Running ‘testthat.R’ [105s/136s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(statgenSTA)
  > 
  > test_check("statgenSTA")
  Saving _problems/test-STA-31.R
  Saving _problems/test-fitTDLme4-36.R
  Saving _problems/test-fitTDLme4-36.R
  Saving _problems/test-fitTDLme4-36.R
  Saving _problems/test-fitTDLme4-75.R
  Saving _problems/test-fitTDLme4-36.R
  Saving _problems/test-fitTDLme4-87.R
  Saving _problems/test-fitTDLme4-113.R
  Saving _problems/test-outliers-39.R
  Saving _problems/test-outliers-56.R
  Saving _problems/test-outliers-57.R
  Saving _problems/test-outliers-60.R
  Saving _problems/test-outliers-67.R
  Saving _problems/test-outliers-68.R
  Saving _problems/test-outliers-74.R
  Saving _problems/test-outliers-75.R
  Saving _problems/test-outliers-76.R
  Saving _problems/test-outliers-85.R
  Saving _problems/test-outliers-86.R
  Saving _problems/test-outliers-87.R
  [ FAIL 20 | WARN 27 | SKIP 9 | PASS 663 ]
  
  ══ Skipped tests (9) ═══════════════════════════════════════════════════════════
  • On CRAN (2): 'test-STA.R:200:3', 'test-STA.R:219:3'
  • empty test (2): ,
  • {Matrix} is not installed. (2): 'test-ExtractLme4.R:7:3',
    'test-ExtractLme4.R:13:1'
  • {asreml} is not installed (3): 'test-STA.R:43:3', 'test-STA.R:57:3',
    'test-STA.R:113:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-STA.R:31:3'): summary.STA produces correct output for lme4 ─────
  Error in `summary.STA(modelLm)`: No fitted model found for t1 in E1.
  
  Backtrace:
      ▆
   1. ├─base::summary(modelLm) at test-STA.R:31:3
   2. └─statgenSTA:::summary.STA(modelLm)
  ── Failure ('test-fitTDLme4.R:36:25'): running models creates objects with correct structure / "mRand" in modelLm has correct structure ──
  Expected `STAMod[[trait]]` to inherit from "character".
  Actual inheritance: "NULL"
  ── Failure ('test-fitTDLme4.R:36:25'): option what produces expected output / "mRand" in modelLmR has correct structure ──
  Expected `STAMod[[trait]]` to inherit from "character".
  Actual inheritance: "NULL"
  ── Failure ('test-fitTDLme4.R:36:25'): option covariates produces expected output structure / "mRand" in modelLmCov has correct structure ──
  Expected `STAMod[[trait]]` to inherit from "character".
  Actual inheritance: "NULL"
  ── Error ('test-fitTDLme4.R:75:3'): option covariates produces expected output structure ──
  Error in `modelLmCov[["E1"]]$mRand$t1@frame`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
      ▆
   1. ├─testthat::expect_true("repId" %in% colnames(modelLmCov[["E1"]]$mRand$t1@frame)) at test-fitTDLme4.R:75:3
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─"repId" %in% colnames(modelLmCov[["E1"]]$mRand$t1@frame)
   5. └─base::colnames(modelLmCov[["E1"]]$mRand$t1@frame)
   6.   └─base::is.data.frame(x)
  ── Failure ('test-fitTDLme4.R:36:25'): option useCheckId produces expected output structure / "mRand" in modelLmCi has correct structure ──
  Expected `STAMod[[trait]]` to inherit from "character".
  Actual inheritance: "NULL"
  ── Error ('test-fitTDLme4.R:87:3'): option useCheckId produces expected output structure ──
  Error in `modelLmCi[["E1"]]$mRand$t1@frame`: no applicable method for `@` applied to an object of class "NULL"
  Backtrace:
      ▆
   1. ├─testthat::expect_true("checkId" %in% colnames(modelLmCi[["E1"]]$mRand$t1@frame)) at test-fitTDLme4.R:87:3
   2. │ └─testthat::quasi_label(enquo(object), label)
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─"checkId" %in% colnames(modelLmCi[["E1"]]$mRand$t1@frame)
   5. └─base::colnames(modelLmCi[["E1"]]$mRand$t1@frame)
   6.   └─base::is.data.frame(x)
  ── Failure ('test-fitTDLme4.R:112:3'): Fitting models functions properly when trait contains space ──
  Expected `... <- NULL` to produce messages.
  ── Failure ('test-outliers.R:39:3'): outliersSTA functions properly for multiple traits ──
  Expected `out14$indicator[["E1"]]` to have names `paste0("t", 1:4)`.
  Differences:
  `actual` is NULL
  `expected` is a character vector ('t1', 't2', 't3', 't4')
  
  ── Failure ('test-outliers.R:56:3'): option rLimit funtions properly ───────────
  Expected `out1$indicator[["E1"]][["t1"]]` to have length 6.
  Actual length: 0.
  ── Failure ('test-outliers.R:57:3'): option rLimit funtions properly ───────────
  Expected `nrow(out1$outliers)` to equal 6.
  Differences:
  target is NULL, current is numeric
  ── Failure ('test-outliers.R:58:3'): option rLimit funtions properly ───────────
  Expected `out1$outliers$res` to equal `c(...)`.
  Differences:
  target is NULL, current is numeric
  ── Failure ('test-outliers.R:66:3'): option rLimit funtions properly for multiple traits ──
  Expected `sapply(X = out14$indicator[["E1"]], FUN = length)` to be equivalent to `c(6, 10, 0, 2)`.
  Length mismatch: comparison on first 0 components
  ── Failure ('test-outliers.R:68:3'): option rLimit funtions properly for multiple traits ──
  Expected `nrow(out14$outliers)` to equal 18.
  Differences:
  target is NULL, current is numeric
  ── Failure ('test-outliers.R:74:3'): option commonFactors functions properly ───
  Expected `out1$indicator[["E1"]][["t1"]]` to have length 6.
  Actual length: 0.
  ── Failure ('test-outliers.R:75:3'): option commonFactors functions properly ───
  Expected `nrow(out1$outliers)` to equal 18.
  Differences:
  target is NULL, current is numeric
  ── Failure ('test-outliers.R:76:3'): option commonFactors functions properly ───
  Expected `sum(out1$outliers$outlier)` to equal 6.
  Differences:
  1/1 mismatches
  [1] 0 - 6 == -6
  ── Failure ('test-outliers.R:85:3'): option verbose functions properly ─────────
  Expected `printOut1` to equal "No large standardized residuals.".
  Differences:
  Lengths differ: 0 is not 1
  ── Failure ('test-outliers.R:86:3'): option verbose functions properly ─────────
  Expected `"Large standardized residuals." %in% printOut2` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-outliers.R:87:3'): option verbose functions properly ─────────
  Expected `any(grepl(pattern = "1.082710", x = printOut2))` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 20 | WARN 27 | SKIP 9 | PASS 663 ]
  Error:
  ! Test failures.
  Execution halted