Running ‘spelling.R’
  Running ‘testthat.R’ [125s/170s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cauphy)
  Loading required package: ape
  > 
  > test_check("cauphy")
  [ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('testAncestralStateReconstruction.R:148:3'): testAncestralFit ──────
  MAP$par (`actual`) not equal to -0.5086788 (`expected`).
  
    `actual`: -1.12
  `expected`: -0.51
  ── Failure ('testCauchyLikelihood.R:258:3'): testLikelihoodFunction ────────────
  ff$disp (`actual`) not equal to 0.06785236 (`expected`).
  
    `actual`: 0.040
  `expected`: 0.068
  ── Failure ('testFitFunctions.R:33:3'): optim ──────────────────────────────────
  ... <= res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:41:3'): optim ──────────────────────────────────
  unname(sqrt(diag(vcov(res)))) (`actual`) not equal to c(0.03243854, 0.0180895) (`expected`).
  
    `actual`: 0.024 0.011
  `expected`: 0.032 0.018
  ── Failure ('testFitFunctions.R:87:3'): optim, random root ─────────────────────
  ... <= res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:100:3'): optim, random root ────────────────────
  reslam$logLik > res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:104:3'): optim, random root ────────────────────
  unname(sqrt(diag(vcov(reslam)))) (`actual`) not equal to c(0.0285, 0.0415) (`expected`).
  
    `actual`: NaN NaN
  `expected`: 0.0 0.0
  ── Failure ('testFitFunctions.R:147:3'): optim, reml ───────────────────────────
  ... <= res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:160:3'): optim, reml ───────────────────────────
  unname(sqrt(diag(vcov(res)))) (`actual`) not equal to c(0.02016588) (`expected`).
  
    `actual`: 0.008
  `expected`: 0.020
  ── Failure ('testFitFunctions.R:164:3'): optim, reml ───────────────────────────
  reslam$logLik > res$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:168:3'): optim, reml ───────────────────────────
  unname(sqrt(diag(vcov(reslam)))) (`actual`) not equal to c(0.0283, 0.0574) (`expected`).
  
    `actual`: NaN NaN
  `expected`: 0.0 0.1
  ── Failure ('testFitFunctions.R:324:3'): cauphylm helper functions ─────────────
  logLik(reslmdat) (`actual`) not equal to 13.296526 (`expected`).
  
    `actual`: -Inf
  `expected`: 13.3
  ── Failure ('testFitFunctions.R:325:3'): cauphylm helper functions ─────────────
  AIC(reslmdat) (`actual`) not equal to -20.5930517 (`expected`).
  
    `actual`:   Inf
  `expected`: -20.6
  ── Failure ('testFitFunctions.R:330:3'): cauphylm helper functions ─────────────
  unname(sqrt(diag(vcov(reslmdat)))) (`actual`) not equal to c(0.04988679, 0.065175, 0.18057543) (`expected`).
  
    `actual`: 0.030 0.035 0.303
  `expected`: 0.050 0.065 0.181
  ── Failure ('testFitFunctions.R:390:3'): profile likelihood ────────────────────
  max(pr$lambda$profLogLik) (`actual`) not equal to fit$logLik (`expected`).
  
    `actual`: 12.6
  `expected`: -Inf
  ── Failure ('testFitFunctions.R:391:3'): profile likelihood ────────────────────
  mean(pr$x0$profLogLik) <= fit$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:392:3'): profile likelihood ────────────────────
  mean(pr$disp$profLogLik) <= fit$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testFitFunctions.R:393:3'): profile likelihood ────────────────────
  mean(pr$lambda$profLogLik) <= fit$logLik is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('testIncrementReconstruction.R:206:3'): testAncestralIncrementFit ──
  MAP$par (`actual`) not equal to 0.2811777 (`expected`).
  
    `actual`: 0.48
  `expected`: 0.28
  ── Failure ('testIncrementReconstruction.R:273:3'): testHDI ────────────────────
  dim(hdi_all[[1]]) (`actual`) not equal to c(2, 2) (`expected`).
  
    `actual`: 1.0 2.0
  `expected`: 2.0 2.0
  
  [ FAIL 20 | WARN 2 | SKIP 0 | PASS 265 ]
  Error: Test failures
  Execution halted