##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TRONCO
###
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* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* preparing ‘TRONCO’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘f1_introduction.rmd’ using rmarkdown
--- finished re-building ‘f1_introduction.rmd’

--- re-building ‘f2_loading_data.Rmd’ using rmarkdown
--- finished re-building ‘f2_loading_data.Rmd’

--- re-building ‘f3_data_visualization.Rmd’ using rmarkdown
2025-09-11 17:54:15.958 R[417:218604211] XType: Using static font registry.
--- finished re-building ‘f3_data_visualization.Rmd’

--- re-building ‘f4_data_manipulation.Rmd’ using rmarkdown
--- finished re-building ‘f4_data_manipulation.Rmd’

--- re-building ‘f5_model_inference.Rmd’ using rmarkdown
--- finished re-building ‘f5_model_inference.Rmd’

--- re-building ‘f6_post_reconstruction.Rmd’ using rmarkdown

Quitting from f6_post_reconstruction.Rmd:227-231 [unnamed-chunk-15]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `{
    event = events[i]
    posterr.adj.col = array(list(NA), c(nrow(adj.matrix), 1))
    colnames(posterr.adj.col) = event
    rownames(posterr.adj.col) = rownames(adj.matrix)
    for (pre in rownames(posterr.adj.col)) {
      if (adj.matrix[pre, event] == 1) {
        comp = bnlearn::bn.cv(bndata, bnnet, loss = "pred-lw", loss.args = list(
          target = event, from = pre), runs = runs, k = k, fit = "bayes",
        fit.args = list(iss = 1))
        res = NULL
        for (i in 1:runs) {
          res = c(res, attributes(comp[[i]])$mean)
        }
        posterr.adj.col[[pre, event]] = res
      }
    }
    posterr.adj.col
  }`:
! task 1 failed - "valid loss function(s) are "logl" (Log-Likelihood Loss), "pred" (Classification Error), "cor" (Predictive Correlation), "mse" (Mean Squared Error), "f1" (F1 Score), "auroc" (Area under the ROC Curve), "pred-exact" (Classification Error (Posterior, exact)). See ?bn.cv for details."
---
Backtrace:
    ▆
 1. └─TRONCO::tronco.kfold.posterr(model.boot, runs = 2, cores.ratio = 0)
 2.   └─... %dopar% ...
 3.     └─e$fun(obj, substitute(ex), parent.frame(), e$data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'f6_post_reconstruction.Rmd' failed with diagnostics:
task 1 failed - "valid loss function(s) are "logl" (Log-Likelihood Loss), "pred" (Classification Error), "cor" (Predictive Correlation), "mse" (Mean Squared Error), "f1" (F1 Score), "auroc" (Area under the ROC Curve), "pred-exact" (Classification Error (Posterior, exact)). See ?bn.cv for details."
--- failed re-building ‘f6_post_reconstruction.Rmd’

--- re-building ‘f7_import_export.Rmd’ using rmarkdown
--- finished re-building ‘f7_import_export.Rmd’

SUMMARY: processing the following file failed:
  ‘f6_post_reconstruction.Rmd’

Error: Vignette re-building failed.
Execution halted