--- Begin Message ---
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
--- End Message ---
