Last updated on 2025-12-20 13:50:33 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 11.99 | 120.57 | 132.56 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 8.54 | 85.43 | 93.97 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 21.00 | 183.69 | 204.69 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 20.00 | 187.83 | 207.83 | ERROR | |
| r-devel-windows-x86_64 | 0.2.0 | 14.00 | 134.00 | 148.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 12.26 | 136.39 | 148.65 | OK | |
| r-release-linux-x86_64 | 0.1.3 | 11.25 | 111.06 | 122.31 | ERROR | |
| r-release-macos-arm64 | 0.2.0 | 3.00 | 33.00 | 36.00 | OK | |
| r-release-macos-x86_64 | 0.2.0 | 9.00 | 107.00 | 116.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 17.00 | 142.00 | 159.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | 3.00 | 36.00 | 39.00 | OK | |
| r-oldrel-macos-x86_64 | 0.2.0 | 9.00 | 129.00 | 138.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.0 | 19.00 | 176.00 | 195.00 | OK |
Version: 0.2.0
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 using long-format SHAP values
> ### Aliases: shap.plot.summary
>
> ### ** Examples
>
> # Example: Basic workflow for SHAP summary plot
> # Note: For xgboost 3.x, use xgb.DMatrix + xgb.train, and convert factor labels to numeric
>
> data("iris")
> X1 = as.matrix(iris[,1:4])
> y1 = as.numeric(iris[[5]]) - 1 # Convert factor to numeric
> dtrain = xgboost::xgb.DMatrix(data = X1, label = y1)
> params = list(learning_rate = 1, min_split_loss = 0, reg_lambda = 0,
+ objective = 'reg:squarederror', nthread = 1)
> mod1 = xgboost::xgb.train(params = params, data = dtrain,
+ nrounds = 1, verbose = 0)
>
> # Get SHAP values and feature importance
> shap_values <- shap.values(xgb_model = mod1, X_train = X1)
> shap_values$mean_shap_score # Ranked features by mean|SHAP|
Petal.Length Petal.Width Sepal.Length Sepal.Width
0.6307042 0.2135736 0.0300757 0.0000000
> shap_values_iris <- shap_values$shap_score
>
> # Prepare long-format data for plotting
> shap_long_iris <- shap.prep(xgb_model = mod1, X_train = X1)
Error in `[.data.table`(fv_sub_long, , `:=`(stdfvalue, std1(rfvalue)), :
attempt access index 2/2 in VECTOR_ELT
Calls: shap.prep -> [ -> [.data.table
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shap.plot.dependence 4.852 0.092 6.162
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.0
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`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─SHAPforxgboost::shap.prep(fit, X_train = X)
2. ├─fv_sub_long[, `:=`(stdfvalue, std1(rfvalue)), by = "variable"]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'basic_workflow.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- 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-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
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 using long-format SHAP values
> ### Aliases: shap.plot.summary
>
> ### ** Examples
>
> # Example: Basic workflow for SHAP summary plot
> # Note: For xgboost 3.x, use xgb.DMatrix + xgb.train, and convert factor labels to numeric
>
> data("iris")
> X1 = as.matrix(iris[,1:4])
> y1 = as.numeric(iris[[5]]) - 1 # Convert factor to numeric
> dtrain = xgboost::xgb.DMatrix(data = X1, label = y1)
> params = list(learning_rate = 1, min_split_loss = 0, reg_lambda = 0,
+ objective = 'reg:squarederror', nthread = 1)
> mod1 = xgboost::xgb.train(params = params, data = dtrain,
+ nrounds = 1, verbose = 0)
>
> # Get SHAP values and feature importance
> shap_values <- shap.values(xgb_model = mod1, X_train = X1)
> shap_values$mean_shap_score # Ranked features by mean|SHAP|
Petal.Length Petal.Width Sepal.Length Sepal.Width
0.6307042 0.2135736 0.0300757 0.0000000
> shap_values_iris <- shap_values$shap_score
>
> # Prepare long-format data for plotting
> shap_long_iris <- shap.prep(xgb_model = mod1, X_train = X1)
Error in `[.data.table`(fv_sub_long, , `:=`(stdfvalue, std1(rfvalue)), :
attempt access index 2/2 in VECTOR_ELT
Calls: shap.prep -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
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 using long-format SHAP values
> ### Aliases: shap.plot.summary
>
> ### ** Examples
>
> # Example: Basic workflow for SHAP summary plot
> # Note: For xgboost 3.x, use xgb.DMatrix + xgb.train, and convert factor labels to numeric
>
> data("iris")
> X1 = as.matrix(iris[,1:4])
> y1 = as.numeric(iris[[5]]) - 1 # Convert factor to numeric
> dtrain = xgboost::xgb.DMatrix(data = X1, label = y1)
> params = list(learning_rate = 1, min_split_loss = 0, reg_lambda = 0,
+ objective = 'reg:squarederror', nthread = 1)
> mod1 = xgboost::xgb.train(params = params, data = dtrain,
+ nrounds = 1, verbose = 0)
>
> # Get SHAP values and feature importance
> shap_values <- shap.values(xgb_model = mod1, X_train = X1)
> shap_values$mean_shap_score # Ranked features by mean|SHAP|
Petal.Length Petal.Width Sepal.Length Sepal.Width
0.6307042 0.2135736 0.0300757 0.0000000
> shap_values_iris <- shap_values$shap_score
>
> # Prepare long-format data for plotting
> shap_long_iris <- shap.prep(xgb_model = mod1, X_train = X1)
Error in `[.data.table`(fv_sub_long, , `:=`(stdfvalue, std1(rfvalue)), :
attempt access index 2/2 in VECTOR_ELT
Calls: shap.prep -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
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`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─SHAPforxgboost::shap.prep(fit, X_train = X)
2. ├─fv_sub_long[, `:=`(stdfvalue, std1(rfvalue)), by = "variable"]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'basic_workflow.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- 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
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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
shap.plot.dependence 4.254 0.129 6.046
Flavor: r-release-linux-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
Flavor: r-release-linux-x86_64