CRAN Package Check Results for Maintainer ‘Devin Incerti <devin.incerti at gmail.com>’

Last updated on 2025-12-28 01:49:07 CET.

Package	ERROR	WARN	NOTE	OK
hesim	1	4	3	5

Package hesim

Current CRAN status: ERROR: 1, WARN: 4, NOTE: 3, OK: 5

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-clang/Work/PKGS/hesim.Rcheck/00install.out’ for details. * used C++ compiler: ‘Debian clang version 21.1.8 (1)’ Flavor: r-devel-linux-x86_64-debian-clang

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 15.2.0-12) 15.2.0’ 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: 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: whether package can be installed
Result: WARN Found the following significant warnings: Warning: src/Makevars.win: Unknown C++C++11 standard was ignored See 'd:/Rcompile/CRANpkg/local/4.6/hesim.Rcheck/00install.out' for details. * used C++ compiler: 'g++.exe (GCC) 14.3.0' Flavor: r-devel-windows-x86_64

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 2.03467701 3: 1 1 1 1 1 2 0 2.03467701 2.27235976 4: 1 1 1 1 2 3 1 2.27235976 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-windows-x86_64

Version: 0.5.7
Check: tests
Result: ERROR Running 'testthat.R' [42s] 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-windows-x86_64

Version: 0.5.7
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'cea.Rmd' using rmarkdown --- 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$sim_stateprobs(t = c(0:10)) 2. └─hesim:::indiv_ctstm_sim_stateprobs(...) 3. ├─disprog[, `:=`(strategy_index, .GRP), by = "strategy_id"] 4. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'intro.Rmd' failed with diagnostics: attempt access index 9/9 in VECTOR_ELT --- failed re-building 'intro.Rmd' --- re-building 'markov-cohort.Rmd' using rmarkdown --- finished re-building 'markov-cohort.Rmd' --- re-building 'markov-inhomogeneous-cohort.Rmd' using rmarkdown --- finished re-building 'markov-inhomogeneous-cohort.Rmd' --- re-building 'markov-inhomogeneous-indiv.Rmd' using rmarkdown Quitting from markov-inhomogeneous-indiv.Rmd:438-440 [unnamed-chunk-30] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 9/9 in VECTOR_ELT --- Backtrace: ▆ 1. └─econmod$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 --- 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 --- 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-windows-x86_64

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