Last updated on 2026-10-24 15:51:39 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2026.03.11 | 230.69 | 335.10 | 565.79 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2026.03.11 | 157.09 | 175.89 | 332.98 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2026.03.11 | 159.00 | 210.62 | 369.62 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2026.03.11 | 175.00 | 199.18 | 374.18 | OK | |
| r-devel-windows-x86_64 | 2026.03.11 | 260.00 | 411.00 | 671.00 | OK | |
| r-patched-linux-x86_64 | 2026.03.11 | 212.40 | 317.99 | 530.39 | OK | |
| r-release-linux-x86_64 | 2026.03.11 | 217.05 | 318.94 | 535.99 | OK | |
| r-release-macos-arm64 | 2026.03.11 | 43.00 | 44.00 | 87.00 | OK | |
| r-release-macos-x86_64 | 2026.03.11 | 129.00 | 442.00 | 571.00 | OK | |
| r-release-windows-x86_64 | 2026.03.11 | 250.00 | 334.00 | 584.00 | OK | |
| r-oldrel-macos-arm64 | 2026.03.11 | 37.00 | 49.00 | 86.00 | OK | |
| r-oldrel-macos-x86_64 | 2026.03.11 | 130.00 | 108.00 | 238.00 | OK | |
| r-oldrel-windows-x86_64 | 2026.03.11 | 298.00 | 453.00 | 751.00 | OK |
Version: 2026.03.11
Check: examples
Result: ERROR
Running examples in ‘riskRegression-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CSC
> ### Title: Cause-specific Cox proportional hazard regression
> ### Aliases: CSC
> ### Keywords: survival
>
> ### ** Examples
>
>
> library(prodlim)
> library(survival)
> data(Melanoma)
> ## fit two cause-specific Cox models
> ## different formula for the two causes
> fit1 <- CSC(list(Hist(time,status)~sex+age,Hist(time,status)~invasion+epicel+log(thick)),
+ data=Melanoma)
> print(fit1)
CSC(formula = list(Hist(time, status) ~ sex + age, Hist(time,
status) ~ invasion + epicel + log(thick)), data = Melanoma)
Right-censored response of a competing.risks model
No.Observations: 205
Pattern:
Cause event right.censored
1 57 0
2 14 0
unknown 0 134
----------> Cause: 1
Call:
coxph(formula = survival::Surv(time, status) ~ sex + age, x = TRUE,
y = TRUE)
n= 205, number of events= 57
coef exp(coef) se(coef) z Pr(>|z|)
sexMale 0.598259 1.818949 0.267639 2.235 0.0254 *
age 0.016542 1.016679 0.008663 1.910 0.0562 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
exp(coef) exp(-coef) lower .95 upper .95
sexMale 1.819 0.5498 1.0765 3.074
age 1.017 0.9836 0.9996 1.034
Concordance= 0.631 (se = 0.037 )
Likelihood ratio test= 9.94 on 2 df, p=0.007
Wald test = 10 on 2 df, p=0.007
Score (logrank) test = 10.26 on 2 df, p=0.006
----------> Cause: 2
Call:
coxph(formula = survival::Surv(time, status) ~ invasion + epicel +
log(thick), x = TRUE, y = TRUE)
n= 205, number of events= 14
coef exp(coef) se(coef) z Pr(>|z|)
invasionlevel.1 -0.7315 0.4812 0.6492 -1.127 0.2599
invasionlevel.2 -2.2593 0.1044 1.2478 -1.811 0.0702 .
epicelpresent 1.0840 2.9564 0.5738 1.889 0.0589 .
log(thick) 0.8954 2.4484 0.3959 2.262 0.0237 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
exp(coef) exp(-coef) lower .95 upper .95
invasionlevel.1 0.4812 2.0781 0.134806 1.718
invasionlevel.2 0.1044 9.5768 0.009051 1.205
epicelpresent 2.9564 0.3383 0.960134 9.103
log(thick) 2.4484 0.4084 1.126881 5.320
Concordance= 0.648 (se = 0.1 )
Likelihood ratio test= 7.41 on 4 df, p=0.1
Wald test = 7.72 on 4 df, p=0.1
Score (logrank) test = 7.44 on 4 df, p=0.1
>
> ## Not run:
> ##D library(rms)
> ##D fit1a <- CSC(list(Hist(time,status)~sex+rcs(age,3),Hist(time,status)~invasion+epicel+log(thick)),
> ##D data=Melanoma,fitter="cph")
> ##D print(fit1a)
> ## End(Not run)
> ## Not run:
> ##D library(glmnet)
> ##D # lasso
> ##D fit1b <- CSC(list(Hist(time,status)~sex+age,Hist(time,status)~invasion+epicel+log(thick)),
> ##D data=Melanoma,fitter="glmnet")
> ##D # rigde regression
> ##D fit1c <- CSC(list(Hist(time,status)~sex+age,Hist(time,status)~invasion+epicel+log(thick)),
> ##D data=Melanoma,fitter="glmnet")
> ##D print(fit1b)
> ## End(Not run)
> ## Not run:
> ##D library(Publish)
> ##D publish(fit1)
> ## End(Not run)
>
> ## model hazard of all cause mortality instead of hazard of type 2
> fit1a <- CSC(list(Hist(time,status)~sex+age,Hist(time,status)~invasion+epicel+log(thick)),
+ data=Melanoma,
+ surv.type="surv")
>
> ## the predicted probabilities are similar
> plot(predictRisk(fit1,times=500,cause=1,newdata=Melanoma),
+ predictRisk(fit1a,times=500,cause=1,newdata=Melanoma))
Error in a$specials[[i]] : subscript out of bounds
Calls: plot ... lapply -> FUN -> coxVariableName -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2026.03.11
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/17s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(riskRegression)
riskRegression version 2026.03.11
>
> test_check("riskRegression")
Saving _problems/test-AUC-13.R
Saving _problems/test-BinomialRegression-12.R
Saving _problems/test-BinomialRegression-34.R
Saving _problems/test-BrierScore-14.R
Saving _problems/test-CauseSpecificCoxRegression-11.R
Saving _problems/test-CauseSpecificCoxRegression-43.R
Saving _problems/test-CauseSpecificCoxRegression-84.R
Saving _problems/test-FineGrayRegression-10.R
[iidCox] internal consistency
Saving _problems/test-iidCox-50.R
[predictCox] Estimation of the baseline hazard (no strata)
Saving _problems/test-predictCox-42.R
Saving _problems/test-predictCox-62.R
Saving _problems/test-predictCox-74.R
[predictCox] Estimation of the baseline hazard (strata)
[predictCox] Estimation of the baseline hazard (time varying cov, no strata)
Saving _problems/test-predictCox-171.R
[predictCox] Estimation of the baseline hazard (time varying cov, strata)
[predictCox] Predictions (no strata, continuous)
Saving _problems/test-predictCox-240.R
Saving _problems/test-predictCox-249.R
[predictRisk.rfsrc]
[predictRisk.CauseSpecificCox]
Saving _problems/test-predictRisk-68.R
[predictRisk.glm] vs. lava
Saving _problems/test-score-train-test-42.R
Saving _problems/test-score-train-test-42.R
Saving _problems/test-score-90.R
Saving _problems/test-score-119.R
Saving _problems/test-score-149.R
[1] "binary"
[1] "survival"
Saving _problems/test-summary-score-44.R
[ FAIL 22 | WARN 4 | SKIP 0 | PASS 93 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-AUC.R:13:5'): AUC censored data: order ─────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-AUC.R:13:5
2. │ └─base::withCallingHandlers(...)
3. ├─riskRegression::Score(...)
4. └─riskRegression::Score.list(...)
5. └─riskRegression:::getNullModel(...)
6. └─prodlim::prodlim(nullform, data)
7. └─prodlim::EventHistory.frame(...)
8. └─prodlim::model.design(...)
9. └─stats::delete.response(terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-BinomialRegression.R:12:5'): Absolute risk regression ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::ARR(...) at test-BinomialRegression.R:12:5
2. └─riskRegression::riskRegression(...)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-BinomialRegression.R:34:5'): Logistic risk regression ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::LRR(Hist(time, event) ~ X1 + X2, data = d, cause = 1) at test-BinomialRegression.R:34:5
2. └─riskRegression::riskRegression(...)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-BrierScore.R:14:5'): Brier score censored data order ───────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─riskRegression::Score(...) at test-BrierScore.R:14:5
2. └─riskRegression::Score.list(...)
3. └─riskRegression:::getNullModel(...)
4. └─prodlim::prodlim(nullform, data)
5. └─prodlim::EventHistory.frame(...)
6. └─prodlim::model.design(...)
7. └─stats::delete.response(terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-CauseSpecificCoxRegression.R:11:5'): CSC vs prodlim ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─prodlim::prodlim(Hist(time, status) ~ 1, data = Melanoma) at test-CauseSpecificCoxRegression.R:11:5
2. └─prodlim::EventHistory.frame(...)
3. └─prodlim::model.design(...)
4. └─stats::delete.response(terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-CauseSpecificCoxRegression.R:43:9'): predictSurv ───────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─riskRegression::predictRisk(...) at test-CauseSpecificCoxRegression.R:43:9
2. └─riskRegression:::predictRisk.coxph(...)
3. └─riskRegression::predictCox(...)
4. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
5. └─stats::delete.response(...)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-CauseSpecificCoxRegression.R:84:5'): strat and strata ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─riskRegression::predictRisk(...) at test-CauseSpecificCoxRegression.R:84:5
2. └─riskRegression:::predictRisk.CauseSpecificCox(...)
3. ├─stats::predict(...)
4. └─riskRegression:::predict.CauseSpecificCox(...)
5. ├─riskRegression::coxLP(...)
6. └─riskRegression:::coxLP.coxph(...)
7. └─riskRegression:::reconstructData(object)
8. ├─base::as.data.frame(cbind(coxModelFrame(object), splitStrataVar(object)))
9. ├─base::cbind(coxModelFrame(object), splitStrataVar(object))
10. │ └─data.table (local) cbind(deparse.level, ...)
11. └─riskRegression:::splitStrataVar(object)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test-FineGrayRegression.R:10:5'): Formula interface ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::FGR(Hist(time, event) ~ X1 + X2, data = d) at test-FineGrayRegression.R:10:5
2. └─prodlim::EventHistory.frame(...)
3. └─prodlim::model.design(...)
4. └─stats::delete.response(terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-iidCox.R:50:1'): (code run outside of `test_that()`) ───────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─riskRegression::iidCox(coxph.fit, return.object = FALSE) at test-iidCox.R:50:1
2. └─riskRegression:::iidCox.coxph(coxph.fit, return.object = FALSE)
3. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
4. └─stats::delete.response(...)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-predictCox.R:41:3'): baseline hazard (no strata): compare to survival::basehaz ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-predictCox.R:41:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─riskRegression::predictCox(fit.coxph, centered = FALSE)
5. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
6. └─stats::delete.response(...)
7. └─stats (local) off(a$specials[[i]])
── Error ('test-predictCox.R:62:5'): baseline hazard (no strata): number of events ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::predictCox(fit.coxph) at test-predictCox.R:62:5
2. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
3. └─stats::delete.response(...)
4. └─stats (local) off(a$specials[[i]])
── Error ('test-predictCox.R:73:5'): product limit baseline survival (no strata): product limit ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::predictCox(...) at test-predictCox.R:73:5
2. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
3. └─stats::delete.response(...)
4. └─stats (local) off(a$specials[[i]])
── Error ('test-predictCox.R:170:5'): baseline hazard (no strata, time varying): compare to survival::basehaz ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-predictCox.R:170:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::suppressWarnings(predictCox(fit.coxphTV, centered = FALSE)$cumhazard)
5. │ └─base::withCallingHandlers(...)
6. └─riskRegression::predictCox(fit.coxphTV, centered = FALSE)
7. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
8. └─stats::delete.response(...)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-predictCox.R:240:3'): [predictCox] - consistency of hazard/cumhazard/survival ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::predictCox(...) at test-predictCox.R:240:3
2. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
3. └─stats::delete.response(...)
4. └─stats (local) off(a$specials[[i]])
── Error ('test-predictCox.R:248:1'): (code run outside of `test_that()`) ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::predictCox(...) at test-predictCox.R:248:1
2. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
3. └─stats::delete.response(...)
4. └─stats (local) off(a$specials[[i]])
── Error ('test-predictRisk.R:68:5'): Prediction with CSC - categorical cause ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─riskRegression::predictRisk(...) at test-predictRisk.R:68:5
2. └─riskRegression:::predictRisk.CauseSpecificCox(...)
3. ├─stats::predict(...)
4. └─riskRegression:::predict.CauseSpecificCox(...)
5. ├─riskRegression::coxLP(...)
6. └─riskRegression:::coxLP.coxph(...)
7. └─riskRegression:::reconstructData(object)
8. ├─base::as.data.frame(cbind(coxModelFrame(object), splitStrataVar(object)))
9. ├─base::cbind(coxModelFrame(object), splitStrataVar(object))
10. │ └─data.table (local) cbind(deparse.level, ...)
11. └─riskRegression:::splitStrataVar(object)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test-score-train-test.R:42:7'): Survival outcome ────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::do.call(Score, input.score) at test-score-train-test.R:42:7
2. ├─riskRegression (local) `<fn>`(...)
3. └─riskRegression::Score.list(...)
4. └─riskRegression:::getNullModel(...)
5. └─prodlim::prodlim(nullform, data)
6. └─prodlim::EventHistory.frame(...)
7. └─prodlim::model.design(...)
8. └─stats::delete.response(terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-score-train-test.R:42:7'): Competing risks outcome ─────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::do.call(Score, input.score) at test-score-train-test.R:42:7
2. ├─riskRegression (local) `<fn>`(...)
3. └─riskRegression::Score.list(...)
4. └─riskRegression:::getNullModel(...)
5. └─prodlim::prodlim(nullform, data)
6. └─prodlim::EventHistory.frame(...)
7. └─prodlim::model.design(...)
8. └─stats::delete.response(terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-score.R:90:9'): survival outcome,Brier Score, external prediction ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─pec::pec(...) at test-score.R:90:9
2. └─prodlim::prodlim(formula = ProdLimform, data = data)
3. └─prodlim::EventHistory.frame(...)
4. └─prodlim::model.design(...)
5. └─stats::delete.response(terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-score.R:115:9'): integrated Brier score ────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-score.R:115:9
2. │ └─base::withCallingHandlers(...)
3. ├─riskRegression::Score(...)
4. └─riskRegression::Score.list(...)
5. └─riskRegression:::getNullModel(...)
6. └─prodlim::prodlim(nullform, data)
7. └─prodlim::EventHistory.frame(...)
8. └─prodlim::model.design(...)
9. └─stats::delete.response(terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-score.R:149:9'): survival outcome uncensored ───────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─riskRegression::Score(...) at test-score.R:149:9
2. └─riskRegression::Score.list(...)
3. └─riskRegression:::getNullModel(...)
4. └─prodlim::prodlim(nullform, data)
5. └─prodlim::EventHistory.frame(...)
6. └─prodlim::model.design(...)
7. └─stats::delete.response(terms)
8. └─stats (local) off(a$specials[[i]])
── Error ('test-summary-score.R:44:5'): (code run outside of `test_that()`) ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─riskRegression::Score(...) at test-summary-score.R:44:5
2. └─riskRegression::Score.list(...)
3. └─riskRegression:::getNullModel(...)
4. └─prodlim::prodlim(nullform, data)
5. └─prodlim::EventHistory.frame(...)
6. └─prodlim::model.design(...)
7. └─stats::delete.response(terms)
8. └─stats (local) off(a$specials[[i]])
[ FAIL 22 | WARN 4 | SKIP 0 | PASS 93 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc