Running ‘testthat.R’ [226s/227s]
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 = 23.757629
    Scaled convergence tolerance is 2.38576
  Stepsize computed as 0.203177
  BUILD              6 29.061508 23.757629
  HI-REDUCTION       8 26.607666 23.757629
  Exiting from Nelder Mead minimizer
      10 function evaluations used
  [1] "New improvement found, resetting step counter"
          step    negloglik     sigma.sq           mu           SE           bt 
   3.000000000 23.757629269  0.119989054  2.031770706  0.007193124  0.910914370 
            vh 
   0.007833514 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 23.840866
    Scaled convergence tolerance is 2.39409
  Stepsize computed as 0.209007
  BUILD              6 29.086870 23.840866
  HI-REDUCTION       8 26.583512 23.840866
  Exiting from Nelder Mead minimizer
      10 function evaluations used
          step    negloglik     sigma.sq           mu           SE           bt 
   4.000000000 23.757629269  0.119989054  2.031770706  0.007193124  0.910914370 
            vh 
   0.007833514 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 23.941276
    Scaled convergence tolerance is 2.40413
  Stepsize computed as 0.190223
  BUILD              6 28.600244 23.867942
  HI-REDUCTION       8 26.293536 23.867942
  Exiting from Nelder Mead minimizer
      10 function evaluations used
          step    negloglik     sigma.sq           mu           SE           bt 
   5.000000000 23.757629269  0.119989054  2.031770706  0.007193124  0.910914370 
            vh 
   0.007833514 
  [1] "100 of 100 done"
  [1] "Now starting analysis"
  [1] "Starting with initial values"
     sigma.sq          mu          SE          bt          vh 
   3.46228575 -0.19436421  0.03462286  1.00000000  0.03462286 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 10.383891
    Scaled convergence tolerance is 1.04839
  Stepsize computed as 0.346229
  Exiting from Nelder Mead minimizer
      6 function evaluations used
         step   negloglik    sigma.sq          mu          SE          bt 
   1.00000000  9.48533648  3.46228575 -0.19436421  0.03462286  1.34622858 
           vh 
   0.03462286 
    Nelder-Mead direct search function minimizer
  function value for initial parameters = 9.485336
    Scaled convergence tolerance is 0.958534
  Stepsize computed as 0.346229
  Exiting from Nelder Mead minimizer
      6 function evaluations used
  [1] "New improvement found, resetting step counter"
         step   negloglik    sigma.sq          mu          SE          bt 
   2.00000000  8.92067596  3.46228575 -0.19436421  0.03462286  1.69245715 
           vh 
   0.03462286 
    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: 8 | FAILED: 1 ]
  1. Error: Simulation works (@test_condition.R#31) 
  
  Error: testthat unit tests failed
  Execution halted