Running ‘testthat.R’ [27s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > #Need to execute the following for manual checking
  > #Sys.setenv(NOT_CRAN = "true")
  > #setwd("~/Analyses/R/asremlPlus/tests/")
  > #test_check("asremlPlus", filter = "3Wheat")
  > #test_check("asremlPlus", filter = "4Wheat")
  > #test_check("asremlPlus", filter = "3")
  > test_check("asremlPlus", filter = "4")
  Loading required package: asremlPlus
  ASReml-R needs to be loaded if the mixed-model functions are to be used.
  
  ASReml-R is available from VSNi. Please visit http://www.vsni.co.uk/ for more information.
  
  #### Test for changeTerms using wheat example with asreml4
  #### Test estimateV for chick pea example with asreml4
  #### Test estimateV for Wheat example with asreml4
  #### Test estimateV specials for Cane with asreml4
  #### Test estimateV specials for HEB25 with asreml4
  #### Test estimateV at, fa, rr functions for MET data with asreml4
  #### Test estimateV str, spl & dev for orange with asreml4
  #### Test for predictions.frame on Oats with asreml4
  #### Test for Intercept prediction on Oats with asreml4
  #### Test for predictPlus.asreml4
  #### Test for plotPredictions.asreml4
  #### Test for predictPresent.asreml4
  #### Test for plotPvalues.asreml4
  #### Test for plotPvalues.asreml4
  #### Test for factor combinations asreml4
  #### Test for recalcLSD.alldiffs4
  #### Test for LSDby4
  #### Test for REMLRT with asreml4
  #### Test for chooseModel.asrtests with asreml4
  #### Test for spline testing with asreml4
  #### Test for reparamSigDevn.asrtests with asreml4
  #### Test for simulate.asreml with asreml4
  #### Test for sort.alldiffs on Smarthouse with asreml4
  #### Test for sort.alldiffs on Oats with asreml4
  #### Test for sort in standard order for classify on Oats with asreml4
  #### Test variofaces using Atieno with asreml4
  #### Test for wheat example with asreml4
  #### Test for allDifferences.data.frame sort.alldiffs on Oats with asreml4
  #### Test for sort.alldiffs on Smarthouse with asreml4
  #### Test for sort.alldiffs on WaterRunoff with asreml4
  #### Test for sort.alldiffs on Oats with asreml4
  #### Test for subset.alldiffs on Smarthouse with asreml4
  #### Test for facCombine.alldiffs on Ladybird with asreml4
  #### Test for linear.transformation on Oats with asreml4
  #### Test for linear.transformation on WaterRunoff with asreml4
  #### Test for predictions.frame on Oats with lme4
  #### Test for allDifferences.data.frame on Oats with lme4
  #### Test for alldiffs validity on Oats with lme4
  #### Test for linTransform on WaterRunoff with lme4
  
  
  #### Predictions for  transform(s) transform(s) from Sources:Species
  
  The original predictions, obtained as described below, have
  been linearly transformed. 
  The original predictions, obtained as described below, have
  been linearly transformed to form estimated marginal means. 
       Combination predicted.value standard.error upper.Confidence.limit
  1 S. iqscjbogxah     -0.04097328     0.07296427              0.1028683
  2 S. oymwjrcnepv     -0.26708439     0.07296427             -0.1232428
  3 S. ocphawvtlgi     -0.30086748     0.07347407             -0.1560209
  4 S. hbpgtylxqku     -0.39587830     0.07338042             -0.2512163
  5 S. orcxszbujml     -0.42885687     0.07309091             -0.2847656
  6 S. xeqackngdrt     -0.49632334     0.11711989             -0.2654334
  7 S. tkujbvipoyr     -0.55659120     0.11715667             -0.3256288
    lower.Confidence.limit est.status
  1             -0.1848149  Estimable
  2             -0.4109260  Estimable
  3             -0.4457141  Estimable
  4             -0.5405403  Estimable
  5             -0.5729481  Estimable
  6             -0.7272132  Estimable
  7             -0.7875536  Estimable
  
  
  LSD values 
  
  minimum LSD =  0.1252489 
  
  mean LSD =  0.1868838 
  
  maximum LSD =  0.2751421 
  
  (sed range / mean sed =  0.802 )
  
  #### Test for alldiffs functions on WaterRunoff with lme4
  ── 1. Error: alldiffs_lme4 (@test4alldiffslme.r#254)  ──────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: plotPvalues(TS.diffs, gridspacing = rep(c(3, 4), c(4, 2)), show.sig = TRUE) at testthat/test4alldiffslme.r:254
  2: plotPvalues.alldiffs(TS.diffs, gridspacing = rep(c(3, 4), c(4, 2)), show.sig = TRUE)
  3: plotPvalues.data.frame(object = p, x = "X1", y = "X2", gridspacing = gridspacing, 
         show.sig = show.sig, triangles = triangles, axis.labels = pairname, colours = colours, 
         ggplotFuncs = ggplotFuncs)
  4: print(plt)
  5: print.ggplot(plt)
  6: ggplot_gtable(data)
  7: ggplot_gtable.ggplot_built(data)
  8: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  9: guides_gengrob(gdefs, theme)
  10: lapply(gdefs, guide_gengrob, theme)
  ...
  19: pushvpgp(x)
  20: pushgrobvp(x$vp)
  21: pushgrobvp.viewport(x$vp)
  22: pushViewport(vp, recording = FALSE)
  23: lapply(vps, push.vp, recording)
  24: FUN(X[[i]], ...)
  25: push.vp.vpTree(X[[i]], ...)
  26: push.vp(vp$parent, recording)
  27: push.vp.viewport(vp$parent, recording)
  28: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  #### Test for sort.alldiffs on Smarthouse with lme4
  #### Test for sort.alldiffs on WateRunoff with lme4
  #### Test for facCombine.alldiffs on Ladybird with lme4
  #### Test for as.predictions.frame on Ladybird with lme4
  ── 2. Error: as.predictions.frame_lme4 (@test4alldiffslme.r#531)  ──────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: testthat::expect_silent(plotPredictions(HCL.preds, y = "predicted.value", "Host:Cadavers:Ladybird")) at testthat/test4alldiffslme.r:531
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: plotPredictions(HCL.preds, y = "predicted.value", "Host:Cadavers:Ladybird")
  10: plotPredictions.data.frame(HCL.preds, y = "predicted.value", "Host:Cadavers:Ladybird")
  ...
  13: ggplot_gtable(data)
  14: ggplot_gtable.ggplot_built(data)
  15: layout$render(geom_grobs, data, theme, plot$labels)
  16: f(..., self = self)
  17: self$facet$draw_panels(panels, self$layout, self$panel_scales_x, self$panel_scales_y, 
         self$panel_params, self$coord, data, theme, self$facet_params)
  18: f(...)
  19: render_strips(col_vars, row_vars, params$labeller, theme)
  20: build_strip(x, labeller, theme, TRUE)
  21: ggstrip(grobs, theme, element, gp, horizontal, clip = "on")
  22: Summary.unit(structure(c(4.4, 4.4), unit = 8L, class = c("margin", "unit")), na.rm = FALSE)
  
  #### Test for boot using wheat example with asreml4
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 80 SKIPPED: 36 FAILED: 2
  1. Error: alldiffs_lme4 (@test4alldiffslme.r#254) 
  2. Error: as.predictions.frame_lme4 (@test4alldiffslme.r#531) 
  
  Error: testthat unit tests failed
  Execution halted