When I try to install app-sci/biopython-1.21, I get an error message about missing dependencies and an unexpected EOF. The ebuild is thus broken on my system. I use the stable x86 branch. Here is the output of $ emerge biopython : Calculating dependencies ...done! >>> emerge (1 of 1) app-sci/biopython-1.21 to / >>> md5 src_uri ;-) biopython-1.21.tar.gz >>> Unpacking source... >>> Unpacking biopython-1.21.tar.gz to /var/tmp/portage/biopython-1.21/work >>> Source unpacked. running build running build_py creating build creating build/lib.linux-i686-2.3 creating build/lib.linux-i686-2.3/Bio copying Bio/triefind.py -> build/lib.linux-i686-2.3/Bio copying Bio/FormatIO.py -> build/lib.linux-i686-2.3/Bio copying Bio/Translate.py -> build/lib.linux-i686-2.3/Bio copying Bio/MarkupEditor.py -> build/lib.linux-i686-2.3/Bio copying Bio/SVM.py -> build/lib.linux-i686-2.3/Bio copying Bio/distance.py -> build/lib.linux-i686-2.3/Bio copying Bio/HotRand.py -> build/lib.linux-i686-2.3/Bio copying Bio/Seq.py -> build/lib.linux-i686-2.3/Bio copying Bio/Std.py -> build/lib.linux-i686-2.3/Bio copying Bio/ParserSupport.py -> build/lib.linux-i686-2.3/Bio copying Bio/pairwise2.py -> build/lib.linux-i686-2.3/Bio copying Bio/PropertyManager.py -> build/lib.linux-i686-2.3/Bio copying Bio/SGMLExtractor.py -> build/lib.linux-i686-2.3/Bio copying Bio/xkMeans.py -> build/lib.linux-i686-2.3/Bio copying Bio/sequtils.py -> build/lib.linux-i686-2.3/Bio copying Bio/Search.py -> build/lib.linux-i686-2.3/Bio copying Bio/listfns.py -> build/lib.linux-i686-2.3/Bio copying Bio/NetCatch.py -> build/lib.linux-i686-2.3/Bio copying Bio/biblio.py -> build/lib.linux-i686-2.3/Bio copying Bio/SeqFeature.py -> build/lib.linux-i686-2.3/Bio copying Bio/crc.py -> build/lib.linux-i686-2.3/Bio copying Bio/Index.py -> build/lib.linux-i686-2.3/Bio copying Bio/kNN.py -> build/lib.linux-i686-2.3/Bio copying Bio/DocSQL.py -> build/lib.linux-i686-2.3/Bio copying Bio/FilteredReader.py -> build/lib.linux-i686-2.3/Bio copying Bio/lcc.py -> build/lib.linux-i686-2.3/Bio copying Bio/Writer.py -> build/lib.linux-i686-2.3/Bio copying Bio/ReseekFile.py -> build/lib.linux-i686-2.3/Bio copying Bio/StdHandler.py -> build/lib.linux-i686-2.3/Bio copying Bio/stringfns.py -> build/lib.linux-i686-2.3/Bio copying Bio/MaxEntropy.py -> build/lib.linux-i686-2.3/Bio copying Bio/File.py -> build/lib.linux-i686-2.3/Bio copying Bio/MarkovModel.py -> build/lib.linux-i686-2.3/Bio copying Bio/RecordFile.py -> build/lib.linux-i686-2.3/Bio copying Bio/NaiveBayes.py -> build/lib.linux-i686-2.3/Bio copying Bio/Transcribe.py -> build/lib.linux-i686-2.3/Bio copying Bio/DBXRef.py -> build/lib.linux-i686-2.3/Bio copying Bio/__init__.py -> build/lib.linux-i686-2.3/Bio copying Bio/kMeans.py -> build/lib.linux-i686-2.3/Bio copying Bio/mathfns.py -> build/lib.linux-i686-2.3/Bio copying Bio/LogisticRegression.py -> build/lib.linux-i686-2.3/Bio copying Bio/PubMed.py -> build/lib.linux-i686-2.3/Bio copying Bio/Decode.py -> build/lib.linux-i686-2.3/Bio copying Bio/SeqRecord.py -> build/lib.linux-i686-2.3/Bio copying Bio/utils.py -> build/lib.linux-i686-2.3/Bio creating build/lib.linux-i686-2.3/Bio/Ais copying Bio/Ais/example_ais2.py -> build/lib.linux-i686-2.3/Bio/Ais copying Bio/Ais/__init__.py -> build/lib.linux-i686-2.3/Bio/Ais creating build/lib.linux-i686-2.3/Bio/Align copying Bio/Align/FormatConvert.py -> build/lib.linux-i686-2.3/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-i686-2.3/Bio/Align copying Bio/Align/Generic.py -> build/lib.linux-i686-2.3/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-i686-2.3/Bio/Align creating build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/Scanner.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/AlignAceStandalone.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/Motif.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/Applications.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/Parser.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/__init__.py -> build/lib.linux-i686-2.3/Bio/AlignAce creating build/lib.linux-i686-2.3/Bio/Alphabet copying Bio/Alphabet/IUPAC.py -> build/lib.linux-i686-2.3/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-i686-2.3/Bio/Alphabet creating build/lib.linux-i686-2.3/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-i686-2.3/Bio/Application creating build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/Record.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/NCBIStandalone.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-i686-2.3/Bio/Blast creating build/lib.linux-i686-2.3/Bio/builders copying Bio/builders/__init__.py -> build/lib.linux-i686-2.3/Bio/builders creating build/lib.linux-i686-2.3/Bio/builders/Search copying Bio/builders/Search/search.py -> build/lib.linux-i686-2.3/Bio/builders/Search copying Bio/builders/Search/__init__.py -> build/lib.linux-i686-2.3/Bio/builders/Search creating build/lib.linux-i686-2.3/Bio/builders/SeqRecord copying Bio/builders/SeqRecord/sequence.py -> build/lib.linux-i686-2.3/Bio/builders/SeqRecord copying Bio/builders/SeqRecord/__init__.py -> build/lib.linux-i686-2.3/Bio/builders/SeqRecord creating build/lib.linux-i686-2.3/Bio/CDD copying Bio/CDD/Record.py -> build/lib.linux-i686-2.3/Bio/CDD copying Bio/CDD/cdd_format.py -> build/lib.linux-i686-2.3/Bio/CDD copying Bio/CDD/__init__.py -> build/lib.linux-i686-2.3/Bio/CDD creating build/lib.linux-i686-2.3/Bio/Clustalw copying Bio/Clustalw/clustal_format.py -> build/lib.linux-i686-2.3/Bio/Clustalw copying Bio/Clustalw/__init__.py -> build/lib.linux-i686-2.3/Bio/Clustalw creating build/lib.linux-i686-2.3/Bio/Cluster copying Bio/Cluster/data.py -> build/lib.linux-i686-2.3/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-i686-2.3/Bio/Cluster creating build/lib.linux-i686-2.3/Bio/config copying Bio/config/DBRegistry.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/_support.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/Registry.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/SeqDBRegistry.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/FormatRegistry.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/_stanzaformat.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/__init__.py -> build/lib.linux-i686-2.3/Bio/config creating build/lib.linux-i686-2.3/Bio/Crystal copying Bio/Crystal/__init__.py -> build/lib.linux-i686-2.3/Bio/Crystal creating build/lib.linux-i686-2.3/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-i686-2.3/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-i686-2.3/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-i686-2.3/Bio/Data creating build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/prosite.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/genbank.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/interpro.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/_support.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/embl.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/pdb.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/prodoc.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/__init__.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/swissprot.py -> build/lib.linux-i686-2.3/Bio/dbdefs creating build/lib.linux-i686-2.3/Bio/ECell copying Bio/ECell/Record.py -> build/lib.linux-i686-2.3/Bio/ECell copying Bio/ECell/ecell_format.py -> build/lib.linux-i686-2.3/Bio/ECell copying Bio/ECell/__init__.py -> build/lib.linux-i686-2.3/Bio/ECell creating build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/primersearch_format.py -> build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/primer3_format.py -> build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/Primer.py -> build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-i686-2.3/Bio/Emboss creating build/lib.linux-i686-2.3/Bio/Encodings copying Bio/Encodings/IUPACEncoding.py -> build/lib.linux-i686-2.3/Bio/Encodings copying Bio/Encodings/__init__.py -> build/lib.linux-i686-2.3/Bio/Encodings creating build/lib.linux-i686-2.3/Bio/Enzyme copying Bio/Enzyme/__init__.py -> build/lib.linux-i686-2.3/Bio/Enzyme creating build/lib.linux-i686-2.3/Bio/expressions copying Bio/expressions/genbank.py -> build/lib.linux-i686-2.3/Bio/expressions copying Bio/expressions/fasta.py -> build/lib.linux-i686-2.3/Bio/expressions copying Bio/expressions/__init__.py -> build/lib.linux-i686-2.3/Bio/expressions copying Bio/expressions/blocks.py -> build/lib.linux-i686-2.3/Bio/expressions creating build/lib.linux-i686-2.3/Bio/expressions/blast copying Bio/expressions/blast/wublast.py -> build/lib.linux-i686-2.3/Bio/expressions/blast copying Bio/expressions/blast/ncbiblast.py -> build/lib.linux-i686-2.3/Bio/expressions/blast copying Bio/expressions/blast/__init__.py -> build/lib.linux-i686-2.3/Bio/expressions/blast creating build/lib.linux-i686-2.3/Bio/expressions/embl copying Bio/expressions/embl/embl65.py -> build/lib.linux-i686-2.3/Bio/expressions/embl copying Bio/expressions/embl/__init__.py -> build/lib.linux-i686-2.3/Bio/expressions/embl creating build/lib.linux-i686-2.3/Bio/expressions/swissprot copying Bio/expressions/swissprot/sprot38.py -> build/lib.linux-i686-2.3/Bio/expressions/swissprot copying Bio/expressions/swissprot/sprot40.py -> build/lib.linux-i686-2.3/Bio/expressions/swissprot copying Bio/expressions/swissprot/speclist.py -> build/lib.linux-i686-2.3/Bio/expressions/swissprot copying Bio/expressions/swissprot/__init__.py -> build/lib.linux-i686-2.3/Bio/expressions/swissprot creating build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/DBIdsClient.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/POM.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/sourcegen.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/parse.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/Mixins.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/MultiDict.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/Datatypes.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/HistoryClient.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/ThinClient.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/ReseekFile.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/dtd2py.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/setup.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/Config.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/__init__.py -> build/lib.linux-i686-2.3/Bio/EUtils creating build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/ePost_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/eSummary_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/eLink_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/LinkOut.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/eInfo_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/eSearch_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/__init__.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs creating build/lib.linux-i686-2.3/Bio/Fasta copying Bio/Fasta/FastaAlign.py -> build/lib.linux-i686-2.3/Bio/Fasta copying Bio/Fasta/__init__.py -> build/lib.linux-i686-2.3/Bio/Fasta creating build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/genbank.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/sequence.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/embl.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/search.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/__init__.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/swissprot.py -> build/lib.linux-i686-2.3/Bio/formatdefs creating build/lib.linux-i686-2.3/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> build/lib.linux-i686-2.3/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> build/lib.linux-i686-2.3/Bio/FSSP copying Bio/FSSP/__init__.py -> build/lib.linux-i686-2.3/Bio/FSSP creating build/lib.linux-i686-2.3/Bio/GA copying Bio/GA/Evolver.py -> build/lib.linux-i686-2.3/Bio/GA copying Bio/GA/Organism.py -> build/lib.linux-i686-2.3/Bio/GA copying Bio/GA/__init__.py -> build/lib.linux-i686-2.3/Bio/GA creating build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/TwoPoint.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/Uniform.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/General.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/GeneralPoint.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/__init__.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/Point.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover creating build/lib.linux-i686-2.3/Bio/GA/Mutation copying Bio/GA/Mutation/Simple.py -> build/lib.linux-i686-2.3/Bio/GA/Mutation copying Bio/GA/Mutation/General.py -> build/lib.linux-i686-2.3/Bio/GA/Mutation copying Bio/GA/Mutation/__init__.py -> build/lib.linux-i686-2.3/Bio/GA/Mutation creating build/lib.linux-i686-2.3/Bio/GA/Repair copying Bio/GA/Repair/__init__.py -> build/lib.linux-i686-2.3/Bio/GA/Repair copying Bio/GA/Repair/Stabilizing.py -> build/lib.linux-i686-2.3/Bio/GA/Repair creating build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/Diversity.py -> build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/Abstract.py -> build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/RouletteWheel.py -> build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/Tournament.py -> build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/__init__.py -> build/lib.linux-i686-2.3/Bio/GA/Selection creating build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/genbank_format.py -> build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/LocationParser.py -> build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-i686-2.3/Bio/GenBank creating build/lib.linux-i686-2.3/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-i686-2.3/Bio/Geo copying Bio/Geo/geo_format.py -> build/lib.linux-i686-2.3/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-i686-2.3/Bio/Geo creating build/lib.linux-i686-2.3/Bio/GFF copying Bio/GFF/easy.py -> build/lib.linux-i686-2.3/Bio/GFF copying Bio/GFF/__init__.py -> build/lib.linux-i686-2.3/Bio/GFF copying Bio/GFF/GenericTools.py -> build/lib.linux-i686-2.3/Bio/GFF copying Bio/GFF/binning.py -> build/lib.linux-i686-2.3/Bio/GFF creating build/lib.linux-i686-2.3/Bio/Gobase copying Bio/Gobase/__init__.py -> build/lib.linux-i686-2.3/Bio/Gobase creating build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-i686-2.3/Bio/Graphics creating build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-i686-2.3/Bio/HMM creating build/lib.linux-i686-2.3/Bio/IntelliGenetics copying Bio/IntelliGenetics/Record.py -> build/lib.linux-i686-2.3/Bio/IntelliGenetics copying Bio/IntelliGenetics/intelligenetics_format.py -> build/lib.linux-i686-2.3/Bio/IntelliGenetics copying Bio/IntelliGenetics/__init__.py -> build/lib.linux-i686-2.3/Bio/IntelliGenetics creating build/lib.linux-i686-2.3/Bio/InterPro copying Bio/InterPro/__init__.py -> build/lib.linux-i686-2.3/Bio/InterPro creating build/lib.linux-i686-2.3/Bio/Kabat copying Bio/Kabat/kabat_format.py -> build/lib.linux-i686-2.3/Bio/Kabat copying Bio/Kabat/Record.py -> build/lib.linux-i686-2.3/Bio/Kabat copying Bio/Kabat/__init__.py -> build/lib.linux-i686-2.3/Bio/Kabat creating build/lib.linux-i686-2.3/Bio/KDTree copying Bio/KDTree/__init__.py -> build/lib.linux-i686-2.3/Bio/KDTree copying Bio/KDTree/_KDTree.py -> build/lib.linux-i686-2.3/Bio/KDTree creating build/lib.linux-i686-2.3/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-i686-2.3/Bio/KEGG creating build/lib.linux-i686-2.3/Bio/KEGG/Compound copying Bio/KEGG/Compound/compound_format.py -> build/lib.linux-i686-2.3/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-i686-2.3/Bio/KEGG/Compound creating build/lib.linux-i686-2.3/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/enzyme_format.py -> build/lib.linux-i686-2.3/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-i686-2.3/Bio/KEGG/Enzyme creating build/lib.linux-i686-2.3/Bio/KEGG/Map copying Bio/KEGG/Map/map_format.py -> build/lib.linux-i686-2.3/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-i686-2.3/Bio/KEGG/Map creating build/lib.linux-i686-2.3/Bio/LocusLink copying Bio/LocusLink/locus_format.py -> build/lib.linux-i686-2.3/Bio/LocusLink copying Bio/LocusLink/__init__.py -> build/lib.linux-i686-2.3/Bio/LocusLink copying Bio/LocusLink/web_parse.py -> build/lib.linux-i686-2.3/Bio/LocusLink creating build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/nlmmedline_010319_format.py -> build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/NLMMedlineXML.py -> build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/nlmmedline_011101_format.py -> build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/nlmmedline_001211_format.py -> build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-i686-2.3/Bio/Medline creating build/lib.linux-i686-2.3/Bio/MetaTool copying Bio/MetaTool/Record.py -> build/lib.linux-i686-2.3/Bio/MetaTool copying Bio/MetaTool/Input.py -> build/lib.linux-i686-2.3/Bio/MetaTool copying Bio/MetaTool/__init__.py -> build/lib.linux-i686-2.3/Bio/MetaTool copying Bio/MetaTool/metatool_format.py -> build/lib.linux-i686-2.3/Bio/MetaTool creating build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/FlatDB.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/XPath.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/Location.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/compression.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/BaseDB.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/SimpleSeqRecord.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/BerkeleyDB.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/__init__.py -> build/lib.linux-i686-2.3/Bio/Mindy creating build/lib.linux-i686-2.3/Bio/MultiProc copying Bio/MultiProc/Scheduler.py -> build/lib.linux-i686-2.3/Bio/MultiProc copying Bio/MultiProc/copen.py -> build/lib.linux-i686-2.3/Bio/MultiProc copying Bio/MultiProc/Task.py -> build/lib.linux-i686-2.3/Bio/MultiProc copying Bio/MultiProc/__init__.py -> build/lib.linux-i686-2.3/Bio/MultiProc creating build/lib.linux-i686-2.3/Bio/NBRF copying Bio/NBRF/Record.py -> build/lib.linux-i686-2.3/Bio/NBRF copying Bio/NBRF/nbrf_format.py -> build/lib.linux-i686-2.3/Bio/NBRF copying Bio/NBRF/ValSeq.py -> build/lib.linux-i686-2.3/Bio/NBRF copying Bio/NBRF/__init__.py -> build/lib.linux-i686-2.3/Bio/NBRF creating build/lib.linux-i686-2.3/Bio/Ndb copying Bio/Ndb/__init__.py -> build/lib.linux-i686-2.3/Bio/Ndb creating build/lib.linux-i686-2.3/Bio/NeuralNetwork copying Bio/NeuralNetwork/StopTraining.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork copying Bio/NeuralNetwork/Training.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork copying Bio/NeuralNetwork/__init__.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork creating build/lib.linux-i686-2.3/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/Network.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/Layer.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/__init__.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/BackPropagation creating build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Motif.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Pattern.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Signature.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/__init__.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Schema.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene creating build/lib.linux-i686-2.3/Bio/Parsers copying Bio/Parsers/spark.py -> build/lib.linux-i686-2.3/Bio/Parsers copying Bio/Parsers/__init__.py -> build/lib.linux-i686-2.3/Bio/Parsers creating build/lib.linux-i686-2.3/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-i686-2.3/Bio/Pathway creating build/lib.linux-i686-2.3/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-i686-2.3/Bio/Pathway/Rep copying Bio/Pathway/Rep/HashSet.py -> build/lib.linux-i686-2.3/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-i686-2.3/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-i686-2.3/Bio/Pathway/Rep creating build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-i686-2.3/Bio/PDB creating build/lib.linux-i686-2.3/Bio/Prosite copying Bio/Prosite/Prodoc.py -> build/lib.linux-i686-2.3/Bio/Prosite copying Bio/Prosite/Pattern.py -> build/lib.linux-i686-2.3/Bio/Prosite copying Bio/Prosite/__init__.py -> build/lib.linux-i686-2.3/Bio/Prosite creating build/lib.linux-i686-2.3/Bio/Rebase copying Bio/Rebase/Rebase.py -> build/lib.linux-i686-2.3/Bio/Rebase copying Bio/Rebase/__init__.py -> build/lib.linux-i686-2.3/Bio/Rebase creating build/lib.linux-i686-2.3/Bio/Saf copying Bio/Saf/Record.py -> build/lib.linux-i686-2.3/Bio/Saf copying Bio/Saf/saf_format.py -> build/lib.linux-i686-2.3/Bio/Saf copying Bio/Saf/__init__.py -> build/lib.linux-i686-2.3/Bio/Saf creating build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/FileIndex.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-i686-2.3/Bio/SCOP creating build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testResidues.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testCla.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testDes.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testDom.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testScop.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testHie.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testRaf.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/__init__.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests creating build/lib.linux-i686-2.3/Bio/SeqIO copying Bio/SeqIO/generic.py -> build/lib.linux-i686-2.3/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-i686-2.3/Bio/SeqIO copying Bio/SeqIO/FASTA.py -> build/lib.linux-i686-2.3/Bio/SeqIO creating build/lib.linux-i686-2.3/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-i686-2.3/Bio/SeqUtils creating build/lib.linux-i686-2.3/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> build/lib.linux-i686-2.3/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> build/lib.linux-i686-2.3/Bio/SubsMat copying Bio/SubsMat/__init__.py -> build/lib.linux-i686-2.3/Bio/SubsMat creating build/lib.linux-i686-2.3/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/SVDSuperimposer.py -> build/lib.linux-i686-2.3/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-i686-2.3/Bio/SVDSuperimposer creating build/lib.linux-i686-2.3/Bio/SwissProt copying Bio/SwissProt/SProt.py -> build/lib.linux-i686-2.3/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-i686-2.3/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-i686-2.3/Bio/SwissProt creating build/lib.linux-i686-2.3/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-i686-2.3/Bio/UniGene creating build/lib.linux-i686-2.3/Bio/writers copying Bio/writers/__init__.py -> build/lib.linux-i686-2.3/Bio/writers creating build/lib.linux-i686-2.3/Bio/writers/SeqRecord copying Bio/writers/SeqRecord/fasta.py -> build/lib.linux-i686-2.3/Bio/writers/SeqRecord copying Bio/writers/SeqRecord/empty.py -> build/lib.linux-i686-2.3/Bio/writers/SeqRecord copying Bio/writers/SeqRecord/__init__.py -> build/lib.linux-i686-2.3/Bio/writers/SeqRecord creating build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/SCOP.py -> build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/NCBI.py -> build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/InterPro.py -> build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/ExPASy.py -> build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/__init__.py -> build/lib.linux-i686-2.3/Bio/WWW creating build/lib.linux-i686-2.3/BioSQL copying BioSQL/Loader.py -> build/lib.linux-i686-2.3/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-i686-2.3/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-i686-2.3/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-i686-2.3/BioSQL copying BioSQL/__init__.py -> build/lib.linux-i686-2.3/BioSQL creating build/lib.linux-i686-2.3/Martel copying Martel/LAX.py -> build/lib.linux-i686-2.3/Martel copying Martel/msre_parse.py -> build/lib.linux-i686-2.3/Martel copying Martel/Iterator.py -> build/lib.linux-i686-2.3/Martel copying Martel/IterParser.py -> build/lib.linux-i686-2.3/Martel copying Martel/Generate.py -> build/lib.linux-i686-2.3/Martel copying Martel/convert_re.py -> build/lib.linux-i686-2.3/Martel copying Martel/Dispatch.py -> build/lib.linux-i686-2.3/Martel copying Martel/Expression.py -> build/lib.linux-i686-2.3/Martel copying Martel/Parser.py -> build/lib.linux-i686-2.3/Martel copying Martel/msre_constants.py -> build/lib.linux-i686-2.3/Martel copying Martel/optimize.py -> build/lib.linux-i686-2.3/Martel copying Martel/setup.py -> build/lib.linux-i686-2.3/Martel copying Martel/Time.py -> build/lib.linux-i686-2.3/Martel copying Martel/__init__.py -> build/lib.linux-i686-2.3/Martel copying Martel/RecordReader.py -> build/lib.linux-i686-2.3/Martel running build_ext building 'Bio.cSVM' extension creating build/temp.linux-i686-2.3 creating build/temp.linux-i686-2.3/Bio gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/csupport.c -o build/temp.linux-i686-2.3/Bio/csupport.o gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cSVMmodule.c -o build/temp.linux-i686-2.3/Bio/cSVMmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cSVMmodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cSVM.so building 'Bio.ckMeans' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/ckMeansmodule.c -o build/temp.linux-i686-2.3/Bio/ckMeansmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/ckMeansmodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/ckMeans.so building 'Bio.clistfns' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -I/usr/include/python2.3 -c Bio/clistfnsmodule.c -o build/temp.linux-i686-2.3/Bio/clistfnsmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/clistfnsmodule.o -o build/lib.linux-i686-2.3/Bio/clistfns.so building 'Bio.cmathfns' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cmathfnsmodule.c -o build/temp.linux-i686-2.3/Bio/cmathfnsmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cmathfnsmodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cmathfns.so building 'Bio.cstringfns' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -I/usr/include/python2.3 -c Bio/cstringfnsmodule.c -o build/temp.linux-i686-2.3/Bio/cstringfnsmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cstringfnsmodule.o -o build/lib.linux-i686-2.3/Bio/cstringfns.so building 'Bio.cdistance' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cdistancemodule.c -o build/temp.linux-i686-2.3/Bio/cdistancemodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cdistancemodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cdistance.so building 'Bio.cpairwise2' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cpairwise2module.c -o build/temp.linux-i686-2.3/Bio/cpairwise2module.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cpairwise2module.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cpairwise2.so building 'Bio.trie' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/trie.c -o build/temp.linux-i686-2.3/Bio/trie.o Bio/trie.c: Dans la fonction
When I try to install app-sci/biopython-1.21, I get an error message about missing dependencies and an unexpected EOF. The ebuild is thus broken on my system. I use the stable x86 branch. Here is the output of $ emerge biopython : Calculating dependencies ...done! >>> emerge (1 of 1) app-sci/biopython-1.21 to / >>> md5 src_uri ;-) biopython-1.21.tar.gz >>> Unpacking source... >>> Unpacking biopython-1.21.tar.gz to /var/tmp/portage/biopython-1.21/work >>> Source unpacked. running build running build_py creating build creating build/lib.linux-i686-2.3 creating build/lib.linux-i686-2.3/Bio copying Bio/triefind.py -> build/lib.linux-i686-2.3/Bio copying Bio/FormatIO.py -> build/lib.linux-i686-2.3/Bio copying Bio/Translate.py -> build/lib.linux-i686-2.3/Bio copying Bio/MarkupEditor.py -> build/lib.linux-i686-2.3/Bio copying Bio/SVM.py -> build/lib.linux-i686-2.3/Bio copying Bio/distance.py -> build/lib.linux-i686-2.3/Bio copying Bio/HotRand.py -> build/lib.linux-i686-2.3/Bio copying Bio/Seq.py -> build/lib.linux-i686-2.3/Bio copying Bio/Std.py -> build/lib.linux-i686-2.3/Bio copying Bio/ParserSupport.py -> build/lib.linux-i686-2.3/Bio copying Bio/pairwise2.py -> build/lib.linux-i686-2.3/Bio copying Bio/PropertyManager.py -> build/lib.linux-i686-2.3/Bio copying Bio/SGMLExtractor.py -> build/lib.linux-i686-2.3/Bio copying Bio/xkMeans.py -> build/lib.linux-i686-2.3/Bio copying Bio/sequtils.py -> build/lib.linux-i686-2.3/Bio copying Bio/Search.py -> build/lib.linux-i686-2.3/Bio copying Bio/listfns.py -> build/lib.linux-i686-2.3/Bio copying Bio/NetCatch.py -> build/lib.linux-i686-2.3/Bio copying Bio/biblio.py -> build/lib.linux-i686-2.3/Bio copying Bio/SeqFeature.py -> build/lib.linux-i686-2.3/Bio copying Bio/crc.py -> build/lib.linux-i686-2.3/Bio copying Bio/Index.py -> build/lib.linux-i686-2.3/Bio copying Bio/kNN.py -> build/lib.linux-i686-2.3/Bio copying Bio/DocSQL.py -> build/lib.linux-i686-2.3/Bio copying Bio/FilteredReader.py -> build/lib.linux-i686-2.3/Bio copying Bio/lcc.py -> build/lib.linux-i686-2.3/Bio copying Bio/Writer.py -> build/lib.linux-i686-2.3/Bio copying Bio/ReseekFile.py -> build/lib.linux-i686-2.3/Bio copying Bio/StdHandler.py -> build/lib.linux-i686-2.3/Bio copying Bio/stringfns.py -> build/lib.linux-i686-2.3/Bio copying Bio/MaxEntropy.py -> build/lib.linux-i686-2.3/Bio copying Bio/File.py -> build/lib.linux-i686-2.3/Bio copying Bio/MarkovModel.py -> build/lib.linux-i686-2.3/Bio copying Bio/RecordFile.py -> build/lib.linux-i686-2.3/Bio copying Bio/NaiveBayes.py -> build/lib.linux-i686-2.3/Bio copying Bio/Transcribe.py -> build/lib.linux-i686-2.3/Bio copying Bio/DBXRef.py -> build/lib.linux-i686-2.3/Bio copying Bio/__init__.py -> build/lib.linux-i686-2.3/Bio copying Bio/kMeans.py -> build/lib.linux-i686-2.3/Bio copying Bio/mathfns.py -> build/lib.linux-i686-2.3/Bio copying Bio/LogisticRegression.py -> build/lib.linux-i686-2.3/Bio copying Bio/PubMed.py -> build/lib.linux-i686-2.3/Bio copying Bio/Decode.py -> build/lib.linux-i686-2.3/Bio copying Bio/SeqRecord.py -> build/lib.linux-i686-2.3/Bio copying Bio/utils.py -> build/lib.linux-i686-2.3/Bio creating build/lib.linux-i686-2.3/Bio/Ais copying Bio/Ais/example_ais2.py -> build/lib.linux-i686-2.3/Bio/Ais copying Bio/Ais/__init__.py -> build/lib.linux-i686-2.3/Bio/Ais creating build/lib.linux-i686-2.3/Bio/Align copying Bio/Align/FormatConvert.py -> build/lib.linux-i686-2.3/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-i686-2.3/Bio/Align copying Bio/Align/Generic.py -> build/lib.linux-i686-2.3/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-i686-2.3/Bio/Align creating build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/Scanner.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/AlignAceStandalone.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/Motif.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/Applications.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/Parser.py -> build/lib.linux-i686-2.3/Bio/AlignAce copying Bio/AlignAce/__init__.py -> build/lib.linux-i686-2.3/Bio/AlignAce creating build/lib.linux-i686-2.3/Bio/Alphabet copying Bio/Alphabet/IUPAC.py -> build/lib.linux-i686-2.3/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-i686-2.3/Bio/Alphabet creating build/lib.linux-i686-2.3/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-i686-2.3/Bio/Application creating build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/Record.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/NCBIStandalone.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-i686-2.3/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-i686-2.3/Bio/Blast creating build/lib.linux-i686-2.3/Bio/builders copying Bio/builders/__init__.py -> build/lib.linux-i686-2.3/Bio/builders creating build/lib.linux-i686-2.3/Bio/builders/Search copying Bio/builders/Search/search.py -> build/lib.linux-i686-2.3/Bio/builders/Search copying Bio/builders/Search/__init__.py -> build/lib.linux-i686-2.3/Bio/builders/Search creating build/lib.linux-i686-2.3/Bio/builders/SeqRecord copying Bio/builders/SeqRecord/sequence.py -> build/lib.linux-i686-2.3/Bio/builders/SeqRecord copying Bio/builders/SeqRecord/__init__.py -> build/lib.linux-i686-2.3/Bio/builders/SeqRecord creating build/lib.linux-i686-2.3/Bio/CDD copying Bio/CDD/Record.py -> build/lib.linux-i686-2.3/Bio/CDD copying Bio/CDD/cdd_format.py -> build/lib.linux-i686-2.3/Bio/CDD copying Bio/CDD/__init__.py -> build/lib.linux-i686-2.3/Bio/CDD creating build/lib.linux-i686-2.3/Bio/Clustalw copying Bio/Clustalw/clustal_format.py -> build/lib.linux-i686-2.3/Bio/Clustalw copying Bio/Clustalw/__init__.py -> build/lib.linux-i686-2.3/Bio/Clustalw creating build/lib.linux-i686-2.3/Bio/Cluster copying Bio/Cluster/data.py -> build/lib.linux-i686-2.3/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-i686-2.3/Bio/Cluster creating build/lib.linux-i686-2.3/Bio/config copying Bio/config/DBRegistry.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/_support.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/Registry.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/SeqDBRegistry.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/FormatRegistry.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/_stanzaformat.py -> build/lib.linux-i686-2.3/Bio/config copying Bio/config/__init__.py -> build/lib.linux-i686-2.3/Bio/config creating build/lib.linux-i686-2.3/Bio/Crystal copying Bio/Crystal/__init__.py -> build/lib.linux-i686-2.3/Bio/Crystal creating build/lib.linux-i686-2.3/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-i686-2.3/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-i686-2.3/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-i686-2.3/Bio/Data creating build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/prosite.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/genbank.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/interpro.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/_support.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/embl.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/pdb.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/prodoc.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/__init__.py -> build/lib.linux-i686-2.3/Bio/dbdefs copying Bio/dbdefs/swissprot.py -> build/lib.linux-i686-2.3/Bio/dbdefs creating build/lib.linux-i686-2.3/Bio/ECell copying Bio/ECell/Record.py -> build/lib.linux-i686-2.3/Bio/ECell copying Bio/ECell/ecell_format.py -> build/lib.linux-i686-2.3/Bio/ECell copying Bio/ECell/__init__.py -> build/lib.linux-i686-2.3/Bio/ECell creating build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/primersearch_format.py -> build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/primer3_format.py -> build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/Primer.py -> build/lib.linux-i686-2.3/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-i686-2.3/Bio/Emboss creating build/lib.linux-i686-2.3/Bio/Encodings copying Bio/Encodings/IUPACEncoding.py -> build/lib.linux-i686-2.3/Bio/Encodings copying Bio/Encodings/__init__.py -> build/lib.linux-i686-2.3/Bio/Encodings creating build/lib.linux-i686-2.3/Bio/Enzyme copying Bio/Enzyme/__init__.py -> build/lib.linux-i686-2.3/Bio/Enzyme creating build/lib.linux-i686-2.3/Bio/expressions copying Bio/expressions/genbank.py -> build/lib.linux-i686-2.3/Bio/expressions copying Bio/expressions/fasta.py -> build/lib.linux-i686-2.3/Bio/expressions copying Bio/expressions/__init__.py -> build/lib.linux-i686-2.3/Bio/expressions copying Bio/expressions/blocks.py -> build/lib.linux-i686-2.3/Bio/expressions creating build/lib.linux-i686-2.3/Bio/expressions/blast copying Bio/expressions/blast/wublast.py -> build/lib.linux-i686-2.3/Bio/expressions/blast copying Bio/expressions/blast/ncbiblast.py -> build/lib.linux-i686-2.3/Bio/expressions/blast copying Bio/expressions/blast/__init__.py -> build/lib.linux-i686-2.3/Bio/expressions/blast creating build/lib.linux-i686-2.3/Bio/expressions/embl copying Bio/expressions/embl/embl65.py -> build/lib.linux-i686-2.3/Bio/expressions/embl copying Bio/expressions/embl/__init__.py -> build/lib.linux-i686-2.3/Bio/expressions/embl creating build/lib.linux-i686-2.3/Bio/expressions/swissprot copying Bio/expressions/swissprot/sprot38.py -> build/lib.linux-i686-2.3/Bio/expressions/swissprot copying Bio/expressions/swissprot/sprot40.py -> build/lib.linux-i686-2.3/Bio/expressions/swissprot copying Bio/expressions/swissprot/speclist.py -> build/lib.linux-i686-2.3/Bio/expressions/swissprot copying Bio/expressions/swissprot/__init__.py -> build/lib.linux-i686-2.3/Bio/expressions/swissprot creating build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/DBIdsClient.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/POM.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/sourcegen.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/parse.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/Mixins.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/MultiDict.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/Datatypes.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/HistoryClient.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/ThinClient.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/ReseekFile.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/dtd2py.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/setup.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/Config.py -> build/lib.linux-i686-2.3/Bio/EUtils copying Bio/EUtils/__init__.py -> build/lib.linux-i686-2.3/Bio/EUtils creating build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/ePost_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/eSummary_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/eLink_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/LinkOut.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/eInfo_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/eSearch_020511.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/__init__.py -> build/lib.linux-i686-2.3/Bio/EUtils/DTDs creating build/lib.linux-i686-2.3/Bio/Fasta copying Bio/Fasta/FastaAlign.py -> build/lib.linux-i686-2.3/Bio/Fasta copying Bio/Fasta/__init__.py -> build/lib.linux-i686-2.3/Bio/Fasta creating build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/genbank.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/sequence.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/embl.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/search.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/__init__.py -> build/lib.linux-i686-2.3/Bio/formatdefs copying Bio/formatdefs/swissprot.py -> build/lib.linux-i686-2.3/Bio/formatdefs creating build/lib.linux-i686-2.3/Bio/FSSP copying Bio/FSSP/fssp_rec.py -> build/lib.linux-i686-2.3/Bio/FSSP copying Bio/FSSP/FSSPTools.py -> build/lib.linux-i686-2.3/Bio/FSSP copying Bio/FSSP/__init__.py -> build/lib.linux-i686-2.3/Bio/FSSP creating build/lib.linux-i686-2.3/Bio/GA copying Bio/GA/Evolver.py -> build/lib.linux-i686-2.3/Bio/GA copying Bio/GA/Organism.py -> build/lib.linux-i686-2.3/Bio/GA copying Bio/GA/__init__.py -> build/lib.linux-i686-2.3/Bio/GA creating build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/TwoPoint.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/Uniform.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/General.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/GeneralPoint.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/__init__.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover copying Bio/GA/Crossover/Point.py -> build/lib.linux-i686-2.3/Bio/GA/Crossover creating build/lib.linux-i686-2.3/Bio/GA/Mutation copying Bio/GA/Mutation/Simple.py -> build/lib.linux-i686-2.3/Bio/GA/Mutation copying Bio/GA/Mutation/General.py -> build/lib.linux-i686-2.3/Bio/GA/Mutation copying Bio/GA/Mutation/__init__.py -> build/lib.linux-i686-2.3/Bio/GA/Mutation creating build/lib.linux-i686-2.3/Bio/GA/Repair copying Bio/GA/Repair/__init__.py -> build/lib.linux-i686-2.3/Bio/GA/Repair copying Bio/GA/Repair/Stabilizing.py -> build/lib.linux-i686-2.3/Bio/GA/Repair creating build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/Diversity.py -> build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/Abstract.py -> build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/RouletteWheel.py -> build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/Tournament.py -> build/lib.linux-i686-2.3/Bio/GA/Selection copying Bio/GA/Selection/__init__.py -> build/lib.linux-i686-2.3/Bio/GA/Selection creating build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/genbank_format.py -> build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/LocationParser.py -> build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-i686-2.3/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-i686-2.3/Bio/GenBank creating build/lib.linux-i686-2.3/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-i686-2.3/Bio/Geo copying Bio/Geo/geo_format.py -> build/lib.linux-i686-2.3/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-i686-2.3/Bio/Geo creating build/lib.linux-i686-2.3/Bio/GFF copying Bio/GFF/easy.py -> build/lib.linux-i686-2.3/Bio/GFF copying Bio/GFF/__init__.py -> build/lib.linux-i686-2.3/Bio/GFF copying Bio/GFF/GenericTools.py -> build/lib.linux-i686-2.3/Bio/GFF copying Bio/GFF/binning.py -> build/lib.linux-i686-2.3/Bio/GFF creating build/lib.linux-i686-2.3/Bio/Gobase copying Bio/Gobase/__init__.py -> build/lib.linux-i686-2.3/Bio/Gobase creating build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-i686-2.3/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-i686-2.3/Bio/Graphics creating build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-i686-2.3/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-i686-2.3/Bio/HMM creating build/lib.linux-i686-2.3/Bio/IntelliGenetics copying Bio/IntelliGenetics/Record.py -> build/lib.linux-i686-2.3/Bio/IntelliGenetics copying Bio/IntelliGenetics/intelligenetics_format.py -> build/lib.linux-i686-2.3/Bio/IntelliGenetics copying Bio/IntelliGenetics/__init__.py -> build/lib.linux-i686-2.3/Bio/IntelliGenetics creating build/lib.linux-i686-2.3/Bio/InterPro copying Bio/InterPro/__init__.py -> build/lib.linux-i686-2.3/Bio/InterPro creating build/lib.linux-i686-2.3/Bio/Kabat copying Bio/Kabat/kabat_format.py -> build/lib.linux-i686-2.3/Bio/Kabat copying Bio/Kabat/Record.py -> build/lib.linux-i686-2.3/Bio/Kabat copying Bio/Kabat/__init__.py -> build/lib.linux-i686-2.3/Bio/Kabat creating build/lib.linux-i686-2.3/Bio/KDTree copying Bio/KDTree/__init__.py -> build/lib.linux-i686-2.3/Bio/KDTree copying Bio/KDTree/_KDTree.py -> build/lib.linux-i686-2.3/Bio/KDTree creating build/lib.linux-i686-2.3/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-i686-2.3/Bio/KEGG creating build/lib.linux-i686-2.3/Bio/KEGG/Compound copying Bio/KEGG/Compound/compound_format.py -> build/lib.linux-i686-2.3/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-i686-2.3/Bio/KEGG/Compound creating build/lib.linux-i686-2.3/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/enzyme_format.py -> build/lib.linux-i686-2.3/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-i686-2.3/Bio/KEGG/Enzyme creating build/lib.linux-i686-2.3/Bio/KEGG/Map copying Bio/KEGG/Map/map_format.py -> build/lib.linux-i686-2.3/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-i686-2.3/Bio/KEGG/Map creating build/lib.linux-i686-2.3/Bio/LocusLink copying Bio/LocusLink/locus_format.py -> build/lib.linux-i686-2.3/Bio/LocusLink copying Bio/LocusLink/__init__.py -> build/lib.linux-i686-2.3/Bio/LocusLink copying Bio/LocusLink/web_parse.py -> build/lib.linux-i686-2.3/Bio/LocusLink creating build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/nlmmedline_010319_format.py -> build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/NLMMedlineXML.py -> build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/nlmmedline_011101_format.py -> build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/nlmmedline_001211_format.py -> build/lib.linux-i686-2.3/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-i686-2.3/Bio/Medline creating build/lib.linux-i686-2.3/Bio/MetaTool copying Bio/MetaTool/Record.py -> build/lib.linux-i686-2.3/Bio/MetaTool copying Bio/MetaTool/Input.py -> build/lib.linux-i686-2.3/Bio/MetaTool copying Bio/MetaTool/__init__.py -> build/lib.linux-i686-2.3/Bio/MetaTool copying Bio/MetaTool/metatool_format.py -> build/lib.linux-i686-2.3/Bio/MetaTool creating build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/FlatDB.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/XPath.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/Location.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/compression.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/BaseDB.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/SimpleSeqRecord.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/BerkeleyDB.py -> build/lib.linux-i686-2.3/Bio/Mindy copying Bio/Mindy/__init__.py -> build/lib.linux-i686-2.3/Bio/Mindy creating build/lib.linux-i686-2.3/Bio/MultiProc copying Bio/MultiProc/Scheduler.py -> build/lib.linux-i686-2.3/Bio/MultiProc copying Bio/MultiProc/copen.py -> build/lib.linux-i686-2.3/Bio/MultiProc copying Bio/MultiProc/Task.py -> build/lib.linux-i686-2.3/Bio/MultiProc copying Bio/MultiProc/__init__.py -> build/lib.linux-i686-2.3/Bio/MultiProc creating build/lib.linux-i686-2.3/Bio/NBRF copying Bio/NBRF/Record.py -> build/lib.linux-i686-2.3/Bio/NBRF copying Bio/NBRF/nbrf_format.py -> build/lib.linux-i686-2.3/Bio/NBRF copying Bio/NBRF/ValSeq.py -> build/lib.linux-i686-2.3/Bio/NBRF copying Bio/NBRF/__init__.py -> build/lib.linux-i686-2.3/Bio/NBRF creating build/lib.linux-i686-2.3/Bio/Ndb copying Bio/Ndb/__init__.py -> build/lib.linux-i686-2.3/Bio/Ndb creating build/lib.linux-i686-2.3/Bio/NeuralNetwork copying Bio/NeuralNetwork/StopTraining.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork copying Bio/NeuralNetwork/Training.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork copying Bio/NeuralNetwork/__init__.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork creating build/lib.linux-i686-2.3/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/Network.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/Layer.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/BackPropagation copying Bio/NeuralNetwork/BackPropagation/__init__.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/BackPropagation creating build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Motif.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Pattern.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Signature.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/__init__.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene copying Bio/NeuralNetwork/Gene/Schema.py -> build/lib.linux-i686-2.3/Bio/NeuralNetwork/Gene creating build/lib.linux-i686-2.3/Bio/Parsers copying Bio/Parsers/spark.py -> build/lib.linux-i686-2.3/Bio/Parsers copying Bio/Parsers/__init__.py -> build/lib.linux-i686-2.3/Bio/Parsers creating build/lib.linux-i686-2.3/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-i686-2.3/Bio/Pathway creating build/lib.linux-i686-2.3/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-i686-2.3/Bio/Pathway/Rep copying Bio/Pathway/Rep/HashSet.py -> build/lib.linux-i686-2.3/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-i686-2.3/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-i686-2.3/Bio/Pathway/Rep creating build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-i686-2.3/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-i686-2.3/Bio/PDB creating build/lib.linux-i686-2.3/Bio/Prosite copying Bio/Prosite/Prodoc.py -> build/lib.linux-i686-2.3/Bio/Prosite copying Bio/Prosite/Pattern.py -> build/lib.linux-i686-2.3/Bio/Prosite copying Bio/Prosite/__init__.py -> build/lib.linux-i686-2.3/Bio/Prosite creating build/lib.linux-i686-2.3/Bio/Rebase copying Bio/Rebase/Rebase.py -> build/lib.linux-i686-2.3/Bio/Rebase copying Bio/Rebase/__init__.py -> build/lib.linux-i686-2.3/Bio/Rebase creating build/lib.linux-i686-2.3/Bio/Saf copying Bio/Saf/Record.py -> build/lib.linux-i686-2.3/Bio/Saf copying Bio/Saf/saf_format.py -> build/lib.linux-i686-2.3/Bio/Saf copying Bio/Saf/__init__.py -> build/lib.linux-i686-2.3/Bio/Saf creating build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/FileIndex.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-i686-2.3/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-i686-2.3/Bio/SCOP creating build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testResidues.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testCla.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testDes.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testDom.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testScop.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testHie.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/testRaf.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests copying Bio/SCOP/tests/__init__.py -> build/lib.linux-i686-2.3/Bio/SCOP/tests creating build/lib.linux-i686-2.3/Bio/SeqIO copying Bio/SeqIO/generic.py -> build/lib.linux-i686-2.3/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-i686-2.3/Bio/SeqIO copying Bio/SeqIO/FASTA.py -> build/lib.linux-i686-2.3/Bio/SeqIO creating build/lib.linux-i686-2.3/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-i686-2.3/Bio/SeqUtils creating build/lib.linux-i686-2.3/Bio/SubsMat copying Bio/SubsMat/FreqTable.py -> build/lib.linux-i686-2.3/Bio/SubsMat copying Bio/SubsMat/MatrixInfo.py -> build/lib.linux-i686-2.3/Bio/SubsMat copying Bio/SubsMat/__init__.py -> build/lib.linux-i686-2.3/Bio/SubsMat creating build/lib.linux-i686-2.3/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/SVDSuperimposer.py -> build/lib.linux-i686-2.3/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-i686-2.3/Bio/SVDSuperimposer creating build/lib.linux-i686-2.3/Bio/SwissProt copying Bio/SwissProt/SProt.py -> build/lib.linux-i686-2.3/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-i686-2.3/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-i686-2.3/Bio/SwissProt creating build/lib.linux-i686-2.3/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-i686-2.3/Bio/UniGene creating build/lib.linux-i686-2.3/Bio/writers copying Bio/writers/__init__.py -> build/lib.linux-i686-2.3/Bio/writers creating build/lib.linux-i686-2.3/Bio/writers/SeqRecord copying Bio/writers/SeqRecord/fasta.py -> build/lib.linux-i686-2.3/Bio/writers/SeqRecord copying Bio/writers/SeqRecord/empty.py -> build/lib.linux-i686-2.3/Bio/writers/SeqRecord copying Bio/writers/SeqRecord/__init__.py -> build/lib.linux-i686-2.3/Bio/writers/SeqRecord creating build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/SCOP.py -> build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/NCBI.py -> build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/InterPro.py -> build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/ExPASy.py -> build/lib.linux-i686-2.3/Bio/WWW copying Bio/WWW/__init__.py -> build/lib.linux-i686-2.3/Bio/WWW creating build/lib.linux-i686-2.3/BioSQL copying BioSQL/Loader.py -> build/lib.linux-i686-2.3/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-i686-2.3/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-i686-2.3/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-i686-2.3/BioSQL copying BioSQL/__init__.py -> build/lib.linux-i686-2.3/BioSQL creating build/lib.linux-i686-2.3/Martel copying Martel/LAX.py -> build/lib.linux-i686-2.3/Martel copying Martel/msre_parse.py -> build/lib.linux-i686-2.3/Martel copying Martel/Iterator.py -> build/lib.linux-i686-2.3/Martel copying Martel/IterParser.py -> build/lib.linux-i686-2.3/Martel copying Martel/Generate.py -> build/lib.linux-i686-2.3/Martel copying Martel/convert_re.py -> build/lib.linux-i686-2.3/Martel copying Martel/Dispatch.py -> build/lib.linux-i686-2.3/Martel copying Martel/Expression.py -> build/lib.linux-i686-2.3/Martel copying Martel/Parser.py -> build/lib.linux-i686-2.3/Martel copying Martel/msre_constants.py -> build/lib.linux-i686-2.3/Martel copying Martel/optimize.py -> build/lib.linux-i686-2.3/Martel copying Martel/setup.py -> build/lib.linux-i686-2.3/Martel copying Martel/Time.py -> build/lib.linux-i686-2.3/Martel copying Martel/__init__.py -> build/lib.linux-i686-2.3/Martel copying Martel/RecordReader.py -> build/lib.linux-i686-2.3/Martel running build_ext building 'Bio.cSVM' extension creating build/temp.linux-i686-2.3 creating build/temp.linux-i686-2.3/Bio gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/csupport.c -o build/temp.linux-i686-2.3/Bio/csupport.o gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cSVMmodule.c -o build/temp.linux-i686-2.3/Bio/cSVMmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cSVMmodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cSVM.so building 'Bio.ckMeans' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/ckMeansmodule.c -o build/temp.linux-i686-2.3/Bio/ckMeansmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/ckMeansmodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/ckMeans.so building 'Bio.clistfns' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -I/usr/include/python2.3 -c Bio/clistfnsmodule.c -o build/temp.linux-i686-2.3/Bio/clistfnsmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/clistfnsmodule.o -o build/lib.linux-i686-2.3/Bio/clistfns.so building 'Bio.cmathfns' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cmathfnsmodule.c -o build/temp.linux-i686-2.3/Bio/cmathfnsmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cmathfnsmodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cmathfns.so building 'Bio.cstringfns' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -I/usr/include/python2.3 -c Bio/cstringfnsmodule.c -o build/temp.linux-i686-2.3/Bio/cstringfnsmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cstringfnsmodule.o -o build/lib.linux-i686-2.3/Bio/cstringfns.so building 'Bio.cdistance' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cdistancemodule.c -o build/temp.linux-i686-2.3/Bio/cdistancemodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cdistancemodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cdistance.so building 'Bio.cpairwise2' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cpairwise2module.c -o build/temp.linux-i686-2.3/Bio/cpairwise2module.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cpairwise2module.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cpairwise2.so building 'Bio.trie' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/trie.c -o build/temp.linux-i686-2.3/Bio/trie.o Bio/trie.c: Dans la fonction « Trie_has_prefix »: Bio/trie.c:443: AVERTISSEMENT: return transforme en entier un pointeur sans transtypage gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/triemodule.c -o build/temp.linux-i686-2.3/Bio/triemodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/triemodule.o build/temp.linux-i686-2.3/Bio/trie.o -o build/lib.linux-i686-2.3/Bio/trie.so building 'Bio.cMarkovModel' extension gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio -I/usr/include/python2.3 -c Bio/cMarkovModelmodule.c -o build/temp.linux-i686-2.3/Bio/cMarkovModelmodule.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/cMarkovModelmodule.o build/temp.linux-i686-2.3/Bio/csupport.o -o build/lib.linux-i686-2.3/Bio/cMarkovModel.so building 'Bio.Cluster.cluster' extension creating build/temp.linux-i686-2.3/Bio/Cluster gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio/Cluster -I/usr/include/python2.3 -c Bio/Cluster/linpack.c -o build/temp.linux-i686-2.3/Bio/Cluster/linpack.o gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio/Cluster -I/usr/include/python2.3 -c Bio/Cluster/clustermodule.c -o build/temp.linux-i686-2.3/Bio/Cluster/clustermodule.o gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio/Cluster -I/usr/include/python2.3 -c Bio/Cluster/ranlib.c -o build/temp.linux-i686-2.3/Bio/Cluster/ranlib.o gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio/Cluster -I/usr/include/python2.3 -c Bio/Cluster/cluster.c -o build/temp.linux-i686-2.3/Bio/Cluster/cluster.o gcc -fno-strict-aliasing -DNDEBUG -march=pentium3 -O3 -pipe -fPIC -IBio/Cluster -I/usr/include/python2.3 -c Bio/Cluster/com.c -o build/temp.linux-i686-2.3/Bio/Cluster/com.o gcc -pthread -shared -march=pentium3 -O3 -pipe build/temp.linux-i686-2.3/Bio/Cluster/clustermodule.o build/temp.linux-i686-2.3/Bio/Cluster/cluster.o build/temp.linux-i686-2.3/Bio/Cluster/ranlib.o build/temp.linux-i686-2.3/Bio/Cluster/com.o build/temp.linux-i686-2.3/Bio/Cluster/linpack.o -o build/lib.linux-i686-2.3/Bio/Cluster/cluster.so >>> Install biopython-1.21 into /var/tmp/portage/biopython-1.21/image/ category app-sci running install *** mxTextTools *** is either not installed or out of date. This package is required for many Biopython features. Please install it before you install Biopython. You can find mxTextTools at http://www.lemburg.com/files/python/mxExtensions.html. Do you want to continue this installation? (y/N) *** Martel *** is either not installed or out of date. This package is required for many Biopython features. Please install it before you install Biopython. You can find Martel at http://www.biopython.org/~dalke/Martel/. Do you want to continue this installation? (y/N) Traceback (most recent call last): File "setup.py", line 383, in ? ext_modules=EXTENSIONS, File "/usr/lib/python2.3/distutils/core.py", line 149, in setup dist.run_commands() File "/usr/lib/python2.3/distutils/dist.py", line 907, in run_commands self.run_command(cmd) File "/usr/lib/python2.3/distutils/dist.py", line 927, in run_command cmd_obj.run() File "setup.py", line 131, in run if self.check_dependencies(): File "setup.py", line 111, in check_dependencies if not get_yes_or_no( File "setup.py", line 48, in get_yes_or_no response = raw_input().lower() EOFError: EOF when reading a line !!! ERROR: app-sci/biopython-1.21 failed. !!! Function src_install, Line 27, Exitcode 1 !!! (no error message) Reproducible: Always Steps to Reproduce: 1. 2. 3.
Biopython 1.23 is now in portage stable. Could you check if this version solves your problems?
No, biopython-1.23 doesn't fix it either, and newer newer version will. Those are separate packages. Introduce them into protage tree and make biopython package depend on them: http://numpy.sourceforge.net - go for Numeric-23.1.tar.gz, unpack, "python setup.py install". Same for egenix-mx-base-2.0.5.tar.gz from http://www.egenix.com/files/python/eGenix-mx-Extensions.html Also, install ReportLab from http://www.reportlab.org/downloads.html . BTW: I saw some errors anyway: copying Bio/EUtils/DTDs/LinkOut.dtd -> /var/tmp/portage/biopython-1.23/image/usr/lib/python2.3/site-packages/Bio/EUtils/DTDs copying Bio/EUtils/DTDs/ePost_020511.dtd -> /var/tmp/portage/biopython-1.23/image/usr/lib/python2.3/site-packages/Bio/EUtils/DTDs install: `Doc/examples' is a directory gzip: /var/tmp/portage/biopython-1.23/image/usr/share/doc/biopython-1.23/examples: No such file or directory install: `Doc/install' is a directory gzip: /var/tmp/portage/biopython-1.23/image/usr/share/doc/biopython-1.23/install: No such file or directory man: prepallstrip: strip:
Looks like current packages have the necessary dependencies. Closing this bug.
