Date: Tue, 1 Jul 2008 02:47:23 GMT From: Wen heping <wenheping@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/125134: [Update]biology/py-biopython:update to 1.45 Message-ID: <200807010247.m612lN95026351@www.freebsd.org> Resent-Message-ID: <200807010250.m612o8kW094270@freefall.freebsd.org>
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>Number: 125134 >Category: ports >Synopsis: [Update]biology/py-biopython:update to 1.45 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Tue Jul 01 02:50:07 UTC 2008 >Closed-Date: >Last-Modified: >Originator: Wen heping >Release: FreeBSD 7.0 release >Organization: ChangAn Middle School >Environment: FreeBSD fb7.wenjing.com 7.0-RELEASE FreeBSD 7.0-RELEASE #0: Sun Feb 24 19:59:52 UTC 2008 root@logan.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC i386 >Description: update to 1.45 from 1.43 >How-To-Repeat: >Fix: Patch attached with submission follows: --- Makefile.orig 2008-07-01 09:25:01.000000000 +0000 +++ Makefile 2008-07-01 09:25:15.000000000 +0000 @@ -6,7 +6,7 @@ # PORTNAME= biopython -PORTVERSION= 1.43 +PORTVERSION= 1.45 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} --- distinfo.orig 2007-05-30 06:57:20.000000000 +0000 +++ distinfo 2008-07-01 09:26:06.000000000 +0000 @@ -1,3 +1,3 @@ -MD5 (biopython-1.43.tar.gz) = 3c275b321bb1db7d8bda764913aaedcd -SHA256 (biopython-1.43.tar.gz) = eb424da9efddbf376c31660786ecb34ff893ea752bf7300f4a06d1b8c6ba175b -SIZE (biopython-1.43.tar.gz) = 3867907 +MD5 (biopython-1.45.tar.gz) = 049ff32be28297b77c25624082118629 +SHA256 (biopython-1.45.tar.gz) = ea9af15729aed1a3eb9d8bc65bced919390b50d0f93622a69ef9aaeb3ff56020 +SIZE (biopython-1.45.tar.gz) = 3978249 --- pkg-plist.orig 2008-07-01 09:25:06.000000000 +0000 +++ pkg-plist 2008-07-01 09:51:05.000000000 +0000 @@ -221,6 +221,9 @@ %%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Encodings/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Entrez/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.pyo @@ -338,9 +341,6 @@ %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/Geo/geo_format.py -%%PYTHON_SITELIBDIR%%/Bio/Geo/geo_format.pyc -%%PYTHON_SITELIBDIR%%/Bio/Geo/geo_format.pyo %%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.pyo @@ -405,33 +405,15 @@ %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.py %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/compound_format.py -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/compound_format.pyc -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/compound_format.pyo %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/__init__.py %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/enzyme_format.py -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/enzyme_format.pyc -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/enzyme_format.pyo %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/__init__.py %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/map_format.py -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/map_format.pyc -%%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/map_format.pyo %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.py %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/Kabat/Record.py -%%PYTHON_SITELIBDIR%%/Bio/Kabat/Record.pyc -%%PYTHON_SITELIBDIR%%/Bio/Kabat/Record.pyo -%%PYTHON_SITELIBDIR%%/Bio/Kabat/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/Kabat/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/Kabat/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/Kabat/kabat_format.py -%%PYTHON_SITELIBDIR%%/Bio/Kabat/kabat_format.pyc -%%PYTHON_SITELIBDIR%%/Bio/Kabat/kabat_format.pyo %%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.py %%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.pyo @@ -688,6 +670,9 @@ %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.py %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/PDB/parse_pdb_header.py %%PYTHON_SITELIBDIR%%/Bio/PDB/parse_pdb_header.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/parse_pdb_header.pyo @@ -715,6 +700,58 @@ %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Async.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Async.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Async.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Controller.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Controller.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Controller.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Utils.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Utils.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Utils.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyo +%%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/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Async.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Async.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Async.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Cache.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Cache.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Cache.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Controller.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Controller.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Controller.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Template.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Template.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Template.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/bottle.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/decline_lambda.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/decline_split.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/island.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/simple.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/split_island.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/split_ssm_1d.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/split_ssm_2d.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/ssm_1d.par +%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/ssm_2d.par %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.py %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.pyc %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.pyo @@ -845,6 +882,12 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.py %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.py %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyo @@ -1094,6 +1137,9 @@ %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.py %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyc %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyo +%%PYTHON_SITELIBDIR%%/Bio/ExPASy.py +%%PYTHON_SITELIBDIR%%/Bio/ExPASy.pyc +%%PYTHON_SITELIBDIR%%/Bio/ExPASy.pyo %%PYTHON_SITELIBDIR%%/Bio/kNN.py %%PYTHON_SITELIBDIR%%/Bio/kNN.pyc %%PYTHON_SITELIBDIR%%/Bio/kNN.pyo @@ -1213,6 +1259,7 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils @dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss @dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez @dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme @dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP @dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta @@ -1234,7 +1281,6 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme @dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map @dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG -@dirrm %%PYTHON_SITELIBDIR%%/Bio/Kabat @dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink @dirrm %%PYTHON_SITELIBDIR%%/Bio/MEME @dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline @@ -1248,6 +1294,13 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene @dirrm %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork @dirrm %%PYTHON_SITELIBDIR%%/Bio/Nexus +@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data +@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal +@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop +@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist +@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async +@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen +@dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF @dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB @dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers @dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep >Release-Note: >Audit-Trail: >Unformatted:
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