.............   23 tests OK 
    test-add_pvalue.R.............   23 tests OK 
    test-add_pvalue.R.............   24 tests OK 
    test-add_pvalue.R.............   25 tests OK 
    test-add_pvalue.R.............   25 tests OK 
    test-add_pvalue.R.............   25 tests OK 
    test-add_pvalue.R.............   26 tests OK 
    test-add_pvalue.R.............   27 tests OK 
    test-add_pvalue.R.............   27 tests OK 
    test-add_pvalue.R.............   27 tests OK 
    test-add_pvalue.R.............   28 tests OK 
    test-add_pvalue.R.............   29 tests OK 
    test-add_pvalue.R.............   29 tests OK 
    test-add_pvalue.R.............   29 tests OK 
    test-add_pvalue.R.............   30 tests OK 
    test-add_pvalue.R.............   31 tests OK 
    test-add_pvalue.R.............   31 tests OK 
    test-add_pvalue.R.............   31 tests OK 
    test-add_pvalue.R.............   32 tests OK 
    test-add_pvalue.R.............   33 tests OK 
    test-add_pvalue.R.............   33 tests OK 
    test-add_pvalue.R.............   33 tests OK 
    test-add_pvalue.R.............   34 tests OK 
    test-add_pvalue.R.............   35 tests OK 
    test-add_pvalue.R.............   35 tests OK 
    test-add_pvalue.R.............   36 tests OK 
    test-add_pvalue.R.............   36 tests OK 
    test-add_pvalue.R.............   37 tests OK 
    test-add_pvalue.R.............   37 tests OK 
    test-add_pvalue.R.............   38 tests OK 
    test-add_pvalue.R.............   38 tests OK 
    test-add_pvalue.R.............   39 tests OK 
    test-add_pvalue.R.............   39 tests OK 
    test-add_pvalue.R.............   40 tests OK 
    test-add_pvalue.R.............   40 tests OK 
    test-add_pvalue.R.............   40 tests OK 
    test-add_pvalue.R.............   41 tests OK 
    test-add_pvalue.R.............   41 tests OK 
    test-add_pvalue.R.............   41 tests OK 
    test-add_pvalue.R.............   42 tests OK 
    test-add_pvalue.R.............   42 tests OK 
    test-add_pvalue.R.............   43 tests OK 
    test-add_pvalue.R.............   43 tests OK 
    test-add_pvalue.R.............   44 tests OK 
    test-add_pvalue.R.............   44 tests OK 
    test-add_pvalue.R.............   45 tests OK 
    test-add_pvalue.R.............   46 tests OK 
    test-add_pvalue.R.............   47 tests OK 
    test-add_pvalue.R.............   47 tests OK 
    test-add_pvalue.R.............   47 tests OK 
    test-add_pvalue.R.............   47 tests OK 
    test-add_pvalue.R.............   47 tests OK 
    test-add_pvalue.R.............   48 tests OK 
    test-add_pvalue.R.............   49 tests OK 
    test-add_pvalue.R.............   50 tests OK 12.0s
    
    test-annotation_ticks.R.......    0 tests    
    test-annotation_ticks.R.......    0 tests    
    test-annotation_ticks.R.......    0 tests    
    test-annotation_ticks.R.......    1 tests OK 
    test-annotation_ticks.R.......    1 tests OK 
    test-annotation_ticks.R.......    2 tests OK 
    test-annotation_ticks.R.......    3 tests OK 
    test-annotation_ticks.R.......    4 tests OK 
    test-annotation_ticks.R.......    4 tests OK 
    test-annotation_ticks.R.......    4 tests OK 
    test-annotation_ticks.R.......    4 tests OK 
    test-annotation_ticks.R.......    5 tests OK 
    test-annotation_ticks.R.......    6 tests OK 
    test-annotation_ticks.R.......    7 tests OK 
    test-annotation_ticks.R.......    8 tests OK 
    test-annotation_ticks.R.......    9 tests OK 
    test-annotation_ticks.R.......   10 tests OK 
    test-annotation_ticks.R.......   11 tests OK 
    test-annotation_ticks.R.......   11 tests OK 
    test-annotation_ticks.R.......   12 tests OK 
    test-annotation_ticks.R.......   12 tests OK 
    test-annotation_ticks.R.......   13 tests OK 
    test-annotation_ticks.R.......   13 tests OK 
    test-annotation_ticks.R.......   14 tests OK 
    test-annotation_ticks.R.......   14 tests OK 
    test-annotation_ticks.R.......   15 tests OK 
    test-annotation_ticks.R.......   16 tests OK 
    test-annotation_ticks.R.......   16 tests OK 
    test-annotation_ticks.R.......   16 tests OK 
    test-annotation_ticks.R.......   17 tests OK 
    test-annotation_ticks.R.......   18 tests OK 
    test-annotation_ticks.R.......   19 tests OK 
    test-annotation_ticks.R.......   20 tests OK 
    test-annotation_ticks.R.......   21 tests OK 2.3s
    
    test-guide_prism_bracket.R....    0 tests    
    test-guide_prism_bracket.R....    0 tests    
    test-guide_prism_bracket.R....    0 tests    
    test-guide_prism_bracket.R....    0 tests    
    test-guide_prism_bracket.R....    0 tests    
    test-guide_prism_bracket.R....    1 tests OK 
    test-guide_prism_bracket.R....    2 tests OK 
    test-guide_prism_bracket.R....    2 tests OK 
    test-guide_prism_bracket.R....    2 tests OK 
    test-guide_prism_bracket.R....    3 tests OK 
    test-guide_prism_bracket.R....    3 tests OK 
    test-guide_prism_bracket.R....    3 tests OK 
    test-guide_prism_bracket.R....    4 tests OK 
    test-guide_prism_bracket.R....    5 tests OK 
    test-guide_prism_bracket.R....    5 tests OK 
    test-guide_prism_bracket.R....    5 tests OK 
    test-guide_prism_bracket.R....    6 tests OK 
    test-guide_prism_bracket.R....    6 tests OK 
    test-guide_prism_bracket.R....    6 tests OK 
    test-guide_prism_bracket.R....    7 tests OK 
    test-guide_prism_bracket.R....    8 tests OK 
    test-guide_prism_bracket.R....    8 tests OK 
    test-guide_prism_bracket.R....    8 tests OK 
    test-guide_prism_bracket.R....    8 tests OK 
    test-guide_prism_bracket.R....    8 tests OK 
    test-guide_prism_bracket.R....    9 tests OK 
    test-guide_prism_bracket.R....   10 tests OK 
    test-guide_prism_bracket.R....   10 tests OK 
    test-guide_prism_bracket.R....   10 tests OK 
    test-guide_prism_bracket.R....   10 tests OK 
    test-guide_prism_bracket.R....   10 tests OK 
    test-guide_prism_bracket.R....   11 tests OK 
    test-guide_prism_bracket.R....   11 tests OK 
    test-guide_prism_bracket.R....   12 tests OK 2.7s
    
    test-guide_prism_minor.R......    0 tests    
    test-guide_prism_minor.R......    0 tests    
    test-guide_prism_minor.R......    0 tests    
    test-guide_prism_minor.R......    0 tests    
    test-guide_prism_minor.R......    0 tests    
    test-guide_prism_minor.R......    1 tests OK 
    test-guide_prism_minor.R......    2 tests OK 
    test-guide_prism_minor.R......    2 tests OK 
    test-guide_prism_minor.R......    2 tests OK 
    test-guide_prism_minor.R......    3 tests OK 
    test-guide_prism_minor.R......    3 tests OK 
    test-guide_prism_minor.R......    3 tests OK 
    test-guide_prism_minor.R......    4 tests OK 
    test-guide_prism_minor.R......    5 tests OK 
    test-guide_prism_minor.R......    5 tests OK 
    test-guide_prism_minor.R......    5 tests OK 
    test-guide_prism_minor.R......    6 tests OK 
    test-guide_prism_minor.R......    6 tests OK 
    test-guide_prism_minor.R......    7 tests OK 
    test-guide_prism_minor.R......    7 tests OK 
    test-guide_prism_minor.R......    8 tests OK 
    test-guide_prism_minor.R......    8 tests OK 
    test-guide_prism_minor.R......    8 tests OK 
    test-guide_prism_minor.R......    9 tests OK 
    test-guide_prism_minor.R......   10 tests OK 1.4s
    
    test-guide_prism_offset.R.....    0 tests    
    test-guide_prism_offset.R.....    0 tests    
    test-guide_prism_offset.R.....    0 tests    
    test-guide_prism_offset.R.....    0 tests    
    test-guide_prism_offset.R.....    0 tests    
    test-guide_prism_offset.R.....    1 tests OK 
    test-guide_prism_offset.R.....    2 tests OK 
    test-guide_prism_offset.R.....    2 tests OK 
    test-guide_prism_offset.R.....    2 tests OK 
    test-guide_prism_offset.R.....    3 tests OK 
    test-guide_prism_offset.R.....    3 tests OK 
    test-guide_prism_offset.R.....    3 tests OK 
    test-guide_prism_offset.R.....    4 tests OK 
    test-guide_prism_offset.R.....    5 tests OK 
    test-guide_prism_offset.R.....    5 tests OK 
    test-guide_prism_offset.R.....    5 tests OK 
    test-guide_prism_offset.R.....    6 tests OK 
    test-guide_prism_offset.R.....    6 tests OK 
    test-guide_prism_offset.R.....    6 tests OK 
    test-guide_prism_offset.R.....    7 tests OK 
    test-guide_prism_offset.R.....    8 tests OK 
    test-guide_prism_offset.R.....    8 tests OK 
    test-guide_prism_offset.R.....    8 tests OK 
    test-guide_prism_offset.R.....    9 tests OK 1.9s
    
    test-guide_prism_offset_minor.R    0 tests    
    test-guide_prism_offset_minor.R    0 tests    
    test-guide_prism_offset_minor.R    0 tests    
    test-guide_prism_offset_minor.R    0 tests    
    test-guide_prism_offset_minor.R    0 tests    
    test-guide_prism_offset_minor.R    1 tests OK 
    test-guide_prism_offset_minor.R    2 tests OK 
    test-guide_prism_offset_minor.R    2 tests OK 
    test-guide_prism_offset_minor.R    2 tests OK 
    test-guide_prism_offset_minor.R    3 tests OK 
    test-guide_prism_offset_minor.R    3 tests OK 
    test-guide_prism_offset_minor.R    3 tests OK 
    test-guide_prism_offset_minor.R    4 tests OK 
    test-guide_prism_offset_minor.R    5 tests OK 
    test-guide_prism_offset_minor.R    5 tests OK 
    test-guide_prism_offset_minor.R    5 tests OK 
    test-guide_prism_offset_minor.R    6 tests OK 
    test-guide_prism_offset_minor.R    6 tests OK 
    test-guide_prism_offset_minor.R    7 tests OK 
    test-guide_prism_offset_minor.R    7 tests OK 
    test-guide_prism_offset_minor.R    8 tests OK 
    test-guide_prism_offset_minor.R    8 tests OK 
    test-guide_prism_offset_minor.R    8 tests OK 
    test-guide_prism_offset_minor.R    9 tests OK 
    test-guide_prism_offset_minor.R   10 tests OK 1.8s
    
    test-preview_theme.R..........    0 tests    
    test-preview_theme.R..........    1 tests OK Error in `parent %+replace% t`:
    ! `%+replace%` requires two theme objects
    Backtrace:
         ▆
      1. └─tinytest::test_package("ggprism")
      2.   └─tinytest::run_test_dir(...)
      3.     └─base::lapply(...)
      4.       └─tinytest (local) FUN(X[[i]], ...)
      5.         └─base::eval(expr, envir = e)
      6.           └─base::eval(expr, envir = e)
      7.             └─ggprism::preview_theme("floral")
      8.               └─ggprism::theme_prism(palette = palette)
      9.                 └─parent %+replace% t
     10.                   └─cli::cli_abort("{.code %+replace%} requires two theme objects")
     11.                     └─rlang::abort(...)
    Warning messages:
    1: `aes_string()` was deprecated in ggplot2 3.0.0.
    ℹ Please use tidy evaluation idioms with `aes()`.
    ℹ See also `vignette("ggplot2-in-packages")` for more information.
    ℹ The deprecated feature was likely used in the ggprism package.
      Please report the issue at <https://github.com/csdaw/ggprism/issues>. 
    2: The S3 guide system was deprecated in ggplot2 3.5.0.
    ℹ It has been replaced by a ggproto system that can be extended. 
    3: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
    ℹ Please use the `linewidth` argument instead.
    ℹ The deprecated feature was likely used in the ggprism package.
      Please report the issue at <https://github.com/csdaw/ggprism/issues>. 
    4: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
    ℹ Please use the `linewidth` argument instead.
    ℹ The deprecated feature was likely used in the ggprism package.
      Please report the issue at <https://github.com/csdaw/ggprism/issues>. 
    Execution halted

Package: ggraph
Check: examples
New result: ERROR
  Running examples in ‘ggraph-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: geom_conn_bundle
  > ### Title: Create hierarchical edge bundles between node connections
  > ### Aliases: geom_conn_bundle geom_conn_bundle2 geom_conn_bundle0
  > 
  > ### ** Examples
  > 
  > # Create a graph of the flare class system
  > library(tidygraph)
  
  Attaching package: ‘tidygraph’
  
  The following object is masked from ‘package:stats’:
  
      filter
  
  > flareGraph <- tbl_graph(flare$vertices, flare$edges) %>%
  +   mutate(
  +     class = map_bfs_chr(node_is_root(), .f = function(node, dist, path, ...) {
  +       if (dist <= 1) {
  +         return(shortName[node])
  +       }
  +       path$result[[nrow(path)]]
  +     })
  +   )
  > importFrom <- match(flare$imports$from, flare$vertices$name)
  > importTo <- match(flare$imports$to, flare$vertices$name)
  > 
  > # Use class inheritance for layout but plot class imports as bundles
  > ggraph(flareGraph, 'dendrogram', circular = TRUE) +
  +   geom_conn_bundle(aes(colour = after_stat(index)),
  +     data = get_con(importFrom, importTo),
  +     edge_alpha = 0.25
  +   ) +
  +   geom_node_point(aes(filter = leaf, colour = class)) +
  +   scale_edge_colour_distiller('', direction = 1, guide = 'edge_direction') +
  +   coord_fixed() +
  +   ggforce::theme_no_axes()
  Error in get_layer_key(...) : 
    unused argument (list(<object>, <object>, <object>, <object>, <object>, <object>, <object>, 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, <object>, <object>, <object>, NULL, <object>, NULL, <object>, <object>, <object>, <object>, NULL, <object>, NULL, <object>, NULL, <object>, <object>, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, <object>, NULL, NULL, NULL, NULL, NULL, NULL, 
      NULL, NULL, <object>, NULL, 2, NULL, NULL, NULL, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, <object>, NULL, <object>, NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), <object>, 2, <object>, <object>, NULL, NULL, NULL, <object>, NULL, <object>, NULL, NULL, NULL, NULL, FALSE, NULL, NULL, <object>, <object>, "panel", <object>, <object>, "panel", <object>, "topleft", NULL, NULL, <object>, NULL, N
  Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> process_layers -> <Anonymous>
  Execution halted

Package: ggraph
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Edges.Rmd’ using rmarkdown
  
  Quitting from Edges.Rmd:318-322 [unnamed-chunk-20]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `get_layer_key()`:
  ! unused argument (list(<object>, <object>, <object>, <object>, <object>, <object>, <object>, 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, <object>, <object>, <object>, NULL, <object>, NULL, <object>, <object>, <object>, <object>, NULL, <object>, NULL, <object>, NULL, <object>, <object>, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, <object>, NULL, NULL, NULL, NULL, NULL, NULL, 
      NULL, NULL, <object>, NULL, 2, NULL, NULL, <object>, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, <object>, NULL, <object>, NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), <object>, 2, <object>, <object>, NULL, NULL, NULL, <object>, NULL, <object>, NULL, NULL, NULL, NULL, FALSE, NULL, NULL, <object>, <object>, "panel", <object>, <object>, "panel", <object>, "topleft", NULL, c(1, 1, 1, 1), <object>, NULL, NULL, "on", 
      "inside", <object>, NULL, NULL, NULL, <object>, <object>, NULL, 2.75, 2.75, <object>, <object>, <object>))
  ---
  Backtrace:
       ▆
    1. └─tools:::.buildOneVignette(...)
    2.   ├─base::tryCatch(...)
    3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    6.   └─engine$weave(file, quiet = quiet, encoding = enc)
    7.     └─knitr:::vweave_rmarkdown(...)
    8.       └─rmarkdown::render(...)
    9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
   10.           └─knitr:::process_file(text, output)
   11.             ├─xfun:::handle_error(...)
   12.             ├─base::withCallingHandlers(...)
   13.             └─knitr:::process_group(group)
   14.               └─knitr:::call_block(x)
   15.                 └─knitr:::block_exec(params)
   16.                   └─knitr:::eng_r(options)
   17.                     ├─knitr:::in_input_dir(...)
   18.                     │ └─knitr:::in_dir(input_dir(), expr)
   19.                     └─knitr (local) evaluate(...)
   20.                       └─evaluate::evaluate(...)
   21.                         ├─base::withRestarts(...)
   22.                         │ └─base (local) withRestartList(expr, restarts)
   23.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
   24.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
   25.                         │   └─base (local) withRestartList(expr, restarts[-nr])
   26.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
   27.                         │       └─base (local) doWithOneRestart(return(expr), restart)
   28.                         ├─evaluate:::with_handlers(...)
   29.                         │ ├─base::eval(call)
   30.                         │ │ └─base::eval(call)
   31.                         │ └─base::withCallingHandlers(...)
   32.                         └─watcher$print_value(ev$value, ev$visible, envir)
   33.                           ├─base::withVisible(handle_value(handler, value, visible, envir))
   34.                           └─evaluate:::handle_value(handler, value, visible, envir)
   35.                             └─handler$value(value, visible)
   36.                               └─knitr (local) fun(x, options = options)
   37.                                 ├─base::withVisible(knit_print(x, ...))
   38.                                 ├─knitr::knit_print(x, ...)
   39.                                 └─knitr:::knit_print.default(x, ...)
   40.                                   └─knitr::normal_print(x)
   41.                                     ├─base::print(x)
   42.                                     └─ggplot2 (local) `print.ggplot2::ggplot`(x)
   43.                                       ├─ggplot2::ggplot_build(x)
   44.                                       ├─ggraph:::ggplot_build.ggraph(x)
   45.                                       ├─base::NextMethod()
   46.                                       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
   47.                                         └─plot@guides$build(npscales, plot@layers, plot@labels, data, plot@theme)
   48.                                           └─ggplot2 (local) build(..., self = self)
   49.                                             └─guides$process_layers(layers, layer_data, theme)
   50.                                               └─ggplot2 (local) process_layers(..., self = self)
   51.                                                 └─base::Map(...)
   52.                                                   └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
   53.                                                     └─ggplot2 (local) `<fn>`(guide = dots[[1L]][[1L]], param = dots[[2L]][[1L]])
   54.                                                       └─guide$process_layers(param, layers, data, theme)
   55.                                                         └─ggplot2 (local) process_layers(..., self = self)
   56.                                                           └─self$get_layer_key(params, layers[include], data[include], theme)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Edges.Rmd' failed with diagnostics:
  unused argument (list(<object>, <object>, <object>, <object>, <object>, <object>, <object>, 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, <object>, <object>, <object>, NULL, <object>, NULL, <object>, <object>, <object>, <object>, NULL, <object>, NULL, <object>, NULL, <object>, <object>, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.5, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.75, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, <object>, NULL, NULL, NULL, NULL, NULL, NULL, 
      NULL, NULL, <object>, NULL, 2, NULL, NULL, <object>, 1.2, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0.2, NULL, <object>, NULL, <object>, NULL, "right", NULL, NULL, NULL, "center", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, c(0, 0, 0, 0), <object>, 2, <object>, <object>, NULL, NULL, NULL, <object>, NULL, <object>, NULL, NULL, NULL, NULL, FALSE, NULL, NULL, <object>, <object>, "panel", <object>, <object>, "panel", <object>, "topleft", NULL, c(1, 1, 1, 1), <object>, NULL, NULL, "on", 
      "inside", <object>, NULL, NULL, NULL, <object>, <object>, NULL, 2.75, 2.75, <object>, <object>, <object>))
  --- failed re-building ‘Edges.Rmd’
  
  --- re-building ‘Layouts.Rmd’ using rmarkdown
  --- finished re-building ‘Layouts.Rmd’
  
  --- re-building ‘Nodes.Rmd’ using rmarkdown
  --- finished re-building ‘Nodes.Rmd’
  
  --- re-building ‘tidygraph.Rmd’ using rmarkdown
  --- finished re-building ‘tidygraph.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Edges.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggraph
Check: S3 generic/method consistency
New result: WARNING
  ggplot_build:
    function(plot, ...)
  ggplot_build.ggraph:
    function(plot)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: ggResidpanel
Check: examples
New result: ERROR
  Running examples in ‘ggResidpanel-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: resid_panel
  > ### Title: Panel of Diagnostic Residual Plots.
  > ### Aliases: resid_panel
  > 
  > ### ** Examples
  > 
  > 
  > # Fit a model to the penguin data
  > penguin_model <- lme4::lmer(heartrate ~ depth + duration + (1|bird), data = penguins)
  > 
  > # Create the default panel
  > resid_panel(penguin_model)
  > 
  > # Select all plots to include in the panel and set the smoother option to TRUE
  > resid_panel(penguin_model, plots = "all", smoother = TRUE)
  `geom_smooth()` using formula = 'y ~ x'
  `geom_smooth()` using formula = 'y ~ x'
  > 
  > # Select only the residual plot and qq-plot to be included in the panel,
  > # request confidence bands on the qq plot, and set the number of rows to 2
  > resid_panel(penguin_model, plots = c("resid", "qq"), qqbands = TRUE, nrow = 2)
  Error in `stat_qq_band()`:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  Backtrace:
       ▆
    1. ├─ggResidpanel::resid_panel(...)
    2. │ ├─base::suppressWarnings(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ └─cowplot::plot_grid(...)
    5. │   └─cowplot::align_plots(...)
    6. │     └─base::lapply(...)
    7. │       └─cowplot (local) FUN(X[[i]], ...)
    8. │         ├─cowplot::as_gtable(x)
    9. │         └─cowplot:::as_gtable.default(x)
   10. │           ├─cowplot::as_grob(plot)
   11. │           └─cowplot:::as_grob.ggplot(plot)
   12. │             └─ggplot2::ggplotGrob(plot)
   13. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
   14. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
   15. │                 └─ggplot2:::by_layer(...)
   16. │                   ├─rlang::try_fetch(...)
   17. │                   │ ├─base::tryCatch(...)
   18. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   19. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   20. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   21. │                   │ └─base::withCallingHandlers(...)
   22. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   23. │                     └─l$draw_geom(d, layout)
   24. │                       └─ggplot2 (local) draw_geom(..., self = self)
   25. │                         └─self$geom$draw_layer(...)
   26. │                           └─ggplot2 (local) draw_layer(..., self = self)
   27. │                             └─base::lapply(...)
   28. │                               └─ggplot2 (local) FUN(X[[i]], ...)
   29. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   30. │                                 └─self$draw_panel(data, panel_params, coord)
   31. │                                   └─ggplot2 (local) draw_panel(..., self = self)
   32. │                                     └─base::lapply(...)
   33. │                                       └─ggplot2 (local) FUN(X[[i]], ...)
   34. │                                         └─self$draw_group(group, panel_params, coord, ...)
   35. │                                           └─ggplot2 (local) draw_group(...)
   36. │                                             └─ggplot2 (local) draw_group(..., self = self)
   37. └─base::.handleSimpleError(...)
   38.   └─rlang (local) h(simpleError(msg, call))
   39.     └─handlers[[1L]](cnd)
   40.       └─cli::cli_abort(...)
   41.         └─rlang::abort(...)
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
  resid_interact 9.290  0.247   9.691
  resid_compare  6.597  0.325   6.960

Package: ggResidpanel
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘introduction.Rmd’ using rmarkdown
  
  Quitting from introduction.Rmd:219-227 [unnamed-chunk-16]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'introduction.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  --- failed re-building ‘introduction.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘introduction.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggResidpanel
Check: tests
New result: ERROR
    Running ‘testthat.R’ [43s/43s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggResidpanel)
    
    Attaching package: 'ggResidpanel'
    
    The following object is masked from 'package:datasets':
    
        penguins
    
    > 
    > test_check("ggResidpanel")
    [ FAIL 1 | WARN 4 | SKIP 9 | PASS 18 ]
    
    ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
    • On CRAN (9): 'test-resid_panel.R:113:3', 'test-resid_panel.R:133:3',
      'test-resid_panel.R:148:3', 'test-resid_panel.R:163:3',
      'test-resid_panel.R:178:3', 'test-resid_panel.R:191:3',
      'test-resid_panel.R:201:3', 'test-resid_panel.R:219:3',
      'test-resid_panel.R:240:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-resid_panel.R:79:3'): formatting options ───────────────────────
    Error in `stat_qq_band()`: Problem while converting geom to grob.
    ℹ Error occurred in the 1st layer.
    Caused by error in `check_linewidth()`:
    ! could not find function "check_linewidth"
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-resid_panel.R:79:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   └─vdiffr:::print_plot(plot, title)
      4. ├─ggResidpanel::resid_panel(...)
      5. │ ├─base::suppressWarnings(...)
      6. │ │ └─base::withCallingHandlers(...)
      7. │ └─cowplot::plot_grid(...)
      8. │   └─cowplot::align_plots(...)
      9. │     └─base::lapply(...)
     10. │       └─cowplot (local) FUN(X[[i]], ...)
     11. │         ├─cowplot::as_gtable(x)
     12. │         └─cowplot:::as_gtable.default(x)
     13. │           ├─cowplot::as_grob(plot)
     14. │           └─cowplot:::as_grob.ggplot(plot)
     15. │             └─ggplot2::ggplotGrob(plot)
     16. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     17. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     18. │                 └─ggplot2:::by_layer(...)
     19. │                   ├─rlang::try_fetch(...)
     20. │                   │ ├─base::tryCatch(...)
     21. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     22. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     23. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     24. │                   │ └─base::withCallingHandlers(...)
     25. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     26. │                     └─l$draw_geom(d, layout)
     27. │                       └─ggplot2 (local) draw_geom(..., self = self)
     28. │                         └─self$geom$draw_layer(...)
     29. │                           └─ggplot2 (local) draw_layer(..., self = self)
     30. │                             └─base::lapply(...)
     31. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     32. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     33. │                                 └─self$draw_panel(data, panel_params, coord)
     34. │                                   └─ggplot2 (local) draw_panel(..., self = self)
     35. │                                     └─base::lapply(...)
     36. │                                       └─ggplot2 (local) FUN(X[[i]], ...)
     37. │                                         └─self$draw_group(group, panel_params, coord, ...)
     38. │                                           └─ggplot2 (local) draw_group(...)
     39. │                                             └─ggplot2 (local) draw_group(..., self = self)
     40. └─base::.handleSimpleError(...)
     41.   └─rlang (local) h(simpleError(msg, call))
     42.     └─handlers[[1L]](cnd)
     43.       └─cli::cli_abort(...)
     44.         └─rlang::abort(...)
    
    [ FAIL 1 | WARN 4 | SKIP 9 | PASS 18 ]
    Error: Test failures
    Execution halted

Package: ggRtsy
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Vignette.Rmd’ using rmarkdown
  
  Quitting from Vignette.Rmd:47-49 [unnamed-chunk-2]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
  Can't extract rows past the end.
  ℹ Location 1 doesn't exist.
  ℹ There are only 0 rows.
  --- failed re-building ‘Vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggRtsy
Check: tests
New result: ERROR
    Running ‘testthat.R’ [3s/3s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggplot2)
    > library(dplyr)
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    > 
    > library(ggRtsy)
    > 
    > test_check("ggRtsy")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-RectangleFiller.R:7:3'): Rectangle Filler works ────────────────
    <vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
    Error in `data[[1, 1]]`: Can't extract rows past the end.
    i Location 1 doesn't exist.
    i There are only 0 rows.
    Backtrace:
         ▆
      1. ├─ggRtsy::RectangleFiller(...) at test-RectangleFiller.R:7:3
      2. │ ├─data[[1, 1]]
      3. │ └─tibble:::`[[.tbl_df`(data, 1, 1)
      4. │   └─tibble:::vectbl_as_row_location2(i, fast_nrow(x), i_arg)
      5. │     ├─tibble:::subclass_row_index_errors(...)
      6. │     │ └─base::withCallingHandlers(...)
      7. │     └─vctrs::vec_as_location2(i, n, call = call)
      8. │       ├─vctrs:::result_get(...)
      9. │       └─vctrs:::vec_as_location2_result(...)
     10. │         ├─base::tryCatch(...)
     11. │         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     12. │         │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     13. │         │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     14. │         └─vctrs::vec_as_location(i, n, names = names, arg = arg, call = call)
     15. └─vctrs (local) `<fn>`()
     16.   └─vctrs:::stop_subscript_oob(...)
     17.     └─vctrs:::stop_subscript(...)
     18.       └─rlang::abort(...)
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
    Error: Test failures
    Execution halted

Package: ggside
Check: examples
New result: ERROR
  Running examples in ‘ggside-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: geom_xsidebar
  > ### Title: Side bar Charts
  > ### Aliases: geom_xsidebar geom_*sidebar geom_ysidebar geom_xsidecol
  > ###   geom_ysidecol
  > 
  > ### ** Examples
  > 
  > 
  > p <-ggplot(iris, aes(Sepal.Width, Sepal.Length, color = Species, fill = Species)) +
  + geom_point()
  > 
  > #sidebar - uses StatCount
  > p +
  + geom_xsidebar() +
  + geom_ysidebar()
  Error in `geom_bar()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `setup_params()`:
  ! `stat_xsidecount()` must only have an x or y aesthetic.
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. └─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3.   ├─ggplot2::ggplot_build(x)
    4.   └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    5.     └─ggplot2:::by_layer(...)
    6.       ├─rlang::try_fetch(...)
    7.       │ ├─base::tryCatch(...)
    8.       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11.       │ └─base::withCallingHandlers(...)
   12.       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13.         └─l$compute_statistic(d, layout)
   14.           └─ggside (local) compute_statistic(..., self = self)
   15.             └─ggplot2 (local) ggproto_parent_method(self = self, data = data, layout = layout)
   16.               └─self$stat$setup_params(data, self$stat_params)
   17.                 └─ggplot2 (local) setup_params(..., self = self)
   18.                   └─cli::cli_abort("{.fn {snake_class(self)}} must only have an {.field x} {.emph or} {.field y} aesthetic.")
   19.                     └─rlang::abort(...)
  Execution halted

Package: ggside
Check: for code/documentation mismatches
New result: WARNING
  Codoc mismatches from Rd file 'geom_xsideabline.Rd':
  geom_xsidehline
    Code: function(mapping = NULL, data = NULL, position = "identity",
                   ..., yintercept, na.rm = FALSE, show.legend = NA)
    Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm =
                   FALSE, show.legend = NA)
    Argument names in code not in docs:
      position
    Mismatches in argument names (first 3):
      Position: 3 Code: position Docs: ...
      Position: 4 Code: ... Docs: yintercept
      Position: 5 Code: yintercept Docs: na.rm
  geom_ysidehline
    Code: function(mapping = NULL, data = NULL, position = "identity",
                   ..., yintercept, na.rm = FALSE, show.legend = NA)
    Docs: function(mapping = NULL, data = NULL, ..., yintercept, na.rm =
                   FALSE, show.legend = NA)
    Argument names in code not in docs:
      position
    Mismatches in argument names (first 3):
      Position: 3 Code: position Docs: ...
      Position: 4 Code: ... Docs: yintercept
      Position: 5 Code: yintercept Docs: na.rm
  geom_xsidevline
    Code: function(mapping = NULL, data = NULL, position = "identity",
                   ..., xintercept, na.rm = FALSE, show.legend = NA)
    Docs: function(mapping = NULL, data = NULL, ..., xintercept, na.rm =
                   FALSE, show.legend = NA)
    Argument names in code not in docs:
      position
    Mismatches in argument names (first 3):
      Position: 3 Code: position Docs: ...
      Position: 4 Code: ... Docs: xintercept
      Position: 5 Code: xintercept Docs: na.rm
  geom_ysidevline
    Code: function(mapping = NULL, data = NULL, position = "identity",
                   ..., xintercept, na.rm = FALSE, show.legend = NA)
    Docs: function(mapping = NULL, data = NULL, ..., xintercept, na.rm =
                   FALSE, show.legend = NA)
    Argument names in code not in docs:
      position
    Mismatches in argument names (first 3):
      Position: 3 Code: position Docs: ...
      Position: 4 Code: ... Docs: xintercept
      Position: 5 Code: xintercept Docs: na.rm
  
  Codoc mismatches from Rd file 'geom_xsidebar.Rd':
  geom_xsidebar
    Code: function(mapping = NULL, data = NULL, stat = "count", position
                   = "stack", ..., just = 0.5, lineend = "butt", linejoin
                   = "mitre", na.rm = FALSE, show.legend = NA,
                   inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "count", position
                   = "stack", ..., just = 0.5, width = NULL, na.rm =
                   FALSE, orientation = "x", show.legend = NA,
                   inherit.aes = TRUE)
    Argument names in code not in docs:
      lineend linejoin
    Argument names in docs not in code:
      width orientation
    Mismatches in argument names:
      Position: 7 Code: lineend Docs: width
      Position: 8 Code: linejoin Docs: na.rm
      Position: 9 Code: na.rm Docs: orientation
  geom_ysidebar
    Code: function(mapping = NULL, data = NULL, stat = "count", position
                   = "stack", ..., just = 0.5, lineend = "butt", linejoin
                   = "mitre", na.rm = FALSE, show.legend = NA,
                   inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "count", position
                   = "stack", ..., just = 0.5, width = NULL, na.rm =
                   FALSE, orientation = "y", show.legend = NA,
                   inherit.aes = TRUE)
    Argument names in code not in docs:
      lineend linejoin
    Argument names in docs not in code:
      width orientation
    Mismatches in argument names:
      Position: 7 Code: lineend Docs: width
      Position: 8 Code: linejoin Docs: na.rm
      Position: 9 Code: na.rm Docs: orientation
  geom_xsidecol
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "stack", ..., just = 0.5, lineend = "butt",
                   linejoin = "mitre", na.rm = FALSE, show.legend = NA,
                   inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, position = "stack", ...,
                   just = 0.5, width = NULL, na.rm = FALSE, show.legend =
                   NA, inherit.aes = TRUE)
    Argument names in code not in docs:
      stat lineend linejoin
    Argument names in docs not in code:
      width
    Mismatches in argument names (first 3):
      Position: 3 Code: stat Docs: position
      Position: 4 Code: position Docs: ...
      Position: 5 Code: ... Docs: just
  geom_ysidecol
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "stack", ..., just = 0.5, lineend = "butt",
                   linejoin = "mitre", na.rm = FALSE, show.legend = NA,
                   inherit.aes = TRUE, orientation = "y")
    Docs: function(mapping = NULL, data = NULL, position = "stack", ...,
                   just = 0.5, width = NULL, na.rm = FALSE, show.legend =
                   NA, inherit.aes = TRUE, orientation = "y")
    Argument names in code not in docs:
      stat lineend linejoin
    Argument names in docs not in code:
      width
    Mismatches in argument names (first 3):
      Position: 3 Code: stat Docs: position
      Position: 4 Code: position Docs: ...
      Position: 5 Code: ... Docs: just
  
  Codoc mismatches from Rd file 'geom_xsideboxplot.Rd':
  geom_xsideboxplot
    Code: function(mapping = NULL, data = NULL, stat = "boxplot",
                   position = "dodge2", ..., outliers = TRUE,
                   outlier.colour = NULL, outlier.color = NULL,
                   outlier.fill = NULL, outlier.shape = NULL,
                   outlier.size = NULL, outlier.stroke = 0.5,
                   outlier.alpha = NULL, whisker.colour = NULL,
                   whisker.color = NULL, whisker.linetype = NULL,
                   whisker.linewidth = NULL, staple.colour = NULL,
                   staple.color = NULL, staple.linetype = NULL,
                   staple.linewidth = NULL, median.colour = NULL,
                   median.color = NULL, median.linetype = NULL,
                   median.linewidth = NULL, box.colour = NULL, box.color
                   = NULL, box.linetype = NULL, box.linewidth = NULL,
                   notch = FALSE, notchwidth = 0.5, staplewidth = 0,
                   varwidth = FALSE, na.rm = FALSE, orientation = "x",
                   show.legend = NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "boxplot",
                   position = "dodge2", ..., outliers = TRUE,
                   outlier.colour = NULL, outlier.color = NULL,
                   outlier.fill = NULL, outlier.shape = 19, outlier.size
                   = 1.5, outlier.stroke = 0.5, outlier.alpha = NULL,
                   notch = FALSE, notchwidth = 0.5, staplewidth = 0,
                   varwidth = FALSE, na.rm = FALSE, orientation = "x",
                   show.legend = NA, inherit.aes = TRUE)
    Argument names in code not in docs:
      whisker.colour whisker.color whisker.linetype whisker.linewidth
      staple.colour staple.color staple.linetype staple.linewidth
      median.colour median.color median.linetype median.linewidth
      box.colour box.color box.linetype box.linewidth
    Mismatches in argument names (first 3):
      Position: 14 Code: whisker.colour Docs: notch
      Position: 15 Code: whisker.color Docs: notchwidth
      Position: 16 Code: whisker.linetype Docs: staplewidth
    Mismatches in argument default values:
      Name: 'outlier.shape' Code: NULL Docs: 19
      Name: 'outlier.size' Code: NULL Docs: 1.5
  geom_ysideboxplot
    Code: function(mapping = NULL, data = NULL, stat = "boxplot",
                   position = "dodge2", ..., outliers = TRUE,
                   outlier.colour = NULL, outlier.color = NULL,
                   outlier.fill = NULL, outlier.shape = NULL,
                   outlier.size = NULL, outlier.stroke = 0.5,
                   outlier.alpha = NULL, whisker.colour = NULL,
                   whisker.color = NULL, whisker.linetype = NULL,
                   whisker.linewidth = NULL, staple.colour = NULL,
                   staple.color = NULL, staple.linetype = NULL,
                   staple.linewidth = NULL, median.colour = NULL,
                   median.color = NULL, median.linetype = NULL,
                   median.linewidth = NULL, box.colour = NULL, box.color
                   = NULL, box.linetype = NULL, box.linewidth = NULL,
                   notch = FALSE, notchwidth = 0.5, staplewidth = 0,
                   varwidth = FALSE, na.rm = FALSE, orientation = "y",
                   show.legend = NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "boxplot",
                   position = "dodge2", ..., outliers = TRUE,
                   outlier.colour = NULL, outlier.color = NULL,
                   outlier.fill = NULL, outlier.shape = 19, outlier.size
                   = 1.5, outlier.stroke = 0.5, outlier.alpha = NULL,
                   notch = FALSE, notchwidth = 0.5, staplewidth = 0,
                   varwidth = FALSE, na.rm = FALSE, orientation = "y",
                   show.legend = NA, inherit.aes = TRUE)
    Argument names in code not in docs:
      whisker.colour whisker.color whisker.linetype whisker.linewidth
      staple.colour staple.color staple.linetype staple.linewidth
      median.colour median.color median.linetype median.linewidth
      box.colour box.color box.linetype box.linewidth
    Mismatches in argument names (first 3):
      Position: 14 Code: whisker.colour Docs: notch
      Position: 15 Code: whisker.color Docs: notchwidth
      Position: 16 Code: whisker.linetype Docs: staplewidth
    Mismatches in argument default values:
      Name: 'outlier.shape' Code: NULL Docs: 19
      Name: 'outlier.size' Code: NULL Docs: 1.5
  
  Codoc mismatches from Rd file 'geom_xsidedensity.Rd':
  geom_xsidedensity
    Code: function(mapping = NULL, data = NULL, stat = "density",
                   position = "identity", ..., outline.type = "upper",
                   lineend = "butt", linejoin = "round", linemitre = 10,
                   na.rm = FALSE, show.legend = NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "density",
                   position = "identity", ..., na.rm = FALSE, orientation
                   = "x", show.legend = NA, inherit.aes = TRUE,
                   outline.type = "upper")
    Argument names in code not in docs:
      lineend linejoin linemitre
    Argument names in docs not in code:
      orientation
    Mismatches in argument names (first 3):
      Position: 6 Code: outline.type Docs: na.rm
      Position: 7 Code: lineend Docs: orientation
      Position: 8 Code: linejoin Docs: show.legend
  geom_ysidedensity
    Code: function(mapping = NULL, data = NULL, stat = "density",
                   position = "identity", ..., outline.type = "upper",
                   lineend = "butt", linejoin = "round", linemitre = 10,
                   na.rm = FALSE, show.legend = NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "density",
                   position = "identity", ..., na.rm = FALSE, orientation
                   = "y", show.legend = NA, inherit.aes = TRUE,
                   outline.type = "upper")
    Argument names in code not in docs:
      lineend linejoin linemitre
    Argument names in docs not in code:
      orientation
    Mismatches in argument names (first 3):
      Position: 6 Code: outline.type Docs: na.rm
      Position: 7 Code: lineend Docs: orientation
      Position: 8 Code: linejoin Docs: show.legend
  
  Codoc mismatches from Rd file 'geom_xsidefunction.Rd':
  geom_xsidefunction
    Code: function(mapping = NULL, data = NULL, stat = "function",
                   position = "identity", ..., arrow = NULL, arrow.fill =
                   NULL, lineend = "butt", linejoin = "round", linemitre
                   = 10, na.rm = FALSE, show.legend = NA, inherit.aes =
                   TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "function",
                   position = "identity", ..., na.rm = FALSE, show.legend
                   = NA, inherit.aes = TRUE)
    Argument names in code not in docs:
      arrow arrow.fill lineend linejoin linemitre
    Mismatches in argument names:
      Position: 6 Code: arrow Docs: na.rm
      Position: 7 Code: arrow.fill Docs: show.legend
      Position: 8 Code: lineend Docs: inherit.aes
  
  Codoc mismatches from Rd file 'geom_xsidehistogram.Rd':
  geom_xsidehistogram
    Code: function(mapping = NULL, data = NULL, stat = "bin", position =
                   "stack", ..., binwidth = NULL, bins = NULL,
                   orientation = "x", lineend = "butt", linejoin =
                   "mitre", na.rm = FALSE, show.legend = NA, inherit.aes
                   = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "bin", position =
                   "stack", ..., binwidth = NULL, bins = NULL, na.rm =
                   FALSE, orientation = "x", show.legend = NA,
                   inherit.aes = TRUE)
    Argument names in code not in docs:
      lineend linejoin
    Mismatches in argument names (first 3):
      Position: 8 Code: orientation Docs: na.rm
      Position: 9 Code: lineend Docs: orientation
      Position: 10 Code: linejoin Docs: show.legend
  geom_ysidehistogram
    Code: function(mapping = NULL, data = NULL, stat = "bin", position =
                   "stack", ..., binwidth = NULL, bins = NULL,
                   orientation = "y", lineend = "butt", linejoin =
                   "mitre", na.rm = FALSE, show.legend = NA, inherit.aes
                   = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "bin", position =
                   "stack", ..., binwidth = NULL, bins = NULL, na.rm =
                   FALSE, orientation = "y", show.legend = NA,
                   inherit.aes = TRUE)
    Argument names in code not in docs:
      lineend linejoin
    Mismatches in argument names (first 3):
      Position: 8 Code: orientation Docs: na.rm
      Position: 9 Code: lineend Docs: orientation
      Position: 10 Code: linejoin Docs: show.legend
  
  Codoc mismatches from Rd file 'geom_xsidelabel.Rd':
  geom_xsidelabel
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "nudge", ..., parse = FALSE, label.padding
                   = unit(0.25, "lines"), label.r = unit(0.15, "lines"),
                   label.size = deprecated(), border.colour = NULL,
                   border.color = NULL, text.colour = NULL, text.color =
                   NULL, size.unit = "mm", na.rm = FALSE, show.legend =
                   NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., parse = FALSE, nudge_x =
                   0, nudge_y = 0, label.padding = unit(0.25, "lines"),
                   label.r = unit(0.15, "lines"), label.size = 0.25,
                   size.unit = "mm", na.rm = FALSE, show.legend = NA,
                   inherit.aes = TRUE)
    Argument names in code not in docs:
      border.colour border.color text.colour text.color
    Argument names in docs not in code:
      nudge_x nudge_y
    Mismatches in argument names (first 3):
      Position: 7 Code: label.padding Docs: nudge_x
      Position: 8 Code: label.r Docs: nudge_y
      Position: 9 Code: label.size Docs: label.padding
    Mismatches in argument default values:
      Name: 'position' Code: "nudge" Docs: "identity"
      Name: 'label.size' Code: deprecated() Docs: 0.25
  geom_ysidelabel
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "nudge", ..., parse = FALSE, label.padding
                   = unit(0.25, "lines"), label.r = unit(0.15, "lines"),
                   label.size = deprecated(), border.colour = NULL,
                   border.color = NULL, text.colour = NULL, text.color =
                   NULL, size.unit = "mm", na.rm = FALSE, show.legend =
                   NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., parse = FALSE, nudge_x =
                   0, nudge_y = 0, label.padding = unit(0.25, "lines"),
                   label.r = unit(0.15, "lines"), label.size = 0.25,
                   size.unit = "mm", na.rm = FALSE, show.legend = NA,
                   inherit.aes = TRUE)
    Argument names in code not in docs:
      border.colour border.color text.colour text.color
    Argument names in docs not in code:
      nudge_x nudge_y
    Mismatches in argument names (first 3):
      Position: 7 Code: label.padding Docs: nudge_x
      Position: 8 Code: label.r Docs: nudge_y
      Position: 9 Code: label.size Docs: label.padding
    Mismatches in argument default values:
      Name: 'position' Code: "nudge" Docs: "identity"
      Name: 'label.size' Code: deprecated() Docs: 0.25
  
  Codoc mismatches from Rd file 'geom_xsideline.Rd':
  geom_xsideline
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., orientation = "x", arrow =
                   NULL, arrow.fill = NULL, lineend = "butt", linejoin =
                   "round", linemitre = 10, na.rm = FALSE, show.legend =
                   NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", na.rm = FALSE, orientation =
                   "x", show.legend = NA, inherit.aes = TRUE, ...)
    Argument names in code not in docs:
      arrow arrow.fill lineend linejoin linemitre
    Mismatches in argument names (first 3):
      Position: 5 Code: ... Docs: na.rm
      Position: 7 Code: arrow Docs: show.legend
      Position: 8 Code: arrow.fill Docs: inherit.aes
  geom_ysideline
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., orientation = "y", arrow =
                   NULL, arrow.fill = NULL, lineend = "butt", linejoin =
                   "round", linemitre = 10, na.rm = FALSE, show.legend =
                   NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", na.rm = FALSE, orientation =
                   "y", show.legend = NA, inherit.aes = TRUE, ...)
    Argument names in code not in docs:
      arrow arrow.fill lineend linejoin linemitre
    Mismatches in argument names (first 3):
      Position: 5 Code: ... Docs: na.rm
      Position: 7 Code: arrow Docs: show.legend
      Position: 8 Code: arrow.fill Docs: inherit.aes
  geom_xsidepath
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., arrow = NULL, arrow.fill =
                   NULL, lineend = "butt", linejoin = "round", linemitre
                   = 10, na.rm = FALSE, show.legend = NA, inherit.aes =
                   TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., lineend = "butt", linejoin
                   = "round", linemitre = 10, arrow = NULL, na.rm =
                   FALSE, show.legend = NA, inherit.aes = TRUE)
    Argument names in code not in docs:
      arrow.fill
    Mismatches in argument names (first 3):
      Position: 6 Code: arrow Docs: lineend
      Position: 7 Code: arrow.fill Docs: linejoin
      Position: 8 Code: lineend Docs: linemitre
  geom_ysidepath
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., arrow = NULL, arrow.fill =
                   NULL, lineend = "butt", linejoin = "round", linemitre
                   = 10, na.rm = FALSE, show.legend = NA, inherit.aes =
                   TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., lineend = "butt", linejoin
                   = "round", linemitre = 10, arrow = NULL, na.rm =
                   FALSE, show.legend = NA, inherit.aes = TRUE)
    Argument names in code not in docs:
      arrow.fill
    Mismatches in argument names (first 3):
      Position: 6 Code: arrow Docs: lineend
      Position: 7 Code: arrow.fill Docs: linejoin
      Position: 8 Code: lineend Docs: linemitre
  
  Codoc mismatches from Rd file 'geom_xsidetext.Rd':
  geom_xsidetext
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "nudge", ..., parse = FALSE, check_overlap
                   = FALSE, size.unit = "mm", na.rm = FALSE, show.legend
                   = NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., parse = FALSE, nudge_x =
                   0, nudge_y = 0, check_overlap = FALSE, size.unit =
                   "mm", na.rm = FALSE, show.legend = NA, inherit.aes =
                   TRUE)
    Argument names in docs not in code:
      nudge_x nudge_y
    Mismatches in argument names (first 3):
      Position: 7 Code: check_overlap Docs: nudge_x
      Position: 8 Code: size.unit Docs: nudge_y
      Position: 9 Code: na.rm Docs: check_overlap
    Mismatches in argument default values:
      Name: 'position' Code: "nudge" Docs: "identity"
  geom_ysidetext
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "nudge", ..., parse = FALSE, check_overlap
                   = FALSE, size.unit = "mm", na.rm = FALSE, show.legend
                   = NA, inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., parse = FALSE, nudge_x =
                   0, nudge_y = 0, check_overlap = FALSE, size.unit =
                   "mm", na.rm = FALSE, show.legend = NA, inherit.aes =
                   TRUE)
    Argument names in docs not in code:
      nudge_x nudge_y
    Mismatches in argument names (first 3):
      Position: 7 Code: check_overlap Docs: nudge_x
      Position: 8 Code: size.unit Docs: nudge_y
      Position: 9 Code: na.rm Docs: check_overlap
    Mismatches in argument default values:
      Name: 'position' Code: "nudge" Docs: "identity"
  
  Codoc mismatches from Rd file 'geom_xsidetile.Rd':
  geom_xsidetile
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., lineend = "butt", linejoin
                   = "mitre", na.rm = FALSE, show.legend = NA,
                   inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., linejoin = "mitre", na.rm
                   = FALSE, show.legend = NA, inherit.aes = TRUE)
    Argument names in code not in docs:
      lineend
    Mismatches in argument names (first 3):
      Position: 6 Code: lineend Docs: linejoin
      Position: 7 Code: linejoin Docs: na.rm
      Position: 8 Code: na.rm Docs: show.legend
  geom_ysidetile
    Code: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., lineend = "butt", linejoin
                   = "mitre", na.rm = FALSE, show.legend = NA,
                   inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "identity",
                   position = "identity", ..., linejoin = "mitre", na.rm
                   = FALSE, show.legend = NA, inherit.aes = TRUE)
    Argument names in code not in docs:
      lineend
    Mismatches in argument names (first 3):
      Position: 6 Code: lineend Docs: linejoin
      Position: 7 Code: linejoin Docs: na.rm
      Position: 8 Code: na.rm Docs: show.legend
  
  Codoc mismatches from Rd file 'geom_xsideviolin.Rd':
  geom_xsideviolin
    Code: function(mapping = NULL, data = NULL, stat = "ydensity",
                   position = "dodge", ..., trim = TRUE, bounds = c(-Inf,
                   Inf), quantile.colour = NULL, quantile.color = NULL,
                   quantile.linetype = 0L, quantile.linewidth = NULL,
                   draw_quantiles = deprecated(), scale = "area", na.rm =
                   FALSE, orientation = "x", show.legend = NA,
                   inherit.aes = TRUE)
    Docs: function(mapping = NULL, data = NULL, stat = "ydensity",
                   position = "dodge", ..., draw_quantiles = NULL, trim =
                   TRUE, bounds = c(-Inf, Inf), scale = "area", na.rm =
                   FALSE, orientation = "x", show.legend = NA,
                   inherit.aes = TRUE)
    Argument names in code not in docs:
      quantile.colour quantile.color quantile.linetype quantile.linewidth
    Mismatches in argument names (first 3):
      Position: 6 Code: trim Docs: draw_quantiles
      Position: 7 Code: bounds Docs: trim
      Position: 8 Code: quantile.colour Docs: bounds
    Mismatches in argument default values:
      Name: 'draw_quantiles' Code: deprecated() Docs: NULL
  geom_ysideviolin
    Code: function(mapping = NULL, data = NULL, stat = "ydensity",
                   position = "dodge", ..., trim = TRUE, bounds = c(-Inf,
                   Inf), quantile.colour = NULL, quantile.color = NULL,
                   quantile.linetype = 0L, quantile.linewidth = NULL,
                   draw_quantiles = deprecated(), scale = "area", na.rm =
                   FALSE, show.legend = NA, inherit.aes = TRUE,
                   orientation = "y")
    Docs: function(mapping = NULL, data = NULL, stat = "ydensity",
                   position = "dodge", ..., draw_quantiles = NULL, trim =
                   TRUE, bounds = c(-Inf, Inf), scale = "area", na.rm =
                   FALSE, show.legend = NA, inherit.aes = TRUE,
                   orientation = "y")
    Argument names in code not in docs:
      quantile.colour quantile.color quantile.linetype quantile.linewidth
    Mismatches in argument names (first 3):
      Position: 6 Code: trim Docs: draw_quantiles
      Position: 7 Code: bounds Docs: trim
      Position: 8 Code: quantile.colour Docs: bounds
    Mismatches in argument default values:
      Name: 'draw_quantiles' Code: deprecated() Docs: NULL

Package: ggside
Check: R code for possible problems
New result: NOTE
  geom_xsidelabel: no visible global function definition for ‘deprecated’
  geom_xsideviolin: no visible global function definition for
    ‘deprecated’
  geom_ysidelabel: no visible global function definition for ‘deprecated’
  geom_ysideviolin: no visible global function definition for
    ‘deprecated’
  Undefined global functions or variables:
    deprecated

Package: ggside
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘ggside_aes_mapping.Rmd’ using rmarkdown
  
  Quitting from ggside_aes_mapping.Rmd:42-46 [ggside_updated_aes_usage]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'ggside_aes_mapping.Rmd' failed with diagnostics:
  Problem while setting up geom.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `ggproto_parent_method()`:
  ! `geom_xsidedensity()` requires the following missing aesthetics: y.
  --- failed re-building ‘ggside_aes_mapping.Rmd’
  
  --- re-building ‘ggside_basic_usage.Rmd’ using rmarkdown
  
  Quitting from ggside_basic_usage.Rmd:172-176 [base_example_FacetWrap]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'ggside_basic_usage.Rmd' failed with diagnostics:
  Cannot update 0 guides with a list of parameters of length 4.
  --- failed re-building ‘ggside_basic_usage.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘ggside_aes_mapping.Rmd’ ‘ggside_basic_usage.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggside
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggside_scale:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggside_layer:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggside_options:
    function(object, plot, object_name)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: ggside
Check: tests
New result: ERROR
    Running ‘testthat.R’ [102s/103s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggplot2)
    > library(ggside)
    Registered S3 method overwritten by 'ggside':
      method from   
      +.gg   ggplot2
    > 
    > if ((nzchar(Sys.getenv("CI")) ||
    +      !nzchar(Sys.getenv("NOT_CRAN"))) &&
    +     identical(Sys.getenv("VDIFFR_RUN_TESTS"), 'false')) {
    +   #if we are running tests remotely AND
    +   # we are opting out of using vdiffr
    +   # assigning a dummy function
    + 
    +   expect_doppelganger <- function(...) {
    +     testthat::skip("`VDIFFR_RUN_TESTS` set to false on this remote check")
    +   }
    + } else {
    +   expect_doppelganger <- vdiffr::expect_doppelganger
    + }
    > 
    > test_check("ggside")
    [ FAIL 14 | WARN 1449 | SKIP 39 | PASS 83 ]
    
    ══ Skipped tests (39) ══════════════════════════════════════════════════════════
    • On CRAN (39): 'test_FacetGrid_ggside_themes.R:11:3',
      'test_FacetGrid_ggside_themes.R:23:3', 'test_FacetNull_ggside_themes.R:11:3',
      'test_FacetNull_ggside_themes.R:23:3', 'test_FacetWrap_ggside_themes.R:11:3',
      'test_FacetWrap_ggside_themes.R:23:3', 'test_continuous_date_axis.R:28:3',
      'test_continuous_date_axis.R:34:3', 'test_continuous_date_axis.R:40:3',
      'test_continuous_date_axis.R:46:3', 'test_ggside_axis_polts.R:9:3',
      'test_ggside_axis_polts.R:16:3', 'test_ggside_axis_polts.R:27:3',
      'test_ggside_axis_polts.R:40:3', 'test_ggside_respect_labels.R:32:3',
      'test_ggside_respect_labels.R:41:3', 'test_ggside_scales.R:77:3',
      'test_ggside_scales.R:127:3', 'test_ggside_scales.R:148:3',
      'test_non_aes_mapping_legend.R:11:3', 'test_ops_meaningful.R:17:3',
      'test_side_layers.R:13:3', 'test_side_layers.R:27:3',
      'test_side_layers.R:39:3', 'test_side_layers.R:53:3',
      'test_side_layers.R:60:3', 'test_side_layers.R:67:3',
      'test_side_layers.R:74:3', 'test_side_layers.R:88:3',
      'test_side_layers.R:95:3', 'test_side_layers.R:102:3',
      'test_side_layers.R:110:3', 'test_side_layers.R:117:3',
      'test_side_layers.R:124:3', 'test_side_layers.R:138:3',
      'test_vdiff_diamondplots.R:40:3', 'test_vdiff_diamondplots.R:67:3',
      'test_vdiff_irisScatter.R:10:3', 'test_vdiff_irisScatter.R:28:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_add_gg.R:44:3'): add_gg errors ─────────────────────────────────
    <getvarError/missingArgError/error/condition>
    Error in `Ops.S7_object(p)`: argument "e2" is missing, with no default
    Backtrace:
         ▆
      1. ├─testthat::expect_error(+p, "with a single argument. Did you accidentally put") at test_add_gg.R:44:3
      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. └─S7:::Ops.S7_object(p)
      8.   ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
      9.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     10.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     11.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     12.   └─base_ops[[.Generic]](e1, e2)
     13.     └─S7::S7_dispatch()
    ── Error ('test_axis_render_position.R:9:3'): axis may be rendered in between plots ──
    Error in `geom_density(mapping = mapping, data = data, stat = stat, position = position, 
        outline.type = outline.type, lineend = lineend, linejoin = linejoin, 
        linemitre = linemitre, na.rm = na.rm, show.legend = show.legend, 
        inherit.aes = inherit.aes)`: Problem while setting up geom.
    i Error occurred in the 2nd layer.
    Caused by error in `ggproto_parent_method()`:
    ! `geom_xsidedensity()` requires the following missing aesthetics: y.
    ── Failure ('test_continuous_date_axis.R:19:3'): default ggplot2 error ─────────
    `ggplot_build(p)` did not throw the expected error.
    ── Error ('test_ggside_axis_polts.R:58:3'): ggside FacetGrid strip option works ──
    Error in `upgradeUnit.default(x)`: Not a unit object
    Backtrace:
         ▆
      1. └─vdiffr::expect_doppelganger(...) at test_ggside_axis_polts.R:58:3
      2.   └─vdiffr (local) writer(fig, testcase, title)
      3.     ├─vdiffr:::print_plot(plot, title)
      4.     └─vdiffr:::print_plot.ggplot(plot, title)
      5.       ├─base::print(p)
      6.       └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7.         ├─ggplot2::ggplot_gtable(data)
      8.         └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
      9.           └─layout$render(geom_grobs, data, theme, plot@labels)
     10.             └─ggplot2 (local) render(..., self = self)
     11.               └─self$facet$draw_panels(...)
     12.                 └─ggside (local) draw_panels(...)
     13.                   └─grid::convertUnit(theme$strip.switch.pad.wrap, "cm")
     14.                     ├─grid:::upgradeUnit(x)
     15.                     └─grid:::upgradeUnit.default(x)
    ── Error ('test_ggside_classes.R:16:3'): geom_*side* returns ggside_layer ──────
    Error in `deprecated()`: could not find function "deprecated"
    Backtrace:
         ▆
      1. ├─testthat::expect_s3_class(geom_xsideviolin(), "ggside_layer") at test_ggside_classes.R:16:3
      2. │ └─testthat::quasi_label(enquo(object), arg = "object")
      3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
      4. └─ggside::geom_xsideviolin()
      5.   ├─ggside:::call_layer_param_aware(...)
      6.   │ └─base::eval(call, envir = env)
      7.   │   └─base::eval(call, envir = env)
      8.   └─ggplot2::geom_violin(...)
      9.     └─lifecycle::is_present(draw_quantiles)
     10.       ├─rlang::is_missing(maybe_missing(arg))
     11.       └─rlang::maybe_missing(arg)
     12.         └─rlang::is_missing(x)
    ── Error ('test_ggside_classes.R:41:5'): adding ggside_layer to ggplot makes ggside object ──
    Error in `deprecated()`: could not find function "deprecated"
    Backtrace:
         ▆
      1. ├─ggside (local) expect_is_ggside(p, geom_xsideviolin()) at test_ggside_classes.R:57:3
      2. └─ggside::geom_xsideviolin() at test_ggside_classes.R:41:5
      3.   ├─ggside:::call_layer_param_aware(...)
      4.   │ └─base::eval(call, envir = env)
      5.   │   └─base::eval(call, envir = env)
      6.   └─ggplot2::geom_violin(...)
      7.     └─lifecycle::is_present(draw_quantiles)
      8.       ├─rlang::is_missing(maybe_missing(arg))
      9.       └─rlang::maybe_missing(arg)
     10.         └─rlang::is_missing(x)
    ── Error ('test_ggside_extended_themes.R:14:3'): ggside themes functions work ──
    Error in `geom_density(mapping = mapping, data = data, stat = stat, position = position, 
        outline.type = outline.type, lineend = lineend, linejoin = linejoin, 
        linemitre = linemitre, na.rm = na.rm, show.legend = show.legend, 
        inherit.aes = inherit.aes)`: Problem while setting up geom.
    i Error occurred in the 2nd layer.
    Caused by error in `ggproto_parent_method()`:
    ! `geom_xsidedensity()` requires the following missing aesthetics: y.
    ── Error ('test_ggside_extended_themes.R:30:3'): ggside theme inheritence work ──
    Error in `geom_density(mapping = mapping, data = data, stat = stat, position = position, 
        outline.type = outline.type, lineend = lineend, linejoin = linejoin, 
        linemitre = linemitre, na.rm = na.rm, show.legend = show.legend, 
        inherit.aes = inherit.aes)`: Problem while setting up geom.
    i Error occurred in the 2nd layer.
    Caused by error in `ggproto_parent_method()`:
    ! `geom_xsidedensity()` requires the following missing aesthetics: y.
    ── Error ('test_ggside_respect_labels.R:23:3'): ggside `respect_side_labels` works on xsides ──
    Error in `element_render(theme, use_ggside_ele("panel.background", side = side, 
        family = "rect", theme = theme))`: Theme element `ggside.rect` has `NULL` property without default: linejoin.
    Backtrace:
         ▆
      1. └─vdiffr::expect_doppelganger("xside respect default", px) at test_ggside_respect_labels.R:23:3
      2.   └─vdiffr (local) writer(fig, testcase, title)
      3.     ├─vdiffr:::print_plot(plot, title)
      4.     └─vdiffr:::print_plot.ggplot(plot, title)
      5.       ├─base::print(p)
      6.       └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7.         ├─ggplot2::ggplot_gtable(data)
      8.         └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
      9.           └─layout$render(geom_grobs, data, theme, plot@labels)
     10.             └─ggplot2 (local) render(..., self = self)
     11.               └─self$facet$draw_panel_content(...)
     12.                 └─ggplot2 (local) draw_panel_content(..., self = self)
     13.                   └─base::lapply(...)
     14.                     └─ggplot2 (local) FUN(X[[i]], ...)
     15.                       └─coord$draw_panel(panel, ranges[[i]], theme)
     16.                         └─ggplot2 (local) draw_panel(..., self = self)
     17.                           └─self$render_bg(params, theme)
     18.                             └─ggside (local) render_bg(...)
     19.                               └─ggside:::ggside_guide_grid(...)
     20.                                 ├─ggside:::ggname(...)
     21.                                 │ └─grid::grobName(grob, prefix)
     22.                                 ├─grid::grobTree(...)
     23.                                 │ ├─grid::gTree(...)
     24.                                 │ │ └─grid::setChildren(gt, children)
     25.                                 │ └─grid::gList(...)
     26.                                 └─ggplot2::element_render(...)
     27.                                   └─ggplot2::calc_element(element, theme)
     28.                                     └─base::lapply(...)
     29.                                       └─ggplot2 (local) FUN(X[[i]], ...)
     30.                                         └─cli::cli_abort(...)
     31.                                           └─rlang::abort(...)
    ── Error ('test_ggside_respect_labels.R:61:3'): ggside `respect_side_labels` works as expected with other parameters and facets ──
    Error in `update_params(..., self = self)`: Cannot update 0 guides with a list of parameters of length 4.
    Backtrace:
         ▆
      1. └─vdiffr::expect_doppelganger(...) at test_ggside_respect_labels.R:61:3
      2.   └─vdiffr (local) writer(fig, testcase, title)
      3.     ├─vdiffr:::print_plot(plot, title)
      4.     └─vdiffr:::print_plot.ggplot(plot, title)
      5.       ├─base::print(p)
      6.       └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7.         ├─ggplot2::ggplot_build(x)
      8.         └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
      9.           └─layout$setup_panel_guides(plot@guides, plot@layers)
     10.             └─ggplot2 (local) setup_panel_guides(..., self = self)
     11.               └─base::lapply(...)
     12.                 └─ggplot2 (local) FUN(X[[i]], ...)
     13.                   └─ggplot2 (local) setup_panel_guides(..., self = self)
     14.                     └─guides$update_params(guide_params)
     15.                       └─ggplot2 (local) update_params(..., self = self)
     16.                         └─cli::cli_abort(...)
     17.                           └─rlang::abort(...)
    ── Error ('test_side_layers.R:19:3'): plot bar ─────────────────────────────────
    Error in `geom_bar(mapping = mapping, data = data, stat = stat, position = position, 
        just = just, lineend = lineend, linejoin = linejoin, na.rm = na.rm, 
        show.legend = show.legend, inherit.aes = inherit.aes)`: Problem while computing stat.
    i Error occurred in the 2nd layer.
    Caused by error in `setup_params()`:
    ! `stat_xsidecount()` must only have an x or y aesthetic.
    ── Error ('test_side_layers.R:46:3'): plot density ─────────────────────────────
    Error in `geom_density(mapping = mapping, data = data, stat = stat, position = position, 
        outline.type = outline.type, lineend = lineend, linejoin = linejoin, 
        linemitre = linemitre, na.rm = na.rm, show.legend = show.legend, 
        inherit.aes = inherit.aes)`: Problem while setting up geom.
    i Error occurred in the 2nd layer.
    Caused by error in `ggproto_parent_method()`:
    ! `geom_xsidedensity()` requires the following missing aesthetics: y.
    ── Error ('test_side_layers.R:78:3'): plot label ───────────────────────────────
    Error in `deprecated()`: could not find function "deprecated"
    Backtrace:
        ▆
     1. └─ggside::geom_xsidelabel(aes(y = 2, label = letters[1:3])) at test_side_layers.R:78:3
     2.   ├─ggside:::call_layer_param_aware(...)
     3.   │ └─base::eval(call, envir = env)
     4.   │   └─base::eval(call, envir = env)
     5.   └─ggplot2::geom_label(...)
     6.     └─lifecycle::is_present(label.size)
     7.       ├─rlang::is_missing(maybe_missing(arg))
     8.       └─rlang::maybe_missing(arg)
     9.         └─rlang::is_missing(x)
    ── Error ('test_side_layers.R:128:3'): plot violin ─────────────────────────────
    Error in `deprecated()`: could not find function "deprecated"
    Backtrace:
        ▆
     1. └─ggside::geom_xsideviolin() at test_side_layers.R:128:3
     2.   ├─ggside:::call_layer_param_aware(...)
     3.   │ └─base::eval(call, envir = env)
     4.   │   └─base::eval(call, envir = env)
     5.   └─ggplot2::geom_violin(...)
     6.     └─lifecycle::is_present(draw_quantiles)
     7.       ├─rlang::is_missing(maybe_missing(arg))
     8.       └─rlang::maybe_missing(arg)
     9.         └─rlang::is_missing(x)
    
    [ FAIL 14 | WARN 1449 | SKIP 39 | PASS 83 ]
    Deleting unused snapshots:
    • FacetGrid_ggside_themes/grid-xside-ggside-panel-scale-5.svg
    • FacetGrid_ggside_themes/grid-xside-ggside-panel-scale-y-5.svg
    • FacetGrid_ggside_themes/grid-xside-ggside-panel-spacing-10pt.svg
    • FacetGrid_ggside_themes/grid-xside-ggside-panel-spacing-y-10pt.svg
    • FacetGrid_ggside_themes/grid-xyside-ggside-panel-scale-5.svg
    • FacetGrid_ggside_themes/grid-xyside-ggside-panel-scale-x-5.svg
    • FacetGrid_ggside_themes/grid-xyside-ggside-panel-scale-y-5.svg
    • FacetGrid_ggside_themes/grid-xyside-ggside-panel-spacing-10pt.svg
    • FacetGrid_ggside_themes/grid-xyside-ggside-panel-spacing-x-10pt.svg
    • FacetGrid_ggside_themes/grid-xyside-ggside-panel-spacing-y-10pt.svg
    • FacetGrid_ggside_themes/grid-yside-ggside-panel-scale-5.svg
    • FacetGrid_ggside_themes/grid-yside-ggside-panel-scale-x-5.svg
    • FacetGrid_ggside_themes/grid-yside-ggside-panel-scale-y-5.svg
    • FacetGrid_ggside_themes/grid-yside-ggside-panel-spacing-10pt.svg
    • FacetGrid_ggside_themes/grid-yside-ggside-panel-spacing-x-10pt.svg
    • FacetGrid_ggside_themes/grid-yside-ggside-panel-spacing-y-10pt.svg
    • FacetNull_ggside_themes/xside-ggside-panel-scale-5.svg
    • FacetNull_ggside_themes/xside-ggside-panel-scale-y-5.svg
    • FacetNull_ggside_themes/xside-ggside-panel-spacing-10pt.svg
    • FacetNull_ggside_themes/xside-ggside-panel-spacing-y-10pt.svg
    • FacetNull_ggside_themes/xyside-ggside-panel-scale-5.svg
    • FacetNull_ggside_themes/xyside-ggside-panel-scale-x-5.svg
    • FacetNull_ggside_themes/xyside-ggside-panel-scale-y-5.svg
    • FacetNull_ggside_themes/xyside-ggside-panel-spacing-10pt.svg
    • FacetNull_ggside_themes/xyside-ggside-panel-spacing-x-10pt.svg
    • FacetNull_ggside_themes/xyside-ggside-panel-spacing-y-10pt.svg
    • FacetNull_ggside_themes/yside-ggside-panel-scale-5.svg
    • FacetNull_ggside_themes/yside-ggside-panel-scale-x-5.svg
    • FacetNull_ggside_themes/yside-ggside-panel-scale-y-5.svg
    • FacetNull_ggside_themes/yside-ggside-panel-spacing-10pt.svg
    • FacetNull_ggside_themes/yside-ggside-panel-spacing-x-10pt.svg
    • FacetNull_ggside_themes/yside-ggside-panel-spacing-y-10pt.svg
    • FacetWrap_ggside_themes/wrap-xside-ggside-panel-scale-5.svg
    • FacetWrap_ggside_themes/wrap-xside-ggside-panel-scale-y-5.svg
    • FacetWrap_ggside_themes/wrap-xside-ggside-panel-spacing-10pt.svg
    • FacetWrap_ggside_themes/wrap-xside-ggside-panel-spacing-y-10pt.svg
    • FacetWrap_ggside_themes/wrap-xyside-ggside-panel-scale-5.svg
    • FacetWrap_ggside_themes/wrap-xyside-ggside-panel-scale-x-5.svg
    • FacetWrap_ggside_themes/wrap-xyside-ggside-panel-scale-y-5.svg
    • FacetWrap_ggside_themes/wrap-xyside-ggside-panel-spacing-10pt.svg
    • FacetWrap_ggside_themes/wrap-xyside-ggside-panel-spacing-x-10pt.svg
    • FacetWrap_ggside_themes/wrap-xyside-ggside-panel-spacing-y-10pt.svg
    • FacetWrap_ggside_themes/wrap-yside-ggside-panel-scale-5.svg
    • FacetWrap_ggside_themes/wrap-yside-ggside-panel-scale-x-5.svg
    • FacetWrap_ggside_themes/wrap-yside-ggside-panel-scale-y-5.svg
    • FacetWrap_ggside_themes/wrap-yside-ggside-panel-spacing-10pt.svg
    • FacetWrap_ggside_themes/wrap-yside-ggside-panel-spacing-x-10pt.svg
    • FacetWrap_ggside_themes/wrap-yside-ggside-panel-spacing-y-10pt.svg
    • axis_render_position/grid-default.svg
    • axis_render_position/grid-x-on-main-pos-bot.svg
    • axis_render_position/grid-x-on-main-top.svg
    • axis_render_position/grid-x-on-side-pos-bot.svg
    • axis_render_position/grid-x-on-side.svg
    • axis_render_position/grid-y-on-main-pos-left.svg
    • axis_render_position/grid-y-on-main-right.svg
    • axis_render_position/grid-y-on-side-pos-left.svg
    • axis_render_position/grid-y-on-side.svg
    • axis_render_position/wrap-default.svg
    • axis_render_position/wrap-x-on-main-pos-bot.svg
    • axis_render_position/wrap-x-on-main-top.svg
    • axis_render_position/wrap-x-on-side-pos-bot.svg
    • axis_render_position/wrap-x-on-side.svg
    • axis_render_position/wrap-y-on-main-pos-left.svg
    • axis_render_position/wrap-y-on-main-right.svg
    • axis_render_position/wrap-y-on-side-pos-left.svg
    • axis_render_position/wrap-y-on-side.svg
    • axis_render_position/x-on-main-pos-bot.svg
    • axis_render_position/x-on-main-top.svg
    • axis_render_position/x-on-side-pos-bot.svg
    • axis_render_position/x-on-side.svg
    • axis_render_position/y-on-main-pos-left.svg
    • axis_render_position/y-on-main-right.svg
    • axis_render_position/y-on-side-pos-left.svg
    • axis_render_position/y-on-side.svg
    • ggside_axis_polts/xside-bot-pos-top-grid.svg
    • ggside_axis_polts/xside-bot-pos-top.svg
    • ggside_axis_polts/xside-bottom.svg
    • ggside_axis_polts/xside-top-noaxis.svg
    • ggside_axis_polts/xside-top-pos-top-wrap.svg
    • ggside_axis_polts/xside-top-pos-top.svg
    • ggside_axis_polts/xyside-facet-grid.svg
    • ggside_axis_polts/xyside-lb-pos-swap.svg
    • ggside_axis_polts/xyside-lb.svg
    • ggside_axis_polts/xyside-no-x-text.svg
    • ggside_axis_polts/xyside-no-y-text.svg
    • ggside_axis_polts/xyside-xb-pos-top.svg
    • ggside_axis_polts/xyside-xb.svg
    • ggside_axis_polts/xyside-yl-pos-right.svg
    • ggside_axis_polts/xyside-yl.svg
    • ggside_axis_polts/yside-left-pos-right-grid.svg
    • ggside_axis_polts/yside-left-pos-right.svg
    • ggside_axis_polts/yside-left.svg
    • ggside_axis_polts/yside-right-noaxis.svg
    • ggside_axis_polts/yside-right-pos-right-wrap.svg
    • ggside_axis_polts/yside-right-pos-right.svg
    • ggside_extended_themes/bw.svg
    • ggside_extended_themes/classic.svg
    • ggside_extended_themes/dark.svg
    • ggside_extended_themes/gray.svg
    • ggside_extended_themes/light.svg
    • ggside_extended_themes/linedraw.svg
    • ggside_extended_themes/minimal.svg
    • ggside_extended_themes/side-panel-background.svg
    • ggside_extended_themes/side-panel-border.svg
    • ggside_extended_themes/void.svg
    • ggside_respect_labels/xside-respect-all.svg
    • ggside_respect_labels/xside-respect-none.svg
    • ggside_respect_labels/xside-respect-x.svg
    • ggside_respect_labels/xside-respect-y.svg
    • ggside_respect_labels/xyside-facet-grid-respect-default-free-scales.svg
    • ggside_respect_labels/xyside-facet-grid-respect-none-free-scales.svg
    • ggside_respect_labels/xyside-facet-grid-respect-none.svg
    • ggside_respect_labels/xyside-xb-respect-all.svg
    • ggside_respect_labels/xyside-xb-respect-default.svg
    • ggside_respect_labels/xyside-xb-respect-none.svg
    • ggside_respect_labels/xyside-xb-respect-x.svg
    • ggside_respect_labels/xyside-xb-respect-y.svg
    • ggside_respect_labels/xyside-yl-respect-all.svg
    • ggside_respect_labels/xyside-yl-respect-default.svg
    • ggside_respect_labels/xyside-yl-respect-none.svg
    • ggside_respect_labels/xyside-yl-respect-x.svg
    • ggside_respect_labels/xyside-yl-respect-y.svg
    • ggside_respect_labels/yside-respect-all.svg
    • ggside_respect_labels/yside-respect-none.svg
    • ggside_respect_labels/yside-respect-x.svg
    • ggside_respect_labels/yside-respect-y.svg
    • ggside_scales/xsidey-ysidex-facetgrid.svg
    • ggside_scales/xsidey-ysidex-facetwrap.svg
    • non_aes_mapping_legend/non-aes-color-blue.svg
    • non_aes_mapping_legend/non-aes-xcolor-red.svg
    • ops_meaningful/alpha-0-5-from-function.svg
    • side_layers/boxplot2.svg
    • side_layers/label.svg
    • side_layers/violin.svg
    • vdiff_irisScatter/collapsed-histo.svg
    • vdiff_irisScatter/facetgrid-collapsed-density.svg
    • vdiff_irisScatter/facetgrid-histo.svg
    • vdiff_irisScatter/facetgrid-side-density.svg
    • vdiff_irisScatter/stacked-side-density.svg
    • vdiff_irisScatter/yside-histo.svg
    Error: Test failures
    Execution halted

Package: ggspatial
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.fixed_plot_aspect:
    function(object, plot, object_name)
  
  ggplot_build:
    function(plot, ...)
  ggplot_build.gg_fixed_plot_aspect:
    function(plot)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: ggstatsplot
Check: tests
New result: ERROR
    Running ‘testthat.R’ [189s/96s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # graphics engine changed in this version, and so snapshots generated on
    > # previous R version won't work
    > if (getRversion() >= "4.4.0") {
    +   library(testthat)
    +   suppressPackageStartupMessages(library(ggstatsplot))
    +   test_check("ggstatsplot")
    + }
    Starting 2 test processes
    [ FAIL 1 | WARN 151 | SKIP 47 | PASS 8 ]
    
    ══ Skipped tests (47) ══════════════════════════════════════════════════════════
    • On CRAN (47): 'test-combine-plots.R:19:5', 'test-extract-stats.R:8:5',
      'test-ggbetweenstats.R:11:5', 'test-ggbetweenstats.R:64:5',
      'test-ggbetweenstats.R:95:5', 'test-ggcoefstats.R:4:3',
      'test-ggcoefstats.R:13:3', 'test-ggcoefstats.R:63:3',
      'test-ggcoefstats.R:98:5', 'test-ggcoefstats.R:145:5',
      'test-ggcoefstats.R:164:5', 'test-ggcorrmat.R:5:5', 'test-ggcorrmat.R:24:5',
      'test-ggcorrmat.R:67:5', 'test-ggcorrmat.R:92:5', 'test-ggbarstats.R:22:5',
      'test-ggbarstats.R:66:5', 'test-ggbarstats.R:166:5',
      'test-ggbarstats.R:208:5', 'test-ggbarstats.R:225:5',
      'test-ggbarstats.R:251:5', 'test-ggdotplotstats.R:23:5',
      'test-ggdotplotstats.R:43:5', 'test-ggdotplotstats.R:104:5',
      'test-gghistostats.R:7:5', 'test-gghistostats.R:26:5',
      'test-gghistostats.R:51:5', 'test-gghistostats.R:95:5',
      'test-ggscatterstats.R:7:5', 'test-ggscatterstats.R:26:5',
      'test-ggscatterstats.R:54:3', 'test-ggscatterstats.R:112:5',
      'test-ggscatterstats.R:142:5', 'test-ggwithinstats.R:12:5',
      'test-ggwithinstats.R:50:5', 'test-ggwithinstats.R:81:5',
      'test-ggpiestats.R:21:5', 'test-ggpiestats.R:77:5',
      'test-ggpiestats.R:152:5', 'test-ggpiestats.R:196:5',
      'test-ggpiestats.R:204:5', 'test-ggpiestats.R:249:5', 'test-utils.R:7:5',
      'test-utils.R:22:5', 'test-pairwise-ggsignif.R:7:5',
      'test-pairwise-ggsignif.R:162:5', 'test-pairwise-ggsignif.R:318:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-extract-stats.R:83:5'): checking if extract_stats works for grouped plots ──
    <purrr_error_indexed/rlang_error/error/condition>
    Error in `purrr::map(seq_along(p), ~purrr::pluck(p, .x))`: i In index: 1.
    Caused by error in `pluck_raw()`:
    ! Index 1 must be a string, not an integer.
    Backtrace:
        ▆
     1. └─testthat::expect_snapshot(...) at test-extract-stats.R:83:5
     2.   └─rlang::cnd_signal(state$error)
    
    [ FAIL 1 | WARN 151 | SKIP 47 | PASS 8 ]
    Deleting unused snapshots:
    • ggbarstats/changing-aesthetics-works.svg
    • ggbarstats/checking-count-labels.svg
    • ggbarstats/checking-paired-two-way-table-with-na.svg
    • ggbarstats/checking-paired-two-way-table-without-na.svg
    • ggbarstats/checking-percentage-and-count-labels.svg
    • ggbarstats/checking-unpaired-two-way-table-with-na.svg
    • ggbarstats/label-repelling-works.svg
    • ggbarstats/prop-test-fails-with-dropped-levels.svg
    • ggbetweenstats/default-plot-as-expected.svg
    • ggbetweenstats/mean-shown-with-scarce-data.svg
    • ggbetweenstats/plot-with-outliers-as-expected.svg
    • ggbetweenstats/specific-geoms-removed.svg
    • ggcoefstats/chi2-statistic.svg
    • ggcoefstats/f-statistic-with-omega.svg
    • ggcoefstats/f-statistic.svg
    • ggcoefstats/meta-analysis-works.svg
    • ggcoefstats/sorting-works.svg
    • ggcoefstats/z-statistic.svg
    • ggcorrmat/applying-ggplot2-function-works.svg
    • ggcorrmat/non-parametric-correlation-with-nas.svg
    • ggcorrmat/with-nas.svg
    • ggdotplotstats/further-modification-with-ggplot-works.svg
    • ggdotplotstats/robust-with-na.svg
    • gghistostats/modification-with-ggplot2-works.svg
    • gghistostats/robust-with-na.svg
    • ggpiestats/changing-aesthetics-works.svg
    • ggpiestats/checking-count-labels.svg
    • ggpiestats/checking-one-way-table-with-na.svg
    • ggpiestats/checking-paired-two-way-table-with-na.svg
    • ggpiestats/checking-paired-two-way-table-without-na.svg
    • ggpiestats/checking-percentage-and-count-labels.svg
    • ggpiestats/checking-unpaired-two-way-table-with-na.svg
    • ggpiestats/checking-unpaired-two-way-table-without-na.svg
    • ggpiestats/empty-groups-in-factors-not-dropped.svg
    • ggpiestats/grouped-ggpiestats-with-two-way-table.svg
    • ggpiestats/label-repelling-works.svg
    • ggpiestats/prop-test-fails-with-dropped-levels.svg
    • ggscatterstats/aesthetic-modifications-work.svg
    • ggscatterstats/no-label-variable-but-expression.svg
    • ggscatterstats/robust-correlation-with-nas.svg
    • ggwithinstats/centrality-path-can-be-turned-off.svg
    • ggwithinstats/defaults-plots-more-than-two-groups.svg
    • ggwithinstats/defaults-plots-two-groups.svg
    • ggwithinstats/grouped-plots-default.svg
    • pairwise-ggsignif/between-bayes.svg
    • pairwise-ggsignif/between-non-parametric-all.svg
    • pairwise-ggsignif/between-non-parametric-only-non-significant.svg
    • pairwise-ggsignif/between-non-parametric-only-significant.svg
    • pairwise-ggsignif/between-parametric-all.svg
    • pairwise-ggsignif/between-parametric-only-significant.svg
    • pairwise-ggsignif/between-robust-all.svg
    • pairwise-ggsignif/between-robust-only-non-significant.svg
    • pairwise-ggsignif/between-robust-only-significant.svg
    • pairwise-ggsignif/within-bayes.svg
    • pairwise-ggsignif/within-non-parametric-all.svg
    • pairwise-ggsignif/within-non-parametric-only-non-significant.svg
    • pairwise-ggsignif/within-non-parametric-only-significant.svg
    • pairwise-ggsignif/within-parametric-all.svg
    • pairwise-ggsignif/within-parametric-only-significant.svg
    • pairwise-ggsignif/within-robust-all.svg
    • pairwise-ggsignif/within-robust-only-non-significant.svg
    • pairwise-ggsignif/within-robust-only-significant.svg
    Error: Test failures
    Execution halted

Package: ggstream
Check: tests
New result: ERROR
    Running ‘testthat.R’ [2s/2s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggstream)
    > 
    > test_check("ggstream")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-geom_stream.R:4:3'): geom_stream ─────────────────────────────
    class(...) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
    Error: Test failures
    Execution halted

Package: ggsurvfit
Check: examples
New result: ERROR
  Running examples in ‘ggsurvfit-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: add_risktable
  > ### Title: Add risk table
  > ### Aliases: add_risktable
  > 
  > ### ** Examples
  > 
  > p <-
  +   survfit2(Surv(time, status) ~ sex, data = df_lung) %>%
  +   ggsurvfit() +
  +   add_censor_mark() +
  +   add_confidence_interval() +
  +   scale_ggsurvfit()
  > 
  > # using the function defaults
  > p + add_risktable()
  Error in .construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}",  : 
    argument "risktable_height" is missing, with no default
  Calls: <Anonymous> ... ggsurvfit_build -> <Anonymous> -> .construct_risktable
  Execution halted

Package: ggsurvfit
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘themes.Rmd’ using rmarkdown
  
  Quitting from themes.Rmd:61-68 [unnamed-chunk-4]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `.construct_risktable()`:
  ! argument "risktable_height" is missing, with no default
  ---
  Backtrace:
       ▆
    1. └─tools::buildVignettes(...)
    2.   ├─base::tryCatch(...)
    3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    6.   └─engine$weave(file, quiet = quiet, encoding = enc)
    7.     └─knitr:::vweave_rmarkdown(...)
    8.       └─rmarkdown::render(...)
    9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
   10.           └─knitr:::process_file(text, output)
   11.             ├─xfun:::handle_error(...)
   12.             ├─base::withCallingHandlers(...)
   13.             └─knitr:::process_group(group)
   14.               └─knitr:::call_block(x)
   15.                 └─knitr:::block_exec(params)
   16.                   └─knitr:::eng_r(options)
   17.                     ├─knitr:::in_input_dir(...)
   18.                     │ └─knitr:::in_dir(input_dir(), expr)
   19.                     └─knitr (local) evaluate(...)
   20.                       └─evaluate::evaluate(...)
   21.                         ├─base::withRestarts(...)
   22.                         │ └─base (local) withRestartList(expr, restarts)
   23.                         │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
   24.                         │   │ └─base (local) doWithOneRestart(return(expr), restart)
   25.                         │   └─base (local) withRestartList(expr, restarts[-nr])
   26.                         │     └─base (local) withOneRestart(expr, restarts[[1L]])
   27.                         │       └─base (local) doWithOneRestart(return(expr), restart)
   28.                         ├─evaluate:::with_handlers(...)
   29.                         │ ├─base::eval(call)
   30.                         │ │ └─base::eval(call)
   31.                         │ └─base::withCallingHandlers(...)
   32.                         └─watcher$print_value(ev$value, ev$visible, envir)
   33.                           ├─base::withVisible(handle_value(handler, value, visible, envir))
   34.                           └─evaluate:::handle_value(handler, value, visible, envir)
   35.                             └─handler$value(value, visible)
   36.                               └─knitr (local) fun(x, options = options)
   37.                                 ├─base::withVisible(knit_print(x, ...))
   38.                                 ├─knitr::knit_print(x, ...)
   39.                                 └─knitr:::knit_print.default(x, ...)
   40.                                   └─knitr::normal_print(x)
   41.                                     ├─base::print(x)
   42.                                     └─ggsurvfit:::print.ggsurvfit(x)
   43.                                       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
   44.                                         ├─rlang::inject(...)
   45.                                         └─ggsurvfit:::.construct_risktable(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'themes.Rmd' failed with diagnostics:
  argument "risktable_height" is missing, with no default
  --- failed re-building ‘themes.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘themes.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ggsurvfit
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.scale_ggsurvfit:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.add_risktable:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.add_quantile:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.add_risktable_strata_symbol:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.add_pvalue:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.add_confidence_interval:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.add_legend_title:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.add_censor_mark:
    function(object, plot, object_name)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: ggsurvfit
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [84s/85s]
  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(ggsurvfit)
    Loading required package: ggplot2
    > 
    > test_check("ggsurvfit")
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Ignoring unknown labels:
    * fill : "Time from Surgery to Treatment"
    * linetype : "Time from Surgery to Treatment"
    Ignoring unknown labels:
    * linetype : "Time from Surgery to Treatment"
    Ignoring unknown labels:
    * linetype : "Time from Surgery to Treatment"
    Ignoring unknown labels:
    * fill : "cyl"
    * linetype : "cyl"
    ! `add_pvalue()` works with objects created with `survfit2()` or `tidycmprsk::cuminc()`.
    i `add_pvalue()` has been ignored.
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    ! Setting start time to -9.83572895277207.
    i Specify `ggsurvfit::survfit2(start.time)` to override this default.
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Plotting outcome "death from cancer".
    Saving 7 x 7 in image
    Saving 7 x 7 in image
    [ FAIL 36 | WARN 0 | SKIP 17 | PASS 204 ]
    
    ══ Skipped tests (17) ══════════════════════════════════════════════════════════
    • On CRAN (17): 'test-add_censor_mark.R:15:3', 'test-add_censor_mark.R:48:3',
      'test-add_censor_mark.R:63:3', 'test-add_confidence_interval.R:20:3',
      'test-add_confidence_interval.R:64:3', 'test-add_confidence_interval.R:85:3',
      'test-add_pvalue.R:47:3', 'test-add_quantile.R:78:3',
      'test-add_quantile.R:160:3', 'test-add_quantile.R:174:3',
      'test-add_quantile.R:205:3', 'test-ggcuminc.R:36:3', 'test-ggcuminc.R:63:3',
      'test-ggsurvfit.R:10:3', 'test-ggsurvfit_options.R:45:3',
      'test-stat_stepribbon.R:27:3', 'test-tidy_survfit.R:211:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-add_risktable.R:12:3'): add_risktable() works with ggsurvfit() ──
    `lst_survfit2_risktable %>% lapply(function(x) print(x))` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:12:3
      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. ├─lst_survfit2_risktable %>% lapply(function(x) print(x))
      8. └─base::lapply(., function(x) print(x))
      9.   └─ggsurvfit (local) FUN(X[[i]], ...)
     10.     ├─base::print(x) at test-add_risktable.R:14:14
     11.     └─ggsurvfit:::print.ggsurvfit(x)
     12.       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     13.         ├─rlang::inject(...)
     14.         └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:19:3'): add_risktable() works with ggsurvfit() ──
    ``%>%`(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:19:3
      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. ├─list(sf1, sf2, sf3) %>% ...
      8. ├─base::lapply(...)
      9. │ └─ggsurvfit (local) FUN(X[[i]], ...)
     10. │   └─... %>% print() at test-add_risktable.R:23:11
     11. ├─base::print(.)
     12. └─ggsurvfit:::print.ggsurvfit(.)
     13.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14.     ├─rlang::inject(...)
     15.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:31:3'): add_risktable() works with ggsurvfit() ──
    ``%>%`(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:31:3
      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. ├─list(sf1, sf2, sf3) %>% ...
      8. ├─base::lapply(...)
      9. │ └─ggsurvfit (local) FUN(X[[i]], ...)
     10. │   └─... %>% print() at test-add_risktable.R:35:11
     11. ├─base::print(.)
     12. └─ggsurvfit:::print.ggsurvfit(.)
     13.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14.     ├─rlang::inject(...)
     15.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:43:3'): add_risktable() works with ggsurvfit() ──
    ``%>%`(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:43:3
      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. ├─list(sf2, sf3) %>% ...
      8. ├─base::lapply(...)
      9. │ └─ggsurvfit (local) FUN(X[[i]], ...)
     10. │   └─... %>% print() at test-add_risktable.R:45:14
     11. ├─base::print(.)
     12. └─ggsurvfit:::print.ggsurvfit(.)
     13.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14.     ├─rlang::inject(...)
     15.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:49:3'): add_risktable() works with ggsurvfit() ──
    ``%>%`(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:49:3
      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. ├─list(sf2, sf3) %>% ...
      8. ├─base::lapply(...)
      9. │ └─ggsurvfit (local) FUN(X[[i]], ...)
     10. │   └─... %>% print() at test-add_risktable.R:51:14
     11. ├─base::print(.)
     12. └─ggsurvfit:::print.ggsurvfit(.)
     13.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14.     ├─rlang::inject(...)
     15.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:63:3'): add_risktable() works with ggsurvfit() ──
    `print(risktable_overall1)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(print(risktable_overall1), NA) at test-add_risktable.R:63:3
      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. ├─base::print(risktable_overall1)
      8. └─ggsurvfit:::print.ggsurvfit(risktable_overall1)
      9.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     10.     ├─rlang::inject(...)
     11.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:73:3'): add_risktable() works with ggsurvfit() ──
    `print(risktable_overall2)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(print(risktable_overall2), NA) at test-add_risktable.R:73:3
      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. ├─base::print(risktable_overall2)
      8. └─ggsurvfit:::print.ggsurvfit(risktable_overall2)
      9.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     10.     ├─rlang::inject(...)
     11.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:90:3'): add_risktable() works with ggsurvfit() ──
    `print(risktable_with_weights)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(print(risktable_with_weights), NA) at test-add_risktable.R:90:3
      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. ├─base::print(risktable_with_weights)
      8. └─ggsurvfit:::print.ggsurvfit(risktable_with_weights)
      9.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     10.     ├─rlang::inject(...)
     11.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:98:3'): add_risktable() works with ggsurvfit() ──
    `print(`sf1-risktable-height`)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(print(`sf1-risktable-height`), NA) at test-add_risktable.R:98:3
      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. ├─base::print(`sf1-risktable-height`)
      8. └─ggsurvfit:::print.ggsurvfit(`sf1-risktable-height`)
      9.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     10.     ├─rlang::inject(...)
     11.     └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-add_risktable.R:103:3'): add_risktable() works with ggsurvfit() ──
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "auto", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
        ▆
     1. └─vdiffr::expect_doppelganger("sf1-risktable", lst_survfit2_risktable[[1]]) at test-add_risktable.R:103:3
     2.   └─vdiffr (local) writer(fig, testcase, title)
     3.     ├─vdiffr:::print_plot(plot, title)
     4.     └─vdiffr:::print_plot.ggplot(plot, title)
     5.       ├─base::print(p)
     6.       └─ggsurvfit:::print.ggsurvfit(p)
     7.         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     8.           ├─rlang::inject(...)
     9.           └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:143:3'): add_risktable() works with ggcuminc() ──
    `lst_cuminc_risktable %>% lapply(function(x) print(x))` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:143:3
      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. ├─lst_cuminc_risktable %>% lapply(function(x) print(x))
      8. └─base::lapply(., function(x) print(x))
      9.   └─ggsurvfit (local) FUN(X[[i]], ...)
     10.     ├─base::print(x) at test-add_risktable.R:145:14
     11.     └─ggsurvfit:::print.ggcuminc(x)
     12.       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     13.         ├─rlang::inject(...)
     14.         └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:149:3'): add_risktable() works with ggcuminc() ──
    ``%>%`(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:149:3
      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. ├─list(cuminc1, cuminc2, cuminc3) %>% ...
      8. ├─base::lapply(...)
      9. │ └─ggsurvfit (local) FUN(X[[i]], ...)
     10. │   └─... %>% print() at test-add_risktable.R:153:11
     11. ├─base::print(.)
     12. └─ggsurvfit:::print.ggcuminc(.)
     13.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14.     ├─rlang::inject(...)
     15.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:161:3'): add_risktable() works with ggcuminc() ──
    ``%>%`(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:161:3
      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. ├─list(cuminc2, cuminc3) %>% ...
      8. ├─base::lapply(...)
      9. │ └─ggsurvfit (local) FUN(X[[i]], ...)
     10. │   └─... %>% print() at test-add_risktable.R:163:14
     11. ├─base::print(.)
     12. └─ggsurvfit:::print.ggcuminc(.)
     13.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14.     ├─rlang::inject(...)
     15.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:167:3'): add_risktable() works with ggcuminc() ──
    ``%>%`(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:167:3
      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. ├─list(cuminc2, cuminc3) %>% ...
      8. ├─base::lapply(...)
      9. │ └─ggsurvfit (local) FUN(X[[i]], ...)
     10. │   └─(ggcuminc(x) + add_risktable(combine_groups = TRUE)) %>% ... at test-add_risktable.R:169:14
     11. ├─base::print(.)
     12. └─ggsurvfit:::print.ggcuminc(.)
     13.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14.     ├─rlang::inject(...)
     15.     └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-add_risktable.R:174:3'): add_risktable() works with ggcuminc() ──
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "auto", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
        ▆
     1. └─vdiffr::expect_doppelganger("cuminc1-risktable", lst_cuminc_risktable[[1]]) at test-add_risktable.R:174:3
     2.   └─vdiffr (local) writer(fig, testcase, title)
     3.     ├─vdiffr:::print_plot(plot, title)
     4.     └─vdiffr:::print_plot.ggplot(plot, title)
     5.       ├─base::print(p)
     6.       └─ggsurvfit:::print.ggcuminc(p)
     7.         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     8.           ├─rlang::inject(...)
     9.           └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:186:3'): add_risktable() works with ggcuminc() and multiple outcomes ──
    `lst_cuminc_risktable_outcomes %>% lapply(function(x) print(x))` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:186:3
      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. ├─lst_cuminc_risktable_outcomes %>% ...
      8. └─base::lapply(., function(x) print(x))
      9.   └─ggsurvfit (local) FUN(X[[i]], ...)
     10.     ├─base::print(x) at test-add_risktable.R:187:46
     11.     └─ggsurvfit:::print.ggcuminc(x)
     12.       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     13.         ├─rlang::inject(...)
     14.         └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-add_risktable.R:193:3'): add_risktable() works with ggcuminc() and multiple outcomes ──
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "auto", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
        ▆
     1. └─vdiffr::expect_doppelganger(...) at test-add_risktable.R:193:3
     2.   └─vdiffr (local) writer(fig, testcase, title)
     3.     ├─vdiffr:::print_plot(plot, title)
     4.     └─vdiffr:::print_plot.ggplot(plot, title)
     5.       ├─base::print(p)
     6.       └─ggsurvfit:::print.ggcuminc(p)
     7.         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     8.           ├─rlang::inject(...)
     9.           └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-add_risktable.R:208:3'): add_risktable() throws messages ───────
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "auto", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
         ▆
      1. ├─testthat::expect_message(...) at test-add_risktable.R:208:3
      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. ├─base::print(...)
      8. └─ggsurvfit:::print.ggsurvfit(...)
      9.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     10.     ├─rlang::inject(...)
     11.     └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:237:3'): add_risktable() custom stats ────────
    `lst_custom_stats %>% lapply(function(x) print(x))` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:237:3
      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. ├─lst_custom_stats %>% lapply(function(x) print(x))
      8. └─base::lapply(., function(x) print(x))
      9.   └─ggsurvfit (local) FUN(X[[i]], ...)
     10.     ├─base::print(x) at test-add_risktable.R:237:44
     11.     └─ggsurvfit:::print.ggsurvfit(x)
     12.       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     13.         ├─rlang::inject(...)
     14.         └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:253:3'): add_risktable() custom stats ────────
    `lst_custom_stats2 %>% lapply(function(x) print(x))` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:253:3
      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. ├─lst_custom_stats2 %>% lapply(function(x) print(x))
      8. └─base::lapply(., function(x) print(x))
      9.   └─ggsurvfit (local) FUN(X[[i]], ...)
     10.     ├─base::print(x) at test-add_risktable.R:253:45
     11.     └─ggsurvfit:::print.ggsurvfit(x)
     12.       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     13.         ├─rlang::inject(...)
     14.         └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-add_risktable.R:257:3'): add_risktable() custom stats ──────────
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk} ({cum.event})", 
    "{round(estimate*100)}% ({round(conf.low*100)}, {round(conf.high*100)})"
    ), geom_blank.stats_label = c("At Risk (Cum. Events)", "Survival (95% CI)"
    ), geom_blank.combine_groups = FALSE, geom_blank.risktable_group = "auto", 
        geom_blank.risktable_height = NULL, geom_blank.theme = list(
            structure(list(line = <object>, rect = <object>, text = <object>, 
                title = <object>, point = <object>, polygon = <object>, 
                geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
                5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
                "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                    r = 0, b = 0, l = 0, unit = "pt", ...) 
                {
                    warn_dots_empty()
                    lens <- c(length(t), length(r), length(b), length(l))
                    if (any(lens != 1)) {
                      incorrect <- c("t", "r", "b", "l")[lens != 
                        1]
                      s <- if (length(incorrect) > 1) 
                        "s"
                      else ""
                      cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                        i = "Argument{s} get(s) truncated to length 1."))
                      t <- t[1]
                      r <- r[1]
                      b <- b[1]
                      l <- l[1]
                    }
                    u <- unit(c(t, r, b, l), unit)
                    S7::new_object(u)
                }, name = "margin", parent = structure(list(class = c("simpleUnit", 
                "unit", "unit_v2"), constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                    r = 0, b = 0, l = 0, unit = "pt", ...) 
                {
                    warn_dots_empty()
                    lens <- c(length(t), length(r), length(b), length(l))
                    if (any(lens != 1)) {
                      incorrect <- c("t", "r", "b", "l")[lens != 
                        1]
                      s <- if (length(incorrect) > 1) 
                        "s"
                      else ""
                      cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                        i = "Argument{s} get(s) truncated to length 1."))
                      t <- t[1]
                      r <- r[1]
                      b <- b[1]
                      l <- l[1]
                    }
                    u <- unit(c(t, r, b, l), unit)
                    S7::new_object(u)
                }, class = c("S7_class", "S7_object")), unit = 8L), 
                aspect.ratio = NULL, axis.title = NULL, axis.title.x = <object>, 
                axis.title.x.top = <object>, axis.title.x.bottom = NULL, 
                axis.title.y = <object>, axis.title.y.left = NULL, 
                axis.title.y.right = <object>, axis.text = <object>, 
                axis.text.x = <object>, axis.text.x.top = <object>, 
                axis.text.x.bottom = NULL, axis.text.y = <object>, 
                axis.text.y.left = NULL, axis.text.y.right = <object>, 
                axis.text.theta = NULL, axis.text.r = <object>, axis.ticks = <object>, 
                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 = structure(0.5, class = "rel"), 
                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 = structure(0.75, class = "rel"), 
                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 = <object>, 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 = <object>, 
                legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
                legend.spacing.x = NULL, legend.spacing.y = NULL, 
                legend.key = NULL, legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
                "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
                legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
                legend.key.spacing.y = NULL, legend.key.justification = NULL, 
                legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
                legend.axis.line = NULL, legend.text = <object>, 
                legend.text.position = NULL, legend.title = <object>, 
                legend.title.position = NULL, legend.position = "right", 
                legend.position.inside = NULL, legend.direction = NULL, 
                legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
                0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
                "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                    r = 0, b = 0, l = 0, unit = "pt", ...) 
                {
                    warn_dots_empty()
                    lens <- c(length(t), length(r), length(b), length(l))
                    if (any(lens != 1)) {
                      incorrect <- c("t", "r", "b", "l")[lens != 
                        1]
                      s <- if (length(incorrect) > 1) 
                        "s"
                      else ""
                      cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                        i = "Argument{s} get(s) truncated to length 1."))
                      t <- t[1]
                      r <- r[1]
                      b <- b[1]
                      l <- l[1]
                    }
                    u <- unit(c(t, r, b, l), unit)
                    S7::new_object(u)
                }, name = "margin", parent = structure(list(class = c("simpleUnit", 
                "unit", "unit_v2"), constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                    r = 0, b = 0, l = 0, unit = "pt", ...) 
                {
                    warn_dots_empty()
                    lens <- c(length(t), length(r), length(b), length(l))
                    if (any(lens != 1)) {
                      incorrect <- c("t", "r", "b", "l")[lens != 
                        1]
                      s <- if (length(incorrect) > 1) 
                        "s"
                      else ""
                      cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                        i = "Argument{s} get(s) truncated to length 1."))
                      t <- t[1]
                      r <- r[1]
                      b <- b[1]
                      l <- l[1]
                    }
                    u <- unit(c(t, r, b, l), unit)
                    S7::new_object(u)
                }, class = c("S7_class", "S7_object")), unit = 8L), 
                legend.box.background = <object>, legend.box.spacing = structure(2, class = "rel"), 
                panel.background = <object>, panel.border = <object>, 
                panel.spacing = NULL, panel.spacing.x = NULL, panel.spacing.y = NULL, 
                panel.grid = <object>, panel.grid.major = NULL, panel.grid.minor = <object>, 
                panel.grid.major.x = NULL, panel.grid.major.y = NULL, 
                panel.grid.minor.x = NULL, panel.grid.minor.y = NULL, 
                panel.ontop = FALSE, panel.widths = NULL, panel.heights = NULL, 
                plot.background = <object>, plot.title = <object>, 
                plot.title.position = "panel", plot.subtitle = <object>, 
                plot.caption = <object>, plot.caption.position = "panel", 
                plot.tag = <object>, plot.tag.position = "topleft", 
                plot.tag.location = NULL, plot.margin = NULL, strip.background = <object>, 
                strip.background.x = NULL, strip.background.y = NULL, 
                strip.clip = "on", strip.placement = "inside", strip.text = <object>, 
                strip.text.x = NULL, strip.text.x.bottom = NULL, 
                strip.text.x.top = NULL, strip.text.y = <object>, 
                strip.text.y.left = <object>, strip.text.y.right = NULL, 
                strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
        ▆
     1. └─vdiffr::expect_doppelganger(...) at test-add_risktable.R:257:3
     2.   └─vdiffr (local) writer(fig, testcase, title)
     3.     ├─vdiffr:::print_plot(plot, title)
     4.     └─vdiffr:::print_plot.ggplot(plot, title)
     5.       ├─base::print(p)
     6.       └─ggsurvfit:::print.ggsurvfit(p)
     7.         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     8.           ├─rlang::inject(...)
     9.           └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable.R:273:3'): add_risktable() works with Cox models ──
    `(ggsurvfit(sf_cox) + add_risktable()) %>% ggsurvfit_build()` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable.R:273:3
      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. ├─(ggsurvfit(sf_cox) + add_risktable()) %>% ggsurvfit_build()
      8. └─ggsurvfit::ggsurvfit_build(.)
      9.   ├─rlang::inject(...)
     10.   └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-add_risktable.R:319:3'): add_risktable() works with ggsurvfit() `start.time` and negative times ──
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "auto", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
        ▆
     1. └─vdiffr::expect_doppelganger("sf-negative_time", sf_negative_time) at test-add_risktable.R:319:3
     2.   └─vdiffr (local) writer(fig, testcase, title)
     3.     ├─vdiffr:::print_plot(plot, title)
     4.     └─vdiffr:::print_plot.ggplot(plot, title)
     5.       ├─base::print(p)
     6.       └─ggsurvfit:::print.ggsurvfit(p)
     7.         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     8.           ├─rlang::inject(...)
     9.           └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable_strata_symbol.R:10:3'): add_risktable_strata_symbol() works ──
    `(p + add_risktable_strata_symbol(symbol = "O")) %>% ggsurvfit_build()` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable_strata_symbol.R:10:3
      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. ├─(p + add_risktable_strata_symbol(symbol = "O")) %>% ...
      8. └─ggsurvfit::ggsurvfit_build(.)
      9.   ├─rlang::inject(...)
     10.   └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-add_risktable_strata_symbol.R:14:3'): add_risktable_strata_symbol() works ──
    `(p + add_risktable_strata_symbol(symbol = "O")) %>% ggsurvfit_build()` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-add_risktable_strata_symbol.R:14:3
      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. ├─(p + add_risktable_strata_symbol(symbol = "O")) %>% ...
      8. └─ggsurvfit::ggsurvfit_build(.)
      9.   ├─rlang::inject(...)
     10.   └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-add_risktable_strata_symbol.R:32:3'): add_risktable_strata_symbol() works ──
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "risktable_stats", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
        ▆
     1. └─vdiffr::expect_doppelganger(...) at test-add_risktable_strata_symbol.R:32:3
     2.   └─vdiffr (local) writer(fig, testcase, title)
     3.     ├─vdiffr:::print_plot(plot, title)
     4.     └─vdiffr:::print_plot.ggplot(plot, title)
     5.       ├─base::print(p)
     6.       └─ggsurvfit:::print.ggsurvfit(p)
     7.         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     8.           ├─rlang::inject(...)
     9.           └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-add_risktable_strata_symbol.R:56:3'): add_risktable_strata_symbol() messaging works ──
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "auto", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
         ▆
      1. ├─testthat::expect_message(...) at test-add_risktable_strata_symbol.R:56:3
      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. ├─base::print(...)
      8. └─ggsurvfit:::print.ggsurvfit(...)
      9.   └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     10.     ├─rlang::inject(...)
     11.     └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-ggsurvfit.R:193:3'): ggsurvfit() works with geoms with new data ──
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "risktable_stats", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
        ▆
     1. └─vdiffr::expect_doppelganger("sf2-ggsurvfit_new_data_geom1", p1) at test-ggsurvfit.R:193:3
     2.   └─vdiffr (local) writer(fig, testcase, title)
     3.     ├─vdiffr:::print_plot(plot, title)
     4.     └─vdiffr:::print_plot.ggplot(plot, title)
     5.       ├─base::print(p)
     6.       └─ggsurvfit:::print.ggsurvfit(p)
     7.         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     8.           ├─rlang::inject(...)
     9.           └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-ggsurvfit_build.R:7:3'): ggsurvfit_build() works ─────────────
    `built_p <- ggsurvfit_build(p, combine_plots = FALSE)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
        ▆
     1. ├─testthat::expect_error(...) at test-ggsurvfit_build.R:7:3
     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. └─ggsurvfit::ggsurvfit_build(p, combine_plots = FALSE)
     8.   ├─rlang::inject(...)
     9.   └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-ggsurvfit_build.R:12:3'): ggsurvfit_build() works ──────────────
    Error in `eval(code, test_env)`: object 'built_p' not found
    Backtrace:
        ▆
     1. ├─testthat::expect_true(inherits(built_p, "list")) at test-ggsurvfit_build.R:12:3
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─base::inherits(built_p, "list")
    ── Failure ('test-grid.draw_ggsurvfit.R:8:3'): grid.draw() works ───────────────
    `save_image_png(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-grid.draw_ggsurvfit.R:8:3
      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. ├─ggsurvfit (local) save_image_png(...)
      8. │ └─ggplot2::ggsave(filename = path, plot = x) at test-grid.draw_ggsurvfit.R:4:5
      9. │   └─base::lapply(plot, grid.draw)
     10. │     ├─grid (local) FUN(X[[i]], ...)
     11. │     └─ggsurvfit:::grid.draw.ggsurvfit(X[[i]], ...)
     12. │       ├─ggsurvfit_build(x, combine_plots = TRUE) %>% ...
     13. │       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14. │         ├─rlang::inject(...)
     15. │         └─ggsurvfit:::.construct_risktable(...)
     16. └─grid::grid.draw(., recording = recording)
    ── Failure ('test-grid.draw_ggsurvfit.R:17:3'): grid.draw() works ──────────────
    `save_image_png(...)` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-grid.draw_ggsurvfit.R:17:3
      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. ├─ggsurvfit (local) save_image_png(...)
      8. │ └─ggplot2::ggsave(filename = path, plot = x) at test-grid.draw_ggsurvfit.R:4:5
      9. │   └─base::lapply(plot, grid.draw)
     10. │     ├─grid (local) FUN(X[[i]], ...)
     11. │     └─ggsurvfit:::grid.draw.ggcuminc(X[[i]], ...)
     12. │       ├─ggsurvfit_build(x, combine_plots = TRUE) %>% ...
     13. │       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     14. │         ├─rlang::inject(...)
     15. │         └─ggsurvfit:::.construct_risktable(...)
     16. └─grid::grid.draw(., recording = recording)
    ── Failure ('test-theme_risktable.R:12:3'): theme_risktable works ──────────────
    `lst_survfit2_default %>% lapply(function(x) print(x))` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-theme_risktable.R:12:3
      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. ├─lst_survfit2_default %>% lapply(function(x) print(x))
      8. └─base::lapply(., function(x) print(x))
      9.   └─ggsurvfit (local) FUN(X[[i]], ...)
     10.     ├─base::print(x) at test-theme_risktable.R:12:48
     11.     └─ggsurvfit:::print.ggsurvfit(x)
     12.       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     13.         ├─rlang::inject(...)
     14.         └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-theme_risktable.R:21:3'): theme_risktable works ──────────────
    `lst_survfit2_boxed %>% lapply(function(x) print(x))` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-theme_risktable.R:21:3
      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. ├─lst_survfit2_boxed %>% lapply(function(x) print(x))
      8. └─base::lapply(., function(x) print(x))
      9.   └─ggsurvfit (local) FUN(X[[i]], ...)
     10.     ├─base::print(x) at test-theme_risktable.R:21:46
     11.     └─ggsurvfit:::print.ggsurvfit(x)
     12.       └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     13.         ├─rlang::inject(...)
     14.         └─ggsurvfit:::.construct_risktable(...)
    ── Failure ('test-theme_risktable.R:29:3'): theme_risktable works ──────────────
    `lst_survfit2_boxed_symbol %>% lapply(function(x) ggsurvfit_build(x))` threw an unexpected error.
    Message: argument "risktable_height" is missing, with no default
    Class:   getvarError/missingArgError/error/condition
    Backtrace:
         ▆
      1. ├─testthat::expect_error(...) at test-theme_risktable.R:29:3
      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. ├─lst_survfit2_boxed_symbol %>% ...
      8. └─base::lapply(., function(x) ggsurvfit_build(x))
      9.   └─ggsurvfit (local) FUN(X[[i]], ...)
     10.     └─ggsurvfit::ggsurvfit_build(x) at test-theme_risktable.R:29:53
     11.       ├─rlang::inject(...)
     12.       └─ggsurvfit:::.construct_risktable(...)
    ── Error ('test-theme_risktable.R:33:3'): theme_risktable works ────────────────
    <getvarError/missingArgError/error/condition>
    Error in `.construct_risktable(x, geom_blank.times = NULL, geom_blank.risktable_stats = c("{n.risk}", 
    "{cum.event}"), geom_blank.stats_label = NULL, geom_blank.combine_groups = FALSE, 
        geom_blank.risktable_group = "auto", geom_blank.risktable_height = NULL, 
        geom_blank.theme = list(structure(list(line = <object>, rect = <object>, 
            text = <object>, title = <object>, point = <object>, 
            polygon = <object>, geom = <object>, spacing = structure(5.5, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), margins = structure(c(5.5, 5.5, 
            5.5, 5.5), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), aspect.ratio = NULL, 
            axis.title = NULL, axis.title.x = <object>, axis.title.x.top = <object>, 
            axis.title.x.bottom = NULL, axis.title.y = <object>, 
            axis.title.y.left = NULL, axis.title.y.right = <object>, 
            axis.text = <object>, axis.text.x = <object>, axis.text.x.top = <object>, 
            axis.text.x.bottom = NULL, axis.text.y = <object>, axis.text.y.left = NULL, 
            axis.text.y.right = <object>, axis.text.theta = NULL, 
            axis.text.r = <object>, axis.ticks = <object>, 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 = structure(0.5, class = "rel"), 
            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 = structure(0.75, class = "rel"), 
            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 = <object>, 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 = <object>, legend.margin = NULL, legend.spacing = structure(2, class = "rel"), 
            legend.spacing.x = NULL, legend.spacing.y = NULL, legend.key = NULL, 
            legend.key.size = structure(1.2, unit = 3L, class = c("simpleUnit", 
            "unit", "unit_v2")), legend.key.height = NULL, legend.key.width = NULL, 
            legend.key.spacing = NULL, legend.key.spacing.x = NULL, 
            legend.key.spacing.y = NULL, legend.key.justification = NULL, 
            legend.frame = NULL, legend.ticks = NULL, legend.ticks.length = structure(0.2, class = "rel"), 
            legend.axis.line = NULL, legend.text = <object>, legend.text.position = NULL, 
            legend.title = <object>, legend.title.position = NULL, 
            legend.position = "right", legend.position.inside = NULL, 
            legend.direction = NULL, legend.byrow = NULL, legend.justification = "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 = structure(c(0, 
            0, 0, 0), class = c("ggplot2::margin", "simpleUnit", 
            "unit", "unit_v2", "S7_object"), S7_class = structure(function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, name = "margin", parent = structure(list(class = c("simpleUnit", 
            "unit", "unit_v2"), constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (t = 0, 
                r = 0, b = 0, l = 0, unit = "pt", ...) 
            {
                warn_dots_empty()
                lens <- c(length(t), length(r), length(b), length(l))
                if (any(lens != 1)) {
                    incorrect <- c("t", "r", "b", "l")[lens != 1]
                    s <- if (length(incorrect) > 1) 
                      "s"
                    else ""
                    cli::cli_warn(c("In {.fn margin}, the argument{s} {.and {.arg {incorrect}}} should \\\n        have length 1, not length {.and {lens[lens != 1]}}.", 
                      i = "Argument{s} get(s) truncated to length 1."))
                    t <- t[1]
                    r <- r[1]
                    b <- b[1]
                    l <- l[1]
                }
                u <- unit(c(t, r, b, l), unit)
                S7::new_object(u)
            }, class = c("S7_class", "S7_object")), unit = 8L), legend.box.background = <object>, 
            legend.box.spacing = structure(2, class = "rel"), panel.background = <object>, 
            panel.border = <object>, panel.spacing = NULL, panel.spacing.x = NULL, 
            panel.spacing.y = NULL, panel.grid = <object>, panel.grid.major = NULL, 
            panel.grid.minor = <object>, panel.grid.major.x = NULL, 
            panel.grid.major.y = NULL, panel.grid.minor.x = NULL, 
            panel.grid.minor.y = NULL, panel.ontop = FALSE, panel.widths = NULL, 
            panel.heights = NULL, plot.background = <object>, plot.title = <object>, 
            plot.title.position = "panel", plot.subtitle = <object>, 
            plot.caption = <object>, plot.caption.position = "panel", 
            plot.tag = <object>, plot.tag.position = "topleft", plot.tag.location = NULL, 
            plot.margin = NULL, strip.background = <object>, strip.background.x = NULL, 
            strip.background.y = NULL, strip.clip = "on", strip.placement = "inside", 
            strip.text = <object>, strip.text.x = NULL, strip.text.x.bottom = NULL, 
            strip.text.x.top = NULL, strip.text.y = <object>, strip.text.y.left = <object>, 
            strip.text.y.right = NULL, strip.switch.pad.grid = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2")), strip.switch.pad.wrap = structure(2.75, unit = 8L, class = c("simpleUnit", 
            "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
        "gg", "S7_object"), S7_class = structure(function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, name = "theme", parent = structure(list(class = "gg", 
            constructor = function (.data) 
            {
                stop(sprintf("S3 class <%s> doesn't have a constructor", 
                    class[[1]]), call. = FALSE)
            }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
            complete = structure(list(name = "complete", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property"), 
            validate = structure(list(name = "validate", class = structure(list(
                class = "logical", constructor_name = "logical", 
                constructor = function (.data = logical(0)) 
                .data, validator = function (object) 
                {
                    if (base_class(object) != name) {
                      sprintf("Underlying data must be <%s> not <%s>", 
                        name, base_class(object))
                    }
                }), class = "S7_base_class"), getter = NULL, setter = NULL, 
                validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
            ..., complete = FALSE, validate = TRUE) 
        {
            warn_dots_empty()
            S7::new_object(elements, complete = complete, validate = validate)
        }, class = c("S7_class", "S7_object")), complete = TRUE, validate = TRUE), 
            structure(list(axis.title.x = <object>, axis.text.x = <object>, 
                axis.text.y = <object>, axis.ticks = <object>, axis.line = <object>, 
                legend.position = "none", panel.border = <object>, 
                panel.grid.major = <object>, panel.grid.minor = <object>, 
                plot.title = <object>, plot.margin = structure(c(0, 
                5.5, 0, 5.5), unit = 8L, class = c("simpleUnit", 
                "unit", "unit_v2"))), class = c("theme", "ggplot2::theme", 
            "gg", "S7_object"), S7_class = structure(function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, name = "theme", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(
                complete = structure(list(name = "complete", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property"), 
                validate = structure(list(name = "validate", class = structure(list(
                    class = "logical", constructor_name = "logical", 
                    constructor = function (.data = logical(0)) 
                    .data, validator = function (object) 
                    {
                      if (base_class(object) != name) {
                        sprintf("Underlying data must be <%s> not <%s>", 
                          name, base_class(object))
                      }
                    }), class = "S7_base_class"), getter = NULL, 
                    setter = NULL, validator = NULL, default = NULL), class = "S7_property")), abstract = FALSE, constructor = function (elements = list(), 
                ..., complete = FALSE, validate = TRUE) 
            {
                warn_dots_empty()
                S7::new_object(elements, complete = complete, validate = validate)
            }, class = c("S7_class", "S7_object")), complete = FALSE, validate = TRUE), 
            structure(list(x = NULL), class = c("ggplot2::labels", 
            "gg", "S7_object"), S7_class = structure(function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object"))), structure(list(
                y = NULL), class = c("ggplot2::labels", "gg", "S7_object"
            ), S7_class = structure(function (labels = list(), ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, name = "labels", parent = structure(list(class = "gg", 
                constructor = function (.data) 
                {
                    stop(sprintf("S3 class <%s> doesn't have a constructor", 
                      class[[1]]), call. = FALSE)
                }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (labels = list(), 
                ...) 
            {
                warn_dots_empty()
                S7::new_object(labels)
            }, validator = function (self) 
            {
                if (!is.list(self)) {
                    return("labels must be a list.")
                }
                if (!is_named2(self)) {
                    return("every label must be named.")
                }
                dups <- unique(names(self)[duplicated(names(self))])
                if (length(dups) > 0) {
                    dups <- oxford_comma(dups, final = "and")
                    return(paste0("labels cannot contain duplicate names (", 
                      dups, ")."))
                }
                return(NULL)
            }, class = c("S7_class", "S7_object")))), geom_blank.size = 3.5, 
        combine_plots = combine_plots, risktable_symbol_args = risktable_symbol_args)`: argument "risktable_height" is missing, with no default
    Backtrace:
        ▆
     1. └─vdiffr::expect_doppelganger(...) at test-theme_risktable.R:33:3
     2.   └─vdiffr (local) writer(fig, testcase, title)
     3.     ├─vdiffr:::print_plot(plot, title)
     4.     └─vdiffr:::print_plot.ggplot(plot, title)
     5.       ├─base::print(p)
     6.       └─ggsurvfit:::print.ggsurvfit(p)
     7.         └─ggsurvfit::ggsurvfit_build(x, combine_plots = TRUE)
     8.           ├─rlang::inject(...)
     9.           └─ggsurvfit:::.construct_risktable(...)
    
    [ FAIL 36 | WARN 0 | SKIP 17 | PASS 204 ]
    Deleting unused snapshots:
    • add_censor_mark/cuminc2-censor-mark-all-outcomes.svg
    • add_censor_mark/cuminc2-censor-mark.svg
    • add_censor_mark/cuminc3-censor-mark-all-outcomes.svg
    • add_censor_mark/cuminc3-censor-mark.svg
    • add_censor_mark/sf2-censor-mark.svg
    • add_censor_mark/sf3-censor-mark.svg
    • add_confidence_interval/cuminc2-confidence-interval-all-outcomes.svg
    • add_confidence_interval/cuminc2-confidence-interval.svg
    • add_confidence_interval/cuminc3-confidence-interval-all-outcomes.svg
    • add_confidence_interval/cuminc3-confidence-interval.svg
    • add_confidence_interval/sf2-confidence-interval.svg
    • add_confidence_interval/sf3-confidence-interval.svg
    • add_pvalue/cuminc2-pvalue.svg
    • add_pvalue/sf2-pvalue-annotation-risk.svg
    • add_pvalue/sf2-pvalue-annotation.svg
    • add_pvalue/sf2-pvalue-with-survfit.svg
    • add_quantile/cuminc2-quantile-all-outcomes.svg
    • add_quantile/cuminc2-quantile.svg
    • add_quantile/cuminc3-quantile-all-outcomes.svg
    • add_quantile/cuminc3-quantile.svg
    • add_quantile/sf-mtcars-decreasing-many-quantiles.svg
    • add_quantile/sf-mtcars-decreasing.svg
    • add_quantile/sf-mtcars-increasing-many-quantiles.svg
    • add_quantile/sf-mtcars-increasing.svg
    • add_quantile/sf-mtcars-timing.svg
    • add_quantile/sf2-colon-quantile-no-line.svg
    • add_quantile/sf2-colon-quantile.svg
    • add_quantile/sf2-quantile-x-value-not-all-groups.svg
    • add_quantile/sf2-quantile-x-value-out-of-bounds.svg
    • add_quantile/sf2-quantile.svg
    • add_quantile/sf3-quantile.svg
    • add_risktable/add-risktable-overall1.svg
    • add_risktable/add-risktable-overall2.svg
    • add_risktable/add-risktable-weights.svg
    • add_risktable/cuminc2-risktable-all-outcomes.svg
    • add_risktable/cuminc2-risktable.svg
    • add_risktable/cuminc3-risktable-all-outcomes.svg
    • add_risktable/cuminc3-risktable.svg
    • add_risktable/sf-start-time.svg
    • add_risktable/sf1-risktable-custom-stats-and-label2.svg
    • add_risktable/sf1-risktable-height.svg
    • add_risktable/sf2-risktable-custom-stats-and-label.svg
    • add_risktable/sf2-risktable-custom-stats-and-label2.svg
    • add_risktable/sf2-risktable.svg
    • add_risktable/sf3-risktable-custom-stats-and-label.svg
    • add_risktable/sf3-risktable-custom-stats-and-label2.svg
    • add_risktable/sf3-risktable.svg
    • add_risktable_strata_symbol/add-risktable-strata-symbol-circle.svg
    • add_risktable_strata_symbol/add-risktable-strata-symbol-uni.svg
    • ggcuminc/cuminc1-ggcuminc-sf-all-outcomes.svg
    • ggcuminc/cuminc1-ggcuminc.svg
    • ggcuminc/cuminc2-ggcuminc-all-outcomes.svg
    • ggcuminc/cuminc2-ggcuminc-sf-all-outcomes.svg
    • ggcuminc/cuminc2-ggcuminc.svg
    • ggcuminc/cuminc3-ggcuminc-all-outcomes.svg
    • ggcuminc/cuminc3-ggcuminc-sf-all-outcomes.svg
    • ggcuminc/cuminc3-ggcuminc.svg
    • ggcuminc/sf-cuminc2-ggcuminc.svg
    • ggcuminc/sf-cuminc3-ggcuminc.svg
    • ggsurvfit/sf1-ggsurvfit-cloglog.svg
    • ggsurvfit/sf1-ggsurvfit-cumhaz.svg
    • ggsurvfit/sf1-ggsurvfit-custom.svg
    • ggsurvfit/sf1-ggsurvfit-kmunicate.svg
    • ggsurvfit/sf1-ggsurvfit-risk.svg
    • ggsurvfit/sf2-ggsurvfit-cloglog.svg
    • ggsurvfit/sf2-ggsurvfit-cumhaz.svg
    • ggsurvfit/sf2-ggsurvfit-custom.svg
    • ggsurvfit/sf2-ggsurvfit-kmunicate.svg
    • ggsurvfit/sf2-ggsurvfit-linetype.svg
    • ggsurvfit/sf2-ggsurvfit-new-data-geom2.svg
    • ggsurvfit/sf2-ggsurvfit-risk.svg
    • ggsurvfit/sf2-ggsurvfit-strata-transformation.svg
    • ggsurvfit/sf2-ggsurvfit.svg
    • ggsurvfit/sf3-ggsurvfit-cloglog.svg
    • ggsurvfit/sf3-ggsurvfit-cumhaz.svg
    • ggsurvfit/sf3-ggsurvfit-custom.svg
    • ggsurvfit/sf3-ggsurvfit-kmunicate.svg
    • ggsurvfit/sf3-ggsurvfit-linetype.svg
    • ggsurvfit/sf3-ggsurvfit-risk.svg
    • ggsurvfit/sf3-ggsurvfit.svg
    • ggsurvfit_options/ggci-outcomes-linetype.svg
    • ggsurvfit_options/ggci-outcomes.svg
    • ggsurvfit_options/ggci-strata.svg
    • stat_stepribbon/gg-stepribbon2.svg
    • theme_risktable/sf1-ggsurvfit-theme-risktable-boxed-symbol.svg
    • theme_risktable/sf1-ggsurvfit-theme-risktable-boxed.svg
    • theme_risktable/sf2-ggsurvfit-theme-risktable-boxed-symbol.svg
    • theme_risktable/sf2-ggsurvfit-theme-risktable-boxed.svg
    • theme_risktable/sf2-ggsurvfit-theme-risktable-default.svg
    • theme_risktable/sf3-ggsurvfit-theme-risktable-boxed-symbol.svg
    • theme_risktable/sf3-ggsurvfit-theme-risktable-boxed.svg
    • theme_risktable/sf3-ggsurvfit-theme-risktable-default.svg
    Error: Test failures
    Execution halted

Package: ggtern
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: ggtikz
Check: tests
New result: ERROR
    Running ‘testthat.R’ [48s/49s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(ggtikz)
    > 
    > test_check("ggtikz")
    [ FAIL 9 | WARN 0 | SKIP 0 | PASS 283 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-ggtikzCanvas.R:127:5'): Panel viewport names are determined correctly ──
    `vp_name` (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-2-1.10-9-10-9"
    `expected`: "panel-1-2.10-9-10-9"
    Backtrace:
        ▆
     1. └─ggtikz (local) expect_vp_name_equal(p_grid1, 2, 1, "panel-1-2.10-9-10-9") at test-ggtikzCanvas.R:127:5
     2.   └─testthat::expect_equal(vp_name, expect) at test-ggtikzCanvas.R:107:5
    ── Failure ('test-ggtikzCanvas.R:128:5'): Panel viewport names are determined correctly ──
    `vp_name` (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-1-2.12-7-12-7"
    `expected`: "panel-2-1.12-7-12-7"
    Backtrace:
        ▆
     1. └─ggtikz (local) expect_vp_name_equal(p_grid1, 1, 2, "panel-2-1.12-7-12-7") at test-ggtikzCanvas.R:128:5
     2.   └─testthat::expect_equal(vp_name, expect) at test-ggtikzCanvas.R:107:5
    ── Failure ('test-ggtikzCanvas.R:130:5'): Panel viewport names are determined correctly ──
    `vp_name` (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-1-3.14-7-14-7"
    `expected`: "panel-3-1.14-7-14-7"
    Backtrace:
        ▆
     1. └─ggtikz (local) expect_vp_name_equal(p_grid1, 1, 3, "panel-3-1.14-7-14-7") at test-ggtikzCanvas.R:130:5
     2.   └─testthat::expect_equal(vp_name, expect) at test-ggtikzCanvas.R:107:5
    ── Failure ('test-ggtikzCanvas.R:131:5'): Panel viewport names are determined correctly ──
    `vp_name` (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-2-3.14-9-14-9"
    `expected`: "panel-3-2.14-9-14-9"
    Backtrace:
        ▆
     1. └─ggtikz (local) expect_vp_name_equal(p_grid1, 2, 3, "panel-3-2.14-9-14-9") at test-ggtikzCanvas.R:131:5
     2.   └─testthat::expect_equal(vp_name, expect) at test-ggtikzCanvas.R:107:5
    ── Failure ('test-ggtikzCanvas.R:135:5'): Panel viewport names are determined correctly ──
    `vp_name` (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-2-1.10-9-10-9"
    `expected`: "panel-1-2.10-9-10-9"
    Backtrace:
        ▆
     1. └─ggtikz (local) expect_vp_name_equal(p_grid1, 2, 1, "panel-1-2.10-9-10-9") at test-ggtikzCanvas.R:135:5
     2.   └─testthat::expect_equal(vp_name, expect) at test-ggtikzCanvas.R:107:5
    ── Failure ('test-ggtikzCanvas.R:136:5'): Panel viewport names are determined correctly ──
    `vp_name` (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-1-2.12-7-12-7"
    `expected`: "panel-2-1.12-7-12-7"
    Backtrace:
        ▆
     1. └─ggtikz (local) expect_vp_name_equal(p_grid1, 1, 2, "panel-2-1.12-7-12-7") at test-ggtikzCanvas.R:136:5
     2.   └─testthat::expect_equal(vp_name, expect) at test-ggtikzCanvas.R:107:5
    ── Failure ('test-ggtikzCanvas.R:138:5'): Panel viewport names are determined correctly ──
    `vp_name` (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-1-3.14-7-14-7"
    `expected`: "panel-3-1.14-7-14-7"
    Backtrace:
        ▆
     1. └─ggtikz (local) expect_vp_name_equal(p_grid1, 1, 3, "panel-3-1.14-7-14-7") at test-ggtikzCanvas.R:138:5
     2.   └─testthat::expect_equal(vp_name, expect) at test-ggtikzCanvas.R:107:5
    ── Failure ('test-ggtikzCanvas.R:139:5'): Panel viewport names are determined correctly ──
    `vp_name` (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-2-3.14-9-14-9"
    `expected`: "panel-3-2.14-9-14-9"
    Backtrace:
        ▆
     1. └─ggtikz (local) expect_vp_name_equal(p_grid1, 2, 3, "panel-3-2.14-9-14-9") at test-ggtikzCanvas.R:139:5
     2.   └─testthat::expect_equal(vp_name, expect) at test-ggtikzCanvas.R:107:5
    ── Failure ('test-ggtikzCanvas.R:161:5'): Panel viewports can be activated ─────
    grid::current.viewport()$name (`actual`) not equal to `expect` (`expected`).
    
    `actual`:   "panel-2-3.14-9-14-9"
    `expected`: "panel-3-2.14-9-14-9"
    Backtrace:
        ▆
     1. └─ggtikz (local) check_activated_vp(p_grid1, 2, 3, "panel-3-2.14-9-14-9") at test-ggtikzCanvas.R:161:5
     2.   └─ggtikz (local) expect_cur_vp_equal(expect) at test-ggtikzCanvas.R:152:5
     3.     └─testthat::expect_equal(grid::current.viewport()$name, expect) at test-ggtikzCanvas.R:144:5
    
    [ FAIL 9 | WARN 0 | SKIP 0 | PASS 283 ]
    Error: Test failures
    Execution halted

Package: ggtime
Check: tests
New result: ERROR
    Running ‘testthat.R’ [20s/20s]
  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(ggtime)
    Registered S3 methods overwritten by 'ggtime':
      method           from      
      autolayer.tbl_ts fabletools
      autoplot.dcmp_ts fabletools
      autoplot.tbl_ts  fabletools
    > 
    > test_check("ggtime")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-plot-helpers.R:192:3'): gg_tsdisplay() plots ───────────────────
    Error in `UseMethod("ggplot_build")`: no applicable method for 'ggplot_build' applied to an object of class "NULL"
    Backtrace:
        ▆
     1. └─ggplot2::ggplot_build(p[[1]]) at test-plot-helpers.R:192:3
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]
    Error: Test failures
    Execution halted

Package: ggtranslate
Check: examples
New result: ERROR
  Running examples in ‘ggtranslate-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ggtranslate
  > ### Title: Translate all text elements in a ggplot2 object
  > ### Aliases: ggtranslate
  > 
  > ### ** Examples
  > 
  > library(ggplot2)
  > 
  > df <- data.frame(
  +   day = factor(c("Monday", "Tuesday"), levels = c("Monday", "Tuesday")),
  +   value = c(10, 12)
  + )
  > translation_fr <- list(
  +   "Monday" = "Lundi",
  +   "Tuesday" = "Mardi",
  +   "Weekly Report" = "Rapport Hebdomadaire"
  + )
  > p_en <- ggplot(df, aes(x = day, y = value)) +
  +   geom_col() +
  +   labs(title = "Weekly Report")
  > p_fr <- ggtranslate(p_en, translation_fr)
  Error: <ggplot2::ggplot> object properties are invalid:
  - @labels must be <ggplot2::labels>, not <list>
  Execution halted

Package: gpmap
Check: differences from ‘gpmap-Ex.Rout’ to ‘gpmap-Ex.Rout.save’
New result: NOTE
  419,427d418
  < Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
  < ℹ Please use tidy evaluation idioms with `aes()`.
  < ℹ See also `vignette("ggplot2-in-packages")` for more information.
  < ℹ The deprecated feature was likely used in the gpmap package.
  <   Please report the issue to the authors.
  < Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
  < ℹ Please use `linewidth` instead.
  < ℹ The deprecated feature was likely used in the gpmap package.
  <   Please report the issue to the authors.

Package: gpmap
Check: tests
New result: NOTE
    Running ‘genotype_test.R’ [1s/1s]
    Comparing ‘genotype_test.Rout’ to ‘genotype_test.Rout.save’ ... OK
    Running ‘test_code_example.R’ [3s/3s]
    Comparing ‘test_code_example.Rout’ to ‘test_code_example.Rout.save’ ...27,36d26
  < Warning messages:
  < 1: `aes_string()` was deprecated in ggplot2 3.0.0.
  < ℹ Please use tidy evaluation idioms with `aes()`.
  < ℹ See also `vignette("ggplot2-in-packages")` for more information.
  < ℹ The deprecated feature was likely used in the gpmap package.
  <   Please report the issue to the authors. 
  < 2: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
  < ℹ Please use `linewidth` instead.
  < ℹ The deprecated feature was likely used in the gpmap package.
  <   Please report the issue to the authors.

Package: grafify
Check: tests
New result: ERROR
    Running ‘testthat.R’ [13s/14s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(grafify)
    Loading required package: ggplot2
    > library(rlang)
    
    Attaching package: 'rlang'
    
    The following objects are masked from 'package:testthat':
    
        is_false, is_null, is_true
    
    > library(dplyr)
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    > library(tidyr)
    
    Attaching package: 'tidyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    > library(Matrix)
    
    Attaching package: 'Matrix'
    
    The following objects are masked from 'package:tidyr':
    
        expand, pack, unpack
    
    > library(lme4)
    > 
    > 
    > test_check("grafify")
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). See help for details.
    boundary (singular) fit: see help('isSingular')
    boundary (singular) fit: see help('isSingular')
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). See help for details.
    boundary (singular) fit: see help('isSingular')
    boundary (singular) fit: see help('isSingular')
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    The new argument `AvgRF` is set to TRUE by default in >=5.0.0). Response variable is averaged over levels of Fixed and Random factors. Use help for details.
    [ FAIL 5 | WARN 0 | SKIP 0 | PASS 180 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-plot_3d_scatterbar.R:53:3'): Check 3d scatter bars ─────────────
    Error in `expect_match(sb1$labels$y, "PI")`: is.character(act$val) is not TRUE
    Backtrace:
        ▆
     1. └─testthat::expect_match(sb1$labels$y, "PI") at test-plot_3d_scatterbar.R:53:3
     2.   └─base::stopifnot(is.character(act$val))
    ── Error ('test-plot_3d_scatterbox.R:49:3'): Check 3d scatter box ──────────────
    Error in `expect_match(sb1$labels$y, "PI")`: is.character(act$val) is not TRUE
    Backtrace:
        ▆
     1. └─testthat::expect_match(sb1$labels$y, "PI") at test-plot_3d_scatterbox.R:49:3
     2.   └─base::stopifnot(is.character(act$val))
    ── Error ('test-plot_befafter_colors.R:17:3'): Check before-after colors plots ──
    Error in `expect_match(db1$labels$y, "PI")`: is.character(act$val) is not TRUE
    Backtrace:
        ▆
     1. └─testthat::expect_match(db1$labels$y, "PI") at test-plot_befafter_colors.R:17:3
     2.   └─base::stopifnot(is.character(act$val))
    ── Error ('test-plot_befafter_colors.R:37:3'): Check before-after colour plots ──
    Error in `expect_match(db2$labels$y, "PI")`: is.character(act$val) is not TRUE
    Backtrace:
        ▆
     1. └─testthat::expect_match(db2$labels$y, "PI") at test-plot_befafter_colors.R:37:3
     2.   └─base::stopifnot(is.character(act$val))
    ── Failure ('test-plot_qqline.R:14:3'): Check QQ plots ─────────────────────────
    as.character(db1$labels$y) is empty.
    
    [ FAIL 5 | WARN 0 | SKIP 0 | PASS 180 ]
    Error: Test failures
    Execution halted

Package: graphPAF
Check: examples
New result: ERROR
  Running examples in ‘graphPAF-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot.SAF_summary
  > ### Title: Produce plots of sequential and average PAF
  > ### Aliases: plot.SAF_summary
  > 
  > ### ** Examples
  > 
  > library(splines)
  > library(survival)
  > library(parallel)
  > options(boot.parallel="snow")
  > options(boot.ncpus=2)
  > #  Simulated data on occupational and environmental exposure to
  > # chronic cough from Eide, 1995
  > # First specify the causal graph, in terms of the parents of each node.  Then put into a list
  > parent_urban.rural <- c()
  > parent_smoking.category <- c("urban.rural")
  > parent_occupational.exposure <- c("urban.rural")
  > parent_y <- c("urban.rural","smoking.category","occupational.exposure")
  > parent_list <- list(parent_urban.rural, parent_smoking.category,
  + parent_occupational.exposure, parent_y)
  > # also specify nodes of graph, in order from root to leaves
  > node_vec <- c("urban.rural","smoking.category","occupational.exposure", "y")
  > model_list=automatic_fit(Hordaland_data,
  + parent_list=parent_list, node_vec=node_vec, prev=.09)
  Warning in eval(family$initialize) :
    non-integer #successes in a binomial glm!
  Warning in eval(family$initialize) :
    non-integer #successes in a binomial glm!
  Warning in eval(family$initialize) :
    non-integer #successes in a binomial glm!
  Warning in eval(family$initialize) :
    non-integer #successes in a binomial glm!
  > out <- average_paf(data=model_list[[length(model_list)]]$data,
  +  model_list=model_list,
  + parent_list=parent_list, node_vec=node_vec, prev=.09, nperm=10,
  + riskfactor_vec = c("urban.rural","occupational.exposure"),ci=FALSE)
  > plot(out)
  Warning in fortify(data, ...) : Arguments in `...` must be used.
  ✖ Problematic argument:
  • size = point.size
  ℹ Did you misspell an argument name?
  Error: Can't find method for generic `+(e1, e2)`:
  - e1: <ggplot2::element_text>
  - e2: <theme>
  Execution halted

Package: gratia
Check: differences from ‘gratia-Ex.Rout’ to ‘gratia-Ex.Rout.save’
New result: NOTE
  302,303d301
  < Warning: annotation$theme is not a valid theme.
  < Please use `theme()` to construct themes.
  527,528d524
  < Ignoring unknown labels:
  < * fill : "x2"

Package: GRShiny
Check: tests
New result: ERROR
    Running ‘testthat.R’ [7s/7s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(GRShiny)
    > 
    > test_check("GRShiny")
    
    F1 =~ NA*y1+l1*y1+l2*y2
    
     
    F1~~ 1*F1
    F1~ 0*1  
     | t11*t1;
    NAt21*t1;
    NAt10*t0;
    NAt20*t0;
    
    F1 =~ NA*y1+l1*y1+l2*y2+l3*y3+l4*y4+l5*y5+l6*y6
    
     
    F1~~ 1*F1
    F1~ 0*1  
    y1 | t11*t1;
    y2 | t21*t1;
    y3 | t31*t1;
    y4 | t41*t1;
    y5 | t51*t1;
    y6 | t61*t1;
    y1 | t12*t2;
    y2 | t22*t2;
    y3 | t32*t2;
    y4 | t42*t2;
    y5 | t52*t2;
    y6 | t62*t2;
    
    F1 =~ NA*y1+l1*y1+l2*y2+l3*y3+l4*y4+l5*y5+l6*y6
    
     
    F1~~ 1*F1
    F1~ 0*1  
    y1 | t11*t1;
    y2 | t21*t1;
    y3 | t31*t1;
    y4 | t41*t1;
    y5 | t51*t1;
    y6 | t61*t1;
    y1 | t12*t2;
    y2 | t22*t2;
    y3 | t32*t2;
    y4 | t42*t2;
    y5 | t52*t2;
    y6 | t62*t2;
    
    F1 =~ NA*y1+l1*y1+l2*y2+l3*y3+l4*y4+l5*y5+l6*y6
    
     
    F1~~ 1*F1
    F1~ 0*1  
    y1 | t11*t1;
    y2 | t21*t1;
    y3 | t31*t1;
    y4 | t41*t1;
    y5 | t51*t1;
    y6 | t61*t1;
    y1 | t12*t2;
    y2 | t22*t2;
    y3 | t32*t2;
    y4 | t42*t2;
    y5 | t52*t2;
    y6 | t62*t2;
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-gendata.r:73:3'): Plotting functions work ────────────────────
    `res` is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
    Error: Test failures
    Execution halted

Package: grwat
Check: tests
New result: ERROR
    Running ‘testthat.R’ [112s/112s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > suppressPackageStartupMessages(library(grwat))
    > 
    > test_check("grwat")
    [ FAIL 7 | WARN 0 | SKIP 1 | PASS 165 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • On CRAN (1): 'test-gr_report.R:1:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-gr_plot_acf.R:8:3'): ACF ggplot has the correct content ──────
    `plt` has type 'object', not 'list'.
    ── Failure ('test-gr_plot_hori.R:11:3'): Horizon plot has the correct content ──
    `plt` has type 'object', not 'list'.
    ── Failure ('test-gr_plot_matrix.R:7:3'): Matrix ggplot has the correct content ──
    `plt` has type 'object', not 'list'.
    ── Failure ('test-gr_plot_matrix.R:12:3'): Matrix ggplot has the correct content ──
    `plt` has type 'object', not 'list'.
    ── Failure ('test-gr_plot_matrix.R:17:3'): Matrix ggplot has the correct content ──
    `plt` has type 'object', not 'list'.
    ── Failure ('test-gr_plot_ridge.R:9:3'): Ridgeline plot has the correct content ──
    `plt` has type 'object', not 'list'.
    ── Failure ('test-gr_plot_tests.R:10:3'): Tests plot has the correct content ───
    `plt` has type 'object', not 'list'.
    
    [ FAIL 7 | WARN 0 | SKIP 1 | PASS 165 ]
    Error: Test failures
    Execution halted

Package: gsaot
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘gaussian-model-sensitivity.Rmd’ using rmarkdown
  
  Quitting from gaussian-model-sensitivity.Rmd:66-85 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'gaussian-model-sensitivity.Rmd' failed with diagnostics:
  Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  --- failed re-building ‘gaussian-model-sensitivity.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘gaussian-model-sensitivity.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: gsDesign
Check: tests
New result: ERROR
    Running ‘testthat.R’ [152s/153s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(gsDesign)
    > 
    > test_check("gsDesign")
    Symmetric two-sided group sequential design with
    90 % power and 2.5 % Type I Error.
    Spending computations assume trial stops
    if a bound is crossed.
    
                  
      Analysis  N   Z   Nominal p  Spend
             1  21 3.25    0.0006 0.0006
             2  41 2.99    0.0014 0.0013
             3  62 2.69    0.0036 0.0028
             4  82 2.37    0.0088 0.0063
             5 103 2.03    0.0214 0.0140
         Total                    0.0250 
    
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3      4      5 Total  E{N}
      0.0000 0.0006 0.0013 0.0028 0.0063 0.0140 0.025 101.6
      0.3242 0.0370 0.1512 0.2647 0.2699 0.1771 0.900  73.7
    
    Lower boundary (futility or Type II Error)
              Analysis
       Theta     1      2      3      4     5 Total
      0.0000 6e-04 0.0013 0.0028 0.0063 0.014 0.025
      0.3242 0e+00 0.0000 0.0000 0.0000 0.000 0.000
    Symmetric two-sided group sequential design with
    90 % power and 2.5 % Type I Error.
    Spending computations assume trial stops
    if a bound is crossed.
    
                  
      Analysis  N   Z   Nominal p  Spend
             1  21 3.25    0.0006 0.0006
             2  41 2.99    0.0014 0.0013
             3  62 2.69    0.0036 0.0028
             4  82 2.37    0.0088 0.0063
             5 103 2.03    0.0214 0.0140
         Total                    0.0250 
    
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3      4      5  Total  E{N}
      0.0000 0.0006 0.0013 0.0028 0.0063 0.0140 0.0250 101.6
      0.0162 0.0007 0.0018 0.0041 0.0092 0.0202 0.0359 101.6
      0.0324 0.0009 0.0024 0.0058 0.0131 0.0282 0.0505 101.4
      0.0486 0.0012 0.0033 0.0082 0.0183 0.0386 0.0696 101.2
      0.0648 0.0015 0.0045 0.0112 0.0251 0.0514 0.0938 100.9
      0.0810 0.0020 0.0061 0.0153 0.0338 0.0667 0.1238 100.4
      0.0972 0.0025 0.0080 0.0205 0.0445 0.0845 0.1599  99.9
      0.1135 0.0031 0.0106 0.0270 0.0574 0.1044 0.2024  99.1
      0.1297 0.0038 0.0137 0.0351 0.0726 0.1258 0.2511  98.2
      0.1459 0.0048 0.0177 0.0450 0.0901 0.1479 0.3055  97.2
      0.1621 0.0059 0.0225 0.0568 0.1097 0.1696 0.3645  95.9
      0.1783 0.0072 0.0284 0.0707 0.1308 0.1898 0.4270  94.4
      0.1945 0.0088 0.0356 0.0867 0.1531 0.2073 0.4914  92.8
      0.2107 0.0107 0.0441 0.1048 0.1756 0.2209 0.5561  90.9
      0.2269 0.0130 0.0541 0.1248 0.1977 0.2299 0.6194  88.8
      0.2431 0.0157 0.0657 0.1465 0.2183 0.2335 0.6796  86.6
      0.2593 0.0188 0.0791 0.1696 0.2364 0.2316 0.7355  84.2
      0.2755 0.0224 0.0943 0.1936 0.2514 0.2243 0.7859  81.6
      0.2917 0.0266 0.1114 0.2179 0.2622 0.2122 0.8303  79.0
      0.3079 0.0315 0.1304 0.2418 0.2685 0.1961 0.8683  76.4
      0.3242 0.0370 0.1512 0.2647 0.2699 0.1771 0.9000  73.7
      0.3404 0.0434 0.1738 0.2859 0.2664 0.1562 0.9257  71.0
      0.3566 0.0506 0.1980 0.3046 0.2582 0.1347 0.9461  68.3
      0.3728 0.0587 0.2236 0.3202 0.2457 0.1136 0.9617  65.7
      0.3890 0.0677 0.2502 0.3322 0.2297 0.0936 0.9735  63.1
      0.4052 0.0779 0.2776 0.3401 0.2110 0.0754 0.9820  60.7
      0.4214 0.0891 0.3053 0.3438 0.1905 0.0594 0.9881  58.3
      0.4376 0.1015 0.3330 0.3430 0.1689 0.0458 0.9923  56.1
      0.4538 0.1152 0.3602 0.3380 0.1473 0.0345 0.9952  53.9
      0.4700 0.1300 0.3864 0.3289 0.1262 0.0255 0.9970  51.9
      0.4862 0.1462 0.4112 0.3161 0.1063 0.0184 0.9982  50.0
      0.5024 0.1637 0.4341 0.3001 0.0881 0.0130 0.9990  48.2
      0.5186 0.1824 0.4547 0.2815 0.0718 0.0090 0.9994  46.5
      0.5349 0.2025 0.4726 0.2610 0.0576 0.0061 0.9997  44.9
      0.5511 0.2238 0.4875 0.2391 0.0454 0.0040 0.9998  43.4
      0.5673 0.2463 0.4992 0.2166 0.0352 0.0026 0.9999  41.9
      0.5835 0.2700 0.5074 0.1940 0.0269 0.0017 1.0000  40.6
      0.5997 0.2947 0.5122 0.1718 0.0202 0.0010 1.0000  39.3
      0.6159 0.3205 0.5135 0.1504 0.0150 0.0006 1.0000  38.1
      0.6321 0.3472 0.5112 0.1303 0.0109 0.0004 1.0000  37.0
      0.6483 0.3746 0.5057 0.1116 0.0078 0.0002 1.0000  35.9
    
    Lower boundary (futility or Type II Error)
              Analysis
       Theta     1      2      3      4      5  Total
      0.0000 6e-04 0.0013 0.0028 0.0063 0.0140 0.0250
      0.0162 4e-04 0.0009 0.0019 0.0042 0.0095 0.0170
      0.0324 3e-04 0.0006 0.0013 0.0028 0.0063 0.0114
      0.0486 3e-04 0.0004 0.0009 0.0018 0.0041 0.0074
      0.0648 2e-04 0.0003 0.0006 0.0011 0.0025 0.0047
      0.0810 1e-04 0.0002 0.0004 0.0007 0.0016 0.0030
      0.0972 1e-04 0.0001 0.0002 0.0004 0.0009 0.0018
      0.1135 1e-04 0.0001 0.0001 0.0003 0.0005 0.0011
      0.1297 1e-04 0.0001 0.0001 0.0001 0.0003 0.0007
      0.1459 0e+00 0.0000 0.0001 0.0001 0.0002 0.0004
      0.1621 0e+00 0.0000 0.0000 0.0000 0.0001 0.0002
      0.1783 0e+00 0.0000 0.0000 0.0000 0.0000 0.0001
      0.1945 0e+00 0.0000 0.0000 0.0000 0.0000 0.0001
      0.2107 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2269 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2431 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2593 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2755 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2917 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3079 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3242 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3404 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3566 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3728 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3890 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4052 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4214 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4376 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4538 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4700 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4862 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5024 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5186 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5349 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5511 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5673 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5835 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5997 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.6159 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.6321 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.6483 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
    Symmetric two-sided group sequential design with
    90 % power and 2.5 % Type I Error.
    Spending computations assume trial stops
    if a bound is crossed.
    
                  
      Analysis  N   Z   Nominal p  Spend
             1  21 3.25    0.0006 0.0006
             2  41 2.99    0.0014 0.0013
             3  62 2.69    0.0036 0.0028
             4  82 2.37    0.0088 0.0063
             5 103 2.03    0.0214 0.0140
         Total                    0.0250 
    
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3      4      5 Total  E{N}
      0.0000 0.0006 0.0013 0.0028 0.0063 0.0140 0.025 101.6
      0.3242 0.0370 0.1512 0.2647 0.2699 0.1771 0.900  73.7
    
    Lower boundary (futility or Type II Error)
              Analysis
       Theta     1      2      3      4     5 Total
      0.0000 6e-04 0.0013 0.0028 0.0063 0.014 0.025
      0.3242 0e+00 0.0000 0.0000 0.0000 0.000 0.000
    Symmetric two-sided group sequential design with
    90 % power and 2.5 % Type I Error.
    Spending computations assume trial stops
    if a bound is crossed.
    
                  
      Analysis  N   Z   Nominal p  Spend
             1  21 3.25    0.0006 0.0006
             2  41 2.99    0.0014 0.0013
             3  62 2.69    0.0036 0.0028
             4  82 2.37    0.0088 0.0063
             5 103 2.03    0.0214 0.0140
         Total                    0.0250 
    
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3      4      5 Total  E{N}
      0.0000 0.0006 0.0013 0.0028 0.0063 0.0140 0.025 101.6
      0.3242 0.0370 0.1512 0.2647 0.2699 0.1771 0.900  73.7
    
    Lower boundary (futility or Type II Error)
              Analysis
       Theta     1      2      3      4     5 Total
      0.0000 6e-04 0.0013 0.0028 0.0063 0.014 0.025
      0.3242 0e+00 0.0000 0.0000 0.0000 0.000 0.000
    NULL
    Symmetric two-sided group sequential design with
    90 % power and 2.5 % Type I Error.
    Spending computations assume trial stops
    if a bound is crossed.
    
                  
      Analysis  N   Z   Nominal p  Spend
             1  21 3.25    0.0006 0.0006
             2  41 2.99    0.0014 0.0013
             3  62 2.69    0.0036 0.0028
             4  82 2.37    0.0088 0.0063
             5 103 2.03    0.0214 0.0140
         Total                    0.0250 
    
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3      4      5  Total  E{N}
      0.0000 0.0006 0.0013 0.0028 0.0063 0.0140 0.0250 101.6
      0.0162 0.0007 0.0018 0.0041 0.0092 0.0202 0.0359 101.6
      0.0324 0.0009 0.0024 0.0058 0.0131 0.0282 0.0505 101.4
      0.0486 0.0012 0.0033 0.0082 0.0183 0.0386 0.0696 101.2
      0.0648 0.0015 0.0045 0.0112 0.0251 0.0514 0.0938 100.9
      0.0810 0.0020 0.0061 0.0153 0.0338 0.0667 0.1238 100.4
      0.0972 0.0025 0.0080 0.0205 0.0445 0.0845 0.1599  99.9
      0.1135 0.0031 0.0106 0.0270 0.0574 0.1044 0.2024  99.1
      0.1297 0.0038 0.0137 0.0351 0.0726 0.1258 0.2511  98.2
      0.1459 0.0048 0.0177 0.0450 0.0901 0.1479 0.3055  97.2
      0.1621 0.0059 0.0225 0.0568 0.1097 0.1696 0.3645  95.9
      0.1783 0.0072 0.0284 0.0707 0.1308 0.1898 0.4270  94.4
      0.1945 0.0088 0.0356 0.0867 0.1531 0.2073 0.4914  92.8
      0.2107 0.0107 0.0441 0.1048 0.1756 0.2209 0.5561  90.9
      0.2269 0.0130 0.0541 0.1248 0.1977 0.2299 0.6194  88.8
      0.2431 0.0157 0.0657 0.1465 0.2183 0.2335 0.6796  86.6
      0.2593 0.0188 0.0791 0.1696 0.2364 0.2316 0.7355  84.2
      0.2755 0.0224 0.0943 0.1936 0.2514 0.2243 0.7859  81.6
      0.2917 0.0266 0.1114 0.2179 0.2622 0.2122 0.8303  79.0
      0.3079 0.0315 0.1304 0.2418 0.2685 0.1961 0.8683  76.4
      0.3242 0.0370 0.1512 0.2647 0.2699 0.1771 0.9000  73.7
      0.3404 0.0434 0.1738 0.2859 0.2664 0.1562 0.9257  71.0
      0.3566 0.0506 0.1980 0.3046 0.2582 0.1347 0.9461  68.3
      0.3728 0.0587 0.2236 0.3202 0.2457 0.1136 0.9617  65.7
      0.3890 0.0677 0.2502 0.3322 0.2297 0.0936 0.9735  63.1
      0.4052 0.0779 0.2776 0.3401 0.2110 0.0754 0.9820  60.7
      0.4214 0.0891 0.3053 0.3438 0.1905 0.0594 0.9881  58.3
      0.4376 0.1015 0.3330 0.3430 0.1689 0.0458 0.9923  56.1
      0.4538 0.1152 0.3602 0.3380 0.1473 0.0345 0.9952  53.9
      0.4700 0.1300 0.3864 0.3289 0.1262 0.0255 0.9970  51.9
      0.4862 0.1462 0.4112 0.3161 0.1063 0.0184 0.9982  50.0
      0.5024 0.1637 0.4341 0.3001 0.0881 0.0130 0.9990  48.2
      0.5186 0.1824 0.4547 0.2815 0.0718 0.0090 0.9994  46.5
      0.5349 0.2025 0.4726 0.2610 0.0576 0.0061 0.9997  44.9
      0.5511 0.2238 0.4875 0.2391 0.0454 0.0040 0.9998  43.4
      0.5673 0.2463 0.4992 0.2166 0.0352 0.0026 0.9999  41.9
      0.5835 0.2700 0.5074 0.1940 0.0269 0.0017 1.0000  40.6
      0.5997 0.2947 0.5122 0.1718 0.0202 0.0010 1.0000  39.3
      0.6159 0.3205 0.5135 0.1504 0.0150 0.0006 1.0000  38.1
      0.6321 0.3472 0.5112 0.1303 0.0109 0.0004 1.0000  37.0
      0.6483 0.3746 0.5057 0.1116 0.0078 0.0002 1.0000  35.9
    
    Lower boundary (futility or Type II Error)
              Analysis
       Theta     1      2      3      4      5  Total
      0.0000 6e-04 0.0013 0.0028 0.0063 0.0140 0.0250
      0.0162 4e-04 0.0009 0.0019 0.0042 0.0095 0.0170
      0.0324 3e-04 0.0006 0.0013 0.0028 0.0063 0.0114
      0.0486 3e-04 0.0004 0.0009 0.0018 0.0041 0.0074
      0.0648 2e-04 0.0003 0.0006 0.0011 0.0025 0.0047
      0.0810 1e-04 0.0002 0.0004 0.0007 0.0016 0.0030
      0.0972 1e-04 0.0001 0.0002 0.0004 0.0009 0.0018
      0.1135 1e-04 0.0001 0.0001 0.0003 0.0005 0.0011
      0.1297 1e-04 0.0001 0.0001 0.0001 0.0003 0.0007
      0.1459 0e+00 0.0000 0.0001 0.0001 0.0002 0.0004
      0.1621 0e+00 0.0000 0.0000 0.0000 0.0001 0.0002
      0.1783 0e+00 0.0000 0.0000 0.0000 0.0000 0.0001
      0.1945 0e+00 0.0000 0.0000 0.0000 0.0000 0.0001
      0.2107 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2269 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2431 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2593 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2755 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.2917 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3079 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3242 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3404 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3566 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3728 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.3890 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4052 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4214 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4376 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4538 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4700 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.4862 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5024 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5186 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5349 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5511 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5673 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5835 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.5997 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.6159 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.6321 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.6483 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
    Symmetric two-sided group sequential design with
    90 % power and 2.5 % Type I Error.
    Spending computations assume trial stops
    if a bound is crossed.
    
                  
      Analysis  N   Z   Nominal p  Spend
             1  21 3.25    0.0006 0.0006
             2  41 2.99    0.0014 0.0013
             3  62 2.69    0.0036 0.0028
             4  82 2.37    0.0088 0.0063
             5 103 2.03    0.0214 0.0140
         Total                    0.0250 
    
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3      4      5 Total  E{N}
      0.0000 0.0006 0.0013 0.0028 0.0063 0.0140 0.025 101.6
      0.3242 0.0370 0.1512 0.2647 0.2699 0.1771 0.900  73.7
    
    Lower boundary (futility or Type II Error)
              Analysis
       Theta     1      2      3      4     5 Total
      0.0000 6e-04 0.0013 0.0028 0.0063 0.014 0.025
      0.3242 0e+00 0.0000 0.0000 0.0000 0.000 0.000
    Time to event group sequential design with HR= 0.5 
    Equal randomization:          ratio=1
    Asymmetric two-sided group sequential design with
    90 % power and 2.5 % Type I Error.
    Upper bound spending computations assume
    trial continues if lower bound is crossed.
    
                    ----Lower bounds----  ----Upper bounds-----
      Analysis  N   Z   Nominal p Spend+  Z   Nominal p Spend++
             1  38 0.55    0.7089 0.0577 3.01    0.0013  0.0013
             2  75 1.30    0.9027 0.0239 2.55    0.0054  0.0049
             3 112 2.00    0.9772 0.0184 2.00    0.0228  0.0188
         Total                    0.1000                 0.0250 
    + lower bound beta spending (under H1):
     Kim-DeMets (power) spending function with rho = 0.5.
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3  Total E{N}
      0.0000 0.0013 0.0048 0.0130 0.0191 50.6
      0.0174 0.0018 0.0073 0.0197 0.0289 52.7
      0.0349 0.0026 0.0109 0.0290 0.0425 55.0
      0.0523 0.0036 0.0159 0.0414 0.0608 57.5
      0.0698 0.0049 0.0226 0.0573 0.0848 60.2
      0.0872 0.0066 0.0317 0.0770 0.1152 62.9
      0.1047 0.0088 0.0434 0.1004 0.1526 65.6
      0.1221 0.0117 0.0583 0.1271 0.1970 68.3
      0.1396 0.0153 0.0767 0.1563 0.2483 70.9
      0.1570 0.0199 0.0991 0.1868 0.3058 73.2
      0.1744 0.0257 0.1255 0.2170 0.3681 75.3
      0.1919 0.0327 0.1559 0.2451 0.4337 77.1
      0.2093 0.0413 0.1900 0.2694 0.5006 78.5
      0.2268 0.0516 0.2274 0.2881 0.5671 79.4
      0.2442 0.0638 0.2672 0.3001 0.6310 79.8
      0.2617 0.0782 0.3083 0.3044 0.6909 79.8
      0.2791 0.0949 0.3495 0.3010 0.7454 79.4
      0.2965 0.1141 0.3895 0.2902 0.7938 78.5
      0.3140 0.1359 0.4268 0.2729 0.8356 77.3
      0.3314 0.1604 0.4600 0.2505 0.8709 75.8
      0.3489 0.1877 0.4879 0.2244 0.9000 74.0
      0.3663 0.2176 0.5095 0.1964 0.9235 72.1
      0.3838 0.2501 0.5241 0.1679 0.9422 70.0
      0.4012 0.2851 0.5313 0.1404 0.9567 67.9
      0.4187 0.3222 0.5310 0.1147 0.9679 65.7
      0.4361 0.3611 0.5235 0.0917 0.9763 63.6
      0.4535 0.4016 0.5094 0.0717 0.9827 61.5
      0.4710 0.4431 0.4894 0.0548 0.9874 59.4
      0.4884 0.4853 0.4645 0.0411 0.9909 57.4
      0.5059 0.5277 0.4357 0.0301 0.9934 55.5
      0.5233 0.5697 0.4040 0.0216 0.9953 53.7
      0.5408 0.6110 0.3705 0.0152 0.9967 51.9
      0.5582 0.6510 0.3362 0.0104 0.9976 50.3
      0.5757 0.6894 0.3019 0.0070 0.9983 48.8
      0.5931 0.7259 0.2683 0.0046 0.9988 47.4
      0.6105 0.7601 0.2361 0.0030 0.9992 46.0
      0.6280 0.7919 0.2057 0.0019 0.9995 44.8
      0.6454 0.8210 0.1775 0.0012 0.9996 43.7
      0.6629 0.8474 0.1516 0.0007 0.9998 42.7
      0.6803 0.8711 0.1283 0.0004 0.9998 41.9
      0.6978 0.8921 0.1075 0.0002 0.9999 41.1
    
    Lower boundary (futility or Type II Error)
              Analysis
       Theta      1      2      3  Total
      0.0000 0.7089 0.2112 0.0608 0.9809
      0.0174 0.6715 0.2247 0.0749 0.9711
      0.0349 0.6322 0.2352 0.0900 0.9575
      0.0523 0.5916 0.2423 0.1053 0.9392
      0.0698 0.5499 0.2454 0.1200 0.9152
      0.0872 0.5076 0.2442 0.1329 0.8848
      0.1047 0.4653 0.2389 0.1432 0.8474
      0.1221 0.4234 0.2296 0.1501 0.8030
      0.1396 0.3823 0.2166 0.1528 0.7517
      0.1570 0.3425 0.2006 0.1511 0.6942
      0.1744 0.3043 0.1824 0.1452 0.6319
      0.1919 0.2682 0.1627 0.1354 0.5663
      0.2093 0.2344 0.1424 0.1226 0.4994
      0.2268 0.2031 0.1222 0.1077 0.4329
      0.2442 0.1744 0.1028 0.0918 0.3690
      0.2617 0.1485 0.0848 0.0758 0.3091
      0.2791 0.1252 0.0686 0.0608 0.2546
      0.2965 0.1047 0.0543 0.0472 0.2062
      0.3140 0.0867 0.0422 0.0356 0.1644
      0.3314 0.0711 0.0321 0.0259 0.1291
      0.3489 0.0577 0.0239 0.0184 0.1000
      0.3663 0.0465 0.0175 0.0126 0.0765
      0.3838 0.0370 0.0125 0.0083 0.0578
      0.4012 0.0292 0.0087 0.0054 0.0433
      0.4187 0.0228 0.0060 0.0033 0.0321
      0.4361 0.0176 0.0040 0.0020 0.0237
      0.4535 0.0135 0.0026 0.0012 0.0173
      0.4710 0.0102 0.0017 0.0007 0.0126
      0.4884 0.0077 0.0011 0.0004 0.0091
      0.5059 0.0057 0.0007 0.0002 0.0066
      0.5233 0.0042 0.0004 0.0001 0.0047
      0.5408 0.0030 0.0002 0.0000 0.0033
      0.5582 0.0022 0.0001 0.0000 0.0024
      0.5757 0.0016 0.0001 0.0000 0.0017
      0.5931 0.0011 0.0000 0.0000 0.0012
      0.6105 0.0008 0.0000 0.0000 0.0008
      0.6280 0.0005 0.0000 0.0000 0.0005
      0.6454 0.0004 0.0000 0.0000 0.0004
      0.6629 0.0002 0.0000 0.0000 0.0002
      0.6803 0.0002 0.0000 0.0000 0.0002
      0.6978 0.0001 0.0000 0.0000 0.0001
                 T         n    Events HR futility HR efficacy
    IA 1  14.62151  94.04674  37.07307       0.835       0.372
    IA 2  23.01537 148.03673  74.14613       0.740       0.554
    Final 36.00000 154.36995 111.21920       0.684       0.684
    Accrual rates:
         Stratum 1
    0-24      6.43
    Control event rates (H1):
          Stratum 1
    0-Inf      0.12
    Censoring rates:
          Stratum 1
    0-Inf      0.02
    One-sided group sequential design with
    90 % power and 2.5 % Type I Error.
               Sample
                Size 
      Analysis Ratio*  Z   Nominal p  Spend
             1  0.205 3.25    0.0006 0.0006
             2  0.409 2.99    0.0014 0.0013
             3  0.614 2.69    0.0036 0.0028
             4  0.819 2.37    0.0088 0.0063
             5  1.023 2.03    0.0214 0.0140
         Total                       0.0250 
    
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    * Sample size ratio compared to fixed design with no interim
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3      4      5  Total   E{N}
      0.0000 0.0006 0.0013 0.0028 0.0063 0.0140 0.0250 1.0197
      0.1621 0.0007 0.0018 0.0041 0.0092 0.0202 0.0359 1.0182
      0.3242 0.0009 0.0024 0.0058 0.0131 0.0282 0.0505 1.0161
      0.4862 0.0012 0.0033 0.0082 0.0183 0.0386 0.0696 1.0133
      0.6483 0.0015 0.0045 0.0112 0.0251 0.0514 0.0938 1.0096
      0.8104 0.0020 0.0061 0.0153 0.0338 0.0667 0.1238 1.0049
      0.9725 0.0025 0.0080 0.0205 0.0445 0.0845 0.1599 0.9990
      1.1345 0.0031 0.0106 0.0270 0.0574 0.1044 0.2024 0.9916
      1.2966 0.0038 0.0137 0.0351 0.0726 0.1258 0.2511 0.9826
      1.4587 0.0048 0.0177 0.0450 0.0901 0.1479 0.3055 0.9718
      1.6208 0.0059 0.0225 0.0568 0.1097 0.1696 0.3645 0.9591
      1.7828 0.0072 0.0284 0.0707 0.1308 0.1898 0.4270 0.9443
      1.9449 0.0088 0.0356 0.0867 0.1531 0.2073 0.4914 0.9275
      2.1070 0.0107 0.0441 0.1048 0.1756 0.2209 0.5561 0.9088
      2.2691 0.0130 0.0541 0.1248 0.1977 0.2299 0.6194 0.8881
      2.4311 0.0157 0.0657 0.1465 0.2183 0.2335 0.6796 0.8656
      2.5932 0.0188 0.0791 0.1696 0.2364 0.2316 0.7355 0.8417
      2.7553 0.0224 0.0943 0.1936 0.2514 0.2243 0.7859 0.8165
      2.9174 0.0266 0.1114 0.2179 0.2622 0.2122 0.8303 0.7904
      3.0794 0.0315 0.1304 0.2418 0.2685 0.1961 0.8683 0.7636
      3.2415 0.0370 0.1512 0.2647 0.2699 0.1771 0.9000 0.7366
      3.4036 0.0434 0.1738 0.2859 0.2664 0.1562 0.9257 0.7096
      3.5657 0.0506 0.1980 0.3046 0.2582 0.1347 0.9461 0.6829
      3.7277 0.0587 0.2236 0.3202 0.2457 0.1136 0.9617 0.6567
      3.8898 0.0677 0.2502 0.3322 0.2297 0.0936 0.9735 0.6313
      4.0519 0.0779 0.2776 0.3401 0.2110 0.0754 0.9820 0.6068
      4.2140 0.0891 0.3053 0.3438 0.1905 0.0594 0.9881 0.5832
      4.3760 0.1015 0.3330 0.3430 0.1689 0.0458 0.9923 0.5608
      4.5381 0.1152 0.3602 0.3380 0.1473 0.0345 0.9952 0.5394
      4.7002 0.1300 0.3864 0.3289 0.1262 0.0255 0.9970 0.5192
      4.8623 0.1462 0.4112 0.3161 0.1063 0.0184 0.9982 0.5001
      5.0243 0.1637 0.4341 0.3001 0.0881 0.0130 0.9990 0.4820
      5.1864 0.1824 0.4547 0.2815 0.0718 0.0090 0.9994 0.4650
      5.3485 0.2025 0.4726 0.2610 0.0576 0.0061 0.9997 0.4489
      5.5106 0.2238 0.4875 0.2391 0.0454 0.0040 0.9998 0.4337
      5.6727 0.2463 0.4992 0.2166 0.0352 0.0026 0.9999 0.4194
      5.8347 0.2700 0.5074 0.1940 0.0269 0.0017 1.0000 0.4059
      5.9968 0.2947 0.5122 0.1718 0.0202 0.0010 1.0000 0.3931
      6.1589 0.3205 0.5135 0.1504 0.0150 0.0006 1.0000 0.3811
      6.3210 0.3472 0.5112 0.1303 0.0109 0.0004 1.0000 0.3697
      6.4830 0.3746 0.5057 0.1116 0.0078 0.0002 1.0000 0.3589
                   Lower bounds   Upper bounds
      Analysis  N    Z   Nominal p  Z   Nominal p
             1  21 -3.25    0.0006 3.25    0.0006
             2  41 -2.99    0.0014 2.99    0.0014
             3  62 -2.69    0.0036 2.69    0.0036
             4  82 -2.37    0.0088 2.37    0.0088
             5 103 -2.03    0.0214 2.03    0.0214
    
    Boundary crossing probabilities and expected sample size assume
    any cross stops the trial
    
    Upper boundary
              Analysis
      Theta      1      2      3      4      5  Total  E{N}
      0.000 0.0006 0.0013 0.0028 0.0063 0.0140 0.0250 101.6
      0.025 0.0008 0.0021 0.0050 0.0112 0.0243 0.0434 101.5
      0.050 0.0012 0.0034 0.0084 0.0188 0.0396 0.0714 101.2
      0.075 0.0018 0.0054 0.0137 0.0303 0.0607 0.1119 100.6
      0.100 0.0026 0.0084 0.0215 0.0465 0.0877 0.1667  99.8
      0.125 0.0036 0.0127 0.0326 0.0680 0.1195 0.2365  98.5
      0.150 0.0050 0.0188 0.0479 0.0949 0.1535 0.3201  96.9
      0.175 0.0069 0.0272 0.0677 0.1264 0.1859 0.4141  94.7
      0.200 0.0094 0.0383 0.0926 0.1607 0.2124 0.5134  92.1
      0.225 0.0127 0.0528 0.1223 0.1951 0.2291 0.6120  89.1
      0.250 0.0169 0.0711 0.1562 0.2263 0.2334 0.7039  85.6
      0.275 0.0223 0.0938 0.1928 0.2509 0.2246 0.7844  81.7
      0.300 0.0290 0.1208 0.2302 0.2660 0.2044 0.8505  77.7
      0.325 0.0374 0.1524 0.2659 0.2699 0.1760 0.9015  73.5
      0.350 0.0475 0.1880 0.2974 0.2620 0.1434 0.9384  69.4
      0.375 0.0598 0.2272 0.3221 0.2437 0.1107 0.9636  65.3
      0.400 0.0745 0.2688 0.3381 0.2173 0.0810 0.9796  61.5
      0.425 0.0918 0.3115 0.3440 0.1857 0.0562 0.9892  57.8
      0.450 0.1118 0.3539 0.3395 0.1523 0.0370 0.9946  54.4
      0.475 0.1349 0.3942 0.3253 0.1200 0.0231 0.9975  51.3
      0.500 0.1610 0.4308 0.3027 0.0907 0.0137 0.9989  48.5
    
    Lower boundary
              Analysis
      Theta     1      2      3      4      5  Total
      0.000 6e-04 0.0013 0.0028 0.0063 0.0140 0.0250
      0.025 4e-04 0.0007 0.0016 0.0034 0.0076 0.0137
      0.050 3e-04 0.0004 0.0008 0.0017 0.0039 0.0071
      0.075 2e-04 0.0002 0.0004 0.0008 0.0019 0.0036
      0.100 1e-04 0.0001 0.0002 0.0004 0.0009 0.0017
      0.125 1e-04 0.0001 0.0001 0.0002 0.0004 0.0008
      0.150 0e+00 0.0000 0.0000 0.0001 0.0001 0.0003
      0.175 0e+00 0.0000 0.0000 0.0000 0.0001 0.0001
      0.200 0e+00 0.0000 0.0000 0.0000 0.0000 0.0001
      0.225 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.250 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.275 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.300 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.325 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.350 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.375 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.400 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.425 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.450 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.475 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.500 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
                   Lower bounds   Upper bounds
      Analysis  N    Z   Nominal p  Z   Nominal p
             1  21 -3.25    0.0006 3.25    0.0006
             2  41 -2.99    0.0014 2.99    0.0014
             3  62 -2.69    0.0036 2.69    0.0036
             4  82 -2.37    0.0088 2.37    0.0088
             5 103 -2.03    0.0214 2.03    0.0214
    
    Boundary crossing probabilities and expected sample size assume
    any cross stops the trial
    
    Upper boundary
              Analysis
      Theta      1      2      3      4      5  Total  E{N}
      0.000 0.0006 0.0013 0.0028 0.0063 0.0140 0.0250 101.6
      0.025 0.0008 0.0021 0.0050 0.0112 0.0243 0.0434 101.5
      0.050 0.0012 0.0034 0.0084 0.0188 0.0396 0.0714 101.2
      0.075 0.0018 0.0054 0.0137 0.0303 0.0607 0.1119 100.6
      0.100 0.0026 0.0084 0.0215 0.0465 0.0877 0.1667  99.8
      0.125 0.0036 0.0127 0.0326 0.0680 0.1195 0.2365  98.5
      0.150 0.0050 0.0188 0.0479 0.0949 0.1535 0.3201  96.9
      0.175 0.0069 0.0272 0.0677 0.1264 0.1859 0.4141  94.7
      0.200 0.0094 0.0383 0.0926 0.1607 0.2124 0.5134  92.1
      0.225 0.0127 0.0528 0.1223 0.1951 0.2291 0.6120  89.1
      0.250 0.0169 0.0711 0.1562 0.2263 0.2334 0.7039  85.6
      0.275 0.0223 0.0938 0.1928 0.2509 0.2246 0.7844  81.7
      0.300 0.0290 0.1208 0.2302 0.2660 0.2044 0.8505  77.7
      0.325 0.0374 0.1524 0.2659 0.2699 0.1760 0.9015  73.5
      0.350 0.0475 0.1880 0.2974 0.2620 0.1434 0.9384  69.4
      0.375 0.0598 0.2272 0.3221 0.2437 0.1107 0.9636  65.3
      0.400 0.0745 0.2688 0.3381 0.2173 0.0810 0.9796  61.5
      0.425 0.0918 0.3115 0.3440 0.1857 0.0562 0.9892  57.8
      0.450 0.1118 0.3539 0.3395 0.1523 0.0370 0.9946  54.4
      0.475 0.1349 0.3942 0.3253 0.1200 0.0231 0.9975  51.3
      0.500 0.1610 0.4308 0.3027 0.0907 0.0137 0.9989  48.5
    
    Lower boundary
              Analysis
      Theta     1      2      3      4      5  Total
      0.000 6e-04 0.0013 0.0028 0.0063 0.0140 0.0250
      0.025 4e-04 0.0007 0.0016 0.0034 0.0076 0.0137
      0.050 3e-04 0.0004 0.0008 0.0017 0.0039 0.0071
      0.075 2e-04 0.0002 0.0004 0.0008 0.0019 0.0036
      0.100 1e-04 0.0001 0.0002 0.0004 0.0009 0.0017
      0.125 1e-04 0.0001 0.0001 0.0002 0.0004 0.0008
      0.150 0e+00 0.0000 0.0000 0.0001 0.0001 0.0003
      0.175 0e+00 0.0000 0.0000 0.0000 0.0001 0.0001
      0.200 0e+00 0.0000 0.0000 0.0000 0.0000 0.0001
      0.225 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.250 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.275 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.300 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.325 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.350 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.375 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.400 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.425 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.450 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.475 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.500 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
    Asymmetric two-sided group sequential design with
    90 % power and 2.5 % Type I Error.
    Spending computations assume trial stops
    if a bound is crossed.
    
                     ----Lower bounds----  ----Upper bounds-----
      Analysis  N    Z   Nominal p Spend+  Z   Nominal p Spend++
             1  21 -3.25    0.0006 0.0006 3.25    0.0006  0.0006
             2  41 -2.99    0.0014 0.0013 2.99    0.0014  0.0013
             3  62 -2.69    0.0036 0.0028 2.69    0.0036  0.0028
             4  82 -2.37    0.0088 0.0063 2.37    0.0088  0.0063
             5 103 -2.03    0.0214 0.0140 2.03    0.0214  0.0140
         Total                     0.0250                 0.0250 
    + lower bound beta spending (under H1):
     Hwang-Shih-DeCani spending function with gamma = -4.
    ++ alpha spending:
     Hwang-Shih-DeCani spending function with gamma = -4.
    
    Boundary crossing probabilities and expected sample size
    assume any cross stops the trial
    
    Upper boundary (power or Type I Error)
              Analysis
       Theta      1      2      3      4      5 Total  E{N}
      0.0000 0.0006 0.0013 0.0028 0.0063 0.0140 0.025 101.6
      0.3242 0.0370 0.1512 0.2647 0.2699 0.1771 0.900  73.7
    
    Lower boundary (futility or Type II Error)
              Analysis
       Theta     1      2      3      4     5 Total
      0.0000 6e-04 0.0013 0.0028 0.0063 0.014 0.025
      0.3242 0e+00 0.0000 0.0000 0.0000 0.000 0.000
                   Lower bounds   Upper bounds
      Analysis  N    Z   Nominal p  Z   Nominal p
             1  21 -3.25    0.0006 3.25    0.0006
             2  41 -2.99    0.0014 2.99    0.0014
             3  62 -2.69    0.0036 2.69    0.0036
             4  82 -2.37    0.0088 2.37    0.0088
             5 103 -2.03    0.0214 2.03    0.0214
    
    Boundary crossing probabilities and expected sample size assume
    any cross stops the trial
    
    Upper boundary
              Analysis
      Theta      1      2      3      4      5  Total  E{N}
      0.000 0.0006 0.0013 0.0028 0.0063 0.0140 0.0250 101.6
      0.025 0.0008 0.0021 0.0050 0.0112 0.0243 0.0434 101.5
      0.050 0.0012 0.0034 0.0084 0.0188 0.0396 0.0714 101.2
      0.075 0.0018 0.0054 0.0137 0.0303 0.0607 0.1119 100.6
      0.100 0.0026 0.0084 0.0215 0.0465 0.0877 0.1667  99.8
      0.125 0.0036 0.0127 0.0326 0.0680 0.1195 0.2365  98.5
      0.150 0.0050 0.0188 0.0479 0.0949 0.1535 0.3201  96.9
      0.175 0.0069 0.0272 0.0677 0.1264 0.1859 0.4141  94.7
      0.200 0.0094 0.0383 0.0926 0.1607 0.2124 0.5134  92.1
      0.225 0.0127 0.0528 0.1223 0.1951 0.2291 0.6120  89.1
      0.250 0.0169 0.0711 0.1562 0.2263 0.2334 0.7039  85.6
      0.275 0.0223 0.0938 0.1928 0.2509 0.2246 0.7844  81.7
      0.300 0.0290 0.1208 0.2302 0.2660 0.2044 0.8505  77.7
      0.325 0.0374 0.1524 0.2659 0.2699 0.1760 0.9015  73.5
      0.350 0.0475 0.1880 0.2974 0.2620 0.1434 0.9384  69.4
      0.375 0.0598 0.2272 0.3221 0.2437 0.1107 0.9636  65.3
      0.400 0.0745 0.2688 0.3381 0.2173 0.0810 0.9796  61.5
      0.425 0.0918 0.3115 0.3440 0.1857 0.0562 0.9892  57.8
      0.450 0.1118 0.3539 0.3395 0.1523 0.0370 0.9946  54.4
      0.475 0.1349 0.3942 0.3253 0.1200 0.0231 0.9975  51.3
      0.500 0.1610 0.4308 0.3027 0.0907 0.0137 0.9989  48.5
    
    Lower boundary
              Analysis
      Theta     1      2      3      4      5  Total
      0.000 6e-04 0.0013 0.0028 0.0063 0.0140 0.0250
      0.025 4e-04 0.0007 0.0016 0.0034 0.0076 0.0137
      0.050 3e-04 0.0004 0.0008 0.0017 0.0039 0.0071
      0.075 2e-04 0.0002 0.0004 0.0008 0.0019 0.0036
      0.100 1e-04 0.0001 0.0002 0.0004 0.0009 0.0017
      0.125 1e-04 0.0001 0.0001 0.0002 0.0004 0.0008
      0.150 0e+00 0.0000 0.0000 0.0001 0.0001 0.0003
      0.175 0e+00 0.0000 0.0000 0.0000 0.0001 0.0001
      0.200 0e+00 0.0000 0.0000 0.0000 0.0000 0.0001
      0.225 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.250 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.275 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.300 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.325 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.350 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.375 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.400 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.425 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.450 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.475 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.500 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
                   Lower bounds   Upper bounds
      Analysis  N    Z   Nominal p  Z   Nominal p
             1  21 -3.25    0.0006 3.25    0.0006
             2  41 -2.99    0.0014 2.99    0.0014
             3  62 -2.69    0.0036 2.69    0.0036
             4  82 -2.37    0.0088 2.37    0.0088
             5 103 -2.03    0.0214 2.03    0.0214
    
    Boundary crossing probabilities and expected sample size assume
    any cross stops the trial
    
    Upper boundary
              Analysis
      Theta      1      2      3      4      5  Total  E{N}
      0.000 0.0006 0.0013 0.0028 0.0063 0.0140 0.0250 101.6
      0.025 0.0008 0.0021 0.0050 0.0112 0.0243 0.0434 101.5
      0.050 0.0012 0.0034 0.0084 0.0188 0.0396 0.0714 101.2
      0.075 0.0018 0.0054 0.0137 0.0303 0.0607 0.1119 100.6
      0.100 0.0026 0.0084 0.0215 0.0465 0.0877 0.1667  99.8
      0.125 0.0036 0.0127 0.0326 0.0680 0.1195 0.2365  98.5
      0.150 0.0050 0.0188 0.0479 0.0949 0.1535 0.3201  96.9
      0.175 0.0069 0.0272 0.0677 0.1264 0.1859 0.4141  94.7
      0.200 0.0094 0.0383 0.0926 0.1607 0.2124 0.5134  92.1
      0.225 0.0127 0.0528 0.1223 0.1951 0.2291 0.6120  89.1
      0.250 0.0169 0.0711 0.1562 0.2263 0.2334 0.7039  85.6
      0.275 0.0223 0.0938 0.1928 0.2509 0.2246 0.7844  81.7
      0.300 0.0290 0.1208 0.2302 0.2660 0.2044 0.8505  77.7
      0.325 0.0374 0.1524 0.2659 0.2699 0.1760 0.9015  73.5
      0.350 0.0475 0.1880 0.2974 0.2620 0.1434 0.9384  69.4
      0.375 0.0598 0.2272 0.3221 0.2437 0.1107 0.9636  65.3
      0.400 0.0745 0.2688 0.3381 0.2173 0.0810 0.9796  61.5
      0.425 0.0918 0.3115 0.3440 0.1857 0.0562 0.9892  57.8
      0.450 0.1118 0.3539 0.3395 0.1523 0.0370 0.9946  54.4
      0.475 0.1349 0.3942 0.3253 0.1200 0.0231 0.9975  51.3
      0.500 0.1610 0.4308 0.3027 0.0907 0.0137 0.9989  48.5
    
    Lower boundary
              Analysis
      Theta     1      2      3      4      5  Total
      0.000 6e-04 0.0013 0.0028 0.0063 0.0140 0.0250
      0.025 4e-04 0.0007 0.0016 0.0034 0.0076 0.0137
      0.050 3e-04 0.0004 0.0008 0.0017 0.0039 0.0071
      0.075 2e-04 0.0002 0.0004 0.0008 0.0019 0.0036
      0.100 1e-04 0.0001 0.0002 0.0004 0.0009 0.0017
      0.125 1e-04 0.0001 0.0001 0.0002 0.0004 0.0008
      0.150 0e+00 0.0000 0.0000 0.0001 0.0001 0.0003
      0.175 0e+00 0.0000 0.0000 0.0000 0.0001 0.0001
      0.200 0e+00 0.0000 0.0000 0.0000 0.0000 0.0001
      0.225 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.250 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.275 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.300 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.325 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.350 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.375 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.400 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.425 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.450 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.475 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
      0.500 0e+00 0.0000 0.0000 0.0000 0.0000 0.0000
    NULL
    NULL
    Linear spending function with none = [ FAIL 7 | WARN 10 | SKIP 112 | PASS 1879 ]
    
    ══ Skipped tests (112) ═════════════════════════════════════════════════════════
    • On CRAN (112): 'test-independent-test-as_gt.R:2:3',
      'test-independent-test-as_rtf.R:2:3', 'test-independent-test-as_rtf.R:14:3',
      'test-independent-test-as_rtf.R:28:3', 'test-independent-test-as_rtf.R:41:3',
      'test-independent-test-as_rtf.R:53:3',
      'test-independent-test-gsBoundSummary.R:9:3',
      'test-independent-test-gsBoundSummary.R:16:3',
      'test-independent-test-gsBoundSummary.R:23:3',
      'test-independent-test-gsBoundSummary.R:31:3',
      'test-independent-test-gsBoundSummary.R:39:3',
      'test-independent-test-gsBoundSummary.R:47:3',
      'test-independent-test-gsBoundSummary.R:56:3',
      'test-independent-test-plot.binomialSPRT.R:11:3',
      'test-independent-test-plot.binomialSPRT.R:27:3',
      'test-independent-test-plot.gsBinomialExact.R:10:3',
      'test-independent-test-plot.gsBinomialExact.R:25:3',
      'test-independent-test-plot.gsBinomialExact.R:40:3',
      'test-independent-test-plot.gsBinomialExact.R:55:3',
      'test-independent-test-plot.gsBinomialExact.R:70:3',
      'test-independent-test-plot.gsDesign.R:4:3',
      'test-independent-test-plot.gsDesign.R:13:3',
      'test-independent-test-plot.gsDesign.R:22:3',
      'test-independent-test-plot.gsDesign.R:31:3',
      'test-independent-test-plot.gsDesign.R:40:3',
      'test-independent-test-plot.gsDesign.R:49:3',
      'test-independent-test-plot.gsDesign.R:58:3',
      'test-independent-test-plot.gsDesign.R:67:3',
      'test-independent-test-plot.gsDesign.R:76:3',
      'test-independent-test-plot.gsDesign.R:85:3',
      'test-independent-test-plot.gsDesign.R:94:3',
      'test-independent-test-plot.gsDesign.R:107:3',
      'test-independent-test-plot.gsDesign.R:120:3',
      'test-independent-test-plot.gsDesign.R:129:3',
      'test-independent-test-plot.gsProbability.R:5:3',
      'test-independent-test-plot.gsProbability.R:12:3',
      'test-independent-test-plot.gsProbability.R:19:3',
      'test-independent-test-plot.gsProbability.R:26:3',
      'test-independent-test-plot.gsProbability.R:33:3',
      'test-independent-test-plot.gsProbability.R:40:3',
      'test-independent-test-plot.gsProbability.R:47:3',
      'test-independent-test-plot.gsProbability.R:54:3',
      'test-independent-test-plot.gsProbability.R:61:3',
      'test-independent-test-plot.ssrCP.R:16:3',
      'test-independent-test-plotASN.R:67:3',
      'test-independent-test-plotASN.R:71:3',
      'test-independent-test-plotBval.R:51:3',
      'test-independent-test-plotHR.R:47:3', 'test-independent-test-plotRR.R:48:3',
      'test-independent-test-plotgsCP.R:42:3',
      'test-independent-test-plotgsCP.R:54:3',
      'test-independent-test-plotgsPower.R:39:3',
      'test-independent-test-plotgsPower.R:96:3',
      'test-independent-test-plotgsZ.R:55:3',
      'test-independent-test-plotsf.R:40:3', 'test-independent-test-plotsf.R:52:3',
      'test-independent-test-plotsf.R:64:3',
      'test-independent-test-print.eEvents.R:18:3',
      'test-independent-test-print.gsBoundSummary.R:11:3',
      'test-independent-test-print.gsDesign.R:9:3',
      'test-independent-test-print.gsDesign.R:16:3',
      'test-independent-test-print.gsDesign.R:23:3',
      'test-independent-test-print.gsDesign.R:30:3',
      'test-independent-test-print.gsDesign.R:37:3',
      'test-independent-test-print.gsDesign.R:44:3',
      'test-independent-test-print.gsDesign.R:51:3',
      'test-independent-test-print.gsDesign.R:58:3',
      'test-independent-test-print.gsDesign.R:65:3',
      'test-independent-test-print.gsProbability.R:8:3',
      'test-independent-test-print.gsProbability.R:18:3',
      'test-independent-test-print.gsProbability.R:26:3',
      'test-independent-test-print.gsSurv.R:15:3',
      'test-independent-test-print.gsSurv.R:29:3',
      'test-independent-test-print.gsSurv.R:39:3',
      'test-independent-test-print.gsSurv.R:49:3',
      'test-independent-test-print.gsSurv.R:58:3',
      'test-independent-test-print.nSurv.R:19:3',
      'test-independent-test-print.nSurv.R:30:3',
      'test-independent-test-print.nSurv.R:42:3',
      'test-independent-test-print.nSurvival.R:19:3',
      'test-independent-test-print.nSurvival.R:29:3',
      'test-independent-test-print.nSurvival.R:40:3',
      'test-independent-test-print.nSurvival.R:51:3',
      'test-independent-test-print.nSurvival.R:63:3',
      'test-independent-test-print.nSurvival.R:75:3',
      'test-independent-test-print.nSurvival.R:87:3',
      'test-independent-test-sfprint.R:12:5',
      'test-independent-test-sfprint.R:20:3',
      'test-independent-test-sfprint.R:28:3',
      'test-independent-test-sfprint.R:38:3',
      'test-independent-test-sfprint.R:48:3',
      'test-independent-test-sfprint.R:58:3',
      'test-independent-test-summary.gsDesign.R:8:3',
      'test-independent-test-summary.gsDesign.R:15:3',
      'test-independent-test-summary.gsDesign.R:24:5',
      'test-independent-test-summary.gsDesign.R:34:5',
      'test-independent-test-summary.gsDesign.R:44:5',
      'test-independent-test-summary.gsDesign.R:54:5',
      'test-independent-test-summary.gsDesign.R:92:3',
      'test-independent-test-summary.gsDesign.R:107:3',
      'test-independent-test-summary.gsDesign.R:116:3',
      'test-independent-test-summary.gsDesign.R:125:5',
      'test-independent-test-summary.spendfn.R:18:3',
      'test-independent-test-summary.spendfn.R:25:3',
      'test-independent-test-summary.spendfn.R:32:3',
      'test-independent-test-summary.spendfn.R:42:3',
      'test-independent-test-summary.spendfn.R:51:3',
      'test-independent-test-summary.spendfn.R:60:3',
      'test-independent-test-xprint.R:13:5',
      'test-independent-test-xtable.gsSurv.R:12:5',
      'test-independent-test-xtable.gsSurv.R:23:5',
      'test-independent-test-xtable.gsSurv.R:37:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-independent-test-hGraph.R:3:3'): hGraph: Basic graph layout ────
    Error in `stat_ellipse(data = ellipseData, aes(x = x, y = y, group = n, 
        fill = as.factor(fill)), geom = "polygon")`: Problem while computing stat.
    ℹ Error occurred in the 1st layer.
    Caused by error in `setup_params()`:
    ! The package "MASS" is required for calculating ellipses with `type =
      "t"`.
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger("basic layout", x) at test-independent-test-hGraph.R:3:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_build(x)
      8. │       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$compute_statistic(d, layout)
     18. │               └─ggplot2 (local) compute_statistic(..., self = self)
     19. │                 └─self$stat$setup_params(data, self$stat_params)
     20. │                   └─ggplot2 (local) setup_params(...)
     21. │                     └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
     22. │                       └─base::stop(cnd)
     23. └─rlang (local) `<fn>`(`<rlb_r___>`)
     24.   └─handlers[[1L]](cnd)
     25.     └─cli::cli_abort(...)
     26.       └─rlang::abort(...)
    ── Error ('test-independent-test-hGraph.R:8:3'): hGraph: Note clockwise ordering ──
    Error in `stat_ellipse(data = ellipseData, aes(x = x, y = y, group = n, 
        fill = as.factor(fill)), geom = "polygon")`: Problem while computing stat.
    ℹ Error occurred in the 1st layer.
    Caused by error in `setup_params()`:
    ! The package "MASS" is required for calculating ellipses with `type =
      "t"`.
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger("clockwise order", x) at test-independent-test-hGraph.R:8:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_build(x)
      8. │       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$compute_statistic(d, layout)
     18. │               └─ggplot2 (local) compute_statistic(..., self = self)
     19. │                 └─self$stat$setup_params(data, self$stat_params)
     20. │                   └─ggplot2 (local) setup_params(...)
     21. │                     └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
     22. │                       └─base::stop(cnd)
     23. └─rlang (local) `<fn>`(`<rlb_r___>`)
     24.   └─handlers[[1L]](cnd)
     25.     └─cli::cli_abort(...)
     26.       └─rlang::abort(...)
    ── Error ('test-independent-test-hGraph.R:13:3'): hGraph: Add colors (default is 3 gray shades) ──
    Error in `stat_ellipse(data = ellipseData, aes(x = x, y = y, group = n, 
        fill = as.factor(fill)), geom = "polygon")`: Problem while computing stat.
    ℹ Error occurred in the 1st layer.
    Caused by error in `setup_params()`:
    ! The package "MASS" is required for calculating ellipses with `type =
      "t"`.
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger("gray shades", x) at test-independent-test-hGraph.R:13:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_build(x)
      8. │       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$compute_statistic(d, layout)
     18. │               └─ggplot2 (local) compute_statistic(..., self = self)
     19. │                 └─self$stat$setup_params(data, self$stat_params)
     20. │                   └─ggplot2 (local) setup_params(...)
     21. │                     └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
     22. │                       └─base::stop(cnd)
     23. └─rlang (local) `<fn>`(`<rlb_r___>`)
     24.   └─handlers[[1L]](cnd)
     25.     └─cli::cli_abort(...)
     26.       └─rlang::abort(...)
    ── Error ('test-independent-test-hGraph.R:18:3'): hGraph: Use a hue palette ────
    Error in `stat_ellipse(data = ellipseData, aes(x = x, y = y, group = n, 
        fill = as.factor(fill)), geom = "polygon")`: Problem while computing stat.
    ℹ Error occurred in the 1st layer.
    Caused by error in `setup_params()`:
    ! The package "MASS" is required for calculating ellipses with `type =
      "t"`.
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger("hue palette", x) at test-independent-test-hGraph.R:18:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_build(x)
      8. │       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$compute_statistic(d, layout)
     18. │               └─ggplot2 (local) compute_statistic(..., self = self)
     19. │                 └─self$stat$setup_params(data, self$stat_params)
     20. │                   └─ggplot2 (local) setup_params(...)
     21. │                     └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
     22. │                       └─base::stop(cnd)
     23. └─rlang (local) `<fn>`(`<rlb_r___>`)
     24.   └─handlers[[1L]](cnd)
     25.     └─cli::cli_abort(...)
     26.       └─rlang::abort(...)
    ── Error ('test-independent-test-hGraph.R:31:3'): hGraph: Different alpha allocation, hypotheses names, and transitions ──
    Error in `stat_ellipse(data = ellipseData, aes(x = x, y = y, group = n, 
        fill = as.factor(fill)), geom = "polygon")`: Problem while computing stat.
    ℹ Error occurred in the 1st layer.
    Caused by error in `setup_params()`:
    ! The package "MASS" is required for calculating ellipses with `type =
      "t"`.
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-independent-test-hGraph.R:31:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_build(x)
      8. │       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$compute_statistic(d, layout)
     18. │               └─ggplot2 (local) compute_statistic(..., self = self)
     19. │                 └─self$stat$setup_params(data, self$stat_params)
     20. │                   └─ggplot2 (local) setup_params(...)
     21. │                     └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
     22. │                       └─base::stop(cnd)
     23. └─rlang (local) `<fn>`(`<rlb_r___>`)
     24.   └─handlers[[1L]](cnd)
     25.     └─cli::cli_abort(...)
     26.       └─rlang::abort(...)
    ── Error ('test-independent-test-hGraph.R:51:3'): hGraph: Custom position and size of ellipses, change text to multi-line text ──
    Error in `stat_ellipse(data = ellipseData, aes(x = x, y = y, group = n, 
        fill = as.factor(fill)), geom = "polygon")`: Problem while computing stat.
    ℹ Error occurred in the 1st layer.
    Caused by error in `setup_params()`:
    ! The package "MASS" is required for calculating ellipses with `type =
      "t"`.
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger("custom ellipses multiline", x) at test-independent-test-hGraph.R:51:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_build(x)
      8. │       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$compute_statistic(d, layout)
     18. │               └─ggplot2 (local) compute_statistic(..., self = self)
     19. │                 └─self$stat$setup_params(data, self$stat_params)
     20. │                   └─ggplot2 (local) setup_params(...)
     21. │                     └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
     22. │                       └─base::stop(cnd)
     23. └─rlang (local) `<fn>`(`<rlb_r___>`)
     24.   └─handlers[[1L]](cnd)
     25.     └─cli::cli_abort(...)
     26.       └─rlang::abort(...)
    ── Error ('test-independent-test-hGraph.R:60:3'): hGraph: Number of digits to show for alphaHypotheses ──
    Error in `stat_ellipse(data = ellipseData, aes(x = x, y = y, group = n, 
        fill = as.factor(fill)), geom = "polygon")`: Problem while computing stat.
    ℹ Error occurred in the 1st layer.
    Caused by error in `setup_params()`:
    ! The package "MASS" is required for calculating ellipses with `type =
      "t"`.
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger("alpha digits", x) at test-independent-test-hGraph.R:60:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_build(x)
      8. │       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$compute_statistic(d, layout)
     18. │               └─ggplot2 (local) compute_statistic(..., self = self)
     19. │                 └─self$stat$setup_params(data, self$stat_params)
     20. │                   └─ggplot2 (local) setup_params(...)
     21. │                     └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
     22. │                       └─base::stop(cnd)
     23. └─rlang (local) `<fn>`(`<rlb_r___>`)
     24.   └─handlers[[1L]](cnd)
     25.     └─cli::cli_abort(...)
     26.       └─rlang::abort(...)
    
    [ FAIL 7 | WARN 10 | SKIP 112 | PASS 1879 ]
    Error: Test failures
    Execution halted

Package: gtExtras
Check: tests
New result: ERROR
    Running ‘testthat.R’ [56s/29s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(gtExtras)
    Loading required package: gt
    
    Attaching package: 'gt'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    
    Attaching package: 'gtExtras'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    > 
    > test_check("gtExtras")
    Starting 2 test processes
    [ FAIL 6 | WARN 4 | SKIP 19 | PASS 104 ]
    
    ══ Skipped tests (19) ══════════════════════════════════════════════════════════
    • On CRAN (19): 'test-fmt_pad_num.R:3:3', 'test-fmt_symbol_first.R:56:3',
      'test-fmt_symbol_first.R:61:3', 'test-fmt_symbol_first.R:66:3',
      'test-fmt_symbol_first.R:71:3', 'test-fontawesome-icons.R:3:3',
      'test-fontawesome-icons.R:101:3', 'test-fmt_pct_extra.R:3:3',
      'test-gt_image_multi_rows.R:3:3', 'test-gt_image_rows.R:3:3',
      'test-gt_img_circle.R:3:3', 'test-gt_summary_table.R:25:3',
      'test-gt_text_img.R:3:3', 'test-gtsave_extra.R:4:3',
      'test-html-helpers.R:24:3', 'test-icon_fun.R:3:3', 'test-img_header.R:3:3',
      'test-two-column-layouts.R:4:3', 'test-two-column-layouts.R:27:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-gt_pct_bar.R:93:3'): gt_pct_bar SVG is created and has specific palette ──
    round(bar_vals, 2) (`actual`) not equal to c(0, 119.06, 0, 124.02, 0, 85.04, 0, 85.04) (`expected`).
    
      `actual`: 0 0 119.06 0 0 124.02 0 0 85.04 0 and 2 more...
    `expected`: 0   119.06   0 124.02   0 85.04             ...
    ── Failure ('test-gt_pct_bar.R:97:3'): gt_pct_bar SVG is created and has specific palette ──
    `bar_colors` (`actual`) not equal to c(...) (`expected`).
    
    actual vs expected
    - "fill: none; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; stroke-width: 0.00; stroke: none;"
      "FF4343;"
      "BFBFBF;"
    - "fill: none; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; stroke-width: 0.00; stroke: none;"
      "FF4343;"
      "BFBFBF;"
    - "fill: none; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; stroke-width: 0.00; stroke: none;"
      "FF4343;"
      "BFBFBF;"
    - "fill: none; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; stroke-width: 0.00; stroke: none;"
    and 2 more ...
    ── Failure ('test-gt_plt_bar.R:43:3'): gt_plt_bar svg is created and has specific values ──
    `bar_vals` (`actual`) not equal to c("90.61", "90.61", "98.37", "92.33", "80.68", "78.10") (`expected`).
    
         actual   | expected               
     [1] "113.39" -                        
     [2] "90.61"  | "90.61"  [1]           
     [3] "113.39" -                        
     [4] "90.61"  | "90.61"  [2]           
     [5] "113.39" -                        
     [6] "98.37"  | "98.37"  [3]           
     [7] "113.39" -                        
     [8] "92.33"  | "92.33"  [4]           
     [9] "113.39" -                        
    [10] "80.68"  | "80.68"  [5]           
     ... ...        ...      and 2 more ...
    ── Failure ('test-gt_plt_bar.R:47:3'): gt_plt_bar svg is created and has specific values ──
    `bar_neg_vals` (`actual`) not equal to c("49.19", "32.79", "16.40", "16.40", "32.79", "49.19") (`expected`).
    
         actual   | expected               
     [1] "113.39" -                        
     [2] "49.19"  | "49.19"  [1]           
     [3] "113.39" -                        
     [4] "32.79"  | "32.79"  [2]           
     [5] "113.39" -                        
     [6] "16.40"  | "16.40"  [3]           
     [7] "113.39" -                        
     [8] "16.40"  | "16.40"  [4]           
     [9] "113.39" -                        
    [10] "32.79"  | "32.79"  [5]           
     ... ...        ...      and 2 more ...
    ── Error ('test-gt_plt_conf_int.R:4:3'): gt_plt_conf_int generates correct points/text ──
    Error in `geom_label(aes(x = .data$ci2, label = do.call(scales::label_number, 
        text_args)(.data$ci2)), color = pal_vals[4], hjust = 1.1, 
        size = text_size, vjust = 0, fill = "transparent", position = position_nudge(y = 0.25), 
        family = "mono", fontface = "bold", label.size = unit(0, 
            "lines"), label.padding = unit(0.05, "lines"), label.r = unit(0, 
            "lines"))`: Problem while converting geom to grob.
    i Error occurred in the 3rd layer.
    Caused by error in `Ops.unit()`:
    ! operator '==' not meaningful for units
    Backtrace:
         ▆
      1. ├─... %>% rvest::read_html() at test-gt_plt_conf_int.R:4:3
      2. ├─rvest::read_html(.)
      3. ├─gt::as_raw_html(.)
      4. │ ├─htmltools::as.tags(data)
      5. │ └─gt:::as.tags.gt_tbl(data)
      6. │   ├─htmltools::HTML(render_as_html(data = x))
      7. │   └─gt:::render_as_html(data = x)
      8. │     └─gt:::build_data(data = data, context = "html")
      9. │       └─gt:::perform_text_transforms(data = data)
     10. │         ├─gt:::text_transform_at_location(...)
     11. │         └─gt:::text_transform_at_location.cells_body(...)
     12. │           └─gtExtras (local) fn(body[[col]][stub_df$rownum_i %in% loc$rows])
     13. │             └─base::mapply(...)
     14. │               └─gtExtras (local) `<fn>`(...)
     15. │                 └─ggplot2::ggsave(...)
     16. │                   └─base::lapply(plot, grid.draw)
     17. │                     ├─grid (local) FUN(X[[i]], ...)
     18. │                     └─ggplot2 (local) `grid.draw.ggplot2::ggplot`(X[[i]], ...)
     19. │                       ├─base::print(x)
     20. │                       └─ggplot2 (local) `print.ggplot2::ggplot`(x)
     21. │                         ├─ggplot2::ggplot_gtable(data)
     22. │                         └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
     23. │                           └─ggplot2:::by_layer(...)
     24. │                             ├─rlang::try_fetch(...)
     25. │                             │ ├─base::tryCatch(...)
     26. │                             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     27. │                             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28. │                             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     29. │                             │ └─base::withCallingHandlers(...)
     30. │                             └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     31. │                               └─l$draw_geom(d, layout)
     32. │                                 └─ggplot2 (local) draw_geom(..., self = self)
     33. │                                   └─self$geom$draw_layer(...)
     34. │                                     └─ggplot2 (local) draw_layer(..., self = self)
     35. │                                       └─base::lapply(...)
     36. │                                         └─ggplot2 (local) FUN(X[[i]], ...)
     37. │                                           ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     38. │                                           └─self$draw_panel(...)
     39. │                                             └─ggplot2 (local) draw_panel(..., self = self)
     40. │                                               └─grid:::Ops.unit(data$linewidth, 0)
     41. │                                                 └─base::stop(...)
     42. └─base::.handleSimpleError(...)
     43.   └─rlang (local) h(simpleError(msg, call))
     44.     └─handlers[[1L]](cnd)
     45.       └─cli::cli_abort(...)
     46.         └─rlang::abort(...)
    ── Error ('test-gt_plt_conf_int.R:62:3'): gt_plt_conf_int uses correct points/text/colors ──
    Error in `geom_label(aes(x = .data$ci2, label = do.call(scales::label_number, 
        text_args)(.data$ci2)), color = pal_vals[4], hjust = 1.1, 
        size = text_size, vjust = 0, fill = "transparent", position = position_nudge(y = 0.25), 
        family = "mono", fontface = "bold", label.size = unit(0, 
            "lines"), label.padding = unit(0.05, "lines"), label.r = unit(0, 
            "lines"))`: Problem while converting geom to grob.
    i Error occurred in the 3rd layer.
    Caused by error in `Ops.unit()`:
    ! operator '==' not meaningful for units
    Backtrace:
         ▆
      1. ├─... %>% rvest::read_html() at test-gt_plt_conf_int.R:62:3
      2. ├─rvest::read_html(.)
      3. ├─gt::as_raw_html(.)
      4. │ ├─htmltools::as.tags(data)
      5. │ └─gt:::as.tags.gt_tbl(data)
      6. │   ├─htmltools::HTML(render_as_html(data = x))
      7. │   └─gt:::render_as_html(data = x)
      8. │     └─gt:::build_data(data = data, context = "html")
      9. │       └─gt:::perform_text_transforms(data = data)
     10. │         ├─gt:::text_transform_at_location(...)
     11. │         └─gt:::text_transform_at_location.cells_body(...)
     12. │           └─gtExtras (local) fn(body[[col]][stub_df$rownum_i %in% loc$rows])
     13. │             └─base::mapply(...)
     14. │               └─gtExtras (local) `<fn>`(...)
     15. │                 └─ggplot2::ggsave(...)
     16. │                   └─base::lapply(plot, grid.draw)
     17. │                     ├─grid (local) FUN(X[[i]], ...)
     18. │                     └─ggplot2 (local) `grid.draw.ggplot2::ggplot`(X[[i]], ...)
     19. │                       ├─base::print(x)
     20. │                       └─ggplot2 (local) `print.ggplot2::ggplot`(x)
     21. │                         ├─ggplot2::ggplot_gtable(data)
     22. │                         └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
     23. │                           └─ggplot2:::by_layer(...)
     24. │                             ├─rlang::try_fetch(...)
     25. │                             │ ├─base::tryCatch(...)
     26. │                             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     27. │                             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28. │                             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     29. │                             │ └─base::withCallingHandlers(...)
     30. │                             └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     31. │                               └─l$draw_geom(d, layout)
     32. │                                 └─ggplot2 (local) draw_geom(..., self = self)
     33. │                                   └─self$geom$draw_layer(...)
     34. │                                     └─ggplot2 (local) draw_layer(..., self = self)
     35. │                                       └─base::lapply(...)
     36. │                                         └─ggplot2 (local) FUN(X[[i]], ...)
     37. │                                           ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     38. │                                           └─self$draw_panel(...)
     39. │                                             └─ggplot2 (local) draw_panel(..., self = self)
     40. │                                               └─grid:::Ops.unit(data$linewidth, 0)
     41. │                                                 └─base::stop(...)
     42. └─base::.handleSimpleError(...)
     43.   └─rlang (local) h(simpleError(msg, call))
     44.     └─handlers[[1L]](cnd)
     45.       └─cli::cli_abort(...)
     46.         └─rlang::abort(...)
    
    [ FAIL 6 | WARN 4 | SKIP 19 | PASS 104 ]
    Error: Test failures
    Execution halted

Package: harmony
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Seurat.Rmd’ using rmarkdown
  Calculating gene variances
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating feature variances of standardized and clipped values
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating gene variances
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating feature variances of standardized and clipped values
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Using method 'umap'
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  --- finished re-building ‘Seurat.Rmd’
  
  --- re-building ‘detailedWalkthrough.Rmd’ using rmarkdown
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
  Quitting from detailedWalkthrough.Rmd:778-788 [unnamed-chunk-36]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::labels> object is invalid:
  - every label must be named.
  ---
  Backtrace:
      ▆
   1. └─ggplot2::labs(...)
   2.   └─ggplot2::class_labels(args)
   3.     └─S7::new_object(labels)
   4.       └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'detailedWalkthrough.Rmd' failed with diagnostics:
  <ggplot2::labels> object is invalid:
  - every label must be named.
  --- failed re-building ‘detailedWalkthrough.Rmd’
  
  --- re-building ‘quickstart.Rmd’ using rmarkdown
  --- finished re-building ‘quickstart.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘detailedWalkthrough.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: hesim
Check: tests
New result: ERROR
    Running ‘testthat.R’ [36s/36s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(hesim)
    > 
    > test_check("hesim")
    sample = 1
    sample = 2
    [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1121 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot.R:52:3'): autoplot.survival() allows confidence intervals ──
    p$labels$fill not equal to "curve".
    target is NULL, current is character
    ── Failure ('test-plot.R:56:3'): autoplot.survival() allows confidence intervals ──
    p$labels$fill not equal to "curve".
    target is NULL, current is character
    ── Failure ('test-plot.R:95:3'): autoplot.stateprobs() allows confidence intervals ──
    p$labels$fill not equal to "strategy_id".
    target is NULL, current is character
    ── Failure ('test-plot.R:99:3'): autoplot.stateprobs() allows confidence intervals ──
    p$labels$fill not equal to "strategy_id".
    target is NULL, current is character
    
    [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1121 ]
    Error: Test failures
    Execution halted

Package: hmde
Check: tests
New result: ERROR
    Running ‘testthat.R’ [17s/17s]
  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(hmde)
    > 
    > test_check("hmde")
    
    SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
    Chain 1: 
    Chain 1: Gradient evaluation took 1.4e-05 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.14 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1: 
    Chain 1: 
    Chain 1: WARNING: No variance estimation is
    Chain 1:          performed for num_warmup < 20
    Chain 1: 
    Chain 1: Iteration:  1 / 20 [  5%]  (Warmup)
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    Chain 1: Iteration: 20 / 20 [100%]  (Sampling)
    Chain 1: 
    Chain 1:  Elapsed Time: 0 seconds (Warm-up)
    Chain 1:                0 seconds (Sampling)
    Chain 1:                0 seconds (Total)
    Chain 1: 
    
    SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 1).
    Chain 1: 
    Chain 1: Gradient evaluation took 0.001336 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 13.36 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1: 
    Chain 1: 
    Chain 1: WARNING: No variance estimation is
    Chain 1:          performed for num_warmup < 20
    Chain 1: 
    Chain 1: Iteration:  1 / 20 [  5%]  (Warmup)
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    Chain 1: Iteration: 20 / 20 [100%]  (Sampling)
    Chain 1: 
    Chain 1:  Elapsed Time: 2.83 seconds (Warm-up)
    Chain 1:                0.047 seconds (Sampling)
    Chain 1:                2.877 seconds (Total)
    Chain 1: 
    
    SAMPLING FOR MODEL 'canham_multi_ind' NOW (CHAIN 2).
    Chain 2: 
    Chain 2: Gradient evaluation took 0.001376 seconds
    Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 13.76 seconds.
    Chain 2: Adjust your expectations accordingly!
    Chain 2: 
    Chain 2: 
    Chain 2: WARNING: No variance estimation is
    Chain 2:          performed for num_warmup < 20
    Chain 2: 
    Chain 2: Iteration:  1 / 20 [  5%]  (Warmup)
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    Chain 2: Iteration: 20 / 20 [100%]  (Sampling)
    Chain 2: 
    Chain 2:  Elapsed Time: 0.265 seconds (Warm-up)
    Chain 2:                0.086 seconds (Sampling)
    Chain 2:                0.351 seconds (Total)
    Chain 2: 
    
    SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
    Chain 1: 
    Chain 1: Gradient evaluation took 1.3e-05 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.13 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1: 
    Chain 1: 
    Chain 1: Iteration:   1 / 1000 [  0%]  (Warmup)
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    Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
    Chain 1: 
    Chain 1:  Elapsed Time: 0.274 seconds (Warm-up)
    Chain 1:                0.568 seconds (Sampling)
    Chain 1:                0.842 seconds (Total)
    Chain 1: 
    
    SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
    Chain 1: 
    Chain 1: Gradient evaluation took 2e-05 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1: 
    Chain 1: 
    Chain 1: WARNING: No variance estimation is
    Chain 1:          performed for num_warmup < 20
    Chain 1: 
    Chain 1: Iteration:  1 / 20 [  5%]  (Warmup)
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    Chain 1: 
    Chain 1:  Elapsed Time: 0.001 seconds (Warm-up)
    Chain 1:                0 seconds (Sampling)
    Chain 1:                0.001 seconds (Total)
    Chain 1: 
    
    SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 2).
    Chain 2: 
    Chain 2: Gradient evaluation took 9e-06 seconds
    Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
    Chain 2: Adjust your expectations accordingly!
    Chain 2: 
    Chain 2: 
    Chain 2: WARNING: No variance estimation is
    Chain 2:          performed for num_warmup < 20
    Chain 2: 
    Chain 2: Iteration:  1 / 20 [  5%]  (Warmup)
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    Chain 2: Iteration: 20 / 20 [100%]  (Sampling)
    Chain 2: 
    Chain 2:  Elapsed Time: 0.001 seconds (Warm-up)
    Chain 2:                0.006 seconds (Sampling)
    Chain 2:                0.007 seconds (Total)
    Chain 2: 
    
    SAMPLING FOR MODEL 'vb_single_ind' NOW (CHAIN 1).
    Chain 1: 
    Chain 1: Gradient evaluation took 2.8e-05 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1: 
    Chain 1: 
    Chain 1: Iteration:   1 / 1000 [  0%]  (Warmup)
    Chain 1: Iteration: 100 / 1000 [ 10%]  (Warmup)
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    Chain 1: Iteration: 900 / 1000 [ 90%]  (Sampling)
    Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
    Chain 1: 
    Chain 1:  Elapsed Time: 0.609 seconds (Warm-up)
    Chain 1:                0.657 seconds (Sampling)
    Chain 1:                1.266 seconds (Total)
    Chain 1: 
    
    SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 1).
    Chain 1: 
    Chain 1: Gradient evaluation took 3.9e-05 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1: 
    Chain 1: 
    Chain 1: WARNING: No variance estimation is
    Chain 1:          performed for num_warmup < 20
    Chain 1: 
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    Chain 1: Iteration: 18 / 20 [ 90%]  (Sampling)
    Chain 1: Iteration: 20 / 20 [100%]  (Sampling)
    Chain 1: 
    Chain 1:  Elapsed Time: 0.003 seconds (Warm-up)
    Chain 1:                0.001 seconds (Sampling)
    Chain 1:                0.004 seconds (Total)
    Chain 1: 
    
    SAMPLING FOR MODEL 'vb_multi_ind' NOW (CHAIN 2).
    Chain 2: 
    Chain 2: Gradient evaluation took 1.7e-05 seconds
    Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds.
    Chain 2: Adjust your expectations accordingly!
    Chain 2: 
    Chain 2: 
    Chain 2: WARNING: No variance estimation is
    Chain 2:          performed for num_warmup < 20
    Chain 2: 
    Chain 2: Iteration:  1 / 20 [  5%]  (Warmup)
    Chain 2: Iteration:  2 / 20 [ 10%]  (Warmup)
    Chain 2: Iteration:  4 / 20 [ 20%]  (Warmup)
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    Chain 2: Iteration:  8 / 20 [ 40%]  (Warmup)
    Chain 2: Iteration: 10 / 20 [ 50%]  (Warmup)
    Chain 2: Iteration: 11 / 20 [ 55%]  (Sampling)
    Chain 2: Iteration: 12 / 20 [ 60%]  (Sampling)
    Chain 2: Iteration: 14 / 20 [ 70%]  (Sampling)
    Chain 2: Iteration: 16 / 20 [ 80%]  (Sampling)
    Chain 2: Iteration: 18 / 20 [ 90%]  (Sampling)
    Chain 2: Iteration: 20 / 20 [100%]  (Sampling)
    Chain 2: 
    Chain 2:  Elapsed Time: 0.001 seconds (Warm-up)
    Chain 2:                0.001 seconds (Sampling)
    Chain 2:                0.002 seconds (Total)
    Chain 2: 
    
    SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
    Chain 1: 
    Chain 1: Gradient evaluation took 3.2e-05 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1: 
    Chain 1: 
    Chain 1: WARNING: There aren't enough warmup iterations to fit the
    Chain 1:          three stages of adaptation as currently configured.
    Chain 1:          Reducing each adaptation stage to 15%/75%/10% of
    Chain 1:          the given number of warmup iterations:
    Chain 1:            init_buffer = 3
    Chain 1:            adapt_window = 20
    Chain 1:            term_buffer = 2
    Chain 1: 
    Chain 1: Iteration:  1 / 50 [  2%]  (Warmup)
    Chain 1: Iteration:  5 / 50 [ 10%]  (Warmup)
    Chain 1: Iteration: 10 / 50 [ 20%]  (Warmup)
    Chain 1: Iteration: 15 / 50 [ 30%]  (Warmup)
    Chain 1: Iteration: 20 / 50 [ 40%]  (Warmup)
    Chain 1: Iteration: 25 / 50 [ 50%]  (Warmup)
    Chain 1: Iteration: 26 / 50 [ 52%]  (Sampling)
    Chain 1: Iteration: 30 / 50 [ 60%]  (Sampling)
    Chain 1: Iteration: 35 / 50 [ 70%]  (Sampling)
    Chain 1: Iteration: 40 / 50 [ 80%]  (Sampling)
    Chain 1: Iteration: 45 / 50 [ 90%]  (Sampling)
    Chain 1: Iteration: 50 / 50 [100%]  (Sampling)
    Chain 1: 
    Chain 1:  Elapsed Time: 0.016 seconds (Warm-up)
    Chain 1:                0.036 seconds (Sampling)
    Chain 1:                0.052 seconds (Total)
    Chain 1: 
    
    SAMPLING FOR MODEL 'constant_multi_ind' NOW (CHAIN 1).
    Chain 1: 
    Chain 1: Gradient evaluation took 4.5e-05 seconds
    Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.45 seconds.
    Chain 1: Adjust your expectations accordingly!
    Chain 1: 
    Chain 1: 
    Chain 1: WARNING: There aren't enough warmup iterations to fit the
    Chain 1:          three stages of adaptation as currently configured.
    Chain 1:          Reducing each adaptation stage to 15%/75%/10% of
    Chain 1:          the given number of warmup iterations:
    Chain 1:            init_buffer = 3
    Chain 1:            adapt_window = 20
    Chain 1:            term_buffer = 2
    Chain 1: 
    Chain 1: Iteration:  1 / 50 [  2%]  (Warmup)
    Chain 1: Iteration:  5 / 50 [ 10%]  (Warmup)
    Chain 1: Iteration: 10 / 50 [ 20%]  (Warmup)
    Chain 1: Iteration: 15 / 50 [ 30%]  (Warmup)
    Chain 1: Iteration: 20 / 50 [ 40%]  (Warmup)
    Chain 1: Iteration: 25 / 50 [ 50%]  (Warmup)
    Chain 1: Iteration: 26 / 50 [ 52%]  (Sampling)
    Chain 1: Iteration: 30 / 50 [ 60%]  (Sampling)
    Chain 1: Iteration: 35 / 50 [ 70%]  (Sampling)
    Chain 1: Iteration: 40 / 50 [ 80%]  (Sampling)
    Chain 1: Iteration: 45 / 50 [ 90%]  (Sampling)
    Chain 1: Iteration: 50 / 50 [100%]  (Sampling)
    Chain 1: 
    Chain 1:  Elapsed Time: 0.114 seconds (Warm-up)
    Chain 1:                0.032 seconds (Sampling)
    Chain 1:                0.146 seconds (Total)
    Chain 1: 
    [ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-hmde_plot_de_pieces.R:17:3'): Execution and output: plot_de_pieces function ──
    `plot` does not have names.
    ── Failure ('test-hmde_plot_de_pieces.R:21:3'): Execution and output: plot_de_pieces function ──
    `plot` has type 'object', not 'list'.
    ── Failure ('test-hmde_plot_obs_est_inds.R:5:3'): Execution and output: plot_obs_est_inds function ──
    `plot` does not have names.
    ── Failure ('test-hmde_plot_obs_est_inds.R:9:3'): Execution and output: plot_obs_est_inds function ──
    `plot` has type 'object', not 'list'.
    
    [ FAIL 4 | WARN 0 | SKIP 0 | PASS 85 ]
    Error: Test failures
    Execution halted

Package: horseshoe
Check: examples
New result: ERROR
  Running examples in ‘horseshoe-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: HS.normal.means
  > ### Title: The horseshoe prior for the sparse normal means problem
  > ### Aliases: HS.normal.means
  > 
  > ### ** Examples
  > 
  > #Empirical Bayes example with 20 signals, rest is noise
  > #Posterior mean for the signals is plotted
  > #And variable selection is performed using the credible intervals
  > #And the credible intervals are plotted
  > truth <- c(rep(0, 80), rep(8, 20))
  > data <-  truth + rnorm(100, 1)
  > tau.hat <- HS.MMLE(data, Sigma2 = 1)
  > res.HS1 <- HS.normal.means(data, method.tau = "fixed", tau = tau.hat,
  + method.sigma = "fixed", Sigma2 = 1)
  [1] 1000
  [1] 2000
  [1] 3000
  [1] 4000
  [1] 5000
  [1] 6000
  > #Plot the posterior mean against the data (signals in blue)
  > plot(data, res.HS1$BetaHat, col = c(rep("black", 80), rep("blue", 20)))
  > #Find the selected betas (ideally, the last 20 are equal to 1)
  > HS.var.select(res.HS1, data, method = "intervals")
    [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
   [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
   [75] 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
  > #Plot the credible intervals
  > library(Hmisc)
  
  Attaching package: ‘Hmisc’
  
  The following objects are masked from ‘package:base’:
  
      format.pval, units
  
  > xYplot(Cbind(res.HS1$BetaHat, res.HS1$LeftCI, res.HS1$RightCI) ~ 1:100)
  Error in sRequire("lattice") : 
    package lattice is required but not installed
  Calls: xYplot -> sRequire
  Execution halted

Package: hrbrthemes
Check: tests
New result: ERROR
    Running ‘test-all.R’ [5s/5s]
  Running the tests in ‘tests/test-all.R’ failed.
  Complete output:
    > library(testthat)
    > test_check("hrbrthemes")
    Loading required package: hrbrthemes
    [ FAIL 1 | WARN 0 | SKIP 2 | PASS 9 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test-hrbrthemes.R:71:3', 'test-themes.R:4:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-hrbrthemes.R:16:3'): we can do something ─────────────────────
    `gg_check(gg_tmp)` did not produce any messages.
    
    [ FAIL 1 | WARN 0 | SKIP 2 | PASS 9 ]
    Deleting unused snapshots:
    • themes/theme-ipsum-rc.svg
    • themes/theme-ipsum.svg
    Error: Test failures
    Execution halted

Package: hyperoverlap
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘hyperoverlap’

Package: hypsoLoop
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘ggplot2::set_theme’ by ‘sjPlot::set_theme’ when loading ‘hypsoLoop’

Package: ibdsim2
Check: examples
New result: ERROR
  Running examples in ‘ibdsim2-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plotSegmentDistribution
  > ### Title: Scatter plots of IBD segment distributions
  > ### Aliases: plotSegmentDistribution
  > 
  > ### ** Examples
  > 
  > 
  > # Simulation parameters used in the below examples.
  > map = uniformMap(M = 10)   # recombination map
  > N = 5                      # number of sims
  > 
  > # For more realistic results, replace with e.g.:
  > # map = loadMap("decode19")
  > # N = 1000
  > 
  > 
  > #################################################################
  > # EXAMPLE 1
  > # Comparison of IBD segment distributions
  > # between paternal and maternal half siblings.
  > #################################################################
  > 
  > # Define the pedigrees
  > xPat = halfSibPed()
  > xMat = swapSex(xPat, 1)
  Changing sex of spouses as well: 2
  Changing sex of spouses as well: 3
  > 
  > simPat = ibdsim(xPat, N = N, map = map)
  Simulation parameters:
  Simulations  : 5
  Chromosomes  : 1
  Genome length: 1000 Mb
                 1000 cM (male)
                 1000 cM (female)
  Recomb model : chi
  Target indivs: 1-5
  Skip recomb  : -
  Total time used: 0.00613 secs
  > simMat = ibdsim(xMat, N = N, map = map)
  Simulation parameters:
  Simulations  : 5
  Chromosomes  : 1
  Genome length: 1000 Mb
                 1000 cM (male)
                 1000 cM (female)
  Recomb model : chi
  Target indivs: 1-5
  Skip recomb  : -
  Total time used: 0.00638 secs
  > 
  > # By default, the IBD segments of the "leaves" are computed and plotted
  > plotSegmentDistribution(simPat, simMat, type = "ibd1", ids = 4:5,
  +                         labels = c("HSpat", "HSmat"))
  Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
  ℹ Please use tidy evaluation idioms with `aes()`.
  ℹ See also `vignette("ggplot2-in-packages")` for more information.
  ℹ The deprecated feature was likely used in the ibdsim2 package.
    Please report the issue to the authors.
  Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
  ℹ Please use `linewidth` instead.
  ℹ The deprecated feature was likely used in the ibdsim2 package.
    Please report the issue to the authors.
  Error in `stat_ellipse()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `setup_params()`:
  ! The package "MASS" is required for calculating ellipses with `type =
    "t"`.
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_build(x)
    4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$compute_statistic(d, layout)
   14. │         └─ggplot2 (local) compute_statistic(..., self = self)
   15. │           └─self$stat$setup_params(data, self$stat_params)
   16. │             └─ggplot2 (local) setup_params(...)
   17. │               └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
   18. │                 └─base::stop(cnd)
   19. └─rlang (local) `<fn>`(`<S3: rlib_error_package_not_found>`)
   20.   └─handlers[[1L]](cnd)
   21.     └─cli::cli_abort(...)
   22.       └─rlang::abort(...)
  Execution halted

Package: ImHD
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘ImHD’

Package: implicitMeasures
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [26s/26s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(implicitMeasures)
    > 
    > test_check("implicitMeasures")
    [ FAIL 4 | WARN 1 | SKIP 2 | PASS 75 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test-compute_iat.R:36:3', 'test-compute_iat.R:60:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-d_density_d_plot.R:25:3'): d_point produces a ggplot fot the IAT ──
    class(d_point(iat_dscore))[[1]] not equal to "gg".
    1/1 mismatches
    x[1]: "ggplot2::ggplot"
    y[1]: "gg"
    ── Failure ('test-d_density_d_plot.R:47:3'): d_point produces a ggplot fot the SC-IAT ──
    class(d_point(d_sciat1))[[1]] not equal to "gg".
    1/1 mismatches
    x[1]: "ggplot2::ggplot"
    y[1]: "gg"
    ── Failure ('test-d_density_d_plot.R:77:3'): d_density produces a ggplot fot the IAT ──
    class(d_density(iat_dscore))[[1]] not equal to "gg".
    1/1 mismatches
    x[1]: "ggplot2::ggplot"
    y[1]: "gg"
    ── Failure ('test-d_density_d_plot.R:99:3'): d_density produces a ggplot fot the SC-IAT ──
    class(d_density(d_sciat1))[[1]] not equal to "gg".
    1/1 mismatches
    x[1]: "ggplot2::ggplot"
    y[1]: "gg"
    
    [ FAIL 4 | WARN 1 | SKIP 2 | PASS 75 ]
    Error: Test failures
    Execution halted

Package: imputeTS
Check: tests
New result: ERROR
    Running ‘testthat.R’ [47s/48s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > test_check("imputeTS")
    Loading required package: imputeTS
    [ FAIL 43 | WARN 18 | SKIP 52 | PASS 411 ]
    
    ══ Skipped tests (52) ══════════════════════════════════════════════════════════
    • On CRAN (52): 'test-ggplot_na_distribution.R:59:3',
      'test-ggplot_na_distribution.R:124:3', 'test-ggplot_na_distribution.R:178:3',
      'test-ggplot_na_distribution2.R:64:3',
      'test-ggplot_na_distribution2.R:108:3',
      'test-ggplot_na_distribution2.R:134:3', 'test-ggplot_na_gapsize.R:66:3',
      'test-ggplot_na_gapsize.R:110:3', 'test-ggplot_na_gapsize.R:138:3',
      'test-ggplot_na_imputations.R:133:3', 'test-ggplot_na_imputations.R:198:3',
      'test-input-na_advanced-tsObjects.R:5:3',
      'test-input-na_advanced-tsObjects.R:27:3',
      'test-input-na_advanced-tsObjects.R:51:3',
      'test-input-na_advanced-tsObjects.R:74:3',
      'test-input-na_advanced-tsObjects.R:100:3',
      'test-input-na_advanced-tsObjects.R:127:3',
      'test-input-na_advanced-tsObjects.R:149:3',
      'test-input-na_advanced-tsObjects.R:180:3',
      'test-input-na_advanced-tsObjects.R:203:3',
      'test-input-na_advanced-tsObjects.R:228:3',
      'test-input-na_advanced-tsObjects.R:251:3',
      'test-input-na_advanced-tsObjects.R:268:3',
      'test-input-na_advanced-tsObjects.R:284:3',
      'test-input-na_advanced-tsObjects.R:301:3',
      'test-input-na_advanced-tsObjects.R:319:3', 'test-na_interpolation.R:8:3',
      'test-na_interpolation.R:22:3', 'test-na_interpolation.R:37:3',
      'test-na_kalman.R:13:3', 'test-na_kalman.R:24:3', 'test-na_kalman.R:36:3',
      'test-na_locf.R:8:3', 'test-na_locf.R:26:3', 'test-na_locf.R:45:3',
      'test-na_ma.R:8:3', 'test-na_ma.R:24:3', 'test-na_ma.R:41:3',
      'test-na_mean.R:8:3', 'test-na_mean.R:21:3', 'test-na_mean.R:35:3',
      'test-na_replace.R:9:3', 'test-na_replace.R:21:3', 'test-na_replace.R:34:3',
      'test-na_seadec.R:8:3', 'test-na_seadec.R:23:3', 'test-na_seadec.R:44:3',
      'test-na_seadec.R:140:3', 'test-na_seasplit.R:8:3',
      'test-na_seasplit.R:23:3', 'test-na_seasplit.R:39:3',
      'test-na_seasplit.R:137:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-ggplot_na_distribution.R:15:5'): Check that all parameters of plot run without error ──
    is.list(ggplot_na_distribution(tsAirgap)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution.R:16:5'): Check that all parameters of plot run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:20:5'): Check that all parameters of plot  run without error ──
    is.recursive(ggplot_na_distribution2(tsAirgap)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:21:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_distribution2(tsAirgap)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:22:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_distribution2(tsAirgap, number_intervals = 8)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:23:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_distribution2(tsAirgap, interval_size = 25)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:24:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_distribution2(tsNH4, measure = "count")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:25:5'): Check that all parameters of plot  run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:29:5'): Check that all parameters of plot  run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:33:5'): Check that all parameters of plot  run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:38:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_distribution2(tsAirgap, color_border = "black")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_distribution2.R:39:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_distribution2(tsAirgap, theme = ggplot2::theme_classic())) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:16:5'): Check that all parameters of plot  run without error ──
    is.recursive(ggplot_na_gapsize(tsAirgap)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:17:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:18:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, ranked_by = "total")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:19:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsNH4, limit = 2)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:20:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, legend = F)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:21:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, orientation = "horizontal")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:22:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, include_total = F)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:23:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, color_occurrence = "blue")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:24:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, limit = 1)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:25:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, include_total = F)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:26:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, ranked_by = "total")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:27:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, color_occurrence = "gold")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:28:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, color_total = "green")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:29:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, title = "test")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:30:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, subtitle = "test2")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:31:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, xlab = "test")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:32:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, ylab = "test")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:33:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, orientation = "vertical")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:34:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, label_occurrence = "occ")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:35:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, label_total = "total")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_gapsize.R:36:5'): Check that all parameters of plot  run without error ──
    is.list(ggplot_na_gapsize(tsAirgap, theme = ggplot2::theme_classic())) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:18:5'): Check that all parameters of plot run without error ──
    is.recursive(ggplot_na_imputations(tsAirgap, imp_mean)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:19:5'): Check that all parameters of plot run without error ──
    is.recursive(ggplot_na_imputations(tsAirgap, imp_mean, tsAirgapComplete)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:21:5'): Check that all parameters of plot run without error ──
    is.list(ggplot_na_imputations(x_with_na = tsAirgap, x_with_imputations = imp_mean)) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:27:5'): Check that all parameters of plot run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:37:5'): Check that all parameters of plot run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:46:5'): Check that all parameters of plot run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:55:5'): Check that all parameters of plot run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:65:5'): Check that all parameters of plot run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:73:5'): Check that all parameters of plot run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot_na_imputations.R:81:5'): Check that all parameters of plot run without error ──
    is.list(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 43 | WARN 18 | SKIP 52 | PASS 411 ]
    Error: Test failures
    Execution halted

Package: inTextSummaryTable
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘inTextSummaryTable-advanced.Rmd’ using rmarkdown
  --- finished re-building ‘inTextSummaryTable-advanced.Rmd’
  
  --- re-building ‘inTextSummaryTable-aesthetics.Rmd’ using rmarkdown
  
  Quitting from inTextSummaryTable-aesthetics.Rmd:210-224 [aesthetics-defaultsVisualization]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'inTextSummaryTable-aesthetics.Rmd' failed with diagnostics:
  Problem while setting up geom aesthetics.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `list_sizes()`:
  ! `x$size` must be a vector, not a <quosure> object.
  --- failed re-building ‘inTextSummaryTable-aesthetics.Rmd’
  
  --- re-building ‘inTextSummaryTable-createTables.Rmd’ using rmarkdown
  --- finished re-building ‘inTextSummaryTable-createTables.Rmd’
  
  --- re-building ‘inTextSummaryTable-exportTables.Rmd’ using rmarkdown
  --- finished re-building ‘inTextSummaryTable-exportTables.Rmd’
  
  --- re-building ‘inTextSummaryTable-introduction.Rmd’ using rmarkdown
  --- finished re-building ‘inTextSummaryTable-introduction.Rmd’
  
  --- re-building ‘inTextSummaryTable-standardTables.Rmd’ using rmarkdown
  --- finished re-building ‘inTextSummaryTable-standardTables.Rmd’
  
  --- re-building ‘inTextSummaryTable-visualization.Rmd’ using rmarkdown
  
  Quitting from inTextSummaryTable-visualization.Rmd:154-172 [visualization-a4document]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'inTextSummaryTable-visualization.Rmd' failed with diagnostics:
  The `plot.margin` theme element must be a <unit> vector of length 4
  --- failed re-building ‘inTextSummaryTable-visualization.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘inTextSummaryTable-aesthetics.Rmd’
    ‘inTextSummaryTable-visualization.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: inTextSummaryTable
Check: tests
New result: ERROR
    Running ‘testthat.R’ [61s/61s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(inTextSummaryTable)
    > 
    > test_check("inTextSummaryTable")
    [ FAIL 59 | WARN 0 | SKIP 0 | PASS 881 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:15:2'): A color variable is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:48:2'): A color palette is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:82:2'): A label for the color variable is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:108:2'): Line types are correctly used to differenciate the groups of the color variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:143:2'): A linetype palette is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:178:2'): Shapes are correctly used to differenciate the groups of the color variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:213:2'): A shape palette is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:246:2'): Points are correctly labelled with the y-variable values ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:280:2'): Points are correctly labelled with an expression of the data variables ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:351:2'): Points are correctly labelled with a text justified based on data variables ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-aesthetics.R:397:2'): The padding between points and labels is correctly set when specified ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-byVar.R:16:2'): A plot is correctly created by a variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-byVar.R:58:2'): A warning is generated if the 'by' variable is not available in the data ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-byVar.R:81:2'): Titles are correctly set by group of a variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-byVar.R:107:2'): Labels for the y-axis are correctly set by group of a variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-byVar.R:130:2'): Vertical and horizontal lines are correctly set by group of a variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 3rd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-byVar.R:185:2'): Extra ggplot specifications are correctly set by group of a variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:26:2'): The plot is correctly facetted based on a variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:62:3'): The scale of the facet is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:83:2'): Horizontal lines are correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 4th layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:117:3'): Horizontal lines are correctly set by facet ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 4th layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:141:2'): Vertical lines are correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 4th layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:176:4'): A table is successfully included in a plot ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:209:4'): A table with specific height is correctly included in a plot ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Failure ('test_subjectProfileSummaryPlot-general.R:246:2'): An error is generated if the height for the table is not correctly specified ──
    `subjectProfileSummaryPlot(...)` threw an error with unexpected message.
    Expected match: "Table height should be between 0 and 1."
    Actual message: "Problem while setting up geom aesthetics.\nℹ Error occurred in the 2nd layer.\nCaused by error in `list_sizes()`:\n! `x$size` must be a vector, not a <quosure> object."
    ── Error ('test_subjectProfileSummaryPlot-general.R:267:2'): A warning is generated if the facet and text variables are specified ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:289:3'): Extra ggplot with a data point outside the plot range is correctly included ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-general.R:314:3'): Extra ggplot specified as a function is correctly included ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-labels.R:12:2'): A label is correctly specified for a x variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-labels.R:30:2'): The label for the y variable is correctly set by default ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-labels.R:47:2'): A label is correctly set for a y variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-labels.R:66:2'): A title is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-labels.R:86:2'): A caption is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-labels.R:108:2'): The variable labels are correctly extracted from the labels of all variables ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-theme.R:31:2'): The line size is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-theme.R:52:2'): The label size is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:13:2'): A plot is correctly created with a continuous x variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:34:2'): A plot is successfully created with a continuous x variable with only one element ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:59:2'): A plot is correctly created with a discrete x variable ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:84:2'): The x-axis labels are correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:111:2'): A x-axis gap is correctly set ──
    Error in `geom_text(data = dataGapSym, mapping = do.call(aes, aesArgs), 
        show.legend = FALSE, inherit.aes = FALSE, size = sizeLabel, 
        hjust = "center", vjust = 1)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:188:2'): A warning is generated if a x-axis gap is not of length 2 ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:206:2'): The range of the x-axis gap is correctly set to a specified value ──
    Error in `geom_text(data = dataGapSym, mapping = do.call(aes, aesArgs), 
        show.legend = FALSE, inherit.aes = FALSE, size = sizeLabel, 
        hjust = "center", vjust = 1)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:244:2'): A jitter is correctly set for the x-axis  ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:268:2'): The limits are correctly set for the x-axis ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-xVar.R:288:2'): The x-axis is correctly expanded ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:13:2'): The mean data is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:39:2'): The standard error data is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:73:2'): The data with the minimum and maximum values are correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:100:2'): A warning is generated if a variable is specified for the minimum value but not for the maximum value ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:121:2'): A warning is generated if a variable is specified for the maximum value but not for the minimum value ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:141:2'): A y-axis transformation is correctly set ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:171:2'): A warning is generated if the y-axis transformation is not set as a character ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:188:2'): A warning is generated if the y-axis transformation is not available ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:206:2'): Negative values are correctly set to a default minimum value with a log10 transformation with a warning ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:235:2'): Negative values are correctly set to a specified minimum value with a log10 transformation with a warning ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:261:2'): The limits are correctly set for the y-axis ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:281:2'): The y-axis is correctly expanded ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    ── Error ('test_subjectProfileSummaryPlot-yVar.R:306:2'): A warning is generated if the old specification to expand the y-axis is used ──
    Error in `geom_point(mapping = do.call(aes, c(aesBase, list(y = sym("meanVar")), 
        if (!is.null(colorVar) & useShape) list(shape = sym("colorVar")))), 
        position = pd, size = sizePoint, data = data)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 2nd layer.
    Caused by error in `list_sizes()`:
    ! `x$size` must be a vector, not a <quosure> object.
    
    [ FAIL 59 | WARN 0 | SKIP 0 | PASS 881 ]
    Error: Test failures
    Execution halted

Package: IRon
Check: examples
New result: ERROR
  Running examples in ‘IRon-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: sera
  > ### Title: Squared Error-Relevance Area (SERA)
  > ### Aliases: sera
  > 
  > ### ** Examples
  > 
  > library(IRon)
  > library(rpart)
  > 
  > if(requireNamespace("rpart")) {
  + 
  +    #' data(accel)
  + 
  +    form <- acceleration ~ .
  + 
  +    ind <- sample(1:nrow(accel),0.75*nrow(accel))
  + 
  +    train <- accel[ind,]
  +    test <- accel[-ind,]
  + 
  +    ph <- phi.control(accel$acceleration)
  + 
  +    m <- rpart::rpart(form, train)
  +    preds <- as.vector(predict(m,test))
  + 
  +    trues <- test$acceleration
  +    phi.trues <- phi(test$acceleration,ph)
  + 
  +    sera(trues,preds,phi.trues)
  +    sera(trues,preds,phi.trues,pl=TRUE, m.name="Regression Trees")
  +    sera(trues,preds,phi.trues,pl=TRUE, return.err=TRUE)
  + 
  + }
  Error in `ggplot2::geom_smooth()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 1st layer.
  Caused by error in `get()`:
  ! object 'scam' of mode 'function' was not found
  Backtrace:
       ▆
    1. ├─IRon::sera(trues, preds, phi.trues, pl = TRUE, m.name = "Regression Trees")
    2. │ ├─base::print(...)
    3. │ └─ggplot2 (local) `print.ggplot2::ggplot`(...)
    4. │   ├─ggplot2::ggplot_build(x)
    5. │   └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    6. │     └─ggplot2:::by_layer(...)
    7. │       ├─rlang::try_fetch(...)
    8. │       │ ├─base::tryCatch(...)
    9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12. │       │ └─base::withCallingHandlers(...)
   13. │       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   14. │         └─l$compute_statistic(d, layout)
   15. │           └─ggplot2 (local) compute_statistic(..., self = self)
   16. │             └─self$stat$setup_params(data, self$stat_params)
   17. │               └─ggplot2 (local) setup_params(...)
   18. │                 └─base::match.fun(method)
   19. │                   └─base::get(as.character(FUN), mode = "function", envir = envir)
   20. └─base::.handleSimpleError(...)
   21.   └─rlang (local) h(simpleError(msg, call))
   22.     └─handlers[[1L]](cnd)
   23.       └─cli::cli_abort(...)
   24.         └─rlang::abort(...)
  Execution halted

Package: isoorbi
Check: tests
New result: ERROR
    Running ‘testthat.R’ [16s/16s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(dplyr)
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    > 
    > # run the test
    > test_check("isoorbi")
    Loading required package: isoorbi
    
    
    [ FAIL 5 | WARN 1 | SKIP 0 | PASS 350 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_blocks_functions.R:352:3'): test orbi_add_blocks_to_plot() ───
    orbi_add_blocks_to_plot(fig) has type 'object', not 'list'.
    Backtrace:
        ▆
     1. ├─base::suppressMessages(...) at test_blocks_functions.R:352:3
     2. │ └─base::withCallingHandlers(...)
     3. └─testthat::expect_type(orbi_add_blocks_to_plot(fig), "list")
    ── Failure ('test_plotting_functions.R:84:3'): orbi_plot_satellite_peaks() tests ──
    orbi_plot_satellite_peaks(df2) has type 'object', not 'list'.
    ── Failure ('test_plotting_functions.R:107:3'): orbi_plot_raw_data() tests ─────
    orbi_plot_raw_data(df, y = "ratio") has type 'object', not 'list'.
    ── Failure ('test_plotting_functions.R:139:3'): orbi_plot_isotopocule_coverage() tests ──
    `fig` has type 'object', not 'list'.
    ── Failure ('test_shotnoise_functions.R:94:3'): orbi_plot_shot_noise() tests ───
    orbi_plot_shot_noise(df, "time.min") has type 'object', not 'list'.
    
    [ FAIL 5 | WARN 1 | SKIP 0 | PASS 350 ]
    Error: Test failures
    Execution halted

Package: latrend
Check: examples
New result: ERROR
  Running examples in ‘latrend-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: qqPlot
  > ### Title: Quantile-quantile plot
  > ### Aliases: qqPlot
  > 
  > ### ** Examples
  > 
  > data(latrendData)
  > method <- lcMethodLMKM(Y ~ Time, id = "Id", time = "Time", nClusters = 3)
  > model <- latrend(method, latrendData)
  ---------------------------------------------------------------------------
  - Longitudinal clustering using: lm-kmeans
  ---------------------------------------------------------------------------
  Method arguments:
   time:           "Time"
   id:             "Id"
   nClusters:      3
   center:         meanNA
   standardize:    scale
   method:         "qr"
   model:          TRUE
   y:              FALSE
   qr:             TRUE
   singular.ok:    TRUE
   contrasts:      NULL
   iter.max:       10
   nstart:         1
   algorithm:      c("Hartigan-Wong", "Lloyd", "Forgy", "Ma
   formula:        Y ~ Time
  ---------------------------------------------------------------------------
  Checking and transforming the training data format.
  Preparing the training data for fitting...
   Representation step...
  Fitting the method...
   Cluster step...
  Done fitting the method (0.018 secs)
  ---------------------------------------------------------------------------
  > 
  > if (require("ggplot2") && require("qqplotr")) {
  +   qqPlot(model)
  + }
  Loading required package: ggplot2
  Loading required package: qqplotr
  
  Attaching package: ‘qqplotr’
  
  The following objects are masked from ‘package:ggplot2’:
  
      StatQqLine, stat_qq_line
  
  Error in `qqplotr::geom_qq_band()`:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_gtable(data)
    4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$draw_geom(d, layout)
   14. │         └─ggplot2 (local) draw_geom(..., self = self)
   15. │           └─self$geom$draw_layer(...)
   16. │             └─ggplot2 (local) draw_layer(..., self = self)
   17. │               └─base::lapply(...)
   18. │                 └─ggplot2 (local) FUN(X[[i]], ...)
   19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   20. │                   └─self$draw_panel(data, panel_params, coord)
   21. │                     └─ggplot2 (local) draw_panel(..., self = self)
   22. │                       └─base::lapply(...)
   23. │                         └─ggplot2 (local) FUN(X[[i]], ...)
   24. │                           └─self$draw_group(group, panel_params, coord, ...)
   25. │                             └─ggplot2 (local) draw_group(...)
   26. │                               └─ggplot2 (local) draw_group(..., self = self)
   27. └─base::.handleSimpleError(...)
   28.   └─rlang (local) h(simpleError(msg, call))
   29.     └─handlers[[1L]](cnd)
   30.       └─cli::cli_abort(...)
   31.         └─rlang::abort(...)
  Execution halted

Package: latrend
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘demo.Rmd’ using rmarkdown
  ---------------------------------------------------------------------------
  - Longitudinal clustering using: longitudinal k-means (KML)
  ---------------------------------------------------------------------------
  Method arguments:
   time:           getOption("latrend.time")
   id:             getOption("latrend.id")
   nClusters:      2
   nbRedrawing:    1
   maxIt:          200
   imputationMethod:"copyMean"
   distanceName:   "euclidean"
   power:          2
   distance:       function() {}
   centerMethod:   meanNA
   startingCond:   "nearlyAll"
   nbCriterion:    1000
   scale:          TRUE
   response:       "Y"
  ---------------------------------------------------------------------------
  Checking and transforming the training data format.
  Preparing the training data for fitting...
  Fitting the method...
  Done fitting the method (0.27 secs)
  ---------------------------------------------------------------------------
  
  Quitting from demo.Rmd:144-146 [unnamed-chunk-18]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'demo.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  --- failed re-building ‘demo.Rmd’
  
  --- re-building ‘implement.Rmd’ using rmarkdown
  ---------------------------------------------------------------------------
  - Longitudinal clustering using: stratify
  ---------------------------------------------------------------------------
  Method arguments:
   center:         meanNA
   nClusters:      NaN
   clusterNames:   NULL
   time:           getOption("latrend.time")
   id:             getOption("latrend.id")
   name:           "stratify"
   response:       "Y"
   stratify:       Y[1] > 1.6
  ---------------------------------------------------------------------------
  Checking and transforming the training data format.
  Preparing the training data for fitting...
  Fitting the method...
  Done fitting the method (0.041 secs)
  ---------------------------------------------------------------------------
  ---------------------------------------------------------------------------
  - Longitudinal clustering using: stratify
  ---------------------------------------------------------------------------
  Method arguments:
   center:         mean
   nClusters:      NaN
   clusterNames:   NULL
   time:           getOption("latrend.time")
   id:             getOption("latrend.id")
   name:           "stratify"
   response:       "Y"
   stratify:       stratfun
  ---------------------------------------------------------------------------
  Checking and transforming the training data format.
  Preparing the training data for fitting...
  Fitting the method...
  Done fitting the method (0.15 secs)
  ---------------------------------------------------------------------------
  ---------------------------------------------------------------------------
  - Longitudinal clustering using: stratify
  ---------------------------------------------------------------------------
  Method arguments:
   center:         meanNA
   nClusters:      NaN
   clusterNames:   c("Low", "High")
   time:           getOption("latrend.time")
   id:             getOption("latrend.id")
   name:           "stratify"
   response:       "Y"
   stratify:       Intercept[1] > 1.7
  ---------------------------------------------------------------------------
  Checking and transforming the training data format.
  Preparing the training data for fitting...
  Fitting the method...
  Done fitting the method (0.015 secs)
  ---------------------------------------------------------------------------
  ---------------------------------------------------------------------------
  - Longitudinal clustering using: two-step clustering
  ---------------------------------------------------------------------------
  Method arguments:
   standardize:    scale
   center:         meanNA
   time:           getOption("latrend.time")
   id:             getOption("latrend.id")
   response:       "Y"
   representationStep:repStep
   clusterStep:    clusStep
  ---------------------------------------------------------------------------
  Checking and transforming the training data format.
  Preparing the training data for fitting...
  Fitting the method...
  Done fitting the method (0.15 secs)
  ---------------------------------------------------------------------------
  ---------------------------------------------------------------------------
  - Longitudinal clustering using: two-step clustering
  ---------------------------------------------------------------------------
  Method arguments:
   nClusters:      2
   formula:        Y ~ Time
   standardize:    scale
   center:         meanNA
   time:           getOption("latrend.time")
   id:             getOption("latrend.id")
   response:       "Y"
   representationStep:repStep.gen
   clusterStep:    clusStep.gen
  ---------------------------------------------------------------------------
  Checking and transforming the training data format.
  Preparing the training data for fitting...
  Fitting the method...
  Done fitting the method (0.17 secs)
  ---------------------------------------------------------------------------
  --- finished re-building ‘implement.Rmd’
  
  --- re-building ‘simulation.Rmd’ using rmarkdown
  --- finished re-building ‘simulation.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘demo.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: legendry
Check: dependencies in R code
New result: WARNING
  '::' or ':::' import not declared from: ‘S7’

Package: lemon
Check: examples
New result: ERROR
  Running examples in ‘lemon-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: guidebox_as_column
  > ### Title: Guidebox as a column
  > ### Aliases: guidebox_as_column
  > 
  > ### ** Examples
  > 
  > library(ggplot2)
  > 
  > p <- ggplot(diamonds, aes(x=x, y=y, colour=cut)) + geom_point()
  > guidebox_as_column(p)
  Error in lr[1]:(lr[2] - 1) : NA/NaN argument
  Calls: guidebox_as_column -> <Anonymous> -> unit.c -> [ -> [.unit
  Execution halted

Package: lemon
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘capped-axes.Rmd’ using rmarkdown
  --- finished re-building ‘capped-axes.Rmd’
  
  --- re-building ‘facet-rep-labels.Rmd’ using rmarkdown
  --- finished re-building ‘facet-rep-labels.Rmd’
  
  --- re-building ‘geoms.Rmd’ using rmarkdown
  --- finished re-building ‘geoms.Rmd’
  
  --- re-building ‘gtable_show_lemonade.Rmd’ using rmarkdown
  --- finished re-building ‘gtable_show_lemonade.Rmd’
  
  --- re-building ‘legends.Rmd’ using rmarkdown
  
  Quitting from legends.Rmd:178-180 [reposition_legend_facet1]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `reposition_legend()`:
  ! Could not find panel named `panel-1-5`.
  ---
  Backtrace:
      ▆
   1. └─lemon::reposition_legend(d2, "top left", panel = "panel-1-5")
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'legends.Rmd' failed with diagnostics:
  Could not find panel named `panel-1-5`.
  --- failed re-building ‘legends.Rmd’
  
  --- re-building ‘lemon_print.Rmd’ using rmarkdown
  --- finished re-building ‘lemon_print.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘legends.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: lemon
Check: S3 generic/method consistency
New result: WARNING
  ggplot_build:
    function(plot, ...)
  ggplot_build.lemon_plot:
    function(plot)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.axis_annotation:
    function(object, plot, object_name)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: lgpr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [54s/55s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # Short tests
    > #  - focus on testing that everything runs
    > #  - should take less than minute
    > library(testthat)
    > library(lgpr)
    Attached lgpr 1.2.4, using rstan 2.32.7. Type ?lgpr to get started.
    > 
    > test_check("lgpr")
    [ FAIL 2 | WARN 1 | SKIP 0 | PASS 446 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_misc-invgamma.R:34:3'): plotting the inverse gamma distribution works ──
    `c1` not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_misc-invgamma.R:35:3'): plotting the inverse gamma distribution works ──
    `c2` not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 2 | WARN 1 | SKIP 0 | PASS 446 ]
    Error: Test failures
    Execution halted

Package: listdown
Check: examples
New result: ERROR
  Running examples in ‘listdown-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: as_ld_yml
  > ### Title: Turn a Computational Component List into YAML with Class
  > ###   Information
  > ### Aliases: as_ld_yml
  > 
  > ### ** Examples
  > 
  > if (require("ggplot2")) {
  + 
  +   cc_list <- list(
  +     Linear = ggplot(anscombe, aes(x = x1, y = y1)) + geom_point(),
  +    `Non Linear` = ggplot(anscombe, aes(x = x2, y = y2)) + geom_point(),
  +    `Outlier Vertical`= ggplot(anscombe, aes(x = x3, y = y3)) + geom_point(),
  +    `Outlier Horizontal` =  ggplot(anscombe, aes(x = x4, y = y4)) +
  +      geom_point())
  + 
  +   as_ld_yml(cc_list)
  + }
  Loading required package: ggplot2
  Error in parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)),  : 
    <text>:2:1: unexpected symbol
  1: x [[1]]  <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":"))
  2: x
     ^
  Calls: as_ld_yml -> depth_first_copy -> eval -> parse
  Execution halted

Package: listdown
Check: tests
New result: ERROR
    Running ‘testthat.r’ [20s/20s]
  Running the tests in ‘tests/testthat.r’ failed.
  Complete output:
    > library(testthat)
    > library(listdown)
    > 
    > test_check("listdown")
    [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • On CRAN (1): 'test-create-doc.r:27:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ─────────────────────
    Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), 
        ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol
    1: x [[1]]  <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":"))
    2: x
       ^
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. └─listdown::as_ld_yml(cc_list)
     5.   └─listdown (local) depth_first_copy()
     6.     ├─base::eval(...)
     7.     └─base::parse(...)
    ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ────────────────────────
    ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds").
    4 string mismatches
    
    [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ]
    Error: Test failures
    Execution halted

Package: LMD
Check: examples
New result: ERROR
  Running examples in ‘LMD-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_lmd
  > ### Title: LMD Plot
  > ### Aliases: plot_lmd
  > ### Keywords: LMD PF Residue
  > 
  > ### ** Examples
  > 
  > x=1:100
  > y = (2 / 3 )* sin(x * 30) + (2 / 3) * sin(x * 17.5) + (4 / 5) *cos(x * 2)
  > plot_lmd(lmd(y))
  Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
  ℹ Please use `linewidth` instead.
  ℹ The deprecated feature was likely used in the LMD package.
    Please report the issue at
    <https://github.com/shubhra-opensource/LMD/issues>.
  Error: <ggplot2::labels> object is invalid:
  - every label must be named.
  Execution halted

Package: LMD
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Getting_Started_with_LMD.Rmd’ using rmarkdown
  
  Quitting from Getting_Started_with_LMD.Rmd:420-423 [unnamed-chunk-10]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::labels> object is invalid:
  - every label must be named.
  ---
  Backtrace:
      ▆
   1. └─LMD::plot_lmd(lmd_object)
   2.   └─base::lapply(...)
   3.     └─LMD (local) FUN(X[[i]], ...)
   4.       └─LMD (local) uniplot(series, yname)
   5.         └─ggplot2::labs(yname)
   6.           └─ggplot2::class_labels(args)
   7.             └─S7::new_object(labels)
   8.               └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Getting_Started_with_LMD.Rmd' failed with diagnostics:
  <ggplot2::labels> object is invalid:
  - every label must be named.
  --- failed re-building ‘Getting_Started_with_LMD.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Getting_Started_with_LMD.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: longevity
Check: examples
New result: ERROR
  Running examples in ‘longevity-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: autoplot.elife_par
  > ### Title: Goodness-of-fit plots for parametric models
  > ### Aliases: autoplot.elife_par plot.elife_par
  > 
  > ### ** Examples
  > 
  > set.seed(1234)
  > samp <- samp_elife(
  +  n = 200,
  +  scale = 2,
  +  shape = 0.3,
  +  family = "gomp",
  +  lower = 0, upper = runif(200, 0, 10),
  +  type2 = "ltrc")
  > fitted <- fit_elife(
  +  time = samp$dat,
  +  thresh = 0,
  +  event = ifelse(samp$rcens, 0L, 1L),
  +  type = "right",
  +  family = "exp",
  +  export = TRUE)
  > plot(fitted, plot.type = "ggplot")
  Error in get(x = ifelse(packageVersion("ggplot2") >= "3.5.2.9001", "print.ggplot2::ggplot",  : 
    object 'print.ggplot2::ggplot' not found
  Calls: plot -> plot.elife_par -> lapply -> match.fun -> get
  Execution halted

Package: longevity
Check: tests
New result: ERROR
    Running ‘tinytest.R’ [2s/2s]
  Running the tests in ‘tests/tinytest.R’ failed.
  Complete output:
    > 
    > if ( requireNamespace("tinytest", quietly=TRUE) ){
    +   tinytest::test_package("longevity")
    + }
    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    
    test-S3methods.R..............    0 tests    Error in get(x = ifelse(packageVersion("ggplot2") >= "3.5.2.9001", "print.ggplot2::ggplot",  : 
      object 'print.ggplot2::ggplot' not found
    Calls: <Anonymous> ... plot -> plot.elife_par -> lapply -> match.fun -> get
    Execution halted

Package: loon.ggplot
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggmulti’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: ltertools
Check: tests
New result: ERROR
    Running ‘testthat.R’ [3s/6s]
  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(ltertools)
    > 
    > test_check("ltertools")
    Retrieving data for 2022-02-07
    Retrieving data for 2022-02-08
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 36 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-site_timeline.R:15:3'): Outputs are correct ──────────────────
    class(time_gg) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 36 ]
    Error: Test failures
    Execution halted

Package: manymodelr
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘manymodelr’

Package: manynet
Check: examples
New result: ERROR
  Running examples in ‘manynet-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: make_random
  > ### Title: Making unconditional and conditional random networks
  > ### Aliases: make_random generate_random generate_configuration
  > ###   generate_man generate_utilities generate_permutation
  > 
  > ### ** Examples
  > 
  > graphr(generate_random(12, 0.4))
  Error in `patchwork::wrap_plots()`:
  ! Only know how to add <ggplot> and/or <grob> objects
  Backtrace:
      ▆
   1. └─manynet::graphr(generate_random(12, 0.4))
   2.   └─manynet:::.graph_layout(...)
   3.     └─ggraph::ggraph(lo)
   4.       └─manynet:::`+.ggplot`(...)
   5.         └─patchwork::wrap_plots(e1, e2, ...)
   6.           └─cli::cli_abort("Only know how to add {.cls ggplot} and/or {.cls grob} objects")
   7.             └─rlang::abort(...)
  Execution halted

Package: manynet
Check: tests
New result: ERROR
    Running ‘testthat.R’ [43s/28s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(manynet)
    > 
    > test_check("manynet")
    Starting 2 test processes
    [ FAIL 2 | WARN 0 | SKIP 20 | PASS 562 ]
    
    ══ Skipped tests (20) ══════════════════════════════════════════════════════════
    • On CRAN (20): 'test-manip_as.R:86:3', 'test-manip_split.R:49:3',
      'test-map_autograph.R:2:3', 'test-map_autograph.R:17:3',
      'test-map_autograph.R:31:3', 'test-map_autograph.R:47:3',
      'test-map_autograph.R:65:3', 'test-map_autograph.R:91:3',
      'test-map_autograph.R:103:3', 'test-map_autograph.R:113:3',
      'test-map_autograph.R:120:3', 'test-map_autograph.R:127:3',
      'test-map_autograph.R:140:3', 'test-map_autograph.R:171:3',
      'test-map_autograph.R:180:3', 'test-mark_nodes.R:36:3',
      'test-mark_nodes.R:45:3', 'test-mark_nodes.R:81:3', 'test-mark_ties.R:24:3',
      'test-mark_ties.R:33:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-map_theme.R:3:3'): themes graph correctly ──────────────────────
    Error in `patchwork::wrap_plots(e1, e2, ...)`: Only know how to add <ggplot> and/or <grob> objects
    Backtrace:
        ▆
     1. └─manynet::graphr(to_mentoring(ison_brandes)) at test-map_theme.R:3:3
     2.   └─manynet:::.graph_layout(...)
     3.     └─ggraph::ggraph(lo)
     4.       └─manynet:::`+.ggplot`(...)
     5.         └─patchwork::wrap_plots(e1, e2, ...)
     6.           └─cli::cli_abort("Only know how to add {.cls ggplot} and/or {.cls grob} objects")
     7.             └─rlang::abort(...)
    ── Error ('test-map_theme.R:33:3'): scales graph correctly ─────────────────────
    Error in `patchwork::wrap_plots(e1, e2, ...)`: Only know how to add <ggplot> and/or <grob> objects
    Backtrace:
        ▆
     1. ├─... %>% graphr(node_color = color) at test-map_theme.R:33:3
     2. └─manynet::graphr(., node_color = color)
     3.   └─manynet:::.graph_layout(...)
     4.     └─ggraph::ggraph(lo)
     5.       └─manynet:::`+.ggplot`(...)
     6.         └─patchwork::wrap_plots(e1, e2, ...)
     7.           └─cli::cli_abort("Only know how to add {.cls ggplot} and/or {.cls grob} objects")
     8.             └─rlang::abort(...)
    
    [ FAIL 2 | WARN 0 | SKIP 20 | PASS 562 ]
    Error: Test failures
    Execution halted

Package: marquee
Check: examples
New result: ERROR
  Running examples in ‘marquee-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: guide_marquee
  > ### Title: Marquee subtitle guide
  > ### Aliases: guide_marquee
  > 
  > ### ** Examples
  > 
  > ## Don't show: 
  > if (rlang::is_installed("ggplot2", version = "3.5.0")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
  + ## End(Don't show)
  + library(ggplot2)
  + # A standard plot
  + base <- ggplot(mpg, aes(displ, hwy)) +
  +   geom_point()
  + 
  + # Using key glyphs
  + base + aes(shape = drv) +
  +   scale_shape_discrete(
  +     # Same as using <<1>>, <<2>> and <<3>>,
  +     # or ![](1), ![](2) and ![](3)
  +     # or ![](4), ![](f) and ![](r)
  +     name = "Cars with four wheel <<4>>, forward <<f>> or reverse <<r>> drive.",
  +     guide = "marquee"
  +   )
  + 
  + # Recolouring text
  + base <- base +
  +   aes(colour = drv) +
  +   labs(
  +     colour = "Cars with {.4 four wheel}, {.f forward} or {.r reverse} drive."
  +   )
  + base + guides(colour = "marquee")
  + 
  + # Adjust display of labels
  + st <- style(weight = "bold", italic = TRUE, background = NA)
  + base + guides(colour = guide_marquee(style = st))
  + 
  + # Using background instead of text colour by setting it to NULL
  + st <- style(color = "black", background = NULL)
  + base + guides(colour = guide_marquee(style = st))
  + 
  + # Customising style of each label through style sets
  + # Note: tag names must be universal per `vctrs::vec_as_names` and
  + # prefixed with `lab_`.
  + st <- classic_style()
  + st <- modify_style(st, tag = "lab_f", background = NULL, color = "black")
  + st <- modify_style(st, tag = "lab_r", border_size = trbl(1),
  +                    color = "black", background = NA)
  + base + guides(colour = guide_marquee(style = st))
  + 
  + # Alternatively:
  + base + guides(colour = "marquee") +
  +   theme(plot.subtitle = element_marquee(style = st))
  + 
  + # Splicing in labels by number (!!2) or label (!!subcompact)
  + base + aes(colour = class) +
  +   labs(colour = "Cars including !!2 and !!subcompact vehicles") +
  +   guides(colour = "marquee")
  + 
  + # Using automatic detection
  + base + aes(colour = class) +
  +   labs(colour = "Cars including suv and minivan vehicles") +
  +   guides(colour = guide_marquee(detect = TRUE))
  + ## Don't show: 
  + }) # examplesIf
  > library(ggplot2)
  > base <- ggplot(mpg, aes(displ, hwy)) + geom_point()
  > base + aes(shape = drv) + scale_shape_discrete(name = "Cars with four wheel <<4>>, forward <<f>> or reverse <<r>> drive.", 
  +     guide = "marquee")
  Warning: `is.theme()` was deprecated in ggplot2 3.5.2.
  ℹ Please use `is_theme()` instead.
  Warning in split.default(glyphs, rep(seq_len(n_breaks), each = n_layers)) :
    data length is not a multiple of split variable
  Warning in max(unlist(width)) :
    no non-missing arguments to max; returning -Inf
  Warning in max(unlist(height)) :
    no non-missing arguments to max; returning -Inf
  Error in gridGTreeCoords(unname(lapply(x$children[x$childrenOrder], grobCoords,  : 
    Invalid gTree coordinates
  Calls: <Anonymous> ... lapply -> FUN -> grobCoords.gTree -> gridGTreeCoords
  Execution halted

Package: mcStats
Check: tests
New result: ERROR
    Running ‘testthat.R’ [7s/7s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(mcStats)
    > 
    > test_check("mcStats")
    [ FAIL 3 | WARN 2 | SKIP 0 | PASS 5 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('testGraphs.R:10:3'): showT.Test runs error-free ───────────────────
    `showT.Test(x)` generated warnings:
    * Removed 36 rows containing missing values or values outside the scale range
    (`geom_area()`).
    ── Failure ('testGraphs.R:26:3'): showANOVA runs error-free ────────────────────
    `showANOVA(yield ~ N + P + K + block + block:P, npk)` generated warnings:
    * Removed 459 rows containing missing values or values outside the scale range
    (`geom_area()`).
    * Removed 25 rows containing missing values or values outside the scale range
    (`geom_area()`).
    * Removed 281 rows containing missing values or values outside the scale range
    (`geom_area()`).
    * Removed 361 rows containing missing values or values outside the scale range
    (`geom_area()`).
    * Removed 75 rows containing missing values or values outside the scale range
    (`geom_area()`).
    ── Failure ('testGraphs.R:30:3'): showOLS runs error-free ──────────────────────
    `showOLS(mpg ~ cyl + qsec, mtcars)` generated warnings:
    * Removed 420 rows containing missing values or values outside the scale range
    (`geom_area()`).
    * Removed 442 rows containing missing values or values outside the scale range
    (`geom_area()`).
    * Removed 184 rows containing missing values or values outside the scale range
    (`geom_area()`).
    
    [ FAIL 3 | WARN 2 | SKIP 0 | PASS 5 ]
    Error: Test failures
    Execution halted

Package: meme
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘meme.Rmd’ using rmarkdown
  
  Quitting from meme.Rmd:166-177 [unnamed-chunk-12]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `geom_subview()`:
  ! subview must be provided
  ---
  Backtrace:
      ▆
   1. └─ggimage::geom_subview(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'meme.Rmd' failed with diagnostics:
  subview must be provided
  --- failed re-building ‘meme.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘meme.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: metR
Check: examples
New result: ERROR
  Running examples in ‘metR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: geom_contour_fill
  > ### Title: Filled 2d contours of a 3d surface
  > ### Aliases: geom_contour_fill stat_contour_fill StatContourFill
  > ### Keywords: datasets
  > 
  > ### ** Examples
  > 
  > ## Don't show: 
  > if (requireNamespace("reshape2")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
  + ## End(Don't show)
  + ## Don't show: 
  + data.table::setDTthreads(1)
  + ## End(Don't show)
  + 
  + library(ggplot2)
  + surface <- reshape2::melt(volcano)
  + ggplot(surface, aes(Var1, Var2, z = value)) +
  +   geom_contour_fill() +
  +   geom_contour(color = "black", size = 0.1)
  + 
  + ggplot(surface, aes(Var1, Var2, z = value)) +
  +   geom_contour_fill(aes(fill = after_stat(level)))
  + 
  + ggplot(surface, aes(Var1, Var2, z = value)) +
  +   geom_contour_fill(aes(fill = after_stat(level_d)))
  + ## Don't show: 
  + }) # examplesIf
  > data.table::setDTthreads(1)
  > library(ggplot2)
  > surface <- reshape2::melt(volcano)
  > ggplot(surface, aes(Var1, Var2, z = value)) + geom_contour_fill() + geom_contour(color = "black", 
  +     size = 0.1)
  Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
  ℹ Please use `linewidth` instead.
  > ggplot(surface, aes(Var1, Var2, z = value)) + geom_contour_fill(aes(fill = after_stat(level)))
  > ggplot(surface, aes(Var1, Var2, z = value)) + geom_contour_fill(aes(fill = after_stat(level_d)))
  Error in train(..., self = self) : 
    unused argument (call = scale_fill_discretised())
  Calls: <Anonymous> ... <Anonymous> -> train_df -> <Anonymous> -> train -> <Anonymous>
  Execution halted

Package: metR
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Visualization-tools.Rmd’ using knitr
  
  Quitting from Visualization-tools.Rmd:181-184 [unnamed-chunk-12]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `train()`:
  ! unused argument (call = scale_fill_discretised())
  ---
  Backtrace:
       ▆
    1. └─tools:::.buildOneVignette(...)
    2.   ├─base::tryCatch(...)
    3.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    4.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    5.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    6.   └─engine$weave(file, quiet = quiet, encoding = enc)
    7.     └─(if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", ...
    8.       └─knitr::knit(input, text = text, envir = envir, quiet = quiet)
    9.         └─knitr:::process_file(text, output)
   10.           ├─xfun:::handle_error(...)
   11.           ├─base::withCallingHandlers(...)
   12.           └─knitr:::process_group(group)
   13.             └─knitr:::call_block(x)
   14.               └─knitr:::block_exec(params)
   15.                 └─knitr:::eng_r(options)
   16.                   ├─knitr:::in_input_dir(...)
   17.                   │ └─knitr:::in_dir(input_dir(), expr)
   18.                   └─knitr (local) evaluate(...)
   19.                     └─evaluate::evaluate(...)
   20.                       ├─base::withRestarts(...)
   21.                       │ └─base (local) withRestartList(expr, restarts)
   22.                       │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
   23.                       │   │ └─base (local) doWithOneRestart(return(expr), restart)
   24.                       │   └─base (local) withRestartList(expr, restarts[-nr])
   25.                       │     └─base (local) withOneRestart(expr, restarts[[1L]])
   26.                       │       └─base (local) doWithOneRestart(return(expr), restart)
   27.                       ├─evaluate:::with_handlers(...)
   28.                       │ ├─base::eval(call)
   29.                       │ │ └─base::eval(call)
   30.                       │ └─base::withCallingHandlers(...)
   31.                       └─watcher$print_value(ev$value, ev$visible, envir)
   32.                         ├─base::withVisible(handle_value(handler, value, visible, envir))
   33.                         └─evaluate:::handle_value(handler, value, visible, envir)
   34.                           └─handler$value(value, visible)
   35.                             └─knitr (local) fun(x, options = options)
   36.                               ├─base::withVisible(knit_print(x, ...))
   37.                               ├─knitr::knit_print(x, ...)
   38.                               └─knitr:::knit_print.default(x, ...)
   39.                                 └─knitr::normal_print(x)
   40.                                   ├─base::print(x)
   41.                                   └─ggplot2 (local) `print.ggplot2::ggplot`(x)
   42.                                     ├─ggplot2::ggplot_build(x)
   43.                                     └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
   44.                                       └─base::lapply(data, npscales$train_df)
   45.                                         └─ggplot2 (local) FUN(X[[i]], ...)
   46.                                           └─ggplot2 (local) train_df(..., self = self)
   47.                                             └─base::lapply(self$scales, function(scale) scale$train_df(df = df))
   48.                                               └─ggplot2 (local) FUN(X[[i]], ...)
   49.                                                 └─scale$train_df(df = df)
   50.                                                   └─ggplot2 (local) train_df(..., self = self)
   51.                                                     └─self$train(df[[aesthetic]])
   52.                                                       └─ggplot2 (local) train(..., self = self)
   53.                                                         └─self$range$train(x, call = self$call)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics:
  unused argument (call = scale_fill_discretised())
  --- failed re-building ‘Visualization-tools.Rmd’
  
  --- re-building ‘Working-with-data.Rmd’ using knitr
  --- finished re-building ‘Working-with-data.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Visualization-tools.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: metR
Check: tests
New result: ERROR
    Running ‘testthat.R’ [47s/45s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(metR)
    > # library(vdiffr)
    > 
    > on_cran <- !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
    > if (on_cran) data.table::setDTthreads(2)
    > 
    > test_check("metR")
    [ FAIL 1 | WARN 2 | SKIP 19 | PASS 184 ]
    
    ══ Skipped tests (19) ══════════════════════════════════════════════════════════
    • On CRAN (19): 'test-GetTopography.R:3:5', 'test-ReadNetCDF.R:66:5',
      'test-vis-arrow.R:13:5', 'test-vis-arrow.R:39:5', 'test-vis-contour2.R:11:5',
      'test-vis-contour2.R:25:5', 'test-vis-contour2.R:36:5',
      'test-vis-contour2.R:53:5', 'test-vis-contour2.R:72:5',
      'test-vis-contour_fill.R:13:5', 'test-vis-contour_fill.R:27:5',
      'test-vis-contour_fill.R:43:5', 'test-vis-discretised-scale.R:15:5',
      'test-vis-geom-relief.R:11:5', 'test-vis-streamline.R:23:5',
      'test-vis-streamline.R:29:5', 'test-vis-text-contour.R:13:5',
      'test-vis-text-contour.R:69:5', 'test-vis-text-contour.R:80:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-vis-guide_colorstrip.R:14:5'): guide works ─────────────────────
    Error in `upgradeUnit.default(x)`: Not a unit object
    Backtrace:
         ▆
      1. └─vdiffr::expect_doppelganger(...) at test-vis-guide_colorstrip.R:14:5
      2.   └─vdiffr (local) writer(fig, testcase, title)
      3.     ├─vdiffr:::print_plot(plot, title)
      4.     └─vdiffr:::print_plot.ggplot(plot, title)
      5.       ├─base::print(p)
      6.       └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7.         ├─ggplot2::ggplot_gtable(data)
      8.         └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
      9.           └─plot@guides$assemble(theme)
     10.             └─ggplot2 (local) assemble(..., self = self)
     11.               └─self$draw(theme, positions, theme$legend.direction)
     12.                 └─ggplot2 (local) draw(..., self = self)
     13.                   └─guides[[i]]$draw(...)
     14.                     └─ggplot2 (local) draw(..., self = self)
     15.                       ├─ggplot2::guide_gengrob(params, theme)
     16.                       └─metR:::guide_gengrob.colorstrip(params, theme)
     17.                         └─grid::convertWidth(...)
     18.                           └─grid::convertUnit(...)
     19.                             ├─grid:::upgradeUnit(x)
     20.                             └─grid:::upgradeUnit.default(x)
    
    [ FAIL 1 | WARN 2 | SKIP 19 | PASS 184 ]
    Error: Test failures
    Execution halted

Package: mets
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘basic-dutils.Rmd’ using rmarkdown
  --- finished re-building ‘basic-dutils.Rmd’
  
  --- re-building ‘binomial-family.Rmd’ using rmarkdown
  --- finished re-building ‘binomial-family.Rmd’
  
  --- re-building ‘binomial-twin.Rmd’ using rmarkdown
  --- finished re-building ‘binomial-twin.Rmd’
  
  --- re-building ‘binreg-TRS.Rmd’ using rmarkdown
  --- finished re-building ‘binreg-TRS.Rmd’
  
  --- re-building ‘binreg-ate.Rmd’ using rmarkdown
  --- finished re-building ‘binreg-ate.Rmd’
  
  --- re-building ‘binreg.Rmd’ using rmarkdown
  --- finished re-building ‘binreg.Rmd’
  
  --- re-building ‘cifreg.Rmd’ using rmarkdown
  --- finished re-building ‘cifreg.Rmd’
  
  --- re-building ‘cooking-survival-data.Rmd’ using rmarkdown
  --- finished re-building ‘cooking-survival-data.Rmd’
  
  --- re-building ‘glm-utility.Rmd’ using rmarkdown
  --- finished re-building ‘glm-utility.Rmd’
  
  --- re-building ‘haplo-discrete-ttp.Rmd’ using rmarkdown
  --- finished re-building ‘haplo-discrete-ttp.Rmd’
  
  --- re-building ‘interval-discrete-survival.Rmd’ using rmarkdown
  --- finished re-building ‘interval-discrete-survival.Rmd’
  
  --- re-building ‘marginal-cox.Rmd’ using rmarkdown
  --- finished re-building ‘marginal-cox.Rmd’
  
  --- re-building ‘mediation-survival.Rmd’ using rmarkdown
  --- finished re-building ‘mediation-survival.Rmd’
  
  --- re-building ‘phreg_rct.Rmd’ using rmarkdown
  --- finished re-building ‘phreg_rct.Rmd’
  
  --- re-building ‘quantitative-twin.Rmd’ using rmarkdown
  
  Quitting from quantitative-twin.Rmd:113-116 [scatter1]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'quantitative-twin.Rmd' failed with diagnostics:
  Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  --- failed re-building ‘quantitative-twin.Rmd’
  
  --- re-building ‘recurrent-events.Rmd’ using rmarkdown
  --- finished re-building ‘recurrent-events.Rmd’
  
  --- re-building ‘rmst-ate.Rmd’ using rmarkdown
  --- finished re-building ‘rmst-ate.Rmd’
  
  --- re-building ‘survival-ate.Rmd’ using rmarkdown
  --- finished re-building ‘survival-ate.Rmd’
  
  --- re-building ‘time-to-event-family-studies-arev.Rmd’ using rmarkdown
  --- finished re-building ‘time-to-event-family-studies-arev.Rmd’
  
  --- re-building ‘twostage-survival.Rmd’ using rmarkdown
  --- finished re-building ‘twostage-survival.Rmd’
  
  --- re-building ‘while-alive.Rmd’ using rmarkdown
  --- finished re-building ‘while-alive.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘quantitative-twin.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: mikropml
Check: tests
New result: ERROR
    Running ‘testthat.R’ [54s/54s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(mikropml)
    > test_check("mikropml")
    Fraction of data in the training set: 0.778 
    	Groups in the training set: A C D 
    	Groups in the testing set: B
    Fraction of data in the training set: 0.778 
    	Groups in the training set: A C D 
    	Groups in the testing set: B
    Fraction of data in the training set: 0.333 
    	Groups in the training set: A D 
    	Groups in the testing set: A B C D
    Fraction of data in the training set: 0.785 
    	Groups in the training set: A B E F G H 
    	Groups in the testing set: C D
    Fraction of data in the training set: 0.2 
    	Groups in the training set: A B 
    	Groups in the testing set: A B C D E F G H
    Using 'dx' as the outcome column.
    Using 'dx' as the outcome column.
    Using 'dx' as the outcome column.
    Using 'y' as the outcome column.
    Using 'y' as the outcome column.
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    Using 'dx' as the outcome column.
    Groups will not be kept together in CV partitions because the number of groups in the training set is not larger than `kfold`
    Training the model...
    Training complete.
    Fraction of data in the training set: 0.785 
    	Groups in the training set: A B E F G H 
    	Groups in the testing set: C D
    Using 'dx' as the outcome column.
    Using 'dx' as the outcome column.
    [ FAIL 2 | WARN 18 | SKIP 12 | PASS 314 ]
    
    ══ Skipped tests (12) ══════════════════════════════════════════════════════════
    • On CRAN (12): 'test-feature_importance.R:14:3',
      'test-feature_importance.R:142:3', 'test-feature_importance.R:212:3',
      'test-run_ml.R:64:3', 'test-run_ml.R:82:3', 'test-run_ml.R:100:3',
      'test-run_ml.R:116:3', 'test-run_ml.R:135:3', 'test-run_ml.R:150:3',
      'test-run_ml.R:188:3', 'test-run_ml.R:278:3', 'test-train.R:44:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot.R:122:3'): plot_mean_roc uses geom ribbon, line, and abline ──
    ... %>% unlist() (`actual`) not equal to c(...) (`expected`).
    
    `names(actual)` is a character vector ('geom_ribbon1', 'geom_ribbon2', 'geom_ribbon3', 'geom_ribbon4', 'geom_line1', ...)
    `names(expected)` is absent
    ── Failure ('test-plot.R:140:3'): plot_mean_prc uses geom ribbon, line, and hline ──
    ... %>% unlist() (`actual`) not equal to c(...) (`expected`).
    
    `names(actual)` is a character vector ('geom_ribbon1', 'geom_ribbon2', 'geom_ribbon3', 'geom_ribbon4', 'geom_line1', ...)
    `names(expected)` is absent
    
    [ FAIL 2 | WARN 18 | SKIP 12 | PASS 314 ]
    Error: Test failures
    Execution halted

Package: MiMIR
Check: examples
New result: ERROR
  Running examples in ‘MiMIR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: MetaboWAS
  > ### Title: MetaboWAS
  > ### Aliases: MetaboWAS
  > 
  > ### ** Examples
  > 
  > require(MiMIR)
  > require(plotly)
  Loading required package: plotly
  Loading required package: ggplot2
  
  Attaching package: ‘plotly’
  
  The following object is masked from ‘package:ggplot2’:
  
      last_plot
  
  The following object is masked from ‘package:stats’:
  
      filter
  
  The following object is masked from ‘package:graphics’:
  
      layout
  
  > require(ggplot2)
  > 
  > #' #load the dataset
  > metabolic_measures <- synthetic_metabolic_dataset
  > phenotypes <- synthetic_phenotypic_dataset
  > 
  > #Computing a MetaboWAS for age corrected by sex
  > MetaboWAS(met=metabolic_measures, pheno=phenotypes, test_variable="age", covariates= "sex")
  Error in `ggplot2::scale_y_continuous()`:
  ! `limits` must be a vector of length 2, not length 7.
  Backtrace:
      ▆
   1. └─MiMIR::MetaboWAS(...)
   2.   └─ggplot2::scale_y_continuous(expand = c(0, 0), limits = c(0, ylim))
   3.     └─ggplot2::continuous_scale(...)
   4.       └─ggplot2:::check_continuous_limits(limits, call = call)
   5.         └─ggplot2:::check_length(limits, 2L, arg = arg, call = call)
   6.           └─cli::cli_abort(msg, call = call, arg = arg)
   7.             └─rlang::abort(...)
  Execution halted

Package: miRetrieve
Check: tests
New result: ERROR
    Running ‘testthat.R’ [30s/30s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(miRetrieve)
    > 
    > test_check("miRetrieve")
    [ FAIL 6 | WARN 15 | SKIP 0 | PASS 204 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-fitlda.R:35:5'): Tests that 'plot_lda_term' returns a plot ───
    `plot_lda` has type 'object', not 'list'.
    ── Failure ('test-jointargets.R:69:5'): Tests that targets can be plotted ──────
    typeof(plot_target) not equal to "list".
    1/1 mismatches
    x[1]: "object"
    y[1]: "list"
    ── Failure ('test-plotscore.R:41:5'): Tests plotting scores ────────────────────
    typeof(plot_animal) not equal to "list".
    1/1 mismatches
    x[1]: "object"
    y[1]: "list"
    ── Failure ('test-plotscore.R:42:5'): Tests plotting scores ────────────────────
    typeof(plot_patients) not equal to "list".
    1/1 mismatches
    x[1]: "object"
    y[1]: "list"
    ── Failure ('test-plotscore.R:43:5'): Tests plotting scores ────────────────────
    typeof(plot_biomarker) not equal to "list".
    1/1 mismatches
    x[1]: "object"
    y[1]: "list"
    ── Failure ('test-plotscore.R:44:5'): Tests plotting scores ────────────────────
    typeof(plot_own) not equal to "list".
    1/1 mismatches
    x[1]: "object"
    y[1]: "list"
    
    [ FAIL 6 | WARN 15 | SKIP 0 | PASS 204 ]
    Error: Test failures
    Execution halted

Package: MiscMetabar
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [107s/64s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(MiscMetabar)
    Loading required package: phyloseq
    Loading required package: ggplot2
    Loading required package: dada2
    Loading required package: Rcpp
    Loading required package: dplyr
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    Loading required package: purrr
    
    Attaching package: 'purrr'
    
    The following object is masked from 'package:testthat':
    
        is_null
    
    > 
    > test_check("MiscMetabar")
    Starting 2 test processes
    [ FAIL 1 | WARN 2 | SKIP 74 | PASS 82 ]
    
    ══ Skipped tests (74) ══════════════════════════════════════════════════════════
    • On CRAN (74): 'test_adonis.R:1:1', 'test_controls.R:7:3',
      'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',
      'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',
      'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',
      'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',
      'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',
      'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',
      'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',
      'test_deseq2_edgeR.R:59:3', 'test_figures_biplot.R:14:3',
      'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',
      'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',
      'test_figures_misc.R:35:3', 'test_figures_summary_plot.R:9:3',
      'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3',
      'test_figures_beta_div.R:22:3', 'test_figures_beta_div.R:73:5',
      'test_figures_beta_div.R:92:3', 'test_figures_beta_div.R:102:5',
      'test_figures_beta_div.R:159:5', 'test_figures_beta_div.R:209:3',
      'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',
      'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',
      'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',
      'test_figures_beta_div.R:387:3', 'test_figures_beta_div.R:402:3',
      'test_figures_beta_div.R:414:3', 'test_krona.R:7:3',
      'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',
      'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',
      'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',
      'test_figures_taxo.R:379:3', 'test_figures_taxo.R:414:3',
      'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',
      'test_phyloseq_class.R:95:3', 'test_rw.R:8:3', 'test_rw.R:24:3',
      'test_rw.R:39:3', 'test_subset.R:7:3', 'test_subset.R:18:3',
      'test_table_functions.R:6:3', 'test_table_functions.R:19:3',
      'test_table_functions.R:34:5', 'test_table_functions.R:47:5',
      'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',
      'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',
      'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',
      'test_misc.R:30:3', 'test_misc.R:97:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_figures_beta_div.R:72:5'): graph_test_pq works ───────────────
    `graph_test_pq(data_fungi_mini, fact = "Tree_name")` produced warnings.
    
    [ FAIL 1 | WARN 2 | SKIP 74 | PASS 82 ]
    Error: Test failures
    Execution halted

Package: mistral
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘mistral’
  See ‘/home/hornik/tmp/CRAN_recheck/mistral.Rcheck/00install.out’ for details.
  Used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’

Package: MKpower
Check: examples
New result: ERROR
  Running examples in ‘MKpower-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: qqunif
  > ### Title: qq-Plots for Uniform Distribution
  > ### Aliases: qqunif qqunif.default qqunif.sim.power.ttest
  > ###   qqunif.sim.power.wtest
  > ### Keywords: hplot
  > 
  > ### ** Examples
  > 
  > ## default
  > qqunif(runif(100))
  Error in `stat_qq_band()`:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_gtable(data)
    4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$draw_geom(d, layout)
   14. │         └─ggplot2 (local) draw_geom(..., self = self)
   15. │           └─self$geom$draw_layer(...)
   16. │             └─ggplot2 (local) draw_layer(..., self = self)
   17. │               └─base::lapply(...)
   18. │                 └─ggplot2 (local) FUN(X[[i]], ...)
   19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   20. │                   └─self$draw_panel(data, panel_params, coord)
   21. │                     └─ggplot2 (local) draw_panel(..., self = self)
   22. │                       └─base::lapply(...)
   23. │                         └─ggplot2 (local) FUN(X[[i]], ...)
   24. │                           └─self$draw_group(group, panel_params, coord, ...)
   25. │                             └─ggplot2 (local) draw_group(...)
   26. │                               └─ggplot2 (local) draw_group(..., self = self)
   27. └─base::.handleSimpleError(...)
   28.   └─rlang (local) h(simpleError(msg, call))
   29.     └─handlers[[1L]](cnd)
   30.       └─cli::cli_abort(...)
   31.         └─rlang::abort(...)
  Execution halted

Package: model4you
Check: tests
New result: NOTE
    Running ‘test-pmodel-test.R’ [18s/18s]
    Running ‘test-pmodel.R’ [30s/30s]
    Comparing ‘test-pmodel.Rout’ to ‘test-pmodel.Rout.save’ ... OK
    Running ‘test-pmtree.R’ [17s/17s]
    Comparing ‘test-pmtree.Rout’ to ‘test-pmtree.Rout.save’ ...13,18d12
  < Warning message:
  < `aes_string()` was deprecated in ggplot2 3.0.0.
  < ℹ Please use tidy evaluation idioms with `aes()`.
  < ℹ See also `vignette("ggplot2-in-packages")` for more information.
  < ℹ The deprecated feature was likely used in the model4you package.
  <   Please report the issue to the authors.

Package: modeldb
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/6s]
  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(dplyr)
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    > library(purrr)
    
    Attaching package: 'purrr'
    
    The following object is masked from 'package:testthat':
    
        is_null
    
    > library(modeldb)
    > 
    > test_check("modeldb")
    [ FAIL 1 | WARN 33 | SKIP 0 | PASS 18 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_kmeans_viz.R:5:3'): plot_kmeans() returns a ggplot2 object ───
    class(plot_kmeans(mtcars, mpg, wt, group = am)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 1 | WARN 33 | SKIP 0 | PASS 18 ]
    Error: Test failures
    Execution halted

Package: Momocs
Check: examples
New result: ERROR
  Running examples in ‘Momocs-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_CV
  > ### Title: Plots a cross-validation table as an heatmap
  > ### Aliases: plot_CV plot_CV.default plot_CV.LDA
  > 
  > ### ** Examples
  > 
  > h <- hearts %>%
  +      fgProcrustes(0.01) %>% coo_slide(ldk=2) %T>% stack %>%
  +      efourier(6, norm=FALSE) %>% LDA(~aut)
  iteration:  1 	gain: 30322 
  iteration:  2 	gain: 1.2498 
  iteration:  3 	gain: 0.34194 
  iteration:  4 	gain: 0.0062954 
  > 
  > h %>% plot_CV()
  Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
  ℹ Please use the `linewidth` argument instead.
  ℹ The deprecated feature was likely used in the Momocs package.
    Please report the issue at <https://github.com/MomX/Momocs/issues>.
  Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
  of ggplot2 3.3.4.
  ℹ The deprecated feature was likely used in the Momocs package.
    Please report the issue at <https://github.com/MomX/Momocs/issues>.
  > h %>% plot_CV(freq=FALSE, rm0=FALSE, fill=FALSE)
  > # you can customize the returned gg with some ggplot2 functions
  > h %>% plot_CV(labels=FALSE, fill=TRUE, axis.size=5) + ggplot2::ggtitle("A confusion matrix")
  > 
  > # or build your own using the prepared data_frame:
  > df <- h %>% plot_CV() %$% data
  Error in eval(substitute(expr), data, enclos = parent.frame()) : 
    invalid 'envir' argument of type 'object'
  Calls: %$% -> <Anonymous> -> with.default -> eval
  Execution halted

Package: mosaic
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Resampling.Rmd’ using rmarkdown
  
  Quitting from Resampling.Rmd:438-440 [unnamed-chunk-13]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Resampling.Rmd' failed with diagnostics:
  `orientation` must be a string or character vector.
  --- failed re-building ‘Resampling.Rmd’
  
  --- re-building ‘mosaic-resources.Rmd’ using rmarkdown
  --- finished re-building ‘mosaic-resources.Rmd’
  
  --- re-building ‘MinimalRgg.Rnw’ using knitr
  
  Quitting from MinimalRgg.Rnw:494-496 [bwplot]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'MinimalRgg.Rnw' failed with diagnostics:
  `orientation` must be a string
  or character vector.
  --- failed re-building ‘MinimalRgg.Rnw’
  
  SUMMARY: processing the following files failed:
    ‘Resampling.Rmd’ ‘MinimalRgg.Rnw’
  
  Error: Vignette re-building failed.
  Execution halted

Package: mpactr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [54s/41s]
  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(mpactr)
    > 
    > test_check("mpactr")
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 61 ions failed the cv_filter filter, 423 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1303 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 796 ions failed the Blanks filter, 507 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 86 ions failed the cv_filter filter, 398 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 86 ions failed the cv_filter filter, 398 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    ! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 86 ions failed the cv_filter filter, 398 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 61 ions failed the cv_filter filter, 423 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Checking 1289 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 65 ions failed the mispicked filter, 1224 ions remain.
    i Parsing 1224 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 698 ions failed the Blanks filter, 526 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for insource ions.
    v 27 ions failed the insource filter, 457 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    ! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
    v 70 ions failed the mispicked filter, 1303 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    ! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
    v 70 ions failed the mispicked filter, 1303 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    ! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 86 ions failed the cv_filter filter, 398 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 86 ions failed the cv_filter filter, 398 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 61 ions failed the cv_filter filter, 423 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 61 ions failed the cv_filter filter, 423 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for insource ions.
    v 27 ions failed the insource filter, 457 ions remain.
    i Parsing 484 peaks for insource ions.
    v 27 ions failed the insource filter, 457 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for replicability across technical replicates.
    v 61 ions failed the cv_filter filter, 423 ions remain.
    i Parsing 423 peaks for insource ions.
    v 23 ions failed the insource filter, 400 ions remain.
    Found duplicate compound values, will add a suffix to unique the value.
    Found duplicate compound values, will add a suffix to unique the value.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Coculture.
    i Argument remove_ions is: TRUE.Removing peaks from Coculture.
    v 354 ions failed the Coculture filter, 879 ions remain.
    Rows: 1306 Columns: 21
    -- Column specification --------------------------------------------------------
    Delimiter: ","
    dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
    
    i Use `spec()` to retrieve the full column specification for this data.
    i Specify the column types or set `show_col_types = FALSE` to quiet this message.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for insource ions.
    v 27 ions failed the insource filter, 457 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks based on the sample group: Coculture.
    i Argument remove_ions is: TRUE.Removing peaks from Coculture.
    v 293 ions failed the Coculture filter, 191 ions remain.
    i Parsing 191 peaks for insource ions.
    v 15 ions failed the insource filter, 176 ions remain.
    i Checking 1303 peaks for mispicked peaks.
    i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
    v 70 ions failed the mispicked filter, 1233 ions remain.
    i Parsing 1233 peaks based on the sample group: Blanks.
    i Argument remove_ions is: TRUE.Removing peaks from Blanks.
    v 749 ions failed the Blanks filter, 484 ions remain.
    i Parsing 484 peaks for insource ions.
    v 27 ions failed the insource filter, 457 ions remain.
    [ FAIL 2 | WARN 0 | SKIP 1 | PASS 165 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • empty test (1): 'test-peak_table_formatter.R:32:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
    class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-quality_control.R:44:3'): qc plot returns a generates a plot ──
    class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 2 | WARN 0 | SKIP 1 | PASS 165 ]
    Error: Test failures
    Execution halted

Package: mshap
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(mshap)
    > 
    > test_check("mshap")
    [ FAIL 8 | WARN 2 | SKIP 0 | PASS 19 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plots.R:25:3'): Summary Plot Returns ggplot object ───────────
    `p1` has type 'object', not 'list'.
    ── Failure ('test-plots.R:26:3'): Summary Plot Returns ggplot object ───────────
    class(p1) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-plots.R:30:3'): Observation Plot Returns ggplot object ───────
    `p2` has type 'object', not 'list'.
    ── Failure ('test-plots.R:31:3'): Observation Plot Returns ggplot object ───────
    class(p2) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-plots.R:56:3'): Summary Plot Works with all arguments ────────
    `p1_all` has type 'object', not 'list'.
    ── Failure ('test-plots.R:57:3'): Summary Plot Works with all arguments ────────
    class(p1_all) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-plots.R:61:3'): Observation Plot Works with all arguments ────
    `p2_all` has type 'object', not 'list'.
    ── Failure ('test-plots.R:62:3'): Observation Plot Works with all arguments ────
    class(p2_all) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 8 | WARN 2 | SKIP 0 | PASS 19 ]
    Error: Test failures
    Execution halted

Package: mtdesign
Check: tests
New result: ERROR
    Running ‘testthat.R’ [69s/225s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(mtdesign)
    > 
    > test_check("mtdesign")
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: One stage sample size is 15.  Search bounds are 20 to 30.
    testthat 2025-08-19 17:03:17 TRACE test_check: Building grid - nTotal, nStage1: 264
    testthat 2025-08-19 17:03:17 TRACE test_check: Building grid - nTotal, nStage1, rTotal: 6710
    testthat 2025-08-19 17:03:17 TRACE test_check: Building grid - nTotal, nStage1, rTotal, rFutility: 26620
    testthat 2025-08-19 17:03:17 TRACE test_check: Building grid - nTotal, nStage1, rTotal, rFutility, rSuccess: 97571
    testthat 2025-08-19 17:03:17 TRACE test_check: Grid has 97571 rows.
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:17 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Entry
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    testthat 2025-08-19 17:03:18 DEBUG test_check: Exit
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 127 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-powerPlot.R:5:3'): multiplication works ──────────────────────
    class(powerPlot(manderGrid)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-powerPlot.R:6:3'): multiplication works ──────────────────────
    class(powerPlot(simonGrid)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 127 ]
    Error: Test failures
    Execution halted

Package: MultiTraits
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggtern’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: mverse
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘mverse_gettingstarted.Rmd’ using rmarkdown
  --- finished re-building ‘mverse_gettingstarted.Rmd’
  
  --- re-building ‘mverse_intro_glmmodelling.Rmd’ using rmarkdown
  --- finished re-building ‘mverse_intro_glmmodelling.Rmd’
  
  --- re-building ‘mverse_intro_regressionmodelling.Rmd’ using rmarkdown
  
  Quitting from mverse_intro_regressionmodelling.Rmd:127-131 [unnamed-chunk-8]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::labels> object is invalid:
  - every label must be named.
  ---
  Backtrace:
      ▆
   1. └─ggplot2::labs("Significant at 0.05")
   2.   └─ggplot2::class_labels(args)
   3.     └─S7::new_object(labels)
   4.       └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'mverse_intro_regressionmodelling.Rmd' failed with diagnostics:
  <ggplot2::labels> object is invalid:
  - every label must be named.
  --- failed re-building ‘mverse_intro_regressionmodelling.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘mverse_intro_regressionmodelling.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: mxnorm
Check: tests
New result: ERROR
    Running ‘testthat.R’ [20s/20s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(mxnorm)
    > 
    > test_check("mxnorm")
    boundary (singular) fit: see help('isSingular')
    boundary (singular) fit: see help('isSingular')
    boundary (singular) fit: see help('isSingular')
    boundary (singular) fit: see help('isSingular')
    boundary (singular) fit: see help('isSingular')
    boundary (singular) fit: see help('isSingular')
    [ FAIL 2 | WARN 2 | SKIP 6 | PASS 85 ]
    
    ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
    • skimage.filters not available for testing (6): 'test-plot_mx_density.R:21:5',
      'test-plot_mx_discordance.R:21:5', 'test-run_otsu_discordance.R:65:5',
      'test-run_otsu_discordance.R:85:5', 'test-run_otsu_discordance.R:108:5',
      'test-run_otsu_discordance.R:141:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot_mx_proportions.R:14:5'): plotting works ─────────────────
    class(plot_mx_proportions(mx_data)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-plot_mx_umap.R:16:5'): plotting works ────────────────────────
    class(plot_mx_umap(mx_data)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 2 | WARN 2 | SKIP 6 | PASS 85 ]
    Error: Test failures
    Execution halted

Package: NHSRplotthedots
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [59s/59s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(NHSRplotthedots)
    > 
    > test_check("NHSRplotthedots")
    [ FAIL 2 | WARN 733 | SKIP 3 | PASS 430 ]
    
    ══ Skipped tests (3) ═══════════════════════════════════════════════════════════
    • On CRAN (3): 'test-geom_ptd_icon.R:140:3', 'test-ptd_spc.R:303:3',
      'test-ptd_spc_standard.R:22:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-geom_ptd_icon.R:21:3'): it set's up GeomPTDIcon correctly ────
    unclass(GeomPTDIcon$default_aes) (`actual`) not equal to setNames(list(), character()) (`expected`).
    
    `attr(actual, 'S7_class')` is an S7 object of class <S7_class>
    `attr(expected, 'S7_class')` is absent
    ── Failure ('test-ptd_create_ggplot.R:79:3'): it returns a ggplot object ───────
    p$labels (`actual`) not equal to list(...) (`expected`).
    
    `actual` is an S7 object of class <ggplot2::labels>
    `expected` is a list
    
    [ FAIL 2 | WARN 733 | SKIP 3 | PASS 430 ]
    Error: Test failures
    Execution halted

Package: nlmixr2plot
Check: tests
New result: ERROR
    Running ‘testthat.R’ [178s/178s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(nlmixr2plot)
    > 
    > test_check("nlmixr2plot")
    > loading into symengine environment...
    > pruning branches (`if`/`else`) of saem model...
    v done
    > finding duplicate expressions in saem model...
    [====|====|====|====|====|====|====|====|====|====] 0:00:00 
    
    v done
    using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
    
    i calculate uninformed etas
    i done
    rxode2 4.0.3 using 3 threads (see ?getRxThreads)
      no cache: create with `rxCreateCache()`
    Calculating covariance matrix
    [====|====|====|====|====|====|====|====|====|====] 0:00:00 
    
    > loading into symengine environment...
    > pruning branches (`if`/`else`) of saem model...
    v done
    > finding duplicate expressions in saem predOnly model 0...
    [====|====|====|====|====|====|====|====|====|====] 0:00:00 
    
    > finding duplicate expressions in saem predOnly model 1...
    [====|====|====|====|====|====|====|====|====|====] 0:00:00 
    
    > finding duplicate expressions in saem predOnly model 2...
    [====|====|====|====|====|====|====|====|====|====] 0:00:00 
    
    > optimizing duplicate expressions in saem predOnly model 2...
    [====|====|====|====|====|====|====|====|====|====] 0:00:00 
    
    v done
    using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
    
    > Calculating residuals/tables
    v done
    > compress origData in nlmixr2 object, save 14912
    > compress phiM in nlmixr2 object, save 1200
    > compress parHistData in nlmixr2 object, save 2096
    > compress saem0 in nlmixr2 object, save 31632
    using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
    
    using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
    
    Prediction-correction cannot be used together with censored data (<LLOQ or >ULOQ). VPC plot will be shown for non-censored data only!
    Prediction-correction cannot be used together with censored data (<LLOQ or >ULOQ). VPC plot will be shown for non-censored data only!
    Prediction-correction cannot be used together with censored data (<LLOQ or >ULOQ). VPC plot will be shown for non-censored data only!
    Prediction-correction cannot be used together with censored data (<LLOQ or >ULOQ). VPC plot will be shown for non-censored data only!
    using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
    
    [ FAIL 2 | WARN 4 | SKIP 2 | PASS 33 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test-plots-cens.R:2:3', 'test-plots-multiple-endpoints.R:2:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-add.R:42:3'): test addition operator ─────────────────────────
    inherits(p2, "nlmixr2PlotList") is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-add.R:45:3'): test addition operator ─────────────────────────
    ggplot2::is_ggplot(p2[[1]]) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 2 | WARN 4 | SKIP 2 | PASS 33 ]
    Error: Test failures
    Execution halted

Package: nlmixr2rpt
Check: package dependencies
New result: ERROR
  Packages required but not available: 'xpose', 'xpose.nlmixr2'
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: normfluodbf
Check: tests
New result: ERROR
    Running ‘testthat.R’ [32s/33s]
  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(normfluodbf)
    
    == Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
    If you find this package useful, please leave a star:
       https://github.com/AlphaPrime7/normfluodbf
    
    If you want to support me in my learning and development journey:
     https://www.buymeacoffee.com/tingweiadeck
    
    If you encounter a bug or want to request an enhancement please file an issue at:
       https://github.com/AlphaPrime7/normfluodbf/issues
    
    
    Thank you for using normfluodbf!
    
    
    Attaching package: 'normfluodbf'
    
    The following object is masked from 'package:stats':
    
        step
    
    The following object is masked from 'package:utils':
    
        demo
    
    The following object is masked from 'package:base':
    
        subset
    
    > 
    > test_check("normfluodbf")
    Crikee, some values in your original data violate thresholds 🐷 🐫
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Crikee, some values in your original data violate thresholds 🐷 🐫
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Crikee, some values in your original data violate thresholds 🐷 🐫
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Crikee, some values in your original data violate thresholds 🐷 🐫
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Crikee, some values in your original data violate thresholds 🐷 🐫
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "27"
    
    Crikee, some values in your original data violate thresholds 🐷 🐫
    Crikee, some values in your original data violate thresholds 🐷 🐫
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "A01"
    
    [[2]]
    [1] "A02"
    
    [[3]]
    [1] "A03"
    
    [[4]]
    [1] "B01"
    
    [[5]]
    [1] "B02"
    
    [[6]]
    [1] "B03"
    
    [[7]]
    [1] "C01"
    
    [[8]]
    [1] "C02"
    
    [[9]]
    [1] "C03"
    
    Crikee, some values in your original data violate thresholds 🐷 🐫
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "A01"
    
    [[2]]
    [1] "A02"
    
    [[3]]
    [1] "A03"
    
    [[4]]
    [1] "B01"
    
    [[5]]
    [1] "B02"
    
    [[6]]
    [1] "B03"
    
    [[7]]
    [1] "C01"
    
    [[8]]
    [1] "C02"
    
    [[9]]
    [1] "C03"
    
    The upload_data step needs to be completed
    Initializing Data ...
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Data Initialized step DONE...
    DONE (1 seconds)
    The upload_data step needs to be completed
    Initializing Data ...
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "A01"
    
    [[2]]
    [1] "A02"
    
    [[3]]
    [1] "A03"
    
    [[4]]
    [1] "B01"
    
    [[5]]
    [1] "B02"
    
    [[6]]
    [1] "B03"
    
    [[7]]
    [1] "C01"
    
    [[8]]
    [1] "C02"
    
    [[9]]
    [1] "C03"
    
    Data Initialized step DONE...
    DONE (0 seconds)
    The upload_data step needs to be completed
    Initializing Data ...
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Data Initialized step DONE...
    DONE (1 seconds)
    [1] "Steps left:4"
    [1] "Next step function: format_plate_data"
    Formating Plate Data ...
    Data Formatted step DONE...
    DONE (0 seconds)
    [1] "Next step function: normalize_by_well"
    Normalizing Data ...
    Data Normalized step DONE...
    DONE (0 seconds)
    [1] "Next step function: modify_plate_data"
    [1] "Next step function: analyze_ready"
    Process complete
    The upload_data step needs to be completed
    Initializing Data ...
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Data Initialized step DONE...
    DONE (1 seconds)
    [1] "Steps left:4"
    [1] "Next step function: format_plate_data"
    Formating Plate Data ...
    Data Formatted step DONE...
    DONE (0 seconds)
    [1] "Next step function: normalize_by_well"
    Normalizing Data ...
    Data Normalized step DONE...
    DONE (0 seconds)
    [1] "Next step function: modify_plate_data"
    [1] "Next step function: analyze_ready"
    Process complete
    List of 9
     $ plate_meta  : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
      ..$ well    : chr [1:96] "A1" "A2" "A3" "A4" ...
      ..$ sample  : logi [1:96] NA NA NA NA NA NA ...
      ..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
      ..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
      ..$ used    : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
     $ plate_data  : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
      ..$ well         : chr [1:1500] "A1" "A1" "A1" "A1" ...
      ..$ well_row     : chr [1:1500] "A" "A" "A" "A" ...
      ..$ well_col     : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
      ..$ used         : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
      ..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
      ..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
      ..$ outlier      : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
      ..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
     $ steps       : num 0
     $ status      : num 5
     $ dirty       : logi TRUE
     $ version     : chr "2.0.0"
     $ params      :List of 3
      ..$ GENERAL   :List of 5
      .. ..$ X_VAR_ONE      : chr "Time"
      .. ..$ X_VAR_TWO      : chr "Cycle_Number"
      .. ..$ Y_VAR          : chr "FLUORESCENCE"
      .. ..$ X_VAR_ONE_LABEL: chr "TIME"
      .. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
      ..$ THRESHOLDS:List of 4
      .. ..$ MAX_FLUOR         : num 65536
      .. ..$ MIN_FLUOR         : num 128
      .. ..$ CUTOFF_UPPER_LIMIT: num 32768
      .. ..$ CUTOFF_LOWER_LIMIT: num 4096
      ..$ COLORS    :List of 4
      .. ..$ POS    : chr "#7FFFD4"
      .. ..$ TEST   : chr "#0000CD"
      .. ..$ NEG    : chr "#EE3B3B"
      .. ..$ NEUTRAL: chr "#BF3EFF"
     $ dataset_name: chr "dat_1"
     $ data_summary: chr "36 Wells Used"
     - attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
    The upload_data step needs to be completed
    Initializing Data ...
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Data Initialized step DONE...
    DONE (1 seconds)
    [1] "Steps left:4"
    [1] "Next step function: format_plate_data"
    Formating Plate Data ...
    Data Formatted step DONE...
    DONE (0 seconds)
    [1] "Next step function: normalize_by_well"
    Normalizing Data ...
    Data Normalized step DONE...
    DONE (0 seconds)
    [1] "Next step function: modify_plate_data"
    [1] "Next step function: analyze_ready"
    Process complete
    The upload_data step needs to be completed
    Initializing Data ...
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Data Initialized step DONE...
    DONE (1 seconds)
    [1] "Steps left:4"
    [1] "Next step function: format_plate_data"
    Formating Plate Data ...
    Data Formatted step DONE...
    DONE (0 seconds)
    [1] "Next step function: normalize_by_well"
    Normalizing Data ...
    Data Normalized step DONE...
    DONE (0 seconds)
    [1] "Next step function: modify_plate_data"
    [1] "Next step function: analyze_ready"
    Process complete
    Crikee, some values in your original data violate thresholds 🐷 🐫
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    The upload_data step needs to be completed
    Initializing Data ...
    [1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
    [[1]]
    [1] "C9"
    
    Data Initialized step DONE...
    DONE (1 seconds)
    [1] "Steps left:5"
    [1] "Next step function: format_plate_data"
    Formating Plate Data ...
    Data Formatted step DONE...
    DONE (0 seconds)
    [1] "Next step function: remove_outliers"
    [1] "Next step function: normalize_by_well"
    Normalizing Data ...
    Data Normalized step DONE...
    DONE (0 seconds)
    [1] "Next step function: modify_plate_data"
    [1] "Next step function: analyze_ready"
    Process complete
    [ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
    "gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
    
    `actual`:   "gg"             
    `expected`: "ggplot2::ggplot"
    
    [ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
    Error: Test failures
    Execution halted

Package: NPflow
Check: examples
New result: ERROR
  Running examples in ‘NPflow-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: cytoScatter
  > ### Title: Scatterplot of flow cytometry data
  > ### Aliases: cytoScatter
  > 
  > ### ** Examples
  > 
  > 
  > rm(list=ls())
  > #Number of data
  > n <- 500
  > #n <- 2000
  > set.seed(1234)
  > #set.seed(123)
  > #set.seed(4321)
  > 
  > # Sample data
  > m <- matrix(nrow=2, ncol=4, c(-1, 1, 1.5, 2, 2, -2, -1.5, -2))
  > p <- c(0.2, 0.1, 0.4, 0.3) # frequence des clusters
  > 
  > sdev <- array(dim=c(2,2,4))
  > sdev[, ,1] <- matrix(nrow=2, ncol=2, c(0.3, 0, 0, 0.3))
  > sdev[, ,2] <- matrix(nrow=2, ncol=2, c(0.1, 0, 0, 0.3))
  > sdev[, ,3] <- matrix(nrow=2, ncol=2, c(0.3, 0.15, 0.15, 0.3))
  > sdev[, ,4] <- .3*diag(2)
  > c <- rep(0,n)
  > z <- matrix(0, nrow=2, ncol=n)
  > for(k in 1:n){
  +  c[k] = which(rmultinom(n=1, size=1, prob=p)!=0)
  +  z[,k] <- m[, c[k]] + sdev[, , c[k]]%*%matrix(rnorm(2, mean = 0, sd = 1), nrow=2, ncol=1)
  +  #cat(k, "/", n, " observations simulated\n", sep="")
  + }
  > 
  > cytoScatter(z)
  Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
  ℹ Please use tidy evaluation idioms with `aes()`.
  ℹ See also `vignette("ggplot2-in-packages")` for more information.
  ℹ The deprecated feature was likely used in the NPflow package.
    Please report the issue at <https://github.com/sistm/NPflow/issues>.
  Error in `stat_density2d()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  Backtrace:
       ▆
    1. ├─NPflow::cytoScatter(z)
    2. │ ├─base::print(p)
    3. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
    4. │   ├─ggplot2::ggplot_build(x)
    5. │   └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    6. │     └─ggplot2:::by_layer(...)
    7. │       ├─rlang::try_fetch(...)
    8. │       │ ├─base::tryCatch(...)
    9. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12. │       │ └─base::withCallingHandlers(...)
   13. │       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   14. │         └─l$compute_statistic(d, layout)
   15. │           └─ggplot2 (local) compute_statistic(..., self = self)
   16. │             └─self$stat$compute_layer(data, self$computed_stat_params, layout)
   17. │               └─ggplot2 (local) compute_layer(..., self = self)
   18. │                 └─rlang::check_installed("MASS", reason = "for calculating 2D density.")
   19. │                   └─base::stop(cnd)
   20. └─rlang (local) `<fn>`(`<rlb_r___>`)
   21.   └─handlers[[1L]](cnd)
   22.     └─cli::cli_abort(...)
   23.       └─rlang::abort(...)
  Execution halted

Package: nzelect
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘README.Rmd’ using rmarkdown
  
  Quitting from README.Rmd:90-109 [unnamed-chunk-4]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'README.Rmd' failed with diagnostics:
  Problem while setting up geom aesthetics.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `check_aesthetics()`:
  ! Aesthetics must be either length 1 or the same as the data (3104).
  ✖ Fix the following mappings: `group`.
  --- failed re-building ‘README.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘README.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: o2plsda
Check: examples
New result: ERROR
  Running examples in ‘o2plsda-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot.o2plsda
  > ### Title: Score, VIP or loading plot for the O2PLS results
  > ### Aliases: plot.o2plsda
  > 
  > ### ** Examples
  > 
  > X <- matrix(rnorm(50),10,5)
  > Y <- matrix(rnorm(50),10,5)
  > fit <- o2pls(X,Y,2,1,1)
  > yy <- rep(c(0,1),5)
  > fit0 <- oplsda(fit,yy,2)
  > plot(fit0, type="score", group = factor(yy))
  Error in `stat_ellipse()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 3rd layer.
  Caused by error in `setup_params()`:
  ! The package "MASS" is required for calculating ellipses with `type =
    "t"`.
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_build(x)
    4. │ └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$compute_statistic(d, layout)
   14. │         └─ggplot2 (local) compute_statistic(..., self = self)
   15. │           └─self$stat$setup_params(data, self$stat_params)
   16. │             └─ggplot2 (local) setup_params(...)
   17. │               └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
   18. │                 └─base::stop(cnd)
   19. └─rlang (local) `<fn>`(`<rlb_r___>`)
   20.   └─handlers[[1L]](cnd)
   21.     └─cli::cli_abort(...)
   22.       └─rlang::abort(...)
  Execution halted

Package: o2plsda
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘o2plsda.Rmd’ using knitr
  
  Quitting from o2plsda.Rmd:91-96 [unnamed-chunk-5]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'o2plsda.Rmd' failed with diagnostics:
  Problem while computing stat.
  ℹ Error occurred in the 3rd layer.
  Caused by error in `setup_params()`:
  ! The package "MASS" is required for calculating ellipses with `type =
    "t"`.
  --- failed re-building ‘o2plsda.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘o2plsda.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ofpetrial
Check: examples
New result: ERROR
  Running examples in ‘ofpetrial-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: check_ortho_with_chars
  > ### Title: Check the orthogonality with field/topographic characteristics
  > ### Aliases: check_ortho_with_chars
  > 
  > ### ** Examples
  > 
  > data(td_single_input)
  > yield_sf <- sf::st_read(system.file("extdata", "yield-simple1.shp", package = "ofpetrial"))
  Reading layer `yield-simple1' from data source 
    `/home/hornik/tmp/CRAN_recheck/ofpetrial.Rcheck/ofpetrial/extdata/yield-simple1.shp' 
    using driver `ESRI Shapefile'
  Simple feature collection with 3365 features and 1 field
  Geometry type: POINT
  Dimension:     XY
  Bounding box:  xmin: -16.70072 ymin: 39.11962 xmax: -16.69613 ymax: 39.1269
  Geodetic CRS:  WGS 84
  > ssurgo_sf <-
  +   sf::st_read(system.file("extdata", "ssurgo-simple1.shp", package = "ofpetrial")) %>%
  +   dplyr::mutate(mukey = factor(mukey))
  Reading layer `ssurgo-simple1' from data source 
    `/home/hornik/tmp/CRAN_recheck/ofpetrial.Rcheck/ofpetrial/extdata/ssurgo-simple1.shp' 
    using driver `ESRI Shapefile'
  Simple feature collection with 11 features and 9 fields
  Geometry type: POLYGON
  Dimension:     XY
  Bounding box:  xmin: -16.70096 ymin: 39.11957 xmax: -16.69587 ymax: 39.12696
  Geodetic CRS:  WGS 84
  > topo_rast <-
  +   c(
  +     terra::rast(system.file("extdata", "slope.tif", package = "ofpetrial")),
  +     terra::rast(system.file("extdata", "twi.tif", package = "ofpetrial"))
  +   )
  > 
  > checks <-
  +   check_ortho_with_chars(
  +     td = td_single_input,
  +     sp_data_list = list(yield_sf, ssurgo_sf, topo_rast),
  +     vars_list = list("Yld_Vol_Dr", c("mukey", "clay"), names(topo_rast))
  +   )
  Error in `dplyr::mutate()`:
  ℹ In argument: `checks = purrr::pmap(list(trial_design, spatial_data,
    variable), summarize_chars)`.
  Caused by error in `purrr::pmap()`:
  ℹ In index: 2.
  Caused by error in `purrr::map()`:
  ℹ In index: 2.
  Caused by error in `ggplot2::scale_x_continuous()`:
  ! `limits` must be a <numeric> vector, not a character vector.
  Backtrace:
       ▆
    1. ├─ofpetrial::check_ortho_with_chars(...)
    2. │ └─... %>% ...
    3. ├─dplyr::select(., var, input_name, summary_data, summary_fig)
    4. ├─tidyr::unnest(., checks)
    5. ├─dplyr::mutate(...)
    6. ├─dplyr:::mutate.data.frame(...)
    7. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
    8. │   ├─base::withCallingHandlers(...)
    9. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
   10. │     └─mask$eval_all_mutate(quo)
   11. │       └─dplyr (local) eval()
   12. ├─purrr::pmap(list(trial_design, spatial_data, variable), summarize_chars)
   13. │ └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
   14. │   ├─purrr:::with_indexed_errors(...)
   15. │   │ └─base::withCallingHandlers(...)
   16. │   ├─purrr:::call_with_cleanup(...)
   17. │   └─ofpetrial (local) .f(.l[[1L]][[i]], .l[[2L]][[i]], .l[[3L]][[i]], ...)
   18. │     ├─... %>% dplyr::bind_rows()
   19. │     └─purrr::map(char_vars, function(x) summarize_indiv_char(joined_data, var = x))
   20. │       └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
   21. │         ├─purrr:::with_indexed_errors(...)
   22. │         │ └─base::withCallingHandlers(...)
   23. │         ├─purrr:::call_with_cleanup(...)
   24. │         └─ofpetrial (local) .f(.x[[i]], ...)
   25. │           └─ofpetrial:::summarize_indiv_char(joined_data, var = x)
   26. │             └─... %>% ggExtra::ggMarginal(type = "histogram")
   27. ├─dplyr::bind_rows(.)
   28. │ └─rlang::list2(...)
   29. └─ggExtra::ggMarginal(., type = "histogram")
   30.   └─plt$build()
   31.     └─private$addLimits(margThemed)
   32.       └─ggplot2::scale_x_continuous(limits = limits, oob = scales::squish)
   33.         └─ggplot2::continuous_scale(...)
   34.           └─ggplot2:::check_continuous_limits(limits, call = call)
   35.             └─ggplot2:::check_numeric(limits, arg = arg, call = call, allow_na = TRUE)
   36.               └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
   37.                 └─ggplot2:::stop_input_type(...)
   38.                   └─rlang::abort(message, ..., call = call, arg = arg)
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
  check_ortho_inputs 9.909  0.183  10.094

Package: patchwork
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.formula:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.nativeRaster:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.plot_annotation:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.plot_layout:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.raster:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.gt_tbl:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.ggplot:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.grob:
    function(object, plot, object_name)
  
  ggplot_build:
    function(plot, ...)
  ggplot_build.fixed_dim_ggplot:
    function(plot)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: patientProfilesVis
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘patientProfiles-template-SDTM.Rmd’ using rmarkdown
  --- finished re-building ‘patientProfiles-template-SDTM.Rmd’
  
  --- re-building ‘patientProfilesVis-introduction.Rmd’ using rmarkdown
  
  Quitting from patientProfilesVis-introduction.Rmd:167-171 [text-wideFormat-include]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'patientProfilesVis-introduction.Rmd' failed with diagnostics:
  The `plot.margin` theme element must be a <unit> vector of length 4
  --- failed re-building ‘patientProfilesVis-introduction.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘patientProfilesVis-introduction.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: patientProfilesVis
Check: tests
New result: ERROR
    Running ‘testthat.R’ [94s/101s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(patientProfilesVis)
    > 
    > test_check("patientProfilesVis")
    [ FAIL 20 | WARN 23 | SKIP 20 | PASS 332 ]
    
    == Skipped tests (20) ==================================================================================================================================================================================
    * On CRAN (20): 'test_createSubjectProfileReport.R:46:2', 'test_createSubjectProfileReport.R:82:2', 'test_createSubjectProfileReport.R:124:2', 'test_createSubjectProfileReport.R:154:2',
      'test_createSubjectProfileReport.R:197:2', 'test_createSubjectProfileReport.R:252:2', 'test_createSubjectProfileReport.R:316:2', 'test_createSubjectProfileReport.R:381:2',
      'test_createSubjectProfileReport.R:420:2', 'test_createSubjectProfileReport.R:475:2', 'test_createSubjectProfileReport.R:531:2', 'test_createSubjectProfileReport.R:570:2',
      'test_createSubjectProfileReport.R:622:2', 'test_createSubjectProfileReport.R:671:2', 'test_createSubjectProfileReport.R:723:2', 'test_createSubjectProfileReport.R:775:2',
      'test_createSubjectProfileReport.R:820:2', 'test_createSubjectProfileReport.R:878:2', 'test_createSubjectProfileReport.R:908:2', 'test_createSubjectProfileReport.R:939:2'
    
    == Failed tests ========================================================================================================================================================================================
    -- Error ('test_miscellaneous.R:197:3'): The number of lines considered for the plot height is extracted correctly for a text subject profile plot -----------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
         x
      1. +-testthat::expect_equal(...) at test_miscellaneous.R:197:3
      2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
      3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
      4. \-patientProfilesVis::getNLinesSubjectProfile(gg)
      5.   \-ggplot2::layer_data(gg, i = 1)
      6.     +-ggplot2::ggplot_build(plot)
      7.     \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
      8.       \-ggplot2:::plot_theme(plot)
      9.         \-ggplot2:::check_theme(theme)
     10.           \-base::mapply(...)
     11.             \-ggplot2 (local) `<fn>`(...)
     12.               \-cli::cli_abort(...)
     13.                 \-rlang::abort(...)
    -- Error ('test_subjectProfileCombine.R:329:2'): The number of lines to be displayed in the subject profile plot is correctly extracted when plots are combined ----------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
         x
      1. +-testthat::expect_silent(listPlotsWthtNLineCombined <- subjectProfileCombine(listPlotsWthtNLines)) at test_subjectProfileCombine.R:329:9
      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. \-patientProfilesVis::subjectProfileCombine(listPlotsWthtNLines)
     10.   \-patientProfilesVis:::getTimeLimSubjectProfilePlots(...)
     11.     +-base::which(sapply(listPlots, isSubjectProfileTimeVariant, empty = FALSE))
     12.     \-base::sapply(listPlots, isSubjectProfileTimeVariant, empty = FALSE)
     13.       \-base::lapply(X = X, FUN = FUN, ...)
     14.         \-patientProfilesVis (local) FUN(X[[i]], ...)
     15.           \-base::sapply(gg, isSubjectProfileTimeVariant)
     16.             \-base::lapply(X = X, FUN = FUN, ...)
     17.               \-patientProfilesVis (local) FUN(X[[i]], ...)
     18.                 \-base::sapply(gg, isSubjectProfileTimeVariant)
     19.                   \-base::lapply(X = X, FUN = FUN, ...)
     20.                     \-patientProfilesVis (local) FUN(X[[i]], ...)
     21.                       +-base::unlist(...)
     22.                       +-base::lapply(...)
     23.                       +-ggplot2::ggplot_build(gg)
     24.                       \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(gg)
     25.                         \-ggplot2:::plot_theme(plot)
     26.                           \-ggplot2:::check_theme(theme)
     27.                             \-base::mapply(...)
     28.                               \-ggplot2 (local) `<fn>`(...)
     29.                                 \-cli::cli_abort(...)
     30.                                   \-rlang::abort(...)
    -- Error ('test_subjectProfileCombine.R:359:2'): The height of the combined subject profiles is correctly restricted to the specified number of lines --------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
         x
      1. \-patientProfilesVis::subjectProfileCombine(...) at test_subjectProfileCombine.R:359:9
      2.   \-patientProfilesVis:::getTimeLimSubjectProfilePlots(...)
      3.     +-base::which(sapply(listPlots, isSubjectProfileTimeVariant, empty = FALSE))
      4.     \-base::sapply(listPlots, isSubjectProfileTimeVariant, empty = FALSE)
      5.       \-base::lapply(X = X, FUN = FUN, ...)
      6.         \-patientProfilesVis (local) FUN(X[[i]], ...)
      7.           \-base::sapply(gg, isSubjectProfileTimeVariant)
      8.             \-base::lapply(X = X, FUN = FUN, ...)
      9.               \-patientProfilesVis (local) FUN(X[[i]], ...)
     10.                 \-base::sapply(gg, isSubjectProfileTimeVariant)
     11.                   \-base::lapply(X = X, FUN = FUN, ...)
     12.                     \-patientProfilesVis (local) FUN(X[[i]], ...)
     13.                       +-base::unlist(...)
     14.                       +-base::lapply(...)
     15.                       +-ggplot2::ggplot_build(gg)
     16.                       \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(gg)
     17.                         \-ggplot2:::plot_theme(plot)
     18.                           \-ggplot2:::check_theme(theme)
     19.                             \-base::mapply(...)
     20.                               \-ggplot2 (local) `<fn>`(...)
     21.                                 \-cli::cli_abort(...)
     22.                                   \-rlang::abort(...)
    -- Failure ('test_subjectProfileTextPlot.R:43:2'): Parameter variables are correctly displayed for each subject ----------------------------------------------------------------------------------------
    `plots <- subjectProfileTextPlot(data = data, paramValueVar = paramValueVar)` produced warnings.
    -- Error ('test_subjectProfileTextPlot.R:66:5'): Parameter variables are correctly displayed for each subject ------------------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
         x
      1. +-testthat::expect_equal(...) at test_subjectProfileTextPlot.R:60:17
      2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
      3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
      4. \-ggplot2::layer_data(gg, which(isGeomText)) at test_subjectProfileTextPlot.R:66:33
      5.   +-ggplot2::ggplot_build(plot)
      6.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
      7.     \-ggplot2:::plot_theme(plot)
      8.       \-ggplot2:::check_theme(theme)
      9.         \-base::mapply(...)
     10.           \-ggplot2 (local) `<fn>`(...)
     11.             \-cli::cli_abort(...)
     12.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:102:2'): Parameter variables are correctly combined -----------------------------------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_data(gg, which(isGeomText)) at test_subjectProfileTextPlot.R:102:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:128:2'): Parameter values are correctly combined with a specified separator -----------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_data(gg, which(isGeomText)) at test_subjectProfileTextPlot.R:128:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:153:2'): Specified labels for parameter variables are correctly set -------------------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_data(gg, which(isGeomText)) at test_subjectProfileTextPlot.R:153:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:186:2'): Parameter variables and names are correctly displayed ------------------------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_data(gg, which(isGeomText)) at test_subjectProfileTextPlot.R:186:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:240:2'): A specified parameter value function correctly returns a new variable with parameter values ----------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_data(gg, which(isGeomText)) at test_subjectProfileTextPlot.R:240:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Failure ('test_subjectProfileTextPlot.R:266:2'): Parameter variables are correctly represented in a table format ------------------------------------------------------------------------------------
    `... <- NULL` produced warnings.
    -- Error ('test_subjectProfileTextPlot.R:279:2'): Parameter variables are correctly represented in a table format --------------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_grob(gg, which(isGeomTable)) at test_subjectProfileTextPlot.R:279:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:331:2'): Parameter values are correctly ordered/grouped based on grouping variables ---------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_data(gg, which(isGeomText)) at test_subjectProfileTextPlot.R:331:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:370:2'): Parameter values in a table format are correctly ordered/grouped based on grouping variables ---------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_grob(gg, which(isGeomTable)) at test_subjectProfileTextPlot.R:370:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:470:4'): Labels for aesthetic, plot or axis title are correctly extracted from the specified variable labels --------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
         x
      1. +-testthat::expect_equal(...) at test_subjectProfileTextPlot.R:461:9
      2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
      3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
      4. \-ggplot2::layer_scales(gg, which(isGeomText)) at test_subjectProfileTextPlot.R:470:25
      5.   +-ggplot2::ggplot_build(plot)
      6.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
      7.     \-ggplot2:::plot_theme(plot)
      8.       \-ggplot2:::check_theme(theme)
      9.         \-base::mapply(...)
     10.           \-ggplot2 (local) `<fn>`(...)
     11.             \-cli::cli_abort(...)
     12.               \-rlang::abort(...)
    -- Error ('test_subjectProfileTextPlot.R:529:2'): Variables that are too long to fit in one table column will span multiple lines ----------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_grob(gg, which(isGeomTable)) at test_subjectProfileTextPlot.R:529:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Failure ('test_subjectProfileTextPlot.R:586:2'): The widths of the table columns are correctly set --------------------------------------------------------------------------------------------------
    `... <- NULL` produced warnings.
    -- Error ('test_subjectProfileTextPlot.R:599:2'): The widths of the table columns are correctly set ----------------------------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
        x
     1. \-ggplot2::layer_grob(gg, which(isGeomTable)) at test_subjectProfileTextPlot.R:599:9
     2.   +-ggplot2::ggplot_build(plot)
     3.   \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
     4.     \-ggplot2:::plot_theme(plot)
     5.       \-ggplot2:::check_theme(theme)
     6.         \-base::mapply(...)
     7.           \-ggplot2 (local) `<fn>`(...)
     8.             \-cli::cli_abort(...)
     9.               \-rlang::abort(...)
    -- Error ('test_timeAlignment.R:324:2'): A warning is generated if modules to align do not contain a time variable -------------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
         x
      1. +-testthat::expect_warning(...) at test_timeAlignment.R:324:9
      2. | \-testthat:::quasi_capture(...)
      3. |   +-testthat (local) .capture(...)
      4. |   | \-base::withCallingHandlers(...)
      5. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      6. \-patientProfilesVis:::getTimeLimSubjectProfilePlots(...)
      7.   +-base::which(sapply(listPlots, isSubjectProfileTimeVariant, empty = FALSE))
      8.   \-base::sapply(listPlots, isSubjectProfileTimeVariant, empty = FALSE)
      9.     \-base::lapply(X = X, FUN = FUN, ...)
     10.       \-patientProfilesVis (local) FUN(X[[i]], ...)
     11.         \-base::sapply(gg, isSubjectProfileTimeVariant)
     12.           \-base::lapply(X = X, FUN = FUN, ...)
     13.             \-patientProfilesVis (local) FUN(X[[i]], ...)
     14.               \-base::sapply(gg, isSubjectProfileTimeVariant)
     15.                 \-base::lapply(X = X, FUN = FUN, ...)
     16.                   \-patientProfilesVis (local) FUN(X[[i]], ...)
     17.                     +-base::unlist(...)
     18.                     +-base::lapply(...)
     19.                     +-ggplot2::ggplot_build(gg)
     20.                     \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(gg)
     21.                       \-ggplot2:::plot_theme(plot)
     22.                         \-ggplot2:::check_theme(theme)
     23.                           \-base::mapply(...)
     24.                             \-ggplot2 (local) `<fn>`(...)
     25.                               \-cli::cli_abort(...)
     26.                                 \-rlang::abort(...)
    -- Error ('test_timeAlignment.R:346:2'): A warning is generated in case the plot requested to align is not available -----------------------------------------------------------------------------------
    Error in `plot_theme(plot)`: The `plot.margin` theme element must be a <unit> vector of length 4
    Backtrace:
         x
      1. +-testthat::expect_warning(...) at test_timeAlignment.R:346:9
      2. | \-testthat:::quasi_capture(...)
      3. |   +-testthat (local) .capture(...)
      4. |   | \-base::withCallingHandlers(...)
      5. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
      6. \-patientProfilesVis:::getTimeLimSubjectProfilePlots(...)
      7.   +-base::which(sapply(listPlots, isSubjectProfileTimeVariant, empty = FALSE))
      8.   \-base::sapply(listPlots, isSubjectProfileTimeVariant, empty = FALSE)
      9.     \-base::lapply(X = X, FUN = FUN, ...)
     10.       \-patientProfilesVis (local) FUN(X[[i]], ...)
     11.         \-base::sapply(gg, isSubjectProfileTimeVariant)
     12.           \-base::lapply(X = X, FUN = FUN, ...)
     13.             \-patientProfilesVis (local) FUN(X[[i]], ...)
     14.               \-base::sapply(gg, isSubjectProfileTimeVariant)
     15.                 \-base::lapply(X = X, FUN = FUN, ...)
     16.                   \-patientProfilesVis (local) FUN(X[[i]], ...)
     17.                     +-base::unlist(...)
     18.                     +-base::lapply(...)
     19.                     +-ggplot2::ggplot_build(gg)
     20.                     \-ggplot2 (local) `ggplot_build.ggplot2::ggplot`(gg)
     21.                       \-ggplot2:::plot_theme(plot)
     22.                         \-ggplot2:::check_theme(theme)
     23.                           \-base::mapply(...)
     24.                             \-ggplot2 (local) `<fn>`(...)
     25.                               \-cli::cli_abort(...)
     26.                                 \-rlang::abort(...)
    
    [ FAIL 20 | WARN 23 | SKIP 20 | PASS 332 ]
    Error: Test failures
    Execution halted

Package: pcr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [3s/3s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(pcr)
    > 
    > test_check("pcr")
    [ FAIL 12 | WARN 1 | SKIP 0 | PASS 74 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_analyses_fun.R:44:3'): pcr_ddct works ────────────────────────
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_analyses_fun.R:83:3'): pcr_dct works ─────────────────────────
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_analyses_fun.R:144:3'): pcr_curve in separate_tube mode ──────
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_assessment_fun.R:22:3'): pcr_efficiency calculates the correct intercept and slope ──
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_assessment_fun.R:43:3'): pcr_standard calculates the correct intercept and slope ──
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_plotting_fun.R:14:3'): .pcr_plot_analyze returns a ggplot ────
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_plotting_fun.R:23:3'): .pcr_plot_analyze returns a ggplot ────
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_plotting_fun.R:27:3'): .pcr_plot_analyze returns a ggplot ────
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_plotting_fun.R:42:3'): .pcr_plot_analyze returns a dodge columns plot ──
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_plotting_fun.R:57:3'): .pcr_plot_analyze returns a faceted plot ──
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_plotting_fun.R:68:3'): .pcr_plot_assess returns an efficiency plot ──
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_plotting_fun.R:79:3'): .pcr_plot_assess returns standard_curve plots ──
    class(gg) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 12 | WARN 1 | SKIP 0 | PASS 74 ]
    Error: Test failures
    Execution halted

Package: phylepic
Check: S3 generic/method consistency
New result: WARNING
  ggplot_build:
    function(plot, ...)
  ggplot_build.phylepic_ggplot:
    function(plot)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: PieGlyph
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: plantTracker
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Suggested_plantTracker_Workflow.Rmd’ using rmarkdown
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  
  Quitting from Suggested_plantTracker_Workflow.Rmd:821-843 [unnamed-chunk-19]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Suggested_plantTracker_Workflow.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 5th layer.
  Caused by error in `Ops.unit()`:
  ! operator '==' not meaningful for units
  --- failed re-building ‘Suggested_plantTracker_Workflow.Rmd’
  
  --- re-building ‘Using_the_plantTracker_trackSpp_function.Rmd’ using rmarkdown
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_class] <- Map(code_folding_class, options[opts_class],  :
    number of items to replace is not a multiple of replacement length
  Warning in options[opts_attr] <- Map(code_folding_attr, options[opts_attr],  :
    number of items to replace is not a multiple of replacement length
  --- finished re-building ‘Using_the_plantTracker_trackSpp_function.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Suggested_plantTracker_Workflow.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: plotDK
Check: tests
New result: ERROR
    Running ‘testthat.R’ [3s/3s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(plotDK)
    > 
    > test_check("plotDK")
    [ FAIL 3 | WARN 0 | SKIP 0 | PASS 48 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plotDK.R:67:5'): The returned plot has the correct labels ────
    c("x", "y", "group", "subgroup", "text", "fill") (`actual`) and names(labels) (`expected`) don't have the same values.
    * Only in `actual`: "x", "y", "group", "subgroup", "text", "fill"
    
    ── Failure ('test-plotDK.R:72:5'): The returned plot has the correct labels ────
    labels$fill not equal to "test_label".
    target is NULL, current is character
    ── Failure ('test-plotDK.R:81:5'): The returned plot has the correct labels ────
    labels$fill not equal to "fill".
    target is NULL, current is character
    
    [ FAIL 3 | WARN 0 | SKIP 0 | PASS 48 ]
    Error: Test failures
    Execution halted

Package: PlotFTIR
Check: tests
New result: ERROR
    Running ‘testthat.R’ [41s/42s]
  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(PlotFTIR)
    Plotting spectra with PlotFTIR. Please cite if plots are used in publishing (`citation("plotFTIR")`).
    PlotFTIR is set to English as default. Changer au français par la fonction `options("PlotFTIR.lang" = "en")`
    > 
    > test_check("PlotFTIR")
    `PlotFTIR:::read_ftir_csv()` has deduced that input data column `row` is "wavenumber".
    Saving 7 x 7 in image
    Converting ir data to PlotFTIR structure.
    
    Reading 11 files...
    
    
      |                                                                            
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      |=========================                                             |  36%
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      |================================                                      |  45%
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      |======================================                                |  55%
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      |===================================================                   |  73%
      |                                                                            
      |=========================================================             |  82%
      |                                                                            
      |================================================================      |  91%
      |                                                                            
      |======================================================================| 100%
    
    Assigning 11 spectra to 2 groups...
    
    Success!
    
    
    Reading 11 files...
    
    
      |                                                                            
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      |======                                                                |   9%
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      |=========================================================             |  82%
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      |================================================================      |  91%
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      |======================================================================| 100%
    
    Assigning 11 spectra to 11 groups...
    
    Success!
    
    
    Reading 11 files...
    
    
      |                                                                            
      |                                                                      |   0%
      |                                                                            
      |======                                                                |   9%
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      |=============                                                         |  18%
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      |================================================================      |  91%
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      |======================================================================| 100%
    
    Assigning 11 spectra to 2 groups...
    
    Success!
    
    Converting ChemoSpec data to PlotFTIR structure.
    [ FAIL 6 | WARN 58 | SKIP 0 | PASS 513 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-manipulations.R:225:3'): labelled plot is ok ───────────────────
    Error in `add_wavenumber_marker(biodiesel_plot, 1740, "CO Stretch")`: Only knows how to fold ggplot objects together
    Backtrace:
        ▆
     1. └─PlotFTIR::add_wavenumber_marker(biodiesel_plot, 1740, "CO Stretch") at test-manipulations.R:225:3
     2.   └─patchwork:::`-.ggplot`(...)
     3.     └─cli::cli_abort("Only knows how to fold ggplot objects together")
     4.       └─rlang::abort(...)
    ── Failure ('test-manipulations.R:246:3'): -.gg is ok ──────────────────────────
    `biodiesel_plot - NULL` did not throw the expected error.
    ── Error ('test-manipulations.R:502:3'): add_band is ok ────────────────────────
    Error in `add_band(biodiesel_plot, c(1000, 2000))`: Only knows how to fold ggplot objects together
    Backtrace:
        ▆
     1. └─PlotFTIR::add_band(biodiesel_plot, c(1000, 2000)) at test-manipulations.R:502:3
     2.   └─patchwork:::`-.ggplot`(...)
     3.     └─cli::cli_abort("Only knows how to fold ggplot objects together")
     4.       └─rlang::abort(...)
    ── Failure ('test-plot_ftir.R:26:3'): Plots are generated ──────────────────────
    p3$label$y (`actual`) not equal to "% Transmittance" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('% Transmittance')
    ── Failure ('test-plot_ftir.R:27:3'): Plots are generated ──────────────────────
    p4$label$y (`actual`) not equal to "Transmittance (a.u.)" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('Transmittance (a.u.)')
    ── Failure ('test-plot_ftir.R:28:3'): Plots are generated ──────────────────────
    p5$label$y (`actual`) not equal to "Normalized Absorbance" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('Normalized Absorbance')
    
    [ FAIL 6 | WARN 58 | SKIP 0 | PASS 513 ]
    Error: Test failures
    Execution halted

Package: plotROC
Check: examples
New result: ERROR
  Running examples in ‘plotROC-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: calc_auc
  > ### Title: Calculate the Area under the ROC curve
  > ### Aliases: calc_auc
  > 
  > ### ** Examples
  > 
  > D.ex <- rbinom(50, 1, .5)
  > rocdata <- data.frame(D = c(D.ex, D.ex),
  +                      M = c(rnorm(50, mean = D.ex, sd = .4), rnorm(50, mean = D.ex, sd = 1)),
  +                      Z = c(rep("A", 50), rep("B", 50)))
  > 
  > ggroc <- ggplot(rocdata, aes(m = M, d = D)) + geom_roc()
  > calc_auc(ggroc)
  Error in `rlang::quo_get_expr()`:
  ! `quo` must be a quosure
  Backtrace:
      ▆
   1. ├─plotROC::calc_auc(ggroc)
   2. │ └─rlang::quo_get_expr(l2$plot$mapping[current_name][[1]])
   3. └─rlang::abort(message = message)
  Execution halted

Package: plotROC
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘examples.Rmd’ using rmarkdown
  
  Quitting from examples.Rmd:249-256 [auctab]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'examples.Rmd' failed with diagnostics:
  `quo` must be a quosure
  --- failed re-building ‘examples.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘examples.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: plotROC
Check: tests
New result: ERROR
    Running ‘testthat.R’ [3s/3s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(plotROC)
    Loading required package: ggplot2
    > 
    > test_check("plotROC")
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-calc.R:67:13'): Calc AUC modification works ────────────────────
    Error in `rlang::quo_get_expr(l2$plot$mapping[current_name][[1]])`: `quo` must be a quosure
    Backtrace:
        ▆
     1. ├─testthat::expect_equal(nrow(calc_auc(ggroc_p)), 1) at test-calc.R:67:13
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::nrow(calc_auc(ggroc_p))
     5. ├─plotROC::calc_auc(ggroc_p)
     6. │ └─rlang::quo_get_expr(l2$plot$mapping[current_name][[1]])
     7. └─rlang::abort(message = message)
    
    [ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
    Error: Test failures
    Execution halted

Package: plotthis
Check: examples
New result: ERROR
  Running examples in ‘plotthis-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: QQPlot
  > ### Title: QQ plot
  > ### Aliases: QQPlot
  > 
  > ### ** Examples
  > 
  > set.seed(8525)
  > data <- data.frame(norm = rnorm(100))
  > 
  > QQPlot(data, val = "norm", band = TRUE)
  Error:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  Backtrace:
       ▆
    1. ├─base (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_gtable(data)
    4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$draw_geom(d, layout)
   14. │         └─ggplot2 (local) draw_geom(..., self = self)
   15. │           └─self$geom$draw_layer(...)
   16. │             └─ggplot2 (local) draw_layer(..., self = self)
   17. │               └─base::lapply(...)
   18. │                 └─ggplot2 (local) FUN(X[[i]], ...)
   19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   20. │                   └─self$draw_panel(data, panel_params, coord)
   21. │                     └─ggplot2 (local) draw_panel(..., self = self)
   22. │                       └─base::lapply(...)
   23. │                         └─ggplot2 (local) FUN(X[[i]], ...)
   24. │                           └─self$draw_group(group, panel_params, coord, ...)
   25. │                             └─ggplot2 (local) draw_group(...)
   26. │                               └─ggplot2 (local) draw_group(..., self = self)
   27. └─base::.handleSimpleError(...)
   28.   └─rlang (local) h(simpleError(msg, call))
   29.     └─handlers[[1L]](cnd)
   30.       └─cli::cli_abort(...)
   31.         └─rlang::abort(...)
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
  PieChart 8.110  0.024   8.134
  LinePlot 6.784  0.208   6.993
  CorPlot  5.130  0.084   5.214
  AreaPlot 4.901  0.200   5.103

Package: pmxTools
Check: tests
New result: ERROR
    Running ‘testthat.R’ [7s/7s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(pmxTools)
    Loading required package: patchwork
    > 
    > test_check("pmxTools")
    [ FAIL 1 | WARN 1 | SKIP 12 | PASS 110 ]
    
    ══ Skipped tests (12) ══════════════════════════════════════════════════════════
    • On CRAN (12): 'test-calc.R:197:3', 'test-misc.R:32:3', 'test-nm.R:4:3',
      'test-nm.R:9:3', 'test-nm.R:14:3', 'test-nm.R:19:3', 'test-nm.R:151:3',
      'test-nm.R:157:3', 'test-nm.R:163:3', 'test-nm.R:167:3', 'test-nm.R:171:3',
      'test-plot.R:14:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-plot.R:9:3'): plot_dist ────────────────────────────────────────
    Error in `gghalves::geom_half_point(side = "l", range_scale = hp_range_scale, 
        alpha = hp_alpha, col = hp_col, transformation = hp_transformation, 
        na.rm = na.rm)`: Problem while converting geom to grob.
    i Error occurred in the 3rd layer.
    Caused by error in `fun()`:
    ! argument "layout" is missing, with no default
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-plot.R:9:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   └─vdiffr:::print_plot(plot, title)
      4. ├─pmxTools::plot_dist(...)
      5. │ ├─base::suppressMessages(print(p))
      6. │ │ └─base::withCallingHandlers(...)
      7. │ ├─base::print(p)
      8. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      9. │   ├─ggplot2::ggplot_gtable(data)
     10. │   └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
     11. │     └─ggplot2:::by_layer(...)
     12. │       ├─rlang::try_fetch(...)
     13. │       │ ├─base::tryCatch(...)
     14. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     15. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     16. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     17. │       │ └─base::withCallingHandlers(...)
     18. │       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     19. │         └─l$draw_geom(d, layout)
     20. │           └─ggplot2 (local) draw_geom(..., self = self)
     21. │             └─self$geom$draw_layer(...)
     22. │               └─ggplot2 (local) draw_layer(..., self = self)
     23. │                 └─base::lapply(...)
     24. │                   └─ggplot2 (local) FUN(X[[i]], ...)
     25. │                     ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     26. │                     └─self$draw_panel(...)
     27. │                       └─ggplot2 (local) draw_panel(..., self = self)
     28. │                         └─base::lapply(...)
     29. │                           └─ggplot2 (local) FUN(X[[i]], ...)
     30. │                             └─self$draw_group(group, panel_params, coord, ...)
     31. │                               └─gghalves (local) draw_group(...)
     32. │                                 └─transformation$compute_layer(transformation_df, transformation_params_new)
     33. │                                   └─ggplot2 (local) compute_layer(..., self = self)
     34. │                                     └─ggplot2:::dapply(...)
     35. │                                       └─base::lapply(...)
     36. │                                         └─ggplot2 (local) FUN(X[[i]], ...)
     37. │                                           └─ggplot2 (local) apply_fun(cur_data)
     38. │                                             └─ggplot2 (local) fun(x, ...)
     39. └─rlang (local) `<fn>`(`<gtvrErrr>`)
     40.   └─handlers[[1L]](cnd)
     41.     └─cli::cli_abort(...)
     42.       └─rlang::abort(...)
    
    [ FAIL 1 | WARN 1 | SKIP 12 | PASS 110 ]
    Deleting unused snapshots:
    • plot/conditioned-distplot.svg
    • plot/perc.svg
    Error: Test failures
    Execution halted

Package: pollster
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘crosstab3way.Rmd’ using rmarkdown
  
  Quitting from crosstab3way.Rmd:40-54 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::labels> object is invalid:
  - every label must be named.
  ---
  Backtrace:
      ▆
   1. └─ggplot2::labs(...)
   2.   └─ggplot2::class_labels(args)
   3.     └─S7::new_object(labels)
   4.       └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'crosstab3way.Rmd' failed with diagnostics:
  <ggplot2::labels> object is invalid:
  - every label must be named.
  --- failed re-building ‘crosstab3way.Rmd’
  
  --- re-building ‘crosstabs.Rmd’ using rmarkdown
  --- finished re-building ‘crosstabs.Rmd’
  
  --- re-building ‘toplines.Rmd’ using rmarkdown
  --- finished re-building ‘toplines.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘crosstab3way.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: PoweREST
Check: examples
New result: ERROR
  Running examples in ‘PoweREST-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: vis_XGBoost
  > ### Title: Visualization of the power estimations from XGBoost
  > ### Aliases: vis_XGBoost
  > 
  > ### ** Examples
  > 
  > data(power_example)
  > # Fit the local power surface of avg_log2FC_abs between 1 and 2
  > avg_log2FC_abs_1_2<-dplyr::filter(power_example,avg_log2FC_abs>1 & avg_log2FC_abs<2)
  > # Fit the model
  > bst<-fit_XGBoost(power_example$power,avg_log2FC=power_example$avg_log2FC_abs,
  + avg_PCT=power_example$mean_pct,replicates=power_example$sample_size)
  [17:48:12] WARNING: src/objective/regression_obj.cu:213: reg:linear is now deprecated in favor of reg:squarederror.
  [1]	train-rmse:3.899410 
  [2]	train-rmse:3.526278 
  [3]	train-rmse:3.304421 
  [4]	train-rmse:3.162909 
  [5]	train-rmse:3.070662 
  [6]	train-rmse:3.022160 
  [7]	train-rmse:2.985705 
  [8]	train-rmse:2.960430 
  [9]	train-rmse:2.897214 
  [10]	train-rmse:2.851660 
  [11]	train-rmse:2.802100 
  [12]	train-rmse:2.767539 
  [13]	train-rmse:2.738521 
  [14]	train-rmse:2.721141 
  [15]	train-rmse:2.704307 
  [16]	train-rmse:2.691786 
  [17]	train-rmse:2.675275 
  [18]	train-rmse:2.653118 
  [19]	train-rmse:2.634277 
  [20]	train-rmse:2.612226 
  [21]	train-rmse:2.597224 
  [22]	train-rmse:2.591398 
  [23]	train-rmse:2.576851 
  [24]	train-rmse:2.561155 
  [25]	train-rmse:2.549148 
  [26]	train-rmse:2.541995 
  [27]	train-rmse:2.534172 
  [28]	train-rmse:2.531158 
  [29]	train-rmse:2.523874 
  [30]	train-rmse:2.513346 
  [31]	train-rmse:2.504330 
  [32]	train-rmse:2.499985 
  [33]	train-rmse:2.494602 
  [34]	train-rmse:2.490118 
  [35]	train-rmse:2.485187 
  [36]	train-rmse:2.481274 
  [37]	train-rmse:2.478983 
  [38]	train-rmse:2.474464 
  [39]	train-rmse:2.472630 
  [40]	train-rmse:2.470462 
  [41]	train-rmse:2.465974 
  [42]	train-rmse:2.463282 
  [43]	train-rmse:2.461544 
  [44]	train-rmse:2.459646 
  [45]	train-rmse:2.457870 
  [46]	train-rmse:2.457458 
  [47]	train-rmse:2.456774 
  [48]	train-rmse:2.454137 
  [49]	train-rmse:2.451836 
  [50]	train-rmse:2.448660 
  [51]	train-rmse:2.447398 
  [52]	train-rmse:2.446590 
  [53]	train-rmse:2.446181 
  [54]	train-rmse:2.445337 
  [55]	train-rmse:2.440712 
  [56]	train-rmse:2.439058 
  [57]	train-rmse:2.438639 
  [58]	train-rmse:2.438273 
  [59]	train-rmse:2.437549 
  [60]	train-rmse:2.436880 
  [61]	train-rmse:2.436747 
  [62]	train-rmse:2.436142 
  [63]	train-rmse:2.436074 
  [64]	train-rmse:2.436004 
  [65]	train-rmse:2.435452 
  [66]	train-rmse:2.435168 
  [67]	train-rmse:2.434432 
  [68]	train-rmse:2.434199 
  [69]	train-rmse:2.434129 
  [70]	train-rmse:2.433798 
  [71]	train-rmse:2.433172 
  [72]	train-rmse:2.432885 
  [73]	train-rmse:2.432878 
  [74]	train-rmse:2.432361 
  [75]	train-rmse:2.431104 
  [76]	train-rmse:2.430946 
  [77]	train-rmse:2.430928 
  [78]	train-rmse:2.430922 
  [79]	train-rmse:2.430885 
  [80]	train-rmse:2.430406 
  [81]	train-rmse:2.429241 
  [82]	train-rmse:2.428940 
  [83]	train-rmse:2.428897 
  [84]	train-rmse:2.428869 
  [85]	train-rmse:2.426834 
  [86]	train-rmse:2.425378 
  [87]	train-rmse:2.425094 
  [88]	train-rmse:2.425047 
  [89]	train-rmse:2.424926 
  [90]	train-rmse:2.424915 
  [91]	train-rmse:2.424905 
  [92]	train-rmse:2.424811 
  [93]	train-rmse:2.424751 
  [94]	train-rmse:2.424695 
  [95]	train-rmse:2.424657 
  [96]	train-rmse:2.424631 
  [97]	train-rmse:2.424603 
  [98]	train-rmse:2.424565 
  [99]	train-rmse:2.424548 
  [100]	train-rmse:2.424535 
  > pred<-pred_XGBoost(bst,n.grid=30,xlim=c(0,1.5),ylim=c(0,0.1),replicates=3)
  > vis_XGBoost(pred,view='2D',legend_name='Power',xlab='avg_log2FC_abs',ylab='mean_pct')
  Error in `rayshader::plot_gg()`:
  ! Base operators are not defined for quosures. Do you need to unquote
    the quosure?
  
  # Bad: myquosure * rhs
  
  # Good: !!myquosure * rhs
  Backtrace:
      ▆
   1. └─PoweREST::vis_XGBoost(...)
   2.   ├─base::eval(parse(text = txt3))
   3.   │ └─base::eval(parse(text = txt3))
   4.   └─rayshader::plot_gg(mtplot, width = 3.5, raytrace = FALSE, preview = TRUE)
   5.     └─rlang:::Ops.quosure(ggplotobj2$layers[[i]]$geom$default_aes$size, pointcontract)
   6.       └─rlang::abort(...)
  Execution halted

Package: precintcon
Check: examples
New result: ERROR
  Running examples in ‘precintcon-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: pplot.deciles
  > ### Title: Plot deciles
  > ### Aliases: pplot.deciles precintcon.plot.deciles
  > ### Keywords: deciles precipitation
  > 
  > ### ** Examples
  > 
  > ## Loading the monthly precipitation serie.
  > #
  > data(monthly)
  > 
  > ## Performing the a set of statistical analysis
  > #
  > pplot.deciles(monthly)
  Error:
  ! The `show_guide` argument of `layer()` was deprecated in ggplot2 2.0.0
    and is now defunct.
  ℹ Please use the `show.legend` argument instead.
  Backtrace:
      ▆
   1. └─precintcon::pplot.deciles(monthly)
   2.   └─precintcon::precintcon.plot.deciles(...)
   3.     └─base::mapply(...)
   4.       └─precintcon (local) `<fn>`(...)
   5.         └─ggplot2::geom_boxplot(...)
   6.           └─ggplot2::layer(...)
   7.             └─lifecycle::deprecate_stop("2.0.0", "layer(show_guide)", "layer(show.legend)")
   8.               └─lifecycle:::deprecate_stop0(msg)
   9.                 └─rlang::cnd_signal(...)
  Execution halted

Package: predict3d
Check: examples
New result: ERROR
  Running examples in ‘predict3d-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ggPredict
  > ### Title: Visualize predictions from the multiple regression models.
  > ### Aliases: ggPredict
  > 
  > ### ** Examples
  > 
  > fit=loess(mpg~hp*wt*am,data=mtcars)
  Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
    pseudoinverse used at 1.1217 2.8465 -0.010111
  Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
    neighborhood radius 5.2631
  Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
    reciprocal condition number  5.8021e-17
  Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,  :
    There are other near singularities as well. 40.381
  > ggPredict(fit)
  Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
    pseudoinverse used at 1.1217 2.8465 -0.010111
  Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
    neighborhood radius 5.2631
  Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
    reciprocal condition number  5.8021e-17
  Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
    There are other near singularities as well. 40.381
  Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
    pseudoinverse used at 1.1217 2.8465 -0.010111
  Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
    neighborhood radius 5.2631
  Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
    reciprocal condition number  5.8021e-17
  Warning in predLoess(object$y, object$x, newx = if (is.null(newdata)) object$x else if (is.data.frame(newdata)) as.matrix(model.frame(delete.response(terms(object)),  :
    There are other near singularities as well. 40.381
  Error in UseMethod("ggplot_build") : 
    no applicable method for 'ggplot_build' applied to an object of class "c('gg', 'ggplot', 'ggPredict')"
  Calls: ggPredict -> getAspectRatio -> layer_scales -> ggplot_build
  Execution halted

Package: predict3d
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘predict3d.Rmd’ using rmarkdown
  
  Quitting from predict3d.Rmd:54-58 [unnamed-chunk-4]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `UseMethod()`:
  ! no applicable method for 'ggplot_build' applied to an object of class "c('gg', 'ggplot', 'ggPredict')"
  ---
  Backtrace:
      ▆
   1. └─predict3d::ggPredict(fit1, digits = 1)
   2.   └─predict3d::getAspectRatio(p)
   3.     └─ggplot2::layer_scales(p)
   4.       └─ggplot2::ggplot_build(plot)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
  no applicable method for 'ggplot_build' applied to an object of class "c('gg', 'ggplot', 'ggPredict')"
  --- failed re-building ‘predict3d.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘predict3d.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: PredPsych
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘PredPsych’

Package: priorsense
Check: tests
New result: ERROR
    Running ‘testthat.R’ [362s/367s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(priorsense)
    > 
    > test_check("priorsense")
    [ FAIL 1 | WARN 0 | SKIP 2 | PASS 91 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test_cmdstan.R:5:3', 'test_moment_matching.R:15:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_plots.R:103:5'): pagination of plots works as expected ───────
    powerscale_plot_quantities(ps, variables_per_page = Inf) has length 1, not length 11.
    
    [ FAIL 1 | WARN 0 | SKIP 2 | PASS 91 ]
    Error: Test failures
    Execution halted

Package: profiplots
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘how-to-use.Rmd’ using rmarkdown
  Warning in doTryCatch(return(expr), name, parentenv, handler) :
    "lwd.ticks" is not a graphical parameter
  Warning in doTryCatch(return(expr), name, parentenv, handler) :
    "lwd.ticks" is not a graphical parameter
  Warning in doTryCatch(return(expr), name, parentenv, handler) :
    "lwd.ticks" is not a graphical parameter
  Warning in doTryCatch(return(expr), name, parentenv, handler) :
    "lwd.ticks" is not a graphical parameter
  --- finished re-building ‘how-to-use.Rmd’
  
  --- re-building ‘plots-gallery.Rmd’ using rmarkdown
  
  Quitting from plots-gallery.Rmd:1148-1150 [unnamed-chunk-47]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'plots-gallery.Rmd' failed with diagnostics:
  Problem while computing stat.
  ℹ Error occurred in the 1st layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  --- failed re-building ‘plots-gallery.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘plots-gallery.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: ProteinPCA
Check: examples
New result: ERROR
  Running examples in ‘ProteinPCA-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: pca_analysis
  > ### Title: Principal Component Analysis (PCA) Tool on Protein Expression
  > ###   Data
  > ### Aliases: pca_analysis
  > 
  > ### ** Examples
  > 
  > set.seed(123)
  > data_matrix <- matrix(rnorm(100 * 20), nrow = 100, ncol = 20)
  > rownames(data_matrix) <- paste0('Sample_', 1:100)
  > colnames(data_matrix) <- paste0('Protein_', 1:20)
  > groups <- sample(c("Group A", "Group B"), 100, replace = TRUE)
  > result <- pca_analysis(data_matrix, groups = groups)
  Error in `ggplot2::stat_ellipse()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `setup_params()`:
  ! The package "MASS" is required for calculating ellipses with `type =
    "t"`.
  Backtrace:
       ▆
    1. ├─ProteinPCA::pca_analysis(data_matrix, groups = groups)
    2. │ └─gridExtra::grid.arrange(p1, p2, ncol = 2)
    3. │   └─gridExtra::arrangeGrob(...)
    4. │     └─base::lapply(grobs[toconv], ggplot2::ggplotGrob)
    5. │       └─ggplot2 (local) FUN(X[[i]], ...)
    6. │         ├─ggplot2::ggplot_gtable(ggplot_build(x))
    7. │         │ └─ggplot2:::attach_plot_env(data@plot@plot_env)
    8. │         │   └─base::options(ggplot2_plot_env = env)
    9. │         ├─ggplot2::ggplot_build(x)
   10. │         └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
   11. │           └─ggplot2:::by_layer(...)
   12. │             ├─rlang::try_fetch(...)
   13. │             │ ├─base::tryCatch(...)
   14. │             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   15. │             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   16. │             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   17. │             │ └─base::withCallingHandlers(...)
   18. │             └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   19. │               └─l$compute_statistic(d, layout)
   20. │                 └─ggplot2 (local) compute_statistic(..., self = self)
   21. │                   └─self$stat$setup_params(data, self$stat_params)
   22. │                     └─ggplot2 (local) setup_params(...)
   23. │                       └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
   24. │                         └─base::stop(cnd)
   25. └─rlang (local) `<fn>`(`<S3: rlib_error_package_not_found>`)
   26.   └─handlers[[1L]](cnd)
   27.     └─cli::cli_abort(...)
   28.       └─rlang::abort(...)
  Execution halted

Package: psborrow
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.

Package: psc
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘psc-vignette.Rmd’ using rmarkdown
  
  Quitting from psc-vignette.Rmd:176-178 [unnamed-chunk-5]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'psc-vignette.Rmd' failed with diagnostics:
  ℹ In index: 1.
  Caused by error in `UseMethod()`:
  ! no applicable method for 'ggplot_build' applied to an object of class "c('gg', 'ggplot')"
  --- failed re-building ‘psc-vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘psc-vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: pubh
Check: examples
New result: ERROR
  Running examples in ‘pubh-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: axis_labs
  > ### Title: Apply labels from variables to axis-labels in plots.
  > ### Aliases: axis_labs
  > 
  > ### ** Examples
  > 
  > data(kfm, package = "ISwR")
  > require(sjlabelled, quietly = TRUE)
  
  Attaching package: ‘sjlabelled’
  
  The following object is masked from ‘package:ggplot2’:
  
      as_label
  
  > kfm <- kfm |>
  +   var_labels(
  +     dl.milk = "Breast-milk intake (dl/day)",
  +     sex = "Sex",
  +     weight = "Child weight (kg)",
  +     ml.suppl = "Milk substitute (ml/day)",
  +     mat.weight = "Maternal weight (kg)",
  +     mat.height = "Maternal height (cm)"
  +   )
  > 
  > kfm |>
  +   gf_point(weight ~ dl.milk) |>
  +   gf_lm(col = 2, interval = "confidence", col = 2) |>
  +   axis_labs()
  Warning in rep(yes, length.out = len) :
    'x' is NULL so the result will be NULL
  Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : 
    replacement has length zero
  Calls: axis_labs -> ifelse
  Execution halted

Package: qad
Check: tests
New result: ERROR
    Running ‘testthat.R’ [11s/11s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(qad)
    > 
    > test_check("qad")
    Intervalls for the variable x2 
      Interval lowerBound upperBound
    1       I1          1          4
    2       I2          4         16
    3       I3         16         36
    4       I4         36         64
    
    Probability that X2 given X1=x1 lies in the interval I_i :
         I1 I2 I3 I4
    x1=1  1  0  0  0
    x1=3  0  1  0  0
    x1=5  0  0  1  0
    x1=7  0  0  0  1
    Intervalls for the variable x2 
       Interval   lowerBound   upperBound
    1        I1 -0.096486699 -0.053395374
    2        I2 -0.053395374  0.002087639
    3        I3  0.002087639  0.066711530
    4        I4  0.066711530  0.099509880
    5        I5  0.099509880  0.131427673
    6        I6  0.131427673  0.191538016
    7        I7  0.191538016  0.249979026
    8        I8  0.249979026  0.307634802
    9        I9  0.307634802  0.367007563
    10      I10  0.367007563  0.464833934
    11      I11  0.464833934  0.558460326
    12      I12  0.558460326  0.656561580
    13      I13  0.656561580  0.734241443
    14      I14  0.734241443  0.882390495
    15      I15  0.882390495  1.049379193
    
    Probability that X2 given X1=x1 lies in the interval I_i :
              I1   I2   I3   I4   I5   I6   I7   I8   I9  I10 I11 I12 I13 I14 I15
    x1=0    0.32 0.26 0.24 0.18 0.00 0.00 0.00 0.00 0.00 0.00   0   0   0   0   0
    x1=0.5  0.00 0.00 0.00 0.00 0.00 0.18 0.32 0.26 0.16 0.08   0   0   0   0   0
    x1=-0.5 0.00 0.00 0.00 0.04 0.06 0.12 0.30 0.30 0.18 0.00   0   0   0   0   0
    Intervalls for the variable x2 
       Interval  lowerBound  upperBound
    1        I1 -2.57950318 -1.34040838
    2        I2 -1.34040838 -1.00396718
    3        I3 -1.00396718 -0.64810453
    4        I4 -0.64810453 -0.33029574
    5        I5 -0.33029574 -0.21994356
    6        I6 -0.21994356  0.04462126
    7        I7  0.04462126  0.28878267
    8        I8  0.28878267  0.40811969
    9        I9  0.40811969  0.91540807
    10      I10  0.91540807  1.24743173
    11      I11  1.24743173  2.63602417
    
    Probability that X2 given X1=x1 lies in the interval I_i :
                I1        I2   I3   I4   I5   I6 I7 I8 I9 I10  I11
    x1=0 0.1154545 0.1645455 0.11 0.06 0.11 0.33  0  0  0   0 0.11
    Intervalls for the variable x2 
       Interval  lowerBound  upperBound
    1        I1 -2.88733453 -1.28351547
    2        I2 -1.28351547 -0.68187142
    3        I3 -0.68187142 -0.38763785
    4        I4 -0.38763785 -0.09317142
    5        I5 -0.09317142  0.10731113
    6        I6  0.10731113  0.36070504
    7        I7  0.36070504  0.53181638
    8        I8  0.53181638  0.79584583
    9        I9  0.79584583  1.11295501
    10      I10  1.11295501  1.63424046
    11      I11  1.63424046  2.30770520
    
    Probability that X2 given X1=x1 lies in the interval I_i :
           I1 I2 I3   I4   I5   I6 I7 I8   I9  I10  I11
    x1=0 0.11  0  0 0.11 0.11 0.28  0  0 0.11 0.11 0.17
    [1] "computation process..."
    [1] "computation process: 2 / 3"
    [1] "computation process: 3 / 3"
    p.values are adjusted by using the method fdr
    
    quantification of asymmetric dependencies: 
    
    
    Sample Size: 100
    Number of unique ranks: x1: 100
                            x2: 100
                       (x1,x2): 100
    Resolution: 10 x 10
    
    Dependence measures:
                        q p.values
     q(x1,x2)       0.294    0.206
     q(x2,x1)       0.183    0.980
     max.dependence 0.294    0.348
    
                         a p.values
     asymmetry       0.111       NA
    [ FAIL 10 | WARN 26 | SKIP 0 | PASS 71 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-predict.R:42:3'): plot is returned by prediction ─────────────
    class(pred[[2]]) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-qad.R:79:3'): heatmap.qad ────────────────────────────────────
    class(qad::heatmap.qad(pw_fit, select = "dependence")) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-qad.R:80:3'): heatmap.qad ────────────────────────────────────
    class(...) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-utilityfunctions.R:24:3'): plot.qad ──────────────────────────
    class(plot(fit)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-utilityfunctions.R:25:3'): plot.qad ──────────────────────────
    class(plot(fit, addSample = TRUE)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-utilityfunctions.R:26:3'): plot.qad ──────────────────────────
    class(plot(fit, copula = TRUE)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-utilityfunctions.R:27:3'): plot.qad ──────────────────────────
    class(plot(fit, density = TRUE)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-utilityfunctions.R:28:3'): plot.qad ──────────────────────────
    class(plot(fit, margins = TRUE)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-utilityfunctions.R:29:3'): plot.qad ──────────────────────────
    class(plot(fit, panel.grid = FALSE)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-utilityfunctions.R:33:3'): plot_density ──────────────────────
    class(plot_density(fit$mass_matrix)) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 10 | WARN 26 | SKIP 0 | PASS 71 ]
    Error: Test failures
    Execution halted

Package: qdap
Check: tests
New result: ERROR
    Running ‘testthat.R’ [18s/15s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library("testthat")
    > library("qdap")
    Loading required package: qdapDictionaries
    Loading required package: qdapRegex
    Loading required package: qdapTools
    Loading required package: RColorBrewer
    
    Attaching package: 'qdap'
    
    The following objects are masked from 'package:base':
    
        Filter, proportions
    
    > 
    > 
    > test_check("qdap")
    
      |                                                                            
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      |======                                                                |   9%
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      |=============                                                         |  18%
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      |===================                                                   |  27%
      |                                                                            
      |=========================                                             |  36%
      |                                                                            
      |================================                                      |  45%
      |                                                                            
      |======================================                                |  55%
      |                                                                            
      |=============================================                         |  64%
      |                                                                            
      |===================================================                   |  73%
      |                                                                            
      |=========================================================             |  82%
      |                                                                            
      |================================================================      |  91%
      |                                                                            
      |======================================================================| 100%
    
      |                                                                            
      |                                                                      |   0%
      |                                                                            
      |======                                                                |   9%
      |                                                                            
      |=============                                                         |  18%
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      |===================                                                   |  27%
      |                                                                            
      |=========================                                             |  36%
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      |================================                                      |  45%
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      |======================================                                |  55%
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      |=============================================                         |  64%
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      |===================================================                   |  73%
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      |=========================================================             |  82%
      |                                                                            
      |================================================================      |  91%
      |                                                                            
      |======================================================================| 100%
    [ FAIL 1 | WARN 3 | SKIP 0 | PASS 217 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-dispersion_plot.R:6:5'): dispersion_plot outputs a ggplot object ──
    all(class(m) == c("gg", "ggplot")) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 1 | WARN 3 | SKIP 0 | PASS 217 ]
    Error: Test failures
    Execution halted

Package: quickReg
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘quickReg.Rmd’ using rmarkdown
  
  Quitting from quickReg.Rmd:130-162 [plot]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::labels> object is invalid:
  - every label must be named.
  ---
  Backtrace:
      ▆
   1. └─ggplot2::labs(list(title = "Regression Model", x = "variables"))
   2.   └─ggplot2::class_labels(args)
   3.     └─S7::new_object(labels)
   4.       └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'quickReg.Rmd' failed with diagnostics:
  <ggplot2::labels> object is invalid:
  - every label must be named.
  --- failed re-building ‘quickReg.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘quickReg.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: quollr
Check: examples
New result: ERROR
  Running examples in ‘quollr-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_rmse_layouts
  > ### Title: Arrange RMSE plot and 2-D layouts
  > ### Aliases: plot_rmse_layouts
  > 
  > ### ** Examples
  > 
  > design <- gen_design(n_right = 4, ncol_right = 2)
  > plot_rmse_layouts(plots = scurve_plts, design = design)
  Error in `patchwork::wrap_plots()`:
  ! Only know how to add <ggplot> and/or <grob> objects
  Backtrace:
      ▆
   1. └─quollr::plot_rmse_layouts(plots = scurve_plts, design = design)
   2.   └─patchwork::wrap_plots(plots)
   3.     └─cli::cli_abort("Only know how to add {.cls ggplot} and/or {.cls grob} objects")
   4.       └─rlang::abort(...)
  Execution halted

Package: quollr
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘quollr1quickstart.Rmd’ using rmarkdown
  --- finished re-building ‘quollr1quickstart.Rmd’
  
  --- re-building ‘quollr2dataprocessing.Rmd’ using rmarkdown
  --- finished re-building ‘quollr2dataprocessing.Rmd’
  
  --- re-building ‘quollr3hexbin.Rmd’ using rmarkdown
  --- finished re-building ‘quollr3hexbin.Rmd’
  
  --- re-building ‘quollr4algo.Rmd’ using rmarkdown
  --- finished re-building ‘quollr4algo.Rmd’
  
  --- re-building ‘quollr5summary.Rmd’ using rmarkdown
  --- finished re-building ‘quollr5summary.Rmd’
  
  --- re-building ‘quollr6bestbinwidth.Rmd’ using rmarkdown
  --- finished re-building ‘quollr6bestbinwidth.Rmd’
  
  --- re-building ‘quollr7bestfit.Rmd’ using rmarkdown
  
  Quitting from quollr7bestfit.Rmd:44-47 [unnamed-chunk-3]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'quollr7bestfit.Rmd' failed with diagnostics:
  Only know how to add <ggplot> and/or <grob> objects
  --- failed re-building ‘quollr7bestfit.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘quollr7bestfit.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: quollr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [11s/11s]
  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(quollr)
    > library(vdiffr)
    > 
    > test_check("quollr")
    New names:
    * `` -> `...1`
    * `` -> `...2`
    New names:
    * `` -> `...1`
    * `` -> `...2`
    [ FAIL 1 | WARN 0 | SKIP 33 | PASS 4 ]
    
    ══ Skipped tests (33) ══════════════════════════════════════════════════════════
    • On CRAN (30): 'test-2d.R:6:3', 'test-2d.R:16:3', 'test-2d.R:26:3',
      'test-2d.R:35:3', 'test-2d.R:43:3', 'test-2d.R:49:3', 'test-2d.R:56:3',
      'test-2d.R:69:3', 'test-2d.R:80:3', 'test-2d.R:94:3', 'test-2d.R:102:3',
      'test-2d.R:115:3', 'test-2d.R:122:3', 'test-data_processing.R:2:3',
      'test-geom_hexgrid.R:5:3', 'test-geom_trimesh.R:6:3', 'test-highd.R:4:3',
      'test-highd.R:11:3', 'test-link_plots.R:3:3', 'test-link_plots.R:31:3',
      'test-model.R:3:3', 'test-parameters.R:3:3', 'test-parameters.R:11:3',
      'test-prediction.R:3:3', 'test-prediction.R:11:3', 'test-prediction.R:20:3',
      'test-prediction.R:28:3', 'test-projection.R:7:3', 'test-projection.R:20:3',
      'test-projection.R:45:3'
    • empty test (3): 'test-highd.R:18:1', 'test-link_plots.R:10:1',
      'test-link_plots.R:40:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-prediction.R:36:3'): plot_rmse_layouts() works ─────────────────
    Error in `patchwork::wrap_plots(plots)`: Only know how to add <ggplot> and/or <grob> objects
    Backtrace:
        ▆
     1. └─quollr::plot_rmse_layouts(plots = scurve_plts, design = design) at test-prediction.R:36:3
     2.   └─patchwork::wrap_plots(plots)
     3.     └─cli::cli_abort("Only know how to add {.cls ggplot} and/or {.cls grob} objects")
     4.       └─rlang::abort(...)
    
    [ FAIL 1 | WARN 0 | SKIP 33 | PASS 4 ]
    Deleting unused snapshots:
    • geom_hexgrid/geom-hexgrid-basic-with-all-bin-centroids.svg
    • geom_trimesh/geom-hexgrid-basic-with-all-bin-centroids.svg
    Error: Test failures
    Execution halted

Package: RamanMP
Check: examples
New result: ERROR
  Running examples in ‘RamanMP-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: peak.finder
  > ### Title: Peaks identification
  > ### Aliases: peak.finder
  > ### Keywords: peaks
  > 
  > ### ** Examples
  > 
  > data("MPdatabase")
  > peak.data<-peak.finder(MPdatabase[,c(1,7)], threshold = 500, m=7)
  Error: <ggplot2::element_text> object properties are invalid:
  - @size must be <NULL>, <integer>, or <double>, not <character>
  Execution halted

Package: rasterdiv
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘rasterdiv_01_Basics.Rmd’ using rmarkdown
  --- finished re-building ‘rasterdiv_01_Basics.Rmd’
  
  --- re-building ‘rasterdiv_02_Area_based_Rao.Rmd’ using rmarkdown
  --- finished re-building ‘rasterdiv_02_Area_based_Rao.Rmd’
  
  --- re-building ‘rasterdiv_03_Advanced_multidimension_Rao.Rmd’ using rmarkdown
  --- finished re-building ‘rasterdiv_03_Advanced_multidimension_Rao.Rmd’
  
  --- re-building ‘rasterdiv_04_Accumulation_Rao.Rmd’ using rmarkdown
  
  Quitting from rasterdiv_04_Accumulation_Rao.Rmd:126-144 [unnamed-chunk-12]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'rasterdiv_04_Accumulation_Rao.Rmd' failed with diagnostics:
  Problem while setting up geom aesthetics.
  ℹ Error occurred in the 5th layer.
  Caused by error in `list_sizes()`:
  ! `x$label` must be a vector, not an expression vector.
  --- failed re-building ‘rasterdiv_04_Accumulation_Rao.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘rasterdiv_04_Accumulation_Rao.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: reda
Check: tests
New result: ERROR
    Running ‘tinytest.R’ [4s/4s]
  Running the tests in ‘tests/tinytest.R’ failed.
  Complete output:
    > if (requireNamespace("tinytest", quietly = TRUE) &&
    +     utils::packageVersion("tinytest") >= "1.1.0") {
    + 
    +     ## Set a seed to make the test deterministic
    +     set.seed(808)
    + 
    +     tinytest::test_package("reda", ncpu = NULL,
    +                            side_effects = TRUE)
    + }
    
    test_Recur.R..................    0 tests    
    test_Recur.R..................    0 tests    
    test_Recur.R..................    0 tests    
    test_Recur.R..................    0 tests    
    test_Recur.R..................    0 tests    
    test_Recur.R..................    0 tests    
    test_Recur.R..................    1 tests OK 
    test_Recur.R..................    2 tests OK 
    test_Recur.R..................    3 tests OK 
    test_Recur.R..................    4 tests OK 
    test_Recur.R..................    5 tests OK 
    test_Recur.R..................    6 tests OK 
    test_Recur.R..................    7 tests OK 
    test_Recur.R..................    8 tests OK 
    test_Recur.R..................    9 tests OK 
    test_Recur.R..................   10 tests OK 
    test_Recur.R..................   11 tests OK 
    test_Recur.R..................   11 tests OK 
    test_Recur.R..................   12 tests OK 
    test_Recur.R..................   13 tests OK 
    test_Recur.R..................   14 tests OK 
    test_Recur.R..................   15 tests OK 
    test_Recur.R..................   16 tests OK 
    test_Recur.R..................   17 tests OK 
    test_Recur.R..................   18 tests OK 
    test_Recur.R..................   19 tests OK 
    test_Recur.R..................   20 tests OK 
    test_Recur.R..................   21 tests OK 
    test_Recur.R..................   22 tests OK 
    test_Recur.R..................   22 tests OK 
    test_Recur.R..................   22 tests OK 
    test_Recur.R..................   22 tests OK 
    test_Recur.R..................   22 tests OK 
    test_Recur.R..................   23 tests OK 
    test_Recur.R..................   24 tests OK 
    test_Recur.R..................   25 tests OK 
    test_Recur.R..................   26 tests OK 
    test_Recur.R..................   27 tests OK 
    test_Recur.R..................   28 tests OK 
    test_Recur.R..................   29 tests OK 
    test_Recur.R..................   30 tests OK 
    test_Recur.R..................   31 tests OK 
    test_Recur.R..................   32 tests OK 
    test_Recur.R..................   33 tests OK 
    test_Recur.R..................   33 tests OK 
    test_Recur.R..................   34 tests OK 
    test_Recur.R..................   34 tests OK 
    test_Recur.R..................   35 tests OK 
    test_Recur.R..................   36 tests OK 
    test_Recur.R..................   37 tests OK 
    test_Recur.R..................   38 tests OK 
    test_Recur.R..................   39 tests OK 
    test_Recur.R..................   40 tests OK 
    test_Recur.R..................   41 tests OK 
    test_Recur.R..................   42 tests OK 
    test_Recur.R..................   43 tests OK 
    test_Recur.R..................   44 tests OK 
    test_Recur.R..................   45 tests OK 
    test_Recur.R..................   45 tests OK 
    test_Recur.R..................   45 tests OK 
    test_Recur.R..................   46 tests OK 
    test_Recur.R..................   47 tests OK 
    test_Recur.R..................   48 tests OK 
    test_Recur.R..................   49 tests OK 
    test_Recur.R..................   50 tests OK 
    test_Recur.R..................   50 tests OK 
    test_Recur.R..................   51 tests OK 
    test_Recur.R..................   52 tests OK 
    test_Recur.R..................   53 tests OK 
    test_Recur.R..................   54 tests OK 
    test_Recur.R..................   55 tests OK 
    test_Recur.R..................   56 tests OK 
    test_Recur.R..................   57 tests OK 
    test_Recur.R..................   58 tests OK 
    test_Recur.R..................   59 tests OK 
    test_Recur.R..................   60 tests OK 
    test_Recur.R..................   61 tests OK 
    test_Recur.R..................   62 tests OK 
    test_Recur.R..................   63 tests OK 
    test_Recur.R..................   64 tests OK 0.2s
    
    test_Survr.R..................    0 tests    
    test_Survr.R..................    0 tests    
    test_Survr.R..................    0 tests    
    test_Survr.R..................    0 tests    
    test_Survr.R..................    1 tests OK 
    test_Survr.R..................    2 tests OK 
    test_Survr.R..................    3 tests OK 
    test_Survr.R..................    3 tests OK 
    test_Survr.R..................    3 tests OK 
    test_Survr.R..................    4 tests OK 
    test_Survr.R..................    5 tests OK 
    test_Survr.R..................    6 tests OK 
    test_Survr.R..................    6 tests OK 
    test_Survr.R..................    6 tests OK 
    test_Survr.R..................    7 tests OK 
    test_Survr.R..................    7 tests OK 
    test_Survr.R..................    7 tests OK 
    test_Survr.R..................    8 tests OK 
    test_Survr.R..................    8 tests OK 
    test_Survr.R..................    8 tests OK 
    test_Survr.R..................    9 tests OK 
    test_Survr.R..................    9 tests OK 
    test_Survr.R..................    9 tests OK 
    test_Survr.R..................   10 tests OK 
    test_Survr.R..................   10 tests OK 
    test_Survr.R..................   10 tests OK 
    test_Survr.R..................   11 tests OK 
    test_Survr.R..................   11 tests OK 
    test_Survr.R..................   11 tests OK 
    test_Survr.R..................   12 tests OK 
    test_Survr.R..................   12 tests OK 
    test_Survr.R..................   12 tests OK 
    test_Survr.R..................   13 tests OK 
    test_Survr.R..................   13 tests OK 
    test_Survr.R..................   13 tests OK 
    test_Survr.R..................   14 tests OK 85ms
    
    test_mcf.formula.R............    0 tests    
    test_mcf.formula.R............    0 tests    
    test_mcf.formula.R............    0 tests    
    test_mcf.formula.R............    1 tests OK 
    test_mcf.formula.R............    1 tests OK 
    test_mcf.formula.R............    1 tests OK Observations with missing value in covariates are removed.
    Checking the new dataset again...
    Done!
    
    test_mcf.formula.R............    1 tests OK 
    test_mcf.formula.R............    2 tests OK 
    test_mcf.formula.R............    2 tests OK 
    test_mcf.formula.R............    3 tests OK 
    test_mcf.formula.R............    4 tests OK 
    test_mcf.formula.R............    5 tests OK 
    test_mcf.formula.R............    6 tests OK 
    test_mcf.formula.R............    6 tests OK 
    test_mcf.formula.R............    6 tests OK 
    test_mcf.formula.R............    7 tests OK 
    test_mcf.formula.R............    8 tests OK 
    test_mcf.formula.R............    9 tests OK Formula:
    Recur(Days, ID, No.) ~ 1
    <environment: 0x5584827567a0>
    
    MCF:
       time numRisk   instRate        MCF         se        lower      upper
    1    61      41 0.02439024 0.02439024 0.02409097 -0.022827181 0.07160767
    2    76      41 0.02439024 0.04878049 0.03364120 -0.017155058 0.11471603
    3    84      41 0.02439024 0.07317073 0.04067023 -0.006541457 0.15288292
    4    87      41 0.02439024 0.09756098 0.04633990  0.006736445 0.18838551
    5    92      41 0.02439024 0.12195122 0.05110466  0.021787935 0.22211450
    6    98      41 0.02439024 0.14634146 0.05519934  0.038152751 0.25453018
    7   120      41 0.02439024 0.17073171 0.05876418  0.055556027 0.28590739
    8   139      41 0.04878049 0.21951220 0.07326981  0.075906003 0.36311839
    9   165      41 0.02439024 0.24390244 0.07541665  0.096088517 0.39171636
    10  166      41 0.02439024 0.26829268 0.07731661  0.116754905 0.41983046
    11  202      41 0.02439024 0.29268293 0.07898751  0.137870245 0.44749561
    12  206      41 0.02439024 0.31707317 0.08752683  0.145523746 0.48862260
    13  249      41 0.02439024 0.34146341 0.08867963  0.167654539 0.51527229
    14  254      41 0.02439024 0.36585366 0.08965595  0.190131233 0.54157608
    15  258      41 0.02439024 0.39024390 0.09046150  0.212942628 0.56754518
    16  265      41 0.02439024 0.41463415 0.09110081  0.236079844 0.59318845
    17  276      41 0.02439024 0.43902439 0.09785797  0.247226302 0.63082248
    18  298      41 0.02439024 0.46341463 0.10960728  0.248588321 0.67824095
    19  323      41 0.02439024 0.48780488 0.10973957  0.272719270 0.70289049
    20  326      41 0.02439024 0.51219512 0.10973957  0.297109514 0.72728073
    21  328      41 0.02439024 0.53658537 0.11490658  0.311372601 0.76179813
    22  344      41 0.02439024 0.56097561 0.11465376  0.336258363 0.78569286
    23  348      41 0.02439024 0.58536585 0.12424961  0.341841096 0.82889061
    24  349      41 0.02439024 0.60975610 0.12378162  0.367148574 0.85236362
    25  367      41 0.02439024 0.63414634 0.12319414  0.392690260 0.87560242
    26  377      41 0.02439024 0.65853659 0.13184165  0.400131703 0.91694147
    27  389      41 0.00000000 0.65853659 0.13184165  0.400131703 0.91694147
    28  404      40 0.02500000 0.68353659 0.13593896  0.417101125 0.94997205
    29  408      40 0.02500000 0.70853659 0.13980461  0.434524578 0.98254859
    30  410      40 0.02500000 0.73353659 0.13914201  0.460823266 1.00624990
    31  449      40 0.02500000 0.75853659 0.14270223  0.478845347 1.03822782
    32  479      40 0.02500000 0.78353659 0.14606884  0.497246910 1.06982626
    33  497      40 0.02500000 0.80853659 0.14925494  0.516002277 1.10107089
    34  538      40 0.02500000 0.83353659 0.15227185  0.535089238 1.13198393
    35  539      40 0.02500000 0.85853659 0.15512945  0.554488445 1.16258473
    36  561      40 0.02500000 0.88353659 0.16174773  0.566516867 1.20055630
    37  563      40 0.02500000 0.90853659 0.16425059  0.586611342 1.23046183
    38  570      40 0.02500000 0.93353659 0.17033184  0.599692308 1.26738086
    39  573      40 0.02500000 0.95853659 0.16895814  0.627384709 1.28968846
    40  578      40 0.00000000 0.95853659 0.16895814  0.627384709 1.28968846
    41  581      38 0.02631579 0.98485237 0.17120360  0.649299489 1.32040526
    42  582      38 0.00000000 0.98485237 0.17120360  0.649299489 1.32040526
    43  585      36 0.00000000 0.98485237 0.17120360  0.649299489 1.32040526
    44  586      34 0.02941176 1.01426414 0.17384433  0.673535517 1.35499276
    45  587      33 0.00000000 1.01426414 0.17384433  0.673535517 1.35499276
    46  589      31 0.00000000 1.01426414 0.17384433  0.673535517 1.35499276
    47  593      29 0.00000000 1.01426414 0.17384433  0.673535517 1.35499276
    48  594      28 0.00000000 1.01426414 0.17384433  0.673535517 1.35499276
    49  595      27 0.00000000 1.01426414 0.17384433  0.673535517 1.35499276
    50  596      26 0.00000000 1.01426414 0.17384433  0.673535517 1.35499276
    51  601      25 0.00000000 1.01426414 0.17384433  0.673535517 1.35499276
    52  603      23 0.00000000 1.01426414 0.17384433  0.673535517 1.35499276
    53  604      22 0.04545455 1.05971868 0.18506099  0.697005813 1.42243156
    54  606      22 0.00000000 1.05971868 0.18506099  0.697005813 1.42243156
    55  608      21 0.00000000 1.05971868 0.18506099  0.697005813 1.42243156
    56  611      20 0.00000000 1.05971868 0.18506099  0.697005813 1.42243156
    57  613      19 0.00000000 1.05971868 0.18506099  0.697005813 1.42243156
    58  614      18 0.00000000 1.05971868 0.18506099  0.697005813 1.42243156
    59  621      17 0.05882353 1.11854221 0.20750288  0.711844037 1.52524039
    60  631      17 0.00000000 1.11854221 0.20750288  0.711844037 1.52524039
    61  635      16 0.06250000 1.18104221 0.20690835  0.775509306 1.58657512
    62  640      16 0.06250000 1.24354221 0.22632442  0.799954507 1.68712992
    63  641      16 0.00000000 1.24354221 0.22632442  0.799954507 1.68712992
    64  642      15 0.00000000 1.24354221 0.22632442  0.799954507 1.68712992
    65  644      14 0.00000000 1.24354221 0.22632442  0.799954507 1.68712992
    66  646      13 0.07692308 1.32046529 0.22850515  0.872603417 1.76832717
    67  648      13 0.00000000 1.32046529 0.22850515  0.872603417 1.76832717
    68  649      12 0.00000000 1.32046529 0.22850515  0.872603417 1.76832717
    69  650      11 0.00000000 1.32046529 0.22850515  0.872603417 1.76832717
    70  651      10 0.00000000 1.32046529 0.22850515  0.872603417 1.76832717
    71  653       9 0.22222222 1.54268751 0.31165607  0.931852831 2.15352220
    72  663       7 0.00000000 1.54268751 0.31165607  0.931852831 2.15352220
    73  665       6 0.00000000 1.54268751 0.31165607  0.931852831 2.15352220
    74  667       5 0.00000000 1.54268751 0.31165607  0.931852831 2.15352220
    75  759       2 0.00000000 1.54268751 0.31165607  0.931852831 2.15352220
    76  761       1 0.00000000 1.54268751 0.31165607  0.931852831 2.15352220
    
    test_mcf.formula.R............   10 tests OK 0.9s
    
    test_mcfDiff.R................    0 tests    
    test_mcfDiff.R................    0 tests    
    test_mcfDiff.R................    0 tests    
    test_mcfDiff.R................    0 tests    
    test_mcfDiff.R................    0 tests    
    test_mcfDiff.R................    0 tests    
    test_mcfDiff.R................    0 tests    
    test_mcfDiff.R................    1 tests OK 
    test_mcfDiff.R................    2 tests OK 
    test_mcfDiff.R................    3 tests OK 
    test_mcfDiff.R................    4 tests OK 
    test_mcfDiff.R................    5 tests OK 
    test_mcfDiff.R................    6 tests OK 
    test_mcfDiff.R................    7 tests OK 
    test_mcfDiff.R................    8 tests OK 
    test_mcfDiff.R................    9 tests OK 
    test_mcfDiff.R................   10 tests OK 
    test_mcfDiff.R................   11 tests OK 
    test_mcfDiff.R................   12 tests OK 
    test_mcfDiff.R................   13 tests OK 
    test_mcfDiff.R................   13 tests OK 
    test_mcfDiff.R................   14 tests OK 
    test_mcfDiff.R................   14 tests OK 
    test_mcfDiff.R................   15 tests OK 
    test_mcfDiff.R................   16 tests 1 fails Call: 
    mcfDiff(mcf1 = mcf1, mcf2 = mcf2)
    
    Two-Sample Pseudo-Score Tests:
                     Statistic   Variance      Chisq DF Pr(>Chisq)
    Constant Weight -0.3338763 13.7090222  0.0081314  1     0.9281
    Linear Weight    1.1518140  2.8036059  0.4732033  1     0.4915
    
    Variance Estimator: robust 
    
    test_mcfDiff.R................   17 tests 1 fails 
    test_mcfDiff.R................   17 tests 1 fails 
    test_mcfDiff.R................   17 tests 1 fails 
    test_mcfDiff.R................   17 tests 1 fails 
    test_mcfDiff.R................   18 tests 1 fails 
    test_mcfDiff.R................   19 tests 1 fails 
    test_mcfDiff.R................   20 tests 1 fails 
    test_mcfDiff.R................   21 tests 1 fails 
    test_mcfDiff.R................   22 tests 1 fails 
    test_mcfDiff.R................   23 tests 1 fails 
    test_mcfDiff.R................   24 tests 1 fails 
    test_mcfDiff.R................   25 tests 1 fails 
    test_mcfDiff.R................   26 tests 1 fails 
    test_mcfDiff.R................   27 tests 1 fails 
    test_mcfDiff.R................   28 tests 1 fails 
    test_mcfDiff.R................   28 tests 1 fails 
    test_mcfDiff.R................   29 tests 1 fails 
    test_mcfDiff.R................   30 tests 1 fails 
    test_mcfDiff.R................   30 tests 1 fails 
    test_mcfDiff.R................   30 tests 1 fails 
    test_mcfDiff.R................   31 tests 1 fails Two-Sample Pseudo-Score Tests:
                    Statistic Variance Chisq DF Pr(>Chisq)
    Constant Weight         0        0   NaN  1        NaN
    Linear Weight           0        0   NaN  1        NaN
    
    Variance Estimator: robust 
    
    test_mcfDiff.R................   32 tests 1 fails 0.4s
    
    test_rateReg.R................    0 tests    
    test_rateReg.R................    0 tests    
    test_rateReg.R................    0 tests    
    test_rateReg.R................    0 tests    
    test_rateReg.R................    1 tests OK 
    test_rateReg.R................    2 tests OK 
    test_rateReg.R................    3 tests OK 
    test_rateReg.R................    4 tests OK 
    test_rateReg.R................    5 tests OK 
    test_rateReg.R................    6 tests OK 
    test_rateReg.R................    7 tests OK 
    test_rateReg.R................    8 tests OK 
    test_rateReg.R................    9 tests OK 
    test_rateReg.R................   10 tests OK 
    test_rateReg.R................   11 tests OK 
    test_rateReg.R................   11 tests OK 
    test_rateReg.R................   11 tests OK Observations with missing value in covariates are removed.
    Checking the new dataset again...
    Done!
    
    test_rateReg.R................   12 tests OK 
    test_rateReg.R................   13 tests OK 
    test_rateReg.R................   14 tests OK 
    test_rateReg.R................   14 tests OK 
    test_rateReg.R................   14 tests OK 
    test_rateReg.R................   14 tests OK 
    test_rateReg.R................   14 tests OK 
    test_rateReg.R................   15 tests OK 
    test_rateReg.R................   16 tests OK 
    test_rateReg.R................   17 tests OK 
    test_rateReg.R................   18 tests OK 
    test_rateReg.R................   19 tests OK 
    test_rateReg.R................   20 tests OK 
    test_rateReg.R................   21 tests OK 
    test_rateReg.R................   22 tests OK 
    test_rateReg.R................   23 tests OK 
    test_rateReg.R................   23 tests OK 
    test_rateReg.R................   24 tests OK 
    test_rateReg.R................   25 tests OK 
    test_rateReg.R................   26 tests 1 fails 
    test_rateReg.R................   26 tests 1 fails 
    test_rateReg.R................   26 tests 1 fails 
    test_rateReg.R................   26 tests 1 fails 
    test_rateReg.R................   27 tests 1 fails 
    test_rateReg.R................   28 tests 1 fails 
    test_rateReg.R................   29 tests 1 fails 
    test_rateReg.R................   30 tests 1 fails 
    test_rateReg.R................   31 tests 1 fails 
    test_rateReg.R................   32 tests 2 fails 
    test_rateReg.R................   33 tests 3 fails 
    test_rateReg.R................   34 tests 4 fails Call: 
    rateReg(formula = Recur(time, ID, event) ~ x1 + group + gender, 
        data = testDat, knots = seq.int(28, 140, 28))
    
    Coefficients of covariates: 
            x1 groupTreat gendermale 
     0.2876191 -0.8955805  0.3465096 
    
    Frailty parameter:  0.6983293 
    
    Internal knots: 
    28, 56, 84, 112, 140
    
    Boundary knots: 
    0, 168
    
    Coefficients of pieces:
    M-spline1 M-spline2 M-spline3 M-spline4 M-spline5 M-spline6 
    0.8951422 0.8951428 0.6103266 1.0042103 1.0276077 1.5064373 
    
    test_rateReg.R................   35 tests 4 fails Call: 
    rateReg(formula = Recur(time, ID, event) ~ x1 + group + gender, 
        data = testDat, knots = c(60, 90, 120), degree = 3, spline = "mSplines")
    
    Coefficients of covariates: 
            x1 groupTreat gendermale 
     0.2834071 -0.8953501  0.3545572 
    
    Frailty parameter:  0.700646 
    
    Internal knots: 
    60, 90, 120
    
    Boundary knots: 
    0, 168
    
    Coefficients of spline bases:
    M-spline1 M-spline2 M-spline3 M-spline4 M-spline5 M-spline6 M-spline7 
    0.3357607 1.2053217 0.3099513 1.5969252 0.2864276 1.8674454 0.2948529 
    
    test_rateReg.R................   36 tests 4 fails Call: 
    rateReg(formula = Recur(time, ID, event) ~ x1 + group + gender, 
        data = testDat, knots = seq.int(28, 140, 28))
    
    Coefficients of covariates: 
                   coef exp(coef) se(coef)       z Pr(>|z|)  
    x1          0.28762   1.33325  0.24006  1.1981  0.23087  
    groupTreat -0.89558   0.40837  0.39915 -2.2437  0.02485 *
    gendermale  0.34651   1.41412  0.39299  0.8817  0.37792  
    ---
    Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    
    Parameter of frailty: 
            parameter        se
    Frailty 0.6983293 0.1768623
    
    Internal knots: 
    28, 56, 84, 112, 140
    
    Boundary knots:
    0, 168
    
    Degree of spline bases: 0 
    
    Coefficients of spline bases:
                 coef se(coef)
    M-spline1 0.89514   0.2760
    M-spline2 0.89514   0.2760
    M-spline3 0.61033   0.1984
    M-spline4 1.00421   0.3109
    M-spline5 1.02761   0.3216
    M-spline6 1.50644   0.4863
    
    Loglikelihood:  -988.9471 
    
    test_rateReg.R................   37 tests 4 fails Formula:
    Recur(time, ID, event) ~ x1 + group + gender
    <environment: 0x558484e4ea60>
    
    New data:
      x1 groupTreat gendermale
    1  0          0          0
    
    Confidence level: 95% 
    
    MCF:
                time         MCF       lower       upper
    1      0.0000000 0.000000000 0.000000000 0.000000000
    2      0.1681682 0.005440165 0.002490306 0.008390025
    3      0.3363363 0.010880331 0.004980611 0.016780051
    4      0.5045045 0.016320496 0.007470917 0.025170076
    5      0.6726727 0.021760662 0.009961223 0.033560101
    6      0.8408408 0.027200827 0.012451528 0.041950126
    7      1.0090090 0.032640993 0.014941834 0.050340152
    8      1.1771772 0.038081158 0.017432140 0.058730177
    9      1.3453453 0.043521324 0.019922446 0.067120202
    10     1.5135135 0.048961489 0.022412751 0.075510227
    11     1.6816817 0.054401655 0.024903057 0.083900253
    12     1.8498498 0.059841820 0.027393363 0.092290278
    13     2.0180180 0.065281986 0.029883668 0.100680303
    14     2.1861862 0.070722151 0.032373974 0.109070329
    15     2.3543544 0.076162317 0.034864280 0.117460354
    16     2.5225225 0.081602482 0.037354585 0.125850379
    17     2.6906907 0.087042648 0.039844891 0.134240404
    18     2.8588589 0.092482813 0.042335197 0.142630430
    19     3.0270270 0.097922979 0.044825502 0.151020455
    20     3.1951952 0.103363144 0.047315808 0.159410480
    21     3.3633634 0.108803310 0.049806114 0.167800505
    22     3.5315315 0.114243475 0.052296420 0.176190531
    23     3.6996997 0.119683641 0.054786725 0.184580556
    24     3.8678679 0.125123806 0.057277031 0.192970581
    25     4.0360360 0.130563972 0.059767337 0.201360607
    26     4.2042042 0.136004137 0.062257642 0.209750632
    27     4.3723724 0.141444303 0.064747948 0.218140657
    28     4.5405405 0.146884468 0.067238254 0.226530682
    29     4.7087087 0.152324634 0.069728559 0.234920708
    30     4.8768769 0.157764799 0.072218865 0.243310733
    31     5.0450450 0.163204964 0.074709171 0.251700758
    32     5.2132132 0.168645130 0.077199476 0.260090783
    33     5.3813814 0.174085295 0.079689782 0.268480809
    34     5.5495495 0.179525461 0.082180088 0.276870834
    35     5.7177177 0.184965626 0.084670394 0.285260859
    36     5.8858859 0.190405792 0.087160699 0.293650885
    37     6.0540541 0.195845957 0.089651005 0.302040910
    38     6.2222222 0.201286123 0.092141311 0.310430935
    39     6.3903904 0.206726288 0.094631616 0.318820960
    40     6.5585586 0.212166454 0.097121922 0.327210986
    41     6.7267267 0.217606619 0.099612228 0.335601011
    42     6.8948949 0.223046785 0.102102533 0.343991036
    43     7.0630631 0.228486950 0.104592839 0.352381061
    44     7.2312312 0.233927116 0.107083145 0.360771087
    45     7.3993994 0.239367281 0.109573450 0.369161112
    46     7.5675676 0.244807447 0.112063756 0.377551137
    47     7.7357357 0.250247612 0.114554062 0.385941163
    48     7.9039039 0.255687778 0.117044368 0.394331188
    49     8.0720721 0.261127943 0.119534673 0.402721213
    50     8.2402402 0.266568109 0.122024979 0.411111238
    51     8.4084084 0.272008274 0.124515285 0.419501264
    52     8.5765766 0.277448440 0.127005590 0.427891289
    53     8.7447447 0.282888605 0.129495896 0.436281314
    54     8.9129129 0.288328771 0.131986202 0.444671339
    55     9.0810811 0.293768936 0.134476507 0.453061365
    56     9.2492492 0.299209102 0.136966813 0.461451390
    57     9.4174174 0.304649267 0.139457119 0.469841415
    58     9.5855856 0.310089433 0.141947424 0.478231441
    59     9.7537538 0.315529598 0.144437730 0.486621466
    60     9.9219219 0.320969763 0.146928036 0.495011491
    61    10.0900901 0.326409929 0.149418342 0.503401516
    62    10.2582583 0.331850094 0.151908647 0.511791542
    63    10.4264264 0.337290260 0.154398953 0.520181567
    64    10.5945946 0.342730425 0.156889259 0.528571592
    65    10.7627628 0.348170591 0.159379564 0.536961617
    66    10.9309309 0.353610756 0.161869870 0.545351643
    67    11.0990991 0.359050922 0.164360176 0.553741668
    68    11.2672673 0.364491087 0.166850481 0.562131693
    69    11.4354354 0.369931253 0.169340787 0.570521719
    70    11.6036036 0.375371418 0.171831093 0.578911744
    71    11.7717718 0.380811584 0.174321398 0.587301769
    72    11.9399399 0.386251749 0.176811704 0.595691794
    73    12.1081081 0.391691915 0.179302010 0.604081820
    74    12.2762763 0.397132080 0.181792316 0.612471845
    75    12.4444444 0.402572246 0.184282621 0.620861870
    76    12.6126126 0.408012411 0.186772927 0.629251895
    77    12.7807808 0.413452577 0.189263233 0.637641921
    78    12.9489489 0.418892742 0.191753538 0.646031946
    79    13.1171171 0.424332908 0.194243844 0.654421971
    80    13.2852853 0.429773073 0.196734150 0.662811997
    81    13.4534535 0.435213239 0.199224455 0.671202022
    82    13.6216216 0.440653404 0.201714761 0.679592047
    83    13.7897898 0.446093570 0.204205067 0.687982072
    84    13.9579580 0.451533735 0.206695372 0.696372098
    85    14.1261261 0.456973901 0.209185678 0.704762123
    86    14.2942943 0.462414066 0.211675984 0.713152148
    87    14.4624625 0.467854232 0.214166290 0.721542173
    88    14.6306306 0.473294397 0.216656595 0.729932199
    89    14.7987988 0.478734562 0.219146901 0.738322224
    90    14.9669670 0.484174728 0.221637207 0.746712249
    91    15.1351351 0.489614893 0.224127512 0.755102275
    92    15.3033033 0.495055059 0.226617818 0.763492300
    93    15.4714715 0.500495224 0.229108124 0.771882325
    94    15.6396396 0.505935390 0.231598429 0.780272350
    95    15.8078078 0.511375555 0.234088735 0.788662376
    96    15.9759760 0.516815721 0.236579041 0.797052401
    97    16.1441441 0.522255886 0.239069346 0.805442426
    98    16.3123123 0.527696052 0.241559652 0.813832452
    99    16.4804805 0.533136217 0.244049958 0.822222477
    100   16.6486486 0.538576383 0.246540264 0.830612502
    101   16.8168168 0.544016548 0.249030569 0.839002527
    102   16.9849850 0.549456714 0.251520875 0.847392553
    103   17.1531532 0.554896879 0.254011181 0.855782578
    104   17.3213213 0.560337045 0.256501486 0.864172603
    105   17.4894895 0.565777210 0.258991792 0.872562628
    106   17.6576577 0.571217376 0.261482098 0.880952654
    107   17.8258258 0.576657541 0.263972403 0.889342679
    108   17.9939940 0.582097707 0.266462709 0.897732704
    109   18.1621622 0.587537872 0.268953015 0.906122730
    110   18.3303303 0.592978038 0.271443320 0.914512755
    111   18.4984985 0.598418203 0.273933626 0.922902780
    112   18.6666667 0.603858369 0.276423932 0.931292805
    113   18.8348348 0.609298534 0.278914238 0.939682831
    114   19.0030030 0.614738700 0.281404543 0.948072856
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    993  166.8228228 5.396644159 2.470383247 8.322905071
    994  166.9909910 5.402084324 2.472873552 8.331295096
    995  167.1591592 5.407524490 2.475363858 8.339685122
    996  167.3273273 5.412964655 2.477854164 8.348075147
    997  167.4954955 5.418404821 2.480344469 8.356465172
    998  167.6636637 5.423844986 2.482834775 8.364855197
    999  167.8318318 5.429285152 2.485325081 8.373245223
    1000 168.0000000 5.434725317 2.487815387 8.381635248
    
    test_rateReg.R................   38 tests 4 fails 0.7s
    
    test_simEvent.R...............    1 tests OK 
    test_simEvent.R...............    2 tests OK 
    test_simEvent.R...............    3 tests OK 
    test_simEvent.R...............    4 tests OK 
    test_simEvent.R...............    5 tests OK 
    test_simEvent.R...............    6 tests OK 
    test_simEvent.R...............    7 tests OK 
    test_simEvent.R...............    8 tests OK 
    test_simEvent.R...............    9 tests OK 
    test_simEvent.R...............   10 tests OK 
    test_simEvent.R...............   11 tests OK 
    test_simEvent.R...............   12 tests OK 
    test_simEvent.R...............   13 tests OK 
    test_simEvent.R...............   14 tests OK 
    test_simEvent.R...............   15 tests OK 
    test_simEvent.R...............   16 tests OK 
    test_simEvent.R...............   17 tests OK 
    test_simEvent.R...............   18 tests OK 
    test_simEvent.R...............   19 tests OK 
    test_simEvent.R...............   19 tests OK 'simEvent' S4 class object:
    [1] 0.2668173 0.3422368 0.9858833
    
    test_simEvent.R...............   20 tests OK 
    test_simEvent.R...............   21 tests OK 
    test_simEvent.R...............   22 tests OK 
    test_simEvent.R...............   23 tests OK 
    test_simEvent.R...............   24 tests OK 
    test_simEvent.R...............   25 tests OK 
    test_simEvent.R...............   26 tests OK 
    test_simEvent.R...............   27 tests OK 
    test_simEvent.R...............   28 tests OK 
    test_simEvent.R...............   29 tests OK 
    test_simEvent.R...............   30 tests OK 
    test_simEvent.R...............   31 tests OK 
    test_simEvent.R...............   32 tests OK 
    test_simEvent.R...............   33 tests OK 59ms
    ----- FAILED[data]: test_mcfDiff.R<55--57>
     call| expect_equal(class(plot(mcfDiff(mcf0, testVariance = "none"), 
     call| -->    addOrigin = TRUE)), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[data]: test_rateReg.R<121--122>
     call| expect_equivalent(class(plot(br_constFit, conf.int = TRUE)), 
     call| -->    c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[data]: test_rateReg.R<146--148>
     call| expect_equivalent(class(plot(mcf_constFit, conf.int = TRUE, lty = 2, 
     call| -->    col = "red")), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[data]: test_rateReg.R<149--151>
     call| expect_equivalent(class(plot(mcf_splineFit, conf.int = TRUE, 
     call| -->    lty = 1:4, col = 1:4)), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    ----- FAILED[data]: test_rateReg.R<152--152>
     call| expect_equivalent(class(plot(mcf_splineFit)), c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    Error: 5 out of 191 tests failed
    In addition: There were 16 warnings (use warnings() to see them)
    Execution halted

Package: rempsyc
Check: examples
New result: ERROR
  Running examples in ‘rempsyc-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: nice_normality
  > ### Title: Easy normality check per group
  > ### Aliases: nice_normality
  > ### Keywords: QQ density distribution normality plots
  > 
  > ### ** Examples
  > 
  > ## Don't show: 
  > if (requireNamespace("ggplot2", quietly = TRUE) && requireNamespace("see", quietly = TRUE) && requireNamespace("patchwork", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
  + ## End(Don't show)
  + # Make the basic plot
  + nice_normality(
  +   data = iris,
  +   variable = "Sepal.Length",
  +   group = "Species"
  + )
  + 
  + # Further customization
  + nice_normality(
  +   data = iris,
  +   variable = "Sepal.Length",
  +   group = "Species",
  +   colours = c(
  +     "#00BA38",
  +     "#619CFF",
  +     "#F8766D"
  +   ),
  +   groups.labels = c(
  +     "(a) Setosa",
  +     "(b) Versicolor",
  +     "(c) Virginica"
  +   ),
  +   grid = FALSE,
  +   shapiro = TRUE
  + )
  + ## Don't show: 
  + }) # examplesIf
  > nice_normality(data = iris, variable = "Sepal.Length", group = "Species")
  Error in `qqplotr::stat_qq_band()`:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  Backtrace:
       ▆
    1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
    2. │ └─base::source(...)
    3. │   ├─base::print(yy$value)
    4. │   └─patchwork:::print.patchwork(yy$value)
    5. │     └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
    6. │       └─base::lapply(x$plots, plot_table, guides = guides)
    7. │         ├─patchwork (local) FUN(X[[i]], ...)
    8. │         └─patchwork:::plot_table.ggplot(X[[i]], ...)
    9. │           └─ggplot2::ggplotGrob(x)
   10. │             ├─ggplot2::ggplot_gtable(ggplot_build(x))
   11. │             └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
   12. │               └─ggplot2:::by_layer(...)
   13. │                 ├─rlang::try_fetch(...)
   14. │                 │ ├─base::tryCatch(...)
   15. │                 │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   16. │                 │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   17. │                 │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   18. │                 │ └─base::withCallingHandlers(...)
   19. │                 └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   20. │                   └─l$draw_geom(d, layout)
   21. │                     └─ggplot2 (local) draw_geom(..., self = self)
   22. │                       └─self$geom$draw_layer(...)
   23. │                         └─ggplot2 (local) draw_layer(..., self = self)
   24. │                           └─base::lapply(...)
   25. │                             └─ggplot2 (local) FUN(X[[i]], ...)
   26. │                               ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   27. │                               └─self$draw_panel(data, panel_params, coord)
   28. │                                 └─ggplot2 (local) draw_panel(..., self = self)
   29. │                                   └─base::lapply(...)
   30. │                                     └─ggplot2 (local) FUN(X[[i]], ...)
   31. │                                       └─self$draw_group(group, panel_params, coord, ...)
   32. │                                         └─ggplot2 (local) draw_group(...)
   33. │                                           └─ggplot2 (local) draw_group(..., self = self)
   34. └─base::.handleSimpleError(...)
   35.   └─rlang (local) h(simpleError(msg, call))
   36.     └─handlers[[1L]](cnd)
   37.       └─cli::cli_abort(...)
   38.         └─rlang::abort(...)
  Execution halted

Package: rempsyc
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘assumptions.Rmd’ using rmarkdown
  
  Quitting from assumptions.Rmd:134-140 [unnamed-chunk-11]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'assumptions.Rmd' failed with diagnostics:
  Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `check_linewidth()`:
  ! could not find function "check_linewidth"
  --- failed re-building ‘assumptions.Rmd’
  
  --- re-building ‘contrasts.Rmd’ using rmarkdown
  --- finished re-building ‘contrasts.Rmd’
  
  --- re-building ‘moderation.Rmd’ using rmarkdown
  --- finished re-building ‘moderation.Rmd’
  
  --- re-building ‘scatter.Rmd’ using rmarkdown
  --- finished re-building ‘scatter.Rmd’
  
  --- re-building ‘t-test.Rmd’ using rmarkdown
  --- finished re-building ‘t-test.Rmd’
  
  --- re-building ‘table.Rmd’ using rmarkdown
  --- finished re-building ‘table.Rmd’
  
  --- re-building ‘violin.Rmd’ using rmarkdown
  --- finished re-building ‘violin.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘assumptions.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: rempsyc
Check: tests
New result: ERROR
    Running ‘testthat.R’ [16s/17s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(rempsyc)
    Suggested APA citation: Thériault, R. (2023). rempsyc: Convenience functions for psychology. 
    Journal of Open Source Software, 8(87), 5466. https://doi.org/10.21105/joss.05466
    > 
    > test_check("rempsyc")
    Ignoring unknown labels:
    * legend.title : ""
    Ignoring unknown labels:
    * legend.title : ""
    [ FAIL 2 | WARN 0 | SKIP 20 | PASS 44 ]
    
    ══ Skipped tests (20) ══════════════════════════════════════════════════════════
    • On CRAN (20): 'test-best_duplicate.R:8:3', 'test-cormatrix_excel.R:5:3',
      'test-extract_duplicates.R:8:3', 'test-find_mad.R:2:3',
      'test-format_value.R:2:3', 'test-nice_assumptions.R:9:3',
      'test-nice_contrasts.R:7:3', 'test-nice_lm.R:5:3',
      'test-nice_lm_contrasts.R:12:3', 'test-nice_lm_slopes.R:5:3',
      'test-nice_mod.R:4:3', 'test-nice_na.R:2:3', 'test-nice_randomize.R:5:3',
      'test-nice_reverse.R:3:3', 'test-nice_slopes.R:4:3',
      'test-nice_t_test.R:5:3', 'test-nice_table.R:13:3', 'test-nice_var.R:2:3',
      'test-scale_mad.R:2:3', 'test-winsorize_mad.R:2:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-nice_normality.R:15:3'): nice_normality ────────────────────────
    Error in `qqplotr::stat_qq_band()`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `check_linewidth()`:
    ! could not find function "check_linewidth"
    Backtrace:
         ▆
      1. ├─ggplot2::ggsave(...) at test-nice_normality.R:15:3
      2. │ └─base::lapply(plot, grid.draw)
      3. │   ├─grid (local) FUN(X[[i]], ...)
      4. │   └─ggplot2 (local) `grid.draw.ggplot2::ggplot`(X[[i]], ...)
      5. │     ├─base::print(x)
      6. │     └─patchwork:::print.patchwork(x)
      7. │       └─patchwork:::build_patchwork(plot, plot$layout$guides %||% "auto")
      8. │         └─base::lapply(x$plots, plot_table, guides = guides)
      9. │           ├─patchwork (local) FUN(X[[i]], ...)
     10. │           └─patchwork:::plot_table.ggplot(X[[i]], ...)
     11. │             └─ggplot2::ggplotGrob(x)
     12. │               ├─ggplot2::ggplot_gtable(ggplot_build(x))
     13. │               └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(ggplot_build(x))
     14. │                 └─ggplot2:::by_layer(...)
     15. │                   ├─rlang::try_fetch(...)
     16. │                   │ ├─base::tryCatch(...)
     17. │                   │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     18. │                   │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     19. │                   │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     20. │                   │ └─base::withCallingHandlers(...)
     21. │                   └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     22. │                     └─l$draw_geom(d, layout)
     23. │                       └─ggplot2 (local) draw_geom(..., self = self)
     24. │                         └─self$geom$draw_layer(...)
     25. │                           └─ggplot2 (local) draw_layer(..., self = self)
     26. │                             └─base::lapply(...)
     27. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     28. │                                 ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     29. │                                 └─self$draw_panel(data, panel_params, coord)
     30. │                                   └─ggplot2 (local) draw_panel(..., self = self)
     31. │                                     └─base::lapply(...)
     32. │                                       └─ggplot2 (local) FUN(X[[i]], ...)
     33. │                                         └─self$draw_group(group, panel_params, coord, ...)
     34. │                                           └─ggplot2 (local) draw_group(...)
     35. │                                             └─ggplot2 (local) draw_group(..., self = self)
     36. └─base::.handleSimpleError(...)
     37.   └─rlang (local) h(simpleError(msg, call))
     38.     └─handlers[[1L]](cnd)
     39.       └─cli::cli_abort(...)
     40.         └─rlang::abort(...)
    ── Error ('test-nice_qq.R:16:3'): nice_qq ──────────────────────────────────────
    Error in `qqplotr::stat_qq_band()`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `check_linewidth()`:
    ! could not find function "check_linewidth"
    Backtrace:
         ▆
      1. ├─ggplot2::ggsave(...) at test-nice_qq.R:16:3
      2. │ └─base::lapply(plot, grid.draw)
      3. │   ├─grid (local) FUN(X[[i]], ...)
      4. │   └─ggplot2 (local) `grid.draw.ggplot2::ggplot`(X[[i]], ...)
      5. │     ├─base::print(x)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(x)
      7. │       ├─ggplot2::ggplot_gtable(data)
      8. │       └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$draw_geom(d, layout)
     18. │               └─ggplot2 (local) draw_geom(..., self = self)
     19. │                 └─self$geom$draw_layer(...)
     20. │                   └─ggplot2 (local) draw_layer(..., self = self)
     21. │                     └─base::lapply(...)
     22. │                       └─ggplot2 (local) FUN(X[[i]], ...)
     23. │                         ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     24. │                         └─self$draw_panel(data, panel_params, coord)
     25. │                           └─ggplot2 (local) draw_panel(..., self = self)
     26. │                             └─base::lapply(...)
     27. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     28. │                                 └─self$draw_group(group, panel_params, coord, ...)
     29. │                                   └─ggplot2 (local) draw_group(...)
     30. │                                     └─ggplot2 (local) draw_group(..., self = self)
     31. └─base::.handleSimpleError(...)
     32.   └─rlang (local) h(simpleError(msg, call))
     33.     └─handlers[[1L]](cnd)
     34.       └─cli::cli_abort(...)
     35.         └─rlang::abort(...)
    
    [ FAIL 2 | WARN 0 | SKIP 20 | PASS 44 ]
    Error: Test failures
    Execution halted

Package: rmweather
Check: tests
New result: ERROR
    Running ‘testthat.R’ [10s/10s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(dplyr)
    
    Attaching package: 'dplyr'
    
    The following object is masked from 'package:testthat':
    
        matches
    
    The following objects are masked from 'package:stats':
    
        filter, lag
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, setequal, union
    
    > library(rmweather)
    > 
    > test_check("rmweather")
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 40 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_02_rmw_functions.R:83:3'): Test training function ────────────
    class(rmw_plot_importance(df_importance)) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_02_rmw_functions.R:90:3'): Test training function ────────────
    class(plot_test) not identical to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 40 ]
    Error: Test failures
    Execution halted

Package: robCompositions
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘robCompositions’
  See ‘/home/hornik/tmp/CRAN_recheck/robCompositions.Rcheck/00install.out’ for details.
  Used C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
  Used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’

Package: robustbase
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘fastMcd-kmini.Rnw’ using Sweave
  Loading required package: robustbase
  --- finished re-building ‘fastMcd-kmini.Rnw’
  
  --- re-building ‘lmrob_simulation.Rnw’ using Sweave
  Loading required package: xtable
  Loading required package: robustbase
  Loading required package: ggplot2
  Loading required package: GGally
  Loading required package: grid
  Loading required package: reshape2
  
  Error: processing vignette 'lmrob_simulation.Rnw' failed with diagnostics:
   chunk 2 (label = graphics-setup) 
  Error : is.list(theme_G <- theme$panel.grid.major %||% theme$panel.grid) is not TRUE
  
  --- failed re-building ‘lmrob_simulation.Rnw’
  
  --- re-building ‘psi_functions.Rnw’ using Sweave
  Loading required package: robustbase
  --- finished re-building ‘psi_functions.Rnw’
  
  SUMMARY: processing the following file failed:
    ‘lmrob_simulation.Rnw’
  
  Error: Vignette re-building failed.
  Execution halted

Package: RSDA
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘RSDA’

Package: RTIGER
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘RTIGER’

Package: RVA
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘RVA.Rmd’ using rmarkdown
  
  Quitting from RVA.Rmd:179-181 [unnamed-chunk-15]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `S7::prop(x, "meta")[[i]]`:
  ! subscript out of bounds
  ---
  Backtrace:
      ▆
   1. ├─knitr::kable(head(cutoff.result.list[[1]]))
   2. ├─utils::head(cutoff.result.list[[1]])
   3. ├─cutoff.result.list[[1]]
   4. └─ggplot2 (local) `[[.ggplot2::gg`(cutoff.result.list, 1)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'RVA.Rmd' failed with diagnostics:
  subscript out of bounds
  --- failed re-building ‘RVA.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘RVA.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: RVenn
Check: tests
New result: ERROR
    Running ‘testthat.R’ [6s/6s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(RVenn)
    > 
    > test_check("RVenn")
    [ FAIL 4 | WARN 1 | SKIP 0 | PASS 31 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_ggvenn.R:9:3'): ggvenn: plot for 2 and 3 sets ────────────────
    class(g1) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_ggvenn.R:10:3'): ggvenn: plot for 2 and 3 sets ───────────────
    class(g2) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_ggvenn.R:16:3'): ggvenn: slices ──────────────────────────────
    class(ggvenn(v1, slice = c(2, 4))) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test_ggvenn.R:17:3'): ggvenn: slices ──────────────────────────────
    class(ggvenn(v1, slice = c("A", "B", "C"))) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 4 | WARN 1 | SKIP 0 | PASS 31 ]
    Error: Test failures
    Execution halted

Package: Rwtss
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [5s/6s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(Rwtss)
    Rwtss - R interface to Web Time Series Service.
    Loaded Rwtss v0.9.2.
            See ?Rwtss for help, citation("Rwtss") for use in publication.
            See demo(package = "Rwtss") for examples.
    > 
    > test_check("Rwtss")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_wtss.R:60:9'): Plot ──────────────────────────────────────────
    unname(summary(g)[1, 2]) == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    Backtrace:
        ▆
     1. ├─vcr::use_cassette(...) at test_wtss.R:53:5
     2. │ └─base::withCallingHandlers(...)
     3. └─testthat::expect_true(unname(summary(g)[1, 2]) == "gg") at test_wtss.R:60:9
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 57 ]
    Error: Test failures
    In addition: Warning message:
    `check_cassette_names()` was deprecated in vcr 2.0.0. 
    Execution halted

Package: saros
Check: examples
New result: ERROR
  Running examples in ‘saros-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: girafe
  > ### Title: Pull global plotting settings before displaying plot
  > ### Aliases: girafe
  > 
  > ### ** Examples
  > 
  > plot <- makeme(data = ex_survey, dep = b_1)
  Warning in fortify(data, ...) : Arguments in `...` must be used.
  ✖ Problematic argument:
  • cumulative = TRUE
  ℹ Did you misspell an argument name?
  Warning in (function (title = waiver(), theme = NULL, position = NULL, direction = NULL,  :
    Arguments in `...` must be used.
  ✖ Problematic argument:
  • data_id = "fill.guide"
  ℹ Did you misspell an argument name?
  > girafe(plot)
  Error:
  ! Problem while converting geom to grob.
  ℹ Error occurred in the 1st layer.
  Caused by error in `draw_panel()`:
  ! unused arguments (lineend = "butt", linejoin = "mitre")
  Backtrace:
       ▆
    1. ├─saros::girafe(plot)
    2. │ └─ggiraph::girafe(...)
    3. │   ├─base::tryCatch(...)
    4. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5. │   ├─base::print(ggobj)
    6. │   └─ggplot2 (local) `print.ggplot2::ggplot`(ggobj)
    7. │     ├─ggplot2::ggplot_gtable(data)
    8. │     └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    9. │       └─ggplot2:::by_layer(...)
   10. │         ├─rlang::try_fetch(...)
   11. │         │ ├─base::tryCatch(...)
   12. │         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   13. │         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   14. │         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   15. │         │ └─base::withCallingHandlers(...)
   16. │         └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   17. │           └─l$draw_geom(d, layout)
   18. │             └─ggplot2 (local) draw_geom(..., self = self)
   19. │               └─self$geom$draw_layer(...)
   20. │                 └─ggplot2 (local) draw_layer(..., self = self)
   21. │                   └─base::lapply(...)
   22. │                     └─ggplot2 (local) FUN(X[[i]], ...)
   23. │                       ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   24. │                       └─self$draw_panel(...)
   25. └─base::.handleSimpleError(...)
   26.   └─rlang (local) h(simpleError(msg, call))
   27.     └─handlers[[1L]](cnd)
   28.       └─cli::cli_abort(...)
   29.         └─rlang::abort(...)
  Execution halted

Package: saros
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [24s/16s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(saros)
    > 
    > testthat::test_check("saros")
    Starting 2 test processes
    [ FAIL 1 | WARN 2 | SKIP 0 | PASS 224 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-make_content.cat_plot_html.R:2:5'): show.legend works with unused categories ──
    Error in `(function (mapping = NULL, data = NULL, stat = "identity", position = "stack", 
        ..., just = 0.5, lineend = "butt", linejoin = "mitre", na.rm = FALSE, 
        show.legend = NA, inherit.aes = TRUE) 
    {
        layer(mapping = mapping, data = data, geom = "col", stat = stat, 
            position = position, show.legend = show.legend, inherit.aes = inherit.aes, 
            params = list2(na.rm = na.rm, just = just, lineend = lineend, 
                linejoin = linejoin, ...))
    })(mapping = structure(list(), class = c("ggplot2::mapping", 
    "uneval", "gg", "S7_object"), S7_class = structure(function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, name = "mapping", parent = structure(list(class = "gg", constructor = function (.data) 
    {
        stop(sprintf("S3 class <%s> doesn't have a constructor", 
            class[[1]]), call. = FALSE)
    }, validator = NULL), class = "S7_S3_class"), package = "ggplot2", properties = list(), abstract = FALSE, constructor = function (x = list(), 
        ..., env = globalenv()) 
    {
        warn_dots_empty()
        check_object(x, is.list, "a {.cls list}")
        x <- lapply(x, new_aesthetic, env = env)
        x <- S7::new_object(x)
        class(x) <- union(c("ggplot2::mapping", "uneval"), class(x))
        x
    }, class = c("S7_class", "S7_object")), names = character(0)), 
        position = <environment>, na.rm = TRUE, show.legend = TRUE)`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `draw_panel()`:
    ! unused arguments (lineend = "butt", linejoin = "mitre")
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-make_content.cat_plot_html.R:2:5
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_gtable(data)
      8. │       └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$draw_geom(d, layout)
     18. │               └─ggplot2 (local) draw_geom(..., self = self)
     19. │                 └─self$geom$draw_layer(...)
     20. │                   └─ggplot2 (local) draw_layer(..., self = self)
     21. │                     └─base::lapply(...)
     22. │                       └─ggplot2 (local) FUN(X[[i]], ...)
     23. │                         ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     24. │                         └─self$draw_panel(...)
     25. └─base::.handleSimpleError(...)
     26.   └─rlang (local) h(simpleError(msg, call))
     27.     └─handlers[[1L]](cnd)
     28.       └─cli::cli_abort(...)
     29.         └─rlang::abort(...)
    
    [ FAIL 1 | WARN 2 | SKIP 0 | PASS 224 ]
    Error: Test failures
    Execution halted

Package: scCustomize
Check: examples
New result: ERROR
  Running examples in ‘scCustomize-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: Plot_Median_Genes
  > ### Title: Plot Median Genes per Cell per Sample
  > ### Aliases: Plot_Median_Genes
  > 
  > ### ** Examples
  > 
  > library(Seurat)
  > # Create example groups
  > pbmc_small$sample_id <- sample(c("sample1", "sample2"), size = ncol(pbmc_small), replace = TRUE)
  > 
  > # Plot
  > Plot_Median_Genes(seurat_object = pbmc_small, sample_col = "orig.ident",  group_by = "sample_id")
  Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
  ℹ Please use the `linewidth` argument instead.
  ℹ The deprecated feature was likely used in the ggprism package.
    Please report the issue at <https://github.com/csdaw/ggprism/issues>.
  Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
  ℹ Please use the `linewidth` argument instead.
  ℹ The deprecated feature was likely used in the ggprism package.
    Please report the issue at <https://github.com/csdaw/ggprism/issues>.
  Error in `parent %+replace% t`:
  ! `%+replace%` requires two theme objects
  Backtrace:
      ▆
   1. └─scCustomize::Plot_Median_Genes(...)
   2.   └─scCustomize::theme_ggprism_mod()
   3.     ├─... %+replace% ...
   4.     │ └─ggplot2::is_theme(e1)
   5.     │   └─S7::S7_inherits(x, class_theme)
   6.     └─ggprism::theme_prism(...)
   7.       └─parent %+replace% t
   8.         └─cli::cli_abort("{.code %+replace%} requires two theme objects")
   9.           └─rlang::abort(...)
  Execution halted

Package: scoringutils
Check: examples
New result: ERROR
  Running examples in ‘scoringutils-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: get_pit_histogram.forecast_quantile
  > ### Title: Probability integral transformation histogram
  > ### Aliases: get_pit_histogram.forecast_quantile
  > ###   get_pit_histogram.forecast_sample get_pit_histogram
  > ###   get_pit_histogram.default
  > ### Keywords: scoring
  > 
  > ### ** Examples
  > 
  > library("ggplot2")
  > 
  > result <- get_pit_histogram(example_sample_continuous, by = "model")
  > ggplot(result,  aes(x = mid, y = density)) +
  +   geom_col() +
  +   facet_wrap(. ~ model) +
  +   labs(x = "Quantile", "Density")
  Error: <ggplot2::labels> object is invalid:
  - every label must be named.
  Execution halted

Package: SCpubr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [145s/146s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # nolint start
    > library(testthat)
    > library(SCpubr)
    
    
    ── SCpubr 2.0.2 ────────────────────────────────────────────────────────────────
    
    ℹ Have a look at extensive tutorials in SCpubr's book.
    
    ✔ If you use SCpubr in your research, please cite it accordingly.
    
    ★ If the package is useful to you, consider leaving a Star in the GitHub repository.
    
    ! Keep track of the package updates on Twitter (@Enblacar) or in the Official NEWS website.
    
    ♥ Happy plotting!
    
    
    
    ── Tips! ──
    
    ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
    
    ✖ To suppress this startup message, use: suppressPackageStartupMessages(library(SCpubr))
    ✖ Alternatively, you can also set the following option: options("SCpubr.verbose" = FALSE)
      And then load the package normally (and faster) as: library(SCpubr)
    
    ────────────────────────────────────────────────────────────────────────────────
    > # nolint end
    > test_check("SCpubr")
    
    
    [ FAIL 58 | WARN 16 | SKIP 391 | PASS 29 ]
    
    ══ Skipped tests (391) ═════════════════════════════════════════════════════════
    • On CRAN (391): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
      'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
      'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
      'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
      'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
      'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
      'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
      'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
      'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
      'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
      'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
      'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
      'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
      'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
      'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
      'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
      'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
      'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
      'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
      'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
      'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
      'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
      'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
      'test-do_CellularStatesPlot.R:50:5', 'test-do_CellularStatesPlot.R:78:5',
      'test-do_CellularStatesPlot.R:152:5', 'test-do_CellularStatesPlot.R:284:5',
      'test-do_CellularStatesPlot.R:305:5', 'test-do_CellularStatesPlot.R:327:5',
      'test-do_CellularStatesPlot.R:349:5', 'test-do_CellularStatesPlot.R:415:5',
      'test-do_CellularStatesPlot.R:436:5', 'test-do_CellularStatesPlot.R:458:5',
      'test-do_CellularStatesPlot.R:478:5', 'test-do_CellularStatesPlot.R:499:5',
      'test-do_CellularStatesPlot.R:519:5', 'test-do_CellularStatesPlot.R:539:5',
      'test-do_CellularStatesPlot.R:559:5', 'test-do_CellularStatesPlot.R:580:5',
      'test-do_CellularStatesPlot.R:598:5', 'test-do_CellularStatesPlot.R:616:5',
      'test-do_CellularStatesPlot.R:634:5', 'test-do_CellularStatesPlot.R:653:5',
      'test-do_CellularStatesPlot.R:683:5', 'test-do_CellularStatesPlot.R:705:5',
      'test-do_CellularStatesPlot.R:727:5', 'test-do_CellularStatesPlot.R:746:5',
      'test-do_CellularStatesPlot.R:765:5', 'test-do_CellularStatesPlot.R:784:5',
      'test-do_CellularStatesPlot.R:803:5', 'test-do_CellularStatesPlot.R:835:5',
      'test-do_CellularStatesPlot.R:858:5', 'test-do_CellularStatesPlot.R:882:5',
      'test-do_CellularStatesPlot.R:902:5', 'test-do_CellularStatesPlot.R:922:5',
      'test-do_CellularStatesPlot.R:942:5', 'test-do_CellularStatesPlot.R:962:5',
      'test-do_CellularStatesPlot.R:982:5', 'test-do_ChordDiagramPlot.R:19:5',
      'test-do_ChordDiagramPlot.R:49:5', 'test-do_ChordDiagramPlot.R:150:5',
      'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
      'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
      'test-do_CopyNumberVariantPlot.R:74:5',
      'test-do_CopyNumberVariantPlot.R:83:5',
      'test-do_CopyNumberVariantPlot.R:96:5',
      'test-do_CopyNumberVariantPlot.R:109:5',
      'test-do_CopyNumberVariantPlot.R:130:5', 'test-do_CorrelationPlot.R:16:5',
      'test-do_CorrelationPlot.R:34:5', 'test-do_CorrelationPlot.R:58:5',
      'test-do_CorrelationPlot.R:70:5', 'test-do_DimPlot.R:19:5',
      'test-do_DimPlot.R:27:5', 'test-do_DimPlot.R:134:5',
      'test-do_DimPlot.R:170:5', 'test-do_DimPlot.R:191:5',
      'test-do_DimPlot.R:211:5', 'test-do_DimPlot.R:246:5',
      'test-do_DimPlot.R:258:5', 'test-do_DimPlot.R:268:5',
      'test-do_DimPlot.R:278:5', 'test-do_DimPlot.R:298:5',
      'test-do_DimPlot.R:307:5', 'test-do_DimPlot.R:316:5',
      'test-do_DimPlot.R:325:5', 'test-do_DimPlot.R:334:5',
      'test-do_DimPlot.R:341:5', 'test-do_DimPlot.R:352:5',
      'test-do_DimPlot.R:360:5', 'test-do_DimPlot.R:368:5',
      'test-do_DimPlot.R:376:5', 'test-do_DimPlot.R:384:5',
      'test-do_DimPlot.R:392:5', 'test-do_DimPlot.R:400:5',
      'test-do_DimPlot.R:424:5', 'test-do_DimPlot.R:432:5',
      'test-do_DimPlot.R:440:5', 'test-do_DimPlot.R:448:5',
      'test-do_DimPlot.R:456:5', 'test-do_DimPlot.R:463:5',
      'test-do_DimPlot.R:470:5', 'test-do_DimPlot.R:477:5',
      'test-do_DimPlot.R:484:5', 'test-do_DimPlot.R:501:5',
      'test-do_DimPlot.R:509:5', 'test-do_DimPlot.R:517:5',
      'test-do_DimPlot.R:524:5', 'test-do_DimPlot.R:531:5',
      'test-do_DimPlot.R:538:5', 'test-do_DimPlot.R:546:5',
      'test-do_DimPlot.R:557:5', 'test-do_DimPlot.R:566:5',
      'test-do_DimPlot.R:575:5', 'test-do_DimPlot.R:585:5',
      'test-do_DimPlot.R:596:5', 'test-do_DimPlot.R:605:5',
      'test-do_DimPlot.R:614:5', 'test-do_DotPlot.R:16:5',
      'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
      'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
      'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
      'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
      'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
      'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
      'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
      'test-do_DotPlot.R:295:5', 'test-do_EnrichmentHeatmap.R:19:5',
      'test-do_EnrichmentHeatmap.R:193:5', 'test-do_EnrichmentHeatmap.R:224:5',
      'test-do_EnrichmentHeatmap.R:241:5', 'test-do_EnrichmentHeatmap.R:275:5',
      'test-do_EnrichmentHeatmap.R:314:5', 'test-do_EnrichmentHeatmap.R:337:5',
      'test-do_EnrichmentHeatmap.R:356:5', 'test-do_ExpressionHeatmap.R:12:5',
      'test-do_ExpressionHeatmap.R:150:5', 'test-do_ExpressionHeatmap.R:168:5',
      'test-do_ExpressionHeatmap.R:186:5', 'test-do_ExpressionHeatmap.R:215:5',
      'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:24:5',
      'test-do_FeaturePlot.R:429:5', 'test-do_FeaturePlot.R:470:5',
      'test-do_FeaturePlot.R:577:5', 'test-do_FeaturePlot.R:598:5',
      'test-do_FeaturePlot.R:616:5', 'test-do_FeaturePlot.R:633:5',
      'test-do_FeaturePlot.R:642:5', 'test-do_FeaturePlot.R:652:5',
      'test-do_FeaturePlot.R:662:5', 'test-do_FeaturePlot.R:672:5',
      'test-do_FeaturePlot.R:682:5', 'test-do_FeaturePlot.R:692:5',
      'test-do_FeaturePlot.R:702:5', 'test-do_FeaturePlot.R:712:5',
      'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
      'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
      'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
      'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
      'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
      'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
      'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
      'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
      'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
      'test-do_FeaturePlot.R:925:5', 'test-do_FeaturePlot.R:937:5',
      'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
      'test-do_FeaturePlot.R:970:5', 'test-do_FeaturePlot.R:978:5',
      'test-do_FeaturePlot.R:987:5', 'test-do_FunctionalAnnotationPlot.R:15:5',
      'test-do_GeyserPlot.R:18:5', 'test-do_GeyserPlot.R:64:5',
      'test-do_GeyserPlot.R:93:5', 'test-do_GeyserPlot.R:154:5',
      'test-do_GeyserPlot.R:170:5', 'test-do_GeyserPlot.R:189:5',
      'test-do_GeyserPlot.R:208:5', 'test-do_GeyserPlot.R:225:5',
      'test-do_GeyserPlot.R:242:5', 'test-do_GeyserPlot.R:262:5',
      'test-do_GeyserPlot.R:280:5', 'test-do_GeyserPlot.R:293:5',
      'test-do_GroupedGOTermPlot.R:16:5', 'test-do_GroupwiseDEPlot.R:26:5',
      'test-do_GroupwiseDEPlot.R:111:5', 'test-do_GroupwiseDEPlot.R:139:5',
      'test-do_GroupwiseDEPlot.R:165:5', 'test-do_GroupwiseDEPlot.R:189:5',
      'test-do_NebulosaPlot.R:19:5', 'test-do_NebulosaPlot.R:102:5',
      'test-do_NebulosaPlot.R:112:5', 'test-do_NebulosaPlot.R:122:5',
      'test-do_NebulosaPlot.R:134:5', 'test-do_NebulosaPlot.R:143:5',
      'test-do_NebulosaPlot.R:152:5', 'test-do_NebulosaPlot.R:161:5',
      'test-do_NebulosaPlot.R:171:5', 'test-do_NebulosaPlot.R:185:5',
      'test-do_NebulosaPlot.R:194:5', 'test-do_NebulosaPlot.R:204:5',
      'test-do_NebulosaPlot.R:215:5', 'test-do_NebulosaPlot.R:227:5',
      'test-do_NebulosaPlot.R:239:5', 'test-do_NebulosaPlot.R:252:5',
      'test-do_NebulosaPlot.R:262:5', 'test-do_NebulosaPlot.R:272:5',
      'test-do_NebulosaPlot.R:282:5', 'test-do_NebulosaPlot.R:292:5',
      'test-do_NebulosaPlot.R:302:5', 'test-do_NebulosaPlot.R:314:5',
      'test-do_PathwayActivityPlot.R:12:5', 'test-do_PathwayActivityPlot.R:66:5',
      'test-do_PathwayActivityPlot.R:78:5', 'test-do_PathwayActivityPlot.R:117:5',
      'test-do_RidgePlot.R:41:5', 'test-do_RidgePlot.R:137:5',
      'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
      'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
      'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
      'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
      'test-do_TFActivityPlot.R:72:5', 'test-do_TFActivityPlot.R:85:5',
      'test-do_TFActivityPlot.R:99:5', 'test-do_TermEnrichmentPlot.R:11:5',
      'test-do_TermEnrichmentPlot.R:24:5', 'test-do_TermEnrichmentPlot.R:31:5',
      'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
      'test-do_TermEnrichmentPlot.R:56:5', 'test-do_ViolinPlot.R:10:5',
      'test-do_ViolinPlot.R:25:5', 'test-do_ViolinPlot.R:37:5',
      'test-do_ViolinPlot.R:49:5', 'test-do_ViolinPlot.R:65:5',
      'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
      'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
      'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
      'test-do_ViolinPlot.R:170:5', 'test-do_ViolinPlot.R:182:5',
      'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
      'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
      'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
      'test-do_ViolinPlot.R:304:5', 'test-do_VolcanoPlot.R:12:5',
      'test-do_VolcanoPlot.R:39:5', 'test-do_VolcanoPlot.R:49:5',
      'test-do_VolcanoPlot.R:64:5', 'test-do_VolcanoPlot.R:79:5',
      'test-do_VolcanoPlot.R:102:5', 'test-utils.R:4:5', 'test-utils.R:9:5',
      'test-utils.R:14:5', 'test-utils.R:19:5', 'test-utils.R:30:5',
      'test-utils.R:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
      'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
      'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
      'test-utils.R:107:5', 'test-utils.R:123:5', 'test-utils.R:134:5',
      'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
      'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
      'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
      'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
      'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
      'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
      'test-utils.R:318:5', 'test-utils.R:329:5', 'test-utils.R:340:5',
      'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
      'test-utils.R:380:5', 'test-utils.R:393:5', 'test-utils.R:400:5',
      'test-utils.R:410:5', 'test-utils.R:421:5', 'test-utils.R:427:5',
      'test-utils.R:437:5', 'test-utils.R:446:5', 'test-utils.R:461:5',
      'test-utils.R:468:5', 'test-utils.R:475:5', 'test-utils.R:482:5',
      'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
      'test-utils.R:518:5', 'test-utils.R:525:5', 'test-utils.R:535:5',
      'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
      'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
      'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
      'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
      'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
      'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
      'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
      'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
      'test-utils.R:843:5', 'test-utils.R:850:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-do_AlluvialPlot.R:9:5'): do_AlluvialPlot: CRAN essential tests ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:82:5'): do_AlluvialPlot: factors ───────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:92:5'): do_AlluvialPlot: factors ───────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:102:5'): do_AlluvialPlot: geom_flow ────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:110:5'): do_AlluvialPlot: geom_flow ────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:122:5'): do_AlluvialPlot: stratum.fill.conditional ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:131:5'): do_AlluvialPlot: stratum.fill.conditional ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:142:5'): do_AlluvialPlot: use_viridis ──────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:151:5'): do_AlluvialPlot: use_viridis ──────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:161:5'): do_AlluvialPlot: colors.use ───────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:180:5'): do_AlluvialPlot: test_numbers ─────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:190:5'): do_AlluvialPlot: test_numbers ─────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:201:5'): do_AlluvialPlot: test_numbers ─────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:213:5'): do_AlluvialPlot: test_numbers ─────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:226:5'): do_AlluvialPlot: test_numbers ─────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:240:5'): do_AlluvialPlot: test_numbers ─────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_AlluvialPlot.R:255:5'): do_AlluvialPlot: test_numbers ─────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_BarPlot.R:9:5'): do_BarPlot: CRAN essential tests ─────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_BarPlot.R:16:5'): do_BarPlot: CRAN essential tests ────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_BarPlot.R:22:5'): do_BarPlot: CRAN essential tests ────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_BeeSwarmPlot.R:8:5'): do_BeeSwarmPlot: CRAN essentials ────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_BeeSwarmPlot.R:14:5'): do_BeeSwarmPlot: CRAN essentials ───
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_BoxPlot.R:6:5'): do_BoxPlot: CRAN essentials ──────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_BoxPlot.R:13:5'): do_BoxPlot: CRAN essentials ─────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_BoxPlot.R:18:5'): do_BoxPlot: CRAN essentials ─────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_CellularStatesPlot.R:19:5'): do_CellularStatesPlot: CRAN essentials ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_ColorPalette.R:41:5'): do_BarPlot: PASS - color vectors plot = TRUERUE ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_ColorPalette.R:44:5'): do_BarPlot: PASS - color vectors plot = TRUERUE ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_ColorPalette.R:47:5'): do_BarPlot: PASS - color vectors plot = TRUERUE ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_ColorPalette.R:50:5'): do_BarPlot: PASS - color vectors plot = TRUERUE ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_ColorPalette.R:53:5'): do_BarPlot: PASS - color vectors plot = TRUERUE ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_ColorPalette.R:56:5'): do_BarPlot: PASS - color vectors plot = TRUERUE ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_ColorPalette.R:59:5'): do_BarPlot: PASS - color vectors plot = TRUERUE ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_CopyNumberVariantPlot.R:8:5'): do_BarPlot: CRAN essentials ──
    `out` has type 'object', not 'list'.
    ── Failure ('test-do_DimPlot.R:5:5'): do_DimPlot: CRAN essentials ──────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_DimPlot.R:8:5'): do_DimPlot: CRAN essentials ──────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_DimPlot.R:11:5'): do_DimPlot: CRAN essentials ─────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_DimPlot.R:15:5'): do_DimPlot: CRAN essentials ─────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_DotPlot.R:7:5'): do_DotPlot: CRAN essentials ──────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_DotPlot.R:12:5'): do_DotPlot: CRAN essentials ─────────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_FeaturePlot.R:6:5'): do_FeaturePlot: CRAN essential ───────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_FeaturePlot.R:11:5'): do_FeaturePlot: CRAN essential ──────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_FunctionalAnnotationPlot.R:10:5'): do_FunctionalAnnotationPlot: CRAN essential tests ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_GeyserPlot.R:7:5'): do_GeyserPlot: CRAN essentials ────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_GeyserPlot.R:13:5'): do_GeyserPlot: CRAN essentials ───────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_GroupedGOTermPlot.R:11:5'): do_GroupedGOTermPlot: CRAN essential tests ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_GroupwiseDEPlot.R:16:5'): do_GroupwiseDEPlot: CRAN essentials ──
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_GroupwiseDEPlot.R:22:5'): do_GroupwiseDEPlot: CRAN essentials ──
    `p` has type 'object', not 'list'.
    ── Error ('test-do_NebulosaPlot.R:3:5'): do_NebulosaPlot: CRAN essentials ──────
    <subscriptOutOfBoundsError/error/condition>
    Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
    Backtrace:
        ▆
     1. └─SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1") at test-do_NebulosaPlot.R:3:5
     2.   ├─`*tmp*`[[counter]]
     3.   └─ggplot2 (local) `[[.ggplot2::gg`(`*tmp*`, counter)
    ── Failure ('test-do_PathwayActivityPlot.R:7:5'): do_PathwayActivityPlot: CRAN essentials ──
    `out` has type 'object', not 'list'.
    ── Failure ('test-do_RidgePlot.R:7:5'): do_RidgePlot: CRAN essentials ──────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_RidgePlot.R:14:5'): do_RidgePlot: CRAN essentials ─────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_RidgePlot.R:21:5'): do_RidgePlot: CRAN essentials ─────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_RidgePlot.R:29:5'): do_RidgePlot: CRAN essentials ─────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_RidgePlot.R:36:5'): do_RidgePlot: CRAN essentials ─────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_TFActivityPlot.R:6:5'): do_TFActivityPlot: PASS - minimal input ──
    `out` has type 'object', not 'list'.
    ── Failure ('test-do_ViolinPlot.R:6:5'): do_ViolinPlot: CRAN essentials ────────
    `p` has type 'object', not 'list'.
    ── Failure ('test-do_VolcanoPlot.R:8:5'): do_VolcanoPlot: CRAN essentials ──────
    `p` has type 'object', not 'list'.
    
    [ FAIL 58 | WARN 16 | SKIP 391 | PASS 29 ]
    Error: Test failures
    Execution halted

Package: scrutiny
Check: examples
New result: ERROR
  Running examples in ‘scrutiny-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: debit_plot
  > ### Title: Visualize DEBIT results
  > ### Aliases: debit_plot
  > 
  > ### ** Examples
  > 
  > # Run `debit_plot()` on the output
  > # of `debit_map()`:
  > pigs3 %>%
  +   debit_map() %>%
  +   debit_plot()
  Error: <ggplot2::element_line> object properties are invalid:
  - @colour cannot be a decimal number, but could be an integer.
  - @arrow.fill cannot be a decimal number, but could be an integer.
  Execution halted

Package: scrutiny
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘consistency-tests-in-depth.Rmd’ using rmarkdown
  --- finished re-building ‘consistency-tests-in-depth.Rmd’
  
  --- re-building ‘consistency-tests-simple.Rmd’ using rmarkdown
  --- finished re-building ‘consistency-tests-simple.Rmd’
  
  --- re-building ‘debit.Rmd’ using rmarkdown
  
  Quitting from debit.Rmd:116-124 [unnamed-chunk-8]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::element_line> object properties are invalid:
  - @colour cannot be a decimal number, but could be an integer.
  - @arrow.fill cannot be a decimal number, but could be an integer.
  ---
  Backtrace:
      ▆
   1. ├─pigs3 %>% debit_map() %>% debit_plot()
   2. └─scrutiny::debit_plot(.)
   3.   ├─ggplot2::theme(...)
   4.   │ └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
   5.   │   └─base::mget(args, envir = env)
   6.   └─ggplot2::element_line(seq(0, 0.5, 0.1))
   7.     └─S7::new_object(...)
   8.       └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'debit.Rmd' failed with diagnostics:
  <ggplot2::element_line> object properties are invalid:
  - @colour cannot be a decimal number, but could be an integer.
  - @arrow.fill cannot be a decimal number, but could be an integer.
  --- failed re-building ‘debit.Rmd’
  
  --- re-building ‘devtools.Rmd’ using rmarkdown
  --- finished re-building ‘devtools.Rmd’
  
  --- re-building ‘duplicates.Rmd’ using rmarkdown
  --- finished re-building ‘duplicates.Rmd’
  
  --- re-building ‘grim.Rmd’ using rmarkdown
  --- finished re-building ‘grim.Rmd’
  
  --- re-building ‘grimmer.Rmd’ using rmarkdown
  --- finished re-building ‘grimmer.Rmd’
  
  --- re-building ‘related.Rmd’ using rmarkdown
  --- finished re-building ‘related.Rmd’
  
  --- re-building ‘rounding-in-depth.Rmd’ using rmarkdown
  --- finished re-building ‘rounding-in-depth.Rmd’
  
  --- re-building ‘rounding-options.Rmd’ using rmarkdown
  --- finished re-building ‘rounding-options.Rmd’
  
  --- re-building ‘wrangling.Rmd’ using rmarkdown
  --- finished re-building ‘wrangling.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘debit.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: scrutiny
Check: tests
New result: ERROR
    Running ‘testthat.R’ [60s/60s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > 
    > 
    > library(testthat)
    > library(scrutiny)
    > 
    > test_check("scrutiny")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 523 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-debit-plot.R:3:1'): (code run outside of `test_that()`) ────────
    Error: <ggplot2::element_line> object properties are invalid:
    - @colour cannot be a decimal number, but could be an integer.
    - @arrow.fill cannot be a decimal number, but could be an integer.
    Backtrace:
        ▆
     1. ├─pigs3 %>% debit_map() %>% debit_plot() at test-debit-plot.R:3:1
     2. └─scrutiny::debit_plot(.)
     3.   ├─ggplot2::theme(...)
     4.   │ └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
     5.   │   └─base::mget(args, envir = env)
     6.   └─ggplot2::element_line(seq(0, 0.5, 0.1))
     7.     └─S7::new_object(...)
     8.       └─S7::validate(object, recursive = !parent_validated)
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 523 ]
    Error: Test failures
    Execution halted

Package: scUtils
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(scUtils)
    > 
    > test_check("scUtils")
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plots.R:59:3'): all kinds of colnames are allowed ────────────
    p$labels not equal to list(y = "Dim2", x = "Dim1", colour = "expression").
    Attributes: < names for target but not for current >
    Attributes: < Length mismatch: comparison on first 0 components >
    Length mismatch: comparison on first 2 components
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 32 ]
    Error: Test failures
    Execution halted

Package: SDMtune
Check: tests
New result: ERROR
    Running ‘testthat.R’ [29s/29s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(SDMtune)
    
       _____  ____   __  ___ __
      / ___/ / __ \ /  |/  // /_ __  __ ____   ___
      \__ \ / / / // /|_/ // __// / / // __ \ / _ \
     ___/ // /_/ // /  / // /_ / /_/ // / / //  __/
    /____//_____//_/  /_/ \__/ \__,_//_/ /_/ \___/  version 1.3.2
    
    To cite this package in publications type: citation("SDMtune").
    > 
    > test_check("SDMtune")
    [ FAIL 2 | WARN 0 | SKIP 55 | PASS 315 ]
    
    ══ Skipped tests (55) ══════════════════════════════════════════════════════════
    • On CRAN (55): 'test-ANN-class.R:1:1', 'test-BRT-class.R:1:1',
      'test-Maxent-class.R:3:3', 'test-Maxnet-class.R:3:3', 'test-RF-class.R:1:1',
      'test-SDMmodel-class.R:3:3', 'test-SDMmodel2MaxEnt.R:13:3',
      'test-SDMmodelCV-class.R:3:3', 'test-SDMtune-class.R:42:3',
      'test-SWD-class.R:3:3', 'test-addSamplesToBg.R:22:3', 'test-aicc.R:1:1',
      'test-auc.R:1:1', 'test-checkMaxentInstallation.R:2:3',
      'test-confMatrix.R:1:1', 'test-convertFolds.R:126:3', 'test-corVar.R:4:3',
      'test-doJk.R:1:1', 'test-gridSearch.R:1:1', 'test-maxentTh.R:2:3',
      'test-maxentVarImp.R:2:3', 'test-mergeSWD.R:34:3', 'test-mergeSWD.R:46:3',
      'test-modelReport.R:1:1', 'test-optimizeModel.R:1:1', 'test-plotJk.R:36:3',
      'test-plotPA.R:27:3', 'test-plotPA.R:39:3', 'test-plotPred.R:6:3',
      'test-plotPred.R:26:3', 'test-plotResponse.R:1:1',
      'test-predct-Maxnet.R:1:1', 'test-predict-ANN.R:1:1',
      'test-predict-BRT.R:1:1', 'test-predict-Maxent.R:1:1',
      'test-predict-RF.R:1:1', 'test-predict-SDMmodel.R:1:1',
      'test-predict-SDMmodelCV.R:1:1', 'test-prepareSWD.R:1:1',
      'test-randomFolds.R:4:3', 'test-randomSearch.R:1:1', 'test-reduceVar.R:1:1',
      'test-swd2csv.R:30:3', 'test-thinData.R:1:1', 'test-train.R:1:1',
      'test-trainANN.R:1:1', 'test-trainBRT.R:1:1', 'test-trainMaxent.R:1:1',
      'test-trainMaxnet.R:1:1', 'test-trainRF.R:1:1', 'test-trainValTest.R:4:3',
      'test-tss.R:1:1', 'test-utils.R:1:1', 'test-varImp.R:1:1',
      'test-varSel.R:1:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plotCor.R:5:3'): The plot has the correct labels and text size ──
    p$labels$x (`actual`) not equal to "Var2" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('Var2')
    ── Failure ('test-plotCor.R:6:3'): The plot has the correct labels and text size ──
    p$labels$y (`actual`) not equal to "Var1" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('Var1')
    
    [ FAIL 2 | WARN 0 | SKIP 55 | PASS 315 ]
    Error: Test failures
    Execution halted

Package: seAMLess
Check: examples
New result: ERROR
  Running examples in ‘seAMLess-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ternaryPlot
  > ### Title: Given the immune compositions (ICs) of bulk-RNA samples, this
  > ###   function creates a ternary plot similar to ALOT tube from EuroFlow
  > ###   analysis and Figure 1E of our paper.
  > ### Aliases: ternaryPlot
  > 
  > ### ** Examples
  > 
  > library(seAMLess)
  > 
  > data(minRes)
  > ternaryPlot(minRes)
  Error in loadNamespace(x) : there is no package called ‘ggtern’
  Calls: ternaryPlot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted

Package: see
Check: examples
New result: ERROR
  Running examples in ‘see-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: geom_from_list
  > ### Title: Create ggplot2 geom(s) from a list
  > ### Aliases: geom_from_list geoms_from_list
  > 
  > ### ** Examples
  > 
  > ## Don't show: 
  > if (require("ggside") && require("ggplot2")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
  + ## End(Don't show)
  + library(ggplot2)
  + 
  + # Example 1 (basic geoms and labels) --------------------------
  + l1 <- list(
  +   geom = "point",
  +   data = mtcars,
  +   aes = list(x = "mpg", y = "wt", size = "hp", color = "hp"),
  +   show.legend = c("size" = FALSE)
  + )
  + l2 <- list(
  +   geom = "labs",
  +   title = "A Title"
  + )
  + 
  + ggplot() +
  +   geom_from_list(l1) +
  +   geom_from_list(l2)
  + 
  + ggplot() +
  +   geoms_from_list(list(l1 = l1, l2 = l2))
  + 
  + # Example 2 (Violin, boxplots, ...) --------------------------
  + l1 <- list(
  +   geom = "violin",
  +   data = iris,
  +   aes = list(x = "Species", y = "Sepal.Width")
  + )
  + l2 <- list(
  +   geom = "boxplot",
  +   data = iris,
  +   aes = list(x = "Species", y = "Sepal.Width"),
  +   outlier.shape = NA
  + )
  + l3 <- list(
  +   geom = "jitter",
  +   data = iris,
  +   width = 0.1,
  +   aes = list(x = "Species", y = "Sepal.Width")
  + )
  + 
  + ggplot() +
  +   geom_from_list(l1) +
  +   geom_from_list(l2) +
  +   geom_from_list(l3)
  + 
  + # Example 3 (2D density) --------------------------
  + ggplot() +
  +   geom_from_list(list(
  +     geom = "density_2d", data = iris,
  +     aes = list(x = "Sepal.Width", y = "Petal.Length")
  +   ))
  + ggplot() +
  +   geom_from_list(list(
  +     geom = "density_2d_filled", data = iris,
  +     aes = list(x = "Sepal.Width", y = "Petal.Length")
  +   ))
  + ggplot() +
  +   geom_from_list(list(
  +     geom = "density_2d_polygon", data = iris,
  +     aes = list(x = "Sepal.Width", y = "Petal.Length")
  +   ))
  + ggplot() +
  +   geom_from_list(list(
  +     geom = "density_2d_raster", data = iris,
  +     aes = list(x = "Sepal.Width", y = "Petal.Length")
  +   )) +
  +   scale_x_continuous(expand = c(0, 0)) +
  +   scale_y_continuous(expand = c(0, 0))
  + 
  + # Example 4 (facet and coord flip) --------------------------
  + 
  + ggplot(iris, aes(x = Sepal.Length, y = Petal.Width)) +
  +   geom_point() +
  +   geom_from_list(list(geom = "hline", yintercept = 2)) +
  +   geom_from_list(list(geom = "coord_flip")) +
  +   geom_from_list(list(geom = "facet_wrap", facets = "~ Species", scales = "free"))
  + 
  + # Example 5 (theme and scales) --------------------------
  + ggplot(iris, aes(x = Sepal.Length, y = Petal.Width, color = Species)) +
  +   geom_point() +
  +   geom_from_list(list(geom = "scale_color_viridis_d", option = "inferno")) +
  +   geom_from_list(list(geom = "theme", legend.position = "top"))
  + 
  + ggplot(iris, aes(x = Sepal.Length, y = Petal.Width, color = Species)) +
  +   geom_point() +
  +   geom_from_list(list(geom = "scale_color_material_d", palette = "rainbow")) +
  +   geom_from_list(list(geom = "theme_void"))
  + 
  + # Example 5 (Smooths and side densities) --------------------------
  + 
  + ggplot(iris, aes(x = Sepal.Length, y = Petal.Width)) +
  +   geom_from_list(list(geom = "point")) +
  +   geom_from_list(list(geom = "smooth", color = "red")) +
  +   geom_from_list(list(aes = list(x = "Sepal.Length"), geom = "ggside::geom_xsidedensity")) +
  +   geom_from_list(list(geom = "ggside::scale_xsidey_continuous", breaks = NULL))
  + ## Don't show: 
  + }) # examplesIf
  Loading required package: ggside
  Loading required package: ggplot2
  > library(ggplot2)
  > l1 <- list(geom = "point", data = mtcars, aes = list(x = "mpg", y = "wt", 
  +     size = "hp", color = "hp"), show.legend = c(size = FALSE))
  > l2 <- list(geom = "labs", title = "A Title")
  > ggplot() + geom_from_list(l1) + geom_from_list(l2)
  > ggplot() + geoms_from_list(list(l1 = l1, l2 = l2))
  > l1 <- list(geom = "violin", data = iris, aes = list(x = "Species", y = "Sepal.Width"))
  > l2 <- list(geom = "boxplot", data = iris, aes = list(x = "Species", y = "Sepal.Width"), 
  +     outlier.shape = NA)
  > l3 <- list(geom = "jitter", data = iris, width = 0.1, aes = list(x = "Species", 
  +     y = "Sepal.Width"))
  > ggplot() + geom_from_list(l1) + geom_from_list(l2) + geom_from_list(l3)
  Warning in geom_from_list(l2) :
    Ignoring unknown parameters: `outlier.shape`
  > ggplot() + geom_from_list(list(geom = "density_2d", data = iris, aes = list(x = "Sepal.Width", 
  +     y = "Petal.Length")))
  > ggplot() + geom_from_list(list(geom = "density_2d_filled", data = iris, 
  +     aes = list(x = "Sepal.Width", y = "Petal.Length")))
  > ggplot() + geom_from_list(list(geom = "density_2d_polygon", data = iris, 
  +     aes = list(x = "Sepal.Width", y = "Petal.Length")))
  > ggplot() + geom_from_list(list(geom = "density_2d_raster", data = iris, 
  +     aes = list(x = "Sepal.Width", y = "Petal.Length"))) + scale_x_continuous(expand = c(0, 
  +     0)) + scale_y_continuous(expand = c(0, 0))
  Error in `geom_from_list()`:
  ! Problem while mapping stat to aesthetics.
  ℹ Error occurred in the 1st layer.
  Caused by error:
  ! Aesthetics must be valid computed stats.
  ✖ The following aesthetics are invalid:
  • `fill = after_stat(density)`
  ℹ Did you map your stat in the wrong layer?
  Backtrace:
       ▆
    1. └─(if (getRversion() >= "3.4") withAutoprint else force)(...)
    2.   └─base::source(...)
    3.     ├─base::print(yy$value)
    4.     └─ggplot2 (local) `print.ggplot2::ggplot`(yy$value)
    5.       ├─ggplot2::ggplot_build(x)
    6.       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    7.         └─ggplot2:::by_layer(...)
    8.           ├─rlang::try_fetch(...)
    9.           │ ├─base::tryCatch(...)
   10.           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11.           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12.           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   13.           │ └─base::withCallingHandlers(...)
   14.           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   15.             └─l$map_statistic(d, plot)
   16.               └─ggplot2 (local) map_statistic(..., self = self)
   17.                 └─ggplot2:::check_nondata_cols(...)
   18.                   └─cli::cli_abort(c(problem, issues, i = hint), call = NULL)
   19.                     └─rlang::abort(...)
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
  add_plot_attributes 6.129  0.384   6.149

Package: see
Check: tests
New result: ERROR
    Running ‘testthat.R’ [63s/32s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # graphics engine changed in R 4.4, and so snapshots generated on
    > # previous R version won't work
    > if (getRversion() >= "4.4.0") {
    +   library(testthat)
    +   library(see)
    + 
    +   test_check("see")
    + }
    Starting 2 test processes
    [ FAIL 1 | WARN 3 | SKIP 23 | PASS 34 ]
    
    ══ Skipped tests (23) ══════════════════════════════════════════════════════════
    • On CRAN (22): 'test-check_model.R:2:3', 'test-plot.check_collinearity.R:7:3',
      'test-plot.compare_parameters.R:20:3', 'test-plot.effectsize_table.R:5:3',
      'test-plot.check_dag.R:17:3', 'test-plot.check_dag.R:68:3',
      'test-plot.check_dag.R:90:3', 'test-plot.estimate_density.R:14:3',
      'test-plot.n_factors.R:7:3', 'test-plot.p_direction.R:11:1',
      'test-plot.p_significance.R:11:1', 'test-plot.performance_pp_check.R:6:3',
      'test-plot.performance_roc.R:14:3', 'test-plot.parameters_model.R:7:3',
      'test-plot.parameters_model.R:35:3', 'test-plot.parameters_model.R:90:3',
      'test-plot.parameters_model.R:104:3', 'test-scale_color_colorhex_c.R:3:3',
      'test-vdiffr_bayestestr_plots.R:11:3', 'test-vdiffr_geoms_coords.R:9:3',
      'test-vdiffr_scale_color.R:2:3', 'test-vdiffr_themes.R:22:3'
    • TRUE is TRUE (1): 'test-plot.simulate_parameters.R:1:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-plot.check_normality.R:18:3'): `plot.see_check_normality()` works ──
    Error in `qqplotr::stat_qq_band(alpha = alpha_level, detrend = detrend, 
        bandType = method)`: Problem while converting geom to grob.
    i Error occurred in the 1st layer.
    Caused by error in `check_linewidth()`:
    ! could not find function "check_linewidth"
    Backtrace:
         ▆
      1. ├─vdiffr::expect_doppelganger(...) at test-plot.check_normality.R:18:3
      2. │ └─vdiffr (local) writer(fig, testcase, title)
      3. │   ├─vdiffr:::print_plot(plot, title)
      4. │   └─vdiffr:::print_plot.ggplot(plot, title)
      5. │     ├─base::print(p)
      6. │     └─ggplot2 (local) `print.ggplot2::ggplot`(p)
      7. │       ├─ggplot2::ggplot_gtable(data)
      8. │       └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
      9. │         └─ggplot2:::by_layer(...)
     10. │           ├─rlang::try_fetch(...)
     11. │           │ ├─base::tryCatch(...)
     12. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     13. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     14. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
     15. │           │ └─base::withCallingHandlers(...)
     16. │           └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
     17. │             └─l$draw_geom(d, layout)
     18. │               └─ggplot2 (local) draw_geom(..., self = self)
     19. │                 └─self$geom$draw_layer(...)
     20. │                   └─ggplot2 (local) draw_layer(..., self = self)
     21. │                     └─base::lapply(...)
     22. │                       └─ggplot2 (local) FUN(X[[i]], ...)
     23. │                         ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
     24. │                         └─self$draw_panel(data, panel_params, coord)
     25. │                           └─ggplot2 (local) draw_panel(..., self = self)
     26. │                             └─base::lapply(...)
     27. │                               └─ggplot2 (local) FUN(X[[i]], ...)
     28. │                                 └─self$draw_group(group, panel_params, coord, ...)
     29. │                                   └─ggplot2 (local) draw_group(...)
     30. │                                     └─ggplot2 (local) draw_group(..., self = self)
     31. └─base::.handleSimpleError(...)
     32.   └─rlang (local) h(simpleError(msg, call))
     33.     └─handlers[[1L]](cnd)
     34.       └─cli::cli_abort(...)
     35.         └─rlang::abort(...)
    
    [ FAIL 1 | WARN 3 | SKIP 23 | PASS 34 ]
    Error: Test failures
    Execution halted

Package: seedreg
Check: examples
New result: ERROR
  Running examples in ‘seedreg-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: multicurve
  > ### Title: Graph: Merge multiple curves into a single graph
  > ### Aliases: multicurve
  > 
  > ### ** Examples
  > 
  > library(seedreg)
  > data("aristolochia")
  > attach(aristolochia)
  > a=LM_model(trat,germ)
  
  $Coefficients
              Estimate Std Error   t value      P-value   
  (Intercept)   -52.50 8.0436071 -6.526922 6.166973e-09 **
  trat            3.54 0.3095986 11.434161 2.398736e-18 **
  
  $test
                         Parameter      values
  1            Optimum temperature  35.0000000
  2   Optimum temperature response  71.4000000
  3            Minimal temperature  15.0000000
  4   Minimal temperature response   0.6000000
  5  Predicted maximum basal value          NA
  6  Predicted minimum basal value          NA
  7                            AIC 706.9321172
  8                            BIC 714.0781971
  9                      r-squared   0.7443336
  10                          RMSE  19.3344253
  
  [[3]]
  
  > b=LL_model(trat,germ,npar = "LL.3")
  $Coefficients
                 Estimate Std Error   t value      P-value   
  b:(Intercept) -19.40819 7.2234673 -2.686825 8.834104e-03 **
  d:(Intercept)  63.94663 2.6591940 24.047373 7.589711e-38 **
  e:(Intercept)  23.57567 0.7028374 33.543565 5.265615e-48 **
  
  $values
                         Parameter      values
  1            Optimum temperature  35.0000000
  2   Optimum temperature response  63.9167699
  3            Minimal temperature  15.0000000
  4   Minimal temperature response   0.0098744
  5  Predicted maximum basal value          NA
  6  Predicted minimum basal value  18.3683368
  7                            AIC 661.2956178
  8                            BIC 670.8237244
  9                      r-squared   0.7900000
  10                          RMSE  14.3558723
  
  [[3]]
  
  > c=BC_model(trat,germ, npar = "BC.4")
  $Coefficients
                  Estimate  Std Error   t value      P-value   
  b:(Intercept) -13.957213  3.6556392 -3.817995 2.726669e-04 **
  d:(Intercept) 250.774747 60.3259646  4.156995 8.380546e-05 **
  e:(Intercept)  25.505952  0.6951316 36.692263 2.126565e-50 **
  f:(Intercept)  -5.617971  1.7401792 -3.228387 1.838928e-03 **
  
  $values
                         Parameter      values
  1            Optimum temperature  29.1414141
  2   Optimum temperature response  75.3297253
  3            Minimal temperature  15.0000000
  4   Minimal temperature response   0.1007687
  5  Predicted maximum basal value          NA
  6  Predicted minimum basal value  16.9061906
  7                            AIC 642.3420163
  8                            BIC 654.2521495
  9                      r-squared   0.8400000
  10                          RMSE  12.5937300
  
  [[3]]
  
  > d=CD_model(trat,germ, npar = "CRS.4")
  $Coefficients
                   Estimate    Std Error   t value      P-value   
  b:(Intercept)   -14.42145    3.5312045 -4.084003 1.085486e-04 **
  d:(Intercept)  6110.38908 1944.3164277  3.142693 2.387074e-03 **
  e:(Intercept)    25.81624    0.7578171 34.066589 4.361048e-48 **
  f:(Intercept) -6231.70537 2001.2831503 -3.113855 2.603523e-03 **
  
  $values
                         Parameter      values
  1            optimum temperature  28.9633963
  2   Optimum temperature response  75.7505378
  3            Minimal temperature  15.0000000
  4   Minimal temperature response   0.1115036
  5  Predicted maximum basal value          NA
  6  Predicted minimum basal value  16.8361836
  7                            AIC 642.3427825
  8                            BIC 654.2529157
  9                      r-squared   0.8400000
  10                          RMSE  12.5937903
  
  [[3]]
  
  > multicurve(list(a,b,c,d))
  Error in equation[[i]] <- plots[[i]][[3]]$plot$s : 
    replacement has length zero
  Calls: multicurve
  Execution halted

Package: shinyMixR
Check: tests
New result: ERROR
    Running ‘testthat.R’ [6s/6s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > # see https://github.com/rstudio/shinytest2/issues/351 
    > options(chromote.timeout = 120)
    > 
    > library(testthat)
    > library(shinyMixR)
    Loading required package: shiny
    Loading required package: ggplot2
    > library(nlmixr2)
    ── Attaching packages ───────────────────────────────────────── nlmixr2 4.0.0 ──
    ✔ lotri        1.0.1     ✔ nlmixr2extra 3.0.2
    ✔ nlmixr2data  2.0.9     ✔ nlmixr2plot  3.0.2
    ✔ nlmixr2est   4.0.2     ✔ rxode2       4.0.3
    ── Optional Packages Loaded/Ignored ─────────────────────────── nlmixr2 4.0.0 ──
    ✔ shinyMixR     ✖ nlmixr2lib
    ✖ babelmixr2     ✖ nlmixr2rpt
    ✖ ggPMX     ✖ nonmem2rx
    ✖ monolix2rx     ✖ xpose.nlmixr2
    ── Conflicts ───────────────────────────────────────────── nlmixr2conflicts() ──
    ✖ rxode2::boxCox()     masks nlmixr2est::boxCox()
    ✖ rxode2::yeoJohnson() masks nlmixr2est::yeoJohnson()
    > 
    > test_check("shinyMixR")
    xdg-open: file '/home/hornik/tmp/scratch/Rtmp6xpzeX/files/analysis/run1/par_table.html' does not exist
    [ FAIL 2 | WARN 0 | SKIP 11 | PASS 21 ]
    
    ══ Skipped tests (11) ══════════════════════════════════════════════════════════
    • On CRAN (11): 'test-module_dataexplore.R:3:3', 'test-module_metadata.R:3:3',
      'test-module_report.R:4:3', 'test-module_run.R:3:3',
      'test-module_script.R:3:3', 'test-module_settings.R:3:3',
      'test-run_nmx.R:3:3', 'test-run_shinymixr.R:3:3',
      'test-shinymixr-01-model-run1.R:8:3',
      'test-shinymixr-02-parameter-table.R:6:3',
      'test-shinymixr-03-create-newmodel.R:6:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-fit_plot.R:8:3'): fit_plot works as expected ───────────────────
    <packageNotFoundError/error/condition>
    Error in `loadNamespace(x)`: there is no package called 'xpose.nlmixr2'
    Backtrace:
        ▆
     1. ├─base::suppressWarnings(fit_plot(res)) at test-fit_plot.R:8:3
     2. │ └─base::withCallingHandlers(...)
     3. ├─shinyMixR::fit_plot(res)
     4. └─base::loadNamespace(x)
     5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     6.     └─base (local) withOneRestart(expr, restarts[[1L]])
     7.       └─base (local) doWithOneRestart(return(expr), restart)
    ── Error ('test-gof_plot.R:10:3'): gof_plot works as expected ──────────────────
    <packageNotFoundError/error/condition>
    Error in `loadNamespace(x)`: there is no package called 'xpose.nlmixr2'
    Backtrace:
        ▆
     1. ├─base::suppressWarnings(gof_plot(res, ptype = "all", type = "xpose")) at test-gof_plot.R:10:3
     2. │ └─base::withCallingHandlers(...)
     3. ├─shinyMixR::gof_plot(res, ptype = "all", type = "xpose")
     4. └─base::loadNamespace(x)
     5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
     6.     └─base (local) withOneRestart(expr, restarts[[1L]])
     7.       └─base (local) doWithOneRestart(return(expr), restart)
    
    [ FAIL 2 | WARN 0 | SKIP 11 | PASS 21 ]
    Error: Test failures
    Execution halted

Package: shortIRT
Check: examples
New result: ERROR
  Running examples in ‘shortIRT-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: bp
  > ### Title: Benchmark Procedure
  > ### Aliases: bp
  > 
  > ### ** Examples
  > 
  > # set a seed to replicate the results
  > set.seed(999)
  > # Simulate person and item parameters
  > true_theta <- rnorm(1000)
  > b <- runif(30, -3, 3)
  > a <- runif(30, 0.6, 2)
  > parameters <- data.frame(b, a)
  > # simulate data
  > data <- sirt::sim.raschtype(true_theta, b = b, fixed.a = a)
  > stf <- bp(data, starting_theta = true_theta, item_par = parameters, num_item = 5)
  Error: Package 'MASS' is needed for applying this
              function. Please install it.
  Execution halted

Package: simplecolors
Check: tests
New result: ERROR
    Running ‘testthat.R’ [3s/3s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(simplecolors)
    > 
    > test_check("simplecolors")
    [ FAIL 3 | WARN 1 | SKIP 0 | PASS 22 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-sc_across.R:15:3'): sc_across returns ggplot ─────────────────
    is(x) not equal to "gg".
    1/1 mismatches
    x[1]: "ggplot2::ggplot"
    y[1]: "gg"
    ── Failure ('test-sc_within.R:19:3'): sc_within returns ggplot ─────────────────
    is(x) not equal to "gg".
    1/1 mismatches
    x[1]: "ggplot2::ggplot"
    y[1]: "gg"
    ── Failure ('test-show_colors.R:5:3'): show_colors retuns gglot ────────────────
    is(x) not equal to "gg".
    1/1 mismatches
    x[1]: "ggplot2::ggplot"
    y[1]: "gg"
    
    [ FAIL 3 | WARN 1 | SKIP 0 | PASS 22 ]
    Error: Test failures
    Execution halted

Package: SimSurvey
Check: data for non-ASCII characters
New result: WARNING
    Failed with error:  'there is no package called 'Matrix''
    Error loading dataset 'survey_lite_mesh':
     Error in .requirePackage(package) : 
      unable to load required package 'Matrix'
    
    Failed with error:  'there is no package called 'Matrix''
    Error loading dataset 'survey_mesh':
     Error in .requirePackage(package) : 
      unable to load required package 'Matrix'
    
    The dataset(s) may use package(s) not declared in Depends/Imports.

Package: sjSDM
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggtern’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: smer
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘smer.Rmd’ using rmarkdown
  
  Quitting from smer.Rmd:197-207 [h2_plot]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'smer.Rmd' failed with diagnostics:
  Problem while setting up geom aesthetics.
  ℹ Error occurred in the 3rd layer.
  Caused by error in `list_sizes()`:
  ! `x$label` must be a vector, not an expression vector.
  --- failed re-building ‘smer.Rmd’
  
  --- re-building ‘study-erythroid-differentiation-data.Rmd’ using rmarkdown
  --- finished re-building ‘study-erythroid-differentiation-data.Rmd’
  
  --- re-building ‘tutorial-cite-us.Rmd’ using rmarkdown
  --- finished re-building ‘tutorial-cite-us.Rmd’
  
  --- re-building ‘tutorial-create-mask-file.Rmd’ using rmarkdown
  --- finished re-building ‘tutorial-create-mask-file.Rmd’
  
  --- re-building ‘tutorial-memory-optimization.Rmd’ using rmarkdown
  --- finished re-building ‘tutorial-memory-optimization.Rmd’
  
  --- re-building ‘tutorial-simulate-traits.Rmd’ using rmarkdown
  --- finished re-building ‘tutorial-simulate-traits.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘smer.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: spacejamr
Check: tests
New result: ERROR
    Running ‘testthat.R’ [18s/19s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(spacejamr)
    > 
    > test_check("spacejamr")
        Density Mean Degree Mean Closeness Mean Betweenness Largest Component Size
    pl        0           0            NaN                0                      1
    apl       0           0            NaN                0                      1
        Density Mean Degree Mean Closeness Mean Betweenness Largest Component Size
    pl        0           0            NaN                0                      1
    apl       0           0            NaN                0                      1
    window: polygonal boundary
    enclosing rectangle: [257656.9, 323005.8] x [4558224, 4654702] units
    PointSim Object
    
    window: polygonal boundary
    enclosing rectangle: [257656.9, 323005.8] x [4558224, 4654702] units
    
    Points:3IGRAPH 256f8fa UN-- 3 0 -- 
    + attr: name (v/c)
    + edges from 256f8fa (vertex names):
    IGRAPH 256f8fa UN-- 3 0 -- 
    + attr: name (v/c)
    + edges from 256f8fa (vertex names):
    Using the projected CRS WGS 84 / UTM zone 19N which uses 'm' for measurement units. Please visit https://spatialreference.org/ref/epsg/32619/ for more information about this CRS.
    [ FAIL 3 | WARN 3 | SKIP 0 | PASS 20 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-generics.R:11:5'): we can plot objects created with the spacejamr package ──
    class(plot(RI)) (`actual`) not identical to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-generics.R:14:5'): we can plot objects created with the spacejamr package ──
    class(plot(ri_points)) (`actual`) not identical to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-generics.R:17:5'): we can plot objects created with the spacejamr package ──
    class(plot(pl)) (`actual`) not identical to c("ggraph", "gg", "ggplot") (`expected`).
    
        actual            | expected    
    [1] "ggraph"          - "gg"     [2]
    [2] "ggplot2::ggplot" -             
    [3] "ggplot"          -             
    [4] "ggplot2::gg"     -             
    [5] "S7_object"       -             
    [6] "gg"              - "ggplot" [3]
    
    [ FAIL 3 | WARN 3 | SKIP 0 | PASS 20 ]
    Error: Test failures
    Execution halted

Package: spectralR
Check: tests
New result: ERROR
    Running ‘tinytest.R’ [5s/5s]
  Running the tests in ‘tests/tinytest.R’ failed.
  Complete output:
    > if ( requireNamespace("tinytest", quietly=TRUE) ){
    +   tinytest::test_package("spectralR")
    + }
    
    test_get.pixel.data.R.........    1 tests OK 0.1s
    
    test_prepare.vector.data.R....    1 tests OK 
    test_prepare.vector.data.R....    2 tests OK 
    test_prepare.vector.data.R....    3 tests OK 
    test_prepare.vector.data.R....    4 tests OK 
    test_prepare.vector.data.R....    4 tests OK 
    test_prepare.vector.data.R....    4 tests OK 
    test_prepare.vector.data.R....    5 tests OK 
    test_prepare.vector.data.R....    6 tests OK 
    test_prepare.vector.data.R....    7 tests OK 
    test_prepare.vector.data.R....    8 tests OK 
    test_prepare.vector.data.R....    9 tests OK 
    test_prepare.vector.data.R....   10 tests OK 
    test_prepare.vector.data.R....   11 tests OK 
    test_prepare.vector.data.R....   12 tests OK 0.1s
    
    test_spectral.curves.plot.R...    1 tests OK Joining with `by = join_by(variable)`
    Error in if (msg != "") { : the condition has length > 1
    Calls: <Anonymous> ... lapply -> FUN -> eval -> eval -> expect_silent -> fun
    Execution halted

Package: spinifex
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [95s/90s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(spinifex)
    Loading required package: tourr
    --------------------------------------------------------
    spinifex --- version 0.3.8
    Please share bugs, suggestions, and feature requests at:
    https://github.com/nspyrison/spinifex/issues/
    --------------------------------------------------------
    
    Attaching package: 'spinifex'
    
    The following objects are masked from 'package:tourr':
    
        is_orthonormal, save_history
    
    > 
    > test_check("spinifex")
    Target: 0.921, 20.4% better 
    Target: 0.965, 4.8% better 
    Target: 0.980, 1.5% better 
    Target: 0.987, 0.7% better 
    Target: 0.992, 0.5% better 
    Target: 0.995, 0.3% better 
    Target: 0.996, 0.1% better 
    No better bases found after 25 tries.  Giving up.
    Final projection: 
    -0.701  -0.450  
     0.096  -0.241  
    -0.649   0.259  
    -0.210  -0.124  
     0.186  -0.810  
    Target: 0.653, 48.8% better 
    Target: 0.747, 14.4% better 
    Target: 0.909, 21.6% better 
    Target: 0.936, 3.0% better 
    Target: 0.963, 2.9% better 
    Target: 0.980, 1.8% better 
    Target: 1.014, 3.4% better 
    Target: 1.023, 0.9% better 
    Target: 1.039, 1.6% better 
    Target: 1.043, 0.3% better 
    Target: 1.044, 0.1% better 
    No better bases found after 25 tries.  Giving up.
    Final projection: 
     0.253  -0.109  
    -0.578   0.347  
    -0.436  -0.433  
    -0.588   0.274  
     0.258   0.778  
    Target: 0.373, 98.7% better 
    Target: 0.468, 25.5% better 
    Target: 0.631, 34.9% better 
    Target: 0.655, 3.8% better 
    Target: 0.681, 4.0% better 
    Target: 0.717, 5.4% better 
    Target: 0.735, 2.5% better 
    Target: 0.743, 1.1% better 
    Target: 0.744, 0.2% better 
    Target: 0.745, 0.1% better 
    Target: 0.746, 0.1% better 
    Target: 0.747, 0.1% better 
    Target: 0.748, 0.1% better 
    Target: 0.749, 0.1% better 
    No better bases found after 30 tries.  Giving up.
    Final projection: 
     0.013   0.560  
    -0.530   0.385  
    -0.425  -0.627  
     0.723  -0.156  
    -0.125  -0.347  
    
    Attaching package: 'ggplot2'
    
    The following objects are masked from 'package:spinifex':
    
        scale_colour_discrete, scale_fill_discrete
    
    Target: 0.733, 83.0% better 
    Target: 0.926, 26.4% better 
    `nframes` and `fps` adjusted to match transition
    [ FAIL 11 | WARN 0 | SKIP 0 | PASS 80 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-0_util.R:106:3'): theme_spinifex: class ──────────────────────
    class(g) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_ggproto_visualize.r:30:3'): ggtourr ────────────────────────
    class(gg_mt) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_ggproto_visualize.r:31:3'): ggtourr ────────────────────────
    class(gg_gt) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_ggproto_visualize.r:32:3'): ggtourr ────────────────────────
    class(gg_mt1d) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-2_ggproto_visualize.r:33:3'): ggtourr ────────────────────────
    class(gg_gt1d) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Error ('test-2_ggproto_visualize.r:53:1'): (code run outside of `test_that()`) ──
    Error in `UseMethod("layout")`: no applicable method for 'layout' applied to an object of class "c('ggplot2::ggplot', 'ggplot', 'ggplot2::gg', 'S7_object', 'gg')"
    Backtrace:
        ▆
     1. ├─spinifex::animate_plotly(gg_mt) at test-2_ggproto_visualize.r:53:1
     2. │ └─... %>% ...
     3. └─plotly::layout(...)
    ── Failure ('test-zDepricated_2_render.R:29:3'): render_, class and dim ────────
    class(ret) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-zDepricated_3_visualize.r:76:3'): view_frame: gganimate class and length ──
    class(ret_light) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-zDepricated_3_visualize.r:77:3'): view_frame: gganimate class and length ──
    class(ret_heavy) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-zDepricated_3_visualize.r:93:3'): view_manip_space: gganimate class and length ──
    class(ret_light) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    ── Failure ('test-zDepricated_3_visualize.r:94:3'): view_manip_space: gganimate class and length ──
    class(ret_heavy) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 11 | WARN 0 | SKIP 0 | PASS 80 ]
    Error: Test failures
    Execution halted

Package: sport
Check: tests
New result: ERROR
    Running ‘testthat.R’ [21s/21s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > 
    > test_check("sport")
    Loading required package: sport
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 238 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_output.R:30:3'): Scale is labelled 'r' ───────────────────────
    p$labels$y not identical to "r".
    target is NULL, current is character
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 238 ]
    Error: Test failures
    Execution halted

Package: ssd4mosaic
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [141s/142s]
  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(ssd4mosaic)
    > 
    > test_check("ssd4mosaic")
    [ FAIL 3 | WARN 0 | SKIP 1 | PASS 66 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • On CRAN (1): 'test-golem-recommended.R:72:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-fct_ci_plots.R:23:3'): Confidence intervals are added to plots ──
    plot_ci$layers has length 16, not length 11.
    ── Failure ('test-fct_ci_plots.R:24:3'): Confidence intervals are added to plots ──
    plot_cens_ci$layers has length 11, not length 7.
    ── Error ('test-fct_options_plots.R:8:3'): Uncensored data can be coloured by group ──
    Error in `order(p$layers[[1]]$data$group)`: argument 1 is not a vector
    Backtrace:
        ▆
     1. └─base::order(p$layers[[1]]$data$group) at test-fct_options_plots.R:8:3
    
    [ FAIL 3 | WARN 0 | SKIP 1 | PASS 66 ]
    Error: Test failures
    Execution halted

Package: sssc
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘sssc’

Package: stacomiR
Check: examples
New result: ERROR
  Running examples in ‘stacomiR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: report_silver_eel-class
  > ### Title: Class "report_silver_eel"
  > ### Aliases: report_silver_eel-class report_silver_eel
  > ### Keywords: classes
  > 
  > ### ** Examples
  > 
  > # launching stacomi without selecting the scheme or interface
  > stacomi(	database_expected=FALSE)
  > # the following script will load data from the two Anguillere monitored in the Somme
  > 
  > # If you have a working database
  > # the following line of code will create the r_silver dataset 
  > # from the "fd80." schema in the database
  > ## Not run: 
  > ##D 	stacomi(database_expected=TRUE, sch="fd80.")	# overrides the default option sch = 'iav'
  > ##D 	# prompt for user and password, you can set these in the options, 
  > ##D 	# including dbname and host
  > ##D 	if (interactive()){
  > ##D 		if (!exists("user")){
  > ##D 			user <- readline(prompt="Enter user: ")
  > ##D 			password <- readline(prompt="Enter password: ")	
  > ##D 		}	
  > ##D 	}
  > ##D 	options(					
  > ##D 			stacomiR.dbname = "bd_contmig_nat",
  > ##D 			stacomiR.host ="localhost",
  > ##D 			stacomiR.port = "5432",
  > ##D 			stacomiR.user = user,
  > ##D 			stacomiR.user = password						
  > ##D 	)	
  > ##D 	
  > ##D   #create an instance of the class
  > ##D   r_silver<-new("report_silver_eel")
  > ##D   r_silver<-choice_c(r_silver,
  > ##D 	  dc=c(2,6),			
  > ##D 	  horodatedebut="2010-09-01",
  > ##D 	  horodatefin="2016-10-04",
  > ##D 	  silent=FALSE)
  > ##D   r_silver<-connect(r_silver)	
  > ## End(Not run)
  > 	
  > # load the dataset generated by previous lines
  > data("r_silver")
  > # the calculation will fill the slot calcdata
  > r_silver<-calcule(r_silver)
  > # stages are in r_silver@calcdata[["6"]][,"stage"] 
  > #look at data structure using str(r_silver@calcdata[["6"]])
  > 
  > # standard plot as drawn by Laurent Beaulaton (Analyse des donnees d'argenture acquises en France)
  > # showing Durif's stage according to size and eye diameter
  > plot(r_silver, plot.type=1)
  > 
  > # number per month or year and Durif's stage (year if number of dc >1)
  > plot(r_silver, plot.type="2")
  > 
  > # plot showing fulton's coefficient, and size weight graphs
  > # inspired from Acou et al., 2009 
  > # Differential Production and Condition Indices of Premigrant
  > # Eels in Two Small Atlantic Coastal Catchments
  > # of France
  > plot(r_silver, plot.type="3")
  Error in loadNamespace(x) : there is no package called ‘MASS’
  Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted

Package: stacomiR
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘stacomir.Rmd’ using rmarkdown
  
  Quitting from stacomir.Rmd:349-366 [silver]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `loadNamespace()`:
  ! there is no package called 'MASS'
  ---
  Backtrace:
      ▆
   1. ├─base::plot(r_silver, plot.type = "3")
   2. ├─stacomiR::plot(r_silver, plot.type = "3")
   3. │ └─stacomiR (local) .local(x, ...)
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base (local) withOneRestart(expr, restarts[[1L]])
   7.       └─base (local) doWithOneRestart(return(expr), restart)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
  there is no package called 'MASS'
  --- failed re-building ‘stacomir.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘stacomir.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: states
Check: tests
New result: ERROR
    Running ‘testthat.R’ [3s/3s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library("testthat")
    > library("states")
    
    Attaching package: 'states'
    
    The following object is masked from 'package:testthat':
    
        compare
    
    > 
    > test_check("states")
    [ FAIL 3 | WARN 0 | SKIP 0 | PASS 106 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot-missing.R:72:3'): plot_missing accepts all input options ──
    plot_missing(...) has type 'object', not 'list'.
    ── Failure ('test-plot-missing.R:77:3'): plot_missing accepts all input options ──
    plot_missing(...) has type 'object', not 'list'.
    ── Failure ('test-plot-missing.R:82:3'): plot_missing accepts all input options ──
    plot_missing(...) has type 'object', not 'list'.
    
    [ FAIL 3 | WARN 0 | SKIP 0 | PASS 106 ]
    Error: Test failures
    Execution halted

Package: stRoke
Check: tests
New result: ERROR
    Running ‘testthat.R’ [8s/8s]
  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(stRoke)
    > 
    > test_check("stRoke")
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    Waiting for profiling to be done...
    OBS: as per 2007 not all valid CPR numbers apply to modulus 11 rule.
        
    See the vignette 'Toolbox'
    
    > 2 + 2
    [1] 4
    
    > 2 + 2
    [1] 4
    
    > 2 + 2
    [1] 4
    [ FAIL 3 | WARN 2 | SKIP 0 | PASS 47 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-index_plot.R:2:3'): index_plot() works! ──────────────────────
    index_plot(stRoke::score[score$event == "A", ]) has type 'object', not 'list'.
    ── Failure ('test-index_plot.R:5:3'): index_plot() works! ──────────────────────
    index_plot(stRoke::score[score$event == "A", ], sub_plot = "_per") has type 'object', not 'list'.
    ── Failure ('test-index_plot.R:17:3'): index_plot() works! ─────────────────────
    index_plot(stRoke::score, sub_plot = "_per", facet.by = "event") has type 'object', not 'list'.
    
    [ FAIL 3 | WARN 2 | SKIP 0 | PASS 47 ]
    Error: Test failures
    Execution halted

Package: Superpower
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [59s/59s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(Superpower)
    > 
    > 
    > test_check("Superpower")
    [1] "condition_one" "sad_1"        
    [ FAIL 1 | WARN 18 | SKIP 13 | PASS 399 ]
    
    ══ Skipped tests (13) ══════════════════════════════════════════════════════════
    • On CRAN (13): 'test-ANOVA_compromise.R:45:3', 'test-anova_exact.R:152:3',
      'test-anova_power.R:93:3', 'test-anova_power.R:119:3',
      'test-anova_power.R:160:3', 'test-anova_power.R:193:3',
      'test-anova_power.R:232:3', 'test-emmeans_power.R:44:3',
      'test-justifieR.R:29:3', 'test-plot_power.R:43:3', 'test-plot_power.R:102:3',
      'test-plot_power.R:148:3', 'test-plot_power.R:169:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-morey.R:109:3'): No error messages ftest ─────────────────────
    class(test)[1] not equal to "gg".
    1/1 mismatches
    x[1]: "ggplot2::ggplot"
    y[1]: "gg"
    
    [ FAIL 1 | WARN 18 | SKIP 13 | PASS 399 ]
    Error: Test failures
    Execution halted

Package: survminer
Check: examples
New result: ERROR
  Running examples in ‘survminer-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: add_ggsurvplot
  > ### Title: Add Components to a ggsurvplot
  > ### Aliases: add_ggsurvplot +.ggsurv %++%
  > 
  > ### ** Examples
  > 
  > # Fit survival curves
  > require("survival")
  Loading required package: survival
  
  Attaching package: ‘survival’
  
  The following object is masked from ‘package:survminer’:
  
      myeloma
  
  > fit<- survfit(Surv(time, status) ~ sex, data = lung)
  > 
  > # Basic survival curves
  > p <- ggsurvplot(fit, data = lung, risk.table = TRUE,
  +    main = "Survival curve",
  +    submain = "Based on Kaplan-Meier estimates",
  +    caption = "created with survminer"
  +    )
  Warning: ggtheme is not a valid theme.
  Please use `theme()` to construct themes.
  Ignoring unknown labels:
  • fill : "Strata"
  • linetype : "1"
  Warning: ggtheme is not a valid theme.
  Please use `theme()` to construct themes.
  Warning: tables.theme is not a valid theme.
  Please use `theme()` to construct themes.
  > p
  Ignoring unknown labels:
  • fill : "Strata"
  • linetype : "1"
  Ignoring unknown labels:
  • fill : "Strata"
  • linetype : "1"
  Ignoring unknown labels:
  • fill : "Strata"
  • linetype : "1"
  Ignoring unknown labels:
  • colour : "Strata"
  > 
  > # Customizing the plots
  > p + theme_survminer(
  +      font.main = c(16, "bold", "darkblue"),
  +      font.submain = c(15, "bold.italic", "purple"),
  +      font.caption = c(14, "plain", "orange"),
  +      font.x = c(14, "bold.italic", "red"),
  +      font.y = c(14, "bold.italic", "darkred"),
  +      font.tickslab = c(12, "plain", "darkgreen")
  + )
  Warning: e2 is not a valid theme.
  Please use `theme()` to construct themes.
  Warning: e2 is not a valid theme.
  Please use `theme()` to construct themes.
  Error in `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`:
  ! Can't merge the `axis.text.y` theme element.
  Caused by error in `method(merge_element, list(ggplot2::element, class_any))`:
  ! Only elements of the same class can be merged.
  Backtrace:
       ▆
    1. └─survminer:::`+.ggsurv`(...)
    2.   └─S7:::Ops.S7_object(p, e2)
    3.     ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
    4.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    5.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
    6.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
    7.     └─base_ops[[.Generic]](e1, e2)
    8.       ├─S7::S7_dispatch()
    9.       └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
   10.         └─ggplot2:::add_ggplot(e1, e2, e2name)
   11.           ├─ggplot2::ggplot_add(object, p, objectname)
   12.           └─ggplot2:::ggplot_add.default(object, p, objectname)
   13.             └─ggplot2::update_ggplot(object = object, plot = plot, ...)
   14.               ├─S7::S7_dispatch()
   15.               └─ggplot2 (local) `method(update_ggplot, list(class_any, ggplot2::ggplot))`(...)
   16.                 └─ggplot2::update_ggplot(object, plot)
   17.                   ├─S7::S7_dispatch()
   18.                   └─ggplot2 (local) `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`(...)
   19.                     ├─S7::set_props(plot, theme = add_theme(plot@theme, object))
   20.                     └─ggplot2:::add_theme(plot@theme, object)
   21.                       ├─rlang::try_fetch(...)
   22.                       │ ├─base::tryCatch(...)
   23.                       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   24.                       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   25.                       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   26.                       │ └─base::withCallingHandlers(...)
   27.                       └─ggplot2::merge_element(t2[[item]], t1[[item]])
   28.                         ├─S7::S7_dispatch()
   29.                         └─ggplot2 (local) `method(merge_element, list(ggplot2::element, class_any))`(new = `<ggpl2::_>`, old = `<elmnt_mr>`, ...)
   30.                           └─cli::cli_abort("Only elements of the same class can be merged.")
   31.                             └─rlang::abort(...)
  Execution halted

Package: survminer
Check: tests
New result: ERROR
    Running ‘testthat.R’ [10s/10s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(survminer)
    Loading required package: ggplot2
    Loading required package: ggpubr
    > 
    > test_check("survminer")
    
    Attaching package: 'survival'
    
    The following object is masked from 'package:survminer':
    
        myeloma
    
    [ FAIL 1 | WARN 20 | SKIP 0 | PASS 11 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-ggsurvplot_facet.R:19:3'): ggsurvplot_facet calculates pvalue for each facet ──
    nrow(.build$plot$layer[[4]][["data"]]) not equal to length(unique(kidney[["disease"]])).
    target is NULL, current is numeric
    
    [ FAIL 1 | WARN 20 | SKIP 0 | PASS 11 ]
    Error: Test failures
    Execution halted

Package: SynergyLMM
Check: tests
New result: ERROR
    Running ‘testthat.R’ [290s/292s]
  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(SynergyLMM)
    > 
    > test_check("SynergyLMM")
    
    Normality Test of Random Effects
    $Time
    
    Title:
     Shapiro - Wilk Normality Test
    
    Test Results:
      STATISTIC:
        W: 0.9678
      P VALUE:
        0.8702 
    
    Description:
     Normality Test of Time random effects
    
    
    Normalized Residuals Levene Homoscedasticity Test by Sample
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  9  0.5417 0.8398
          80               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Sample
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by SampleID
    Fligner-Killeen:med chi-squared = 5.1645, df = 9, p-value = 0.8197
    
    
    Normality Test of Random Effects
    $Time
    
    Title:
     Shapiro - Wilk Normality Test
    
    Test Results:
      STATISTIC:
        W: 0.9678
      P VALUE:
        0.8702 
    
    Description:
     Normality Test of Time random effects
    
    
    Normalized Residuals Levene Homoscedasticity Test by Sample
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  9  0.5417 0.8398
          80               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Sample
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by SampleID
    Fligner-Killeen:med chi-squared = 5.1645, df = 9, p-value = 0.8197
    
    
    Normality Test of Random Effects
    $Time
    
    Title:
     Shapiro - Wilk Normality Test
    
    Test Results:
      STATISTIC:
        W: 0.9678
      P VALUE:
        0.8702 
    
    Description:
     Normality Test of Time random effects
    
    
    Normalized Residuals Levene Homoscedasticity Test by Sample
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  9  0.5417 0.8398
          80               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Sample
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by SampleID
    Fligner-Killeen:med chi-squared = 5.1645, df = 9, p-value = 0.8197
    
    
    Normalized Residuals Normality Test
    
    Title:
     Shapiro - Wilk Normality Test
    
    Test Results:
      STATISTIC:
        W: 0.7822
      P VALUE:
        3.211e-10 
    
    
    Normalized Residuals Levene Homoscedasticity Test by Time
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  8  0.5553 0.8111
          81               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Time
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by as.factor(Time)
    Fligner-Killeen:med chi-squared = 5.6845, df = 8, p-value = 0.6825
    
    
    Normalized Residuals Levene Homoscedasticity Test by Treatment
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  3  0.9028 0.4433
          86               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Treatment
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by Treatment
    Fligner-Killeen:med chi-squared = 1.5828, df = 3, p-value = 0.6633
    
    
    Outlier observations
       SampleID Time Treatment   TV      RTV   logRTV      TV0 normalized_resid
    90       10    9    Drug_A 1000 8.342366 2.121347 119.8701         6.124042
    
    Normalized Residuals Normality Test
    
    Title:
     Shapiro - Wilk Normality Test
    
    Test Results:
      STATISTIC:
        W: 0.7822
      P VALUE:
        3.211e-10 
    
    
    Normalized Residuals Levene Homoscedasticity Test by Time
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  8  0.5553 0.8111
          81               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Time
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by as.factor(Time)
    Fligner-Killeen:med chi-squared = 5.6845, df = 8, p-value = 0.6825
    
    
    Normalized Residuals Levene Homoscedasticity Test by Treatment
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  3  0.9028 0.4433
          86               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Treatment
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by Treatment
    Fligner-Killeen:med chi-squared = 1.5828, df = 3, p-value = 0.6633
    
    
    Outlier observations
       SampleID Time Treatment   TV      RTV   logRTV      TV0 normalized_resid
    90       10    9    Drug_A 1000 8.342366 2.121347 119.8701         6.124042
    
    Normalized Residuals Normality Test
    
    Title:
     Shapiro - Wilk Normality Test
    
    Test Results:
      STATISTIC:
        W: 0.7822
      P VALUE:
        3.211e-10 
    
    
    Normalized Residuals Levene Homoscedasticity Test by Time
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  8  0.5553 0.8111
          81               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Time
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by as.factor(Time)
    Fligner-Killeen:med chi-squared = 5.6845, df = 8, p-value = 0.6825
    
    
    Normalized Residuals Levene Homoscedasticity Test by Treatment
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  3  0.9028 0.4433
          86               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Treatment
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by Treatment
    Fligner-Killeen:med chi-squared = 1.5828, df = 3, p-value = 0.6633
    
    
    Outlier observations
       SampleID Time Treatment   TV      RTV   logRTV      TV0 normalized_resid
    90       10    9    Drug_A 1000 8.342366 2.121347 119.8701         6.124042
    
    Normalized Residuals Normality Test
    
    Title:
     Shapiro - Wilk Normality Test
    
    Test Results:
      STATISTIC:
        W: 0.7822
      P VALUE:
        3.211e-10 
    
    
    Normalized Residuals Levene Homoscedasticity Test by Time
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  8  0.5553 0.8111
          81               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Time
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by as.factor(Time)
    Fligner-Killeen:med chi-squared = 5.6845, df = 8, p-value = 0.6825
    
    
    Normalized Residuals Levene Homoscedasticity Test by Treatment
    Levene's Test for Homogeneity of Variance (center = median)
          Df F value Pr(>F)
    group  3  0.9028 0.4433
          86               
    
    Normalized Residuals Fligner-Killeen Homoscedasticity Test by Treatment
    
    	Fligner-Killeen test of homogeneity of variances
    
    data:  normalized_resid by Treatment
    Fligner-Killeen:med chi-squared = 1.5828, df = 3, p-value = 0.6633
    
    
    Outlier observations
       SampleID Time Treatment   TV      RTV   logRTV      TV0 normalized_resid
    90       10    9    Drug_A 1000 8.342366 2.121347 119.8701         6.124042
    Random effect variances not available. Returned R2 does not account for random effects.
    Random effect variances not available. Returned R2 does not account for random effects.
    No subject with a log-likelihood displacement greater than: 3.976
    [1] "Outliers with Log Likelihood displacement greater than: 4.977"
          4 
    6.55449 
    No subject with a log-likelihood displacement greater than: 1000
    [1] "Outliers with Log Likelihood displacement greater than: -1000"
             1          2          3          4          5          6          7 
    0.08258159 2.00421829 3.20399631 1.04719077 0.29520400 1.85948923 3.28403183 
             8          9         10 
    1.09210541 0.36262353 0.02277539 
    No subject with a log-likelihood displacement greater than: 3.976
    No subject with a Cook's distance greater than: 0.919
    No subject with a Cook's distance greater than: 0.582
    [1] "Subjects with Cook's distance greater than: -10"
               1            2            3            4            5            6 
    0.0097363880 0.4406576193 0.8019684428 0.2264886706 0.0670661290 0.4616129833 
               7            8            9           10 
    0.8019684428 0.2264886706 0.0256954978 0.0002433785 
    No subject with a Cook's distance greater than: 0.919
    `geom_line()`: Each group consists of only one observation.
    i Do you need to adjust the group aesthetic?
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 2.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 6.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 1.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 2.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 3.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 4.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 5.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 6.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 7.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 8.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 9.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 1.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 2.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 3.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 4.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 5.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 6.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 7.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 8.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 9.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 3.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 4.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 5.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 6.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 7.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 8.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    Some Combination Index values were infinite (+Inf) due to zero denominators for time: 9.
                       These values have been capped at a maximum of 100 to preserve interpretability.
    [ FAIL 1 | WARN 1357 | SKIP 0 | PASS 328 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-plot_SynergyLMM.R:37:3'): plot_lmmSynergy runs without error on valid input ──
    class(...) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 1 | WARN 1357 | SKIP 0 | PASS 328 ]
    Error: Test failures
    Execution halted

Package: tastypie
Check: tests
New result: ERROR
    Running ‘testthat.R’ [17s/17s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(tastypie)
                $$  $$  $$
              __||__||__||__
             | * * * * * * *|
             |* * * * * * * |
             | * * * * * * *|
             |______________|
     _              _              _
    | |_  ___  ___ | |_  _ _  ___ |_| ___
    |  _|| .'||_ -||  _|| | || . || || -_|
    |_|  |__,||___||_|  |_  ||  _||_||___|
                        |___||_|          
    > 
    > test_check("tastypie")
    [ FAIL 45 | WARN 38 | SKIP 0 | PASS 74 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-addimages.R:18:3'): output is a 'ggplot' object and title specification ──
    class\(imgpie\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(class(imgpie), "gg") at test-addimages.R:18:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:15:3'): output has 'list' type ────────────────────────
    pie_bake(a, template = "basic1") has type 'object', not 'list'.
    ── Failure ('test-bake.R:16:3'): output has 'list' type ────────────────────────
    pie_bake(a, template = "basic2") has type 'object', not 'list'.
    ── Failure ('test-bake.R:17:3'): output has 'list' type ────────────────────────
    pie_bake(a, template = "basic3") has type 'object', not 'list'.
    ── Failure ('test-bake.R:18:3'): output has 'list' type ────────────────────────
    pie_bake(a, template = "basic4") has type 'object', not 'list'.
    ── Failure ('test-bake.R:19:3'): output has 'list' type ────────────────────────
    pie_bake(a, template = "basic5", title = "tt") has type 'object', not 'list'.
    ── Failure ('test-bake.R:24:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "basic5", perc = T\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:24:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:25:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "basic4", perc = T\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:25:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:26:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "basic3", perc = T\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:26:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:27:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "basic2", perc = T\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:27:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:28:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "basic1", perc = T\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:28:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:29:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "bw1", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:29:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:30:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "bw2", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:30:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:31:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "bw3", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:31:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:32:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "bw4", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:32:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:33:3'): output is a 'ggplot' object ───────────────────
    class\(pie_bake\(a, template = "bw5", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:33:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:88:3'): also tibbles can be baked ─────────────────────
    class\(pie_bake\(tibble::as_tibble\(a\), template = "blue1"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:88:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:89:3'): also tibbles can be baked ─────────────────────
    class\(pie_bake\(b, template = "blue3"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:89:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake.R:90:3'): also tibbles can be baked ─────────────────────
    class\(pie_bake\(c, template = "blue4"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake.R:90:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:15:3'): output has 'list' type ────────────────────
    pie_bake_pro(a, template = "dart1") has type 'object', not 'list'.
    ── Failure ('test-bake_pro.R:16:3'): output has 'list' type ────────────────────
    pie_bake_pro(a, template = "dart3", title = "tt") has type 'object', not 'list'.
    ── Failure ('test-bake_pro.R:21:3'): output is a 'ggplot' object ───────────────
    class\(pie_bake_pro\(a, template = "eaten3"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:21:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:22:3'): output is a 'ggplot' object ───────────────
    class\(pie_bake_pro\(a, template = "eaten1", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:22:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:23:3'): output is a 'ggplot' object ───────────────
    class\(pie_bake_pro\(a, template = "cirbar1", title = "prova"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:23:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:24:3'): output is a 'ggplot' object ───────────────
    class\(pie_bake_pro\(a, template = "cirbar2"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:24:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:25:3'): output is a 'ggplot' object ───────────────
    class\(pie_bake_pro\(a, template = "cirbar3", title = "ciao"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:25:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:26:3'): output is a 'ggplot' object ───────────────
    class\(pie_bake_pro\(a, template = "cirbar4", title = "nop"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:26:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:27:3'): output is a 'ggplot' object ───────────────
    class\(pie_bake_pro\(a, template = "cirbar5"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:27:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:60:3'): also tibbles can be baked ─────────────────
    class\(pie_bake_pro\(tibble::as_tibble\(a\), template = "dart2"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:60:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:61:3'): also tibbles can be baked ─────────────────
    class\(pie_bake_pro\(b, template = "dart4"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:61:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bake_pro.R:62:3'): also tibbles can be baked ─────────────────
    class\(pie_bake_pro\(c, template = "dart5"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bake_pro.R:62:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:17:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub1"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:17:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:18:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub2"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:18:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:19:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub3"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:19:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:20:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub4"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:20:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:21:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub5"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:21:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:22:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub1", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:22:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:23:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub2", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:23:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:24:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub3", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:24:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:25:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub4", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:25:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:26:3'): output is a 'ggplot' object ─────────────────
    class\(bubble_blow\(a, template = "bub5", title = "gg"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:26:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:51:3'): also tibbles can be blown ───────────────────
    class\(bubble_blow\(tibble::as_tibble\(a\), template = "bub3", perc = "right"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:51:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:52:3'): also tibbles can be blown ───────────────────
    class\(bubble_blow\(b, template = "bub4", perc = "right"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:52:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-bubble.R:53:3'): also tibbles can be blown ───────────────────
    class\(bubble_blow\(c, template = "bub5", perc = "right"\)\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(...) at test-bubble.R:53:3
     2.   └─testthat:::expect_match_(...)
    ── Failure ('test-templates.R:37:3'): pie discover works properly ──────────────
    class\(b\) does not match "gg".
    Actual values:
    * ggplot2::ggplot
    * ggplot
    * ggplot2::gg
    * S7_object
    * gg
    Backtrace:
        ▆
     1. └─testthat::expect_match(class(b), "gg") at test-templates.R:37:3
     2.   └─testthat:::expect_match_(...)
    
    [ FAIL 45 | WARN 38 | SKIP 0 | PASS 74 ]
    Error: Test failures
    Execution halted

Package: teal.modules.general
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggmosaic’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: teal.widgets
Check: tests
New result: ERROR
    Running ‘testthat.R’ [20s/20s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > pkg_name <- "teal.widgets"
    > library(pkg_name, character.only = TRUE)
    > testthat::test_check(pkg_name)
    [ FAIL 3 | WARN 0 | SKIP 21 | PASS 203 ]
    
    ══ Skipped tests (21) ══════════════════════════════════════════════════════════
    • testing depth 3 is below current testing specification 5 (21):
      'test-plot_with_settings_ui.R:68:5', 'test-plot_with_settings_ui.R:91:5',
      'test-plot_with_settings_ui.R:163:5', 'test-plot_with_settings_ui.R:227:5',
      'test-plot_with_settings_ui.R:273:5', 'test-plot_with_settings_ui.R:321:5',
      'test-plot_with_settings_ui.R:364:5', 'test-plot_with_settings_ui.R:385:5',
      'test-plot_with_settings_ui.R:403:3', 'test-plot_with_settings_ui.R:448:3',
      'test-plot_with_settings_ui.R:469:3', 'test-table_with_settings_ui.R:48:5',
      'test-table_with_settings_ui.R:68:5', 'test-table_with_settings_ui.R:115:5',
      'test-table_with_settings_ui.R:181:5', 'test-table_with_settings_ui.R:209:5',
      'test-table_with_settings_ui.R:243:5', 'test-table_with_settings_ui.R:309:5',
      'test-table_with_settings_ui.R:336:5', 'test-table_with_settings_ui.R:359:3',
      'test-verbatim_popup_ui.R:33:5'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-ggplot2_args.R:196:3'): parse_ggplot2_args, deparse needed to expand ggplot2 objects like element_blank ──
    identical(...) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test-ggplot2_args.R:208:5'): resolve_ggplot2_args priorotizes input in the order: user_plot, user_default, teal.ggplot2_args and module_plot ──
    withr::with_options(...) not identical to ggplot2_args(...).
    Component "theme": Component "axis.text": target is ggplot2::element_blank, current is element_blank
    ── Failure ('test-ggplot2_args.R:267:5'): parse_ggplot2_args, when resolve_ggplot2_args priorotizes input in the order: user_plot, user_default, teal.ggplot2_args and module_plot ──
    deparse(parsed_all$theme, 500) not identical to "ggplot2::theme(axis.text = structure(list(), class = c(\"element_blank\", \"element\")))".
    1/1 mismatches
    x[1]: "ggplot2::theme(axis.text = <object>)"
    y[1]: "ggplot2::theme(axis.text = structure(list(), class = c(\"element_blank\",
    y[1]:  \"element\")))"
    
    [ FAIL 3 | WARN 0 | SKIP 21 | PASS 203 ]
    Error: Test failures
    Execution halted

Package: tepr
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘tepr.Rmd’ using rmarkdown
  
  Quitting from tepr.Rmd:509-512 [plotaucpval]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'tepr.Rmd' failed with diagnostics:
  Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  --- failed re-building ‘tepr.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘tepr.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: TestGardener
Check: examples
New result: ERROR
  Running examples in ‘TestGardener-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: Ffuns_plot
  > ### Title: Plot a selection of fit criterion F functions and their first
  > ###   two derivatives.
  > ### Aliases: Ffuns_plot
  > 
  > ### ** Examples
  > 
  > #  Example 1.  Display fit criterion values and derivatives for the 
  > #  short SweSAT multiple choice test with 24 items and 1000 examinees
  > chcemat   <- Quant_13B_problem_dataList$chcemat
  > index     <- Quant_13B_problem_parmList$index
  > SfdList   <- Quant_13B_problem_parmList$SfdList
  > plotindex <- 1:3
  > indfine   <- seq(0,100,len=101)
  > Ffuns_plot(indfine, index, SfdList, chcemat, plotindex)
  Error: <ggplot2::labels> object is invalid:
  - every label must be named.
  Execution halted

Package: tidyEdSurvey
Check: tests
New result: ERROR
    Running ‘testthat.R’ [39s/39s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(EdSurvey)
    Loading required package: car
    Loading required package: carData
    Loading required package: lfactors
    lfactors v1.0.4
    
    Loading required package: Dire
    Dire v2.2.0
    
    EdSurvey v4.0.7
    
    > library(tidyEdSurvey)
    tidyEdSurvey v0.1.3
    A package for using 'dplyr' and 'ggplot2' with student level data in an edsurvey.data.frame. To work with teacher or school level data, see ?EdSurvey::getData
    
    Attaching package: 'tidyEdSurvey'
    
    The following object is masked from 'package:base':
    
        attach
    
    > test_check('tidyEdSurvey')
    [ FAIL 2 | WARN 0 | SKIP 1 | PASS 10 ]
    
    ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
    • On CRAN (1): 'test-dplyr-TIMSS.R:1:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-ggplot.R:13:3'): density plot with facets and PVs ────────────
    class(p) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    ── Failure ('test-ggplot.R:21:3'): boxplot with facets and PVs ─────────────────
    class(p) not equal to c("gg", "ggplot").
    Lengths differ: 5 is not 2
    
    [ FAIL 2 | WARN 0 | SKIP 1 | PASS 10 ]
    Error: Test failures
    Execution halted

Package: tidypaleo
Check: S3 generic/method consistency
New result: WARNING
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.rotate_facet_label_spec:
    function(object, plot, object_name)
  
  ggplot_add:
    function(object, plot, ...)
  ggplot_add.sequential_layer_facet_spec:
    function(object, plot, object_name)
  See section ‘Generic functions and methods’ in the ‘Writing R
  Extensions’ manual.

Package: tidysdm
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘a0_tidysdm_overview.Rmd’ using rmarkdown
  Warning in grid.Call.graphics(C_path, x$x, x$y, index, switch(x$rule, winding = 1L,  :
    supplied color is neither numeric nor character
  --- finished re-building ‘a0_tidysdm_overview.Rmd’
  
  --- re-building ‘a1_palaeodata_application.Rmd’ using rmarkdown
  
  Quitting from a1_palaeodata_application.Rmd:257-259 [unnamed-chunk-10]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'a1_palaeodata_application.Rmd' failed with diagnostics:
  There was 1 workflow that had no results.
  --- failed re-building ‘a1_palaeodata_application.Rmd’
  
  --- re-building ‘a2_tidymodels_additions.Rmd’ using rmarkdown
  --- finished re-building ‘a2_tidymodels_additions.Rmd’
  
  --- re-building ‘a3_troubleshooting.Rmd’ using rmarkdown
  
  Quitting from a3_troubleshooting.Rmd:306-309 [unnamed-chunk-15]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  NULL
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'a3_troubleshooting.Rmd' failed with diagnostics:
  No method for objects of class: NULL
  --- failed re-building ‘a3_troubleshooting.Rmd’
  
  SUMMARY: processing the following files failed:
    ‘a1_palaeodata_application.Rmd’ ‘a3_troubleshooting.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: tradeoffaucdim
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [49s/49s]
  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(tradeoffaucdim)
    Loading required package: SuperLearner
    Loading required package: nnls
    Loading required package: gam
    Loading required package: splines
    Loading required package: foreach
    Loaded gam 1.22-5
    
    Super Learner
    Version: 2.0-29
    Package created on 2024-02-06
    
    > 
    > test_check("tradeoffaucdim" )
    fitting model SL.glm ======>------------------------   20% |  ETA: 14s
    fitting model SL.glm ===========>-------------------   36% |  ETA: 12s
    fitting model SL.glm ================>--------------   53% |  ETA:  9s
    fitting model SL.glm ====================>----------   66% |  ETA:  7s
    fitting model SL.glm ========================>------   79% |  ETA:  4s
    fitting model SL.glm ===========================>---   92% |  ETA:  2s
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 38 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-05-plot_curve.R:11:3'): output ───────────────────────────────
    plot_curve(obj4)$plot_performance has type 'object', not 'list'.
    ── Failure ('test-05-plot_curve.R:12:3'): output ───────────────────────────────
    plot_curve(obj4)$plot_time has type 'object', not 'list'.
    
    [ FAIL 2 | WARN 0 | SKIP 0 | PASS 38 ]
    Error: Test failures
    Execution halted

Package: TransProR
Check: examples
New result: ERROR
  Running examples in ‘TransProR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: highlight_by_node
  > ### Title: Highlight Nodes in a Phylogenetic Tree with Custom Fill Colors
  > ###   and Transparency
  > ### Aliases: highlight_by_node
  > 
  > ### ** Examples
  > 
  > plot_file <- system.file("extdata", "tree_plot.rds", package = "TransProR")
  > p2_plot <- readRDS(plot_file)
  > 
  > # Please replace the following vectors with your specific values
  > nodes <- c(117, 129, 125, 127, 119,
  +            123, 139, 166, 124, 131, 217) # x-values of the nodes you want to highlight
  > fill_colors <- c("#CD6600", "#CD6600", "#CD6600",
  +                  "#CD6600", "#009933", "#009933",
  +                  "#009933", "#009933", "#9B30FF",
  +                  "#9B30FF", "#9B30FF") # Fill colors
  > alpha_values <- c(0.3, 0.3, 0.3, 0.3, 0.2, 0.3,
  +                   0.3, 0.3, 0.3, 0.3, 0.3) # Transparency values
  > extend_values <- c(25, 24, 24, 25, 25, 25,
  +                    24, 24, 25, 24, 24) # Values for the 'extend' parameter
  > 
  > p2 <- highlight_by_node(
  +   p2_plot,
  +   nodes,
  +   fill_colors,
  +   alpha_values,
  +   extend_values
  + )
  Error in ggtree_object + layer : non-numeric argument to binary operator
  Calls: highlight_by_node
  Execution halted
  Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
  DESeq2_analyze 6.585  0.564    7.18

Package: tricolore
Check: package dependencies
New result: ERROR
  Package required but not available: ‘ggtern’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: triplot
Check: examples
New result: ERROR
  Running examples in ‘triplot-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot.triplot
  > ### Title: Plots triplot
  > ### Aliases: plot.triplot
  > 
  > ### ** Examples
  > 
  > library(DALEX)
  Welcome to DALEX (version: 2.5.2).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  > set.seed(123)
  > apartments_num <- apartments[,unlist(lapply(apartments, is.numeric))]
  > apartments_num_lm_model <- lm(m2.price ~ ., data = apartments_num)
  > apartments_num_new_observation <- apartments_num[30, ]
  > explainer_apartments <- explain(model = apartments_num_lm_model,
  +                                 data = apartments_num[,-1],
  +                                 y = apartments_num[, 1],
  +                                 verbose = FALSE)
  > apartments_tri <- calculate_triplot(x = explainer_apartments,
  +  new_observation = apartments_num_new_observation[-1])
  > plot(apartments_tri)
  Error: <ggplot2::ggplot> object properties are invalid:
  - @labels must be <ggplot2::labels>, not <character>
  Execution halted

Package: triplot
Check: tests
New result: ERROR
    Running ‘testthat.R’ [16s/16s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(triplot)
    > 
    > test_check("triplot")
    Welcome to DALEX (version: 2.5.2).
    Find examples and detailed introduction at: http://ema.drwhy.ai/
    Additional features will be available after installation of: ggpubr.
    Use 'install_dependencies()' to get all suggested dependencies
    [ FAIL 2 | WARN 3 | SKIP 0 | PASS 74 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_triplot.R:86:3'): check plot.calculate_triplot function ────────
    Error: <ggplot2::ggplot> object properties are invalid:
    - @labels must be <ggplot2::labels>, not <character>
    Backtrace:
         ▆
      1. ├─base::plot(apartments_tri) at test_triplot.R:86:3
      2. └─triplot:::plot.triplot(apartments_tri)
      3.   └─S7:::Ops.S7_object(p3, theme(axis.title = element_text(size = axis_lab_size)))
      4.     ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
      5.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      6.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      7.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
      8.     └─base_ops[[.Generic]](e1, e2)
      9.       ├─S7::S7_dispatch()
     10.       └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     11.         └─ggplot2:::add_ggplot(e1, e2, e2name)
     12.           ├─ggplot2::ggplot_add(object, p, objectname)
     13.           └─ggplot2:::ggplot_add.default(object, p, objectname)
     14.             └─ggplot2::update_ggplot(object = object, plot = plot, ...)
     15.               ├─S7::S7_dispatch()
     16.               └─ggplot2 (local) `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`(...)
     17.                 └─S7::set_props(plot, theme = add_theme(plot@theme, object))
     18.                   └─S7::`props<-`(`*tmp*`, value = list(...))
     19.                     └─S7::validate(object)
    ── Error ('test_triplot.R:112:3'): check plot.calculate_triplot function for FI ──
    Error: <ggplot2::ggplot> object properties are invalid:
    - @labels must be <ggplot2::labels>, not <character>
    Backtrace:
         ▆
      1. ├─base::plot(apartments_tri, abbrev_labels = 5) at test_triplot.R:112:3
      2. └─triplot:::plot.triplot(apartments_tri, abbrev_labels = 5)
      3.   └─S7:::Ops.S7_object(p3, theme(axis.title = element_text(size = axis_lab_size)))
      4.     ├─base::tryCatch(return(base_ops[[.Generic]](e1, e2)), S7_error_method_not_found = function(cnd) cnd)
      5.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
      6.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
      7.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
      8.     └─base_ops[[.Generic]](e1, e2)
      9.       ├─S7::S7_dispatch()
     10.       └─ggplot2 (local) `method(+, list(ggplot2::ggplot, class_any))`(...)
     11.         └─ggplot2:::add_ggplot(e1, e2, e2name)
     12.           ├─ggplot2::ggplot_add(object, p, objectname)
     13.           └─ggplot2:::ggplot_add.default(object, p, objectname)
     14.             └─ggplot2::update_ggplot(object = object, plot = plot, ...)
     15.               ├─S7::S7_dispatch()
     16.               └─ggplot2 (local) `method(update_ggplot, list(ggplot2::theme, ggplot2::ggplot))`(...)
     17.                 └─S7::set_props(plot, theme = add_theme(plot@theme, object))
     18.                   └─S7::`props<-`(`*tmp*`, value = list(...))
     19.                     └─S7::validate(object)
    
    [ FAIL 2 | WARN 3 | SKIP 0 | PASS 74 ]
    Error: Test failures
    Execution halted

Package: umx
Check: examples
New result: ERROR
  Running examples in ‘umx-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: umxDiffMZ
  > ### Title: MZ differences method for testing evidence for causality.
  > ### Aliases: umxDiffMZ
  > 
  > ### ** Examples
  > 
  > data(twinData)
  > umxDiffMZ(x="ht", y="wt", labxy = c(-.5, 3), data = twinData, sep = "")
  umxDiffMZ is pre-alpha quality: Internals are stubs and parameter names may change!
  The `method` was set to "gam", but mgcv is not installed.
  ! Falling back to `method = "lm"`.
  ℹ Install mgcv or change the `method` argument to resolve this issue.
  `geom_smooth()` using method = 'gam' and formula = 'y ~ x'
  Warning: Removed 96 rows containing non-finite outside the scale range
  (`stat_smooth()`).
  Error in `annotate()`:
  ! Problem while setting up geom aesthetics.
  ℹ Error occurred in the 4th layer.
  Caused by error in `list_sizes()`:
  ! `x$label` must be a vector, not a call.
  Backtrace:
       ▆
    1. ├─umx::umxDiffMZ(...)
    2. │ ├─base::print(p)
    3. │ ├─base::print(p)
    4. │ └─ggplot2 (local) `print.ggplot2::ggplot`(p)
    5. │   ├─ggplot2::ggplot_build(x)
    6. │   └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
    7. │     └─ggplot2:::by_layer(...)
    8. │       ├─rlang::try_fetch(...)
    9. │       │ ├─base::tryCatch(...)
   10. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   13. │       │ └─base::withCallingHandlers(...)
   14. │       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   15. │         └─l$compute_geom_2(d, theme = plot@theme)
   16. │           └─ggplot2 (local) compute_geom_2(..., self = self)
   17. │             └─self$geom$use_defaults(...)
   18. │               └─ggplot2 (local) use_defaults(..., self = self)
   19. │                 └─ggplot2:::check_aesthetics(new_params, nrow(data))
   20. │                   └─vctrs::list_sizes(x)
   21. └─vctrs:::stop_scalar_type(...)
   22.   └─vctrs:::stop_vctrs(...)
   23.     └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  Execution halted

Package: umx
Check: tests
New result: ERROR
    Running ‘testthat.R’ [470s/339s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library("testthat")
    > library("umx")
    Loading required package: OpenMx
    For an overview type '?umx'
    
    Attaching package: 'umx'
    
    The following object is masked from 'package:stats':
    
        loadings
    
    > 
    > test_check("umx")
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    Table: Table of Model Comparisons
    
    |Model  | EP|Δ Fit  |Δ df |p       |      AIC|Δ AIC  |Compare with Model |Fit units |
    |:------|--:|:------|:----|:-------|--------:|:------|:------------------|:---------|
    |CP3fac | 51|       |     |        | 184511.3|0      |                   |-2lnL     |
    |dropC  | 42|237.47 |9    |< 0.001 | 184730.8|219.47 |CP3fac             |-2lnL     |
    
    
    Table: Common Factor Paths
    
    |                |A    |C  |    E|
    |:---------------|:----|:--|----:|
    |Common.factor.1 |0.79 |.  | 0.62|
    |Common.factor.2 |.    |.  | 1.00|
    |Common.factor.3 |0.64 |.  | 0.76|
    
    
    Table: Loadings of each trait on the Common Factors
    
    |    |   CP1|   CP2|   CP3|
    |:---|-----:|-----:|-----:|
    |gff |  0.44|  0.05|  0.35|
    |fc  |  0.99|  0.02| -0.05|
    |qol |  0.31|  0.05|  0.71|
    |hap |  0.24|  0.76|  0.58|
    |sat |  0.27|  0.38|  0.65|
    |AD  | -0.31| -0.20| -0.45|
    
    
    Table: Specific-factor loadings
    
    |           |gff  |fc   |qol  |hap  |sat  |AD   |
    |:----------|:----|:----|:----|:----|:----|:----|
    |Specific a |0.45 |.    |0.17 |0.13 |0.16 |0.38 |
    |Specific c |.    |.    |.    |.    |.    |.    |
    |Specific e |0.7  |0.16 |0.61 |.    |0.58 |0.73 |
    
    
    Table: Means (from model$top$expMean)
    
    |          | gff_T1|  fc_T1| qol_T1| hap_T1| sat_T1| AD_T1| gff_T2|  fc_T2| qol_T2| hap_T2| sat_T2| AD_T2|
    |:---------|------:|------:|------:|------:|------:|-----:|------:|------:|------:|------:|------:|-----:|
    |intercept |  38.39| -13.37|   7.81|  22.97|  27.56|  4.09|  38.39| -13.37|   7.81|  22.97|  27.56|  4.09|
    
    
    Table: Table of Model Comparisons
    
    |Model  | EP|Δ Fit   |Δ df |p       |      AIC|Δ AIC   |Compare with Model |Fit units |
    |:------|--:|:-------|:----|:-------|--------:|:-------|:------------------|:---------|
    |CP3fac | 51|        |     |        | 184511.3|0       |                   |-2lnL     |
    |dropC  | 42|237.469 |9    |< 0.001 | 184730.8|219.469 |CP3fac             |-2lnL     |
    
    
    
    
    
    
            lbound estimate ubound lbound Code ubound Code
    G_to_x1  0.367    0.397  0.429           0           0
            lbound estimate ubound lbound Code ubound Code
    G_to_x1  0.367    0.397  0.429           0           0
               lbound estimate ubound lbound Code ubound Code
    G_to_x1     0.367    0.397  0.429           0           0
    G_to_x2     0.469    0.503  0.541           0           0
    G_to_x3     0.538    0.577  0.619           0           0
    G_to_x4     0.657    0.702  0.751           0           0
    G_to_x5     0.746    0.795  0.850           0           0
    x1_with_x1  0.036    0.041  0.047           0           0
    x2_with_x2  0.033    0.038  0.044           0           0
    x3_with_x3  0.035    0.041  0.047           0           0
    x4_with_x4  0.033    0.039  0.047           0           0
    x5_with_x5  0.030    0.036  0.044           0           0
            lbound estimate ubound lbound Code ubound Code
    G_to_x1  0.367    0.397  0.429           0           0
    G_to_x2  0.469    0.503  0.541           0           0
    G_to_x3  0.538    0.577  0.619           0           0
    G_to_x4  0.657    0.702  0.751           0           0
    G_to_x5  0.746    0.795  0.850           0           0
            lbound estimate ubound lbound Code ubound Code
    G_to_x1  0.367    0.397  0.429           0           0
    The hypothesis that 'drop_path_2_x2' was tested by dropping drop_path_2_x2 from 'One Factor'. This caused a significant loss of fit (χ²(1) = 946, p = < 0.001: AIC = -2696.599 change in AIC = 943.998).
    
    Table: Table of Model Comparisons
    
    |Model          | EP|Δ Fit   |Δ df |p       |       AIC|Δ AIC   |Compare with Model |Fit units |
    |:--------------|--:|:-------|:----|:-------|---------:|:-------|:------------------|:---------|
    |One Factor     | 10|        |     |        | -3640.597|0       |                   |-2lnL     |
    |drop_path_2_x2 |  9|945.998 |1    |< 0.001 | -2696.599|943.998 |One Factor         |-2lnL     |
    
    
    Table: Table of Model Comparisons
    
    |Model          | EP|Δ Fit   |Δ df |p       |       AIC|Δ AIC   |Compare with Model |Fit units |
    |:--------------|--:|:-------|:----|:-------|---------:|:-------|:------------------|:---------|
    |One Factor     | 10|        |     |        | -3640.597|0       |                   |-2lnL     |
    |drop_path_2_x2 |  9|945.998 |1    |< 0.001 | -2696.599|943.998 |One Factor         |-2lnL     |
    <table class=" lightable-paper lightable-striped" style='font-family: "Arial Narrow", arial, helvetica, sans-serif; width: auto !important; margin-left: auto; margin-right: auto;'>
    <caption>Table of Model Comparisons</caption>
     <thead>
      <tr>
       <th style="text-align:left;"> Model </th>
       <th style="text-align:right;"> EP </th>
       <th style="text-align:left;"> Δ Fit </th>
       <th style="text-align:left;"> Δ df </th>
       <th style="text-align:left;"> p </th>
       <th style="text-align:right;"> AIC </th>
       <th style="text-align:left;"> Δ AIC </th>
       <th style="text-align:left;"> Compare with Model </th>
       <th style="text-align:left;"> Fit units </th>
      </tr>
     </thead>
    <tbody>
      <tr>
       <td style="text-align:left;"> One Factor </td>
       <td style="text-align:right;"> 10 </td>
       <td style="text-align:left;">  </td>
       <td style="text-align:left;">  </td>
       <td style="text-align:left;">  </td>
       <td style="text-align:right;"> -3640.597 </td>
       <td style="text-align:left;"> 0 </td>
       <td style="text-align:left;">  </td>
       <td style="text-align:left;"> -2lnL </td>
      </tr>
      <tr>
       <td style="text-align:left;"> drop_path_2_x2 </td>
       <td style="text-align:right;"> 9 </td>
       <td style="text-align:left;"> 945.998 </td>
       <td style="text-align:left;"> 1 </td>
       <td style="text-align:left;"> &lt; 0.001 </td>
       <td style="text-align:right;"> -2696.599 </td>
       <td style="text-align:left;"> 943.998 </td>
       <td style="text-align:left;"> One Factor </td>
       <td style="text-align:left;"> -2lnL </td>
      </tr>
    </tbody>
    </table>
    
    Table: Table of Model Comparisons
    
    |Model                | EP|Δ Fit    |Δ df |p       |       AIC|Δ AIC    |Compare with Model |Fit units |
    |:--------------------|--:|:--------|:----|:-------|---------:|:--------|:------------------|:---------|
    |One Factor           | 10|         |     |        | -3640.597|0        |                   |-2lnL     |
    |drop_path_2_x2       |  9|945.998  |1    |< 0.001 | -2696.599|943.998  |One Factor         |-2lnL     |
    |drop_path_2_x2_and_3 |  8|1939.339 |2    |< 0.001 | -1705.258|1935.339 |One Factor         |-2lnL     |
    
    
    Table: Table of Model Comparisons
    
    |Model                | EP|Δ Fit    |Δ df |p       |       AIC|Δ AIC    |Compare with Model |Fit units |
    |:--------------------|--:|:--------|:----|:-------|---------:|:--------|:------------------|:---------|
    |One Factor           | 10|         |     |        | -3640.597|0        |                   |-2lnL     |
    |drop_path_2_x2       |  9|945.998  |1    |< 0.001 | -2696.599|943.998  |One Factor         |-2lnL     |
    |drop_path_2_x2_and_3 |  8|1939.339 |2    |< 0.001 | -1705.258|1935.339 |One Factor         |-2lnL     |
    The  'One Factor'  model is the best fitting model according to AIC.AIC weight-based  {Wagenmakers, 2004, 192-196} conditional probabilities of being the best model for  'One Factor', 'drop_path_2_x2', and 'drop_path_2_x2_and_3'  respectively are:  '1', '0', and '0'  Using MuMIn::Weights(AIC()).
    
    Table: Table of Model Comparisons
    
    |Model                | EP|Δ Fit    |Δ df |p       |       AIC|Δ AIC    |Compare with Model |Fit units |
    |:--------------------|--:|:--------|:----|:-------|---------:|:--------|:------------------|:---------|
    |One Factor           | 10|         |     |        | -3640.597|0        |                   |-2lnL     |
    |drop_path_2_x2       |  9|945.998  |1    |< 0.001 | -2696.599|943.998  |One Factor         |-2lnL     |
    |drop_path_2_x2_and_3 |  8|1939.339 |2    |< 0.001 | -1705.258|1935.339 |One Factor         |-2lnL     |
    |drop_path_2_x2       |  9|         |     |        | -2696.599|943.998  |                   |-2lnL     |
    |drop_path_2_x2       |  9|0        |0    |        | -2696.599|943.998  |drop_path_2_x2     |-2lnL     |
    |drop_path_2_x2_and_3 |  8|993.341  |1    |< 0.001 | -1705.258|1935.339 |drop_path_2_x2     |-2lnL     |
    
    
    Table: Parameter loadings for model 'One Factor'
    
    |   |name       | Std.Estimate|Std.SE |CI                |type            |
    |:--|:----------|------------:|:------|:-----------------|:---------------|
    |11 |G_with_G   |         1.00|0      |1 [1, 1]          |Factor Variance |
    |1  |G_to_x1    |         0.89|0.01   |0.89 [0.87, 0.91] |Factor loading  |
    |2  |G_to_x2    |         0.93|0.01   |0.93 [0.92, 0.95] |Factor loading  |
    |3  |G_to_x3    |         0.94|0.01   |0.94 [0.93, 0.95] |Factor loading  |
    |4  |G_to_x4    |         0.96|0      |0.96 [0.95, 0.97] |Factor loading  |
    |5  |G_to_x5    |         0.97|0      |0.97 [0.97, 0.98] |Factor loading  |
    |6  |x1_with_x1 |         0.21|0.02   |0.21 [0.17, 0.24] |Residual        |
    |7  |x2_with_x2 |         0.13|0.01   |0.13 [0.11, 0.15] |Residual        |
    |8  |x3_with_x3 |         0.11|0.01   |0.11 [0.09, 0.13] |Residual        |
    |9  |x4_with_x4 |         0.07|0.01   |0.07 [0.06, 0.09] |Residual        |
    |10 |x5_with_x5 |         0.05|0.01   |0.05 [0.04, 0.07] |Residual        |
    
    
    Table: Parameter loadings for model 'One Factor'
    
    |   |name       | Std.Estimate|Std.SE |CI                |type            |
    |:--|:----------|------------:|:------|:-----------------|:---------------|
    |11 |G_with_G   |         1.00|0      |1 [1, 1]          |Factor Variance |
    |1  |G_to_x1    |         0.89|0.01   |0.89 [0.87, 0.91] |Factor loading  |
    |2  |G_to_x2    |         0.93|0.01   |0.93 [0.92, 0.95] |Factor loading  |
    |3  |G_to_x3    |         0.94|0.01   |0.94 [0.93, 0.95] |Factor loading  |
    |4  |G_to_x4    |         0.96|0      |0.96 [0.95, 0.97] |Factor loading  |
    |5  |G_to_x5    |         0.97|0      |0.97 [0.97, 0.98] |Factor loading  |
    |6  |x1_with_x1 |         0.21|0.02   |0.21 [0.17, 0.24] |Residual        |
    |7  |x2_with_x2 |         0.13|0.01   |0.13 [0.11, 0.15] |Residual        |
    |8  |x3_with_x3 |         0.11|0.01   |0.11 [0.09, 0.13] |Residual        |
    |9  |x4_with_x4 |         0.07|0.01   |0.07 [0.06, 0.09] |Residual        |
    |10 |x5_with_x5 |         0.05|0.01   |0.05 [0.04, 0.07] |Residual        |
    
    
    Table: Parameter loadings for model 'One Factor'
    
    |   |name       | Estimate|SE   |type            |
    |:--|:----------|--------:|:----|:---------------|
    |11 |G_with_G   |     1.00|0    |Factor Variance |
    |1  |G_to_x1    |     0.40|0.02 |Factor loading  |
    |2  |G_to_x2    |     0.50|0.02 |Factor loading  |
    |3  |G_to_x3    |     0.58|0.02 |Factor loading  |
    |4  |G_to_x4    |     0.70|0.02 |Factor loading  |
    |5  |G_to_x5    |     0.80|0.03 |Factor loading  |
    |6  |x1_with_x1 |     0.04|0    |Residual        |
    |7  |x2_with_x2 |     0.04|0    |Residual        |
    |8  |x3_with_x3 |     0.04|0    |Residual        |
    |9  |x4_with_x4 |     0.04|0    |Residual        |
    |10 |x5_with_x5 |     0.04|0    |Residual        |
    
    
    Table: Parameter loadings for model 'One Factor'
    
    |   |name      | Std.Estimate| Std.SE|CI                  |type |
    |:--|:---------|------------:|------:|:-------------------|:----|
    |12 |one_to_x1 |        -0.02|    0.1|-0.02 [-0.22, 0.18] |Mean |
    |13 |one_to_x2 |        -0.10|    0.1|-0.1 [-0.3, 0.1]    |Mean |
    |14 |one_to_x3 |        -0.08|    0.1|-0.08 [-0.28, 0.11] |Mean |
    |15 |one_to_x4 |        -0.07|    0.1|-0.07 [-0.27, 0.12] |Mean |
    |16 |one_to_x5 |        -0.07|    0.1|-0.07 [-0.26, 0.13] |Mean |
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |   a1|c1 |   e1|
    |:---|----:|:--|----:|
    |bmi | 0.86|.  | 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.648| 21.648|
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |   a1|c1 |   e1|
    |:---|----:|:--|----:|
    |bmi | 0.86|.  | 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.648| 21.648|
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |   a1|c1 |   e1|
    |:---|----:|:--|----:|
    |bmi | 0.86|.  | 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.648| 21.648|
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |   a1|c1 |   e1|
    |:---|----:|:--|----:|
    |bmi | 0.86|.  | 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.648| 21.648|
    
    
    
    
    |name    |Estimate |Std.Error |
    |:-------|:--------|:---------|
    |a_r1c1  |-0.82    |0.1       |
    |c_r1c1  |-0.07    |0.24      |
    |e_r1c1  |0.31     |0.03      |
    |am_r1c1 |0        |0         |
    |cm_r1c1 |-0.01    |0.01      |
    |em_r1c1 |0.01     |0         |
    |mean    |20.57    |0.15      |
    |lin11   |0.05     |0.01      |
    |quad11  |0        |0         |
    
    
    |name    |Estimate |Std.Error |
    |:-------|:--------|:---------|
    |a_r1c1  |-0.82    |0.1       |
    |c_r1c1  |-0.07    |0.24      |
    |e_r1c1  |0.31     |0.03      |
    |am_r1c1 |0        |0         |
    |cm_r1c1 |-0.01    |0.01      |
    |em_r1c1 |0.01     |0         |
    |mean    |20.57    |0.15      |
    |lin11   |0.05     |0.01      |
    |quad11  |0        |0         |
    
    
    |name    |Estimate |Std.Error |
    |:-------|:--------|:---------|
    |a_r1c1  |-0.82    |0.1       |
    |c_r1c1  |-0.07    |0.24      |
    |e_r1c1  |0.31     |0.03      |
    |am_r1c1 |0        |0         |
    |cm_r1c1 |-0.01    |0.01      |
    |em_r1c1 |0.01     |0         |
    |mean    |20.57    |0.15      |
    |lin11   |0.05     |0.01      |
    |quad11  |0        |0         |
    
    
    |name    |Estimate |Std.Error |
    |:-------|:--------|:---------|
    |a_r1c1  |-0.82    |0.1       |
    |c_r1c1  |-0.07    |0.24      |
    |e_r1c1  |0.31     |0.03      |
    |am_r1c1 |0        |0         |
    |cm_r1c1 |-0.01    |0.01      |
    |em_r1c1 |0.01     |0         |
    |mean    |20.57    |0.15      |
    |lin11   |0.05     |0.01      |
    |quad11  |0        |0         |
    
    
    |name    |Estimate |Std.Error |
    |:-------|:--------|:---------|
    |a_r1c1  |-0.82    |0.1       |
    |c_r1c1  |-0.07    |0.24      |
    |e_r1c1  |0.31     |0.03      |
    |am_r1c1 |0        |0         |
    |cm_r1c1 |-0.01    |0.01      |
    |em_r1c1 |0.01     |0         |
    |mean    |20.57    |0.15      |
    |lin11   |0.05     |0.01      |
    |quad11  |0        |0         |
    
    
    Table: General Independent Pathway path loadings
    
    |    |   ai1|   ci1|   ei1|
    |:---|-----:|-----:|-----:|
    |hap |  0.47|  0.24|  0.77|
    |sat |  0.51|  0.20|  0.56|
    |AD  | -0.54| -0.06| -0.27|
    
    
    Table: Specific factor loadings
    
    |           |hap  |sat  |AD   |
    |:----------|:----|:----|:----|
    |Specific a |0.14 |0.3  |0.45 |
    |Specific c |.    |.    |.    |
    |Specific e |0.32 |0.54 |0.65 |
    
    
    Table: Means (from model$top$expMean)
    
    |          | hap_T1| sat_T1| AD_T1| hap_T2| sat_T2| AD_T2|
    |:---------|------:|------:|-----:|------:|------:|-----:|
    |intercept |  22.98|  27.56|  4.14|  22.98|  27.56|  4.14|
    Error in generateNormalData(model, nrows, subname, empirical, returnModel,  : 
      Definition variable(s) found, but the number of rows in the data do not match the number of rows requested for data generation.
    
    
    Table: Parameter loadings for model 'tim'
    
    |   |name               | Std.Estimate|Std.SE |CI                   |type          |
    |:--|:------------------|------------:|:------|:--------------------|:-------------|
    |5  |litres_with_wt     |         0.89|0.04   |0.89 [0.81, 0.96]    |Manifest Cov  |
    |1  |wt_to_mpg          |        -0.54|0.17   |-0.54 [-0.89, -0.2]  |Manifest path |
    |2  |litres_to_mpg      |        -0.36|0.18   |-0.36 [-0.71, -0.02] |Manifest path |
    |7  |one_to_mpg         |         5.89|0.68   |5.89 [4.56, 7.22]    |Mean          |
    |8  |one_to_wt          |         3.34|0.45   |3.34 [2.45, 4.23]    |Mean          |
    |9  |one_to_litres      |         1.89|0.3    |1.89 [1.31, 2.47]    |Mean          |
    |3  |mpg_with_mpg       |         0.22|0.07   |0.22 [0.08, 0.35]    |Residual      |
    |4  |wt_with_wt         |         1.00|0      |1 [1, 1]             |Residual      |
    |6  |litres_with_litres |         1.00|0      |1 [1, 1]             |Residual      |
    
    
    Table: Raw parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |   |   a1|  c1|   e1|
    |:--|----:|---:|----:|
    |ht | 0.61| 0.1| 0.24|
    
    
    Table: Means (from model$top$expMean)
    
    |          |    ht1|    ht2|
    |:---------|------:|------:|
    |intercept | 16.252| 16.252|
    
    
    Table: Table of Model Comparisons
    
    |Model | EP|Δ Fit  |Δ df |p  |      AIC|Δ AIC  |Compare with Model |Fit units |
    |:-----|--:|:------|:----|:--|--------:|:------|:------------------|:---------|
    |ADE   |  4|       |     |   | 5987.341|0      |                   |-2lnL     |
    |ACE   |  4|-0.139 |0    |   | 5987.202|-0.139 |ADE                |-2lnL     |
    
    
    Table: Table of Model Comparisons
    
    |Model | EP|Δ Fit |Δ df |p  |     AIC|Δ AIC |Compare with Model |Fit units |
    |:-----|--:|:-----|:----|:--|-------:|:-----|:------------------|:---------|
    |ACE   |  4|      |     |   | 5987.20|0     |                   |-2lnL     |
    |ADE   |  4|0.14  |0    |   | 5987.34|0.14  |ACE                |-2lnL     |
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; D: dominance effects; E: unique environment.
    
    |   |   a1|d1 |   e1|
    |:--|----:|:--|----:|
    |ht | 0.93|.  | 0.36|
    
    
    Table: Means (from model$top$expMean)
    
    |          |    ht1|    ht2|
    |:---------|------:|------:|
    |intercept | 16.252| 16.252|
    (Intercept) B = 60.201 [59.505, 60.898], t = 169.359, p < 0.001
    age B = 0.106 [0.088, 0.125], t = 11.183, p < 0.001
    R² = 0.017 (adj = 0.016)(Intercept) B = 1.711 [1.705, 1.717], t = 590.26, p < 0.001
    age B = -0.001 [-0.001, -0.001], t = -12.358, p < 0.001
    R² = 0.02 (adj = 0.02)
    
    Table: Standardized parameter estimates from a 2-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |   |   a1|a2   |    c1|c2 |   e1|e2  |
    |:--|----:|:----|-----:|:--|----:|:---|
    |ht | 0.76|     |  0.43|   | 0.49|    |
    |wt | 0.60|0.68 | -0.10|.  | 0.02|0.4 |
    
    
    Table: Means (from model$top$expMean)
    
    |          |   ht1|    wt1|   ht2|    wt2|
    |:---------|-----:|------:|-----:|------:|
    |intercept | -0.39| -0.532| -0.39| -0.532|
    'data.frame':	80 obs. of  18 variables:
     $ fam     : int  1 2 3 4 5 6 7 8 9 10 ...
     $ age     : int  21 24 21 21 19 26 23 29 24 28 ...
     $ zyg     : int  1 1 1 1 1 1 1 1 1 1 ...
     $ part    : int  2 2 2 2 2 2 2 2 2 2 ...
     $ wt1     : num  -0.502 -0.844 -0.758 0.181 -1.185 ...
     $ wt2     : num  -0.588 -0.929 -1.185 1.035 -1.356 ...
     $ ht1     : num  1.7 1.63 1.65 1.57 1.61 ...
     $ ht2     : num  1.7 1.63 1.68 1.65 1.63 ...
     $ htwt1   : num  20.1 20.3 20.2 26.8 19.3 ...
     $ htwt2   : num  19.7 19.9 17.7 27.9 18.1 ...
     $ bmi1    : num  21 21.1 21 23 20.7 ...
     $ bmi2    : num  20.9 21 20.1 23.3 20.3 ...
     $ cohort  : chr  "younger" "younger" "younger" "younger" ...
     $ zygosity: Factor w/ 5 levels "MZFF","MZMM",..: 1 1 1 1 1 1 1 1 1 1 ...
     $ age1    : int  21 24 21 21 19 26 23 29 24 28 ...
     $ age2    : int  21 24 21 21 19 26 23 29 24 28 ...
     $ obese1  : Ord.factor w/ 3 levels "normal"<"overweight"<..: 2 2 2 3 1 3 2 1 1 3 ...
     $ obese2  : Ord.factor w/ 3 levels "normal"<"overweight"<..: 1 1 1 3 1 3 2 1 1 2 ...
    
    
    Table: Standardized parameter estimates from a 2-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |      |   a1|a2   |   c1|c2 |   e1|e2   |
    |:-----|----:|:----|----:|:--|----:|:----|
    |wt    | 0.87|     | 0.06|   | 0.48|     |
    |obese | 0.63|0.52 | 0.25|.  | 0.40|0.33 |
    
    
    Table: Means (from model$top$expMean)
    
    |          |    wt1|obese1 |    wt2|obese2 |
    |:---------|------:|:------|------:|:------|
    |intercept | -0.414|0      | -0.414|0      |
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |   |   a1|c1 |   e1|
    |:--|----:|:--|----:|
    |wt | 0.87|.  | 0.49|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.58|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.698| 21.698|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.89| 0.45|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.305| 21.305|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.89| 0.45|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.313| 21.313|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.89| 0.46|
    
    
    Table: Means (from model$top$expMean)
    
    |          |  bmi1|  bmi2|
    |:---------|-----:|-----:|
    |intercept | 21.32| 21.32|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.89| 0.46|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.329| 21.329|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.89| 0.47|
    
    
    Table: Means (from model$top$expMean)
    
    |          |  bmi1|  bmi2|
    |:---------|-----:|-----:|
    |intercept | 21.34| 21.34|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.88| 0.47|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.351| 21.351|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.88| 0.48|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.364| 21.364|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.88| 0.48|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.378| 21.378|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.87| 0.49|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.394| 21.394|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.87| 0.49|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.411| 21.411|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|  e1|
    |:---|:--|----:|---:|
    |bmi |.  | 0.87| 0.5|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.429| 21.429|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.86| 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.449| 21.449|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.86| 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |  bmi1|  bmi2|
    |:---------|-----:|-----:|
    |intercept | 21.47| 21.47|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.85| 0.52|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.492| 21.492|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.85| 0.53|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.514| 21.514|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.85| 0.53|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.536| 21.536|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.84| 0.54|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.558| 21.558|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.84| 0.55|
    
    
    Table: Means (from model$top$expMean)
    
    |          |  bmi1|  bmi2|
    |:---------|-----:|-----:|
    |intercept | 21.58| 21.58|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.83| 0.56|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.601| 21.601|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.83| 0.56|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.621| 21.621|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.82| 0.57|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.641| 21.641|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.82| 0.57|
    
    
    Table: Means (from model$top$expMean)
    
    |          |  bmi1|  bmi2|
    |:---------|-----:|-----:|
    |intercept | 21.66| 21.66|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.58|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.679| 21.679|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.58|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.698| 21.698|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.718| 21.718|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.739| 21.739|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |  c1|   e1|
    |:---|:--|---:|----:|
    |bmi |.  | 0.8| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.763| 21.763|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |  c1|  e1|
    |:---|:--|---:|---:|
    |bmi |.  | 0.8| 0.6|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.788| 21.788|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |  c1|  e1|
    |:---|:--|---:|---:|
    |bmi |.  | 0.8| 0.6|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.816| 21.816|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |  c1|  e1|
    |:---|:--|---:|---:|
    |bmi |.  | 0.8| 0.6|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.847| 21.847|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |  c1|  e1|
    |:---|:--|---:|---:|
    |bmi |.  | 0.8| 0.6|
    
    
    Table: Means (from model$top$expMean)
    
    |          |  bmi1|  bmi2|
    |:---------|-----:|-----:|
    |intercept | 21.88| 21.88|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |  c1|   e1|
    |:---|:--|---:|----:|
    |bmi |.  | 0.8| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.914| 21.914|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.949| 21.949|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.985| 21.985|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.019| 22.019|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.051| 22.051|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.58|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.081| 22.081|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.82| 0.58|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.108| 22.108|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.82| 0.57|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.131| 22.131|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.82| 0.57|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.152| 22.152|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.83| 0.56|
    
    
    Table: Means (from model$top$expMean)
    
    |          |  bmi1|  bmi2|
    |:---------|-----:|-----:|
    |intercept | 22.17| 22.17|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.83| 0.56|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.185| 22.185|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.84| 0.55|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.197| 22.197|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.84| 0.54|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.208| 22.208|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.84| 0.54|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.216| 22.216|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.85| 0.53|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.223| 22.223|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.85| 0.52|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.229| 22.229|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.86| 0.52|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.233| 22.233|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.86| 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.238| 22.238|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.86| 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.242| 22.242|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|  e1|
    |:---|:--|----:|---:|
    |bmi |.  | 0.86| 0.5|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.246| 22.246|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|  e1|
    |:---|:--|----:|---:|
    |bmi |.  | 0.87| 0.5|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.251| 22.251|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|  e1|
    |:---|:--|----:|---:|
    |bmi |.  | 0.87| 0.5|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.256| 22.256|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.87| 0.49|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.261| 22.261|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.87| 0.49|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.266| 22.266|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.87| 0.49|
    
    
    Table: Means (from model$top$expMean)
    
    |          |  bmi1|  bmi2|
    |:---------|-----:|-----:|
    |intercept | 22.27| 22.27|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|  e1|
    |:---|:--|----:|---:|
    |bmi |.  | 0.87| 0.5|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.272| 22.272|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|  e1|
    |:---|:--|----:|---:|
    |bmi |.  | 0.87| 0.5|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.272| 22.272|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.86| 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.268| 22.268|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.86| 0.51|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.259| 22.259|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.85| 0.52|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.244| 22.244|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.85| 0.53|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.223| 22.223|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.84| 0.55|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.194| 22.194|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.82| 0.57|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.158| 22.158|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.81| 0.59|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.115| 22.115|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.78| 0.62|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.066| 22.066|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.76| 0.66|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 22.015| 22.015|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.72| 0.69|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.961| 21.961|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.68| 0.73|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.909| 21.909|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.63| 0.77|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.859| 21.859|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.58| 0.81|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.814| 21.814|
    
    
    
    
    Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |a1 |   c1|   e1|
    |:---|:--|----:|----:|
    |bmi |.  | 0.53| 0.85|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.776| 21.776|
    polite note: in future, please use report = 'markdown', not file='markdown'. file is for choosing a custom html file when writing to the browser with report= 'html'
    
    Table: Standardized parameter estimates from a 1-factor Direct variance ACE model. A: additive genetic; C: common environment; E: unique environment.
    
    |    |    A1|     C1|    E1|
    |:---|-----:|------:|-----:|
    |bmi | 0.807| -0.063| 0.256|
    
    
    Table: Means (from model$top$expMean)
    
    |          |   bmi1|   bmi2|
    |:---------|------:|------:|
    |intercept | 21.649| 21.649|
    
    
    
    
    
    
    Table: Parameter loadings for model 'check_model_ex'
    
    |   |name       | Estimate|SE   |type            |
    |:--|:----------|--------:|:----|:---------------|
    |11 |G_with_G   |     1.00|0    |Factor Variance |
    |1  |G_to_x1    |     0.89|0.02 |Factor loading  |
    |2  |G_to_x2    |     0.93|0.02 |Factor loading  |
    |3  |G_to_x3    |     0.94|0.02 |Factor loading  |
    |4  |G_to_x4    |     0.96|0.02 |Factor loading  |
    |5  |G_to_x5    |     0.97|0.03 |Factor loading  |
    |6  |x1_with_x1 |     0.21|0    |Residual        |
    |7  |x2_with_x2 |     0.13|0    |Residual        |
    |8  |x3_with_x3 |     0.11|0    |Residual        |
    |9  |x4_with_x4 |     0.07|0    |Residual        |
    |10 |x5_with_x5 |     0.05|0    |Residual        |
    [1] "cyl"
    [1] "cylinder"
    (Intercept) B = 34.661 [29.452, 39.87], t = 13.609, p < 0.001
    cyl B = -1.587 [-3.043, -0.131], t = -2.23, p = 0.034
    disp B = -0.021 [-0.042, 0], t = -2.007, p = 0.054
    R² = 0.76 (adj = 0.743)(Intercept) B = 53.445 [31.077, 75.814], t = 4.894, p < 0.001
    cyl B = -8.367 [-16.359, -0.376], t = -2.145, p = 0.041
    I(cyl^2) B = 0.597 [-0.096, 1.291], t = 1.766, p = 0.088
    disp B = -0.027 [-0.049, -0.006], t = -2.574, p = 0.016
    R² = 0.784 (adj = 0.76)(Intercept) B = 34.661 [31.149, 38.173], t = 19.737, p < 0.001
    cyl B = -1.587 [-2.569, -0.606], t = -3.234, p = 0.002
    disp B = -0.021 [-0.035, -0.006], t = -2.91, p = 0.005
    R² = 0.76 (adj = 0.752)(Intercept) B = 34.661 [29.452, 39.87], t = 13.609, p < 0.001
    cyl B = -1.587 [-3.043, -0.131], t = -2.23, p = 0.034
    disp B = -0.021 [-0.042, 0], t = -2.007, p = 0.054
    R² = 0.76 (adj = 0.743)(Intercept) B = -32.432 [-98.452, 33.589], t = -1.005, p = 0.323
    cyl B = 24.515 [6.063, 42.966], t = 2.717, p = 0.011
    disp B = 0.119 [-0.147, 0.385], t = 0.915, p = 0.368
    R² = 0.702 (adj = 0.681)[ FAIL 1 | WARN 9 | SKIP 25 | PASS 352 ]
    
    ══ Skipped tests (25) ══════════════════════════════════════════════════════════
    • empty test (25): 'test_poly.r:6:1', 'test_umxBuild_run_modify.r:94:1',
      'test_umxBuild_run_modify.r:131:1', 'test_umxBuild_run_modify.r:150:1',
      'test_umxBuild_run_modify.r:195:1', 'test_umxCP.r:4:1',
      'test_umxFactorScores.r:9:1', 'test_umxFitAndReporting.r:191:1',
      'test_umxFitAndReporting.r:205:1', 'test_umxMatrixFree.R:6:1',
      'test_umxPath.r:7:1', 'test_umx_ACE_etc.r:6:1', 'test_umx_ACE_etc.r:26:1',
      'test_umx_ACE_etc.r:69:2', 'test_umx_ACE_etc.r:118:2',
      'test_umx_ACE_etc.r:135:2', 'test_umx_ACE_etc.r:163:2',
      'test_umx_ACE_etc.r:185:2', 'test_umx_ACE_etc.r:222:1',
      'test_umx_ACE_etc.r:236:1', 'test_umx_ACE_etc.r:248:1',
      'test_umx_misc.r:54:1', 'test_umx_misc.r:96:1', 'test_umx_misc.r:111:1',
      'test_umx_misc.r:161:1'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test_umx_DOC_etc.r:12:2'): testing umxDiffMZ ────────────────────────
    Error in `annotate("text", x = labxy[1], y = labxy[2], label = blurb)`: Problem while setting up geom aesthetics.
    ℹ Error occurred in the 4th layer.
    Caused by error in `list_sizes()`:
    ! `x$label` must be a vector, not a call.
    
    [ FAIL 1 | WARN 9 | SKIP 25 | PASS 352 ]
    Error: Test failures
    Execution halted

Package: UnalR
Check: tests
New result: ERROR
    Running ‘testthat.R’ [17s/11s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(UnalR)
    > 
    > test_check("UnalR")
    Starting 2 test processes
    [ FAIL 1 | WARN 4 | SKIP 2 | PASS 73 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test-Plot_Boxplot.R:48:3', 'test-Tabla.R:40:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-Plot_Series.R:110:3'): Plot.Series() captura de algunos valores claves a retornar ──
    `output_PlotSeries` has type 'object', not 'list'.
    
    [ FAIL 1 | WARN 4 | SKIP 2 | PASS 73 ]
    Error: Test failures
    Execution halted

Package: vaccine
Check: tests
New result: ERROR
    Running ‘testthat.R’ [157s/157s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(vaccine)
    vaccine (version 1.3.0).
    Type ?vaccine to get started.
    > 
    > test_check("vaccine")
    Loading required package: nnls
    Loading required package: gam
    Loading required package: splines
    Loading required package: foreach
    Loaded gam 1.22-5
    
    Super Learner
    Version: 2.0-29
    Package created on 2024-02-06
    
    Loading required namespace: ranger
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 165 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-test-core-functions.R:320:3'): plot_ce ───────────────────────
    class(p) (`actual`) not equal to c("gg", "ggplot") (`expected`).
    
    `actual`:        "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"    
    `expected[2:2]`:                                                      "ggplot"
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 165 ]
    Error: Test failures
    Execution halted

Package: vaccineff
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘testthat.R’ [22s/22s]
  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
    > 
    > # nolint start
    > library(testthat)
    > library(vaccineff)
    > # nolint end
    > 
    > test_check("vaccineff")
    [ FAIL 2 | WARN 0 | SKIP 6 | PASS 100 ]
    
    ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
    • On CRAN (6): 'test-coh_immunization.R:344:3',
      'test-coh_immunization.R:369:3', 'test-coh_match.R:55:5',
      'test-coh_match_utils.R:251:3', 'test-coh_time_to_event.R:64:3',
      'test-handler_warnings.R:17:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-utils_coverage.R:38:3'): `plot_coverage`: default plot ───────
    plt$labels$y (`actual`) not identical to "coverage * max(dose_plot)" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('coverage * max(dose_plot)')
    ── Failure ('test-utils_coverage.R:50:3'): `plot_coverage`: cumulative plot ────
    plt$labels$y (`actual`) not identical to "coverage * max(dose_plot)" (`expected`).
    
    `actual` is NULL
    `expected` is a character vector ('coverage * max(dose_plot)')
    
    [ FAIL 2 | WARN 0 | SKIP 6 | PASS 100 ]
    Error: Test failures
    Execution halted

Package: vanquish
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘vanquish’

Package: VarSelLCM
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘VarSelLCM.Rmd’ using rmarkdown
  
  Quitting from VarSelLCM.Rmd:112-115 [unnamed-chunk-10]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `rep()`:
  ! attempt to replicate an object of type 'object'
  ---
  Backtrace:
      x
   1. +-base::plot(res_with, y = "Sex")
   2. \-VarSelLCM::plot(res_with, y = "Sex")
   3.   \-VarSelLCM (local) .local(x, y, ...)
   4.     \-base::ifelse(...)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'VarSelLCM.Rmd' failed with diagnostics:
  attempt to replicate an object of type 'object'
  --- failed re-building ‘VarSelLCM.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘VarSelLCM.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: vDiveR
Check: examples
New result: ERROR
  Running examples in ‘vDiveR-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_conservation_level
  > ### Title: Conservation Levels Distribution Plot
  > ### Aliases: plot_conservation_level
  > 
  > ### ** Examples
  > 
  > plot_conservation_level(proteins_1host, conservation_label = 1,alpha=0.8, base_size = 15)
  Ignoring unknown labels:
  • fill : "Conservation level"
  Error in `geom_half_point()`:
  ! 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 (local) `<fn>`(x)
    2. ├─ggplot2 (local) `print.ggplot2::ggplot`(x)
    3. │ ├─ggplot2::ggplot_gtable(data)
    4. │ └─ggplot2 (local) `ggplot_gtable.ggplot2::ggplot_built`(data)
    5. │   └─ggplot2:::by_layer(...)
    6. │     ├─rlang::try_fetch(...)
    7. │     │ ├─base::tryCatch(...)
    8. │     │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9. │     │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10. │     │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   11. │     │ └─base::withCallingHandlers(...)
   12. │     └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   13. │       └─l$draw_geom(d, layout)
   14. │         └─ggplot2 (local) draw_geom(..., self = self)
   15. │           └─self$geom$draw_layer(...)
   16. │             └─ggplot2 (local) draw_layer(..., self = self)
   17. │               └─base::lapply(...)
   18. │                 └─ggplot2 (local) FUN(X[[i]], ...)
   19. │                   ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
   20. │                   └─self$draw_panel(...)
   21. │                     └─ggplot2 (local) draw_panel(..., self = self)
   22. │                       └─base::lapply(...)
   23. │                         └─ggplot2 (local) FUN(X[[i]], ...)
   24. │                           └─self$draw_group(group, panel_params, coord, ...)
   25. │                             └─gghalves (local) draw_group(...)
   26. │                               └─transformation$compute_layer(transformation_df, transformation_params_new)
   27. │                                 └─ggplot2 (local) compute_layer(..., self = self)
   28. │                                   └─ggplot2:::dapply(...)
   29. │                                     └─base::lapply(...)
   30. │                                       └─ggplot2 (local) FUN(X[[i]], ...)
   31. │                                         └─ggplot2 (local) apply_fun(cur_data)
   32. │                                           └─ggplot2 (local) fun(x, ...)
   33. └─rlang (local) `<fn>`(`<gtvrErrr>`)
   34.   └─handlers[[1L]](cnd)
   35.     └─cli::cli_abort(...)
   36.       └─rlang::abort(...)
  Execution halted

Package: vip
Check: tests
New result: ERROR
    Running ‘tinytest.R’ [10s/10s]
  Running the tests in ‘tests/tinytest.R’ failed.
  Complete output:
    > if (requireNamespace("tinytest", quietly = TRUE)) {
    +   home <- length(unclass(packageVersion("vip"))[[1L]]) == 4
    +   tinytest::test_package("vip", at_home = home)
    + }
    
    Attaching package: 'vip'
    
    The following object is masked from 'package:utils':
    
        vi
    
    
    test_get_feature_names.R......    0 tests    
    test_get_feature_names.R......    0 tests    
    test_get_feature_names.R......    0 tests    
    test_get_feature_names.R......    1 tests OK 
    test_get_feature_names.R......    2 tests OK 
    test_get_feature_names.R......    3 tests OK 
    test_get_feature_names.R......    3 tests OK 
    test_get_feature_names.R......    3 tests OK 
    test_get_feature_names.R......    3 tests OK 
    test_get_feature_names.R......    3 tests OK 
    test_get_feature_names.R......    3 tests OK 
    test_get_feature_names.R......    4 tests OK 
    test_get_feature_names.R......    5 tests OK 0.1s
    
    test_pkg_C50.R................    0 tests    1ms [Exited at #12: Package 'C50' missing]
    
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    test_pkg_nnet.R...............    0 tests    
    test_pkg_nnet.R...............    0 tests    
    test_pkg_nnet.R...............    1 tests OK 
    test_pkg_nnet.R...............    2 tests OK 
    test_pkg_nnet.R...............    3 tests OK 
    test_pkg_nnet.R...............    3 tests OK 
    test_pkg_nnet.R...............    4 tests 1 fails 1.6s
    
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    test_pkg_party.R..............    1 tests OK 
    test_pkg_party.R..............    2 tests OK 
    test_pkg_party.R..............    3 tests OK 
    test_pkg_party.R..............    4 tests OK 
    test_pkg_party.R..............    5 tests OK 
    test_pkg_party.R..............    6 tests OK 5.4s
    
    test_pkg_partykit.R...........    0 tests    3ms [Exited at #7: Package 'partykit' missing]
    
    test_pkg_pls.R................    0 tests    1ms [Exited at #5: Package 'caret' missing]
    
    test_pkg_randomForest.R.......    0 tests    2ms [Exited at #12: Package 'randomForest' missing]
    
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    test_pkg_stats.R..............    0 tests    
    test_pkg_stats.R..............    1 tests OK 
    test_pkg_stats.R..............    2 tests OK 
    test_pkg_stats.R..............    3 tests OK 
    test_pkg_stats.R..............    4 tests OK 20ms
    
    test_pkg_tidymodels.R.........    0 tests    2ms [Exited at #5: Package 'ranger' missing]
    
    test_pkg_xgboost.R............    0 tests    1ms [Exited at #12: Package 'xgboost' missing]
    
    test_vi_firm.R................    0 tests    15ms [Exited at #8: 'requireNamespace("ranger", quietly = TRUE)' is not TRUE]
    
    test_vi_permute.R.............    0 tests    2ms [Exited at #7: 'requireNamespace("ranger", quietly = TRUE)' is not TRUE]
    
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    test_vi_shap.R................    0 tests    
    test_vi_shap.R................    0 tests    
    test_vi_shap.R................    0 tests    
    test_vi_shap.R................    0 tests    
    test_vi_shap.R................    0 tests    
    test_vi_shap.R................    0 tests    
    test_vi_shap.R................    0 tests    2.6s
    
    test_vip.R....................    0 tests    
    test_vip.R....................    0 tests    
    test_vip.R....................    0 tests    
    test_vip.R....................    0 tests    
    test_vip.R....................    1 tests OK 
    test_vip.R....................    2 tests OK 
    test_vip.R....................    3 tests OK 11ms
    ----- FAILED[data]: test_pkg_nnet.R<47--50>
     call| expect_identical(current = class(p), target = c("gg", "ggplot"))
     diff| Lengths (2, 5) differ (string compare on first 2)
     diff| 1 string mismatch
    Error: 1 out of 22 tests failed
    Execution halted

Package: visualpred
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘visualpred’

Package: VoronoiBiomedPlot
Check: examples
New result: ERROR
  Running examples in ‘VoronoiBiomedPlot-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: VoronoiBiomedPlot-package
  > ### Title: Projection Visualization Plots for Dimensionally Reduced Data
  > ### Aliases: VoronoiBiomedPlot-package VoronoiBiomedPlot
  > ### Keywords: package visualization multivariate biomedical
  > 
  > ### ** Examples
  > 
  > # Load the iris dataset
  > data <- iris[, c("Sepal.Length", "Petal.Length", "Species")]
  > 
  > # Create comprehensive projection plots
  > plots <- create_projection_plots(
  +   data = data,
  +   class_column = "Species",
  +   legend_position = "bottom",
  +   add_grid_lines = FALSE
  + )
  Error in `ggplot2::stat_ellipse()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 2nd layer.
  Caused by error in `setup_params()`:
  ! The package "MASS" is required for calculating ellipses with `type =
    "t"`.
  Backtrace:
       ▆
    1. ├─VoronoiBiomedPlot::create_projection_plots(...)
    2. │ ├─VoronoiBiomedPlot (local) compute_voronoi_diagram(...)
    3. │ ├─base::unlist(get_plot_limits(ellipse_plot))
    4. │ └─VoronoiBiomedPlot (local) get_plot_limits(ellipse_plot)
    5. │   ├─ggplot2::ggplot_build(plot)
    6. │   └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(plot)
    7. │     └─ggplot2:::by_layer(...)
    8. │       ├─rlang::try_fetch(...)
    9. │       │ ├─base::tryCatch(...)
   10. │       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   11. │       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   12. │       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   13. │       │ └─base::withCallingHandlers(...)
   14. │       └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   15. │         └─l$compute_statistic(d, layout)
   16. │           └─ggplot2 (local) compute_statistic(..., self = self)
   17. │             └─self$stat$setup_params(data, self$stat_params)
   18. │               └─ggplot2 (local) setup_params(...)
   19. │                 └─rlang::check_installed("MASS", "for calculating ellipses with `type = \"t\"`.")
   20. │                   └─base::stop(cnd)
   21. └─rlang (local) `<fn>`(`<S3: rlib_error_package_not_found>`)
   22.   └─handlers[[1L]](cnd)
   23.     └─cli::cli_abort(...)
   24.       └─rlang::abort(...)
  Execution halted

Package: vvshiny
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  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
    > 
    > testthat::test_check("vvshiny")
    Loading required package: vvshiny
    [ FAIL 2 | WARN 2 | SKIP 0 | PASS 59 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-basic_plot.R:15:3'): basic_plot function test ────────────────
    `test_plot1` has type 'object', not 'list'.
    ── Failure ('test-basic_plot.R:19:3'): basic_plot function test ────────────────
    `test_plot2` has type 'object', not 'list'.
    
    [ FAIL 2 | WARN 2 | SKIP 0 | PASS 59 ]
    Error: Test failures
    Execution halted

Package: washi
Check: tests
New result: ERROR
    Running ‘testthat.R’ [5s/5s]
  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(washi)
    > 
    > test_check("washi")
    Couldn't find 'sans'. Defaulting to 'sans'.
    a flextable object.
    col_keys: `a`, `b` 
    header has 1 row(s) 
    body has 5 row(s) 
    original dataset sample: 
      a  b
    1 1  6
    2 2  7
    3 3  8
    4 4  9
    5 5 10
    NULL
    Couldn't find 'sans'. Defaulting to 'sans'.
    Couldn't find 'sans'. Defaulting to 'sans'.
    Couldn't find 'sans'. Defaulting to 'sans'.
    Couldn't find 'sans'. Defaulting to 'sans'.
    [ FAIL 2 | WARN 4 | SKIP 5 | PASS 13 ]
    
    ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
    • On CRAN (5): 'test-flextable.R:9:3', 'test-fonts.R:3:3',
      'test-palettes.R:48:3', 'test-scales.R:42:3', 'test-theme.R:34:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test-theme.R:30:3'): washi_theme() works ──────────────────────────
    length(theme$panel.grid.major.x) (`actual`) not equal to 0 (`expected`).
    
      `actual`: 1.0
    `expected`: 0.0
    ── Failure ('test-theme.R:31:3'): washi_theme() works ──────────────────────────
    length(theme$panel.grid.major.y) (`actual`) not equal to 0 (`expected`).
    
      `actual`: 1.0
    `expected`: 0.0
    
    [ FAIL 2 | WARN 4 | SKIP 5 | PASS 13 ]
    Error: Test failures
    Execution halted

Package: windfarmGA
Check: tests
New result: ERROR
    Running ‘testthat.R’ [182s/127s]
  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(windfarmGA)
    > 
    > test_check("windfarmGA")
    Starting 2 test processes
    [ FAIL 2 | WARN 0 | SKIP 2 | PASS 703 ]
    
    ══ Skipped tests (2) ═══════════════════════════════════════════════════════════
    • On CRAN (2): 'test_parallel.R:3:3', 'test_terrain.R:8:3'
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure ('test_plots.R:29:3'): Test Plotting Functions ──────────────────────
    is.recursive(a0) is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    ── Failure ('test_plots.R:126:3'): Test Plotting Functions ─────────────────────
    class(windr_res)[1] == "gg" is not TRUE
    
    `actual`:   FALSE
    `expected`: TRUE 
    
    [ FAIL 2 | WARN 0 | SKIP 2 | PASS 703 ]
    Error: Test failures
    Execution halted

Package: wql
Check: examples
New result: ERROR
  Running examples in ‘wql-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: eofNum
  > ### Title: Plot EOF percent variance
  > ### Aliases: eofNum
  > ### Keywords: Graphics ts
  > 
  > ### ** Examples
  > 
  > 
  > # Create an annual time series data matrix from sfbay chlorophyll data
  > # Average over each year
  > chla1 <- aggregate(sfbayChla, 1, mean, na.rm = TRUE)  
  > chla1 <- chla1[, 1:12]  # remove stations with missing years
  > eofNum(chla1)
  Error: <ggplot2::labels> object is invalid:
  - every label must be named.
  Execution halted

Package: wql
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘wql-package.Rmd’ using rmarkdown
  
  Quitting from wql-package.Rmd:240-244 [unnamed-chunk-25]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  ! <ggplot2::labels> object is invalid:
  - every label must be named.
  ---
  Backtrace:
      ▆
   1. └─wql::eofNum(chla1)
   2.   └─ggplot2::labs(list(x = "Rank", y = "Eigenvalue"))
   3.     └─ggplot2::class_labels(args)
   4.       └─S7::new_object(labels)
   5.         └─S7::validate(object, recursive = !parent_validated)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'wql-package.Rmd' failed with diagnostics:
  <ggplot2::labels> object is invalid:
  - every label must be named.
  --- failed re-building ‘wql-package.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘wql-package.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: WVPlots
Check: examples
New result: ERROR
  Running examples in ‘WVPlots-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: ScatterHist
  > ### Title: Plot a scatter plot with marginals.
  > ### Aliases: ScatterHist
  > 
  > ### ** Examples
  > 
  > 
  > if (requireNamespace('data.table', quietly = TRUE)) {
  + 	# don't multi-thread during CRAN checks
  + 		data.table::setDTthreads(1)
  + }
  > 
  > set.seed(34903490)
  > x = rnorm(50)
  > y = 0.5*x^2 + 2*x + rnorm(length(x))
  > frm = data.frame(x=x,y=y)
  > WVPlots::ScatterHist(frm, "x", "y",
  +   title= "Example Fit",
  +   smoothmethod = "gam",
  +   contour = TRUE)
  Error in `ggplot2::geom_density2d()`:
  ! Problem while computing stat.
  ℹ Error occurred in the 3rd layer.
  Caused by error in `compute_layer()`:
  ! The package "MASS" is required for calculating 2D density.
  Backtrace:
       ▆
    1. ├─WVPlots::ScatterHist(...)
    2. │ └─WVPlots:::designYLabelPadFunction(...)
    3. │   └─WVPlots:::getYLabs(p1)
    4. │     ├─ggplot2::ggplot_build(p)
    5. │     └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(p)
    6. │       └─ggplot2:::by_layer(...)
    7. │         ├─rlang::try_fetch(...)
    8. │         │ ├─base::tryCatch(...)
    9. │         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10. │         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11. │         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   12. │         │ └─base::withCallingHandlers(...)
   13. │         └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
   14. │           └─l$compute_statistic(d, layout)
   15. │             └─ggplot2 (local) compute_statistic(..., self = self)
   16. │               └─self$stat$compute_layer(data, self$computed_stat_params, layout)
   17. │                 └─ggplot2 (local) compute_layer(..., self = self)
   18. │                   └─rlang::check_installed("MASS", reason = "for calculating 2D density.")
   19. │                     └─base::stop(cnd)
   20. └─rlang (local) `<fn>`(`<rlb_r___>`)
   21.   └─handlers[[1L]](cnd)
   22.     └─cli::cli_abort(...)
   23.       └─rlang::abort(...)
  Execution halted

Package: xpose
Check: whether package can be installed
New result: ERROR
  Installation failed.

Package: xpose.nlmixr2
Check: package dependencies
New result: ERROR
  Package required but not available: ‘xpose’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: xpose.xtras
Check: package dependencies
New result: ERROR
  Package required but not available: ‘xpose’
  
  See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
  manual.

Package: ZetaSuite
Check: whether package can be installed
New result: WARNING
  Found the following significant warnings:
    Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘ZetaSuite’