Checking if your kit is complete... Looks good Writing Makefile for Bio::NEXUS cp lib/Bio/NEXUS/DataBlock.pm blib/lib/Bio/NEXUS/DataBlock.pm cp lib/Bio/NEXUS/CodonsBlock.pm blib/lib/Bio/NEXUS/CodonsBlock.pm cp lib/Bio/NEXUS/NotesBlock.pm blib/lib/Bio/NEXUS/NotesBlock.pm cp lib/Bio/NEXUS/HistoryBlock.pm blib/lib/Bio/NEXUS/HistoryBlock.pm cp lib/Bio/NEXUS/TaxUnit.pm blib/lib/Bio/NEXUS/TaxUnit.pm cp lib/Bio/NEXUS/CharactersBlock.pm blib/lib/Bio/NEXUS/CharactersBlock.pm cp lib/Bio/NEXUS/SpanBlock.pm blib/lib/Bio/NEXUS/SpanBlock.pm cp lib/Bio/NEXUS/UnalignedBlock.pm blib/lib/Bio/NEXUS/UnalignedBlock.pm cp lib/Bio/NEXUS/TaxUnitSet.pm blib/lib/Bio/NEXUS/TaxUnitSet.pm cp lib/Bio/NEXUS/DistancesBlock.pm blib/lib/Bio/NEXUS/DistancesBlock.pm cp lib/Bio/NEXUS/MatrixBlock.pm blib/lib/Bio/NEXUS/MatrixBlock.pm cp lib/Bio/NEXUS/UnknownBlock.pm blib/lib/Bio/NEXUS/UnknownBlock.pm cp lib/Bio/NEXUS/Node.pm blib/lib/Bio/NEXUS/Node.pm cp lib/Bio/NEXUS/Tree.pm blib/lib/Bio/NEXUS/Tree.pm cp lib/Bio/NEXUS/WeightSet.pm blib/lib/Bio/NEXUS/WeightSet.pm cp lib/Bio/NEXUS/TaxaBlock.pm blib/lib/Bio/NEXUS/TaxaBlock.pm cp lib/Bio/NEXUS/TreesBlock.pm blib/lib/Bio/NEXUS/TreesBlock.pm cp lib/Bio/NEXUS/SetsBlock.pm blib/lib/Bio/NEXUS/SetsBlock.pm cp lib/Bio/NEXUS/AssumptionsBlock.pm blib/lib/Bio/NEXUS/AssumptionsBlock.pm cp lib/Bio/NEXUS/Block.pm blib/lib/Bio/NEXUS/Block.pm cp lib/Bio/NEXUS.pm blib/lib/Bio/NEXUS.pm cp lib/Bio/NEXUS/Functions.pm blib/lib/Bio/NEXUS/Functions.pm cp exec/nextool.pl blib/script/nextool.pl /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/nextool.pl cp exec/nex2text_tree.pl blib/script/nex2text_tree.pl /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/nex2text_tree.pl cp exec/nexplot.pl blib/script/nexplot.pl /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/nexplot.pl Manifying blib/man1/nextool.pl.1 Manifying blib/man1/nex2text_tree.pl.1 Manifying blib/man1/nexplot.pl.1 Manifying blib/man3/Bio::NEXUS::DataBlock.3 Manifying blib/man3/Bio::NEXUS::CodonsBlock.3 Manifying blib/man3/Bio::NEXUS::NotesBlock.3 Manifying blib/man3/Bio::NEXUS::HistoryBlock.3 Manifying blib/man3/Bio::NEXUS::TaxUnit.3 Manifying blib/man3/Bio::NEXUS::CharactersBlock.3 Manifying blib/man3/Bio::NEXUS::SpanBlock.3 Manifying blib/man3/Bio::NEXUS::UnalignedBlock.3 Manifying blib/man3/Bio::NEXUS::TaxUnitSet.3 Manifying blib/man3/Bio::NEXUS::DistancesBlock.3 Manifying blib/man3/Bio::NEXUS::MatrixBlock.3 Manifying blib/man3/Bio::NEXUS::UnknownBlock.3 Manifying blib/man3/Bio::NEXUS::Node.3 Manifying blib/man3/Bio::NEXUS::Tree.3 Manifying blib/man3/Bio::NEXUS::WeightSet.3 Manifying blib/man3/Bio::NEXUS::SetsBlock.3 Manifying blib/man3/Bio::NEXUS::TaxaBlock.3 Manifying blib/man3/Bio::NEXUS::TreesBlock.3 Manifying blib/man3/Bio::NEXUS::AssumptionsBlock.3 Manifying blib/man3/Bio::NEXUS::Block.3 Manifying blib/man3/Bio::NEXUS::Functions.3 Manifying blib/man3/Bio::NEXUS.3 PERL_DL_NONLAZY=1 /home/cpanrun/pa-risc1.1/build/5.8.2/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/01_nexus................. ---- Empty NEXUS object creation ok 1 - NEXUS object and Bio::NEXUS::Tree object created successfully without error ok 2 - NEXUS object defined isa Bio::NEXUS ok 3 - Tree object defined isa Bio::NEXUS::Tree ok 4 - NEXUS file parsed successfully without error ok 5 - NEXUS object defined isa Bio::NEXUS ---- Contents of t/data/01_basic.nex ok 6 - NEXUS file parsed and object created successfully ok 7 - Blocks are defined ok 8 - 3 blocks are present ok 9 - Bio::NEXUS::TaxaBlock object present isa Bio::NEXUS::TaxaBlock ok 10 - Bio::NEXUS::CharactersBlock object present isa Bio::NEXUS::CharactersBlock ok 11 - Bio::NEXUS::TreesBlock object present isa Bio::NEXUS::TreesBlock ok 12 - Bio::NEXUS::TREE Object defined isa Bio::NEXUS::Tree ---- Contents of Taxa block ok 13 - 4 taxa labels defined ok 14 - 5 characters defined ok 15 - Bio::NEXUS::Tree object present ok 16 - 4 OTU defined ok 17 - 7 Nodes defined: 4 OTUs + 3 internal 1..17 ok t/02_wrong_format..........Use of uninitialized value in concatenation (.) or string at /home/cpanrun/depot/main/contrib-patched/perl/CPAN/src/Bio-NEXUS/blib/lib/Bio/NEXUS.pm line 212. ok 1 - Wrong NEXUS file format identified successfully Wrong input NEXUS format - Error message : ERROR: '' does not begin with the '#NEXUS' token; it does not appear to be a NEXUS file. at t/02_wrong_format.t line 49 1..1 ok t/03_trees................. ---- Bush rake:basal polytomy, all branch lengths = 1 ok 1 - TreesBlock object created and parsed ok 2 - 9 nodes defined: 8 otus + 1 root ok 3 - 8 OTUs defined ---- maximally asymmetric tree, branch lengths = time ok 4 - TreesBlock object created and parsed ok 5 - 15 nodes defined: 8 otus + 7 root ok 6 - 8 OTUs 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..0 # Skip Test::Pod required for testing POD skipped all skipped: Test::Pod required for testing POD t/11_podcoverage...........1..0 # Skip Test::Pod::Coverage required for testing POD coverage skipped all skipped: Test::Pod::Coverage required for testing POD coverage All tests successful, 2 tests skipped. Files=10, Tests=117, 22 wallclock secs (20.33 cusr + 0.91 csys = 21.24 CPU) Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/DataBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/CodonsBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/NotesBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/HistoryBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/TaxUnit.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/CharactersBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/SpanBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/UnalignedBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/TaxUnitSet.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/DistancesBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/MatrixBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/UnknownBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/Node.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/Tree.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/WeightSet.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/TaxaBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/TreesBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/SetsBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/AssumptionsBlock.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/Block.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/lib/site_perl/5.8.2/Bio/NEXUS/Functions.pm Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man1/nextool.pl.1 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man1/nex2text_tree.pl.1 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man1/nexplot.pl.1 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::DataBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::CodonsBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::NotesBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::HistoryBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::TaxUnit.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::CharactersBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::SpanBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::UnalignedBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::TaxUnitSet.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::DistancesBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::MatrixBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::UnknownBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::Node.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::Tree.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::WeightSet.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::SetsBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::TaxaBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::TreesBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::AssumptionsBlock.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::Block.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS::Functions.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/man/man3/Bio::NEXUS.3 Installing /home/cpanrun/pa-risc1.1/build/5.8.2/bin/nextool.pl Installing /home/cpanrun/pa-risc1.1/build/5.8.2/bin/nex2text_tree.pl Installing /home/cpanrun/pa-risc1.1/build/5.8.2/bin/nexplot.pl Appending installation info to /home/cpanrun/pa-risc1.1/build/5.8.2/lib/5.8.2/PA-RISC1.1-thread-multi/perllocal.pod