Last updated on 2025-03-12 08:53:19 CET.
Package | ERROR | NOTE | OK |
---|---|---|---|
douconca | 15 | ||
factReg | 15 | ||
isatabr | 2 | 13 | |
LMMsolver | 15 | ||
statgenGWAS | 10 | 5 | |
statgenGxE | 2 | 8 | 5 |
statgenHTP | 8 | 7 | |
statgenIBD | 6 | 9 | |
statgenMPP | 15 | ||
statgenQTLxT | 7 | 8 | |
statgenSTA | 2 | 8 | 5 |
Current CRAN status: OK: 15
Current CRAN status: OK: 15
Current CRAN status: NOTE: 2, OK: 13
Version: 1.0.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘xcms’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 15
Current CRAN status: NOTE: 10, OK: 5
Version: 1.0.10
Check: top-level files
Result: NOTE
possible bashism in configure.ac line 31 (should be 'b = a'):
if test x"${RSysinfoName}" == x"Darwin"; then
possible bashism in configure.ac line 42 (should be 'b = a'):
if test x"${hasOpenMP}" == x""; then
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
Version: 1.0.10
Check: installed package size
Result: NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 2.7Mb
libs 5.1Mb
Flavors: 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
Version: 1.0.10
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Version: 1.0.10
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘snpStats’
Flavor: r-oldrel-macos-arm64
Current CRAN status: ERROR: 2, NOTE: 8, OK: 5
Version: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [62s/147s]
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$vcov not equivalent to c(...).
9/9 mismatches (average diff: 7.95)
[1] 31.6 - 25.90 == 5.68
[2] 14.3 - 5.25 == 9.09
[3] 14.3 - 5.25 == 9.09
[4] 14.3 - 5.25 == 9.09
[5] 31.6 - 25.90 == 5.68
[6] 14.3 - 5.25 == 9.09
[7] 14.3 - 5.25 == 9.09
[8] 14.3 - 5.25 == 9.09
[9] 31.6 - 25.90 == 5.68
[ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [56s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(statgenGxE)
>
> test_check("statgenGxE")
[ FAIL 14 | WARN 47 | SKIP 17 | PASS 434 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-gxeMegaEnv.R:72:3', 'test-gxeMegaEnv.R:103:3',
'test-gxeVarComp.R:52:3', 'test-gxeVarComp.R:116:3',
'test-gxeVarComp.R:151:3', 'test-gxeVarComp.R:187:3',
'test-gxeVarComp.R:216:3', 'test-gxeVarCov.R:24:3', 'test-gxeVarCov.R:37:3',
'test-gxeVarCov.R:78:3', 'test-gxeVarCov.R:90:3', 'test-gxeVarCov.R:100:3',
'test-report.R:7:3', 'test-report.R:21:3', 'test-report.R:31:3',
'test-report.R:41:3', 'test-summaries.R:75:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gxeMegaEnv.R:68:3'): predict.megaEnv functions correctly ─────
geTabLm$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
Current CRAN status: NOTE: 8, OK: 7
Version: 1.0.7
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
Version: 1.0.7
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 3.5Mb
Flavor: r-release-macos-arm64
Current CRAN status: NOTE: 6, OK: 9
Version: 1.0.8
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘statgenGWAS’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.8
Check: installed package size
Result: NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
extdata 2.4Mb
libs 4.2Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 15
Current CRAN status: NOTE: 7, OK: 8
Version: 1.0.2
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
runMultiTraitGwas.Rd: GWAS
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: 1.0.2
Check: installed package size
Result: NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
libs 6.4Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: ERROR: 2, NOTE: 8, OK: 5
Version: 1.0.14
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘mapproj’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.14
Check: tests
Result: ERROR
Running ‘testthat.R’ [135s/364s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(statgenSTA)
>
> test_check("statgenSTA")
[ FAIL 21 | WARN 19 | SKIP 6 | PASS 757 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-STA.R:200:3', 'test-STA.R:219:3'
• empty test (1): 'test-fitTDSpATS.R:67:1'
• {asreml} is not installed (3): 'test-STA.R:43:3', 'test-STA.R:57:3',
'test-STA.R:113:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ExtractLme4.R:37:3'): BLUPs are computed correctly ───────────
extLm$BLUPs$t1 not equal to c(...).
15/15 mismatches (average diff: 7.36)
[1] 83.5 - 79.4 == 4.17
[2] 68.7 - 79.4 == -10.63
[3] 87.5 - 79.4 == 8.14
[4] 76.4 - 79.4 == -2.95
[5] 85.4 - 79.4 == 6.03
[6] 72.3 - 79.4 == -7.05
[7] 72.6 - 79.4 == -6.77
[8] 70.8 - 79.4 == -8.63
[9] 83.6 - 79.4 == 4.23
...
── Failure ('test-ExtractLme4.R:49:3'): SE of BLUPs are computed correctly ─────
extLm$seBLUPs$t1 not equal to rep(x = 0, times = 15).
15/15 mismatches (average diff: 11.8)
[1] 11.8 - 0 == 11.8
[2] 11.8 - 0 == 11.8
[3] 11.8 - 0 == 11.8
[4] 11.8 - 0 == 11.8
[5] 11.8 - 0 == 11.8
[6] 11.8 - 0 == 11.8
[7] 11.8 - 0 == 11.8
[8] 11.8 - 0 == 11.8
[9] 11.8 - 0 == 11.8
...
── Failure ('test-ExtractLme4.R:63:3'): heritability is computed correctly ─────
extLm$heritability not equivalent to 0.
1/1 mismatches
[1] 0.55 - 0 == 0.55
── Failure ('test-ExtractLme4.R:70:3'): heritability can be coerced to data.frame correctly ──
herit[1, 2] not equal to 0.
1/1 mismatches
[1] 0.55 - 0 == 0.55
── Failure ('test-ExtractLme4.R:77:3'): varGen is computed correctly ───────────
extLm$varGen not equivalent to 0.
1/1 mismatches
[1] 309 - 0 == 309
── Failure ('test-ExtractLme4.R:84:3'): varErr is computed correctly ───────────
extLm$varErr not equivalent to 638.590646884335.
1/1 mismatches
[1] 504 - 639 == -134
── Failure ('test-ExtractLme4.R:142:3'): rMeans are computed correctly ─────────
extLm$rMeans$t1 not equal to c(...).
30/30 mismatches (average diff: 7.36)
[1] 99.3 - 81.3 == 17.99
[2] 89.4 - 81.3 == 8.14
[3] 83.5 - 77.5 == 6.03
[4] 70.0 - 81.3 == -11.24
[5] 81.4 - 77.5 == 3.96
[6] 79.8 - 77.5 == 2.32
[7] 70.7 - 81.3 == -10.63
[8] 68.8 - 77.5 == -8.63
[9] 95.5 - 77.5 == 17.99
...
── Failure ('test-ExtractLme4.R:159:3'): random effects are computed correctly ──
extLm$ranEf$t1 not equal to c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0).
15/15 mismatches (average diff: 7.36)
[1] 4.17 - 0 == 4.17
[2] -10.63 - 0 == -10.63
[3] 8.14 - 0 == 8.14
[4] -2.95 - 0 == -2.95
[5] 6.03 - 0 == 6.03
[6] -7.05 - 0 == -7.05
[7] -6.77 - 0 == -6.77
[8] -8.63 - 0 == -8.63
[9] 4.23 - 0 == 4.23
...
── Failure ('test-ExtractLme4.R:167:3'): residuals are computed correctly for genotype random ──
extLm$residR$t1 not equal to c(...).
30/30 mismatches (average diff: 7.36)
[1] 7.07 - 25.1 == -17.99
[2] -1.04 - 7.1 == -8.14
[3] 13.73 - 19.8 == -6.03
[4] -32.05 - -43.3 == 11.24
[5] 36.02 - 40.0 == -3.96
[6] 6.78 - 9.1 == -2.32
[7] -18.65 - -29.3 == 10.63
[8] -8.92 - -17.5 == 8.63
[9] 22.34 - 40.3 == -17.99
...
── Failure ('test-ExtractLme4.R:184:3'): standardized residuals are computed correctly ──
extLm$stdResR$t1 not equal to c(...).
30/30 mismatches (average diff: 0.264)
[1] 0.3147 - 0.992 == -0.6769
[2] -0.0462 - 0.281 == -0.3273
[3] 0.6115 - 0.782 == -0.1708
[4] -1.4272 - -1.713 == 0.2860
[5] 1.6039 - 1.582 == 0.0219
[6] 0.3017 - 0.360 == -0.0584
[7] -0.8303 - -1.159 == 0.3283
[8] -0.3972 - -0.694 == 0.2972
[9] 0.9945 - 1.596 == -0.6012
...
── Failure ('test-STA.R:36:3'): summary.STA produces correct output for lme4 ───
sumLm$heritability not equivalent to 0.
1/1 mismatches
[1] 0.52 - 0 == 0.52
── Failure ('test-fitTDLme4.R:112:3'): Fitting models functions properly when trait contains space ──
`... <- NULL` did not produce any messages.
── Failure ('test-outliers.R:56:3'): option rLimit funtions properly ───────────
out1$indicator[["E1"]][["t1"]] has length 4, not length 6.
── Failure ('test-outliers.R:57:3'): option rLimit funtions properly ───────────
nrow(out1$outliers) not equal to 6.
1/1 mismatches
[1] 4 - 6 == -2
── Failure ('test-outliers.R:58:3'): option rLimit funtions properly ───────────
out1$outliers$res not equal to c(...).
Lengths differ: 4 is not 6
── Failure ('test-outliers.R:66:3'): option rLimit funtions properly for multiple traits ──
sapply(X = out14$indicator[["E1"]], FUN = length) not equivalent to c(6, 10, 0, 2).
2/4 mismatches (average diff: 3)
[1] 4 - 6 == -2
[2] 6 - 10 == -4
── Failure ('test-outliers.R:68:3'): option rLimit funtions properly for multiple traits ──
nrow(out14$outliers) not equal to 18.
1/1 mismatches
[1] 12 - 18 == -6
── Failure ('test-outliers.R:74:3'): option commonFactors functions properly ───
out1$indicator[["E1"]][["t1"]] has length 4, not length 6.
── Failure ('test-outliers.R:75:3'): option commonFactors functions properly ───
nrow(out1$outliers) not equal to 18.
1/1 mismatches
[1] 12 - 18 == -6
── Failure ('test-outliers.R:76:3'): option commonFactors functions properly ───
sum(out1$outliers$outlier) not equal to 6.
1/1 mismatches
[1] 4 - 6 == -2
── Failure ('test-outliers.R:87:3'): option verbose functions properly ─────────
any(grepl(pattern = "1.082710", x = printOut2)) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 21 | WARN 19 | SKIP 6 | PASS 757 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.14
Check: tests
Result: ERROR
Running ‘testthat.R’ [116s/155s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(statgenSTA)
>
> test_check("statgenSTA")
[ FAIL 21 | WARN 19 | SKIP 6 | PASS 757 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-STA.R:200:3', 'test-STA.R:219:3'
• empty test (1): 'test-fitTDSpATS.R:67:1'
• {asreml} is not installed (3): 'test-STA.R:43:3', 'test-STA.R:57:3',
'test-STA.R:113:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ExtractLme4.R:37:3'): BLUPs are computed correctly ───────────
extLm$BLUPs$t1 not equal to c(...).
15/15 mismatches (average diff: 7.36)
[1] 83.5 - 79.4 == 4.17
[2] 68.7 - 79.4 == -10.63
[3] 87.5 - 79.4 == 8.14
[4] 76.4 - 79.4 == -2.95
[5] 85.4 - 79.4 == 6.03
[6] 72.3 - 79.4 == -7.05
[7] 72.6 - 79.4 == -6.77
[8] 70.8 - 79.4 == -8.63
[9] 83.6 - 79.4 == 4.23
...
── Failure ('test-ExtractLme4.R:49:3'): SE of BLUPs are computed correctly ─────
extLm$seBLUPs$t1 not equal to rep(x = 0, times = 15).
15/15 mismatches (average diff: 11.8)
[1] 11.8 - 0 == 11.8
[2] 11.8 - 0 == 11.8
[3] 11.8 - 0 == 11.8
[4] 11.8 - 0 == 11.8
[5] 11.8 - 0 == 11.8
[6] 11.8 - 0 == 11.8
[7] 11.8 - 0 == 11.8
[8] 11.8 - 0 == 11.8
[9] 11.8 - 0 == 11.8
...
── Failure ('test-ExtractLme4.R:63:3'): heritability is computed correctly ─────
extLm$heritability not equivalent to 0.
1/1 mismatches
[1] 0.55 - 0 == 0.55
── Failure ('test-ExtractLme4.R:70:3'): heritability can be coerced to data.frame correctly ──
herit[1, 2] not equal to 0.
1/1 mismatches
[1] 0.55 - 0 == 0.55
── Failure ('test-ExtractLme4.R:77:3'): varGen is computed correctly ───────────
extLm$varGen not equivalent to 0.
1/1 mismatches
[1] 309 - 0 == 309
── Failure ('test-ExtractLme4.R:84:3'): varErr is computed correctly ───────────
extLm$varErr not equivalent to 638.590646884335.
1/1 mismatches
[1] 504 - 639 == -134
── Failure ('test-ExtractLme4.R:142:3'): rMeans are computed correctly ─────────
extLm$rMeans$t1 not equal to c(...).
30/30 mismatches (average diff: 7.36)
[1] 99.3 - 81.3 == 17.99
[2] 89.4 - 81.3 == 8.14
[3] 83.5 - 77.5 == 6.03
[4] 70.0 - 81.3 == -11.24
[5] 81.4 - 77.5 == 3.96
[6] 79.8 - 77.5 == 2.32
[7] 70.7 - 81.3 == -10.63
[8] 68.8 - 77.5 == -8.63
[9] 95.5 - 77.5 == 17.99
...
── Failure ('test-ExtractLme4.R:159:3'): random effects are computed correctly ──
extLm$ranEf$t1 not equal to c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0).
15/15 mismatches (average diff: 7.36)
[1] 4.17 - 0 == 4.17
[2] -10.63 - 0 == -10.63
[3] 8.14 - 0 == 8.14
[4] -2.95 - 0 == -2.95
[5] 6.03 - 0 == 6.03
[6] -7.05 - 0 == -7.05
[7] -6.77 - 0 == -6.77
[8] -8.63 - 0 == -8.63
[9] 4.23 - 0 == 4.23
...
── Failure ('test-ExtractLme4.R:167:3'): residuals are computed correctly for genotype random ──
extLm$residR$t1 not equal to c(...).
30/30 mismatches (average diff: 7.36)
[1] 7.07 - 25.1 == -17.99
[2] -1.04 - 7.1 == -8.14
[3] 13.73 - 19.8 == -6.03
[4] -32.05 - -43.3 == 11.24
[5] 36.02 - 40.0 == -3.96
[6] 6.78 - 9.1 == -2.32
[7] -18.65 - -29.3 == 10.63
[8] -8.92 - -17.5 == 8.63
[9] 22.34 - 40.3 == -17.99
...
── Failure ('test-ExtractLme4.R:184:3'): standardized residuals are computed correctly ──
extLm$stdResR$t1 not equal to c(...).
30/30 mismatches (average diff: 0.264)
[1] 0.3147 - 0.992 == -0.6769
[2] -0.0462 - 0.281 == -0.3273
[3] 0.6115 - 0.782 == -0.1708
[4] -1.4272 - -1.713 == 0.2860
[5] 1.6039 - 1.582 == 0.0219
[6] 0.3017 - 0.360 == -0.0584
[7] -0.8303 - -1.159 == 0.3283
[8] -0.3972 - -0.694 == 0.2972
[9] 0.9945 - 1.596 == -0.6012
...
── Failure ('test-STA.R:36:3'): summary.STA produces correct output for lme4 ───
sumLm$heritability not equivalent to 0.
1/1 mismatches
[1] 0.52 - 0 == 0.52
── Failure ('test-fitTDLme4.R:112:3'): Fitting models functions properly when trait contains space ──
`... <- NULL` did not produce any messages.
── Failure ('test-outliers.R:56:3'): option rLimit funtions properly ───────────
out1$indicator[["E1"]][["t1"]] has length 4, not length 6.
── Failure ('test-outliers.R:57:3'): option rLimit funtions properly ───────────
nrow(out1$outliers) not equal to 6.
1/1 mismatches
[1] 4 - 6 == -2
── Failure ('test-outliers.R:58:3'): option rLimit funtions properly ───────────
out1$outliers$res not equal to c(...).
Lengths differ: 4 is not 6
── Failure ('test-outliers.R:66:3'): option rLimit funtions properly for multiple traits ──
sapply(X = out14$indicator[["E1"]], FUN = length) not equivalent to c(6, 10, 0, 2).
2/4 mismatches (average diff: 3)
[1] 4 - 6 == -2
[2] 6 - 10 == -4
── Failure ('test-outliers.R:68:3'): option rLimit funtions properly for multiple traits ──
nrow(out14$outliers) not equal to 18.
1/1 mismatches
[1] 12 - 18 == -6
── Failure ('test-outliers.R:74:3'): option commonFactors functions properly ───
out1$indicator[["E1"]][["t1"]] has length 4, not length 6.
── Failure ('test-outliers.R:75:3'): option commonFactors functions properly ───
nrow(out1$outliers) not equal to 18.
1/1 mismatches
[1] 12 - 18 == -6
── Failure ('test-outliers.R:76:3'): option commonFactors functions properly ───
sum(out1$outliers$outlier) not equal to 6.
1/1 mismatches
[1] 4 - 6 == -2
── Failure ('test-outliers.R:87:3'): option verbose functions properly ─────────
any(grepl(pattern = "1.082710", x = printOut2)) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 21 | WARN 19 | SKIP 6 | PASS 757 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.0.14
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