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

[Dirk Eddelbuettel]

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 <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.

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 | edd at debian.org