Last updated on 2025-12-04 09:49:59 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.4.3 | 26.93 | 162.84 | 189.77 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.4.3 | 23.52 | 121.05 | 144.57 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.4.3 | 140.00 | 158.89 | 298.89 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.4.3 | 201.00 | 158.61 | 359.61 | ERROR | |
| r-devel-windows-x86_64 | 0.1.4.3 | 30.00 | 155.00 | 185.00 | OK | |
| r-patched-linux-x86_64 | 0.1.4.3 | 28.29 | 154.75 | 183.04 | OK | |
| r-release-linux-x86_64 | 0.1.4.3 | 26.03 | 154.94 | 180.97 | OK | |
| r-release-macos-arm64 | 0.1.4.3 | OK | ||||
| r-release-macos-x86_64 | 0.1.4.3 | 25.00 | 254.00 | 279.00 | OK | |
| r-release-windows-x86_64 | 0.1.4.3 | 30.00 | 156.00 | 186.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.4.3 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.1.4.3 | 27.00 | 210.00 | 237.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.1.4.3 | 40.00 | 207.00 | 247.00 | OK |
Version: 0.1.4.3
Check: examples
Result: ERROR
Running examples in ‘MBMethPred-Ex.R’ failed
The error most likely occurred in:
> ### Name: ModelMetrics
> ### Title: Model metrics
> ### Aliases: ModelMetrics
>
> ### ** Examples
>
> xgboost <- XGBoostModel(SplitRatio = 0.2,
+ CV = 2,
+ NCores = 1,
+ NewData = NULL)
Warning in throw_err_or_depr_msg("Parameter(s) have been removed from this function: ", :
Parameter(s) have been removed from this function: params. This warning will become an error in a future version.
Warning in throw_err_or_depr_msg("Passed unrecognized parameters: ", paste(head(names_unrecognized), :
Passed unrecognized parameters: verbose, num_class. 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.
Error in prescreen.objective(objective) :
Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
Calls: XGBoostModel ... lapply -> FUN -> <Anonymous> -> prescreen.objective
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.4.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [34s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MBMethPred)
>
> test_check("MBMethPred")
y_pred
y_true Group3 SHH Group4
Group3 1 0 0
SHH 1 1 0
Group4 0 0 1
y_pred
y_true Group3 SHH WNT Group4
Group3 8 0 0 0
SHH 0 24 2 0
WNT 0 0 24 0
Group4 1 0 0 31
y_pred
y_true Group3 SHH WNT Group4
Group3 20 0 0 1
SHH 0 20 0 0
WNT 0 0 18 0
Group4 1 0 0 32
y_pred
y_true Group3 SHH WNT Group4
Group3 18 0 0 1
SHH 0 41 0 0
WNT 0 0 37 0
Group4 6 2 0 52
y_pred
y_true Group3 SHH WNT Group4
Group3 26 0 1 0
SHH 0 41 0 0
WNT 0 0 38 0
Group4 1 1 0 53
y_pred
y_true Group3 SHH WNT Group4
Group3 27 0 0 0
SHH 0 43 0 0
WNT 0 0 37 0
Group4 4 2 0 54
y_pred
y_true Group3 SHH WNT Group4
Group3 23 0 0 3
SHH 0 42 0 0
WNT 0 0 35 0
Group4 6 1 0 55
y_pred
y_true Group3 SHH WNT Group4
Group3 26 0 0 1
SHH 0 38 1 0
WNT 0 0 39 0
Group4 5 0 0 52
y_pred
y_true Group3 SHH WNT Group4
Group3 26 0 0 2
SHH 0 41 0 0
WNT 0 0 39 0
Group4 0 0 0 57
y_pred
y_true Group3 SHH WNT Group4
Group3 27 0 0 2
SHH 0 41 0 0
WNT 0 0 39 0
Group4 3 1 1 53
y_pred
y_true Group3 SHH WNT Group4
Group3 21 0 0 3
SHH 0 42 0 0
WNT 0 0 37 0
Group4 6 0 0 54
y_pred
y_true Group3 SHH WNT Group4
Group3 20 0 1 5
SHH 0 42 0 0
WNT 0 0 37 0
Group4 6 1 0 46
y_pred
y_true Group3 SHH WNT Group4
Group3 27 0 0 1
SHH 0 41 1 0
WNT 0 0 40 0
Group4 6 0 0 57
Saving _problems/test-ModelMetrics-2.R
y_pred
y_true Group3 SHH WNT Group4
Group3 13 0 0 0
SHH 0 27 0 0
WNT 0 0 22 1
Group4 1 0 0 24
y_pred
y_true Group3 SHH WNT Group4
Group3 15 0 0 1
SHH 0 19 0 0
WNT 0 0 19 0
Group4 4 0 0 36
Saving _problems/test-NewDataPredictionResult-10.R
y_pred
y_true Group3 SHH WNT Group4
Group3 15 0 0 2
SHH 0 18 0 0
WNT 0 0 18 0
Group4 0 0 0 34
y_pred
y_true Group3 SHH WNT Group4
Group3 11 0 0 1
SHH 0 27 0 1
WNT 0 0 24 0
Group4 0 0 0 31
The NMI score is: 0.903790812437385
y_pred
y_true Group3 SHH WNT Group4
Group3 12 0 0 1
SHH 0 26 0 0
WNT 1 0 20 0
Group4 0 0 0 31
y_pred
y_true Group3 SHH WNT Group4
Group3 15 0 0 1
SHH 0 20 0 0
WNT 0 0 21 0
Group4 2 0 0 32
Saving _problems/test-XGBoostModel-2.R
[ FAIL 3 | WARN 12 | SKIP 0 | PASS 9 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ModelMetrics.r:2:3'): ModelMetrics returns correct class. ──────
Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
Backtrace:
▆
1. └─MBMethPred::XGBoostModel(...) at test-ModelMetrics.r:2:3
2. └─parallel::mclapply(...)
3. └─base::lapply(X = X, FUN = FUN, ...)
4. └─MBMethPred (local) FUN(X[[i]], ...)
5. └─xgboost::xgboost(...)
6. └─xgboost:::prescreen.objective(objective)
── Error ('test-NewDataPredictionResult.R:10:3'): NewDataPredictionResult returns correct type ──
Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
Backtrace:
▆
1. └─MBMethPred::XGBoostModel(...) at test-NewDataPredictionResult.R:10:3
2. └─parallel::mclapply(...)
3. └─base::lapply(X = X, FUN = FUN, ...)
4. └─MBMethPred (local) FUN(X[[i]], ...)
5. └─xgboost::xgboost(...)
6. └─xgboost:::prescreen.objective(objective)
── Error ('test-XGBoostModel.R:2:3'): XGBoostModel returns correct class. ──────
Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
Backtrace:
▆
1. ├─testthat::expect_type(...) at test-XGBoostModel.R:2:3
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MBMethPred::XGBoostModel(...)
5. └─parallel::mclapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─MBMethPred (local) FUN(X[[i]], ...)
8. └─xgboost::xgboost(...)
9. └─xgboost:::prescreen.objective(objective)
[ FAIL 3 | WARN 12 | SKIP 0 | PASS 9 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.4.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [35s/127s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MBMethPred)
>
> test_check("MBMethPred")
y_pred
y_true Group3 SHH Group4
Group3 1 0 0
SHH 1 1 0
Group4 0 0 1
y_pred
y_true Group3 SHH WNT Group4
Group3 8 0 0 0
SHH 0 24 2 0
WNT 0 0 24 0
Group4 1 0 0 31
y_pred
y_true Group3 SHH WNT Group4
Group3 20 0 0 1
SHH 0 20 0 0
WNT 0 0 18 0
Group4 1 0 0 32
y_pred
y_true Group3 SHH WNT Group4
Group3 18 0 0 1
SHH 0 41 0 0
WNT 0 0 37 0
Group4 6 2 0 52
y_pred
y_true Group3 SHH WNT Group4
Group3 26 0 1 0
SHH 0 41 0 0
WNT 0 0 38 0
Group4 1 1 0 53
y_pred
y_true Group3 SHH WNT Group4
Group3 27 0 0 0
SHH 0 43 0 0
WNT 0 0 37 0
Group4 4 2 0 54
y_pred
y_true Group3 SHH WNT Group4
Group3 23 0 0 3
SHH 0 42 0 0
WNT 0 0 35 0
Group4 6 1 0 55
y_pred
y_true Group3 SHH WNT Group4
Group3 26 0 0 1
SHH 0 38 1 0
WNT 0 0 39 0
Group4 5 0 0 52
y_pred
y_true Group3 SHH WNT Group4
Group3 26 0 0 2
SHH 0 41 0 0
WNT 0 0 39 0
Group4 0 0 0 57
y_pred
y_true Group3 SHH WNT Group4
Group3 27 0 0 2
SHH 0 41 0 0
WNT 0 0 39 0
Group4 3 1 1 53
y_pred
y_true Group3 SHH WNT Group4
Group3 21 0 0 3
SHH 0 42 0 0
WNT 0 0 37 0
Group4 6 0 0 54
y_pred
y_true Group3 SHH WNT Group4
Group3 20 0 1 5
SHH 0 42 0 0
WNT 0 0 37 0
Group4 6 1 0 46
y_pred
y_true Group3 SHH WNT Group4
Group3 27 0 0 1
SHH 0 41 1 0
WNT 0 0 40 0
Group4 6 0 0 57
Saving _problems/test-ModelMetrics-2.R
y_pred
y_true Group3 SHH WNT Group4
Group3 13 0 0 0
SHH 0 27 0 0
WNT 0 0 22 1
Group4 1 0 0 24
y_pred
y_true Group3 SHH WNT Group4
Group3 15 0 0 1
SHH 0 19 0 0
WNT 0 0 19 0
Group4 4 0 0 36
Saving _problems/test-NewDataPredictionResult-10.R
y_pred
y_true Group3 SHH WNT Group4
Group3 15 0 0 2
SHH 0 18 0 0
WNT 0 0 18 0
Group4 0 0 0 34
y_pred
y_true Group3 SHH WNT Group4
Group3 11 0 0 1
SHH 0 27 0 1
WNT 0 0 24 0
Group4 0 0 0 31
The NMI score is: 0.903790812437385
y_pred
y_true Group3 SHH WNT Group4
Group3 12 0 0 1
SHH 0 26 0 0
WNT 1 0 20 0
Group4 0 0 0 31
y_pred
y_true Group3 SHH WNT Group4
Group3 15 0 0 1
SHH 0 20 0 0
WNT 0 0 21 0
Group4 2 0 0 32
Saving _problems/test-XGBoostModel-2.R
[ FAIL 3 | WARN 12 | SKIP 0 | PASS 9 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ModelMetrics.r:2:3'): ModelMetrics returns correct class. ──────
Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
Backtrace:
▆
1. └─MBMethPred::XGBoostModel(...) at test-ModelMetrics.r:2:3
2. └─parallel::mclapply(...)
3. └─base::lapply(X = X, FUN = FUN, ...)
4. └─MBMethPred (local) FUN(X[[i]], ...)
5. └─xgboost::xgboost(...)
6. └─xgboost:::prescreen.objective(objective)
── Error ('test-NewDataPredictionResult.R:10:3'): NewDataPredictionResult returns correct type ──
Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
Backtrace:
▆
1. └─MBMethPred::XGBoostModel(...) at test-NewDataPredictionResult.R:10:3
2. └─parallel::mclapply(...)
3. └─base::lapply(X = X, FUN = FUN, ...)
4. └─MBMethPred (local) FUN(X[[i]], ...)
5. └─xgboost::xgboost(...)
6. └─xgboost:::prescreen.objective(objective)
── Error ('test-XGBoostModel.R:2:3'): XGBoostModel returns correct class. ──────
Error in `prescreen.objective(objective)`: Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
Backtrace:
▆
1. ├─testthat::expect_type(...) at test-XGBoostModel.R:2:3
2. │ └─testthat::quasi_label(enquo(object))
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─MBMethPred::XGBoostModel(...)
5. └─parallel::mclapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─MBMethPred (local) FUN(X[[i]], ...)
8. └─xgboost::xgboost(...)
9. └─xgboost:::prescreen.objective(objective)
[ FAIL 3 | WARN 12 | SKIP 0 | PASS 9 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.4.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘MBMethPred_introduction.Rmd’ using knitr
Quitting from MBMethPred_introduction.Rmd:229-242 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `prescreen.objective()`:
! Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
---
Backtrace:
▆
1. └─MBMethPred::XGBoostModel(...)
2. └─parallel::mclapply(...)
3. └─base::lapply(X = X, FUN = FUN, ...)
4. └─MBMethPred (local) FUN(X[[i]], ...)
5. └─xgboost::xgboost(...)
6. └─xgboost:::prescreen.objective(objective)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MBMethPred_introduction.Rmd' failed with diagnostics:
Objectives with non-default prediction mode (reg:logistic, binary:logitraw, multi:softmax) are not supported in 'xgboost()'. Try 'xgb.train()'.
--- failed re-building ‘MBMethPred_introduction.Rmd’
SUMMARY: processing the following file failed:
‘MBMethPred_introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.4.3
Check: installed package size
Result: NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
R 1.1Mb
data 3.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64