Running ‘spelling.R’
  Running ‘testthat.R’ [110s/239s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(Colossus)
  > 
  > test_check("Colossus")
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  [ FAIL 83 | WARN 12 | SKIP 15 | PASS 777 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • Cran Skip (15): 'test-Assigned.R:74:5', 'test-CoxRegression.R:215:5',
    'test-Logbound.R:24:5', 'test-Logbound.R:110:5', 'test-Logbound.R:161:5',
    'test-Logbound.R:203:5', 'test-Logbound.R:251:5', 'test-Logbound.R:329:5',
    'test-Logbound.R:357:5', 'test-Omnibus.R:21:5', 'test-Omnibus.R:67:5',
    'test-Omnibus.R:147:5', 'test-Omnibus.R:214:5', 'test-Omnibus.R:256:5',
    'test-Omnibus.R:453:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-CaseControl.R:72:11'): threshold nonfail ─────────────────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 62.1
  `expected`: 63.5
  
  ── Failure ('test-CaseControl.R:72:11'): threshold nonfail ─────────────────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 62.1
  `expected`: 63.5
  
  ── Failure ('test-CaseControl.R:72:11'): threshold nonfail ─────────────────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 62.1
  `expected`: 63.5
  
  ── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 2383.2
  `expected`: 2365.3
  
  ── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 1472.9
  `expected`:  895.6
  
  ── Failure ('test-CaseControl.R:223:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 661.6
  `expected`: 662.9
  
  ── Failure ('test-CaseControl.R:261:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 134.5
  `expected`:  68.7
  
  ── Failure ('test-CaseControl.R:261:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 71.6
  `expected`: 63.5
  
  ── Failure ('test-CaseControl.R:261:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 113.6
  `expected`:  57.4
  
  ── Failure ('test-CaseControl.R:280:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`:  67.0
  `expected`: 113.1
  
  ── Failure ('test-CaseControl.R:280:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 128.3
  `expected`:  70.0
  
  ── Failure ('test-CaseControl.R:280:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 66.5
  `expected`: 63.3
  
  ── Failure ('test-CaseControl.R:280:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 95.8
  `expected`: 70.0
  
  ── Failure ('test-CaseControl.R:280:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 62.252
  `expected`: 62.188
  
  ── Failure ('test-CaseControl.R:280:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`: 62.94
  `expected`: 63.29
  
  ── Failure ('test-CaseControl.R:280:13'): threshold nonfail, gradient ──────────
  Expected `e$Deviation` to equal `devs[i_index]`.
  Differences:
    `actual`:  67.0
  `expected`: 113.1
  
  ── Failure ('test-CaseControl.R:342:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[1]` to equal `model0_sdo[i_index]`.
  Differences:
    `actual`: 0.0116
  `expected`: 0.0140
  
  ── Failure ('test-CaseControl.R:343:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model0_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.394
  `expected`: 0.490
  
  ── Failure ('test-CaseControl.R:344:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model0_sde[i_index]`.
  Differences:
    `actual`: 0.01418
  `expected`: 0.01403
  
  ── Failure ('test-CaseControl.R:345:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model0_sde[i_index + 1]`.
  Differences:
    `actual`: 0.4956
  `expected`: 0.4901
  
  ── Failure ('test-CaseControl.R:349:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[1]` to equal `model1_sdo[i_index]`.
  Differences:
    `actual`: 0.0098
  `expected`: 0.0138
  
  ── Failure ('test-CaseControl.R:350:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model1_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.32
  `expected`: 0.43
  
  ── Failure ('test-CaseControl.R:351:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model1_sde[i_index]`.
  Differences:
    `actual`: 0.0152
  `expected`: 0.0141
  
  ── Failure ('test-CaseControl.R:352:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model1_sde[i_index + 1]`.
  Differences:
    `actual`: 0.517
  `expected`: 0.482
  
  ── Failure ('test-CaseControl.R:358:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model2_sde[i_index]`.
  Differences:
    `actual`: 0.0033
  `expected`: 0.0047
  
  ── Failure ('test-CaseControl.R:359:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model2_sde[i_index + 1]`.
  Differences:
    `actual`: 0.098
  `expected`: 0.138
  
  ── Failure ('test-CaseControl.R:365:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model3_sde[i_index]`.
  Differences:
    `actual`: 0.00470
  `expected`: 0.00425
  
  ── Failure ('test-CaseControl.R:366:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model3_sde[i_index + 1]`.
  Differences:
    `actual`: 0.114
  `expected`: 0.149
  
  ── Failure ('test-CaseControl.R:344:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model0_sde[i_index]`.
  Differences:
    `actual`: 0.0145
  `expected`: 0.0205
  
  ── Failure ('test-CaseControl.R:345:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model0_sde[i_index + 1]`.
  Differences:
    `actual`: 0.41
  `expected`: 0.57
  
  ── Failure ('test-CaseControl.R:350:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model1_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.39616
  `expected`: 0.39577
  
  ── Failure ('test-CaseControl.R:351:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model1_sde[i_index]`.
  Differences:
    `actual`: 0.0145
  `expected`: 0.0205
  
  ── Failure ('test-CaseControl.R:352:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model1_sde[i_index + 1]`.
  Differences:
    `actual`: 0.28
  `expected`: 0.40
  
  ── Failure ('test-CaseControl.R:363:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[1]` to equal `model3_sdo[i_index]`.
  Differences:
    `actual`: 0.0039
  `expected`: 0.0056
  
  ── Failure ('test-CaseControl.R:364:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model3_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.114
  `expected`: 0.161
  
  ── Failure ('test-CaseControl.R:365:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model3_sde[i_index]`.
  Differences:
    `actual`: 0.0039
  `expected`: 0.0056
  
  ── Failure ('test-CaseControl.R:366:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model3_sde[i_index + 1]`.
  Differences:
    `actual`: 0.114
  `expected`: 0.161
  
  ── Failure ('test-CaseControl.R:349:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[1]` to equal `model1_sdo[i_index]`.
  Differences:
    `actual`: 0.0164
  `expected`: 0.0232
  
  ── Failure ('test-CaseControl.R:350:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model1_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.36
  `expected`: 0.51
  
  ── Failure ('test-CaseControl.R:351:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model1_sde[i_index]`.
  Differences:
    `actual`: 0.0164
  `expected`: 0.0232
  
  ── Failure ('test-CaseControl.R:352:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model1_sde[i_index + 1]`.
  Differences:
    `actual`: 0.36
  `expected`: 0.51
  
  ── Failure ('test-CaseControl.R:358:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model2_sde[i_index]`.
  Differences:
    `actual`: 0.0039
  `expected`: 0.0056
  
  ── Failure ('test-CaseControl.R:359:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model2_sde[i_index + 1]`.
  Differences:
    `actual`: 0.143
  `expected`: 0.202
  
  ── Failure ('test-CaseControl.R:363:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[1]` to equal `model3_sdo[i_index]`.
  Differences:
    `actual`: 0.0039
  `expected`: 0.0056
  
  ── Failure ('test-CaseControl.R:364:7'): information matrix calculations ───────
  Expected `eo$Standard_Deviation[2]` to equal `model3_sdo[i_index + 1]`.
  Differences:
    `actual`: 0.114
  `expected`: 0.161
  
  ── Failure ('test-CaseControl.R:365:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[1]` to equal `model3_sde[i_index]`.
  Differences:
    `actual`: 0.0039
  `expected`: 0.0056
  
  ── Failure ('test-CaseControl.R:366:7'): information matrix calculations ───────
  Expected `ee$Standard_Deviation[2]` to equal `model3_sde[i_index + 1]`.
  Differences:
    `actual`: 0.114
  `expected`: 0.161
  
  ── Failure ('test-CoxPlot.R:211:5'): Coxph risk no error ───────────────────────
  Expected `ep$"y:lower"[7]` to equal 0.01537157.
  Differences:
    `actual`: 0.044
  `expected`: 0.015
  
  ── Failure ('test-CoxPlot.R:212:5'): Coxph risk no error ───────────────────────
  Expected `ep$"y:upper"[7]` to equal 19.59424.
  Differences:
    `actual`:  6.9
  `expected`: 19.6
  
  ── Failure ('test-CoxRegression.R:153:3'): Coxph loglin_M Single ───────────────
  Expected `e$AIC` to equal 1056.299.
  Differences:
    `actual`: 2108.6
  `expected`: 1056.3
  
  ── Failure ('test-Formula.R:231:3'): Checking model and formula can be input ───
  Expected `e0$beta_0` to equal `e1$beta_0`.
  Differences:
    `actual`: 0.69901 -0.41653
  `expected`: 0.69833 -0.41604
  
  ── Failure ('test-Formula.R:519:3'): Multiplicative model check ────────────────
  Expected `res0$beta_0` to equal `res1$beta_0`.
  Differences:
    `actual`: -0.869 -0.069
  `expected`: -0.741 -0.069
  
  ── Failure ('test-Gradient.R:64:3'): Coxph gradient methods ────────────────────
  Expected `e3$beta_0` to equal `c(0.6594536, 0.7276018)`.
  Differences:
    `actual`: 0.6655 0.7311
  `expected`: 0.6595 0.7276
  
  ── Failure ('test-Multidose.R:41:3'): Coxph multidose ──────────────────────────
  Expected `LL_comp_1[k]` to equal `val[1]`.
  Differences:
    `actual`: -450.7
  `expected`: -901.4
  
  ── Failure ('test-Multidose.R:42:3'): Coxph multidose ──────────────────────────
  Expected `LL_comp_2[k]` to equal `val[2]`.
  Differences:
    `actual`: -449.5
  `expected`: -899.1
  
  ── Failure ('test-Multidose.R:43:3'): Coxph multidose ──────────────────────────
  Expected `LL_comp_3[k]` to equal `val[3]`.
  Differences:
    `actual`: -450.9
  `expected`: -901.7
  
  ── Failure ('test-Multidose.R:125:3'): Coxph multidose negative shift check ────
  Expected `c(-450.724, -449.4633, -449.4633)` to equal `val`.
  Differences:
    `actual`: -450.7 -449.5 -449.5
  `expected`: -901.4 -898.9 -898.9
  
  ── Failure ('test-Multidose.R:316:3'): Coxph multidose MCML repeated column ────
  Expected `e0$LogLik` to equal `e1$LogLik`.
  Differences:
    `actual`: -901.4
  `expected`: -450.7
  
  ── Failure ('test-Multidose.R:388:3'): Coxph multidose MCML swapped columns ────
  Expected `e0$LogLik` to equal `e1$LogLik`.
  Differences:
    `actual`: -453.9
  `expected`: -907.9
  
  ── Failure ('test-Norm.R:58:7'): Checking values converted back ────────────────
  Expected `res$First_Der` to equal `res_max$First_Der`.
  Differences:
    `actual`: -5824.3 13.5
  `expected`: -2912.1  6.7
  
  ── Failure ('test-Norm.R:59:7'): Checking values converted back ────────────────
  Expected `res$First_Der` to equal `res_mean$First_Der`.
  Differences:
    `actual`: -5824.3 13.5
  `expected`: -2912.1  6.7
  
  ── Failure ('test-Norm.R:61:7'): Checking values converted back ────────────────
  Expected `res$Second_Der` to equal `res_max$Second_Der`.
  Differences:
  actual vs expected
                          [,1]      [,2]
  - actual[1, ]   -18207.72716 167.42157
  + expected[1, ]  -9103.86358  83.71079
  - actual[2, ]      167.42157 -42.35621
  + expected[2, ]     83.71079 -21.17810
  
  ── Failure ('test-Norm.R:62:7'): Checking values converted back ────────────────
  Expected `res$Second_Der` to equal `res_mean$Second_Der`.
  Differences:
  actual vs expected
                          [,1]      [,2]
  - actual[1, ]   -18207.72716 167.42157
  + expected[1, ]  -9103.86358  83.71079
  - actual[2, ]      167.42157 -42.35621
  + expected[2, ]     83.71079 -21.17810
  
  ── Failure ('test-Norm.R:67:7'): Checking values converted back ────────────────
  Expected `res$Standard_Deviation` to equal `res_max$Standard_Deviation`.
  Differences:
    `actual`: 0.008 0.157
  `expected`: 0.011 0.221
  
  ── Failure ('test-Norm.R:68:7'): Checking values converted back ────────────────
  Expected `res$Standard_Deviation` to equal `res_mean$Standard_Deviation`.
  Differences:
    `actual`: 0.008 0.157
  `expected`: 0.011 0.221
  
  ── Failure ('test-Norm.R:70:7'): Checking values converted back ────────────────
  Expected `res$Covariance` to equal `res_max$Covariance`.
  Differences:
  actual vs expected
                          [,1]         [,2]
  - actual[1, ]   5.699318e-05 0.0002252772
  + expected[1, ] 1.139864e-04 0.0004505544
  - actual[2, ]   2.252772e-04 0.0244997438
  + expected[2, ] 4.505544e-04 0.0489994876
  
  ── Failure ('test-Norm.R:71:7'): Checking values converted back ────────────────
  Expected `res$Covariance` to equal `res_mean$Covariance`.
  Differences:
  actual vs expected
                          [,1]         [,2]
  - actual[1, ]   5.699318e-05 0.0002252772
  + expected[1, ] 1.139864e-04 0.0004505544
  - actual[2, ]   2.252772e-04 0.0244997438
  + expected[2, ] 4.505544e-04 0.0489994876
  
  ── Failure ('test-Norm.R:58:7'): Checking values converted back ────────────────
  Expected `res$First_Der` to equal `res_max$First_Der`.
  Differences:
    `actual`: 1609.4  -7.6
  `expected`: 3218.9 -15.2
  
  ── Failure ('test-Norm.R:59:7'): Checking values converted back ────────────────
  Expected `res$First_Der` to equal `res_mean$First_Der`.
  Differences:
    `actual`: 1609.4  -7.6
  `expected`: 3218.9 -15.2
  
  ── Failure ('test-Norm.R:61:7'): Checking values converted back ────────────────
  Expected `res$Second_Der` to equal `res_max$Second_Der`.
  Differences:
  actual vs expected
                          [,1]      [,2]
  - actual[1, ]   -15427.13303 -13.38645
  + expected[1, ] -30854.26606 -26.77289
  - actual[2, ]      -13.38645 -19.27044
  + expected[2, ]    -26.77289 -38.54087
  
  ── Failure ('test-Norm.R:62:7'): Checking values converted back ────────────────
  Expected `res$Second_Der` to equal `res_mean$Second_Der`.
  Differences:
  actual vs expected
                          [,1]      [,2]
  - actual[1, ]   -15427.13303 -13.38645
  + expected[1, ] -30854.26606 -26.77289
  - actual[2, ]      -13.38645 -19.27044
  + expected[2, ]    -26.77289 -38.54087
  
  ── Failure ('test-Norm.R:67:7'): Checking values converted back ────────────────
  Expected `res$Standard_Deviation` to equal `res_max$Standard_Deviation`.
  Differences:
    `actual`: 0.008 0.228
  `expected`: 0.006 0.161
  
  ── Failure ('test-Norm.R:68:7'): Checking values converted back ────────────────
  Expected `res$Standard_Deviation` to equal `res_mean$Standard_Deviation`.
  Differences:
    `actual`: 0.008 0.228
  `expected`: 0.006 0.161
  
  ── Failure ('test-Norm.R:58:7'): Checking values converted back ────────────────
  Expected `res$First_Der` to equal `res_max$First_Der`.
  Differences:
    `actual`: -1999.71 -0.62
  `expected`: -3999.42 -1.24
  
  ── Failure ('test-Norm.R:61:7'): Checking values converted back ────────────────
  Expected `res$Second_Der` to equal `res_max$Second_Der`.
  Differences:
  actual vs expected
                          [,1]      [,2]
  - actual[1, ]   -20288.73225  89.01072
  + expected[1, ] -40577.46450 178.02145
  - actual[2, ]       89.01072 -24.61887
  + expected[2, ]    178.02145 -49.23774
  
  ── Failure ('test-Norm.R:67:7'): Checking values converted back ────────────────
  Expected `res$Standard_Deviation` to equal `res_max$Standard_Deviation`.
  Differences:
    `actual`: 0.007 0.203
  `expected`: 0.005 0.144
  
  ── Failure ('test-Norm.R:92:3'): Checking values converted back ────────────────
  Expected `res$First_Der` to equal `res_max$First_Der`.
  Differences:
    `actual`:  -6.73 -18.40 -0.16
  `expected`: -13.46 -36.80 -0.31
  
  ── Failure ('test-Norm.R:172:5'): Checking likelihood bound ────────────────────
  Expected `bound$Parameter_Limits` to equal `bound_max$Parameter_Limits`.
  Differences:
    `actual`: -0.047 -0.025
  `expected`: -0.099 -0.004
  
  ── Failure ('test-Norm.R:173:5'): Checking likelihood bound ────────────────────
  Expected `bound$Parameter_Limits` to equal `bound_mean$Parameter_Limits`.
  Differences:
    `actual`: -0.0465 -0.0249
  `expected`: -0.0464 -0.0249
  
  ── Failure ('test-Omnibus.R:366:3'): check deviation calc, expected cox ────────
  Expected `devs` to equal `c(...)`.
  Differences:
    `actual`: 0.43448 0.38255 0.52225 0.95015 0.45005 0.39804 0.73815 0.97195
  `expected`: 0.61445 0.54101 0.73858 0.95015 0.63646 0.56292 0.73815 0.97195
  
  ── Failure ('test-Omnibus.R:432:3'): check deviation calc, Observed cox ────────
  Expected `devs` to equal `c(...)`.
  Differences:
    `actual[1:4]`: 0.43072 0.53567 0.73858 0.94481
  `expected[1:4]`: 0.60913 0.53567 0.73858 0.94481
  
    `actual[5:8]`: 0.70515 0.58386 0.73815 0.69986
  `expected[5:8]`: 0.70515 0.58386 0.73815 0.98975
  
  ── Failure ('test-Utility.R:170:3'): Improve Ratio test ────────────────────────
  Expected `val$Difference` to equal 2.200062.
  Differences:
    `actual`: 6.4
  `expected`: 2.2
  
  ── Failure ('test-Utility.R:171:3'): Improve Ratio test ────────────────────────
  Expected `val$"p value"` to equal 0.5319362.
  Differences:
    `actual`: 0.10
  `expected`: 0.53
  
  
  [ FAIL 83 | WARN 12 | SKIP 15 | PASS 777 ]
  Error:
  ! Test failures.
  Execution halted