Running ‘testthat.R’ [33s/36s]
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 error when no predictions.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 wheat76 example with asreml4
  #### Test for IC with wheat94 using asreml4
  #### Test for getFormulae with wheat94 using asreml4
  #### Test for chooseModel.data.frame with asreml4
  #### Test for chooseModel.asrtests with asreml4
  #### Test for testing at terms with asreml4
  #### Test for testing MET at terms with asreml4
  #### Test for at terms in testswapran with asreml4
  #### Test for spline testing with asreml4
  #### Test for reparamSigDevn.asrtests with asreml4
  #### Test for changeModelOnIC with wheat94 using asreml4
  #### Test for changeModelOnIC example using 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 wheat76 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 addBacktransforms 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
  #### Test for alldiffs functions on WaterRunoff with lme4
  #### 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
  #### Test for addBacktransforms on WaterRunoff with lme4
  #### Test for boot using wheat example with asreml4
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  ● On CRAN (1)
  ● asreml cannot be loaded (47)
  
  ══ Warnings ════════════════════════════════════════════════════════════════════
  ── Warning (???): linTransform_lme4 ────────────────────────────────────────────
  qr2rankMatrix(.): QR has negative diag(R) entries
  Backtrace:
   1. lme4::lFormula(...)
   2. lme4:::chkRank.drop.cols(X, kind = rankX.chk, tol = 1e-07)
   3. Matrix::rankMatrix(X, tol = tol, method = method)
   5. Matrix::qr2rankMatrix(q.r, tol = tol, isBqr = x.dense, do.warn = warn.qr)
  ── Warning (???): alldiffs_lme4 ────────────────────────────────────────────────
  qr2rankMatrix(.): QR has negative diag(R) entries
  Backtrace:
   1. lme4::lFormula(...)
   2. lme4:::chkRank.drop.cols(X, kind = rankX.chk, tol = 1e-07)
   3. Matrix::rankMatrix(X, tol = tol, method = method)
   5. Matrix::qr2rankMatrix(q.r, tol = tol, isBqr = x.dense, do.warn = warn.qr)
  ── Warning (???): sort.alldiffsWater_lme4 ──────────────────────────────────────
  qr2rankMatrix(.): QR has negative diag(R) entries
  Backtrace:
   1. lme4::lFormula(...)
   2. lme4:::chkRank.drop.cols(X, kind = rankX.chk, tol = 1e-07)
   3. Matrix::rankMatrix(X, tol = tol, method = method)
   5. Matrix::qr2rankMatrix(q.r, tol = tol, isBqr = x.dense, do.warn = warn.qr)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (???): linTransform_lme4 ──────────────────────────────────────────────
  Error: Dropping columns failed to produce full column rank design matrix
  Backtrace:
      █
   1. └─lme4::lFormula(...)
   2.   └─lme4:::chkRank.drop.cols(X, kind = rankX.chk, tol = 1e-07)
  ── Error (???): alldiffs_lme4 ──────────────────────────────────────────────────
  Error: Dropping columns failed to produce full column rank design matrix
  Backtrace:
      █
   1. └─lme4::lFormula(...)
   2.   └─lme4:::chkRank.drop.cols(X, kind = rankX.chk, tol = 1e-07)
  ── Error (???): sort.alldiffsWater_lme4 ────────────────────────────────────────
  Error: Dropping columns failed to produce full column rank design matrix
  Backtrace:
      █
   1. └─lme4::lFormula(...)
   2.   └─lme4:::chkRank.drop.cols(X, kind = rankX.chk, tol = 1e-07)
  
  [ FAIL 3 | WARN 3 | SKIP 48 | PASS 57 ]
  Error: Test failures
  Execution halted