PATH=C:\mingw\bin;C:\cygwin\bin;C:\cpanfly-5.18\var\megalib\bin;C:\Perl-5.18\site\bin;C:\Perl-5.18\bin;C:\cygwin\bin;C:\Program Files\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\instantclient_11_2;C:\cygwin\bin;C:\Program Files\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\WINDOWS\system32\WindowsPowerShell\v1.0 Start 2014-02-28T21:09:11 ActivePerl-1800 CPAN-2.00 LIB=C:\PROGRA~1\MICROS~3\VC98\Lib\PSDK PATH=C:/CPANFL~1.18/var/libs/bin;C:\mingw\bin;C:\cygwin\bin;C:\CPANFL~1.18\var\megalib\bin;C:\Perl-5.18\site\bin;C:\Perl-5.18\bin;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\INSTAN~1;C:\cygwin\bin;C:\PROGRA~1\Perforce;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WINDOW~2\v1.0;C:\WINDOWS\system32\WINDOW~2\v1.0 Reading 'C:\cpanfly-5.18\var\cpan\Metadata' Database was generated on Sat, 01 Mar 2014 00:06:17 GMT Running make for C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz Fetching with LWP: http://cpan.nas1.activestate.com/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz Checksum for C:\cpanfly-5.18\var\cpan\sources\authors\id\C\CJ\CJFIELDS\BioPerl-1.6.901.tar.gz ok BioPerl-1.6.901 BioPerl-1.6.901/AUTHORS BioPerl-1.6.901/BioPerl.pm BioPerl-1.6.901/BUGS BioPerl-1.6.901/Build.PL BioPerl-1.6.901/Changes BioPerl-1.6.901/DEPENDENCIES 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BioPerl-1.6.901/t/Tools/Analysis/DNA BioPerl-1.6.901/t/Tools/Analysis/DNA/ESEfinder.t BioPerl-1.6.901/t/Tools/Analysis/Protein BioPerl-1.6.901/t/Tools/Analysis/Protein/Domcut.t BioPerl-1.6.901/t/Tools/Analysis/Protein/ELM.t BioPerl-1.6.901/t/Tools/Analysis/Protein/GOR4.t BioPerl-1.6.901/t/Tools/Analysis/Protein/HNN.t BioPerl-1.6.901/t/Tools/Analysis/Protein/Mitoprot.t BioPerl-1.6.901/t/Tools/Analysis/Protein/NetPhos.t BioPerl-1.6.901/t/Tools/Analysis/Protein/Scansite.t BioPerl-1.6.901/t/Tools/Analysis/Protein/Sopma.t BioPerl-1.6.901/t/Tools/EMBOSS BioPerl-1.6.901/t/Tools/EMBOSS/Palindrome.t BioPerl-1.6.901/t/Tools/EUtilities BioPerl-1.6.901/t/Tools/EUtilities/egquery.t BioPerl-1.6.901/t/Tools/EUtilities/einfo.t BioPerl-1.6.901/t/Tools/EUtilities/elink_acheck.t BioPerl-1.6.901/t/Tools/EUtilities/elink_lcheck.t BioPerl-1.6.901/t/Tools/EUtilities/elink_llinks.t BioPerl-1.6.901/t/Tools/EUtilities/elink_ncheck.t BioPerl-1.6.901/t/Tools/EUtilities/elink_neighbor.t BioPerl-1.6.901/t/Tools/EUtilities/elink_neighbor_history.t BioPerl-1.6.901/t/Tools/EUtilities/elink_scores.t BioPerl-1.6.901/t/Tools/EUtilities/epost.t BioPerl-1.6.901/t/Tools/EUtilities/esearch.t BioPerl-1.6.901/t/Tools/EUtilities/espell.t BioPerl-1.6.901/t/Tools/EUtilities/esummary.t BioPerl-1.6.901/t/Tools/EUtilities/EUtilParameters.t BioPerl-1.6.901/t/Tools/Phylo BioPerl-1.6.901/t/Tools/Phylo/Gerp.t BioPerl-1.6.901/t/Tools/Phylo/Molphy.t BioPerl-1.6.901/t/Tools/Phylo/PAML.t BioPerl-1.6.901/t/Tools/Phylo/Phylip BioPerl-1.6.901/t/Tools/Phylo/Phylip/ProtDist.t BioPerl-1.6.901/t/Tools/Run BioPerl-1.6.901/t/Tools/Run/Dummy.pm BioPerl-1.6.901/t/Tools/Run/RemoteBlast.t BioPerl-1.6.901/t/Tools/Run/RemoteBlast_rpsblast.t BioPerl-1.6.901/t/Tools/Run/StandAloneBlast.t BioPerl-1.6.901/t/Tools/Run/WBCommandExts.t BioPerl-1.6.901/t/Tools/Run/WrapperBase.t BioPerl-1.6.901/t/Tools/Run/Dummy BioPerl-1.6.901/t/Tools/Run/Dummy/Config.pm BioPerl-1.6.901/t/Tools/Signalp BioPerl-1.6.901/t/Tools/Signalp/ExtendedSignalp.t BioPerl-1.6.901/t/Tools/Spidey BioPerl-1.6.901/t/Tools/Spidey/Spidey.t BioPerl-1.6.901/t/Tree BioPerl-1.6.901/t/Tree/Compatible.t BioPerl-1.6.901/t/Tree/Node.t BioPerl-1.6.901/t/Tree/RandomTreeFactory.t BioPerl-1.6.901/t/Tree/Tree.t BioPerl-1.6.901/t/Tree/TreeIO.t BioPerl-1.6.901/t/Tree/TreeStatistics.t BioPerl-1.6.901/t/Tree/PhyloNetwork BioPerl-1.6.901/t/Tree/PhyloNetwork/Factory.t BioPerl-1.6.901/t/Tree/PhyloNetwork/GraphViz.t BioPerl-1.6.901/t/Tree/PhyloNetwork/MuVector.t BioPerl-1.6.901/t/Tree/PhyloNetwork/PhyloNetwork.t BioPerl-1.6.901/t/Tree/PhyloNetwork/RandomFactory.t BioPerl-1.6.901/t/Tree/PhyloNetwork/TreeFactory.t BioPerl-1.6.901/t/Tree/TreeIO BioPerl-1.6.901/t/Tree/TreeIO/lintree.t BioPerl-1.6.901/t/Tree/TreeIO/newick.t BioPerl-1.6.901/t/Tree/TreeIO/nexml.t BioPerl-1.6.901/t/Tree/TreeIO/nexus.t BioPerl-1.6.901/t/Tree/TreeIO/nhx.t BioPerl-1.6.901/t/Tree/TreeIO/phyloxml.t BioPerl-1.6.901/t/Tree/TreeIO/svggraph.t BioPerl-1.6.901/t/Tree/TreeIO/tabtree.t BioPerl-1.6.901/t/Variation BioPerl-1.6.901/t/Variation/AAChange.t BioPerl-1.6.901/t/Variation/AAReverseMutate.t BioPerl-1.6.901/t/Variation/Allele.t BioPerl-1.6.901/t/Variation/DNAMutation.t BioPerl-1.6.901/t/Variation/RNAChange.t BioPerl-1.6.901/t/Variation/SeqDiff.t BioPerl-1.6.901/t/Variation/SNP.t BioPerl-1.6.901/t/Variation/Variation_IO.t CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz >>> C:\Perl-5.18\bin\perl.exe Build.PL could not find ParserDetails.ini in C:/cpanfly-5.18/var/megalib/XML/SAX Checking prerequisites... requires: ! DB_File is not installed recommends: * Convert::Binary::C is not installed * GraphViz is not installed * PostScript::TextBlock is not installed * SOAP::Lite is not installed * XML::DOM::XPath is not installed * YAML is not installed Checking optional features... DB_File Tests.........disabled requires: ! DB_File is not installed EntrezGene............disabled requires: ! Bio::ASN1::EntrezGene is not installed MySQL Tests...........disabled requires: ! DBD::mysql is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation ############################# WARNING ############################# Bio::ASN1::EntrezGene not found. This is an *optional* module; however, because it has a circular dependency with BioPerl we do not include it on our list of recommended modules. If you require EntrezGene functionality, you can install Bio::ASN1::EntrezGene after BioPerl has finished installing. ############################# WARNING ############################# Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl' version '1.006901' ---- Unsatisfied dependencies detected during ---- ---- CJFIELDS/BioPerl-1.6.901.tar.gz ---- DB_File [requires] Running Build test Delayed until after prerequisites Running test for module 'DB_File' ______________________ D i s t r o P r e f s ______________________ DB_File.yml[0] Running make for P/PM/PMQS/DB_File-1.831.tar.gz Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0 PMQS/DB_File-1.831.tar.gz [disabled] -- NA Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0 Running Build for C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz Has already been unwrapped into directory C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.901.tar.gz' failed when processing 'PMQS/DB_File-1.831.tar.gz' with 'unwrapped => NO Disabled via prefs file 'C:\cpanfly-5.18\etc\distroprefs\DB_File.yml' doc 0'. Continuing, but chances to succeed are limited. >>> C:\Perl-5.18\bin\perl.exe ./Build Building BioPerl CJFIELDS/BioPerl-1.6.901.tar.gz C:\Perl-5.18\bin\perl.exe ./Build -- OK Running Build test >>> C:\Perl-5.18\bin\perl.exe ./Build test verbose=1 Copying scripts\utilities\mask_by_search.PLS -> blib\script\mask_by_search.PLS Changing sharpbang in blib\script\mask_by_search.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\mask_by_search.PLS.bak Copying scripts\taxa\query_entrez_taxa.PLS -> blib\script\query_entrez_taxa.PLS Changing sharpbang in blib\script\query_entrez_taxa.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\query_entrez_taxa.PLS.bak Copying scripts\das\das_server.pl -> blib\script\das_server.pl Changing sharpbang in blib\script\das_server.pl to C:\Perl-5.18\bin\perl.exe Deleting blib\script\das_server.pl.bak Copying scripts\seqstats\gccalc.PLS -> blib\script\gccalc.PLS Changing sharpbang in blib\script\gccalc.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\gccalc.PLS.bak Copying scripts\utilities\bp_sreformat.PLS -> blib\script\bp_sreformat.PLS Changing sharpbang in blib\script\bp_sreformat.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_sreformat.PLS.bak Copying scripts\Bio-DB-GFF\genbank2gff.PLS -> blib\script\genbank2gff.PLS Changing sharpbang in blib\script\genbank2gff.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\genbank2gff.PLS.bak Copying scripts\index\bp_seqret.PLS -> blib\script\bp_seqret.PLS Changing sharpbang in blib\script\bp_seqret.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_seqret.PLS.bak Copying scripts\utilities\search2tribe.PLS -> blib\script\search2tribe.PLS Changing sharpbang in blib\script\search2tribe.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\search2tribe.PLS.bak Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_load.PLS -> blib\script\bp_seqfeature_load.PLS Changing sharpbang in blib\script\bp_seqfeature_load.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_seqfeature_load.PLS.bak Copying scripts\DB-HIV\hivq.PLS -> blib\script\hivq.PLS Changing sharpbang in blib\script\hivq.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\hivq.PLS.bak Copying scripts\utilities\download_query_genbank.PLS -> blib\script\download_query_genbank.PLS Changing sharpbang in blib\script\download_query_genbank.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\download_query_genbank.PLS.bak Copying scripts\DB\flanks.PLS -> blib\script\flanks.PLS Changing sharpbang in blib\script\flanks.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\flanks.PLS.bak Copying scripts\Bio-DB-GFF\bulk_load_gff.PLS -> blib\script\bulk_load_gff.PLS Changing sharpbang in blib\script\bulk_load_gff.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bulk_load_gff.PLS.bak Copying scripts\DB\biofetch_genbank_proxy.PLS -> blib\script\biofetch_genbank_proxy.PLS Changing sharpbang in blib\script\biofetch_genbank_proxy.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\biofetch_genbank_proxy.PLS.bak Copying scripts\tree\tree2pag.PLS -> blib\script\tree2pag.PLS Changing sharpbang in blib\script\tree2pag.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\tree2pag.PLS.bak Copying scripts\utilities\remote_blast.PLS -> blib\script\remote_blast.PLS Changing sharpbang in blib\script\remote_blast.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\remote_blast.PLS.bak Copying scripts\utilities\bp_netinstall.PLS -> blib\script\bp_netinstall.PLS Changing sharpbang in blib\script\bp_netinstall.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_netinstall.PLS.bak Copying scripts\Bio-DB-GFF\process_gadfly.PLS -> blib\script\process_gadfly.PLS Changing sharpbang in blib\script\process_gadfly.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\process_gadfly.PLS.bak Copying scripts\utilities\revtrans-motif.PLS -> blib\script\revtrans-motif.PLS Changing sharpbang in blib\script\revtrans-motif.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\revtrans-motif.PLS.bak Copying scripts\taxa\taxonomy2tree.PLS -> blib\script\taxonomy2tree.PLS Changing sharpbang in blib\script\taxonomy2tree.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\taxonomy2tree.PLS.bak Copying scripts\Bio-DB-GFF\load_gff.PLS -> blib\script\load_gff.PLS Changing sharpbang in blib\script\load_gff.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\load_gff.PLS.bak Copying scripts\seq\unflatten_seq.PLS -> blib\script\unflatten_seq.PLS Changing sharpbang in blib\script\unflatten_seq.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\unflatten_seq.PLS.bak Copying scripts\searchio\search2table.PLS -> blib\script\search2table.PLS Changing sharpbang in blib\script\search2table.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\search2table.PLS.bak Copying scripts\biblio\biblio.PLS -> blib\script\biblio.PLS Changing sharpbang in blib\script\biblio.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\biblio.PLS.bak Copying scripts\index\bp_fetch.PLS -> blib\script\bp_fetch.PLS Changing sharpbang in blib\script\bp_fetch.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_fetch.PLS.bak Copying scripts\taxa\local_taxonomydb_query.PLS -> blib\script\local_taxonomydb_query.PLS Changing sharpbang in blib\script\local_taxonomydb_query.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\local_taxonomydb_query.PLS.bak Copying scripts\taxa\classify_hits_kingdom.PLS -> blib\script\classify_hits_kingdom.PLS Changing sharpbang in blib\script\classify_hits_kingdom.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\classify_hits_kingdom.PLS.bak Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_gff3.PLS -> blib\script\bp_seqfeature_gff3.PLS Copying scripts\seq\translate_seq.PLS -> blib\script\translate_seq.PLS Changing sharpbang in blib\script\translate_seq.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\translate_seq.PLS.bak Copying scripts\utilities\bp_mrtrans.PLS -> blib\script\bp_mrtrans.PLS Changing sharpbang in blib\script\bp_mrtrans.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_mrtrans.PLS.bak Copying scripts\Bio-DB-EUtilities\einfo.PLS -> blib\script\einfo.PLS Changing sharpbang in blib\script\einfo.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\einfo.PLS.bak Copying scripts\Bio-DB-GFF\fast_load_gff.PLS -> blib\script\fast_load_gff.PLS Changing sharpbang in blib\script\fast_load_gff.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\fast_load_gff.PLS.bak Copying scripts\DB\biogetseq.PLS -> blib\script\biogetseq.PLS Changing sharpbang in blib\script\biogetseq.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\biogetseq.PLS.bak Copying scripts\seq\seqconvert.PLS -> blib\script\seqconvert.PLS Changing sharpbang in blib\script\seqconvert.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\seqconvert.PLS.bak Copying scripts\Bio-DB-GFF\genbank2gff3.PLS -> blib\script\genbank2gff3.PLS Changing sharpbang in blib\script\genbank2gff3.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\genbank2gff3.PLS.bak Copying scripts\Bio-DB-GFF\meta_gff.PLS -> blib\script\meta_gff.PLS Changing sharpbang in blib\script\meta_gff.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\meta_gff.PLS.bak Copying scripts\searchio\filter_search.PLS -> blib\script\filter_search.PLS Changing sharpbang in blib\script\filter_search.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\filter_search.PLS.bak Copying scripts\searchio\parse_hmmsearch.PLS -> blib\script\parse_hmmsearch.PLS Changing sharpbang in blib\script\parse_hmmsearch.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\parse_hmmsearch.PLS.bak Copying scripts\seq\make_mrna_protein.PLS -> blib\script\make_mrna_protein.PLS Changing sharpbang in blib\script\make_mrna_protein.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\make_mrna_protein.PLS.bak Copying scripts\popgen\heterogeneity_test.PLS -> blib\script\heterogeneity_test.PLS Changing sharpbang in blib\script\heterogeneity_test.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\heterogeneity_test.PLS.bak Copying scripts\seqstats\aacomp.PLS -> blib\script\aacomp.PLS Changing sharpbang in blib\script\aacomp.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\aacomp.PLS.bak Copying scripts\seqstats\oligo_count.PLS -> blib\script\oligo_count.PLS Changing sharpbang in blib\script\oligo_count.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\oligo_count.PLS.bak Copying scripts\utilities\pairwise_kaks.PLS -> blib\script\pairwise_kaks.PLS Changing sharpbang in blib\script\pairwise_kaks.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\pairwise_kaks.PLS.bak Copying scripts\tree\blast2tree.PLS -> blib\script\blast2tree.PLS Changing sharpbang in blib\script\blast2tree.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\blast2tree.PLS.bak Copying scripts\tree\nexus2nh.PLS -> blib\script\nexus2nh.PLS Changing sharpbang in blib\script\nexus2nh.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\nexus2nh.PLS.bak Copying scripts\Bio-DB-SeqFeature-Store\bp_seqfeature_delete.PLS -> blib\script\bp_seqfeature_delete.PLS Changing sharpbang in blib\script\bp_seqfeature_delete.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_seqfeature_delete.PLS.bak Copying scripts\taxa\taxid4species.PLS -> blib\script\taxid4species.PLS Changing sharpbang in blib\script\taxid4species.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\taxid4species.PLS.bak Copying scripts\index\bp_index.PLS -> blib\script\bp_index.PLS Changing sharpbang in blib\script\bp_index.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_index.PLS.bak Copying scripts\seqstats\chaos_plot.PLS -> blib\script\chaos_plot.PLS Changing sharpbang in blib\script\chaos_plot.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\chaos_plot.PLS.bak Copying scripts\DB\bioflat_index.PLS -> blib\script\bioflat_index.PLS Changing sharpbang in blib\script\bioflat_index.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bioflat_index.PLS.bak Copying scripts\Bio-DB-GFF\process_wormbase.PLS -> blib\script\process_wormbase.PLS Changing sharpbang in blib\script\process_wormbase.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\process_wormbase.PLS.bak Copying scripts\seq\extract_feature_seq.PLS -> blib\script\extract_feature_seq.PLS Changing sharpbang in blib\script\extract_feature_seq.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\extract_feature_seq.PLS.bak Copying scripts\utilities\bp_nrdb.PLS -> blib\script\bp_nrdb.PLS Changing sharpbang in blib\script\bp_nrdb.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\bp_nrdb.PLS.bak Copying scripts\searchio\fastam9_to_table.PLS -> blib\script\fastam9_to_table.PLS Changing sharpbang in blib\script\fastam9_to_table.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\fastam9_to_table.PLS.bak Copying scripts\utilities\search2BSML.PLS -> blib\script\search2BSML.PLS Changing sharpbang in blib\script\search2BSML.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\search2BSML.PLS.bak Copying scripts\searchio\hmmer_to_table.PLS -> blib\script\hmmer_to_table.PLS Changing sharpbang in blib\script\hmmer_to_table.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\hmmer_to_table.PLS.bak Copying scripts\seq\split_seq.PLS -> blib\script\split_seq.PLS Changing sharpbang in blib\script\split_seq.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\split_seq.PLS.bak Copying scripts\Bio-DB-GFF\process_sgd.PLS -> blib\script\process_sgd.PLS Changing sharpbang in blib\script\process_sgd.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\process_sgd.PLS.bak Copying scripts\utilities\mutate.PLS -> blib\script\mutate.PLS Changing sharpbang in blib\script\mutate.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\mutate.PLS.bak Copying scripts\seq\seqretsplit.PLS -> blib\script\seqretsplit.PLS Changing sharpbang in blib\script\seqretsplit.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\seqretsplit.PLS.bak Copying scripts\utilities\dbsplit.PLS -> blib\script\dbsplit.PLS Changing sharpbang in blib\script\dbsplit.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\dbsplit.PLS.bak Copying scripts\popgen\composite_LD.PLS -> blib\script\composite_LD.PLS Changing sharpbang in blib\script\composite_LD.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\composite_LD.PLS.bak Copying scripts\utilities\search2alnblocks.PLS -> blib\script\search2alnblocks.PLS Changing sharpbang in blib\script\search2alnblocks.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\search2alnblocks.PLS.bak Copying scripts\utilities\seq_length.PLS -> blib\script\seq_length.PLS Changing sharpbang in blib\script\seq_length.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\seq_length.PLS.bak Copying scripts\utilities\search2gff.PLS -> blib\script\search2gff.PLS Changing sharpbang in blib\script\search2gff.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\search2gff.PLS.bak Copying scripts\Bio-DB-GFF\generate_histogram.PLS -> blib\script\generate_histogram.PLS Changing sharpbang in blib\script\generate_histogram.PLS to C:\Perl-5.18\bin\perl.exe Deleting blib\script\generate_histogram.PLS.bak # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Align/AlignStats.t ......................... 1..45 ok 1 - use Bio::Align::DNAStatistics; ok 2 - use Bio::Align::ProteinStatistics; ok 3 - use Bio::AlignIO; ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 38 - An object of class 'Bio::Matrix::PhylipDist' isa 'Bio::Matrix::PhylipDist' ok 39 ok 40 ok 41 ok 42 - An object of class 'Bio::Seq' isa 'Bio::PrimarySeqI' ok 43 ok 44 - Warn if seqs don't overlap ok 45 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Align/AlignUtil.t .......................... 1..33 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqIO; ok 4 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Align/Graphics.t ........................... 1..41 ok 1 - use Bio::Align::Graphics; ok 2 - require Bio::Align::Graphics; ok 3 - Bio::Align::Graphics->can(...) ok 4 - input is defined ok 5 - AlignIO object is defined ok 6 - An object of class 'Bio::AlignIO::clustalw' isa 'Bio::AlignIO' ok 7 - alignment is there and defined ok 8 - all starts are present ok 9 - all ends are present ok 10 - all colors are present ok 11 - first end is further than first start ok 12 - second end is further than second start ok 13 - third end is further than third start ok 14 - domain labels are present ok 15 - domain starts are present ok 16 - domain ends are present ok 17 - domain colors are present ok 18 - label - first end is further than first start ok 19 - label - second end is further than second start ok 20 - label - third end is further than third start ok 21 - first label start is within domain range ok 22 - second label start is within domain range ok 23 - third label start is within domain range ok 24 - first label end is within domain range ok 25 - second label end is within domain range ok 26 - third label end is within domain range ok 27 - individual labels work ok 28 - An object of class 'Bio::Align::Graphics' isa 'Bio::Align::Graphics' ok 29 - new object is defined ok 30 - pad_bottom is right ok 31 - default pad_top is right ok 32 - start point loaded ok 33 - end point loaded ok 34 - color of domain loaded ok 35 - domain labels loaded ok 36 - label starts loaded ok 37 - label ends loaded ok 38 - label colors loaded ok 39 - labels loaded ok 40 - output file is png ok 41 - wrapping length is not zero ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Align/SimpleAlign.t ........................ 1..199 ok 1 - use Bio::SimpleAlign; ok 2 - use Bio::AlignIO; ok 3 - use Bio::SeqFeature::Generic; ok 4 - use Bio::Location::Simple; ok 5 - use Bio::Location::Split; ok 6 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' ok 7 - pfam input test ok 8 - match_line ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 10 - num_sequences ok 11 - num_sequences ok 12 - select_noncont ok 13 - select_noncont ok 14 - num_sequences ok 15 - select_noncont ok 16 - select_noncont ok 17 - each_seq ok 18 - get_nse ok 19 - id ok 20 - num_gaps ok 21 - each_alphabetically ok 22 - column_from_residue_number ok 23 - display_name get/set ok 24 - display_name get ok 25 - consensus_string ok 26 - consensus_string ok 27 - consensus_string ok 28 ok 29 - each_seq_with_id ok 30 - is_flush ok 31 - id get/set ok 32 - length ok 33 - num_residues ok 34 - num_sequences ok 35 - overall_percentage_identity ok 36 - overall_percentage_identity (align) ok 37 - overall_percentage_identity (short) ok 38 - overall_percentage_identity (long) ok 39 - average_percentage_identity ok 40 ok 41 - set_displayname_count ok 42 ok 43 - set_displayname_flat ok 44 ok 45 - set_displayname_normal ok 46 ok 47 ok 48 - uppercase, map_chars ok 49 - match_line ok 50 - remove_seqs ok 51 - remove_seqs ok 52 - add_seq ok 53 - add_seq ok 54 - get_seq_by_pos ok 55 - get_seq_by_pos ok 56 ok 57 ok 58 ok 59 - purge ok 60 - purge ok 61 - IO::String consensus_iupac ok 62 - IO::String write_aln normal ok 63 - IO::String write_aln slice ok 64 - IO::String write_aln slice ok 65 - IO::String write_aln slice ok 66 - IO::String write_aln slice ok 67 - IO::String write_aln slice ok 68 ok 69 - remove_columns by position ok 70 - remove_columns by position (wrong order) ok 71 - cigar_line ok 72 - cigar_line ok 73 - cigar_line ok 74 - cigar_line ok 75 - sort_alphabetically - before ok 76 ok 77 - sort_alphabetically - after ok 78 - remove_gaps ok 79 - remove_gaps all_gaps_only ok 80 - set_new_reference ok 81 - set_new_reference ok 82 - uniq_seq ok 83 - bug 2099 ok 84 - bug 2099 ok 85 - bug 2793 ok 86 - bug 2793 ok 87 - bug 2793 ok 88 - bug 2793 ok 89 - Bad sequence, bad! ok 90 - added 3 seqs ok 91 - first 2 features added ok 92 - 3rd feature added not ok 93 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 1. # Overriding value [0] with value 1 for Bio::LocatableSeq::end(). # ? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 94 - slice 1 len ok 95 - correct masked seq ok 96 - correct masked seq ok 97 - correct masked seq not ok 98 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 3. # Overriding value [2] with value 3 for Bio::LocatableSeq::end(). # ? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 99 - slice 2 len ok 100 - correct masked seq ok 101 - correct masked seq ok 102 - correct masked seq not ok 103 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 3. # Overriding value [1] with value 3 for Bio::LocatableSeq::end(). # ?? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 104 - slice 3 len ok 105 - correct masked seq ok 106 - correct masked seq ok 107 - correct masked seq not ok 108 # TODO This should pass but dies; see bug 2842 # Failed (TODO) test at t/Align/SimpleAlign.t line 421. # died: Bio::Root::Exception ( # ------------- EXCEPTION: Bio::Root::Exception ------------- # MSG: In sequence one residue count gives end value 6. # Overriding value [4] with value 6 for Bio::LocatableSeq::end(). # ?? # STACK: Error::throw # STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 # STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180 # STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:195 # STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1146 # STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:421 # STACK: t/Align/SimpleAlign.t:421 # ----------------------------------------------------------- # ) ok 109 - slice 4 len ok 110 - correct masked seq ok 111 - correct masked seq ok 112 - correct masked seq ok 113 - initial display id ok ok 114 - safe display id ok ok 115 - restored display id ok ok 116 - sort by list ok ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 - BIC:GGATCCATT[C/C]CTACT ok 124 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT ok 125 - BIC:G[G/C]ATCCATT[C/G]CTACT ok 126 - BIC:GGATCCATT[C/G]CTACT ok 127 - BIC:GGATCCATT[C/G]CTAC[T/A] ok 128 - BIC:GGATCCATT[C/G]CTA[C/G][T/A] ok 129 - BIC:GGATCCATT[C/G]CTACT ok 130 - BIC:GGATCCATT{C.C}CTACT ok 131 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT ok 132 - BIC:G{G.C}ATCCATT{C.G}CTACT ok 133 - BIC:GGATCCATT{C.G}CTACT ok 134 - BIC:GGATCCATT{C.G}CTAC{T.A} ok 135 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A} ok 136 - BIC:GGATCCATT{C.G}CTACT ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 - An object of class 'Bio::SimpleAlign' isa 'Bio::SimpleAlign' ok 195 - consensus string looks ok ok 196 - looks like correct unmasked alignment (from clustalw) ok 197 - looks like correct masked alignment (from clustalw) ok 198 ok 199 - align after looks ok ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Align/TreeBuild.t .......................... 1..13 ok 1 - use Bio::Align::DNAStatistics; ok 2 - use Bio::Align::ProteinStatistics; ok 3 - use Bio::Align::Utilities; ok 4 - use Bio::AlignIO; ok 5 - use Bio::Tree::DistanceFactory; ok 6 - use Bio::TreeIO; ok 7 - 'SimpleAlign object parsed out' isa 'Bio::SimpleAlign' ok 8 - 'Protein distance matrix retrieved' isa 'Bio::Matrix::MatrixI' ok 9 - 'Tree object gotten back' isa 'Bio::Tree::TreeI' ok 10 - NJ calculated Branch length ok 11 - NJ calculated Branch length ok 12 - Make sure two nodes are sister ok 13 - 10 replicates formulated ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Align/Utilities.t .......................... 1..13 ok 1 - use Bio::Align::Utilities; ok 2 - use Bio::SimpleAlign; ok 3 - use Bio::PrimarySeq; ok 4 - use Bio::LocatableSeq; ok 5 - use Bio::AlignIO; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/AlignIO.t .......................... 1..28 ok 1 - use Bio::AlignIO; ok 2 - input filehandle method test : fasta ok 3 - input filehandle method test : clustalw ok 4 - input filehandle method test : psi ok 5 - input filehandle method test : metafasta ok 6 - input filehandle method test : stockholm ok 7 - input filehandle method test : phylip ok 8 - input filehandle method test : nexus ok 9 - input filehandle method test : xmfa ok 10 - input filehandle method test : mase ok 11 - input filehandle method test : arp ok 12 - input filehandle method test : pfam ok 13 - input filehandle method test : selex ok 14 - input filehandle method test : msf ok 15 - input filehandle method test : prodom ok 16 - input filehandle method test : po ok 17 - filehandle output test : fasta ok 18 - filehandle output test : clustalw ok 19 - filehandle output test : psi ok 20 - filehandle output test : metafasta ok 21 - filehandle output test : stockholm ok 22 - filehandle output test : phylip ok 23 - filehandle output test : nexus ok 24 - filehandle output test : xmfa ok 25 - filehandle output test : pfam ok 26 - filehandle output test : selex ok 27 - filehandle output test : msf ok 28 - filehandle output test : po ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/arp.t .............................. 1..48 ok 1 - use Bio::AlignIO::arp; ok 2 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 - ARP get_nse() ok 5 ok 6 - ARP num_sequences() ok 7 - ARP id() ok 8 - ARP description() ok 9 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 10 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 11 ok 12 ok 13 ok 14 ok 15 - An object of class 'Bio::AlignIO::arp' isa 'Bio::AlignIO' ok 16 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 17 - ARP get_nse() ok 18 - ARP num_sequences() ok 19 - ARP id() ok 20 - ARP description() ok 21 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 22 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 23 ok 24 ok 25 ok 26 ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 28 - ARP get_nse() ok 29 - ARP num_sequences() ok 30 - ARP id() ok 31 - ARP description() ok 32 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 33 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 34 ok 35 ok 36 ok 37 ok 38 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 39 - ARP get_nse() ok 40 - ARP num_sequences() ok 41 - ARP id() ok 42 - ARP description() ok 43 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 44 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 45 ok 46 ok 47 ok 48 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/bl2seq.t ........................... 1..3 ok 1 - use Bio::AlignIO::bl2seq; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - BLAST bl2seq format test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/clustalw.t ......................... 1..6 ok 1 - use Bio::AlignIO::clustalw; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - clustalw consensus_string test ok 4 - clustalw (.aln) output test ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 6 - clustalw (.aln) input test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/emboss.t ........................... 1..37 ok 1 - use Bio::AlignIO::emboss; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 11 ok 12 ok 13 ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 15 ok 16 ok 17 ok 18 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 19 ok 20 ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 33 ok 34 ok 35 ok 36 ok 37 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/fasta.t ............................ 1..10 ok 1 - use Bio::AlignIO::fasta; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - fasta input test ok 4 - fasta input test for description ok 5 - fasta input test for id ok 6 - fasta input test for end ok 7 - fasta input test for description ok 8 - fasta output test ok 9 - filehandle input test ok 10 - filehandle output test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/largemultifasta.t .................. 1..7 ok 1 - use Bio::AlignIO::largemultifasta; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - fasta input test ok 4 - fasta input test for description ok 5 - fasta input test for id ok 6 - fasta input test for description ok 7 - fasta output test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/maf.t .............................. 1..11 ok 1 - use Bio::AlignIO::maf; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - maf input test ok 4 ok 5 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 6 - maf input test ok 7 ok 8 - maf input test ok 9 ok 10 - maf input test ok 11 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/mase.t ............................. 1..3 ok 1 - use Bio::AlignIO::mase; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - mase input test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/mega.t ............................. 1..6 ok 1 - use Bio::AlignIO::mega; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 ok 4 ok 5 ok 6 - mega output test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/meme.t ............................. 1..14 ok 1 - use Bio::AlignIO::meme; ok 2 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 ok 6 ok 7 ok 8 - An object of class 'Bio::AlignIO::meme' isa 'Bio::AlignIO' ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 10 ok 11 ok 12 ok 13 ok 14 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/metafasta.t ........................ 1..4 ok 1 - use Bio::AlignIO::metafasta; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - consensus_string on metafasta ok 4 - symbol_chars() using metafasta ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/msf.t .............................. 1..4 ok 1 - use Bio::AlignIO::msf; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - msf input test ok 4 - msf output test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 # WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support t/AlignIO/nexml.t ............................ 1..125 ok 1 - use Bio::AlignIO::nexml; ok 2 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 3 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 4 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 5 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 6 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 7 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 8 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 9 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 10 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 11 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 12 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 13 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 14 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 15 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 16 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 17 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 18 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 19 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 20 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 21 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 22 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 23 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 24 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 25 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 26 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 27 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 28 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 29 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 30 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 31 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 32 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 33 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 34 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 35 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 36 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 37 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 38 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 39 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 40 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 41 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 42 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 43 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 44 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 45 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 46 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 47 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 48 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 49 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 50 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 51 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 52 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 53 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 54 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 55 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 56 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 57 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 58 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 59 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 60 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 61 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 62 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 63 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 64 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 65 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 66 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 67 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 68 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 69 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 70 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 71 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 72 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 73 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 74 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 75 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 76 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 77 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 78 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 79 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 80 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 81 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 82 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 83 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 84 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 85 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 86 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 87 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 88 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 89 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 90 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 91 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 92 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 93 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 94 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 95 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 96 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 97 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 98 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 99 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 100 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 101 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 102 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 103 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 104 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 105 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 106 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 107 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 108 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 109 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 110 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 111 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 112 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 113 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 114 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 115 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 116 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 117 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 118 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 119 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 120 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 121 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 122 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 123 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 124 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok 125 # skip NeXML parsing for NeXML v0.9 is currently very experimental support ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/nexus.t ............................ 1..43 ok 1 - use Bio::AlignIO::nexus; ok 2 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 - nexus output test ok 6 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 7 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 8 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 10 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 11 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 12 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 14 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 15 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 16 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 17 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 18 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 19 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 20 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 21 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 22 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 23 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 24 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 25 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 26 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 27 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 28 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 30 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 31 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 32 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 33 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 34 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 35 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 36 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 37 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 38 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 39 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 40 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 41 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 42 - An object of class 'Bio::AlignIO::nexus' isa 'Bio::AlignIO' ok 43 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/pfam.t ............................. 1..5 ok 1 - use Bio::AlignIO::pfam; ok 2 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 - pfam output test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/phylip.t ........................... 1..16 ok 1 - use Bio::AlignIO::phylip; ok 2 - An object of class 'Bio::AlignIO::phylip' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 - phylip output test ok 6 ok 7 ok 8 not ok 9 # TODO problems with default strand, length? # Failed (TODO) test at t/AlignIO/phylip.t line 44. # got: undef # expected: '0' not ok 10 # TODO problems with default strand, length? # Failed (TODO) test at t/AlignIO/phylip.t line 45. # got: '50' # expected: '47' ok 11 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 12 ok 13 - An object of class 'Bio::AlignIO::phylip' isa 'Bio::AlignIO' ok 14 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 15 ok 16 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/po.t ............................... 1..11 ok 1 - use Bio::AlignIO::po; ok 2 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 - An object of class 'Bio::AlignIO::clustalw' isa 'Bio::AlignIO' ok 6 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 7 - po output test ok 8 - An object of class 'Bio::AlignIO::po' isa 'Bio::AlignIO' ok 9 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 10 ok 11 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/prodom.t ........................... 1..3 ok 1 - use Bio::AlignIO::prodom; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - prodom input test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/psi.t .............................. 1..5 ok 1 - use Bio::AlignIO::psi; ok 2 - An object of class 'Bio::AlignIO::psi' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/selex.t ............................ 1..4 ok 1 - use Bio::AlignIO::selex; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - selex format test ok 4 - selex output test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/stockholm.t ........................ 1..84 ok 1 - use Bio::AlignIO::stockholm; ok 2 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO' ok 3 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 10 - Stockholm annotation ok 11 - Stockholm annotation ok 12 - stockholm output test ok 13 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 - 'Stockholm annotation' isa 'Bio::Annotation::Reference' ok 21 - Stockholm annotation ok 22 - Stockholm annotation ok 23 - Stockholm annotation ok 24 - Stockholm annotation ok 25 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI' ok 26 - Rfam meta data ok 27 - Rfam meta data ok 28 ok 29 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI' ok 36 - Rfam meta data ok 37 - Rfam meta data ok 38 - An object of class 'Bio::AlignIO::stockholm' isa 'Bio::AlignIO' ok 39 ok 40 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 41 ok 42 ok 43 ok 44 ok 45 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' ok 46 - Pfam annotation ok 47 ok 48 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 49 ok 50 ok 51 ok 52 ok 53 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::MetaI' ok 60 - Pfam aln meta data ok 61 - Pfam aln meta data ok 62 - Pfam aln meta data ok 63 - Pfam aln meta data ok 64 - Pfam aln meta data ok 65 - Pfam aln meta data ok 66 - Pfam seq meta data ok 67 - Pfam seq meta data ok 68 - Pfam seq meta data ok 69 - Pfam seq meta data ok 70 ok 71 - An object of class 'Bio::SeqFeature::Generic' isa 'Bio::SeqFeatureI' ok 72 - An object of class 'Bio::Seq::Meta' isa 'Bio::Seq::Meta' ok 73 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI' ok 74 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::DBLink' ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/AlignIO/xmfa.t ............................. 1..30 ok 1 - use Bio::AlignIO::xmfa; ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 3 - xmfa input test ok 4 - xmfa input test for start ok 5 - xmfa input test for end ok 6 - xmfa strand test ok 7 - xmfa input test for id ok 8 - xmfa input test for id ok 9 - xmfa input test ok 10 - xmfa input test for start ok 11 - xmfa input test for end ok 12 - xmfa strand test ok 13 - xmfa input test for id ok 14 - xmfa input test for id ok 15 - xmfa input test ok 16 - xmfa input test for start ok 17 - xmfa input test for end ok 18 - xmfa strand test ok 19 - xmfa input test for id ok 20 - xmfa input test for id ok 21 - xmfa alignment score ok 22 - An object of class 'Bio::SimpleAlign' isa 'Bio::Align::AlignI' ok 23 - xmfa input test ok 24 - xmfa strand ok 25 - xmfa input test for description ok 26 - xmfa input test for id ok 27 - xmfa input test for end ok 28 - xmfa input test for end ok 29 - xmfa alignment score ok 30 - xmfa output test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Alphabet.t ................................. 1..100 ok 1 - use Bio::Symbol::Alphabet; ok 2 - use Bio::Symbol::Symbol; ok 3 - use Bio::Symbol::DNAAlphabet; ok 4 - use Bio::Symbol::ProteinAlphabet; ok 5 - An object of class 'Bio::Symbol::Alphabet' isa 'Bio::Symbol::Alphabet' ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - An object of class 'Bio::Symbol::DNAAlphabet' isa 'Bio::Symbol::AlphabetI' ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 - An object of class 'Bio::Symbol::ProteinAlphabet' isa 'Bio::Symbol::AlphabetI' ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Annotation/Annotation.t .................... 1..159 ok 1 - use Bio::Annotation::Collection; ok 2 - use Bio::Annotation::DBLink; ok 3 - use Bio::Annotation::Comment; ok 4 - use Bio::Annotation::Reference; ok 5 - use Bio::Annotation::SimpleValue; ok 6 - use Bio::Annotation::Target; ok 7 - use Bio::Annotation::AnnotationFactory; ok 8 - use Bio::Annotation::StructuredValue; ok 9 - use Bio::Annotation::TagTree; ok 10 - use Bio::Annotation::Tree; ok 11 - use Bio::Seq; ok 12 - use Bio::SimpleAlign; ok 13 - use Bio::Cluster::UniGene; ok 14 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::AnnotationI' ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 - An object of class 'Bio::Annotation::DBLink' isa 'Bio::AnnotationI' ok 22 ok 23 ok 24 ok 25 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 26 ok 27 ok 28 - An object of class 'Bio::Annotation::Target' isa 'Bio::AnnotationI' ok 29 ok 30 - An object of class 'Bio::Annotation::Reference' isa 'Bio::AnnotationI' ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::AnnotationI' ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 - An object of class 'Bio::Annotation::Collection' isa 'Bio::AnnotationCollectionI' ok 69 ok 70 ok 71 ok 72 ok 73 - An object of class 'Bio::Annotation::StructuredValue' isa 'Bio::Annotation::StructuredValue' ok 74 ok 75 ok 76 ok 77 ok 78 - use Bio::Annotation::OntologyTerm; ok 79 - An object of class 'Bio::Ontology::Term' isa 'Bio::Ontology::Term' ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 - An object of class 'Bio::Seq' isa 'Bio::AnnotatableI' ok 86 - 'isa SeqFeatureI' isa 'Bio::SeqFeatureI' ok 87 - 'isa AnnotatableI' isa 'Bio::AnnotatableI' ok 88 - 'isa SeqFeatureI' isa 'Bio::SeqFeatureI' ok 89 - 'isa AnnotatableI' isa 'Bio::AnnotatableI' ok 90 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::AnnotatableI' ok 91 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::AnnotatableI' ok 92 - An object of class 'Bio::Annotation::AnnotationFactory' isa 'Bio::Factory::ObjectFactoryI' ok 93 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue' ok 94 ok 95 - An object of class 'Bio::Annotation::OntologyTerm' isa 'Bio::Annotation::OntologyTerm' ok 96 - Bio::Annotation::Comment ok 97 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 98 ok 99 - Bio::Annotation::Comment ok 100 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 101 - Bio::Annotation::Comment ok 102 - An object of class 'Bio::Annotation::Comment' isa 'Bio::Annotation::Comment' ok 103 ok 104 - An object of class 'Bio::Annotation::Target' isa 'Bio::Annotation::Target' ok 105 ok 106 ok 107 - An object of class 'Bio::Annotation::Tree' isa 'Bio::AnnotationI' ok 108 - tree_id() ok 109 - tagname() ok 110 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI' ok 111 ok 112 - add tree to AlignI ok 113 - get seq from node id ok 114 ok 115 - An object of class 'Bio::Annotation::Tree' isa 'Bio::Annotation::Tree' ok 116 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 117 - default itext ok 118 - roundtrip ok 119 - itext ok 120 - spxr ok 121 - indent ok 122 - xml ok 123 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 124 ok 125 - child changes ok 126 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 127 ok 128 - child changes ok 129 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 130 ok 131 - child changes ok 132 - child changes in parent node ok 133 - no tags ok 134 - before Stag node ok 135 - after Stag node ok 136 - both stag nodes ok 137 - different instances ok 138 - before TagTree ok 139 - after TagTree ok 140 - both stag nodes ok 141 - different instances ok 142 - before TagTree ok 143 - after TagTree ok 144 - stag nodes ok 145 - same instance ok 146 - before TagTree ok 147 - after TagTree ok 148 - stag nodes ok 149 - different instance ok 150 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::AnnotationI' ok 151 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 152 - child changes ok 153 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 154 - child changes ok 155 - An object of class 'Data::Stag::StagImpl' isa 'Data::Stag::StagI' ok 156 - child changes ok 157 ok 158 ok 159 - An object of class 'Bio::Annotation::TagTree' isa 'Bio::Annotation::TagTree' ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Annotation/AnnotationAdaptor.t ............. 1..23 ok 1 - use Bio::SeqFeature::Generic; ok 2 - use Bio::SeqFeature::AnnotationAdaptor; ok 3 - use Bio::Annotation::DBLink; ok 4 - use Bio::Annotation::Comment; ok 5 - use Bio::Annotation::SimpleValue; ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 Bio::Assembly::IO: could not load tigr - for more details on supported formats please see the Assembly::IO docs Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::Assembly::IO::tigr. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio/SeqFeature/Collection.pm line 146. BEGIN failed--compilation aborted at Bio/SeqFeature/Collection.pm line 146. Compilation failed in require at Bio/Assembly/Singlet.pm line 91. BEGIN failed--compilation aborted at Bio/Assembly/Singlet.pm line 91. Compilation failed in require at Bio\Assembly\IO\tigr.pm line 237. BEGIN failed--compilation aborted at Bio\Assembly\IO\tigr.pm line 237. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:296 STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:138 STACK: t/Assembly/ContigSpectrum.t:12 ----------------------------------------------------------- # Failed test 'undef isa 'Bio::Assembly::IO'' # at t/Assembly/ContigSpectrum.t line 16. # undef isn't defined Can't call method "next_assembly" on an undefined value at t/Assembly/ContigSpectrum.t line 17. # Looks like you planned 236 tests but ran 3. # Looks like you failed 1 test of 3 run. # Looks like your test exited with 2 just after 3. t/Assembly/ContigSpectrum.t .................. 1..236 ok 1 - use Bio::Assembly::IO; ok 2 - use Bio::Assembly::Tools::ContigSpectrum; not ok 3 - undef isa 'Bio::Assembly::IO' Dubious, test returned 2 (wstat 512, 0x200) Failed 234/236 subtests t/Assembly/IO/bowtie.t ....................... skipped: The optional module DB_File (or dependencies thereof) was not installed t/Assembly/IO/sam.t .......................... skipped: The optional module DB_File (or dependencies thereof) was not installed t/Assembly/core.t ............................ skipped: The optional module DB_File (or dependencies thereof) was not installed # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Biblio/Biblio.t ............................ 1..24 ok 1 - use Bio::Biblio; ok 2 - use Bio::Biblio::IO; ok 3 # skip The optional module SOAP::Lite (or dependencies thereof) was not installed ok 4 ok 5 - citation 1 ok 6 - citation 2 ok 7 - citation 3 ok 8 - in callback ok 9 - in callback ok 10 - in callback ok 11 - calling callback ok 12 - citation 1 ok 13 - citation 2 ok 14 - citation 1 ok 15 - citation 2 ok 16 ok 17 - citation 1 ok 18 - citation 2 ok 19 - citation 3 ok 20 - citation 4 ok 21 - filehandle test ok 22 - filehandle test ok 23 - filehandle test ok 24 - filehandle test ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Biblio/References.t ........................ 1..537 ok 1 - use Bio::Biblio::Article; ok 2 - use Bio::Biblio::Book; ok 3 - use Bio::Biblio::BookArticle; ok 4 - use Bio::Biblio::Journal; ok 5 - use Bio::Biblio::JournalArticle; ok 6 - use Bio::Biblio::MedlineArticle; ok 7 - use Bio::Biblio::MedlineBook; ok 8 - use Bio::Biblio::MedlineBookArticle; ok 9 - use Bio::Biblio::MedlineJournal; ok 10 - use Bio::Biblio::MedlineJournalArticle; ok 11 - use Bio::Biblio::Organisation; ok 12 - use Bio::Biblio::Patent; ok 13 - use Bio::Biblio::Person; ok 14 - use Bio::Biblio::Proceeding; ok 15 - use Bio::Biblio::Provider; ok 16 - use Bio::Biblio::Ref; ok 17 - use Bio::Biblio::Service; ok 18 - use Bio::Biblio::TechReport; ok 19 - use Bio::Biblio::Thesis; ok 20 - use Bio::Biblio::WebResource; ok 21 - use Bio::Biblio::PubmedArticle; ok 22 - use Bio::Biblio::PubmedBookArticle; ok 23 - use Bio::Biblio::PubmedJournalArticle; ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 - set 'abstract' ok 48 - get 'abstract' ok 49 - set 'abstract_language' ok 50 - get 'abstract_language' ok 51 - set 'abstract_type' ok 52 - get 'abstract_type' ok 53 - set 'author_list_complete' ok 54 - get 'author_list_complete' ok 55 - set 'cross_references_list_complete' ok 56 - get 'cross_references_list_complete' ok 57 - set 'date' ok 58 - get 'date' ok 59 - set 'date_completed' ok 60 - get 'date_completed' ok 61 - set 'date_created' ok 62 - get 'date_created' ok 63 - set 'date_revised' ok 64 - get 'date_revised' ok 65 - set 'format' ok 66 - get 'format' ok 67 - set 'identifier' ok 68 - get 'identifier' ok 69 - set 'language' ok 70 - get 'language' ok 71 - set 'last_modified_date' ok 72 - get 'last_modified_date' ok 73 - set 'repository_subset' ok 74 - get 'repository_subset' ok 75 - set 'rights' ok 76 - get 'rights' ok 77 - set 'spatial_location' ok 78 - get 'spatial_location' ok 79 - set 'subject_headings_source' ok 80 - get 'subject_headings_source' ok 81 - set 'temporal_period' ok 82 - get 'temporal_period' ok 83 - set 'title' ok 84 - get 'title' ok 85 - set 'toc' ok 86 - get 'toc' ok 87 - set 'toc_type' ok 88 - get 'toc_type' ok 89 - set 'type' ok 90 - get 'type' ok 91 - set 'first_page' ok 92 - get 'first_page' ok 93 - set 'last_page' ok 94 - get 'last_page' ok 95 - set 'issue' ok 96 - get 'issue' ok 97 - set 'issue_supplement' ok 98 - get 'issue_supplement' ok 99 - set 'volume' ok 100 - get 'volume' ok 101 - set 'affiliation' ok 102 - get 'affiliation' ok 103 - set 'citation_owner' ok 104 - get 'citation_owner' ok 105 - set 'date_of_electronic_publication' ok 106 - get 'date_of_electronic_publication' ok 107 - set 'gene_symbols' ok 108 - get 'gene_symbols' ok 109 - set 'grant_list_complete' ok 110 - get 'grant_list_complete' ok 111 - set 'medline_date' ok 112 - get 'medline_date' ok 113 - set 'medline_id' ok 114 - get 'medline_id' ok 115 - set 'medline_page' ok 116 - get 'medline_page' ok 117 - set 'number_of_references' ok 118 - get 'number_of_references' ok 119 - set 'other_languages' ok 120 - get 'other_languages' ok 121 - set 'pmid' ok 122 - get 'pmid' ok 123 - set 'season' ok 124 - get 'season' ok 125 - set 'status' ok 126 - get 'status' ok 127 - set 'vernacular_title' ok 128 - get 'vernacular_title' ok 129 ok 130 - abstract ok 131 - abstract_language ok 132 - abstract_type ok 133 - author_list_complete ok 134 - cross_references_list_complete ok 135 - date ok 136 - date_completed ok 137 - date_created ok 138 - date_revised ok 139 - format ok 140 - identifier ok 141 - language ok 142 - last_modified_date ok 143 - repository_subset ok 144 - rights ok 145 - spatial_location ok 146 - subject_headings_source ok 147 - temporal_period ok 148 - title ok 149 - toc ok 150 - toc_type ok 151 - type ok 152 - first_page ok 153 - last_page ok 154 - issue ok 155 - issue_supplement ok 156 - volume ok 157 - affiliation ok 158 - citation_owner ok 159 - date_of_electronic_publication ok 160 - gene_symbols ok 161 - grant_list_complete ok 162 - medline_date ok 163 - medline_id ok 164 - medline_page ok 165 - number_of_references ok 166 - other_languages ok 167 - pmid ok 168 - season ok 169 - status ok 170 - vernacular_title ok 171 - get 'authors' ok 172 - get 'cross_references' ok 173 - get 'codes' ok 174 - get 'contributors' ok 175 - get 'keywords' ok 176 - get 'publisher' ok 177 - get 'subject_headings' ok 178 - get 'journal' ok 179 - get 'chemicals' ok 180 - get 'comment_ins' ok 181 - get 'comment_ons' ok 182 - get 'erratum_fors' ok 183 - get 'erratum_ins' ok 184 - get 'general_notes' ok 185 - get 'grants' ok 186 - get 'mesh_headings' ok 187 - get 'original_report_ins' ok 188 - get 'other_abstracts' ok 189 - get 'other_ids' ok 190 - get 'republished_froms' ok 191 - get 'republished_ins' ok 192 - get 'retraction_ins' ok 193 - get 'retraction_ofs' ok 194 - get 'summary_for_patients_ins' ok 195 - get 'update_ins' ok 196 - get 'update_ofs' ok 197 - get 'journal' ok 198 - add_author 1 ok 199 - add_author 2 ok 200 - get authors ok 201 - add_contributor 1 ok 202 - add_contributor 2 ok 203 - get contributors ok 204 - add_cross_reference 1 ok 205 - add_cross_reference 2 ok 206 - get cross_references ok 207 - get cross_references ok 208 - set 'abstract' ok 209 - get 'abstract' ok 210 - set 'abstract_language' ok 211 - get 'abstract_language' ok 212 - set 'abstract_type' ok 213 - get 'abstract_type' ok 214 - set 'author_list_complete' ok 215 - get 'author_list_complete' ok 216 - set 'cross_references_list_complete' ok 217 - get 'cross_references_list_complete' ok 218 - set 'date' ok 219 - get 'date' ok 220 - set 'date_completed' ok 221 - get 'date_completed' ok 222 - set 'date_created' ok 223 - get 'date_created' ok 224 - set 'date_revised' ok 225 - get 'date_revised' ok 226 - set 'format' ok 227 - get 'format' ok 228 - set 'identifier' ok 229 - get 'identifier' ok 230 - set 'language' ok 231 - get 'language' ok 232 - set 'last_modified_date' ok 233 - get 'last_modified_date' ok 234 - set 'repository_subset' ok 235 - get 'repository_subset' ok 236 - set 'rights' ok 237 - get 'rights' ok 238 - set 'spatial_location' ok 239 - get 'spatial_location' ok 240 - set 'subject_headings_source' ok 241 - get 'subject_headings_source' ok 242 - set 'temporal_period' ok 243 - get 'temporal_period' ok 244 - set 'title' ok 245 - get 'title' ok 246 - set 'toc' ok 247 - get 'toc' ok 248 - set 'toc_type' ok 249 - get 'toc_type' ok 250 - set 'type' ok 251 - get 'type' ok 252 - set 'first_page' ok 253 - get 'first_page' ok 254 - set 'last_page' ok 255 - get 'last_page' ok 256 - set 'affiliation' ok 257 - get 'affiliation' ok 258 - set 'citation_owner' ok 259 - get 'citation_owner' ok 260 - set 'date_of_electronic_publication' ok 261 - get 'date_of_electronic_publication' ok 262 - set 'gene_symbols' ok 263 - get 'gene_symbols' ok 264 - set 'grant_list_complete' ok 265 - get 'grant_list_complete' ok 266 - set 'medline_date' ok 267 - get 'medline_date' ok 268 - set 'medline_id' ok 269 - get 'medline_id' ok 270 - set 'medline_page' ok 271 - get 'medline_page' ok 272 - set 'number_of_references' ok 273 - get 'number_of_references' ok 274 - set 'other_languages' ok 275 - get 'other_languages' ok 276 - set 'pmid' ok 277 - get 'pmid' ok 278 - set 'season' ok 279 - get 'season' ok 280 - set 'status' ok 281 - get 'status' ok 282 - set 'vernacular_title' ok 283 - get 'vernacular_title' ok 284 ok 285 - abstract ok 286 - abstract_language ok 287 - abstract_type ok 288 - author_list_complete ok 289 - cross_references_list_complete ok 290 - date ok 291 - date_completed ok 292 - date_created ok 293 - date_revised ok 294 - format ok 295 - identifier ok 296 - language ok 297 - last_modified_date ok 298 - repository_subset ok 299 - rights ok 300 - spatial_location ok 301 - subject_headings_source ok 302 - temporal_period ok 303 - title ok 304 - toc ok 305 - toc_type ok 306 - type ok 307 - first_page ok 308 - last_page ok 309 - affiliation ok 310 - citation_owner ok 311 - date_of_electronic_publication ok 312 - gene_symbols ok 313 - grant_list_complete ok 314 - medline_date ok 315 - medline_id ok 316 - medline_page ok 317 - number_of_references ok 318 - other_languages ok 319 - pmid ok 320 - season ok 321 - status ok 322 - vernacular_title ok 323 - get 'authors' ok 324 - get 'cross_references' ok 325 - get 'codes' ok 326 - get 'contributors' ok 327 - get 'keywords' ok 328 - get 'publisher' ok 329 - get 'subject_headings' ok 330 - get 'book' ok 331 - get 'chemicals' ok 332 - get 'comment_ins' ok 333 - get 'comment_ons' ok 334 - get 'erratum_fors' ok 335 - get 'erratum_ins' ok 336 - get 'general_notes' ok 337 - get 'grants' ok 338 - get 'mesh_headings' ok 339 - get 'original_report_ins' ok 340 - get 'other_abstracts' ok 341 - get 'other_ids' ok 342 - get 'republished_froms' ok 343 - get 'republished_ins' ok 344 - get 'retraction_ins' ok 345 - get 'retraction_ofs' ok 346 - get 'summary_for_patients_ins' ok 347 - get 'update_ins' ok 348 - get 'update_ofs' ok 349 - get 'book' ok 350 - set 'abstract' ok 351 - get 'abstract' ok 352 - set 'abstract_language' ok 353 - get 'abstract_language' ok 354 - set 'abstract_type' ok 355 - get 'abstract_type' ok 356 - set 'author_list_complete' ok 357 - get 'author_list_complete' ok 358 - set 'cross_references_list_complete' ok 359 - get 'cross_references_list_complete' ok 360 - set 'date' ok 361 - get 'date' ok 362 - set 'date_completed' ok 363 - get 'date_completed' ok 364 - set 'date_created' ok 365 - get 'date_created' ok 366 - set 'date_revised' ok 367 - get 'date_revised' ok 368 - set 'format' ok 369 - get 'format' ok 370 - set 'identifier' ok 371 - get 'identifier' ok 372 - set 'language' ok 373 - get 'language' ok 374 - set 'last_modified_date' ok 375 - get 'last_modified_date' ok 376 - set 'repository_subset' ok 377 - get 'repository_subset' ok 378 - set 'rights' ok 379 - get 'rights' ok 380 - set 'spatial_location' ok 381 - get 'spatial_location' ok 382 - set 'subject_headings_source' ok 383 - get 'subject_headings_source' ok 384 - set 'temporal_period' ok 385 - get 'temporal_period' ok 386 - set 'title' ok 387 - get 'title' ok 388 - set 'toc' ok 389 - get 'toc' ok 390 - set 'toc_type' ok 391 - get 'toc_type' ok 392 - set 'type' ok 393 - get 'type' ok 394 - set 'edition' ok 395 - get 'edition' ok 396 - set 'isbn' ok 397 - get 'isbn' ok 398 - set 'series' ok 399 - get 'series' ok 400 - set 'volume' ok 401 - get 'volume' ok 402 ok 403 - abstract ok 404 - abstract_language ok 405 - abstract_type ok 406 - author_list_complete ok 407 - cross_references_list_complete ok 408 - date ok 409 - date_completed ok 410 - date_created ok 411 - date_revised ok 412 - format ok 413 - identifier ok 414 - language ok 415 - last_modified_date ok 416 - repository_subset ok 417 - rights ok 418 - spatial_location ok 419 - subject_headings_source ok 420 - temporal_period ok 421 - title ok 422 - toc ok 423 - toc_type ok 424 - type ok 425 - edition ok 426 - isbn ok 427 - series ok 428 - volume ok 429 - get 'authors' ok 430 - get 'cross_references' ok 431 - get 'codes' ok 432 - get 'contributors' ok 433 - get 'keywords' ok 434 - get 'publisher' ok 435 - get 'subject_headings' ok 436 - get 'editor' ok 437 - set 'abbreviation' ok 438 - get 'abbreviation' ok 439 - set 'issn' ok 440 - get 'issn' ok 441 - set 'name' ok 442 - get 'name' ok 443 - set 'coden' ok 444 - get 'coden' ok 445 - set 'country' ok 446 - get 'country' ok 447 - set 'medline_code' ok 448 - get 'medline_code' ok 449 - set 'medline_ta' ok 450 - get 'medline_ta' ok 451 - set 'nlm_unique_id' ok 452 - get 'nlm_unique_id' ok 453 ok 454 - abbreviation ok 455 - issn ok 456 - name ok 457 - coden ok 458 - country ok 459 - medline_code ok 460 - medline_ta ok 461 - nlm_unique_id ok 462 - set 'doc_number' ok 463 - get 'doc_number' ok 464 - set 'doc_office' ok 465 - get 'doc_office' ok 466 - set 'doc_type' ok 467 - get 'doc_type' ok 468 ok 469 - doc_number ok 470 - doc_office ok 471 - doc_type ok 472 - get 'applicants' ok 473 - set 'url' ok 474 - get 'url' ok 475 - set 'estimated_size' ok 476 - get 'estimated_size' ok 477 - set 'cost' ok 478 - get 'cost' ok 479 ok 480 - url ok 481 - estimated_size ok 482 - cost ok 483 - set 'type' ok 484 - get 'type' ok 485 - set 'affiliation' ok 486 - get 'affiliation' ok 487 - set 'email' ok 488 - get 'email' ok 489 - set 'firstname' ok 490 - get 'firstname' ok 491 - set 'forename' ok 492 - get 'forename' ok 493 - set 'initials' ok 494 - get 'initials' ok 495 - set 'lastname' ok 496 - get 'lastname' ok 497 - set 'middlename' ok 498 - get 'middlename' ok 499 - set 'postal_address' ok 500 - get 'postal_address' ok 501 - set 'suffix' ok 502 - get 'suffix' ok 503 ok 504 - type ok 505 - affiliation ok 506 - email ok 507 - firstname ok 508 - forename ok 509 - initials ok 510 - lastname ok 511 - middlename ok 512 - postal_address ok 513 - suffix ok 514 - set 'type' ok 515 - get 'type' ok 516 - set 'name' ok 517 - get 'name' ok 518 ok 519 - type ok 520 - name ok 521 - set 'type' ok 522 - get 'type' ok 523 - set 'name' ok 524 - get 'name' ok 525 ok 526 - type ok 527 - name ok 528 - set 'pubmed_status' ok 529 - get 'pubmed_status' ok 530 - set 'pubmed_provider_id' ok 531 - get 'pubmed_provider_id' ok 532 ok 533 - pubmed_status ok 534 - pubmed_provider_id ok 535 - get 'pubmed_history_list' ok 536 - get 'pubmed_article_id_list' ok 537 - get 'pubmed_url_list' ok t/Biblio/biofetch.t .......................... skipped: Network tests have not been requested t/Biblio/eutils.t ............................ skipped: Network tests have not been requested # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/ClusterIO/ClusterIO.t ...................... 1..12 ok 1 - use Bio::ClusterIO; ok 2 - use Bio::Cluster::ClusterFactory; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI' ok 12 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI' ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/ClusterIO/SequenceFamily.t ................. 1..19 ok 1 - use Bio::SeqIO; ok 2 - use Bio::Cluster::SequenceFamily; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/ClusterIO/unigene.t ........................ 1..73 ok 1 - use Bio::ClusterIO; ok 2 - new Bio::ClusterIO object defined ok 3 ok 4 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::Cluster::UniGeneI' ok 5 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::ClusterI' ok 6 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::IdentifiableI' ok 7 - An object of class 'Bio::Cluster::UniGene' isa 'Bio::DescribableI' ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI' ok 49 ok 50 ok 51 - annotation object defined ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::PrimarySeqI' ok 67 ok 68 - next cluster ok 69 ok 70 ok 71 ok 72 ok 73 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Coordinate/CoordinateBoundaryTest.t ........ 1..174 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 ok 4 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 5 ok 6 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 7 ok 8 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 9 ok 10 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair' ok 11 ok 12 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair' ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' ok 33 ok 34 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 35 ok 36 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' ok 51 ok 52 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 53 ok 54 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' ok 69 ok 70 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 71 ok 72 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 - An object of class 'Bio::Location::Simple' isa 'Bio::LocationI' ok 89 ok 90 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 91 ok 92 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 109 ok 110 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 111 ok 112 - An object of class 'Bio::Location::Simple' isa 'Bio::Location::Simple' ok 113 ok 114 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair' ok 115 ok 116 - An object of class 'Bio::Coordinate::Pair' isa 'Bio::Coordinate::Pair' ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 133 ok 134 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 143 ok 144 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 153 ok 154 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 165 ok 166 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Coordinate/CoordinateGraph.t ............... 1..7 ok 1 - use Bio::Coordinate::Graph; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Coordinate/CoordinateMapper.t .............. 1..175 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 - use Bio::Coordinate::Result::Match; ok 4 - use Bio::Coordinate::Result::Gap; ok 5 - use Bio::Coordinate::Chain; ok 6 - use Bio::Coordinate::Collection; ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Coordinate::Result' ok 15 - An object of class 'Bio::Coordinate::Result' isa 'Bio::Location::SplitLocationI' ok 16 ok 17 ok 18 ok 19 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::LocationI' ok 20 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Coordinate::Result::Match' ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 - An object of class 'Bio::Coordinate::Result::Gap' isa 'Bio::Coordinate::Result::Gap' ok 38 - An object of class 'Bio::Coordinate::Result::Gap' isa 'Bio::LocationI' ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Coordinate::Result::Match' ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 - Match: |314696| Test: 314696| ok 139 ok 140 ok 141 ok 142 - Match: |341| Test: 341| ok 143 ok 144 ok 145 ok 146 - Match: |315843| Test: 315843| ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 - Match: |627011| Test: 627011| ok 153 ok 154 ok 155 ok 156 - Match: |chr1| Test: chr1| ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Coordinate/GeneCoordinateMapper.t .......... 1..116 ok 1 - use Bio::Location::Simple; ok 2 - use Bio::Coordinate::Pair; ok 3 - use Bio::Coordinate::ExtrapolatingPair; ok 4 - use Bio::Coordinate::GeneMapper; ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Location::Simple' ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 - An object of class 'Bio::Coordinate::Result::Match' isa 'Bio::Location::Simple' ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Draw/Pictogram.t ........................... 1..6 ok 1 - use Bio::Draw::Pictogram; ok 2 - use Bio::SeqIO; ok 3 - use Bio::Matrix::PSM::IO; ok 4 - An object of class 'Bio::Draw::Pictogram' isa 'Bio::Draw::Pictogram' ok 5 ok 6 ok t/LiveSeq/Chain.t ............................ 1..45 ok 1 - use Bio::LiveSeq::Chain; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/LiveSeq/LiveSeq.t .......................... 1..48 ok 1 - use Bio::LiveSeq::IO::BioPerl; ok 2 ok 3 ok 4 - Bio::LiveSeq::Gene ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/LiveSeq/Mutation.t ......................... 1..19 ok 1 - use Bio::LiveSeq::Mutation; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/LiveSeq/Mutator.t .......................... 1..24 ok 1 - use Bio::LiveSeq::Mutator; ok 2 - use Bio::LiveSeq::IO::BioPerl; ok 3 - use Bio::Variation::IO; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok t/LocalDB/BioDBGFF.t ......................... skipped: Not compatible with your Operating System # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/LocalDB/DBFasta.t .......................... 1..17 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 - bug 3126 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 - threw Regexp ((?^:FASTA header doesn't match)) ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/LocalDB/DBQual.t ........................... 1..38 ok 1 - use Bio::Root::IO; ok 2 - use File::Copy; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' ok 26 ok 27 ok 28 - An object of class 'Bio::Seq::PrimaryQual' isa 'Bio::Seq::PrimaryQual' ok 29 ok 30 ok 31 ok 32 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' ok 33 ok 34 - An object of class 'Bio::Seq::PrimaryQual::Qual' isa 'Bio::Seq::PrimaryQual' ok 35 ok 36 ok 37 ok 38 ok t/LocalDB/Flat.t ............................. skipped: The optional module DB_File (or dependencies thereof) was not installed # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/LocalDB/Index/Blast.t ...................... 1..26 ok 1 - use Cwd; ok 2 - use Bio::SearchIO; ok 3 - use Bio::Index::Blast; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 --------------------- WARNING --------------------- MSG: overwriting a current value stored for SP130_MOUSE --------------------------------------------------- --------------------- WARNING --------------------- MSG: overwriting a current value stored for SDS3_MOUSE --------------------------------------------------- --------------------- WARNING --------------------- MSG: overwriting a current value stored for IKZF1_MOUSE --------------------------------------------------- t/LocalDB/Index/BlastTable.t ................. 1..27 ok 1 - use Cwd; ok 2 - use Bio::SearchIO; ok 3 - use Bio::Index::BlastTable; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok t/LocalDB/Index/Index.t ...................... skipped: The optional module DB_File (or dependencies thereof) was not installed # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/LocalDB/Registry.t ......................... 1..14 ok 1 - use Bio::DB::Registry; ok 2 - use Bio::DB::Flat; ok 3 ok 4 # skip The optional module DB_File (or dependencies thereof) was not installed ok 5 # skip The optional module DB_File (or dependencies thereof) was not installed ok 6 # skip Network tests have not been requested ok 7 # skip Network tests have not been requested ok 8 # skip Network tests have not been requested ok 9 # skip Network tests have not been requested ok 10 # skip Network tests have not been requested ok 11 # skip Network tests have not been requested ok 12 # skip Network tests have not been requested ok 13 # skip Network tests have not been requested ok 14 # skip Network tests have not been requested ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 # Failed test 'use Bio::DB::SeqFeature::Store::GFF3Loader;' # in t/LocalDB/SeqFeature.t at line 16. # Tried to use 'Bio::DB::SeqFeature::Store::GFF3Loader'. # Error: Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . .. ./t/lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio/DB/SeqFeature/Store/LoadHelper.pm line 38. # BEGIN failed--compilation aborted at t/LocalDB/SeqFeature.t line 16. # Compilation failed in require at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. # Compilation failed in require at (eval 116) line 2. # BEGIN failed--compilation aborted at (eval 116) line 2. # Looks like you planned 116 tests but ran 1 extra. # Looks like you failed 1 test of 117 run. t/LocalDB/SeqFeature.t ....................... 1..116 ok 1 - use Bio::SeqFeature::Generic; ok 2 - use Bio::DB::SeqFeature::Store; not ok 3 - use Bio::DB::SeqFeature::Store::GFF3Loader; ok 4 - use Bio::Root::IO; ok 5 - use Bio::DB::Fasta; ok 6 - use File::Copy; ok 7 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 8 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 9 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 10 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 11 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 12 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 13 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 14 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 15 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 16 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 17 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 18 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 19 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 20 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 21 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 22 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 23 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 24 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 25 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 26 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 27 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 28 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 29 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 30 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 31 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 32 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 33 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 34 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 35 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 36 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 37 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 38 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 39 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 40 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 41 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 42 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 43 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 44 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 45 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 46 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 47 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 48 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 49 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 50 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 51 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 52 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 53 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 54 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 55 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 56 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 57 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 58 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 59 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 60 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 61 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 62 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 63 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 64 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 65 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 66 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 67 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 68 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 69 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 70 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 71 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 72 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 73 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 74 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 75 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 76 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 77 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 78 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 79 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 80 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 81 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 82 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 83 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 84 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 85 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 86 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 87 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 88 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 89 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 90 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 91 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 92 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 93 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 94 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 95 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 96 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 97 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 98 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 99 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 100 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 101 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 102 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 103 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 104 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 105 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 106 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 107 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 108 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 109 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 110 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 111 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 112 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 113 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 114 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 115 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 116 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # ok 117 # skip DB load failed? Skipping all! Attempt to reload Bio/DB/SeqFeature/Store/GFF3Loader.pm aborted. # Compilation failed in require at Bio/DB/SeqFeature/Store/memory.pm line 124. # BEGIN failed--compilation aborted at Bio/DB/SeqFeature/Store/memory.pm line 124. # Compilation failed in require at (eval 130) line 2. # at t/LocalDB/SeqFeature.t line 32. # Dubious, test returned 1 (wstat 256, 0x100) Failed 1/116 subtests (less 111 skipped subtests: 4 okay) # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio\DB\Taxonomy\flatfile.pm line 89. BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114 STACK: t/LocalDB/transfac_pro.t:18 ----------------------------------------------------------- Bio::DB::Taxonomy: flatfile cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio\DB\Taxonomy\flatfile.pm line 89. BEGIN failed--compilation aborted at Bio\DB\Taxonomy\flatfile.pm line 89. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::Taxonomy::_load_tax_module Bio/DB/Taxonomy.pm:263 STACK: Bio::DB::Taxonomy::new Bio/DB/Taxonomy.pm:114 STACK: t/LocalDB/transfac_pro.t:18 ----------------------------------------------------------- For more information about the Bio::DB::Taxonomy system please see the Bio::DB::Taxonomy docs. This includes ways of checking for formats at compile time, not run time. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio\DB\TFBS\transfac_pro.pm line 118. BEGIN failed--compilation aborted at Bio\DB\TFBS\transfac_pro.pm line 118. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151 STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130 STACK: t/LocalDB/transfac_pro.t:25 ----------------------------------------------------------- Bio::DB::TFBS: transfac_pro cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::DB::TFBS::transfac_pro. Can't locate DB_File.pm in @INC (you may need to install the DB_File module) (@INC contains: . C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\lib C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj\blib\arch C:/cpanfly-5.18/var/cpan/build/BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\cpan\build\BioPerl-1.6.901-nWgCFj C:\cpanfly-5.18\var\megalib C:/cpanfly-5.18/var/megalib C:/Perl-5.18/site/lib C:/Perl-5.18/lib) at Bio\DB\TFBS\transfac_pro.pm line 118. BEGIN failed--compilation aborted at Bio\DB\TFBS\transfac_pro.pm line 118. Compilation failed in require at Bio/Root/Root.pm line 543. STACK: Error::throw STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472 STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545 STACK: Bio::DB::TFBS::_load_tax_module Bio/DB/TFBS.pm:151 STACK: Bio::DB::TFBS::new Bio/DB/TFBS.pm:130 STACK: t/LocalDB/transfac_pro.t:25 ----------------------------------------------------------- For more information about the Bio::DB::TFBS system please see the Bio::DB::TFBS docs. This includes ways of checking for formats at compile time, not run time. # Failed test at t/LocalDB/transfac_pro.t line 25. Can't call method "get_reference_ids" on an undefined value at t/LocalDB/transfac_pro.t line 33. # Looks like you planned 115 tests but ran 4. # Looks like you failed 1 test of 4 run. # Looks like your test exited with 2 just after 4. t/LocalDB/transfac_pro.t ..................... 1..115 ok 1 - use Bio::Matrix::PSM::IO; ok 2 - use Bio::DB::TFBS; ok 3 - use Bio::DB::Taxonomy; not ok 4 Dubious, test returned 2 (wstat 512, 0x200) Failed 112/115 subtests # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Map/Cyto.t ................................. 1..110 ok 1 - use Bio::Map::CytoMap; ok 2 - use Bio::Map::CytoPosition; ok 3 - use Bio::Map::CytoMarker; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - An object of class 'Bio::Map::CytoPosition' isa 'Bio::Map::CytoPosition' ok 15 ok 16 ok 17 ok 18 - An object of class 'Bio::Range' isa 'Bio::Range' ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Map/Linkage.t .............................. 1..18 ok 1 - use Bio::Map::LinkagePosition; ok 2 - use Bio::Map::Microsatellite; ok 3 - use Bio::Map::LinkageMap; ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 # Failed test at t/Map/Map.t line 322. # got: 'Bio::Map::Position=HASH(0x1735784)' # expected: 'Bio::Map::Position=HASH(0x17353c4)' # Failed test at t/Map/Map.t line 323. # got: 'Bio::Map::Position=HASH(0x17353c4)' # expected: 'Bio::Map::Position=HASH(0x1735784)' # Failed test at t/Map/Map.t line 324. # got: undef # expected: 'Bio::Map::Position=HASH(0x1735b74)' Can't call method "toString" on an undefined value at t/Map/Map.t line 325. # Looks like you planned 267 tests but ran 134. # Looks like you failed 3 tests of 134 run. # Looks like your test exited with 255 just after 134. t/Map/Map.t .................................. 1..267 ok 1 - use Bio::Map::SimpleMap; ok 2 - use Bio::Map::Marker; ok 3 - use Bio::Map::Position; ok 4 - use Bio::Map::Relative; ok 5 - use Bio::Map::Mappable; ok 6 ok 7 ok 8 ok 9 ok 10 - Length is 0 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 not ok 132 not ok 133 not ok 134 Dubious, test returned 255 (wstat 65280, 0xff00) Failed 136/267 subtests # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Map/MapIO.t ................................ 1..51 ok 1 - use Bio::MapIO; ok 2 ok 3 - An object of class 'Bio::Map::SimpleMap' isa 'Bio::Map::MapI' ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Map/MicrosatelliteMarker.t ................. 1..8 ok 1 - use Bio::Map::SimpleMap; ok 2 - use Bio::Map::Position; ok 3 - use Bio::Map::Microsatellite; ok 4 ok 5 ok 6 ok 7 ok 8 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Map/Physical.t ............................. 1..39 ok 1 - use Bio::Map::Physical; ok 2 - use Bio::MapIO; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 - code holds and returns a string, definition requires a boolean ok 13 - code holds and returns a string, definition requires a boolean ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Matrix/IO/masta.t .......................... 1..16 ok 1 - use Bio::Matrix::PSM::IO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Matrix/IO/psm.t ............................ 1..63 ok 1 - use Bio::Matrix::PSM::IO; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Matrix/InstanceSite.t ...................... 1..6 ok 1 - use Bio::Matrix::PSM::InstanceSite; ok 2 ok 3 ok 4 ok 5 ok 6 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Matrix/Matrix.t ............................ 1..77 ok 1 - use Bio::Matrix::Generic; ok 2 - use Bio::Matrix::IO; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 - An object of class 'Bio::Matrix::Scoring' isa 'Bio::Matrix::Scoring' ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 - An object of class 'Bio::Matrix::Scoring' isa 'Bio::Matrix::Scoring' ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Matrix/ProtMatrix.t ........................ 1..14 ok 1 - use Bio::Matrix::PSM::ProtMatrix; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Matrix/ProtPsm.t ........................... 1..14 ok 1 - use Bio::Matrix::PSM::IO; ok 2 ok 3 ok 4 ok 5 # skip TODO: Module incomplete ok 6 # skip TODO: Module incomplete ok 7 # skip TODO: Module incomplete ok 8 # skip TODO: Module incomplete ok 9 # skip TODO: Module incomplete ok 10 # skip TODO: Module incomplete ok 11 # skip TODO: Module incomplete ok 12 # skip TODO: Module incomplete ok 13 # skip TODO: Module incomplete ok 14 # skip TODO: Module incomplete ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Matrix/SiteMatrix.t ........................ 1..14 ok 1 - use Bio::Matrix::PSM::SiteMatrix; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Ontology/GOterm.t .......................... 1..62 ok 1 - use Bio::Ontology::GOterm; ok 2 - use Bio::Ontology::Ontology; ok 3 - use Bio::Annotation::DBLink; ok 4 - An object of class 'Bio::Ontology::GOterm' isa 'Bio::Ontology::GOterm' ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Ontology/GraphAdaptor.t .................... 1..28 ok 1 - use Bio::Ontology::SimpleGOEngine::GraphAdaptor; ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Ontology/IO/go.t ........................... 1..102 ok 1 - use Bio::OntologyIO; ok 2 ok 3 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::OntologyI' ok 4 ok 5 - An object of class 'Bio::Ontology::OBOEngine' isa 'Bio::Ontology::OntologyEngineI' ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok # Acme::Override::INET replaced IO::Socket::INET with IO::Socket::IP 0.29 t/Ontology/IO/interpro.t ..................... 1..69 ok 1 - use Bio::OntologyIO; ok 2 - An object of class 'Bio::OntologyIO::InterProParser' isa 'Bio::OntologyIO::InterProParser' ok 3 ok 4 - get_dbxrefs on leaf terms is non-empty ok 5 - get_dbxrefs(member_list) on leaf terms is non-empty ok 6 - get_dbxrefs(sec_list) on leaf terms is non-empty ok 7 - get_dbxrefs(class_list) on leaf terms is non-empty ok 8 - get_dbxrefs(pub_list) on leaf terms is non-empty ok 9 - get_dbxrefs(example_list) on leaf terms is non-empty ok 10 - get_dbxrefs(external_doc_list) on leaf terms is non-empty ok 11 - get_members on leaf terms is non-empty ok 12 - class_list on leaf terms is non-empty ok 13 - get_examples on leaf terms is non-empty ok 14 - get_external_documents on leaf terms is non-empty ok 15 - get_references on leaf terms is non-empty ok 16 - protein_count on leaf terms is non-empty ok 17 - to_string looks reasonable ok 18 - There are 8 root InterPro terms ok 19 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 20 - term Kringle in ontology InterPro ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 22 - term Helix-turn-helix, AraC type in ontology InterPro ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 24 - term post-translational modification in ontology InterPro ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 26 - term Active Site in ontology InterPro ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 28 - term Repeat in ontology InterPro ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 30 - term Cdc20/Fizzy in ontology InterPro ok 31 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 32 - term Integrins alpha chain in ontology InterPro ok 33 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 34 - term Conserved Site in ontology InterPro ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 36 - term Binding Site in ontology InterPro ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 38 - term Region in ontology InterPro ok 39 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 40 - term Active Site in ontology InterPro ok 41 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 42 - term Binding Site in ontology InterPro ok 43 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 44 - term Conserved Site in ontology InterPro ok 45 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 46 - term Domain in ontology InterPro ok 47 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 48 - term Family in ontology InterPro ok 49 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 50 - term Region in ontology InterPro ok 51 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 52 - term Repeat in ontology InterPro ok 53 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology' ok 54 - term post-translational modification in ontology InterPro ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 - Kringle term has one parent ok 62 - Kringle term has one ancestor ok 63 - Helix-turn-helix, AraC type term has one parent ok 64 - Helix-turn-helix, AraC type term has one ancestor ok 65 - Cdc20/Fizzy term has one parent ok 66 - Cdc20/Fizzy term has one ancestor ok 67 - Integrins alpha chain term has one parent ok 68 - Integrins alpha chain term has one ancestor ok 69 - secondary accession map has 2 keys ok Timeout (max run time is 300s) C:\Perl-5.18\bin\perl.exe exits with 37.