- 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