Last updated on 2025-12-06 00:48:34 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.0 | 14.50 | 381.94 | 396.44 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.0 | 9.68 | 188.65 | 198.33 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.0 | 27.00 | 559.94 | 586.94 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.3.0 | 25.00 | 546.13 | 571.13 | OK | |
| r-devel-windows-x86_64 | 1.3.0 | 14.00 | 328.00 | 342.00 | OK | |
| r-patched-linux-x86_64 | 1.3.0 | 13.18 | 367.30 | 380.48 | OK | |
| r-release-linux-x86_64 | 1.3.0 | 13.39 | 367.07 | 380.46 | OK | |
| r-release-macos-arm64 | 1.3.0 | OK | ||||
| r-release-macos-x86_64 | 1.3.0 | 12.00 | 323.00 | 335.00 | OK | |
| r-release-windows-x86_64 | 1.3.0 | 15.00 | 326.00 | 341.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.0 | OK | ||||
| r-oldrel-macos-x86_64 | 1.3.0 | 14.00 | 351.00 | 365.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.0 | 20.00 | 470.00 | 490.00 | OK |
Version: 1.3.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'ggstatsplot', 'gtsummary', 'knitr', 'lme4', 'merDeriv', 'qs',
'rmarkdown', 'UCSCXenaShiny'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.0
Check: examples
Result: ERROR
Running examples in ‘bregr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: br_show_forest_ggstatsplot
> ### Title: Show a forest plot with 'ggstatsplot' interface
> ### Aliases: br_show_forest_ggstatsplot
>
> ### ** Examples
>
> if (rlang::is_installed("ggstats")) {
+ m <- br_pipeline(mtcars,
+ y = "mpg",
+ x = colnames(mtcars)[2:4],
+ x2 = "vs",
+ method = "gaussian"
+ )
+ br_show_forest_ggstatsplot(m)
+ }
Error in br_show_forest_ggstatsplot(m) :
The package "ggstatsplot" is required.
Calls: br_show_forest_ggstatsplot -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [85s/86s]
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 1.3.0
Project home : https://github.com/WangLabCSU/bregr
Documentation: https://wanglabcsu.github.io/bregr/
Cite as : https://doi.org/10.1002/mdr2.70028
Wang, S., Peng, Y., Shu, C., Wang, C., Yang, Y., Zhao, Y., Cui, Y., Hu, D. and Zhou, J.-G. (2025),
bregr: An R Package for Streamlined Batch Processing and Visualization of Biomedical Regression Models. Med Research.
=======================================================================
>
> 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
Saving _problems/test-roxytest-testexamples-04-show-45.R
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 1 | 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 ════════════════════════════════════════════════════════════════
── Error ('test-roxytest-testexamples-04-show.R:45:5'): Function br_show_forest_ggstatsplot() @ L344 ──
<rlib_error_package_not_found/rlang_error/error/condition>
Error in `br_show_forest_ggstatsplot(m)`: The package "ggstatsplot" is required.
Backtrace:
▆
1. └─bregr::br_show_forest_ggstatsplot(m) at test-roxytest-testexamples-04-show.R:45:5
2. └─rlang::check_installed("ggstatsplot")
[ FAIL 1 | WARN 1 | SKIP 6 | PASS 112 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.0
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc