[Bioperl-guts-l] [bioperl/bioperl-live] 8ab208: Removed Bio::Root

noreply at github.com noreply at github.com
Mon Aug 8 19:42:03 EDT 2011 

  Branch: refs/heads/reorganization_2.x
  Home:   https://github.com/bioperl/bioperl-live

  Commit: 8ab208f6b8507b3c7d54ebcbf9102d541c41d8b9
      https://github.com/bioperl/bioperl-live/commit/8ab208f6b8507b3c7d54ebcbf9102d541c41d8b9
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-06-13 (Mon, 13 Jun 2011)

  Changed paths:
    R Bio/Root/Build.pm
  R Bio/Root/Exception.pm
  R Bio/Root/HTTPget.pm
  R Bio/Root/IO.pm
  R Bio/Root/Root.pm
  R Bio/Root/RootI.pm
  R Bio/Root/Storable.pm
  R Bio/Root/Test.pm
  R Bio/Root/Test/Warn.pm
  R Bio/Root/Utilities.pm
  R Bio/Root/Version.pm

  Log Message:
  -----------
  Removed Bio::Root


  Commit: e41e90049c0164f1141a25727441a68a3b13a4c5
      https://github.com/bioperl/bioperl-live/commit/e41e90049c0164f1141a25727441a68a3b13a4c5
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-06-13 (Mon, 13 Jun 2011)

  Changed paths:
    R t/Root/Exception.t
  R t/Root/RootI.t
  R t/Root/RootIO.t
  R t/Root/Storable.t
  R t/Root/Tempfile.t
  R t/Root/Utilities.t

  Log Message:
  -----------
  Removed Bio::Root test files


  Commit: 59a40bf15fa49542a8923e50aa3a30067a67171a
      https://github.com/bioperl/bioperl-live/commit/59a40bf15fa49542a8923e50aa3a30067a67171a
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-06-14 (Tue, 14 Jun 2011)

  Changed paths:
    R Bio/Das/FeatureTypeI.pm
  R Bio/Das/SegmentI.pm
  R Bio/Event/EventGeneratorI.pm
  R Bio/Event/EventHandlerI.pm

  Log Message:
  -----------
  Removed Bio::Das and Bio::Event to own dists


  Commit: 254efc2ca2adaee3bfde16498036fa8abeeb2656
      https://github.com/bioperl/bioperl-live/commit/254efc2ca2adaee3bfde16498036fa8abeeb2656
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-06-17 (Fri, 17 Jun 2011)

  Changed paths:
    A Bio/Root/HTTPget.pm
  A Bio/Root/Version.pm

  Log Message:
  -----------
  Replaced files to Bio/Root that will not be in the Root dist


  Commit: f511844e5e469cff4d4484fcc7abedf6c53a30d5
      https://github.com/bioperl/bioperl-live/commit/f511844e5e469cff4d4484fcc7abedf6c53a30d5
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-06-22 (Wed, 22 Jun 2011)

  Changed paths:
    M Build.PL

  Log Message:
  -----------
  Added Bio::Root dependency to Build.PL


  Commit: f004554e798466610336e45ae50003c7c3e68ca3
      https://github.com/bioperl/bioperl-live/commit/f004554e798466610336e45ae50003c7c3e68ca3
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-06-22 (Wed, 22 Jun 2011)

  Changed paths:
    M Build.PL

  Log Message:
  -----------
  Added Bio::Das and Bio::Event dependencies


  Commit: 05f599a0ac49c9079a43341bab15896d9b52cc78
      https://github.com/bioperl/bioperl-live/commit/05f599a0ac49c9079a43341bab15896d9b52cc78
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-06-26 (Sun, 26 Jun 2011)

  Changed paths:
    R Bio/DasI.pm
  M Build.PL

  Log Message:
  -----------
  Updated dependencies in Build.PL


  Commit: 3b93d5029fbfd7bf28aa2f3f5c3f16806bee2eb9
      https://github.com/bioperl/bioperl-live/commit/3b93d5029fbfd7bf28aa2f3f5c3f16806bee2eb9
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-06-26 (Sun, 26 Jun 2011)

  Changed paths:
    R Bio/Location/Atomic.pm
  R Bio/Location/AvWithinCoordPolicy.pm
  R Bio/Location/CoordinatePolicyI.pm
  R Bio/Location/Fuzzy.pm
  R Bio/Location/FuzzyLocationI.pm
  R Bio/Location/NarrowestCoordPolicy.pm
  R Bio/Location/Simple.pm
  R Bio/Location/Split.pm
  R Bio/Location/SplitLocationI.pm
  R Bio/Location/WidestCoordPolicy.pm
  R Bio/Range.pm
  R Bio/RangeI.pm
  M Build.PL

  Log Message:
  -----------
  Extracted Bio-Location


  Commit: 24aba52b3949a8ef93f8a9568f17c591f59c3496
      https://github.com/bioperl/bioperl-live/commit/24aba52b3949a8ef93f8a9568f17c591f59c3496
  Author: Sheena Scroggins <sheena.scroggins at gmail.com>
  Date:   2011-08-02 (Tue, 02 Aug 2011)

  Changed paths:
    R Bio/Factory/AnalysisI.pm
  R Bio/Factory/ApplicationFactoryI.pm
  R Bio/Factory/DriverFactory.pm
  R Bio/Factory/FTLocationFactory.pm
  R Bio/Factory/LocationFactoryI.pm
  R Bio/Factory/MapFactoryI.pm
  R Bio/Factory/ObjectBuilderI.pm
  R Bio/Factory/ObjectFactory.pm
  R Bio/Factory/ObjectFactoryI.pm
  R Bio/Factory/SeqAnalysisParserFactory.pm
  R Bio/Factory/SeqAnalysisParserFactoryI.pm
  R Bio/Factory/SequenceFactoryI.pm
  R Bio/Factory/SequenceProcessorI.pm
  R Bio/Factory/SequenceStreamI.pm
  R Bio/Factory/TreeFactoryI.pm

  Log Message:
  -----------
  Removed Bio::Factory


  Commit: f5da50b4e10228fd3aab4286c20b6ca666afe346
      https://github.com/bioperl/bioperl-live/commit/f5da50b4e10228fd3aab4286c20b6ca666afe346
  Author: Robert Buels <rmb32 at cornell.edu>
  Date:   2011-08-08 (Mon, 08 Aug 2011)

  Changed paths:
    M Bio/AlignIO/stockholm.pm
  M Bio/AnalysisResultI.pm
  M Bio/Annotation/Reference.pm
  M Bio/Annotation/StructuredValue.pm
  M Bio/Assembly/Contig.pm
  M Bio/Assembly/IO/ace.pm
  M Bio/Assembly/IO/phrap.pm
  M Bio/Assembly/IO/tigr.pm
  M Bio/Biblio.pm
  M Bio/Cluster/FamilyI.pm
  M Bio/ClusterI.pm
  M Bio/DB/BiblioI.pm
  M Bio/DB/Fasta.pm
  M Bio/DB/GFF.pm
  M Bio/DB/GFF/Adaptor/dbi/mysql.pm
  M Bio/DB/GFF/Adaptor/dbi/pg_fts.pm
  M Bio/DB/GFF/Aggregator/clone.pm
  M Bio/DB/HIV.pm
  M Bio/DB/HIV/HIVQueryHelper.pm
  M Bio/DB/MeSH.pm
  M Bio/DB/Qual.pm
  M Bio/DB/SeqFeature/Store.pm
  M Bio/DB/SeqFeature/Store/DBI/Pg.pm
  M Bio/DB/SeqFeature/Store/DBI/mysql.pm
  M Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
  M Bio/DB/SeqFeature/Store/GFF2Loader.pm
  M Bio/DB/SeqFeature/Store/GFF3Loader.pm
  M Bio/DB/SeqFeature/Store/LoadHelper.pm
  M Bio/DB/SeqFeature/Store/Loader.pm
  M Bio/DB/SeqFeature/Store/memory.pm
  M Bio/DB/Taxonomy/flatfile.pm
  M Bio/DB/WebDBSeqI.pm
  M Bio/DBLinkContainerI.pm
  M Bio/FeatureIO/ptt.pm
  M Bio/Index/Stockholm.pm
  M Bio/LiveSeq/IO/Loader.pm
  M Bio/LiveSeq/Mutation.pm
  M Bio/LiveSeq/SeqI.pm
  M Bio/LiveSeq/Transcript.pm
  M Bio/LiveSeq/Translation.pm
  M Bio/Map/CytoPosition.pm
  M Bio/Map/GeneMap.pm
  M Bio/Map/Marker.pm
  M Bio/Map/PositionI.pm
  M Bio/Matrix/PSM/SiteMatrix.pm
  M Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
  M Bio/OntologyIO/simplehierarchy.pm
  M Bio/Perl.pm
  M Bio/Phenotype/MeSH/Term.pm
  M Bio/PhyloNetwork.pm
  M Bio/PopGen/HtSNP.pm
  M Bio/PopGen/TagHaplotype.pm
  M Bio/PullParserI.pm
  M Bio/Restriction/Analysis.pm
  M Bio/Root/Version.pm
  M Bio/Search/Hit/GenericHit.pm
  M Bio/Search/Tiling/MapTiling.pm
  M Bio/SearchIO/blast.pm
  M Bio/SearchIO/blastxml.pm
  M Bio/SearchIO/fasta.pm
  M Bio/SearchIO/hmmer.pm
  M Bio/SearchIO/hmmer2.pm
  M Bio/SearchIO/hmmer3.pm
  M Bio/Seq.pm
  M Bio/Seq/LargeSeqI.pm
  M Bio/Seq/Meta.pm
  M Bio/Seq/Meta/Array.pm
  M Bio/Seq/Quality.pm
  M Bio/Seq/SeqBuilder.pm
  A Bio/Seq/SimulatedRead.pm
  M Bio/SeqEvolution/Factory.pm
  M Bio/SeqFeature/Annotated.pm
  M Bio/SeqFeature/Collection.pm
  M Bio/SeqFeature/Generic.pm
  M Bio/SeqFeature/Primer.pm
  M Bio/SeqFeature/Tools/IDHandler.pm
  M Bio/SeqFeatureI.pm
  M Bio/SeqI.pm
  M Bio/SeqIO.pm
  M Bio/SeqIO/bsml.pm
  M Bio/SeqIO/chaos.pm
  M Bio/SeqIO/embl.pm
  M Bio/SeqIO/fastq.pm
  M Bio/SeqIO/genbank.pm
  M Bio/SeqIO/mbsout.pm
  M Bio/SeqIO/msout.pm
  M Bio/SeqIO/swiss.pm
  M Bio/SeqUtils.pm
  M Bio/SimpleAlign.pm
  M Bio/Structure/Entry.pm
  M Bio/Structure/Residue.pm
  M Bio/Structure/SecStr/DSSP/Res.pm
  M Bio/Structure/SecStr/STRIDE/Res.pm
  M Bio/Taxon.pm
  M Bio/Tools/Alignment/Consed.pm
  M Bio/Tools/HMMER/Domain.pm
  M Bio/Tools/QRNA.pm
  M Bio/Tools/RandomDistFunctions.pm
  M Bio/Tools/Run/RemoteBlast.pm
  M Bio/Tools/Run/StandAloneBlast.pm
  M Bio/Tools/Run/StandAloneNCBIBlast.pm
  M Bio/Tools/Run/WrapperBase.pm
  M Bio/Tools/Run/WrapperBase/CommandExts.pm
  M Bio/Tools/Signalp/ExtendedSignalp.pm
  M Bio/Tools/TargetP.pm
  M Bio/Tools/dpAlign.pm
  M Build.PL
  M Changes
  M INSTALL
  R MANIFEST
  M MANIFEST.SKIP
  M README
  M doc/Deobfuscator/bin/deob_index.pl
  M doc/Deobfuscator/cgi-bin/deob_detail.cgi
  M doc/Deobfuscator/cgi-bin/deob_interface.cgi
  M examples/align/align_on_codons.pl
  M examples/align/aligntutorial.pl
  M examples/biblio/biblio-eutils-example.pl
  M examples/biblio/biblio-soap-example.pl
  M examples/biblio/biblio_soap.pl
  M examples/contributed/nmrpdb_parse.pl
  M examples/contributed/prosite2perl.pl
  M examples/db/est_tissue_query.pl
  M examples/db/gb2features.pl
  M examples/db/getGenBank.pl
  M examples/db/get_seqs.pl
  M examples/db/use_registry.pl
  M examples/generate_random_seq.pl
  M examples/longorf.pl
  M examples/make_primers.pl
  M examples/popgen/parse_calc_stats.pl
  M examples/revcom_dir.pl
  M examples/searchio/blast_example.pl
  M examples/searchio/waba2gff.pl
  M examples/searchio/waba2gff3.pl
  M examples/sirna/rnai_finder.cgi
  M examples/structure/structure-io.pl
  M examples/tk/gsequence.pl
  M examples/tk/hitdisplay.pl
  M examples/tools/extract_genes.pl
  M examples/tools/gb_to_gff.pl
  M examples/tools/parse_codeml.pl
  M examples/tools/reverse-translate.pl
  M examples/tools/run_primer3.pl
  M maintenance/authors.pl
  M maintenance/check_NAME.pl
  M maintenance/check_URLs.pl
  M maintenance/dependencies.pl
  M maintenance/deprecated.pl
  M maintenance/find_mod_deps.pl
  M maintenance/module_usage.pl
  M maintenance/modules.pl
  M maintenance/ncbi_blast_switches.pl
  M maintenance/pod.pl
  M maintenance/symlink_script.pl
  M maintenance/version.pl
  A scripts/Bio-DB-EUtilities/bp_einfo.pl
  R scripts/Bio-DB-EUtilities/einfo.PLS
  A scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
  A scripts/Bio-DB-GFF/bp_fast_load_gff.pl
  A scripts/Bio-DB-GFF/bp_genbank2gff.pl
  A scripts/Bio-DB-GFF/bp_genbank2gff3.pl
  A scripts/Bio-DB-GFF/bp_generate_histogram.pl
  A scripts/Bio-DB-GFF/bp_load_gff.pl
  A scripts/Bio-DB-GFF/bp_meta_gff.pl
  A scripts/Bio-DB-GFF/bp_process_gadfly.pl
  A scripts/Bio-DB-GFF/bp_process_sgd.pl
  A scripts/Bio-DB-GFF/bp_process_wormbase.pl
  R scripts/Bio-DB-GFF/bulk_load_gff.PLS
  R scripts/Bio-DB-GFF/fast_load_gff.PLS
  R scripts/Bio-DB-GFF/genbank2gff.PLS
  R scripts/Bio-DB-GFF/genbank2gff3.PLS
  R scripts/Bio-DB-GFF/generate_histogram.PLS
  R scripts/Bio-DB-GFF/load_gff.PLS
  R scripts/Bio-DB-GFF/meta_gff.PLS
  R scripts/Bio-DB-GFF/process_gadfly.PLS
  R scripts/Bio-DB-GFF/process_sgd.PLS
  R scripts/Bio-DB-GFF/process_wormbase.PLS
  A scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
  A scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
  A scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
  R scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
  R scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
  R scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
  A scripts/DB-HIV/bp_hivq.pl
  R scripts/DB-HIV/hivq.PLS
  R scripts/DB/biofetch_genbank_proxy.PLS
  R scripts/DB/bioflat_index.PLS
  R scripts/DB/biogetseq.PLS
  A scripts/DB/bp_biofetch_genbank_proxy.pl
  A scripts/DB/bp_bioflat_index.pl
  A scripts/DB/bp_biogetseq.pl
  A scripts/DB/bp_flanks.pl
  R scripts/DB/flanks.PLS
  R scripts/biblio/biblio.PLS
  A scripts/biblio/bp_biblio.pl
  R scripts/bioperl_netinstall.pl
  A scripts/das/bp_das_server.pl
  R scripts/das/das_server.pl
  R scripts/index/bp_fetch.PLS
  A scripts/index/bp_fetch.pl
  R scripts/index/bp_index.PLS
  A scripts/index/bp_index.pl
  R scripts/index/bp_seqret.PLS
  A scripts/index/bp_seqret.pl
  A scripts/popgen/bp_composite_LD.pl
  A scripts/popgen/bp_heterogeneity_test.pl
  R scripts/popgen/composite_LD.PLS
  R scripts/popgen/heterogeneity_test.PLS
  A scripts/searchio/bp_fastam9_to_table.pl
  A scripts/searchio/bp_filter_search.pl
  A scripts/searchio/bp_hmmer_to_table.pl
  A scripts/searchio/bp_parse_hmmsearch.pl
  A scripts/searchio/bp_search2table.pl
  R scripts/searchio/fastam9_to_table.PLS
  R scripts/searchio/filter_search.PLS
  R scripts/searchio/hmmer_to_table.PLS
  R scripts/searchio/parse_hmmsearch.PLS
  R scripts/searchio/search2table.PLS
  A scripts/seq/bp_extract_feature_seq.pl
  A scripts/seq/bp_make_mrna_protein.pl
  A scripts/seq/bp_seqconvert.pl
  A scripts/seq/bp_seqretsplit.pl
  A scripts/seq/bp_split_seq.pl
  A scripts/seq/bp_translate_seq.pl
  A scripts/seq/bp_unflatten_seq.pl
  R scripts/seq/extract_feature_seq.PLS
  R scripts/seq/make_mrna_protein.PLS
  R scripts/seq/seqconvert.PLS
  R scripts/seq/seqretsplit.PLS
  R scripts/seq/split_seq.PLS
  R scripts/seq/translate_seq.PLS
  R scripts/seq/unflatten_seq.PLS
  R scripts/seqstats/aacomp.PLS
  A scripts/seqstats/bp_aacomp.pl
  A scripts/seqstats/bp_chaos_plot.pl
  A scripts/seqstats/bp_gccalc.pl
  A scripts/seqstats/bp_oligo_count.pl
  R scripts/seqstats/chaos_plot.PLS
  R scripts/seqstats/gccalc.PLS
  R scripts/seqstats/oligo_count.PLS
  A scripts/taxa/bp_classify_hits_kingdom.pl
  A scripts/taxa/bp_local_taxonomydb_query.pl
  A scripts/taxa/bp_query_entrez_taxa.pl
  A scripts/taxa/bp_taxid4species.pl
  A scripts/taxa/bp_taxonomy2tree.pl
  R scripts/taxa/classify_hits_kingdom.PLS
  R scripts/taxa/local_taxonomydb_query.PLS
  R scripts/taxa/query_entrez_taxa.PLS
  R scripts/taxa/taxid4species.PLS
  R scripts/taxa/taxonomy2tree.PLS
  R scripts/tree/blast2tree.PLS
  A scripts/tree/bp_blast2tree.pl
  A scripts/tree/bp_nexus2nh.pl
  A scripts/tree/bp_tree2pag.pl
  R scripts/tree/nexus2nh.PLS
  R scripts/tree/tree2pag.PLS
  A scripts/utilities/bp_dbsplit.pl
  A scripts/utilities/bp_download_query_genbank.pl
  A scripts/utilities/bp_mask_by_search.pl
  R scripts/utilities/bp_mrtrans.PLS
  A scripts/utilities/bp_mrtrans.pl
  A scripts/utilities/bp_mutate.pl
  A scripts/utilities/bp_netinstall.pl
  R scripts/utilities/bp_nrdb.PLS
  A scripts/utilities/bp_nrdb.pl
  A scripts/utilities/bp_pairwise_kaks.pl
  A scripts/utilities/bp_remote_blast.pl
  A scripts/utilities/bp_revtrans-motif.pl
  A scripts/utilities/bp_search2BSML.pl
  A scripts/utilities/bp_search2alnblocks.pl
  A scripts/utilities/bp_search2gff.pl
  A scripts/utilities/bp_search2tribe.pl
  A scripts/utilities/bp_seq_length.pl
  R scripts/utilities/bp_sreformat.PLS
  A scripts/utilities/bp_sreformat.pl
  R scripts/utilities/dbsplit.PLS
  R scripts/utilities/download_query_genbank.PLS
  R scripts/utilities/mask_by_search.PLS
  R scripts/utilities/mutate.PLS
  R scripts/utilities/pairwise_kaks.PLS
  R scripts/utilities/remote_blast.PLS
  R scripts/utilities/revtrans-motif.PLS
  R scripts/utilities/search2BSML.PLS
  R scripts/utilities/search2alnblocks.PLS
  R scripts/utilities/search2gff.PLS
  R scripts/utilities/search2tribe.PLS
  R scripts/utilities/seq_length.PLS
  M t/Align/Graphics.t
  M t/Align/SimpleAlign.t
  M t/AlignIO/nexml.t
  M t/AlignIO/stockholm.t
  M t/Assembly/IO/sam.t
  M t/Assembly/core.t
  A t/Coordinate/CoordinateBoundaryTest.t
  M t/LocalDB/BioDBGFF.t
  M t/LocalDB/DBFasta.t
  M t/LocalDB/Index/Index.t
  M t/LocalDB/SeqFeature.t
  M t/Map/Map.t
  M t/Ontology/Ontology.t
  M t/Perl.t
  M t/RemoteDB/HIV/HIV.t
  M t/SearchIO/Tiling.t
  M t/SearchIO/blast.t
  M t/SearchIO/blasttable.t
  M t/SearchIO/fasta.t
  M t/SearchIO/hmmer.t
  M t/Seq/MetaSeq.t
  A t/Seq/SimulatedRead.t
  M t/SeqFeature/FeatureIO.t
  M t/SeqIO/SeqIO.t
  M t/SeqIO/fastq.t
  M t/SeqIO/gbxml.t
  M t/SeqIO/mbsout.t
  M t/SeqIO/msout.t
  M t/SeqIO/nexml.t
  M t/SeqIO/swiss.t
  M t/Tools/Run/RemoteBlast_rpsblast.t
  M t/Tools/Run/WrapperBase.t
  M t/Tree/TreeIO/nexml.t
  A t/data/badfasta.fa
  R t/data/characters.nexml.xml
  A t/data/fastq/zero_qual.fastq
  A t/data/msout/msout_infile1
  A t/data/msout/msout_infile2
  A t/data/msout/msout_infile3
  A t/data/msout/msout_infile4
  R t/data/msout_infile1
  R t/data/msout_infile1.gz
  R t/data/msout_infile2
  R t/data/msout_infile2.gz
  A t/data/nexml/characters.nexml.8.xml
  A t/data/nexml/characters.nexml.xml
  A t/data/nexml/trees.nexml.8.xml
  A t/data/nexml/trees.nexml.xml
  A t/data/spaced_fasta.fa
  M t/data/testaln.stockholm
  A t/data/tiny.stk
  R t/data/trees.nexml.xml
  R t/lib/Array/Compare.pm
  R t/lib/Sub/Uplevel.pm
  R t/lib/Test/Builder.pm
  R t/lib/Test/Builder/Module.pm
  R t/lib/Test/Builder/Tester.pm
  R t/lib/Test/Builder/Tester/Color.pm
  R t/lib/Test/Exception.pm
  R t/lib/Test/Harness.pm
  R t/lib/Test/Harness/Assert.pm
  R t/lib/Test/Harness/Iterator.pm
  R t/lib/Test/Harness/Point.pm
  R t/lib/Test/Harness/Results.pm
  R t/lib/Test/Harness/Straps.pm
  R t/lib/Test/Harness/TAP.pod
  R t/lib/Test/Harness/Util.pm
  R t/lib/Test/More.pm
  R t/lib/Test/Simple.pm
  R t/lib/Test/Tutorial.pod
  R t/lib/Test/Warn.pm
  R t/lib/Tree/DAG_Node.pm
  M t/nexml.t

  Log Message:
  -----------
  Merge branch 'master' of github.com:bioperl/bioperl-live into reorganization_2.x

Conflicts:
	Bio/Location/Split.pm
	Bio/Root/Build.pm
	Bio/Root/Exception.pm
	Bio/Root/IO.pm
	Bio/Root/RootI.pm
	Bio/Root/Storable.pm
	Bio/Root/Test.pm
	Build.PL
	t/Root/RootIO.t


Compare: https://github.com/bioperl/bioperl-live/compare/8ab208f^...f5da50b

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