CRAN Package Check Results for Package InformativeCensoring

Last updated on 2026-10-24 17:51:34 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.3.6	8.94	522.10	531.04	OK
r-devel-linux-x86_64-debian-gcc	0.3.6	7.31	73.97	81.28	ERROR
r-devel-linux-x86_64-fedora-clang	0.3.6			365.31	OK
r-devel-linux-x86_64-fedora-gcc	0.3.6			353.58	OK
r-devel-windows-x86_64	0.3.6	12.00	278.00	290.00	OK	--no-vignettes
r-patched-linux-x86_64	0.3.6	9.25	499.94	509.19	OK
r-release-linux-x86_64	0.3.6	9.21	498.22	507.43	OK
r-release-macos-arm64	0.3.6	2.00	105.00	107.00	OK
r-release-macos-x86_64	0.3.6	6.00	564.00	570.00	OK
r-release-windows-x86_64	0.3.6	12.00	245.00	257.00	OK	--no-vignettes
r-oldrel-macos-arm64	0.3.6				OK
r-oldrel-macos-x86_64	0.3.6	6.00	447.00	453.00	OK
r-oldrel-windows-x86_64	0.3.6	16.00	320.00	336.00	OK	--no-vignettes

Check Details

Version: 0.3.6
Check: tests
Result: ERROR Running ‘testthat.R’ [7s/8s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library("InformativeCensoring") Loading required package: survival Attaching package: 'InformativeCensoring' The following object is masked from 'package:survival': cox.zph > > test_check("InformativeCensoring") Saving _problems/test-gammaImputedata-16.R Saving _problems/test-gammaImputedata-47.R Saving _problems/test-gammaImputedata-72.R Saving _problems/test-gammaImputedata-111.R Saving _problems/test-gammaImputedata-143.R Saving _problems/test-gammaImputedata-169.R Saving _problems/test-gammaImputedata-207.R Saving _problems/test-gammaImputedata-225.R Saving _problems/test-gammaStat-10.R Saving _problems/test-gammaStat-51.R Saving _problems/test-gammaStat-85.R Saving _problems/test-gammaStat-103.R Saving _problems/test-gammaStat-134.R Saving _problems/test-scoreExtract-16.R Saving _problems/test-scoreExtract-67.R Saving _problems/test-scoreSystem-73.R Saving _problems/test-scoreSystem-118.R Saving _problems/test-scoreSystem-140.R Saving _problems/test-scoreSystem-177.R Saving _problems/test-scoreSystem-216.R Saving _problems/test-scoreSystem-256.R Saving _problems/test-validationGamma-26.R Saving _problems/test-validationGamma-39.R [ FAIL 23 | WARN 0 | SKIP 0 | PASS 376 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-gammaImputedata.R:12:3'): GammaImputeSet_object ──────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaImputedata.R:12:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaImputedata.R:43:3'): gamma.factor ───────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaImputedata.R:43:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaImputedata.R:68:3'): inf.gamma.factor ───────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaImputedata.R:68:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaImputedata.R:108:3'): impute.times.non_stochastic_tests ─── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. ├─InformativeCensoring::ExtractSingle(...) at test-gammaImputedata.R:108:3 2. └─InformativeCensoring::gammaImpute(...) 3. └─base::lapply(...) 4. └─InformativeCensoring (local) FUN(X[[i]], ...) 5. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 6. │ ├─"strata" %in% colnames(base.hazard) 7. │ └─base::colnames(base.hazard) 8. │ └─base::is.data.frame(x) 9. └─survival::basehaz(model) 10. ├─survival::survfit(fit, se.fit = FALSE) 11. └─survival:::survfit.coxph(fit, se.fit = FALSE) 12. └─survival:::model.matrix.coxph(object, data = mf) 13. └─stats::delete.response(object$terms) 14. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaImputedata.R:140:3'): internal_gamma_val_same_with_colname_or_vect ── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaImputedata.R:140:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaImputedata.R:165:3'): gamma_and_gamma_factor ────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaImputedata.R:165:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaImputedata.R:203:3'): DCO.time_vector ───────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaImputedata.R:203:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaImputedata.R:221:3'): DCO.time_different_inputs_agree ───── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaImputedata.R:221:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaStat.R:7:3'): GammaStat ─────────────────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaStat.R:7:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaStat.R:48:3'): weibull_and_exponential ──────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaStat.R:48:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaStat.R:82:3'): default_formula_behaves_as_expected ──────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaStat.R:82:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaStat.R:100:3'): GammaStatSet ────────────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaStat.R:100:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-gammaStat.R:131:3'): GammaStatSet_multiplecovar ──────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::gammaImpute(...) at test-gammaStat.R:131:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 5. │ ├─"strata" %in% colnames(base.hazard) 6. │ └─base::colnames(base.hazard) 7. │ └─base::is.data.frame(x) 8. └─survival::basehaz(model) 9. ├─survival::survfit(fit, se.fit = FALSE) 10. └─survival:::survfit.coxph(fit, se.fit = FALSE) 11. └─survival:::model.matrix.coxph(object, data = mf) 12. └─stats::delete.response(object$terms) 13. └─stats (local) off(a$specials[[i]]) ── Error ('test-scoreExtract.R:8:3'): ScoreImputeSet_extract ─────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::ScoreImpute(...) at test-scoreExtract.R:8:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─base::by(...) 5. └─base::by.data.frame(...) 6. ├─base::structure(...) 7. └─base::eval(...) 8. └─base::eval(...) 9. └─base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 10. └─base::lapply(X = ans[index], FUN = FUN, ...) 11. └─base (local) FUN(X[[i]], ...) 12. └─InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 13. └─InformativeCensoring:::.imputeTimes(...) 14. └─InformativeCensoring:::.calcscores(...) 15. ├─base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 16. └─InformativeCensoring (local) lin.comb(model.fits[[1]]) 17. ├─stats::predict(model.fit, type = "lp") 18. └─survival:::predict.coxph(model.fit, type = "lp") 19. └─stats::delete.response(Terms) 20. └─stats (local) off(a$specials[[i]]) ── Error ('test-scoreExtract.R:58:3'): ExtractSingle.Stat ────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::ScoreImpute(...) at test-scoreExtract.R:58:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─base::by(...) 5. └─base::by.data.frame(...) 6. ├─base::structure(...) 7. └─base::eval(...) 8. └─base::eval(...) 9. └─base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 10. └─base::lapply(X = ans[index], FUN = FUN, ...) 11. └─base (local) FUN(X[[i]], ...) 12. └─InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 13. └─InformativeCensoring:::.imputeTimes(...) 14. └─InformativeCensoring:::.calcscores(...) 15. ├─base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 16. └─InformativeCensoring (local) lin.comb(model.fits[[1]]) 17. ├─stats::predict(model.fit, type = "lp") 18. └─survival:::predict.coxph(model.fit, type = "lp") 19. └─stats::delete.response(Terms) 20. └─stats (local) off(a$specials[[i]]) ── Error ('test-scoreSystem.R:70:3'): ScoreImputedDataOutput ─────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::ScoreImpute(...) at test-scoreSystem.R:70:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─base::by(...) 5. └─base::by.data.frame(...) 6. ├─base::structure(...) 7. └─base::eval(...) 8. └─base::eval(...) 9. └─base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 10. └─base::lapply(X = ans[index], FUN = FUN, ...) 11. └─base (local) FUN(X[[i]], ...) 12. └─InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 13. └─InformativeCensoring:::.imputeTimes(...) 14. └─InformativeCensoring:::.calcscores(...) 15. ├─base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 16. └─InformativeCensoring (local) lin.comb(model.fits[[1]]) 17. ├─stats::predict(model.fit, type = "lp") 18. └─survival:::predict.coxph(model.fit, type = "lp") 19. └─stats::delete.response(Terms) 20. └─stats (local) off(a$specials[[i]]) ── Error ('test-scoreSystem.R:116:3'): algorithm_is_stochastic ───────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::ScoreImpute(...) at test-scoreSystem.R:116:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─base::by(...) 5. └─base::by.data.frame(...) 6. ├─base::structure(...) 7. └─base::eval(...) 8. └─base::eval(...) 9. └─base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 10. └─base::lapply(X = ans[index], FUN = FUN, ...) 11. └─base (local) FUN(X[[i]], ...) 12. └─InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 13. └─InformativeCensoring:::.imputeTimes(...) 14. └─InformativeCensoring:::.calcscores(...) 15. ├─base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 16. └─InformativeCensoring (local) lin.comb(model.fits[[1]]) 17. ├─stats::predict(model.fit, type = "lp") 18. └─survival:::predict.coxph(model.fit, type = "lp") 19. └─stats::delete.response(Terms) 20. └─stats (local) off(a$specials[[i]]) ── Error ('test-scoreSystem.R:138:3'): factor_numeric_character_Id_same_answer ── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::ScoreImpute(...) at test-scoreSystem.R:138:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─base::by(...) 5. └─base::by.data.frame(...) 6. ├─base::structure(...) 7. └─base::eval(...) 8. └─base::eval(...) 9. └─base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 10. └─base::lapply(X = ans[index], FUN = FUN, ...) 11. └─base (local) FUN(X[[i]], ...) 12. └─InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 13. └─InformativeCensoring:::.imputeTimes(...) 14. └─InformativeCensoring:::.calcscores(...) 15. ├─base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 16. └─InformativeCensoring (local) lin.comb(model.fits[[1]]) 17. ├─stats::predict(model.fit, type = "lp") 18. └─survival:::predict.coxph(model.fit, type = "lp") 19. └─stats::delete.response(Terms) 20. └─stats (local) off(a$specials[[i]]) ── Error ('test-scoreSystem.R:174:3'): using_censor_type_gives_same_result_as_not_if_no_administrative_censoring ── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::ScoreImpute(...) at test-scoreSystem.R:174:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─base::by(...) 5. └─base::by.data.frame(...) 6. ├─base::structure(...) 7. └─base::eval(...) 8. └─base::eval(...) 9. └─base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 10. └─base::lapply(X = ans[index], FUN = FUN, ...) 11. └─base (local) FUN(X[[i]], ...) 12. └─InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 13. └─InformativeCensoring:::.imputeTimes(...) 14. └─InformativeCensoring:::.calcscores(...) 15. ├─base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 16. └─InformativeCensoring (local) lin.comb(model.fits[[1]]) 17. ├─stats::predict(model.fit, type = "lp") 18. └─survival:::predict.coxph(model.fit, type = "lp") 19. └─stats::delete.response(Terms) 20. └─stats (local) off(a$specials[[i]]) ── Error ('test-scoreSystem.R:207:3'): Sfn_time_dep ──────────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-scoreSystem.R:207:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─InformativeCensoring::ScoreImpute(...) 7. └─base::lapply(...) 8. └─InformativeCensoring (local) FUN(X[[i]], ...) 9. ├─base::by(...) 10. └─base::by.data.frame(...) 11. ├─base::structure(...) 12. └─base::eval(...) 13. └─base::eval(...) 14. └─base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 15. └─base::lapply(X = ans[index], FUN = FUN, ...) 16. └─base (local) FUN(X[[i]], ...) 17. └─InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 18. └─InformativeCensoring:::.imputeTimes(...) 19. └─base::lapply(...) 20. └─InformativeCensoring (local) FUN(X[[i]], ...) 21. └─InformativeCensoring:::.calcscores(...) 22. ├─base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 23. └─InformativeCensoring (local) lin.comb(model.fits[[1]]) 24. ├─stats::predict(model.fit, type = "lp") 25. └─survival:::predict.coxph(model.fit, type = "lp") 26. └─stats::delete.response(Terms) 27. └─stats (local) off(a$specials[[i]]) ── Error ('test-scoreSystem.R:253:3'): ordering_timeindep ────────────────────── <subscriptOutOfBoundsError/error/condition> Error in `a$specials[[i]]`: subscript out of bounds Backtrace: ▆ 1. └─InformativeCensoring::ScoreImpute(...) at test-scoreSystem.R:253:3 2. └─base::lapply(...) 3. └─InformativeCensoring (local) FUN(X[[i]], ...) 4. ├─base::by(...) 5. └─base::by.data.frame(...) 6. ├─base::structure(...) 7. └─base::eval(...) 8. └─base::eval(...) 9. └─base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 10. └─base::lapply(X = ans[index], FUN = FUN, ...) 11. └─base (local) FUN(X[[i]], ...) 12. └─InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 13. └─InformativeCensoring:::.imputeTimes(...) 14. └─InformativeCensoring:::.calcscores(...) 15. ├─base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 16. └─InformativeCensoring (local) lin.comb(model.fits[[1]]) 17. ├─stats::predict(model.fit, type = "lp") 18. └─survival:::predict.coxph(model.fit, type = "lp") 19. └─stats::delete.response(Terms) 20. └─stats (local) off(a$specials[[i]]) ── Failure ('test-validationGamma.R:23:3'): invalid_rhs_formula ──────────────── `gammaImpute(...)` threw an error. Message: subscript out of bounds Class: subscriptOutOfBoundsError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-validationGamma.R:23:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─InformativeCensoring::gammaImpute(...) 7. └─base::lapply(...) 8. └─InformativeCensoring (local) FUN(X[[i]], ...) 9. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 10. │ ├─"strata" %in% colnames(base.hazard) 11. │ └─base::colnames(base.hazard) 12. │ └─base::is.data.frame(x) 13. └─survival::basehaz(model) 14. ├─survival::survfit(fit, se.fit = FALSE) 15. └─survival:::survfit.coxph(fit, se.fit = FALSE) 16. └─survival:::model.matrix.coxph(object, data = mf) 17. └─stats::delete.response(object$terms) 18. └─stats (local) off(a$specials[[i]]) ── Failure ('test-validationGamma.R:36:3'): validate_gamma_arguments_lhs_formula ── `gammaImpute(...)` threw an error. Message: subscript out of bounds Class: subscriptOutOfBoundsError/error/condition Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-validationGamma.R:36:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─InformativeCensoring::gammaImpute(...) 7. └─base::lapply(...) 8. └─InformativeCensoring (local) FUN(X[[i]], ...) 9. ├─InformativeCensoring:::.SetupStrataBaseHaz(...) 10. │ ├─"strata" %in% colnames(base.hazard) 11. │ └─base::colnames(base.hazard) 12. │ └─base::is.data.frame(x) 13. └─survival::basehaz(model) 14. ├─survival::survfit(fit, se.fit = FALSE) 15. └─survival:::survfit.coxph(fit, se.fit = FALSE) 16. └─survival:::model.matrix.coxph(object, data = mf) 17. └─stats::delete.response(object$terms) 18. └─stats (local) off(a$specials[[i]]) [ FAIL 23 | WARN 0 | SKIP 0 | PASS 376 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.3.6
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘gamma_imputation_Jackson_2014.Rnw’ using knitr Quitting from gamma_imputation_Jackson_2014.Rnw:118-123 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `a$specials[[i]]`: ! subscript out of bounds --- Backtrace: x 1. \-InformativeCensoring::gammaImpute(...) 2. \-base::lapply(...) 3. \-InformativeCensoring (local) FUN(X[[i]], ...) 4. +-InformativeCensoring:::.SetupStrataBaseHaz(...) 5. | +-"strata" %in% colnames(base.hazard) 6. | \-base::colnames(base.hazard) 7. | \-base::is.data.frame(x) 8. \-survival::basehaz(model) 9. +-survival::survfit(fit, se.fit = FALSE) 10. \-survival:::survfit.coxph(fit, se.fit = FALSE) 11. \-survival:::model.matrix.coxph(object, data = mf) 12. \-stats::delete.response(object$terms) 13. \-stats (local) off(a$specials[[i]]) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'gamma_imputation_Jackson_2014.Rnw' failed with diagnostics: subscript out of bounds --- failed re-building ‘gamma_imputation_Jackson_2014.Rnw’ --- re-building ‘risk_score_imputation_Hsu_2009.Rnw’ using knitr Quitting from risk_score_imputation_Hsu_2009.Rnw:140-145 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `a$specials[[i]]`: ! subscript out of bounds --- Backtrace: x 1. \-InformativeCensoring::ScoreImpute(...) 2. \-base::lapply(...) 3. \-InformativeCensoring (local) FUN(X[[i]], ...) 4. +-base::by(...) 5. \-base::by.data.frame(...) 6. +-base::structure(...) 7. \-base::eval(...) 8. \-base::eval(...) 9. \-base::tapply(seq_len(400L), `<named list>`, `<fn>`, simplify = FALSE) 10. \-base::lapply(X = ans[index], FUN = FUN, ...) 11. \-base (local) FUN(X[[i]], ...) 12. \-InformativeCensoring (local) FUN(data[x, , drop = FALSE], ...) 13. \-InformativeCensoring:::.imputeTimes(...) 14. \-InformativeCensoring:::.calcscores(...) 15. +-base::data.frame(Rs.f = lin.comb(model.fits[[1]]), Rs.c = lin.comb(model.fits[[2]])) 16. \-InformativeCensoring (local) lin.comb(model.fits[[1]]) 17. +-stats::predict(model.fit, type = "lp") 18. \-survival:::predict.coxph(model.fit, type = "lp") 19. \-stats::delete.response(Terms) 20. \-stats (local) off(a$specials[[i]]) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'risk_score_imputation_Hsu_2009.Rnw' failed with diagnostics: subscript out of bounds --- failed re-building ‘risk_score_imputation_Hsu_2009.Rnw’ SUMMARY: processing the following files failed: ‘gamma_imputation_Jackson_2014.Rnw’ ‘risk_score_imputation_Hsu_2009.Rnw’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc