CRAN Package Check Results for Maintainer ‘Yang Liu <lyhello at gmail.com>’

Last updated on 2025-12-06 10:51:14 CET.

Package	ERROR	OK
SHAPforxgboost	4	9

Package SHAPforxgboost

Current CRAN status: ERROR: 4, OK: 9

Version: 0.1.3
Check: examples
Result: 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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.3
Check: re-building of vignette outputs
Result: 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 Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.1.3
Check: examples
Result: ERROR Running examples in ‘SHAPforxgboost-Ex.R’ failed The error most likely occurred in: > ### 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64

Version: 0.1.3
Check: re-building of vignette outputs
Result: 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 Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64