Last updated on 2025-12-28 05:50:39 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| pec | 13 | ||
| prodlim | 13 | ||
| Publish | 1 | 12 | |
| riskRegression | 1 | 2 | 10 |
| SmoothHazard | 13 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 2025.07.24
Check: examples
Result: ERROR
Running examples in 'Publish-Ex.R' failed
The error most likely occurred in:
> ### Name: publish.Score
> ### Title: Publish predictive accuracy results
> ### Aliases: publish.Score
>
> ### ** Examples
>
> if (requireNamespace("riskRegression",quietly=TRUE)){
+ library(riskRegression)
+ library(survival)
+ learn = sampleData(100)
+ val= sampleData(100)
+ f1=CSC(Hist(time,event)~X1+X8,data=learn)
+ f2=CSC(Hist(time,event)~X1+X5+X6+X8,learn)
+ xs=Score(list(f1,f2),data=val,formula=Hist(time,event)~1)
+ publish(xs)
+ }
riskRegression version 2025.09.17
Error in `[.data.table`(DT, , `:=`(IC0, residuals - mean(residuals)), :
attempt access index 11/11 in VECTOR_ELT
Calls: Score ... do.call -> Brier.competing.risks -> [ -> [.data.table
Execution halted
Flavor: r-devel-windows-x86_64
Current CRAN status: ERROR: 1, NOTE: 2, OK: 10
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-windows-x86_64
Version: 2025.09.17
Check: tests
Result: ERROR
Running 'testthat.R' [33s]
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-windows-x86_64
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
Current CRAN status: OK: 13
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.