Microsoft (R) Program Maintenance Utility Version 7.00.8882 Copyright (C) Microsoft Corp 1988-2000. All rights reserved. C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp exec/nextool.pl blib\script\nextool.pl pl2bat.bat blib\script\nextool.pl C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp exec/nex2text_tree.pl blib\script\nex2text_tree.pl pl2bat.bat blib\script\nex2text_tree.pl C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp exec/nexplot.pl blib\script\nexplot.pl pl2bat.bat blib\script\nexplot.pl Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\AssumptionsBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\Block.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\CharactersBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\CodonsBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\DataBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\DistancesBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\Functions.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\HistoryBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\MatrixBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\Node.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\NotesBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\SetsBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\SpanBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\TaxaBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\TaxUnit.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\TaxUnitSet.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\Tree.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\TreesBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\UnalignedBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\UnknownBlock.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\NEXUS\WeightSet.pm Installing C:\cpanrun-5.8\build\5-8-0\bin\nex2text_tree.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\nex2text_tree.pl Installing C:\cpanrun-5.8\build\5-8-0\bin\nexplot.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\nexplot.pl Installing C:\cpanrun-5.8\build\5-8-0\bin\nextool.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\nextool.pl Writing C:\cpanrun-5.8\build\5-8-0\site\lib\auto\Bio\NEXUS\.packlist Appending installation info to C:\cpanrun-5.8\build\5-8-0\lib/perllocal.pod defined ---- symmetric bifurcating tree, all branch lengths = 1 ok 7 - TreesBlock object created and parsed ok 8 - 15 nodes defined: 8 otus + 7 root ok 9 - 8 OTUs defined 1..9 ok t\04_labels................ ---- very long names in various places (OTU, char, tree labels) ok 1 - NEXUS object created and parsed ok 2 - 15 nodes defined: 8 otus + 7 root ok 3 - 8 OTUs defined ok 4 - Long string properly set in Taxa block ok 5 - Long string properly set in Characters block ok 6 - Long string properly set in node of the Tree ok 7 - Long string properly set in Tree name 1..7 ok t\05_radical_whitespace.... ---- Radical white-space (legal) in the NEXUS data ok 1 - NEXUS object created and parsed ok 2 - taxa label C parsed correctly in Taxa block ok 3 - taxa label 'NE' not present in Taxa block ok 4 - taxa label C parsed correctly in Characters Block ok 5 - character label '5' parsed correctly in Characters Block ok 6 - taxa label C parsed correctly in the Tree ok 7 - tree name 'radical_whitespace' parsed correctly 1..7 ok t\06_tree_parse............tree 'basal-trifurcation' = (((A:1,B:1):1,(C:1,D:1):1):1,(E:1,F:1):2,(G:1,H:1):2); ok 1 - TreesBlock object created and parsed ok 2 - 14 nodes defined: 8 otus + 6 root ok 3 - 8 OTUs defined ok 4 - the quoted tree name basal-trifurcation parsed correctly tree bush = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1); ok 5 - TreesBlock object created and parsed ok 6 - 15 nodes defined: 8 otus + 7 root ok 7 - 8 OTUs defined ok 8 - the quoted tree name bush parsed correctly tree 'bush-branchlength-negative' = (((A:1,B:1):1,(C:1,D:1):-0.25):1,((E:1,F:1):1,(G:1,H:1):1):1); ok 9 - TreesBlock object created and parsed ok 10 - 15 nodes defined: 8 otus + 7 root ok 11 - 8 OTUs defined ok 12 - the quoted tree name bush-branchlength-negative parsed correctly tree 'bush-branchlength-scientific' = (((A:1,B:2e+01):1,(C:9e-01,D:1):1):1,((E:1,F:9E-01):1,(G:2E+01,H:1):1):1); ok 13 - TreesBlock object created and parsed ok 14 - 15 nodes defined: 8 otus + 7 root ok 15 - 8 OTUs defined ok 16 - the quoted tree name bush-branchlength-scientific parsed correctly ok 17 - Node name 'B' parsed correctly ok 18 - Branch length (scientific notation) read correctly tree 'bush-branchlength-zero' = (((A:1,B:1):1,(C:0,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1); ok 19 - TreesBlock object created and parsed ok 20 - 15 nodes defined: 8 otus + 7 root ok 21 - 8 OTUs defined ok 22 - the quoted tree name bush-branchlength-zero parsed correctly tree 'bush-cladogram' = (((A,B),(C,D)),((E,F),(G,H))); ok 23 - TreesBlock object created and parsed ok 24 - 15 nodes defined: 8 otus + 7 root ok 25 - 8 OTUs defined ok 26 - the quoted tree name bush-cladogram parsed correctly tree 'bush-extended-root-branch' = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1):1; ok 27 - TreesBlock object created and parsed ok 28 - 15 nodes defined: 8 otus + 7 root ok 29 - 8 OTUs defined ok 30 - the quoted tree name bush-extended-root-branch parsed correctly tree 'bush-inode-labels' = (((A:1,B:1)AB:1,(C:1,D:1)CD:1)ABCD:1,((E:1,F:1)EF:1,(G:1,H:1)GH:1)EFGH:1); ok 31 - TreesBlock object created and parsed ok 32 - 15 nodes defined: 8 otus + 7 root ok 33 - 8 OTUs defined ok 34 - the quoted tree name bush-inode-labels parsed correctly tree 'bush-inode-labels-partial' = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1)EF:1,(G:1,H:1)GH:1)EFGH:1); ok 35 - TreesBlock object created and parsed ok 36 - 15 nodes defined: 8 otus + 7 root ok 37 - 8 OTUs defined ok 38 - the quoted tree name bush-inode-labels-partial parsed correctly tree 'bush-inode-labels-quoted1' = (((A:1,B:1)'inode AB':1,(C:1,D:1)'inode CD':1)'inode ABCD':1,((E:1,F:1)'inode EF':1,(G:1,H:1)'inode GH':1)'inode EFGH':1); ok 39 - TreesBlock object created and parsed ok 40 - 15 nodes defined: 8 otus + 7 root ok 41 - 8 OTUs defined ok 42 - the quoted tree name bush-inode-labels-quoted1 parsed correctly tree 'bush quoted string name1' = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1); ok 43 - TreesBlock object created and parsed ok 44 - 15 nodes defined: 8 otus + 7 root ok 45 - 8 OTUs defined ok 46 - the quoted tree name bush_quoted_string_name1 parsed correctly tree 'bush-uneven' = (((A:1,B:2):1,(C:1,D:2):1):1,((E:1,F:2):1,(G:1,H:2):1):1); ok 47 - TreesBlock object created and parsed ok 48 - 15 nodes defined: 8 otus + 7 root ok 49 - 8 OTUs defined ok 50 - the quoted tree name bush-uneven parsed correctly tree ladder = (((((((A:1,B:1):1,C:2):1,D:3):1,E:4):1,F:5):1,G:6):1,H:7); ok 51 - TreesBlock object created and parsed ok 52 - 15 nodes defined: 8 otus + 7 root ok 53 - 8 OTUs defined ok 54 - the quoted tree name ladder parsed correctly tree 'ladder-cladogram' = (((((((A,B),C),D),E),F),G),H); ok 55 - TreesBlock object created and parsed ok 56 - 15 nodes defined: 8 otus + 7 root ok 57 - 8 OTUs defined ok 58 - the quoted tree name ladder-cladogram parsed correctly tree 'ladder-uneven' = (((((((A:1,B:2):1,C:2):1,D:4):1,E:4):1,F:6):1,G:6):1,H:8); ok 59 - TreesBlock object created and parsed ok 60 - 15 nodes defined: 8 otus + 7 root ok 61 - 8 OTUs defined ok 62 - the quoted tree name ladder-uneven parsed correctly tree rake = (A:1,B:1,C:1,D:1,E:1,F:1,G:1,H:1); ok 63 - TreesBlock object created and parsed ok 64 - 9 nodes defined: 8 otus + 1 root ok 65 - 8 OTUs defined ok 66 - the quoted tree name rake parsed correctly tree 'rake-cladogram' = (A,B,C,D,E,F,G,H); ok 67 - TreesBlock object created and parsed ok 68 - 9 nodes defined: 8 otus + 1 root ok 69 - 8 OTUs defined ok 70 - the quoted tree name rake-cladogram parsed correctly 1..70 ok t\07_quoted_labels......... ---- Quoted string - 1 ; a) OTU name 'OTU C' (single quotes) ,b) charlabel "Char 3",and c) tree name "the ladder tree" ok 1 - NEXUS object created and parsed ok 2 - taxa label 'OTU C' parsed correctly in Taxa block ok 3 - taxa label 'OTU C' parsed correctly in Characters Block ok 4 - taxa label 'OTU C' parsed correctly in the Tree ok 5 - the quoted tree name 'the ladder tree' parsed correctly 1..5 ok t\09_todo..................ok 1 - Bio::NEXUS module loaded successfully 1..1 ok t\10_perlpod...............1..25 ok 1 - blib\script\nex2text_tree.pl ok 2 - blib\script\nexplot.pl ok 3 - blib\script\nextool.pl ok 4 - blib\lib\Bio\NEXUS.pm ok 5 - blib\lib\Bio\NEXUS\AssumptionsBlock.pm ok 6 - blib\lib\Bio\NEXUS\Block.pm ok 7 - blib\lib\Bio\NEXUS\CharactersBlock.pm ok 8 - blib\lib\Bio\NEXUS\CodonsBlock.pm ok 9 - blib\lib\Bio\NEXUS\DataBlock.pm ok 10 - blib\lib\Bio\NEXUS\DistancesBlock.pm ok 11 - blib\lib\Bio\NEXUS\Functions.pm ok 12 - blib\lib\Bio\NEXUS\HistoryBlock.pm ok 13 - blib\lib\Bio\NEXUS\MatrixBlock.pm ok 14 - blib\lib\Bio\NEXUS\Node.pm ok 15 - blib\lib\Bio\NEXUS\NotesBlock.pm ok 16 - blib\lib\Bio\NEXUS\SetsBlock.pm ok 17 - blib\lib\Bio\NEXUS\SpanBlock.pm ok 18 - blib\lib\Bio\NEXUS\TaxaBlock.pm ok 19 - blib\lib\Bio\NEXUS\TaxUnit.pm ok 20 - blib\lib\Bio\NEXUS\TaxUnitSet.pm ok 21 - blib\lib\Bio\NEXUS\Tree.pm ok 22 - blib\lib\Bio\NEXUS\TreesBlock.pm ok 23 - blib\lib\Bio\NEXUS\UnalignedBlock.pm ok 24 - blib\lib\Bio\NEXUS\UnknownBlock.pm ok 25 - blib\lib\Bio\NEXUS\WeightSet.pm ok t\11_podcoverage...........1..22 ok 1 - Pod coverage on Bio::NEXUS ok 2 - Pod coverage on Bio::NEXUS::AssumptionsBlock ok 3 - Pod coverage on Bio::NEXUS::Block ok 4 - Pod coverage on Bio::NEXUS::CharactersBlock ok 5 - Pod coverage on Bio::NEXUS::CodonsBlock ok 6 - Pod coverage on Bio::NEXUS::DataBlock ok 7 - Pod coverage on Bio::NEXUS::DistancesBlock # Bio::NEXUS::Functions: no public symbols defined ok 8 - Pod coverage on Bio::NEXUS::Functions ok 9 - Pod coverage on Bio::NEXUS::HistoryBlock ok 10 - Pod coverage on Bio::NEXUS::MatrixBlock ok 11 - Pod coverage on Bio::NEXUS::Node # Bio::NEXUS::NotesBlock: no public symbols defined ok 12 - Pod coverage on Bio::NEXUS::NotesBlock ok 13 - Pod coverage on Bio::NEXUS::SetsBlock ok 14 - Pod coverage on Bio::NEXUS::SpanBlock ok 15 - Pod coverage on Bio::NEXUS::TaxaBlock ok 16 - Pod coverage on Bio::NEXUS::TaxUnit ok 17 - Pod coverage on Bio::NEXUS::TaxUnitSet ok 18 - Pod coverage on Bio::NEXUS::Tree ok 19 - Pod coverage on Bio::NEXUS::TreesBlock ok 20 - Pod coverage on Bio::NEXUS::UnalignedBlock ok 21 - Pod coverage on Bio::NEXUS::UnknownBlock ok 22 - Pod coverage on Bio::NEXUS::WeightSet ok All tests successful. Files=10, Tests=164, 4 wallclock secs ( 0.00 cusr + 0.00 csys = 0.00 CPU)