Last updated on 2025-02-14 02:49:38 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.1.1 | 141.47 | 178.80 | 320.27 | OK | --no-tests |
| r-devel-linux-x86_64-debian-gcc | 3.1.1 | 101.77 | 121.11 | 222.88 | OK | --no-tests |
| r-devel-linux-x86_64-fedora-clang | 3.1.1 | 1001.96 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 3.1.1 | 985.72 | ERROR | |||
| r-devel-windows-x86_64 | 3.1.1 | 149.00 | 319.00 | 468.00 | OK | |
| r-patched-linux-x86_64 | 3.1.1 | 140.70 | 164.53 | 305.23 | NOTE | --no-tests |
| r-release-linux-x86_64 | 3.1.1 | 140.22 | 163.55 | 303.77 | NOTE | --no-tests |
| r-release-macos-arm64 | 3.1.1 | 467.00 | ERROR | |||
| r-release-macos-x86_64 | 3.1.1 | 1006.00 | ERROR | |||
| r-release-windows-x86_64 | 3.1.1 | 153.00 | 306.00 | 459.00 | NOTE | |
| r-oldrel-macos-arm64 | 3.1.1 | 583.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 3.1.1 | 1484.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 3.1.1 | 179.00 | 390.00 | 569.00 | ERROR |
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [7m/10m]
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
>
> library(testthat)
> library(abn)
abn version 3.1.1 (2024-05-22) is loaded.
To cite the package 'abn' in publications call: citation('abn').
Attaching package: 'abn'
The following object is masked from 'package:base':
factorial
>
> require(RhpcBLASctl)
Loading required package: RhpcBLASctl
> omp_set_num_threads(2)
>
> test_check("abn")
Loading required package: Matrix
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
[ FAIL 9 | WARN 0 | SKIP 55 | PASS 448 ]
══ Skipped tests (55) ══════════════════════════════════════════════════════════
• BuildScoreCache(method=mle) crashes with Poisson nodes (1):
'test-fitabn_mle.R:138:3'
• INLA is not tested on CRAN (1): 'test-search_hillclimber.R:79:7'
• On CRAN (52): 'test-Coutput.R:1:1', 'test-abn-methods.R:29:3',
'test-abn-methods.R:55:3', 'test-abn-methods.R:76:3',
'test-abn-methods.R:102:3', 'test-abn-methods.R:125:3',
'test-abn-methods.R:154:3', 'test-abn-methods.R:177:3',
'test-abn-methods.R:200:3', 'test-abn-methods.R:228:3',
'test-abn-methods.R:253:3', 'test-abn-methods.R:278:3',
'test-abn-methods.R:303:3', 'test-abn-methods.R:328:3',
'test-abn-methods.R:353:3', 'test-abn-methods.R:378:3',
'test-abn-methods.R:403:3', 'test-abn-methods.R:428:3',
'test-build_score_cache.R:122:3', 'test-build_score_cache.R:181:3',
'test-build_score_cache.R:331:3', 'test-build_score_cache.R:386:3',
'test-build_score_cache.R:434:3', 'test-build_score_cache_bayes.R:2:3',
'test-build_score_cache_bayes.R:33:3', 'test-build_score_cache_bayes.R:91:3',
'test-build_score_cache_bayes.R:127:3', 'test-calc_node_inla_glm.R:2:3',
'test-calc_node_inla_glmm.R:2:3', 'test-fitabn.R:26:3', 'test-fitabn.R:56:3',
'test-fitabn.R:75:3', 'test-fitabn.R:94:3', 'test-fitabn.R:136:3',
'test-fitabn.R:190:3', 'test-fitabn.R:379:3', 'test-fitabn_bayes.R:2:3',
'test-fitabn_mle.R:562:11', 'test-fitabn_mle.R:674:11',
'test-mostprobable.R:2:3', 'test-mostprobable.R:12:3',
'test-mostprobable.R:79:3', 'test-mostprobable.R:169:3',
'test-mostprobable.R:211:3', 'test-plot-abn.R:34:3', 'test-plot-abn.R:125:3',
'test-search_heuristic.R:2:3', 'test-search_hillclimber.R:16:3',
'test-search_hillclimber.R:84:3', 'test-simulateabn.R:508:3',
'test-simulateabn.R:810:3', 'test-tographviz.R:27:3'
• Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-simulateabn.R:780:13'): simulateAbn() simulation works with method 'mle' ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
DAG matrix contains trivial cycles (nonzero values on diagonal)
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-simulateabn.R:761:5
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-simulateabn.R:762:7
4. │ └─base::withCallingHandlers(...)
5. ├─utils::capture.output(...) at test-simulateabn.R:763:9
6. │ └─base::withVisible(...elt(i))
7. └─testthat::expect_no_error(...) at test-simulateabn.R:779:11
── Failure ('test-simulateabn.R:783:13'): simulateAbn() simulation works with method 'mle' ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
object 'myres.mle.grp' not found
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-simulateabn.R:761:5
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-simulateabn.R:762:7
4. │ └─base::withCallingHandlers(...)
5. ├─utils::capture.output(...) at test-simulateabn.R:763:9
6. │ └─base::withVisible(...elt(i))
7. └─testthat::expect_no_error(...) at test-simulateabn.R:782:11
── Error ('test-simulateabn.R:794:5'): simulateAbn() simulation works with method 'mle' ──
Error in `eval(code, test_env)`: object 'mysim.grp' not found
Backtrace:
▆
1. ├─base::prop.table(table(mysim.grp$Outdoor)) at test-simulateabn.R:794:5
2. └─base::table(mysim.grp$Outdoor)
── Error ('test-simulateabn.R:953:13'): simulateAbn() works with grouping in real data. ──
Error in `validate_abnDag(dag, data.df = data.df, returnDag = TRUE)`: DAG matrix contains trivial cycles (nonzero values on diagonal)
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-simulateabn.R:914:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressWarnings(...) at test-simulateabn.R:915:5
4. │ └─base::withCallingHandlers(...)
5. ├─utils::capture.output(...) at test-simulateabn.R:917:9
6. │ └─base::withVisible(...elt(i))
7. └─abn::fitAbn(object = mydag, method = "mle") at test-simulateabn.R:953:13
8. └─abn::fitAbn.mle(...)
9. └─abn::createAbnDag(dag, data.df = data.df, data.dists = data.dists)
10. └─abn::validate_abnDag(dag, data.df = data.df, returnDag = TRUE)
── Failure ('test-tographviz.R:80:11'): toGraphviz() works with all distributions. ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
DAG matrix contains trivial cycles (nonzero values on diagonal)
Backtrace:
▆
1. ├─utils::capture.output(...) at test-tographviz.R:53:3
2. │ └─base::withVisible(...elt(i))
3. ├─base::suppressMessages(...) at test-tographviz.R:54:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-tographviz.R:78:7
── Failure ('test-tographviz.R:89:5'): toGraphviz() works with all distributions. ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
object 'myres.mle' not found
── Failure ('test-tographviz.R:97:5'): toGraphviz() works with all distributions. ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
object 'myres.mle' not found
── Failure ('test-tographviz.R:105:5'): toGraphviz() works with all distributions. ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
'dag' must comprise only 1's or 0's
── Error ('test-tographviz.R:134:5'): toGraphviz() works with all distributions. ──
Error in `eval(code, test_env)`: object 'myres.mle' not found
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-tographviz.R:133:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─abn::toGraphviz(...) at test-tographviz.R:134:5
[ FAIL 9 | WARN 0 | SKIP 55 | PASS 448 ]
Deleting unused snapshots:
• tographviz/graph.dot
• tographviz/graph1.dot
• tographviz/graph_group.dot
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 3.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘data_simulation.Rmd’ using rmarkdown
--- finished re-building ‘data_simulation.Rmd’
--- re-building ‘mixed_effect_BN_model.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/abn.Rcheck/vign_test/abn/vignettes/mixed_effect_BN_model_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 10733 bytes
Input file size = 10823 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8278
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8278
Output IDAT size = 8278 bytes (2455 bytes decrease)
Output file size = 8356 bytes (2467 bytes = 22.79% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/abn.Rcheck/vign_test/abn/vignettes/mixed_effect_BN_model_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13423 bytes
Input file size = 13513 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9984
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9984
Output IDAT size = 9984 bytes (3439 bytes decrease)
Output file size = 10062 bytes (3451 bytes = 25.54% decrease)
Quitting from lines 153-159 [unnamed-chunk-5] (mixed_effect_BN_model.Rmd)
Error: processing vignette 'mixed_effect_BN_model.Rmd' failed with diagnostics:
DAG matrix contains trivial cycles (nonzero values on diagonal)
--- failed re-building ‘mixed_effect_BN_model.Rmd’
--- re-building ‘model_specification.Rmd’ using rmarkdown
--- finished re-building ‘model_specification.Rmd’
--- re-building ‘multiprocessing.Rmd’ using rmarkdown
--- finished re-building ‘multiprocessing.Rmd’
--- re-building ‘parameter_learning.Rmd’ using rmarkdown
--- finished re-building ‘parameter_learning.Rmd’
--- re-building ‘quick_start_example.Rmd’ using rmarkdown
--- finished re-building ‘quick_start_example.Rmd’
--- re-building ‘structure_learning.Rmd’ using rmarkdown
--- finished re-building ‘structure_learning.Rmd’
SUMMARY: processing the following file failed:
‘mixed_effect_BN_model.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [6m/13m]
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
>
> library(testthat)
> library(abn)
abn version 3.1.1 (2024-05-22) is loaded.
To cite the package 'abn' in publications call: citation('abn').
Attaching package: 'abn'
The following object is masked from 'package:base':
factorial
>
> require(RhpcBLASctl)
Loading required package: RhpcBLASctl
> omp_set_num_threads(2)
>
> test_check("abn")
Loading required package: Matrix
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
[ FAIL 9 | WARN 0 | SKIP 55 | PASS 448 ]
══ Skipped tests (55) ══════════════════════════════════════════════════════════
• BuildScoreCache(method=mle) crashes with Poisson nodes (1):
'test-fitabn_mle.R:138:3'
• INLA is not tested on CRAN (1): 'test-search_hillclimber.R:79:7'
• On CRAN (52): 'test-Coutput.R:1:1', 'test-abn-methods.R:29:3',
'test-abn-methods.R:55:3', 'test-abn-methods.R:76:3',
'test-abn-methods.R:102:3', 'test-abn-methods.R:125:3',
'test-abn-methods.R:154:3', 'test-abn-methods.R:177:3',
'test-abn-methods.R:200:3', 'test-abn-methods.R:228:3',
'test-abn-methods.R:253:3', 'test-abn-methods.R:278:3',
'test-abn-methods.R:303:3', 'test-abn-methods.R:328:3',
'test-abn-methods.R:353:3', 'test-abn-methods.R:378:3',
'test-abn-methods.R:403:3', 'test-abn-methods.R:428:3',
'test-build_score_cache.R:122:3', 'test-build_score_cache.R:181:3',
'test-build_score_cache.R:331:3', 'test-build_score_cache.R:386:3',
'test-build_score_cache.R:434:3', 'test-build_score_cache_bayes.R:2:3',
'test-build_score_cache_bayes.R:33:3', 'test-build_score_cache_bayes.R:91:3',
'test-build_score_cache_bayes.R:127:3', 'test-calc_node_inla_glm.R:2:3',
'test-calc_node_inla_glmm.R:2:3', 'test-fitabn.R:26:3', 'test-fitabn.R:56:3',
'test-fitabn.R:75:3', 'test-fitabn.R:94:3', 'test-fitabn.R:136:3',
'test-fitabn.R:190:3', 'test-fitabn.R:379:3', 'test-fitabn_bayes.R:2:3',
'test-fitabn_mle.R:562:11', 'test-fitabn_mle.R:674:11',
'test-mostprobable.R:2:3', 'test-mostprobable.R:12:3',
'test-mostprobable.R:79:3', 'test-mostprobable.R:169:3',
'test-mostprobable.R:211:3', 'test-plot-abn.R:34:3', 'test-plot-abn.R:125:3',
'test-search_heuristic.R:2:3', 'test-search_hillclimber.R:16:3',
'test-search_hillclimber.R:84:3', 'test-simulateabn.R:508:3',
'test-simulateabn.R:810:3', 'test-tographviz.R:27:3'
• Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-simulateabn.R:780:13'): simulateAbn() simulation works with method 'mle' ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
DAG matrix contains trivial cycles (nonzero values on diagonal)
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-simulateabn.R:761:5
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-simulateabn.R:762:7
4. │ └─base::withCallingHandlers(...)
5. ├─utils::capture.output(...) at test-simulateabn.R:763:9
6. │ └─base::withVisible(...elt(i))
7. └─testthat::expect_no_error(...) at test-simulateabn.R:779:11
── Failure ('test-simulateabn.R:783:13'): simulateAbn() simulation works with method 'mle' ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
object 'myres.mle.grp' not found
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-simulateabn.R:761:5
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-simulateabn.R:762:7
4. │ └─base::withCallingHandlers(...)
5. ├─utils::capture.output(...) at test-simulateabn.R:763:9
6. │ └─base::withVisible(...elt(i))
7. └─testthat::expect_no_error(...) at test-simulateabn.R:782:11
── Error ('test-simulateabn.R:794:5'): simulateAbn() simulation works with method 'mle' ──
Error in `eval(code, test_env)`: object 'mysim.grp' not found
Backtrace:
▆
1. ├─base::prop.table(table(mysim.grp$Outdoor)) at test-simulateabn.R:794:5
2. └─base::table(mysim.grp$Outdoor)
── Error ('test-simulateabn.R:953:13'): simulateAbn() works with grouping in real data. ──
Error in `validate_abnDag(dag, data.df = data.df, returnDag = TRUE)`: DAG matrix contains trivial cycles (nonzero values on diagonal)
Backtrace:
▆
1. ├─base::suppressMessages(...) at test-simulateabn.R:914:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressWarnings(...) at test-simulateabn.R:915:5
4. │ └─base::withCallingHandlers(...)
5. ├─utils::capture.output(...) at test-simulateabn.R:917:9
6. │ └─base::withVisible(...elt(i))
7. └─abn::fitAbn(object = mydag, method = "mle") at test-simulateabn.R:953:13
8. └─abn::fitAbn.mle(...)
9. └─abn::createAbnDag(dag, data.df = data.df, data.dists = data.dists)
10. └─abn::validate_abnDag(dag, data.df = data.df, returnDag = TRUE)
── Failure ('test-tographviz.R:80:11'): toGraphviz() works with all distributions. ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
DAG matrix contains trivial cycles (nonzero values on diagonal)
Backtrace:
▆
1. ├─utils::capture.output(...) at test-tographviz.R:53:3
2. │ └─base::withVisible(...elt(i))
3. ├─base::suppressMessages(...) at test-tographviz.R:54:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-tographviz.R:78:7
── Failure ('test-tographviz.R:89:5'): toGraphviz() works with all distributions. ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
object 'myres.mle' not found
── Failure ('test-tographviz.R:97:5'): toGraphviz() works with all distributions. ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
object 'myres.mle' not found
── Failure ('test-tographviz.R:105:5'): toGraphviz() works with all distributions. ──
Expected `{ ... }` to run without any errors.
i Actually got a <simpleError> with text:
'dag' must comprise only 1's or 0's
── Error ('test-tographviz.R:134:5'): toGraphviz() works with all distributions. ──
Error in `eval(code, test_env)`: object 'myres.mle' not found
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-tographviz.R:133:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─abn::toGraphviz(...) at test-tographviz.R:134:5
[ FAIL 9 | WARN 0 | SKIP 55 | PASS 448 ]
Deleting unused snapshots:
• tographviz/graph.dot
• tographviz/graph1.dot
• tographviz/graph_group.dot
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 3.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘data_simulation.Rmd’ using rmarkdown
--- finished re-building ‘data_simulation.Rmd’
--- re-building ‘mixed_effect_BN_model.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/abn.Rcheck/vign_test/abn/vignettes/mixed_effect_BN_model_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 10733 bytes
Input file size = 10823 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8278
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8278
Output IDAT size = 8278 bytes (2455 bytes decrease)
Output file size = 8356 bytes (2467 bytes = 22.79% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/abn.Rcheck/vign_test/abn/vignettes/mixed_effect_BN_model_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13423 bytes
Input file size = 13513 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9984
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9984
Output IDAT size = 9984 bytes (3439 bytes decrease)
Output file size = 10062 bytes (3451 bytes = 25.54% decrease)
Quitting from lines 153-159 [unnamed-chunk-5] (mixed_effect_BN_model.Rmd)
Error: processing vignette 'mixed_effect_BN_model.Rmd' failed with diagnostics:
DAG matrix contains trivial cycles (nonzero values on diagonal)
--- failed re-building ‘mixed_effect_BN_model.Rmd’
--- re-building ‘model_specification.Rmd’ using rmarkdown
--- finished re-building ‘model_specification.Rmd’
--- re-building ‘multiprocessing.Rmd’ using rmarkdown
--- finished re-building ‘multiprocessing.Rmd’
--- re-building ‘parameter_learning.Rmd’ using rmarkdown
--- finished re-building ‘parameter_learning.Rmd’
--- re-building ‘quick_start_example.Rmd’ using rmarkdown
--- finished re-building ‘quick_start_example.Rmd’
--- re-building ‘structure_learning.Rmd’ using rmarkdown
--- finished re-building ‘structure_learning.Rmd’
SUMMARY: processing the following file failed:
‘mixed_effect_BN_model.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 3.1.1
Flags: --no-tests
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘INLA’
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 3.1.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘INLA’
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 3.1.1
Check: installed package size
Result: NOTE
installed size is 13.3Mb
sub-directories of 1Mb or more:
data 1.0Mb
extdata 2.9Mb
libs 8.2Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [331s/347s]
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
>
> library(testthat)
> library(abn)
abn version 3.1.1 (2024-05-22) is loaded.
To cite the package 'abn' in publications call: citation('abn').
Attaching package: 'abn'
The following object is masked from 'package:base':
factorial
>
> require(RhpcBLASctl)
Loading required package: RhpcBLASctl
> omp_set_num_threads(2)
>
> test_check("abn")
Loading required package: Matrix
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
[ FAIL 7 | WARN 0 | SKIP 56 | PASS 438 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• BuildScoreCache(method=mle) crashes with Poisson nodes (1):
'test-fitabn_mle.R:138:3'
• INLA is not tested on CRAN (1): 'test-search_hillclimber.R:79:7'
• On CRAN (53): 'test-Coutput.R:1:1', 'test-abn-methods.R:29:3',
'test-abn-methods.R:55:3', 'test-abn-methods.R:76:3',
'test-abn-methods.R:102:3', 'test-abn-methods.R:125:3',
'test-abn-methods.R:154:3', 'test-abn-methods.R:177:3',
'test-abn-methods.R:200:3', 'test-abn-methods.R:228:3',
'test-abn-methods.R:253:3', 'test-abn-methods.R:278:3',
'test-abn-methods.R:303:3', 'test-abn-methods.R:328:3',
'test-abn-methods.R:353:3', 'test-abn-methods.R:378:3',
'test-abn-methods.R:403:3', 'test-abn-methods.R:428:3',
'test-build_score_cache.R:122:3', 'test-build_score_cache.R:181:3',
'test-build_score_cache.R:331:3', 'test-build_score_cache.R:386:3',
'test-build_score_cache.R:434:3', 'test-build_score_cache_bayes.R:2:3',
'test-build_score_cache_bayes.R:33:3', 'test-build_score_cache_bayes.R:91:3',
'test-build_score_cache_bayes.R:127:3', 'test-calc_node_inla_glm.R:2:3',
'test-calc_node_inla_glmm.R:2:3', 'test-fitabn.R:26:3', 'test-fitabn.R:56:3',
'test-fitabn.R:75:3', 'test-fitabn.R:94:3', 'test-fitabn.R:136:3',
'test-fitabn.R:190:3', 'test-fitabn.R:379:3', 'test-fitabn_bayes.R:2:3',
'test-fitabn_mle.R:562:11', 'test-fitabn_mle.R:674:11',
'test-mostprobable.R:2:3', 'test-mostprobable.R:12:3',
'test-mostprobable.R:79:3', 'test-mostprobable.R:169:3',
'test-mostprobable.R:211:3', 'test-plot-abn.R:34:3', 'test-plot-abn.R:125:3',
'test-search_heuristic.R:2:3', 'test-search_hillclimber.R:16:3',
'test-search_hillclimber.R:84:3', 'test-simulateabn.R:508:3',
'test-simulateabn.R:810:3', 'test-tographviz.R:27:3',
'test-tographviz.R:171:3'
• Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-build_score_cache.R:41:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(buildScoreCache(data.df = df, data.dists = dists)) at test-build_score_cache.R:41:7
── Failure ('test-build_score_cache.R:42:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "Bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:42:7
── Failure ('test-build_score_cache.R:43:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:43:7
── Failure ('test-build_score_cache.R:49:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:49:7
── Failure ('test-build_score_cache.R:53:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:53:7
── Failure ('test-build_score_cache.R:62:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:62:7
── Error ('test-build_score_cache.R:66:7'): buildScoreCache() checks work fine ──
<packageNotFoundError/error/condition>
Error in `library(p, character.only = TRUE)`: there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. ├─testthat::expect_warning(...) at test-build_score_cache.R:66:7
6. │ └─testthat:::expect_condition_matching(...)
7. │ └─testthat:::quasi_capture(...)
8. │ ├─testthat (local) .capture(...)
9. │ │ └─base::withCallingHandlers(...)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─abn::buildScoreCache(...)
12. └─abn::buildScoreCache.bayes(...)
13. └─... %do% ...
14. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
15. └─base::library(p, character.only = TRUE)
[ FAIL 7 | WARN 0 | SKIP 56 | PASS 438 ]
Deleting unused snapshots:
• tographviz/graph.dot
• tographviz/graph1.dot
• tographviz/graph_group.dot
Error: Test failures
Execution halted
Flavor: r-release-macos-arm64
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [10m/14m]
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
>
> library(testthat)
> library(abn)
abn version 3.1.1 (2024-05-22) is loaded.
To cite the package 'abn' in publications call: citation('abn').
Attaching package: 'abn'
The following object is masked from 'package:base':
factorial
>
> require(RhpcBLASctl)
Loading required package: RhpcBLASctl
> omp_set_num_threads(2)
>
> test_check("abn")
Loading required package: Matrix
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
[ FAIL 7 | WARN 0 | SKIP 56 | PASS 438 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• BuildScoreCache(method=mle) crashes with Poisson nodes (1):
'test-fitabn_mle.R:138:3'
• INLA is not tested on CRAN (1): 'test-search_hillclimber.R:79:7'
• On CRAN (53): 'test-Coutput.R:1:1', 'test-abn-methods.R:29:3',
'test-abn-methods.R:55:3', 'test-abn-methods.R:76:3',
'test-abn-methods.R:102:3', 'test-abn-methods.R:125:3',
'test-abn-methods.R:154:3', 'test-abn-methods.R:177:3',
'test-abn-methods.R:200:3', 'test-abn-methods.R:228:3',
'test-abn-methods.R:253:3', 'test-abn-methods.R:278:3',
'test-abn-methods.R:303:3', 'test-abn-methods.R:328:3',
'test-abn-methods.R:353:3', 'test-abn-methods.R:378:3',
'test-abn-methods.R:403:3', 'test-abn-methods.R:428:3',
'test-build_score_cache.R:122:3', 'test-build_score_cache.R:181:3',
'test-build_score_cache.R:331:3', 'test-build_score_cache.R:386:3',
'test-build_score_cache.R:434:3', 'test-build_score_cache_bayes.R:2:3',
'test-build_score_cache_bayes.R:33:3', 'test-build_score_cache_bayes.R:91:3',
'test-build_score_cache_bayes.R:127:3', 'test-calc_node_inla_glm.R:2:3',
'test-calc_node_inla_glmm.R:2:3', 'test-fitabn.R:26:3', 'test-fitabn.R:56:3',
'test-fitabn.R:75:3', 'test-fitabn.R:94:3', 'test-fitabn.R:136:3',
'test-fitabn.R:190:3', 'test-fitabn.R:379:3', 'test-fitabn_bayes.R:2:3',
'test-fitabn_mle.R:562:11', 'test-fitabn_mle.R:674:11',
'test-mostprobable.R:2:3', 'test-mostprobable.R:12:3',
'test-mostprobable.R:79:3', 'test-mostprobable.R:169:3',
'test-mostprobable.R:211:3', 'test-plot-abn.R:34:3', 'test-plot-abn.R:125:3',
'test-search_heuristic.R:2:3', 'test-search_hillclimber.R:16:3',
'test-search_hillclimber.R:84:3', 'test-simulateabn.R:508:3',
'test-simulateabn.R:810:3', 'test-tographviz.R:27:3',
'test-tographviz.R:171:3'
• Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-build_score_cache.R:41:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(buildScoreCache(data.df = df, data.dists = dists)) at test-build_score_cache.R:41:7
── Failure ('test-build_score_cache.R:42:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "Bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:42:7
── Failure ('test-build_score_cache.R:43:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:43:7
── Failure ('test-build_score_cache.R:49:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:49:7
── Failure ('test-build_score_cache.R:53:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:53:7
── Failure ('test-build_score_cache.R:62:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:62:7
── Error ('test-build_score_cache.R:66:7'): buildScoreCache() checks work fine ──
<packageNotFoundError/error/condition>
Error in `library(p, character.only = TRUE)`: there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. ├─testthat::expect_warning(...) at test-build_score_cache.R:66:7
6. │ └─testthat:::expect_condition_matching(...)
7. │ └─testthat:::quasi_capture(...)
8. │ ├─testthat (local) .capture(...)
9. │ │ └─base::withCallingHandlers(...)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─abn::buildScoreCache(...)
12. └─abn::buildScoreCache.bayes(...)
13. └─... %do% ...
14. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
15. └─base::library(p, character.only = TRUE)
[ FAIL 7 | WARN 0 | SKIP 56 | PASS 438 ]
Deleting unused snapshots:
• tographviz/graph.dot
• tographviz/graph1.dot
• tographviz/graph_group.dot
Error: Test failures
Execution halted
Flavor: r-release-macos-x86_64
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [410s/443s]
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
>
> library(testthat)
> library(abn)
abn version 3.1.1 (2024-05-22) is loaded.
To cite the package 'abn' in publications call: citation('abn').
Attaching package: 'abn'
The following object is masked from 'package:base':
factorial
>
> require(RhpcBLASctl)
Loading required package: RhpcBLASctl
> omp_set_num_threads(2)
>
> test_check("abn")
Loading required package: Matrix
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
[ FAIL 7 | WARN 0 | SKIP 56 | PASS 438 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• BuildScoreCache(method=mle) crashes with Poisson nodes (1):
'test-fitabn_mle.R:138:3'
• INLA is not tested on CRAN (1): 'test-search_hillclimber.R:79:7'
• On CRAN (53): 'test-Coutput.R:1:1', 'test-abn-methods.R:29:3',
'test-abn-methods.R:55:3', 'test-abn-methods.R:76:3',
'test-abn-methods.R:102:3', 'test-abn-methods.R:125:3',
'test-abn-methods.R:154:3', 'test-abn-methods.R:177:3',
'test-abn-methods.R:200:3', 'test-abn-methods.R:228:3',
'test-abn-methods.R:253:3', 'test-abn-methods.R:278:3',
'test-abn-methods.R:303:3', 'test-abn-methods.R:328:3',
'test-abn-methods.R:353:3', 'test-abn-methods.R:378:3',
'test-abn-methods.R:403:3', 'test-abn-methods.R:428:3',
'test-build_score_cache.R:122:3', 'test-build_score_cache.R:181:3',
'test-build_score_cache.R:331:3', 'test-build_score_cache.R:386:3',
'test-build_score_cache.R:434:3', 'test-build_score_cache_bayes.R:2:3',
'test-build_score_cache_bayes.R:33:3', 'test-build_score_cache_bayes.R:91:3',
'test-build_score_cache_bayes.R:127:3', 'test-calc_node_inla_glm.R:2:3',
'test-calc_node_inla_glmm.R:2:3', 'test-fitabn.R:26:3', 'test-fitabn.R:56:3',
'test-fitabn.R:75:3', 'test-fitabn.R:94:3', 'test-fitabn.R:136:3',
'test-fitabn.R:190:3', 'test-fitabn.R:379:3', 'test-fitabn_bayes.R:2:3',
'test-fitabn_mle.R:562:11', 'test-fitabn_mle.R:674:11',
'test-mostprobable.R:2:3', 'test-mostprobable.R:12:3',
'test-mostprobable.R:79:3', 'test-mostprobable.R:169:3',
'test-mostprobable.R:211:3', 'test-plot-abn.R:34:3', 'test-plot-abn.R:125:3',
'test-search_heuristic.R:2:3', 'test-search_hillclimber.R:16:3',
'test-search_hillclimber.R:84:3', 'test-simulateabn.R:508:3',
'test-simulateabn.R:810:3', 'test-tographviz.R:27:3',
'test-tographviz.R:171:3'
• Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-build_score_cache.R:41:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(buildScoreCache(data.df = df, data.dists = dists)) at test-build_score_cache.R:41:7
── Failure ('test-build_score_cache.R:42:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "Bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:42:7
── Failure ('test-build_score_cache.R:43:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:43:7
── Failure ('test-build_score_cache.R:49:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:49:7
── Failure ('test-build_score_cache.R:53:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:53:7
── Failure ('test-build_score_cache.R:62:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:62:7
── Error ('test-build_score_cache.R:66:7'): buildScoreCache() checks work fine ──
<packageNotFoundError/error/condition>
Error in `library(p, character.only = TRUE)`: there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. ├─testthat::expect_warning(...) at test-build_score_cache.R:66:7
6. │ └─testthat:::expect_condition_matching(...)
7. │ └─testthat:::quasi_capture(...)
8. │ ├─testthat (local) .capture(...)
9. │ │ └─base::withCallingHandlers(...)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─abn::buildScoreCache(...)
12. └─abn::buildScoreCache.bayes(...)
13. └─... %do% ...
14. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
15. └─base::library(p, character.only = TRUE)
[ FAIL 7 | WARN 0 | SKIP 56 | PASS 438 ]
Deleting unused snapshots:
• tographviz/graph.dot
• tographviz/graph1.dot
• tographviz/graph_group.dot
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 3.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [12m/21m]
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
>
> library(testthat)
> library(abn)
abn version 3.1.1 (2024-05-22) is loaded.
To cite the package 'abn' in publications call: citation('abn').
Attaching package: 'abn'
The following object is masked from 'package:base':
factorial
>
> require(RhpcBLASctl)
Loading required package: RhpcBLASctl
> omp_set_num_threads(2)
>
> test_check("abn")
Loading required package: Matrix
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
[ FAIL 7 | WARN 0 | SKIP 56 | PASS 438 ]
══ Skipped tests (56) ══════════════════════════════════════════════════════════
• BuildScoreCache(method=mle) crashes with Poisson nodes (1):
'test-fitabn_mle.R:138:3'
• INLA is not tested on CRAN (1): 'test-search_hillclimber.R:79:7'
• On CRAN (53): 'test-Coutput.R:1:1', 'test-abn-methods.R:29:3',
'test-abn-methods.R:55:3', 'test-abn-methods.R:76:3',
'test-abn-methods.R:102:3', 'test-abn-methods.R:125:3',
'test-abn-methods.R:154:3', 'test-abn-methods.R:177:3',
'test-abn-methods.R:200:3', 'test-abn-methods.R:228:3',
'test-abn-methods.R:253:3', 'test-abn-methods.R:278:3',
'test-abn-methods.R:303:3', 'test-abn-methods.R:328:3',
'test-abn-methods.R:353:3', 'test-abn-methods.R:378:3',
'test-abn-methods.R:403:3', 'test-abn-methods.R:428:3',
'test-build_score_cache.R:122:3', 'test-build_score_cache.R:181:3',
'test-build_score_cache.R:331:3', 'test-build_score_cache.R:386:3',
'test-build_score_cache.R:434:3', 'test-build_score_cache_bayes.R:2:3',
'test-build_score_cache_bayes.R:33:3', 'test-build_score_cache_bayes.R:91:3',
'test-build_score_cache_bayes.R:127:3', 'test-calc_node_inla_glm.R:2:3',
'test-calc_node_inla_glmm.R:2:3', 'test-fitabn.R:26:3', 'test-fitabn.R:56:3',
'test-fitabn.R:75:3', 'test-fitabn.R:94:3', 'test-fitabn.R:136:3',
'test-fitabn.R:190:3', 'test-fitabn.R:379:3', 'test-fitabn_bayes.R:2:3',
'test-fitabn_mle.R:562:11', 'test-fitabn_mle.R:674:11',
'test-mostprobable.R:2:3', 'test-mostprobable.R:12:3',
'test-mostprobable.R:79:3', 'test-mostprobable.R:169:3',
'test-mostprobable.R:211:3', 'test-plot-abn.R:34:3', 'test-plot-abn.R:125:3',
'test-search_heuristic.R:2:3', 'test-search_hillclimber.R:16:3',
'test-search_hillclimber.R:84:3', 'test-simulateabn.R:508:3',
'test-simulateabn.R:810:3', 'test-tographviz.R:27:3',
'test-tographviz.R:171:3'
• Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-build_score_cache.R:41:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(buildScoreCache(data.df = df, data.dists = dists)) at test-build_score_cache.R:41:7
── Failure ('test-build_score_cache.R:42:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "Bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:42:7
── Failure ('test-build_score_cache.R:43:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:43:7
── Failure ('test-build_score_cache.R:49:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:49:7
── Failure ('test-build_score_cache.R:53:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:53:7
── Failure ('test-build_score_cache.R:62:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:62:7
── Error ('test-build_score_cache.R:66:7'): buildScoreCache() checks work fine ──
<packageNotFoundError/error/condition>
Error in `library(p, character.only = TRUE)`: there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. ├─testthat::expect_warning(...) at test-build_score_cache.R:66:7
6. │ └─testthat:::expect_condition_matching(...)
7. │ └─testthat:::quasi_capture(...)
8. │ ├─testthat (local) .capture(...)
9. │ │ └─base::withCallingHandlers(...)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─abn::buildScoreCache(...)
12. └─abn::buildScoreCache.bayes(...)
13. └─... %do% ...
14. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
15. └─base::library(p, character.only = TRUE)
[ FAIL 7 | WARN 0 | SKIP 56 | PASS 438 ]
Deleting unused snapshots:
• tographviz/graph.dot
• tographviz/graph1.dot
• tographviz/graph_group.dot
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 3.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [120s]
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
>
> library(testthat)
> library(abn)
abn version 3.1.1 (2024-05-22) is loaded.
To cite the package 'abn' in publications call: citation('abn').
Attaching package: 'abn'
The following object is masked from 'package:base':
factorial
>
> require(RhpcBLASctl)
Loading required package: RhpcBLASctl
> omp_set_num_threads(2)
>
> test_check("abn")
Loading required package: Matrix
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
Running in single core mode. 'cluster.type' is ignored.
[ FAIL 7 | WARN 0 | SKIP 82 | PASS 295 ]
══ Skipped tests (82) ══════════════════════════════════════════════════════════
• BuildScoreCache(method=mle) crashes with Poisson nodes (1):
'test-fitabn_mle.R:138:3'
• INLA is not tested on CRAN (1): 'test-search_hillclimber.R:79:7'
• On CRAN (51): 'test-Coutput.R:1:1', 'test-abn-methods.R:29:3',
'test-abn-methods.R:55:3', 'test-abn-methods.R:76:3',
'test-abn-methods.R:102:3', 'test-abn-methods.R:125:3',
'test-abn-methods.R:154:3', 'test-abn-methods.R:177:3',
'test-abn-methods.R:200:3', 'test-abn-methods.R:228:3',
'test-abn-methods.R:253:3', 'test-abn-methods.R:278:3',
'test-abn-methods.R:303:3', 'test-abn-methods.R:328:3',
'test-abn-methods.R:353:3', 'test-abn-methods.R:378:3',
'test-abn-methods.R:403:3', 'test-abn-methods.R:428:3',
'test-build_score_cache.R:122:3', 'test-build_score_cache.R:181:3',
'test-build_score_cache.R:331:3', 'test-build_score_cache.R:386:3',
'test-build_score_cache.R:434:3', 'test-build_score_cache_bayes.R:2:3',
'test-build_score_cache_bayes.R:33:3', 'test-build_score_cache_bayes.R:91:3',
'test-build_score_cache_bayes.R:127:3', 'test-calc_node_inla_glm.R:2:3',
'test-calc_node_inla_glmm.R:2:3', 'test-fitabn.R:26:3', 'test-fitabn.R:56:3',
'test-fitabn.R:75:3', 'test-fitabn.R:94:3', 'test-fitabn.R:136:3',
'test-fitabn.R:190:3', 'test-fitabn.R:379:3', 'test-fitabn_bayes.R:2:3',
'test-mostprobable.R:2:3', 'test-mostprobable.R:12:3',
'test-mostprobable.R:79:3', 'test-mostprobable.R:169:3',
'test-mostprobable.R:211:3', 'test-plot-abn.R:34:3', 'test-plot-abn.R:125:3',
'test-search_heuristic.R:2:3', 'test-search_hillclimber.R:16:3',
'test-search_hillclimber.R:84:3', 'test-simulateabn.R:508:3',
'test-simulateabn.R:810:3', 'test-tographviz.R:27:3',
'test-tographviz.R:171:3'
• Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'
• `buildScoreCache.mle()` is tested mainly on Unix-like systems. (6):
'test-build_score_cache_mle.R:32:5', 'test-build_score_cache_mle.R:84:5',
'test-build_score_cache_mle.R:121:5', 'test-build_score_cache_mle.R:159:5',
'test-build_score_cache_mle.R:220:5', 'test-build_score_cache_mle.R:260:5'
• empty test (2): 'test-abn-methods.R:15:1',
'test-build_score_cache_mle.R:264:1'
• fitAbn.mle() is tested mainly on Unix-like systems (8):
'test-fitabn_mle.R:32:7', 'test-fitabn_mle.R:83:7',
'test-fitabn_mle.R:132:7', 'test-fitabn_mle.R:286:7',
'test-fitabn_mle.R:384:7', 'test-fitabn_mle.R:482:7',
'test-fitabn_mle.R:592:9', 'test-fitabn_mle.R:704:9'
• simulateAbn() is tested mainly on Unix-like systems (12):
'test-simulateabn.R:35:5', 'test-simulateabn.R:90:5',
'test-simulateabn.R:139:5', 'test-simulateabn.R:188:5',
'test-simulateabn.R:236:5', 'test-simulateabn.R:304:5',
'test-simulateabn.R:373:5', 'test-simulateabn.R:422:5',
'test-simulateabn.R:471:5', 'test-simulateabn.R:704:5',
'test-simulateabn.R:805:5', 'test-simulateabn.R:994:9'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-build_score_cache.R:41:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(buildScoreCache(data.df = df, data.dists = dists)) at test-build_score_cache.R:41:7
── Failure ('test-build_score_cache.R:42:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "Bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:42:7
── Failure ('test-build_score_cache.R:43:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(data.df = df, data.dists = dists, method = "bayes")` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:43:7
── Failure ('test-build_score_cache.R:49:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:49:7
── Failure ('test-build_score_cache.R:53:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:53:7
── Failure ('test-build_score_cache.R:62:7'): buildScoreCache() checks work fine ──
Expected `buildScoreCache(...)` to run without any errors.
i Actually got a <packageNotFoundError> with text:
there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. └─testthat::expect_no_error(...) at test-build_score_cache.R:62:7
── Error ('test-build_score_cache.R:66:7'): buildScoreCache() checks work fine ──
<packageNotFoundError/error/condition>
Error in `library(p, character.only = TRUE)`: there is no package called 'INLA'
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-build_score_cache.R:33:3
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(...) at test-build_score_cache.R:34:5
4. │ └─base::withCallingHandlers(...)
5. ├─testthat::expect_warning(...) at test-build_score_cache.R:66:7
6. │ └─testthat:::expect_condition_matching(...)
7. │ └─testthat:::quasi_capture(...)
8. │ ├─testthat (local) .capture(...)
9. │ │ └─base::withCallingHandlers(...)
10. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
11. └─abn::buildScoreCache(...)
12. └─abn::buildScoreCache.bayes(...)
13. └─... %do% ...
14. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
15. └─base::library(p, character.only = TRUE)
[ FAIL 7 | WARN 0 | SKIP 82 | PASS 295 ]
Deleting unused snapshots:
• tographviz/graph.dot
• tographviz/graph1.dot
• tographviz/graph_group.dot
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64