CRAN Package Check Results for Package popEpi

Last updated on 2025-12-28 01:48:47 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.4.13	19.78	257.96	277.74	OK
r-devel-linux-x86_64-debian-gcc	0.4.13	11.14	179.96	191.10	OK
r-devel-linux-x86_64-fedora-clang	0.4.13	33.00	395.33	428.33	OK
r-devel-linux-x86_64-fedora-gcc	0.4.13	34.00	444.36	478.36	OK
r-devel-windows-x86_64	0.4.13	22.00	178.00	200.00	ERROR
r-patched-linux-x86_64	0.4.13	18.88	315.29	334.17	OK
r-release-linux-x86_64	0.4.13	18.33	329.64	347.97	OK
r-release-macos-arm64	0.4.13				OK
r-release-macos-x86_64	0.4.13	12.00	225.00	237.00	OK
r-release-windows-x86_64	0.4.13	20.00	254.00	274.00	OK
r-oldrel-macos-arm64	0.4.13				OK
r-oldrel-macos-x86_64	0.4.13	12.00	290.00	302.00	OK
r-oldrel-windows-x86_64	0.4.13	27.00	331.00	358.00	OK

Additional issues

M1mac

Check Details

Version: 0.4.13
Check: examples
Result: ERROR Running examples in 'popEpi-Ex.R' failed The error most likely occurred in: > ### Name: aggre > ### Title: Aggregation of split 'Lexis' data > ### Aliases: aggre > > ### ** Examples > > > ## form a Lexis object > library(Epi) > data(sibr) > x <- sibr[1:10,] > x[1:5,]$sex <- 0 ## pretend some are male > x <- Lexis(data = x, + entry = list(AGE = dg_age, CAL = get.yrs(dg_date)), + exit = list(CAL = get.yrs(ex_date)), + entry.status=0, exit.status = status) > x <- splitMulti(x, breaks = list(CAL = seq(1993, 2013, 5), + AGE = seq(0, 100, 50))) Error in `[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), : attempt access index 12/12 in VECTOR_ELT Calls: splitMulti -> [ -> [.data.table Execution halted Flavor: r-devel-windows-x86_64

Version: 0.4.13
Check: tests
Result: ERROR Running 'testthat.R' [33s] Running the tests in 'tests/testthat.R' failed. Complete output: > > if (requireNamespace("testthat")) { + library("testthat") + library("popEpi") + library("data.table") + + using_r_devel <- grepl(pattern = "devel", x = R.version$status) + if (using_r_devel) { + ## memory leak problem in data.table 1.11.2 in R-devel (3.6.0 atm) + requireNamespace("data.table") + data.table::setDTthreads(threads = 1L) + } + + testthat::test_check("popEpi") + } Loading required namespace: testthat Attaching package: 'data.table' The following object is masked from 'package:base': %notin% Saving _problems/test_aggre-8.R Saving _problems/test_aggre-31.R Saving _problems/test_aggre-43.R Saving _problems/test_aggre-103.R Saving _problems/test_aggre-138.R Saving _problems/test_lexpand-51.R Saving _problems/test_lexpand-187.R Saving _problems/test_lexpand-239.R Saving _problems/test_lexpand-289.R Saving _problems/test_rate-16.R Saving _problems/test_rate-83.R Saving _problems/test_rate-104.R Saving _problems/test_rate-167.R Saving _problems/test_rate-194.R Saving _problems/test_rate-200.R Saving _problems/test_rate-232.R Saving _problems/test_sir-58.R Saving _problems/test_splitMulti-124.R Saving _problems/test_splitting_attributes-29.R NOTE: entry.status has been set to "DM" for all. Saving _problems/test_survtab_bad_surv_ints-11.R Saving _problems/test_survtab_bad_surv_ints-49.R Saving _problems/test_survtab_observed-13.R Saving _problems/test_survtab_observed-142.R Saving _problems/test_survtab_relative-61.R Saving _problems/test_survtab_relative-178.R Saving _problems/test_survtab_usage-261.R Saving _problems/test_survtab_usage-286.R Saving _problems/test_survtab_usage-334.R Saving _problems/test_survtab_usage-381.R Saving _problems/test_survtab_usage-408.R Saving _problems/test_utils-206.R Saving _problems/test_utils-229.R [ FAIL 32 | WARN 0 | SKIP 39 | PASS 71 ] ══ Skipped tests (39) ══════════════════════════════════════════════════════════ • Unit tests skipped normally (39): 'test_aggre.R:162:3', 'test_aggre.R:199:3', 'test_expo.R:4:3', 'test_lexpand.R:5:3', 'test_lexpand.R:29:3', 'test_lexpand.R:59:3', 'test_lexpand.R:78:3', 'test_lexpand.R:99:3', 'test_lexpand.R:137:3', 'test_lexpand.R:213:3', 'test_lexpand.R:249:3', 'test_lexpand.R:342:3', 'test_relpois_mean_curve.R:4:3', 'test_splitLexisDT.R:4:3', 'test_splitMulti.R:9:3', 'test_splitting_breaks.R:5:3', 'test_splitting_breaks.R:39:3', 'test_splitting_randomly_on_fixed_data.R:9:3', 'test_splitting_randomly_on_random_data.R:9:3', 'test_survmean.R:6:3', 'test_survmean.R:76:3', 'test_survmean.R:117:3', 'test_survmean.R:166:3', 'test_survmean.R:265:3', 'test_survtab_adjusted.R:4:3', 'test_survtab_observed.R:67:3', 'test_survtab_relative.R:81:5', 'test_survtab_usage.R:6:3', 'test_survtab_usage.R:121:3', 'test_survtab_usage.R:198:3', 'test_survtab_usage.R:432:3', 'test_utils.R:4:3', 'test_utils.R:27:3', 'test_utils.R:138:3', 'test_utils.R:179:3', 'test_weighter.R:5:3', 'test_weighter.R:47:3', 'test_weighter.R:99:3', 'test_weighter.R:122:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_aggre.R:7:3'): aggre leaves original data untouched ──────────── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_aggre.R:7:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_aggre.R:30:3'): aggre works with by = NULL ───────────────────── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_aggre.R:30:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_aggre.R:42:3'): aggre and lexpand produce the same results ───── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_aggre.R:42:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_aggre.R:103:5'): aggre()'s by argument works flexibly ────────── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::splitMulti(x, breaks = BL) at test_aggre.R:103:5 2. ├─...[] 3. └─data.table:::`[.data.table`(...) ── Error ('test_aggre.R:137:3'): subset argument works properly ──────────────── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_aggre.R:137:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_lexpand.R:46:3'): pp not added to data if pp = FALSE but pop.haz is ── Error in ``[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id)`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_lexpand.R:46:3 2. ├─l[, `:=`(lex.multi, 1:.N), by = lex.id] 3. └─data.table:::`[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id) ── Error ('test_lexpand.R:185:3'): lexpanding and aggregating to years works ─── Error in ``[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id)`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_lexpand.R:185:3 2. ├─l[, `:=`(lex.multi, 1:.N), by = lex.id] 3. └─data.table:::`[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id) ── Error ('test_lexpand.R:235:3'): lexpand aggre: multistate column names correct ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_lexpand.R:235:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_lexpand.R:286:3'): different specifications of time vars work with event defined and overlapping=FALSE ── Error in ``[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_lexpand.R:286:3 2. ├─l[, `:=`(lex.multi, 1:.N), by = lex.id] 3. └─data.table:::`[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id) ── Error ('test_rate.R:16:3'): rate works with different weights ─────────────── Error in ``[.data.table`(data, , eval(k), by = print)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::rate(...) at test_rate.R:16:3 2. └─popEpi:::rate_est(...) 3. ├─data[, eval(k), by = print] 4. └─data.table:::`[.data.table`(data, , eval(k), by = print) ── Error ('test_rate.R:83:3'): names dont cause problems ─────────────────────── Error in ``[.data.table`(data, , eval(k), by = print)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::rate(...) at test_rate.R:83:3 2. └─popEpi:::rate_est(...) 3. ├─data[, eval(k), by = print] 4. └─data.table:::`[.data.table`(data, , eval(k), by = print) ── Error ('test_rate.R:104:3'): rate works with different weights an subset ──── Error in ``[.data.table`(data, , eval(k), by = print)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::rate(...) at test_rate.R:104:3 2. └─popEpi:::rate_est(...) 3. ├─data[, eval(k), by = print] 4. └─data.table:::`[.data.table`(data, , eval(k), by = print) ── Error ('test_rate.R:167:3'): rate works with different weights and syntaxies ── Error in ``[.data.table`(data, , eval(k), by = print)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::rate(...) at test_rate.R:167:3 2. └─popEpi:::rate_est(...) 3. ├─data[, eval(k), by = print] 4. └─data.table:::`[.data.table`(data, , eval(k), by = print) ── Error ('test_rate.R:194:3'): in rate levels of adjust are printable ───────── Error in ``[.data.table`(data, , eval(k), by = print)`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::rate(...) at test_rate.R:194:3 2. └─popEpi:::rate_est(...) 3. ├─data[, eval(k), by = print] 4. └─data.table:::`[.data.table`(data, , eval(k), by = print) ── Error ('test_rate.R:200:3'): rate.plot doesnt throw an error ──────────────── Error in ``[.data.table`(data, , eval(k), by = print)`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::rate(...) at test_rate.R:200:3 2. └─popEpi:::rate_est(...) 3. ├─data[, eval(k), by = print] 4. └─data.table:::`[.data.table`(data, , eval(k), by = print) ── Error ('test_rate.R:232:3'): rate_ratio works ─────────────────────────────── Error in ``[.data.table`(data, , eval(k), by = print)`: attempt access index 7/7 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::rate(...) at test_rate.R:232:3 2. └─popEpi:::rate_est(...) 3. ├─data[, eval(k), by = print] 4. └─data.table:::`[.data.table`(data, , eval(k), by = print) ── Error ('test_sir.R:56:1'): (code run outside of `test_that()`) ────────────── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_sir.R:56:1 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_splitMulti.R:124:3'): splitMulti agrees with splitLexis, vol. II ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::splitMulti(lex, breaks = BL, drop = FALSE) at test_splitMulti.R:124:3 2. ├─...[] 3. └─data.table:::`[.data.table`(...) ── Error ('test_splitting_attributes.R:29:3'): popEpi splitters produce correct attributes ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 17/17 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::splitMulti(sire, breaks = BL, drop = TRUE) at test_splitting_attributes.R:29:3 2. ├─...[] 3. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_bad_surv_ints.R:10:3'): removing consecutively bad surv.ints is logical w/ & w/out adjusting ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_survtab_bad_surv_ints.R:10:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_bad_surv_ints.R:47:3'): survtab_ag messages & results due to non-consecutively bad surv.ints are OK ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_survtab_bad_surv_ints.R:47:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_observed.R:10:3'): surv.obs about the same as Kaplan-Meier & CIFs close to Aalen-Johansen ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_survtab_observed.R:10:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_observed.R:138:3'): survtab works with more complicated estimation ── Error in ``[.data.table`(data, , `:=`("surv.int", 1:.N), by = eval(byVars))`: attempt access index 9/9 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::survtab(...) at test_survtab_observed.R:138:3 2. └─popEpi::survtab_ag(...) 3. ├─data[, `:=`("surv.int", 1:.N), by = eval(byVars)] 4. └─data.table:::`[.data.table`(data, , `:=`("surv.int", 1:.N), by = eval(byVars)) ── Error ('test_survtab_relative.R:60:5'): relative survivals about the same as relsurv's ── Error in ``[.data.table`(lex, , `:=`(c(tmpPCS), list(exp(-cumsum(.SD[[1L]] * lex.dur)))), by = lex.id, .SDcols = c(haz, "lex.dur"))`: attempt access index 14/14 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::survtab(...) at test_survtab_relative.R:60:5 2. └─popEpi:::comp_pp_weights(...) 3. ├─...[] 4. ├─Epi::`[.Lexis`(...) 5. ├─base::NextMethod(x) 6. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_relative.R:178:5'): Ederer I expected survival curve agrees with survival::survexp ── Error in ``[.data.table`(y, , `:=`(surv.exp, cumsum(haz)), by = eval(tmpID))`: attempt access index 3/3 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi:::comp_e1(x, breaks = list(fot = fb), pophaz = pm, survScale = "fot") at test_survtab_relative.R:178:5 2. ├─y[, `:=`(surv.exp, cumsum(haz)), by = eval(tmpID)] 3. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_usage.R:256:3'): getCall & formula methods for survtab work ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_survtab_usage.R:256:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_usage.R:281:3'): survtab_ag allows for certain arguments to be length > 1 ── Error in ``[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id)`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_survtab_usage.R:281:3 2. ├─l[, `:=`(lex.multi, 1:.N), by = lex.id] 3. └─data.table:::`[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id) ── Error ('test_survtab_usage.R:329:3'): update() works with survtab objects ─── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_survtab_usage.R:329:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_usage.R:377:3'): internal weights work as intended ───── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_survtab_usage.R:377:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_survtab_usage.R:405:3'): survtab_ag works with bare data.frames ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_survtab_usage.R:405:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_utils.R:204:3'): comp_pp_weighted_figures produces intended results ── Error in ``[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), .SDcols = s1, by = "lex.id")`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_utils.R:204:3 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test_utils.R:228:3'): evalPopFormula & usePopFormula output is stable ── Error in ``[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id)`: attempt access index 8/8 in VECTOR_ELT Backtrace: ▆ 1. └─popEpi::lexpand(...) at test_utils.R:228:3 2. ├─l[, `:=`(lex.multi, 1:.N), by = lex.id] 3. └─data.table:::`[.data.table`(l, , `:=`(lex.multi, 1:.N), by = lex.id) [ FAIL 32 | WARN 0 | SKIP 39 | PASS 71 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Version: 0.4.13
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'sir.Rmd' using rmarkdown Quitting from sir.Rmd:68-79 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 8/8 in VECTOR_ELT --- Backtrace: ▆ 1. └─popEpi::lexpand(...) 2. └─popEpi::splitMulti(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'sir.Rmd' failed with diagnostics: attempt access index 8/8 in VECTOR_ELT --- failed re-building 'sir.Rmd' --- re-building 'survtab_examples.Rmd' using rmarkdown Quitting from survtab_examples.Rmd:36-66 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 6/6 in VECTOR_ELT --- Backtrace: ▆ 1. └─popEpi::survtab(...) 2. └─popEpi::survtab_ag(...) 3. ├─data[, `:=`("surv.int", 1:.N), by = eval(byVars)] 4. └─data.table:::`[.data.table`(data, , `:=`("surv.int", 1:.N), by = eval(byVars)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'survtab_examples.Rmd' failed with diagnostics: attempt access index 6/6 in VECTOR_ELT --- failed re-building 'survtab_examples.Rmd' SUMMARY: processing the following files failed: 'sir.Rmd' 'survtab_examples.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64