• using R Under development (unstable) (2025-09-04 r88794)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 21.1.0     flang version 21.1.0
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘mlsurvlrnrs/DESCRIPTION’ ... OK
• this is package ‘mlsurvlrnrs’ version ‘0.0.5’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘mlsurvlrnrs’ can be installed ... [12s/12s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking whether startup messages can be suppressed ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [122s/405s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [50s/47s] OK
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs