• using R Under development (unstable) (2025-02-15 r87726)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)     GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘rptR/DESCRIPTION’ ... OK
• this is package ‘rptR’ version ‘0.9.22’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘rptR’ can be installed ... [7s/20s] OK See the install log for details.
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘methods’   All declared Imports should be used.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [13s/39s] OK
• checking Rd files ... 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.}        | ^
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [29s/85s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [150s/425s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [32s/92s] OK
• checking PDF version of manual ... [8s/23s] OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR, 2 NOTEs