Last updated on 2026-10-24 21:51:39 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.0 | 10.19 | 161.00 | 171.19 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.0 | 6.91 | 77.02 | 83.93 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.0 | 115.93 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.0 | 107.78 | OK | |||
| r-devel-windows-x86_64 | 1.3.0 | 11.00 | 154.00 | 165.00 | OK | |
| r-patched-linux-x86_64 | 1.3.0 | 9.92 | 149.68 | 159.60 | OK | |
| r-release-linux-x86_64 | 1.3.0 | 9.15 | 152.74 | 161.89 | OK | |
| r-release-macos-arm64 | 1.3.0 | 3.00 | 36.00 | 39.00 | OK | |
| r-release-macos-x86_64 | 1.3.0 | 7.00 | 243.00 | 250.00 | OK | |
| r-release-windows-x86_64 | 1.3.0 | 10.00 | 148.00 | 158.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.0 | OK | ||||
| r-oldrel-macos-x86_64 | 1.3.0 | 6.00 | 123.00 | 129.00 | OK | |
| r-oldrel-windows-x86_64 | 1.3.0 | 14.00 | 196.00 | 210.00 | OK |
Version: 1.3.0
Check: examples
Result: ERROR
Running examples in ‘JointFPM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: JointFPM
> ### Title: Joint FPMs for recurrent and competing events.
> ### Aliases: JointFPM
>
> ### ** Examples
>
> JointFPM(Surv(time = start,
+ time2 = stop,
+ event = event,
+ type = 'counting') ~ 1,
+ re_model = ~ pyridoxine + thiotepa,
+ ce_model = ~ pyridoxine + thiotepa,
+ re_indicator = "re",
+ ce_indicator = "ce",
+ df_ce = 3,
+ df_re = 3,
+ tvc_ce_terms = list(pyridoxine = 2,
+ thiotepa = 2),
+ tvc_re_terms = list(pyridoxine = 2,
+ thiotepa = 2),
+ cluster = "id",
+ data = bladder1_stacked)
Error in a$specials[[i]] : subscript out of bounds
Calls: JointFPM ... gsm -> <Anonymous> -> as.vector -> pmin -> pmax -> Shat
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(JointFPM)
>
> test_check("JointFPM")
Starting 2 test processes.
Saving _problems/test-JointFPM-18.R
Saving _problems/test-JointFPM-38.R
Saving _problems/test-JointFPM-58.R
Saving _problems/test-JointFPM-79.R
Saving _problems/test-JointFPM-101.R
Saving _problems/test-JointFPM-117.R
Saving _problems/test-summary.JointFPM-15.R
Saving _problems/test-test_dfs_JointFPM-19.R
Saving _problems/test-test_dfs_JointFPM-38.R
Saving _problems/test-predict.JointFPM-21.R
Saving _problems/test-predict.JointFPM-37.R
Saving _problems/test-predict.JointFPM-196.R
Saving _problems/test-predict.JointFPM-244.R
Saving _problems/test-predict.JointFPM-291.R
Saving _problems/test-predict.JointFPM-337.R
Saving _problems/test-predict.JointFPM-361.R
Saving _problems/test-predict.JointFPM-409.R
Saving _problems/test-predict.JointFPM-433.R
Saving _problems/test-predict.JointFPM-459.R
Saving _problems/test-predict.JointFPM-482.R
Saving _problems/test-predict.JointFPM-518.R
Saving _problems/test-predict.JointFPM-535.R
[ FAIL 22 | WARN 0 | SKIP 6 | PASS 11 ]
══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-mean_no.R:1:1', 'test-mean_no.R:16:1',
'test-predict.JointFPM.R:78:3', 'test-predict.JointFPM.R:103:3',
'test-predict.JointFPM.R:130:3', 'test-predict.JointFPM.R:156:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-JointFPM.R:2:3'): Test model with same varaibles for re and ce model ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "object 'test' not found", call = eval(expr, envir), name = test, mode = "any"), class = c("objectNotFoundError", "error", "condition")))`: error in evaluating the argument 'object' in selecting a method for function 'coef': object 'test' not found
Backtrace:
▆
1. ├─base::print(coef(test$model), digits = 3)
2. ├─stats::coef(test$model)
3. └─base (local) `<fn>`(`<S3: objectNotFoundError>`)
── Error ('test-JointFPM.R:22:3'): Test model with different varaibles for re and ce model ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "object 'test' not found", call = eval(expr, envir), name = test, mode = "any"), class = c("objectNotFoundError", "error", "condition")))`: error in evaluating the argument 'object' in selecting a method for function 'coef': object 'test' not found
Backtrace:
▆
1. ├─base::print(coef(test$model), digits = 3)
2. ├─stats::coef(test$model)
3. └─base (local) `<fn>`(`<S3: objectNotFoundError>`)
── Error ('test-JointFPM.R:42:3'): Test model with different dfs for ce and re model ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "object 'test' not found", call = eval(expr, envir), name = test, mode = "any"), class = c("objectNotFoundError", "error", "condition")))`: error in evaluating the argument 'object' in selecting a method for function 'coef': object 'test' not found
Backtrace:
▆
1. ├─base::print(coef(test$model), digits = 3)
2. ├─stats::coef(test$model)
3. └─base (local) `<fn>`(`<S3: objectNotFoundError>`)
── Error ('test-JointFPM.R:62:3'): Test model with re_tvc_terms ────────────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "object 'test' not found", call = eval(expr, envir), name = test, mode = "any"), class = c("objectNotFoundError", "error", "condition")))`: error in evaluating the argument 'object' in selecting a method for function 'coef': object 'test' not found
Backtrace:
▆
1. ├─base::print(coef(test$model), digits = 3)
2. ├─stats::coef(test$model)
3. └─base (local) `<fn>`(`<S3: objectNotFoundError>`)
── Error ('test-JointFPM.R:83:3'): Test model with re_tvc_term and ce_tvc_term ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "object 'test' not found", call = eval(expr, envir), name = test, mode = "any"), class = c("objectNotFoundError", "error", "condition")))`: error in evaluating the argument 'object' in selecting a method for function 'coef': object 'test' not found
Backtrace:
▆
1. ├─base::print(coef(test$model), digits = 3)
2. ├─stats::coef(test$model)
3. └─base (local) `<fn>`(`<S3: objectNotFoundError>`)
── Error ('test-JointFPM.R:106:5'): Correct model specification ────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-JointFPM.R:105:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─JointFPM::JointFPM(...) at test-JointFPM.R:106:5
5. └─rstpm2::stpm2(...)
6. └─base::eval(m, data, parent.frame())
7. └─base::eval(m, data, parent.frame())
8. └─rstpm2::gsm(...)
9. ├─link$link(...)
10. │ └─base::as.vector(S)
11. ├─base::pmin(...)
12. ├─base::pmax(...)
13. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
14. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
15. │ └─base::withCallingHandlers(...)
16. ├─survival::survfit(obj, se.fit = FALSE)
17. └─survival:::survfit.coxph(obj, se.fit = FALSE)
18. └─survival:::model.matrix.coxph(object, data = mf)
19. └─stats::delete.response(object$terms)
20. └─stats (local) off(a$specials[[i]])
── Failure ('test-summary.JointFPM.R:2:3'): Summary output is stable ───────────
Expected `{ ... }` not to throw any conditions.
Actually got a <simpleError> with message:
error in evaluating the argument 'object' in selecting a method for function 'summary': subscript out of bounds
── Error ('test-test_dfs_JointFPM.R:2:3'): Stable output of test run ───────────
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─JointFPM::test_dfs_JointFPM(...)
2. └─JointFPM::JointFPM(...)
3. └─rstpm2::stpm2(...)
4. └─base::eval(m, data, parent.frame())
5. └─base::eval(m, data, parent.frame())
6. └─rstpm2::gsm(...)
7. ├─link$link(...)
8. │ └─base::as.vector(S)
9. ├─base::pmin(...)
10. ├─base::pmax(...)
11. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
12. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
13. │ └─base::withCallingHandlers(...)
14. ├─survival::survfit(obj, se.fit = FALSE)
15. └─survival:::survfit.coxph(obj, se.fit = FALSE)
16. └─survival:::model.matrix.coxph(object, data = mf)
17. └─stats::delete.response(object$terms)
18. └─stats (local) off(a$specials[[i]])
── Error ('test-test_dfs_JointFPM.R:25:5'): Stable output of test run ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-test_dfs_JointFPM.R:23:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─JointFPM::test_dfs_JointFPM(...) at test-test_dfs_JointFPM.R:25:5
5. └─JointFPM::JointFPM(...)
6. └─rstpm2::stpm2(...)
7. └─base::eval(m, data, parent.frame())
8. └─base::eval(m, data, parent.frame())
9. └─rstpm2::gsm(...)
10. ├─link$link(...)
11. │ └─base::as.vector(S)
12. ├─base::pmin(...)
13. ├─base::pmax(...)
14. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
15. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
16. │ └─base::withCallingHandlers(...)
17. ├─survival::survfit(obj, se.fit = FALSE)
18. └─survival:::survfit.coxph(obj, se.fit = FALSE)
19. └─survival:::model.matrix.coxph(object, data = mf)
20. └─stats::delete.response(object$terms)
21. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:2:3'): Mean number of events in bladder did not change ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "object 'bldr_model' not found", call = eval(expr, envir), name = bldr_model, mode = "any"), class = c("objectNotFoundError", "error", "condition")))`: error in evaluating the argument 'object' in selecting a method for function 'predict': object 'bldr_model' not found
Backtrace:
▆
1. ├─stats::predict(...)
2. └─base (local) `<fn>`(`<S3: objectNotFoundError>`)
── Error ('test-predict.JointFPM.R:26:5'): Difference is correct ───────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-predict.JointFPM.R:25:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:26:5
5. └─rstpm2::stpm2(...)
6. └─base::eval(m, data, parent.frame())
7. └─base::eval(m, data, parent.frame())
8. └─rstpm2::gsm(...)
9. ├─link$link(...)
10. │ └─base::as.vector(S)
11. ├─base::pmin(...)
12. ├─base::pmax(...)
13. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
14. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
15. │ └─base::withCallingHandlers(...)
16. ├─survival::survfit(obj, se.fit = FALSE)
17. └─survival:::survfit.coxph(obj, se.fit = FALSE)
18. └─survival:::model.matrix.coxph(object, data = mf)
19. └─stats::delete.response(object$terms)
20. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:185:5'): S_M(t|x) == S(t|x) ─────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-predict.JointFPM.R:183:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:185:5
5. └─rstpm2::stpm2(...)
6. └─base::eval(m, data, parent.frame())
7. └─base::eval(m, data, parent.frame())
8. └─rstpm2::gsm(...)
9. ├─link$link(...)
10. │ └─base::as.vector(S)
11. ├─base::pmin(...)
12. ├─base::pmax(...)
13. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
14. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
15. │ └─base::withCallingHandlers(...)
16. ├─survival::survfit(obj, se.fit = FALSE)
17. └─survival:::survfit.coxph(obj, se.fit = FALSE)
18. └─survival:::model.matrix.coxph(object, data = mf)
19. └─stats::delete.response(object$terms)
20. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:233:5'): Point estimate is the same if ci_fit == TRUE or FALSE ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-predict.JointFPM.R:231:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:233:5
5. └─rstpm2::stpm2(...)
6. └─base::eval(m, data, parent.frame())
7. └─base::eval(m, data, parent.frame())
8. └─rstpm2::gsm(...)
9. ├─link$link(...)
10. │ └─base::as.vector(S)
11. ├─base::pmin(...)
12. ├─base::pmax(...)
13. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
14. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
15. │ └─base::withCallingHandlers(...)
16. ├─survival::survfit(obj, se.fit = FALSE)
17. └─survival:::survfit.coxph(obj, se.fit = FALSE)
18. └─survival:::model.matrix.coxph(object, data = mf)
19. └─stats::delete.response(object$terms)
20. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:280:7'): S_M(t|x0) - S_M(t|x1) == S(t|x0) - S(t|x1) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-predict.JointFPM.R:278:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:280:7
5. └─rstpm2::stpm2(...)
6. └─base::eval(m, data, parent.frame())
7. └─base::eval(m, data, parent.frame())
8. └─rstpm2::gsm(...)
9. ├─link$link(...)
10. │ └─base::as.vector(S)
11. ├─base::pmin(...)
12. ├─base::pmax(...)
13. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
14. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
15. │ └─base::withCallingHandlers(...)
16. ├─survival::survfit(obj, se.fit = FALSE)
17. └─survival:::survfit.coxph(obj, se.fit = FALSE)
18. └─survival:::model.matrix.coxph(object, data = mf)
19. └─stats::delete.response(object$terms)
20. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:326:5'): Error when newdata is not a data.frame ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-predict.JointFPM.R:325:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:326:5
8. └─rstpm2::stpm2(...)
9. └─base::eval(m, data, parent.frame())
10. └─base::eval(m, data, parent.frame())
11. └─rstpm2::gsm(...)
12. ├─link$link(...)
13. │ └─base::as.vector(S)
14. ├─base::pmin(...)
15. ├─base::pmax(...)
16. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
17. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
18. │ └─base::withCallingHandlers(...)
19. ├─survival::survfit(obj, se.fit = FALSE)
20. └─survival:::survfit.coxph(obj, se.fit = FALSE)
21. └─survival:::model.matrix.coxph(object, data = mf)
22. └─stats::delete.response(object$terms)
23. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:350:5'): Error when newdata has more than one row ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-predict.JointFPM.R:349:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:350:5
8. └─rstpm2::stpm2(...)
9. └─base::eval(m, data, parent.frame())
10. └─base::eval(m, data, parent.frame())
11. └─rstpm2::gsm(...)
12. ├─link$link(...)
13. │ └─base::as.vector(S)
14. ├─base::pmin(...)
15. ├─base::pmax(...)
16. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
17. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
18. │ └─base::withCallingHandlers(...)
19. ├─survival::survfit(obj, se.fit = FALSE)
20. └─survival:::survfit.coxph(obj, se.fit = FALSE)
21. └─survival:::model.matrix.coxph(object, data = mf)
22. └─stats::delete.response(object$terms)
23. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:398:5'): Error when forgetting to specify exposed ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-predict.JointFPM.R:397:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:398:5
8. └─rstpm2::stpm2(...)
9. └─base::eval(m, data, parent.frame())
10. └─base::eval(m, data, parent.frame())
11. └─rstpm2::gsm(...)
12. ├─link$link(...)
13. │ └─base::as.vector(S)
14. ├─base::pmin(...)
15. ├─base::pmax(...)
16. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
17. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
18. │ └─base::withCallingHandlers(...)
19. ├─survival::survfit(obj, se.fit = FALSE)
20. └─survival:::survfit.coxph(obj, se.fit = FALSE)
21. └─survival:::model.matrix.coxph(object, data = mf)
22. └─stats::delete.response(object$terms)
23. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:422:5'): Error when exposed is not a function ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-predict.JointFPM.R:421:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:422:5
8. └─rstpm2::stpm2(...)
9. └─base::eval(m, data, parent.frame())
10. └─base::eval(m, data, parent.frame())
11. └─rstpm2::gsm(...)
12. ├─link$link(...)
13. │ └─base::as.vector(S)
14. ├─base::pmin(...)
15. ├─base::pmax(...)
16. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
17. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
18. │ └─base::withCallingHandlers(...)
19. ├─survival::survfit(obj, se.fit = FALSE)
20. └─survival:::survfit.coxph(obj, se.fit = FALSE)
21. └─survival:::model.matrix.coxph(object, data = mf)
22. └─stats::delete.response(object$terms)
23. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:448:5'): Error when var is not included in newdata ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-predict.JointFPM.R:447:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:448:5
8. └─rstpm2::stpm2(...)
9. └─base::eval(m, data, parent.frame())
10. └─base::eval(m, data, parent.frame())
11. └─rstpm2::gsm(...)
12. ├─link$link(...)
13. │ └─base::as.vector(S)
14. ├─base::pmin(...)
15. ├─base::pmax(...)
16. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
17. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
18. │ └─base::withCallingHandlers(...)
19. ├─survival::survfit(obj, se.fit = FALSE)
20. └─survival:::survfit.coxph(obj, se.fit = FALSE)
21. └─survival:::model.matrix.coxph(object, data = mf)
22. └─stats::delete.response(object$terms)
23. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:471:5'): Test integration when t == 0 ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-predict.JointFPM.R:470:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:471:5
5. └─rstpm2::stpm2(...)
6. └─base::eval(m, data, parent.frame())
7. └─base::eval(m, data, parent.frame())
8. └─rstpm2::gsm(...)
9. ├─link$link(...)
10. │ └─base::as.vector(S)
11. ├─base::pmin(...)
12. ├─base::pmax(...)
13. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
14. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
15. │ └─base::withCallingHandlers(...)
16. ├─survival::survfit(obj, se.fit = FALSE)
17. └─survival:::survfit.coxph(obj, se.fit = FALSE)
18. └─survival:::model.matrix.coxph(object, data = mf)
19. └─stats::delete.response(object$terms)
20. └─stats (local) off(a$specials[[i]])
── Error ('test-predict.JointFPM.R:496:3'): Integration with GQ works ──────────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "object 'bldr_model' not found", call = eval(expr, envir), name = bldr_model, mode = "any"), class = c("objectNotFoundError", "error", "condition")))`: error in evaluating the argument 'object' in selecting a method for function 'predict': object 'bldr_model' not found
Backtrace:
▆
1. ├─stats::predict(...)
2. └─base (local) `<fn>`(`<S3: objectNotFoundError>`)
── Error ('test-predict.JointFPM.R:524:5'): GQ gives results similar to Romberg Integration ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-predict.JointFPM.R:522:3
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─JointFPM::JointFPM(...) at test-predict.JointFPM.R:524:5
5. └─rstpm2::stpm2(...)
6. └─base::eval(m, data, parent.frame())
7. └─base::eval(m, data, parent.frame())
8. └─rstpm2::gsm(...)
9. ├─link$link(...)
10. │ └─base::as.vector(S)
11. ├─base::pmin(...)
12. ├─base::pmax(...)
13. └─rstpm2:::Shat(coxph.obj, data, control$old.init)
14. ├─base::suppressWarnings(survfit(obj, se.fit = FALSE))
15. │ └─base::withCallingHandlers(...)
16. ├─survival::survfit(obj, se.fit = FALSE)
17. └─survival:::survfit.coxph(obj, se.fit = FALSE)
18. └─survival:::model.matrix.coxph(object, data = mf)
19. └─stats::delete.response(object$terms)
20. └─stats (local) off(a$specials[[i]])
[ FAIL 22 | WARN 0 | SKIP 6 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc