Last updated on 2025-09-07 09:49:46 CEST.
| Package | ERROR | OK |
|---|---|---|
| autonewsmd | 13 | |
| BiasCorrector | 13 | |
| DQAgui | 13 | |
| DQAstats | 13 | |
| kdry | 13 | |
| mlexperiments | 13 | |
| mllrnrs | 1 | 12 |
| mlsurvlrnrs | 1 | 12 |
| rBiasCorrection | 13 | |
| sjtable2df | 13 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 0.0.5
Check: examples
Result: ERROR
Running examples in ‘mllrnrs-Ex.R’ failed
The error most likely occurred in:
> ### Name: LearnerGlmnet
> ### Title: R6 Class to construct a Glmnet learner
> ### Aliases: LearnerGlmnet
>
> ### ** Examples
>
> # binary classification
>
> library(mlbench)
> data("PimaIndiansDiabetes2")
> dataset <- PimaIndiansDiabetes2 |>
+ data.table::as.data.table() |>
+ na.omit()
>
> seed <- 123
> feature_cols <- colnames(dataset)[1:8]
>
> train_x <- model.matrix(
+ ~ -1 + .,
+ dataset[, .SD, .SDcols = feature_cols]
+ )
> train_y <- as.integer(dataset[, get("diabetes")]) - 1L
>
> fold_list <- splitTools::create_folds(
+ y = train_y,
+ k = 3,
+ type = "stratified",
+ seed = seed
+ )
> glmnet_cv <- mlexperiments::MLCrossValidation$new(
+ learner = mllrnrs::LearnerGlmnet$new(
+ metric_optimization_higher_better = FALSE
+ ),
+ fold_list = fold_list,
+ ncores = 2,
+ seed = 123
+ )
> glmnet_cv$learner_args <- list(
+ alpha = 1,
+ lambda = 0.1,
+ family = "binomial",
+ type.measure = "class",
+ standardize = TRUE
+ )
> glmnet_cv$predict_args <- list(type = "response")
> glmnet_cv$performance_metric_args <- list(positive = "1")
> glmnet_cv$performance_metric <- mlexperiments::metric("auc")
Error: Package "measures" must be installed to use function 'metric()'.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> # https://github.com/Rdatatable/data.table/issues/5658
> Sys.setenv("OMP_THREAD_LIMIT" = 2)
> Sys.setenv("Ncpu" = 2)
>
> library(testthat)
> library(mllrnrs)
>
> test_check("mllrnrs")
[ FAIL 17 | WARN 0 | SKIP 1 | PASS 0 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-lints.R:10:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-glmnet_binary.R:88:5'): test nested cv, bayesian, binary - glmnet ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("prauc") at test-glmnet_binary.R:88:5
── Error ('test-glmnet_binary.R:134:5'): test nested cv, grid - glmnet, errors ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("prauc") at test-glmnet_binary.R:134:5
── Error ('test-glmnet_multiclass.R:89:5'): test nested cv, bayesian, multiclass - glmnet ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("bacc") at test-glmnet_multiclass.R:89:5
── Error ('test-glmnet_regression.R:87:5'): test nested cv, bayesian, regression - glmnet ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("rmsle") at test-glmnet_regression.R:87:5
── Error ('test-glmnet_regression.R:134:5'): test nested cv, grid - glmnet ─────
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("rmsle") at test-glmnet_regression.R:134:5
── Error ('test-lightgbm_binary.R:99:5'): test nested cv, bayesian, binary - lightgbm ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("auc") at test-lightgbm_binary.R:99:5
── Error ('test-lightgbm_multiclass.R:101:5'): test nested cv, bayesian, multiclass - lightgbm ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("bacc") at test-lightgbm_multiclass.R:101:5
── Error ('test-lightgbm_regression.R:99:5'): test nested cv, bayesian, regression - lightgbm ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("msle") at test-lightgbm_regression.R:99:5
── Error ('test-lightgbm_regression.R:141:5'): test nested cv, grid - lightgbm ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("msle") at test-lightgbm_regression.R:141:5
── Error ('test-ranger_binary.R:92:5'): test nested cv, bayesian, binary - ranger ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("auc") at test-ranger_binary.R:92:5
── Error ('test-ranger_multiclass.R:93:5'): test nested cv, bayesian, regression - ranger ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("bacc") at test-ranger_multiclass.R:93:5
── Error ('test-ranger_regression.R:87:5'): test nested cv, bayesian, regression - ranger ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("msle") at test-ranger_regression.R:87:5
── Error ('test-ranger_regression.R:125:5'): test nested cv, grid - ranger ─────
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("msle") at test-ranger_regression.R:125:5
── Error ('test-xgboost_binary.R:83:5'): test nested cv, bayesian, binary:logistic - xgboost ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("auc") at test-xgboost_binary.R:83:5
── Error ('test-xgboost_multiclass.R:86:5'): test nested cv, bayesian, multi:softprob - xgboost, with weights ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("bacc") at test-xgboost_multiclass.R:86:5
── Error ('test-xgboost_regression.R:82:5'): test nested cv, bayesian, reg:squarederror - xgboost ──
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("msle") at test-xgboost_regression.R:82:5
── Error ('test-xgboost_regression.R:125:5'): test nested cv, grid - xgboost ───
Error: Package "measures" must be installed to use function 'metric()'.
Backtrace:
▆
1. └─mlexperiments::metric("msle") at test-xgboost_regression.R:125:5
[ FAIL 17 | WARN 0 | SKIP 1 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: ERROR: 1, OK: 12
Version: 0.0.5
Check: examples
Result: ERROR
Running examples in ‘mlsurvlrnrs-Ex.R’ failed
The error most likely occurred in:
> ### Name: LearnerSurvCoxPHCox
> ### Title: R6 Class to construct a Cox proportional hazards survival
> ### learner
> ### Aliases: LearnerSurvCoxPHCox
>
> ### ** Examples
>
> # survival analysis
>
> dataset <- survival::colon |>
+ data.table::as.data.table() |>
+ na.omit()
> dataset <- dataset[get("etype") == 2, ]
>
> seed <- 123
> surv_cols <- c("status", "time", "rx")
>
> feature_cols <- colnames(dataset)[3:(ncol(dataset) - 1)]
>
> split_vector <- splitTools::multi_strata(
+ df = dataset[, .SD, .SDcols = surv_cols],
+ strategy = "kmeans",
+ k = 4
+ )
>
> train_x <- model.matrix(
+ ~ -1 + .,
+ dataset[, .SD, .SDcols = setdiff(feature_cols, surv_cols[1:2])]
+ )
> train_y <- survival::Surv(
+ event = (dataset[, get("status")] |>
+ as.character() |>
+ as.integer()),
+ time = dataset[, get("time")],
+ type = "right"
+ )
>
> fold_list <- splitTools::create_folds(
+ y = split_vector,
+ k = 3,
+ type = "stratified",
+ seed = seed
+ )
>
>
> surv_coxph_cox_optimizer <- mlexperiments::MLCrossValidation$new(
+ learner = LearnerSurvCoxPHCox$new(),
+ fold_list = fold_list,
+ ncores = 1L,
+ seed = seed
+ )
> surv_coxph_cox_optimizer$performance_metric <- c_index
>
> # set data
> surv_coxph_cox_optimizer$set_data(
+ x = train_x,
+ y = train_y
+ )
>
> surv_coxph_cox_optimizer$execute()
CV fold: Fold1
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.
CV fold: Fold2
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.
CV fold: Fold3
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.
Error: Package "measures" must be installed to use function 'metric_types_helper()'.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [122s/405s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> Sys.setenv("OMP_THREAD_LIMIT" = 2)
> Sys.setenv("Ncpu" = 2)
>
> library(testthat)
> library(mlsurvlrnrs)
>
> test_check("mlsurvlrnrs")
CV fold: Fold1
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.
CV fold: Fold2
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.
CV fold: Fold3
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.
CV fold: Fold1
Registering parallel backend using 2 cores.
Running initial scoring function 6 times in 2 thread(s)... 9.703 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 2.43 seconds
3) Running FUN 2 times in 2 thread(s)... 1.483 seconds
CV fold: Fold2
Registering parallel backend using 2 cores.
Running initial scoring function 6 times in 2 thread(s)... 9.873 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 2.606 seconds
3) Running FUN 2 times in 2 thread(s)... 1.493 seconds
CV fold: Fold3
Registering parallel backend using 2 cores.
Running initial scoring function 6 times in 2 thread(s)... 9.365 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 1.402 seconds
3) Running FUN 2 times in 2 thread(s)... 1.432 seconds
CV fold: Fold1
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.202 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
- Could not obtain meaningful lengthscales.
2) Running local optimum search...
- Convergence Not Found. Trying again with tighter parameters...
- Convergence Not Found. Trying again with tighter parameters...
- Convergence Not Found. Trying again with tighter parameters...
- Maximum convergence attempts exceeded - process is probably sampling random points. 112 seconds
3) Running FUN 2 times in 2 thread(s)... 0.641 seconds
CV fold: Fold2
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.292 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 31.118 seconds
3) Running FUN 2 times in 2 thread(s)... 0.814 seconds
CV fold: Fold3
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.399 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 4.91 seconds
3) Running FUN 2 times in 2 thread(s)... 0.673 seconds
CV fold: Fold1
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.433 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 0.918 seconds
3) Running FUN 2 times in 2 thread(s)... 0.557 seconds
CV fold: Fold2
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.36 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 1.135 seconds
3) Running FUN 2 times in 2 thread(s)... 1.036 seconds
CV fold: Fold3
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.618 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 0.936 seconds
3) Running FUN 2 times in 2 thread(s)... 0.621 seconds
CV fold: Fold1
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.403 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 18.456 seconds
3) Running FUN 2 times in 2 thread(s)... 0.807 seconds
CV fold: Fold2
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.621 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 5.441 seconds
3) Running FUN 2 times in 2 thread(s)... 0.796 seconds
CV fold: Fold3
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 7.38 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 11.006 seconds
3) Running FUN 2 times in 2 thread(s)... 0.761 seconds
CV fold: Fold1
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 6.81 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 6.841 seconds
3) Running FUN 2 times in 2 thread(s)... 0.465 seconds
CV fold: Fold2
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 6.855 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
- Could not obtain meaningful lengthscales.
2) Running local optimum search...
- Convergence Not Found. Trying again with tighter parameters...
- Convergence Not Found. Trying again with tighter parameters... 14.425 seconds
3) Running FUN 2 times in 2 thread(s)... 0.639 seconds
CV fold: Fold3
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 10 rows.
Registering parallel backend using 2 cores.
Running initial scoring function 10 times in 2 thread(s)... 6.37 seconds
Starting Epoch 1
1) Fitting Gaussian Process...
2) Running local optimum search... 8.252 seconds
3) Running FUN 2 times in 2 thread(s)... 0.52 seconds
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 0 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-lints.R:10:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-surv_coxph_cox.R:56:5'): test cv - surv_coxph_cox ──────────────
Error: Package "measures" must be installed to use function 'metric_types_helper()'.
Backtrace:
▆
1. └─surv_coxph_cox_optimizer$execute() at test-surv_coxph_cox.R:56:5
2. └─mlexperiments:::.run_cv(self = self, private = private)
3. └─mlexperiments:::.cv_postprocessing(...)
4. └─mlexperiments:::.compute_performance(...)
5. └─base::sapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─mlexperiments (local) FUN(X[[i]], ...)
8. └─mlexperiments::metric_types_helper(...)
── Error ('test-surv_glmnet_cox.R:99:5'): test nested cv, grid - surv_glmnet_cox ──
Error: Package "measures" must be installed to use function 'metric_types_helper()'.
Backtrace:
▆
1. └─surv_glmnet_cox_optimizer$execute() at test-surv_glmnet_cox.R:99:5
2. └─mlexperiments:::.run_cv(self = self, private = private)
3. └─mlexperiments:::.cv_postprocessing(...)
4. └─mlexperiments:::.compute_performance(...)
5. └─base::sapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─mlexperiments (local) FUN(X[[i]], ...)
8. └─mlexperiments::metric_types_helper(...)
── Error ('test-surv_ranger_cox.R:110:5'): test nested cv, bayesian - surv_ranger_cox ──
Error: Package "measures" must be installed to use function 'metric_types_helper()'.
Backtrace:
▆
1. └─surv_ranger_cox_optimizer$execute() at test-surv_ranger_cox.R:110:5
2. └─mlexperiments:::.run_cv(self = self, private = private)
3. └─mlexperiments:::.cv_postprocessing(...)
4. └─mlexperiments:::.compute_performance(...)
5. └─base::sapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─mlexperiments (local) FUN(X[[i]], ...)
8. └─mlexperiments::metric_types_helper(...)
── Error ('test-surv_rpart_cox.R:108:5'): test nested cv, bayesian - surv_rpart_cox ──
Error: Package "measures" must be installed to use function 'metric_types_helper()'.
Backtrace:
▆
1. └─surv_rpart_cox_optimizer$execute() at test-surv_rpart_cox.R:108:5
2. └─mlexperiments:::.run_cv(self = self, private = private)
3. └─mlexperiments:::.cv_postprocessing(...)
4. └─mlexperiments:::.compute_performance(...)
5. └─base::sapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─mlexperiments (local) FUN(X[[i]], ...)
8. └─mlexperiments::metric_types_helper(...)
── Error ('test-surv_xgboost_aft.R:116:5'): test nested cv, bayesian - surv_xgboost_aft ──
Error: Package "measures" must be installed to use function 'metric_types_helper()'.
Backtrace:
▆
1. └─surv_xgboost_aft_optimizer$execute() at test-surv_xgboost_aft.R:116:5
2. └─mlexperiments:::.run_cv(self = self, private = private)
3. └─mlexperiments:::.cv_postprocessing(...)
4. └─mlexperiments:::.compute_performance(...)
5. └─base::sapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─mlexperiments (local) FUN(X[[i]], ...)
8. └─mlexperiments::metric_types_helper(...)
── Error ('test-surv_xgboost_cox.R:115:5'): test nested cv, bayesian - surv_xgboost_cox ──
Error: Package "measures" must be installed to use function 'metric_types_helper()'.
Backtrace:
▆
1. └─surv_xgboost_cox_optimizer$execute() at test-surv_xgboost_cox.R:115:5
2. └─mlexperiments:::.run_cv(self = self, private = private)
3. └─mlexperiments:::.cv_postprocessing(...)
4. └─mlexperiments:::.compute_performance(...)
5. └─base::sapply(...)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─mlexperiments (local) FUN(X[[i]], ...)
8. └─mlexperiments::metric_types_helper(...)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: OK: 13
Current CRAN status: OK: 13