Running ‘testthat.R’ [80s/111s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rptR)
  > 
  > test_check("rptR")
  Bootstrap Progress:
  Bootstrap Progress:
  Permutation Progress for Population :
  Bootstrap Progress:
  Permutation Progress for Container:
  Bootstrap Progress:
  Permutation Progress for Population:
  Bootstrap Progress:
  Permutation Progress for Population:
  Bootstrap Progress:
  Permutation Progress for Population:
  Bootstrap Progress:
  ── 1. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_5$CI_emp$CI_org["Container", "97.5%"]) not equal to 0.008368035.
  1/1 mismatches
  [1] 0 - 0.00837 == -0.00837
  
  ── 2. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_5$CI_emp$CI_org["Population", "2.5%"]) not equal to 0.09174017.
  1/1 mismatches
  [1] 0.135 - 0.0917 == 0.0435
  
  ── 3. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_5$CI_emp$CI_org["Population", "97.5%"]) not equal to 0.2063018.
  1/1 mismatches
  [1] 0.299 - 0.206 == 0.0922
  
  ── 4. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_5$CI_emp$CI_link["Container", "97.5%"]) not equal to 0.0084029.
  1/1 mismatches
  [1] 0 - 0.0084 == -0.0084
  
  ── 5. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_5$CI_emp$CI_link["Population", "2.5%"]) not equal to 0.09218286.
  1/1 mismatches
  [1] 0.137 - 0.0922 == 0.0445
  
  ── 6. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_5$CI_emp$CI_link["Population", "97.5%"]) not equal to 0.2095188.
  1/1 mismatches
  [1] 0.314 - 0.21 == 0.104
  
  ── 7. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_5$CI_emp$CI_link["Residual", "2.5%"]) not equal to 0.7902657.
  1/1 mismatches
  [1] 0.686 - 0.79 == -0.104
  
  ── 8. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_5$CI_emp$CI_link["Residual", "97.5%"]) not equal to 0.8994142.
  1/1 mismatches
  [1] 0.863 - 0.899 == -0.0361
  
  Permutation Progress for Container:
  Permutation Progress for Population:
  Bootstrap Progress:
  Permutation Progress for Container:
  Permutation Progress for Population:
  Bootstrap Progress:
  Permutation Progress for Population :
  Bootstrap Progress:
  ── 9. Failure: rpt estimation works for two random effect, boot, no permut, no p
  as.numeric(R_est_6$CI_emp[1, "2.5%"]) not equal to 0.3837608.
  1/1 mismatches
  [1] 0.418 - 0.384 == 0.0347
  
  ── 10. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_6$CI_emp[1, "97.5%"]) not equal to 0.5347381.
  1/1 mismatches
  [1] 0.596 - 0.535 == 0.061
  
  ── 11. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_6$CI_emp[2, "2.5%"]) not equal to 0.1587494.
  1/1 mismatches
  [1] 0.0849 - 0.159 == -0.0738
  
  ── 12. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_6$CI_emp[2, "97.5%"]) not equal to 0.3445943.
  1/1 mismatches
  [1] 0.363 - 0.345 == 0.0182
  
  Permutation Progress for Container :
  Permutation Progress for Population :
  ── 13. Failure: rpt estimation works for two random effect, no boot, permut, no 
  R_est_7$P$P_permut[2] not equal to 0.4.
  1/1 mismatches
  [1] 0.6 - 0.4 == 0.2
  
  Bootstrap Progress:
  Permutation Progress for Container :
  Permutation Progress for Population :
  ── 14. Failure: Variance estimation works for two random effects with residual a
  R_est_8$CI_emp["Container", "2.5%"] not equal to 1.772372.
  1/1 mismatches
  [1] 1.68 - 1.77 == -0.0885
  
  ── 15. Failure: Variance estimation works for two random effects with residual a
  R_est_8$CI_emp["Population", "2.5%"] not equal to 1.296191.
  1/1 mismatches
  [1] 1.16 - 1.3 == -0.137
  
  ── 16. Failure: Variance estimation works for two random effects with residual a
  R_est_8$CI_emp["Residual", "2.5%"] not equal to 1.227603.
  1/1 mismatches
  [1] 1.14 - 1.23 == -0.0898
  
  ── 17. Failure: Variance estimation works for two random effects with residual a
  R_est_8$CI_emp["Overdispersion", "2.5%"] not equal to 1.227603.
  1/1 mismatches
  [1] 1.14 - 1.23 == -0.0898
  
  Bootstrap Progress:
  Permutation Progress for Container:
  Bootstrap Progress:
  ── 18. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_org[1, "2.5%"]) not equal to 0.02431758.
  1/1 mismatches
  [1] 0.031 - 0.0243 == 0.00667
  
  ── 19. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_org[1, "97.5%"]) not equal to 0.0256355.
  1/1 mismatches
  [1] 0.0856 - 0.0256 == 0.06
  
  ── 20. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_org[2, "2.5%"]) not equal to 0.2346106.
  1/1 mismatches
  [1] 0.296 - 0.235 == 0.061
  
  ── 21. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_org[2, "97.5%"]) not equal to 0.5839979.
  1/1 mismatches
  [1] 0.625 - 0.584 == 0.0409
  
  ── 22. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_link[1, "2.5%"]) not equal to 0.02642277.
  1/1 mismatches
  [1] 0.0386 - 0.0264 == 0.0122
  
  ── 23. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_link[1, "97.5%"]) not equal to 0.03203479.
  1/1 mismatches
  [1] 0.0943 - 0.032 == 0.0623
  
  ── 24. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_link[2, "2.5%"]) not equal to 0.2449164.
  1/1 mismatches
  [1] 0.31 - 0.245 == 0.0654
  
  ── 25. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_link[2, "97.5%"]) not equal to 0.5944401.
  1/1 mismatches
  [1] 0.634 - 0.594 == 0.0397
  
  Permutation Progress for Container:
  Permutation Progress for Population:
  ── 26. Failure: rpt estimation works for two random effect, no boot, permut, no 
  R_est_3$P$P_permut_org[1] not equal to 0.2.
  1/1 mismatches
  [1] 0.4 - 0.2 == 0.2
  
  ── 27. Failure: rpt estimation works for two random effect, no boot, permut, no 
  R_est_3$P$P_permut_link[1] not equal to 0.2.
  1/1 mismatches
  [1] 0.6 - 0.2 == 0.4
  
  Bootstrap Progress:
  Permutation Progress for Container:
  Bootstrap Progress:
  Permutation Progress for Container:
  Permutation Progress for Habitat:
  Bootstrap Progress:
  Permutation Progress for Population:
  Bootstrap Progress:
  ── 28. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_org[1, "2.5%"]) not equal to 0.0001784753.
  1/1 mismatches
  [1] 0.00543 - 0.000178 == 0.00525
  
  ── 29. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_org[2, "2.5%"]) not equal to 0.1085067.
  1/1 mismatches
  [1] 0.104 - 0.109 == -0.00416
  
  ── 30. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_org[2, "97.5%"]) not equal to 0.1204242.
  1/1 mismatches
  [1] 0.207 - 0.12 == 0.0863
  
  ── 31. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_link[1, "2.5%"]) not equal to 0.0001784753.
  1/1 mismatches
  [1] 0.0055 - 0.000178 == 0.00532
  
  ── 32. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_link[2, "2.5%"]) not equal to 0.1085067.
  1/1 mismatches
  [1] 0.105 - 0.109 == -0.00397
  
  ── 33. Failure: rpt estimation works for two random effect, boot, no permut, no 
  as.numeric(R_est_2$CI_emp$CI_link[2, "97.5%"]) not equal to 0.1204242.
  1/1 mismatches
  [1] 0.209 - 0.12 == 0.089
  
  Permutation Progress for Container:
  Permutation Progress for Population:
  Bootstrap Progress:
  Permutation Progress for Population :
  Bootstrap Progress:
  Permutation Progress for Container:
  Bootstrap Progress:
  Permutation Progress for Population:
  Bootstrap Progress:
  Permutation Progress for Population:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 195 SKIPPED: 0 FAILED: 33
  1. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptBinary.R#119) 
  2. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptBinary.R#121) 
  3. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptBinary.R#122) 
  4. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptBinary.R#131) 
  5. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptBinary.R#133) 
  6. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptBinary.R#134) 
  7. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptBinary.R#136) 
  8. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptBinary.R#137) 
  9. Failure: rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link (@test-rptGaussian.R#84) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted