--- Makefile.orig 2010-01-02 09:24:55.000000000 +0800 +++ Makefile 2010-01-01 11:43:59.000000000 +0800 @@ -6,7 +6,7 @@ # PORTNAME= biopython -PORTVERSION= 1.51 +PORTVERSION= 1.53 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} --- distinfo.orig 2010-01-02 09:25:26.000000000 +0800 +++ distinfo 2010-01-01 11:44:42.000000000 +0800 @@ -1,3 +1,3 @@ -MD5 (biopython-1.51.tar.gz) = e973cb96b44b47526d31b6a0039c686f -SHA256 (biopython-1.51.tar.gz) = 0ebf44e6376d7b44fb2857e751d388f30402d6a81798821e40a7f7b92a4b036b -SIZE (biopython-1.51.tar.gz) = 5557548 +MD5 (biopython-1.53.tar.gz) = df1004ec64b9b593c0e690c14a20667a +SHA256 (biopython-1.53.tar.gz) = 0db8bf8d37641fdfc6a8aac248de3d8cb4111e55484deb43f67e8d7ad082013f +SIZE (biopython-1.53.tar.gz) = 4284683 --- pkg-plist.orig 2010-01-02 09:25:37.000000000 +0800 +++ pkg-plist 2010-01-01 19:06:04.000000000 +0800 @@ -162,75 +162,6 @@ %%PYTHON_SITELIBDIR%%/Bio/DocSQL.py %%PYTHON_SITELIBDIR%%/Bio/DocSQL.pyc %%PYTHON_SITELIBDIR%%/Bio/DocSQL.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DBIdsClient.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DBIdsClient.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DBIdsClient.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/LinkOut.dtd -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/LinkOut.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/LinkOut.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/LinkOut.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eInfo_020511.dtd -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eInfo_020511.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eInfo_020511.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eInfo_020511.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eLink_020511.dtd -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eLink_020511.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eLink_020511.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eLink_020511.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/ePost_020511.dtd -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/ePost_020511.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/ePost_020511.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/ePost_020511.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSearch_020511.dtd -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSearch_020511.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSearch_020511.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSearch_020511.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSummary_020511.dtd -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSummary_020511.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSummary_020511.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs/eSummary_020511.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Datatypes.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Datatypes.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Datatypes.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/HistoryClient.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/HistoryClient.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/HistoryClient.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Mixins.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Mixins.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/Mixins.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/MultiDict.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/MultiDict.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/MultiDict.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/POM.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/POM.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/POM.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/ReseekFile.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/ReseekFile.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/ReseekFile.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/ThinClient.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/ThinClient.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/ThinClient.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/dtd2py.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/dtd2py.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/dtd2py.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/parse.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/parse.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/parse.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/setup.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/setup.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/setup.pyo -%%PYTHON_SITELIBDIR%%/Bio/EUtils/sourcegen.py -%%PYTHON_SITELIBDIR%%/Bio/EUtils/sourcegen.pyc -%%PYTHON_SITELIBDIR%%/Bio/EUtils/sourcegen.pyo %%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.py %%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.pyc %%PYTHON_SITELIBDIR%%/Bio/EZRetrieve.pyo @@ -295,10 +226,14 @@ %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSpell.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSummary_041029.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/egquery.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pmc-1.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/pubmed_100101.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_080101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmcommon_090101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_080101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedline_090101.dtd +%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmserials_080101.dtd @@ -566,6 +501,9 @@ %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.py %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyc %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MEME.pyo +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.py +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.pyc +%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/MAST.pyo %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyo @@ -591,9 +529,6 @@ %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.py %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.pyc %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.pyo -%%PYTHON_SITELIBDIR%%/Bio/Ndb/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/Ndb/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/Ndb/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/NetCatch.py %%PYTHON_SITELIBDIR%%/Bio/NetCatch.pyc %%PYTHON_SITELIBDIR%%/Bio/NetCatch.pyo @@ -778,6 +713,12 @@ %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Controller.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/EasyController.pyo %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.py %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyo @@ -821,10 +762,9 @@ %%PYTHON_SITELIBDIR%%/Bio/Prosite/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Prosite/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Prosite/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/PubMed.py -%%PYTHON_SITELIBDIR%%/Bio/PubMed.pyc -%%PYTHON_SITELIBDIR%%/Bio/PubMed.pyo -%%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.so +%%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.py +%%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.pyc +%%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.pyo %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.py %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.pyc %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.pyo @@ -849,6 +789,9 @@ %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.py %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyc %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyo @@ -858,9 +801,6 @@ %%PYTHON_SITELIBDIR%%/Bio/SCOP/Dom.py %%PYTHON_SITELIBDIR%%/Bio/SCOP/Dom.pyc %%PYTHON_SITELIBDIR%%/Bio/SCOP/Dom.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/FileIndex.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/FileIndex.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/FileIndex.pyo %%PYTHON_SITELIBDIR%%/Bio/SCOP/Hie.py %%PYTHON_SITELIBDIR%%/Bio/SCOP/Hie.pyc %%PYTHON_SITELIBDIR%%/Bio/SCOP/Hie.pyo @@ -870,9 +810,6 @@ %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.py %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.pyc %%PYTHON_SITELIBDIR%%/Bio/SCOP/Residues.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.py %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyc %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/SVDSuperimposer.pyo @@ -888,6 +825,12 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.py %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqFeature.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.py +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_convert.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.py +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqIO/_index.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.py %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqIO/AceIO.pyo @@ -957,6 +900,12 @@ %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.py +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.pyc +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications/_Novoalign.pyo %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyo @@ -993,9 +942,9 @@ %%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.py %%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/UniGene/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.py +%%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyc +%%PYTHON_SITELIBDIR%%/Bio/UniGene/UniGene.pyo %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyo @@ -1009,13 +958,7 @@ %%PYTHON_SITELIBDIR%%/Bio/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/cMarkovModel.so -%%PYTHON_SITELIBDIR%%/Bio/clistfns.so -%%PYTHON_SITELIBDIR%%/Bio/cmathfns.so %%PYTHON_SITELIBDIR%%/Bio/cpairwise2.so -%%PYTHON_SITELIBDIR%%/Bio/cstringfns.so -%%PYTHON_SITELIBDIR%%/Bio/distance.py -%%PYTHON_SITELIBDIR%%/Bio/distance.pyc -%%PYTHON_SITELIBDIR%%/Bio/distance.pyo %%PYTHON_SITELIBDIR%%/Bio/kNN.py %%PYTHON_SITELIBDIR%%/Bio/kNN.pyc %%PYTHON_SITELIBDIR%%/Bio/kNN.pyo @@ -1052,8 +995,6 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/Compass @dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal @dirrm %%PYTHON_SITELIBDIR%%/Bio/Data -@dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs -@dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils @dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss @dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings @dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs @@ -1085,7 +1026,6 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers @dirrm %%PYTHON_SITELIBDIR%%/Bio/Motif @dirrm %%PYTHON_SITELIBDIR%%/Bio/NMR -@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ndb @dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation @dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene @dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork @@ -1108,11 +1048,11 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer @dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqIO @dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqUtils +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Sequencing/Applications @dirrm %%PYTHON_SITELIBDIR%%/Bio/Sequencing @dirrm %%PYTHON_SITELIBDIR%%/Bio/Statistics @dirrm %%PYTHON_SITELIBDIR%%/Bio/SubsMat @dirrm %%PYTHON_SITELIBDIR%%/Bio/SwissProt @dirrm %%PYTHON_SITELIBDIR%%/Bio/UniGene -@dirrm %%PYTHON_SITELIBDIR%%/Bio/WWW @dirrm %%PYTHON_SITELIBDIR%%/Bio/Wise @dirrm %%PYTHON_SITELIBDIR%%/Bio