Running 'test-all.R' [24s]
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:
  n5, t5, t6
   
  These nodes are invalid:
  n8
   
  Root node `x` not in ndlst
   
  These nodes are invalid:
  n7
   
  These nodes are invalid:
  n7
   
  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 9.58
    ..@ 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 2 2 3 4 6 3 5 7 ...
    ..@ root        : chr "n1"
    ..@ othr_slt_nms: logi(0) 
  [1] "TreeMan Object of [10] tips"
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + With node matrix
    + Binary
    + PD 9.08
    + Root node is "n1"
  -- 1. Error: rmClade() works (@test-manip-methods.R#153)  ----------------------
  Invalid margin
  1: getAge(t2) at testthat/test-manip-methods.R:153
  2: .getTreeAgeFrmMtrx(tree@ndmtrx, all_ids, tids, spns, parallel)
  3: .getNdsPrdstsFrmMtrx(ndmtrx, all_ids, tids, spns, parallel = parallel, progress = "none")
  4: plyr::adply(ndmtrx[, all_ids %in% ids], .margins = 2, .fun = .get, .parallel = parallel, 
         .progress = progress)
  5: splitter_a(.data, .margins, .expand, .id)
  6: stop("Invalid margin")
  
  Node (internal node):
    + ID: "n9"
    + prid: "n6"
    + ptid: "t1", "t2"
    + nkids: 2
    + spn: 0.031
    + predist: 1.4
    + pd: 1.5
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + Binary
    + PD 8.53
    + Root node is "n1"
    + With additional node slots:
      [binary_val]
  Tree (TreeMan Object):
    + 10 tips
    + 9 internal nodes
    + Binary
    + PD 6.17
    + Root node is "n1"
  [1] "TreeMen Object of [3] trees"
  TreeMen Object of [3] trees== testthat results  ===========================================================
  OK: 244 SKIPPED: 8 WARNINGS: 3 FAILED: 1
  1. Error: rmClade() works (@test-manip-methods.R#153) 
  
  Error: testthat unit tests failed
  Execution halted