Last updated on 2024-11-08 00:49:45 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.10 | 7.64 | 89.15 | 96.79 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.10 | 5.76 | 61.31 | 67.07 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.10 | 161.96 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.10 | 139.93 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.10 | 10.00 | 94.00 | 104.00 | OK | |
| r-patched-linux-x86_64 | 1.0.10 | 7.22 | 84.57 | 91.79 | OK | |
| r-release-linux-x86_64 | 1.0.10 | 7.98 | 84.86 | 92.84 | OK | |
| r-release-macos-arm64 | 1.0.10 | 47.00 | OK | |||
| r-release-macos-x86_64 | 1.0.10 | 83.00 | OK | |||
| r-release-windows-x86_64 | 1.0.10 | 10.00 | 103.00 | 113.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.10 | 50.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.10 | 80.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.10 | 12.00 | 121.00 | 133.00 | OK |
Version: 1.0.10
Check: examples
Result: ERROR
Running examples in ‘wally-Ex.R’ failed
The error most likely occurred in:
> ### Name: wallyPlot
> ### Title: Wally plots to assess calibration of a risk or survival
> ### prediction
> ### Aliases: wallyPlot
>
> ### ** Examples
>
>
> # Survival setting
> library(prodlim)
> library(data.table)
> library(survival)
> set.seed(180)
> d = SimSurv(180)
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: 1.0.10
Check: tests
Result: ERROR
Running ‘Reproduce-Fig-paper.R’ [17s/60s]
Running ‘test-wally-function.R’ [8s/13s]
Running the tests in ‘tests/test-wally-function.R’ failed.
Complete output:
>
> # {{{ load packages
> library(survival)
> library(data.table)
> library(testthat)
> library(prodlim)
> library(riskRegression)
riskRegression version 2023.12.21
> library(wally)
> # }}}
>
>
> # {{{ "Wally for survival weird formula and hanging"
> test_that("Wally for survival weird formula and hanging",{
+ set.seed(10)
+ d <- sampleData(138,outcome="survival")
+ setnames(d,c("time","event"),c("truc","toto"))
+ f <- coxph(Surv(truc,toto)~X6+X7,data=d,x=TRUE)
+ d$pi <- predictRisk(f,times=2,newdata=d)
+ pred <- as.matrix(d$pi,ncol=1)
+ ## matrix input
+ u <- wallyPlot(pred,
+ time=2,
+ formula=as.formula(paste("Hist(","truc",",","toto",")~1")),
+ data=d,
+ hanging=TRUE,
+ seed=5987,
+ colbox="red",
+ superuser.hide=FALSE,
+ superuser.choice=NULL,
+ q=13)
+ ## model input
+ v <- wallyPlot(f,
+ time=2,
+ formula=as.formula(paste("Hist(","truc",",","toto",")~1")),
+ data=d,
+ hanging=TRUE,
+ seed=5987,
+ colbox="red",
+ superuser.hide=FALSE,
+ superuser.choice=NULL,
+ q=13)
+ expect_equal(u,v)
+ })
── Error: Wally for survival weird formula and hanging ─────────────────────────
Error in `cbind(idxM, pidxM)`: cannot get data pointer of 'NULL' objects
Backtrace:
▆
1. └─riskRegression::sampleData(138, outcome = "survival")
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 failed
Backtrace:
▆
1. ├─testthat::test_that(...)
2. │ └─withr (local) `<fn>`()
3. └─reporter$stop_if_needed()
4. └─rlang::abort("Test failed", call = NULL)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc