Last updated on 2025-12-20 11:50:32 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.13 | 18.28 | 167.08 | 185.36 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.4.13 | 12.57 | 115.60 | 128.17 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.4.13 | 34.00 | 267.96 | 301.96 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.4.13 | 33.00 | 269.39 | 302.39 | ERROR | |
| r-devel-windows-x86_64 | 0.4.13 | 22.00 | 270.00 | 292.00 | OK | |
| r-patched-linux-x86_64 | 0.4.13 | 19.24 | 337.25 | 356.49 | OK | |
| r-release-linux-x86_64 | 0.4.13 | 17.21 | 331.08 | 348.29 | 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 | 19.00 | 251.00 | 270.00 | 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 | 30.00 | 321.00 | 351.00 | OK |
Version: 0.4.13
Check: examples
Result: ERROR
Running examples in ‘popEpi-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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,]$sex <- 0 ## pretend some are male
> x <- Lexis(data = x,
+ entry = list(AGE = dg_age, CAL = get.yrs(dg_date)),
+ exit = list(CAL = get.yrs(ex_date)),
+ entry.status=0, exit.status = status)
> x <- splitMulti(x, breaks = list(CAL = seq(1993, 2013, 5),
+ AGE = seq(0, 100, 50)))
Error in `[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")), :
attempt access index 12/12 in VECTOR_ELT
Calls: splitMulti -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.4.13
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
>
> if (requireNamespace("testthat")) {
+ library("testthat")
+ library("popEpi")
+ library("data.table")
+
+ using_r_devel <- grepl(pattern = "devel", x = R.version$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-linux-x86_64-debian-clang
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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.4.13
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/24s]
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-linux-x86_64-debian-gcc
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.4.13
Check: tests
Result: ERROR
Running ‘testthat.R’ [45s/77s]
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-linux-x86_64-fedora-clang
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.4.13
Check: tests
Result: ERROR
Running ‘testthat.R’ [47s/85s]
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-linux-x86_64-fedora-gcc