Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("treespace")
  Loading required package: treespace
  Loading required package: ape
  Loading required package: ade4
  Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
  == Failed tests ================================================================
  -- Failure (testbasics.R:41:3): treeDist equals corresponding entry of multiDist --
  treeDist(trees[[1]], trees[[2]]) not equal to multiDist(trees)[[1]].
  Classes differ: 'numeric' is not 'dist'
  -- Failure (testbasics.R:42:3): treeDist equals corresponding entry of multiDist --
  treeDist(trees[[1]], trees[[2]], emphasise.tips = c("t1", "t2")) not equal to multiDist(trees, emphasise.tips = c("t1", "t2"))[[1]].
  Classes differ: 'numeric' is not 'dist'
  -- Failure (testbasics.R:54:3): multiDist equals the distance matrix from treespace --
  multidistMatrixFunction(0)[[n]] not equal to treedistMatrix[[n]].
  names for current but not for target
  Attributes: < Names: 4 string mismatches >
  Attributes: < Length mismatch: comparison on first 5 components >
  Attributes: < Component 2: Modes: numeric, character >
  Attributes: < Component 2: target is numeric, current is character >
  Attributes: < Component 3: Modes: logical, numeric >
  Attributes: < Component 3: target is logical, current is numeric >
  Attributes: < Component 4: Modes of target, current: call, logical >
  Attributes: < Component 4: target, current do not match when deparsed >
  ...
  -- Failure (testbasics.R:55:3): multiDist equals the distance matrix from treespace --
  multidistMatrixFunction(l)[[n]] not equal to treedistMatrix0.5[[n]].
  names for current but not for target
  Attributes: < Names: 4 string mismatches >
  Attributes: < Length mismatch: comparison on first 5 components >
  Attributes: < Component 2: Modes: numeric, character >
  Attributes: < Component 2: target is numeric, current is character >
  Attributes: < Component 3: Modes: logical, numeric >
  Attributes: < Component 3: target is logical, current is numeric >
  Attributes: < Component 4: Modes of target, current: call, logical >
  Attributes: < Component 4: target, current do not match when deparsed >
  ...
  -- Failure (testbasics.R:56:3): multiDist equals the distance matrix from treespace --
  treespace(trees, nf = 2, emphasise.tips = c("t1", "t2"))$D[[n]] not equal to multiDist(trees, emphasise.tips = c("t1", "t2"))[[n]].
  names for target but not for current
  Attributes: < Names: 4 string mismatches >
  Attributes: < Length mismatch: comparison on first 5 components >
  Attributes: < Component 2: Modes: character, numeric >
  Attributes: < Component 2: target is character, current is numeric >
  Attributes: < Component 3: Modes: numeric, logical >
  Attributes: < Component 3: target is numeric, current is logical >
  Attributes: < Component 4: Modes: logical, call >
  Attributes: < Component 4: Lengths: 1, 2 >
  ...
  -- Failure (testbasics.R:86:3): indTree and catTree should be identical by relatedTreeDist measure --
  relatedTreeDist(list(indTree1, indTree2), df)[[1]] not equal to 0.
  Lengths: 0, 1
  Attributes: < Modes: list, NULL >
  Attributes: < Lengths: 5, 0 >
  Attributes: < names for target but not for current >
  Attributes: < current is not list-like >
  target is dist, current is numeric
  -- Failure (testbasics.R:176:3): transmission tree distances are independent of the node naming order --
  0 not equal to wiwTreeDist(matList, sampled = 1:7)[[1]].
  Classes differ: 'numeric' is not 'dist'
  
  [ FAIL 7 | WARN 0 | SKIP 0 | PASS 40 ]
  Error: Test failures
  Execution halted