Running ‘test-all.R’ [21s/26s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("treeman")
  Loading required package: treeman
  [4] in treelst is not a TreeMan object
  These nodes are invalid:
  n3, t6, t9
   
  These nodes are invalid:
  n6
   
  Root node `x` not in ndlst
   
  These nodes are invalid:
  n8
   
  These nodes are invalid:
  n4, n8
   
  ── Skip (test-display-methods.R:11:1): show() works ────────────────────────────
  Reason: empty test
  
  Formal class 'TreeMan' [package "treeman"] with 17 slots
    ..@ ndlst       :List of 19
    ..@ nds         : chr [1:9] "n1" "n2" "n3" "n4" ...
    ..@ nnds        : int 9
    ..@ tips        : chr [1:10] "t1" "t10" "t2" "t3" ...
    ..@ ntips       : int 10
    ..@ all         : chr [1:19] "n1" "n2" "n3" "n4" ...
    ..@ nall        : int 19
    ..@ pd          : num 7.44
    ..@ wspn        : logi TRUE
    ..@ wtxnyms     : logi FALSE
    ..@ ply         : logi FALSE
    ..@ updtd       : logi TRUE
    ..@ ndmtrx      :Formal class 'big.matrix' [package "bigmemory"] with 1 slot
    ..@ tinds       : int [1:10] 10 11 12 13 14 15 16 17 18 19
    ..@ prinds      : num [1:19] 1 1 1 3 4 2 5 2 5 9 ...
    ..@ root        : chr "n1"
    ..@ othr_slt_nms: logi(0) 
  [1] "TreeMan Object of [10] tips"
  ── Skip (test-display-methods.R:17:1): print() works ───────────────────────────
  Reason: empty test
  
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + Binary
    + PD 10.5
    + Root node is "n1"
  ── Skip (test-display-methods.R:20:1): summary() works ─────────────────────────
  Reason: empty test
  
  ── Warning (test-manip-methods.R:151:3): rmClade() works ───────────────────────
  Coercing vector to a single-column matrix.
  
  ── ERROR (test-manip-methods.R:153:3): rmClade() works ─────────────────────────
  Error: Invalid margin
  Backtrace:
      █
   1. └─treeman::getAge(t2) test-manip-methods.R:153:2
   2.   └─treeman:::.getTreeAgeFrmMtrx(...)
   3.     └─treeman:::.getNdsPrdstsFrmMtrx(...)
   4.       └─plyr::adply(...)
   5.         └─plyr:::splitter_a(.data, .margins, .expand, .id)
  
  ── Skip (test-node.R:17:1): Node works (rooted + w/o spns) ─────────────────────
  Reason: empty test
  
  Node (internal node):
    + ID: "n4"
    + prid: "n1"
    + ptid: "t3", "t8"
    + nkids: 2
    + spn: 0.32
    + predist: 0.32
    + pd: 0.93
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + Binary
    + PD 9.47
    + Root node is "n1"
    + With additional node slots:
      [binary_val]
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + Binary
    + PD 10
    + Root node is "n1"
  [1] "TreeMen Object of [3] trees"
  ── Skip (test-treemen.R:11:1): print() works ───────────────────────────────────
  Reason: empty test
  
  TreeMen Object of [3] trees── Skip (test-treemen.R:14:1): show() works ────────────────────────────────────
  Reason: empty test
  
  ── Skipped tests  ──────────────────────────────────────────────────────────────
  ● empty test (6)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  Warning (test-manip-methods.R:151:3): rmClade() works
  ERROR (test-manip-methods.R:153:3): rmClade() works
  
  [ FAIL 1 | WARN 1 | SKIP 6 | PASS 246 ]
  Error: Test failures
  Execution halted