Running ‘testthat.R’ [31s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RevGadgets)
  > 
  > test_check("RevGadgets")
  
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  [ FAIL 7 | WARN 4 | SKIP 0 | PASS 94 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_dropTip.R:11:3'): drops tips ───────────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─RevGadgets::rerootPhylo(tree = tree, outgroup = "Galeopterus_variegatus") at test_dropTip.R:11:2
    2.   ├─dplyr::full_join(tree[[i]][[j]]@data, node_names_new, by = "node_name")
    3.   └─dplyr:::full_join.data.frame(...)
    4.     └─dplyr:::join_mutate(...)
    5.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    6.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.             ├─base::withCallingHandlers(...)
   10.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test_plotAncStatesMAP.R:20:3'): plots MAP of ancestral states ───────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─RevGadgets::plotAncStatesMAP(t = example) at test_plotAncStatesMAP.R:20:2
    2. │ └─ggtree::ggtree(t, layout = tree_layout, ...)
    3. │   ├─ggplot2::ggplot(...)
    4. │   └─ggplot2:::ggplot.default(...)
    5. │     ├─ggplot2::fortify(data, ...)
    6. │     └─ggtree:::fortify.treedata(data, ...)
    7. │       └─ggtree:::fortify.phylo(...)
    8. │         ├─as_tibble(model) %>% ...
    9. │         ├─tibble::as_tibble(model)
   10. │         └─tidytree:::as_tibble.treedata(model)
   11. │           ├─tibble::as_tibble(x@phylo)
   12. │           └─tidytree:::as_tibble.phylo(x@phylo)
   13. │             ├─dplyr::full_join(res, label.df, by = "node")
   14. │             └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   15. │               └─dplyr:::join_mutate(...)
   16. │                 ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   17. │                 └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   18. │                   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   19. │                     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   20. │                       ├─base::withCallingHandlers(...)
   21. │                       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   22. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  ── Error ('test_plotAncStatesPie.R:41:3'): plots pies of ancestral states ──────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─RevGadgets::plotAncStatesPie(...) at test_plotAncStatesPie.R:41:2
    2. │ └─ggtree::ggtree(t, ...)
    3. │   ├─ggplot2::ggplot(...)
    4. │   └─ggplot2:::ggplot.default(...)
    5. │     ├─ggplot2::fortify(data, ...)
    6. │     └─ggtree:::fortify.treedata(data, ...)
    7. │       └─ggtree:::fortify.phylo(...)
    8. │         ├─as_tibble(model) %>% ...
    9. │         ├─tibble::as_tibble(model)
   10. │         └─tidytree:::as_tibble.treedata(model)
   11. │           ├─tibble::as_tibble(x@phylo)
   12. │           └─tidytree:::as_tibble.phylo(x@phylo)
   13. │             ├─dplyr::full_join(res, label.df, by = "node")
   14. │             └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   15. │               └─dplyr:::join_mutate(...)
   16. │                 ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   17. │                 └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   18. │                   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   19. │                     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   20. │                       ├─base::withCallingHandlers(...)
   21. │                       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   22. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  ── Error ('test_plotFBDTree.R:12:3'): plots FBD tree ───────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─RevGadgets::plotFBDTree(...) at test_plotFBDTree.R:12:2
    2. │ └─RevGadgets:::plotTreeFull(...)
    3. │   └─ggtree::ggtree(...)
    4. │     ├─ggplot2::ggplot(...)
    5. │     └─ggplot2:::ggplot.default(...)
    6. │       ├─ggplot2::fortify(data, ...)
    7. │       └─ggtree:::fortify.treedata(data, ...)
    8. │         └─ggtree:::fortify.phylo(...)
    9. │           ├─as_tibble(model) %>% ...
   10. │           ├─tibble::as_tibble(model)
   11. │           └─tidytree:::as_tibble.treedata(model)
   12. │             ├─tibble::as_tibble(x@phylo)
   13. │             └─tidytree:::as_tibble.phylo(x@phylo)
   14. │               ├─dplyr::full_join(res, label.df, by = "node")
   15. │               └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   16. │                 └─dplyr:::join_mutate(...)
   17. │                   ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   18. │                   └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   19. │                     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   20. │                       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   21. │                         ├─base::withCallingHandlers(...)
   22. │                         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   23. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  ── Error ('test_plotTree.R:10:3'): plot basic, not-yet-rooted phylogeny ────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─RevGadgets::plotTree(tree = tree, node_labels = "posterior") at test_plotTree.R:10:2
    2. │ └─RevGadgets:::plotTreeFull(...)
    3. │   └─ggtree::ggtree(...)
    4. │     ├─ggplot2::ggplot(...)
    5. │     └─ggplot2:::ggplot.default(...)
    6. │       ├─ggplot2::fortify(data, ...)
    7. │       └─ggtree:::fortify.treedata(data, ...)
    8. │         └─ggtree:::fortify.phylo(...)
    9. │           ├─as_tibble(model) %>% ...
   10. │           ├─tibble::as_tibble(model)
   11. │           └─tidytree:::as_tibble.treedata(model)
   12. │             ├─tibble::as_tibble(x@phylo)
   13. │             └─tidytree:::as_tibble.phylo(x@phylo)
   14. │               ├─dplyr::full_join(res, label.df, by = "node")
   15. │               └─dplyr:::full_join.data.frame(res, label.df, by = "node")
   16. │                 └─dplyr:::join_mutate(...)
   17. │                   ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   18. │                   └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   19. │                     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   20. │                       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   21. │                         ├─base::withCallingHandlers(...)
   22. │                         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   23. └─dplyr::mutate(., isTip = !.data$node %in% .data$parent)
  ── Error ('test_processBranchData.R:13:3'): compare annotated tree from documentation example ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─RevGadgets::processBranchData(tree, branch_data, summary = "median") at test_processBranchData.R:13:2
    2.   ├─tibble::as_tibble(tree)
    3.   └─tidytree:::as_tibble.treedata(tree)
    4.     ├─tibble::as_tibble(x@phylo)
    5.     └─tidytree:::as_tibble.phylo(x@phylo)
    6.       ├─dplyr::full_join(res, label.df, by = "node")
    7.       └─dplyr:::full_join.data.frame(res, label.df, by = "node")
    8.         └─dplyr:::join_mutate(...)
    9.           ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   10.           └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   11.             └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   12.               └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   13.                 ├─base::withCallingHandlers(...)
   14.                 └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test_rerootPhylo.R:11:3'): reroots tree ─────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─RevGadgets::rerootPhylo(tree = tree, outgroup = "Galeopterus_variegatus") at test_rerootPhylo.R:11:2
    2.   ├─dplyr::full_join(tree[[i]][[j]]@data, node_names_new, by = "node_name")
    3.   └─dplyr:::full_join.data.frame(...)
    4.     └─dplyr:::join_mutate(...)
    5.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    6.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.             ├─base::withCallingHandlers(...)
   10.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 7 | WARN 4 | SKIP 0 | PASS 94 ]
  Error: Test failures
  Execution halted