[R-pkg-team] Bug#1070842: r-bioc-mutationalpatterns: autopkgtest regression with r-base 4.4.0

[Graham Inggs]

Source: r-bioc-mutationalpatterns
Version: 3.12.0+dfsg-1
Severity: serious
X-Debbugs-Cc: Dirk Eddelbuettel <edd at debian.org>
User: debian-ci at 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