Attachment #99034 for bug #138038

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#

PORTNAME=	biopython
PORTVERSION=	1.51
CATEGORIES=	biology python
MASTER_SITES=	http://www.biopython.org/DIST/
PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}

MAINTAINER=	mauricio@arareko.net
COMMENT=	A collection of Python modules for bioinformatics

BUILD_DEPENDS=	${PYNUMPY} \
		${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
RUN_DEPENDS=	${BUILD_DEPENDS}

USE_PYTHON=	2.4+

USE_PYTHON=	2.3+
USE_PYDISTUTILS=yes

.if !defined(WITHOUT_REPORTLAB)

Lines 1-3 Link Here

(-)py-biopython.new/distinfo (-3 / +3 lines)
1	MD5 (biopython-1.48.tar.gz) = b049e3af8128bea68e4e86b55c6d0996	1	MD5 (biopython-1.51.tar.gz) = e973cb96b44b47526d31b6a0039c686f
2	SHA256 (biopython-1.48.tar.gz) = cfb3a1774d1d4b01a66b3428cec7b4c943517b2485e0ca577a6b540818f29cb0	2	SHA256 (biopython-1.51.tar.gz) = 0ebf44e6376d7b44fb2857e751d388f30402d6a81798821e40a7f7b92a4b036b
3	SIZE (biopython-1.48.tar.gz) = 4149100	3	SIZE (biopython-1.51.tar.gz) = 5557548




--- setup.py.orig	Sat Mar 17 13:21:04 2007
+++ setup.py	Mon May 28 17:01:45 2007
@@ -112,7 +112,7 @@
         
     
     # Compile KDTree ? Not compiled by default
-    print "\n*** Bio.KDTree *** NOT built by default "
+#    print "\n*** Bio.KDTree *** NOT built by default "
     kdtree_msg = """
 The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
 which in turn, depends on C++ code that does not compile cleanly on
@@ -120,14 +120,14 @@
 
 Would you like to build Bio.KDTree ?"""
 
-    if get_yes_or_no (kdtree_msg, 0):
-        NUMPY_PACKAGES.append("Bio.KDTree")
-        NUMPY_EXTENSIONS.append(
-            CplusplusExtension('Bio.KDTree._CKDTree', 
-                               ["Bio/KDTree/KDTree.cpp",
-                                "Bio/KDTree/KDTree.swig.cpp"],
-                               libraries=["stdc++"],
-                               language="c++"))
+#    if get_yes_or_no (kdtree_msg, 0):
+    NUMPY_PACKAGES.append("Bio.KDTree")
+    NUMPY_EXTENSIONS.append(
+        CplusplusExtension('Bio.KDTree._CKDTree', 
+                           ["Bio/KDTree/KDTree.cpp",
+                            "Bio/KDTree/KDTree.swig.cpp"],
+                           libraries=["stdc++"],
+                           language="c++"))
     
     
     return 1




%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.py
%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyc
%%PYTHON_SITELIBDIR%%/BioSQL/BioSeq.pyo
%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.py
%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyc
%%PYTHON_SITELIBDIR%%/BioSQL/BioSeqDatabase.pyo
%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.py
%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyc
%%PYTHON_SITELIBDIR%%/BioSQL/DBUtils.pyo
%%PYTHON_SITELIBDIR%%/BioSQL/Loader.py
%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyc
%%PYTHON_SITELIBDIR%%/BioSQL/Loader.pyo
%%PYTHON_SITELIBDIR%%/BioSQL/__init__.py
%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyc
%%PYTHON_SITELIBDIR%%/BioSQL/__init__.pyo
@dirrm %%PYTHON_SITELIBDIR%%/BioSQL
%%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/Ais/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Ais/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.py
%%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/AlignInfo.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Clustalw.py
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Clustalw.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Clustalw.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Dialign.py
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Dialign.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Dialign.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Mafft.py
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Mafft.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Mafft.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Muscle.py
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Muscle.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Muscle.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Prank.py
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Prank.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Prank.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Probcons.py
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Probcons.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_Probcons.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_TCoffee.py
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_TCoffee.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/_TCoffee.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/Applications/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.py
%%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.pyc
%%PYTHON_SITELIBDIR%%/Bio/Align/FormatConvert.pyo

%%PYTHON_SITELIBDIR%%/Bio/CAPS/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/CAPS/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/CAPS/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/CDD/Record.py
%%PYTHON_SITELIBDIR%%/Bio/CDD/Record.pyc
%%PYTHON_SITELIBDIR%%/Bio/CDD/Record.pyo
%%PYTHON_SITELIBDIR%%/Bio/CDD/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/CDD/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/CDD/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/CDD/cdd_format.py
%%PYTHON_SITELIBDIR%%/Bio/CDD/cdd_format.pyc
%%PYTHON_SITELIBDIR%%/Bio/CDD/cdd_format.pyo
%%PYTHON_SITELIBDIR%%/Bio/Clustalw/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Clustalw/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Clustalw/__init__.pyo

%%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Crystal/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/DBXRef.py
%%PYTHON_SITELIBDIR%%/Bio/DBXRef.pyc
%%PYTHON_SITELIBDIR%%/Bio/DBXRef.pyo
%%PYTHON_SITELIBDIR%%/Bio/Data/CodonTable.py
%%PYTHON_SITELIBDIR%%/Bio/Data/CodonTable.pyc
%%PYTHON_SITELIBDIR%%/Bio/Data/CodonTable.pyo

%%PYTHON_SITELIBDIR%%/Bio/Data/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Data/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Data/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Decode.py
%%PYTHON_SITELIBDIR%%/Bio/Decode.pyc
%%PYTHON_SITELIBDIR%%/Bio/Decode.pyo
%%PYTHON_SITELIBDIR%%/Bio/DocSQL.py
%%PYTHON_SITELIBDIR%%/Bio/DocSQL.pyc
%%PYTHON_SITELIBDIR%%/Bio/DocSQL.pyo
%%PYTHON_SITELIBDIR%%/Bio/ECell/Record.py
%%PYTHON_SITELIBDIR%%/Bio/ECell/Record.pyc
%%PYTHON_SITELIBDIR%%/Bio/ECell/Record.pyo
%%PYTHON_SITELIBDIR%%/Bio/ECell/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/ECell/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/ECell/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/ECell/ecell_format.py
%%PYTHON_SITELIBDIR%%/Bio/ECell/ecell_format.pyc
%%PYTHON_SITELIBDIR%%/Bio/ECell/ecell_format.pyo
%%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.py
%%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.pyc
%%PYTHON_SITELIBDIR%%/Bio/EUtils/Config.pyo

%%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.py
%%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyc
%%PYTHON_SITELIBDIR%%/Bio/Emboss/Applications.pyo
%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.py
%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.pyc
%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer.pyo
%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.py
%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.pyc
%%PYTHON_SITELIBDIR%%/Bio/Emboss/Primer3.pyo

%%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Emboss/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Emboss/primer3_format.py
%%PYTHON_SITELIBDIR%%/Bio/Emboss/primer3_format.pyc
%%PYTHON_SITELIBDIR%%/Bio/Emboss/primer3_format.pyo
%%PYTHON_SITELIBDIR%%/Bio/Emboss/primersearch_format.py
%%PYTHON_SITELIBDIR%%/Bio/Emboss/primersearch_format.pyc
%%PYTHON_SITELIBDIR%%/Bio/Emboss/primersearch_format.pyo
%%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.py
%%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.pyc
%%PYTHON_SITELIBDIR%%/Bio/Encodings/IUPACEncoding.pyo
%%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/Entrez/DTDs/EMBL_General.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/GenBank_General.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/HomoloGene.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/HomoloGene.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd

%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/eSummary_041029.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/egquery.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/nlmmedlinecitation_080101.dtd
%%PYTHON_SITELIBDIR%%/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd
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%%PYTHON_SITELIBDIR%%/Bio/Entrez/Parser.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
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.py
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.pyc
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Enzyme.pyo
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prodoc.py
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prodoc.pyc
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prodoc.pyo
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prosite.py
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prosite.pyc
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/Prosite.pyo
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/ScanProsite.py
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/ScanProsite.pyc
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/ScanProsite.pyo
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/ExPASy/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/FSSP/FSSPTools.py
%%PYTHON_SITELIBDIR%%/Bio/FSSP/FSSPTools.pyc
%%PYTHON_SITELIBDIR%%/Bio/FSSP/FSSPTools.pyo

%%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/BasicChromosome.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/BasicChromosome.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/BasicChromosome.pyo

%%PYTHON_SITELIBDIR%%/Bio/Graphics/Distribution.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/Distribution.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/Distribution.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_AbstractDrawer.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_AbstractDrawer.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_CircularDrawer.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_CircularDrawer.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_CircularDrawer.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Colors.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Colors.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Colors.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Diagram.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Diagram.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Diagram.pyo
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%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Feature.pyo
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%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_FeatureSet.pyo
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%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Graph.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_GraphSet.py
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%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_GraphSet.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_LinearDrawer.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Track.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Track.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/_Track.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Graphics/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Graphics/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Graphics/__init__.pyo

%%PYTHON_SITELIBDIR%%/Bio/Index.py
%%PYTHON_SITELIBDIR%%/Bio/Index.pyc
%%PYTHON_SITELIBDIR%%/Bio/Index.pyo
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/Record.py
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/Record.pyc
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/Record.pyo
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/intelligenetics_format.py
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/intelligenetics_format.pyc
%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics/intelligenetics_format.pyo
%%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/InterPro/__init__.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/KEGG/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/locus_format.py
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/locus_format.pyc
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/locus_format.pyo
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/web_parse.py
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/web_parse.pyc
%%PYTHON_SITELIBDIR%%/Bio/LocusLink/web_parse.pyo
%%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.py
%%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.pyc
%%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.pyo

%%PYTHON_SITELIBDIR%%/Bio/Medline/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Medline/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Medline/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Motif/Applications/_AlignAce.py
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%%PYTHON_SITELIBDIR%%/Bio/Motif/Applications/_AlignAce.pyo
%%PYTHON_SITELIBDIR%%/Bio/Motif/Applications/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Motif/Applications/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Motif/Applications/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.py
%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.pyc
%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/AlignAce.pyo
%%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/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Motif/Parsers/__init__.pyo
%%PYTHON_SITELIBDIR%%/Bio/Motif/Thresholds.py
%%PYTHON_SITELIBDIR%%/Bio/Motif/Thresholds.pyc
%%PYTHON_SITELIBDIR%%/Bio/Motif/Thresholds.pyo
%%PYTHON_SITELIBDIR%%/Bio/Motif/_Motif.py
%%PYTHON_SITELIBDIR%%/Bio/Motif/_Motif.pyc
%%PYTHON_SITELIBDIR%%/Bio/Motif/_Motif.pyo
%%PYTHON_SITELIBDIR%%/Bio/Motif/__init__.py
%%PYTHON_SITELIBDIR%%/Bio/Motif/__init__.pyc
%%PYTHON_SITELIBDIR%%/Bio/Motif/__init__.pyo
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%%PYTHON_SITELIBDIR%%/Martel/Generate.pyo
%%PYTHON_SITELIBDIR%%/Martel/IterParser.py
%%PYTHON_SITELIBDIR%%/Martel/IterParser.pyc
%%PYTHON_SITELIBDIR%%/Martel/IterParser.pyo
%%PYTHON_SITELIBDIR%%/Martel/Iterator.py
%%PYTHON_SITELIBDIR%%/Martel/Iterator.pyc
%%PYTHON_SITELIBDIR%%/Martel/Iterator.pyo
%%PYTHON_SITELIBDIR%%/Martel/LAX.py
%%PYTHON_SITELIBDIR%%/Martel/LAX.pyc
%%PYTHON_SITELIBDIR%%/Martel/LAX.pyo
%%PYTHON_SITELIBDIR%%/Martel/Parser.py
%%PYTHON_SITELIBDIR%%/Martel/Parser.pyc
%%PYTHON_SITELIBDIR%%/Martel/Parser.pyo
%%PYTHON_SITELIBDIR%%/Martel/RecordReader.py
%%PYTHON_SITELIBDIR%%/Martel/RecordReader.pyc
%%PYTHON_SITELIBDIR%%/Martel/RecordReader.pyo
%%PYTHON_SITELIBDIR%%/Martel/Time.py
%%PYTHON_SITELIBDIR%%/Martel/Time.pyc
%%PYTHON_SITELIBDIR%%/Martel/Time.pyo
%%PYTHON_SITELIBDIR%%/Martel/__init__.py
%%PYTHON_SITELIBDIR%%/Martel/__init__.pyc
%%PYTHON_SITELIBDIR%%/Martel/__init__.pyo
%%PYTHON_SITELIBDIR%%/Martel/convert_re.py
%%PYTHON_SITELIBDIR%%/Martel/convert_re.pyc
%%PYTHON_SITELIBDIR%%/Martel/convert_re.pyo
%%PYTHON_SITELIBDIR%%/Martel/msre_constants.py
%%PYTHON_SITELIBDIR%%/Martel/msre_constants.pyc
%%PYTHON_SITELIBDIR%%/Martel/msre_constants.pyo
%%PYTHON_SITELIBDIR%%/Martel/msre_parse.py
%%PYTHON_SITELIBDIR%%/Martel/msre_parse.pyc
%%PYTHON_SITELIBDIR%%/Martel/msre_parse.pyo
%%PYTHON_SITELIBDIR%%/Martel/optimize.py
%%PYTHON_SITELIBDIR%%/Martel/optimize.pyc
%%PYTHON_SITELIBDIR%%/Martel/optimize.pyo
%%PYTHON_SITELIBDIR%%/Martel/setup.py
%%PYTHON_SITELIBDIR%%/Martel/setup.pyc
%%PYTHON_SITELIBDIR%%/Martel/setup.pyo
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Affy
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align/Applications
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Align
@dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignAce
@dirrm %%PYTHON_SITELIBDIR%%/Bio/AlignIO

@dirrm %%PYTHON_SITELIBDIR%%/Bio/Application
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast
@dirrm %%PYTHON_SITELIBDIR%%/Bio/CAPS
@dirrm %%PYTHON_SITELIBDIR%%/Bio/CDD
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Clustalw
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Cluster
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Compass
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Crystal
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Data
@dirrm %%PYTHON_SITELIBDIR%%/Bio/ECell
@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
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
@dirrm %%PYTHON_SITELIBDIR%%/Bio/ExPASy
@dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta
@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover

@dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF
@dirrm %%PYTHON_SITELIBDIR%%/Bio/GenBank
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Geo
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics/GenomeDiagram
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Graphics
@dirrm %%PYTHON_SITELIBDIR%%/Bio/HMM
@dirrm %%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics
@dirrm %%PYTHON_SITELIBDIR%%/Bio/InterPro
@dirrm %%PYTHON_SITELIBDIR%%/Bio/KDTree
@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound
@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme
@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map
@dirrm %%PYTHON_SITELIBDIR%%/Bio/KEGG
@dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink
@dirrm %%PYTHON_SITELIBDIR%%/Bio/MEME
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Motif/Applications
@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
@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
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/Async
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal
@dirrm %%PYTHON_SITELIBDIR%%/Bio/PopGen
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Prosite
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Rebase
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update
@dirrm %%PYTHON_SITELIBDIR%%/Bio/Restriction
@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/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

Return to bug 138038

Lines 6-12 Link Here

(-)py-biopython.new/Makefile (-5 / +3 lines)
6	#	6	#
7		7
8	PORTNAME= biopython	8	PORTNAME= biopython
9	PORTVERSION= 1.48	9	PORTVERSION= 1.51
10	CATEGORIES= biology python	10	CATEGORIES= biology python
11	MASTER_SITES= http://www.biopython.org/DIST/	11	MASTER_SITES= http://www.biopython.org/DIST/
12	PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}	12	PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
Lines 14-26 Link Here
14	MAINTAINER= mauricio@arareko.net	14	MAINTAINER= mauricio@arareko.net
15	COMMENT= A collection of Python modules for bioinformatics	15	COMMENT= A collection of Python modules for bioinformatics
16		16
17	BUILD_DEPENDS= ${PYNUMERIC} \	17	BUILD_DEPENDS= ${PYNUMPY} \
18	${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base	18	${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
19	RUN_DEPENDS= ${BUILD_DEPENDS}	19	RUN_DEPENDS= ${BUILD_DEPENDS}
20		20
21	CONFLICTS= py-martel-[0-9]	21	USE_PYTHON= 2.4+
22
23	USE_PYTHON= 2.3+
24	USE_PYDISTUTILS=yes	22	USE_PYDISTUTILS=yes
25		23
26	.if !defined(WITHOUT_REPORTLAB)	24	.if !defined(WITHOUT_REPORTLAB)

Lines 1-34 Link Here

(-)py-biopython.new/files/patch-setup.py (-34 lines)
1	--- setup.py.orig Sat Mar 17 13:21:04 2007
2	+++ setup.py Mon May 28 17:01:45 2007
3	@@ -112,7 +112,7 @@
4
5
6	# Compile KDTree ? Not compiled by default
7	- print "\n* Bio.KDTree * NOT built by default "
8	+# print "\n* Bio.KDTree * NOT built by default "
9	kdtree_msg = """
10	The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
11	which in turn, depends on C++ code that does not compile cleanly on
12	@@ -120,14 +120,14 @@
13
14	Would you like to build Bio.KDTree ?"""
15
16	- if get_yes_or_no (kdtree_msg, 0):
17	- NUMPY_PACKAGES.append("Bio.KDTree")
18	- NUMPY_EXTENSIONS.append(
19	- CplusplusExtension('Bio.KDTree._CKDTree',
20	- ["Bio/KDTree/KDTree.cpp",
21	- "Bio/KDTree/KDTree.swig.cpp"],
22	- libraries=["stdc++"],
23	- language="c++"))
24	+# if get_yes_or_no (kdtree_msg, 0):
25	+ NUMPY_PACKAGES.append("Bio.KDTree")
26	+ NUMPY_EXTENSIONS.append(
27	+ CplusplusExtension('Bio.KDTree._CKDTree',
28	+ ["Bio/KDTree/KDTree.cpp",
29	+ "Bio/KDTree/KDTree.swig.cpp"],
30	+ libraries=["stdc++"],
31	+ language="c++"))
32
33
34	return 1