Last updated on 2025-12-20 10:50:42 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.7 | 245.49 | 423.29 | 668.78 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.5.7 | 177.44 | 224.48 | 401.92 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.5.7 | 493.00 | 517.82 | 1010.82 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.5.7 | 519.00 | 499.09 | 1018.09 | ERROR | |
| r-devel-windows-x86_64 | 0.5.7 | 277.00 | 445.00 | 722.00 | OK | |
| r-patched-linux-x86_64 | 0.5.7 | 272.65 | 358.95 | 631.60 | OK | |
| r-release-linux-x86_64 | 0.5.7 | 267.65 | 360.50 | 628.15 | OK | |
| r-release-macos-arm64 | 0.5.7 | OK | ||||
| r-release-macos-x86_64 | 0.5.7 | 147.00 | 266.00 | 413.00 | OK | |
| r-release-windows-x86_64 | 0.5.7 | 276.00 | 443.00 | 719.00 | OK | |
| r-oldrel-macos-arm64 | 0.5.7 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.5.7 | 143.00 | 329.00 | 472.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.5.7 | 353.00 | 575.00 | 928.00 | NOTE |
Version: 0.5.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: src/Makevars: Unknown C++ standard ‘C++11’ was ignored
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hesim.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.5.7
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: IndivCtstm
> ### Title: Individual-level continuous time state transition model
> ### Aliases: IndivCtstm
>
> ### ** Examples
>
> library("flexsurv")
Loading required package: survival
>
> # Treatment strategies, target population, and model structure
> strategies <- data.frame(strategy_id = c(1, 2))
> patients <- data.frame(patient_id = seq(1, 3),
+ age = c(45, 50, 60),
+ female = c(0, 0, 1))
> states <- data.frame(state_id = c(1, 2))
> hesim_dat <- hesim_data(strategies = strategies,
+ patients = patients,
+ states = states)
>
> # Parameter estimation
> ## Multi-state model
> tmat <- rbind(c(NA, 1, 2),
+ c(3, NA, 4),
+ c(NA, NA, NA))
> fits <- vector(length = max(tmat, na.rm = TRUE), mode = "list")
> surv_dat <- data.frame(mstate3_exdata$transitions)
> for (i in 1:length(fits)){
+ fits[[i]] <- flexsurvreg(Surv(years, status) ~ factor(strategy_id),
+ data = surv_dat,
+ subset = (trans == i),
+ dist = "weibull")
+ }
> fits <- flexsurvreg_list(fits)
>
> ## Utility
> utility_tbl <- stateval_tbl(data.frame(state_id = states$state_id,
+ mean = mstate3_exdata$utility$mean,
+ se = mstate3_exdata$utility$se),
+ dist = "beta")
> ## Costs
> drugcost_tbl <- stateval_tbl(data.frame(strategy_id = strategies$strategy_id,
+ est = mstate3_exdata$costs$drugs$costs),
+ dist = "fixed")
> medcost_tbl <- stateval_tbl(data.frame(state_id = states$state_id,
+ mean = mstate3_exdata$costs$medical$mean,
+ se = mstate3_exdata$costs$medical$se),
+ dist = "gamma")
>
> # Economic model
> n_samples = 2
>
> ## Construct model
> ### Transitions
> transmod_data <- expand(hesim_dat)
> transmod <- create_IndivCtstmTrans(fits, input_data = transmod_data,
+ trans_mat = tmat,
+ n = n_samples)
>
> ### Utility
> utilitymod <- create_StateVals(utility_tbl, n = n_samples, hesim_data = hesim_dat)
>
> ### Costs
> drugcostmod <- create_StateVals(drugcost_tbl, n = n_samples, hesim_data = hesim_dat)
> medcostmod <- create_StateVals(medcost_tbl, n = n_samples, hesim_data = hesim_dat)
> costmods <- list(drugs = drugcostmod,
+ medical = medcostmod)
>
> ### Combine
> ictstm <- IndivCtstm$new(trans_model = transmod,
+ utility_model = utilitymod,
+ cost_models = costmods)
>
>
> ## Simulate outcomes
> head(ictstm$sim_disease()$disprog_)
sample strategy_id patient_id grp_id from to final time_start time_stop
<num> <int> <int> <int> <num> <num> <int> <num> <num>
1: 1 1 1 1 1 2 0 0.00000000 0.42756667
2: 1 1 1 1 2 1 0 0.42756667 2.03467700
3: 1 1 1 1 1 2 0 2.03467700 2.27235975
4: 1 1 1 1 2 3 1 2.27235975 2.85620102
5: 1 1 2 1 1 2 0 0.00000000 0.05681537
6: 1 1 2 1 2 1 0 0.05681537 0.55861667
> head(ictstm$sim_stateprobs(t = c(0, 5, 10))$stateprobs_[t == 5])
Error in `[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id") :
attempt access index 9/9 in VECTOR_ELT
Calls: head ... <Anonymous> -> indiv_ctstm_sim_stateprobs -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.5.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
Saving _problems/test-cpp-distributions-103.R
Saving _problems/test-ctstm-215.R
Saving _problems/test-ctstm-271.R
Saving _problems/test-ctstm-309.R
Saving _problems/test-ctstm-387.R
Saving _problems/test-ctstm-392.R
sample = 1
sample = 2
Saving _problems/test-ctstm-595.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 1095 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-cpp-distributions.R:100:1'): (code run outside of `test_that()`) ──
`new(PwExp, rate = c(1, 2), time = c(0, 2, 4))` threw an error with unexpected message.
Expected match: "'time' and 'rate' must be the same length."
Actual message: "object 'PwExp' not found"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-cpp-distributions.R:100:1
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─methods::new(PwExp, rate = c(1, 2), time = c(0, 2, 4))
7. └─methods::getClass(Class, where = topenv(parent.frame()))
8. └─methods::getClassDef(Class, where)
9. └─methods:::.getClassesFromCache(Class)
── Error ('test-ctstm.R:215:3'): IndivCtstmTrans - transition specific ─────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─mstate_list$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:215:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(disprog, self, t)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:271:3'): IndivCtstmTrans - joint ───────────────────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-ctstm.R:271:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::inherits(mstate$sim_stateprobs(t = c(0, 1, 2)), "data.table")
5. └─mstate$sim_stateprobs(t = c(0, 1, 2))
6. └─hesim:::indiv_ctstm_sim_stateprobs(disprog, self, t)
7. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
8. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:309:3'): Simulate disease progression with transition specific models ──
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:309:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Failure ('test-ctstm.R:387:3'): Simulate costs and QALYs ────────────────────
`ictstm$sim_qalys(dr = 0.03)$qalys_` threw an error.
Message: attempt access index 9/9 in VECTOR_ELT
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(ictstm$sim_qalys(dr = 0.03)$qalys_, NA) at test-ctstm.R:387:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─ictstm$sim_qalys(dr = 0.03)
7. └─private$sim_ev(...)
8. ├─self$disprog_[, `:=`(strategy_idx, .GRP), by = "strategy_id"]
9. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:392:3'): Simulate costs and QALYs ──────────────────────
Error in ``[.data.table`(self$disprog_, , `:=`(strategy_idx, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_qalys(dr = 0.03, by_patient = TRUE) at test-ctstm.R:392:3
2. └─private$sim_ev(...)
3. ├─self$disprog_[, `:=`(strategy_idx, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:595:3'): IndivCtstm - joint ────────────────────────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:595:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 1095 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.5.7
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cea.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘cea.Rmd’
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from intro.Rmd:301-304 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 9/9 in VECTOR_ELT
---
Backtrace:
▆
1. └─ictstm$sim_stateprobs(t = c(0:10))
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'intro.Rmd' failed with diagnostics:
attempt access index 9/9 in VECTOR_ELT
--- failed re-building ‘intro.Rmd’
--- re-building ‘markov-cohort.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘markov-cohort.Rmd’
--- re-building ‘markov-inhomogeneous-cohort.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘markov-inhomogeneous-cohort.Rmd’
--- re-building ‘markov-inhomogeneous-indiv.Rmd’ using rmarkdown
Quitting from markov-inhomogeneous-indiv.Rmd:438-440 [unnamed-chunk-30]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 9/9 in VECTOR_ELT
---
Backtrace:
▆
1. └─econmod$sim_stateprobs(t = 0:60)
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'markov-inhomogeneous-indiv.Rmd' failed with diagnostics:
attempt access index 9/9 in VECTOR_ELT
--- failed re-building ‘markov-inhomogeneous-indiv.Rmd’
--- re-building ‘mlogit.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘mlogit.Rmd’
--- re-building ‘mstate.Rmd’ using rmarkdown
Quitting from mstate.Rmd:247-249 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 9/9 in VECTOR_ELT
---
Backtrace:
▆
1. └─econmod_cr$sim_stateprobs(t = seq(0, 20, 1/12))
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'mstate.Rmd' failed with diagnostics:
attempt access index 9/9 in VECTOR_ELT
--- failed re-building ‘mstate.Rmd’
--- re-building ‘psm.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘psm.Rmd’
SUMMARY: processing the following files failed:
‘intro.Rmd’ ‘markov-inhomogeneous-indiv.Rmd’ ‘mstate.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.5.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: src/Makevars: Unknown C++ standard ‘C++11’ was ignored
See ‘/data/gannet/ripley/R/packages/tests-clang/hesim.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 21.1.8’
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5.7
Check: examples
Result: ERROR
Running examples in ‘hesim-Ex.R’ failed
The error most likely occurred in:
> ### Name: IndivCtstm
> ### Title: Individual-level continuous time state transition model
> ### Aliases: IndivCtstm
>
> ### ** Examples
>
> library("flexsurv")
Loading required package: survival
>
> # Treatment strategies, target population, and model structure
> strategies <- data.frame(strategy_id = c(1, 2))
> patients <- data.frame(patient_id = seq(1, 3),
+ age = c(45, 50, 60),
+ female = c(0, 0, 1))
> states <- data.frame(state_id = c(1, 2))
> hesim_dat <- hesim_data(strategies = strategies,
+ patients = patients,
+ states = states)
>
> # Parameter estimation
> ## Multi-state model
> tmat <- rbind(c(NA, 1, 2),
+ c(3, NA, 4),
+ c(NA, NA, NA))
> fits <- vector(length = max(tmat, na.rm = TRUE), mode = "list")
> surv_dat <- data.frame(mstate3_exdata$transitions)
> for (i in 1:length(fits)){
+ fits[[i]] <- flexsurvreg(Surv(years, status) ~ factor(strategy_id),
+ data = surv_dat,
+ subset = (trans == i),
+ dist = "weibull")
+ }
> fits <- flexsurvreg_list(fits)
>
> ## Utility
> utility_tbl <- stateval_tbl(data.frame(state_id = states$state_id,
+ mean = mstate3_exdata$utility$mean,
+ se = mstate3_exdata$utility$se),
+ dist = "beta")
> ## Costs
> drugcost_tbl <- stateval_tbl(data.frame(strategy_id = strategies$strategy_id,
+ est = mstate3_exdata$costs$drugs$costs),
+ dist = "fixed")
> medcost_tbl <- stateval_tbl(data.frame(state_id = states$state_id,
+ mean = mstate3_exdata$costs$medical$mean,
+ se = mstate3_exdata$costs$medical$se),
+ dist = "gamma")
>
> # Economic model
> n_samples = 2
>
> ## Construct model
> ### Transitions
> transmod_data <- expand(hesim_dat)
> transmod <- create_IndivCtstmTrans(fits, input_data = transmod_data,
+ trans_mat = tmat,
+ n = n_samples)
>
> ### Utility
> utilitymod <- create_StateVals(utility_tbl, n = n_samples, hesim_data = hesim_dat)
>
> ### Costs
> drugcostmod <- create_StateVals(drugcost_tbl, n = n_samples, hesim_data = hesim_dat)
> medcostmod <- create_StateVals(medcost_tbl, n = n_samples, hesim_data = hesim_dat)
> costmods <- list(drugs = drugcostmod,
+ medical = medcostmod)
>
> ### Combine
> ictstm <- IndivCtstm$new(trans_model = transmod,
+ utility_model = utilitymod,
+ cost_models = costmods)
>
>
> ## Simulate outcomes
> head(ictstm$sim_disease()$disprog_)
sample strategy_id patient_id grp_id from to final time_start time_stop
<num> <int> <int> <int> <num> <num> <int> <num> <num>
1: 1 1 1 1 1 2 0 0.00000000 0.42756667
2: 1 1 1 1 2 1 0 0.42756667 2.03467700
3: 1 1 1 1 1 2 0 2.03467700 2.27235975
4: 1 1 1 1 2 3 1 2.27235975 2.85620102
5: 1 1 2 1 1 2 0 0.00000000 0.05681537
6: 1 1 2 1 2 1 0 0.05681537 0.55861667
> head(ictstm$sim_stateprobs(t = c(0, 5, 10))$stateprobs_[t == 5])
Error in `[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id") :
attempt access index 9/9 in VECTOR_ELT
Calls: head ... <Anonymous> -> indiv_ctstm_sim_stateprobs -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.5.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [72s/122s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
Saving _problems/test-cpp-distributions-103.R
Saving _problems/test-ctstm-215.R
Saving _problems/test-ctstm-271.R
Saving _problems/test-ctstm-309.R
Saving _problems/test-ctstm-387.R
Saving _problems/test-ctstm-392.R
sample = 1
sample = 2
Saving _problems/test-ctstm-595.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 1095 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-cpp-distributions.R:100:1'): (code run outside of `test_that()`) ──
`new(PwExp, rate = c(1, 2), time = c(0, 2, 4))` threw an error with unexpected message.
Expected match: "'time' and 'rate' must be the same length."
Actual message: "object 'PwExp' not found"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-cpp-distributions.R:100:1
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─methods::new(PwExp, rate = c(1, 2), time = c(0, 2, 4))
7. └─methods::getClass(Class, where = topenv(parent.frame()))
8. └─methods::getClassDef(Class, where)
9. └─methods:::.getClassesFromCache(Class)
── Error ('test-ctstm.R:215:3'): IndivCtstmTrans - transition specific ─────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─mstate_list$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:215:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(disprog, self, t)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:271:3'): IndivCtstmTrans - joint ───────────────────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-ctstm.R:271:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::inherits(mstate$sim_stateprobs(t = c(0, 1, 2)), "data.table")
5. └─mstate$sim_stateprobs(t = c(0, 1, 2))
6. └─hesim:::indiv_ctstm_sim_stateprobs(disprog, self, t)
7. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
8. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:309:3'): Simulate disease progression with transition specific models ──
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:309:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Failure ('test-ctstm.R:387:3'): Simulate costs and QALYs ────────────────────
`ictstm$sim_qalys(dr = 0.03)$qalys_` threw an error.
Message: attempt access index 9/9 in VECTOR_ELT
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(ictstm$sim_qalys(dr = 0.03)$qalys_, NA) at test-ctstm.R:387:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─ictstm$sim_qalys(dr = 0.03)
7. └─private$sim_ev(...)
8. ├─self$disprog_[, `:=`(strategy_idx, .GRP), by = "strategy_id"]
9. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:392:3'): Simulate costs and QALYs ──────────────────────
Error in ``[.data.table`(self$disprog_, , `:=`(strategy_idx, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_qalys(dr = 0.03, by_patient = TRUE) at test-ctstm.R:392:3
2. └─private$sim_ev(...)
3. ├─self$disprog_[, `:=`(strategy_idx, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:595:3'): IndivCtstm - joint ────────────────────────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:595:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 1095 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5.7
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘cea.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘cea.Rmd’
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from intro.Rmd:301-304 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 9/9 in VECTOR_ELT
---
Backtrace:
▆
1. └─ictstm$sim_stateprobs(t = c(0:10))
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'intro.Rmd' failed with diagnostics:
attempt access index 9/9 in VECTOR_ELT
--- failed re-building ‘intro.Rmd’
--- re-building ‘markov-cohort.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘markov-cohort.Rmd’
--- re-building ‘markov-inhomogeneous-cohort.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘markov-inhomogeneous-cohort.Rmd’
--- re-building ‘markov-inhomogeneous-indiv.Rmd’ using rmarkdown
Quitting from markov-inhomogeneous-indiv.Rmd:438-440 [unnamed-chunk-30]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 9/9 in VECTOR_ELT
---
Backtrace:
▆
1. └─econmod$sim_stateprobs(t = 0:60)
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'markov-inhomogeneous-indiv.Rmd' failed with diagnostics:
attempt access index 9/9 in VECTOR_ELT
--- failed re-building ‘markov-inhomogeneous-indiv.Rmd’
--- re-building ‘mlogit.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘mlogit.Rmd’
--- re-building ‘mstate.Rmd’ using rmarkdown
Quitting from mstate.Rmd:247-249 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 9/9 in VECTOR_ELT
---
Backtrace:
▆
1. └─econmod_cr$sim_stateprobs(t = seq(0, 20, 1/12))
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'mstate.Rmd' failed with diagnostics:
attempt access index 9/9 in VECTOR_ELT
--- failed re-building ‘mstate.Rmd’
--- re-building ‘psm.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘psm.Rmd’
SUMMARY: processing the following files failed:
‘intro.Rmd’ ‘markov-inhomogeneous-indiv.Rmd’ ‘mstate.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.5.7
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Warning: src/Makevars: Unknown C++ standard ‘C++11’ was ignored
See ‘/data/gannet/ripley/R/packages/tests-devel/hesim.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.5.7
Check: tests
Result: ERROR
Running ‘testthat.R’ [63s/90s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
Saving _problems/test-cpp-distributions-103.R
Saving _problems/test-ctstm-215.R
Saving _problems/test-ctstm-271.R
Saving _problems/test-ctstm-309.R
Saving _problems/test-ctstm-387.R
Saving _problems/test-ctstm-392.R
sample = 1
sample = 2
Saving _problems/test-ctstm-595.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 1095 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-cpp-distributions.R:100:1'): (code run outside of `test_that()`) ──
`new(PwExp, rate = c(1, 2), time = c(0, 2, 4))` threw an error with unexpected message.
Expected match: "'time' and 'rate' must be the same length."
Actual message: "object 'PwExp' not found"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-cpp-distributions.R:100:1
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─methods::new(PwExp, rate = c(1, 2), time = c(0, 2, 4))
7. └─methods::getClass(Class, where = topenv(parent.frame()))
8. └─methods::getClassDef(Class, where)
9. └─methods:::.getClassesFromCache(Class)
── Error ('test-ctstm.R:215:3'): IndivCtstmTrans - transition specific ─────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─mstate_list$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:215:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(disprog, self, t)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:271:3'): IndivCtstmTrans - joint ───────────────────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_true(...) at test-ctstm.R:271:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::inherits(mstate$sim_stateprobs(t = c(0, 1, 2)), "data.table")
5. └─mstate$sim_stateprobs(t = c(0, 1, 2))
6. └─hesim:::indiv_ctstm_sim_stateprobs(disprog, self, t)
7. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
8. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:309:3'): Simulate disease progression with transition specific models ──
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:309:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Failure ('test-ctstm.R:387:3'): Simulate costs and QALYs ────────────────────
`ictstm$sim_qalys(dr = 0.03)$qalys_` threw an error.
Message: attempt access index 9/9 in VECTOR_ELT
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(ictstm$sim_qalys(dr = 0.03)$qalys_, NA) at test-ctstm.R:387:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─ictstm$sim_qalys(dr = 0.03)
7. └─private$sim_ev(...)
8. ├─self$disprog_[, `:=`(strategy_idx, .GRP), by = "strategy_id"]
9. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:392:3'): Simulate costs and QALYs ──────────────────────
Error in ``[.data.table`(self$disprog_, , `:=`(strategy_idx, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_qalys(dr = 0.03, by_patient = TRUE) at test-ctstm.R:392:3
2. └─private$sim_ev(...)
3. ├─self$disprog_[, `:=`(strategy_idx, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
── Error ('test-ctstm.R:595:3'): IndivCtstm - joint ────────────────────────────
Error in ``[.data.table`(disprog, , `:=`(strategy_index, .GRP), by = "strategy_id")`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─ictstm$sim_stateprobs(t = c(0, 1, 2, 3)) at test-ctstm.R:595:3
2. └─hesim:::indiv_ctstm_sim_stateprobs(...)
3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"]
4. └─data.table:::`[.data.table`(...)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 1095 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.5.7
Check: installed package size
Result: NOTE
installed size is 23.9Mb
sub-directories of 1Mb or more:
doc 2.2Mb
libs 19.8Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64