Date: Sun, 5 Sep 2004 14:55:11 +0200 (CEST) From: Stefan Walter <sw@gegenunendlich.de> To: FreeBSD-gnats-submit@FreeBSD.org Cc: wjv@FreeBSD.org Subject: ports/71400: [PATCH] biology/py23-biopython: unbreak/update to 1.30 Message-ID: <20040905125511.4BD143E37@kyuzo.dunkelkammer.void> Resent-Message-ID: <200409051300.i85D0XnF005960@freefall.freebsd.org>
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>Number: 71400 >Category: ports >Synopsis: [PATCH] biology/py23-biopython: unbreak/update to 1.30 >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: Sun Sep 05 13:00:33 GMT 2004 >Closed-Date: >Last-Modified: >Originator: Stefan Walter >Release: FreeBSD 5.2-CURRENT i386 >Organization: Infinity Approximation Task Force >Environment: System: FreeBSD kyuzo.dunkelkammer.void 5.2-CURRENT FreeBSD 5.2-CURRENT #0: Wed Jul 28 20:21:17 CEST 2004 >Description: - Unbreak build by fixing dependency list - Update to 1.30, which really honors PREFIX - USE_PYDISTUTILS Port maintainer (wjv@FreeBSD.org) is cc'd. Generated with FreeBSD Port Tools 0.50 >How-To-Repeat: >Fix: --- py23-biopython-1.30.patch begins here --- diff -ruN --exclude=CVS /usr/ports/biology/py-biopython.old/Makefile /usr/ports/biology/py-biopython/Makefile --- /usr/ports/biology/py-biopython.old/Makefile Sun Sep 5 13:44:19 2004 +++ /usr/ports/biology/py-biopython/Makefile Sun Sep 5 14:16:13 2004 @@ -6,7 +6,7 @@ # PORTNAME= biopython -PORTVERSION= 1.23 +PORTVERSION= 1.30 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/files/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -16,26 +16,16 @@ CONFLICTS= py*-martel-* -BROKEN= "Does not build" - -BUILD_DEPENDS= ${PYDISTUTILS} -RUN_DEPENDS= ${PYNUMERIC} \ +BUILD_DEPENDS= ${PYNUMERIC} \ ${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base +RUN_DEPENDS= ${BUILD_DEPENDS} -USE_PERL5_BUILD=yes -USE_PYTHON= 2.0+ -PYTHON_SETUP= ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py -CPIO= cpio --quiet -pdum -R -EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME} +USE_PYTHON= 2.2+ +USE_PYDISTUTILS=yes .if !defined(WITHOUT_REPORTLAB) +BUILD_DEPENDS+= ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab .endif - -do-build: - (cd ${WRKSRC} && ${PYTHON_SETUP} build) - -do-install: - (cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 --prefix=${PREFIX}) .include <bsd.port.mk> diff -ruN --exclude=CVS /usr/ports/biology/py-biopython.old/distinfo /usr/ports/biology/py-biopython/distinfo --- /usr/ports/biology/py-biopython.old/distinfo Sun Sep 5 13:44:19 2004 +++ /usr/ports/biology/py-biopython/distinfo Sun Sep 5 14:17:08 2004 @@ -1,2 +1,2 @@ -MD5 (biopython-1.23.tar.gz) = 45ea628621c6b04d471f029ef5873aaf -SIZE (biopython-1.23.tar.gz) = 2241300 +MD5 (biopython-1.30.tar.gz) = d8df866a40be20962b8ef52baa5376c1 +SIZE (biopython-1.30.tar.gz) = 3186467 diff -ruN --exclude=CVS /usr/ports/biology/py-biopython.old/pkg-plist /usr/ports/biology/py-biopython/pkg-plist --- /usr/ports/biology/py-biopython.old/pkg-plist Sun Sep 5 13:44:19 2004 +++ /usr/ports/biology/py-biopython/pkg-plist Sun Sep 5 14:29:33 2004 @@ -1,3 +1,10 @@ +%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.py +%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyc +%%PYTHON_SITELIBDIR%%/Bio/Affy/CelFile.pyo +%%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Affy/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Affy/_cel.so %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyo @@ -37,6 +44,9 @@ %%PYTHON_SITELIBDIR%%/Bio/Alphabet/IUPAC.py %%PYTHON_SITELIBDIR%%/Bio/Alphabet/IUPAC.pyc %%PYTHON_SITELIBDIR%%/Bio/Alphabet/IUPAC.pyo +%%PYTHON_SITELIBDIR%%/Bio/Alphabet/Reduced.py +%%PYTHON_SITELIBDIR%%/Bio/Alphabet/Reduced.pyc +%%PYTHON_SITELIBDIR%%/Bio/Alphabet/Reduced.pyo %%PYTHON_SITELIBDIR%%/Bio/Alphabet/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Alphabet/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Alphabet/__init__.pyo @@ -52,6 +62,9 @@ %%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIWWW.py %%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIWWW.pyc %%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIWWW.pyo +%%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIXML.py +%%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIXML.pyc +%%PYTHON_SITELIBDIR%%/Bio/Blast/NCBIXML.pyo %%PYTHON_SITELIBDIR%%/Bio/Blast/ParseBlastTable.py %%PYTHON_SITELIBDIR%%/Bio/Blast/ParseBlastTable.pyc %%PYTHON_SITELIBDIR%%/Bio/Blast/ParseBlastTable.pyo @@ -83,6 +96,9 @@ %%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 %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.pyo @@ -119,24 +135,30 @@ %%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 @@ -176,6 +198,9 @@ %%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 %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.py %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyc %%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyo @@ -302,9 +327,6 @@ %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.py %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/GenBank/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/GenBank/genbank_format.py -%%PYTHON_SITELIBDIR%%/Bio/GenBank/genbank_format.pyc -%%PYTHON_SITELIBDIR%%/Bio/GenBank/genbank_format.pyo %%PYTHON_SITELIBDIR%%/Bio/GenBank/utils.py %%PYTHON_SITELIBDIR%%/Bio/GenBank/utils.pyc %%PYTHON_SITELIBDIR%%/Bio/GenBank/utils.pyo @@ -368,9 +390,13 @@ %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.py %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/KDTree/_KDTree.py -%%PYTHON_SITELIBDIR%%/Bio/KDTree/_KDTree.pyc -%%PYTHON_SITELIBDIR%%/Bio/KDTree/_KDTree.pyo +%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.py +%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.pyc +%%PYTHON_SITELIBDIR%%/Bio/KDTree/CKDTree.pyo +%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.py +%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.pyc +%%PYTHON_SITELIBDIR%%/Bio/KDTree/KDTree.pyo +%%PYTHON_SITELIBDIR%%/Bio/KDTree/_CKDTree.so %%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.py %%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.pyo @@ -500,6 +526,15 @@ %%PYTHON_SITELIBDIR%%/Bio/NBRF/nbrf_format.py %%PYTHON_SITELIBDIR%%/Bio/NBRF/nbrf_format.pyc %%PYTHON_SITELIBDIR%%/Bio/NBRF/nbrf_format.pyo +%%PYTHON_SITELIBDIR%%/Bio/NMR/NOEtools.py +%%PYTHON_SITELIBDIR%%/Bio/NMR/NOEtools.pyc +%%PYTHON_SITELIBDIR%%/Bio/NMR/NOEtools.pyo +%%PYTHON_SITELIBDIR%%/Bio/NMR/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/NMR/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/NMR/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/NMR/xpktools.py +%%PYTHON_SITELIBDIR%%/Bio/NMR/xpktools.pyc +%%PYTHON_SITELIBDIR%%/Bio/NMR/xpktools.pyo %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.py %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.pyc %%PYTHON_SITELIBDIR%%/Bio/NaiveBayes.pyo @@ -548,9 +583,18 @@ %%PYTHON_SITELIBDIR%%/Bio/PDB/Chain.py %%PYTHON_SITELIBDIR%%/Bio/PDB/Chain.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/Chain.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.pyo %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.py %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/FragmentMapper.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/FragmentMapper.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/FragmentMapper.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/HSExposure.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/HSExposure.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/HSExposure.pyo %%PYTHON_SITELIBDIR%%/Bio/PDB/MMCIF2Dict.py %%PYTHON_SITELIBDIR%%/Bio/PDB/MMCIF2Dict.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/MMCIF2Dict.pyo @@ -569,6 +613,9 @@ %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBIO.py %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBIO.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBIO.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/PDBList.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/PDBList.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/PDBList.pyo %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.py %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/PDBParser.pyo @@ -578,15 +625,27 @@ %%PYTHON_SITELIBDIR%%/Bio/PDB/Residue.py %%PYTHON_SITELIBDIR%%/Bio/PDB/Residue.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/Residue.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/ResidueDepth.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/ResidueDepth.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/ResidueDepth.pyo %%PYTHON_SITELIBDIR%%/Bio/PDB/Selection.py %%PYTHON_SITELIBDIR%%/Bio/PDB/Selection.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/Selection.pyo %%PYTHON_SITELIBDIR%%/Bio/PDB/Structure.py %%PYTHON_SITELIBDIR%%/Bio/PDB/Structure.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/Structure.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/StructureAlignment.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/StructureAlignment.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/StructureAlignment.pyo %%PYTHON_SITELIBDIR%%/Bio/PDB/StructureBuilder.py %%PYTHON_SITELIBDIR%%/Bio/PDB/StructureBuilder.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/StructureBuilder.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/Superimposer.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/Superimposer.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/Superimposer.pyo +%%PYTHON_SITELIBDIR%%/Bio/PDB/Vector.py +%%PYTHON_SITELIBDIR%%/Bio/PDB/Vector.pyc +%%PYTHON_SITELIBDIR%%/Bio/PDB/Vector.pyo %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.py %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyo @@ -594,6 +653,9 @@ %%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 %%PYTHON_SITELIBDIR%%/Bio/ParserSupport.py %%PYTHON_SITELIBDIR%%/Bio/ParserSupport.pyc %%PYTHON_SITELIBDIR%%/Bio/ParserSupport.pyo @@ -633,9 +695,6 @@ %%PYTHON_SITELIBDIR%%/Bio/PubMed.py %%PYTHON_SITELIBDIR%%/Bio/PubMed.pyc %%PYTHON_SITELIBDIR%%/Bio/PubMed.pyo -%%PYTHON_SITELIBDIR%%/Bio/Rebase/Rebase.py -%%PYTHON_SITELIBDIR%%/Bio/Rebase/Rebase.pyc -%%PYTHON_SITELIBDIR%%/Bio/Rebase/Rebase.pyo %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.py %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/Rebase/__init__.pyo @@ -669,30 +728,6 @@ %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.py %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/SCOP/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/__init__.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/__init__.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/__init__.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testCla.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testCla.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testCla.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDes.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDes.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDes.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDom.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDom.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testDom.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testHie.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testHie.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testHie.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testRaf.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testRaf.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testRaf.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testResidues.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testResidues.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testResidues.pyo -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testScop.py -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testScop.pyc -%%PYTHON_SITELIBDIR%%/Bio/SCOP/tests/testScop.pyo %%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.py %%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.pyc %%PYTHON_SITELIBDIR%%/Bio/SGMLExtractor.pyo @@ -735,9 +770,42 @@ %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.py %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsageIndices.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsageIndices.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsageIndices.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/IsoelectricPoint.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/IsoelectricPoint.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/IsoelectricPoint.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/MeltingTemp.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/MeltingTemp.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/MeltingTemp.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParam.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParam.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParam.pyo +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParamData.py +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParamData.pyc +%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/ProtParamData.pyo %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.py %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.py +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyc +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Ace.pyo +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.py +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyc +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/Phd.pyo +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Sequencing/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Statistics/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Statistics/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Statistics/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Statistics/lowess.py +%%PYTHON_SITELIBDIR%%/Bio/Statistics/lowess.pyc +%%PYTHON_SITELIBDIR%%/Bio/Statistics/lowess.pyo %%PYTHON_SITELIBDIR%%/Bio/Std.py %%PYTHON_SITELIBDIR%%/Bio/Std.pyc %%PYTHON_SITELIBDIR%%/Bio/Std.pyo @@ -786,6 +854,15 @@ %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.py %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/WWW/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.py +%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyc +%%PYTHON_SITELIBDIR%%/Bio/Wise/__init__.pyo +%%PYTHON_SITELIBDIR%%/Bio/Wise/dnal.py +%%PYTHON_SITELIBDIR%%/Bio/Wise/dnal.pyc +%%PYTHON_SITELIBDIR%%/Bio/Wise/dnal.pyo +%%PYTHON_SITELIBDIR%%/Bio/Wise/psw.py +%%PYTHON_SITELIBDIR%%/Bio/Wise/psw.pyc +%%PYTHON_SITELIBDIR%%/Bio/Wise/psw.pyo %%PYTHON_SITELIBDIR%%/Bio/Writer.py %%PYTHON_SITELIBDIR%%/Bio/Writer.pyc %%PYTHON_SITELIBDIR%%/Bio/Writer.pyo @@ -851,12 +928,18 @@ %%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.py %%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.pyc %%PYTHON_SITELIBDIR%%/Bio/dbdefs/embl.pyo +%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.py +%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.pyc +%%PYTHON_SITELIBDIR%%/Bio/dbdefs/fasta.pyo %%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.py %%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.pyc %%PYTHON_SITELIBDIR%%/Bio/dbdefs/genbank.pyo %%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.py %%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.pyc %%PYTHON_SITELIBDIR%%/Bio/dbdefs/interpro.pyo +%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.py +%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.pyc +%%PYTHON_SITELIBDIR%%/Bio/dbdefs/medline.pyo %%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.py %%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.pyc %%PYTHON_SITELIBDIR%%/Bio/dbdefs/pdb.pyo @@ -899,6 +982,9 @@ %%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.py %%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.pyc %%PYTHON_SITELIBDIR%%/Bio/expressions/genbank.pyo +%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.py +%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.pyc +%%PYTHON_SITELIBDIR%%/Bio/expressions/hmmpfam.pyo %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.py %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyc %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyo @@ -1035,83 +1121,88 @@ 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+@dirrm %%PYTHON_SITELIBDIR%%/Bio/SCOP +@dirrm %%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer +@dirrm %%PYTHON_SITELIBDIR%%/Bio/Saf +@dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqIO +@dirrm %%PYTHON_SITELIBDIR%%/Bio/SeqUtils +@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/builders/Search +@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord +@dirrm %%PYTHON_SITELIBDIR%%/Bio/builders +@dirrm %%PYTHON_SITELIBDIR%%/Bio/config +@dirrm %%PYTHON_SITELIBDIR%%/Bio/dbdefs +@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/blast +@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/embl +@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot +@dirrm %%PYTHON_SITELIBDIR%%/Bio/expressions +@dirrm %%PYTHON_SITELIBDIR%%/Bio/formatdefs +@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord +@dirrm %%PYTHON_SITELIBDIR%%/Bio/writers @dirrm %%PYTHON_SITELIBDIR%%/Bio +@dirrm %%PYTHON_SITELIBDIR%%/BioSQL +@dirrm %%PYTHON_SITELIBDIR%%/Martel --- py23-biopython-1.30.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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