Date: Fri, 20 Oct 2006 18:22:38 -0400 (EDT) From: Thomas Abthorpe <thomas@goodking.ca> To: FreeBSD-gnats-submit@FreeBSD.org Cc: mauricio@arareko.net, thomas@goodking.ca Subject: ports/104635: [PATCH] biology/py24-biopython: update to 1.42 Message-ID: <200610202222.k9KMMcna030261@goodking.goodking.ca> Resent-Message-ID: <200610202230.k9KMUI4B084865@freefall.freebsd.org>
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>Number: 104635 >Category: ports >Synopsis: [PATCH] biology/py24-biopython: update to 1.42 >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: Fri Oct 20 22:30:18 GMT 2006 >Closed-Date: >Last-Modified: >Originator: Thomas Abthorpe >Release: FreeBSD 6.2-PRERELEASE i386 >Organization: GoodKing.Ca >Environment: System: FreeBSD goodking.goodking.ca 6.2-PRERELEASE FreeBSD 6.2-PRERELEASE #2: Mon Oct 2 02:05:54 EDT >Description: - Update to 1.42 Port maintainer (mauricio@arareko.net) is cc'd. Generated with FreeBSD Port Tools 0.77 >How-To-Repeat: >Fix: --- py24-biopython-1.42.patch begins here --- Index: Makefile =================================================================== RCS file: /home/ncvs/ports/biology/py-biopython/Makefile,v retrieving revision 1.21 diff -u -r1.21 Makefile --- Makefile 11 Nov 2005 01:15:34 -0000 1.21 +++ Makefile 20 Oct 2006 22:21:57 -0000 @@ -6,9 +6,9 @@ # PORTNAME= biopython -PORTVERSION= 1.41 +PORTVERSION= 1.42 CATEGORIES= biology python -MASTER_SITES= http://www.biopython.org/files/ +MASTER_SITES= http://www.biopython.org/DIST/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= mauricio@arareko.net Index: distinfo =================================================================== RCS file: /home/ncvs/ports/biology/py-biopython/distinfo,v retrieving revision 1.12 diff -u -r1.12 distinfo --- distinfo 11 Nov 2005 01:15:34 -0000 1.12 +++ distinfo 20 Oct 2006 22:21:57 -0000 @@ -1,3 +1,3 @@ -MD5 (biopython-1.41.tar.gz) = 03f8efc258fb49b07d1a2b642fa8362e -SHA256 (biopython-1.41.tar.gz) = 15b708b7635fd993aad3c53fd4cfc28601da6d4332b027d09899f1cb5178cef9 -SIZE (biopython-1.41.tar.gz) = 3807547 +MD5 (biopython-1.42.tar.gz) = 6d9bf58d0fcfa5a3b2053ad419069ff3 +SHA256 (biopython-1.42.tar.gz) = ba4d00fdf7de67196ecba317dee09a14850b40596bd83d73e458c5f19fc9fc58 +SIZE (biopython-1.42.tar.gz) = 3933507 Index: pkg-plist =================================================================== RCS file: /home/ncvs/ports/biology/py-biopython/pkg-plist,v retrieving revision 1.11 diff -u -r1.11 pkg-plist --- pkg-plist 11 Nov 2005 01:15:34 -0000 1.11 +++ pkg-plist 20 Oct 2006 22:21:57 -0000 @@ -7,9 +7,6 @@ %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/Ais/example_ais2.py -%%PYTHON_SITELIBDIR%%/Bio/Ais/example_ais2.pyc -%%PYTHON_SITELIBDIR%%/Bio/Ais/example_ais2.pyo %%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.py %%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.pyc %%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.pyo @@ -98,9 +95,6 @@ %%PYTHON_SITELIBDIR%%/Bio/Cluster/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Cluster/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/Cluster/cluster.so -%%PYTHON_SITELIBDIR%%/Bio/Cluster/data.py -%%PYTHON_SITELIBDIR%%/Bio/Cluster/data.pyc -%%PYTHON_SITELIBDIR%%/Bio/Cluster/data.pyo %%PYTHON_SITELIBDIR%%/Bio/Compass/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Compass/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Compass/__init__.pyo @@ -678,10 +672,6 @@ %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.py %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF/MMCIFlex.so -%%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 @@ -727,12 +717,6 @@ %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/RecordFile.py -%%PYTHON_SITELIBDIR%%/Bio/RecordFile.pyc -%%PYTHON_SITELIBDIR%%/Bio/RecordFile.pyo -%%PYTHON_SITELIBDIR%%/Bio/ReseekFile.py -%%PYTHON_SITELIBDIR%%/Bio/ReseekFile.pyc -%%PYTHON_SITELIBDIR%%/Bio/ReseekFile.pyo %%PYTHON_SITELIBDIR%%/Bio/Restriction/DNAUtils.so %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.py %%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.pyc @@ -791,9 +775,6 @@ %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/__init__.py %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/SVM.py -%%PYTHON_SITELIBDIR%%/Bio/SVM.pyc -%%PYTHON_SITELIBDIR%%/Bio/SVM.pyo %%PYTHON_SITELIBDIR%%/Bio/Saf/Record.py %%PYTHON_SITELIBDIR%%/Bio/Saf/Record.pyc %%PYTHON_SITELIBDIR%%/Bio/Saf/Record.pyo @@ -942,9 +923,7 @@ %%PYTHON_SITELIBDIR%%/Bio/builders/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/builders/__init__.pyo %%PYTHON_SITELIBDIR%%/Bio/cMarkovModel.so -%%PYTHON_SITELIBDIR%%/Bio/cSVM.so %%PYTHON_SITELIBDIR%%/Bio/cdistance.so -%%PYTHON_SITELIBDIR%%/Bio/ckMeans.so %%PYTHON_SITELIBDIR%%/Bio/clistfns.so %%PYTHON_SITELIBDIR%%/Bio/cmathfns.so %%PYTHON_SITELIBDIR%%/Bio/config/DBRegistry.py @@ -1075,9 +1054,6 @@ %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.py %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyc %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyo -%%PYTHON_SITELIBDIR%%/Bio/kMeans.py -%%PYTHON_SITELIBDIR%%/Bio/kMeans.pyc -%%PYTHON_SITELIBDIR%%/Bio/kMeans.pyo %%PYTHON_SITELIBDIR%%/Bio/kNN.py %%PYTHON_SITELIBDIR%%/Bio/kNN.pyc %%PYTHON_SITELIBDIR%%/Bio/kNN.pyo @@ -1093,9 +1069,6 @@ %%PYTHON_SITELIBDIR%%/Bio/pairwise2.py %%PYTHON_SITELIBDIR%%/Bio/pairwise2.pyc %%PYTHON_SITELIBDIR%%/Bio/pairwise2.pyo -%%PYTHON_SITELIBDIR%%/Bio/sequtils.py -%%PYTHON_SITELIBDIR%%/Bio/sequtils.pyc -%%PYTHON_SITELIBDIR%%/Bio/sequtils.pyo %%PYTHON_SITELIBDIR%%/Bio/stringfns.py %%PYTHON_SITELIBDIR%%/Bio/stringfns.pyc %%PYTHON_SITELIBDIR%%/Bio/stringfns.pyo @@ -1121,9 +1094,6 @@ %%PYTHON_SITELIBDIR%%/Bio/writers/__init__.py %%PYTHON_SITELIBDIR%%/Bio/writers/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/writers/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/xkMeans.py -%%PYTHON_SITELIBDIR%%/Bio/xkMeans.pyc -%%PYTHON_SITELIBDIR%%/Bio/xkMeans.pyo %%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py %%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc %%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo @@ -1184,92 +1154,91 @@ %%PYTHON_SITELIBDIR%%/Martel/setup.py %%PYTHON_SITELIBDIR%%/Martel/setup.pyc %%PYTHON_SITELIBDIR%%/Martel/setup.pyo -@dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy -@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ais -@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align -@dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce -@dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet -@dirrm 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%%PYTHON_SITELIBDIR%%/Bio/GenBank +@dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF +@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Selection +@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Repair +@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Mutation +@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover +@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta +@dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss +@dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs +@dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils +@dirrm %%PYTHON_SITELIBDIR%%/Bio/ECell +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Data +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Compass +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Cluster +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Clustalw +@dirrm %%PYTHON_SITELIBDIR%%/Bio/CDD +@dirrm %%PYTHON_SITELIBDIR%%/Bio/CAPS +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Application +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet +@dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Ais +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy @dirrm %%PYTHON_SITELIBDIR%%/Bio -@dirrm %%PYTHON_SITELIBDIR%%/BioSQL -@dirrm %%PYTHON_SITELIBDIR%%/Martel --- py24-biopython-1.42.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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