Last updated on 2025-09-12 03:50:11 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.0 | 11.64 | 352.82 | 364.46 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.0 | 9.27 | 307.30 | 316.57 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.0 | 619.11 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.0 | 614.81 | OK | |||
| r-devel-windows-x86_64 | 1.2.0 | 13.00 | 301.00 | 314.00 | OK | |
| r-patched-linux-x86_64 | 1.2.0 | 13.34 | 334.46 | 347.80 | OK | |
| r-release-linux-x86_64 | 1.2.0 | 10.97 | 342.38 | 353.35 | OK | |
| r-release-macos-arm64 | 1.2.0 | 168.00 | OK | |||
| r-release-macos-x86_64 | 1.2.0 | 302.00 | OK | |||
| r-release-windows-x86_64 | 1.2.0 | 13.00 | 310.00 | 323.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.0 | 171.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.2.0 | 313.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.2.0 | 18.00 | 413.00 | 431.00 | OK |
Version: 1.2.0
Check: tests
Result: ERROR
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
Flavor: r-devel-linux-x86_64-fedora-clang