Running ‘testthat.R’ [7m/18m]
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