Last updated on 2026-10-24 12:51:39 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.8 | 6.70 | 115.16 | 121.86 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.0.8 | 4.29 | 83.19 | 87.48 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0.8 | 105.10 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0.8 | 100.61 | OK | |||
| r-devel-windows-x86_64 | 0.0.8 | 9.00 | 129.00 | 138.00 | OK | |
| r-patched-linux-x86_64 | 0.0.8 | 7.06 | 104.69 | 111.75 | OK | |
| r-release-linux-x86_64 | 0.0.8 | 6.38 | 109.95 | 116.33 | OK | |
| r-release-macos-arm64 | 0.0.8 | 1.00 | 28.00 | 29.00 | OK | |
| r-release-macos-x86_64 | 0.0.8 | 4.00 | 124.00 | 128.00 | OK | |
| r-release-windows-x86_64 | 0.0.8 | 8.00 | 119.00 | 127.00 | OK | |
| r-oldrel-macos-arm64 | 0.0.8 | 1.00 | 26.00 | 27.00 | OK | |
| r-oldrel-macos-x86_64 | 0.0.8 | 4.00 | 102.00 | 106.00 | OK | |
| r-oldrel-windows-x86_64 | 0.0.8 | 11.00 | 148.00 | 159.00 | OK |
Version: 0.0.8
Check: examples
Result: ERROR
Running examples in ‘mlsurvlrnrs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LearnerSurvCoxPHCox
> ### Title: R6 Class to construct a Cox proportional hazards survival
> ### learner
> ### Aliases: LearnerSurvCoxPHCox
>
> ### ** Examples
>
> # survival analysis
> if (requireNamespace("survival", quietly = TRUE) &&
+ requireNamespace("glmnet", quietly = TRUE) &&
+ requireNamespace("splitTools", quietly = TRUE)) {
+
+ 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$execute()
+ }
CV fold: Fold1
Parameter 'ncores' is ignored for learner 'LearnerSurvCoxPHCox'.
Error in a$specials[[i]] : subscript out of bounds
Calls: <Anonymous> ... <Anonymous> -> predict.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/29s]
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'.
Saving _problems/test-surv_coxph_cox-67.R
CV fold: Fold1
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 4 rows.
elapsed = 0.964 Round = 1 alpha = 0.4000 Value = 0.6385853
elapsed = 0.719 Round = 2 alpha = 1.0000 Value = 0.6392989
elapsed = 0.826 Round = 3 alpha = 0.2000 Value = 0.6383342
elapsed = 0.705 Round = 4 alpha = 0.6000 Value = 0.6378678
elapsed = 0.764 Round = 5 alpha = 0.9473769 Value = 0.6392761
elapsed = 0.725 Round = 6 alpha = 2.220446e-16 Value = 0.6386236
Best Parameters Found:
Round = 2 alpha = 1.0000 Value = 0.6392989
CV fold: Fold2
CV progress [==================================>-----------------] 2/3 ( 67%)
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 4 rows.
elapsed = 0.565 Round = 1 alpha = 0.4000 Value = 0.6711017
elapsed = 0.625 Round = 2 alpha = 1.0000 Value = 0.6713381
elapsed = 0.898 Round = 3 alpha = 0.2000 Value = 0.6714672
elapsed = 0.722 Round = 4 alpha = 0.6000 Value = 0.6709781
elapsed = 0.794 Round = 5 alpha = 0.01416867 Value = 0.6709011
elapsed = 0.729 Round = 6 alpha = 0.1916107 Value = 0.6713719
Best Parameters Found:
Round = 3 alpha = 0.2000 Value = 0.6714672
CV fold: Fold3
CV progress [====================================================] 3/3 (100%)
Number of rows of initialization grid > than 'options("mlexperiments.bayesian.max_init")'...
... reducing initialization grid to 4 rows.
elapsed = 0.716 Round = 1 alpha = 0.4000 Value = 0.6568598
elapsed = 0.577 Round = 2 alpha = 1.0000 Value = 0.6567473
elapsed = 0.957 Round = 3 alpha = 0.2000 Value = 0.6574278
elapsed = 0.656 Round = 4 alpha = 0.6000 Value = 0.6563444
elapsed = 0.898 Round = 5 alpha = 0.01111365 Value = 0.6574339
elapsed = 0.613 Round = 6 alpha = 0.1115121 Value = 0.6577871
Best Parameters Found:
Round = 6 alpha = 0.1115121 Value = 0.6577871
CV fold: Fold1
Parameter settings [=============================================] 3/3 (100%)
CV fold: Fold2
CV progress [==================================>-----------------] 2/3 ( 67%)
Parameter settings [=============================================] 3/3 (100%)
CV fold: Fold3
CV progress [====================================================] 3/3 (100%)
Parameter settings [=============================================] 3/3 (100%)
CV fold: Fold1
CV fold: Fold2
CV progress [==================================>-----------------] 2/3 ( 67%)
CV fold: Fold3
CV progress [====================================================] 3/3 (100%)
[ FAIL 1 | WARN 75 | SKIP 5 | PASS 9 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-lints.R:10:5'
• {rBayesianOptimizaion} is not installed (4): 'test-surv_ranger_cox.R:93:3',
'test-surv_rpart_cox.R:88:3', 'test-surv_xgboost_aft.R:91:3',
'test-surv_xgboost_cox.R:89:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-surv_coxph_cox.R:67:3'): test cv - surv_coxph_cox ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─surv_coxph_cox_optimizer$execute() at test-surv_coxph_cox.R:67:3
2. └─mlexperiments:::.run_cv(self = self, private = private)
3. └─mlexperiments:::.fold_looper(self, private)
4. ├─base::do.call(private$cv_run_model, run_args)
5. └─mlexperiments (local) `<fn>`(train_index = `<int>`, fold_train = `<list>`, fold_test = `<list>`)
6. ├─base::do.call(.cv_fit_model, args)
7. └─mlexperiments (local) `<fn>`(...)
8. ├─base::do.call(self$learner$predict, pred_args)
9. └─mlexperiments (local) `<fn>`(...)
10. ├─base::do.call(private$fun_predict, kwargs)
11. └─mlsurvlrnrs (local) `<fn>`(...)
12. ├─base::do.call(stats::predict, args)
13. ├─stats (local) `<fn>`(...)
14. └─survival:::predict.coxph(...)
15. └─stats::delete.response(Terms)
16. └─stats (local) off(a$specials[[i]])
[ FAIL 1 | WARN 75 | SKIP 5 | PASS 9 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc