Date: Tue, 8 Jan 2002 23:39:58 -0800 (PST) From: Hye-Shik Chang <perky@fallin.lv> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/33719: Update port: biology/py-biopython Message-ID: <200201090739.g097dwa01952@freefall.freebsd.org>
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>Number: 33719 >Category: ports >Synopsis: Update port: biology/py-biopython >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Jan 08 23:40:01 PST 2002 >Closed-Date: >Last-Modified: >Originator: Hye-Shik Chang >Release: FreeBSD 4.4 >Organization: Yonsei University >Environment: FreeBSD perky.dnip.net 4.5-PRERELEASE FreeBSD 4.5-PRERELEASE #0: Fri Dec 28 21:27:47 KST 2001 root@perky.dnip.net:/usr/src/sys/compile/KENNY i386 >Description: update to 1.00.a4 >How-To-Repeat: >Fix: diff -ruN py-biopython.orig/Makefile py-biopython/Makefile --- py-biopython.orig/Makefile Mon Oct 8 13:02:33 2001 +++ py-biopython/Makefile Wed Jan 9 16:36:18 2002 @@ -6,8 +6,7 @@ # PORTNAME= biopython -PORTVERSION= 1.00.a3 -PORTREVISION= 1 +PORTVERSION= 1.00.a4 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/Download/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -73,6 +72,10 @@ PLIST_OMNIORB= "@comment " PLIST_FNORB= "@comment " .endif # defined(WITH_CORBA) + +.if !defined(WITHOUT_REPORTLAB) +RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab +.endif pre-fetch: .if !defined(BATCH) && !defined(WITH_CORBA) diff -ruN py-biopython.orig/distinfo py-biopython/distinfo --- py-biopython.orig/distinfo Mon Oct 8 13:02:33 2001 +++ py-biopython/distinfo Wed Jan 9 16:39:34 2002 @@ -1,2 +1,2 @@ -MD5 (biopython-1.00a3.tar.gz) = be59a12eeb2c0bcdd82a73dfd7bcc615 +MD5 (biopython-1.00a4.tar.gz) = bca77b4242c9a8495f60c7475b884c5d MD5 (biopython-corba-0.3.0.tar.gz) = 4465f240d22b113314c70b1dc8ebc41c diff -ruN py-biopython.orig/pkg-plist py-biopython/pkg-plist --- py-biopython.orig/pkg-plist Mon Oct 8 13:02:33 2001 +++ py-biopython/pkg-plist Wed Jan 9 16:33:22 2002 @@ -203,17 +203,22 @@ %%PORTDOCS%%share/doc/biopython/Blast.txt %%PORTDOCS%%share/doc/biopython/Enzyme.txt %%PORTDOCS%%share/doc/biopython/Fasta.txt +%%PORTDOCS%%share/doc/biopython/IntelliGenetics.txt +%%PORTDOCS%%share/doc/biopython/InterPro.txt %%PORTDOCS%%share/doc/biopython/KEGG.txt %%PORTDOCS%%share/doc/biopython/Medline.txt %%PORTDOCS%%share/doc/biopython/Parser.txt %%PORTDOCS%%share/doc/biopython/Prosite.txt %%PORTDOCS%%share/doc/biopython/References.txt -%%PORTDOCS%%share/doc/biopython/SCOP.txt %%PORTDOCS%%share/doc/biopython/SwissProt.txt %%PORTDOCS%%share/doc/biopython/Tutorial.pdf %%PORTDOCS%%share/doc/biopython/Tutorial.tex %%PORTDOCS%%share/doc/biopython/Tutorial.txt %%PORTDOCS%%share/doc/biopython/make_api_docs.py +%%PORTDOCS%%share/doc/biopython/metatool.txt +%%PORTDOCS%%share/examples/biopython/GenBank/check_output.py +%%PORTDOCS%%share/examples/biopython/GenBank/check_output_simple.py +%%PORTDOCS%%share/examples/biopython/GenBank/find_parser_problems.py %%PORTDOCS%%share/examples/biopython/SeqGui/SeqGui.py %%PORTDOCS%%share/examples/biopython/clustal_run.py %%PORTDOCS%%share/examples/biopython/fasta_consumer.py @@ -228,6 +233,7 @@ %%PORTDOCS%%share/examples/biopython/pubmed_search.py %%PORTDOCS%%share/examples/biopython/query_entrez.py %%PORTDOCS%%share/examples/biopython/query_pubmed.py +%%PORTDOCS%%share/examples/biopython/scop_pdb.py %%PORTDOCS%%share/examples/biopython/swissprot.py %%PORTDOCS%%share/examples/biopython/www_blast.py %%PORTDOCS%%share/examples/biopython/xbbtools/README @@ -236,7 +242,9 @@ %%PORTDOCS%%share/examples/biopython/xbbtools/testrp.fas %%PORTDOCS%%share/examples/biopython/xbbtools/xbb_blast.py %%PORTDOCS%%share/examples/biopython/xbbtools/xbb_blastbg.py +%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_help.py %%PORTDOCS%%share/examples/biopython/xbbtools/xbb_io.py +%%PORTDOCS%%share/examples/biopython/xbbtools/xbb_search.py %%PORTDOCS%%share/examples/biopython/xbbtools/xbb_sequence.py %%PORTDOCS%%share/examples/biopython/xbbtools/xbb_translations.py %%PORTDOCS%%share/examples/biopython/xbbtools/xbb_utils.py @@ -254,6 +262,8 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/cfastpairwise.so +lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/csupport.so lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Align/fastpairwise.pyo @@ -269,6 +279,12 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Application/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Application/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Application/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/Applications.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/Applications.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/Applications.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/NCBIStandalone.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/NCBIStandalone.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/NCBIStandalone.pyo @@ -296,6 +312,21 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Data/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Data/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Data/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/Applications.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/Applications.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/Applications.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/Primer.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/Primer.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/Primer.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/primer3_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/primer3_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/primer3_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/primersearch_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/primersearch_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss/primersearch_format.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Encodings/IUPACEncoding.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Encodings/IUPACEncoding.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Encodings/IUPACEncoding.pyo @@ -323,6 +354,54 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/File.py lib/%%PYTHON_VERSION%%/site-packages/Bio/File.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/File.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/General.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/General.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/General.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/Point.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/Point.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/Point.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Evolver.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Evolver.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Evolver.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/General.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/General.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/General.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/Simple.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/Simple.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/Simple.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Organism.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Organism.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Organism.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Repair/Stabilizing.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Repair/Stabilizing.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Repair/Stabilizing.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Repair/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Repair/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Repair/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Abstract.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Abstract.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Abstract.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Diversity.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Diversity.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Diversity.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/RouletteWheel.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/RouletteWheel.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/RouletteWheel.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Tournament.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Tournament.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/Tournament.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/__init__.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/LocationParser.py lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/LocationParser.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/LocationParser.pyo @@ -335,12 +414,54 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/genbank_format.py lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/genbank_format.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/genbank_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/utils.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/utils.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank/utils.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/BasicChromosome.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/BasicChromosome.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/BasicChromosome.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/Comparative.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/Comparative.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/Comparative.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/DisplayRepresentation.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/DisplayRepresentation.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/DisplayRepresentation.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/Distribution.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/Distribution.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/Distribution.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/DynamicProgramming.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/DynamicProgramming.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/DynamicProgramming.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/MarkovModel.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/MarkovModel.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/MarkovModel.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/Trainer.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/Trainer.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/Trainer.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/Utilities.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/Utilities.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/Utilities.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM/__init__.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/Record.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/Record.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/Record.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/intelligenetics_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/intelligenetics_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics/intelligenetics_format.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro/__init__.pyo @@ -356,6 +477,12 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.py lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme/enzyme_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Map/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Map/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Map/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Map/map_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Map/map_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Map/map_format.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/__init__.pyo @@ -368,18 +495,99 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/kabat_format.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/kabat_format.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat/kabat_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/NLMMedlineXML.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/NLMMedlineXML.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/NLMMedlineXML.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/PubMed.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/PubMed.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/PubMed.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_001211_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_001211_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_001211_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_010319_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_010319_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_010319_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_011101_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_011101_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/nlmmedline_011101_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/Input.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/Input.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/Input.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/Record.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/Record.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/Record.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/metatool_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/metatool_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool/metatool_format.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/Record.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/Record.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/Record.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/ValSeq.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/ValSeq.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/ValSeq.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/nbrf_format.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/nbrf_format.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF/nbrf_format.pyo 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+lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep/HashSet.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep/HashSet.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep/MultiGraph.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep/MultiGraph.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep/MultiGraph.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/__init__.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/__init__.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/__init__.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/PropertyManager.py lib/%%PYTHON_VERSION%%/site-packages/Bio/PropertyManager.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/PropertyManager.pyo @@ -401,15 +609,27 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/RecordFile.py lib/%%PYTHON_VERSION%%/site-packages/Bio/RecordFile.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/RecordFile.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Cla.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Cla.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Cla.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Des.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Des.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Des.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Dom.py lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Dom.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Dom.pyo -lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Lin.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Lin.pyc -lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Lin.pyo -lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Location.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Location.pyc -lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Location.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/FileIndex.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/FileIndex.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/FileIndex.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Hie.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Hie.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Hie.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Raf.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Raf.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Raf.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Residues.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Residues.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/Residues.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP/__init__.pyo @@ -425,6 +645,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqIO/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqIO/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqIO/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqIO/generic.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqIO/generic.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqIO/generic.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqRecord.py lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqRecord.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqRecord.pyo @@ -446,6 +669,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.py lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/LogisticRegression.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/LogisticRegression.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/LogisticRegression.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.py lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/Tools/Classification/MaxEntropy.pyo @@ -516,6 +742,9 @@ lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/ExPASy.py lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/ExPASy.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/ExPASy.pyo +lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/InterPro.py +lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/InterPro.pyc +lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/InterPro.pyo lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/NCBI.py lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/NCBI.pyc lib/%%PYTHON_VERSION%%/site-packages/Bio/WWW/NCBI.pyo @@ -547,22 +776,40 @@ @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/SCOP @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Rebase @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Prosite +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway/Rep +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Pathway @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/PDB +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/NeuralNetwork/Gene +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/NeuralNetwork/BackPropagation +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/NeuralNetwork +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/NBRF +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/MetaTool @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Kabat +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Map @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Enzyme @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG/Compound @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/KEGG @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/InterPro +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/IntelliGenetics +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/HMM +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Graphics @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Gobase @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GenBank +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Selection +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Repair +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Mutation +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GA/Crossover +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/GA @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/FSSP @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Enzyme @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Encodings +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Emboss @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Data @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Clustalw @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast +@dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Application @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Alphabet @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio/Align @dirrm lib/%%PYTHON_VERSION%%/site-packages/Bio @@ -570,6 +817,7 @@ %%PORTDOCS%%%%PLIST_CORBA%%@dirrm share/doc/biopython/BioCorba %%PORTDOCS%%@dirrm share/examples/biopython/xbbtools %%PORTDOCS%%@dirrm share/examples/biopython/SeqGui +%%PORTDOCS%%@dirrm share/examples/biopython/GenBank %%PORTDOCS%%@dirrm share/examples/biopython %%PORTDOCS%%@dirrm share/doc/biopython %%PLIST_OMNIORB%%@dirrm lib/%%PYTHON_VERSION%%/site-packages/BioCorba/bsane__POA/seqcore >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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