Running ‘testthat.R’ [19s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(deeptime)
  > 
  > test_check("deeptime")
  NULL
  [ FAIL 5 | WARN 0 | SKIP 16 | PASS 36 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (16)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-coord_geo.R:126:3'): ggtree scale works ────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─ggtree::ggtree(mammal.tree) at test-coord_geo.R:126:2
    2. │ ├─ggplot2::ggplot(...)
    3. │ └─ggplot2:::ggplot.default(...)
    4. │   ├─ggplot2::fortify(data, ...)
    5. │   └─ggtree:::fortify.phylo(data, ...)
    6. │     ├─as_tibble(model) %>% ...
    7. │     ├─tibble::as_tibble(model)
    8. │     └─tidytree:::as_tibble.phylo(model)
    9. │       ├─dplyr::full_join(res, label.df, by = "node")
   10. │       └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   11. │         └─dplyr:::join_mutate(...)
   12. │           ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   13. │           └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   14. │             └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   15. │               └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   16. │                 ├─base::withCallingHandlers(...)
   17. │                 └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   18. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  ── Error ('test-coord_geo.R:138:3'): ggtree scale works with only fossil taxa ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─ggtree::ggtree(ceratopsianTreeRaia, position = position_nudge(x = -ceratopsianTreeRaia$root.time)) at test-coord_geo.R:138:2
    2. │ ├─ggplot2::ggplot(...)
    3. │ └─ggplot2:::ggplot.default(...)
    4. │   ├─ggplot2::fortify(data, ...)
    5. │   └─ggtree:::fortify.phylo(data, ...)
    6. │     ├─as_tibble(model) %>% ...
    7. │     ├─tibble::as_tibble(model)
    8. │     └─tidytree:::as_tibble.phylo(model)
    9. │       ├─dplyr::full_join(res, label.df, by = "node")
   10. │       └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   11. │         └─dplyr:::join_mutate(...)
   12. │           ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   13. │           └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   14. │             └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   15. │               └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   16. │                 ├─base::withCallingHandlers(...)
   17. │                 └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   18. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  ── Error ('test-coord_geo_polar.R:4:3'): coord_geo_polar works ─────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─ggtree::revts(ggtree(tree)) at test-coord_geo_polar.R:4:2
    2. ├─ggtree::ggtree(tree)
    3. │ ├─ggplot2::ggplot(...)
    4. │ └─ggplot2:::ggplot.default(...)
    5. │   ├─ggplot2::fortify(data, ...)
    6. │   └─ggtree:::fortify.phylo(data, ...)
    7. │     ├─as_tibble(model) %>% ...
    8. │     ├─tibble::as_tibble(model)
    9. │     └─tidytree:::as_tibble.phylo(model)
   10. │       ├─dplyr::full_join(res, label.df, by = "node")
   11. │       └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   12. │         └─dplyr:::join_mutate(...)
   13. │           ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   14. │           └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   15. │             └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   16. │               └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   17. │                 ├─base::withCallingHandlers(...)
   18. │                 └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   19. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  ── Error ('test-coord_geo_polar.R:17:3'): stacking scales works ────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─ggtree::revts(ggtree(mammal.tree)) at test-coord_geo_polar.R:17:2
    2. ├─ggtree::ggtree(mammal.tree)
    3. │ ├─ggplot2::ggplot(...)
    4. │ └─ggplot2:::ggplot.default(...)
    5. │   ├─ggplot2::fortify(data, ...)
    6. │   └─ggtree:::fortify.phylo(data, ...)
    7. │     ├─as_tibble(model) %>% ...
    8. │     ├─tibble::as_tibble(model)
    9. │     └─tidytree:::as_tibble.phylo(model)
   10. │       ├─dplyr::full_join(res, label.df, by = "node")
   11. │       └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   12. │         └─dplyr:::join_mutate(...)
   13. │           ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   14. │           └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   15. │             └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   16. │               └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   17. │                 ├─base::withCallingHandlers(...)
   18. │                 └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   19. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  ── Error ('test-coord_geo_polar.R:29:3'): ggtree scale works with only fossil taxa ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─ggtree::ggtree(ceratopsianTreeRaia, position = position_nudge(x = -ceratopsianTreeRaia$root.time)) at test-coord_geo_polar.R:29:2
    2. │ ├─ggplot2::ggplot(...)
    3. │ └─ggplot2:::ggplot.default(...)
    4. │   ├─ggplot2::fortify(data, ...)
    5. │   └─ggtree:::fortify.phylo(data, ...)
    6. │     ├─as_tibble(model) %>% ...
    7. │     ├─tibble::as_tibble(model)
    8. │     └─tidytree:::as_tibble.phylo(model)
    9. │       ├─dplyr::full_join(res, label.df, by = "node")
   10. │       └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   11. │         └─dplyr:::join_mutate(...)
   12. │           ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   13. │           └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   14. │             └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   15. │               └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   16. │                 ├─base::withCallingHandlers(...)
   17. │                 └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   18. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  
  [ FAIL 5 | WARN 0 | SKIP 16 | PASS 36 ]
  Deleting unused snapshots:
  • coord_geo/scale-on-all-facets-new.svg
  • coord_geo/scale-on-all-facets-old.svg
  • coord_geo/scale-on-fossil-ggtree-new.svg
  • coord_geo/scale-on-fossil-ggtree-old.svg
  • coord_geo/scale-on-ggtree-new.svg
  • coord_geo/scale-on-ggtree-old.svg
  • coord_geo/scales-on-different-sides1-new.svg
  • coord_geo/scales-on-different-sides1-old.svg
  • coord_geo/scales-on-different-sides2-new.svg
  • coord_geo/scales-on-different-sides2-old.svg
  • coord_geo_polar/coord-geo-polar-new.svg
  • coord_geo_polar/coord-geo-polar-old.svg
  • coord_geo_polar/scale-on-fossil-ggtree-new.svg
  • coord_geo_polar/scale-on-fossil-ggtree-old.svg
  • coord_geo_polar/stacked-scales-new.svg
  • coord_geo_polar/stacked-scales-old.svg
  • coord_trans_xy/coord-trans-xy-with-expansion-new.svg
  • coord_trans_xy/coord-trans-xy-with-expansion-old.svg
  • ggarrange2/double-ggarrange2-layout-new.svg
  • ggarrange2/double-ggarrange2-layout-old.svg
  • ggarrange2/double-ggarrange2-new.svg
  • ggarrange2/double-ggarrange2-old.svg
  • ggarrange2/ggarrange2-layout-new.svg
  • ggarrange2/ggarrange2-layout-old.svg
  • ggarrange2/ggarrange2-with-layout-layout-new.svg
  • ggarrange2/ggarrange2-with-layout-layout-old.svg
  • ggarrange2/ggarrange2-with-layout-new.svg
  • ggarrange2/ggarrange2-with-layout-old.svg
  • gggeo_scale/gggeo-scale-left-and-right-new.svg
  • gggeo_scale/gggeo-scale-left-and-right-old.svg
  • gggeo_scale/gggeo-scale-top-new.svg
  • gggeo_scale/gggeo-scale-top-old.svg
  Error: Test failures
  Execution halted