- using R Under development (unstable) (2024-06-28 r86850)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 18.1.8
flang-new version 18.1.8
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘mlr3viz/DESCRIPTION’ ... OK
- this is package ‘mlr3viz’ version ‘0.8.0’
- 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 ‘mlr3viz’ can be installed ... [11s/29s] OK
See the install log for details.
- checking installed package size ... OK
- checking package 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 ... [17s/51s] 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 examples ... [54s/139s] ERROR
Running examples in ‘mlr3viz-Ex.R’ failed
The error most likely occurred in:
> ### Name: autoplot.TuningInstanceSingleCrit
> ### Title: Plots for Tuning Instances
> ### Aliases: autoplot.TuningInstanceSingleCrit
>
> ### ** Examples
>
> if (requireNamespace("mlr3tuning") && requireNamespace("patchwork")) {
+ library(mlr3tuning)
+
+ learner = lrn("classif.rpart")
+ learner$param_set$values$cp = to_tune(0.001, 0.1)
+ learner$param_set$values$minsplit = to_tune(1, 10)
+
+ instance = TuningInstanceSingleCrit$new(
+ task = tsk("iris"),
+ learner = learner,
+ resampling = rsmp("holdout"),
+ measure = msr("classif.ce"),
+ terminator = trm("evals", n_evals = 10))
+
+ tuner = tnr("random_search")
+
+ tuner$optimize(instance)
+
+ # plot performance versus batch number
+ autoplot(instance, type = "performance")
+
+ # plot cp values versus performance
+ autoplot(instance, type = "marginal", cols_x = "cp")
+
+ # plot transformed parameter values versus batch number
+ autoplot(instance, type = "parameter", trafo = TRUE)
+
+ # plot parallel coordinates plot
+ autoplot(instance, type = "parallel")
+
+ # plot pairs
+ autoplot(instance, type = "pairs")
+ }
Loading required namespace: mlr3tuning
Loading required package: mlr3
Loading required package: paradox
TuningInstanceSingleCrit is deprecated. Use TuningInstanceBatchSingleCrit instead.
INFO [10:04:56.002] [bbotk] Starting to optimize 2 parameter(s) with '<OptimizerBatchRandomSearch>' and '<TerminatorEvals> [n_evals=10, k=0]'
INFO [10:04:56.103] [bbotk] Evaluating 1 configuration(s)
INFO [10:04:56.129] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:04:56.214] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:04:56.266] [mlr3] Finished benchmark
INFO [10:04:56.362] [bbotk] Result of batch 1:
INFO [10:04:56.374] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:04:56.374] [bbotk] 0.008452299 3 0.06 0 0 0.033
INFO [10:04:56.374] [bbotk] uhash
INFO [10:04:56.374] [bbotk] 64775c28-c47b-4766-8e4d-dd73aeb6af4e
INFO [10:04:56.407] [bbotk] Evaluating 1 configuration(s)
INFO [10:04:56.433] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:04:56.449] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:04:56.506] [mlr3] Finished benchmark
INFO [10:04:56.607] [bbotk] Result of batch 2:
INFO [10:04:56.616] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:04:56.616] [bbotk] 0.08961432 5 0.04 0 0 0.039
INFO [10:04:56.616] [bbotk] uhash
INFO [10:04:56.616] [bbotk] ca856bcf-7791-49fb-a6fe-fdef6a09245f
INFO [10:04:56.649] [bbotk] Evaluating 1 configuration(s)
INFO [10:04:56.677] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:04:56.693] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:04:56.748] [mlr3] Finished benchmark
INFO [10:04:56.843] [bbotk] Result of batch 3:
INFO [10:04:56.851] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:04:56.851] [bbotk] 0.0418993 1 0.04 0 0 0.035
INFO [10:04:56.851] [bbotk] uhash
INFO [10:04:56.851] [bbotk] c5564361-b274-4850-91cd-eff1b69cd838
INFO [10:04:56.884] [bbotk] Evaluating 1 configuration(s)
INFO [10:04:56.907] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:04:56.923] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:04:56.977] [mlr3] Finished benchmark
INFO [10:04:57.075] [bbotk] Result of batch 4:
INFO [10:04:57.083] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:04:57.083] [bbotk] 0.03442392 7 0.04 0 0 0.035
INFO [10:04:57.083] [bbotk] uhash
INFO [10:04:57.083] [bbotk] 904912ae-d4f2-49c8-b36c-62c58bd01fa6
INFO [10:04:57.116] [bbotk] Evaluating 1 configuration(s)
INFO [10:04:57.142] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:04:57.176] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:04:57.342] [mlr3] Finished benchmark
INFO [10:04:57.492] [bbotk] Result of batch 5:
INFO [10:04:58.109] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:04:58.109] [bbotk] 0.03974457 4 0.04 0 0 0.118
INFO [10:04:58.109] [bbotk] uhash
INFO [10:04:58.109] [bbotk] 96fc4f3e-4133-4bcd-95fc-1aea2f757016
INFO [10:04:58.245] [bbotk] Evaluating 1 configuration(s)
INFO [10:04:58.305] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:04:58.338] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:04:58.405] [mlr3] Finished benchmark
INFO [10:04:58.536] [bbotk] Result of batch 6:
INFO [10:04:58.546] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:04:58.546] [bbotk] 0.07436679 7 0.04 0 0 0.042
INFO [10:04:58.546] [bbotk] uhash
INFO [10:04:58.546] [bbotk] 9297a84e-366b-4943-a0ba-011a61d23118
INFO [10:04:58.579] [bbotk] Evaluating 1 configuration(s)
INFO [10:04:58.701] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:04:58.828] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:04:59.042] [mlr3] Finished benchmark
INFO [10:04:59.421] [bbotk] Result of batch 7:
INFO [10:04:59.461] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:04:59.461] [bbotk] 0.01993475 9 0.04 0 0 0.153
INFO [10:04:59.461] [bbotk] uhash
INFO [10:04:59.461] [bbotk] db6b0b69-e04f-4ddf-93e5-ba55d3b230a0
INFO [10:04:59.574] [bbotk] Evaluating 1 configuration(s)
INFO [10:04:59.655] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:04:59.741] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:05:00.106] [mlr3] Finished benchmark
INFO [10:05:00.680] [bbotk] Result of batch 8:
INFO [10:05:00.689] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:05:00.689] [bbotk] 0.01973017 8 0.04 0 0 0.266
INFO [10:05:00.689] [bbotk] uhash
INFO [10:05:00.689] [bbotk] 2d539514-f744-4869-a9c3-9157b603f55d
INFO [10:05:00.723] [bbotk] Evaluating 1 configuration(s)
INFO [10:05:00.748] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:05:00.767] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:05:00.830] [mlr3] Finished benchmark
INFO [10:05:00.941] [bbotk] Result of batch 9:
INFO [10:05:00.952] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:05:00.952] [bbotk] 0.05521701 8 0.04 0 0 0.042
INFO [10:05:00.952] [bbotk] uhash
INFO [10:05:00.952] [bbotk] d8b656c8-fa2b-43d5-88c6-66c04f0c1433
INFO [10:05:00.989] [bbotk] Evaluating 1 configuration(s)
INFO [10:05:01.016] [mlr3] Running benchmark with 1 resampling iterations
INFO [10:05:01.034] [mlr3] Applying learner 'classif.rpart' on task 'iris' (iter 1/1)
INFO [10:05:01.106] [mlr3] Finished benchmark
INFO [10:05:01.450] [bbotk] Result of batch 10:
INFO [10:05:01.480] [bbotk] cp minsplit classif.ce warnings errors runtime_learners
INFO [10:05:01.480] [bbotk] 0.09280291 3 0.04 0 0 0.047
INFO [10:05:01.480] [bbotk] uhash
INFO [10:05:01.480] [bbotk] 5493921e-66ed-4aaa-a411-5dd094d51a09
INFO [10:05:01.560] [bbotk] Finished optimizing after 10 evaluation(s)
INFO [10:05:01.562] [bbotk] Result:
INFO [10:05:01.571] [bbotk] cp minsplit learner_param_vals x_domain classif.ce
INFO [10:05:01.571] [bbotk] <num> <int> <list> <list> <num>
INFO [10:05:01.571] [bbotk] 0.08961432 5 <list[3]> <list[2]> 0.04
Error in `fortify()`:
! `data` must be a <data.frame>, or an object coercible by `fortify()`,
or a valid <data.frame>-like object coercible by `as.data.frame()`.
Caused by error in `.prevalidate_data_frame_like_object()`:
! `dim(data)` must return an <integer> of length 2.
Backtrace:
▆
1. ├─ggplot2::autoplot(instance, type = "performance")
2. └─mlr3viz:::autoplot.TuningInstanceSingleCrit(instance, type = "performance")
3. └─mlr3viz:::autoplot.OptimInstanceSingleCrit(...)
4. ├─ggplot2::fortify(object)
5. └─ggplot2:::fortify.default(object)
6. ├─rlang::try_fetch(...)
7. │ ├─base::tryCatch(...)
8. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ └─base::withCallingHandlers(...)
12. └─ggplot2:::validate_as_data_frame(model)
13. └─ggplot2:::.prevalidate_data_frame_like_object(data)
14. └─cli::cli_abort(paste0("{.code dim(data)} must return ", "an {.cls integer} of length 2."))
15. └─rlang::abort(...)
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [129s/88s] ERROR
Running ‘testthat.R’ [129s/86s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> if (requireNamespace("testthat", quietly = TRUE)) {
+ library("testthat")
+ library("mlr3viz")
+ test_check("mlr3viz")
+ }
Starting 2 test processes
[ FAIL 1 | WARN 0 | SKIP 27 | PASS 86 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test_Filter.R:10:3', 'test_LearnerClassif.R:8:3',
'test_LearnerClassif.R:18:3', 'test_BenchmarkResult.R:20:3',
'test_BenchmarkResult.R:49:3', 'test_LearnerClassifCVGlmnet.R:13:3',
'test_LearnerClassifRpart.R:10:3', 'test_LearnerClasssifGlmnet.R:13:3',
'test_LearnerRegr.R:8:3', 'test_LearnerRegr.R:18:3',
'test_LearnerRegr.R:28:3', 'test_LearnerClustHierarchical.R:7:3',
'test_LearnerRegrCVGlmnet.R:13:3', 'test_LearnerRegrGlmnet.R:12:3',
'test_LearnerRegrRpart.R:10:3', 'test_PredictionClassif.R:11:3',
'test_OptimInstanceSingleCrit.R:47:7', 'test_PredictionRegr.R:10:3',
'test_PredictionClust.R:8:3', 'test_TaskClassif.R:8:3',
'test_TaskClust.R:10:3', 'test_TaskRegr.R:8:3', 'test_ResampleResult.R:21:3',
'test_plot_learner_prediction.R:10:3', 'test_plot_learner_prediction.R:43:3',
'test_plot_learner_prediction.R:53:3', 'test_TuningInstanceSingleCrit.R:33:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_TuningInstanceSingleCrit.R:28:3'): fortify.TuningInstanceSingleCrit ──
Error in `fortify(instance)`: `data` must be a <data.frame>, or an object coercible by `fortify()`, or a valid <data.frame>-like object coercible by `as.data.frame()`.
Caused by error in `.prevalidate_data_frame_like_object()`:
! `dim(data)` must return an <integer> of length 2.
[ FAIL 1 | WARN 0 | SKIP 27 | PASS 86 ]
Deleting unused snapshots:
• BenchmarkResult/bmr-prc.svg
• BenchmarkResult/bmr-roc.svg
• Filter/filter-2.svg
• LearnerClustHierarchical/learner-clust-agnes.svg
• LearnerClustHierarchical/learner-clust-hclust.svg
• OptimInstanceSingleCrit/tisc-marginal-02.svg
• OptimInstanceSingleCrit/tisc-marginal-trafo-01.svg
• OptimInstanceSingleCrit/tisc-marginal-trafo-02.svg
• OptimInstanceSingleCrit/tisc-marginal-x-domain-01.svg
• OptimInstanceSingleCrit/tisc-parallel.svg
• OptimInstanceSingleCrit/tisc-parameter-01.svg
• OptimInstanceSingleCrit/tisc-parameter-02.svg
• OptimInstanceSingleCrit/tisc-parameter-return-list-01.svg
• OptimInstanceSingleCrit/tisc-parameter-return-list-02.svg
• OptimInstanceSingleCrit/tisc-parameter-trafo-01.svg
• OptimInstanceSingleCrit/tisc-parameter-trafo-02.svg
• OptimInstanceSingleCrit/tisc-parameter-x-domain-01.svg
• OptimInstanceSingleCrit/tisc-performance.svg
• OptimInstanceSingleCrit/tisc-points.svg
• OptimInstanceSingleCrit/tisc-surface-grid-50.svg
• OptimInstanceSingleCrit/tisc-surface-regr-lm.svg
• OptimInstanceSingleCrit/tisc-surface.svg
• PredictionClassif/predictionclassif-prc.svg
• PredictionClassif/predictionclassif-roc.svg
• PredictionClassif/predictionclassif-threshold.svg
• PredictionClust/predictionclust-pca.svg
• PredictionClust/predictionclust-scatter.svg
• PredictionClust/predictionclust-sil.svg
• PredictionRegr/predictionregr-confidence.svg
• PredictionRegr/predictionregr-histogram.svg
• PredictionRegr/predictionregr-residual.svg
• ResampleResult/resampleresult-histogram.svg
• ResampleResult/resampleresult-prc.svg
• ResampleResult/resampleresult-roc.svg
• TaskClassif/taskclassif-duo.svg
• TaskClassif/taskclassif-pairs.svg
• TaskRegr/taskregr-pairs.svg
• TuningInstanceSingleCrit/tisc-incumbent.svg
• TuningInstanceSingleCrit/tisc-marginal-01.svg
• TuningInstanceSingleCrit/tisc-marginal-02.svg
• TuningInstanceSingleCrit/tisc-marginal-trafo-01.svg
• TuningInstanceSingleCrit/tisc-marginal-trafo-02.svg
• TuningInstanceSingleCrit/tisc-marginal-x-domain-01.svg
• TuningInstanceSingleCrit/tisc-parallel.svg
• TuningInstanceSingleCrit/tisc-parameter-01.svg
• TuningInstanceSingleCrit/tisc-parameter-02.svg
• TuningInstanceSingleCrit/tisc-parameter-return-list-01.svg
• TuningInstanceSingleCrit/tisc-parameter-return-list-02.svg
• TuningInstanceSingleCrit/tisc-parameter-trafo-01.svg
• TuningInstanceSingleCrit/tisc-parameter-trafo-02.svg
• TuningInstanceSingleCrit/tisc-parameter-x-domain-01.svg
• TuningInstanceSingleCrit/tisc-performance.svg
• TuningInstanceSingleCrit/tisc-points.svg
• TuningInstanceSingleCrit/tisc-surface-grid-50.svg
• TuningInstanceSingleCrit/tisc-surface-regr-lm.svg
• TuningInstanceSingleCrit/tisc-surface.svg
• plot_learner_prediction/learner-prediction-1d-se.svg
• plot_learner_prediction/learner-prediction-binary-prob.svg
• plot_learner_prediction/learner-prediction-binary-response.svg
• plot_learner_prediction/learner-prediction-categorical.svg
• plot_learner_prediction/learner-prediction-prob.svg
Error: Test failures
Execution halted
- checking PDF version of manual ... [9s/27s] 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