--selftest failure of binary distribution on linux

[rrnewton]

Stefanie Hartmann reported this failed test output of the binary distribution:

../software/phybin-0.3.x86_64_linux --selftest
### Failure in: 0:3:annotateWLabLists      
expected: ["A","B","C","D"]
 but got: ["D","C","B","A"]
### Failure in: 0:4:normalize1             
expected: "(C, D, E, (A, B))"
 but got: "(E, D, C, (B, A));"
### Failure in: 0:5:normalize2A            
expected: "(C, D, E, (A, B))"
 but got: "FullTree   NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 2,\n                                                   NTLeaf (StandardDecor 0.0 Nothing) 3,\n                                                   NTLeaf (StandardDecor 0.0 Nothing) 4,\n                                                   NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 0,\n                                                                                           NTLeaf (StandardDecor 0.0 Nothing) 1]]"
### Failure in: 0:6:normalize2B            
expected: "(C, D, E, (A, B))"
 but got: "FullTree   NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 2,\n                                                   NTLeaf (StandardDecor 0.0 Nothing) 3,\n                                                   NTLeaf (StandardDecor 0.0 Nothing) 4,\n                                                   NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 0,\n                                                                                           NTLeaf (StandardDecor 0.0 Nothing) 1]]"
### Failure in: 0:7:normalize3             
expected: "(((BB, BJ)), (MB, ML), (RE, (SD, SM)))"
 but got: "FullTree   NTInterior (StandardDecor 0.0 Nothing) [NTInterior (StandardDecor 0.0 Nothing) [NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 0,\n                                                                                                                                   NTLeaf (StandardDecor 0.0 Nothing) 1]],\n                                                   NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 5,\n                                                                                           NTLeaf (StandardDecor 0.0 Nothing) 6],\n                                                   NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 4,\n                                                                                           NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 2,\n                                                                                                                                   NTLeaf (StandardDecor 0.0 Nothing) 3]]]"
### Error in:   3:bipTreeConversion         
./tests/t3_consensus/cluster1_284_alltrees.tr: openFile: does not exist (No such file or directory)
### Error in:   4:t3                        
./tests/t3_consensus/cluster1_284_consensus.tr: openFile: does not exist (No such file or directory)
### Error in:   5:t4                        
./tests/t4_consensus/cluster1_16_consensus.tr: openFile: does not exist (No such file or directory)
### Error in:   6:t5                        
./tests/t5_consensus/cluster1_35_consensus.tr: openFile: does not exist (No such file or directory)
Cases: 31  Tried: 31  Errors: 4  Failures: 5

[alexweisberg]

I also get this error using the precompiled linux executable when I run the selftest.

The program also exits with errors if I try to run it with my dataset anyway: `phybin --namesep= --graphbins --tolerant -v ./*tre ... Number of input tree files: 636 Number of VALID trees (correct # of leaves/taxa): 636 Total tree nodes contained in valid trees: 15349 Average branch len over valid trees: 1.3280990778664684e-2 Max/Min branch lengths: (27.903559695134344,0.0) Time to compute distance matrix: 15.033477s Clustering using method UPGMA [finished] Wrote full dendrogram to file dendrogram.txt Sanity checked dendrogram of size: 636 [async] writing dendrogram as a graph to dendrogram.dot [finished] Wrote contents of each cluster to cluster.txt [finished] Wrote representative (consensus) trees to cluster_consensus.tr Next start the time consuming operation of writing out graphviz visualizations: [finished] Wrote visual representations of consensus trees to cluster.pdf Waiting for 2 asynchronous tasks to finish...

phybin: bipsToTree: Internal error! No match for bip: fromList [62,63] out is [(fromList [0],NTLeaf () 0),(fromList [1],NTLeaf () 1),(fromList [2],NTLeaf () 2),(fromList [3],NTLeaf () 3)] and remaining bips 0 when processing orig bip set: fromList [fromList [62,63]]`

Despite the output text, the only output files are dendrogram.txt and distance_matrix.txt

[alexweisberg]

Just to update this, I also compiled Phybin 0.3 from source on a mac (the pre-compiled mac 0.3 version dies with "Killed 9" on El Capitan) and it gives the same error message on --selftest.