[R-pkg-team] Bug#1039638: r-bioc-mutationalpatterns: autopkgtest failure with r-base (4.3.1-1)

[Bas Couwenberg]

Source: r-bioc-mutationalpatterns
Version: 3.8.1+dfsg-1
Severity: serious
Justification: autopkgtest failure

Dear Maintainer,

The autopkgtest of your package fails with r-base (4.3.1-1):

 147s [ FAIL 4 | WARN 4 | SKIP 0 | PASS 271 ]
 147s 
 147s ══ Failed tests ════════════════════════════════════════════════════════════════
 147s ── Error ('test-fit_to_signatures_bootstrapped.R:12'): Output has correct class ──
 147s Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
 147s Backtrace:
 147s      ▆
 147s   1. ├─MutationalPatterns::fit_to_signatures_bootstrapped(...) at test-fit_to_signatures_bootstrapped.R:12:2
 147s   2. │ └─MutationalPatterns::fit_to_signatures_strict(...)
 147s   3. │   └─... %>% purrr::reduce(dplyr::full_join, by = "rowname")
 147s   4. └─purrr::reduce(., dplyr::full_join, by = "rowname")
 147s   5.   └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
 147s   6.     ├─dplyr (local) fn(out, elt, ...)
 147s   7.     └─dplyr:::full_join.data.frame(out, elt, ...)
 147s   8.       └─dplyr:::join_mutate(...)
 147s   9.         ├─base::`[<-`(`*tmp*`, new_rows, names(y_key), value = `<tibble[,1]>`)
 147s  10.         └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, names(y_key), value = `<tibble[,1]>`)
 147s  11.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 147s  12.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg)
 147s  13.               ├─base::withCallingHandlers(...)
 147s  14.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
 147s ── Error ('test-fit_to_signatures_bootstrapped.R:31'): Output is equal to expected ──
 147s Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
 147s Backtrace:
 147s      ▆
 147s   1. ├─MutationalPatterns::fit_to_signatures_bootstrapped(...) at test-fit_to_signatures_bootstrapped.R:31:2
 147s   2. │ └─MutationalPatterns::fit_to_signatures_strict(...)
 147s   3. │   └─... %>% purrr::reduce(dplyr::full_join, by = "rowname")
 147s   4. └─purrr::reduce(., dplyr::full_join, by = "rowname")
 147s   5.   └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
 147s   6.     ├─dplyr (local) fn(out, elt, ...)
 147s   7.     └─dplyr:::full_join.data.frame(out, elt, ...)
 147s   8.       └─dplyr:::join_mutate(...)
 147s   9.         ├─base::`[<-`(`*tmp*`, new_rows, names(y_key), value = `<tibble[,1]>`)
 147s  10.         └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, names(y_key), value = `<tibble[,1]>`)
 147s  11.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 147s  12.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg)
 147s  13.               ├─base::withCallingHandlers(...)
 147s  14.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
 147s ── Error ('test-fit_to_signatures_strict.R:11'): (code run outside of `test_that()`) ──
 147s Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
 147s Backtrace:
 147s      ▆
 147s   1. ├─MutationalPatterns::fit_to_signatures_strict(...) at test-fit_to_signatures_strict.R:11:0
 147s   2. │ └─... %>% purrr::reduce(dplyr::full_join, by = "rowname")
 147s   3. └─purrr::reduce(., dplyr::full_join, by = "rowname")
 147s   4.   └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
 147s   5.     ├─dplyr (local) fn(out, elt, ...)
 147s   6.     └─dplyr:::full_join.data.frame(out, elt, ...)
 147s   7.       └─dplyr:::join_mutate(...)
 147s   8.         ├─base::`[<-`(`*tmp*`, new_rows, names(y_key), value = `<tibble[,1]>`)
 147s   9.         └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, names(y_key), value = `<tibble[,1]>`)
 147s  10.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 147s  11.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg)
 147s  12.               ├─base::withCallingHandlers(...)
 147s  13.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
 147s ── Error ('test-plot_lesion_segregation.R:22'): (code run outside of `test_that()`) ──
 147s Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
 147s Backtrace:
 147s      ▆
 147s   1. ├─MutationalPatterns::plot_lesion_segregation(grl, subsample = 0.1) at test-plot_lesion_segregation.R:22:0
 147s   2. │ └─... %>% ...
 147s   3. ├─dplyr::mutate(., sample = factor(sample, levels = levels(tb$sample)))
 147s   4. ├─dplyr::filter(., n >= min_muts_mean)
 147s   5. ├─dplyr::right_join(...)
 147s   6. └─dplyr:::right_join.data.frame(...)
 147s   7.   └─dplyr:::join_mutate(...)
 147s   8.     ├─base::`[<-`(`*tmp*`, new_rows, names(y_key), value = `<tibble[,2]>`)
 147s   9.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, names(y_key), value = `<tibble[,2]>`)
 147s  10.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 147s  11.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg)
 147s  12.           ├─base::withCallingHandlers(...)
 147s  13.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
 147s 
 147s [ FAIL 4 | WARN 4 | SKIP 0 | PASS 271 ]

https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-bioc-mutationalpatterns/34908839/log.gz