Last updated on 2025-12-19 14:50:33 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2025.09.17 | 200.73 | 339.92 | 540.65 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2025.09.17 | 129.61 | 223.46 | 353.07 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2025.09.17 | 424.00 | 536.88 | 960.88 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2025.09.17 | 378.00 | 423.64 | 801.64 | ERROR | |
| r-devel-windows-x86_64 | 2025.09.17 | 223.00 | 343.00 | 566.00 | OK | |
| r-patched-linux-x86_64 | 2025.09.17 | 193.55 | 310.26 | 503.81 | OK | |
| r-release-linux-x86_64 | 2025.09.17 | 199.02 | 308.84 | 507.86 | OK | |
| r-release-macos-arm64 | 2025.09.17 | OK | ||||
| r-release-macos-x86_64 | 2025.09.17 | 125.00 | 270.00 | 395.00 | OK | |
| r-release-windows-x86_64 | 2025.09.17 | 231.00 | 326.00 | 557.00 | OK | |
| r-oldrel-macos-arm64 | 2025.09.17 | NOTE | ||||
| r-oldrel-macos-x86_64 | 2025.09.17 | 119.00 | 267.00 | 386.00 | NOTE | |
| r-oldrel-windows-x86_64 | 2025.09.17 | 277.00 | 433.00 | 710.00 | OK |
Version: 2025.09.17
Check: examples
Result: ERROR
Running examples in ‘riskRegression-Ex.R’ failed
The error most likely occurred in:
> ### Name: IPA
> ### Title: Explained variation for settings with binary, survival and
> ### competing risk outcome
> ### Aliases: IPA rsquared rsquared.default rsquared.glm rsquared.coxph
> ### rsquared.CauseSpecificCox IPA.default IPA.glm IPA.coxph
> ### IPA.CauseSpecificCox
>
> ### ** Examples
>
> library(prodlim)
> library(data.table)
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
> # binary outcome
> library(lava)
> set.seed(18)
> learndat <- sampleData(48,outcome="binary")
> lr1 = glm(Y~X1+X2+X7+X9,data=learndat,family=binomial)
> IPA(lr1)
Variable Brier IPA IPA.drop
<fctr> <char> <char> <char>
1: Null model 24.8 0.0 37.1
2: Full model 15.6 37.1 0.0
3: X1 19.5 21.6 15.5
4: X2 15.8 36.3 0.8
5: X7 16.0 35.4 1.7
6: X9 21.2 14.6 22.5
NOTE: Values are multiplied by 100 and given in %.
NOTE: The higher IPA the better.
NOTE: IPA.drop = IPA(Full model) - IPA. The higher the drop
the more important is the variable for the full model.
>
> ## validation data
> valdat=sampleData(94,outcome="binary")
> IPA(lr1,newdata=valdat)
Variable Brier IPA IPA.drop
<fctr> <char> <char> <char>
1: Null model 23.6 0.0 -1.3
2: Full model 23.9 -1.3 0.0
3: X1 23.9 -0.9 -0.3
4: X2 23.2 1.9 -3.1
5: X7 24.0 -1.7 0.4
6: X9 23.5 0.5 -1.8
NOTE: Values are multiplied by 100 and given in %.
NOTE: The higher IPA the better.
NOTE: IPA.drop = IPA(Full model) - IPA. The higher the drop
the more important is the variable for the full model.
>
> ## predicted risks externally given
> p1=predictRisk(lr1,newdata=valdat)
> IPA(p1,formula=Y~1,valdat)
model IPA Brier
<fctr> <char> <char>
1: Null model 0.0 23.6
2: numeric -1.3 23.9
NOTE: Values are multiplied by 100 and given in %.
NOTE: The higher IPA the better.
NOTE: IPA.drop = IPA(Full model) - IPA. The higher the drop
the more important is the variable for the full model.
>
> # survival
> library(survival)
> data(pbc)
> pbc=na.omit(pbc)
> pbctest=(1:NROW(pbc)) %in% sample(1:NROW(pbc),size=.632*NROW(pbc))
> pbclearn=pbc[pbctest,]
> cox1= coxph(Surv(time,status!=0)~age+sex+log(bili)+log(albumin)+log(protime),
+ data=pbclearn,x=TRUE)
>
> ## same data
> IPA(cox1,formula=Surv(time,status!=0)~1,times=1000)
Error in `[.data.table`(score, , `:=`(IPA, 1 - Brier/Brier[model == "Null model"]), :
attempt access index 3/3 in VECTOR_ELT
Calls: IPA ... computePerformance -> IPACompute -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2025.09.17
Check: tests
Result: ERROR
Running ‘testthat.R’ [57s/80s]
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 2025.09.17
>
> test_check("riskRegression")
Saving _problems/test-AUC-13.R
Saving _problems/test-BrierScore-14.R
[iidCox] internal consistency
[iidCox] compare to timereg - no strata, no interaction, continuous
[iidCox] compare to timereg - no strata, interaction, continuous
[iidCox] compare to timereg - no covariate
[iidCox] compare to timereg - no strata, no interaction, categorical
[iidCox] compare to timereg - ties
[iidCox] compare to timereg - strata
[iidCox] compare to timereg - Melanoma
[predictCox] Estimation of the baseline hazard (no strata)
[predictCox] Estimation of the baseline hazard (strata)
[predictCox] Estimation of the baseline hazard (time varying cov, no strata)
[predictCox] Estimation of the baseline hazard (time varying cov, strata)
[predictCox] Predictions (no strata, continuous)
[predictCox] Predictions (no strata, categorical)
[predictCox] Predictions (strata)
[predictCox] SE/CI check against manual computation
[predictCox] Argument 'diag'
[predictCox] Confidence band vs timereg
[predictCox] Check same result store.iid=minimal vs. full
[predictCox] Does not handle weights
[predictCox] dealing with negative timepoints or NA
[predictCox] Previous bug
[predictRisk.rfsrc]
[predictRisk.CauseSpecificCox]
[predictRisk.glm] vs. lava
Saving _problems/test-score-train-test-42.R
Saving _problems/test-score-train-test-42.R
Saving _problems/test-score-38.R
Saving _problems/test-score-92.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 9 | WARN 0 | SKIP 0 | PASS 371 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-AUC.R:13:5'): AUC censored data: order ─────────────────────────
Error in ``[.data.table`(aucDT, , `:=`(TPR, cumsum(ipcwCases)/sum(ipcwCases)), by = list(model, times))`: attempt access index 12/12 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-AUC.R:13:5
2. │ └─base::withCallingHandlers(...)
3. ├─riskRegression::Score(...)
4. └─riskRegression::Score.list(...)
5. └─riskRegression:::computePerformance(...)
6. ├─base::do.call(paste(m, response.type, sep = "."), input)
7. └─riskRegression:::AUC.survival(...)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-BrierScore.R:14:5'): Brier score censored data order ───────────
Error in ``[.data.table`(DT, , `:=`(IC0, residuals - mean(residuals)), by = list(model, times))`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. ├─riskRegression::Score(...) at test-BrierScore.R:14:5
2. └─riskRegression::Score.list(...)
3. └─riskRegression:::computePerformance(...)
4. ├─base::do.call(paste(m, response.type, sep = "."), input)
5. └─riskRegression:::Brier.survival(...)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-score-train-test.R:42:7'): Survival outcome ────────────────────
Error in ``[.data.table`(DT, , `:=`(IC0, residuals - mean(residuals)), by = list(model, times))`: attempt access index 10/10 in VECTOR_ELT
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:::computePerformance(...)
5. ├─base::do.call(paste(m, response.type, sep = "."), input)
6. └─riskRegression:::Brier.survival(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-score-train-test.R:42:7'): Competing risks outcome ─────────────
Error in ``[.data.table`(DT, , `:=`(IC0, residuals - mean(residuals)), by = list(model, times))`: attempt access index 11/11 in VECTOR_ELT
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:::computePerformance(...)
5. ├─base::do.call(paste(m, response.type, sep = "."), input)
6. └─riskRegression:::Brier.competing.risks(...)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
── Error ('test-score.R:38:3'): R squared/IPA ──────────────────────────────────
Error in ``[.data.table`(DT, , `:=`(Brier, sum(residuals)/N), by = list(model))`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─riskRegression::Score(...) at test-score.R:38:3
2. └─riskRegression::Score.list(...)
3. └─riskRegression:::computePerformance(...)
4. ├─base::do.call(paste(m, response.type, sep = "."), input)
5. └─riskRegression:::Brier.binary(...)
6. ├─DT[, `:=`(Brier, sum(residuals)/N), by = list(model)]
7. └─data.table:::`[.data.table`(...)
── Error ('test-score.R:92:9'): survival outcome,Brier Score, external prediction ──
Error in ``[.data.table`(aucDT, , `:=`(TPR, cumsum(ipcwCases)/sum(ipcwCases)), by = list(model, times))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─riskRegression::Score(...) at test-score.R:92:9
2. └─riskRegression::Score.list(...)
3. └─riskRegression:::computePerformance(...)
4. ├─base::do.call(paste(m, response.type, sep = "."), input)
5. └─riskRegression:::AUC.survival(...)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
── Error ('test-score.R:115:9'): integrated Brier score ────────────────────────
Error in ``[.data.table`(aucDT, , `:=`(TPR, cumsum(ipcwCases)/sum(ipcwCases)), by = list(model, times))`: attempt access index 13/13 in VECTOR_ELT
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-score.R:115:9
2. │ └─base::withCallingHandlers(...)
3. ├─riskRegression::Score(...)
4. └─riskRegression::Score.list(...)
5. └─riskRegression:::computePerformance(...)
6. ├─base::do.call(paste(m, response.type, sep = "."), input)
7. └─riskRegression:::AUC.survival(...)
8. ├─...[]
9. └─data.table:::`[.data.table`(...)
── Error ('test-score.R:149:9'): survival outcome uncensored ───────────────────
Error in ``[.data.table`(out[["Brier"]][["score"]], , `:=`(IBS, sapply(times, function(t) { Dint(x = c(0, times), y = c(0, Brier), range = c(0, t)) })), by = c("model"))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─riskRegression::Score(...) at test-score.R:149:9
2. └─riskRegression::Score.list(...)
3. └─riskRegression:::computePerformance(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-summary-score.R:44:5'): (code run outside of `test_that()`) ────
Error in ``[.data.table`(DT, , `:=`(IC0, residuals - mean(residuals)), by = list(model, times))`: attempt access index 10/10 in VECTOR_ELT
Backtrace:
▆
1. ├─riskRegression::Score(...) at test-summary-score.R:44:5
2. └─riskRegression::Score.list(...)
3. └─riskRegression:::computePerformance(...)
4. ├─base::do.call(paste(m, response.type, sep = "."), input)
5. └─riskRegression:::Brier.survival(...)
6. ├─...[]
7. └─data.table:::`[.data.table`(...)
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 371 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2025.09.17
Check: installed package size
Result: NOTE
installed size is 12.0Mb
sub-directories of 1Mb or more:
R 2.0Mb
libs 9.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64