Running ‘testthat.R’ [119s/225s]
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