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. 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
