RUNIT TEST PROTOCOL--Mon Dec 6 13:20:26 2010

Number of test functions: 97

Number of errors: 0

Number of failures: 4

1 Test suite

Failures

Details

Test Suite: phylobase unit testing

• Test file: runit.badnex.R
  • test.checkTree: (1 checks) ... OK (0.01 seconds)
    
• Test file: runit.class-phylo4d.R
  • test.phylo4d.matrix: (0 checks) ... OK (0 seconds)
    
  • test.phylo4d.phylo: (21 checks) ... OK (0.3 seconds)
    
  • test.phylo4d.phylo4: (39 checks) ... OK (0.43 seconds)
    
  • test.phylo4d.phylo4d: (1 checks) ... OK (0.01 seconds)
    
• Test file: runit.class-phylo4.R
  • test.phylo4.matrix: (12 checks) ... OK (0.02 seconds)
    
  • test.phylo4.phylo: (12 checks) ... OK (0.07 seconds)
    
• Test file: runit.formatData.R
  • test.formatData: (48 checks) ... OK (0.51 seconds)
    
  • test.formatDataWithDup: (45 checks) ... OK (0.58 seconds)
    
• Test file: runit.methods-oldclasses.R
  • test.reorder.phylo: (0 checks) ... OK (0 seconds)
    
• Test file: runit.methods-phylo4d.R
  • test.addData.phylo4: (0 checks) ... OK (0 seconds)
    
  • test.addData.phylo4d: (0 checks) ... OK (0 seconds)
    
  • test.hasNodeData.phylo4d: (0 checks) ... OK (0 seconds)
    
  • test.na.omit.phylo4d: (0 checks) ... OK (0 seconds)
    
  • test.nData: (1 checks) ... OK (0 seconds)
    
  • test.nodeData.phylo4d: (3 checks) ... OK (0.01 seconds)
    
  • test.Replace.nodeData.phylo4d: (1 checks) ... OK (0.02 seconds)
    
  • test.Replace.tdata.phylo4d: (3 checks) ... OK (0.06 seconds)
    
  • test.Replace.tipData.phylo4d: (1 checks) ... OK (0.02 seconds)
    
  • test.summary.phylo4d: (0 checks) ... OK (0 seconds)
    
  • test.tdata.phylo4d: (8 checks) ... OK (0.04 seconds)
    
  • test.tipData.phylo4d: (3 checks) ... OK (0.01 seconds)
    
• Test file: runit.methods-phylo4.R
  • test.edgeId.phylo4: (5 checks) ... OK (0 seconds)
    
  • test.edgeLabels.phylo4: (4 checks) ... OK (0 seconds)
    
  • test.edgeLength.phylo4: (5 checks) ... OK (0.01 seconds)
    
  • test.edgeOrder.phylo4: (3 checks) ... OK (0.01 seconds)
    
  • test.edges.phylo4: (2 checks) ... OK (0 seconds)
    
  • test.hasEdgeLabels.phylo4: (2 checks) ... OK (0 seconds)
    
  • test.hasEdgeLength.phylo4: (2 checks) ... OK (0 seconds)
    
  • test.hasNodeLabels.phylo4: (2 checks) ... OK (0.01 seconds)
    
  • test.head.phylo4: (0 checks) ... OK (0 seconds)
    
  • test.isRooted.phylo4: (1 checks) ... OK (0 seconds)
    
  • test.labels.phylo4: (4 checks) ... OK (0 seconds)
    
  • test.names.phylo4: (0 checks) ... OK (0 seconds)
    
  • test.nEdges.phylo4: (1 checks) ... OK (0 seconds)
    
  • test.nNodes.phylo4: (1 checks) ... OK (0 seconds)
    
  • test.nodeId.phylo4: (5 checks) ... OK (0 seconds)
    
  • test.nodeLabels.phylo4: (1 checks) ... OK (0 seconds)
    
  • test.nodeType.phylo4: (1 checks) ... OK (0 seconds)
    
  • test.nTips.ANY: (1 checks) ... OK (0 seconds)
    
  • test.nTips.phylo4: (1 checks) ... OK (0 seconds)
    
  • test.reorder.phylo4: (0 checks) ... OK (0 seconds)
    
  • test.Replace.edgeLabels.phylo4: (8 checks) ... OK (0.03 seconds)
    
  • test.Replace.edgeLength.phylo4: (14 checks) ... OK (0.04 seconds)
    
  • test.Replace.labels.phylo4: (20 checks) ... OK (0.1 seconds)
    
  • test.Replace.nodeLabels.phylo4: (8 checks) ... OK (0.04 seconds)
    
  • test.Replace.rootNode.phylo4: (0 checks) ... OK (0 seconds)
    
  • test.Replace.tipLabels.phylo4: (7 checks) ... OK (0.04 seconds)
    
  • test.rootNode.phylo4: (1 checks) ... OK (0 seconds)
    
  • test.sumEdgeLength.phylo4: (0 checks) ... OK (0 seconds)
    
  • test.summary.phylo4: (12 checks) ... OK (0.03 seconds)
    
  • test.tail.phylo4: (0 checks) ... OK (0 seconds)
    
  • test.tipLabels.phylo4: (1 checks) ... OK (0 seconds)
    
• Test file: runit.pdata.R
  • test.assign.pdata: (0 checks) ... OK (0 seconds)
    
  • test.check_pdata: (0 checks) ... OK (0 seconds)
    
  • test.extract.pdata: (0 checks) ... OK (0 seconds)
    
  • test.pdata: (0 checks) ... OK (0 seconds)
    
  • test.plot.pdata: (0 checks) ... OK (0 seconds)
    
• Test file: runit.phylo4.R
  • test..genlab: (0 checks) ... OK (0 seconds)
    
• Test file: runit.phylobase.options.R
  • test.phylobase.options: (6 checks) ... OK (0.01 seconds)
    
• Test file: runit.prune.R
  • test.prune.phylo4: (1 checks) ... OK (0.02 seconds)
    
  • test.prune.phylo4d: (1 checks) ... OK (0.1 seconds)
    
• Test file: runit.readNCL.R
  • test.readNCL: (127 checks) ... OK (1.83 seconds)
    
• Test file: runit.readNexus.R
  • test.readNexus: (112 checks) ... OK (1.7 seconds)
    
• Test file: runit.setAs-Methods.R
  • test.multiPhylo4.As.multiPhylo: (0 checks) ... OK (0 seconds)
    
  • test.multiPhylo.As.multiPhylo4: (0 checks) ... OK (0 seconds)
    
  • test.phylo4.As.data.frame: (2 checks) ... OK (0.02 seconds)
    
  • test.phylo4.As.phylo: FAILURE !! (check number 1) Error in checkEquals(suppressWarnings(as(phy, "phylo")), tr) : Names: 2 string mismatches Component 2: Numeric: lengths (8, 1) differ Component 4: Numeric: lengths (1, 8) differ
    
  • test.phylo4.As.phylog: (0 checks) ... OK (0 seconds)
    
  • test.phylo4d.As.phylo: FAILURE !! (check number 1) Error in checkEquals(as(phyd, "phylo"), tr) : Names: 2 string mismatches Component 2: Numeric: lengths (8, 1) differ Component 4: Numeric: lengths (1, 8) differ
    
  • test.phylo4ToDataFrame: (5 checks) ... OK (0.01 seconds)
    
  • test.phylo.As.phylo4: FAILURE !! (check number 10) Error in checkEquals(tr, as(phy, "phylo")) : Names: 2 string mismatches Component 2: Numeric: lengths (1, 8) differ Component 4: Numeric: lengths (8, 1) differ
    
  • test.phylo.As.phylo4d: FAILURE !! (check number 3) Error in checkEquals(tr, as(phyd, "phylo")) : Names: 2 string mismatches Component 2: Numeric: lengths (1, 8) differ Component 4: Numeric: lengths (8, 1) differ
    
• Test file: runit.subset.R
  • test.extractTree: (2 checks) ... OK (0 seconds)
    
  • test.subset.phylo4: (22 checks) ... OK (0.16 seconds)
    
  • test.subset.phylo4d: (21 checks) ... OK (0.45 seconds)
    
• Test file: runit.tbind.R
  • test.tbind: (0 checks) ... OK (0 seconds)
    
• Test file: runit.treePlot.R
  • test..bubLegendGrob: (0 checks) ... OK (0 seconds)
    
  • test.drawDetails.bubLegend: (0 checks) ... OK (0 seconds)
    
  • test.phylobubbles: (0 checks) ... OK (0 seconds)
    
  • test.phyloXXYY: (0 checks) ... OK (0 seconds)
    
  • test.plotOneTree: (0 checks) ... OK (0 seconds)
    
  • test.plot.phylo4: (0 checks) ... OK (0 seconds)
    
  • test.tip.data.plot: (0 checks) ... OK (0 seconds)
    
  • test.treePlot: (0 checks) ... OK (0 seconds)
    
• Test file: runit.treestruc.R
  • test.hasPoly: (2 checks) ... OK (0.05 seconds)
    
  • test.hasRetic: (1 checks) ... OK (0 seconds)
    
  • test.hasSingle: (1 checks) ... OK (0 seconds)
    
• Test file: runit.treewalk.R
  • test.ancestor: (0 checks) ... OK (0 seconds)
    
  • test.ancestors: (0 checks) ... OK (0 seconds)
    
  • test.children: (0 checks) ... OK (0 seconds)
    
  • test.descendants: (8 checks) ... OK (0.07 seconds)
    
  • test.getEdge: (29 checks) ... OK (0.13 seconds)
    
  • test.getNode: (13 checks) ... OK (0.02 seconds)
    
  • test.MRCA: (0 checks) ... OK (0 seconds)
    
  • test.shortestPath: (0 checks) ... OK (0 seconds)
    
  • test.siblings: (0 checks) ... OK (0 seconds)