Last updated on 2026-09-11 21:51:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.1 | 50.54 | 228.81 | 279.35 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.1 | 37.37 | 179.56 | 216.93 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.0 | 46.00 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.1 | 43.00 | 154.90 | 197.90 | ERROR | |
| r-devel-windows-x86_64 | 0.2.1 | 57.00 | 330.00 | 387.00 | OK | |
| r-patched-linux-x86_64 | 0.2.1 | 51.09 | 223.76 | 274.85 | OK | |
| r-release-linux-x86_64 | 0.2.1 | 54.48 | 221.89 | 276.37 | OK | |
| r-release-macos-arm64 | 0.2.1 | 12.00 | 74.00 | 86.00 | OK | |
| r-release-macos-x86_64 | 0.2.1 | 38.00 | 252.00 | 290.00 | OK | |
| r-release-windows-x86_64 | 0.2.1 | 58.00 | 349.00 | 407.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.1 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.1 | 39.00 | 290.00 | 329.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.1 | 80.00 | 340.00 | 420.00 | OK |
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/18s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(normalblockr)
>
> test_check("normalblockr")
number of blocks = 1
number of blocks = 2
number of blocks = 3
number of blocks = 2
number of blocks = 3
number of blocks = 4
number of blocks = 2
penalty = 0.2315772
penalty = 0.1975743
penalty = 0.168564
penalty = 0.1438134
penalty = 0.122697
penalty = 0.1046811
penalty = 0.08931055
penalty = 0.07619689
penalty = 0.06500874
penalty = 0.05546336
penalty = 0.04731956
penalty = 0.04037153
penalty = 0.03444369
penalty = 0.02938625
penalty = 0.0250714
penalty = 0.02139011
penalty = 0.01824936
penalty = 0.01556977
penalty = 0.01328362
penalty = 0.01133316
penalty = 0.009669088
penalty = 0.008249355
penalty = 0.007038085
penalty = 0.006004668
penalty = 0.005122989
penalty = 0.00437077
penalty = 0.003729
penalty = 0.003181463
penalty = 0.002714322
penalty = 0.002315772
number of blocks = 3
penalty = 0.2959283
penalty = 0.2524765
penalty = 0.2154049
penalty = 0.1837765
penalty = 0.1567922
penalty = 0.1337701
penalty = 0.1141283
penalty = 0.09737062
penalty = 0.08307348
penalty = 0.07087562
penalty = 0.0604688
penalty = 0.05159004
penalty = 0.04401496
penalty = 0.03755215
penalty = 0.03203829
penalty = 0.02733404
penalty = 0.02332052
penalty = 0.01989632
penalty = 0.0169749
penalty = 0.01448244
penalty = 0.01235595
penalty = 0.0105417
penalty = 0.00899384
penalty = 0.007673255
penalty = 0.006546575
penalty = 0.005585327
penalty = 0.004765222
penalty = 0.004065534
penalty = 0.003468583
penalty = 0.002959283
number of blocks = 4
penalty = 0.3171464
penalty = 0.2705791
penalty = 0.2308494
penalty = 0.1969533
penalty = 0.1680342
penalty = 0.1433614
penalty = 0.1223113
penalty = 0.1043521
penalty = 0.08902984
penalty = 0.0759574
penalty = 0.06480441
penalty = 0.05528904
penalty = 0.04717083
penalty = 0.04024464
penalty = 0.03433543
penalty = 0.02929389
penalty = 0.0249926
penalty = 0.02132288
penalty = 0.018192
penalty = 0.01552083
penalty = 0.01324187
penalty = 0.01129754
penalty = 0.009638698
penalty = 0.008223427
penalty = 0.007015964
penalty = 0.005985795
penalty = 0.005106888
penalty = 0.004357032
penalty = 0.00371728
penalty = 0.003171464
number of blocks = 2
penalty = 0.3050263
penalty = 0.2602386
penalty = 0.2220272
penalty = 0.1894265
penalty = 0.1616126
penalty = 0.1378827
penalty = 0.1176371
penalty = 0.1003642
penalty = 0.08562747
penalty = 0.0730546
penalty = 0.06232784
penalty = 0.05317611
penalty = 0.04536815
penalty = 0.03870664
penalty = 0.03302326
penalty = 0.02817439
penalty = 0.02403748
penalty = 0.02050801
penalty = 0.01749677
penalty = 0.01492768
penalty = 0.01273582
penalty = 0.01086579
penalty = 0.009270344
penalty = 0.00790916
penalty = 0.006747841
penalty = 0.005757041
penalty = 0.004911722
penalty = 0.004190523
penalty = 0.00357522
penalty = 0.003050263
number of blocks = 3
penalty = 0.3303011
penalty = 0.2818023
penalty = 0.2404246
penalty = 0.2051226
penalty = 0.175004
penalty = 0.1493078
penalty = 0.1273846
penalty = 0.1086804
penalty = 0.09272265
penalty = 0.07910799
penalty = 0.06749239
penalty = 0.05758234
penalty = 0.0491274
penalty = 0.04191392
penalty = 0.03575961
penalty = 0.03050895
penalty = 0.02602925
penalty = 0.02220732
penalty = 0.01894657
penalty = 0.01616461
penalty = 0.01379112
penalty = 0.01176614
penalty = 0.0100385
penalty = 0.008564521
penalty = 0.007306974
penalty = 0.006234076
penalty = 0.005318713
penalty = 0.004537755
penalty = 0.003871467
penalty = 0.003303011
number of blocks = 4
penalty = 0.5085554
penalty = 0.4338831
penalty = 0.3701751
penalty = 0.3158215
penalty = 0.2694488
penalty = 0.229885
penalty = 0.1961305
penalty = 0.1673322
penalty = 0.1427625
penalty = 0.1218004
penalty = 0.1039162
penalty = 0.08865792
penalty = 0.07564009
penalty = 0.06453369
penalty = 0.05505807
penalty = 0.04697378
penalty = 0.04007652
penalty = 0.034192
penalty = 0.02917151
penalty = 0.0248882
penalty = 0.02123381
penalty = 0.018116
penalty = 0.01545599
penalty = 0.01318656
penalty = 0.01125034
penalty = 0.009598433
penalty = 0.008189074
penalty = 0.006986655
penalty = 0.005960789
penalty = 0.005085554
No model with this penalty in the collection. Returning model with closest penalty: 0.0927226549989336 Collection penalty values can be found via $sparsity
penalty = 0.2959283
penalty = 0.2524765
penalty = 0.2154049
penalty = 0.1837765
penalty = 0.1567922
penalty = 0.1337701
penalty = 0.1141283
penalty = 0.09737062
penalty = 0.08307348
penalty = 0.07087562
penalty = 0.0604688
penalty = 0.05159004
penalty = 0.04401496
penalty = 0.03755215
penalty = 0.03203829
penalty = 0.02733404
penalty = 0.02332052
penalty = 0.01989632
penalty = 0.0169749
penalty = 0.01448244
penalty = 0.01235595
penalty = 0.0105417
penalty = 0.00899384
penalty = 0.007673255
penalty = 0.006546575
penalty = 0.005585327
penalty = 0.004765222
penalty = 0.004065534
penalty = 0.003468583
penalty = 0.002959283
penalty = 0.3303011
penalty = 0.2818023
penalty = 0.2404246
penalty = 0.2051226
penalty = 0.175004
penalty = 0.1493078
penalty = 0.1273846
penalty = 0.1086804
penalty = 0.09272265
penalty = 0.07910799
penalty = 0.06749239
penalty = 0.05758234
penalty = 0.0491274
penalty = 0.04191392
penalty = 0.03575961
penalty = 0.03050895
penalty = 0.02602925
penalty = 0.02220732
penalty = 0.01894657
penalty = 0.01616461
penalty = 0.01379112
penalty = 0.01176614
penalty = 0.0100385
penalty = 0.008564521
penalty = 0.007306974
penalty = 0.006234076
penalty = 0.005318713
penalty = 0.004537755
penalty = 0.003871467
penalty = 0.003303011
A diagonal normal-block-var model with 3 unknown blocks .
===========================================================================
nb_param q n_edges sparsity loglik deviance BIC ICL EBIC niter
48 3 3 0 -912.19 1824.379 2034.716 1727.892 2041.308 8
===========================================================================
* Useful fields
$model_par, $posterior_par / $var_par, $clustering
$loglik, $BIC, $ICL, $objective, $nb_param, $criteria
* Useful S3 methods
print(), summary(), plot(), coef(), sigma(), fitted(), predict()
A diagonal normal-block-var model with unknown q
===========================================================================
3 model(s) explored
q ranging from 2 to 4
===========================================================================
* Useful fields
$models, $criteria
* Useful methods
print(), summary(), plot(), $get_best_model()
Saving _problems/test-clustering-heuristics-18.R
Saving _problems/test-clustering-heuristics-58.R
Saving _problems/test-clustering-heuristics-90.R
A sequential mean-then-variance normal-block fit
===========================================================================
mean-block stage : 3 clusters -- diagonal normal-block-mean model with fixed blocks
variance-block stage: 2 clusters -- diagonal normal-block-var model with 2 unknown blocks
ARI between the two partitions: -0.032
(near 0 means the two structures are unrelated, as is usual)
===========================================================================
* Useful fields
$mean, $var (both ordinary fitted models), $residuals
Saving _problems/test-shared-initialization-186.R
Saving _problems/test-shared-initialization-204.R
Saving _problems/test-shared-initialization-210.R
Saving _problems/test-shared-initialization-237.R
Saving _problems/test-shared-initialization-244.R
Saving _problems/test-shared-initialization-253.R
[ FAIL 9 | WARN 59 | SKIP 0 | PASS 560 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-clustering-heuristics.R:18:5'): every user-selectable clustering heuristic name produces a valid q-cluster init ──
Expected `model$optimize(control = list(niter = 2, threshold = -1))` not to throw any errors.
Actually got a <functionNotFoundError> with message:
could not find function "initRefFields"
── Error ('test-clustering-heuristics.R:58:3'): the heuristics reach comparable optima on a variance-block model ──
<functionNotFoundError/objectNotFoundError/error/condition>
Error in `initRefFields(.self, .refClassDef, as.environment(.self), list(...))`: could not find function "initRefFields"
Backtrace:
▆
1. └─model_sbm$optimize() at test-clustering-heuristics.R:58:3
2. └─private$optimizer(control)
3. └─private$optim_initialize()
4. └─private$get_heuristic_parameters()
5. └─private$heuristic_clustering(reg_res$R)
6. └─private$clustering_methods[[private$clustering_approx]](R, self$q)
7. └─sbm::estimateSimpleSBM(cov(R), "gaussian", estimOptions = options)
8. └─mySBM$optimize(currentOptions)
9. ├─base::do.call(paste0("BM_", model_type), args)
10. └─blockmodels::BM_gaussian(...)
11. └─methods::new(`<chr>`, ...)
12. ├─methods::initialize(value, ...)
13. └─methods::initialize(value, ...)
14. └─.Object$initialize(...)
15. └─.self$initFields(...)
── Error ('test-clustering-heuristics.R:90:3'): the heuristics reach comparable optima on a zero-inflated model ──
<functionNotFoundError/objectNotFoundError/error/condition>
Error in `initRefFields(.self, .refClassDef, as.environment(.self), list(...))`: could not find function "initRefFields"
Backtrace:
▆
1. └─model_sbm$optimize() at test-clustering-heuristics.R:90:3
2. └─private$optimizer(control)
3. └─private$optim_initialize()
4. └─private$get_heuristic_parameters()
5. └─private$heuristic_clustering(zi_diag$R)
6. └─private$clustering_methods[[private$clustering_approx]](R, self$q)
7. └─sbm::estimateSimpleSBM(cov(R), "gaussian", estimOptions = options)
8. └─mySBM$optimize(currentOptions)
9. ├─base::do.call(paste0("BM_", model_type), args)
10. └─blockmodels::BM_gaussian(...)
11. └─methods::new(`<chr>`, ...)
12. ├─methods::initialize(value, ...)
13. └─methods::initialize(value, ...)
14. └─.Object$initialize(...)
15. └─.self$initFields(...)
── Error ('test-shared-initialization.R:186:3'): sbm_clustering_path() returns one valid membership vector per q, named by q, never NULL ──
<functionNotFoundError/objectNotFoundError/error/condition>
Error in `initRefFields(.self, .refClassDef, as.environment(.self), list(...))`: could not find function "initRefFields"
Backtrace:
▆
1. └─normalblockr:::sbm_clustering_path(sbm_R, q_list) at test-shared-initialization.R:186:3
2. └─sbm::estimateSimpleSBM(stats::cov(R), "gaussian", estimOptions = options)
3. └─mySBM$optimize(currentOptions)
4. ├─base::do.call(paste0("BM_", model_type), args)
5. └─blockmodels::BM_gaussian(...)
6. └─methods::new(`<chr>`, ...)
7. ├─methods::initialize(value, ...)
8. └─methods::initialize(value, ...)
9. └─.Object$initialize(...)
10. └─.self$initFields(...)
── Error ('test-shared-initialization.R:204:3'): sbm_clustering_path() falls back to a cheap ward2 clustering for q's the SBM exploration doesn't reach ──
<functionNotFoundError/objectNotFoundError/error/condition>
Error in `initRefFields(.self, .refClassDef, as.environment(.self), list(...))`: could not find function "initRefFields"
Backtrace:
▆
1. └─normalblockr:::sbm_clustering_path(sbm_R, q_list) at test-shared-initialization.R:204:3
2. └─sbm::estimateSimpleSBM(stats::cov(R), "gaussian", estimOptions = options)
3. └─mySBM$optimize(currentOptions)
4. ├─base::do.call(paste0("BM_", model_type), args)
5. └─blockmodels::BM_gaussian(...)
6. └─methods::new(`<chr>`, ...)
7. ├─methods::initialize(value, ...)
8. └─methods::initialize(value, ...)
9. └─.Object$initialize(...)
10. └─.self$initFields(...)
── Error ('test-shared-initialization.R:210:3'): NormalBlockVarCollectionClusters with clustering_init = 'sbm' eagerly resolves it from the shared path ──
<functionNotFoundError/objectNotFoundError/error/condition>
Error in `initRefFields(.self, .refClassDef, as.environment(.self), list(...))`: could not find function "initRefFields"
Backtrace:
▆
1. └─NormalBlockVarCollectionClusters$new(...) at test-shared-initialization.R:210:3
2. └─normalblockr (local) initialize(...)
3. └─normalblockr:::clustering_path_for_family(...)
4. └─normalblockr:::clustering_path_for_collection(R, q_list, method)
5. └─normalblockr:::sbm_clustering_path(R, q_list)
6. └─sbm::estimateSimpleSBM(stats::cov(R), "gaussian", estimOptions = options)
7. └─mySBM$optimize(currentOptions)
8. ├─base::do.call(paste0("BM_", model_type), args)
9. └─blockmodels::BM_gaussian(...)
10. └─methods::new(`<chr>`, ...)
11. ├─methods::initialize(value, ...)
12. └─methods::initialize(value, ...)
13. └─.Object$initialize(...)
14. └─.self$initFields(...)
── Error ('test-shared-initialization.R:235:3'): NormalBlockVarCollectionClustersSparsity also uses the shared sbm path ──
<functionNotFoundError/objectNotFoundError/error/condition>
Error in `initRefFields(.self, .refClassDef, as.environment(.self), list(...))`: could not find function "initRefFields"
Backtrace:
▆
1. └─NormalBlockVarCollectionClustersSparsity$new(...) at test-shared-initialization.R:235:3
2. └─normalblockr (local) initialize(...)
3. └─normalblockr:::clustering_path_for_family(...)
4. └─normalblockr:::clustering_path_for_collection(R, q_list, method)
5. └─normalblockr:::sbm_clustering_path(R, q_list)
6. └─sbm::estimateSimpleSBM(stats::cov(R), "gaussian", estimOptions = options)
7. └─mySBM$optimize(currentOptions)
8. ├─base::do.call(paste0("BM_", model_type), args)
9. └─blockmodels::BM_gaussian(...)
10. └─methods::new(`<chr>`, ...)
11. ├─methods::initialize(value, ...)
12. └─methods::initialize(value, ...)
13. └─.Object$initialize(...)
14. └─.self$initFields(...)
── Error ('test-shared-initialization.R:244:3'): sbm_clustering_path()'s ward2 fallback does not error on a (near-)constant column ──
<functionNotFoundError/objectNotFoundError/error/condition>
Error in `initRefFields(.self, .refClassDef, as.environment(.self), list(...))`: could not find function "initRefFields"
Backtrace:
▆
1. ├─testthat::expect_no_warning(...) at test-shared-initialization.R:244:3
2. │ └─testthat:::expect_no_(...)
3. │ └─testthat:::quasi_capture(enquo(object), NULL, capture)
4. │ ├─testthat (local) .capture(...)
5. │ │ ├─base::withRestarts(...)
6. │ │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
7. │ │ │ └─base (local) doWithOneRestart(return(expr), restart)
8. │ │ └─base::withCallingHandlers(...)
9. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
10. └─normalblockr:::sbm_clustering_path(sbm_R_const, 2:20)
11. └─sbm::estimateSimpleSBM(stats::cov(R), "gaussian", estimOptions = options)
12. └─mySBM$optimize(currentOptions)
13. ├─base::do.call(paste0("BM_", model_type), args)
14. └─blockmodels::BM_gaussian(...)
15. └─methods::new(`<chr>`, ...)
16. ├─methods::initialize(value, ...)
17. └─methods::initialize(value, ...)
18. └─.Object$initialize(...)
19. └─.self$initFields(...)
── Error ('test-shared-initialization.R:252:3'): zero-inflated collections also use the shared sbm path, clustering on zi_residuals() instead of ols_residuals() ──
<functionNotFoundError/objectNotFoundError/error/condition>
Error in `initRefFields(.self, .refClassDef, as.environment(.self), list(...))`: could not find function "initRefFields"
Backtrace:
▆
1. └─NormalBlockVarCollectionClusters$new(...) at test-shared-initialization.R:252:3
2. └─normalblockr (local) initialize(...)
3. └─normalblockr:::clustering_path_for_family(...)
4. └─normalblockr:::clustering_path_for_collection(R, q_list, method)
5. └─normalblockr:::sbm_clustering_path(R, q_list)
6. └─sbm::estimateSimpleSBM(stats::cov(R), "gaussian", estimOptions = options)
7. └─mySBM$optimize(currentOptions)
8. ├─base::do.call(paste0("BM_", model_type), args)
9. └─blockmodels::BM_gaussian(...)
10. └─methods::new(`<chr>`, ...)
11. ├─methods::initialize(value, ...)
12. └─methods::initialize(value, ...)
13. └─.Object$initialize(...)
14. └─.self$initFields(...)
[ FAIL 9 | WARN 59 | SKIP 0 | PASS 560 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘breast-cancer-proteomics.Rmd’ using rmarkdown
malloc(): unsorted double linked list corrupted
--- re-building ‘normal-block.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘normal-block.Rmd’
--- re-building ‘zero-inflated-normal-block.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘zero-inflated-normal-block.Rmd’
SUMMARY: processing the following file failed:
‘breast-cancer-proteomics.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc