Last updated on 2024-10-19 02:49:24 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2023.12.21 | 205.87 | 285.50 | 491.37 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2023.12.21 | 134.13 | 190.56 | 324.69 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2023.12.21 | 910.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2023.12.21 | 632.26 | ERROR | |||
| r-devel-windows-x86_64 | 2023.12.21 | 209.00 | 311.00 | 520.00 | NOTE | |
| r-patched-linux-x86_64 | 2023.12.21 | OK | ||||
| r-release-linux-x86_64 | 2023.12.21 | 187.34 | 269.28 | 456.62 | OK | |
| r-release-macos-arm64 | 2023.12.21 | 185.00 | NOTE | |||
| r-release-macos-x86_64 | 2023.12.21 | 237.00 | NOTE | |||
| r-release-windows-x86_64 | 2023.12.21 | 204.00 | 324.00 | 528.00 | OK | |
| r-oldrel-macos-arm64 | 2023.12.21 | 222.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2023.12.21 | 346.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2023.12.21 | 249.00 | 390.00 | 639.00 | OK |
Version: 2023.12.21
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
CSC.Rd: coxph
FGR.Rd: Hist
ate.Rd: as.data.table
plot.riskRegression.Rd: SmartControl
plotBrier.Rd: SmartControl
plotCalibration.Rd: SmartControl
plotEffects.Rd: SmartControl
plotPredictRisk.Rd: SmartControl
plotROC.Rd: SmartControl
plotRisk.Rd: SmartControl
selectCox.Rd: fastbw
summary.ate.Rd: as.data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 2023.12.21
Check: examples
Result: ERROR
Running examples in ‘riskRegression-Ex.R’ failed
The error most likely occurred in:
> ### Name: Ctree
> ### Title: S3-Wrapper for ctree.
> ### Aliases: Ctree
>
> ### ** Examples
>
> if (require("party",quietly=TRUE)){
+ library(prodlim)
+ library(party)
+ library(survival)
+ set.seed(50)
+ d <- SimSurv(50)
+ nd <- data.frame(X1=c(0,1,0),X2=c(-1,0,1))
+ f <- Ctree(Surv(time,status)~X1+X2,data=d)
+ predictRisk(f,newdata=nd,times=c(3,8))
+ }
Attaching package: ‘zoo’
The following objects are masked from ‘package:base’:
as.Date, as.Date.numeric
Error in cbind(idxM, pidxM) : cannot get data pointer of 'NULL' objects
Calls: SimSurv ... exogenous<- -> exogenous<-.lvm -> reindex -> mat.lvm -> cbind
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2023.12.21
Check: tests
Result: ERROR
Running ‘testthat.R’
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 2023.12.21
>
> test_check("riskRegression")
[iidCox] internal consistency
[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)
[predictCoxPL] Check baseline hazard estimation vs survfit
[predictRisk.rfsrc]
[predictRisk.CauseSpecificCox]
[predictRisk.glm] vs. lava
Testing binary data with
Testing survival data with
Testing competing.risks data with
[1] "binary"
[ FAIL 24 | WARN 4 | SKIP 0 | PASS 43 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-BinomialRegression.R:11:5'): Absolute risk regression ──────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(300, outcome = "competing.risks") at test-BinomialRegression.R:11:5
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-BinomialRegression.R:33:5'): Logistic risk regression ──────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─prodlim::SimCompRisk(100) at test-BinomialRegression.R:33:5
2. └─prodlim::crModel()
3. ├─lava::`distribution<-`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
4. └─lava:::`distribution<-.lvm`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
6. └─lava:::`addvar<-.lvm`(...)
7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
9. └─lava::procformula(object, value, ...)
10. ├─lava::`exogenous<-`(...)
11. └─lava:::`exogenous<-.lvm`(...)
12. └─lava::reindex(x)
13. └─lava:::mat.lvm(x, res)
14. └─base::cbind(idxM, pidxM)
── Error ('test-CauseSpecificCoxRegression.R:40:9'): predictSurv ───────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─prodlim::SimSurv(100) at test-CauseSpecificCoxRegression.R:40:9
2. └─prodlim::survModel()
3. └─lava::lvm(~eventtime + censtime)
4. ├─lava::`regression<-`(`*tmp*`, messages = messages, value = myvar)
5. └─lava:::`regression<-.lvm`(`*tmp*`, messages = messages, value = myvar)
6. └─lava::procformula(object, value, ...)
7. ├─lava::`exogenous<-`(...)
8. └─lava:::`exogenous<-.lvm`(...)
9. └─lava::reindex(x)
10. └─lava:::mat.lvm(x, res)
11. └─base::cbind(idxM, pidxM)
── Error ('test-CauseSpecificCoxRegression.R:54:5'): Cox models ────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─prodlim::SimCompRisk(100) at test-CauseSpecificCoxRegression.R:54:5
2. └─prodlim::crModel()
3. ├─lava::`distribution<-`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
4. └─lava:::`distribution<-.lvm`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
6. └─lava:::`addvar<-.lvm`(...)
7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
9. └─lava::procformula(object, value, ...)
10. ├─lava::`exogenous<-`(...)
11. └─lava:::`exogenous<-.lvm`(...)
12. └─lava::reindex(x)
13. └─lava:::mat.lvm(x, res)
14. └─base::cbind(idxM, pidxM)
── Error ('test-CauseSpecificCoxRegression.R:67:5'): strata ────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─prodlim::SimCompRisk(100) at test-CauseSpecificCoxRegression.R:67:5
2. └─prodlim::crModel()
3. ├─lava::`distribution<-`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
4. └─lava:::`distribution<-.lvm`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
6. └─lava:::`addvar<-.lvm`(...)
7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
9. └─lava::procformula(object, value, ...)
10. ├─lava::`exogenous<-`(...)
11. └─lava:::`exogenous<-.lvm`(...)
12. └─lava::reindex(x)
13. └─lava:::mat.lvm(x, res)
14. └─base::cbind(idxM, pidxM)
── Error ('test-FineGrayRegression.R:9:5'): Formula interface ──────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─prodlim::SimCompRisk(100) at test-FineGrayRegression.R:9:5
2. └─prodlim::crModel()
3. ├─lava::`distribution<-`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
4. └─lava:::`distribution<-.lvm`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
6. └─lava:::`addvar<-.lvm`(...)
7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
9. └─lava::procformula(object, value, ...)
10. ├─lava::`exogenous<-`(...)
11. └─lava:::`exogenous<-.lvm`(...)
12. └─lava::reindex(x)
13. └─lava:::mat.lvm(x, res)
14. └─base::cbind(idxM, pidxM)
── Error ('test-iidCox.R:35:1'): (code run outside of `test_that()`) ───────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(20, outcome = "survival") at test-iidCox.R:35:1
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-phreg.R:32:1'): (code run outside of `test_that()`) ────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(50, outcome = "survival") at test-phreg.R:32:1
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-plotRisk.R:27:2'): More than one competing risk ────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(80, outcome = "competing.risk") at test-plotRisk.R:27:2
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-predictCox.R:191:1'): (code run outside of `test_that()`) ──────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(50, outcome = "survival") at test-predictCox.R:191:1
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-predictCoxPL.R:27:1'): (code run outside of `test_that()`) ─────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(25, outcome = "survival") at test-predictCoxPL.R:27:1
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-predictRisk-TD.R:51:5'): start stop CauseSpecificCox ───────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(201, outcome = "competing.risk") at test-predictRisk-TD.R:51:5
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-predictRisk.R:49:5'): Prediction with CSC - categorical cause ──
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─prodlim::SimCompRisk(n) at test-predictRisk.R:49:5
2. └─prodlim::crModel()
3. ├─lava::`distribution<-`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
4. └─lava:::`distribution<-.lvm`(`*tmp*`, "eventtime1", value = lava::coxWeibull.lvm(scale = 1/100))
5. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
6. └─lava:::`addvar<-.lvm`(...)
7. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
8. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
9. └─lava::procformula(object, value, ...)
10. ├─lava::`exogenous<-`(...)
11. └─lava:::`exogenous<-.lvm`(...)
12. └─lava::reindex(x)
13. └─lava:::mat.lvm(x, res)
14. └─base::cbind(idxM, pidxM)
── Error ('test-predictRisk.R:90:1'): (code run outside of `test_that()`) ──────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(n, outcome = "binary") at test-predictRisk.R:90:1
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score-train-test.R:20:7'): Testing binary data with ───────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(n = train.sample.size, outcome = typ$data) at test-score-train-test.R:20:7
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score-train-test.R:20:7'): Testing survival data with ─────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(n = train.sample.size, outcome = typ$data) at test-score-train-test.R:20:7
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score-train-test.R:20:7'): Testing competing.risks data with ──
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(n = train.sample.size, outcome = typ$data) at test-score-train-test.R:20:7
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score.R:33:5'): R squared/IPA ──────────────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(43, outcome = "binary") at test-score.R:33:5
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score.R:47:5'): binary outcome: robustness against order of data set ──
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(43, outcome = "binary") at test-score.R:47:5
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score.R:79:9'): survival outcome,Brier Score, external prediction ──
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(n, outcome = "survival") at test-score.R:79:9
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score.R:107:9'): integrated Brier score ────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(100, outcome = "survival") at test-score.R:107:9
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score.R:145:9'): survival outcome uncensored ───────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(100, outcome = "survival") at test-score.R:145:9
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-score.R:158:5'): binary outcome: Brier ─────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(n = 47, outcome = "binary") at test-score.R:158:5
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
── Error ('test-summary-score.R:26:5'): (code run outside of `test_that()`) ────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(n = 112, outcome = y) at test-summary-score.R:26:5
2. ├─lava::`distribution<-`(...)
3. └─lava:::`distribution<-.lvm`(...)
4. ├─lava::`addvar<-`(`*tmp*`, value = as.formula(paste("~", variable)))
5. └─lava:::`addvar<-.lvm`(...)
6. ├─lava::`regression<-`(`*tmp*`, ..., value = value)
7. └─lava:::`regression<-.lvm`(`*tmp*`, ..., value = value)
8. └─lava::procformula(object, value, ...)
9. ├─lava::`exogenous<-`(...)
10. └─lava:::`exogenous<-.lvm`(...)
11. └─lava::reindex(x)
12. └─lava:::mat.lvm(x, res)
13. └─base::cbind(idxM, pidxM)
[ FAIL 24 | WARN 4 | SKIP 0 | PASS 43 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2023.12.21
Check: installed package size
Result: NOTE
installed size is 10.2Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 8.7Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64