Last updated on 2025-02-18 02:50:50 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.9 | 10.60 | 195.82 | 206.42 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.9 | 6.69 | 138.06 | 144.75 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.9 | 322.35 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.9 | 337.01 | ERROR | |||
| r-devel-macos-arm64 | 1.0.9 | 116.00 | OK | |||
| r-devel-macos-x86_64 | 1.0.9 | 243.00 | OK | |||
| r-devel-windows-x86_64 | 1.0.9 | 13.00 | 194.00 | 207.00 | OK | |
| r-patched-linux-x86_64 | 1.0.9 | 9.26 | 186.96 | 196.22 | NOTE | |
| r-release-linux-x86_64 | 1.0.9 | 7.75 | 186.31 | 194.06 | NOTE | |
| r-release-macos-arm64 | 1.0.9 | 115.00 | NOTE | |||
| r-release-macos-x86_64 | 1.0.9 | 216.00 | NOTE | |||
| r-release-windows-x86_64 | 1.0.9 | 11.00 | 197.00 | 208.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.0.9 | 112.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.0.9 | 191.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.0.9 | 15.00 | 233.00 | 248.00 | NOTE |
Version: 1.0.9
Check: tests
Result: 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$vcov not equivalent to c(...).
9/9 mismatches (average diff: 7.95)
[1] 31.6 - 25.90 == 5.68
[2] 14.3 - 5.25 == 9.09
[3] 14.3 - 5.25 == 9.09
[4] 14.3 - 5.25 == 9.09
[5] 31.6 - 25.90 == 5.68
[6] 14.3 - 5.25 == 9.09
[7] 14.3 - 5.25 == 9.09
[8] 14.3 - 5.25 == 9.09
[9] 31.6 - 25.90 == 5.68
[ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [55s/73s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(statgenGxE)
>
> test_check("statgenGxE")
[ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-gxeMegaEnv.R:72:3', 'test-gxeMegaEnv.R:103:3',
'test-gxeVarComp.R:52:3', 'test-gxeVarComp.R:116:3',
'test-gxeVarComp.R:151:3', 'test-gxeVarComp.R:187:3',
'test-gxeVarComp.R:216:3', 'test-gxeVarCov.R:24:3', 'test-gxeVarCov.R:37:3',
'test-gxeVarCov.R:78:3', 'test-gxeVarCov.R:90:3', 'test-gxeVarCov.R:100:3',
'test-report.R:7:3', 'test-report.R:21:3', 'test-report.R:31:3',
'test-report.R:41:3', 'test-summaries.R:75:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gxeMegaEnv.R:68:3'): predict.megaEnv functions correctly ─────
geTabLm$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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.9
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘asreml’
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64