Running ‘testthat.R’ [438s/441s]
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 = 24.497385
    Scaled convergence tolerance is 2.45974
  Stepsize computed as 0.196344
  BUILD              6 29.390968 24.497385
  HI-REDUCTION       8 27.126568 24.497385
  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 
  35.9586494 -0.2122948  0.3595865  1.0000000  0.3595865 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 13.505546
    Scaled convergence tolerance is 1.36055
  Stepsize computed as 3.595865
  Exiting from Nelder Mead minimizer
      6 function evaluations used
        step  negloglik   sigma.sq         mu         SE         bt         vh 
   1.0000000 13.2410990 35.9586494 -0.2122948  3.9554514  1.0000000  0.3595865 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 13.241099
    Scaled convergence tolerance is 1.33411
  Stepsize computed as 3.595865
  Exiting from Nelder Mead minimizer
      6 function evaluations used
        step  negloglik   sigma.sq         mu         SE         bt         vh 
   2.0000000 13.2410990 35.9586494 -0.2122948  3.9554514  1.0000000  0.3595865 
    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