PATH=/opt/SUNWspro/bin:/usr/local/bin:/opt/csw/bin:/usr/ccs/bin:/usr/bin:/usr/sbin
Start 2013-09-15T02:35:31
ActivePerl-1402 CPAN-2.00
Reading '/export/home/fly1432/var/cpan/Metadata'
  Database was generated on Sun, 15 Sep 2013 08:17:02 GMT
Running make for C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz
Checksum for /net/nas/data/cpan/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz ok
BioPerl-1.6.922
BioPerl-1.6.922/.travis.yml
BioPerl-1.6.922/AUTHORS
BioPerl-1.6.922/BioPerl.pm
BioPerl-1.6.922/BUGS
BioPerl-1.6.922/Build.PL
BioPerl-1.6.922/Changes
BioPerl-1.6.922/DEPENDENCIES
BioPerl-1.6.922/DEPRECATED
BioPerl-1.6.922/INSTALL
BioPerl-1.6.922/INSTALL.SKIP
BioPerl-1.6.922/INSTALL.WIN
BioPerl-1.6.922/LICENSE
BioPerl-1.6.922/MANIFEST
BioPerl-1.6.922/META.json
BioPerl-1.6.922/META.yml
BioPerl-1.6.922/README
BioPerl-1.6.922/README.md
BioPerl-1.6.922/Bio
BioPerl-1.6.922/Bio/AlignIO.pm
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BioPerl-1.6.922/doc/Deobfuscator
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BioPerl-1.6.922/doc/Deobfuscator/lib
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BioPerl-1.6.922/examples
BioPerl-1.6.922/examples/bioperl.pl
BioPerl-1.6.922/examples/generate_random_seq.pl
BioPerl-1.6.922/examples/longorf.pl
BioPerl-1.6.922/examples/make_primers.pl
BioPerl-1.6.922/examples/rev_and_trans.pl
BioPerl-1.6.922/examples/revcom_dir.pl
BioPerl-1.6.922/examples/subsequence.cgi
BioPerl-1.6.922/examples/align
BioPerl-1.6.922/examples/align/align_on_codons.pl
BioPerl-1.6.922/examples/align/aligntutorial.pl
BioPerl-1.6.922/examples/align/clustalw.pl
BioPerl-1.6.922/examples/align/FastAlign.pl
BioPerl-1.6.922/examples/align/simplealign.pl
BioPerl-1.6.922/examples/Bio-DB-GFF
BioPerl-1.6.922/examples/Bio-DB-GFF/load_ucsc.pl
BioPerl-1.6.922/examples/cluster
BioPerl-1.6.922/examples/cluster/dbsnp.pl
BioPerl-1.6.922/examples/contributed
BioPerl-1.6.922/examples/contributed/nmrpdb_parse.pl
BioPerl-1.6.922/examples/contributed/prosite2perl.pl
BioPerl-1.6.922/examples/contributed/rebase2list.pl
BioPerl-1.6.922/examples/db
BioPerl-1.6.922/examples/db/dbfetch
BioPerl-1.6.922/examples/db/est_tissue_query.pl
BioPerl-1.6.922/examples/db/gb2features.pl
BioPerl-1.6.922/examples/db/get_seqs.pl
BioPerl-1.6.922/examples/db/getGenBank.pl
BioPerl-1.6.922/examples/db/rfetch.pl
BioPerl-1.6.922/examples/db/use_registry.pl
BioPerl-1.6.922/examples/liveseq
BioPerl-1.6.922/examples/liveseq/change_gene.pl
BioPerl-1.6.922/examples/popgen
BioPerl-1.6.922/examples/popgen/parse_calc_stats.pl
BioPerl-1.6.922/examples/quality
BioPerl-1.6.922/examples/quality/svgtrace.pl
BioPerl-1.6.922/examples/root
BioPerl-1.6.922/examples/root/exceptions1.pl
BioPerl-1.6.922/examples/root/exceptions2.pl
BioPerl-1.6.922/examples/root/exceptions3.pl
BioPerl-1.6.922/examples/root/exceptions4.pl
BioPerl-1.6.922/examples/root/README
BioPerl-1.6.922/examples/root/lib
BioPerl-1.6.922/examples/root/lib/TestInterface.pm
BioPerl-1.6.922/examples/root/lib/TestObject.pm
BioPerl-1.6.922/examples/searchio
BioPerl-1.6.922/examples/searchio/blast_example.pl
BioPerl-1.6.922/examples/searchio/custom_writer.pl
BioPerl-1.6.922/examples/searchio/hitwriter.pl
BioPerl-1.6.922/examples/searchio/hspwriter.pl
BioPerl-1.6.922/examples/searchio/htmlwriter.pl
BioPerl-1.6.922/examples/searchio/psiblast_features.pl
BioPerl-1.6.922/examples/searchio/psiblast_iterations.pl
BioPerl-1.6.922/examples/searchio/rawwriter.pl
BioPerl-1.6.922/examples/searchio/resultwriter.pl
BioPerl-1.6.922/examples/searchio/waba2gff.pl
BioPerl-1.6.922/examples/searchio/waba2gff3.pl
BioPerl-1.6.922/examples/sirna
BioPerl-1.6.922/examples/sirna/rnai_finder.cgi
BioPerl-1.6.922/examples/sirna/TAG
BioPerl-1.6.922/examples/structure
BioPerl-1.6.922/examples/structure/structure-io.pl
BioPerl-1.6.922/examples/tk
BioPerl-1.6.922/examples/tk/gsequence.pl
BioPerl-1.6.922/examples/tk/hitdisplay.pl
BioPerl-1.6.922/examples/tools
BioPerl-1.6.922/examples/tools/extract_genes.pl
BioPerl-1.6.922/examples/tools/gb_to_gff.pl
BioPerl-1.6.922/examples/tools/gff2ps.pl
BioPerl-1.6.922/examples/tools/parse_codeml.pl
BioPerl-1.6.922/examples/tools/psw.pl
BioPerl-1.6.922/examples/tools/reverse-translate.pl
BioPerl-1.6.922/examples/tools/run_genscan.pl
BioPerl-1.6.922/examples/tools/run_primer3.pl
BioPerl-1.6.922/examples/tools/seq_pattern.pl
BioPerl-1.6.922/examples/tools/standaloneblast.pl
BioPerl-1.6.922/examples/tree
BioPerl-1.6.922/examples/tree/paup2phylip.pl
BioPerl-1.6.922/ide
BioPerl-1.6.922/ide/bioperl.komodo
BioPerl-1.6.922/ide/bioperl-mode
BioPerl-1.6.922/ide/bioperl-mode/README
BioPerl-1.6.922/ide/bioperl-mode/dist
BioPerl-1.6.922/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
BioPerl-1.6.922/ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
BioPerl-1.6.922/ide/bioperl-mode/dist/bioperl-mode.tar
BioPerl-1.6.922/ide/bioperl-mode/dist/bioperl-mode.tar.md5
BioPerl-1.6.922/ide/bioperl-mode/dist/Changes
BioPerl-1.6.922/ide/bioperl-mode/dist/package-me
BioPerl-1.6.922/ide/bioperl-mode/dist/SKIP
BioPerl-1.6.922/ide/bioperl-mode/etc
BioPerl-1.6.922/ide/bioperl-mode/etc/images
BioPerl-1.6.922/ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
BioPerl-1.6.922/ide/bioperl-mode/etc/images/bpmode-tool.xpm
BioPerl-1.6.922/ide/bioperl-mode/site-lisp
BioPerl-1.6.922/ide/bioperl-mode/site-lisp/bioperl-init.el
BioPerl-1.6.922/ide/bioperl-mode/site-lisp/bioperl-mode.el
BioPerl-1.6.922/ide/bioperl-mode/site-lisp/bioperl-skel.el
BioPerl-1.6.922/ide/bioperl-mode/site-lisp/pod.el
BioPerl-1.6.922/maintenance
BioPerl-1.6.922/maintenance/authors.pl
BioPerl-1.6.922/maintenance/check_NAME.pl
BioPerl-1.6.922/maintenance/check_URLs.pl
BioPerl-1.6.922/maintenance/cvs2cl_by_file.pl
BioPerl-1.6.922/maintenance/dependencies.pl
BioPerl-1.6.922/maintenance/deprecated.pl
BioPerl-1.6.922/maintenance/find_mod_deps.pl
BioPerl-1.6.922/maintenance/module_usage.pl
BioPerl-1.6.922/maintenance/modules.pl
BioPerl-1.6.922/maintenance/ncbi_blast_switches.pl
BioPerl-1.6.922/maintenance/perltidy.conf
BioPerl-1.6.922/maintenance/pod.pl
BioPerl-1.6.922/maintenance/README
BioPerl-1.6.922/maintenance/symlink_script.pl
BioPerl-1.6.922/maintenance/version.pl
BioPerl-1.6.922/maintenance/big_split
BioPerl-1.6.922/maintenance/big_split/file_classification.csv
BioPerl-1.6.922/maintenance/big_split/rbuels_notes.txt
BioPerl-1.6.922/models
BioPerl-1.6.922/models/biblio.dia
BioPerl-1.6.922/models/bio_liveseq_variation.dia
BioPerl-1.6.922/models/bio_map.dia
BioPerl-1.6.922/models/bio_restriction.dia
BioPerl-1.6.922/models/bioperl.dia
BioPerl-1.6.922/models/coordinatemapper.dia
BioPerl-1.6.922/models/map_proposal.txt
BioPerl-1.6.922/models/maps_and_markers.dia
BioPerl-1.6.922/models/popgen.dia
BioPerl-1.6.922/models/population_proposal.txt
BioPerl-1.6.922/models/README
BioPerl-1.6.922/scripts
BioPerl-1.6.922/scripts/README
BioPerl-1.6.922/scripts/Bio-DB-GFF
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_fast_load_gff.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_genbank2gff.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_genbank2gff3.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_generate_histogram.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_load_gff.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_meta_gff.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_process_gadfly.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_process_sgd.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/bp_process_wormbase.pl
BioPerl-1.6.922/scripts/Bio-DB-GFF/README
BioPerl-1.6.922/scripts/Bio-DB-SeqFeature-Store
BioPerl-1.6.922/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
BioPerl-1.6.922/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
BioPerl-1.6.922/scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
BioPerl-1.6.922/scripts/das
BioPerl-1.6.922/scripts/das/bp_das_server.pl
BioPerl-1.6.922/scripts/das/README
BioPerl-1.6.922/scripts/das/TAG
BioPerl-1.6.922/scripts/DB
BioPerl-1.6.922/scripts/DB/bp_biofetch_genbank_proxy.pl
BioPerl-1.6.922/scripts/DB/bp_bioflat_index.pl
BioPerl-1.6.922/scripts/DB/bp_biogetseq.pl
BioPerl-1.6.922/scripts/DB/bp_flanks.pl
BioPerl-1.6.922/scripts/DB/TAG
BioPerl-1.6.922/scripts/DB-HIV
BioPerl-1.6.922/scripts/DB-HIV/bp_hivq.pl
BioPerl-1.6.922/scripts/index
BioPerl-1.6.922/scripts/index/bp_fetch.pl
BioPerl-1.6.922/scripts/index/bp_index.pl
BioPerl-1.6.922/scripts/index/bp_seqret.pl
BioPerl-1.6.922/scripts/index/TAG
BioPerl-1.6.922/scripts/popgen
BioPerl-1.6.922/scripts/popgen/bp_composite_LD.pl
BioPerl-1.6.922/scripts/popgen/bp_heterogeneity_test.pl
BioPerl-1.6.922/scripts/searchio
BioPerl-1.6.922/scripts/searchio/bp_fastam9_to_table.pl
BioPerl-1.6.922/scripts/searchio/bp_filter_search.pl
BioPerl-1.6.922/scripts/searchio/bp_hmmer_to_table.pl
BioPerl-1.6.922/scripts/searchio/bp_parse_hmmsearch.pl
BioPerl-1.6.922/scripts/searchio/bp_search2table.pl
BioPerl-1.6.922/scripts/searchio/README
BioPerl-1.6.922/scripts/searchio/TAG
BioPerl-1.6.922/scripts/seq
BioPerl-1.6.922/scripts/seq/bp_extract_feature_seq.pl
BioPerl-1.6.922/scripts/seq/bp_make_mrna_protein.pl
BioPerl-1.6.922/scripts/seq/bp_seqconvert.pl
BioPerl-1.6.922/scripts/seq/bp_seqcut.pl
BioPerl-1.6.922/scripts/seq/bp_seqpart.pl
BioPerl-1.6.922/scripts/seq/bp_seqretsplit.pl
BioPerl-1.6.922/scripts/seq/bp_split_seq.pl
BioPerl-1.6.922/scripts/seq/bp_translate_seq.pl
BioPerl-1.6.922/scripts/seq/bp_unflatten_seq.pl
BioPerl-1.6.922/scripts/seq/TAG
BioPerl-1.6.922/scripts/seqstats
BioPerl-1.6.922/scripts/seqstats/bp_aacomp.pl
BioPerl-1.6.922/scripts/seqstats/bp_chaos_plot.pl
BioPerl-1.6.922/scripts/seqstats/bp_gccalc.pl
BioPerl-1.6.922/scripts/seqstats/bp_oligo_count.pl
BioPerl-1.6.922/scripts/seqstats/TAG
BioPerl-1.6.922/scripts/taxa
BioPerl-1.6.922/scripts/taxa/bp_classify_hits_kingdom.pl
BioPerl-1.6.922/scripts/taxa/bp_local_taxonomydb_query.pl
BioPerl-1.6.922/scripts/taxa/bp_query_entrez_taxa.pl
BioPerl-1.6.922/scripts/taxa/bp_taxid4species.pl
BioPerl-1.6.922/scripts/taxa/bp_taxonomy2tree.pl
BioPerl-1.6.922/scripts/taxa/TAG
BioPerl-1.6.922/scripts/tree
BioPerl-1.6.922/scripts/tree/bp_blast2tree.pl
BioPerl-1.6.922/scripts/tree/bp_nexus2nh.pl
BioPerl-1.6.922/scripts/tree/bp_tree2pag.pl
BioPerl-1.6.922/scripts/tree/TAG
BioPerl-1.6.922/scripts/utilities
BioPerl-1.6.922/scripts/utilities/bp_dbsplit.pl
BioPerl-1.6.922/scripts/utilities/bp_download_query_genbank.pl
BioPerl-1.6.922/scripts/utilities/bp_mask_by_search.pl
BioPerl-1.6.922/scripts/utilities/bp_mrtrans.pl
BioPerl-1.6.922/scripts/utilities/bp_mutate.pl
BioPerl-1.6.922/scripts/utilities/bp_netinstall.pl
BioPerl-1.6.922/scripts/utilities/bp_nrdb.pl
BioPerl-1.6.922/scripts/utilities/bp_pairwise_kaks.pl
BioPerl-1.6.922/scripts/utilities/bp_remote_blast.pl
BioPerl-1.6.922/scripts/utilities/bp_revtrans-motif.pl
BioPerl-1.6.922/scripts/utilities/bp_search2alnblocks.pl
BioPerl-1.6.922/scripts/utilities/bp_search2BSML.pl
BioPerl-1.6.922/scripts/utilities/bp_search2gff.pl
BioPerl-1.6.922/scripts/utilities/bp_search2tribe.pl
BioPerl-1.6.922/scripts/utilities/bp_seq_length.pl
BioPerl-1.6.922/scripts/utilities/bp_sreformat.pl
BioPerl-1.6.922/scripts/utilities/README
BioPerl-1.6.922/scripts/utilities/TAG
BioPerl-1.6.922/t
BioPerl-1.6.922/t/Alphabet.t
BioPerl-1.6.922/t/nexml.t
BioPerl-1.6.922/t/Perl.t
BioPerl-1.6.922/t/PodSyntax.t
BioPerl-1.6.922/t/SearchDist.t
BioPerl-1.6.922/t/SeqEvolution.t
BioPerl-1.6.922/t/Species.t
BioPerl-1.6.922/t/Symbol.t
BioPerl-1.6.922/t/TaxonTree.t
BioPerl-1.6.922/t/Align
BioPerl-1.6.922/t/Align/AlignStats.t
BioPerl-1.6.922/t/Align/AlignUtil.t
BioPerl-1.6.922/t/Align/Graphics.t
BioPerl-1.6.922/t/Align/SimpleAlign.t
BioPerl-1.6.922/t/Align/TreeBuild.t
BioPerl-1.6.922/t/Align/Utilities.t
BioPerl-1.6.922/t/AlignIO
BioPerl-1.6.922/t/AlignIO/AlignIO.t
BioPerl-1.6.922/t/AlignIO/arp.t
BioPerl-1.6.922/t/AlignIO/bl2seq.t
BioPerl-1.6.922/t/AlignIO/clustalw.t
BioPerl-1.6.922/t/AlignIO/emboss.t
BioPerl-1.6.922/t/AlignIO/fasta.t
BioPerl-1.6.922/t/AlignIO/largemultifasta.t
BioPerl-1.6.922/t/AlignIO/maf.t
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BioPerl-1.6.922/t/AlignIO/mega.t
BioPerl-1.6.922/t/AlignIO/meme.t
BioPerl-1.6.922/t/AlignIO/metafasta.t
BioPerl-1.6.922/t/AlignIO/msf.t
BioPerl-1.6.922/t/AlignIO/nexml.t
BioPerl-1.6.922/t/AlignIO/nexus.t
BioPerl-1.6.922/t/AlignIO/pfam.t
BioPerl-1.6.922/t/AlignIO/phylip.t
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BioPerl-1.6.922/t/AlignIO/prodom.t
BioPerl-1.6.922/t/AlignIO/psi.t
BioPerl-1.6.922/t/AlignIO/selex.t
BioPerl-1.6.922/t/AlignIO/stockholm.t
BioPerl-1.6.922/t/AlignIO/xmfa.t
BioPerl-1.6.922/t/Annotation
BioPerl-1.6.922/t/Annotation/Annotation.t
BioPerl-1.6.922/t/Annotation/AnnotationAdaptor.t
BioPerl-1.6.922/t/Assembly
BioPerl-1.6.922/t/Assembly/ContigSpectrum.t
BioPerl-1.6.922/t/Assembly/core.t
BioPerl-1.6.922/t/Assembly/IO
BioPerl-1.6.922/t/Assembly/IO/bowtie.t
BioPerl-1.6.922/t/Assembly/IO/sam.t
BioPerl-1.6.922/t/Cluster
BioPerl-1.6.922/t/Cluster/UniGene.t
BioPerl-1.6.922/t/ClusterIO
BioPerl-1.6.922/t/ClusterIO/ClusterIO.t
BioPerl-1.6.922/t/ClusterIO/SequenceFamily.t
BioPerl-1.6.922/t/ClusterIO/unigene.t
BioPerl-1.6.922/t/Coordinate
BioPerl-1.6.922/t/Coordinate/CoordinateBoundaryTest.t
BioPerl-1.6.922/t/Coordinate/CoordinateGraph.t
BioPerl-1.6.922/t/Coordinate/CoordinateMapper.t
BioPerl-1.6.922/t/Coordinate/GeneCoordinateMapper.t
BioPerl-1.6.922/t/data
BioPerl-1.6.922/t/data/01_basic.xml
BioPerl-1.6.922/t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml
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BioPerl-1.6.922/t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml
BioPerl-1.6.922/t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml
BioPerl-1.6.922/t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml
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BioPerl-1.6.922/t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml
BioPerl-1.6.922/t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml
BioPerl-1.6.922/t/data/03_bootstraps.xml
BioPerl-1.6.922/t/data/03_bootstraps_in_tag.xml
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BioPerl-1.6.922/t/data/1BPT.pdb
BioPerl-1.6.922/t/data/1ZZ19XR301R-Alignment.tblastn
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BioPerl-1.6.922/t/data/27-contig_Newbler.ace
BioPerl-1.6.922/t/data/503384.MEGABLAST.0
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BioPerl-1.6.922/t/data/5X_1895.FASTXY
BioPerl-1.6.922/t/data/8HVP.pdb
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BioPerl-1.6.922/t/data/catalase-webblast.BLASTP
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BioPerl-1.6.922/t/data/cysprot1b.fa
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BioPerl-1.6.922/t/data/cysprot1b.msf
BioPerl-1.6.922/t/data/cysprot1b.newick
BioPerl-1.6.922/t/data/cysprot_vs_gadfly.FASTA
BioPerl-1.6.922/t/data/D10483.gbk
BioPerl-1.6.922/t/data/D12555.gbk
BioPerl-1.6.922/t/data/dcr1_sp.WUBLASTP
BioPerl-1.6.922/t/data/dmel_2Lchunk.gb
BioPerl-1.6.922/t/data/dna1.fa
BioPerl-1.6.922/t/data/dna2.fa
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BioPerl-1.6.922/t/data/dnaEbsub_ecoli.wublastx
BioPerl-1.6.922/t/data/dnaEbsub_ecoli.wutblastn
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BioPerl-1.6.922/t/Ontology/IO/obo.t
BioPerl-1.6.922/t/Phenotype
BioPerl-1.6.922/t/Phenotype/Correlate.t
BioPerl-1.6.922/t/Phenotype/Measure.t
BioPerl-1.6.922/t/Phenotype/MeSH.t
BioPerl-1.6.922/t/Phenotype/MiniMIMentry.t
BioPerl-1.6.922/t/Phenotype/OMIMentry.t
BioPerl-1.6.922/t/Phenotype/OMIMentryAllelicVariant.t
BioPerl-1.6.922/t/Phenotype/OMIMparser.t
BioPerl-1.6.922/t/Phenotype/Phenotype.t
BioPerl-1.6.922/t/PopGen
BioPerl-1.6.922/t/PopGen/Coalescent.t
BioPerl-1.6.922/t/PopGen/HtSNP.t
BioPerl-1.6.922/t/PopGen/MK.t
BioPerl-1.6.922/t/PopGen/PopGen.t
BioPerl-1.6.922/t/PopGen/PopGenSims.t
BioPerl-1.6.922/t/PopGen/TagHaplotype.t
BioPerl-1.6.922/t/RemoteDB
BioPerl-1.6.922/t/RemoteDB/BioFetch.t
BioPerl-1.6.922/t/RemoteDB/CUTG.t
BioPerl-1.6.922/t/RemoteDB/EMBL.t
BioPerl-1.6.922/t/RemoteDB/EntrezGene.t
BioPerl-1.6.922/t/RemoteDB/GenBank.t
BioPerl-1.6.922/t/RemoteDB/GenPept.t
BioPerl-1.6.922/t/RemoteDB/MeSH.t
BioPerl-1.6.922/t/RemoteDB/RefSeq.t
BioPerl-1.6.922/t/RemoteDB/SeqHound.t
BioPerl-1.6.922/t/RemoteDB/SeqRead_fail.t
BioPerl-1.6.922/t/RemoteDB/SeqVersion.t
BioPerl-1.6.922/t/RemoteDB/SwissProt.t
BioPerl-1.6.922/t/RemoteDB/Taxonomy.t
BioPerl-1.6.922/t/RemoteDB/HIV
BioPerl-1.6.922/t/RemoteDB/HIV/HIV.t
BioPerl-1.6.922/t/RemoteDB/HIV/HIVAnnotProcessor.t
BioPerl-1.6.922/t/RemoteDB/HIV/HIVQuery.t
BioPerl-1.6.922/t/RemoteDB/HIV/HIVQueryHelper.t
BioPerl-1.6.922/t/RemoteDB/Query
BioPerl-1.6.922/t/RemoteDB/Query/GenBank.t
BioPerl-1.6.922/t/Restriction
BioPerl-1.6.922/t/Restriction/Analysis-refac.t
BioPerl-1.6.922/t/Restriction/Analysis.t
BioPerl-1.6.922/t/Restriction/Gel.t
BioPerl-1.6.922/t/Restriction/IO.t
BioPerl-1.6.922/t/Root
BioPerl-1.6.922/t/Root/Exception.t
BioPerl-1.6.922/t/Root/HTTPget.t
BioPerl-1.6.922/t/Root/RootI.t
BioPerl-1.6.922/t/Root/RootIO.t
BioPerl-1.6.922/t/Root/Storable.t
BioPerl-1.6.922/t/Root/Tempfile.t
BioPerl-1.6.922/t/Root/Utilities.t
BioPerl-1.6.922/t/SearchIO
BioPerl-1.6.922/t/SearchIO/axt.t
BioPerl-1.6.922/t/SearchIO/blast.t
BioPerl-1.6.922/t/SearchIO/blast_pull.t
BioPerl-1.6.922/t/SearchIO/blasttable.t
BioPerl-1.6.922/t/SearchIO/blastxml.t
BioPerl-1.6.922/t/SearchIO/CigarString.t
BioPerl-1.6.922/t/SearchIO/cross_match.t
BioPerl-1.6.922/t/SearchIO/erpin.t
BioPerl-1.6.922/t/SearchIO/exonerate.t
BioPerl-1.6.922/t/SearchIO/fasta.t
BioPerl-1.6.922/t/SearchIO/gmap_f9.t
BioPerl-1.6.922/t/SearchIO/hmmer.t
BioPerl-1.6.922/t/SearchIO/hmmer_pull.t
BioPerl-1.6.922/t/SearchIO/infernal.t
BioPerl-1.6.922/t/SearchIO/megablast.t
BioPerl-1.6.922/t/SearchIO/psl.t
BioPerl-1.6.922/t/SearchIO/rnamotif.t
BioPerl-1.6.922/t/SearchIO/SearchIO.t
BioPerl-1.6.922/t/SearchIO/sim4.t
BioPerl-1.6.922/t/SearchIO/SimilarityPair.t
BioPerl-1.6.922/t/SearchIO/Tiling.t
BioPerl-1.6.922/t/SearchIO/waba.t
BioPerl-1.6.922/t/SearchIO/wise.t
BioPerl-1.6.922/t/SearchIO/Writer
BioPerl-1.6.922/t/SearchIO/Writer/GbrowseGFF.t
BioPerl-1.6.922/t/SearchIO/Writer/HitTableWriter.t
BioPerl-1.6.922/t/SearchIO/Writer/HSPTableWriter.t
BioPerl-1.6.922/t/SearchIO/Writer/HTMLWriter.t
BioPerl-1.6.922/t/SearchIO/Writer/TextWriter.t
BioPerl-1.6.922/t/Seq
BioPerl-1.6.922/t/Seq/DBLink.t
BioPerl-1.6.922/t/Seq/EncodedSeq.t
BioPerl-1.6.922/t/Seq/LargeLocatableSeq.t
BioPerl-1.6.922/t/Seq/LargePSeq.t
BioPerl-1.6.922/t/Seq/LocatableSeq.t
BioPerl-1.6.922/t/Seq/MetaSeq.t
BioPerl-1.6.922/t/Seq/PrimaryQual.t
BioPerl-1.6.922/t/Seq/PrimarySeq.t
BioPerl-1.6.922/t/Seq/PrimedSeq.t
BioPerl-1.6.922/t/Seq/Quality.t
BioPerl-1.6.922/t/Seq/Seq.t
BioPerl-1.6.922/t/Seq/SimulatedRead.t
BioPerl-1.6.922/t/Seq/WithQuality.t
BioPerl-1.6.922/t/SeqFeature
BioPerl-1.6.922/t/SeqFeature/Amplicon.t
BioPerl-1.6.922/t/SeqFeature/Clone.t
BioPerl-1.6.922/t/SeqFeature/Collection.t
BioPerl-1.6.922/t/SeqFeature/Computation.t
BioPerl-1.6.922/t/SeqFeature/FeaturePair.t
BioPerl-1.6.922/t/SeqFeature/Gene.t
BioPerl-1.6.922/t/SeqFeature/Generic.t
BioPerl-1.6.922/t/SeqFeature/Location.t
BioPerl-1.6.922/t/SeqFeature/LocationFactory.t
BioPerl-1.6.922/t/SeqFeature/Primer.t
BioPerl-1.6.922/t/SeqFeature/Range.t
BioPerl-1.6.922/t/SeqFeature/RangeI.t
BioPerl-1.6.922/t/SeqFeature/SeqAnalysisParser.t
BioPerl-1.6.922/t/SeqFeature/SubSeq.t
BioPerl-1.6.922/t/SeqFeature/Unflattener.t
BioPerl-1.6.922/t/SeqFeature/Unflattener2.t
BioPerl-1.6.922/t/SeqIO
BioPerl-1.6.922/t/SeqIO/abi.t
BioPerl-1.6.922/t/SeqIO/ace.t
BioPerl-1.6.922/t/SeqIO/agave.t
BioPerl-1.6.922/t/SeqIO/alf.t
BioPerl-1.6.922/t/SeqIO/asciitree.t
BioPerl-1.6.922/t/SeqIO/bsml.t
BioPerl-1.6.922/t/SeqIO/bsml_sax.t
BioPerl-1.6.922/t/SeqIO/chadoxml.t
BioPerl-1.6.922/t/SeqIO/chaos.t
BioPerl-1.6.922/t/SeqIO/chaosxml.t
BioPerl-1.6.922/t/SeqIO/ctf.t
BioPerl-1.6.922/t/SeqIO/embl.t
BioPerl-1.6.922/t/SeqIO/entrezgene.t
BioPerl-1.6.922/t/SeqIO/excel.t
BioPerl-1.6.922/t/SeqIO/exp.t
BioPerl-1.6.922/t/SeqIO/fasta.t
BioPerl-1.6.922/t/SeqIO/fastq.t
BioPerl-1.6.922/t/SeqIO/flybase_chadoxml.t
BioPerl-1.6.922/t/SeqIO/game.t
BioPerl-1.6.922/t/SeqIO/gbxml.t
BioPerl-1.6.922/t/SeqIO/gcg.t
BioPerl-1.6.922/t/SeqIO/genbank.t
BioPerl-1.6.922/t/SeqIO/Handler.t
BioPerl-1.6.922/t/SeqIO/interpro.t
BioPerl-1.6.922/t/SeqIO/kegg.t
BioPerl-1.6.922/t/SeqIO/largefasta.t
BioPerl-1.6.922/t/SeqIO/lasergene.t
BioPerl-1.6.922/t/SeqIO/locuslink.t
BioPerl-1.6.922/t/SeqIO/mbsout.t
BioPerl-1.6.922/t/SeqIO/metafasta.t
BioPerl-1.6.922/t/SeqIO/msout.t
BioPerl-1.6.922/t/SeqIO/MultiFile.t
BioPerl-1.6.922/t/SeqIO/Multiple_fasta.t
BioPerl-1.6.922/t/SeqIO/nexml.t
BioPerl-1.6.922/t/SeqIO/phd.t
BioPerl-1.6.922/t/SeqIO/pir.t
BioPerl-1.6.922/t/SeqIO/pln.t
BioPerl-1.6.922/t/SeqIO/qual.t
BioPerl-1.6.922/t/SeqIO/raw.t
BioPerl-1.6.922/t/SeqIO/scf.t
BioPerl-1.6.922/t/SeqIO/SeqBuilder.t
BioPerl-1.6.922/t/SeqIO/SeqIO.t
BioPerl-1.6.922/t/SeqIO/seqxml.t
BioPerl-1.6.922/t/SeqIO/Splicedseq.t
BioPerl-1.6.922/t/SeqIO/strider.t
BioPerl-1.6.922/t/SeqIO/swiss.t
BioPerl-1.6.922/t/SeqIO/tab.t
BioPerl-1.6.922/t/SeqIO/table.t
BioPerl-1.6.922/t/SeqIO/tigr.t
BioPerl-1.6.922/t/SeqIO/tigrxml.t
BioPerl-1.6.922/t/SeqIO/tinyseq.t
BioPerl-1.6.922/t/SeqIO/ztr.t
BioPerl-1.6.922/t/SeqTools
BioPerl-1.6.922/t/SeqTools/Backtranslate.t
BioPerl-1.6.922/t/SeqTools/CodonTable.t
BioPerl-1.6.922/t/SeqTools/ECnumber.t
BioPerl-1.6.922/t/SeqTools/GuessSeqFormat.t
BioPerl-1.6.922/t/SeqTools/OddCodes.t
BioPerl-1.6.922/t/SeqTools/SeqPattern.t
BioPerl-1.6.922/t/SeqTools/SeqStats.t
BioPerl-1.6.922/t/SeqTools/SeqUtils.t
BioPerl-1.6.922/t/SeqTools/SeqWords.t
BioPerl-1.6.922/t/Structure
BioPerl-1.6.922/t/Structure/IO.t
BioPerl-1.6.922/t/Structure/Structure.t
BioPerl-1.6.922/t/Tools
BioPerl-1.6.922/t/Tools/AmpliconSearch.t
BioPerl-1.6.922/t/Tools/ePCR.t
BioPerl-1.6.922/t/Tools/Est2Genome.t
BioPerl-1.6.922/t/Tools/FootPrinter.t
BioPerl-1.6.922/t/Tools/Geneid.t
BioPerl-1.6.922/t/Tools/Genewise.t
BioPerl-1.6.922/t/Tools/Genomewise.t
BioPerl-1.6.922/t/Tools/Genpred.t
BioPerl-1.6.922/t/Tools/GFF.t
BioPerl-1.6.922/t/Tools/GuessSeqFormat.t
BioPerl-1.6.922/t/Tools/Hmmer.t
BioPerl-1.6.922/t/Tools/IUPAC.t
BioPerl-1.6.922/t/Tools/Lucy.t
BioPerl-1.6.922/t/Tools/Match.t
BioPerl-1.6.922/t/Tools/pICalculator.t
BioPerl-1.6.922/t/Tools/Primer3.t
BioPerl-1.6.922/t/Tools/Promoterwise.t
BioPerl-1.6.922/t/Tools/Pseudowise.t
BioPerl-1.6.922/t/Tools/QRNA.t
BioPerl-1.6.922/t/Tools/RandDistFunctions.t
BioPerl-1.6.922/t/Tools/RepeatMasker.t
BioPerl-1.6.922/t/Tools/rnamotif.t
BioPerl-1.6.922/t/Tools/Seg.t
BioPerl-1.6.922/t/Tools/Sigcleave.t
BioPerl-1.6.922/t/Tools/Signalp.t
BioPerl-1.6.922/t/Tools/Sim4.t
BioPerl-1.6.922/t/Tools/SiRNA.t
BioPerl-1.6.922/t/Tools/TandemRepeatsFinder.t
BioPerl-1.6.922/t/Tools/TargetP.t
BioPerl-1.6.922/t/Tools/Tmhmm.t
BioPerl-1.6.922/t/Tools/tRNAscanSE.t
BioPerl-1.6.922/t/Tools/Alignment
BioPerl-1.6.922/t/Tools/Alignment/Consed.t
BioPerl-1.6.922/t/Tools/Analysis
BioPerl-1.6.922/t/Tools/Analysis/DNA
BioPerl-1.6.922/t/Tools/Analysis/DNA/ESEfinder.t
BioPerl-1.6.922/t/Tools/Analysis/Protein
BioPerl-1.6.922/t/Tools/Analysis/Protein/Domcut.t
BioPerl-1.6.922/t/Tools/Analysis/Protein/ELM.t
BioPerl-1.6.922/t/Tools/Analysis/Protein/GOR4.t
BioPerl-1.6.922/t/Tools/Analysis/Protein/HNN.t
BioPerl-1.6.922/t/Tools/Analysis/Protein/Mitoprot.t
BioPerl-1.6.922/t/Tools/Analysis/Protein/NetPhos.t
BioPerl-1.6.922/t/Tools/Analysis/Protein/Scansite.t
BioPerl-1.6.922/t/Tools/Analysis/Protein/Sopma.t
BioPerl-1.6.922/t/Tools/EMBOSS
BioPerl-1.6.922/t/Tools/EMBOSS/Palindrome.t
BioPerl-1.6.922/t/Tools/Phylo
BioPerl-1.6.922/t/Tools/Phylo/Gerp.t
BioPerl-1.6.922/t/Tools/Phylo/Molphy.t
BioPerl-1.6.922/t/Tools/Phylo/PAML.t
BioPerl-1.6.922/t/Tools/Phylo/Phylip
BioPerl-1.6.922/t/Tools/Phylo/Phylip/ProtDist.t
BioPerl-1.6.922/t/Tools/Run
BioPerl-1.6.922/t/Tools/Run/Dummy.pm
BioPerl-1.6.922/t/Tools/Run/RemoteBlast.t
BioPerl-1.6.922/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-1.6.922/t/Tools/Run/StandAloneBlast.t
BioPerl-1.6.922/t/Tools/Run/WBCommandExts.t
BioPerl-1.6.922/t/Tools/Run/WrapperBase.t
BioPerl-1.6.922/t/Tools/Run/Dummy
BioPerl-1.6.922/t/Tools/Run/Dummy/Config.pm
BioPerl-1.6.922/t/Tools/Signalp
BioPerl-1.6.922/t/Tools/Signalp/ExtendedSignalp.t
BioPerl-1.6.922/t/Tools/Spidey
BioPerl-1.6.922/t/Tools/Spidey/Spidey.t
BioPerl-1.6.922/t/Tree
BioPerl-1.6.922/t/Tree/Compatible.t
BioPerl-1.6.922/t/Tree/Node.t
BioPerl-1.6.922/t/Tree/RandomTreeFactory.t
BioPerl-1.6.922/t/Tree/Tree.t
BioPerl-1.6.922/t/Tree/TreeIO.t
BioPerl-1.6.922/t/Tree/TreeStatistics.t
BioPerl-1.6.922/t/Tree/PhyloNetwork
BioPerl-1.6.922/t/Tree/PhyloNetwork/Factory.t
BioPerl-1.6.922/t/Tree/PhyloNetwork/GraphViz.t
BioPerl-1.6.922/t/Tree/PhyloNetwork/MuVector.t
BioPerl-1.6.922/t/Tree/PhyloNetwork/PhyloNetwork.t
BioPerl-1.6.922/t/Tree/PhyloNetwork/RandomFactory.t
BioPerl-1.6.922/t/Tree/PhyloNetwork/TreeFactory.t
BioPerl-1.6.922/t/Tree/TreeIO
BioPerl-1.6.922/t/Tree/TreeIO/lintree.t
BioPerl-1.6.922/t/Tree/TreeIO/newick.t
BioPerl-1.6.922/t/Tree/TreeIO/nexml.t
BioPerl-1.6.922/t/Tree/TreeIO/nexus.t
BioPerl-1.6.922/t/Tree/TreeIO/nhx.t
BioPerl-1.6.922/t/Tree/TreeIO/phyloxml.t
BioPerl-1.6.922/t/Tree/TreeIO/svggraph.t
BioPerl-1.6.922/t/Tree/TreeIO/tabtree.t
BioPerl-1.6.922/t/Variation
BioPerl-1.6.922/t/Variation/AAChange.t
BioPerl-1.6.922/t/Variation/AAReverseMutate.t
BioPerl-1.6.922/t/Variation/Allele.t
BioPerl-1.6.922/t/Variation/DNAMutation.t
BioPerl-1.6.922/t/Variation/RNAChange.t
BioPerl-1.6.922/t/Variation/SeqDiff.t
BioPerl-1.6.922/t/Variation/SNP.t
BioPerl-1.6.922/t/Variation/Variation_IO.t
BioPerl-1.6.922/travis_scripts
BioPerl-1.6.922/travis_scripts/dependency_installs

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz

>>> /export/home/fly1432/bin/perl Build.PL
could not find ParserDetails.ini in /export/home/fly1432/var/megalib/XML/SAX
Checking prerequisites...
  requires:
    !  DB_File is not installed
  recommends:
    *  GraphViz 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

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 #############################

Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n]   - will not run the BioDBGFF or BioDBSeqFeature live database tests

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 '1.006922'
---- Unsatisfied dependencies detected during ----
----      CJFIELDS/BioPerl-1.6.922.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-1.829.tar.gz
Disabled via prefs file '/export/home/fly1432/etc/distroprefs/DB_File.yml' doc 0
  PMQS/DB_File-1.829.tar.gz
  [disabled] -- NA Disabled via prefs file '/export/home/fly1432/etc/distroprefs/DB_File.yml' doc 0
Running Build for C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz
  Has already been unwrapped into directory /export/home/fly1432/var/cpan/build/BioPerl-1.6.922-5Zg8Xe

  CPAN.pm: Building C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz

Warning: Prerequisite 'DB_File => 0' for 'CJFIELDS/BioPerl-1.6.922.tar.gz' failed when processing 'PMQS/DB_File-1.829.tar.gz' with 'unwrapped => NO Disabled via prefs file '/export/home/fly1432/etc/distroprefs/DB_File.yml' doc 0'. Continuing, but chances to succeed are limited.
>>> ./Build
Building BioPerl
  CJFIELDS/BioPerl-1.6.922.tar.gz
  ./Build -- OK
Running Build test
>>> ./Build test verbose=1
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 - The object 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 - The object 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 - The object isa Bio::Align::AlignI
ok 32
ok 33
ok 34
ok 35
ok 36
ok 37 - The object isa Bio::Align::AlignI
ok 38 - The object isa Bio::Matrix::PhylipDist
ok 39
ok 40
ok 41
ok 42 - The object isa Bio::PrimarySeqI
ok 43
ok 44 - Warn if seqs don't overlap
ok 45
ok
t/Align/AlignUtil.t .................... 
1..47
ok 1 - use Bio::Align::Utilities;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::SeqIO;
ok 4 - The object 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 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
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 - The object 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 - The object 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
t/Align/SimpleAlign.t .................. 
1..206
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 - The object isa Bio::AlignIO
ok 7 - pfam input test
ok 8 - match_line
ok 9 - The object 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 - select_noncont_by_name
ok 18 - select_noncont_by_name
ok 19 - select_noncont_by_name
ok 20 - select_noncont_by_name
ok 21 - each_seq
ok 22 - get_nse
ok 23 - id
ok 24 - num_gaps
ok 25 - each_alphabetically
ok 26 - column_from_residue_number
ok 27 - display_name get/set
ok 28 - display_name get
ok 29 - consensus_string
ok 30 - consensus_string
ok 31 - consensus_string
ok 32
ok 33 - each_seq_with_id
ok 34 - is_flush
ok 35 - id get/set
ok 36 - length
ok 37 - num_residues
ok 38 - num_sequences
ok 39 - overall_percentage_identity
ok 40 - overall_percentage_identity (align)
ok 41 - overall_percentage_identity (short)
ok 42 - overall_percentage_identity (long)
ok 43 - average_percentage_identity
ok 44
ok 45 - set_displayname_count
ok 46
ok 47 - set_displayname_flat
ok 48
ok 49 - set_displayname_normal
ok 50
ok 51
ok 52 - uppercase, map_chars
ok 53 - match_line
ok 54 - remove_seqs
ok 55 - remove_seqs
ok 56 - add_seq
ok 57 - add_seq
ok 58 - get_seq_by_pos
ok 59 - get_seq_by_pos
ok 60
ok 61
ok 62
ok 63 - purge
ok 64 - purge
ok 65 - IO::String consensus_iupac
ok 66 - IO::String write_aln normal
ok 67 - IO::String write_aln slice
ok 68 - IO::String write_aln slice
ok 69 - IO::String write_aln slice
ok 70 - IO::String write_aln slice
ok 71 - IO::String write_aln slice
ok 72
ok 73 - remove_columns by position
ok 74 - remove_columns by position (wrong order)
ok 75 - cigar_line
ok 76 - cigar_line
ok 77 - cigar_line
ok 78 - cigar_line
ok 79 - sort_alphabetically - before
ok 80
ok 81 - sort_alphabetically - after
ok 82 - remove_gaps
ok 83 - remove_gaps all_gaps_only
ok 84 - set_new_reference
ok 85 - set_new_reference
ok 86 - uniq_seq
ok 87 - bug 2099
ok 88 - bug 2099
ok 89 - bug 2793
ok 90 - bug 2793
ok 91 - bug 2793
ok 92 - bug 2793
ok 93 - Bad sequence, bad!
ok 94 - The object isa Bio::AnnotatableI
ok 95 - added 3 seqs
ok 96 - first 2 features added
ok 97 - 3rd feature added
not ok 98 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# 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:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 99 - slice 1 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 432.
# 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:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 104 - slice 2 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 432.
# 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:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 109 - slice 3 len
ok 110 - correct masked seq
ok 111 - correct masked seq
ok 112 - correct masked seq
not ok 113 # TODO This should pass but dies; see bug 2842

#   Failed (TODO) test at t/Align/SimpleAlign.t line 432.
# 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:486
# STACK: Bio::Root::RootI::warn Bio/Root/RootI.pm:180
# STACK: Bio::LocatableSeq::end Bio/LocatableSeq.pm:201
# STACK: Bio::SimpleAlign::slice Bio/SimpleAlign.pm:1167
# STACK: Test::Exception::lives_ok t/Align/SimpleAlign.t:432
# STACK: t/Align/SimpleAlign.t:432
# -----------------------------------------------------------
# )
ok 114 - slice 4 len
ok 115 - correct masked seq
ok 116 - correct masked seq
ok 117 - correct masked seq
ok 118 - initial display id ok
ok 119 - safe display id ok
ok 120 - restored display id ok
ok 121 - sort by list ok
ok 122
ok 123
ok 124
ok 125
ok 126
ok 127
ok 128 - BIC:GGATCCATT[C/C]CTACT
ok 129 - BIC:GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
ok 130 - BIC:G[G/C]ATCCATT[C/G]CTACT
ok 131 - BIC:GGATCCATT[C/G]CTACT
ok 132 - BIC:GGATCCATT[C/G]CTAC[T/A]
ok 133 - BIC:GGATCCATT[C/G]CTA[C/G][T/A]
ok 134 - BIC:GGATCCATT[C/G]CTACT
ok 135 - BIC:GGATCCATT{C.C}CTACT
ok 136 - BIC:GGAT{C.-}{C.-}ATT{C.C}CT{A.C}CT
ok 137 - BIC:G{G.C}ATCCATT{C.G}CTACT
ok 138 - BIC:GGATCCATT{C.G}CTACT
ok 139 - BIC:GGATCCATT{C.G}CTAC{T.A}
ok 140 - BIC:GGATCCATT{C.G}CTA{C.G}{T.A}
ok 141 - BIC:GGATCCATT{C.G}CTACT
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
ok 195
ok 196
ok 197
ok 198
ok 199 - The object isa Bio::SimpleAlign
ok 200 - consensus string looks ok
ok 201 - conservation length
ok 202 - conservation scores
ok 203 - looks like correct unmasked alignment (from clustalw)
ok 204 - looks like correct masked alignment (from clustalw)
ok 205
ok 206 - align after looks ok
ok

Timeout (max run time is 300s)
/export/home/fly1432/bin/perl killed by signal 15