CRAN Package Check Results for Maintainer ‘Edris Sharif Rahmani <rahmani.biotech at gmail.com>’

Last updated on 2025-12-04 07:51:56 CET.

Package	ERROR	NOTE	OK
MBMethPred	2	2	9

Package MBMethPred

Current CRAN status: ERROR: 2, NOTE: 2, OK: 9

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