On 10 May 2024 at 11:01, Graham Inggs wrote: | Source: r-bioc-mutationalpatterns | Version: 3.12.0+dfsg-1 | Severity: serious | X-Debbugs-Cc: Dirk Eddelbuettel <e...@debian.org> | User: debian...@lists.debian.org | Usertags: regression | | Hi Maintainer | | r-bioc-mutationalpatterns' autopkgtest regresses when tested with r-base 4.4.0 | [1]. I've copied what I hope is the relevant part of the log below.
FYI, I am not the maintainer of r-bioc-mutationalpatterns. As you likely know, BioConductor aligns its releases with R releases and is now at release 3.19 (matching R 4.4.0) for which this package is now at version 3.14.0. I suggest the maintainer look into upgrading BioConductor to 3.19. Dirk | | Regards | Graham | | | [1] https://ci.debian.net/packages/r/r-bioc-mutationalpatterns/testing/amd64/ | | | 125s > test_check("MutationalPatterns") | 172s [ FAIL 3 | WARN 275 | SKIP 0 | PASS 280 ] | 172s | 172s ══ Failed tests | ════════════════════════════════════════════════════════════════ | 172s ── Error ('test-fit_to_signatures_bootstrapped.R:12:3'): Output | has correct class ── | 172s Error in `FUN(X[[i]], ...)`: isEmpty() is not defined for objects | of class NULL | 172s Backtrace: | 172s ▆ | 172s 1. ├─MutationalPatterns::fit_to_signatures_bootstrapped(...) at | test-fit_to_signatures_bootstrapped.R:12:3 | 172s 2. │ └─MutationalPatterns::fit_to_signatures_strict(...) | 172s 3. │ └─MutationalPatterns:::.strict_refit_backwards_selection_sample(...) | 172s 4. │ └─MutationalPatterns:::.plot_sim_decay(...) | 172s 5. │ ├─sims[!S4Vectors::isEmpty(sims)] %>% unlist() | 172s 6. │ ├─S4Vectors::isEmpty(sims) | 172s 7. │ └─S4Vectors::isEmpty(sims) | 172s 8. │ └─base::vapply(x, isEmpty, logical(1L)) | 172s 9. │ ├─S4Vectors (local) FUN(X[[i]], ...) | 172s 10. │ └─S4Vectors (local) FUN(X[[i]], ...) | 172s 11. └─base::unlist(.) | 172s ── Error ('test-fit_to_signatures_bootstrapped.R:31:3'): Output | is equal to expected ── | 172s Error in `FUN(X[[i]], ...)`: isEmpty() is not defined for objects | of class NULL | 172s Backtrace: | 172s ▆ | 172s 1. ├─MutationalPatterns::fit_to_signatures_bootstrapped(...) at | test-fit_to_signatures_bootstrapped.R:31:3 | 172s 2. │ └─MutationalPatterns::fit_to_signatures_strict(...) | 172s 3. │ └─MutationalPatterns:::.strict_refit_backwards_selection_sample(...) | 172s 4. │ └─MutationalPatterns:::.plot_sim_decay(...) | 172s 5. │ ├─sims[!S4Vectors::isEmpty(sims)] %>% unlist() | 172s 6. │ ├─S4Vectors::isEmpty(sims) | 172s 7. │ └─S4Vectors::isEmpty(sims) | 172s 8. │ └─base::vapply(x, isEmpty, logical(1L)) | 172s 9. │ ├─S4Vectors (local) FUN(X[[i]], ...) | 172s 10. │ └─S4Vectors (local) FUN(X[[i]], ...) | 172s 11. └─base::unlist(.) | 172s ── Error ('test-fit_to_signatures_strict.R:11:1'): (code run | outside of `test_that()`) ── | 172s Error in `FUN(X[[i]], ...)`: isEmpty() is not defined for objects | of class NULL | 172s Backtrace: | 172s ▆ | 172s 1. ├─MutationalPatterns::fit_to_signatures_strict(...) at | test-fit_to_signatures_strict.R:11:1 | 172s 2. │ └─MutationalPatterns:::.strict_refit_backwards_selection_sample(...) | 172s 3. │ └─MutationalPatterns:::.plot_sim_decay(...) | 172s 4. │ ├─sims[!S4Vectors::isEmpty(sims)] %>% unlist() | 172s 5. │ ├─S4Vectors::isEmpty(sims) | 172s 6. │ └─S4Vectors::isEmpty(sims) | 172s 7. │ └─base::vapply(x, isEmpty, logical(1L)) | 172s 8. │ ├─S4Vectors (local) FUN(X[[i]], ...) | 172s 9. │ └─S4Vectors (local) FUN(X[[i]], ...) | 172s 10. └─base::unlist(.) | 172s | 172s [ FAIL 3 | WARN 275 | SKIP 0 | PASS 280 ] | 173s Error: Test failures | 173s Execution halted -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
