* using log directory 'd:/Rcompile/CRANpkg/local/4.4/bregr.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'bregr/DESCRIPTION' ... OK
* this is package 'bregr' version '1.2.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'bregr' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s] OK
* checking loading without being on the library search path ... [4s] OK
* checking whether startup messages can be suppressed ... [4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [17s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [96s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [130s] ERROR
  Running 'testthat.R' [130s]
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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [94s] OK
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [5s] OK
* DONE
Status: 1 ERROR