diff options
| -rw-r--r-- | biology/py-biopython/Makefile | 10 | ||||
| -rw-r--r-- | biology/py-biopython/distinfo | 5 | ||||
| -rw-r--r-- | biology/py-biopython/files/patch-Bio::triemodule.c | 14 | ||||
| -rw-r--r-- | biology/py-biopython/files/patch-setup.py | 11 | ||||
| -rw-r--r-- | biology/py-biopython/pkg-plist | 91 |
5 files changed, 87 insertions, 44 deletions
diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile index 311ce75d386d..58f46fcb30a3 100644 --- a/biology/py-biopython/Makefile +++ b/biology/py-biopython/Makefile @@ -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-* - BUILD_DEPENDS= ${PYNUMERIC} \ ${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base RUN_DEPENDS= ${BUILD_DEPENDS} -USE_PYTHON= 2.2+ +CONFLICTS= py*-martel-[0-9]* + +USE_PYTHON= 2.3+ USE_PYDISTUTILS=yes .if !defined(WITHOUT_REPORTLAB) diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo index cfcff10fce5d..9f9cba1a802f 100644 --- a/biology/py-biopython/distinfo +++ b/biology/py-biopython/distinfo @@ -1,2 +1,3 @@ -MD5 (biopython-1.30.tar.gz) = d8df866a40be20962b8ef52baa5376c1 -SIZE (biopython-1.30.tar.gz) = 3186467 +MD5 (biopython-1.41.tar.gz) = 03f8efc258fb49b07d1a2b642fa8362e +SHA256 (biopython-1.41.tar.gz) = 15b708b7635fd993aad3c53fd4cfc28601da6d4332b027d09899f1cb5178cef9 +SIZE (biopython-1.41.tar.gz) = 3807547 diff --git a/biology/py-biopython/files/patch-Bio::triemodule.c b/biology/py-biopython/files/patch-Bio::triemodule.c deleted file mode 100644 index a1d9ab4ae36d..000000000000 --- a/biology/py-biopython/files/patch-Bio::triemodule.c +++ /dev/null @@ -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 --git a/biology/py-biopython/files/patch-setup.py b/biology/py-biopython/files/patch-setup.py deleted file mode 100644 index fdbd92ff3b60..000000000000 --- a/biology/py-biopython/files/patch-setup.py +++ /dev/null @@ -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 --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist index a3e03d42c880..d7aeff947143 100644 --- a/biology/py-biopython/pkg-plist +++ b/biology/py-biopython/pkg-plist @@ -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 @@ -1128,6 +1191,7 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/Alphabet @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 @@ -1155,13 +1219,13 @@ @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/MEME @dirrm %%PYTHON_SITELIBDIR%%/Bio/Medline @dirrm %%PYTHON_SITELIBDIR%%/Bio/MetaTool @dirrm %%PYTHON_SITELIBDIR%%/Bio/Mindy @@ -1172,6 +1236,7 @@ @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/PDB/mmCIF @dirrm %%PYTHON_SITELIBDIR%%/Bio/PDB @dirrm %%PYTHON_SITELIBDIR%%/Bio/Parsers @@ -1179,6 +1244,8 @@ @dirrm %%PYTHON_SITELIBDIR%%/Bio/Pathway @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 |