Last updated on 2025-02-21 04:52:08 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.14 | 11.63 | 203.25 | 214.88 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.14 | 6.52 | 133.92 | 140.44 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.14 | 331.05 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.14 | 353.93 | ERROR | |||
| r-devel-macos-arm64 | 1.0.14 | 98.00 | OK | |||
| r-devel-macos-x86_64 | 1.0.14 | 217.00 | OK | |||
| r-devel-windows-x86_64 | 1.0.14 | 13.00 | 191.00 | 204.00 | OK | |
| r-patched-linux-x86_64 | 1.0.14 | 9.36 | 192.66 | 202.02 | NOTE | |
| r-release-linux-x86_64 | 1.0.14 | 10.49 | 192.97 | 203.46 | NOTE | |
| r-release-macos-arm64 | 1.0.14 | 96.00 | NOTE | |||
| r-release-macos-x86_64 | 1.0.14 | 182.00 | NOTE | |||
| r-release-windows-x86_64 | 1.0.14 | 13.00 | 189.00 | 202.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.0.14 | 98.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.0.14 | 168.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.0.14 | 16.00 | 233.00 | 249.00 | NOTE |
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’ [113s/140s]
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/148s]
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