Date: Thu, 10 Nov 2005 14:48:52 GMT From: Mauricio Herrera Cuadra <mauricio@arareko.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/88792: [maintainer update] Update port: biology/py-biopython to version 1.41 Message-ID: <200511101448.jAAEmpEq036962@www.freebsd.org> Resent-Message-ID: <200511101450.jAAEoN3X041224@freefall.freebsd.org>
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>Number: 88792
>Category: ports
>Synopsis: [maintainer update] Update port: biology/py-biopython to version 1.41
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Thu Nov 10 14:50:22 GMT 2005
>Closed-Date:
>Last-Modified:
>Originator: Mauricio Herrera Cuadra
>Release: FreeBSD 5.4-STABLE i386
>Organization:
>Environment:
FreeBSD nordwand.arareko.net 5.4-STABLE FreeBSD 5.4-STABLE #0: Wed Oct 12 03:34:59 CDT 2005 root@nordwand.arareko.net:/usr/obj/usr/src/sys/nordwand i386
>Description:
This patch updates the biology/py-biopython port to its 1.41 version.
The previous patches in the 'files' directory are no longer needed, so there's a need to remove them from the ports tree:
biology/py-biopython/files/patch-Bio::triemodule.c
biology/py-biopython/files/patch-setup.py
I'll maintain this port.
>How-To-Repeat:
>Fix:
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
>Release-Note:
>Audit-Trail:
>Unformatted:
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