Last updated on 2025-12-20 01:50:09 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.0 | 18.01 | 331.47 | 349.48 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.9.1 | 14.53 | 120.24 | 134.77 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.9.1 | 36.00 | 276.89 | 312.89 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.9.1 | 37.00 | 270.93 | 307.93 | ERROR | |
| r-devel-windows-x86_64 | 0.9.1 | 27.00 | 347.00 | 374.00 | OK | |
| r-patched-linux-x86_64 | 0.9.1 | 18.53 | 304.46 | 322.99 | OK | |
| r-release-linux-x86_64 | 0.9.0 | 19.33 | 299.58 | 318.91 | OK | |
| r-release-macos-arm64 | 0.9.1 | 4.00 | 87.00 | 91.00 | OK | |
| r-release-macos-x86_64 | 0.9.1 | 13.00 | 325.00 | 338.00 | OK | |
| r-release-windows-x86_64 | 0.9.1 | 21.00 | 324.00 | 345.00 | OK | |
| r-oldrel-macos-arm64 | 0.9.1 | 4.00 | 82.00 | 86.00 | OK | |
| r-oldrel-macos-x86_64 | 0.9.1 | 14.00 | 368.00 | 382.00 | OK | |
| r-oldrel-windows-x86_64 | 0.9.1 | 19.00 | 332.00 | 351.00 | OK |
Version: 0.9.1
Check: examples
Result: ERROR
Running examples in ‘simstudy-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addCompRisk
> ### Title: Generating single competing risk survival variable
> ### Aliases: addCompRisk
>
> ### ** Examples
>
> d1 <- defData(varname = "x1", formula = .5, dist = "binary")
> d1 <- defData(d1, "x2", .5, dist = "binary")
>
> dS <- defSurv(varname = "reinc", formula = "-10 - 0.6*x1 + 0.4*x2", shape = 0.3)
> dS <- defSurv(dS, "death", "-6.5 + 0.3*x1 - 0.5*x2", shape = 0.5)
> dS <- defSurv(dS, "censor", "-7", shape = 0.55)
>
> dd <- genData(10, d1)
> dd <- genSurv(dd, dS)
>
> addCompRisk(dd, c("reinc","death", "censor"), timeName = "time",
+ censorName = "censor", keepEvents = FALSE)
Error in `[.data.table`(dtSurv, , `:=`(..temp_time, min(sapply(1:length(events), :
attempt access index 6/6 in VECTOR_ELT
Calls: addCompRisk -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.9.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hedgehog)
> library(simstudy)
>
> data.table::setDTthreads(2) # added to solve CRAN issue
> test_check("simstudy")
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Saving _problems/test-generate_correlated_data-1038.R
Saving _problems/test-generate_correlated_data-1044.R
Saving _problems/test-generate_correlated_data-1050.R
Saving _problems/test-generate_correlated_data-1055.R
Saving _problems/test-generate_correlated_data-1060.R
Saving _problems/test-generate_correlated_data-1065.R
Saving _problems/test-generate_correlated_data-1072.R
Saving _problems/test-generate_correlated_data-1080.R
Saving _problems/test-generate_correlated_data-1088.R
Saving _problems/test-generate_correlated_data-1179.R
Saving _problems/test-generate_correlated_data-1236.R
Saving _problems/test-generate_correlated_data-1264.R
Saving _problems/test-generate_correlated_data-1281.R
Saving _problems/test-generate_correlated_data-1298.R
Saving _problems/test-generate_correlated_data-1352.R
Saving _problems/test-generate_correlated_data-1380.R
Saving _problems/test-generate_correlated_data-1425.R
Saving _problems/test-generate_correlated_data-1438.R
Saving _problems/test-generate_correlated_data-1480.R
Saving _problems/test-generate_correlated_data-1495.R
Saving _problems/test-generate_correlated_data-1520.R
Saving _problems/test-missing_data-147.R
Saving _problems/test-missing_data-186.R
[ FAIL 23 | WARN 0 | SKIP 307 | PASS 148 ]
══ Skipped tests (307) ═════════════════════════════════════════════════════════
• On CRAN (307): 'test-actual-distributions.R:6:3',
'test-actual-distributions.R:28:3', 'test-add_data.R:7:3',
'test-add_data.R:14:3', 'test-add_data.R:29:3', 'test-add_data.R:36:3',
'test-add_data.R:45:3', 'test-add_data.R:59:3', 'test-add_data.R:73:3',
'test-add_data.R:106:3', 'test-add_data.R:149:3', 'test-add_data.R:181:3',
'test-add_data.R:224:3', 'test-add_data.R:245:3', 'test-add_data.R:267:3',
'test-add_data.R:285:3', 'test-add_data.R:299:3', 'test-add_data.R:313:3',
'test-add_data.R:326:3', 'test-add_data.R:346:3', 'test-add_data.R:374:3',
'test-add_data.R:391:3', 'test-add_data.R:411:3', 'test-asserts.R:7:3',
'test-asserts.R:18:3', 'test-asserts.R:25:3', 'test-asserts.R:34:3',
'test-asserts.R:44:3', 'test-asserts.R:55:3', 'test-asserts.R:62:3',
'test-asserts.R:69:3', 'test-asserts.R:76:3', 'test-asserts.R:83:3',
'test-asserts.R:90:3', 'test-asserts.R:99:3', 'test-asserts.R:108:3',
'test-asserts.R:117:3', 'test-asserts.R:126:3', 'test-asserts.R:137:3',
'test-asserts.R:144:3', 'test-asserts.R:158:3', 'test-asserts.R:174:3',
'test-asserts.R:188:3', 'test-asserts.R:206:3', 'test-asserts.R:224:3',
'test-asserts.R:235:3', 'test-asserts.R:246:3', 'test-asserts.R:257:3',
'test-asserts.R:268:3', 'test-asserts.R:277:3', 'test-asserts.R:285:3',
'test-asserts.R:297:3', 'test-asserts.R:307:3', 'test-asserts.R:326:3',
'test-asserts.R:334:3', 'test-conditions.R:23:3', 'test-conditions.R:52:3',
'test-define_data.R:12:3', 'test-define_data.R:24:3',
'test-define_data.R:36:3', 'test-define_data.R:48:3',
'test-define_data.R:60:3', 'test-define_data.R:72:3',
'test-define_data.R:84:3', 'test-define_data.R:95:3',
'test-define_data.R:106:3', 'test-define_data.R:117:3',
'test-define_data.R:131:3', 'test-define_data.R:146:3',
'test-define_data.R:161:3', 'test-define_data.R:174:3',
'test-define_data.R:187:3', 'test-define_data.R:200:3',
'test-define_data.R:214:3', 'test-define_data.R:229:3',
'test-define_data.R:244:3', 'test-define_data.R:261:3',
'test-define_data.R:269:3', 'test-define_data.R:280:3',
'test-define_data.R:297:3', 'test-define_data.R:305:3',
'test-define_data.R:313:3', 'test-define_data.R:338:3',
'test-define_data.R:348:3', 'test-define_data.R:366:3',
'test-define_data.R:381:3', 'test-define_data.R:394:3',
'test-define_data.R:412:3', 'test-define_data.R:434:3',
'test-define_data.R:441:3', 'test-define_data.R:456:3',
'test-define_data.R:471:3', 'test-define_data.R:493:3',
'test-define_data.R:515:3', 'test-define_data.R:544:3',
'test-define_data.R:558:3', 'test-define_data.R:576:3',
'test-define_data.R:597:3', 'test-define_data.R:619:3',
'test-define_data.R:648:3', 'test-define_data.R:662:3',
'test-define_data.R:673:3', 'test-define_data.R:695:3',
'test-define_data.R:713:3', 'test-define_data.R:731:3',
'test-define_data.R:747:3', 'test-define_data.R:758:3',
'test-define_data.R:767:3', 'test-define_data.R:779:3',
'test-define_data.R:799:3', 'test-define_data.R:817:3',
'test-define_data.R:833:3', 'test-define_data.R:845:3',
'test-define_data.R:860:3', 'test-define_data.R:872:3',
'test-define_data.R:885:3', 'test-define_data.R:899:3',
'test-define_data.R:907:3', 'test-define_data.R:921:3',
'test-define_data.R:931:3', 'test-define_data.R:942:3',
'test-define_data.R:950:3', 'test-define_data.R:978:3',
'test-define_data.R:993:3', 'test-define_data.R:1005:3',
'test-define_data.R:1029:3', 'test-define_data.R:1053:3',
'test-define_data.R:1060:3', 'test-define_data.R:1075:3',
'test-define_data.R:1087:3', 'test-generate_correlated_data.R:8:3',
'test-generate_correlated_data.R:24:3',
'test-generate_correlated_data.R:63:3',
'test-generate_correlated_data.R:100:3',
'test-generate_correlated_data.R:121:3',
'test-generate_correlated_data.R:151:3',
'test-generate_correlated_data.R:211:3',
'test-generate_correlated_data.R:230:3',
'test-generate_correlated_data.R:255:3',
'test-generate_correlated_data.R:332:3',
'test-generate_correlated_data.R:352:3',
'test-generate_correlated_data.R:419:3',
'test-generate_correlated_data.R:1533:3',
'test-generate_correlated_data.R:1595:3',
'test-generate_correlated_data.R:1645:3',
'test-generate_correlated_data.R:1682:3', 'test-generate_data.R:7:3',
'test-generate_data.R:38:3', 'test-generate_data.R:52:3',
'test-generate_data.R:119:3', 'test-generate_data.R:169:3',
'test-generate_data.R:227:3', 'test-generate_data.R:233:3',
'test-generate_data.R:251:3', 'test-generate_data.R:280:3',
'test-generate_data.R:306:3', 'test-generate_data.R:343:3',
'test-generate_data.R:400:3', 'test-generate_data.R:415:3',
'test-generate_data.R:434:3', 'test-generate_data.R:465:3',
'test-generate_data.R:554:3', 'test-generate_data.R:572:3',
'test-generate_data.R:673:3', 'test-generate_data.R:702:3',
'test-generate_data.R:734:3', 'test-generate_data.R:757:3',
'test-generate_data.R:784:3', 'test-generate_data.R:813:3',
'test-generate_data.R:847:3', 'test-generate_data.R:897:3',
'test-generate_data.R:987:3', 'test-generate_data.R:1040:3',
'test-generate_dist.R:7:3', 'test-generate_dist.R:32:3',
'test-generate_dist.R:57:3', 'test-generate_dist.R:71:3',
'test-generate_dist.R:97:3', 'test-generate_dist.R:111:3',
'test-generate_dist.R:129:3', 'test-generate_dist.R:144:3',
'test-generate_dist.R:149:3', 'test-generate_dist.R:162:3',
'test-generate_dist.R:182:3', 'test-generate_dist.R:211:3',
'test-generate_dist.R:233:3', 'test-generate_dist.R:279:3',
'test-generate_dist.R:321:3', 'test-generate_dist.R:367:3',
'test-generate_dist.R:404:3', 'test-generate_dist.R:421:3',
'test-generate_dist.R:436:3', 'test-generate_dist.R:451:3',
'test-generate_dist.R:473:3', 'test-generate_dist.R:495:3',
'test-generate_dist.R:539:3', 'test-generate_dist.R:561:3',
'test-generate_dist.R:587:3', 'test-generate_dist.R:625:3',
'test-generate_dist.R:659:3', 'test-generate_dist.R:693:3',
'test-generate_dist.R:723:3', 'test-generate_dist.R:765:3',
'test-generate_dist.R:791:3', 'test-generate_dist.R:806:3',
'test-generate_dist.R:821:3', 'test-glue.R:8:3', 'test-glue.R:24:3',
'test-glue.R:33:3', 'test-group_data.R:7:3', 'test-group_data.R:73:3',
'test-group_data.R:88:3', 'test-group_data.R:106:3',
'test-group_data.R:117:3', 'test-group_data.R:129:3',
'test-group_data.R:142:3', 'test-group_data.R:156:3',
'test-group_data.R:170:3', 'test-group_data.R:182:3',
'test-group_data.R:194:3', 'test-group_data.R:206:3',
'test-group_data.R:221:3', 'test-group_data.R:238:3',
'test-group_data.R:258:3', 'test-group_data.R:290:3',
'test-group_data.R:313:3', 'test-group_data.R:337:3',
'test-group_data.R:360:3', 'test-group_data.R:368:3',
'test-group_data.R:387:3', 'test-group_data.R:406:3',
'test-group_data.R:425:3', 'test-group_data.R:459:3',
'test-group_data.R:485:3', 'test-group_data.R:511:3',
'test-group_data.R:557:3', 'test-group_data.R:590:3',
'test-group_data.R:603:3', 'test-group_data.R:617:3',
'test-group_data.R:632:3', 'test-group_data.R:642:3',
'test-group_data.R:658:3', 'test-group_data.R:673:3',
'test-group_data.R:682:3', 'test-group_data.R:691:3',
'test-group_data.R:703:3', 'test-group_data.R:714:3',
'test-group_data.R:727:3', 'test-group_data.R:744:3',
'test-group_data.R:764:3', 'test-group_data.R:777:3',
'test-group_data.R:785:3', 'test-group_data.R:796:3',
'test-internal_utility.R:7:3', 'test-internal_utility.R:20:3',
'test-internal_utility.R:36:3', 'test-internal_utility.R:45:3',
'test-internal_utility.R:54:3', 'test-internal_utility.R:66:3',
'test-internal_utility.R:86:3', 'test-internal_utility.R:92:3',
'test-internal_utility.R:103:3', 'test-internal_utility.R:118:3',
'test-internal_utility.R:130:3', 'test-internal_utility.R:142:3',
'test-internal_utility.R:153:3', 'test-internal_utility.R:195:3',
'test-missing_data.R:192:3', 'test-missing_data.R:250:3',
'test-survival.R:8:3', 'test-survival.R:35:3', 'test-survival.R:48:3',
'test-survival.R:72:3', 'test-survival.R:91:3', 'test-survival.R:102:3',
'test-utility.R:11:3', 'test-utility.R:21:3', 'test-utility.R:46:3',
'test-utility.R:62:3', 'test-utility.R:72:3', 'test-utility.R:78:3',
'test-utility.R:84:3', 'test-utility.R:94:3', 'test-utility.R:106:3',
'test-utility.R:120:3', 'test-utility.R:130:3', 'test-utility.R:137:3',
'test-utility.R:155:3', 'test-utility.R:229:3', 'test-utility.R:256:3',
'test-utility.R:263:3', 'test-utility.R:269:3', 'test-utility.R:292:3',
'test-utility.R:298:3', 'test-utility.R:307:3', 'test-utility.R:366:3',
'test-utility.R:375:3', 'test-utility.R:383:3', 'test-utility.R:392:3',
'test-utility.R:401:3', 'test-utility.R:410:3', 'test-utility.R:420:3',
'test-utility.R:426:3', 'test-utility.R:432:3', 'test-utility.R:438:3',
'test-utility.R:444:3', 'test-utility.R:450:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generate_correlated_data.R:1038:3'): genCorGen generates data with correct dimensions ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1038:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1044:3'): genCorGen generates data in wide format ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1044:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1050:3'): genCorGen assigns custom column names ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1050:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1055:3'): genCorGen assigns custom column names when wide is not TRUE ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1055:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1060:3'): genCorGen assigns custom id name ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1060:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1065:3'): genCorGen generates data with specified correlation structure ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1065:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1072:3'): genCorGen generates data with specified correlation matrix ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1072:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1079:3'): number of parameters adjusted ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1079:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1087:3'): All distributions work ────
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1087:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1170:3'): addCorGen basic functionality works ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1170:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1236:3'): addCorGen works with wide format (ungrouped data) ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1236:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1264:3'): addCorGen works with long format (grouped data) ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1264:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1281:3'): addCorGen works with different correlation structures ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1281:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1298:3'): addCorGen works with custom correlation matrices ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1298:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1346:3'): addCorGen works with list of correlation matrices for varying cluster sizes ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1346:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1370:3'): addCorGen works with custom column names ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1370:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1416:3'): addCorGen EP method works correctly ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1416:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1438:3'): addCorGen handles edge cases ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1438:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1480:3'): addCorGen preserves original data ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1480:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1495:3'): addCorGen returns correct data structure ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1495:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1511:3'): addCorGen works with negBinomial distribution ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1511:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-missing_data.R:147:3'): .addLags throws errors. ────────────────
Error in ``[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::trtAssign(data, grpName = "rx") at test-missing_data.R:147:3
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
── Error ('test-missing_data.R:186:3'): LAGS are added as expected. ────────────
Error in ``[.data.table`(lagdt, , `:=`((lags1[i]), shift(.SD[, lags, with = FALSE], n = 1, fill = 0)), by = id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-missing_data.R:186:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─simstudy:::.addLags(dataLong, c(origForm, noLAG))
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
[ FAIL 23 | WARN 0 | SKIP 307 | PASS 148 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.9.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘clustered.Rmd’ using rmarkdown
Quitting from clustered.Rmd:52-67 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::trtAssign(dtSchool, n = 2)
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'clustered.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘clustered.Rmd’
--- re-building ‘corelationmat.Rmd’ using rmarkdown
Quitting from corelationmat.Rmd:70-75 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genCorGen(...)
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'corelationmat.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘corelationmat.Rmd’
--- re-building ‘correlated.Rmd’ using rmarkdown
Quitting from correlated.Rmd:110-116 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genCorGen(...)
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'correlated.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘correlated.Rmd’
--- re-building ‘customdist.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘customdist.Rmd’
--- re-building ‘double_dot_extension.Rmd’ using rmarkdown
Quitting from double_dot_extension.Rmd:180-185 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Error in `[.data.table`(dtSim, , `:=`(newVar, eval(expr)), keyby = def_id): attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genData(4, d)
2. └─simstudy:::.generate(...)
3. └─simstudy:::.gendeterm(...)
4. └─simstudy:::.evalWith(...)
5. └─base::sapply(formula, evalFormula)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─simstudy (local) FUN(X[[i]], ...)
8. ├─base::with(...)
9. └─base::with.default(...)
10. └─base::eval(substitute(expr), data, enclos = parent.frame())
11. └─base::eval(substitute(expr), data, enclos = parent.frame())
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'double_dot_extension.Rmd' failed with diagnostics:
Error in `[.data.table`(dtSim, , `:=`(newVar, eval(expr)), keyby = def_id): attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘double_dot_extension.Rmd’
--- re-building ‘framework.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘framework.Rmd’
--- re-building ‘logisticCoefs.Rmd’ using rmarkdown
Quitting from logisticCoefs.Rmd:38-58 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Error in `[.data.table`(dtSim, , `:=`(newVar, eval(expr)), keyby = def_id): attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genData(5e+05, d1a)
2. └─simstudy:::.generate(...)
3. └─simstudy:::.genbinom(...)
4. └─simstudy:::.getBinaryMean(...)
5. └─simstudy:::.evalWith(...)
6. └─base::sapply(formula, evalFormula)
7. └─base::lapply(X = X, FUN = FUN, ...)
8. └─simstudy (local) FUN(X[[i]], ...)
9. ├─base::with(...)
10. └─base::with.default(...)
11. └─base::eval(substitute(expr), data, enclos = parent.frame())
12. └─base::eval(substitute(expr), data, enclos = parent.frame())
13. └─base::tryCatch(...)
14. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'logisticCoefs.Rmd' failed with diagnostics:
Error in `[.data.table`(dtSim, , `:=`(newVar, eval(expr)), keyby = def_id): attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘logisticCoefs.Rmd’
--- re-building ‘longitudinal.Rmd’ using rmarkdown
Quitting from longitudinal.Rmd:101-104 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::addPeriods(dt)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'longitudinal.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘longitudinal.Rmd’
--- re-building ‘missing.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘missing.Rmd’
--- re-building ‘ordinal.Rmd’ using rmarkdown
Quitting from ordinal.Rmd:185-196 [acuts]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genData(25000, defA)
2. └─simstudy:::.generate(...)
3. └─simstudy:::.genAssign(...)
4. └─simstudy::trtAssign(...)
5. ├─dt[, `:=`(.n, .N), keyby = .stratum]
6. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ordinal.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building ‘ordinal.Rmd’
--- re-building ‘simstudy.Rmd’ using rmarkdown
Quitting from simstudy.Rmd:106-111 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::trtAssign(...)
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'simstudy.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘simstudy.Rmd’
--- re-building ‘spline.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘spline.Rmd’
--- re-building ‘survival.Rmd’ using rmarkdown
Quitting from survival.Rmd:111-122 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genSurv(...)
2. └─simstudy::addCompRisk(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'survival.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘survival.Rmd’
--- re-building ‘treat_and_exposure.Rmd’ using rmarkdown
Quitting from treat_and_exposure.Rmd:93-97 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::trtAssign(...)
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'treat_and_exposure.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘treat_and_exposure.Rmd’
SUMMARY: processing the following files failed:
‘clustered.Rmd’ ‘corelationmat.Rmd’ ‘correlated.Rmd’
‘double_dot_extension.Rmd’ ‘logisticCoefs.Rmd’ ‘longitudinal.Rmd’
‘ordinal.Rmd’ ‘simstudy.Rmd’ ‘survival.Rmd’ ‘treat_and_exposure.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.9.1
Check: examples
Result: ERROR
Running examples in ‘simstudy-Ex.R’ failed
The error most likely occurred in:
> ### Name: addCompRisk
> ### Title: Generating single competing risk survival variable
> ### Aliases: addCompRisk
>
> ### ** Examples
>
> d1 <- defData(varname = "x1", formula = .5, dist = "binary")
> d1 <- defData(d1, "x2", .5, dist = "binary")
>
> dS <- defSurv(varname = "reinc", formula = "-10 - 0.6*x1 + 0.4*x2", shape = 0.3)
> dS <- defSurv(dS, "death", "-6.5 + 0.3*x1 - 0.5*x2", shape = 0.5)
> dS <- defSurv(dS, "censor", "-7", shape = 0.55)
>
> dd <- genData(10, d1)
> dd <- genSurv(dd, dS)
>
> addCompRisk(dd, c("reinc","death", "censor"), timeName = "time",
+ censorName = "censor", keepEvents = FALSE)
Error in `[.data.table`(dtSurv, , `:=`(..temp_time, min(sapply(1:length(events), :
attempt access index 6/6 in VECTOR_ELT
Calls: addCompRisk -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.9.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [32s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hedgehog)
> library(simstudy)
>
> data.table::setDTthreads(2) # added to solve CRAN issue
> test_check("simstudy")
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Saving _problems/test-generate_correlated_data-1038.R
Saving _problems/test-generate_correlated_data-1044.R
Saving _problems/test-generate_correlated_data-1050.R
Saving _problems/test-generate_correlated_data-1055.R
Saving _problems/test-generate_correlated_data-1060.R
Saving _problems/test-generate_correlated_data-1065.R
Saving _problems/test-generate_correlated_data-1072.R
Saving _problems/test-generate_correlated_data-1080.R
Saving _problems/test-generate_correlated_data-1088.R
Saving _problems/test-generate_correlated_data-1179.R
Saving _problems/test-generate_correlated_data-1236.R
Saving _problems/test-generate_correlated_data-1264.R
Saving _problems/test-generate_correlated_data-1281.R
Saving _problems/test-generate_correlated_data-1298.R
Saving _problems/test-generate_correlated_data-1352.R
Saving _problems/test-generate_correlated_data-1380.R
Saving _problems/test-generate_correlated_data-1425.R
Saving _problems/test-generate_correlated_data-1438.R
Saving _problems/test-generate_correlated_data-1480.R
Saving _problems/test-generate_correlated_data-1495.R
Saving _problems/test-generate_correlated_data-1520.R
Saving _problems/test-missing_data-147.R
Saving _problems/test-missing_data-186.R
[ FAIL 23 | WARN 0 | SKIP 307 | PASS 148 ]
══ Skipped tests (307) ═════════════════════════════════════════════════════════
• On CRAN (307): 'test-actual-distributions.R:6:3',
'test-actual-distributions.R:28:3', 'test-add_data.R:7:3',
'test-add_data.R:14:3', 'test-add_data.R:29:3', 'test-add_data.R:36:3',
'test-add_data.R:45:3', 'test-add_data.R:59:3', 'test-add_data.R:73:3',
'test-add_data.R:106:3', 'test-add_data.R:149:3', 'test-add_data.R:181:3',
'test-add_data.R:224:3', 'test-add_data.R:245:3', 'test-add_data.R:267:3',
'test-add_data.R:285:3', 'test-add_data.R:299:3', 'test-add_data.R:313:3',
'test-add_data.R:326:3', 'test-add_data.R:346:3', 'test-add_data.R:374:3',
'test-add_data.R:391:3', 'test-add_data.R:411:3', 'test-asserts.R:7:3',
'test-asserts.R:18:3', 'test-asserts.R:25:3', 'test-asserts.R:34:3',
'test-asserts.R:44:3', 'test-asserts.R:55:3', 'test-asserts.R:62:3',
'test-asserts.R:69:3', 'test-asserts.R:76:3', 'test-asserts.R:83:3',
'test-asserts.R:90:3', 'test-asserts.R:99:3', 'test-asserts.R:108:3',
'test-asserts.R:117:3', 'test-asserts.R:126:3', 'test-asserts.R:137:3',
'test-asserts.R:144:3', 'test-asserts.R:158:3', 'test-asserts.R:174:3',
'test-asserts.R:188:3', 'test-asserts.R:206:3', 'test-asserts.R:224:3',
'test-asserts.R:235:3', 'test-asserts.R:246:3', 'test-asserts.R:257:3',
'test-asserts.R:268:3', 'test-asserts.R:277:3', 'test-asserts.R:285:3',
'test-asserts.R:297:3', 'test-asserts.R:307:3', 'test-asserts.R:326:3',
'test-asserts.R:334:3', 'test-conditions.R:23:3', 'test-conditions.R:52:3',
'test-define_data.R:12:3', 'test-define_data.R:24:3',
'test-define_data.R:36:3', 'test-define_data.R:48:3',
'test-define_data.R:60:3', 'test-define_data.R:72:3',
'test-define_data.R:84:3', 'test-define_data.R:95:3',
'test-define_data.R:106:3', 'test-define_data.R:117:3',
'test-define_data.R:131:3', 'test-define_data.R:146:3',
'test-define_data.R:161:3', 'test-define_data.R:174:3',
'test-define_data.R:187:3', 'test-define_data.R:200:3',
'test-define_data.R:214:3', 'test-define_data.R:229:3',
'test-define_data.R:244:3', 'test-define_data.R:261:3',
'test-define_data.R:269:3', 'test-define_data.R:280:3',
'test-define_data.R:297:3', 'test-define_data.R:305:3',
'test-define_data.R:313:3', 'test-define_data.R:338:3',
'test-define_data.R:348:3', 'test-define_data.R:366:3',
'test-define_data.R:381:3', 'test-define_data.R:394:3',
'test-define_data.R:412:3', 'test-define_data.R:434:3',
'test-define_data.R:441:3', 'test-define_data.R:456:3',
'test-define_data.R:471:3', 'test-define_data.R:493:3',
'test-define_data.R:515:3', 'test-define_data.R:544:3',
'test-define_data.R:558:3', 'test-define_data.R:576:3',
'test-define_data.R:597:3', 'test-define_data.R:619:3',
'test-define_data.R:648:3', 'test-define_data.R:662:3',
'test-define_data.R:673:3', 'test-define_data.R:695:3',
'test-define_data.R:713:3', 'test-define_data.R:731:3',
'test-define_data.R:747:3', 'test-define_data.R:758:3',
'test-define_data.R:767:3', 'test-define_data.R:779:3',
'test-define_data.R:799:3', 'test-define_data.R:817:3',
'test-define_data.R:833:3', 'test-define_data.R:845:3',
'test-define_data.R:860:3', 'test-define_data.R:872:3',
'test-define_data.R:885:3', 'test-define_data.R:899:3',
'test-define_data.R:907:3', 'test-define_data.R:921:3',
'test-define_data.R:931:3', 'test-define_data.R:942:3',
'test-define_data.R:950:3', 'test-define_data.R:978:3',
'test-define_data.R:993:3', 'test-define_data.R:1005:3',
'test-define_data.R:1029:3', 'test-define_data.R:1053:3',
'test-define_data.R:1060:3', 'test-define_data.R:1075:3',
'test-define_data.R:1087:3', 'test-generate_correlated_data.R:8:3',
'test-generate_correlated_data.R:24:3',
'test-generate_correlated_data.R:63:3',
'test-generate_correlated_data.R:100:3',
'test-generate_correlated_data.R:121:3',
'test-generate_correlated_data.R:151:3',
'test-generate_correlated_data.R:211:3',
'test-generate_correlated_data.R:230:3',
'test-generate_correlated_data.R:255:3',
'test-generate_correlated_data.R:332:3',
'test-generate_correlated_data.R:352:3',
'test-generate_correlated_data.R:419:3',
'test-generate_correlated_data.R:1533:3',
'test-generate_correlated_data.R:1595:3',
'test-generate_correlated_data.R:1645:3',
'test-generate_correlated_data.R:1682:3', 'test-generate_data.R:7:3',
'test-generate_data.R:38:3', 'test-generate_data.R:52:3',
'test-generate_data.R:119:3', 'test-generate_data.R:169:3',
'test-generate_data.R:227:3', 'test-generate_data.R:233:3',
'test-generate_data.R:251:3', 'test-generate_data.R:280:3',
'test-generate_data.R:306:3', 'test-generate_data.R:343:3',
'test-generate_data.R:400:3', 'test-generate_data.R:415:3',
'test-generate_data.R:434:3', 'test-generate_data.R:465:3',
'test-generate_data.R:554:3', 'test-generate_data.R:572:3',
'test-generate_data.R:673:3', 'test-generate_data.R:702:3',
'test-generate_data.R:734:3', 'test-generate_data.R:757:3',
'test-generate_data.R:784:3', 'test-generate_data.R:813:3',
'test-generate_data.R:847:3', 'test-generate_data.R:897:3',
'test-generate_data.R:987:3', 'test-generate_data.R:1040:3',
'test-generate_dist.R:7:3', 'test-generate_dist.R:32:3',
'test-generate_dist.R:57:3', 'test-generate_dist.R:71:3',
'test-generate_dist.R:97:3', 'test-generate_dist.R:111:3',
'test-generate_dist.R:129:3', 'test-generate_dist.R:144:3',
'test-generate_dist.R:149:3', 'test-generate_dist.R:162:3',
'test-generate_dist.R:182:3', 'test-generate_dist.R:211:3',
'test-generate_dist.R:233:3', 'test-generate_dist.R:279:3',
'test-generate_dist.R:321:3', 'test-generate_dist.R:367:3',
'test-generate_dist.R:404:3', 'test-generate_dist.R:421:3',
'test-generate_dist.R:436:3', 'test-generate_dist.R:451:3',
'test-generate_dist.R:473:3', 'test-generate_dist.R:495:3',
'test-generate_dist.R:539:3', 'test-generate_dist.R:561:3',
'test-generate_dist.R:587:3', 'test-generate_dist.R:625:3',
'test-generate_dist.R:659:3', 'test-generate_dist.R:693:3',
'test-generate_dist.R:723:3', 'test-generate_dist.R:765:3',
'test-generate_dist.R:791:3', 'test-generate_dist.R:806:3',
'test-generate_dist.R:821:3', 'test-glue.R:8:3', 'test-glue.R:24:3',
'test-glue.R:33:3', 'test-group_data.R:7:3', 'test-group_data.R:73:3',
'test-group_data.R:88:3', 'test-group_data.R:106:3',
'test-group_data.R:117:3', 'test-group_data.R:129:3',
'test-group_data.R:142:3', 'test-group_data.R:156:3',
'test-group_data.R:170:3', 'test-group_data.R:182:3',
'test-group_data.R:194:3', 'test-group_data.R:206:3',
'test-group_data.R:221:3', 'test-group_data.R:238:3',
'test-group_data.R:258:3', 'test-group_data.R:290:3',
'test-group_data.R:313:3', 'test-group_data.R:337:3',
'test-group_data.R:360:3', 'test-group_data.R:368:3',
'test-group_data.R:387:3', 'test-group_data.R:406:3',
'test-group_data.R:425:3', 'test-group_data.R:459:3',
'test-group_data.R:485:3', 'test-group_data.R:511:3',
'test-group_data.R:557:3', 'test-group_data.R:590:3',
'test-group_data.R:603:3', 'test-group_data.R:617:3',
'test-group_data.R:632:3', 'test-group_data.R:642:3',
'test-group_data.R:658:3', 'test-group_data.R:673:3',
'test-group_data.R:682:3', 'test-group_data.R:691:3',
'test-group_data.R:703:3', 'test-group_data.R:714:3',
'test-group_data.R:727:3', 'test-group_data.R:744:3',
'test-group_data.R:764:3', 'test-group_data.R:777:3',
'test-group_data.R:785:3', 'test-group_data.R:796:3',
'test-internal_utility.R:7:3', 'test-internal_utility.R:20:3',
'test-internal_utility.R:36:3', 'test-internal_utility.R:45:3',
'test-internal_utility.R:54:3', 'test-internal_utility.R:66:3',
'test-internal_utility.R:86:3', 'test-internal_utility.R:92:3',
'test-internal_utility.R:103:3', 'test-internal_utility.R:118:3',
'test-internal_utility.R:130:3', 'test-internal_utility.R:142:3',
'test-internal_utility.R:153:3', 'test-internal_utility.R:195:3',
'test-missing_data.R:192:3', 'test-missing_data.R:250:3',
'test-survival.R:8:3', 'test-survival.R:35:3', 'test-survival.R:48:3',
'test-survival.R:72:3', 'test-survival.R:91:3', 'test-survival.R:102:3',
'test-utility.R:11:3', 'test-utility.R:21:3', 'test-utility.R:46:3',
'test-utility.R:62:3', 'test-utility.R:72:3', 'test-utility.R:78:3',
'test-utility.R:84:3', 'test-utility.R:94:3', 'test-utility.R:106:3',
'test-utility.R:120:3', 'test-utility.R:130:3', 'test-utility.R:137:3',
'test-utility.R:155:3', 'test-utility.R:229:3', 'test-utility.R:256:3',
'test-utility.R:263:3', 'test-utility.R:269:3', 'test-utility.R:292:3',
'test-utility.R:298:3', 'test-utility.R:307:3', 'test-utility.R:366:3',
'test-utility.R:375:3', 'test-utility.R:383:3', 'test-utility.R:392:3',
'test-utility.R:401:3', 'test-utility.R:410:3', 'test-utility.R:420:3',
'test-utility.R:426:3', 'test-utility.R:432:3', 'test-utility.R:438:3',
'test-utility.R:444:3', 'test-utility.R:450:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generate_correlated_data.R:1038:3'): genCorGen generates data with correct dimensions ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1038:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1044:3'): genCorGen generates data in wide format ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1044:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1050:3'): genCorGen assigns custom column names ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1050:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1055:3'): genCorGen assigns custom column names when wide is not TRUE ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1055:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1060:3'): genCorGen assigns custom id name ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1060:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1065:3'): genCorGen generates data with specified correlation structure ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1065:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1072:3'): genCorGen generates data with specified correlation matrix ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1072:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1079:3'): number of parameters adjusted ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1079:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1087:3'): All distributions work ────
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1087:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1170:3'): addCorGen basic functionality works ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1170:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1236:3'): addCorGen works with wide format (ungrouped data) ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1236:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1264:3'): addCorGen works with long format (grouped data) ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1264:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1281:3'): addCorGen works with different correlation structures ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1281:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1298:3'): addCorGen works with custom correlation matrices ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1298:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1346:3'): addCorGen works with list of correlation matrices for varying cluster sizes ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1346:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1370:3'): addCorGen works with custom column names ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1370:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1416:3'): addCorGen EP method works correctly ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1416:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1438:3'): addCorGen handles edge cases ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1438:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1480:3'): addCorGen preserves original data ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1480:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1495:3'): addCorGen returns correct data structure ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1495:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1511:3'): addCorGen works with negBinomial distribution ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1511:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-missing_data.R:147:3'): .addLags throws errors. ────────────────
Error in ``[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::trtAssign(data, grpName = "rx") at test-missing_data.R:147:3
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
── Error ('test-missing_data.R:186:3'): LAGS are added as expected. ────────────
Error in ``[.data.table`(lagdt, , `:=`((lags1[i]), shift(.SD[, lags, with = FALSE], n = 1, fill = 0)), by = id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-missing_data.R:186:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─simstudy:::.addLags(dataLong, c(origForm, noLAG))
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
[ FAIL 23 | WARN 0 | SKIP 307 | PASS 148 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘clustered.Rmd’ using rmarkdown
Quitting from clustered.Rmd:52-67 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::trtAssign(dtSchool, n = 2)
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'clustered.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘clustered.Rmd’
--- re-building ‘corelationmat.Rmd’ using rmarkdown
Quitting from corelationmat.Rmd:70-75 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genCorGen(...)
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'corelationmat.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘corelationmat.Rmd’
--- re-building ‘correlated.Rmd’ using rmarkdown
Quitting from correlated.Rmd:110-116 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genCorGen(...)
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'correlated.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘correlated.Rmd’
--- re-building ‘customdist.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘customdist.Rmd’
--- re-building ‘double_dot_extension.Rmd’ using rmarkdown
Quitting from double_dot_extension.Rmd:180-185 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Error in `[.data.table`(dtSim, , `:=`(newVar, eval(expr)), keyby = def_id): attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genData(4, d)
2. └─simstudy:::.generate(...)
3. └─simstudy:::.gendeterm(...)
4. └─simstudy:::.evalWith(...)
5. └─base::sapply(formula, evalFormula)
6. └─base::lapply(X = X, FUN = FUN, ...)
7. └─simstudy (local) FUN(X[[i]], ...)
8. ├─base::with(...)
9. └─base::with.default(...)
10. └─base::eval(substitute(expr), data, enclos = parent.frame())
11. └─base::eval(substitute(expr), data, enclos = parent.frame())
12. └─base::tryCatch(...)
13. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
14. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'double_dot_extension.Rmd' failed with diagnostics:
Error in `[.data.table`(dtSim, , `:=`(newVar, eval(expr)), keyby = def_id): attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘double_dot_extension.Rmd’
--- re-building ‘framework.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘framework.Rmd’
--- re-building ‘logisticCoefs.Rmd’ using rmarkdown
Quitting from logisticCoefs.Rmd:38-58 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! Error in `[.data.table`(dtSim, , `:=`(newVar, eval(expr)), keyby = def_id): attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genData(5e+05, d1a)
2. └─simstudy:::.generate(...)
3. └─simstudy:::.genbinom(...)
4. └─simstudy:::.getBinaryMean(...)
5. └─simstudy:::.evalWith(...)
6. └─base::sapply(formula, evalFormula)
7. └─base::lapply(X = X, FUN = FUN, ...)
8. └─simstudy (local) FUN(X[[i]], ...)
9. ├─base::with(...)
10. └─base::with.default(...)
11. └─base::eval(substitute(expr), data, enclos = parent.frame())
12. └─base::eval(substitute(expr), data, enclos = parent.frame())
13. └─base::tryCatch(...)
14. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'logisticCoefs.Rmd' failed with diagnostics:
Error in `[.data.table`(dtSim, , `:=`(newVar, eval(expr)), keyby = def_id): attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘logisticCoefs.Rmd’
--- re-building ‘longitudinal.Rmd’ using rmarkdown
Quitting from longitudinal.Rmd:101-104 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::addPeriods(dt)
2. ├─...[]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'longitudinal.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘longitudinal.Rmd’
--- re-building ‘missing.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘missing.Rmd’
--- re-building ‘ordinal.Rmd’ using rmarkdown
Quitting from ordinal.Rmd:185-196 [acuts]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 2/2 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genData(25000, defA)
2. └─simstudy:::.generate(...)
3. └─simstudy:::.genAssign(...)
4. └─simstudy::trtAssign(...)
5. ├─dt[, `:=`(.n, .N), keyby = .stratum]
6. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ordinal.Rmd' failed with diagnostics:
attempt access index 2/2 in VECTOR_ELT
--- failed re-building ‘ordinal.Rmd’
--- re-building ‘simstudy.Rmd’ using rmarkdown
Quitting from simstudy.Rmd:106-111 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::trtAssign(...)
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'simstudy.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘simstudy.Rmd’
--- re-building ‘spline.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘spline.Rmd’
--- re-building ‘survival.Rmd’ using rmarkdown
Quitting from survival.Rmd:111-122 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::genSurv(...)
2. └─simstudy::addCompRisk(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'survival.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘survival.Rmd’
--- re-building ‘treat_and_exposure.Rmd’ using rmarkdown
Quitting from treat_and_exposure.Rmd:93-97 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 5/5 in VECTOR_ELT
---
Backtrace:
▆
1. └─simstudy::trtAssign(...)
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'treat_and_exposure.Rmd' failed with diagnostics:
attempt access index 5/5 in VECTOR_ELT
--- failed re-building ‘treat_and_exposure.Rmd’
SUMMARY: processing the following files failed:
‘clustered.Rmd’ ‘corelationmat.Rmd’ ‘correlated.Rmd’
‘double_dot_extension.Rmd’ ‘logisticCoefs.Rmd’ ‘longitudinal.Rmd’
‘ordinal.Rmd’ ‘simstudy.Rmd’ ‘survival.Rmd’ ‘treat_and_exposure.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.9.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [29s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hedgehog)
> library(simstudy)
>
> data.table::setDTthreads(2) # added to solve CRAN issue
> test_check("simstudy")
Attaching package: 'data.table'
The following object is masked from 'package:base':
%notin%
Saving _problems/test-generate_correlated_data-1038.R
Saving _problems/test-generate_correlated_data-1044.R
Saving _problems/test-generate_correlated_data-1050.R
Saving _problems/test-generate_correlated_data-1055.R
Saving _problems/test-generate_correlated_data-1060.R
Saving _problems/test-generate_correlated_data-1065.R
Saving _problems/test-generate_correlated_data-1072.R
Saving _problems/test-generate_correlated_data-1080.R
Saving _problems/test-generate_correlated_data-1088.R
Saving _problems/test-generate_correlated_data-1179.R
Saving _problems/test-generate_correlated_data-1236.R
Saving _problems/test-generate_correlated_data-1264.R
Saving _problems/test-generate_correlated_data-1281.R
Saving _problems/test-generate_correlated_data-1298.R
Saving _problems/test-generate_correlated_data-1352.R
Saving _problems/test-generate_correlated_data-1380.R
Saving _problems/test-generate_correlated_data-1425.R
Saving _problems/test-generate_correlated_data-1438.R
Saving _problems/test-generate_correlated_data-1480.R
Saving _problems/test-generate_correlated_data-1495.R
Saving _problems/test-generate_correlated_data-1520.R
Saving _problems/test-missing_data-147.R
Saving _problems/test-missing_data-186.R
[ FAIL 23 | WARN 0 | SKIP 307 | PASS 148 ]
══ Skipped tests (307) ═════════════════════════════════════════════════════════
• On CRAN (307): 'test-actual-distributions.R:6:3',
'test-actual-distributions.R:28:3', 'test-add_data.R:7:3',
'test-add_data.R:14:3', 'test-add_data.R:29:3', 'test-add_data.R:36:3',
'test-add_data.R:45:3', 'test-add_data.R:59:3', 'test-add_data.R:73:3',
'test-add_data.R:106:3', 'test-add_data.R:149:3', 'test-add_data.R:181:3',
'test-add_data.R:224:3', 'test-add_data.R:245:3', 'test-add_data.R:267:3',
'test-add_data.R:285:3', 'test-add_data.R:299:3', 'test-add_data.R:313:3',
'test-add_data.R:326:3', 'test-add_data.R:346:3', 'test-add_data.R:374:3',
'test-add_data.R:391:3', 'test-add_data.R:411:3', 'test-asserts.R:7:3',
'test-asserts.R:18:3', 'test-asserts.R:25:3', 'test-asserts.R:34:3',
'test-asserts.R:44:3', 'test-asserts.R:55:3', 'test-asserts.R:62:3',
'test-asserts.R:69:3', 'test-asserts.R:76:3', 'test-asserts.R:83:3',
'test-asserts.R:90:3', 'test-asserts.R:99:3', 'test-asserts.R:108:3',
'test-asserts.R:117:3', 'test-asserts.R:126:3', 'test-asserts.R:137:3',
'test-asserts.R:144:3', 'test-asserts.R:158:3', 'test-asserts.R:174:3',
'test-asserts.R:188:3', 'test-asserts.R:206:3', 'test-asserts.R:224:3',
'test-asserts.R:235:3', 'test-asserts.R:246:3', 'test-asserts.R:257:3',
'test-asserts.R:268:3', 'test-asserts.R:277:3', 'test-asserts.R:285:3',
'test-asserts.R:297:3', 'test-asserts.R:307:3', 'test-asserts.R:326:3',
'test-asserts.R:334:3', 'test-conditions.R:23:3', 'test-conditions.R:52:3',
'test-define_data.R:12:3', 'test-define_data.R:24:3',
'test-define_data.R:36:3', 'test-define_data.R:48:3',
'test-define_data.R:60:3', 'test-define_data.R:72:3',
'test-define_data.R:84:3', 'test-define_data.R:95:3',
'test-define_data.R:106:3', 'test-define_data.R:117:3',
'test-define_data.R:131:3', 'test-define_data.R:146:3',
'test-define_data.R:161:3', 'test-define_data.R:174:3',
'test-define_data.R:187:3', 'test-define_data.R:200:3',
'test-define_data.R:214:3', 'test-define_data.R:229:3',
'test-define_data.R:244:3', 'test-define_data.R:261:3',
'test-define_data.R:269:3', 'test-define_data.R:280:3',
'test-define_data.R:297:3', 'test-define_data.R:305:3',
'test-define_data.R:313:3', 'test-define_data.R:338:3',
'test-define_data.R:348:3', 'test-define_data.R:366:3',
'test-define_data.R:381:3', 'test-define_data.R:394:3',
'test-define_data.R:412:3', 'test-define_data.R:434:3',
'test-define_data.R:441:3', 'test-define_data.R:456:3',
'test-define_data.R:471:3', 'test-define_data.R:493:3',
'test-define_data.R:515:3', 'test-define_data.R:544:3',
'test-define_data.R:558:3', 'test-define_data.R:576:3',
'test-define_data.R:597:3', 'test-define_data.R:619:3',
'test-define_data.R:648:3', 'test-define_data.R:662:3',
'test-define_data.R:673:3', 'test-define_data.R:695:3',
'test-define_data.R:713:3', 'test-define_data.R:731:3',
'test-define_data.R:747:3', 'test-define_data.R:758:3',
'test-define_data.R:767:3', 'test-define_data.R:779:3',
'test-define_data.R:799:3', 'test-define_data.R:817:3',
'test-define_data.R:833:3', 'test-define_data.R:845:3',
'test-define_data.R:860:3', 'test-define_data.R:872:3',
'test-define_data.R:885:3', 'test-define_data.R:899:3',
'test-define_data.R:907:3', 'test-define_data.R:921:3',
'test-define_data.R:931:3', 'test-define_data.R:942:3',
'test-define_data.R:950:3', 'test-define_data.R:978:3',
'test-define_data.R:993:3', 'test-define_data.R:1005:3',
'test-define_data.R:1029:3', 'test-define_data.R:1053:3',
'test-define_data.R:1060:3', 'test-define_data.R:1075:3',
'test-define_data.R:1087:3', 'test-generate_correlated_data.R:8:3',
'test-generate_correlated_data.R:24:3',
'test-generate_correlated_data.R:63:3',
'test-generate_correlated_data.R:100:3',
'test-generate_correlated_data.R:121:3',
'test-generate_correlated_data.R:151:3',
'test-generate_correlated_data.R:211:3',
'test-generate_correlated_data.R:230:3',
'test-generate_correlated_data.R:255:3',
'test-generate_correlated_data.R:332:3',
'test-generate_correlated_data.R:352:3',
'test-generate_correlated_data.R:419:3',
'test-generate_correlated_data.R:1533:3',
'test-generate_correlated_data.R:1595:3',
'test-generate_correlated_data.R:1645:3',
'test-generate_correlated_data.R:1682:3', 'test-generate_data.R:7:3',
'test-generate_data.R:38:3', 'test-generate_data.R:52:3',
'test-generate_data.R:119:3', 'test-generate_data.R:169:3',
'test-generate_data.R:227:3', 'test-generate_data.R:233:3',
'test-generate_data.R:251:3', 'test-generate_data.R:280:3',
'test-generate_data.R:306:3', 'test-generate_data.R:343:3',
'test-generate_data.R:400:3', 'test-generate_data.R:415:3',
'test-generate_data.R:434:3', 'test-generate_data.R:465:3',
'test-generate_data.R:554:3', 'test-generate_data.R:572:3',
'test-generate_data.R:673:3', 'test-generate_data.R:702:3',
'test-generate_data.R:734:3', 'test-generate_data.R:757:3',
'test-generate_data.R:784:3', 'test-generate_data.R:813:3',
'test-generate_data.R:847:3', 'test-generate_data.R:897:3',
'test-generate_data.R:987:3', 'test-generate_data.R:1040:3',
'test-generate_dist.R:7:3', 'test-generate_dist.R:32:3',
'test-generate_dist.R:57:3', 'test-generate_dist.R:71:3',
'test-generate_dist.R:97:3', 'test-generate_dist.R:111:3',
'test-generate_dist.R:129:3', 'test-generate_dist.R:144:3',
'test-generate_dist.R:149:3', 'test-generate_dist.R:162:3',
'test-generate_dist.R:182:3', 'test-generate_dist.R:211:3',
'test-generate_dist.R:233:3', 'test-generate_dist.R:279:3',
'test-generate_dist.R:321:3', 'test-generate_dist.R:367:3',
'test-generate_dist.R:404:3', 'test-generate_dist.R:421:3',
'test-generate_dist.R:436:3', 'test-generate_dist.R:451:3',
'test-generate_dist.R:473:3', 'test-generate_dist.R:495:3',
'test-generate_dist.R:539:3', 'test-generate_dist.R:561:3',
'test-generate_dist.R:587:3', 'test-generate_dist.R:625:3',
'test-generate_dist.R:659:3', 'test-generate_dist.R:693:3',
'test-generate_dist.R:723:3', 'test-generate_dist.R:765:3',
'test-generate_dist.R:791:3', 'test-generate_dist.R:806:3',
'test-generate_dist.R:821:3', 'test-glue.R:8:3', 'test-glue.R:24:3',
'test-glue.R:33:3', 'test-group_data.R:7:3', 'test-group_data.R:73:3',
'test-group_data.R:88:3', 'test-group_data.R:106:3',
'test-group_data.R:117:3', 'test-group_data.R:129:3',
'test-group_data.R:142:3', 'test-group_data.R:156:3',
'test-group_data.R:170:3', 'test-group_data.R:182:3',
'test-group_data.R:194:3', 'test-group_data.R:206:3',
'test-group_data.R:221:3', 'test-group_data.R:238:3',
'test-group_data.R:258:3', 'test-group_data.R:290:3',
'test-group_data.R:313:3', 'test-group_data.R:337:3',
'test-group_data.R:360:3', 'test-group_data.R:368:3',
'test-group_data.R:387:3', 'test-group_data.R:406:3',
'test-group_data.R:425:3', 'test-group_data.R:459:3',
'test-group_data.R:485:3', 'test-group_data.R:511:3',
'test-group_data.R:557:3', 'test-group_data.R:590:3',
'test-group_data.R:603:3', 'test-group_data.R:617:3',
'test-group_data.R:632:3', 'test-group_data.R:642:3',
'test-group_data.R:658:3', 'test-group_data.R:673:3',
'test-group_data.R:682:3', 'test-group_data.R:691:3',
'test-group_data.R:703:3', 'test-group_data.R:714:3',
'test-group_data.R:727:3', 'test-group_data.R:744:3',
'test-group_data.R:764:3', 'test-group_data.R:777:3',
'test-group_data.R:785:3', 'test-group_data.R:796:3',
'test-internal_utility.R:7:3', 'test-internal_utility.R:20:3',
'test-internal_utility.R:36:3', 'test-internal_utility.R:45:3',
'test-internal_utility.R:54:3', 'test-internal_utility.R:66:3',
'test-internal_utility.R:86:3', 'test-internal_utility.R:92:3',
'test-internal_utility.R:103:3', 'test-internal_utility.R:118:3',
'test-internal_utility.R:130:3', 'test-internal_utility.R:142:3',
'test-internal_utility.R:153:3', 'test-internal_utility.R:195:3',
'test-missing_data.R:192:3', 'test-missing_data.R:250:3',
'test-survival.R:8:3', 'test-survival.R:35:3', 'test-survival.R:48:3',
'test-survival.R:72:3', 'test-survival.R:91:3', 'test-survival.R:102:3',
'test-utility.R:11:3', 'test-utility.R:21:3', 'test-utility.R:46:3',
'test-utility.R:62:3', 'test-utility.R:72:3', 'test-utility.R:78:3',
'test-utility.R:84:3', 'test-utility.R:94:3', 'test-utility.R:106:3',
'test-utility.R:120:3', 'test-utility.R:130:3', 'test-utility.R:137:3',
'test-utility.R:155:3', 'test-utility.R:229:3', 'test-utility.R:256:3',
'test-utility.R:263:3', 'test-utility.R:269:3', 'test-utility.R:292:3',
'test-utility.R:298:3', 'test-utility.R:307:3', 'test-utility.R:366:3',
'test-utility.R:375:3', 'test-utility.R:383:3', 'test-utility.R:392:3',
'test-utility.R:401:3', 'test-utility.R:410:3', 'test-utility.R:420:3',
'test-utility.R:426:3', 'test-utility.R:432:3', 'test-utility.R:438:3',
'test-utility.R:444:3', 'test-utility.R:450:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generate_correlated_data.R:1038:3'): genCorGen generates data with correct dimensions ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1038:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1044:3'): genCorGen generates data in wide format ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1044:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1050:3'): genCorGen assigns custom column names ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1050:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1055:3'): genCorGen assigns custom column names when wide is not TRUE ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1055:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1060:3'): genCorGen assigns custom id name ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1060:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1065:3'): genCorGen generates data with specified correlation structure ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1065:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1072:3'): genCorGen generates data with specified correlation matrix ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1072:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1079:3'): number of parameters adjusted ──
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1079:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1087:3'): All distributions work ────
Error in ``[.data.table`(dtM, , `:=`(param1, params1[seq]), keyby = seqid)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::genCorGen(...) at test-generate_correlated_data.R:1087:3
2. ├─dtM[, `:=`(param1, params1[seq]), keyby = seqid]
3. └─data.table:::`[.data.table`(...)
── Error ('test-generate_correlated_data.R:1170:3'): addCorGen basic functionality works ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1170:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1236:3'): addCorGen works with wide format (ungrouped data) ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1236:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1264:3'): addCorGen works with long format (grouped data) ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1264:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1281:3'): addCorGen works with different correlation structures ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1281:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1298:3'): addCorGen works with custom correlation matrices ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1298:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1346:3'): addCorGen works with list of correlation matrices for varying cluster sizes ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1346:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1370:3'): addCorGen works with custom column names ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1370:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1416:3'): addCorGen EP method works correctly ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1416:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1438:3'): addCorGen handles edge cases ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1438:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1480:3'): addCorGen preserves original data ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1480:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1495:3'): addCorGen returns correct data structure ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1495:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-generate_correlated_data.R:1511:3'): addCorGen works with negBinomial distribution ──
Error in ``[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)`: attempt access index 9/9 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::addCorGen(...) at test-generate_correlated_data.R:1511:3
2. ├─dtTemp[, `:=`(seq_, 1:.N), keyby = .id]
3. └─data.table:::`[.data.table`(dtTemp, , `:=`(seq_, 1:.N), keyby = .id)
── Error ('test-missing_data.R:147:3'): .addLags throws errors. ────────────────
Error in ``[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)`: attempt access index 2/2 in VECTOR_ELT
Backtrace:
▆
1. └─simstudy::trtAssign(data, grpName = "rx") at test-missing_data.R:147:3
2. ├─dt[, `:=`(.n, .N), keyby = .stratum]
3. └─data.table:::`[.data.table`(dt, , `:=`(.n, .N), keyby = .stratum)
── Error ('test-missing_data.R:186:3'): LAGS are added as expected. ────────────
Error in ``[.data.table`(lagdt, , `:=`((lags1[i]), shift(.SD[, lags, with = FALSE], n = 1, fill = 0)), by = id)`: attempt access index 5/5 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-missing_data.R:186:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─simstudy:::.addLags(dataLong, c(origForm, noLAG))
5. ├─...[]
6. └─data.table:::`[.data.table`(...)
[ FAIL 23 | WARN 0 | SKIP 307 | PASS 148 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc