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Last updated on 2026-10-24 05:51:17 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.8 | 233.06 | 392.09 | 625.15 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.5.8 | 186.87 | 271.08 | 457.95 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.5.8 | 163.00 | 300.65 | 463.65 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.5.8 | 211.00 | 268.48 | 479.48 | OK | |
| r-devel-windows-x86_64 | 0.5.8 | 283.00 | 525.00 | 808.00 | OK | |
| r-patched-linux-x86_64 | 0.5.8 | 256.92 | 363.44 | 620.36 | OK | |
| r-release-linux-x86_64 | 0.5.8 | 254.17 | 366.33 | 620.50 | OK | |
| r-release-macos-arm64 | 0.5.8 | 47.00 | 57.00 | 104.00 | OK | |
| r-release-macos-x86_64 | 0.5.8 | 154.00 | 409.00 | 563.00 | OK | |
| r-release-windows-x86_64 | 0.5.8 | 272.00 | 453.00 | 725.00 | OK | |
| r-oldrel-macos-arm64 | 0.5.8 | 45.00 | 62.00 | 107.00 | OK | |
| r-oldrel-macos-x86_64 | 0.5.8 | 158.00 | 276.00 | 434.00 | OK | |
| r-oldrel-windows-x86_64 | 0.5.8 | 377.00 | 584.00 | 961.00 | OK |
Version: 0.5.8
Check: examples
Result: ERROR
Running examples in ‘hesim-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim_stateprobs.survival
> ### Title: Simulate state probabilities from survival curves
> ### Aliases: sim_stateprobs.survival
>
> ### ** Examples
>
> library("data.table")
Attaching package: ‘data.table’
The following object is masked from ‘package:base’:
%notin%
> library("survival")
>
> # This example shows how to simulate a partitioned survival model by
> # manually constructing a "survival" object. We will consider a case in which
> # Cox proportional hazards models from the survival package---which are not
> # integrated with hesim---are used for parameter estimation. We will use
> # point estimates in the example, but bootstrapping, Bayesian modeling,
> # or other techniques could be used to draw samples for a probabilistic
> # sensitivity analysis.
>
> # (0) We first setup our model per usual by defining the treatment strategies,
> # target population, and health states
> hesim_dat <- hesim_data(
+ strategies = data.table(strategy_id = 1:3,
+ strategy_name = c("SOC", "New 1", "New 2")),
+ patients = data.table(patient_id = 1:2,
+ female = c(0, 1),
+ grp_id = 1),
+ states = data.table(state_id = 1:2,
+ state_name = c("Stable", "Progression"))
+ )
>
> # (1) Next we will estimate Cox models with survival::coxph(). We illustrate
> # by predicting progression free survival (PFS) and overall survival (OS)
> ## Fit models
> onc3_pfs_os <- as_pfs_os(onc3, patient_vars = c("patient_id", "female",
+ "strategy_name"))
> fit_pfs <- coxph(Surv(pfs_time, pfs_status) ~ strategy_name + female,
+ data = onc3_pfs_os)
> fit_os <- coxph(Surv(os_time, pfs_status) ~ strategy_name + female,
+ data = onc3_pfs_os)
>
> ## Predict survival on input data
> surv_input_data <- expand(hesim_dat)
> times <- seq(0, 14, 1/12)
> predict_survival <- function(object, newdata, times) {
+ surv <- summary(survfit(object, newdata = newdata, se.fit = FALSE),
+ t = times)
+ pred <- newdata[rep(seq_len(nrow(newdata)), each = length(times)), ]
+ pred[, sample := 1] # Point estimates only in this example
+ pred[, time := rep(surv$time, times = nrow(newdata))]
+ pred[, survival := c(surv$surv)]
+ return(pred[, ])
+ }
> pfs <- predict_survival(fit_pfs, newdata = surv_input_data, times = times)
Error in a$specials[[i]] : subscript out of bounds
Calls: predict_survival ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.5.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
Saving _problems/test-cpp-distributions-534.R
sample = 1
sample = 2
Saving _problems/test-params_surv-226.R
Saving _problems/test-params_surv_list-97.R
Saving _problems/test-psm-42.R
Saving _problems/test-sim-general-26.R
[ FAIL 5 | WARN 3 | SKIP 0 | PASS 981 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-cpp-distributions.R:532:7'): survspline ────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─hesim (local) test_survspline2(flexsurv_scale = "hazard", timescale = "log") at test-cpp-distributions.R:610:3
2. └─flexsurv::flexsurvspline(...) at test-cpp-distributions.R:532:7
3. ├─base::do.call("flexsurvreg", args)
4. └─flexsurv::flexsurvreg(...)
5. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
6. ├─survival::survfit(cox)
7. └─survival:::survfit.coxph(cox)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test-params_surv.R:225:3'): create_params.flexsurv() ────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-params_surv.R:225:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-params_surv_list.R:96:3'): create_params.partsurvfit() works as expected ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(...) at test-params_surv_list.R:96:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-psm.R:42:3'): (code run outside of `test_that()`) ──────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─flexsurv::flexsurvspline(as.formula(formulas[[i]]), data = surv_est_data) at test-psm.R:42:3
2. ├─base::do.call("flexsurvreg", args)
3. └─flexsurv::flexsurvreg(...)
4. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux)
5. ├─survival::survfit(cox, newdata = newdata)
6. └─survival:::survfit.coxph(cox, newdata = newdata)
7. └─survival:::model.matrix.coxph(object, data = mf)
8. └─stats::delete.response(object$terms)
9. └─stats (local) off(a$specials[[i]])
── Error ('test-sim-general.R:25:3'): (code run outside of `test_that()`) ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─hesim (local) predict_survival(fit_pfs, newdata = newdat, times = times) at test-sim-general.R:33:1
2. ├─base::summary(...) at test-sim-general.R:25:3
3. ├─survival::survfit(object, newdata = newdata, se.fit = FALSE)
4. └─survival:::survfit.coxph(object, newdata = newdata, se.fit = FALSE)
5. └─survival:::model.matrix.coxph(object, data = mf)
6. └─stats::delete.response(object$terms)
7. └─stats (local) off(a$specials[[i]])
[ FAIL 5 | WARN 3 | SKIP 0 | PASS 981 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
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