Last updated on 2026-10-24 12:51:49 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 4.33 | 51.46 | 55.79 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 3.44 | 38.00 | 41.44 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 44.78 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 3.00 | 42.00 | 45.00 | OK | |
| r-release-macos-arm64 | 0.1.0 | 1.00 | 19.00 | 20.00 | OK | |
| r-release-macos-x86_64 | 0.1.0 | 3.00 | 75.00 | 78.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | 2.00 | 26.00 | 28.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.0 | 3.00 | 135.00 | 138.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.0 | 9.00 | 75.00 | 84.00 | OK |
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘ssurvdr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fit_ssurvdr
> ### Title: Fit sparse survival dimension reduction model
> ### Aliases: fit_ssurvdr
>
> ### ** Examples
>
> dat <- simulate_ssurvdr(n = 100, p = 12, active = 1:3, seed = 2026)
> fit <- fit_ssurvdr(dat$X, dat$time, dat$status, d = 2,
+ n_slices = 3, covariance = "mec", backend = "primal")
Error in a$specials[[i]] : subscript out of bounds
Calls: fit_ssurvdr ... <Anonymous> -> predict.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/6s]
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(ssurvdr)
>
> test_check("ssurvdr")
Saving _problems/test-compute_icomp-31.R
Saving _problems/test-compute_icomp-100.R
Saving _problems/test-compute_icomp-142.R
Saving _problems/test-dual-backend-123.R
Saving _problems/test-dual-backend-151.R
Saving _problems/test-dual-backend-183.R
Saving _problems/test-evaluate_ssurvdr-18.R
Saving _problems/test-evaluate_ssurvdr-59.R
Saving _problems/test-evaluate_ssurvdr-101.R
Saving _problems/test-fit-ssurvdr-sparse-path-33.R
Saving _problems/test-fit-ssurvdr-sparse-path-86.R
Saving _problems/test-fit-ssurvdr-sparse-path-142.R
Saving _problems/test-fit_reduced_cox-31.R
Saving _problems/test-fit_reduced_cox-144.R
Saving _problems/test-fit_ssurvdr-17.R
Saving _problems/test-fit_ssurvdr-45.R
Saving _problems/test-fit_ssurvdr-89.R
Saving _problems/test-fit_ssurvdr_grid-18.R
Saving _problems/test-fit_ssurvdr_grid-44.R
Saving _problems/test-summarise_ssurvdr-15.R
Saving _problems/test-summarise_ssurvdr-40.R
[ FAIL 21 | WARN 0 | SKIP 0 | PASS 148 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compute_icomp.R:26:3'): compute_icomp computes all criteria ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_reduced_cox(...) at test-compute_icomp.R:26:3
2. ├─stats::predict(cox_fit, type = "lp")
3. └─survival:::predict.coxph(cox_fit, type = "lp")
4. └─stats::delete.response(Terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-compute_icomp.R:95:3'): compute_icomp rejects invalid eps ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_reduced_cox(...) at test-compute_icomp.R:95:3
2. ├─stats::predict(cox_fit, type = "lp")
3. └─survival:::predict.coxph(cox_fit, type = "lp")
4. └─stats::delete.response(Terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-compute_icomp.R:137:1'): (code run outside of `test_that()`) ───
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_reduced_cox(...) at test-compute_icomp.R:137:1
2. ├─stats::predict(cox_fit, type = "lp")
3. └─survival:::predict.coxph(cox_fit, type = "lp")
4. └─stats::delete.response(Terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-dual-backend.R:113:3'): dual backend handles p greater than n without dense projection ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-dual-backend.R:113:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-dual-backend.R:141:3'): Cox fitting uses preprocessing learned by SAVE ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-dual-backend.R:141:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-dual-backend.R:174:3'): grid search reuses one SAVE kernel per covariance method ──
Error: No model in the grid search completed successfully.
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr_grid(...) at test-dual-backend.R:174:3
── Error ('test-evaluate_ssurvdr.R:11:3'): evaluate_ssurvdr evaluates fitted model against simulation truth ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-evaluate_ssurvdr.R:11:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-evaluate_ssurvdr.R:51:3'): evaluate_ssurvdr works with grid object ──
Error: No model in the grid search completed successfully.
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr_grid(...) at test-evaluate_ssurvdr.R:51:3
── Error ('test-evaluate_ssurvdr.R:100:3'): automatic selection after screening maps back to original predictors ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-evaluate_ssurvdr.R:100:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-fit-ssurvdr-sparse-path.R:23:3'): sparse support path contains the dense benchmark and returns a valid fit ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-fit-ssurvdr-sparse-path.R:23:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-fit-ssurvdr-sparse-path.R:76:3'): full support sparse-path Cox fit is equivalent to dense Cox fit ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-fit-ssurvdr-sparse-path.R:76:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-fit-ssurvdr-sparse-path.R:134:3'): support path automatically adds the dense support candidate ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-fit-ssurvdr-sparse-path.R:134:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-fit_reduced_cox.R:26:3'): fit_reduced_cox fits reduced Cox model correctly ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_reduced_cox(...) at test-fit_reduced_cox.R:26:3
2. ├─stats::predict(cox_fit, type = "lp")
3. └─survival:::predict.coxph(cox_fit, type = "lp")
4. └─stats::delete.response(Terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-fit_reduced_cox.R:139:1'): (code run outside of `test_that()`) ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_reduced_cox(...) at test-fit_reduced_cox.R:139:1
2. ├─stats::predict(cox_fit, type = "lp")
3. └─survival:::predict.coxph(cox_fit, type = "lp")
4. └─stats::delete.response(Terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test-fit_ssurvdr.R:8:3'): fit_ssurvdr runs complete workflow with MEC ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-fit_ssurvdr.R:8:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-fit_ssurvdr.R:38:3'): fit_ssurvdr runs complete workflow with sample covariance ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-fit_ssurvdr.R:38:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-fit_ssurvdr.R:78:1'): (code run outside of `test_that()`) ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-fit_ssurvdr.R:78:1
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-fit_ssurvdr_grid.R:8:3'): fit_ssurvdr_grid runs model comparison ──
Error: No model in the grid search completed successfully.
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr_grid(...) at test-fit_ssurvdr_grid.R:8:3
── Error ('test-fit_ssurvdr_grid.R:36:3'): fit_ssurvdr_grid works with one covariance method ──
Error: No model in the grid search completed successfully.
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr_grid(...) at test-fit_ssurvdr_grid.R:36:3
── Error ('test-summarise_ssurvdr.R:8:3'): summarise_ssurvdr summarises ssurvdr_fit object ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...) at test-summarise_ssurvdr.R:8:3
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
── Error ('test-summarise_ssurvdr.R:32:3'): summarise_ssurvdr summarises ssurvdr_grid object ──
Error: No model in the grid search completed successfully.
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr_grid(...) at test-summarise_ssurvdr.R:32:3
[ FAIL 21 | WARN 0 | SKIP 0 | PASS 148 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction-to-ssurvdr.Rmd’ using rmarkdown
Quitting from introduction-to-ssurvdr.Rmd:18-27 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─ssurvdr::fit_ssurvdr(...)
2. └─ssurvdr::fit_reduced_cox(...)
3. ├─stats::predict(cox_fit, type = "lp")
4. └─survival:::predict.coxph(cox_fit, type = "lp")
5. └─stats::delete.response(Terms)
6. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'introduction-to-ssurvdr.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘introduction-to-ssurvdr.Rmd’
SUMMARY: processing the following file failed:
‘introduction-to-ssurvdr.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc