Running examples in ‘readyomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ready_plots
> ### Title: Generate plots from a differential analysis ('dana') object
> ### Aliases: ready_plots
> 
> ### ** Examples
> 
> set.seed(123)
> mock_X <- matrix(rnorm(20 * 5), nrow = 20)
> colnames(mock_X) <- paste0("feat_", seq_len(5))
> rownames(mock_X) <- paste0("sample_", seq_len(20))
> 
> sample_data <- data.frame(
+   sample_id = rownames(mock_X),
+   group = factor(rep(c("A", "B"), each = 10)),
+   time = factor(rep(c("T1", "T2"), times = 10)),
+   subject_id = factor(rep(seq_len(10), each = 2)),
+   stringsAsFactors = FALSE
+ )
> rownames(sample_data) <- sample_data$sample_id
> 
> fit_df <- data.frame(
+   feat_id = rep(colnames(mock_X), each = 2),
+   Coefficient = rep(c("(Intercept)", "groupB"), 5),
+   Estimate = rnorm(10),
+   `Pr(>|t|)` = runif(10),
+   padj = runif(10),
+   stringsAsFactors = FALSE
+ )
> 
> # Mock dana object
> dana_obj <- list(
+   X = mock_X,
+   sdata = sample_data,
+   formula_rhs = ~ group,
+   fit = fit_df,
+   lrt = data.frame(),  #' empty but valid
+   ranef = data.frame() #' empty but valid
+ )
> class(dana_obj) <- "dana"
> 
> dana_obj <- dana_obj |>
+ ready_plots(
+   term_name = "group",
+   pval_match = "padj",
+   alpha = 0.5,
+   add_labels = FALSE,
+   plot_coeff = TRUE,
+   plot_feat = TRUE,
+   plot_ranef = FALSE,
+   sdata_var = "group",
+   verbose = FALSE
+ )
Error in `ggplot2::geom_violin()`:
! `draw_quantiles` must be a <numeric> vector, not `TRUE`.
Backtrace:
    ▆
 1. └─readyomics::ready_plots(...)
 2.   └─readyomics:::plot_feat(...)
 3.     └─ggplot2::geom_violin(draw_quantiles = TRUE)
 4.       └─ggplot2:::check_numeric(draw_quantiles)
 5.         └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
 6.           └─ggplot2:::stop_input_type(...)
 7.             └─rlang::abort(message, ..., call = call, arg = arg)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
build_phyloseq 8.321  0.542  11.049
dana           7.096  0.181   8.409
mva            6.446  0.298   8.189