* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/shapr.Rcheck’
* using R Under development (unstable) (2025-12-02 r89085)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘shapr/DESCRIPTION’ ... OK
* this is package ‘shapr’ version ‘1.0.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘shapr’ can be installed ... [91s/80s] OK
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [22s/22s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [38s/44s] ERROR
Running examples in ‘shapr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_MSEv_eval_crit
> ### Title: Plots of the MSEv Evaluation Criterion
> ### Aliases: plot_MSEv_eval_crit
> 
> ### ** Examples
> 
> ## No test: 
> if (requireNamespace("xgboost", quietly = TRUE) && requireNamespace("ggplot2", quietly = TRUE)) {
+   # Get the data
+   data("airquality")
+   data <- data.table::as.data.table(airquality)
+   data <- data[complete.cases(data), ]
+ 
+   #' Define the features and the response
+   x_var <- c("Solar.R", "Wind", "Temp", "Month")
+   y_var <- "Ozone"
+ 
+   # Split data into test and training data set
+   ind_x_explain <- 1:25
+   x_train <- data[-ind_x_explain, ..x_var]
+   y_train <- data[-ind_x_explain, get(y_var)]
+   x_explain <- data[ind_x_explain, ..x_var]
+ 
+   # Fitting a basic xgboost model to the training data
+   model <- xgboost::xgboost(
+     data = as.matrix(x_train),
+     label = y_train,
+     nround = 20,
+     verbose = FALSE
+   )
+ 
+   # Specifying the phi_0, i.e. the expected prediction without any features
+   phi0 <- mean(y_train)
+ 
+   # Independence approach
+   explanation_independence <- explain(
+     model = model,
+     x_explain = x_explain,
+     x_train = x_train,
+     approach = "independence",
+     phi0 = phi0,
+     n_MC_samples = 1e2
+   )
+ 
+   # Gaussian 1e1 approach
+   explanation_gaussian_1e1 <- explain(
+     model = model,
+     x_explain = x_explain,
+     x_train = x_train,
+     approach = "gaussian",
+     phi0 = phi0,
+     n_MC_samples = 1e1
+   )
+ 
+   # Gaussian 1e2 approach
+   explanation_gaussian_1e2 <- explain(
+     model = model,
+     x_explain = x_explain,
+     x_train = x_train,
+     approach = "gaussian",
+     phi0 = phi0,
+     n_MC_samples = 1e2
+   )
+ 
+   # ctree approach
+   explanation_ctree <- explain(
+     model = model,
+     x_explain = x_explain,
+     x_train = x_train,
+     approach = "ctree",
+     phi0 = phi0,
+     n_MC_samples = 1e2
+   )
+ 
+   # Combined approach
+   explanation_combined <- explain(
+     model = model,
+     x_explain = x_explain,
+     x_train = x_train,
+     approach = c("gaussian", "independence", "ctree"),
+     phi0 = phi0,
+     n_MC_samples = 1e2
+   )
+ 
+   # Create a list of explanations with names
+   explanation_list_named <- list(
+     "Ind." = explanation_independence,
+     "Gaus. 1e1" = explanation_gaussian_1e1,
+     "Gaus. 1e2" = explanation_gaussian_1e2,
+     "Ctree" = explanation_ctree,
+     "Combined" = explanation_combined
+   )
+ 
+   # Create the default MSEv plot where we average over both the coalitions and observations
+   # with approximate 95% confidence intervals
+   plot_MSEv_eval_crit(explanation_list_named, CI_level = 0.95, plot_type = "overall")
+ 
+   # Can also create plots of the MSEv criterion averaged only over the coalitions or observations.
+   MSEv_figures <- plot_MSEv_eval_crit(explanation_list_named,
+     CI_level = 0.95,
+     plot_type = c("overall", "comb", "explicand")
+   )
+   MSEv_figures$MSEv_bar
+   MSEv_figures$MSEv_coalition_bar
+   MSEv_figures$MSEv_explicand_bar
+ 
+   # When there are many coalitions or observations, then it can be easier to look at line plots
+   MSEv_figures$MSEv_coalition_line_point
+   MSEv_figures$MSEv_explicand_line_point
+ 
+   # We can specify which observations or coalitions to plot
+   plot_MSEv_eval_crit(explanation_list_named,
+     plot_type = "explicand",
+     index_x_explain = c(1, 3:4, 6),
+     CI_level = 0.95
+   )$MSEv_explicand_bar
+   plot_MSEv_eval_crit(explanation_list_named,
+     plot_type = "comb",
+     id_coalition = c(3, 4, 9, 13:15),
+     CI_level = 0.95
+   )$MSEv_coalition_bar
+ 
+   # We can alter the figures if other palette schemes or design is wanted
+   bar_text_n_decimals <- 1
+   MSEv_figures$MSEv_bar +
+     ggplot2::scale_x_discrete(limits = rev(levels(MSEv_figures$MSEv_bar$data$Method))) +
+     ggplot2::coord_flip() +
+     ggplot2::scale_fill_discrete() + #' Default ggplot2 palette
+     ggplot2::theme_minimal() + #' This must be set before the other theme call
+     ggplot2::theme(
+       plot.title = ggplot2::element_text(size = 10),
+       legend.position = "bottom"
+     ) +
+     ggplot2::guides(fill = ggplot2::guide_legend(nrow = 1, ncol = 6)) +
+     ggplot2::geom_text(
+       ggplot2::aes(label = sprintf(
+         paste("%.", sprintf("%d", bar_text_n_decimals), "f", sep = ""),
+         round(MSEv, bar_text_n_decimals)
+       )),
+       vjust = -1.1, # This value must be altered based on the plot dimension
+       hjust = 1.1, # This value must be altered based on the plot dimension
+       color = "black",
+       position = ggplot2::position_dodge(0.9),
+       size = 5
+     )
+ }
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized),  :
  Passed unrecognized parameters: verbose. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '",  :
  Parameter 'label' has been renamed to 'y'. This warning will become an error in a future version.

── Starting `shapr::explain()` at 2025-12-03 11:15:11 ──────────────────────────
ℹ You passed a model to `shapr::explain()` which is not natively supported, and
  did not supply a `get_model_specs` function to `shapr::explain()`.
  Consistency checks between model and data are therefore disabled.
ℹ `max_n_coalitions` is `NULL` or larger than `2^n_features = 16`, and is
  therefore set to `2^n_features = 16`.
Error in `get_predict_model()`:
! You passed a model to `shapr::explain()` that is not natively
  supported and did not supply a 'predict_model' function to
  `shapr::explain()`. See the documentation of `shapr::explain()` or the
  `vignette(shapr::general_usage)` vignette for more information on how to run
  shapr with custom models.
Backtrace:
    ▆
 1. └─shapr::explain(...)
 2.   └─shapr:::get_predict_model(predict_model = predict_model, model = model)
 3.     └─cli::cli_abort(...)
 4.       └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [276s/282s]
 [276s/282s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s/18s] OK
* checking PDF version of manual ... [11s/11s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/shapr.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 8:20.43, 470.58 + 27.80