• using R version 4.5.2 (2025-10-31)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-10) 14.3.0     GNU Fortran (Debian 14.3.0-10) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘SHAPforxgboost/DESCRIPTION’ ... OK
• this is package ‘SHAPforxgboost’ version ‘0.1.3’
• 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 ‘SHAPforxgboost’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [4s/4s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
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• checking loading without being on the library search path ... [4s/5s] OK
• checking use of S3 registration ... 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 ... [17s/21s] OK
• checking Rd files ... [0s/0s] OK
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• checking for missing documentation entries ... OK
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• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
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• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [17s/24s] ERROR Running examples in ‘SHAPforxgboost-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: shap.plot.summary > ### Title: SHAP summary plot core function using the long format SHAP > ### values > ### Aliases: shap.plot.summary > > ### ** Examples > > data("iris") > X1 = as.matrix(iris[,-5]) > mod1 = xgboost::xgboost( + data = X1, label = iris$Species, gamma = 0, eta = 1, + lambda = 0, nrounds = 1, verbose = FALSE, nthread = 1) Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), :   Passed unrecognized parameters: verbose. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :   Parameter 'data' has been renamed to 'x'. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :   Parameter 'label' has been renamed to 'y'. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :   Parameter 'gamma' has been renamed to 'min_split_loss'. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :   Parameter 'eta' has been renamed to 'learning_rate'. This warning will become an error in a future version. Warning in throw_err_or_depr_msg("Parameter '", match_old, "' has been renamed to '", :   Parameter 'lambda' has been renamed to 'reg_lambda'. This warning will become an error in a future version. > > # shap.values(model, X_dataset) returns the SHAP > # data matrix and ranked features by mean|SHAP| > shap_values <- shap.values(xgb_model = mod1, X_train = X1) Warning in `[.data.table`(shap_contrib, , `:=`(BIAS, NULL)) :   Tried to assign NULL to column 'BIAS', but this column does not exist to remove > shap_values$mean_shap_score     setosa versicolor virginica  0.3360065 0.3326459 0.3313476 > shap_values_iris <- shap_values$shap_score > > # shap.prep() returns the long-format SHAP data from either model or > shap_long_iris <- shap.prep(xgb_model = mod1, X_train = X1) Warning in `[.data.table`(shap_contrib, , `:=`(BIAS, NULL)) :   Tried to assign NULL to column 'BIAS', but this column does not exist to remove Error in `[.data.table`(setDT(shap$shap_score), , names(shap$mean_shap_score)[1:top_n], :   column not found: [NA] Calls: shap.prep ... [ -> [.data.table -> stopf -> raise_condition -> signal Execution halted Examples with CPU (user + system) or elapsed time > 5s                       user system elapsed shap.plot.dependence 4.291 0.138 6.366
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [4s/6s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘basic_workflow.Rmd’ using rmarkdown Quitting from basic_workflow.Rmd:62-87 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! column not found: [(Intercept)] --- Backtrace:     ▆  1. └─SHAPforxgboost::shap.prep(fit, X_train = X)  2. ├─...[]  3. └─data.table:::`[.data.table`(...)  4. └─data.table:::stopf(...)  5. └─data.table:::raise_condition(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'basic_workflow.Rmd' failed with diagnostics: column not found: [(Intercept)] --- failed re-building ‘basic_workflow.Rmd’ SUMMARY: processing the following file failed:   ‘basic_workflow.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs