Running ‘testthat.R’ [150s/423s]
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:
  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:
  Permutation Progress for Container :
  Permutation Progress for Population :
  Bootstrap Progress:
  Permutation Progress for Container :
  Permutation Progress for Population :
  Bootstrap Progress:
  Permutation Progress for Container:
  Bootstrap Progress:
  Permutation Progress for Container:
  Permutation Progress for Population:
  Bootstrap Progress:
  Permutation Progress for Container:
  Bootstrap Progress:
  Permutation Progress for Container:
  Permutation Progress for Habitat:
  Bootstrap Progress:
  Permutation Progress for Population:
  Bootstrap Progress:
  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:
  [ FAIL 22 | WARN 153 | SKIP 0 | PASS 206 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-rptGaussian.R:18:9'): rpt estimation works for one random effect, no boot, no permut, no parallelisation, logit link ──
  as.numeric(R_est_1$R) not equal to 0.2985548.
  1/1 mismatches
  [1] 0.289 - 0.299 == -0.00944
  ── Failure ('test-rptGaussian.R:24:9'): LRT works ──────────────────────────────
  R_est_1$P$LRT_P not equal to 9.59e-62.
  1/1 mismatches
  [1] 1 - 9.59e-62 == 1
  ── Failure ('test-rptGaussian.R:33:9'): rpt estimation works for one random effect, boot, no permut, no parallelisation, logit link ──
  as.numeric(R_est_2$CI_emp["2.5%"]) not equal to 0.1881897.
  1/1 mismatches
  [1] 0.289 - 0.188 == 0.101
  ── Failure ('test-rptGaussian.R:34:9'): rpt estimation works for one random effect, boot, no permut, no parallelisation, logit link ──
  as.numeric(R_est_2$CI_emp["97.5%"]) not equal to 0.2463285.
  1/1 mismatches
  [1] 0.289 - 0.246 == 0.0428
  ── Failure ('test-rptGaussian.R:44:9'): rpt estimation works for one random effect, no boot, permut, no parallelisation, logit link ──
  R_est_3$P$P_permut not equal to 0.2.
  1/1 mismatches
  [1] 1 - 0.2 == 0.8
  ── Failure ('test-rptGaussian.R:58:9'): rpt estimation works for two random effect, no boot, no permut, no parallelisation, logit link ──
  R_est_4$R[[1]] not equal to 0.478317.
  1/1 mismatches
  [1] 0.333 - 0.478 == -0.145
  ── Failure ('test-rptGaussian.R:60:9'): rpt estimation works for two random effect, no boot, no permut, no parallelisation, logit link ──
  R_est_4$R[[2]] not equal to 0.2561723.
  1/1 mismatches
  [1] 0.333 - 0.256 == 0.0772
  ── Failure ('test-rptGaussian.R:65:9'): LRTs works ─────────────────────────────
  R_est_4$P[1, "LRT_P"] not equal to 2.292582e-138.
  1/1 mismatches
  [1] NA - 2.29e-138 == NA
  ── Failure ('test-rptGaussian.R:66:9'): LRTs works ─────────────────────────────
  R_est_4$P[2, "LRT_P"] not equal to 2.156259e-07.
  1/1 mismatches
  [1] NA - 2.16e-07 == NA
  ── Failure ('test-rptGaussian.R:85:9'): rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link ──
  as.numeric(R_est_6$CI_emp[1, "2.5%"]) not equal to 0.3837608.
  1/1 mismatches
  [1] 0.333 - 0.384 == -0.0504
  ── Failure ('test-rptGaussian.R:86:9'): rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link ──
  as.numeric(R_est_6$CI_emp[1, "97.5%"]) not equal to 0.5347381.
  1/1 mismatches
  [1] 0.333 - 0.535 == -0.201
  ── Failure ('test-rptGaussian.R:88:9'): rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link ──
  as.numeric(R_est_6$CI_emp[2, "2.5%"]) not equal to 0.1587494.
  1/1 mismatches
  [1] 0.333 - 0.159 == 0.175
  ── Failure ('test-rptGaussian.R:89:9'): rpt estimation works for two random effect, boot, no permut, no parallelisation, logit link ──
  as.numeric(R_est_6$CI_emp[2, "97.5%"]) not equal to 0.3445943.
  1/1 mismatches
  [1] 0.333 - 0.345 == -0.0113
  ── Failure ('test-rptGaussian.R:100:9'): rpt estimation works for two random effect, no boot, permut, no parallelisation, logit link ──
  R_est_7$P$P_permut[1] not equal to 0.2.
  1/1 mismatches
  [1] 1 - 0.2 == 0.8
  ── Failure ('test-rptGaussian.R:101:9'): rpt estimation works for two random effect, no boot, permut, no parallelisation, logit link ──
  R_est_7$P$P_permut[2] not equal to 0.4.
  1/1 mismatches
  [1] 1 - 0.4 == 0.6
  ── Failure ('test-rptGaussian.R:114:9'): Variance estimation works for two random effects with residual and overdispersion and boot and permut ──
  R_est_8$R[[1]] not equal to 2.205629.
  1/1 mismatches
  [1] 1.32 - 2.21 == -0.882
  ── Failure ('test-rptGaussian.R:116:9'): Variance estimation works for two random effects with residual and overdispersion and boot and permut ──
  R_est_8$R[[2]] not equal to 1.181269.
  1/1 mismatches
  [1] 1.32 - 1.18 == 0.142
  ── Failure ('test-rptGaussian.R:118:9'): Variance estimation works for two random effects with residual and overdispersion and boot and permut ──
  R_est_8$CI_emp["Container", "2.5%"] not equal to 1.772372.
  1/1 mismatches
  [1] 1.36 - 1.77 == -0.409
  ── Failure ('test-rptGaussian.R:119:9'): Variance estimation works for two random effects with residual and overdispersion and boot and permut ──
  R_est_8$CI_emp["Population", "2.5%"] not equal to 1.296191.
  1/1 mismatches
  [1] 1.36 - 1.3 == 0.0675
  ── Failure ('test-rptGaussian.R:120:9'): Variance estimation works for two random effects with residual and overdispersion and boot and permut ──
  R_est_8$CI_emp["Residual", "2.5%"] not equal to 1.227603.
  1/1 mismatches
  [1] 1.36 - 1.23 == 0.136
  ── Failure ('test-rptGaussian.R:121:9'): Variance estimation works for two random effects with residual and overdispersion and boot and permut ──
  R_est_8$CI_emp["Overdispersion", "2.5%"] not equal to 1.227603.
  1/1 mismatches
  [1] 1.36 - 1.23 == 0.136
  ── Failure ('test-rptGaussian.R:179:9'): Random Slope repeatability point estimate is correct ──
  R_est_13$R$Population not equal to 0.5015875.
  1/1 mismatches
  [1] 0.6 - 0.502 == 0.0984
  
  [ FAIL 22 | WARN 153 | SKIP 0 | PASS 206 ]
  Error: Test failures
  Execution halted