Last updated on 2026-10-24 01:51:48 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 2.03 | 32.80 | 34.83 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 1.85 | 25.30 | 27.15 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 26.85 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 22.14 | OK | |||
| r-devel-windows-x86_64 | 0.1.0 | 5.00 | 54.00 | 59.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 2.16 | 27.97 | 30.13 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 1.41 | 28.43 | 29.84 | OK | |
| r-release-macos-arm64 | 0.1.0 | 1.00 | 12.00 | 13.00 | OK | |
| r-release-macos-x86_64 | 0.1.0 | 2.00 | 48.00 | 50.00 | OK | |
| r-release-windows-x86_64 | 0.1.0 | 5.00 | 50.00 | 55.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | OK | ||||
| r-oldrel-macos-x86_64 | 0.1.0 | 2.00 | 44.00 | 46.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.0 | 6.00 | 55.00 | 61.00 | OK |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘survC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_risk_score
> ### Title: Compute risk scores from a fitted survival model
> ### Aliases: calc_risk_score
>
> ### ** Examples
>
> if (requireNamespace("survival", quietly = TRUE)) {
+ fit <- survival::coxph(survival::Surv(time, status) ~ age, data = survival::lung)
+ # Linear predictor on the training data
+ calc_risk_score(fit)
+
+ # Risk scale predictions on new data
+ calc_risk_score(fit, survival::lung, type = "risk")
+ }
Error in a$specials[[i]] : subscript out of bounds
Calls: calc_risk_score ... <Anonymous> -> predict.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(survC)
>
> test_check("survC")
Saving _problems/test-calc_risk_score-12.R
Saving _problems/test-calc_risk_score-24.R
Saving _problems/test-cindex_calc-37.R
Attaching package: 'timeROC'
The following object is masked from 'package:testthat':
compare
Saving _problems/test-tdroc_calc-19.R
Saving _problems/test-tdroc_calc-46.R
Saving _problems/test-validation_report-47.R
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-calc_risk_score.R:9:3'): calc_risk_score matches predict() on training data ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-calc_risk_score.R:9:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─survC::calc_risk_score(model)
5. ├─stats::predict(...)
6. └─survival:::predict.coxph(...)
7. └─stats::delete.response(Terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-calc_risk_score.R:21:3'): calc_risk_score supports risk scale and newdata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-calc_risk_score.R:21:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─survC::calc_risk_score(model, type = "risk")
5. ├─stats::predict(...)
6. └─survival:::predict.coxph(...)
7. └─stats::delete.response(Terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-cindex_calc.R:37:3'): cindex_calc accepts newdata and returns bounded result ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─survC::cindex_calc(cox_model, newdata = newdata) at test-cindex_calc.R:37:3
2. ├─survival::concordance(model, newdata = newdata)
3. └─survival:::concordance.coxph(model, newdata = newdata)
4. └─base::lapply(...)
5. └─survival (local) FUN(X[[i]], ...)
6. ├─stats::predict(object, newdata = newdata, na.action = na.omit)
7. └─survival:::predict.coxph(object, newdata = newdata, na.action = na.omit)
8. └─stats::delete.response(Terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-tdroc_calc.R:14:3'): tdroc_calc returns time/AUC table with ROC object attached ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─survC::tdroc_calc(...) at test-tdroc_calc.R:14:3
2. └─timeROC::timeROC(...)
3. ├─pec::ipcw(...)
4. └─pec:::ipcw.marginal(...)
5. └─prodlim::prodlim(formula, data = data, reverse = TRUE)
6. └─prodlim::EventHistory.frame(...)
7. └─prodlim::model.design(...)
8. └─stats::delete.response(terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-tdroc_calc.R:41:3'): tdroc_calc computes ROC curves with expected discrimination ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─survC::tdroc_calc(...) at test-tdroc_calc.R:41:3
2. └─timeROC::timeROC(...)
3. ├─pec::ipcw(...)
4. └─pec:::ipcw.marginal(...)
5. └─prodlim::prodlim(formula, data = data, reverse = TRUE)
6. └─prodlim::EventHistory.frame(...)
7. └─prodlim::model.design(...)
8. └─stats::delete.response(terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-validation_report.R:38:3'): validation_report creates a PPTX with one slide per time point ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─survC::validation_report(...) at test-validation_report.R:38:3
2. └─survC::calc_risk_score(model, data = train_data)
3. ├─stats::predict(...)
4. └─survival:::predict.coxph(...)
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
[ FAIL 6 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc