FreeBSD Bugzilla – Attachment 58983 Details for
Bug 88792
[maintainer update] Update port: biology/py-biopython to version 1.41
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[patch]
file.diff
file.diff (text/plain), 21.32 KB, created by
Mauricio Herrera Cuadra
on 2005-11-10 14:50:22 UTC
(
hide
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Description:
file.diff
Filename:
MIME Type:
Creator:
Mauricio Herrera Cuadra
Created:
2005-11-10 14:50:22 UTC
Size:
21.32 KB
patch
obsolete
>diff -ruN biology/py-biopython.old/Makefile biology/py-biopython/Makefile >--- biology/py-biopython.old/Makefile Wed Nov 9 22:54:18 2005 >+++ biology/py-biopython/Makefile Thu Nov 10 02:46:03 2005 >@@ -6,21 +6,21 @@ > # > > PORTNAME= biopython >-PORTVERSION= 1.30 >+PORTVERSION= 1.41 > CATEGORIES= biology python > MASTER_SITES= http://www.biopython.org/files/ > PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} > >-MAINTAINER= ports@FreeBSD.org >+MAINTAINER= mauricio@arareko.net > COMMENT= A collection of Python modules for bioinformatics > >-CONFLICTS= py*-martel-* >+CONFLICTS= py*-martel-[0-9]* > > BUILD_DEPENDS= ${PYNUMERIC} \ > ${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base > RUN_DEPENDS= ${BUILD_DEPENDS} > >-USE_PYTHON= 2.2+ >+USE_PYTHON= 2.3+ > USE_PYDISTUTILS=yes > > .if !defined(WITHOUT_REPORTLAB) >diff -ruN biology/py-biopython.old/distinfo biology/py-biopython/distinfo >--- biology/py-biopython.old/distinfo Wed Nov 9 22:54:18 2005 >+++ biology/py-biopython/distinfo Wed Nov 9 22:56:46 2005 >@@ -1,2 +1,2 @@ >-MD5 (biopython-1.30.tar.gz) = d8df866a40be20962b8ef52baa5376c1 >-SIZE (biopython-1.30.tar.gz) = 3186467 >+MD5 (biopython-1.41.tar.gz) = 03f8efc258fb49b07d1a2b642fa8362e >+SIZE (biopython-1.41.tar.gz) = 3807547 >diff -ruN biology/py-biopython.old/files/patch-Bio::triemodule.c biology/py-biopython/files/patch-Bio::triemodule.c >--- biology/py-biopython.old/files/patch-Bio::triemodule.c Wed Nov 9 22:54:18 2005 >+++ biology/py-biopython/files/patch-Bio::triemodule.c Wed Dec 31 18:00:00 1969 >@@ -1,14 +0,0 @@ >---- Bio/triemodule.c.orig Thu Dec 2 14:44:14 2004 >-+++ Bio/triemodule.c Thu Dec 2 14:47:57 2004 >-@@ -477,7 +477,11 @@ >- int length; >- int success = 0; >- >-+#ifdef Py_MARSHAL_VERSION >-+ if(!(py_marshalled = PyMarshal_WriteObjectToString(py_value, Py_MARSHAL_VERSION))) >-+#else >- if(!(py_marshalled = PyMarshal_WriteObjectToString(py_value))) >-+#endif >- goto _write_value_to_handle_cleanup; >- if(PyString_AsStringAndSize(py_marshalled, &marshalled, &length) == -1) >- goto _write_value_to_handle_cleanup; >diff -ruN biology/py-biopython.old/files/patch-setup.py biology/py-biopython/files/patch-setup.py >--- biology/py-biopython.old/files/patch-setup.py Wed Nov 9 22:54:18 2005 >+++ biology/py-biopython/files/patch-setup.py Wed Dec 31 18:00:00 1969 >@@ -1,11 +0,0 @@ >---- setup.py.orig Fri May 14 15:17:43 2004 >-+++ setup.py Sun Nov 7 01:02:10 2004 >-@@ -199,7 +199,7 @@ >- self.compiler.set_executable("linker_so", >- cxx + ["-shared"]) >- elif build: # fix for 2.3, only if we are making C++ modules >-- self.compiler.compiler_so = self.compiler.compiler_cxx >-+ self.compiler.compiler_so = self.compiler.compiler_cxx + ["-fPIC"] >- else: >- self.compiler.compiler_so = self._original_compiler_so >- >diff -ruN biology/py-biopython.old/pkg-plist biology/py-biopython/pkg-plist >--- biology/py-biopython.old/pkg-plist Wed Nov 9 22:54:18 2005 >+++ biology/py-biopython/pkg-plist Thu Nov 10 02:03:43 2005 >@@ -4,7 +4,6 @@ > %%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 >@@ -29,6 +28,9 @@ > %%PYTHON_SITELIBDIR%%/Bio/AlignAce/Applications.py > %%PYTHON_SITELIBDIR%%/Bio/AlignAce/Applications.pyc > %%PYTHON_SITELIBDIR%%/Bio/AlignAce/Applications.pyo >+%%PYTHON_SITELIBDIR%%/Bio/AlignAce/CompareAceStandalone.py >+%%PYTHON_SITELIBDIR%%/Bio/AlignAce/CompareAceStandalone.pyc >+%%PYTHON_SITELIBDIR%%/Bio/AlignAce/CompareAceStandalone.pyo > %%PYTHON_SITELIBDIR%%/Bio/AlignAce/Motif.py > %%PYTHON_SITELIBDIR%%/Bio/AlignAce/Motif.pyc > %%PYTHON_SITELIBDIR%%/Bio/AlignAce/Motif.pyo >@@ -74,6 +76,9 @@ > %%PYTHON_SITELIBDIR%%/Bio/Blast/__init__.py > %%PYTHON_SITELIBDIR%%/Bio/Blast/__init__.pyc > %%PYTHON_SITELIBDIR%%/Bio/Blast/__init__.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 >@@ -390,16 +395,6 @@ > %%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/KDTree/_CKDTree.so >-%%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.py >-%%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.pyc >-%%PYTHON_SITELIBDIR%%/Bio/KDTree/__init__.pyo > %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.py > %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.pyc > %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.pyo >@@ -442,6 +437,15 @@ > %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.py > %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.pyc > %%PYTHON_SITELIBDIR%%/Bio/LogisticRegression.pyo >+%%PYTHON_SITELIBDIR%%/Bio/MEME/Motif.py >+%%PYTHON_SITELIBDIR%%/Bio/MEME/Motif.pyc >+%%PYTHON_SITELIBDIR%%/Bio/MEME/Motif.pyo >+%%PYTHON_SITELIBDIR%%/Bio/MEME/Parser.py >+%%PYTHON_SITELIBDIR%%/Bio/MEME/Parser.pyc >+%%PYTHON_SITELIBDIR%%/Bio/MEME/Parser.pyo >+%%PYTHON_SITELIBDIR%%/Bio/MEME/__init__.py >+%%PYTHON_SITELIBDIR%%/Bio/MEME/__init__.pyc >+%%PYTHON_SITELIBDIR%%/Bio/MEME/__init__.pyo > %%PYTHON_SITELIBDIR%%/Bio/MarkovModel.py > %%PYTHON_SITELIBDIR%%/Bio/MarkovModel.pyc > %%PYTHON_SITELIBDIR%%/Bio/MarkovModel.pyo >@@ -466,6 +470,9 @@ > %%PYTHON_SITELIBDIR%%/Bio/Medline/nlmmedline_011101_format.py > %%PYTHON_SITELIBDIR%%/Bio/Medline/nlmmedline_011101_format.pyc > %%PYTHON_SITELIBDIR%%/Bio/Medline/nlmmedline_011101_format.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Medline/nlmmedline_031101_format.py >+%%PYTHON_SITELIBDIR%%/Bio/Medline/nlmmedline_031101_format.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Medline/nlmmedline_031101_format.pyo > %%PYTHON_SITELIBDIR%%/Bio/MetaTool/Input.py > %%PYTHON_SITELIBDIR%%/Bio/MetaTool/Input.pyc > %%PYTHON_SITELIBDIR%%/Bio/MetaTool/Input.pyo >@@ -577,6 +584,22 @@ > %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/__init__.py > %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/__init__.pyc > %%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/__init__.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Nexus.py >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Nexus.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Nexus.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Nodes.py >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Nodes.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Nodes.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Trees.py >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Trees.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/Trees.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/__init__.py >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/__init__.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/__init__.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Nexus/cnexus.so >+%%PYTHON_SITELIBDIR%%/Bio/PDB/AbstractPropertyMap.py >+%%PYTHON_SITELIBDIR%%/Bio/PDB/AbstractPropertyMap.pyc >+%%PYTHON_SITELIBDIR%%/Bio/PDB/AbstractPropertyMap.pyo > %%PYTHON_SITELIBDIR%%/Bio/PDB/Atom.py > %%PYTHON_SITELIBDIR%%/Bio/PDB/Atom.pyc > %%PYTHON_SITELIBDIR%%/Bio/PDB/Atom.pyo >@@ -586,6 +609,9 @@ > %%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.py > %%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.pyc > %%PYTHON_SITELIBDIR%%/Bio/PDB/DSSP.pyo >+%%PYTHON_SITELIBDIR%%/Bio/PDB/Dice.py >+%%PYTHON_SITELIBDIR%%/Bio/PDB/Dice.pyc >+%%PYTHON_SITELIBDIR%%/Bio/PDB/Dice.pyo > %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.py > %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.pyc > %%PYTHON_SITELIBDIR%%/Bio/PDB/Entity.pyo >@@ -604,6 +630,9 @@ > %%PYTHON_SITELIBDIR%%/Bio/PDB/Model.py > %%PYTHON_SITELIBDIR%%/Bio/PDB/Model.pyc > %%PYTHON_SITELIBDIR%%/Bio/PDB/Model.pyo >+%%PYTHON_SITELIBDIR%%/Bio/PDB/NACCESS.py >+%%PYTHON_SITELIBDIR%%/Bio/PDB/NACCESS.pyc >+%%PYTHON_SITELIBDIR%%/Bio/PDB/NACCESS.pyo > %%PYTHON_SITELIBDIR%%/Bio/PDB/NeighborSearch.py > %%PYTHON_SITELIBDIR%%/Bio/PDB/NeighborSearch.pyc > %%PYTHON_SITELIBDIR%%/Bio/PDB/NeighborSearch.pyo >@@ -704,6 +733,31 @@ > %%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 >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/PrintFormat.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/RanaConfig.py >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/RanaConfig.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/RanaConfig.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/Restriction.py >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/Restriction.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/Restriction.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/Restriction_Dictionary.py >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/Restriction_Dictionary.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/Restriction_Dictionary.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/RestrictionCompiler.py >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/RestrictionCompiler.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/RestrictionCompiler.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/Update.py >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/Update.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/Update.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/__init__.py >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/__init__.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update/__init__.pyo >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.py >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyc >+%%PYTHON_SITELIBDIR%%/Bio/Restriction/__init__.pyo > %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.py > %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyc > %%PYTHON_SITELIBDIR%%/Bio/SCOP/Cla.pyo >@@ -988,6 +1042,9 @@ > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.py > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyc > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/__init__.pyo >+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/ipi.py >+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/ipi.pyc >+%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/ipi.pyo > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.py > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.pyc > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/speclist.pyo >@@ -997,6 +1054,9 @@ > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot40.py > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot40.pyc > %%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot/sprot40.pyo >+%%PYTHON_SITELIBDIR%%/Bio/expressions/transfac.py >+%%PYTHON_SITELIBDIR%%/Bio/expressions/transfac.pyc >+%%PYTHON_SITELIBDIR%%/Bio/expressions/transfac.pyo > %%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.py > %%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.pyc > %%PYTHON_SITELIBDIR%%/Bio/formatdefs/__init__.pyo >@@ -1049,6 +1109,9 @@ > %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.py > %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.pyc > %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/__init__.pyo >+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/embl.py >+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/embl.pyc >+%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/embl.pyo > %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.py > %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.pyc > %%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord/empty.pyo >@@ -1121,88 +1184,92 @@ > %%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 %%PYTHON_SITELIBDIR%%/Bio/Application >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Blast >-@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/Enzyme >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Crossover >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Mutation >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Repair >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA/Selection >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GA >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GFF >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/GenBank >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Geo >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Gobase >-@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/Kabat >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/LocusLink >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/MetaTool >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Mindy >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/MultiProc >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/NBRF >-@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/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/Prosite >-@dirrm %%PYTHON_SITELIBDIR%%/Bio/Rebase >-@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 >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Affy 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Ais 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Align 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/AlignAce 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Alphabet 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Application 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Blast 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/CAPS 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/CDD 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Clustalw 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Cluster 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Compass 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Crystal 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Data 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/ECell 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/EUtils 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/EUtils/DTDs 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Emboss 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Encodings 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Enzyme 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/FSSP 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Fasta 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/GA/Crossover 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/GA/Mutation 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/GA/Repair 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/GA/Selection 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/GA 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/GFF 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/GenBank 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Geo 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Gobase 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Graphics 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/HMM 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/IntelliGenetics 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/InterPro 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/KEGG/Map 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/KEGG 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Kabat 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/LocusLink 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/MEME 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Medline 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/MetaTool 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Mindy 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/MultiProc 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/NBRF 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/NMR 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Ndb 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/BackPropagation 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork/Gene 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/NeuralNetwork 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Nexus 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/PDB/mmCIF 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/PDB 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Parsers 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Pathway/Rep 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Pathway 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Prosite 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Rebase 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Restriction/_Update 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Restriction 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/SCOP 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/SVDSuperimposer 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Saf 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/SeqIO 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/SeqUtils 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Sequencing 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Statistics 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/SubsMat 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/SwissProt 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/UniGene 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/WWW 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/Wise 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/builders/Search 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/builders/SeqRecord 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/builders 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/config 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/dbdefs 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/expressions/blast 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/expressions/embl 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/expressions/swissprot 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/expressions 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/formatdefs 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/writers/SeqRecord 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio/writers 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Bio 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/BioSQL 2>/dev/null || true >+@unexec rmdir %D/%%PYTHON_SITELIBDIR%%/Martel 2>/dev/null || true
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bug 88792
: 58983