• using R Under development (unstable) (2025-02-15 r87725)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 19.1.7     flang-new version 19.1.7
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘statgenGxE/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘statgenGxE’ version ‘1.0.9’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘asreml’
• 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 ‘statgenGxE’ can be installed ... [17s/53s] OK See the install log for details.
• checking installed package size ... OK
• 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 whether startup messages can be suppressed ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [32s/56s] OK
• checking Rd files ... OK
• 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 LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [63s/88s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [54s/55s] ERROR   Running ‘testthat.R’ [54s/54s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(statgenGxE)   >   > test_check("statgenGxE")   [ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ]      ══ Skipped tests (17) ══════════════════════════════════════════════════════════   • On CRAN (17): 'test-gxeMegaEnv.R:72:3', 'test-gxeMegaEnv.R:103:3',     'test-gxeVarComp.R:52:3', 'test-gxeVarComp.R:116:3',     'test-gxeVarComp.R:151:3', 'test-gxeVarComp.R:187:3',     'test-gxeVarComp.R:216:3', 'test-gxeVarCov.R:24:3', 'test-gxeVarCov.R:37:3',     'test-gxeVarCov.R:78:3', 'test-gxeVarCov.R:90:3', 'test-gxeVarCov.R:100:3',     'test-report.R:7:3', 'test-report.R:21:3', 'test-report.R:31:3',     'test-report.R:41:3', 'test-summaries.R:75:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-gxeMegaEnv.R:68:3'): predict.megaEnv functions correctly ─────   geTabLm$predictedValue[1, ] not equivalent to c(79.2407761061078, 79.4858110738655).   Component 1: Mean relative difference: 0.01361819   Component 2: Mean relative difference: 0.02727539   ── Failure ('test-gxeMegaEnv.R:70:3'): predict.megaEnv functions correctly ─────   geTabLm$standardError[1, ] not equivalent to c(6.83087991095342, 6.38912904851271).   Component 1: Mean relative difference: 0.2039639   Component 2: Mean relative difference: 0.392072   ── Failure ('test-gxeMegaEnv.R:96:3'): option year in gxeTable functions properly ──   megaEnvPred$predictedValue[1, ] not equivalent to c(75.7340426279225, 72.8307799806527).   Component 1: Mean relative difference: 0.02866731   Component 2: Mean relative difference: 0.04765296   ── Failure ('test-gxeMegaEnv.R:98:3'): option year in gxeTable functions properly ──   megaEnvPred$standardError[1, ] not equivalent to c(5.69948967193805, 7.83055991157765).   Component 1: Mean relative difference: 0.3108429   Component 2: Mean relative difference: 0.1233996   ── Failure ('test-gxeVarComp.R:35:3'): lme4 model gives the correct output ─────   geVCLm$fullRandVC[["vcov"]] not equal to c(0, 79.9668254460519, 306.14928560952).   3/3 mismatches (average diff: 70.4)   [1] 14.8 - 0 == 14.8   [2] 221.2 - 80 == 141.2   [3] 250.9 - 306 == -55.2   ── Failure ('test-gxeVarComp.R:37:3'): lme4 model gives the correct output ─────   geVCLm$fullRandVC[["vcovPerc"]] not equal to c(0, 0.207105642982462, 0.792894357017538).   3/3 mismatches (average diff: 0.185)   [1] 0.0305 - 0.000 == 0.0305   [2] 0.4543 - 0.207 == 0.2471   [3] 0.5153 - 0.793 == -0.2776   ── Failure ('test-gxeVarComp.R:109:3'): predict function functions correctly ───   predVCLm[["predictedValue"]] not equal to c(...).   15/15 mismatches (average diff: 3.33)   [1] 76.9 - 79.3 == -2.425   [2] 72.7 - 76.8 == -4.069   [3] 97.9 - 92.0 == 5.840   [4] 81.8 - 82.3 == -0.492   [5] 77.5 - 79.7 == -2.179   [6] 92.5 - 88.8 == 3.749   [7] 69.7 - 74.9 == -5.263   [8] 93.6 - 89.4 == 4.155   [9] 84.0 - 83.6 == 0.364   ...   ── Failure ('test-gxeVarComp.R:134:3'): option predictLevel in predict function functions correctly ──   predVCLmTr[["predictedValue"]] not equal to c(...).   45/45 mismatches (average diff: 3.33)   [1] 75.1 - 77.5 == -2.425   [2] 70.9 - 75.0 == -4.069   [3] 96.1 - 90.2 == 5.840   [4] 80.0 - 80.5 == -0.492   [5] 75.7 - 77.9 == -2.179   [6] 90.7 - 87.0 == 3.749   [7] 67.9 - 73.1 == -5.263   [8] 91.8 - 87.6 == 4.155   [9] 82.2 - 81.8 == 0.364   ...   ── Failure ('test-gxeVarComp.R:184:3'): vc function functions correctly ────────   vcVCLm[["Component"]] not equal to c(78.7850079727369, 309.69339127849).   2/2 mismatches (average diff: 93.8)   [1] 215 - 78.8 == 136.4   [2] 259 - 309.7 == -51.2   ── Failure ('test-gxeVarComp.R:205:3'): herit function functions correctly ─────   `heritVCLm` not equal to 0.202804089299665.   1/1 mismatches   [1] 0.454 - 0.203 == 0.251   ── Failure ('test-gxeVarCov.R:66:3'): lme4 model gives correct output ──────────   summLm[, "AIC"] not equivalent to 380.14921134723.   1/1 mismatches   [1] Inf - 380 == Inf   ── Failure ('test-gxeVarCov.R:67:3'): lme4 model gives correct output ──────────   summLm[, "BIC"] not equivalent to 383.762536326771.   1/1 mismatches   [1] Inf - 384 == Inf   ── Failure ('test-gxeVarCov.R:68:3'): lme4 model gives correct output ──────────   summLm[, "Deviance"] not equivalent to 376.14921134723.   1/1 mismatches   [1] Inf - 376 == Inf   ── Failure ('test-gxeVarCov.R:70:3'): lme4 model gives correct output ──────────   geVCLm$vcov not equivalent to c(...).   9/9 mismatches (average diff: 7.95)   [1] 31.6 - 25.90 == 5.68   [2] 14.3 - 5.25 == 9.09   [3] 14.3 - 5.25 == 9.09   [4] 14.3 - 5.25 == 9.09   [5] 31.6 - 25.90 == 5.68   [6] 14.3 - 5.25 == 9.09   [7] 14.3 - 5.25 == 9.09   [8] 14.3 - 5.25 == 9.09   [9] 31.6 - 25.90 == 5.68      [ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [73s/73s] OK
• checking PDF version of manual ... 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