Last updated on 2026-10-24 06:51:06 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.5 | 13.45 | 123.36 | 136.81 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.5 | 9.77 | 83.55 | 93.32 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.5 | 11.00 | 82.37 | 93.37 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.1.5 | 10.00 | 75.98 | 85.98 | OK | |
| r-devel-windows-x86_64 | 1.1.5 | 17.00 | 128.00 | 145.00 | OK | |
| r-patched-linux-x86_64 | 1.1.5 | 14.74 | 110.94 | 125.68 | OK | |
| r-release-linux-x86_64 | 1.1.5 | 14.23 | 111.28 | 125.51 | OK | |
| r-release-macos-arm64 | 1.1.5 | 4.00 | 28.00 | 32.00 | OK | |
| r-release-macos-x86_64 | 1.1.5 | 10.00 | 144.00 | 154.00 | OK | |
| r-release-windows-x86_64 | 1.1.5 | 16.00 | 119.00 | 135.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.5 | OK | ||||
| r-oldrel-macos-x86_64 | 1.1.5 | 8.00 | 86.00 | 94.00 | OK | |
| r-oldrel-windows-x86_64 | 1.1.5 | 22.00 | 158.00 | 180.00 | OK |
Version: 1.1.5
Check: examples
Result: ERROR
Running examples in ‘basecamb-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cox.zph.mids
> ### Title: Test cox proportional odds assumption on models using multiple
> ### imputation.
> ### Aliases: cox.zph.mids
>
> ### ** Examples
>
> data <- data.frame(time = 101:200, status = rep(c(0,1), 50), pred = rep(c(1:9, NA), 10))
> imputed_data <- mice::mice(data)
iter imp variable
1 1 pred
1 2 pred
1 3 pred
1 4 pred
1 5 pred
2 1 pred
2 2 pred
2 3 pred
2 4 pred
2 5 pred
3 1 pred
3 2 pred
3 3 pred
3 4 pred
3 5 pred
4 1 pred
4 2 pred
4 3 pred
4 4 pred
4 5 pred
5 1 pred
5 2 pred
5 3 pred
5 4 pred
5 5 pred
> cox_mod <- Hmisc::fit.mult.impute(survival::Surv(time, status) ~ pred,
+ fitter = rms::cph, xtrans = imputed_data)
Wald Statistic Information
Variance Inflation Factors Due to Imputation:
pred
1.07
Fraction of Missing Information:
pred
0.07
d.f. for t-distribution for Tests of Single Coefficients:
pred
917.21
The following fit components were averaged over the 5 model fits:
linear.predictors means stats center
> cox.zph.mids(cox_mod, imputed_data)
Error in a$specials[[i]] : subscript out of bounds
Calls: cox.zph.mids ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(basecamb)
>
> test_check("basecamb")
iter imp variable
1 1 pred
1 2 pred
1 3 pred
1 4 pred
1 5 pred
2 1 pred
2 2 pred
2 3 pred
2 4 pred
2 5 pred
3 1 pred
3 2 pred
3 3 pred
3 4 pred
3 5 pred
4 1 pred
4 2 pred
4 3 pred
4 4 pred
4 5 pred
5 1 pred
5 2 pred
5 3 pred
5 4 pred
5 5 pred
Wald Statistic Information
Variance Inflation Factors Due to Imputation:
pred
1.07
Fraction of Missing Information:
pred
0.07
d.f. for t-distribution for Tests of Single Coefficients:
pred
917.21
The following fit components were averaged over the 5 model fits:
linear.predictors means stats center
Saving _problems/test_cox.zph.mids-11.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_cox.zph.mids.R:11:3'): cox.zph.mids handles cases correctly ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─basecamb::cox.zph.mids(cox_mod, imputed_data, verbose = FALSE) at test_cox.zph.mids.R:11:3
2. └─survival::cox.zph(cox_mod)
3. └─survival:::coxph.getdata(...)
4. ├─stats::model.matrix(fit, data = mf)
5. └─survival:::model.matrix.coxph(fit, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc