Last updated on 2025-02-21 03:52:25 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.22 | 4.16 | 136.96 | 141.12 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.9.22 | 2.98 | 94.69 | 97.67 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.9.22 | 235.12 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.9.22 | 270.31 | ERROR | |||
| r-devel-macos-arm64 | 0.9.22 | 82.00 | NOTE | |||
| r-devel-macos-x86_64 | 0.9.22 | 171.00 | NOTE | |||
| r-devel-windows-x86_64 | 0.9.22 | 5.00 | 174.00 | 179.00 | NOTE | |
| r-patched-linux-x86_64 | 0.9.22 | 6.14 | 134.74 | 140.88 | NOTE | |
| r-release-linux-x86_64 | 0.9.22 | 3.53 | 134.21 | 137.74 | NOTE | |
| r-release-macos-arm64 | 0.9.22 | 67.00 | NOTE | |||
| r-release-macos-x86_64 | 0.9.22 | 101.00 | NOTE | |||
| r-release-windows-x86_64 | 0.9.22 | 6.00 | 171.00 | 177.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.9.22 | 80.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.9.22 | 115.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.9.22 | 7.00 | 217.00 | 224.00 | OK |
Version: 0.9.22
Check: Rd files
Result: NOTE
checkRd: (-1) rptBinary.Rd:89: Lost braces
89 | Note that the distribution might not be symmetrical, in which case the emph{se} is less informative.}
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-arm64, r-devel-macos-x86_64, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 0.9.22
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
rpt.Rd: lmer
rptBinary.Rd: lmer
rptGaussian.Rd: lmer
rptPoisson.Rd: lmer
rptProportion.Rd: lmer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 0.9.22
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.9.22
Check: tests
Result: ERROR
Running ‘testthat.R’ [136s/190s]
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9.22
Check: tests
Result: ERROR
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
Flavor: r-devel-linux-x86_64-fedora-gcc