Running ‘testthat.R’ [170s/383s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(bregr)
  Welcome to 'bregr' package!
  =======================================================================
  You are using bregr version 1.2.0
  
  Project home : https://github.com/WangLabCSU/bregr
  Documentation: https://wanglabcsu.github.io/bregr/
  Cite as      : arXiv:2110.14232
  =======================================================================
                   
  > 
  > test_check("bregr")
  filtered variables: "x2" and "x3"
  filtered variables: "x2"
  Pre-filtering removed 2 out of 2 focal variables (100%)
  filtered variables: "x1" and "x2"
  filtered variables: "x2"
  filtered variables: "x2"
  exponentiate estimates of model(s) constructed from coxph method at default
  `idx` not set, use the first model
  Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models)
  `idx` not set, use the first model
  Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models)
  Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models)
  `idx` not set, use the first model
  `idx` not set, use the first model
  `idx` not set, use the first model
  exponentiate estimates of model(s) constructed from coxph method at default
  exponentiate estimates of model(s) constructed from coxph method at default
  `idx` not set, use the first model
  Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models)
  Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models)
  `idx` not set, use the first model
  exponentiate estimates of model(s) constructed from coxph method at default
  `idx` not set, use the first model
  `type` is not specified, use lp for the model
  exponentiate estimates of model(s) constructed from coxph method at default
  `idx` not set, use the first model
  `idx` not set, use the first model
  `type` is not specified, use response for the model
  `idx` not set, use the first model
  subset model list with idx: 1
  model call: stats::glm(formula = mpg ~ cyl + vs, family = stats::gaussian, data = data)
  model call: stats::glm(formula = mpg ~ cyl + vs, family = stats::gaussian, data = data)
  exponentiate estimates of model(s) constructed from coxph method at default
  exponentiate estimates of model(s) constructed from coxph method at default
  `idx` not set, use the first model
  Cox model: intercept term present but no intercept coefficient (as expected for semi-parametric models)
  `idx` not set, use the first model
  exponentiate estimates of model(s) constructed from coxph method at default
  please note only continuous focal terms analyzed and visualized
  exponentiate estimates of model(s) constructed from coxph method at default
  
  -- Model Diagnostics Summary ---------------------------------------------------
  
  -- Model: "ph.ecog" (coxph) --
  
  Sample size: 227
  Events: 164
  Log-likelihood: -729.23
  Concordance: 12544, 7117, 126, 28, 0, 0.637, and 0.025
  
  Proportional Hazards Test (Schoenfeld Residuals):
  + ph.ecog: χ² = 2.054, df = 1, p = 0.152
  + age: χ² = 0.188, df = 1, p = 0.665
  + sex: χ² = 2.305, df = 1, p = 0.129
  Global test: p = 0.216 - Assumption + SATISFIED
  
  
  -- Model: "ph.karno" (coxph) --
  
  Sample size: 227
  Events: 164
  Log-likelihood: -735.078
  Concordance: 12578, 7145, 65, 28, 0, 0.637, and 0.025
  
  Proportional Hazards Test (Schoenfeld Residuals):
  x ph.karno: χ² = 8.017, df = 1, p = 0.00463
  + age: χ² = 0.478, df = 1, p = 0.489
  + sex: χ² = 3.085, df = 1, p = 0.079
  Global test: p = 0.0157 - Assumption x VIOLATED
  
  
  -- Model: "pat.karno" (coxph) --
  
  Sample size: 225
  Events: 162
  Log-likelihood: -721.587
  Concordance: 12343, 6957, 57, 26, 0, 0.639, and 0.025
  
  Proportional Hazards Test (Schoenfeld Residuals):
  x pat.karno: χ² = 4.226, df = 1, p = 0.0398
  + age: χ² = 0.054, df = 1, p = 0.817
  + sex: χ² = 2.752, df = 1, p = 0.0971
  Global test: p = 0.0819 - Assumption + SATISFIED
  
  
  -- Model: "meal.cal" (coxph) --
  
  Sample size: 181
  Events: 134
  Log-likelihood: -573.568
  Concordance: 7761, 5080, 7, 17, 0, 0.604, and 0.029
  
  Proportional Hazards Test (Schoenfeld Residuals):
  x meal.cal: χ² = 4.65, df = 1, p = 0.031
  + age: χ² = 0.622, df = 1, p = 0.43
  + sex: χ² = 1.481, df = 1, p = 0.224
  Global test: p = 0.0942 - Assumption + SATISFIED
  
  
  -- Model: "wt.loss" (coxph) --
  
  Sample size: 214
  Events: 152
  Log-likelihood: -673.056
  Concordance: 10531, 6672, 10, 22, 0, 0.612, and 0.027
  
  Proportional Hazards Test (Schoenfeld Residuals):
  + wt.loss: χ² = 0.014, df = 1, p = 0.904
  + age: χ² = 0.508, df = 1, p = 0.476
  + sex: χ² = 2.549, df = 1, p = 0.11
  Global test: p = 0.391 - Assumption + SATISFIED
  
  exponentiate estimates of model(s) constructed from coxph method at default
  `idx` not set, use the first model
  `idx` not set, use the first model
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 112 ]
  
  ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-nomogram-interactions.R:2:3'
  • empty test (5): 'test-roxytest-testexamples-02-pipeline.R:5:1',
    'test-roxytest-testexamples-03-accessors.R:5:1',
    'test-roxytest-testexamples-04-show.R:5:1',
    'test-roxytest-testexamples-04-show.R:201:1',
    'test-roxytest-testexamples-05-polar.R:5:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-roxytest-testexamples-04-show.R:106:3'): Function br_show_coxph_diagnostics() @ L478 ──
  `p1` inherits from 'ggalign::AlignPatches'/'S7_object' not 'alignpatches'.
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 112 ]
  Error: Test failures
  Execution halted