Attachment 88343 Details for Bug 125134 – file.diff

[patch] file.diff

file.diff (text/plain), 9.05 KB, created by wenheping on 2008-07-01 03:50:07 UTC

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Creator: wenheping

Created: 2008-07-01 03:50:07 UTC

Size: 9.05 KB

patch

obsolete

>--- Makefile.orig	2008-07-01 09:25:01.000000000 +0000
>+++ Makefile	2008-07-01 09:25:15.000000000 +0000
>@@ -6,7 +6,7 @@
> #
> 
> PORTNAME=	biopython
>-PORTVERSION=	1.43
>+PORTVERSION=	1.45
> CATEGORIES=	biology python
> MASTER_SITES=	http://www.biopython.org/DIST/
> PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
>--- distinfo.orig	2007-05-30 06:57:20.000000000 +0000
>+++ distinfo	2008-07-01 09:26:06.000000000 +0000
>@@ -1,3 +1,3 @@
>-MD5 (biopython-1.43.tar.gz) = 3c275b321bb1db7d8bda764913aaedcd
>-SHA256 (biopython-1.43.tar.gz) = eb424da9efddbf376c31660786ecb34ff893ea752bf7300f4a06d1b8c6ba175b
>-SIZE (biopython-1.43.tar.gz) = 3867907
>+MD5 (biopython-1.45.tar.gz) = 049ff32be28297b77c25624082118629
>+SHA256 (biopython-1.45.tar.gz) = ea9af15729aed1a3eb9d8bc65bced919390b50d0f93622a69ef9aaeb3ff56020
>+SIZE (biopython-1.45.tar.gz) = 3978249
>--- pkg-plist.orig	2008-07-01 09:25:06.000000000 +0000
>+++ pkg-plist	2008-07-01 09:51:05.000000000 +0000
>@@ -221,6 +221,9 @@
> %%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/Enzyme/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/Enzyme/__init__.pyo
>@@ -338,9 +341,6 @@
> %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/Geo/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/Bio/Geo/geo_format.py
>-%%PYTHON_SITELIBDIR%%/Bio/Geo/geo_format.pyc
>-%%PYTHON_SITELIBDIR%%/Bio/Geo/geo_format.pyo
> %%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/Gobase/__init__.pyo
>@@ -405,33 +405,15 @@
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/compound_format.py
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/compound_format.pyc
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Compound/compound_format.pyo
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/enzyme_format.py
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/enzyme_format.pyc
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Enzyme/enzyme_format.pyo
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/map_format.py
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/map_format.pyc
>-%%PYTHON_SITELIBDIR%%/Bio/KEGG/Map/map_format.pyo
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/KEGG/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/Record.py
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/Record.pyc
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/Record.pyo
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/__init__.py
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/__init__.pyc
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/__init__.pyo
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/kabat_format.py
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/kabat_format.pyc
>-%%PYTHON_SITELIBDIR%%/Bio/Kabat/kabat_format.pyo
> %%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/LocusLink/__init__.pyo
>@@ -688,6 +670,9 @@
> %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/PDB/__init__.pyo
>+%%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
>@@ -715,6 +700,58 @@
> %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.py
> %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyc
> %%PYTHON_SITELIBDIR%%/Bio/Pathway/__init__.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/__init__.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/Local.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/__init__.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/__init__.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/Async/__init__.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Async.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Async.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Async.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Controller.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Controller.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Controller.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Utils.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Utils.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/Utils.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/FDist/__init__.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/Utils.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/GenePop/__init__.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Async.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Async.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Async.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Cache.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Cache.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Cache.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Controller.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Controller.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Controller.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Template.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Template.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/Template.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/__init__.py
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/__init__.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/__init__.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/bottle.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/decline_lambda.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/decline_split.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/island.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/simple.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/split_island.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/split_ssm_1d.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/split_ssm_2d.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/ssm_1d.par
>+%%PYTHON_SITELIBDIR%%/Bio/PopGen/SimCoal/data/ssm_2d.par
> %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.py
> %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.pyc
> %%PYTHON_SITELIBDIR%%/Bio/PropertyManager.pyo
>@@ -845,6 +882,12 @@
> %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.py
> %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyc
> %%PYTHON_SITELIBDIR%%/Bio/SeqRecord.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CheckSum.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.py
>+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/SeqUtils/lcc.pyo
> %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.py
> %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyc
> %%PYTHON_SITELIBDIR%%/Bio/SeqUtils/CodonUsage.pyo
>@@ -1094,6 +1137,9 @@
> %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.py
> %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyc
> %%PYTHON_SITELIBDIR%%/Bio/formatdefs/swissprot.pyo
>+%%PYTHON_SITELIBDIR%%/Bio/ExPASy.py
>+%%PYTHON_SITELIBDIR%%/Bio/ExPASy.pyc
>+%%PYTHON_SITELIBDIR%%/Bio/ExPASy.pyo
> %%PYTHON_SITELIBDIR%%/Bio/kNN.py
> %%PYTHON_SITELIBDIR%%/Bio/kNN.pyc
> %%PYTHON_SITELIBDIR%%/Bio/kNN.pyo
>@@ -1213,6 +1259,7 @@
> @dirrm %%PYTHON_SITELIBDIR%%/Bio/EUtils
> @dirrm %%PYTHON_SITELIBDIR%%/Bio/Emboss
> @dirrm %%PYTHON_SITELIBDIR%%/Bio/Encodings
>+@dirrm %%PYTHON_SITELIBDIR%%/Bio/Entrez
> @dirrm %%PYTHON_SITELIBDIR%%/Bio/Enzyme
> @dirrm %%PYTHON_SITELIBDIR%%/Bio/FSSP
> @dirrm %%PYTHON_SITELIBDIR%%/Bio/Fasta
>@@ -1234,7 +1281,6 @@
> @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
>@@ -1248,6 +1294,13 @@
> @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

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Attachments on bug 125134: 88343