Running ‘testthat.R’ [338s/364s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("BMhyb")
  Loading required package: BMhyb
  [1] "Now starting analysis"
  [1] "Starting with initial values"
     sigma.sq          mu          SE          bt          vh 
  0.117682960 2.118832288 0.007956494 1.000000000 0.007956494 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 24.088800
    Scaled convergence tolerance is 2.41888
  Stepsize computed as 0.211883
  BUILD              6 29.371482 24.088800
  HI-REDUCTION       8 26.889548 24.088800
  Exiting from Nelder Mead minimizer
      10 function evaluations used
          step    negloglik     sigma.sq           mu           SE           bt 
   1.000000000 24.088800143  0.117682960  2.118832288  0.007956494  1.000000000 
            vh 
   0.007956494 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 24.088800
    Scaled convergence tolerance is 2.41888
  Stepsize computed as 0.211883
  BUILD              6 29.371482 24.088800
  HI-REDUCTION       8 26.889548 24.088800
  Exiting from Nelder Mead minimizer
      10 function evaluations used
          step    negloglik     sigma.sq           mu           SE           bt 
   2.000000000 24.088800143  0.117682960  2.118832288  0.007956494  1.000000000 
            vh 
   0.007956494 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 24.151683
    Scaled convergence tolerance is 2.42517
  Stepsize computed as 0.232371
  BUILD              6 29.996727 24.151683
  HI-REDUCTION       8 27.354461 24.151683
  Exiting from Nelder Mead minimizer
      10 function evaluations used
          step    negloglik     sigma.sq           mu           SE           bt 
   3.000000000 24.088800143  0.117682960  2.118832288  0.007956494  1.000000000 
            vh 
   0.007956494 
  [1] "100 of 100 done"
  [1] "Now starting analysis"
  [1] "Starting with initial values"
     sigma.sq          mu          SE          bt          vh 
   6.05482797 -0.18627361  0.06054828  1.00000000  0.06054828 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 12.362600
    Scaled convergence tolerance is 1.24626
  Stepsize computed as 0.605483
  BUILD              6 12.362600 10.796056
  EXTENSION          8 12.341983 10.385153
  LO-REDUCTION      10 12.230269 10.385153
  EXTENSION         12 11.211534 9.692381
  Exiting from Nelder Mead minimizer
      14 function evaluations used
        step  negloglik   sigma.sq         mu         SE         bt         vh 
   1.0000000  9.6923808  5.2943416 -0.2444000  0.8743172  1.8137689  0.8743172 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 9.692381
    Scaled convergence tolerance is 0.979238
  Stepsize computed as 0.529434
  Exiting from Nelder Mead minimizer
      6 function evaluations used
  [1] "New improvement found, resetting step counter"
        step  negloglik   sigma.sq         mu         SE         bt         vh 
   2.0000000  9.4697949  5.2943416 -0.2444000  0.8743172  2.3432030  0.8743172 
    Nelder-Mead direct search function minimizer
  ── 1. Error: Simulation works (@test_condition.R#31)  ──────────────────────────
  non-finite value supplied by optim
  1: BMhyb(phy.graph = network, traits = tips, confidence.points = 100, max.steps = 2, 
         control = list(reltol = 0.1, trace = 6)) at testthat/test_condition.R:31
  2: OptimizeThoroughly(phy.graph = phy.graph, traits = traits, free.parameter.names = free.parameter.names, 
         measurement.error = measurement.error, gamma = gamma, do.Higham.correction = do.Higham.correction, 
         do.Brissette.correction = do.Brissette.correction, max.steps = max.steps, verbose = verbose, 
         control = control)
  3: stats::optim(par = starting.values, fn = TryComputeLikelihood, traits = traits, phy.graph = phy.graph, 
         measurement.error = measurement.error, gamma = gamma, do.Higham.correction = do.Higham.correction, 
         do.Brissette.correction = do.Brissette.correction, control = control)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 12 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: Simulation works (@test_condition.R#31) 
  
  Error: testthat unit tests failed
  Execution halted