Microsoft (R) Program Maintenance Utility Version 6.00.8168.0 Copyright (C) Microsoft Corp 1988-1998. All rights reserved. C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp bin/dnd2svg.pl blib\script\dnd2svg.pl pl2bat.bat blib\script\dnd2svg.pl C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp bin/bremer.pl blib\script\bremer.pl pl2bat.bat blib\script\bremer.pl C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp bin/droptip.pl blib\script\droptip.pl pl2bat.bat blib\script\droptip.pl C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp bin/postmb.pl blib\script\postmb.pl pl2bat.bat blib\script\postmb.pl C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp bin/dndtag.pl blib\script\dndtag.pl pl2bat.bat blib\script\dndtag.pl C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp bin/age2bl.pl blib\script\age2bl.pl pl2bat.bat blib\script\age2bl.pl C:\cpanrun-5.8\build\5-8-0\bin\perl.exe -MExtUtils::Command -e cp bin/LRmb.pl blib\script\LRmb.pl pl2bat.bat blib\script\LRmb.pl Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\ObjectCompat.pod Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Adaptor.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Forest.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Generator.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\IO.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Listable.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Manual.pod Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Taxa.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Treedrawer.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Util\CONSTANT.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Util\Exceptions.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Util\IDPool.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Util\Logger.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Util\XMLWritable.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Unparsers\Mrp.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Unparsers\Newick.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Unparsers\Nexus.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Unparsers\Pagel.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Treedrawer\Svg.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Taxa\TaxaLinker.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Taxa\Taxon.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Taxa\TaxonLinker.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Parsers\Newick.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Parsers\Nexus.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Parsers\Table.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Parsers\Taxlist.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Mediators\NodeMediator.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Mediators\TaxaMediator.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datum.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Matrix.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\TypeSafeData.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype\Continuous.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype\Custom.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype\Dna.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype\Mixed.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype\Protein.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype\Restriction.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype\Rna.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Matrices\Datatype\Standard.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Forest\Node.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Forest\Tree.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Adaptor\Bioperl\Datum.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Adaptor\Bioperl\Matrix.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Adaptor\Bioperl\Node.pm Installing C:\cpanrun-5.8\build\5-8-0\site\lib\Bio\Phylo\Adaptor\Bioperl\Tree.pm Installing C:\cpanrun-5.8\build\5-8-0\bin\age2bl.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\age2bl.pl Installing C:\cpanrun-5.8\build\5-8-0\bin\bremer.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\bremer.pl Installing C:\cpanrun-5.8\build\5-8-0\bin\dnd2svg.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\dnd2svg.pl Installing C:\cpanrun-5.8\build\5-8-0\bin\dndtag.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\dndtag.pl Installing C:\cpanrun-5.8\build\5-8-0\bin\droptip.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\droptip.pl Installing C:\cpanrun-5.8\build\5-8-0\bin\LRmb.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\LRmb.pl Installing C:\cpanrun-5.8\build\5-8-0\bin\postmb.bat Installing C:\cpanrun-5.8\build\5-8-0\bin\postmb.pl Writing C:\cpanrun-5.8\build\5-8-0\site\lib\auto\Bio\Phylo\.packlist Appending installation info to C:\cpanrun-5.8\build\5-8-0\lib/perllocal.pod nitialize ok 2 - 2 bad name ok 3 - 3 good name ok 4 - 4 retrieve name ok 5 - 5 bad node ref ok 6 - 6 bad node ref ok 7 - 7 good node ref ok 8 - 8 retrieve node ref ok 9 - 9 set desc ok 10 - 10 get desc ok 11 - 11 bad weight ok 12 - 12 good weight ok 13 - 13 retrieve weight ok 14 - 14 char without type ok 15 - 15 bad type ok 16 - 16 good type ok 17 - 17 retrieve type ok 18 - 18 good DNA ok 19 - 19 bad DNA ok 20 - 20 good RNA ok 21 - 21 bad RNA ok 22 - 22 good STANDARD ok 23 - 23 bad STANDARD ok 24 - 24 good PROTEIN ok 25 - 25 bad PROTEIN ok 26 - 26 good NUCLEOTIDE ok 27 - 27 bad NUCLEOTIDE ok 28 - 28 good CONTINUOUS ok 29 - 29 bad CONTINUOUS ok 30 - 30 retrieve character ok 31 - 31 bad pos ok 32 - 32 good pos ok 33 - 33 retrieve pos ok 34 - 34 bad get ok 35 - 35 good get ok 36 - 36 container ok 37 - 37 container type ok t\09-matrix........1..27 ok 1 - 1 initialize ok 2 - 2 insert bad data ok 3 - 3 insert good data ok 4 - 4 get bad method ok 5 - 5 get good method ok 6 - 6 get data ok 7 - 7 get by value lt ok 8 - 8 get by value le ok 9 - 9 get by value gt ok 10 - 10 get by value ge ok 11 - 11 get by value eq ok 12 - 12 get by value lt ok 13 - 13 get by value le ok 14 - 14 get by value gt ok 15 - 15 get by value ge ok 16 - 16 get by value eq ok 17 - 17 get by value lt ok 18 - 18 get by value le ok 19 - 19 get by value gt ok 20 - 20 get by value ge ok 21 - 21 get by value eq ok 22 - 22 get by re ok 23 - 23 get by re ok 24 - 24 get by re ok 25 - 25 get by re ok 26 - 26 destroy ok 27 - 27 expanded constructor ok t\10-matrices......1..10 ok 1 - 1 initialize obj ok 2 - 2 insert empty ok 3 - 3 insert bad ok 4 - 4 insert good ok 5 - 5 get matrices ok 6 - 6 container ok 7 - 7 container_type ok 8 - 8 cross ref m -> t ok 9 - 9 cross ref m -> t ok 10 - 10 get by regular expression ok t\11-taxon.........1..14 ok 1 - 1 initialize object ok 2 - 2 enter description ok 3 - 3 fetch description ok 4 - 4 enter bad name ok 5 - 5 container ok 6 - 6 container type ok 7 - 7 insert good data ok 8 - 8 insert bad data ok 9 - 9 get data ok 10 - 10 insert good node ok 11 - 11 insert bad node ok 12 - 12 get nodes ok 13 - 13 insert bad data ok 14 - 14 insert bad nodes ok t\12-taxa..........1..4 ok 1 - 1 initialize object ok 2 - 2 insert bad object ok 3 - 3 container ok 4 - 4 container_type ok t\13-listable......1..7 ok 1 - 1 initialize object ok 2 - 2 bad crossref ok 3 - 3 bad crossref ok 4 - 4 insert obj bad ok 5 - 5 get first tree ok 6 - 6 get last tree ok 7 - 7 good crossref ok t\14-nexus.........1..5 -------------------------------------------------------------------- ok 1 - 1 good parse -------------------------------------------------------------------- ok 2 - 2 tree block -------------------------------------------------------------------- ok 3 - 3 bad ntax -------------------------------------------------------------------- ok 4 - 4 bad nchar -------------------------------------------------------------------- ok 5 - 5 file error ok t\15-table.........1..2 ok 1 - 1 init ok 2 - 2 parse table ok t\16-unparse.......1..4 ok 1 ok 2 ok 3 ok 4 ok t\17-parse.........1..6 ok 1 - 1 parse no opts ok 2 - 2 parse wrong args ok 3 - 3 parse bad format ok 4 - 4 parse string ok 5 - 5 parse no format ok 6 - 6 parse taxon list ok t\18-taxlist.......1..1 ok 1 - 1 init obj ok t\19-svg...........1..13 ok 1 - test 1 ok 2 - test 2 ok 3 - test 3 ok 4 - test 4 ok 5 - test 5 ok 6 - test 6 ok 7 - test 7 ok 8 - test 8 ok 9 - test 9 ok 10 - test 10 ok 11 - test 11 ok 12 - test 12 ok 13 - test 13 ok t\pod-coverage.....1..46 ok 1 - Pod coverage on Bio::Phylo ok 2 - Pod coverage on Bio::Phylo::Adaptor ok 3 - Pod coverage on Bio::Phylo::Forest ok 4 - Pod coverage on Bio::Phylo::Generator ok 5 - Pod coverage on Bio::Phylo::IO ok 6 - Pod coverage on Bio::Phylo::Listable ok 7 - Pod coverage on Bio::Phylo::Matrices ok 8 - Pod coverage on Bio::Phylo::Taxa ok 9 - Pod coverage on Bio::Phylo::Treedrawer ok 10 - Pod coverage on Bio::Phylo::Forest::Node ok 11 - Pod coverage on Bio::Phylo::Forest::Tree ok 12 - Pod coverage on Bio::Phylo::Matrices::Datatype ok 13 - Pod coverage on Bio::Phylo::Matrices::Datum ok 14 - Pod coverage on Bio::Phylo::Matrices::Matrix ok 15 - Pod coverage on Bio::Phylo::Matrices::TypeSafeData ok 16 - Pod coverage on Bio::Phylo::Mediators::NodeMediator ok 17 - Pod coverage on Bio::Phylo::Mediators::TaxaMediator # Bio::Phylo::Parsers::Newick: no public symbols defined ok 18 - Pod coverage on Bio::Phylo::Parsers::Newick # Bio::Phylo::Parsers::Nexus: no public symbols defined ok 19 - Pod coverage on Bio::Phylo::Parsers::Nexus # Bio::Phylo::Parsers::Table: no public symbols defined ok 20 - Pod coverage on Bio::Phylo::Parsers::Table ok 21 - Pod coverage on Bio::Phylo::Parsers::Taxlist # Bio::Phylo::Parsers::Taxlist: no public symbols defined ok 22 - Pod coverage on Bio::Phylo::Taxa::TaxaLinker ok 23 - Pod coverage on Bio::Phylo::Taxa::Taxon ok 24 - Pod coverage on Bio::Phylo::Taxa::TaxonLinker # Bio::Phylo::Treedrawer::Svg: no public symbols defined ok 25 - Pod coverage on Bio::Phylo::Treedrawer::Svg # Bio::Phylo::Unparsers::Mrp: no public symbols defined ok 26 - Pod coverage on Bio::Phylo::Unparsers::Mrp # Bio::Phylo::Unparsers::Newick: no public symbols defined ok 27 - Pod coverage on Bio::Phylo::Unparsers::Newick # Bio::Phylo::Unparsers::Nexus: no public symbols defined ok 28 - Pod coverage on Bio::Phylo::Unparsers::Nexus # Bio::Phylo::Unparsers::Pagel: no public symbols defined ok 29 - Pod coverage on Bio::Phylo::Unparsers::Pagel ok 30 - Pod coverage on Bio::Phylo::Util::CONSTANT ok 31 - Pod coverage on Bio::Phylo::Util::Exceptions # Bio::Phylo::Util::IDPool: no public symbols defined ok 32 - Pod coverage on Bio::Phylo::Util::IDPool ok 33 - Pod coverage on Bio::Phylo::Util::Logger ok 34 - Pod coverage on Bio::Phylo::Util::XMLWritable ok 35 - Pod coverage on Bio::Phylo::Adaptor::Bioperl::Datum ok 36 - Pod coverage on Bio::Phylo::Adaptor::Bioperl::Matrix ok 37 - Pod coverage on Bio::Phylo::Adaptor::Bioperl::Node ok 38 - Pod coverage on Bio::Phylo::Adaptor::Bioperl::Tree ok 39 - Pod coverage on Bio::Phylo::Matrices::Datatype::Continuous # Bio::Phylo::Matrices::Datatype::Custom: no public symbols defined ok 40 - Pod coverage on Bio::Phylo::Matrices::Datatype::Custom # Bio::Phylo::Matrices::Datatype::Dna: no public symbols defined ok 41 - Pod coverage on Bio::Phylo::Matrices::Datatype::Dna ok 42 - Pod coverage on Bio::Phylo::Matrices::Datatype::Mixed # Bio::Phylo::Matrices::Datatype::Protein: no public symbols defined ok 43 - Pod coverage on Bio::Phylo::Matrices::Datatype::Protein # Bio::Phylo::Matrices::Datatype::Restriction: no public symbols defined ok 44 - Pod coverage on Bio::Phylo::Matrices::Datatype::Restriction # Bio::Phylo::Matrices::Datatype::Rna: no public symbols defined ok 45 - Pod coverage on Bio::Phylo::Matrices::Datatype::Rna # Bio::Phylo::Matrices::Datatype::Standard: no public symbols defined ok 46 - Pod coverage on Bio::Phylo::Matrices::Datatype::Standard ok t\pod..............1..55 ok 1 - blib\script\age2bl.pl ok 2 - blib\script\bremer.pl ok 3 - blib\script\dnd2svg.pl ok 4 - blib\script\dndtag.pl ok 5 - blib\script\droptip.pl ok 6 - blib\script\LRmb.pl ok 7 - blib\script\postmb.pl ok 8 - blib\lib\Bio\ObjectCompat.pod ok 9 - blib\lib\Bio\Phylo.pm ok 10 - blib\lib\Bio\Phylo\Adaptor.pm ok 11 - blib\lib\Bio\Phylo\Forest.pm ok 12 - blib\lib\Bio\Phylo\Generator.pm ok 13 - blib\lib\Bio\Phylo\IO.pm ok 14 - blib\lib\Bio\Phylo\Listable.pm ok 15 - blib\lib\Bio\Phylo\Manual.pod ok 16 - blib\lib\Bio\Phylo\Matrices.pm ok 17 - blib\lib\Bio\Phylo\Taxa.pm ok 18 - blib\lib\Bio\Phylo\Treedrawer.pm ok 19 - blib\lib\Bio\Phylo\Forest\Node.pm ok 20 - blib\lib\Bio\Phylo\Forest\Tree.pm ok 21 - blib\lib\Bio\Phylo\Matrices\Datatype.pm ok 22 - blib\lib\Bio\Phylo\Matrices\Datum.pm ok 23 - blib\lib\Bio\Phylo\Matrices\Matrix.pm ok 24 - blib\lib\Bio\Phylo\Matrices\TypeSafeData.pm ok 25 - blib\lib\Bio\Phylo\Mediators\NodeMediator.pm ok 26 - blib\lib\Bio\Phylo\Mediators\TaxaMediator.pm ok 27 - blib\lib\Bio\Phylo\Parsers\Newick.pm ok 28 - blib\lib\Bio\Phylo\Parsers\Nexus.pm ok 29 - blib\lib\Bio\Phylo\Parsers\Table.pm ok 30 - blib\lib\Bio\Phylo\Parsers\Taxlist.pm ok 31 - blib\lib\Bio\Phylo\Taxa\TaxaLinker.pm ok 32 - blib\lib\Bio\Phylo\Taxa\Taxon.pm ok 33 - blib\lib\Bio\Phylo\Taxa\TaxonLinker.pm ok 34 - blib\lib\Bio\Phylo\Treedrawer\Svg.pm ok 35 - blib\lib\Bio\Phylo\Unparsers\Mrp.pm ok 36 - blib\lib\Bio\Phylo\Unparsers\Newick.pm ok 37 - blib\lib\Bio\Phylo\Unparsers\Nexus.pm ok 38 - blib\lib\Bio\Phylo\Unparsers\Pagel.pm ok 39 - blib\lib\Bio\Phylo\Util\CONSTANT.pm ok 40 - blib\lib\Bio\Phylo\Util\Exceptions.pm ok 41 - blib\lib\Bio\Phylo\Util\IDPool.pm ok 42 - blib\lib\Bio\Phylo\Util\Logger.pm ok 43 - blib\lib\Bio\Phylo\Util\XMLWritable.pm ok 44 - blib\lib\Bio\Phylo\Adaptor\Bioperl\Datum.pm ok 45 - blib\lib\Bio\Phylo\Adaptor\Bioperl\Matrix.pm ok 46 - blib\lib\Bio\Phylo\Adaptor\Bioperl\Node.pm ok 47 - blib\lib\Bio\Phylo\Adaptor\Bioperl\Tree.pm ok 48 - blib\lib\Bio\Phylo\Matrices\Datatype\Continuous.pm ok 49 - blib\lib\Bio\Phylo\Matrices\Datatype\Custom.pm ok 50 - blib\lib\Bio\Phylo\Matrices\Datatype\Dna.pm ok 51 - blib\lib\Bio\Phylo\Matrices\Datatype\Mixed.pm ok 52 - blib\lib\Bio\Phylo\Matrices\Datatype\Protein.pm ok 53 - blib\lib\Bio\Phylo\Matrices\Datatype\Restriction.pm ok 54 - blib\lib\Bio\Phylo\Matrices\Datatype\Rna.pm ok 55 - blib\lib\Bio\Phylo\Matrices\Datatype\Standard.pm ok t\regress_18208....1..9 ok 1 - 1 parse string ok 2 - found Methanococcus_voltae ok 3 - found 'Pyrococcus furiosus (includes Pyrococcus woesei)' ok 4 - found Pyrococcus_abyssi ok 5 - found Sulfolobus_solfataricus ok 6 - found Sulfolobus_tokodaii ok 7 - found Aeropyrum_pernix ok 8 - found Desulfuroccus_amylolyticus ok 9 - found 'Methanococcus jannaschii (aka Methanocaldococcus jannaschii)' ok t\regress_21209....1..3 ok 1 - 1 parse string ok 2 - 2 have two trees ok 3 - 3 calc symdiff ok t\regress_21417....1..1 ok 1 - 1: remove unbranched internals ok t\regress_22813....1..1 ok 1 - 1: check drawing from synopsis ok t\regress_26332....1..1 ok 1 - 1: multiple draws yields same svg ok All tests successful. Files=27, Tests=396, 12 wallclock secs ( 0.00 cusr + 0.00 csys = 0.00 CPU)