CRAN Package Check Results for Package heemod

Last updated on 2026-10-24 01:51:36 CEST.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.1.0	13.09	329.84	342.93	NOTE
r-devel-linux-x86_64-debian-gcc	1.1.0	8.41	223.43	231.84	ERROR
r-devel-linux-x86_64-fedora-clang	1.1.0	12.00	252.53	264.53	NOTE
r-devel-linux-x86_64-fedora-gcc	1.1.0			226.97	NOTE
r-devel-windows-x86_64	1.1.0	23.00	328.00	351.00	NOTE
r-patched-linux-x86_64	1.1.0	12.92	315.88	328.80	OK
r-release-linux-x86_64	1.1.0	13.42	316.79	330.21	OK
r-release-macos-arm64	1.1.0	3.00	75.00	78.00	OK
r-release-macos-x86_64	1.1.0	9.00	326.00	335.00	OK
r-release-windows-x86_64	1.1.0	24.00	319.00	343.00	OK
r-oldrel-macos-arm64	1.1.0				OK
r-oldrel-macos-x86_64	1.1.0	8.00	266.00	274.00	OK
r-oldrel-windows-x86_64	1.1.0	25.00	428.00	453.00	OK

Check Details

Version: 1.1.0
Check: R code for possible problems
Result: NOTE Found calls to structure() using deprecated special names: heemod/tests/testthat/test_expand.R (.Names: 20) heemod/tests/testthat/test_model.R (.Dim: 6) heemod/tests/testthat/test_probabilistic.R (.Names: 1) heemod/tests/testthat/test_tabular_input.R (.Names: 15) '.Names' should be changed to 'names'. '.Dim' should be changed to 'dim'. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [47s/60s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(heemod) > > test_check("heemod") I: detected use of 'state_time', expanding states: A, B. I: detected use of 'state_time', expanding states: A, B. I: detected use of 'state_time', expanding states: A, B. I: detected use of 'state_time', expanding states: A, B. I: detected use of 'state_time', expanding states: A, B. I: detected use of 'state_time', expanding state: A. I: detected use of 'state_time', expanding state: B. I: detected use of 'state_time', expanding state: C. Updating strategy 'I'... Updating strategy 'II'... Updating strategy 'I'... Updating strategy 'II'... No weights specified in update, using equal weights. Updating strategy 'I'... Updating strategy 'II'... Loading required namespace: diagram I: detected use of 'state_time', expanding state: A. I: detected use of 'state_time', expanding state: A. Updating strategy 'standard'... Updating strategy 'new'... Updating strategy 'standard'... Updating strategy 'new'... Cluster closed. Loading required package: survival Resampling strategy 'I'... Resampling strategy 'II'... Resampling strategy 'I'... Resampling strategy 'II'... Resampling strategy 'I'... Resampling strategy 'II'... Loading required namespace: logitnorm I: detected use of 'state_time', expanding state: X2. II: detected use of 'state_time', expanding state: X2. Resampling strategy 'I'... Resampling strategy 'II'... Saving _problems/test_surv_eval-17.R Resampling strategy 'I'... Resampling strategy 'I'... Resampling strategy 'I'... Resampling strategy 'II'... Resampling strategy 'I'... Resampling strategy 'I'... No covariates provided, returning aggregate survival across all subjects. Resampling strategy 'I'... Resampling strategy 'I'... `km_2` must be a <surv_fit> No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. Resampling strategy 'I'... Resampling strategy 'II'... No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. No covariates provided, returning aggregate survival across all subjects. Resampling strategy 'I'... Resampling strategy 'standard'... Resampling strategy 'new'... Updating strategy 'standard'... Updating strategy 'new'... [ FAIL 1 | WARN 42 | SKIP 1 | PASS 468 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_starting_values.R:200:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_surv_eval.R:11:1'): (code run outside of `test_that()`) ──────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. ├─heemod::define_surv_fit(...) at test_surv_eval.R:11:1 2. │ └─base::structure(enx, class = c("surv_fit", "surv_object"), strata = x$strata) 3. └─flexsurv::flexsurvspline(...) 4. ├─base::do.call("flexsurvreg", args) 5. └─flexsurv::flexsurvreg(...) 6. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux) 7. ├─survival::survfit(cox, newdata = newdata) 8. └─survival:::survfit.coxph(cox, newdata = newdata) 9. └─survival:::model.matrix.coxph(object, data = mf) 10. └─stats::delete.response(object$terms) 11. └─stats (local) off(a$specials[[i]]) [ FAIL 1 | WARN 42 | SKIP 1 | PASS 468 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘a_introduction.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘a_introduction.Rmd’ --- re-building ‘b_time_dependency.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘b_time_dependency.Rmd’ --- re-building ‘c_homogeneous.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘c_homogeneous.Rmd’ --- re-building ‘d_non_homogeneous.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘d_non_homogeneous.Rmd’ --- re-building ‘e_probabilistic.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘e_probabilistic.Rmd’ --- re-building ‘f_sensitivity.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘f_sensitivity.Rmd’ --- re-building ‘g_heterogeneity.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘g_heterogeneity.Rmd’ --- re-building ‘h_tabular.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘h_tabular.Rmd’ --- re-building ‘i_reproduction.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘i_reproduction.Rmd’ --- re-building ‘j_survival.Rmd’ using rmarkdown Quitting from j_survival.Rmd:43-62 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `a$specials[[i]]`: ! subscript out of bounds --- Backtrace: ▆ 1. ├─heemod::define_surv_fit(...) 2. │ └─base::structure(enx, class = c("surv_fit", "surv_object"), strata = x$strata) 3. └─flexsurv::flexsurvspline(...) 4. ├─base::do.call("flexsurvreg", args) 5. └─flexsurv::flexsurvreg(...) 6. └─dlist$inits(t = wt, mf = m, mml = mml, aux = inits.aux) 7. ├─survival::survfit(cox) 8. └─survival:::survfit.coxph(cox) 9. └─survival:::model.matrix.coxph(object, data = mf) 10. └─stats::delete.response(object$terms) 11. └─stats (local) off(a$specials[[i]]) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'j_survival.Rmd' failed with diagnostics: subscript out of bounds --- failed re-building ‘j_survival.Rmd’ --- re-building ‘j_survival_2_psa.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘j_survival_2_psa.Rmd’ --- re-building ‘k_calibration.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘k_calibration.Rmd’ SUMMARY: processing the following file failed: ‘j_survival.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc