CRAN Package Check Results for Package rptR

Last updated on 2025-02-23 19:51:19 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.9.22	3.21	137.51	140.72	NOTE
r-devel-linux-x86_64-debian-gcc	0.9.22	2.39	93.90	96.29	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	7.58	135.84	143.42	NOTE
r-release-linux-x86_64	0.9.22	3.84	135.10	138.94	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	203.00	210.00	OK

Check Details

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