Running ‘testthat.R’ [17m/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 3.0.0 (2023-09-01) is loaded.
  To cite the package 'abn' in publications call: citation('abn').
  
  Attaching package: 'abn'
  
  The following object is masked from 'package:base':
  
      factorial
  
  > 
  > test_check("abn")
  dev.new(): using pdf(file="Rplots1.pdf")
  
  Iteration 1 - deviance = 801.89 - criterion = 2.014199
  Iteration 2 - deviance = 800.5341 - criterion = 0.04426251
  Iteration 3 - deviance = 800.5339 - criterion = 5.210016e-06
  Iteration 4 - deviance = 800.5339 - criterion = 5.363507e-13
  converged
  
  Iteration 1 - deviance = 798.6166 - criterion = 1.874215
  Iteration 2 - deviance = 797.3505 - criterion = 0.03945357
  Iteration 3 - deviance = 797.3503 - criterion = 8.411144e-06
  Iteration 4 - deviance = 797.3503 - criterion = 6.416675e-13
  converged
  
  Iteration 1 - deviance = 800.841 - criterion = 1.953695
  Iteration 2 - deviance = 799.4241 - criterion = 0.04384531
  Iteration 3 - deviance = 799.424 - criterion = 5.262527e-06
  Iteration 4 - deviance = 799.424 - criterion = 7.763524e-13
  converged
  
  Iteration 1 - deviance = 733.9755 - criterion = 1.056032
  Iteration 2 - deviance = 730.6673 - criterion = 0.04998392
  Iteration 3 - deviance = 730.577 - criterion = 0.002808114
  Iteration 4 - deviance = 730.5768 - criterion = 7.365004e-06
  Iteration 5 - deviance = 730.5768 - criterion = 3.999521e-11
  converged
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  
  Iteration 1 - deviance = 733.9755 - criterion = 1.056032
  Iteration 2 - deviance = 730.6673 - criterion = 0.04998392
  Iteration 3 - deviance = 730.577 - criterion = 0.002808114
  Iteration 4 - deviance = 730.5768 - criterion = 7.365004e-06
  Iteration 5 - deviance = 730.5768 - criterion = 3.999521e-11
  converged
  boundary (singular) fit: see help('isSingular')
  
  Iteration 1 - deviance = 801.89 - criterion = 2.014199
  Iteration 2 - deviance = 800.5341 - criterion = 0.04426251
  Iteration 3 - deviance = 800.5339 - criterion = 5.210016e-06
  Iteration 4 - deviance = 800.5339 - criterion = 5.363507e-13
  converged
  
  Iteration 1 - deviance = 798.6166 - criterion = 1.874215
  Iteration 2 - deviance = 797.3505 - criterion = 0.03945357
  Iteration 3 - deviance = 797.3503 - criterion = 8.411144e-06
  Iteration 4 - deviance = 797.3503 - criterion = 6.416675e-13
  converged
  
  Iteration 1 - deviance = 800.841 - criterion = 1.953695
  Iteration 2 - deviance = 799.4241 - criterion = 0.04384531
  Iteration 3 - deviance = 799.424 - criterion = 5.262527e-06
  Iteration 4 - deviance = 799.424 - criterion = 7.763524e-13
  converged
  
  Iteration 1 - deviance = 733.9755 - criterion = 1.056032
  Iteration 2 - deviance = 730.6673 - criterion = 0.04998392
  Iteration 3 - deviance = 730.577 - criterion = 0.002808114
  Iteration 4 - deviance = 730.5768 - criterion = 7.365004e-06
  Iteration 5 - deviance = 730.5768 - criterion = 3.999521e-11
  converged
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  
  Iteration 1 - deviance = 801.89 - criterion = 2.014199
  Iteration 2 - deviance = 800.5341 - criterion = 0.04426251
  Iteration 3 - deviance = 800.5339 - criterion = 5.210016e-06
  Iteration 4 - deviance = 800.5339 - criterion = 5.363507e-13
  converged
  boundary (singular) fit: see help('isSingular')
  [ FAIL 15 | WARN 0 | SKIP 10 | PASS 584 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • BuildScoreCache(method=mle) crashes with Poisson nodes (1):
    'test-fitabn_mle.R:132:3'
  • Numerical results are not tested for method='bayes' (2):
    'test-build_score_cache_bayes.R:51:3', 'test-build_score_cache_bayes.R:104:3'
  • On CRAN (2): 'test-plot-abn.R:34:3', 'test-tographviz.R:27:3'
  • Plot classic view is deprecated. (1): 'test-plot-abn.R:117:3'
  • calc.node.inla.glm() test not yet implemented. (1):
    'test-calc_node_inla_glm.R:2:3'
  • calc.node.inla.glmm() test not yet implemented. (1):
    'test-calc_node_inla_glmm.R:2:3'
  • getmarginals() tests not yet implemented. (1): 'test-getmarginals.R:2:3'
  • plotting for abnHillClimber is not up to date with searchHillClimber()'s
    output. (1): 'test-abn-methods.R:117:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-fitabn.R:65:3'): fitAbn() works with DAG as formula statement ──
  Error in `{
      regressionLoop(i = i, dag = dag, data.df = data.df, data.df.multi = data.df.multi, 
          data.dists = data.dists, group.var = group.var, grouped.vars = grouped.vars, 
          group.ids = group.ids, control = control, nvars = nvars, 
          nobs = nobs, dag.multi = dag.multi, verbose = verbose)
  }`: task 1 failed - ""tcrossprod" is not a BUILTIN function"
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(...) at test-fitabn.R:65:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─abn::fitAbn(...)
   10.   └─abn::fitAbn.mle(...)
   11.     └─... %do% ...
   12.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
  ── Failure ('test-fitabn.R:385:3'): fitabn() works with all distributions, grouping and class abnCache ──
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    task 1 failed - ""tcrossprod" is not a BUILTIN function"
  ── Failure ('test-fitabn.R:426:3'): fitabn() works with all distributions, grouping and class abnCache ──
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    task 1 failed - ""tcrossprod" is not a BUILTIN function"
  ── Failure ('test-fitabn_mle.R:481:3'): fitAbn's regressionLoop() works w/o group.var. ──
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    "tcrossprod" is not a BUILTIN function
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-fitabn_mle.R:481:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─base::suppressMessages(...) at test-fitabn_mle.R:482:4
   4. │ └─base::withCallingHandlers(...)
   5. ├─utils::capture.output(...) at test-fitabn_mle.R:484:8
   6. │ └─base::withVisible(...elt(i))
   7. └─testthat::expect_no_error(...) at test-fitabn_mle.R:485:10
  ── Error ('test-fitabn_mle.R:481:3'): fitAbn's regressionLoop() works w/o group.var. ──
  Error in `eval(code, test_env)`: object 'res' not found
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-fitabn_mle.R:481:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─base::suppressMessages(...) at test-fitabn_mle.R:482:4
   4. │ └─base::withCallingHandlers(...)
   5. ├─utils::capture.output(...) at test-fitabn_mle.R:484:8
   6. │ └─base::withVisible(...elt(i))
   7. └─testthat::expect_equal(...) at test-fitabn_mle.R:502:10
   8.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   9.     └─rlang::eval_bare(expr, quo_get_env(quo))
  ── Failure ('test-fitabn_mle.R:590:3'): fitAbn's regressionLoop() works w/ group.var. ──
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    "tcrossprod" is not a BUILTIN function
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-fitabn_mle.R:590:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─base::suppressMessages(...) at test-fitabn_mle.R:591:4
   4. │ └─base::withCallingHandlers(...)
   5. ├─utils::capture.output(...) at test-fitabn_mle.R:593:8
   6. │ └─base::withVisible(...elt(i))
   7. └─testthat::expect_no_error(...) at test-fitabn_mle.R:594:10
  ── Error ('test-fitabn_mle.R:590:3'): fitAbn's regressionLoop() works w/ group.var. ──
  Error in `eval(code, test_env)`: object 'res' not found
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-fitabn_mle.R:590:2
   2. │ └─base::withCallingHandlers(...)
   3. ├─base::suppressMessages(...) at test-fitabn_mle.R:591:4
   4. │ └─base::withCallingHandlers(...)
   5. ├─utils::capture.output(...) at test-fitabn_mle.R:593:8
   6. │ └─base::withVisible(...elt(i))
   7. └─testthat::expect_equal(...) at test-fitabn_mle.R:611:10
   8.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   9.     └─rlang::eval_bare(expr, quo_get_env(quo))
  ── Failure ('test-simulateabn.R:680:5'): simulateAbn() simulation works ────────
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    task 1 failed - ""tcrossprod" is not a BUILTIN function"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-simulateabn.R:680:4
   2. │ └─base::withCallingHandlers(...)
   3. ├─base::suppressMessages(...) at test-simulateabn.R:681:6
   4. │ └─base::withCallingHandlers(...)
   5. ├─utils::capture.output(...) at test-simulateabn.R:682:8
   6. │ └─base::withVisible(...elt(i))
   7. └─testthat::expect_no_error(...) at test-simulateabn.R:698:10
  ── Failure ('test-simulateabn.R:680:5'): simulateAbn() simulation works ────────
  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:680:4
   2. │ └─base::withCallingHandlers(...)
   3. ├─base::suppressMessages(...) at test-simulateabn.R:681:6
   4. │ └─base::withCallingHandlers(...)
   5. ├─utils::capture.output(...) at test-simulateabn.R:682:8
   6. │ └─base::withVisible(...elt(i))
   7. └─testthat::expect_no_error(...) at test-simulateabn.R:701:10
  ── Error ('test-simulateabn.R:713:5'): simulateAbn() simulation works ──────────
  Error in `eval(code, test_env)`: object 'mysim.grp' not found
  Backtrace:
      ▆
   1. ├─base::prop.table(table(mysim.grp$Outdoor)) at test-simulateabn.R:713:4
   2. └─base::table(mysim.grp$Outdoor)
  ── Error ('test-simulateabn.R:727:3'): simulateAbn() works with grouping in real data. ──
  Error in `{
      regressionLoop(i = i, dag = dag, data.df = data.df, data.df.multi = data.df.multi, 
          data.dists = data.dists, group.var = group.var, grouped.vars = grouped.vars, 
          group.ids = group.ids, control = control, nvars = nvars, 
          nobs = nobs, dag.multi = dag.multi, verbose = verbose)
  }`: task 1 failed - ""tcrossprod" is not a BUILTIN function"
  Backtrace:
       ▆
    1. ├─base::suppressMessages(...) at test-simulateabn.R:727:2
    2. │ └─base::withCallingHandlers(...)
    3. ├─base::suppressWarnings(...) at test-simulateabn.R:728:4
    4. │ └─base::withCallingHandlers(...)
    5. ├─utils::capture.output(...) at test-simulateabn.R:730:8
    6. │ └─base::withVisible(...elt(i))
    7. └─abn::fitAbn(object = mydag, method = "mle") at test-simulateabn.R:766:12
    8.   └─abn::fitAbn.mle(...)
    9.     └─... %do% ...
   10.       └─e$fun(obj, substitute(ex), parent.frame(), e$data)
  ── Failure ('test-tographviz.R:53:3'): toGraphviz() works with all distributions. ──
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    task 1 failed - ""tcrossprod" is not a BUILTIN function"
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test-tographviz.R:53:2
   2. │ └─base::withVisible(...elt(i))
   3. ├─base::suppressMessages(...) at test-tographviz.R:54:4
   4. │ └─base::withCallingHandlers(...)
   5. └─testthat::expect_no_error(...) at test-tographviz.R:78:6
  ── Failure ('test-tographviz.R:88:3'): 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:96:3'): toGraphviz() works with all distributions. ──
  Expected `{ ... }` to run without any errors.
  i Actually got a <simpleError> with text:
    object 'myres.mle' not found
  ── Error ('test-tographviz.R:133:3'): 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:133:2
   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:134:4
  
  [ FAIL 15 | WARN 0 | SKIP 10 | PASS 584 ]
  Deleting unused snapshots:
  • tographviz/graph.dot
  • tographviz/graph1.dot
  • tographviz/graph_group.dot
  Error: Test failures
  Execution halted